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Genetics

  • 2011 Springer Protocols
    Moullier, Philippe; Snyder, Richard O.
    Adeno-associated virus biology / Matthew D. Weitzman and R. Michael Linden -- Design and construction of functional AAV vectors / John T. Gray and Serge Zolotukhin -- AAV capsid structure and cell interactions / Mavis Agbandje-McKenna and Jürgen Kleinschmidt -- Exploring natural diversity of AAV for the design of vectors with novel properties / Guangping Gao, Li Zhong, and Olivier Danos -- Gene therapy in skeletal muscle mediated by adeno-associated virus vectors / Chunping Qiao ... [et al.] -- AAV mediated liver-directed gene therapy / Mark S. Sands -- Recombinant AAV delivery to the central nervous system / Olivier Bockstael ... [et al.] -- Adeno-associated virus mediated gene therapy for retinal degenerative diseases / Knut Steiger ... [et al.] -- Adeno-associated virus vector delivery to the heart / Lawrence T. Bish ... [et al.] -- Evaluation of the fate of rAAV genomes following in vivo administration / K. Reed Clark and Magalie Penaud-Budloo -- Measuring immune responses to recombinant AAV gene transfer / Ashley T. Martino ... [et al.] -- Modificaton and labeling of AAV vector particles / Hildegard Büning ... [et al.] -- AAV mediated gene targeting / Daniel G. Miller -- Preclinical study design for rAAV / Terence R. Flotte, Thomas J. Conlon, and Christian Mueller -- Biodistribution and shedding of AAV vectors / Caroline Le Guiner, Phillipe Moullier, and Valder R. Arruda -- Production and purification of recombinant adeno-associated vectors / Lijun Wang ... [et al.] -- rAAV vector product characterization and stability studies / Richard O. Snyder, Muriel Audit, and Joyce D. Francis -- rAAV human trial experience / Katherine A. High and Patrick Aubourg.
  • 2012 Springer
    Samuel, Charles E.
    ADAR proteins : structure and catalytic mechanism / Rena A. Goodman, Mark R. Macbeth and Peter A. Beal -- ADAR proteins : double-stranded RNA and Z-DNA binding domains / Pierre Barraud and Frédéric H.-T. Allain -- Editing of neurotransmitter receptor and ion channel RNAs in the nervous system / Jennifer L. Hood and Ronald B. Emeson -- Modulation of microRNA expression and function by ADARs / Bjorn-Erik Wulff and Kazuko Nishikura -- Nuclear editing of mRNA 3'-UTRs / Ling-Ling Chen and Gordon G. Carmichael -- Control of ADAR1 editing of hepatitis delta virus RNAs / John L. Casey -- Bioinformatic approaches for identification of A-to-I editing sites / Eli Eisenberg -- ADARs : viruses and innate immunity / Charles E. Samuel -- Role of ADARs in mouse development / Carl R. Walkley, Brian Liddicoat and Jochen C. Hartner -- Regulation and functions of ADAR in Drosophila / Simona Paro, Xianghua Li, Mary A. O'Connell and Liam P. Keegan.
  • 2007 ScienceDirect
    Hughes, Kelly Thomas; Maloy, Stanley R.
    Strain collections and genetic nomenclature / S.R. Maloy ... [et al.] -- Use of antibiotic-resistant transposons for mutagenesis / S.R. Maloy -- In vivo mutagenesis using EZ-Tn5 / J.R. Kirby -- Identification of essential genes in bacteria / D.R. Hillyard ... [et al.] -- Isolation of transposon insertions / S.R. Maloy -- Localized mutagenesis / S.R. Maloy -- Generation of deletions and duplications using transposons as portable regions of homology with emphasis on Mud and Tn10 transposons / K.T. Hughes -- Target-directed proteolysis in vivo / M. Eser ... [et al.] -- Sets of transposon-generated sequence-tagged mutants for structure-function analysis and engineering / B. Traxler ... [et al.] -- Using genomic microarrays to study insertional/transposon mutant libraries / D.N. Baldwin ... [et al.] -- Screening transposon mutant libraries using full-genome oligonucleotide microarrays / K. M. Winterberg ... [et al.] -- Creating recombination-activated genes and sequence-defined mutant libraries using transposons / L. Gallagher ... [et al.] -- Use of operon and gene fusions to study gene regulation in Salmonella / K.T. Hughes ... [et al.] -- Genomic screening for regulatory genes using the T-POP transposon / C. Lee ... [et al.] -- Recombineering: In vivo genetic engineering in E. coli, S. enterica, and beyond / J.A. Sawitzke ... [et al.] -- [lambda]-red genetic engineering in Salmonella enterica serovar Typhimurium / J.E. Karlinsey -- Probing nucleoid structure in bacteria using phage lambda integrase-mediated chromosome rearrangements / N. Garcia-Russell ... [et al.] -- Dissecting nucleic acid-protein interactions using challenge phage / S.R. Maloy ... [et al.] -- Mud-P22 / J.A. Crain ... [et al.] -- Phage metagenomics / V. Casas ... [et al.].
    Also available: Print – 2007
  • 2012 ScienceDirect
    Butler, John M.
    Intended as a companion to the Fundamentals of Forensic DNA Typing volume published in 2009, Advanced Topics in Forensic DNA Typing: Methodology contains 18 chapters with 4 appendices providing up-to-date coverage of essential topics in this important field and citation to more than 2800 articles and internet resources. The book builds upon the previous two editions of John Butler's internationally acclaimed Forensic DNA Typing textbook with forensic DNA analysts as its primary audience. This book provides the most detailed information written to-date on DNA databases, low-level DNA, validation, and numerous other topics including a new chapter on legal aspects of DNA testing to prepare scientists for expert witness testimony. Over half of the content is new compared to previous editions. A forthcoming companion volume will cover interpretation issues. Contains the latest information - hot-topics and new technologies Well edited, attractively laid out, and makes productive use of its four-color format Author John Butler is ranked as the number one "high-impact author in legal medicine and forensic science, 2001 to 2011" by ScienceWatch.com.
  • 2013 Springer
    Alaoui-Jamali, Moulay A.; Aloyz, Raquel; Panasci, Lawrence C.
    Repair of DNA Interstrand Cross-links Produced by Cancer Chemotherapeutic Drugs / Anderson T. Wang, Peter J. McHugh -- DNA-PK, a Pharmacological Target in Cancer Chemotherapy and Radiotherapy? / Bernard Salles D.V.M., Ph.D. -- Growth Factor Receptor Signaling, DNA Damage Response, and Cancer Cell Susceptibility to Chemotherapy and Relapses / Moulay Alaoui-Jamali, Amine Saad, Gerald Batist -- The Relationship Between DNA-Repair Genes, Cellular Radiosensitivity, and the Response of Tumors and Normal Tissues to Radiotherapy / David Murray, Matthew Parliament -- Important Roles of ERCC1 in DNA Repair and Targeted Therapy / Jennifer J. Hu, Joseph de la Garza -- The Role of BRCA1 and BRCA2 in Anticancer Drug Therapy / Andrew Y. Shuen, Jorge S. Reis-Filho -- DNA-PK in CLL Chemotherapy / L. Amrein, D. Davidson, R. Aloyz, L. Panasci -- Poly(ADP) Ribose Polymerase at the Interface of DNA Damage Signaling and DNA Repair / Jana Krietsch, Michele Rouleau, Michel Lebel -- Cellular Protection Against the Antitumor Drug Bleomycin / Dindial Ramotar Ph.D., Mustapha Aouida Ph.D. -- ATR as a Therapeutic Target / Fiona K. Middleton, Nicola J. Curtin -- Telomeres, Telomerase, and DNA Damage Response in Cancer Therapy / Raina A. Tamakawa, Helen B. Fleisig -- RAD51 Is a Key Protein of DNA Repair and Homologous Recombination in Humans / Alexander V. Mazin Ph.D., Olga M. Mazina.
  • 2009 Springer
    Valent, Barbara; Wang, Guo-Liang.
  • 2011
    McElwain, Mark Allan; Kingsley, David M.; Nusse, Roeland; Schneider, David; Talbot, William S.
    Only a few signaling pathways control the majority of biological processes throughout animal development and homeostasis, indicating that each pathway regulates multiple processes. The Wnt family of secreted ligands is one interesting and important example of this paradigm. Evidence abounds that Wnt signaling impacts numerous biological events including embryonic patterning, stem cell self- renewal, cell proliferation, and tissue regeneration. While only a few Wnt proteins have been extensively characterized, it is likely that each family member signals to control a variety of critical biological processes; therefore, it is clear that by understanding the signaling mechanism used by a single Wnt protein, we can understand how many aspects of biology are regulated. WntD is one of 7 Wnt homologs encoded by the Drosophila genome. While most of these Wnt proteins likely signal through a pathway dependent on the [Beta]-catenin homolog Armadillo (Arm), WntD very likely utilizes an Arm-independent mechanism to control embryonic dorsal/ventral (D/V) patterning, migration of the primordial germ cells (PGC) to the embryonic gonad, and the innate immune response. It is therefore of great interest to identify genes involved in this signal transduction pathway and better characterize the effect WntD has on these important biological processes. To this end, a suppressor/enhancer deficiency screen based upon the role of WntD in D/V patterning was previously performed in the laboratory. From this screen, 30 strong candidates for suppressors and 13 strong candidates for enhancers were identified. Here, I present further characterization of two candidate WntD pathway members identified in the screen: Fz4, a likely WntD receptor and Dcerk, a lipid kinase. I show by both in vitro and in vivo assays that both Fz4 and Dcerk function in the WntD signal transduction pathway, and present evidence suggesting that this WntD-Fz4-Dcerk signaling cassette is utilized during both D/V patterning and PGC migration, yet another instance of a single signaling cascade mediating multiple developmental events. Interestingly, I show that both of these novel WntD signal transducers appear to act redundantly with a homologous protein: in both D/V patterning and PGC migration, WntD likely signals through Fz3 and Fz4 receptors to activate the lipid kinases Dcerk and Dmulk. I further show, in collaboration with the Saba Laboratory at Children's Hospital Oakland Research Institute, that these kinases are necessary for wild-type ceramide-1-phosphate (C1P) levels in the adult, and either is sufficient to increase embryonic C1P levels, suggesting that both Dcerk and Dmulk are bona fide ceramide kinases. My data linking WntD-ceramide kinase signaling to PGC migration is consistent with a model in which WntD signaling is responsible for generation of optimal levels of embryonic C1P, which is likely to be the long-undiscovered substrate that is formed into a gradient by the lipid phosphate phosphatases encoded by Wunen and Wunen2. Future experiments will be required to further test this model. Importantly, these results may suggest a mechanism for the regulation of a broad range of migratory cell types, including other cells that migrate to generate a specific tissue or organ during embryonic development, and immune cells that must travel long distances to fight off infections.
  • 2012 Springer Protocols
    Hofreiter, Michael; Shapiro, Beth Alison.
    Setting up an ancient DNA laboratory / Tara L. Fulton -- A phenol-chloroform protocol for extracting DNA from ancient samples / Ross Barnett and Greger Larson -- DNA extraction of ancient animal hard tissue samples via adsorption to silica particles / Nadin Rohland -- Case study : recovery of ancient nuclear DNA from toe pads of the extinct passenger pigeon / Tara L. Fulton, Stephen M. Wagner, and Beth Shapiro -- Extraction of DNA from paleofeces / Melanie Kuch and Hendrik Poinar -- DNA extraction from keratin and chitin / Paula F. Campos and Thomas M.P. Gilbert -- Case study : ancient sloth DNA recovered from hairs preserved in paleofeces / Andrew A. Clack, Ross D.E. MacPhee, and Hendrik N. Poinar -- Ancient DNA extraction from soils and sediments / James Haile -- DNA extraction from fossil eggshell / Charlotte L. Oskam and Michael Bunce -- Ancient DNA extraction from plants / Logan Kistler -- DNA extraction from formalin-fixed material / Paula F. Campos and Thomas M.P. Gilbert -- Case study : ancient DNA recovered from Pleistocene-age remains of a Florida armadillo / Brandon Letts and Beth Shapiro -- Nondestructive DNA extraction from museum specimens / Michael Hofreiter -- Case study : using a nondestructive DNA extraction method to generate mtDNA sequences from historical chimpanzee specimens / Elmira Mohandesan, Stefan Prost, and Michael Hofreiter -- PCR amplification, cloning, and sequencing of ancient DNA / Tara L. Fulton and Mathias Stiller -- Quantitative real-time PCR in aDNA research / Michael Bunce, Charlotte L. Oskam, and Morten E. Allentoft -- Multiplex PCR amplification of ancient DNA / Mathias Stiller and Tara L. Fulton -- Preparation of next-generation sequencing libraries from damaged DNA / Adrian W. Briggs and Patricia Heyn -- Generating barcoded libraries for multiplex high-throughput sequencing / Michael Knapp, Mathias Stiller, and Matthias Meyer -- Case study : targeted high-throughput sequencing of mitochondrial genomes from extinct cave bears via direct multiplex PCR sequencing (DMPS) / Mathias Stiller -- Target enrichment via DNA hybridization capture / Susanne Horn -- Case study : enrichment of ancient mitochondrial DNA by hybridization capture / Susanne Horn -- Analysis of high-throughput ancient DNA sequencing data / Martin Kircher -- Phylogenetic analysis of ancient DNA using BEAST / Simon Y.W. Ho.
  • 2013 Springer
    Wang, Zhou.
    Recent studies demonstrated a key role of the androgen receptor in the development of castration-recurrent or -resistant prostate cancer (CRPC), which is deadly and in urgent need of more effective therapies. Understanding the functions of androgen-responsive genes and their regulation and deregulation in prostate cancer progression may lead to new approaches to prevent and treat prostate cancer patients. This book provides an up-to-date review of the overall androgen-responsive gene expression program and the regulation, function, and clinical relevance of both protein coding and non-coding androgen-responsive genes. Experts in the field of androgen action and prostate cancer research discussed the importance of DNA elements, chromatin structure, cellular signaling, and cell-cell interactions in the regulation of androgen-responsive genes in the context of prostate cancer progression, including the development of CRPC. This book is intended for individuals interested in cancer endocrinology and medical and healthcare professionals involved in prostate cancer research.
  • 2014 Springer Protocols
    Werner, Andreas.
    Targeted small noncoding rna-directed gene activation in human cells -- Isolation of chromatoid bodies from mouse testis as a rich source of short RNAs -- Generation of endo-siRNAs in xenopus laevis oocytes -- Analysis of endo-siRNAs in drosophila -- Methods for studying the biological consequences of endo-siRNA deficiency in drosophila melanogaster -- Small RNA library cloning procedure for deep sequencing of specific endogenous siRNA classes in caenorhabditis elegans -- Assays for direct and indirect effects of c. Elegans endo-siRNAs -- Extraction and nonradioactive detection of small RNA molecules -- P19-mediated enrichment and detection of siRNAs -- Detection of small noncoding RNAs by in situ hybridization using probes of 2'-o-methyl RNA + LNA -- Enhanced detection of small RNAs using a nonradioactive approach -- Computing siRNA and piRNA overlap signatures -- Isolation of small interfering RNAs using viral suppressors of RNA interference -- Computational analysis, biochemical purification, and detection of tRNA-derived small RNA fragments -- Differential DNA methylation patterns in endo-siRNAs mediated silencing of LINE-1 retrotransposons.
  • 2011 Springer Protocols
    Rij, Ronald P. van.
    [Publisher-supplied data] Viruses and RNAi share an intricate relationship at many levels. RNAi is an important antiviral defense mechanism in plants and invertebrates, microRNAs of viral or cellular origin affect many aspects of virus biology, and replication of many, if not all, mammalian viruses can be suppressed by RNAi. Antiviral RNAi: Concepts, Methods, and Applications provides a collection of protocols for the analysis of viral small RNAs and natural antiviral RNAi responses as well as for the development and optimization of RNAi-based antiviral drugs. As RNAi is a central regulatory mechanism in the cell, the methods in this volume can also be applied out of the context of a virus infection. Divided into five convenient parts, this detailed volume reviews important basic concepts in the field of antiviral RNAi, provides experimental and bio-informatic tools for the analysis of small silencing RNAs, covers methods to biochemically dissect RNAi-based antiviral defense and viral counter-defense mechanisms, describes methods for the design, expression, and delivery of therapeutic antiviral siRNAs, and finally presents genome-wide RNAi approaches for the identification of factors involved in virus replication. Written in the highly successful Methods in Molecular Biology series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Antiviral RNAi: Concepts, Methods, and Applications serves as an ideal guide for both novice and experienced researchers alike striving to dissect the role of RNAi in the viral life cycle or to further boost the development of novel therapeutics and experimental tools based on RNAi technology.
  • 2009 Springer
    Foulkes, Andrea S.
  • 2013 CRCnetBASE
    Matson, Robert S.
    Omics & microarrays revisited -- The commercial microarrays -- Supports & surface chemistries -- The arraying processes -- Gene expression microarray-based applications -- Protein microarray applications -- Multiplex assays.
  • 2013 Springer Protocols
    Banerjee, Diponkar; Shah, Sohrab P.
    Array comparative genomic hybridization : an overview of protocols, applications, and technology trends / Diponkar Banerjee -- Ultradense array CGH and discovery of micro-copy number alterations and gene fusions in the cancer genome / Ewa Przybytkowski [and others] -- Epigenomics : sequencing the methylome / Martin Hirst -- Application of array comparative genomic hybridization in chronic myeloid leukemia / Seonyang Park [and others] -- Use of cytogenetic microarrays in myelodysplastic syndrome Characterization / Lisa G. Shaffer, Blake C. Ballif, and Roger A. Schultz -- CGH protocols : chronic lymphocytic leukemia / Esteban Braggio, Rafael Fonseca, and Neil E. Kay -- Analysis of Acquired genomic copy number aberrations and regions of loss of heterozygosity in acute myelogenous leukemia genomes using affymetrix SNP 6.0 arrays and supporting software tools / Peter D. Ouillette [and others] -- Clinical applications of BAC array-CGH to the study of diffuse large B-cell lymphomas / Cristina Robledo, Juan Luis Garcia, and Jesus M. Hernandez -- Genomic profiling of mantle cell lymphoma / Melissa Rieger Menanteau and Jose A. Martinez-Climent -- Copy number analysis in EBV-positive nodal peripheral T cell lymphoma, unspecified / Kyusam Choi, Hyunjeong Ju, and Young Hyeh Ko -- Mycosis fungoides and Sezary syndrome / Blanca Espinet and Rocio Salgado -- Array CGH reveals clonal evolution of adult T-cell leukemia/lymphoma / Akira Umino and Masao Seto -- Array-CGH analysis of cutaneous anaplastic large cell lymphoma / K. Szuhai [and others] -- Genome-wide DNA profiling of HIV-related B-cell lymphomas / Andrea Rinaldi [and others] -- Array comparative genomic hybridization in osteosarcoma / Bekim Sadikovic [and others] -- Comparative genomic hybridization of Wilms' tumor / Shahrad Rod Rassekh and Evica Rajcan-Separovic -- Array-CGH in childhood MDS / Marcel Tauscher, Inka Praulich, and Doris Steinemann -- Nonfamilial breast cancer subtypes / Markus Ringner, Johan Staaf, and Goran Jonsson -- Applications of array-CGH for lung cancer / Kenneth J. Craddock, Wan L. Lam, and Ming-Sound Tsao -- Array CGH in brain tumors / Gayatry Mohapatra, Julia Sharma, and Stephen Yip -- Finding common regions of alteration in copy number data / Oscar M. Rueda, Ramon Diaz-Uriarte, and Carlos Caldas -- Distinguishing somatic and germline copy number events in cancer patient DNA hybridized to whole-genome SNP genotyping arrays / Gavin Ha and Sohrab Shah.
  • 2006 Springer
    Birge, Edward A.
  • 2015 Springer Protocols
    Narayanan, Kumaran.
  • 2010 Springer
    Dame, Remus T.; Dorman, Charles J.
  • 2006 Springer
    Bourke, Billy; Chan, Voon L.; Sherman, Philip M.
    Microbial genomes / Voon Loong Chan -- Evolution and origin of virulence isolates / Voon Loong Chan, Philip M. Sherman, and Billy Bourke -- Genomic approach to understanding of infectious disease mechanisms / Voon Loong Chan, Philip M. Sherman, and Billy Bourke -- Knockout and disease models in toll-like receptor-mediated immunity / Huey-Lan Huang and Wen-Chen Yeh -- Campylobacter from glycome to pathogenesis / John Kelly ... [et al.] -- Genomics of helicobacter species / Zhongming Ge and David B. Schauer -- The organization of leptospira at a genomic level / Dieter M. Bulach ... [et al.] -- Listeria monocytogenes / Keith Ireton -- Mycobacterial genomes / David C. Alexander and Jun Liu -- Mycoplasma / Yuko Sasaki -- Genome comparisons of diverse staphylococcus aureus strains / Martin J. McGavin -- Type III secretion, systems in yersinia pestis, and yersinia pseudotuberculosis / James B. Bliska, Michelle B. Ryndak, and Jens P. Grabenstein -- Genomics and the evolution of pathogenic vibrio cholerae / William S. Jermyn ... [et al.] -- Future directions of infectious disease research / Philip M. Sherman, Billy Bourke, and Voon Loong Chan -- Index.
    Also available: Print – 2006
  • 2015 Springer Protocols
    Fondi, Marco; Galardini, Marco; Mengoni, Alessio.
    Pulsed field gel electrophoresis and genome size estimates/ Rosa Alduina and Annalisa Pisciotta -- Comparative analyses of extrachromosomal bacterial replicons, identification of chromids, and experimental evaluation of their indispensability / Lukasz Dziewit and Dariusz Bartosik -- Choice of next-generation sequencing pipelines / F. Del Chierico ... [et al.] -- Pyrosequencing protocol for bacterial genomes / Ermanno Rizzi -- Bacterial metabarcoding by 16S rRNA gene ion torrent amplicon sequencing / Elio Fantini ... [et al.] -- Illumina-solexa sequencing protocol for bacterial genomes / Zhenfei Hu, Lei Cheng, and Hai Wang -- High-throughput phenomics / Carlo Viti ... [et al.] -- Comparative analysis of gene expression : uncovering expression conservation and divergence between Salmonella enterica serovar typhimurium strains LT2 and 14028S / Paolo Sonego ... [et al.] -- Raw sequence data and quality control / Giovanni Bacci -- Methods for assembling reads and producing contigs / Valerio Orlandini, Marco Fondi, and Renato Fani -- Mapping contigs using CONTIGuator / Marco Galardini, Alessio Mengoni, and Marco Bazzicalupo -- Gene calling and bacterial genome annotation with BG7 / Raquel Tobes ... [et al.] -- Defining orthologs and pangenome size metrics / Emanuele Bosi, Renato Fani, and Marco Fondi -- Robust identification of orthologues and paralogues for microbial pan-genomics using GET HOMOLOGUES : a case study of pIncA/C plasmids / Pablo Vinuesa and Bruno Contreras-Moreira -- Genome-scale metabolic network reconstruction / Marco Fondi and Pietro Liò -- From pangenome to panphenome and back / Marco Galardini, Alessio Mengoni, and Stefano Mocali -- Genome-wide detection of selection and other evolutionary forces / Zhuofei Xu and Rui Zhou -- Integrated microbial genome resource of analysis / Alice Checcucci and Alessio Mengoni.
  • 2012 Springer Protocols
    Keiler, Kenneth C.
    Bioinformatic discovery of bacterial regulatory RNAs using SIPHT / Jonathan Livny -- How to identify CRISPRs in sequencing data / Christine Drevet and Christine Pourcel -- Strategy for identifying noncoding RNAs using whole-genome tiling arrays / Stephen G. Landt and Eduardo Abeliuk -- Genetic screens to identify bacterial sRNA regulators / Pierre Mandin -- Competition assays using barcoded deletion strains to gain insight into small RNA function / Errett C. Hobbs and Gisela Storz -- Use of semi-quantitative northern blot analysis to determine relative quantities of bacterial CRISPR transcripts / Ksenia Pougach and Konstantin Severinov -- RNA visualization in bacteria by fluorescence in situ hybridization / Jay H. Russell and Kenneth C. Keiler -- RNA structure prediction : an overview of methods / Matthew G. Seetin and David H. Mathews -- Crystallization of RNA-protein complexes : from synthesis and purification of individual components to crystals / Anna Perederina and Andrey S. Krasilnikov -- Analysis of RNA folding and ligand binding by conventional and high-throughput calorimetry / Joshua E. Sokoloski and Philip C. Bevilacqua -- Use of aptamer tagging to identify in vivo protein binding partners of small regulatory RNAs / Colin P. Corcoran, Renate Rieder, Dimitri Podkaminski, Benjamin Hofmann, and Jörg Vogel -- Gel mobility shift assays to detect protein-RNA interactions / Alexander V. Yakhnin, Helen Yakhnin, and Paul Babitzke -- RNase footprinting of protein binding sites on an mRNA target of small RNAs / Yi Peng, Toby J. Soper, and Sarah A. Woodson -- Computational identification of sRNA targets / Brian Tjaden -- Detection of sRNA-mRNA interactions by electrophoretic mobility shift assay / Teppei Morita, Kimika Maki, and Hiroji Aiba -- Activity of small RNAs on the stability of targeted mRNAs in vivo / Guillaume Desnoyers and Eric Massé -- Native gel electrophoresis to study the binding and release of RNA polymerase by 6S RNA / Karen M. Wassarman -- Ribosome purification approaches for studying interactions of regulatory proteins and RNAs with the ribosome / Preeti Mehta, Perry Woo, Krirhika Venkataraman, and A. Wali Karzai -- Analysis of aminoacyl- and peptidyl-tRNAs by gel electrophoresis / Brian D. Janssen, Elie J. Diner, and Christopher S. Hayes -- In vitro trans-translation assays / Daisuke Kurita, Akira Muto, and Hyouta Himeno.
  • 2015 Springer Protocols
    Artsimovitch, Irina; Santangelo, Thomas J.
    Mapping the Escherichia coli transcription elongation complex with exonuclease III / Zhaokun Liu and Irina Artsimovitch -- Purification of bacterial RNA polymerase : tools and protocols / Vladimir Svetlov and Irina Artsimovitch -- Monitoring translocation of multisubunit RNA polymerase along the DNA with fluorescent base analogues / Anssi M. Malinen, Matti Turtola, and Georgiy A. Belogurov -- In vitro and in vivo methodologies for studying the sigma-54-dependent transcription / Martin Buck [and nine others] -- Methods for the assembly and analysis of in vitro transcription-coupled-to-translation systems / Daniel Castro-Roa and Nikolay Zenkin -- Site-specific incorporation of probes into RNA polymerase by unnatural-amino-acid mutagenesis and Straudinger-Bertozzi ligation / Anirban Chakraborty [and seven others] -- Reconstruction of factor-dependent, promotor proximal pausing in Drosophila nuclear extracts / Jian Li and David S. Gilmour -- Direct competition assay for transcription fidelity / Lucyna Lubkowska and Maria L. Kireeva -- Single-stranded DNA aptamers for functional probing of bacterial RNA polymerase / Danil Pupov and Andrey Kulbachinskiy -- Biochemical analysis of transcription termination by RNA polymerase III from yeast Saccharomyces cerevisiae / Aneeshkumar G. Arimbasseri and Richard J. Maraia -- Use of RNA polymerase molecular beacon assay to measure RNA polymerase interactions with model promotor fragments / Vladimir Mekler and Konstantin Severinov -- Preparation of cDNA libraries for high-throughput RNA sequencing analysis of RNA 5' ends / Irina O. Vvedenskaya, Seth R. Goldman, and Bryce E. Nickels -- In situ footprinting of E. coli transcription elongation complex with chloroacetaldehyde / A. Rachid Rahmouni and Christine Mosrin-Hauman -- Using solutes and kinetics to probe large conformational changes in the steps of transcription initiation / Emily F. Ruff, Wayne S. Kontur, and M. Thomas Record Jr. -- Manipulating archaeal systems to permit analyses of transcription elongation-termination decisions in vitro / Alexandra M. Gehring and Thomas J. Santangelo -- Purification of active RNA polymerase I from yeast / Francis Dean Appling and David Alan Schneider -- Transcription in archaea : preparation of Methanocaldococcus jannaschii transcription machinery / Katherine Smollet, Fabian Blombach, and Finn Werner -- Transcription in archaea ; in vitro transcription assays for mjRNAP / Katherine Smollet, Fabian Blombach, and Finn Werner -- Experimental analysis of hFACT action during pol II transcription in vitro / Fu-Kai Hsieh, Olga I. Kulaeva, and Vasily M. Studitsky -- ChIP-Seq for genome-scale analysis of bacterial DNA-binding proteins / Richard P. Bonocora and Joseph T. Wade.
  • 2007 Springer Protocols
    Murhammer, David W.
  • 2015 Springer Protocols
    Buchanan, Susan K.; Noinaj, Nicholas.
    The [beta]-barrel assembly machinery complex / Denise L. Leyton, Matthew J. Belousoff, and Trevor Lithgow -- Yeast mitochondria as a model system to study the biogenesis of bacterial [beta]-barrel proteins / Thomas Ulrich [and three others] -- Experimental methods for studying the BAM complex in Neisseria meningitides / Martine P. Bos, Ria Tommassen-van Boxtel, and Jan Tommassen -- Heart modifiability of outer membrane proteins from gram-negative bacteria / Nicholas Noinaj, Adam J. Kuszak, and Susan K. Buchanan -- The role of a destabilized membrane of OMP insertion / Ashlee M. Plummer, Dennis Gessmann, and Karen G. Fleming -- Treponema pallidum in gel microdroplets: a method for topological analysis of BamA (TP0326) and localization of rare outer membrane proteins / Amit Luthra, Arvind Anand, and Justin D. Radolf -- Analyzing the role of periplasmic folding factors in the biogenesis of OMPs and members of the Type V secretion system / Gustavo Bodelón, Elvira Marín, and Luis Ángel Fernandez -- An in vitro assay for substrate translocation by FhaC in liposomes / Enguo Fan, Derrick Norell, and Matthias Müller -- Measuring cell-cell binding using flow-cytometry / Zachary C. Ruhe, Christopher S. Hayes, and David A. Low -- Methods to characterize folding and function of BamA cross-link mutants / Adam J. Kuszak, Nicholas Noinaj, and Susan K. Buchanan -- Small angle X-ray scattering (SAXS) characterization of the POTRA domains of BamA / Pamela Arden Doerner and Marcelo Carlos Sousa -- Assessing the outer membrane insertion and folding of multimeric transmembrane [beta]-barrel proteins / Jack C. Leo, Philipp Oberhettinger, and Dirk Linke -- The expression, purification, and structure determination of BamA from E. coli / Dongchun Ni and Yihua Huang -- Expression and purification of the individual Bam components BamB-E / Suraaj Aulakh, Kelly H. Kim, and Mark Paetzel -- Structure determination of the BAM complex accessory lipoproteins BamB-E / Kornelius Zeth -- An in vitro assay for outer membrane protein assembly by the BAM complex / Giselle Roman-Hernandez and Harris D. Bernstein -- Identification of BamC on the surface of E. coli / Chaille T. Webb and Trevor Lithgow -- Construction and characterization of an E. coli bamD depletion strain / Dante R. Ricci -- Expression, purification, and screening of BamE, a component of the BAM complex, for structural characterization / Mark Jeeves, Pooja Sridhar, and Timothy J. Knowles -- Purification and bicelle crystallization for structure determination of the E. coli outer membrane protein TamA / Fabian Gruss, Sebastian Hiller, and Timm Maier -- Strategies for the analysis of Bam recognition motifs in outer membrane proteins / Nagarajan Paramasivam and Dirk Linke -- Summary and future directions / Nicholas Noinaj and Susan K. Buchanan
  • 2011 CRCnetBASE
    Dey, Dipak; Ghosh, Samiran; Mallick, Bani K.
    Chapter 1. Estimation and Testing in Time-Course Microarray Experiments -- Chapter 2. Classification for Differential Gene Expression Using Bayesian Hierarchical Models -- Chapter 3. Applications of MOSS for Discrete Multi-Way Data -- Chapter 4. Nonparametric Bayesian Bioinformatics -- Chapter 5. Measurement Error and Survival Model for cDNA Microarrays -- Chapter 6. Bayesian Robust Inference for Differential Gene Expression -- Chapter 7. Bayesian Hidden Markov Modeling of Array CGH Data -- Chapter 8. Bayesian Approaches to Phylogenetic Analysis -- Chapter 9. Gene Selection for the Identification of Biomarkers in High-Throughput Data -- Chapter 10. Sparsity Priors for Protein - Protein Interaction Predictions -- Chapter 11. Learning Bayesian Networks for Gene Expression Data -- Chapter 12. In-Vitro to In-Vivo Factor Profiling in Expression Genomics -- Chapter 13. In-Vitro to In-Vivo Factor Profiling in Expression Genomics Machines -- Chapter 14. A Bayesian Mixture Model for Protein Biomarker Discovery -- Chapter 15. Bayesian Methods for Detecting Differentially Expressed Genes -- Chapter 16. Bayes and Empirical Bayes Methods for Spotted Microarray Data Analysis -- Chapter 17. Bayesian Classification Method for QTL Mapping.
  • 2011 Springer
    Edwards-Moulds, JoAnn; Ness, Paul M.; Sloan, Steve R.
    This text is a review of molecular immunohematology (MI). It draws from analyses and case studies around the world and details many techniques used in many labs. It is aimed at anyone interested in how MI is changing blood bank and transfusion medicine.
  • 2012 Springer
    Cryan, J. F.; Reif, Andreas.
  • 2005 Wiley
    Krauss, Gerhard.
    The regulation of gene expression -- The regulation of enzyme activity -- Structure and function of signal pathways -- Signaling by nuclear receptors -- G protein-coupled signal transmission pathways -- Intracellular messenger substance : second messengers -- Ser/Thr-specific protein kinases and protein phosphates -- Signal transmission via transmembrane receptors with tyrosine-specific protein kinase activity -- Signal transmission via ras proteins -- Intracellular signal transduction : the protein cascades of the MAP kinase pathways -- Membrane receptors with associated tyrosine kinase activity -- Other receptor classes -- Regulation of the cell cycle -- Malfunction of signaling pathways and tumorigenesis : oncogenes and tumor suppressor genes -- Apoptosis.
  • 2014 World Scientific
    Friedberg, Errol C.
    Growing up in Brooklyn -- The essential Paul Berg -- College and World War II -- Western Reserve University -- Copenhagen -- Washington University, St. Louis -- Discovering transfer RNA -- Stanford University and its refurbished Department of Biochemistry -- Transcription and translation : new directions -- Making recombinant DNA : the first faltering steps -- Making recombinant DNA : a major breakthrough -- EcoRI restriction endonuclease : a major breakthrough -- "Coincidence is the word we use when we can't see the levers and pulleys" -- Yet another Stanford contribution -- An historic meeting in Hawaii -- The recombinant DNA controversy -- A momentous Gordon Research Conference -- Making recombinant molecules with frog DNA -- The controversy heats up -- Asilomar II -- The dissenters : a different point of view -- The aftermath -- Legislative and revisionist challenges to recombinant DNA -- Asilomar II : lessons learned -- The Nobel Prize in chemistry -- Commercializing the technology -- Life goes on -- The "retirement" years -- Public policy issues : and other interests -- Personal challenges.
    Also available: Print – 2014
  • 2007 Springer
    Xia, Xuhua.
    Also available: Print – 2007
  • 2009 Springer Protocols
    Posada, David.
    Similarity searching using BLAST / Kit J. Menlove, Mark Clement, and Keith A. Crandall -- Gene orthology assessment with OrthologID / Mary Egan ... [et al.] -- Multiple alignment of DNA sequences with MAFFT / Kazutaka Katoh, George Asimenos, and Hiroyuki Toh -- SeqVis : a tool for detecting compositional heterogeneity among aligned nucleotide sequences / Lars Sommer Jermiin ... [et al.] -- Selection of models of DNA evolution with jModelTest / David Posada -- Estimating maximum likelihood phylogenies with PhyML / Stéphane Guindon ... [et al.] -- Trees from trees : construction of phylogenetic supertrees using clann / Christopher J. Creevey and James O. McInerney -- Detecting signatures of selection from DNA sequences using datamonkey / Art F.Y. Poon, Simon D.W. Frost, and Sergei L. Kosakovsky Pond -- Recombination detection and analysis using RDP3 / Darren P. Martin -- CodonExplorer : an interactive online database for the analysis of codon usage and sequence composition / Jesse Zaneveld ... [et al.] -- Genetic code prediction for metazoan mitochondria with GenDecoder / Federico Abascal, Rafael Zardoya, and David Posada -- Computational gene annotation in new genome assemblies using GeneID / Enrique Blanco and Josep F. Abril -- Promoter analysis : gene regulatory motif identification with A-GLAM / Leonardo Mariño-Ramírez ... [et al.] -- Analysis of genomic DNA with the UCSC Genome Browser / Jonathan Pevsner -- Mining for SNPs and SSRs using SNPServer, dbSNP and SSR taxonomy tree / Jacqueline Batley and David Edwards -- Analysis of transposable element sequences using CENSOR and RepeatMasker / Ahsan Huda and I. King Jordan -- DNA sequence polymorphism analysis using DnaSP / Julio Rozas.
  • 2014 CRCnetBASE
    Liu, Yu.
  • 2012 Springer Protocols
    Reske-Kunz, Angelika B.; Sudowe, Stephan.
    Comparison between Agrobacterium-mediated and direct gene transfer using the gene gun / Caixia Gao and Klaus K. Nielsen -- Transient gene expression in epidermal cells of plant leaves by biolistic DNA delivery / Shoko Ueki [and others] -- Transformation of nuclear DNA in meristematic and embryogenic tissues / Mulpuri Sujatha and K.B.R.S. Visarada -- Biolistic DNA delivery to leaf tissue of plants with the non-vacuum gene gun (handygun) / Anssi L. Vuorinen [and others] -- Handgun-mediated inoculation of plants with viral pathogens for mechanistic studies / Victor Gaba, Moshe Lapidot, and Amit Gal-On -- Biolistics-based gene silencing in plants using a modified particle inflow gun / Kevin M. Davies [and others] -- Biolistic transformation of Caenorhabditis elegans / Meltem Isik and Eugene Berezikov -- Improved vectors for selection of transgenic Caenorhabditis elegans / Annabel A. Ferguson [and others] -- Biolistic transformation of Brugia Malayi / Tarig B. Higazi and Thomas R. Unnasch -- Biolistic transfection of human embryonic kidney (HEK) 293 cells / Xiongwei Li [and others] -- Biolistic transfection of tumor tissue samples / Kandan Aravindaram, Shu-Yi Yin, and Ning-Sun Yang -- Biolistic transfection of freshly isolated adult ventricular myocytes / David F. Steele, Ying Dou, and David Fedida -- Biolistic transfection of neurons in organotypic brain slices / John A. O'Brien and Sarah C.R. Lummis -- Biolistic DNA delivery to mice with the low pressure gene gun / Meng-Chi Yen and Ming-Derg Lai -- Chemokine overexpression in the skin by biolistic DNA delivery / Ahmad Jalili -- Enhancement of gene gun-induced vaccine-specific cytotoxic T-cell response by administration of chemotherapeutic drugs / Steve Pascolo -- Dendritic cell-specific biolistic transfection using the Fascin gene promoter / Yvonne Hohn, Stephan Sudowe, and Angelika B. Reske-Kunz -- Particle-mediated administration of plasmid DNA on corneas of BALB/c mice / Dirk Bauer [and others] -- Optimizing particle-mediated epidermal delivery of an influenza DNA vaccine in ferrets / Eric J. Yager [and others] -- Methods for monitoring gene gun-induced HBV and HCV-specific immune responses in mouse models / Gustaf Ahlen, Matti Sallberg, and Lars Frelin -- Gene gun immunization to combat malaria / Elke S. Bergmann-Leitner and Wolfgang W. Leitner -- Identification of T cell epitopes of Mycobacterium tuberculosis with biolistic DNA vaccination / Toshi Nagata and Yukio Koide -- Biolistic DNA vaccination against trypanosoma infection / Marianne Bryan, Siobhan Guyach, and Karen A. Norris -- Biolistic DNA vaccination against melanoma / Julia Steitz and Thomas Tuting -- Biolistic DNA vaccination against cervical cancer / Michal Smahel -- Efficiency of biolistic DNA vaccination in experimental type I allergy / Verena Raker [and others] -- Safety assessment of biolistic DNA vaccination / Barbara Langer [and others] -- DiOlistics: delivery of fluorescent dyes into cells / Nyssa Sherazee and Veronica A. Alvarez -- Protein antigen delivery by gene gun-mediated epidermal antigen incorporation (EAI) / Sandra Scheiblhofer [and others].
  • 2002 Wiley
    Knudsen, Steen.
    Preface xi -- Acknowledgments xiii -- 1 Introduction I -- 1.1 Hybridization 1 -- 1.2 Affymetrix GeneChip Technology 3 -- 1.3 Spotted Arrays 6 -- 1.4 Serial Analysis of Gene Expression (SAGE) 8 -- 1.5 Example: Affymetrix vs. Spotted Arrays 9 -- 1.6 Summary 11 -- 1.7 Further Reading 13 -- 2 Overview of Data Analysis 15 -- 3 Basic Data Analysis 17 -- 3.1 Absolute Measurements 17 -- 3.2 Scaling 18 -- 3.2.1 Example: Linear and Nonlinear Scaling 20 -- 3.3 Detection of Outliers 20 -- 3.4 Fold Change 21 -- 3.5 Significance 22 -- 3.5.1 Nonparametric Tests 24 -- 3.5.2 Correction for Multiple Testing 24 -- 3.5.3 Example I: t-Test and ANOVA 25 -- 3.5.4 Example II: Number of Replicates 26 -- 3.6 Summary 28 -- 3.7 Further Reading 29 -- 4 Visualization by Reduction of Dimensionality 33 -- 4.1 Principal Component Analysis 33 -- 4.2 Example 1: PCA on Small Data Matrix 35 -- 4.3 Example 2: PCA on Real Data 37 -- 4.4 Summary 37 -- 4.5 Further Reading 39 -- 5 Cluster Analysis 41 -- 5.1 Hierarchical Clustering 41 -- 5.2 K-means Clustering 43 -- 5.3 Self-Organizing Maps 44 -- 5.4 Distance Measures 45 -- 5.4.1 Example: Comparison of Distance Measures 47 -- 5.5 Normalization 49 -- 5.6 Visualization of Clusters 50 -- 5.6.1 Example: Visualization of Gene Clusters in -- Bladder Cancer 50 -- 5.7 Summary 50 -- 5.8 Further Reading 52 -- 6 Beyond Cluster Analysis 55 -- 6.1 Function Prediction 55 -- 6.2 Discovery of Regulatory Elements in Promoter -- Regions 56 -- 6.2.1 Example 1: Discovery of Proteasomal Element 57 -- 6.2.2 Example 2: Rediscovery of Mlu Cell Cycle -- Box (MCB) 57 -- 6.3 Integration of data 58 -- 6.4 Summary 59 -- 6.5 Further Reading 59 -- 7 Reverse Engineering of Regulatory Networks 63 -- 7.1 The Time-Series Approach 63 -- 7.2 The Steady-State Approach 64 -- 7.3 Limitations of Network Modeling 65 -- 7.4 Example 1: Steady-State Model 65 -- 7.5 Example 2: Steady-State Model on Real Data 66 -- 7.6 Example 3: Steady-State Model on Real Data 68 -- 7.7 Example 4: Linear Time-Series Model 68 -- 7.8 Further Reading 71 -- 8 Molecular Classifiers 75 -- 8.1 Classification Schemes 76 -- 8.1.1 Nearest Neighbor 76 -- 8.1.2 Neural Networks 76 -- 8.1.3 Support Vector Machine 76 -- 8.2 Example I: Classification of Cancer Subtypes 77 -- 8.3 Example II: Classification of Cancer Subtypes 78 -- 8.4 Summary 79 -- 8.5 Further Reading 79 -- 9 Selection of Genes for Spotting on Arrays 81 -- 9.1 Gene Finding 82 -- 9.2 Selection of Regions Within Genes 82 -- 9.3 Selection of Primers for PCR 83 -- 9.4 Selection of Unique Oligomer Probes 83 -- 9.4.1 Example: Finding PCR Primers for Gene -- AF105374 83 -- 9.5 Experimental Design 84 -- 9.6 Further Reading 84 -- 10 Limitations of Expression Analysis 87 -- 10.1 Relative VersusAbsoluteRNA Quantification 88 -- 10.2 Further Reading 88 -- 11 Genotyping Chips 91 -- 11.1 Example: NeuralNetworksfor GeneChipprediction 91 -- 11.2 Further Reading 93 -- 12 Software Issues and Data Formats 95 -- 12.1 Standardization Efforts 96 -- 12.2 Standard File Format 97 -- 12.2.1 Example: Small Scripts in Awk 97 -- 12.3 Software for Clustering 98 -- 12.3.1 Example: Clustering with ClustArray 99 -- 12.4 Software for Statistical Analysis 99 -- 12.4.1 Example: StatisticalAnalysis with R 99 -- 12.4.2 The affyR Software Package 103 -- 12.4.3 Commercial Statistics Packages 103 -- 12.5 Summary 103 -- 12.6 Further Reading 104 -- 13 Commercial Software Packages 105 -- 14 Bibliography 109 -- Index 123.
  • 2013 Springer
    Dinman, Jonathan D.
    When quantum mechanics was first proposed a century ago, nobody could have anticipated how deeply it would affect our lives. Today, we are connected and powered through devices whose existence is predicated on the basic principles of this strange physics. Not even the biological sciences have escaped its reach. As scientists query the deepest mysteries of the living world, the physical scales probed and the types of questions asked are increasingly blurring the lines between biology and physics. The hybrid field of biophysics represents the new frontier of the 21st century. The ribosome has been at the heart of three Nobel Prizes. Understanding its essential nature and how it interacts with other proteins and nucleic acids to control protein synthesis has been one of the central foundations in our understanding of the biology at the molecular level. With the advent of atomic scale structures, methods to visualize and separate individual molecules, and the computational power to model the complex interactions of over a million atoms at once, our understanding of how gene expression is controlled at the level of protein translation is now deeply ensconced in the biophysical realm. This book provides a premier resource to a wide audience, whether it be the general reader seeking a broad view of the field, a clinician interested in the role of protein translation in human disease, the bench researcher looking for state-of-the-art technologies, or computational scientists involved in cutting edge molecular modeling.
  • 2011 Springer
    Booth, Alan; Landale, Nancy; McHale, Susan.
    "Genes and environment. Biology and behavior. Nature and nurture. The terminology may be clear-cut, but the processes themselves are far from simple: unlike the direct cause-and-effect dichotomies of past frameworks, researchers now recognize these family-based connections as multifaceted, transactional, and emergent. [This book] aims at illuminating a multiplicity of approaches and methodologies for studying family dynamics, to match the complex interplay of physiological factors, environmental challenges, and behavioral adaptations that characterize family life and development. Chapters illustrate physical and social influences on parenting, childhood, adolescence, fertility, and family formation, providing analytical frameworks for understanding key areas such as family behavior, health, development, and adaptation to contextual stressors."--Book jacket.
  • 2012 CRCnetBASE
    Ayyachamy, Manimaran; Gupta, Vijai Kumar.
    Identification of fungal pathogenicity genes by Agrobacterium tumefaciens-mediated transformation / Karunakaran Maruthachalam ... [et al.] -- The genetics and molecular biology of carotenoid biosynthesis in mucorales / Catalina Sanz, Mahdi Shahriari, and Arturo P. Eslava -- Induction and repression of carbohydrate degrading enzymes in fungi with special reference to their coding genes / Pauline Walsh, Alan Hernon, and Anthonia O'Donovan -- Involvement of ADH1, IPT1, and PMT genes in Candida albicans pathogenesis / Mahmoud Rouabhia and Mahmoud Ghannoum -- Enhanced resistance to fungal pathogens in plants through selective utilization of useful fungal genes / B.K. Sarma ... [et al.] -- Genes encoding penicillin and cephalosporin biosinthesis in Acremonium chrysogenum : two separate clusters are required for cephalosporin production / Juan-Francisco Martøn, Carlos Garcia-Estrada, and Ricardo V. Ullon -- A review of the fungal B-galactosidase gene and its biotechnological applications / Anne G. Lydon -- Trichoderma genes involved in interactions with fungi and plants / Mala Mukherjee -- Use of luciferases as a tool to analyze fungal physiology in association with gene transcription / David M. Arana and Jess Pla -- Fungal genes and their respective enzymes in industrial food, bio-based, and pharma applications / Marco van den Berg ... [et al.] -- Fungal metacaspases : an overview / Anthonia O'Donovan, Finola E. Cliffe, and Mary C. Shier -- Signaling molecules in the Arbuscular mycorrhizal fungi / Mohammad Miransari -- Role of pathogenic genes of Fusarium oxysporum, coding cell wall degrading enzymes during wilt infection in plants / Vijai Kumar Gupta, Maria Tuohy, and A. Manimaran -- Engineering fungal expression systems : recombinant expression of two class I alpha-1, 2-mannosidases from the filamentous fungus Aspergillus nidulans / C. Joshua Eades and William E. Hintz -- PCR-diagnostic of Septoria nodorum berk : aggresivenes in wheat tissue / I.V. Maksimov and A.Sh. Valeev -- Detection of toxigeneic and pathogenic fungi targeting metabolic pathway genes / Venkataramana Mudili ... [et al.] -- Pathogenicity genes in entomopathogenic fungia used as biopesticides / K. Uma Devi ... [et al.].
  • 2006 Springer
    Knols, B. G. J.; Louis, C.
    Executive summary -- Report of the working-group meeting / Christos Louis and Bart G.J. Knols -- Review of previous applications of genetics to vector control / Chris F. Curtis -- Genomics and expected benefits for vector entomology / Christos Louis -- Genetic approaches for malaria control / Marcelo Jacobs-Lorena -- Current thoughts about the integration of field and laboratory sciences in genetic control of disease vectors / Thomas W. Scott -- Genetic approaches in Aedes aegypti for control of dengue: an overview / Kenneth Olson .... [et al.] -- Malaria and dengue vector biology and control in West and Central Africa / Didier Fontenille and Pierre Carnevale -- Malaria and dengue vector biology and control in Southern and Eastern Africa / Maureen Coetzee -- Malaria and dengue vector biology and control in Southeast Asia / Pattamaporn Kittayapong -- Malaria and dengue vector biology and control in Latin America / Mario H. Rodriguez -- Transition from the laboratory to the field and effective interplay / Christos Louis -- Evaluation of drive mechanisms (including transgenes and drivers) in different environmental conditions and genetic backgrounds / Anthony A. James ... [et al.] -- Tools for monitoring the genetic structure and stability of mosquito populations / Gregory C. Lanzaro, Sergey Nuzhdin and Frederic Tripet -- What are relevant assays for refractoriness / George K. Christophides ... [et al.] -- Fitness studies: developing a consensus methodology / Thomas W. Scott ... [et al.] -- Mosquito mating behaviour / Willem Takken ... [et al.] -- Pathogen evolution issues in genetically modified mosquito vector strategies / Mario H. Rodriquez -- Models to investigate some issues regarding the feasibility of driving refractoriness genes into mosquito vector populations / Chris F. Curtis -- Identification and characterization of field sites for genetic control of disease vectors / Bart G.J. Knols and Hervé Bossin -- Application of genetically modified mosquitoes in national vector control programmes: thoughts on integrated control / Abraham Mnzava ... [et al.] -- Entomological correlates of epidemiological impacts: how do we know it is working? / Andrew Githeko -- Ethical, legal and social issues in the use of genetically modified vectors for disease control / Yeya T. Touré and Lucien Manga.
  • 2013 ebrary
    Bradley, James T.
    A guide to the rapidly progressing Age of Biotechnology, Brutes or Angels provides basic information on a wide array of new technologies in the life sciences, along with the ethical issues raised by each. With stem cell research, Dolly the cloned sheep, in vitro fertilization, age retardation, and pharmaceutical mind enhancement, humankind is now faced with decisions that it has never before had to consider. The thoughtfulness, or lack of it, that we bring to those decisions will largely determine the future character of the living world.
  • 2015 Springer Protocols
    Biron, David; Haspel, Gal.
    Library construction for mutation identification by whole-genome sequencing / Harold E. Smith -- Fundamentals of comparative genome analysis in caenorhabditis nematodes / Eric S. Haag and Cristel G. Thomas -- Genetic methods for cellular manipulations in C. elegans / Menachem Katz -- Fusion PCR method for expressing genetic tools in C. elegans / Yifat Eliezer and Alon Zaslaver -- Transposon-assisted genetic engineering with Mos1- mediated single-copy insertion (MosSCI) / Christian Frøkjær-Jensen -- Creating genome modifications in C. elegans using the CRISPR/Cas9 system / John A. Calarco and Ari E. Friedland -- Observing and quantifying fluorescent reporters / Michael Hendricks -- Microbial rhodopsin optogenetic tools : application for analyses of synaptic transmission and of neuronal network activity in behavior / Caspar Glock, Jatin Nagpal, and Alexander Gottschalk -- Simultaneous optogenetic stimulation of individual pharyngeal neurons and monitoring of feeding behavior in intact C. elegans / Nicholas F. Trojanowski and Christopher Fang-Yen -- High-pressure freeze and freeze substitution electron microscopy in C. elegans / Laura Manning and Janet Richmond -- Electron tomography methods for C. elegans / David H. Hall and William J. Rice -- Microfluidic devices for behavioral analysis, microscopy, and neuronal imaging in Caenorhabditis elegans / Ross C. Lagoy and Dirk R. Albrecht -- Tracking single C. elegans using a USB microscope on a motorized stage / Eviatar I. Yemini and André E. X. Brown -- Imaging system for C. elegans behavior / Matthew A. Churgin and Christopher Fang-Yen -- Method for obtaining large populations of synchronized Caenorhabditis elegans dauer larvae / Maria C. Ow and Sarah E. Hall -- Sampling and isolation of C. elegans from the natural habitat / Nausicaa Poullet and Christian Braendle -- Primer on prototyping / Dylan Lynch and David Biron -- Primer on quantitative modeling / Iulia Neagu and Erel Levine.
  • 2006 Springer Protocols
    Strange, Kevin.
    An overview of C. elegans biology / Kevin Strange -- Comparative genomics in C. elegans, C. briggsae, and other Caenorhabditis species / Avril Coghlan, Jason E. Stajich, and Todd W. Harris -- WormBase: methods for data mining and coparative genomics / Todd W. Harris and Lincoln D. Stein -- C. elegans deletion mutant screening / Robert J. Barstead and Donald G. Moerman -- Insertional mutagenesis in C. elegans using the drosophila transposon Mos1: a method for the rapid identification of mutated genes / Jean-Louis Bessereau -- Single nucleotide polymorphism mapping / M. Wayne Davis and Marc Hammarlund -- Creation of transgenic lines using microparticle bombardment methods / Vida Praitis -- Construction of plasmids for RNA interference and in vitro transcription of double-stranded RNA / Lisa Timmons -- Delivery methods for RNA interference in C. elegans / Lisa Timmons -- Functional genomic approaches in C. elegans / Todd Lamitina -- Assays for toxicity studies in C. elegans with Bt crystal proteins / Larry J. Bischof, Danielle L. Huffman, and Raffi V. Aroian -- Fluorescent reporter methods / Harald Hutter -- Electrophysiological analysis of neuronal and muscle function in C. elegans / Michael M. Francis and Andres Villu Maricq -- Sperm and oocyte isolation methods for biochemical and proteomic analysis / Michael A. Miller -- Preservation of C. elegans tissue via high-pressure freezing and freeze-substitution for ultrastructural analysis and immunocytochemistry / Robby M. Weimer -- Intracellular pH measurements in vivo using green fluorescent protein variants / Keith Nehrke -- Automated imaging of C. elegans behavior / Christopher J. Cronin, Zhaoyang Feng, and William R. Schafer -- Intracellular Ca2+ imaging in C. elegans / Rex A. Kerr and William R. Schafer -- In vitro culture of C. elegans somatic cells / Kevin Strange and Rebecca Morrison -- Techniques for analysis, sorting, and dispensing of C. elegans on the COPAS flow-sorting system / Rock Pulak.
  • 2011 ScienceDirect
    Rothman, Joel H.; Singson, Andrew.
    Pt.I Genetics and functional genomics : Mapping mutations in C. elegans / Eric J. Lambie -- Specialized chromosomes and their uses in caenorhabditis elegans / Martin R. Jones, Zoe Lohn, Ann M. Rose -- Genome engineering by transgene-instructed gene conversion in C. elegans / Valérie J.P. Robert, Jean-Louis Bessereau -- RNAi methods and screening : RNAi based high-throughput genetic interaction screening / Patricia G. Cipriani, Fabio Piano -- Dissection of genetic pathways in C. elegans / Zheng Wang, David R. Sherwood -- Pt.II Molecular biology and biochemistry : Transgenesis in C. elegans / Vida Praitis, Morris F. Maduro -- RNA processing in C. elegans / J. Jason Morton, Thomas Blumenthal -- Analysis of microRNA expression and function / Priscilla M. Van Wynsberghe, Shih-Peng Chan, Frank J. Slack, Amy E. Pasquinelli -- In situ hybridization of embryos with antisense RNA probes / Gina Broitman-Maduro, Morris F. Maduro -- Gene-centered regulatory network mapping / Albertha J.M. Walhout -- Affinity purification of protein complexes in C. elegans / Esther Zanin, Julien Dumont, RetoGassmann, Iain Cheeseman, Paul Maddox, Shirin Bahmanyar, Ana Carvalho, Sherry Niessen, John R. Yates III, Karen Oegema, Arshad Desai -- Pt.III Development : Cell indentification and cell lineage analysis / Claudiu A. Giurumescu, Andrew D. Chisholm -- The genetics and cell biology of fertilization / Brian D. Geldziler, Mathew R. Marcello, Diane C. Shakes, Andrew Singson -- Imaging embryonic morphogenesis in C. elegans / Jeff Hardin -- Molecular and genetic approaches for the analysis of C. elegans neuronal development / Dong Yan, Yishi Jin -- Methods for evaluating the caenorhabditis elegans dauer state : standard dauer-formation assay using synthetic daumones and proteomic analysis of O-GIcNAc modifications / Jeeyong Lee, Kwang-Youl Kim, Kyoe-Jin Joo, Keekyeong Kim, Pan-Young Jeong, Young-Ki Paik.
  • 2011 Springer Protocols
    Campbell, Lynda J.
    [Publisher-supplied data] Cytogenetic studies of malignancy have become an essential tool in the clinical management of cancer patients. Cancer Cytogenetics: Methods and Protocols presents eminently practical key cytogenetic and FISH techniques for every stage of diagnostic service. Experts in the field describe detailed cytogenetic analysis methods, fluorescence in situ hybridization and array methods currently being applied to investigate and diagnose different varieties of cancer. Written in the highly successful Methods in Molecular Biology series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, and step-by-step, readily reproducible laboratory protocols. The authors of the various chapters have also provided extensive notes to guide individuals who are new to these methods through the pitfalls that bedevil all such testing. Authoritative and accessible, Cancer Cytogenetics: Methods and Protocols serves as an ideal guide to scientists of all backgrounds, allowing them to either establish new techniques in their laboratories or find the different variations of standard methods helpful in improving their results.
  • 2015 Springer Protocols
    Verma, Mukesh.
    Cancer epigenetics : an introduction / Rajnee Kanwal, Karishma Gupta, and Sanjay Gupta -- Community resources and technologies developed through the NIH roadmap epigenomics program / John S. Satterlee ... [et al.] -- Epigenome-wide association studies (EWAS) : past, present, and future / James M. Flanagan -- Epigenetic biomarkers in liver cancer / Krishna K. Banaudha and Mukesh Verma -- Cancer type-specific epigenetic changes : gastric cancer / Danielle Queiroz Calcagno, Marília de Arruda Cardoso Smith, and Rommel Rodriguez Burbano -- Beyond the island : epigenetic biomarkers of colorectal and prostate cancer / Andrea J. Savio and Bharati Bapat -- Prostate cancer epigenome / Swathi Chinaranagari ... [et al.] -- CpG island hypermethylation as a biomarker for the early detection of lung cancer / Yujin Kim and Duk-Hwan Kim -- Analysis of DNA methylation in pancreatic cancer : an update / Christian Pilarsky and Robert Grützmann -- Epigenetics of urothelial carcinoma / Wolfgang A. Schulz ... [et al.] -- Epigenetics of prostate cancer / Tawnya C. McKee and James V. Tricoli -- Methylation profile landscape in mesothelioma : possible implications in early detection, disease progression, and therapeutic options / Xinbo Zhang ... [et al.] -- Techniques to access histone modifications and variants in cancer / Monica Tyagi ... [et al] -- Single base resolution analysis of 5-methylcytosine and 5-hydroxymethylcytosine by RRBS and TAB-RRBS / Maria A. Hahn ... [et al.] -- Quantitative DNA methylation analysis for epigenotyping of colorectal cancer / Atsushi Kaneda and Koichi Yagi -- Histone modifications associated with cancer cell migration and invasion / Miki Hieda, Nariaki Matsuura , and Hiroshi Kimura -- Aberrant epigenetic modifications in radiation-resistant head and neck cancers / Hon-Yi Lin, Tim Hui-Ming Huang, and Michael Wing-Yan Chan -- Cancer-associated infectious agents and epigenetic regulation / Vidya Vedham and Mukesh Verma -- Toxicoepigenomics and cancer : implications for screening / Mukesh Verma -- Human papilloma virus (HPV) modulation of the HNSCC epigenome / Josena K. Stephen and Maria J. Worsham -- Epigenetic regulation of HIV, AIDS, and AIDS-related malignancies / Mukesh Verma -- Epigenetics of colorectal cancer / Wenji Yan and Mingzhou Guo -- Epigenetics in breast and prostate cancer / Yanyuan Wu, Marianna Sarkissyan, and Jaydutt V. Vadgama -- Epigenetic inhibitors / Mukesh Verma and Hirendra Nath Banerjee -- Use of epigenetic modulators as a powerful adjuvant for breast cancer therapies / Aurore Claude-Taupin ... [et al.] -- Epigenetic approaches in glioblastoma multiforme and their implication in screening and diagnosis / Gwyneth Hyman ... [et al.] -- Detection of circulatory microRNAs in prostate cancer/ Anvesha Srivastava ... [et al.] -- Identification and characterization of small-molecule inhibitors of lysine acetyltransferases / Daiqing Liao -- Epigenetic regulation in biopsychosocial pathways / Kristin Litzelman and Mukesh Verma -- Viral epigenetics / Barry I. Milavetz and Lata Balakrishnan -- P53 tumor suppression network in cancer epigenetics / Alok Mishra, Daniel J. Brat, and Mukesh Verma -- Promoter hypermethylation as a biomarker in prostate adenocarcinoma / Jong Y. Park -- Sequencing the cancer methylome / Austin Y. Shull ... [et al.] -- Global DNA methylation profiling technologies and the ovarian cancer methylome / Jessica Tang ... [et al.] -- Recent progress in the discovery of epigenetic inhibitors for the treatment of cancer / Sharad K. Verma -- At the crossroad between obesity and gastric cancer / Jone Garai ... [et al.] -- Detection of epigenetic aberrations in the development of hepatocellular carcinoma / Yujing Zhang -- Specific type epigenetic changes in cervical cancers / Shuping Zhao -- Epigenetics in head and neck cancer / Syeda Marriam Bakhtiar, Amjad Ali, and Debmalya Barh -- Epigenetic therapy for colorectal cancer / Vivek Vaish ... [et al.] -- Epigenetics of gastric cancer / Mingzhou Guo and Wenji Yan.
  • 2014 ScienceDirect
    Arceci, Robert; Berman, Jason N.; Dellaire, Graham.
    Cancer Genomics addresses how recent technological advances in genomics are shaping how we diagnose and treat cancer. Built on the historical context of cancer genetics over the past 30 years, the book provides a snapshot of the current issues and state-of-the-art technologies used in cancer genomics. Subsequent chapters highlight how these approaches have informed our understanding of hereditary cancer syndromes and the diagnosis, treatment and outcome in a variety of adult and pediatric solid tumors and hematologic malignancies. The dramatic increase in cancer genomics research and ever-increasing availability of genomic testing are not without significant ethical issues, which are addressed in the context of the return of research results and the legal considerations underlying the commercialization of genomic discoveries. Finally, the book concludes with "Future Directions", examining the next great challenges to face the field of cancer genomics, namely the contribution of non-coding RNAs to disease pathogenesis and the interaction of the human genome with the environment. Tools such as sidebars, key concept summaries, a glossary, and acronym and abbreviation definitions make this book highly accessible to researchers from several fields associated with cancer genomics.Contributions from thought leaders provide valuable historical perspective to relate the advances in the field to current technologies and literature.
  • 2013 Springer
    Pfeffer, Ulrich.
    Genomic Pathology of Lung Cancer / Kenneth J. Craddock, Shirley Tam, Chang-Qi Zhu, Ming-Sound Tsao -- Understanding Melanoma Progression by Gene Expression Signatures / J. Tímár, T. Barbai, B. Győrffy, E. Rásó -- Prognostic Testing in Uveal Melanoma / Michael Zeschnigk, Dietmar R. Lohmann -- Capturing and Deciphering the Molecular Signatures of Head and Neck Cancer / Thomas J. Belbin, Roberto A. Lleras, Richard V. Smith -- Predictive and Prognostic Biomarkers for Colorectal Cancer / Lara Lipton, Michael Christie, Oliver Sieber -- Expression Profiling of Hepatocellular Carcinoma / Rosina Maria Critelli, Elisabetta Cariani, Erica Villa -- Kidney Cancer Genomics: Paving the Road to a New Paradigm of Personalized Medicine / George M. Yousef, Nicole M. A. White, Andrew H. Girgis -- Pancreatic Cancer Genomics / Vincenzo Corbo, Andrea Mafficini, Eliana Amato, Aldo Scarpa -- Breast Cancer Genomics: From Portraits to Landscapes / Ulrich Pfeffer, Valentina Mirisola, Alessia Isabella Esposito -- Genomic Landscape of Ovarian Cancer / Delia Mezzanzanica, Loris De Cecco, Marina Bagnoli, Patrizia Pinciroli -- Genetics of Endometrial Carcinoma / M. Angeles López-García, Begoña Vieites, M. Angeles Castilla -- Usefulness of Molecular Biology in Follicular-Derived Thyroid Tumors: From Translational Research to Clinical Practice / Alexandre Bozec, Marius Ilie, Paul Hofman -- Sarcomas Genetics: From Point Mutation to Complex Karyotype, from Diagnosis to Therapies / Frédéric Chibon, Alain Aurias, Jean-Michel Coindre -- Novel Molecular Acquisitions in Leukemias / Sabina Chiaretti, Robin Foà -- Where Do We Stand in the Genomics of Lymphomas? / Francesco Bertoni, Zhi-Ming Li, Emanuele Zucca -- The Genomics of Multiple Myeloma and Its Relevance in the Molecular Classification and Risk Stratification of the Disease / Antonino Neri, Luca Agnelli -- Genome-Wide Analysis and Gene Expression Profiling of Neuroblastoma: What Contribution Did They Give to the Tumor Treatment? / Gian Paolo Tonini.
  • 2014 Springer Protocols
    Wajapeyee, Narendra.
    Genome-Wide Mapping Of RNA Pol-II Promoter Usage In Mouse Tissues By Chip-Seq -- Using Native Chromatin Immunoprecipitation To Interrogate Histone Variant Protein Deposition In Embryonic Stem Cells -- Reduced Representation Bisulfite Sequencing To Identify Global Alteration In The DNA Methylation -- A High-Throughput Microrna Expression Profiling System -- Using Pooled Mir30-Shrna Library For Cancer Lethal And Synthetic Lethal Screens -- Genome-Wide RNA Interference Screening To Identify Regulators Of Epigenetic Silencing Of A Tumor Suppressor Gene -- A Diphtheria Toxin Negative Selection In RNA Interference Screening -- Cancer Metabolism: Crosstalk Between Signaling And O-Glcnacylation -- Targeted Genome Modification Via Triple Helix Formation -- Synthesis Of Stabilized Alpha-Helical Peptides -- Arginine-Grafted Biodegradable Polymer: A Versatile Transfection Reagent For Both DNA And Sirna -- Using Laco Arrays To Monitor DNA Double-Strand Break Dynamics In Live Schizosaccharomyces Pombe Cells -- Zebrafish As A Platform To Study Tumor Progression -- Clonal Screens To Find Modifiers Of Partially Penetrant Phenotypes In C. Elegans -- Serum Profiling Using Protein Microarrays To Identify Disease Related Antigens -- Interrogation Of In Vivo Protein-Protein Interactions Using Transgenic Mouse Models And Stable Isotope Labeling -- New Biophysical Methods To Study The Membrane Activity Of Bcl-2 Proteins -- Purification Of Recombinant 2XMBP Tagged Human Proteins From Human Cells -- Computational Analysis In Cancer Exome Sequencing -- Matrix Factorization Methods For Integrative Cancer Genomics -- Computational Methods For DNA Copy-Number Analysis Of Tumors.
  • 2007 Springer Protocols
    Fisher, Paul B.
    Reciprocal subtraction differential RNA display (RSDD) : an efficient technology for cloning differentially expressed genes / Devanand Sarkar, Dong-chul Kang, and Paul B. Fisher -- Cloning differentially expressed genes using rapid subtraction hybridization (RaSH) / Habib Boukerche ... [et al.] -- The application of differential display as a gene profiling tool / Ken Chien-Neng Chang ... [et al.] -- Serial analysis of gene expression (SAGE) / Fred van Ruissen and Frank Baas -- Gene expression profile analysis of tumors / Katia Basso and Riccardo Dalla-Favera -- cDNA microarray and bioinformatic analysis of nuclear factor [kappa]B related genes in squamous cell carcinoma / Zhong Chen ... [et al.] -- Gene profiling uncovers retinoid target genes / Yan Ma ... [et al.] -- Complete open reading frame (C-ORF) technique : rapid and efficient method for obtaining complete protein coding sequences / Dong-chul Kang and Paul B. Fisher -- Chromatin immunoprecipitation assays : molecular analysis of chromatin modification and gene regulation / Piyali Dasgupta and Srikumar P. Chellappan -- Manipulating genes and gene copy number by bacterial artificial chromosome transfection / Stephanie F. Phelps, Sharon Illenye, and Nicholas H. Heintz -- Molecular cytogenetic applications in analysis of the cancer genome / Pulivarthi H. Rao, Subhadra V. Nandula, and Vundavalli V. Murty -- Monitoring methylation and gene expression in cancer / Hetty Carraway and James Herman -- The use of phage display peptide libraries for basic and translational research / Renee Brissette and Neil I. Goldstein -- Yeast and mammalian two-hybrid systems for studying protein-protein interactions / Shu-ichi Matsuzawa and John C. Reed -- Ribonomic and short hairpin RNA gene silencing methods to explore functional gene programs associated with tumor growth arrest / Timothy E. Baroni ... [et al.] -- Surface-epitope masking (SEM) : an immunological subtraction approach for developing monoclonal antibodies targeting surface-expressed molecules / Neil I. Goldstein and Paul B. Fisher -- Approaches for monitoring signal transduction changes in normal and cancer cells / Paul Dent ... [et al.] -- PKR in innate immunity, cancer, and viral oncolysis / Siddharth Balachandran and Glen N. Barber -- Analysis of transformation and tumorigenicity using mouse embryonic fibroblast cells / Hong Sun and Reshma Taneja -- Analysis of growth properties and cell cycle regulation using mouse embryonic fibroblast cells / Hong Sun, Neriman Tuba Gulbagci, and Reshma Taneja -- Reverse phase protein microarrays for monitoring biological responses / Virginia Espina ... [et al.] -- Protein crystallization / Champion Deivanayagam, William J. Cook, and Mark R. Walter.
  • 2007 Springer
    Jurisica, Igor; Wigle, Dennis; Wong, Bill.
    Also available: Print – 2007
  • 2010 CRCnetBASE
    Carninci, Piero.
    The ouput of eukaryotic genomes is much more complex than expected. Genes produce different variants of RNAs from multiple promoters. One of the ultimate targets of biological analysis is to establish a relationship between the messenger RNAs that are transcribed from the genome and the genomic regions that control their expression - the promoters - in order to decipher the networks that regulate gene expression and the transcription factors that act as master regulators of transcriptional control. Novel technologies have recently appeared that allow deciphering of transcriptional network, based on the identification of the starting site of gene transcription, with the simultaneous measurement of expression level and identification of the promoter elements. These tagging technologies (including cap-analysis gene expression - CAGE - and others) are further boosted from the development of the novel generation of sequencing instruments, which allow transcriptional profiling by sequencing at the cost of microarray experiments. This book is a guide for users of new technologies, as it includes accurately proven protocols, allowing readers to prepare their samples for experiments. Additionally, it provides a guide for the bioinformatics tools that are available for the analysis of the obtained tags, including the design of the software, the sources and web information where they can be downloaded. Finally, the book provides examples of the application of these technologies to identify promoters, annotate genomes, identify new RNAs and reconstruct models of transcriptional control. Although examples mainly regard mammalians, the discussion expands to other groups of eukaryotes, where these approaches are complementing genome sequencing.
  • 2015 Springer Protocols
    Ferran, Maureen C.; Skuse, Gary R.
    This volume has been assembled for scientists interested in basic and applied biomedical research directed toward understanding the development, genetics, and function of cardiomyocytes. The methods and protocols contained within it address cell culture techniques, cardiomyocyte differentiation and redifferentiation, experimental induction of cardiomyopathies, introducing genes into cardiomyocytes, genomic approaches to the understanding cardiomyocytes, cryopreservation of neonatal cardiomyocytes, and modeling of cardiomyocyte function. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Practical and current, Cardiomyocytes: Methods and Protocols explores complimentary areas of cardiomyocyte science that, taken together, can inform individuals with a broad range of interests.
  • 2010 Springer
    Perbal, Annick; Perbal, Bernard V.; Takigawa, Masaharu.
    1. A Recent Breakthrough in the CCN Field: Functional Interactions Between CCN2 and CCN3 are Uncovered / Bernard Perbal -- 2. Report on the Fifth International Workshop on the CCN Family of Genes / A. E. Irvine, B. Perbal, and H. Yeger -- 3. Asking the Right Questions: What Can the Structure of the CCN Protein Domains Tell Us? / Kenneth P. Holbourn, Bernard Perbal, and K. Ravi Acharya -- 4. Nucleophosmin/B23: A Multifunctional Regulator that Determines the Fate of CCN2 mRNA / Satoshi Kubota, Yoshiki Mukudai, Harumi Kawaki, Seiji Kondo, Takanori Eguchi, Kumi Sumiyoshi, Toshihiro Ohgawara, Tsuyoshi Shimo, and Masaharu Takigawa -- 5. The CCN Genes as the “Master” Regulators of Angiogenesis, Vasculogenesis, Fibrogenesis and Cell Differentiation/Fate Specification in Mechanical Force-Driven Developmental Processes and Pathological Events / Mary Hanna and Brahim Chaqour -- 6. A Monoclonal Antibody Approach to CCN5 Domain Analysis / Lan Wei, Frank McKeon, Joshua W. Russo, Joan Lemire, and John Castellot -- 7. Matricellular Protein CCN2 Produced by Tubular Epithelial Cells Plays a Pivotal Role in Renal Fibrogenesis / Hirokazu Okada, Tsutomu Inoue, and Hiromichi Suzuki -- 8. Cooperative Regulation of Cell Proliferation and Differentiation by CCN2 and CCN3 / Masaharu Takigawa, Harumi Kawaki, Satoshi Kubota, Karen M. Lyons, and Bernard Perbal -- 9. The Role of CCN3 in Mesenchymal Stem Cells / Ken-Ichi Katsube -- 10. Role of Connective Tissue Growth Factor in Cardiac Fibrosis / Daiji Kawanami, Saptarsi M. Haldar, and Mukesh K. Jain -- 11. Gene Expression of CCN Family Members in Young and Aged Human Skin In Vivo / Taihao Quan, Sharon Shin, Zhaoping Qin, and Gary J. Fisher -- 12. Global Expression Profiling Reveals a Role for CTGF/CCN2 in Lactogenic Differentiation of Mouse Mammary Epithelial Cells / Weihan Wang, Cynthia Jose, Nicholas Kenney, Bethanie Morrison, and Mary Lou Cutler -- 13. CCN3 (NOV): A Negative Regulator of CCN2 (CTGF) Activity and an Endogenous Inhibitor of Fibrosis in Experimental Diabetic Nephropathy / Bruce. L. Riser, Feridoon Najmabadi, Bernard Perbal, Jo Ann Rambow, Melisa L. Riser, Ernest Sukowski, Herman Yeger, Sarah C. Riser, and Darryl R. Peterson -- 14. Inhibitors of Connective Tissue Growth Factor (CCN2)-Mediated Fibrogenesis: Underlying Mechanisms and Prospects for Anti-fibrotic Therapy / David R. Brigstock -- 15. CCN3 Promotes Melanoma Progression by Regulating Integrin Expression, Adhesion and Apoptosis Induced by Cytotoxic Drugs / Viviana Vallacchi, Maria Daniotti, Annamaria De Filippo, Licia Rivoltini, Bernard Perbal, and Monica Rodolfo -- 16. CCN3: A NOVel Growth Factor in Leukaemia / Lynn McCallum and Alexandra E Irvine -- 17. Prognostic Relevance of CCN3 in Bone Sarcomas / Bernard Perbal, Noureddine Lazar, Diana Zambelli, Monia Zuntini, Massimo Serra, Jose Antonio Lopez-Guerrero, Antonio Llombart-Bosch, Piero Picci, and Katia Scotlandi -- 18. CCN6 Regulates Breast Cancer Growth and Invasion Through Modulation of IGF Signaling and Epithelial to Mesenchymal Transition / Anupama Pal, Wei Huang, and Celina G. Kleer -- 19. Novel Transcriptional Regulation of CCN2/CTGF by Nuclear Translocation of MMP3 / Takanori Eguchi, Satoshi Kubota, Kazumi Kawata, Yoshiki Mukudai, Junji Uehara, Toshihiro Ohgawara, Soichiro Ibaragi, Akira Sasaki, Takuo Kuboki, and Masaharu Takigawa -- Fifth International Workshop on the CCN Family of Genes: Abstracts and Posters October 18-22, 2008.
  • 2011 Springer Protocols
    Browse, John; Lu, Chaofu; Wallis, James G.
  • 2009 Springer
    Al-Rubeai, Mohamed.
    Mammalian cell lines command an effective monopoly for the production of therapeutic proteins that require post-translational modifications. This book deals with the methodology involved in the development of cell lines and the cell engineering approach that can be employed to enhance productivity and improve cell function.
  • 2011 Springer Protocols
    Palmer, Ella.
    Cell-Based Microarrays: Overview / Ella Palmer -- Cell-Based Co-transfection Microarrays for Use with HEK293T Cells on a Poly d-Lysine-Coated Polystyrene Microplate / Meenal Soni, Fang Lai -- Large-Scale Cell-Based Microarrays and Their Use with HEK293T Cells and Downstream Apoptotic Assays / Ella Palmer, Tom C. Freeman -- A Novel Fluorescent Transcriptional Reporter for Cell-Based Microarray Assays / Tanya M. Redmond, Michael D. Uhler -- High-Throughput Subcellular Protein Localization Using Transfected-Cell Arrays: Subcellular Protein Localization Using Cell Arrays / Yuhui Hu, Michal Janitz -- Cell Arrays for the Measurement of Organelle Dynamics in Living Cells / Holger Erfle, Tautvydas Lisauskas, Christoph Claas, Jürgen Reymann, Vytaute Starkuviene -- High-Throughput Immunofluorescence Microscopy Using Yeast Spheroplast Cell-Based Microarrays / Wei Niu, G. Traver Hart, Edward M. Marcotte -- Cell-Based Microarrays of Infectious Adenovirus Encoding Short Hairpin RNA (shRNA) / Hansjürgen Volkmer, Frank Weise -- Reverse Transfected Cell Microarrays in Infectious Disease Research / Andreas Konrad, Ramona Jochmann, Elisabeth Kuhn, Elisabeth Naschberger, Priya Chudasama, Michael Stürzl -- Transfected Cell Microarrays for the Expression of Membrane-Displayed Single-Chain Antibodies / Baochuan Lin, James B. Delehanty -- Blood Cell Capture on Antibody Microarrays and Monitoring of the Cell Capture Using Surface Plasmon Resonance Imaging / Yoann Roupioz, Sarah Milgram, André Roget, Thierry Livache -- Immobilized Culture and Transfection Microarray of Non-adherent Cells / Satoshi Yamaguchi, Erika Matsunuma, Teruyuki Nagamune -- Plasma Polymer and PEG-Based Coatings for DNA, Protein and Cell Microarrays / Andrew L. Hook, Nicolas H. Voelcker, Helmut Thissen -- Polymer Microarrays for Cellular High-Content Screening / Salvatore Pernagallo, Juan J. Diaz-Mochon -- High-Throughput Analyses of Gene Functions on a Cell Chip by Electroporation / Koichi Kato, Hiroo Iwata -- Microfluidic Image Cytometry / Ken-ichiro Kamei, Jing Sun, Hsian-Rong Tseng, Robert Damoiseaux.
  • 2014 Springer Protocols
    Furtado, Agnelo; Henry, Robert J.
    DNA Extraction from Vegetative Tissue for Next Generation Sequencing? -- DNA Extraction from Rice Endosperm (Including a Protocol for Extraction of DNA from Ancient Seed Samples) -- RNA Extraction from Cereal Vegetative Tissue -- RNA Extraction from Developing or Mature Wheat Seeds -- cDNA Library Preparation -- Preparation of High Molecular Weight gDNA and Bacterial Artificial Chromosome (BAC) Libraries in Plants -- The Polymerase Chain Reaction (PCR) -- General Methods -- Mutation and Mutation Screening -- The Quantitative Real-Time Polymerase Chain Reaction for the Analysis of Plant Gene Expression -- Cloning of DNA Fragments: Ligation Reactions in Agarose Gel -- Rapid Cloning of Genes and Promoters for Functional Analyses -- Genome Walking -- Functional Analysis by Protein Biochemistry -- Genomic Southern Blot analysis -- Northern Hybridization: A Proficient Method for Detection of Small RNAs and MicroRNAs -- Protein Blotting-Protocol for Beginners -- Genetic Transformation of Wheat via Particle Bombardment -- Sorghum Genetic Transformation by Particle Bombardment -- Genetic Transformation of Wheat via Agrobacterium-mediated DNA Delivery -- A Protocol for High-throughput Agrobacterium-mediated Barley Transformation -- Agrobacterium-mediated Transformation- Rice Transformation -- Agrobacterium-mediated Transformation of Maize (Zea mays) Immature Embryos -- A Technical Platform for PCR-based SNP Screening in Cereals and Other Crops -- A Method for Discovery of Genome-wide SNP Between Any Two Genotypes from Whole Genome Re-sequencing Data.
  • 2005 Springer Protocols
    Zanders, Edward D.
    Also available: Print – 2005
  • 2006 Springer
    Jaroch, S.; Weinmann, Hilmar.
  • 2013 CRCnetBASE
    Darvas, F.; Dormán, G.; Guttman, András.
    Ch. 1. Utilizing small molecules in chemical genomics : toward high-throughput (HT) approaches / György Dormán and Ferenc Darvas -- ch. 2. Development and application of novel analytical methods in lipidomics / Yuqin Wang ... [et al.] -- ch. 3. From chemical genomics to chemical proteomics : the power of microarray technology / Sándor Spisák and András Guttman -- ch. 4. Genomic and proteomic biomarkers in the drug R&D process / László Takács, Anna Debreceni, and István Kurucz -- ch. 5. Quo vadis biomedical sciences in the omics era : toward computational biology and medicine / András Falus ... [et al.] -- ch. 6. Novel chemogenomic approaches to drug design / Didier Rognan.
  • 2012 Springer Protocols
    Morse, Randall H.
    Strain construction and screening methods for a yeast histone H3/H4 mutant library / Junbiao Dai and Jef D. Boeke -- Measuring dynamic changes in histone modifications and nucleosome density during activated transcription in budding yeast / Chhabi K. Govind, Daniel Ginsburg, and Alan G. Hinnebusch -- Monitoring the effects of chromatin remodelers on long-range interactions in vivo / Christine M. Kiefer and Ann Dean -- Measuring nucleosome occupancy in vivo by micrococcal nuclease / Gene O. Bryant -- Analysis of nucleosome positioning using a nucleosome-scanning assay / Juan Jose Infante, G. Lynn Law, and Elton T. Young -- Assaying chromatin structure and remodeling by restriction enzyme accessibility / Kevin W. Trotter and Trevor K. Archer -- Generation of DNA circles in yeast by inducible site-specific recombination / Marc R. Gartenberg -- An efficient purification system for native minichromosome from Saccharomyces cerevisiae / Ashwin Unnikrishnan [and others] -- Simultaneous single-molecule detection of endogenous C-5 DNA methylation and chromatin accessibility using MAPit / Russell P. Darst [and others] -- Analysis of stable and transient protein-protein interactions / Stephanie Byrum [and others] -- Monitoring dynamic binding of chromatin proteins in vivo by fluorescence recovery after photobleaching / Florian Mueller [and others] -- Monitoring dynamic binding of chromatin proteins in vivo by fluorescence correlation spectroscopy and temporal image correlation spectroscopy / Davide Mazza [and others] -- Analysis of chromatin structure in plant cells / Mala Singh [and others] -- Analysis of histones and histone variants in plants / Ila Trivedi [and others] -- Reconstitution of modified chromatin templates for in vitro functional assays / Miyong Yun [and others] -- A defined in vitro system to study ATP-dependent remodeling of short chromatin fibers / Verena K. Maier and Peter B. Becker -- In vitro reconstitution of in vivo-like nucleosome positioning on yeast DNA / Christian J. Wippo and Philipp Korber -- Activator-dependent acetylation of chromatin model systems / Heather J. Szerlong and Jeffrey C. Hansen -- Mapping assembly favored and remodeled nucleosome positions on polynucleosomal templates / Hillel I. Sims, Chuong D. Pham, and Gavin R. Schnitzler -- Analysis of changes in nucleosome conformation using fluorescence resonance energy transfer / Tina Shahian and Geeta J. Narlikar -- Preparation of nucleosomes containing a specific H2A-H2A cross-link forming a DNA-constraining loop structure / Ning Liu and Jeffrey J. Hayes -- Sulfyhydryl-reactive site-directed cross-linking as a method for probing the tetrameric structure of histones H3 and H4 -/ Andrew Bowman and Tom Owen-Hughes -- Genomic approaches for determining nucleosome occupancy in yeast Kyle Tsui [and others] -- Genome-wide approaches to determining nucleosome occupancy in metazoans using MNase-Seq / Kairong Cui and Keji Zhao -- Salt fractionation of nucleosomes for genome-wide profiling / Sheila S. Teves and Steven Henikoff -- Quantitative analysis of genome-wide chromatin remodeling / Songjoon Baek, Myong-Hee Sung, and Gordon L. Hager -- Computational analysis of nucleosome positioning / Itay Tirosh.
  • 2015 Springer Protocols
    Pruett-Miller, Shondra M.
    Genome editing by targeted chromosomal mutagenesis -- Piggybac transposon-based insertional mutagenesis in mouse haploid embryonic stem cells -- Using phage integrases in a site-specific dual integrase cassette exchange strategy -- Therapeutic genome mutagenesis using synthetic donor DNA and triplex-forming molecules -- Genome engineering using adeno-associated virus (AAV) -- Engineering of customized meganucleases via in vitro compartmentalization and in cellulo optimization -- Efficient design and assembly of custom TALENs using the golden gate platform -- Ligation-independent cloning (LIC) assembly of TALEN genes -- Assembly and characterization of megatals for hyperspecific genome engineering applications -- Genome engineering using CRISPR-Cas9 system -- Donor plasmid design for codon and single base genome editing using zinc finger nucleases -- Endogenous gene tagging with fluorescent proteins -- Silencing long noncoding RNAs with genome-editing tools -- Gene editing using ssODNs with engineered endonucleases -- Genome editing in human pluripotent stem cells using site-specific nucleases -- Strategies to increase genome editing frequencies and to facilitate the identification of edited cells -- Using engineered endonucleases to create knockout and knockin zebrafish models -- Creating knockout and knockin rodents using engineered endonucleases via direct embryo injection -- Simple sperm preservation by freeze-drying for conserving animal strains.
  • 2008 Springer Protocols
    Davis, Gregory D.; Kayser, Kevin J.
    Biallelic gene knockouts in Chinese hamster ovary cells / Naoko Yamane-Ohnuki, Kazuya Yamano, and Mitsuo Satoh -- Highly proficient gene targeting by homologous recombination in the human pre-B cell line Nalm-6 / Noritaka Adachi, Aya Kurosawa, and Hideki Koyama -- Robust cell line development using meganucleases / Jean-Pierre Cabaniols and Frédéric Pâques -- Design and testing of zinc finger nucleases for use in mammalian cells / Matthew Porteus -- Gene targeting in Drosophila and Caenorhabditis elegans with zinc-finger nucleases / Dana Carroll ... [et al.] -- Orpheus recombination : a comprehensive bacteriophage system for murine targeting vector construction by transplacement / Knut Woltjen ... [et al.] -- Transposition -mediated mutagenesis in somatic cells : identification of transposon-genomic DNA junctions / David A. Largaespada and Lara S. Collier -- Insertional mutagenesis of the mouse germline with sleeping beauty transposition / Junji Takeda, Zsuzsanna Izsvák, and Zoltán Ivics -- Conditional gene trapping using the FLEx system / Thomas Floss and Frank Schnütgen -- Steps toward targeted insertional mutagenesis with class II transposable elements / Sareina Chiung-Yuan wu ... [et al.] -- Targeting integration of the Saccharomyces Ty5 retrotransposon / Troy L. Brady, Clarice L. Schmidt, and Daniel F. Voytas -- Site-specific chromosomal integration mediated by [phi]C31 integrase / Annahita Keravala and Michele P. Calos-- Triplex-mediated gene modification / Erica B. Schleifman, Joanna Y.Chin, and Peter M. Glazer -- Allelic exchange of unmarked mutations in Mycobacterium tuberculosis / Martin S. Pavelka, Jr. -- Mycobacterial recombineering Julia C. van Kessel and Graham F. Hatfull -- Chromosomal engineering of Clostridium perfringens using group II introns / Phalguni Gupta and Yue Chen.
  • 2008 CRCnetBASE
    Fukui, Kiichi; Ushiki, Tatsuo.
    Mechanical approaches to elucidate mechanisms of chromosome condensation at the nano- and microlevels / Kazushige Kawabata ... [et al.] -- Development of novel AFM probes for chromosome manipulation / Masato Saito, Gen Hashiguchi and Eiichi Tamiya -- Microchamber array-based sequence-specific DNA detection from a single chromosome via trace volume PCR / Masato Saito and Eiichi Tamiya -- On-chip chromosome sorter using electric and magnetic fields / Takahito Inoue ... [et al.] -- Fluorescence microscopy for analysis of chromosome dynamics / Sachihiro Matsunaga -- Fluorescence in situ hybridization (FISH) as a tool for comparative genomics: application of FISH to studies of chromosome evolution in vertebrates / Yoichi Matsuda ... [et al.] -- Immunocytochemistry for analyzing chromosomes / Osamu Hoshi ... [et al.] -- Proteome analysis of human metaphase chromosomes / Kiichi Fukui and Susumu Uchiyama -- Antipeptide antibodies for examining the conformation and molecular assembly of an intracellular protein / Masatoshi Nakagawa ... [et al.] -- Structure and interactions of the imitation SWI-type chromatin-remodeling complex, ATP-dependent chromatin-assembly facter / Tadayasu Ohkubo ... [et al.] -- Dynamic and functional analysis of chromosomal proteins / Nobuko Ohmido ... [et al.] -- Development of a sustainable chromosome imaging database / Kenji Taniguchi ... [et al.] -- Image database and image analysis of chromosome information / Shin-ichi Toyabe ... [et al.]. Transmission and scanning electron microscopy of mammalian metaphase chromosomes / Sumire Inaga, Keiichi Tanaka and Tatsuo Ushiki -- Atomic force microscopy of human chromosomes in relation to their higher-order structure / Osamu Hoshi, Daisuke Fukushi and Tatsuo Ushiki -- Mechanism of higher-order chromatin folding revealed by AFM observation of in vitro reconstituted chromatin / Kohji Hizume ... [et al.] -- Scanning near-field optical/atomic force microscopy as a tool for simultaneous specification of chromosome topography and particular gene location on the nanometer scale / Motoharu Shichiri ... [et al.] -- Isolation of human and plant chromosomes as nanomaterials / Susumu Uchiyama, Tomoyuki Doi and Kiichi Fukui --
  • 2013 Springer
    Garaulet, Marta; Ordovas, J. M.
    Circadian rhythms are such an innate part of our lives that we rarely pause to speculate why they even exist. Perhaps this is the reason why in the medical practice the circadian variability of hormones, metabolites, physiological behaviors or the relevance of time in the presence or absence of different pathologies, have been practically ignored in the past. Some studies have suggested that the disruption of the circadian system may be cause for obesity and manifestations of Metabolic Syndrome (MetS). Shift-work, sleep-deprivation and bright-light-exposure at night are related to increased adiposity (obesity) and prevalence of MetS. Chronobiology and Obesity examines recent advances that have led to researchers to find the relevant link which exists between chronobiology and obesity, but, as it is emphasized throughout the book, there is much more that needs to be explored between the connection.
  • 2015 Springer
    Gahan, Peter B.
  • 2006 Springer Protocols
    Chan, K. C. Allen; Chiu, Rossa W. K.; Lo, Y. M. Dennis.
    Introduction to the polymerase chain reaction / Y.M. Dennis Lo and K.C. Allen Chan -- Setting up a polymerase chain reaction laboratory / Y.M. Dennis Lo and K.C. Allen Chan -- Real-time polymerase chain reaction and melting curve analysis / Robert J. Pryor and Carl T. Wittwer -- Qualitative and quantitative polymerase chain reaction-based methods for DNA methylation analyses / Ivy H.N. Wong -- In-cell polymerase chain reaction: strategy and diagnostic applications / T. Vauvert Hviid -- Qualitative and quantitative DNA and RNA analysis by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry / Chunming Ding -- Analysis of polymerase chain reaction products by denaturing high-performance liquid chromatography / Ching-Wan Lam -- Use of real-time polymerase chain reaction for the detection of fetal aneuploidies / Bernhard Zimmermann ... [et al.] -- Noninvasive prenatal diagnosis by analysis of fetal DNA in maternal plasma / Rossa W. K. Chiu and Y. M. Dennis Lo -- Clinical applications of plasma Epstein-Barr virus DNA analysis and protocols for the quantitative analysis of the size of circulating Epstein-Barr virus DNA / K.C. Allen Chan and Y.M. Dennis Lo -- Molecular analysis of circulating RNA in plasma / Nancy B.Y. Tsui, Enders K.O. Ng, and Y.M. Dennis Lo -- Molecular analysis of mitochondrial DNA point mutations by polymerase chain reaction / Lee-Jun C. Wong, Bryan R. Cobb, and Tian-Jian Chen -- Novel applications of polymerase chain reaction to urinary nucleic acid analysis / Anatoly V. Lichtenstein ... [et al.] -- Detection and quantitation of circulating plasmodium falciparum DNA by polymerase chain reaction / Shira Gal and James S. Wainscoat -- Molecular diagnosis of severe acute respiratory syndrome / Enders K.O. Ng and Y.M. Dennis Lo -- Genomic sequencing of the severe acute respiratory syndrome-coronavirus / Stephen S.C. Chim, Rossa W.K. Chiu, and Y.M. Dennis Lo.
  • 2014 Wellcome Trust
    Jones, Emma M.; Tansey, E. M.
  • 2010
    Grone, Brian Patrick; Brunet, Anne; De Lecea, Luis; Fernald, Russell D.
    In response to changing environments, the brains of vertebrates generate diverse behaviors change their morphology and physiology. Expression of genes in the brain is regulated by light, food, social stresses, and by internal signals including reproductive cycles and metabolism. To understand how these signals can have impact behaviors and the brain, I have studied regulation of reproduction, feeding, and light detection in a cichlid fish, Astatotilapia burtoni, and a circadian rhythm generation in the Siberian hamster, Phodopus sungorus. My experimentals involved measurement of mRNA by in situ hybridization and quantitative reverse transcription-PCR (qRT-PCR). To understand circadian rhythm entrainment, I studied when and where genes involved in circadian light detection are expressed in A. burtoni. mRNA encoding melanopsin, vertebrate ancient opsin, and pituitary adenylate cyclase-activating peptide were found in the inner retina of A. burtoni as well as in the brain. Their locations reveal a network homologous to circadian detection networks in other vertebrates. Melanopsin mRNA levels changed based on light input, as seen for some other opsin genes. Brief light stimuli can suppress circadian rhythms in several species. A two-pulse light treatment induces circadian arrhythmia in locomotor activity in P. sungorus. Loss of circadian rhythmicity in tissues and organisms could occur either through loss of intracellular rhythms or through loss of intercellular synchrony. Following the light treatment, P. sungorus had suppressed levels of mRNA encoding the core clock genes per1, per2, bmal1, and cry1 in the suprachiasmatic nucleus (SCN). Thus, circadian rhythm loss due to light stimuli involves inhibition of intracellular rhythms in the SCN. The brain controls reproductive behavior and physiology in response to relevant external and internal cues. Gonadotropin-releasing hormone (GnRH1) activates the reproductive system and GnRH1 peptide and mRNA levels are higher in dominant male A. burtoni than in subordinate males. Kisspeptin, a neuropeptide acting via the kisspeptin receptor (Kiss1r), increases GnRH1 release. In A. burtoni, I found kiss1r mRNA in GnRH1 and GnRH3 neurons and in many brain nuclei and kiss1r levels were higher in dominant males than in subordinate males. Kisspeptin signaling may regulate many brain functions, including responses to social status. Reproduction requires significant investment of metabolic energy, especially when parents provide care for offspring. Female A. burtoni carry eggs in their mouths for two weeks after spawning, during which time they do not eat. Food deprivation can affect reproductive and feeding behaviors and neuropeptides. To test the hypothesis that food deprivation and reproduction interact in regulating A. burtoni brain gene expression, I measured levels of several neuropeptide and receptor gene mRNAs following mouthbrooding or starvation. Mouthbrooding females had lower levels of gnrh1 mRNA than gravid females, but higher levels of cck and hcrt. In males, food deprivation decreased gnrh1 levels, but increased gnrh2, suggesting a novel feeding role for GnRH2 in fish. Mouthbrooding may inhibit reproduction and modulate feeding neural circuits. I also developed a technique for intracerebroventricular injections in A. burtoni that should facilitate manipulation of neuropeptide receptors including GnRH receptors. Matching behavior and physiology to accommodate changing lighting, social, feeding, and reproductive influences is important for maximizing organismal fitness and I have discovered how these factors regulate several genes that may contribute to adaptive responses in changing environments.
  • 2008 Springer
    Barbieri, Marcello.
    Codes of biosequences / Edward N. Trifonov -- The mechanisms of evolution : natural selection and natural conventions / Marcello Barbieri -- Catalytic propensity of amino acids and the origins of the genetic code and proteins / Ádám Kun ... [et al.] -- Why the genetic code originated : implications for the origin of protein synthesis / Massimo Di Giulio -- Self-referential formation of the genetic system / Romeu Cardoso Guimarães, Carlos Henrique Costa Moreira, and Sávio Torres de Farias -- The mathematical structure of the genetic code / Diego L. Gonzalez -- The arithmetical origin of the genetic code / Vladimir shCherbak -- Protein linguistics and the modular code of the cytoskeleton / Mario Gimona -- A lipid-based code in nuclear signaling / Nadir M. Maraldi -- Biological information transfer beyond the genetic code : the sugar code / Hans-Joachim Gabius -- The immune self code : from correspondence to complexity / Yair Neuman -- Signal transduction codes and cell fate / Marcella Faria -- Towards an understanding of language origins / Eörs Szathmáry -- The codes of language : turtles all the way up? / Stephen J. Cowley -- Code and context in gene expression, cognition, and consciousness / Seán Ó Nualláin -- Neural coding in the neuroheuristic perspective / Alessandro E.P. Villa -- Error detection and correction codes / Diego L. Gonzalez -- The musical code between nature and nurture : ecosemiotic and neurobiological claims / Mark Reybrouck.
  • 2013 Thieme Book
    Passarge, Eberhard.
    Introduction -- Chronology -- Fundamentals -- Prologue -- Molecular basis of genetics -- Analysis of DNA -- Variability of DNA -- Processing of DNA -- Eukaryotic cells -- Formal genetics -- Chromosomes -- Regulation of gene function -- Epigenetic modifications -- Genetic signal pathways -- Genes in embryonic development -- Genomics -- Genetics and medicine -- Imbalanced homeostasis -- Metabolic disorders -- Immune system -- Origins of cancer -- Impaired cell and tissue structure -- Hemoglobin disorders -- Sex determination and differentiation -- Atypical patternns of genetic transmission -- Sensory perception -- Karyotype-phenotype relationnship -- A grief guide to genetic diagnosis -- Morbid anatomy of the human genome - chromosomal locations - alphabetic list -- Appendix -- Supplementary data.
  • 2013 Springer
    Xia, Xuhua.
    This book provides an evolutionary conceptual framework for comparative genomics, with the ultimate objective of understanding the loss and gain of genes during evolution, the interactions among gene products, and the relationship between genotype, phenotype and the environment. The many examples in the book have been carefully chosen from primary research literature based on two criteria: their biological insight and their pedagogical merit. The phylogeny-based comparative methods, involving both continuous and discrete variables, often represent a stumbling block for many students entering the field of comparative genomics. They are numerically illustrated and explained in great detail. The book is intended for researchers new to the field, i.e., advanced undergraduate students, postgraduates and postdoctoral fellows, although professional researchers who are not in the area of comparative genomics will also find the book informative.
  • v. 1-2, 2007 Springer Protocols
    v. 2, 2007 Springer Protocols
    Bergman, Nicholas H.
    v. 1. Genome visualization and annotation ; Sequence alignments ; Identification of conserved sequences and biases in codon usage ; Identification and structural characterization of noncoding RNAs -- v. 2. Comparative analysis of domain and protein families ; Orthologs, synteny, and genome evolution ; Experimental analysis of whole genomes : analysis of copy number and sequence polymorphisms.
  • 2008 CRCnetBASE
    Brown, J. R.
    Introduction : the broad horizons of comparative genomics / James R. Brown -- Advances in next-generation DNA sequencing technologies / Michael L. Metzker -- Large scale phylogenetic reconstruction / Bernard M.E. Moret -- Comparative genomics of viruses using bioinformatics tools / Chris Upton and Elliot J. Lefkowitz -- Archaebacteria and the prokaryote-to-eukaryote transition (and the role of mitochondria therein) / William Martin, Tal Dagan, and Katrin Henze -- Comparative genomics of invertebrates / Takeshi Kawashima ... [et al.] -- Comparative vertebrate genomics / James W. Thomas -- Gaining insight into human population-specific selection pressure / Michael R. Barnes -- Comparative genomics in drug discovery / James R. Brown -- Comparative genomics and the development of novel antimicrobials / Diarmaid Hughes -- Comparative genomics and the development of antimalarial and antiparasitic therapeutics / Emilio F. Merino, Steven A. Sullivan, and Jane M. Carlton -- Comparative genomics in AIDS research / Philippe Lemey, Koen Deforche, and Anne-Mieke Vandamme -- Detailed comparisons of cancer genomes / Timon P.H. Buys ... [et al.] -- Comparative cancer epigenomics / Alice N.C. Kuo ... [et al.] -- G protein-coupled receptors and comparative genomics / Steven M. Foord -- Comparative toxicogenomics in mechanistic and predictive toxicology / Joshua C. Kwekel, Lyle D. Burgoon, and Tim R. Zacharewski -- Comparative genomics and crop improvement / Michael Francki and Rudi Appels -- Domestic animals : a treasure trove for comparative genomics / Leif Andersson.
  • 2006 Springer
    Piškur, Jure; Sunnerhagen, Per.
    Also available: Print – 2006
  • 2014 CRCnetBASE
    Kaushik, Azad K.; Pasman, Yfke.
    1. Variable lymphocyte receptor-based adaptive immunity in the Agnathan Sea Lamprey / Marion J. Parsons, Justin T.H. Chan, Heng Sun, and Götz R.A. Ehrhardt -- 2. Immunoglobulin genes in tetrapods / Yi Sun and Yaofeng Zhao -- 3. The immunoglobulin genes of bats / J.E. Butler, Nancy Wertz, and Michelle L. Baker -- 4. Marsupial and monotreme immunoglobulin genetics / Robert D. Miller and Victoria L. Hansen -- 5. Organization of the immunoglobulin heavy- and light-chain loci in the rat / Peter M. Dammers, Jacobus Hendricks, Peter Terpstra, Nicolaas A. Bos, and Frans G.M. Kroese -- 6. Generation of the antibody repertoire in rabbits : role of gut-associated lymphoid tissues / Kari M. Severson and Katherine L. Knight -- 7. The immunoglobulin genes of domestic swine / J.E. Butler and Nancy Wertz -- 8. Bovine immunoglobulin genetics : a phylogenetic perspective / Yfke Pasman and Azad K. Kaushik -- 9. Informatics tools for immunoglobulin gene sequence analysis / Helena Hazanov, Miri Michaeli, Gitit Lavy-Shahaf, and Ramit Mehr.
  • 2008 ScienceDirect
    Hogstrand, Christer; Kille, Peter.
  • 2006 Springer
    Shmulevich, Ilya; Zhang, Wei.
  • 2015 Springer
    Teschendorff, Andrew E.
    This book introduces the reader to modern computational and statistical tools for translational epigenomics research. Over the last decade, epigenomics has emerged as a key area of molecular biology, epidemiology and genome medicine. Epigenomics not only offers us a deeper understanding of fundamental cellular biology, but also provides us with the basis for an improved understanding and management of complex diseases. From novel biomarkers for risk prediction, early detection, diagnosis and prognosis of common diseases, to novel therapeutic strategies, epigenomics is set to play a key role in the personalized medicine of the future. In this book we introduce the reader to some of the most important computational and statistical methods for analyzing epigenomic data, with a special focus on DNA methylation. Topics include normalization, correction for cellular heterogeneity, batch effects, clustering, supervised analysis and integrative methods for systems epigenomics. This book will be of interest to students and researchers in bioinformatics, biostatistics, biologists and clinicians alike. Dr. Andrew E. Teschendorff is Head of the Computational Systems Genomics Lab at the CAS-MPG Partner Institute for Computational Biology, Shanghai, China, as well as an Honorary Research Fellow at the UCL Cancer Institute, University College London, UK.
  • 2013 CRCnetBASE
    Jacoby, Edgar.
    This book focuses on applications of compound library design and virtual screening to expand the bioactive chemical space, to target hopping of chemotypes to identify synergies within related drug discovery projects or to repurpose known drugs, to propose mechanism of action of compounds, or to identify off-target effects by cross-reactivity analysis. Both ligand-based and structure-based in silico approaches, as reviewed in this book, play important roles for all these applications. Computational chemogenomics is expected to increase the quality and productivity of drug discovery and lead.
  • 2005 Springer
    Peltz, Gary.
    Computational biology: are we there yet? / Gary Peltz -- Statistical theory in QTL mapping / Benjamin Yakir, Anne Pisanté, and Ariel Darvasi -- Haplotype-based computational genetic analysis in mice / Jianmei Wang and Gary Peltz -- Haplotype structure of the mouse genome / Jianmei Wang ... [et al.] -- SNP discovery and genotyping: methods and applications / Jun Wang ... [et al.] -- Genetic and genomic approaches to complex lung disease using mouse models / Michael J. Holtzman, Edy Y. Kim, and Jeffrey D. Morton -- Murine models of osteoporosis / Robert F. Klein -- Murine models of substance and alcohol dependence: unraveling genetic complexities / Kim Cronise and John C. Crabbe -- Murine models of alcoholism: from QTL to gene / Chris Downing, Beth Bennett, and Thomas E. Johnson -- HLA polymorphism and disease susceptibility / -- Henry A. Erlich -- Asthma genetics: a case study / William Cookson.
    Also available: Print – 2005
  • 2011 Atypon
    Nalbantoglu, Ozkan Ufuk; Sayood, Khalid.
    Recent advances in development of sequencing technology has resulted in a deluge of genomic data. In order to make sense of this data, there is an urgent need for algorithms for data processing and quantitative reasoning. An emerging in silico approach, called computational genomic signatures, addresses this need by representing global species-specific features of genomes using simple mathematical models. This text introduces the general concept of computational genomic signatures, and it reviews some of the DNA sequence models which can be used as computational genomic signatures. The text takes the position that a practical computational genomic signature consists of both a model and a measure for computing the distance or similarity between models. Therefore, a discussion of sequence similarity/distance measurement in the context of computational genomic signatures is presented. The remainder of the text covers various applications of computational genomic signatures in the areas of metagenomics, phylogenetics and the detection of horizontal gene transfer.
  • 2010
    Gross, Samuel Solomon; Batzoglou, Serafim; Ng, Andrew Y.; Sidow, Arend.
    In this thesis, I describe three main contributions I have made toward creating more accurate systems for the computational recognition of protein-coding genes. First, I present N-SCAN, a gene predictor based on a hidden Markov model that uses Bayesian networks to model multiple alignments. I also describe CONTRAST, a discriminative gene predictor based on a conditional random field and a set of support vector machines for recognizing coding region boundaries. Both N-SCAN and CONTRAST represented substantial improvements over the state-of-the-art at the time they were introduced. Additionally, I give an algorithm for training conditional random fields that maximizes an approximation to labelwise accuracy, as opposed to the usual maximum likelihood approach. This algorithm proved key to CONTRAST's success.
  • 2007 Springer
    Abuin, A.; Feil, Robert; Metzger, Daniel.
    Conditional somatic mutagenesis in the mouse using site-specific recombinases -- Cre/loxP-mediated chromosome engineering of the mouse genome -- Tetracycline-controlled genetic switches -- Novel gene switches -- Improved embryonic stem cell technologies -- Gene trap mutagenesis -- RNA interference in mice -- Viral vectors: a wide range of choices and high levels of service -- Conditional mutagenesis by cell-permeable proteins: potential, limitations and prospects -- Analysis of mouse development with conditional mutagenesis -- Conditional mouse models of cancer -- Conditional mutagenesis reveals immunological functions of widely expressed genes: activation thresholds, homeostatic mechanisms and disease models -- Conditional transgenesis and recombination to study the molecular mechanisms of brain plasticity and memory -- A novel conditional knockout strategy applied to serotonin receptors -- Conditional mouse models for Friedreich Ataxia, a neurodegenerative disorder associating cardiomyopathy -- Animal models in cardiovascular diseases: new insights from conditional models -- Conditional animal models for the study of lipid metabolism and lipid disorders -- Conditional mouse models to study developmental and pathophysiological gene function in muscle -- Analysis of calcuim channels by conditional mutagenesis -- Conditional mutagenesis of G-protein coupled receptors and G-proteins -- Contribution of targeted conditional somatic mutagenesis to deciphering retinoid X receptor functions and to generating mouse models of human diseases.
  • 2014 Springer
    Rayan, Ghazi M.; Upton, Joseph.
    Physicians often have only partial knowledge of common congenital hand and upper extremity anomalies and their associated syndromes. Surgeons typically find these syndromes to be abstruse, and congenital hand conditions can represent an enigma even to pediatric geneticists. This book is designed to serve as a practical, up-to-date reference that will enable practitioners and students in a variety of disciplines to easily recognize the most common congenital upper extremity anomalies and syndromes. In total, 37 congenital upper extremity anomalies and 127 syndromes are discussed. Salient and common presenting features are described in detail and illustrated with the aid of high-quality digital color photographs whenever possible. In addition, relevant background information is included on such aspects as prevalence, etiology, pathogenesis, and findings elsewhere in the body.
  • 2012 Springer Protocols
    Morozov, Alexei.
    Regulation of Cre Recombinase: Use of Ligand-Regulated and Dimerizable Cre for Transgenesis -- Genetic Manipulations Using Cre and Mutant loxP Sites -- Using Recombinant Adeno-Associated Viral Vectors for Gene Expression in the Brain -- Using Lentiviral Vectors as Delivery Vehicles for Gene Therapy -- Targeting Neurological Disease with siRNA -- In Utero Electroporation for Cellular Transgenesis in the Developing Mammalian Forebrain -- Single-Cell Electroporation of siRNA in Primary Neuronal Cultures -- Development and Application of Membrane-Tethered Toxins for Genetic Analyses of Neuronal Circuits -- Genetic Methods for Anatomical Analysis of Neuronal Circuits -- Functional Circuitry Analysis in Rodents Using Neurotoxins/Immunotoxins -- Analysis of Neuronal Circuits with Optogenetics.
  • 2011
    Yokoo, Rayka; Bejerano, Gill; Fire, Andrew Z.; Pringle, John R.; Villeneuve, Anne.
    The formation of crossovers during meiosis is important both for the reassortment of genetic traits, and for creating a physical connection between homologous chromosomes to ensure faithful segregation. This thesis explores the role of a novel protein, COSA-1 (crossover site associated-1), in forming crossovers in the nematode C. elegans. cosa-1 was isolated in a screen for dead embryos, signaling missegregation of the autosomes, and a high incidence of males, signaling missegregation of the X chromosome. Interestingly, obvious orthologs of COSA-1 are only present in metazoans with the notable exception of Drosophilids. Thus no obvious orthologs of COSA-1 exist in the common model organisms, S. cerevisiae, S. pombe, D. melanogaster, and A. thaliana, making C. elegans one of the few organisms in which COSA-1 could have been isolated and studied. Yet, COSA-1 is conserved into humans suggesting the study of COSA-1 will have implications for human reproduction. Not only does C. elegans cosa-1 play a crucial role in promoting the formation of crossovers, evidenced by the lack of chiasmata in the cosa-1 mutant, GFP::COSA-1 exhibits an interesting localization pattern to presumptive crossover sites. In particular, unlike other crossover promoting proteins MSH-5 and ZHP-3, GFP::COSA-1 does not exhibit an initial broader localization but instead localizes to just 6 foci, 1 focus for the 1 crossover on each of the 6 chromosomes. This localization of GFP::COSA-1 to 6 foci was robust under various conditions. Mathematical modeling of the relationship between irradiation dose and COSA-1 foci revealed a relationship between obligate crossover, the phenomenon in which at least one crossover is formed per chromosome, and crossover interference, the phenomenon in which the formation of a crossover inhibits the formation of other crossovers nearby. In addition, analysis of GFP::COSA-1 foci in mutants that form extra crossovers, in particular rtel-1 and dpy-28, revealed a separation between the number of GFP::COSA-1 foci, 6, and the number of COs made, more than 6, suggesting that interference is still operating on GFP::COSA-1foci. Thus GFP::COSA-1 may serve as a better readout for crossover interference than crossovers per se. The ability to visualize GFP::COSA-1 in live worms holds great potential for elucidating the mechanisms involved in crossover interference, crossover distribution, and crossover designation.
  • 2013 Springer
    Barrangou, Rodolphe; Oost, John van der.
    CRISPR-Cas is a recently discovered defense system which protects bacteria and archaea against invasion by mobile genetic elements such as viruses and plasmids. A wide spectrum of distinct CRISPR-Cas immune systems has been identified in at least half of the available prokaryotic genomes. On-going biochemical and functional analyses have resulted in substantial insight into the functions and possible applications of these fascinating systems, although many secrets remain to be uncovered. In this book, experts summarize the state of the art of this exciting field.
  • 1994- Wiley
    Dracopoli, Nicholas C.
    ch. 1. Genetic Mapping -- ch. 2. Genotyping -- ch. 3. Somatic Cell Hybrids -- ch. 4. Cytogenetics -- ch. 5. Strategies for Large-Insert Cloning and Analysis -- ch. 6. Identifying Candidate Genes in Genomic DNA -- ch. 7. Searching Candidate Genes for Mutations -- ch. 8. Clinical Cytogenetics -- ch. 9. Clinical Molecular Genetics -- ch. 10. Cancer Genetics -- ch. 11. Transcriptional Profiling -- ch. 12. Vectors for Gene Therapy -- ch. 13. Delivery Systems for Gene Therapy -- ch. 14. Forensic Genetics -- ch. 15. Model Systems for the Analysis of Human Disease -- ch. 16. Automation and Robotics in Genetic Analysis -- ch. 17. Biochemical Genetics --ch. 18. High-Throughput Sequencing -- ch. 19. Mitochondrial Genetics -- ch. 20. Epigenetics -- Appendix 1. Abbreviations and Useful Data -- Appendix 2. Laboratory Guidelines, Equipment, and Stock Solutions -- Appendix 3. Commonly Used Techniques -- Appendix 4. Chromosome Karyotyping and Idiograms -- Appendix 5. Genetic Linkage Reference Maps: Access to Internet-Based Resources -- Appendix 6. Human-Mouse Comparative Maps -- Appendix. Suppliers.
    Also available: Print – 1994-2010.
  • v. 1-2, 2008. Springer Protocols
    v. 2, 2008 Springer Protocols
    Posch, Andrew.
    Isolation of mitochondria from plant cell culture / Etienne H. Meyer and A. Harvey Millar -- Isolation and preparation of choroplasts from Arabidopsis thaliana plants / Sybille E. Kubis, Kathryn S. Lilley, and Paul Jarvis -- Isolation of plant cell wall proteins / Elisabeth Jamet ... [et al.] -- Isolation and fractionation of the endoplasmic reticulum from castor bean (Ricinius communis) endosperm for proteomic analyses / William J. Simon, Daniel J. Maltman, and Antoni R. Slabas -- Cell wall fractionation for yeast and fungal proteomics / Aida Pitarch, Césa Nombela, and Concha Gil -- Sample preparation procedure for cellular fungi / Alois Harder -- Isolation and enrichment of secreted proteins from filamentous fungi / Martha L. Medina and Wilson A. Frnacisco -- Isolation and solubilization of cellular membrane proteins from bacteria / Kheir Zuobi-Hasona and L. Jeannine Brady -- Isolation and solubilization of gram-positive bacterial cell wall-associated proteins / Jason N. Cole, Steven P. Djordjevic, and Mark J. Walker -- Cell fractionation of parasitic protozoa / Wanderley de Souza, José Andrés-Morgado-Diaz, and Narcisa L. Cunha-e-Silva Volume 2. Application of fluorescence dye saturation labeling for differential proteome analysis of 1,000 microdissected cells from pancreatic ductal adenocarcinoma precursoe lesions / Barbara Sitek ... [et al.] -- Albumin and immunoglobulin depletion of human plasma / Rosalind e. Jenkins ... [et al.] -- Multi-component immunoaffinity subtraction and reversed-phase chromatography of human serum / James Martosella and Nina Zolotarjova -- Immunoaffinity fractionation of plasma proteins by chicken IgY antibodies / Lei Huang and Xiangming Fang -- Proteomics of cerebrospinal fluid methods for sample processing / John E. Hale ... [et al.] -- Sample preparation of bronchoalveolar lavage fluid / Baptiste Leroy, Paul Falmagne, and Ruddy Wattiez -- Preparation of nasal secretions for peoteome analysis / Begona Casado, Paolo Iadarola, and Lewis K. Pannell -- Preparation of urine samples for proteomic analysis / Rembert Pieper -- Isolation of cytoplasmatic proteins from cultures cells for two-dimensional gel electrophoresis / Ying Wang, Jen-Fu Chiu, and Qing-Yu He -- Sample preparation of culture medium from Madin-Darby Canine Kidney cells / Daniel Ambort, Daniel Lottaz, and Erwin Sterchi -- Sample preparation for mass spectrometry analysis of formalin-fixed paraffin-embedded tissue proteomic analysis of formalin-fixed tissue / Nicolas A. Stewart and Timothy D. Veenstra -- Metalloproteomics in the molecular study of cell physiology and disease / Hermann-Josef Thierse, Stefanie Helm, and Patrick Pankert -- Protein extraction from green plant tissue / Ragnar Flengsrud -- The terminator a device for high-throughput extraction of plant material / B. M. van den Berg -- Volume 1. Mechanical/physical methods of cell disruption and tissue homogenization / Stanley Goldberg -- Bacteria and yeast cell disruption using lytic enzymes / Oriana Salazar -- Sample solublization buffers for two-dimensional electrophoresis / Walter Weiss and Angelika Görg -- Quantitation of protein in samples prepared for 2-D electrophoresis / Tom Berkelman -- Removal of interfering substances in samples prepared for two-dimensional (2-D) electrophoresis / Tom Berkelman -- Protein concentration by hydrophilic interaction chromatography combined with solid phase extraction / Ulrich Schneider -- Difference gel electrophoresis based on lys/cys tagging / Reiner Westermeier and Burghardt Scheibe -- Isotope-coded two-dimensional maps: tagging with deuterated acrylamide and 2-vinylpyridine / Pier Giorgio Righetti, Roberto Sebastiano, and Attilio Citterio.
  • 2011 Springer Protocols
    Eisenacher, Martin; Hamacher, Michael; Stephan, Christian.
    Instruments and methods in proteomics -- In-depth protein characterization by mass spectrometry -- Analysis of phosphoproteomics data -- The origin and early reception of sequence databases -- Laboratory data and sample management for proteomics -- PRIDE and "Database on demand" As valuable tools for computational proteomics -- Analysing proteomics identifications in the context of functional and structural protein annotation: Integrating annotation using PICR, DAS, and BioMart -- Tranche distributed repository and proteomecommons.Org -- Data standardization by the HUPO-PSI: How has the community benefitted? -- mzIdentML: An open community-built standard format for the results of proteomics spectrum identification algorithms -- Spectra, chromatograms, metadata: mzML-the standard data format for mass spectrometer output -- imzML: Imaging mass spectrometry markup language: A common data format for mass spectrometry imaging -- Tandem mass spectrometry spectral libraries and library searching -- Inter-lab proteomics: Data mining in collaborative projects on the basis of the HUPO brain proteome project's pilot studies -- Data management and data integration in the HUPO plasma proteome project -- Statistics in experimental design, preprocessing, and analysis of proteomics data -- The evolution of protein interaction networks -- Cytoscape: Software for visualization and analysis of biological networks -- Text mining for systems modeling -- Identification of alternatively spliced transcripts using a proteomic informatics approach -- Distributions of ion series in ETD and CID spectra: Making a comparison -- Evaluation of peak-picking algorithms for protein mass spectrometry -- OpenMS and TOPP: Open source software for LC-MS data analysis -- LC/MS data processing for label-free quantitative analysis -- Spectral properties of correlation matrices - towards enhanced spectral clustering -- Standards, databases, and modeling tools in systems biology -- Modeling of cellular processes: Methods, data, and requirements.
  • 2012 Springer Protocols
    Bonin, Aurélie; Pompanon, François.
    Sampling and experimental design: Sampling in landscape genomics / Stéphanie Manel, Cécile H. Albert, and Nigel G. Yoccoz. OligoTag : a program for designing sets of tags for next-generation sequencing of multiplexed samples / Eric Coissac. SNP discovery in non-model organisms using 454 next generation sequencing / Christopher W. Wheat. In silico fingerprinting (ISIF) : a user-friendly in silico AFLP program / Margot Paris and Laurence Després -- Producing data: Diversity arrays technology : a generic genome profiling technology on open platforms / Andrzej Kilian [and others]. Two methods to easily obtain nucleotide sequences from AFLP loci of interest / Margot Paris [and others]. Roche genome sequencer flx based high-throughput sequencing of ancient DNA / David E. Alquezar-Planas and Sarah L. Fordyce. Preparation of normalized cDNA libraries for 454 titanium transcriptome sequencing / Zhao Lai [and others]. RAD paired-end sequencing for local de novo assembly and SNP discovery in non-model organisms / Paul D. Etter and Eric Johnson -- Analyzing data: Automated scoring of AFLPs using RawGeno v 2.0, a free R CRAN library / Nils Arrigo, Rolf Holderegger, and Nadir Alvarez. Haplotype inference / Olivier Delaneau and Jean-François Zagury-- Allele identification in assembled genomic sequence datasets / Katrina M. Dlugosch and Aurélie Bonin. Multiple testing in large-scale genetic studies / Matthieu Bouaziz, MArine Jeanmougin, and Mickaël Guedj. Population genomic analysis of model and nonmodel organisms using sequenced RAD tags / Paul A. Hobenlobe, Julian Catchen, and William A. Cresko. Analysis and management of gene and allelic diversity in subdivided populations using the software program METAPOP / Andrés Pérez-Figueroa, Silvia T. Rodriquez-Ramillo, and ARmando Caballero. DetSel : an R-package to detect marker loci responding to selection / Renaud Vitalis. Use of qualitative environmental and phenotypic variables in the context of allele distribution models : detecting signatures of selection in the genome of Lake Victoria cichlids / Stéphane Joost [and others]. Genomic scan as a tool for assessing the genetic component of phenotypic variance in wild populations / Carlos M. Herrera.
  • v. 1-5, 1961-.
    Gedda, Luigi.
    Status: Not Checked OutLane Catalog Record
  • 2011
    Burriesci, Matthew Strecker; Altman, Russ B.; Long, Sharon; Pringle, John R.; Sherlock, Gavin.
    This dissertation describes a general method for identifying and roughly quantifying the metabolites that are produced by symbiotic dinoflagellates and transferred to cnidarian hosts. I developed a system of rapid filtration and gas chromatography-mass spectrometry (GC-MS) to identify these compounds in the anemone tissue and dinoflagellates separately. I used 13C-sodium bicarbonate to label compounds produced from newly-fixed carbon; the principal compound detected in the animal was glucose. I developed a way to visualize these and other large GC-MS datasets using open-source software. I also built tools for analyzing Ultra-High-Throughput-Sequencing (UHTS) data, and these were useful in the de novo assembly of the Aiptasia pallida transcriptome. One tool I developed compares each read to each other read using a MapReduce framework to merge near-duplicate reads and reduce redundancy in the dataset. In addition, our lab sequenced symbiotic animals and therefore often worked with pools of sequences from multiple organisms. I developed a tool for identifying which transcript sequence was produced by which organism in a symbiotic ecosystem: it was 99% accurate on high-quality validation data.
  • 2011
    Shestopalov, Ilya A.; Chen, James K.; Kool, Eric T.; Wender, Paul A.
    Embryonic development is a remarkable program of cell proliferation, migration, and differentiation that transforms a single fertilized egg into a complex multicellular organism. This process depends on spatial and temporal control of gene function, and deciphering the molecular mechanisms that underlie pattern formation requires novel methods for perturbing gene expression with similar precision. Synthetic reagents can help meet this demand, and in this thesis I describe the development and application of caged morpholino (cMO) oligonucleotides for inactivating genes in zebrafish and other optically transparent organisms with spatiotemporal control simply by irradiating embryonic tissues with a focused light beam. In chapter 1 I provide an overview of the zebrafish model system of vertebrate development and survey the capabilities and limitations of various oligonucleotide-based technologies for perturbing RNA function and tracking RNA expression in zebrafish. I examine various light-gated oligonucleotide technologies that exploit the optical transparency of zebrafish embryos, including cMOs, for achieving spatiotemporal control of RNA function. In chapter 2 we describe the initial synthesis of a cMO targeting expression of the no tail a (ntla) transcription factor. By permitting spatiotemporal gene regulation in zebrafish embryos, the ntla cMO was used to make initial observations into the time-dependent role of this gene in notochord formation. In chapter 3 we report optimized methods for the design and synthesis of hairpin cMOs, incorporating a dimethoxynitrobenzyl (DMNB)-based bifunctional linker that permits cMO assembly in only three steps from commercially available reagents. Using this simplified procedure, we have systematically prepared cMOs with differing structural configurations and investigated how the in vitro thermodynamic properties of these reagents correlate with their in vivo activities. Through these studies, I have established general principles for cMO design and successfully applied them to several developmental genes. Our optimized synthetic and design methodologies have also enabled us to prepare a next-generation cMO that contains a bromohydroxyquinoline (BHQ)-based linker for two-photon uncaging. Collectively, these advances established the generality of cMO technologies to facilitate the application of these chemical probes in vivo for functional genomic studies. Finally, in chapter 4 we illustrate the utility of the cMO technology in isolating spatiotemporally-distinct functions of transcription factors -- genes that play diverse roles during embryonic development, with each controlling multiple cellular states in a spatially and temporally defined manner. Resolving the dynamic transcriptional profiles that underlie these patterning processes is essential for understanding embryogenesis at the molecular level; however, probing in vivo gene function with comparable spatiotemporal precision has been a technological challenge. To address this need, I have integrated cMOs with similarly caged fluorophores, fluorescence-activated cell sorting (FACS), and microarray technologies. Using this approach, I have dynamically profiled the No tail-a (Ntla)-dependent transcriptome at different stages of zebrafish mesoderm development, discovering discrete sets of genes that are associated with either notochord cell fate commitment or subsequent changes in cell function. Our studies elucidated the roles of several Ntla-regulated genes in notochord development and demonstrated the activation of multiple transcriptomes within a cell lineage by a single transcription factor.
  • 2006
    King, Robert C.; Mulligan, Pamela Khipple; Stansfield, William D.
    Status: Not Checked OutLane Catalog Record
  • 2013 Springer Protocols
    Eichinger, Ludwig; Rivero-Crespo, Francisco.
    Amoebozoa / Christina Schilde and Pauline Schaap -- Model organism Dictyostelium discoideum / Salvatore Bozzaro -- Comparative genomics of the dictyostelids / William F. Loomis -- One stop shop for everything Dictyostelium : dictyBase and the dicty stock center in 2012 / Petra Fey [and others] -- Fluorescent reporters and methods to analyze fluorescent signals / Annette Müller-Taubenberger and Hellen C. Ishikawa-Ankerhold -- Collection and cultivation of dictyostelids from the wild / Tracy E. Douglas [and others] -- Identification and verification of microRNAs by high-throughput sequencing / Jimmie Hällman [and others] -- Transcriptional profiling of Dictyostelium with RNA sequencing / Edward Roshan Miranda [and others] -- Analysis of chromatin organization by deep sequencing technologies / James L. Platt [and others] -- Pharmacogenetics of resistance to cisplatin and other anticancer drugs and the role of sphingolipid metabolism / Stephen Alexander, William S. Swatson, and Hannah Alexander -- N-glycomic and n-glycoproteomic studies in the social amoebae / Christa L. Feasley -- Measuring cheating, fitness, and segregation in Dictyostelium discoideum / Neil J. Buttery [and others] -- Application of the Cre-loxP system for generating multiple knock-out and knock-in targeted loci / Jan Faix [and others] -- Extrachromosomal inducible expression / Douwe M. Veltman and Peter J.M. Van Haastert -- Isolation of Dictyostelium nuclei for light and electron microscopy / Petros Batsios [and others] -- Investigation of DNA repair pathway activity / Anne-Marie C. Couto, Nicholas D. Lakin, and Catherine J. Pears -- Transcript localization in Dictyostelium discoideum cells by RNA FISH / Patrick Hofmann, Janis Kruse, and Christian Hammann -- Analysis of mitochondrial gene expression / Jessica E. Accari [and others] -- Mitochondrial respiratory complex function and the phenotypic consequences of dysfunction / Sarah J. Annesley [and others] -- Micropipette aspiration for studying cellular mechanosensory responses and mechanics / Yee-Seir Kee and Douglas N. Robinson -- Quantitative analysis of phagocytosis and phagosome maturation / Natascha Sattler, Roger Monroy, and Thierry Soldati -- Setting up and monitoring an infection of Dictyostelium discoideum with mycobacteria / Sonia Arafah [and others] -- Isolation of pathogen-containing vacuoles / Olga Shevchuk and Michael Steinert -- Immunomagnetic purification of fluorescent legionella-containing vacuoles / Ivo Finsel, Christine Hoffmann, and Hubert Hilbi -- Secretory lysosomes in Dictyostelium : visualization, characterization, and dynamics / Wanessa C. Lima and Pierre Cosson -- Monitoring autophagy in Dictyostelium / Ana Mesquita [and others].
  • 2006 Springer Protocols
    Eichinger, Ludwig; Rivero-Crespo, Francisco.
  • 2005 Springer Protocols
    Liang, Peng; Meade, Jonathan D.; Pardee, Arthur B.
    Global analysis of gene expression by differential display : a mathematical model / Shitao Yang and Peng Liang -- Automation of fluorescent differential display with digital readout / Jonathan D. Meade ... [et al.] -- Ordered differential display / Mikhail V. Matz and Ella A. Meleshkevitch -- GeneCalling : transcript profiling coupled to a gene database query / Richard A. Shimkets -- High-density sampling differential display of prokaryotic mRNAs with RAP-PCR / Dana M. Walters and Pierre E. Rouviere -- Vertical arrays : microarrays of complex mixtures of nucleic acids / Rosana Risques ... [et al.] -- Automated pattern ranking in differential display data analysis / Tero Aittokallio ... [et al.] -- Linking cDNA-AFLP-based gene expression patterns and ESTs / Ling Qin, Pjotr Prins, and Johannes Helder -- Differentially expressed genes associated with hepatitis B virus HBx and MHBs protein function in hepatocellular carcinoma / Dae-Ghon Kim -- Identification of disease markers by differential display : prion disease / Michael Clinton ... [et al.] -- Saturation screening for p53 target genes by digital fluorescent differential display / Yong-Jig Cho ... [et al.] -- Identification of p53-regulated genes by the method of differential display / Yunping Lin, Roger P. Leng, and Samuel Benchimol -- Identification by differential display of IL-24 autocrine loop activated by ras oncogenes / Zhongjia Tan, Mai Wang, and Peng Liang -- Comprehensive analysis of ovarian gene expression during ovulation using differential display / Lawrence L. Espey -- Functional analysis of nocturnin : a circadian clock-regulated gene identified by differential display / Julie E. Baggs and Carla B. Green -- Isolation and characterization of anthocyanin 5-0-glucosyltransferase in perilla frutescens var. crispa by differential display / Mami Yamasaki and Kazuki Saito -- Identification of target genes of a yeast transcriptional repressor / Bernard Mai and Linda L. Breeden -- Detection of an mRNA polymorphism by differential display / Shan Liang ... [et al.] -- Silencing in yeast : identification of CLr4 targets / Sergey V. Ivanov and Alla V. Ivanova -- Identification of mRNA bound to RNA binding proteins by differential display / Anne Carr-Schmid, Xinfu Jiao, and Megerditch Kiledjian.
  • 2014 Springer Protocols
    Ackerley, David F.; Copp, Janine N.; Gillam, Elizabeth M. J.
  • 2002 Wiley
    Brakmann, Susanne; Johnsson, Kai.
    ch. 1. Introduction, p. 1-3 / Kai Johnsson and Susanne Brakmann, p. 1-3 -- ch. 2. Evolutionary Biotechnology - From Ideas and Concepts to Experiments and Computer Simulations / Peter Schuster, p. 5-28 -- ch. 3. Using Evolutionary Strategies to Investigate the Structure and Function of Chorismate Mutases / Donald Hilvert, Sean V. Taylor and Peter Kast, p. 29-62 -- ch. 4. Construction of Environmental Libraries for Functional Screening of Enzyme Activity / Rolf Daniel, p. 63-78 -- ch. 5. Investigation of Phage Display for the Directed Evolution of Enzymes / Patrice Soumillion and Jacques Fastrez, p. 79-110 -- ch. 6. Directed Evolution of Binding Proteins by Cell Surface Display: Analysis of the Screening Process / K. Dane Wittrup, p. 111-126 -- ch. 7. Yeast n-Hybrid Systems for Molecular Evolution / Brian T. Carter, Hening Lin and Virginia W. Cornish, p. 127-158 -- ch. 8. Advanced Screening Strategies for Biocatalyst Discovery / Andreas Schwienhorst, p. 159-175 -- ch. 9. Engineering Protein Evolution / Stefan Lutz and Stephen J. Benkovic, p. 177-213 -- ch. 10. Exploring the Diversity of Heme Enzymes through Directed Evolution / Patrick C. Cirino and Frances H. Arnold, p. 215-243 -- ch. 11. Directed Evolution as a Means to Create Enantioselective Enzymes for Use in Organic Chemistry / Manfred T. Reetz and Karl-Erich Jaeger, p. 245-279 -- ch. 12. Applied Molecular Evolution of Enzymes Involved in Synthesis and Repair of DNA / John F. Davidson, Jon Anderson, Haiwei Guo, Daniel Landis and Lawrence A. Loeb, p. 281-307 -- ch. 13. Evolutionary Generation Versus Rational Design of Restriction Endonucleases with Novel Specificity / Thomas Lanio, Albert Jeltsch and Alfred Pingoud, p. 309-327 -- ch. 14. Evolutionary Generation of Enzymes with Novel Substrate Specificities / Uwe T. Bornscheuer, p. 329-341.
  • 2013 Springer
    Vogelsang, Matjaž.
    Lynch syndrome (LS) is the most common cause of inherited colorectal cancer, a disease with a high mortality rate. An estimated 37,000 of diagnosed colorectal cancer cases worldwide are attributed to Lynch syndrome each year. Intensive cancer screening, with early initiation and frequent follow-up, can reduce colorectal cancer incidence and mortality in LS patients. This book provides an up-to-date overview on the genetic and epigenetic basis of Lynch syndrome. It evaluates clinical features of the disease and critically comments on molecular tools available for identifying mutations responsible for Lynch syndrome; in addition the importance of functional assays that can help clarify the clinical nature of identified mutations is also discussed. The book also focuses on challenges in genetic counselling of at-risk individuals and discusses related ethical issues. The purpose of the book is to give a concise knowledge base for the broader scientific and medical community, including genetic counselors, in order to improve awareness on the potential impact that the diagnosis of LS has on treatment, management and surveillance of LS patients.
  • 2014 CRCnetBASE
    Sozer, Amanda C.
    1. Human identification through DNA analysis -- 2. Mass fatalities -- 3. Postmortem functions : body recovery and morgue operations -- 4. Antemortem functions : family assistance operations -- 5. Identification of remains -- 6. Identification and collection of biological samples from human remains -- 7. Identification and collection of DNA reference samples -- 8. Application of DNA technology for human identification -- 9. DNA profile analysis and interpretation -- 10. DNA sample, case, and data tracking using information technology tools -- 11. Implementing and maintaining a quality DNA program -- 12. Laboratory development -- 13. Delivering effective training.
  • 2009 Springer Protocols
    Bugert, Peter.
    PCR-ELISA for high-throughput blood group genotyping / Maryse St-Louis -- Single base extension in multiplex blood group genotyping / Gregory A. Denomme -- Real-time PCR assays for high-throughput blood group genotyping / Fernando Araujo -- Real-time PCR assays for high-throughput human platelet antigen typing / Simon E. McBride -- Multiplex ABO genotyping by minisequencing / Gianmarco Ferri and Susi Pelotti -- Multiplex genotyping for thrombophilia-associated SNPs by universal bead arrays / Susan Bortolin -- Pyrosequencing of toll-like receptor polymorphisms of functional relevance / Parviz Ahmad-Nejad -- Multiplex HLA-typing by pyrosequencing / Ying Lu ... [et al.] -- High-throughput multiplex HLA-typing by ligase detection reaction (LDR) and universal array (UA) approach / Clarissa Consolandi -- Medium- to high-throughput SNP genotyping using VeraCode microbeads / Charles H. Lin ... [et al.] -- The use of maternal plasma for prenatal RhD blood group genotyping / Kirstin Finning, Pete Martin, and Geoff Daniels -- Nanoliter high-throughput PCR for DNA and RNA profiling / Colin J.H. Brenan, Douglas Roberts, and James Hurley -- RNA stabilization of peripheral blood and profiling by bead chip analysis / Svenja Debey-Pascher, Daniela Eggle, and Joachim L. Schultze -- RNA profiling in peripheral blood cells by fluorescent differential display PCR / Martin Steinau and Mangalathu S. Rajeevan -- cDNA amplification by SMART-PCR and suppression subtractive hybridization (SSH)-PCR / Andrew Hillmann, Eimear Dunne, and Dermot Kenny -- Transcript profiling of human platelets using microarray and serial analysis of gene expression (SAGE) / Dmitri V. Gnatenko ... [et al.] -- Genome-wide platelet RNA profiling in clinical samples / Angelika Schedel and Nina Rolf -- PCR-based amplification of platelet mRNA sequences obtained from small-scale platelet samples / Jutta M. Rox, Jens Müller, and Bernd Pötzsch -- MicroRNA profiling of megakaryocytes / Ramiro Garzon -- Serial analysis of gene expression adapted for downsized extracts / SAGE/SADE) analysis in reticulocytes / Béatrice Bonafoux and Thérèse Commes -- Real-time PCR analysis for blood cell lineage specific markers / Louise Edvardsson and Tor Olofsson -- Monitoring the immune response using real-time PCR / Patrick Stordeur.
  • 2002 CRCnetBASE
    Grigorenko, Elena V.
  • 2012 Springer Protocols
    Erickson, David L.; Kress, W. John.
    DNA barcodes : methods and protocols / W. John Kress and David L. Erickson -- Introduction to animal DNA barcoding protocols / Lee A. Weigt [and others] -- DNA barcodes for insects / John James Wilson -- DNA barcoding methods for invertebrates / Nathaniel Evans and Gustav Paulay -- DNA barcoding amphibians and reptiles / Miguel Vences [and others] -- DNA barcoding fishes / Lee A. Weigt -- DNA barcoding birds : from field collection to data analysis / Dario A. Lijtmaer [and others] -- DNA barcoding in mammals / Natalia V. Ivanova, Elizabeth L. Clare, and Alex V. Borisenko -- Methods for DNA barcoding of fungi / Ursula Eberhardt -- Methods for DNA barcoding photosynthetic protists emphasizing the macroalgae and diatoms / Gary W. Saunders and Daniel C. McDevit -- DNA barcoding methods for land plants / Aron J. Fazekas [and others] -- Field information management systems for DNA barcoding / John Deck [and others] -- Laboratory information management systems for DNA barcoding / Meaghan Parker [and others] -- DNA extraction, preservation, and amplification / Thomas Knebelsberger and Isabella Stoger -- DNA mini-barcodes / Mehrdad Hajibabaei and Charly McKenna -- Ways to mix multiple PCR amplicons into single 454 run for DNA barcoding / Ryuji J. Machida and Nancy Knowlton -- Practical evaluation of DNA barcode efficacy / John L. Spouge and Leonardo Marino-Ramirez -- Plant DNA Barcodes, Taxonomic Management and Species Discovery in Tropical Forests / Christopher W. Dick and Campbell O. Webb -- Construction and Analysis of Phylogenetic Trees Using DNA Barcode Data / David L. Erickson and Amy C. Driskell -- Phylogenetic analyses of ecological communities using DNA barcode data / Nathan G. Swenson -- FISH-BOL, a case study for DNA barcodes / Robert D. Ward -- Generating plant DNA barcodes for trees in long-term forest dynamics plots / W. John Kress, Ida C. Lopez, and David L. Erickson -- Future directions / David L. Erickson and W. John Kress.
  • 2014 Springer Protocols
    Lale, Rahmi; Valla, Svein.
    1. BioBrick assembly standards and techniques and associated software tools / Gunvor Røkke, Eirin Korvald, Jarle Pahr, Ove Øyås and Rahmi Lale -- 2. Plasmid construction by SLIC or sequence and ligation- independent cloning / Ryan E. Hill and Julian J. Eaton-Rye -- 3. Quick and clean cloning / Frank Thieme and Sylvestre Marillonnet -- 4. Hierarchical ligation-independent assembly of PCR fragments / Jonathan L. Schmid-Burgk, Zhen Xie, and Yaakov Benenson -- 5. USER-derived cloning methods and their primer design / Bo Salomonsen, Uffe H. Mortensen, and Barbara A. Halkier -- 6. Application of the restriction-free (RF) cloning for multicomponents assembly / Yoav Peleg and Tamar Unger -- 7. A single-tube assembly of DNA using the transfer-PCR (TPCR) platform / Ariel Erijman, Julia M. Shifman, and Yoav Peleg -- 8. Circular polymerase extension cloning / Jiayuan Quan and Jingdong Tian -- 9. Golden gate cloning / Carola Engler and Sylvestre Marillonnet -- 10. Design and construction of multigenic constructs for plant biotechnology using the goldenbraid cloning strategy / Alejandro Sarrion-Perdigones, Jorge Palaci, Antonio Granell and Diego Orzaez -- 11. FX cloning : a simple and robust high-throughput cloning method for protein expression / Eric R. Geertsma -- 12. Minimum GC-rich sequences for overlap extension PCR and primer annealing / Mikiko Nakamura, Ayako Suzuki, Hisashi Hoshida and Rinji Akada -- 13. Simple cloning and DNA assembly in Escherichia coli by prolonged overlap extension PCR / Chun You and Y.-H. Percival Zhang -- 14. Combinatorial assembly of clone libraries using site-specific recombination / Vanessa E. Wall, Leslie A. Garvey, Jennifer L. Mehalko, Lauren V. Procter and Dominic Esposito -- 15. Application of In-Fusion [trademark] cloning for the parallel construction of E. coli expression vectors / Louise E. Bird, Heather Rada, John Flanagan, Jonathan M. Diprose, Robert J.C. Gilbert and Raymond J. Owens -- 16. Seamless ligation cloning extract (SLiCE) cloning method / Yongwei Zhang, Uwe Werling, and Winfried Edelmann -- 17. j5 DNA assembly design automation / Nathan J. Hillson -- 18. FastPCR software for PCR, in silico PCR, and oligonucleotide assembly and analysis / Ruslan Kalendar, David Lee, and Alan H. Schulman.
  • 2005 Springer
    Ohyama, Takashi.
    DNA: alternative conformations and biology / Vladimir N. Potaman and Richard R. Sinden -- Sequence-dependent variability of B-DNA: an update on bending and curvature / Victor B. Zhurkin ... [et al.] -- Curved DNA and prokaryotic promoters: a mechanism for activation of transcription / Munehiko Asayama and Takashi Ohyama -- Repression of transcription by curved DNA and nucleoid protein H-NS: a mode of bacterial gene regulation / Cynthia L. Pon, Stefano Stella and Claudio O. Gualerzi -- Curved DNA and transcription in eukaryotes / Takashi Ohyama -- Putative roles of kin17, a mammalian protein binding -- Curved DNA, in transcription / Jaime F. Angulo ... [et al.] -- Roles for Z- and double-stranded RNA in transcription: encoding genetic information by shape rather than by sequence / Alan Herbert -- Do DNA triple helices or quadruplexes have a role in transcription? / Michael W. Van Dyke -- Nucleic acid structures and the transcription defects in fragile X syndrome and Friedreich's ataxia / Karen Usdin -- Possible roles of DNA supercoiling in transcription / Susumu Hirose and Kuniharu Matsumoto -- Gene regulation by HMGA and HMGB chromosomal proteins and related architectural DNA-binding proteins / Andrew A. Travers -- Molecular mechanisms of male sex determination: the enigma of SRY / Michael A. Weiss -- The role of unusual DNA structures in chromatin organization for transcription / Takashi Ohyama -- DNA bendability and nucleosome positioning in transcriptional regulation / Mensur Dlaki, David W. Ussery and Sren Brunak.
  • 2009 Springer Protocols
    Didenko, Vladimir V.
    In situ detection of apoptosis by the TUNEL assay: An overview of techniques -- Combination of TUNEL assay with immunohistochemistry for simultaneous detection of DNA fragmentation and oxidative cell damage -- EM-ISEL: A useful tool to visualize DNA damage at the ultrastructural level -- In situ labeling of DNA breaks and apoptosis by T7 DNA polymerase -- In situ ligation: A decade and a half of experience -- In situ ligation simplified: Using PCR fragments for detection of double-strand DNA breaks in tissue sections -- 5'OH DNA breaks in apoptosis and their labeling by topoisomerase-based approach -- Detection of DNA strand breaks in apoptotic cells by flow- and image-cytometry -- Fluorochrome-labeled inhibitors of caspases: Convenient in vitro and in vivo markers of apoptotic cells for cytometric analysis -- Combining fluorescent in situ hybridization with the comet assay for targeted examination of DNA damage and repair -- Simultaneous labeling of single- and double-strand DNA breaks by DNA breakage detection-FISH (DBD-FISH) -- Co-localization of DNA repair proteins with UV-induced DNA damage in locally irradiated cells -- Ultrasound imaging of apoptosis: Spectroscopic detection of DNA-damage effects at high and low frequencies -- Quantifying etheno-DNA adducts in human tissues, white blood cells, and urine by ultrasensitive (32)P-postlabeling and immunohistochemistry -- ELISpot assay as a tool to study oxidative stress in peripheral blood mononuclear cells -- Cytokinesis-block micronucleus cytome assay in lymphocytes -- Buccal micronucleus cytome assay -- [Gamma]-H2AX detection in peripheral blood lymphocytes, splenocytes, bone marrow, xenografts, and skin -- Immunologic detection of benzo(a)pyrene-DNA adducts -- Non-invasive assessment of oxidatively damaged DNA: Liquid chromatography-tandem mass spectrometry analysis of urinary 8-oxo-7,8-dihydro-2'-deoxyguanosine -- Assessing sperm DNA fragmentation with the sperm chromatin dispersion test.
  • 2005 CRCnetBASE
    Doetsch, Paul W.; Kow, Yoke Wah; Siede, Wolfram.
  • 2013 Springer Protocols
    Makovets, Svetlana.
    DNA electrophoresis: historical and theoretical perspectives / Gareth A. Roberts and David T.F. Dryden -- Basic DNA electrophoresis in molecular cloning: a comprehensive guide for beginners / Svetlana Makovets -- Analysis of branched DNA replication and recombination intermediates from prokaryotic cells by two-dimensional (2D) native-native agarose gel electrophoresis / Nicholas P. Robinson -- Analysis of DNA structures from eukaryotic cells by two-dimensional native-native DNA agarose gel electrophoresis / Andreas S. Ivessa -- Directionality of replication fork movement determined by two-dimensional native-native DNA agarose gel electrophoresis / Andreas S. Ivessa -- Native/denaturing two-dimensional DNA electrophoresis and its application to the analysis of recombination intermediates / Jessica P. Lao, Shangming Tang, and Neil Hunter -- Plasmid DNA topology assayed by two-dimensional agarose gel electrophoresis / Jorge B. Schvartzman [and three others] -- A neutral glyoxal gel electrophoresis method for the detection and semi-quantitation of DNA single-strand breaks / Brian Pachkowski and Jun Nakamura -- Denaturing gradient gel electrophoresis (DGGE) / Fiona Strathdee and Andrew Free -- Polyacrylamide temperature gradient gel electrophoresis / Viktor Viglasky -- Separation of DNA oligonucleotides using denaturing urea PAGE / Fiona Flett and Heidrun Interthal -- Pulsed-field gel electrophoresis of bacterial chromosomes / Julia S.P. Mawer and David R.F. Leach -- Resolution of budding yeast chromosomes using pulsed-field gel electrophoresis / Aziz El Hage and Jonathan Houseley -- Analysis of DNA damage via single-cell electrophoresis / Diana Anderson and Julian Laubenthal -- Fluorescence in situ hybridization on electrophoresed cells to detect sequence specific DNA damage / Julian Laubenthal and Diana Anderson -- Analysis of DNA-protein interactions using PAGE: band-shift assays / Lynn Powell -- Assaying cooperativity of protein -- DNA interactions using agarose gel electrophoresis / Tanya L. Williams and Daniel L. Levy -- DNA bending by proteins: utilizing plasmid pBendAT as a tool / Fenfei Leng -- Using PCR coupled to PAGE for detection and semiquantitative evaluation of telomerase activity / Laura Gardano.
  • 2012 Springer Protocols
    Alonso, Antonio.
    An overview of DNA typing methods for human identification : past, present, and future / Robyn Thompson, Silvia Zoppis, and Bruce McCord -- Capillary electrophoresis and 5-channel LIF detection of a 26plex autosomal STR asay for human identification / Carolyn R. Hill -- Capillary electrophoresis of miniSTR markers to genotype highly degraded DNA samples / Michael D. Coble -- Interpretation guidelines of a standard Y-chromosome STR 17-plex PCR-CE assay for crime casework / Lutz Roewer and Maria Geppert -- Capillary electrophoresis of an X-chromosome STR decaplex for kinship deficiency cases / Leonor Gusmão [and others] -- A 48-plex autosomal SNP GenPlex Assay for human individualization and relationship testing / Carmen Tomas, Claus Børsting, and Niels Morling -- Typing of 49 autosomal SNPs by single base extension and capillary electrophoresis for forensic genetic testing / Claus Børsting, Carmen Tomas, and Niels Morling -- A 34-plex autosomal SNP single base extension assay for ancestry investigations / C. Phillips, M. Fondevila, and Maria Victoria Lareau -- SNaPshot® minisequencing analysis of multiple ancestry-informative Y-SNPs using capillary electrophoresis / Maria Geppert and Lutz Roewer -- Capillary electrophoresis of 38 noncoding biallelic mini-indels for degraded samples and as complementary tool in paternity testing / Rui Pereira and Leonor Gusmão -- Capillary electrophoresis of an 11-plex mtDNA coding region SNP single base extension assay for discrimination of themost common caucasian HV1/HV2 mitotype / Peter M. Vallone -- Capillary electrophoresis of a multiplex reverse transcription-polymerase chain reaction to target messenger RNA markers for body fluid identification / Cordula Haas, Erin Hanson, and Jack Ballantyne -- DNA extraction from aged skeletal samples for STR typing by capillary electrophoresis / René Huel [and others] -- Interpretation guidelines for multilocus STR forensic profiles from low template DNA samples / Zoran M. Budimlija and Theresa A. Caragine -- Interpretation guidelines for mixed-STR multilocus electrophoretic profiles / Juan Antonio Luque -- Capillary electrophoresis analysis of a 9-plex STR assay for canine genotyping / Barbara van Asch and António Amorim -- Capillary electrophoresis of DNA from Cannabis sativa for correlation of samples to geographic origin / Heather Mller Coyle -- Capillary electrophoresis of multigene barcoding chloroplast markers for species identification of botanical trace evidence / Gianmarco Ferri, Beatrice Corradini, and Milena Alù -- Capillary electrophoresis of big-dye terminator sequencing reactions for human mtDNA control region haplotyping in the identification of human remains / Marta Montesino and Lourdes Prieto -- Capillary electrophoresis of human mtDNA control region sequences from highly degraded samples using short mtDNA amplicons / Odile M. Loreille and Jodi A. Irwin -- Interpretation guidelines of mt DNA control region sequence electropherograms in forensic gnetics / Manuel Crespillo Marquez -- Capillary electrophoresis of mtDNA cytochrome b gene sequences for animal species identification / Adrian Linacre -- Sequence analysis of the canine mitochondrial DNA control region from shed hair samples in criminal investigations / C. Berger, B. Berger, and W. Parson -- Integrated sample cleanup and microchip capillary array electrophoresis for high-performance forensic STR profiling / Peng Liu [and others] -- Microchip capillary electrophoresis protocol to evaluate quality and quantity of mtDNA amplified fragments for DNA sequencing in forensic genetics / Coro Fernández and Antonio Alonso -- Microchip capillary electrophoresis of multi-locus VNTR analysis for genotyping of Bacillus anthracis and Yersinia pestis in microbial forensic cases / Andrea Ciammaruconi.
  • 2005 Springer
    Szyf, Moshe.
    DNA methylation : three decades in search of function / Aharon Razin -- Epigenetic mechanisms of gene regulation : relationships between DNA methylation, histone modification, and chromatin structure / Keith D. Robertson -- DNA hypo- vs. hypermethylation in cancer : tumor specificity, tumor progression, and therapeutic implications / Melanie Ehrlich and Guanchao Jiang -- DNA methylation in urological cancers / Wolfgang A. Schulz and Hans-Helge Seifert -- DNA methylation in colorectal cancer / Jeremy R. Jass ... [et al.] -- CpG island hypermethylation of tumor suppressor genes in human cancer : concepts, methodologies and uses / Michel Herranz and Manel Esteller -- The loss of methyl groups in DNA of tumor cells and tissues : the immunochemical approach / Alain Niveleau ... [et al.] -- Identifying clinicopathological association of DNA hypermethylation in cancers using CpG island microarrays / Susan H. Wei ... [et al.] -- Methylation analysis in cancer : (epi)genomic fast track from discovery to clinical routine / Carolina Haefliger, Sabine Maier and Alexander Olek -- Regulation of DNA methyltransferases in cancer / Nancy Detich and Moshe Szyf -- Inhibition of poly(ADP-ribosyl)ation allows DNA hypermethylation / Anna Reale ... [et al.] -- The role of active demethylation in cancer and its therapeutic potential / Moshe Szyf ... [et al.] -- Purine analogues and their role in methylation and cancer chemotherapy / Katherine L. Seley and Sylvester L. Mosley -- DNA methyltransferase inhibitors : paving the way for epigenetic cancer therapeutics / Gregory K. Reid and A. Robert MacLeod -- Preclinical and clinical studies on 5-aza-2'-deoxycytidine, a potent inhibitor of DNA methylation, in cancer therapy / Richard L. Momparler -- Anticancer gene therapy by in vivo DNA electrotransfer of MBD2 antisense / Pascal Bigey and Daniel Scherman.
  • 2006 Springer
    Böhm, P.; Doerfler, Walter.
    Also available: Print – 2006
  • 2006 Springer
    Böhm, P.; Doerfler, Walter.
    Regulation of chromatin and DNA-methylation patterns in blood cell development / C. Bonifer, P. Lefevre, and H. Tagoh -- Methylation dynamics in the early mammalian embryo : implications of genome reprogramming defects for development / T. Haaf -- Epigenetic regulation in drosophila / F. Lyko ... [et.al.] -- Epimutations in human disease / B. Horsthemke -- Epigenotypes of latent herpesvirus genomes / J. Minarovits -- Epigenetics of complex diseases : from general theory to laboratory experiments / A. Schumacher and A. Petronis -- MSL proteins and the regulation of gene expression / S. Rea and A. Akhtar -- DNA methylation profiles of female steroid hormone-driven human malignancies / M. Campan, D.J. Weisenberger, and P.W. Laird -- Genome-wide analysis of DNA methylation changes in human malignancies / C. Plass and D.J. Smiraglia -- Decreased fidelity in replicating DNA methylation patterns in cancer cells leads to dense methylation of a CpG island / N. Watanabe ... [et.al.] -- Methylation of endogenous human retroelements in health and disease / W. A. Schulz, C. Steinhoff, and A.R. Florl -- Cancer-linked DNA hypomethylation and its relationship to hypermethylation / M. Ehrlich.
    Also available: Print – 2006
  • 2005 Springer
    Esteller, Manel.
  • 2008 CRCnetBASE
    Wang, Sun-Chong; Petronis, Arturas.
  • 2006 CRCnetBASE
    Allison, David B.
    Also available: Print – 2006
  • pt. A-B, 2006. ScienceDirect
    pt. B ScienceDirect
    Kimmel, Alan R.; Oliver, B.
    Pt. A. Array platforms and wet-bench protocols -- pt. B. Databases and statistics.
    Also available: Print – pt. A-B, 2006.
  • 2011 Springer Protocols
    Tsubouchi, Hideo.
    Methods to study mitotic homologous recombination and genome stability / Xiuzhong Zheng, Anastasiya Epstein, and Hannah L. Klein -- Characterizing resection at random and unique chromosome double-strand breaks and telomere ends / Wenjian Ma [and others] -- Characterization of meiotic recombination initiation sites using pulsed-field gel electrophoresis / Sarah Farmer, Wing-Kit Leung, and Hideo Tsubouchi -- Genome-wide detection of meiotic DNA double-strand break hotspots using single-stranded DNA / Hannah G. Blitzblau and Andreas Hochwagen -- Detection of covalent DNA-bound Spo11 and topoisomerase complexes / Edgar Hartsuiker -- Molecular assays to investigate chromatin changes during DNA double-strand break repair in yeast / Scott Houghtaling, Toyoko Tsukuda, and Mary Ann Osley -- Analysis of meiotic recombination intermediates by two-dimensional gel electrophoresis / Jasvinder S. Ahuja and G. Valentin Borner -- Mapping of crossover sites using DNA microarrays / Stacy Y. Chen and Jennifer C. Fung -- Using the semi-synthetic epitope system to identify direct substrates of the meiosis-specific budding yeast kinase, Mek1 / Hsiao-Chi Lo and Nancy M. Hollingsworth -- Genetic and molecular analysis of mitotic recombination in Saccharomyces cerevisiae / Belen Gomez-Gonzalez, Jose F. Ruiz, and Andres Aguilera -- In vivo site-specific mutagenesis and gene collage using the delitto perfetto system in yeast Saccharomyces cerevisiae / Samantha Stuckey, Kuntal Mukherjee, and Francesca Storici -- Detection of RNA-templated double-strand break repair in yeast / Ying Shen and Francesca Storici -- SNP-Based Mapping of crossover recombination in Caenorhabditis elegans / Grace C. Bazan and Kenneth J. Hillers -- Characterization of meiotic crossovers in pollen from Arabidopsis thaliana / Jan Drouaud and Christine Mezard -- Isolation of meiotic recombinants from mouse sperm / Francesca Cole and Maria Jasin -- Homologous recombination assay for interstrand cross-link repair / Koji Nakanishi [and others] -- Evaluation of homologous recombinational repair in chicken B lymphoma cell line, DT40 / Hiroyuki Kitao, Seiki Hirano, and Minoru Takata -- Understanding the immunoglobulin locus specificity of hypermutation / Vera Batrak, Artem Blagodatski, and Jean-Marie Buerstedde -- Quality control of purified proteins involved in homologous recombination / Xiao-Ping Zhang and Wolf-Dietrich Heyer -- Assays for structure-selective DNA endonucleases / William D. Wright, Kirk T. Ehmsen, and Wolf-Dietrich Heyer -- In vitro assays for DNA pairing and recombination-associated DNA synthesis / Jie Liu, Jessica Sneeden, and Wolf-Dietrich Heyer -- In vitro assay for monitoring the formation and branch migration of holliday junctions mediated by a eukaryotic recombinase / Yasuto Murayama and Hiroshi Iwasaki -- Reconstituting the key steps of the DNA double-strand break repair in vitro / Matthew J. Rossi [and others] -- Biochemical studies on human Rad51-mediated homologous recombination / Youngho Kwon, Weixing Zhao, and Patrick Sung -- Studying DNA replication fork stability in xenopus egg extract / Yoshitami Hashimoto and Vincenzo Costanzo -- Supported lipid bilayers and DNA curtains for high-throughput single-molecule studies / Ilya J. Finkelstein and Eric C. Greene -- FRET-based assays to monitor DNA binding and annealing by Rad52 recombination mediator protein / Jill M. Grimme and Maria Spies -- Visualization of human Dmc1 presynaptic filaments / Michael G. Sehorn and Hilarie A. Sehorn -- Tracking of single and multiple genomic loci in living yeast cells / Imen Lassadi and Kerstin Bystricky -- Cell biology of homologous recombination in yeast / Nadine Eckert-Boulet, Rodney Rothstein, and Michael Lisby -- Live cell imaging of meiotic chromosome dynamics in yeast / Harry Scherthan and Caroline Adelfalk -- Chromosome structure and homologous chromosome association during meiotic prophase in Caenorhabditis elegans / Kentaro Nabeshima.
  • pt. A-B, 2006. ScienceDirect
    pt. B ScienceDirect
    Campbell, Judith L.; Modrich, Paul.
    Also available: Print – pt. A-B, 2006.
  • 2012 Springer Protocols
    Bjergbæk, Lotte.
    DNA repair : front and center and not going away! / Vilhelm A. Bohr -- Identification of genes required for damage survival using a cell-based RNAi screen against the Drosophila genome / Dashnamoorthy Ravi and Alexander James Roy Bishop -- Isolating genes involved with genotoxic drug response in the nematode Caenorhabditis elegans using genome-wide RNAi screening / Lone Vedel Schøler [and others] -- Establishment of the DNA repair-defective mutants in DT40 cells / Masamichi Ishiai, Emi Uchida, and Minoru Takata -- Electrophoretic mobility shift assays for protein-DNA complexes involved in DNA repair / Chun Tsai [and others] -- Comet assay : a sensitive genotoxicity test for the detection of DNA damage and repair / Günter Speit and Andreas Rothfuss -- Detection of DNA damage by comet fluorescence in situ hybridization / Wiebke Schlörmann and Michael Glei -- Quantitative DNA damage and repair measurement with the yeast comet assay / Rui Oliveira and Björn Johansson -- Analysis of DNA damage and repair in nuclear and mitochondrial DNA of animal cells using quantitative PCR / Amy M. Furda [and others] -- In vitro DNA mismatch repair in human cells / Liya Gu, Charles M. Ensor, and Guo-Min Li -- Eukaryotic DNA mismatch repair in vitro / Fenghua Yuan [and others] -- Immuno-slot blot assay for detection of UVR-mediated DNA damage / Mahsa Karbaschi [and others] -- Quantification of DNA photoproducts in mammalian cell DNA using radioimmunoassay / Thomas R. Berton and David L. Mitchell -- Measuring the formation and repair of UV damage at the DNA sequence level by ligation-mediated PCR / Ahmad Besaratinia and Gerd P. Pfeifer -- Construction of plasmids containing site-specific DNA interstrand cross-links for biochemical and cell biological studies / Milica Enoiu [and others] -- Replication-coupled DNA interstrand cross-link repair in Xenopus egg extracts / Puck Knipscheer [and others] -- In vitro base excision repair using mammalian cell extracts / Jason L. Parsons and Grigory L. Dianov -- Using Arabidopsis cell extracts to monitor repair of DNA base damage in vitro / Dolores Córdoba-Cañero, Teresa Roldán-Arjona, and Rafael R. Ariza -- In vitro monitoring of base excision repair in Saccharomyces cerevisiae / Simone Moertl and Fred Ahne -- Mitochondrial base excision repair assays / Ricardo Gredilla and Tinna Stevnsner -- O-hydroxylamine-coupled alkaline gel electrophoresis assay for the detection and measurement of DNA single-strand breaks / April M. Luke and Jun Nakamura -- DNA double-strand break damage and repair assessed by pulsed-field gel electrophoresis / Helen E. Bryant -- Quantitative amplification of single-stranded DNA / Eva-Maria Holstein and David Lydall -- Simple, non-radioactive measurement of single-stranded DNA at telomeric, sub-telomeric, and genomic loci in budding yeast / James M. Dewar and David Lydall -- Monitoring DNA recombination initiated by HO endonuclease / Neal Sugawara and James E. Haber -- Monitoring I-SceI-induced double-strand break repair in DT40 Cells / David du Plessis and Julian E. Sale -- I-SceI-based assays to examine distinct repair outcomes of mammalian chromosomal double strand breaks / Amanda Gunn and Jeremy M. Stark -- Studying repair of a single protein-bound nick in vivo using the Flp-nick system / Ida Nielsen, Anni H. Andersen, and Lotte Bjergbæk -- Measurement of diversification in the immunoglobulin light chain gene of DT40 cells / Julian E. Sale -- Live cell microscopy of DNA damage response in Saccharomyces cerevisiae / Sonia Silva [and others] -- Use of gene targeting to study recombination in mammalian cell DNA repair mutants / Jennifer J. Rahn, Gerald M. Adair, and Rodney S. Nairn -- In vitro rejoining of double strand breaks in genomic DNA / George Iliakis, Emil Mladenov, and Nge Cheong -- In vitro DNA double-strand break repair assay based on end-joining of defined duplex oligonucleotides / Kamal Datta [and others] -- Assays of bypass replication of genotoxic lesions in cell-free extracts / Nana Nikolaishvili-Feinberg and Marila Cordeiro-Stone -- Quantitative measurement of translesion DNA synthesis in mammalian cells / Omer Ziv [and others] -- Detection of PCNA modifications in Saccharomyces cerevisiae / Adelina A. Davies and Helle D. Ulrich -- In vitro PCNA modification assays / Joanne L. Parker and Helle D. Ulrich -- Analysis of inhibition of DNA replication in irradiated cells using the SV40 based in vitro assay of DNA replication / George Iliakis [and others] -- CHK1 kinase activity assay / Hong Yan Wang and Ya Wang -- Histone H2AX phosphorylation : a marker for DNA damage / Arishya Sharma, Kamini Singh, and Alexandru Almasan.
  • 2015 Springer Protocols
    Leblanc, Benoît; Rodrigue, Sébastien.
    Electrophoretic mobility shift assay using radiolabeled DNA probes -- In vitro DNase i footprinting -- Determining the architecture of a protein-DNA complex by combining FeBABE cleavage analyses, 3-D printed structures, and the ICM molsoft program -- In cellulo DNA analysis: LMPCR footprinting -- Southwestern blotting assay -- Single-molecule approaches for the characterization of riboswitch folding mechanisms -- Probing of nascent riboswitch transcripts -- Functional studies of DNA-protein interactions using fret techniques -- Precise identification of genome-wide transcription start sites in bacteria by 5'-rapid amplification of cDNA ends (5'-RACE) -- Analysis of DNA supercoiling induced by DNA-protein interactions -- Precise identification of DNA-binding proteins genomic location by exonuclease coupled chromatin immunoprecipitation (ChIP-exo) -- The cruciform DNA mobility shift assay: A tool to study proteins that recognize bent DNA -- Individual and sequential chromatin immunoprecipitation protocols -- Chromatin endogenous cleavage (ChEC) as a method to quantify protein interaction with genomic DNA in saccharomyces cerevisiae -- Selection and validation of spacer sequences for CRISPR-Cas9 genome editing and transcription regulation in bacteria -- Detection of short-range DNA interactions in mammalian cells using high-resolution circular chromosome conformation capture coupled to deep sequencing -- Global mapping of open chromatin regulatory elements by formaldehyde-assisted isolation of regulatory elements followed by sequencing (FAIRE-seq) -- Aggregate and heatmap representations of genome-wide localization data using VAP, a versatile aggregate profiler -- Circular dichroism for the analysis of protein-DNA interactions -- Quantitative investigation of protein-nucleic acid interactions by biosensor surface plasmon resonance -- Identification of nucleic acid high affinity binding sequences of proteins by SELEX.
  • 2002 CRCnetBASE
    Tavantzis, Stylianos Michael.
  • 2002 Springer Protocols
    Vaillancourt, Peter E.
  • 2014 Springer
    Aubin-Horth, Nadia; Landry, Christian R.
    "Researchers in the field of ecological genomics aim to determine how a genome or a population of genomes interacts with its environment across ecological and evolutionary timescales. Ecological genomics is trans-disciplinary by nature. Ecologists have turned to genomics to be able to elucidate the mechanistic bases of the biodiversity their research tries to understand. Genomicists have turned to ecology in order to better explain the functional cellular and molecular variation they observed in their model organisms. Ecological genomics covers 3 fields of research that have most benefited from the recent technological and conceptual developments in the field of ecological genomics: the study of life-history evolution and its impact of genome architectures; the study of the genomic bases of phenotypic plasticity and the study of the genomic bases of adaptation and speciation"-- Publisher's description.
    Also available: Print – 2014
  • 2010
    Esfandyarpour, Hesaam; *Pease, R.; Davis, Ronald W.; Pianetta, Piero.
    The Human Genome Project was accomplished by a reduction in the cost of DNA sequencing by three orders of magnitude. Further cost reductions are required for sequencing to become a standard tool in clinical medicine and to enable personalized medicine via individual genome sequencing. The current cost varies between $50k to $100k over a period of months; depend on the technology, accuracy and read-length. It is desired to reduce the cost to $1000 per genome to enable profiling of individuals genome. To achieve this goal, a highly integrated platform with simplified chemistry is required. In this dissertation, we introduce a novel method for DNA sequencing based on electrical detection of polymerization reaction, called "Thermo/pH sequencing". Our proposed method is based on the direct measurement of the heat release or the pH modulation (change of H+ ion concentration in the solution) during DNA extension. For high throughput DNA sequencing, DNA strands are immobilized to small micron-size beads in a microfluidic platform. The DNA-beads are in a reaction mixture in contact with an array of sensitive micro-machined heat or pH sensors, which detect the electrical signature from incorporation of a complementary base (dNTP) in the presence of appropriate reagents (DNA polymerase, and polymerase reaction buffer). This results to a label-free, long-read and fast chemistry; 10x reduction in reagent cost with 10x increase in throughput can potentially yield to significant improvement in the cost of genome sequencing to less than $1000. In addition, substituting optical detection set-up with microelectronic sensor reduces the capital cost of sequencing instruments from $500k to less than $50k. We demonstrate the proof of concept for this technology at large scale. Then we describe the development of an appropriate microfluidic platform and two micromachined electrical biosensors that employ electrical detection for heat or pH detection. Both versatile platforms can be multiplexed and have the potential of providing rapid and inexpensive measurements without any compromise in the sensitivity, making them good potential candidates for use in the clinical setting. We report a chip-based integrated differential microfluidic nanocalimeters with on-chip injection and multiplexing unit, capable of characterizing the heat of reaction with unprecedented 2-nW resolution in 1 Hz bandwidth for nanoliter scale samples. We successfully demonstrate DNA Thermosequencing with sequential injection of different nucleotides into the integrated microfluidic calorimeter device. In addition, the device can serve as a powerful tool to characterize a variety of the biomedical processes, such as metabolic activities of microorganisms, living cells and catalyzed reactions. We also present a microfabricated device in microfluidics for pH sequencing, called nanoneedle biosensor. The key element for this device is a 10nm wide gap on the end of the needle of total diameter about 100nm. Any change in the population of molecules in this gap results in a change of impedance across the gap; single molecule detection should be possible. In addition, DNA-beads can be allocated iv near the sensors to measure the pH change during DNA extension. The design, fabrication, testing, optimization and a modified structure of the device for higher signal to noise ratio are presented. Toward an integrated sequencer platform, automation and reduced labor cost, higher throughput, accuracy and efficiency for genomics and proteomics analysis; further integration and optimization of the presented systems are required. We envision the integration of our CMOS-compatible devices with a CMOS integrated circuitry into a high throughput gene sequencer or proteomics system. The proteomics system enables multiplex analysis using an array of micro-channels for probing clinically relevant samples such as the human serum for various protein and nucleic acid biomarkers for cancer detection, and also the detection of pathogenic bacteria in solution.
  • 2014 Springer Protocols
    Cutrera, Jeffry; Heller, Richard; Li, Shulin; Teissie, Justin.
    1. Electroporation-based gene therapy; recent evolution in the mechanism description and technology developments / Lluis M. Mir -- 2. Electropermeabilization of the cell membrane / Justin Teissie -- 3. The impact of non-electrical factors on electrical gene transfer / Jiemino Hu, Jeffry Cutrera, and Shulin Li -- 4. Electroporation formulation for cell therapy / Jiemiao Hu and Shulin Li -- 5. Short-fragment DNA-mediated in vivo DNA electroporation delivery / Jinliang Peng, Yonggang Zhao and Yuhong Xu -- 6. Gold nanoparticle-enhanced electroporation for leukemia cell transfection / Shuyan Huang, Yingbo Zu and Shengnian Wang -- 7. siRNA delivery via electropulsation: a review of the basic processes / Muriel Golzio and Justin Teissie -- 8. Continuous cell electroporation for efficient DNA and siRNA delivery based on laminar microfluidic chips / Zewen Wei and Zhihong Li -- 9. Electroporation of siRNA into mouse bone marrow-derived macrophages and dendritic cells / Isabel Siegert, Valentin Schatz, Alexander T. Prechtel, Alexander Steinkasserer, Christian Bogdan and Jonathan Jantsch -- 10. Directo imaging of siRNA electrotransfer at the single-cell level / Justin Teissie and Muriel Golzio -- 11. Electroporation mediated siRNA delivery into tumors / Yashifumi Takei -- 12. Substrate-mediated, high-efficiency siRNA electroporation / Hiroyuki Fujimato and Hiroo Iwata -- 13. Intradermal electroporation / Maria L. Knudsen, Karl Ljungberg, Peter Liljeström and Daniel X. Johansson -- 14. Delivery of DNA into the central nerous system via electroporation / Jochen De Vry, Tim Vanmierlo, Pilar Martínez-Martínez, Mario Losen, Yasin Temel, Harry Steinbusch, Marc De Baets and Jos Prickaerts -- 15. DNA delivery in adult mouse eyes: an update with corneal outcomes / John M. Nickerson, Shannon E. Getz, Jana T. Sellers, Micah A. Chrenek, Penny Goodman, Christiana J. Bernal and Jeffrey H. Boatright -- 16. Delivery of plasmid DNA into dental tissues of developing rat teeth by electroporation / Shaomian Yao, Michael L. Beckley and Dawen Liu -- 17. Electroporation-mediated gene delivery to the lungs / Jennifer L. Young, Michael S. Barravecchia and David A. Dean -- 18. Electroporation-mediated delivery of genes in rodent models of lung contusion / David Machado-Aranda and Krishnan Raghavendran -- 19. In vivo electroporation-mediated gene delivery to the beating heart / Hendrik T. Tevaearai, Amiq Gazdhar, Marie-Noëlle Giraud and Martin Flück -- 20. Managing local swelling following intratumoral electro-chemo-gene therapy / Jeffry Cutrera, Glenn King, Pamela Jones, Elias Gumpel, Xueqing Xia and Shulin Li -- 21. Gene electrotransfer in clinical trials / Julie Gehl -- 22. Electrochemotherapy in veterinary oncology: from rescue to first line therapy / Enrico P. Spugnini and Alfonso Baldi -- 23. Low-energy DC current ablation in a mouse tumor model / Prejesh Philips, Yan Li and Robert C.G. Martin II -- 24. Evolution of electroporated DNA vaccines / Andrea M. Keane-Myers and Matt Bell -- 25. Clinical development of intramuscular electroporation: providing a "boost" for DNA vaccines / Amir S. Khan, Kate E. Broderick and Niranian Y. Sardesai -- 26. Electroporation-mediated administration of candidate DNA vaccines against HIV -1 / Sandhya Vasan -- 27. Electroporation-mediated intradermal delivery of DNA vaccines in nonhuman primates / Lucille Adam, Roger Le Grand and Fré́déric Martinon -- 28. Intramuscular DNA vaccination protocols mediated by electric fields / Pieranna Chiarella and Emanuela Signori -- 29. DNA electroporation of multi-agent vaccines conferring protection against select agent challenge: TriGrid delivery system / Andrea M. Keane-Myers, Matt Bell, Drew Hannaman and Mark Albrecht -- 30. Gene-based vaccination and screening methods to develop monoclonal antibodies / M. Pirouz Daftarian, Aram Vosoughi and Vance Lemmon.
  • pt. A-<D>, 1987-<90>
    Dorian, A. F.
    Status: Not Checked OutLane Catalog Record
    pt. A. General medicine -- pt. B. Anatomy -- pt. C. Biology, genetics and biochemistry -- pt. D. Therapeutic substances.
  • 2005 Wiley
    SU Catalog (SearchWorks) Click LINK above for Print location/circulation status.
    Jorde, Lynn B.
    v. 1. Genetics -- v. 2. Genetics -- v. 3. Genomics -- v. 4. Genomics -- v. 5. Proteomics -- v. 6. Proteomics -- v. 7. Bioinformatics -- v. 8. Bioinformatics.
  • 2008 Springer
    Rédei, G. P.
    v. 1. A-L -- v. 2. M-Z.
  • 2013 Karger
    Stratakis, Constantine A.
    Multiple endocrine neoplasia type 1 / Agarwal, S.K. -- Multiple endocrine neoplasia type 2 / Lodish, M. -- Von Hippel-Lindau syndrome / Chou, A. ... [et al.] -- Carney complex -- Espiard, S., Bertherat, J. -- Multiple endocrine neoplasia type 4 / Lee, M., Pellegata, N.S. -- Novel hereditary forms of pheochromocytomas and paragangliomas / Dahia, P.L.M. -- Carney triad / Carney, J.A. -- Genetics of pituitary adenomas / Gadelha, M.R. ... [et al.] -- Clinical behavior and genetics of nonsyndromic, familial nonmedullary thyroid cancer / Bauer, A.J. -- Genetic defects associated with familial and sporadic hyperparathyroidism / Hendy, G.N., Cole, D.E.C. -- Endocrine tumors associated with neurofibromatosis type 1, Peutz-Jeghers syndrome, and other familial neoplasia syndromes / Kalkan, E., Waguespack, S.G.
  • 2013 Springer
    Jirtle, Randy L.; Tyson, Frederick L.
    The capacity of the epigenome to interpret both internal and external stimuli and alter expression programs is a critical component in normal development, aging, and disease pathogenesis. In the past decade, we have witnessed an explosion of unprecedented research on and support for epigenetics, epigenomics, and their interface with human health and disease. In this volume, Environmental Epigenomics in Health and Disease - Epigenetics and Complex Diseases, a number of leading investigators in the field of epigenetics discuss patterns of epigenomic modifications in normal cells, and how environmentally-induced changes in them are associated with disease pathogenesis. The authors comprehensively review the epigenetic adaptations that occur in human embryonic stem cells, as well as in differentiating cells and organs such as the brain when exposed to environmental factors, and discuss the legal and ethical implications of such alterations. The overall purpose of this volume and its companion, Environmental Epigenomics in Health and Disease - Epigenetics and Disease Origins, is to give readers an overview of how environmental exposures during early development can influence disease formation by disrupting epigenetic programming.
  • 2013 Springer
    Jirtle, Randy L.; Tyson, Frederick L.
    Exposure to environmental toxicants is associated with changes in DNA methylation and gene expression profiles that together can contribute to increased disease susceptibility. The chapters in this volume, Environmental Epigenomics in Health and Disease - Epigenetics and Disease Origins, address a wide range of environmental exposures, such as airborne particulates, cocaine, radiation, tobacco smoke, and xenoestrogens. Particular emphasis is placed on the consequences of environmental exposures during development on epigenetic reprogramming that influences adult disease pathogenesis. Health outcomes associated with these exposures include autoimmune disorders, neurodevelopmental disorders, and cancer. Importantly, dietary supplements and drugs can modify the epigenetic effects induced by these agents, thereby reducing their toxicological impact. The overall purpose of this volume and its companion, Environmental Epigenomics in Health and Disease - Epigenetics and Complex Diseases, is to give readers an overview of how environmental exposures during early development can influence disease formation by disrupting epigenetic processes and developmental programming.
  • 2007 Springer Protocols
    Martin, C. Cristofre.
    Preface -- Contributors -- Pt. 1. Gene expression profiling -- 1. High-throughput whole mount in situ hybridization of zebrafish embryos for analysis of tissue-specific gene expression changes after environmental perturbation / Louise E. Coverdale, Lindsay E. Burton, and C. Cristofre Martin -- 2. Fluorescent RNA arbitrarily primed polymerase chain reaction / Doug Crump ... [et al.] -- 3. Isolation of O₃-response genes from Arabidopsis thaliana using cDNA macroarray / Masanori Tamaoki -- 4. Use of cDNA macroarrays and gene profiling for detection of effects of environmental toxicants / Jason L. Blum ... [et al.] -- 5. Constructing and screening a cDNA library / Kevin Larade and Kenneth B. Storey -- 6. Comparative molecular physiological genomics / Sean F. Eddy and Kenneth B. Storey -- 7. Proteomic analysis of neuroendocrine peptidergic system disruption using the AtT20 pituitary cell line as a model / Fumin Dong ... [et al.] -- 8. Proteomics-based method for risk assessment of peroxisome proliferating pollutants in the marine environment / Susana Cristobal -- 9. Environmental metabolomics using ¹H-NMR spectroscopy / Mark R. Viant -- Pt. 2. Detection of whole genome mutation -- 10. Restriction landmark genome scanning for the detection of mutations / Jun-ichi Asakawa -- 11. Use of the comet assay in environmental toxicology / Loren D. Knopper and James P. McNamee -- 12. The micronucleus assay determination of chromosomal level DNA damage / Michael Fenech -- 13. Fluorescence in situ hybridization for the detection of chromosome aberrations and aneuploidy induced by environmental toxicants / Francesca Pacchierotti and Antonella Sgura -- 14. Laboratory methods for the detection of chromosomal structural aberrations in human and mouse sperm by fluorescence in situ hybridization / Francesco Marchetti, Debby Cabreros, and Andrew J. Wyrobek -- Pt. 3. Determination of species diversity -- 15. Assembling DNA barcodes / Jeremy R. deWaard ... [et al.] -- 16. Application of suppressive subtractive hybridization to uncover the metagenomic diversity of environmental samples / Elizabeth A. Galbraith, Dionysios A. Antonopoulos, and Bryan A. White -- 17. 16S rRNA targeted DGGE fingerprinting of microbial communities / Vesela A. Tzeneva ... [et al.] -- 18. An emulsion polymerase chain reaction-based method for molecular haplotyping / James G. Wetmur and Jia Chen -- Index.
  • 2013 Springer
    Karpf, Adam R.
    Also available: Print – 2013
  • 2013 Springer
    Pascual, Marién; Roa, Sergio.
    Introduction -- Immune System and Atopic Disorders -- Epigenetics -- Epigenetics, Environment, and Allergic Diseases -- Conclusions and Future Perspectives.
  • 2013 ScienceDirect
    Sweatt, J. David.
    Behavioral Epigenetics is the study of how environmental factors affect alterations in behavior, addressing the fundamental mechanisms that shape development and individual vulnerability/resilience to adverse behavioral outcome. With an understanding of the molecular mechanisms involved in epigenetic modulation, researchers believe it will be possible to develop targeted therapies for those individuals in whom it malfunctions. This volume will address current understanding of the roles of epigenetic processes at the molecular/cellular level, their impact on neural development and behavior.
  • 2012 Springer
    Murre, Cornelis.
    Previous observations, generated by many in the field, have provided a first glimpse into the epigenetic mechanisms that underpin lymphocyte and myeloid development. We are only now beginning to merge the multitude of observations into a common framework. At the same time it has become more difficult for the individual mind to comprehend more than a tiny focused fraction of it. The studies described in this volume serve as a starting point to familiarize one self with the multifarious differences in epigenetic designs that orchestrate the progression of developing blood cells. They also may serve as a general paradigm for the mechanisms that underpin the control of eukaryotic gene expression.
  • 2006 CRCnetBASE
    Inui, Akio.
    Also available: Print – 2006
  • 2014 Springer
    Jones, P. A.; Lübbert, Michael.
    The growing knowledge about disturbances of epigenetic gene regulation in hematopoietic stem cell disorders such as myeloid leukemias and preleukemias (myelodysplasias) is now being translated into treatment approaches that target the epigenetic defects pharmacologically. Such approaches include reactivation of tumor suppressor genes and other antiproliferative genes by reversal of DNA hypermethylation through azanucleosides, and use of HDAC inhibitors to reverse gene silencing mediated by chimeric, leukemia-specific transcription factors. This book first presents the latest evidence derived from preclinical models regarding the epigenetic regulation of hematopoietic stem cell differentiation and hemoglobin production. The significance of DNA methylation abnormalities in hematopoietic disorders and of epigenetic disturbances in lung cancer and other solid tumors is then discussed. A major part of the book, however, relates specifically to the translation of basic research and drug development to clinical applications, and in this context both present and future clinical strategies are considered. Individual chapters are devoted to the use of DNA hypomethylating agents and chromatin-modifying agents, and the treatment of hematologic malignancies and solid tumors by means of epigenetic agents is discussed in detail.
  • 2013 Springer
    Sarkar, Fazlul H.
    Systems and Network Biology to Investigate Epigenetic De-regulatory Mechanisms of MicroRNAs in Pancreatic Cancer / Irfana Muqbil, Fazlul H. Sarkar, Ramzi M. Mohammad -- Role of MicroRNAs in Cancer Epigenetics / Kishore B. Challagundla, Petra Wise, Muller Fabbri -- Epigenetic Regulation of EZH2 and Its Targeted MicroRNAs / Sandy Leung-Kuen Au, Irene Oi-Lin Ng, Chun-Ming Wong -- Epigenetics and MicroRNAs in Renal Cancer / Shahana Majid ... [et al.] -- Epigenetic Regulation of MicroRNA in Colon Cancer / Qiong Zhang, Mukesh Verma, Sharad Khare -- Epigenetic Regulation of miRNAs in Breast Cancer Formation and Progression / Zhiqian Zhang ... [et al.] -- Epigenetic Variations of Stem Cell Markers in Cancer / Sripathi M. Sureban, Dongfeng Qu, Courtney W. Houchen -- Recent Updates on Epigenetic Biomarkers for Prostate Cancer / Karen Chiam, Tanya Kate Day, Tina Bianco-Miotto -- Epigenetics and Racial Disparities in Prostate Cancer / Benjamin A. Rybicki -- Epigenetic Signatures of Breast Cancer Genes / Shrikant Anant, Animesh Dhar, Satish Ramalingam -- Exploiting Epigenetic Modifiers to Circumvent Melanoma Dual Resistance to TCR-Engineered Immunotherapy- and BRAF V⁶⁰⁰E-Kinase Inhibitor / Ali R. Jazirehi CLS, -- The Role of Epigenetics in Radiation Therapy and the DNA Damage Response / Steven P. Zielske -- Plant Polyphenols as Epigenetic Modulators of Glutathione S-Transferase P1 Activity / Vijay S. Thakur, Sanjay Gupta -- Epigenetic Regulations of mRNAs and miRNAs by Nutraceuticals / Yiwei Li ... [et al.] -- Towards Curative Cancer Therapy with Maspin: A Unique Window of Opportunity to Target Cancer Dormancy / Alexander Kaplun, M. Margarida Bernardo, Sijana Dzinic.
  • 2005 Springer
    Jeanteur, Ph.
    Chromatin remodeling factors and DNA replication -- Epigenetic inheritance of chromatin states mediated by polycomb and trithorax group proteins in drosophila -- How to pack the genome for a safe trip -- Chromatin modifications on the inactive x chromosome -- Chromatin mechanisms in drosophila dosage compensation -- DNA methylation in epigenetic control of gene expression -- The epigenetic breakdown of cancer cells: from DNA methylation to histone modifications -- Developmental regulation of the beta-globin gene locus -- Epigenetic regulation of mammalian imprinted genes: from primary to functional imprints -- Seed development and genomic imprinting in plants.
  • 2013 Springer
    Greenwood, Celia M. T.; Naumova, Anna K.
    "Epigenetics and Complex Traits provides an overview of basic epigenetic phenomena that influence transmission of genetic traits, including the pivotal roles of epigenetic factors in genome integrity, genetic transmission and phenotypic variation at critical developmental points, interactions between epigenetic marks and genetic variation, as well as a detailed examination of how epigenetic considerations can alter interpretation and analysis of risks for complex traits. Included in this book are several overviews of the impact of inter-individual variation in epigenetic states, from major changes that cause congenital developmental defects to subtle changes and their impact on complex traits. In addition, there are chapters examining the relationship between epigenetic changes and genetic changes in human disease, methods for statistical analysis of epigenetics effects in human disease genetic studies or in population genetics, and a consideration of how epigenetics influences inheritance and analysis of inheritance. Epigenetics and Complex Traits is a resource for those who are working in mammalian genetics or analysis of human genetic data and are interested in the impact of epigenetics on inheritance."-- Back cover.
  • 2011 Springer
    Gasser, Susan M.; Li, En.
    DNA Methylation and Cancer -- Genome-Wide Epigenetic Modifications in Cancer -- DNA Repair and the Control of DNA Methylation -- Errors in Erasure: Links Between Histone Lysine Methylation Removal and Disease -- Histone Modifications in Cancer Biology and Prognosis -- Dynamics of Histone Lysine Methylation: Structures of Methyl Writers and Erasers -- Epigenetic Mechanisms of Mental Retardation -- Histone and DNA Modifications in Mental Retardation -- HDAC Inhibitors and Cancer Therapy -- Epigenetic Mechanisms in Acute Myeloid Leukemia -- The Liver-Specific MicroRNA miR-122: Biology and Therapeutic Potential -- Transcriptional Regulatory Networks in Embryonic Stem Cells -- Small Molecules in Cellular Reprogramming and Differentiation -- Index.
  • 2011 Springer
    Khochbin, Saadi; Rousseaux, Sophie.
    pt. 1. Medical aspects and questions raised on the molecular basis of epigenome involvement in reproduction -- pt. 2. Fundamental aspects of genome and epigenome reprogramming during gametogenesis -- pt. 3. Re-organization of nuclear compartmetns during gametogenesis -- pt. 4. Fundamental aspects of gene expression regulation during gametogenesis.
  • 2012 Springer
    Christen, Yves; Sassone-Corsi, Paolo.
    "What lies at the heart of neuronal plasticity? Accumulating evidence points to epigenetics. This word originally indicated potentially heritable modifications in gene expression that do not involve changes in DNA sequence. Today this definition is much less strict, and epigenetic control is thought to include DNA methylation, histone modifications, histone variants, microRNA metabolic pathways and non-histone proteins modifications. Thus, while neuronal plasticity is rightly thought to be intimately associated to genomic control, it is critical to appreciate that there is much more to the genome than DNA sequence. Recent years have seen spectacular advances in the field of epigenetics. These have attracted the interest of researchers in many fields and evidence connecting epigenetic regulation to brain functions has been accumulating. Neurons daily convert a variety of external stimuli into rapid or long-lasting changes in gene expression. A variety of studies have centered on the molecular mechanisms implicated in epigenetic control and how these may operate in concert. It will be critical to unravel how specificity is achieved. Importantly, specific modifications seem to mediate both developmental processes and adult brain functions, such as synaptic plasticity and memory. Many aspects of the research in neurosciences and endocrinology during the upcoming decade will be dominated by the deciphering of epigenetic control. This book constitutes a compendium of the most updated views in the field"--Publisher.
  • 2009 CRCnetBASE
    Esteller, Manel.
    Epigenetics and cancer: DNA methylation / Santiago Ropero and Manel Esteller -- Epigenetics and cancer: histone modifications / Mario F. Fraga and Manel Esteller -- Epigenetic drugs: DNA demethylating agents / Ehab Atallah, Guillermo Garcia-Manero -- Epigenetic drugs: histone deacetylase inhibitors / Melissa Peart, Ricky W. Johnstone -- Sirtuins in biology and disease / Alejandro Vaquero, Danny Reinberg -- MicroRNAs in cell biology and disease / Muller Fabbri, Carlo M. Croce, George A. Calin -- Chromatin modifications by polycomb complexes / Miguel Vidal -- Epigenetics and its genetic syndromes / Richard J. Gibbons -- Epigenetics and immunity / Esteban Ballestar and Bruce C. Richardson -- Aetiology of major psychosis: why do we need epigenetics? / Gabriel Oh and Arturas Petronis -- Epigenetics and cardiovascular disease / Gertrund Lund and Silvio Zaina -- Epigenetics and plant biology / Luis Valledor ... [et al.] -- Epigenetics, environment, and evolution / Douglas M. Ruden, Parsa Rasouli, Xiangyi Lu -- Epigenetics and epigenomics / Jose Ignacio Martin-Subero, Reiner Siebert.
  • 2010 Springer
    Tollefsbol, Trygve O.
  • 2011 Springer Protocols
    Tollefsbol, Trygve O.
    1. Advances in epigenetic technology / Trygve O. Tollefsbol -- 2. DNA methylation detection: bisulfite genomic sequencing analysis / Yuanyuan Li and Trygve O. Tollefsbol -- 3. Methylation-specific PCR / Ja-Lok Ku, You-Kyung Jeon, and Jae-Gabb Park -- 4. Analysing DNA methylation using bisulphite pyrosequencing / Thomas Mikeska, Jörg Felsberg, Chelsee A. Hewitt, and Alexander Dobrovic -- 5. Closed-tube PCR methods for locus-specific DNA methylation analysis / Ida L.M. Candiloro, Thomas Mikeska, and Alexander Dobrovic -- 6. A combined bisulfite restriction analysis bioinformatics tool: methyl-typing / Cheng-Hong Yang, Yu-Huei Cheng, Li-Yeh Chuang, and Hsueh-Wei Chang -- 7. SIRPH: an HPLC-based SNuPE for quantitative methylation measurement at specific CpG sites / Heike Singer, Nicole Nüsgen, and Osman El-Maarri -- 8. Restriction landmark genome scanning / Hisato Okuizumi, Tomoko Takamiya, Yasushi Okazaki, and Yoshihide Hayashizaki -- 9. Methylated DNA immunoprecipitation genome-wide analysis / Mattia Pelizzola and Annette Molinaro -- 10. Methylated-CpG island recovery assay / Natalie Mitchell, J. Tyson DeAngelis, and Trygve O. Tollefsbol -- 11. Global DNA methylation analysis using the luminometric methylation assay / Mohsen Karimi, Karin Luttropp, and Tomas J. Ekström -- 12. Inhibition of DNA methylation in somatic cells / Angelica M. Giraldo and Kenneth R. Bondioli -- 13. DNA methyltransferase assays / Renata Z. Jurkowska, Alexandre Ceccaldi, Yingying Zhang, Paola B. Arimondo, and Albert Jeltsch -- 14. A chromatin immunoprecipitation protocol for small cell numbers / Philippe Collas -- 15. Native chromatin immunoprecipitation / Céline Cosseau and Christoph Grunau -- 16. Q-PCR in combination with ChIP assays to detect changes in chromatin acetylation / Ryan A. Irvine, Cindy Okitsu, and Chih-Lin Hsieh -- 17. Sequential chromatin immunoprecipitation assay and analysis / Ricardo B. de Medeiros -- 18. Combined chromatin immunoprecipitation and bisulfite methylation sequencing analysis / Yuanyuan Li and Trygve O. Tollefsbol -- 19. Studying RNA-protein interactions in vivo by RNA immunoprecipitation / Luke A. Selth, Pierre Close, and Jesper Q. Svejstrup -- 20. Using ChIP-seq technology to generate high-resolution profiles of histone modifications / Henriette O'Geen, Lorigail Echipare, and Peggy J. Farnham -- 21. Mapping open chromatin with formaldehyde-assisted isolation of regulatory elements / Takao Nammo, Santiago A. Rodriguez-Segui, and Jorge Ferrer -- 22. Inhibition of histone deacetylases / Yi Huang, Patrick G. Shaw, and Nancy E. Davidson -- 23. Computational methods for epigenetic analysis: the protocol of computational analysis for modified methylation-specific digital karyotyping based on massively parallel sequencing / Jian Li, Qian Zhao, and Lars Bolund.
  • 2015 Springer Protocols
    Moore, Jason H.; Williams, Scott M.
    Long-term selection experiments : epistasis and the response to selection / Charles Goodnight -- Finding the epistasis needles in the genome-wide haystack / Marylyn D. Ritchie -- Biological knowledge-driven analysis of epistasis in human GWAS with application to lipid traits / Li Ma, Alon Keinan, and Andrew G. Clark -- Epistasis for quantitative traits in Drosophila / Trudy F. C. Mackay -- Epistasis in the risk of human neuropsychiatric disease / Scott M. Williams -- On the partitioning of genetic variance with epistasis / José M. Álvarez-Castro and Arnaud Le Rouzic -- Measuring gene interactions / Thomas F. Hansen -- Two rules for the detection and quantification of epistasis and other interaction effects / Günter P. Wagner -- Direct approach to modeling epistasis / Rong-Cai Yang -- Capacitating epistasis -- detection and role in the genetic architecture of complex traits / Mats E. Pettersson and Örjan Carlborg -- Compositional epistasis : an epidemiologic perspective / Etsuji Suzuki and Tyler J. VanderWeele -- Identification of genome-wide SNP-SNP and SNP-clinical boolean interactions in age-related macular degeneration / Carlos Riveros [and eight others] -- Epistasis analysis using information theory / Jason H. Moore and Ting Hu -- Genome-wide epistasis and pleiotropy characterized by the bipartite human phenotype network / Christian Darabos and Jason H. Moore -- Network theory for data-driven epistasis networks / Caleb A. Lareau and Brett A. McKinney -- Epistasis analysis using multifactor dimensionality reduction / Jason H. Moore and Peter C. Andrews -- Epistasis analysis using ReliefF / Jason H. Moore -- Epistasis analysis using artificial intelligence / Jason H. Moore and Doug P. Hill.
  • 2008 Springer Protocols
    Mattes, William B.; Mendrick, Donna L.
    Toxicogenomics and classical toxicology, how to improve prediction and mechanistic understanding of human toxicity / Donna L. Mendrick -- Use of traditional endpoints and gene dysregulation to understand mechanisms of toxicity / Wayne R. Buck, Jeffrey F. Waring, Eric A. Blomme -- Quality control of microarray assays for toxicogenomic and in vitro diagnostic applications / Karol L. Thompson and Joseph Hackett -- Role of statistics in toxicogenomics / Michael Elashoff -- Predictive toxicogenomics in preclinical discovery / Scott A. Barros and Rory B. Martin -- In vivo predictive toxicogenomics / Mark W. Porter -- Bioinformatics, databasing and gene annotation / Lyle D. Burgoon and Timothy R. Zacharewski -- Microarray probe mapping and annotation in cross - species comparative toxicogenomics / John N Calley, William B Mattes, Timothy P. Ryan -- Toxicogenomics in biomarker discovery -- Marc F. DeCristofaro, Kellye K. Daniels -- From pharmacogenomics to translational biomarkers / Donna L. Mendrick -- Public consortium efforts in toxicogenomics / William B. Mattes -- Applications of toxicogenomics to nonclinical drug development / Frank D. Sistare, Joseph J. DeGeorge.
  • 2006
    Hartl, Daniel L.; Jones, Elizabeth W.
    Status: Not Checked OutLane Catalog Record
    The genetic code of genes and genomes -- Transmission genetics: heritage from Mendel -- The chromosomal basis of heredity -- Gene linkage and genetic mapping -- Human chromosomes and chromosome behavior -- DNA structure, replication, and manipulation -- The genetics of bacteria and their viruses -- The molecular genetics of gene expression -- Molecular mechanisms of gene regulation -- Genomics, proteomics, and genetic engineering -- The genetic control of development -- Molecular mechanisms of mutation and DNA repair -- Molecular genetics of the cell cycle and cancer -- Molecular evolution and population genetics -- The genetic basis of complex inheritance.
  • 2012 Springer
    Boddington, Paula.
    The "Ethics Job" -- Why Research Ethics? Why Ethics in Genetics? The Case of Genomics Research -- What Ethics Is, What It Is Not, and How We Are Going to Proceed -- Starting Analysis in Ethics: A Practical Guide -- An Overview of Research Ethics and Challenges from Genomics -- Autonomy and Its Limits: The View from Genomics -- The Social and Institutional Setting of Ethics -- Respect for Persons in Research and in Genetics -- Responsibilities of Researchers in Genetics -- Data Sharing in Genomics.
  • 2015 Springer
    Mascalzoni, Deborah.
    Biobank research and genomic information are changing the way we look at health and medicine. Genomics challenges our values and has always been controversial and difficult to regulate. In the future lies the promise of tailored medical treatments and pharmacogenomics but the borders between medical research and clinical practice are becoming blurred. We see sequencing platforms for research that can have diagnostic value for patients. Clinical applications and research have been kept separate, but the blurring lines challenges existing regulations and ethical frameworks.Then how do we regulate it? This book contains an overview of the existing regulatory landscape for biobank research in the Western world and some critical chapters to show how regulations and ethical frameworks are developed and work. How should international sharing work? How design an ethical informed consent? An underlying critique: the regulatory systems are becoming increasingly complex and opaque. The international community is building systems that should respond to that. According to the authors in fact, it is time to turn the ship around. Biobank researchers have a moral responsibility to look at and assess their work in relation to the bigger picture: the shared norms and values of current society. Research ethics shouldn?t only be a matter of bioethicists writing guidelines that professionals have to follow. Ethics should be practiced through discourse and regulatory frameworks need to be part of that public discourse. Ethics review should be then not merely application of bureaucracy and a burden for researchers but an arena where researchers discuss their projects, receive advice and practice their ethics skills.
  • 2005 ScienceDirect
    Gregory, T. Ryan.
    Genome size evolution in animals / T. Ryan Gregory -- Genome size evolution in plants / Michael D. Bennett and Ilia J. Leitch -- Transposable elements / Margaret G. Kidwell -- B chromosomes / Juan Pedro M. Camacho -- Small-scale gene duplications / John S. Taylor and Jeroen Raes -- Large-scale gene and ancient genome duplications / Yves Van de Peer and Axel Meyer -- Polyploidy in plants / Jennifer A. Tate, Douglas E. Soltis, and Pamela S. Soltis -- Polyploidy in animals / T. Ryan Gregory and Barbara K. Mable -- Comparative genomics in eukaryotes / Alan Filipski and Sudhir Kumar -- Comparative genomics in prokaryotes / T. Ryan Gregory and Rob DeSalle -- Macroevolution and the genome / T. Ryan Gregory.
  • 2007 MyiLibrary
    Arnold, Michael L.
    History of investigations -- The role of species concepts -- Testing the hypothesis -- Barriers to gene flow -- Hybrid fitness -- Gene duplication -- Origin of new evolutionary lineages -- Implications for endangered taxa -- Humans and associated lineages -- Emergent properties.
  • 2006 Springer
    Forsdyke, Donald R.
    Also available: Print – 2006
  • 2003 ScienceDirect
    Corne, David; Fogel, Gary.
    An introduction to bioinformatics for computer scientists / David W. Corne and Gary B. Fogel -- An introduction to evolutionary computation for biologists / Gary B. Fogel and David W. Corne -- Determining genome sequences from experimental data using evolutionary computation / Jacek Blazewicz and Marta Kasprzak -- Protein structure alignment using evolutionary computation / Joseph D. Szustakowski and Zhiping Weng -- Using genetic algorithms for pairwise and multiple sequence alignments / Cédric Notredame -- On the evolutionary search for solutions to the protein folding problem / Garrison W. Greenwood and Jae-Min Shin -- Toward effective polypeptide structure prediction with parallel fast messy genetic algorithms / Gary B. Lamont and Laurence D. Merkle -- Application of evolutionary computation to protein folding with specialized operators / Steffen Schulze-Kremer -- Identification of coding regions in DNA sequences using evolved neural networks / Gary B. Fogel, Kumar Chellapilla and David B. Fogel -- Clustering microarray data with evolutionary algorithms / Emanuel Falkenauer and Arnaud Marchand -- Evolutionary computation and fractal visualization of sequence data / Dan Ashlock and Jim Golden -- Identifying metabolic pathways and gene regulation networks with evolutionary algorithms / Junji Kitagawa and Hitoshi Iba --Evolutionary computational support for the characterization of biological systems / Bogdan Filipič and Janez Štrancar -- Discovery of genetic and environmental interactions in disease data using evolutionary computation / Laetitia Jourdan, Clarisse Dhaenens-Flipo and El-Ghazali Talbi -- Feature selection methods based on genetic algorithms for in silico drug design / Mark J. Embrechts, Muhsin Ozdemir, Larry Lockwood, Curt Breneman, Kristin Bennett, Dirk Devogelaere and Marcel Rijckaert --Interpreting analytical spectra with evolutionary computation / Jem J. Rowland.
  • 2012 Springer Protocols
    Fulltext v. 2 (2012) Springer Protocols
    Anisimova, Maria.
    Vol. 1. -- pt. I. Introduction: Bioinformactician's primers: 1. Introduction to genome biology: features, processes, and structures / Aidan Budd ; 2. Diversity of genome organisation / Aidan Budd ; 3. Probability, statistics, and computational science / Niko Beerenwinkel and Juliane Siebourg ; 4. The essentials of computational molecular evolution / Stéphane Aris-Brosou and Nicolas Rodrigue ; -- pt. II. Genomic data assembly, alignment, and homology inference: 5. Next-generation sequencing technologies and fragment assembly algorithms / Heewook Lee and Haixu Tang ; 6. Gene prediction / Tyler Alioto ; 7. Alignment methods: strategies, challenges, benchmarking, and comparative overview / Ari Lötynoja ; 8. Whole-genome alignment / Colin N. Dewey ; 9. Inferring orthology and paralogy / Adrian M. Altenhoff and Christophe Dessimoz ; 10. Detecting laterally transferred genes / Rajeev K. Azad and Jeffrey G. Lawrence ; -- pt. III. Genome evolution: insights from statistical analyses: 11. Genome evolution in outcrossing versus selfing versus asexual species / Sylvain Glémin and Nicolas Galtier ; 12. Transposable elements and their identification / Wojciech Makałowski, Amit Pande, Valer Gotea, and Izabela Makałowska ; 13. Evolution of genome content: population dynamics of transposable elements in flies and humans / Josefa González and Dmitri Petrov ; 14. Detection and phylogenetic assessment of conserved synteny derived from whole genome duplications / Shigehiro Kuraku and Axel Meyer ; 15. Analysis of gene order evolution beyond single-copy genes / Nadia El-Mabrouk and David Sankoff ; 16. Discovering patterns in gene order / Laxmi Parida and Niina Haiminen -- Vol. 2. -- pt. I. Phylogenomics: 1. Tangled trees: the challenge of inferring species trees from coalescent and noncoalescent genes / Christian N.K. Anderson, Liang Liu, Dennis Pearl, and Scott V. Edwards ; 2. Modeling gene family evolution and reconciling phylogenetic discord / Gergely J. Szöllősi and Vincent Daubin ; 3. Genome-wide comparative analysis comparative analysis of phylogenetic trees: the Prokaryotic forest of life / Pere Puigbó, Yuri I. Wolf, and Eugene V. Koonin ; 4. Philosophy and evolution: minding the gap between evolutionary patterns and tree-like patterns / Eric Bapteste, Frédéric Bouchard, and Richard M. Burian ; -- pt. II. Natural selection, recombination, and innovation in genomic sequences: 5. Selection on the protein-coding genome / Carolin Kosiol and Maria Anisimova ; 6. Methods to detect selection on noncoding DNA / Ying Zhen and Peter Andolfatto ; 7. The origin and evolution of new genes / Margarida Cardoso-Moreiera and Manyuan Long ; 8. Evolution of protein domain architectures / Kristoffer Forslund and Erik L.L. Sonnhammer ; 9. Estimating recombination rates from genetic variation in humans / Adam Auton and Gil McVean ; 10. Evolution of viral genomes: interplay between selection, recombination and other forces / Sergei L. Kosakovsky Pond, Ben Murrell, and Art F.Y. Poon ; -- pt. III. Population genomics: 11. Association mapping and disease: evolutionary perspectives / Soren Besenbacher, Thomas Mailund, and Mikkel H. Schierup ; 12. Ancestral population genomics / Julien Y. Dutheil and Asger Hobolth ; 13. Nonredundant representation of ancestral recombinations graphs / Laxmi Parida ; -- pt. IV: The "-OMICS". 14. Using Genomic tools to study regulatory evolution / Yoav Gilad ; 15. Characterization and evolutionary analysis of protein-protein interaction networks / Gabriel Musso, Andrew Emili, and Zhaolei Zhang ; 16. Statistical methods in metabolomics / Alexander Korman, Amy Oh, Alexander Raskind, and David Banks ; 17. Introduction the analysis of environmental sequences: metagenomics with MEGAN / Daniel H. Huson and Suparna Mitra ; 18. Analyzing epigenome data in context of genome evolution and human diseases / Lars Feuerbach, Konstantin Halachev, Yassen Assenov, Fabian Müller, Cahristoph Bock, and Thomas Lengauer ; 19. Genetical genomics for evolutionary studies / Pjotr Prins, Geert Smant, and Ritsert C. Jansen ; -- pt. V. Handling genomic data: resources and computation: 20. Genomics data resources: frameworks and standards / Mark D. Wilkinson ; 21. Sharing programming resources between bio* projects through remote procedure call and native call stack strategies / Pjotr Prins, Naohisa Goto, Andrew Yates, Laurent Gautier, Scotter Willis, Christopher Fields, and Toshiaki Katayama ; 22. Scaleable computing for evoluntionart genomics / Pjotr Prins, Dominique Belhachemi, Steffen Möller, and Geert Smant.
  • 2012 Springer
    Soyer, Orkun S.
    Also available: Print – 2012
  • 2011 Springer
    Pescatello, Linda S.; Roth, Stephen M.
    Fundamental Concepts in Exercise Genomics -- Statistical and Methodological Considerations in Exercise Genomics -- Can You Be Born a Couch Potato? The Genomic Regulation of Physical Activity -- Interaction Between Exercise and Genetics in Type 2 Diabetes Mellitus: An Epidemiological Perspective -- The Interaction Between Genetic Variation and Exercise and Physical Activity in the Determination of Body Composition and Obesity Status -- Interactive Effects of Genetics and Acute Exercise and Exercise Training on Plasma Lipoprotein-Lipid and Blood Pressure Phenotypes -- Genetic Aspects of Muscular Strength and Size -- Genomics of Aerobic Capacity and Endurance Performance: Clinical Implications -- A Synopsis of Exercise Genomics Research and a Vision for its Future Translation into Practice.
  • 2012 Springer Protocols
    Aartsma-Rus, Annemieke.
    DNA diagnostics and exon skipping / Umasuthan Srirangalingam and Shern L. Chew -- Bioinformatics and mutations leading to exon skipping / F.O. Desmet and C. Béroud -- Minigenes to confirm exon skipping mutations / Lourdes R. Desviat, Belén Pérez, and Magdalena Ugarte -- Analysis and interpretation of RNA splicing alterations in genes involved in genetic disorders / Maaike P.G. Vreeswijk and Heleen M. van der Klift -- Exon skipping mutations in neurofibromatosis / Emanuele Buratti and Diana Baralle -- Overview on applications of antisense-mediated exon skipping / Willeke M.C. van Roon-Mom and Annemieke Aartsma-Rus -- Overview on DMD exon skipping / Annemieke Aartsma-Rus -- Overview on AON design / Annemieke Aartsma-Rus -- Optimizing RNA/ENA chimeric antisense oligonucleotides using in vitro splicing / Yasuhiro Takeshima, Mariko Yagi, and Masafumi Matsuo -- Optimizing antisense oligonucleotides using phophorodiamidate morpholino oligomers / Linda J. Popplewell, Alberto Malerba, and George Dickson -- Optimizing splice-switching oligomer sequences using 2'-O-methyl phosphorothioate chemistry / Carl Adkin, Sue Fletcher, and Steve D. Wilton -- Exon skipping quantification by real-time PCR / Alessandra Ferlini and Paola Rimessi -- Antisense-mediated exon skipping to shift alternative splicing to treat cancer / Jing Wan -- Antisense-mediated exon skipping to generate soluble receptors / A. Seda Yilmaz-Elis and J. Sjef Verbeek -- Antisense-mediated exon skipping to reframe transcripts / Sandrina Turczynski [and others] -- U1 snRNA as an effective vector for stable expression of antisense molecules and for the inhibition of the splicing reaction / Julie Martone, Fernanda Gabriella De Angelis, and Irene Bozzoni -- Engineering U7snRNA gene to reframe transcripts / Aurélie Goyenvalle -- Dynamic fluorescent and luminescent reporters for cell-based splicing screens / Claude C. Warzecha, Ruben Hovhannisyan, and Russ P. Carstens -- Antisense-mediated exon-skipping to induce gene knockdown / Petra Disterer and Bernard Khoo -- Antisense-mediated exon inclusion / Yimin Hua and Adrian R. Krainer -- Antisense genes to induce exon inclusion / Rachel Nlend Nlend and Daniel Schümperli -- Using mini-genes to identify factors that modulate alternative splicing / Robert Morse, Adrian G. Todd, and Philip J. Young -- Overview of alternative oligonucleotide chemistries for exon skipping / Amer F. Saleh, Andrey A. Arzumanov, and Michael J. Gait -- Identification of peptides for tissue-specific delivery / Hans Heemskerk -- Systemic delivery of antisense oligomer in animal models and its implications for treating DMD / Qi Long Lu and Bo Wu -- Cell-penetrating peptides enhance systemic delivery of antisense morpholino oligomers / Hong M. Moulton -- Optimizing tissue-specific antisense oligonucleotide-peptide conjugates / Corinne A. Betts [and others].
  • 2009 Springer Protocols
    Parkinson, John.
    Expressed sequence tags : an overview / John Parkinson and Mark Blaxter --Strategies for undertaking expressed sequence tag (EST) projects / Sandra W. Clifton and Makedonka Mitreva -- Construction of cDNA libraries : focus on protists and fungi / Naiara Rodríguez-Ezpeleta ... [et al.] -- Generation of full-length cDNA libraries : focus on plants / Motoaki Seki ... [et al.] -- Preparation of full-length cDNA libraries : focus on metazoans / Masako Harada and Yoshihide Hayashizaki -- Expressed sequence tags : normalization and subtraction of cDNA libraries / Marcelo Bento Soares ... [et al.] -- Generating EST libraries : trans-spliced cDNAs / Cecilia Fernández and Rick M. Maizels -- Large-scale sequencing and analytical processing of ESTs / Makedonka Mitreva and Elaine R. Mardis -- EST processing : from trace to sequence / Ralf Schmid and Mark Blaxter -- Obtaining accurate translations from expressed sequence tags / James Wasmuth and Mark Blaxter -- EST databases and web tools for EST projects /Yao-Qing Shen ... [et al.] -- Phylogenomic analysis of EST datasets / José M. Peregrín-Alvarez and John Parkinson -- Statistical analysis of expressed sequence tags / Edward Susko and Andrew J. Roger -- Application of ESTs in microarray analysis / Weizhong Li ... [et al.] -- Exploiting ESTs in human health / Sandro José de Souza.
  • 2012 Springer Protocols
    Karamanos, Yannis.
    1. DNA microarrays for gene expression analysis in brain tissue and cell lines / Gustavo A. Barisone and Elva Diaz -- 2. Gene expression profiling using the terminal continuation RNA amplification method for small input samples in neuroscience / Stephen D. Ginsberg, Melissa J. Alldred, and Shaoli Che -- 3. Expression profiling in brain disorders / Peter J. Gebicke-Haerter -- 4. Endothelial cell heterogeneity of blood-brain barrier gene expression: analysis by LCM/qRT-PCR / Tyler Demarest, Nivetha Murugesan, Jennifer A. Macdonald, and Joel S. Pachter -- 5. Gene expression profiling using 3' tag digital approach / Yan W. Asmann, E. Aubrey Thompson, and Jean-Pierre A. Kocher -- 6. Sharing expression profiling data with gemma / Anton Zoubarev and Paul Pavlidis -- 7. Two-dimensional protein analysis of neural stem cells / Martin H. Maurer -- 8. iTRAQ proteomics profiling of regulartory proteins during oligodendrocyte differentiation / Mohit Raja Jain, Tong Liu, Teresa L. Wood, and Hong Li -- 9. Protein profiling of the brain: proteomics of isolated tissues and cells / Nicole Haverland and Pawel Ciborowski -- 10. The proteome of brain capillary endothelial cells: toward a molecular characterization of an in vitro blood-brain barrier model / Sophie Duban-Deweer, Christophe Flahaut, and Yannis Karamanos -- 11. MALDI imaging technology applications in neurosciences: from history to perspectives / Michael Salzet, Céline Mériaux, Julien Franck, Maxence Wistorsi, and Isabelle Fournier -- 12. Profiling of HIV proteins in cerebrospinal fluid / Melinda Wojtkiewicz and Pawel Ciborowski -- 13. Proteomic profiling of cerebrospinal fluid / Gwenael Pottiez and Pawel Ciboroski -- 14. New nanotechnology applications in single cell analysis: why and how? / Gradimir N. Misevic, Gerard BenAssaya, Bernard Rasser, Philippe Sales, Jovana Simic-Krstic, Nikola Misevic, and Octavian Popescu.
  • 2007 Karger
    Hoehn, Holger; Schindler, Detlev.
    Why, what, and how can we learn from a rare disease like Fanconi anemia? / Schroeder-Kurth, T. -- Fanconi anemia: a disease with many faces / Dietrich, R., Velleuer, E. -- Milestones in Fanconi anemia research / Digweed, M., Hoehn, H., Sperling K. -- Fanconi anemia genes: structure, mutations, and genotype-phenotype correlations / Kalb, R. ... [et al.] -- Cancer in Fanconi anemia and Fanconi anemia genes in cancer / Neveling, K., Kalb, R., Schindler, D. -- Clonal chromosomal aberrations in bone marrow cells of Fanconi anemia patients: results and implications / Neitzel H. ... [et al.] -- Interphase FISH-assay for the detection of MDS- and AML-associated chromosomal imbalances in native bone marrow and peripheral blood cells / Tönnies, H. ... [et al.] -- Applications of cell cycle testing in Fanconi anemia / Schindler, D. ... [et al.] -- Prenatal diagnosis of Fanconi anemia: functional and molecular testing / Bechtold, A. ... [et al.] -- Revertant mosaicism in Fanconi anemia: natural gene therapy at work / Hoehn, H. ... [et al.] -- Stem cell transplantation in Fanconi anemia, recent advances with alternative donors / Eyrich, M., Winkler, B., Schlegel, P.G. -- Fanconi anemia genes in vertebrates: evolutionary conservation, sex-linkage, and embryonic expression of FANCC and FANCG in avian cells / Nanda, I. ... [et al.] -- Studying homologous recombination in Fanconi anemia / Demuth, I., Digweed, M. -- Functional knock-down of human RAD51 for testing the Fanconi anemia-BRCA connection / Rio, P., Hanenberg, H.
  • 2005 Springer
    Grosjean, Henri.
  • 2006 Springer Protocols
    Didenko, Vladimir V.
  • 2014 CRCnetBASE
    Primorac, Dragan; Schanfield, Moses S.
  • 2005 CRCnetBASE
    Buckleton, John S.; Triggs, Christopher M.; Walsh, Simon J.
  • 2001 ScienceDirect
    Martin, W. N.; Spears, William M.
    Machine generated contents note: Introduction -- Worthy N. Martin and William M. Spears -- Overcoming Fitness Barriers in Multi-Modal Search Spaces 5 -- Martin J. Oates and David Come -- N iches in N K -Landscapes 27 -- Keith E. Mathia, Larry J. Eshelman, and J. David Schaffer -- New Methods for Tunable, Random Landscapes 47 -- R. E. Smith and J. E. Smith -- Analysis of Recombinative Algorithms on a Non-Separable Building-Block Problem 69 -- Richard A. Watson -- Direct Statistical Estimation of GA Landscape Properties 91 -- Colin R. Reeves -- Comparing Population Mean Curves 109 -- B. Naudts and I. Landrieu -- Local Performance of the ((/(I, () -ES in a Noisy Environment 127 -- Dirk V Arnold and Hans-Georg Beyer -- Recursive Conditional Scheme Theorem, Convergence and -- Population Sizing in Genetic Algorithms 143 -- Riccardo Poli -- Towards a Theory of Strong Overgeneral Classifiers 165 -- Tim Kovacs -- Evolutionary Optimization through PAC Learning 185 -- Forbes J. Burkowski -- Continuous Dynamical System Models of Steady-State Genetic Algorithms 209 -- Alden H. Wright and Jonathan E. Rowe -- Mutation-Selection Algorithm: A Large Deviation Approach 227 -- Paul Albuquerque and Christian Mazza -- The Equilibrium and Transient Behavior of Mutation and Recombination 241 -- William M. Spears -- The Mixing Rate of Different Crossover Operators 261 -- Adam Prigel-Bennett -- Dynamic Parameter Control in Simple Evolutionary Algorithms 275 -- Stefan Droste, Thomas Jansen, and Ingo Wegener -- Local Search and High Precision Gray Codes: Convergence Results and Neighborhoods 295 -- Darrell Whitley, Laura Barbulescu, and Jean-Paul Watson -- Burden and Benefits of Redundancy 313 -- Karsten Weicker and Nicole Weicker -- Author Index 335 -- Key Word Index 337.
  • 2010 Springer
    Berry-Kravis, Elizabeth M.; Tassone, Flora.
    Clinical Neurological Phenotype of FXTAS / Maureen A. Leehey, Elizabeth Berry-Kravis, Christopher G. Goetz and Randi J. Hagerman -- The Epidemiology of FXTAS / Deborah A. Hall and Sebastien Jacquemont -- FXTAS: Neuropsychological/Neuropsychiatric Phenotypes / Jim Grigsby, Angela G. Brega, Andreea L. Seritan and James A. Bourgeois -- Radiological Findings in FXTAS / Susan M. Rivera, Glenn T. Stebbins and Jim Grigsby -- The Pathology of FXTAS / Claudia M. Greco, Michael R. Hunsaker and Robert F. Berman -- The Molecular Biology of FXTAS / Flora Tassone and Paul J. Hagerman -- Genotype/Phenotype Relationships in FXTAS / Emily Allen, Maureen A. Leehey, Flora Tassone and Stephanie Sherman -- Animal Models for FXTAS / Rob Willemsen, Yujing Li, Robert F. Berman, Judith R. Brouwer and Ben A. Oostra, et al. -- Treatment and Management of FXTAS / Elizabeth Berry-Kravis, Deborah A. Hall, Maureen A. Leehey and Randi J. Hagerman -- Genetic Counseling for FXTAS and FMR1-Associated Disorders / Louise W. Gane, Katherine Howard and Liane Abrams.
  • 2012 Springer
    Barciszewski, Jan; Erdmann, V. A.
    RNAissance / Juergen Brosius -- Nucleic Acids as Therapeutics / Saraswat Pushpendra, Pareek Arvind and Bhandari Anil -- Thio Effects as a Tool for Mechanistic Studies of the Cleavage of RNA Phosphodiester Bonds: The Chemical Basis / Mikko Ora, Tuomas Lönnberg and Harri Lönnberg -- Off-Target Effects and Safety Aspects of Phosphorothioate Oligonucleotides / Martina Stessl, Christian R. Noe and Johannes Winkler -- Oligonucleotide Conjugates: Rationale, Synthesis, and Applications / Yashveer Singh, Pierre Murat, Nicolas Spinelli and Eric Defrancq -- CRISPR: A Bacterial Immunity System Based on Small RNAs / Rolf Wagner and Ümit Pul -- Antisense Technology: From Unique Laboratory Tool to Novel Anticancer Treatments / Christine Di Cresce, Colin Way, Mateusz Rytelewski, Saman Maleki Vareki and Supritha Nilam, et al. -- Antisense-Mediated Reduction of Eukaryotic Noncoding RNAs / Xue-hai Liang, Timothy A. Vickers and Stanley T. Crooke -- Antisense Oligonucleotides in the Treatment of Malignant Gliomas / Gerardo Caruso, Mariella Caffo, Giuseppe Raudino, Federica Raudino and Mario Venza, et al. -- Natural Antisense Transcripts Mediate Regulation of Gene Expression / Marco Magistri and Mohammad Ali Faghihi -- Activation and Deactivation of Antisense and RNA Interference Function with Light / Jeane M. Govan and Alexander Deiters -- Ribozymes as Molecular Biology Reagents / Sanchita Bhadra, Arti Pothukuchy and Andrew Ellington -- RNA Technologies for Mitochondrial Genetics / André Dietrich, Katarzyna Rolle, Marta Gabryelska, Eliza Wyszko and Romain Val, et al. -- RNA-Based Therapies for Inherited Metabolic Diseases / Belén Pérez, Magdalena Ugarte and Lourdes R. Desviat -- RNA-Cleaving DNA Enzymes and Their Potential Therapeutic Applications as Antibacterial and Antiviral Agents / P. I. Pradeepkumar and Claudia Höbartner -- Hammerhead Ribozymes Against Virus and Viroid RNAs / Alberto Carbonell, Ricardo Flores and Selma Gago -- Suppression of Hepatitis C Viral Genome Replication with RNA-Cleaving Deoxyribozyme / Dal-Hee Min and Dong-Eun Kim -- Design of Synthetic shRNAs for Targeting Hepatitis C: A New Approach to Antiviral Therapeutics / Brian H. Johnston and Qing Ge -- The Diverse Active Sites in Splicing, Debranching, and MicroRNA Processing Around RNA Phosphodiester Bonds / Sourav Kumar Dey, Eduardo Paredes, Molly Evans and Subha R. Das -- MicroRNAs and Their Antagonists as Novel Therapeutics / Jeppe Vinther, Jakob Lewin Rukov and Noam Shomron -- microRNAs in Human Diseases and Viral Infections / Alessandra Mescalchin and Tobias Restle -- Dysregulation of MicroRNA Expression and Human Diseases? / To-Ha Thai -- Noncoding RNAs: Identification of Cancer-Associated MicroRNAs / Muller Fabbri and George A. Calin -- Targeting Non-coding RNAs for Cancer Therapy / Satya K. Kota and Savithri Balasubramanian -- MicroRNA Pathways in Drosophila / Geetanjali Chawla and Nicholas S. Sokol -- Viroids: The Smallest Known Infectious Agents Cause Accumulation of Viroid-Specific Small RNAs / Jaroslav Matoušek, Detlev Riesner and Gerhard Steger.
  • 2014 Springer Protocols
    Blázquez-Castro, Alfonso; Espada, Jesús; Stockert, Juan C.
    Predictive binding geometry of ligands to DNA minor groove : isohelicity and hydrogen-bonding pattern / Juan C. Stockert -- Using microchip gel electrophoresis to probe DNA-drug binding interactions / Nan Shi and Victor M. Ugaz -- Identifying different types of chromatin using Giemsa staining / Juan C. Stockert, Alfonso Blázquez-Castro, and Richard W. Horobin -- Analysis of DNA damage and repair by comet fluorescence in situ hybridization (comet-FISH) / Michael Glei and Wiebke Schlörmann -- Alkaline nuclear dispersion assays for the determination of DNA damage at the single cell level / Piero Sestili and Carmela Fimognari -- Polarization microscopy of extended chromatin fibers / Maria Luiza S. Mello and Benedicto de Campos Vidal -- DNA labeling in vivo : quantification of epidermal stem cell chromatin content in whole mouse hair follicles using Fiji image processing software / Elisa Carrasco, María I. Calvo, and Jesús Espada -- Historical overview of bromo-substituted DNA and sister chromatid differentiation / Roberto Mezzanotte and Mariella Nieddu -- Image analysis of chromatin remodelling / Benedicto de Campos Vidal, Marina B. Felisbino, and Maria Luiza S. Mello -- FISH methods in cytogenetic studies / Miguel Pita, Juan Orellana, Paloma Martínez-Rodríguez, Ángel Martínez-Ramírez, Begoña Fernández-Calvín, and José L. Bella -- Ultrastructural and immunofluorescent methods for the study of the XY body as a biomarker / Roberta B. Sciurano and Alberto J. Solari -- Atomic force microscopy for analyzing metaphase chromosomes : comparison of AFM images with fluorescence labeling images of banding patterns / Osamu Hoshi and Tatsuo Ushiki -- Selective detection of phagocytic phase of apoptosis in fixed tissue sections / Vladimir V. Didenko -- Selective transport of cationized fluorescent topoisomerase into nuclei of live cells for DNA damage studies / Candace L. Minchew and Vladimir V. Didenko -- Visualization and interpretation of eukaryotic DNA replication intermediates in vivo by electron microscopy / Kai J. Neelsen, Arnab Ray Chaudhuri, Cindy Follonier, Raquel Herrador, and Massimo Lopes -- Combined bidimensional electrophoresis and electron microscopy to study specific plasmid DNA replication intermediates in human cells / Cindy Follonier and Massimo Lopes -- Standard DNA methylation analysis in mouse epidermis : bisulfite sequencing, methylation-specific PCR, and 5-methyl-cytosine (5mC) immunological detection / Jesús Espada, Elisa Carrasco, and María I. Calvo -- Methyl-combing : single-molecule analysis of DNA methylation on stretched DNA fibers / Attila Németh -- Investigating 5-hydroxymethylcytosine (5hmC) : the state of the art / Colm E. Nestor, James P. Reddington, Mikael Benson, and Richard R. Meehan -- Hydroxymethylated DNA immunoprecipitation (hmeDIP) / Colm E. Nestor and Richard R. Meehan -- Microscale thermophoresis for the assessment of nuclear protein-binding affinities / Wei Zhang, Stefan Duhr, Philipp Baaske, and Ernest Laue -- Analysis of histone posttranslational modifications from nucleolus-associated chromatin by mass spectrometry / Stefan Dillinger, Ana Villar Garea, Rainer Deutzmann, and Attila Németh -- Salt-urea, sulfopropyl-sepharose, and covalent chromatography methods for histone isolation and fractionation / Pedro Rodriguez-Collazo -- Chromatin immunoprecipitation / Javier Rodríguez-Ubreva and Esteban Ballestar -- Analysis of chromatin composition of repetitive sequences : the ChIP-Chop assay / Raffaella Santoro -- Purification of specific chromatin domains from single- copy gene loci in Saccharomyces cerevisiae / Stephan Hamperl, Christopher R. Brown, Jorge Perez-Fernandez, Katharina Huber, Manuel Wittner, Virginia Babl, Ulrike Stöckl, Hinrich Boeger, Herbert Tschochner, Philipp Milkereit, and Joachim Griesenbeck -- Deep sequencing of small chromatin-associated RNA : isolation and library preparation / Sarah Daniela Diermeier, Thomas Schubert, and Gernot Längst -- Deep sequencing of small chromatin-associated RNA : bioinformatic analysis / Sarah Daniela Diermeier and Gernot Längst.
  • 2012 Springer Protocols
    Kaufmann, M.; Klinger, Claudia.
    Prediction of protein tertiary structures using MUFOLD -- Prediction of protein functions -- Genome-wide screens for expressed hypothetical proteins -- Self-custom-made SFP arrays for nonmodel organisms -- Construction and analysis of full-length and normalized cdna libraries from citrus -- Assembling linear DNA templates for in vitro transcription and translation -- Automated computational analysis of genome-wide DNA methylation profiling data from help-tagging assays -- Detection of RNA editing events in human cells using high-throughput sequencing -- Comparative study of differential gene expression in closely related bacterial species by comparative hybridization -- Whole-genome RT-qPCR microRNA expression profiling -- Using quantitative real-time reverse transcriptase polymerase chain reaction to validate gene regulation by pttg -- FRET-based real-time DNA microarrays -- 2-D gel electrophoresis: Constructing 2D-gel proteome reference maps -- The use of antigen microarrays in antibody profiling -- Limited proteolysis in proteomics using protease-immobilized microreactors -- Mass spectrometry for protein quantification in biomarker discovery -- High-throughput microtitre plate-based assay for DNA topoisomerases -- Microscale thermophoresis as a sensitive method to quantify protein: Nucleic acid interactions in solution -- Bioluminescence resonance energy transfer: An emerging tool for the detection of protein-protein interaction in living cells -- LuMPIS: Luciferase-based MBP-pull-down protein interaction screening system -- Yeast two-hybrid screens: Improvement of array-based screening results by N- and C-terminally tagged fusion proteins -- Inducible microRNA-mediated knockdown of the endogenous human lamin A/C gene -- Multiple-gene silencing using antisense RNAs in escherichia coli -- Functional screen of zebrafish deubiquitylating enzymes by morpholino knockdown and in situ hybridization -- Silencing of gene expression by gymnotic delivery of antisense oligonucleotides -- Polycistronic expression of interfering RNAs from RNA polymerase III promoters -- Metabolite analysis of cannabis sativa l. By NMR spectroscopy -- Metabolome analysis of gram-positive bacteria such as staphylococcus aureus by GC-MS and LC-MS -- Metabolic fingerprinting using comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry.
  • 2006 ScienceDirect
    Bahn, Sabine; Hemby, S. E.
  • 2002 ScienceDirect
    Dorrell, Nick; Wren, Brendan.
    Also available: Print – 2002
  • 2007 Springer
    Berrar, Daniel P.; Dubitzky, Werner; Granzow, Martin.
  • 2011 Springer Protocols
    Bluhm, Burton H.; Xu, Jin-Rong.
    Genome sequencing and assembly / Manfred G. Grabherr, Evan Mauceli, and Li-Jun Ma -- Targeted cloning of fungal telomeres / Mark L. Farman -- Identification and annotation of repetitive sequences in fungal genomes / Braham Dhillon and Stephen B. Goodwin -- Next-generation sequencing and potential applications in fungal genomics / Phillip SanMiguel -- Getting the most out of your fungal microarray data : two cost- and time-effective methods / Sandra M. Mathioni [and others] -- Fusarium graminearum from expression analysis to functional assays / Heather E. Hallen-Adams, Brad L. Cavinder, and Frances Trail -- EST analysis pipeline : use of distributed computing resources / Francisco Javier González and Juan Antonio Vizcaíno -- Application of ChIP-chip analysis in the rice blast pathogen / Soonok Kim and Thomas K. Mitchell -- Proteome studies of filamentous fungi / Scott E. Baker and Ellen A. Panisko -- Bioinformatics pipeline for sequence-based analyses of fungal biodiversity / D. Lee Taylor and Shawn Houston -- Identifying protein complexes by affinity purification and mass spectrometry analysis in the rice blast fungus / Wende Liu [and others] -- Large scale identification of genes involved in plant-fungal interactions using Illumina's sequencing-by-synthesis technology / R.C. Venu [and others] -- High-throughput production of gene replacement mutants in Neurospora crassa / Gyungsoon Park [and others] -- Phenotypic analysis of Neurospora crassa gene deletion strains / Gloria E. Turner -- Efficient approaches for generating GFP fusion and epitope-tagging constructs in filamentous fungi / Xiaoying Zhou, Guotian Li, and Jin-Rong Xu -- Large-scale insertional mutagenesis in Magnaporthe oryzae by Agrobacterium tumefaciens-mediated transformation / Xiao-Lin Chen, Jun Yang, and You-Liang Peng -- Molecular methods for studying the Cryphonectria parasitica -- hypovirus experimental system / Angus L. Dawe [and others] -- Metabolic fingerprinting in Fusarium verticillioides to determine gene function / Jonathon E. Smith and Burton H. Bluhm -- Tapping genomics to unravel ectomycorrhizal symbiosis / Jonathan M. Plett [and others].
  • 2013 Springer
    Hoffman, Barbara; Liebermann, Dan A.
    Emerging evidence indicates that the Gadd45 family of genes play a unique and critical role as sensors of stress, including genotoxic, physiological and oncogenic stress. The stress response Gadd45 family of genes (Gadd45a, Gadd45b & Gadd45g), discovered by Dr. Liebermann and other researchers, encode for small (18 kd) nuclear/cytoplasmic proteins).These genes are rapidly induced by a wide variety of endogenous and exogenous stress stimuli. In spite of marked similarities, Gadd45 genes are regulated differently & exhibit functional diversity. Gadd45 are implicated in cell cycle arrest, DNA demethylation & repair, apoptosis, cell survival, genomic stability, inflammation, & in response to physiological and oncogenic stress. Functions of Gadd45 genes are mediated by protein-protein interactions that modulate structure/function of other cellular proteins implicated in cell cycle regulation and the response of cells to stress; these interactions vary depending upon the biological setting including cell type, developmental stage and stress/stimulus. Protein partners include cdc2/cyclinB1, p21, the p38/JNK stress induced kinase pathways, and PCNA/histones. The purpose of this book is to provide a comprehensive picture of the unique global role Gadd45 genes play as stress sensors & the molecular pathways involved.
    Also available: Print – 2013
  • 2014 Springer
    Huang, He-Feng; Sheng, Jian-Zhong.
    The book Gamete and Embryo-fetal Origins of Adult Diseases introduces various diseases resulting from the abnormal gametogenesis and embryo development, which manifests as growth retardation, birth defects, or increased susceptibility to chronic metabolic diseases such as diabetes, cardiovascular disease and cancer in childhood and adult life, even fertility disorders and the risk of transgenerational transmission. Six common kinds of these diseases are discussed in separate chapters. The authors explore the connections between these diseases and epigenetic reprogramming, rapid cell differentiation and organ formation and environmental influences, including assisted reproductive technology and adverse intrauterine environments. With a summary of findings on the causes and progression of adult diseases at the phase of gametogenesis and embryo development, this book provides insights into the pathogenesis of disease and aids in the treatment and prevention of disease, meeting the requirement for improving the quality of the newborn population, and effectively preventing and curing major diseases at an early stage. This book offers new perspectives and will be an enlightening resource for obstetricians, paediatricians, epidemiologists, endocrinologists and sanitarians.
  • 2007. Karger
    Volff, Jean-Nicolas.
    Coevolution within and between genes / Galtier, N.; Dutheil, J. -- Evolution of protein-protein interaction network / Makino, T.; Gojobori, T. -- Bacterial flagella and type III secretion: case studies in the evolution of complexity / Pallen, M.J.; Gophna, U. -- Comparative genomics and evolutionary trajectories of viral ATP dependent DNA-packaging systems / Burroughs, A.M.; Iyer, L.M.; Aravind, L. -- General trends in the evolution of prokaryotic transcriptional regulatory networks / Madan Babu, M.; Balaji, S.; Aravind, L. -- Divergence of regulatory sequences in duplicated fish genes / Van Hellemont, R. ... [et al.] -- Evolution of gene function on the X chromosome versus the autosomes / Singh, N.D.; Petrov, D.A. -- Amino acid repeats and the structure and evolution of proteins / Albà, M.M.; Tompa, P.; Veitia, R.A. -- Origination of chimeric genes through DNA-level recombination / Arguello, J.R. ... [et al.] -- Exaptation of protein coding sequences from transposable elements / Bowen, N.J.; Jordan, I.K. -- Modulation of host genes by mammalian transposable elements / Makalowski, W.; Toda, Y. -- Modern genomes with retro-look: retrotransposed elements, retroposition and the origin of new genes / Volff, J.-N.; Brosius, J.
  • 2011 CRCnetBASE
    Wu, William; Kaufman, Peter B.; Welsh, Michael J.; Zhang, Helen H.
    "The third edition of this popular reference covers a variety of techniques related to gene manipulation, including DNA isolation, preparation, screening, and analysis. Topics range from very basic methods to current and sophisticated technologies, including methodologies created and tested by the authors. Other topics include approaches to grant funding and SiRNA technology. The authors offer detailed, step-by-step explanations of protocols and helpful troubleshooting guides. This edition features new techniques for every chapter, as well as several new chapters"--Provided by publisher.
  • 2014 Springer Protocols
    Storici, Francesca.
    RecTEPsy-mediated recombineering in Pseudomonas syringae / Bryan Swingle - Genome manipulations with bacterial recombineering and site-specific integration in Drosophila / Yi Zhang, William Schreiner, and Yikang S. Rong -- Multiple genetic manipulations of DT40 cell line / Akira Motegi and Minoru Takata -- Gene targeting of human pluripotent stem cells by homologous recombination / Sara E. Howden and James A. Thomson -- Methods for the assessment of ssODN-mediated gene correction frequencies in muscle cells / Carmen Bertoni -- Small fragment homologous replacement (SFHR) : sequence-specific modification of genomic DNA in eukaryotic cells by small DNA fragments/ Andrea Luchetti, Arianna Malgieri, and Federica Sangiuolo -- Preparation and application of triple helix forming oligonucleotides and single strand oligonucleotide donors for gene correction / Md. Rowshon Alam ... [et al.] -- Triplex-mediated genome targeting and editing / Faisal Reza and Peter M. Glazer -- Targeting piggyBac transposon integrations in the human genome / Daniel L. Galvan, Claudia S. Kettlun, and Matthew H. Wilson -- Gene targeting in human-induced pluripotent stem cells with adenoviral vectors / Kohnosuke Mitani -- Enhanced gene targeting of adult and pluripotent stem cells using evolved adeno-associated virus / Melissa A. Bartel and David V. Schaffer -- Lentiviral vectors encoding zinc-finger nucleases specific for the model target locus HPRT1 / Laetitia P.L. Pelascini and Manuel A.F.V. Gonçalves -- Designing and testing the activities of TAL effector nucleases / Yanni Lin, Thomas J. Cradick, and Gang Bao -- Bacterial one-hybrid system to isolate homing endonuclease variants with altered DNA target specificities / Rakesh Joshi and Frederick S. Gimble -- Design and analysis of site-specific single-strand nicking endonucleases for gene correction / Michael J. Metzger and Michael T. Certo -- CRISPR-Cas-mediated targeted genome editing in human cells / Luhan Yang ... [et al.] -- RNA-guided genome editing of mammalian cells / Neena K. Pyzocha ... [et al.] -- Nuclease-mediated double-strand break (DSB) enhancement of small fragment homologous recombination (SFHR) gene modification in human- induced pluripotent stem cells (hiPSCs) / R. Geoffrey Sargent, Shingo Suzuki, and Dieter C. Gruenert -- AAV-mediated gene editing via double-strand break repair / Matthew L. Hirsch and R. Jude Samulski -- Genetic modification stimulated by the induction of a site- specific break distant from the locus of correction in haploid and diploid yeast Saccharomyces cerevisiae / Samantha Stuckey and Francesca Storici -- Southern blot protocol to detect chimeric nuclease- mediated gene repair / Céline J. Rocca ... [et al.] -- High-throughput cellular screening of engineered nuclease activity using the single-strand annealing assay and luciferase reporter / Thomas J. Cradick, Christopher J. Antico, and Gang Bao -- Unbiased method for detection of genome-wide off- target effects in cell lines treated with zinc finger nucleases / Cory R. Lindsay and David B. Roth -- Identification of off-target cleavage sites of zinc finger nucleases and TAL effector nucleases using predictive models / Eli J. Fine, Thomas J. Cradick, and Gang Bao -- Method for retinal gene repair in neonatal mouse / Marilyn Dernigoghossian ... [et al.] -- In utero delivery of oligodeoxynucleotides for gene correction / Lingzhi Cai ... [et al.] -- Portal vein delivery of viral vectors for gene therapy for hemophilia / Alexandra Sherman ... [et al.] -- Gene correction of induced pluripotent stem cells derived from a murine model of x-linked chronic granulomatous disorder / Sayandip Mukherjee and Adrian J. Thrasher -- Efficient transduction of hematopoietic stem cells and its potential for gene correction of hematopoietic diseases / Dolly Thomas and Gustavo Mostoslavsky.
  • 2015 Springer Protocols
    Bo, Xuenong; Verhaagen, Joost.
    Adeno-Associated Viral Vectors for Gene Delivery to the Nervous System -- Lentiviral Vectors for Gene Delivery to the Nervous System -- Gene Therapy for Parkinson's Disease: AAV-5-Mediated Delivery of Glial Cell Line-Derived Neurotrophic Factor (GDNF) -- Gene Delivery and Gene Therapy for Alzheimer's Disease -- Gene Therapy for Huntington's Disease -- Gene Therapy Approaches to Promoting Axonal Regeneration After Spinal Cord Injury -- Gene Delivery to Neurons of the Dorsal Root Ganglia Using Adeno-Associated Viral Vectors -- Targeted Gene Therapy for Ischemic Stroke -- Adeno-Associated Viral Gene Therapy for Retinal Disorders -- Gene Therapy for Epilepsies -- AAV Gene Therapy Strategies for Lysosomal Storage Disorders with Central Nervous System Involvement -- Gene Therapy in Spinal Muscular Atrophy (SMA) Models Using Intracerebroventricular Injection into Neonatal Mice -- Gene Therapy for Chronic Pain: How to Manipulate and Unravel Pain Control Circuits from the Brain? -- Gene Therapy Approaches Using Reproducible and Fully Penetrant Lentivirus-Mediated Endogenous Glioma Models
  • 2015 Springer Protocols
    Lu, Long Jason.
    Microarray Transposon Tracking for the Mapping of Conditionally Essential Genes in Campylobacter jejuni -- Identifying Essential Streptococcus sanguinis Genes Using Genome-Wide Deletion Mutation -- Defining Essential Genes and Identifying Virulence Factors of Porphyromonas gingivalis by Massively-Parallel Sequencing of Transposon Libraries (Tn-seq) -- Identification of Essential Genes and Synthetic Lethal Gene Combinations in Escherichia coli K-12 -- Identification of Genes Essential for Leptospirosis -- Identifying Essential Genes in Mycobacterium tuberculosis by Global Phenotypic Profiling -- Essential Genes in the Infection Model of Pseudomonas aeruginosa-PCR-Based Signature-Tagged Mutagenesis -- Genome-Wide Synthetic Genetic Screening by Transposon Mutagenesis in Candida albicans -- An Integrated Machine-Learning Model to Predict Prokaryotic Essential Genes -- A Statistical Framework for Improving Genomic Annotations of Transposon Mutagenesis (TM) Assigned Essential Genes -- A Proposed Essential Gene Discovery Pipeline: A Campylobacter jejuni Case Study -- Computational Prediction of Essential Metabolic Genes Using Constraint-Based Approaches -- Three Computational Tools for Predicting Bacterial Essential Genes -- Gene Essentiality Analysis Based on DEG 10, an Updated Database of Essential Genes -- Discovering Essential Domains in Essential Genes.
  • 2006 Springer
    Ma, Jun.
  • 2011 Springer Protocols
    O'Driscoll, Lorraine.
    Real-time PCR and multiplex approaches / Olga L. Gurvich and Mikhail Skoblov -- Reverse-transcriptase polymerase chain reaction to detect extracellular mRNAs / Sweta Rani and Lorraine O'Driscoll -- Microarray analysis of mRNAs : experimental design and data analysis fundamentals / Jai Prakash Mehta -- Software and tools for microarray data analysis / Jai Prakash Mehta and Sweta Rani -- Analysis of gene expression as relevant to cancer cells and circulating tumour cells / Anne M. Friel, John Crown, and Lorraine O'Driscoll -- Gene expression profiling in formalin-fixed, paraffin-embedded tissues using the whole-genome DASL assay / Craig S. April and Jian-Bing Fan -- MicroRNA expression analysis : techniques suitable for studies of intercellular and extracellular MicroRNAs / Erica Hennessy and Lorraine O'Driscoll -- Western blotting analysis as a tool to study receptor tyrosine kinases / Serena Germano and Lorraine O'Driscoll -- 2D gel electrophoresis and mass spectrometry identification and analysis of proteins / Paula Meleady -- Design, construction, and analysis of cell line arrays and tissue microarrays for gene expression analysis / Kathy Gately, Keith Kerr, and Ken O'Byrne -- Immunohistochemical and immunofluorescence procedures for protein analysis / Kishore Reddy Katikireddy and Finbarr O'Sullivan -- Advanced microscopy : laser scanning confocal microscopy / Orla Hanrahan, James Harris, and Chris Egan -- Isolation of exosomes for subsequent mRNA, microRNA, and protein profiling / Sweta Rani [and others] -- Atomic force microscopy and high-content analysis : two innovative technologies for dissecting the relationship between epithelial-mesenchymal transition-related morphological and structural alterations and cell mechanical properties / Stephen T. Buckley, Anthony M. Davies, and Carsten Ehrhardt.
  • 2009 CRCnetBASE
    Göhlmann, Hinrich; Talloen, Willem.
    "Gene expression studies merge three disciplines with different historical backgrounds: molecular biology, bioinformatics, and biostatistics. This book tears down the omnipresent language barriers among researchers of these different backgrounds by explaining the entire process of a gene expression study from conception to interpretation. It covers important technical and statistical pitfalls and problems, helping not only to explain concepts outside the domain of researchers, but to provide additional guidance in their field of expertise. The book also describes technical and statistical methods conceptually with illustrative examples, enabling those inexperienced with gene expression studies to grasp the basic principles"--Provided by publisher.
  • 2014 Springer Protocols
    Ochs, Michael F.
    The Present State and Future Direction of Integrated Gene Function Analysis -- Performing Integrative Functional Genomics Analysis in GeneWeaver.org -- Functional Annotation of Differentially Regulated Gene Set Using WebGestalt: A Gene Set Predictive of Response to Ipilimumab in Tumor Biopsies -- Integrative Data-Mining Tools to Link Gene and Function -- Detection of Driver Protein Complexes in Breast Cancer Metastasis by Large-Scale Transcriptome-Interactome Integration -- Pattern Identification in Time-Course Gene Expression Data with the CoGAPS Matrix Factorization -- Statistical Tools and R Software for Cancer Driver Probabilities -- Predicting the Functional Consequences of Somatic Missense Mutations Found in Tumors -- Determining the Effect of DNA Methylation on Gene Expression in Cancer Cells -- Reverse Engineering Transcriptional Gene Networks -- Integrating In Silico Resources to Map a Signaling Network -- A Method for Inducible Gene Over-Expression and Down-Regulation in Emerging Model Species Using Pogostick -- Construction and Application of Site-Specific Artificial Nucleases for Targeted Gene Editing -- Selection of Recombinant Antibodies from Antibody Gene Libraries -- Construction of Simple and Efficient siRNA Validation Systems for Screening and Identification of Effective RNAi-Targeted Sequences from Mammalian Genes -- Rapid Genetic Modification of Mouse Embryonic Stem Cells by Inducible Cassette Exchange Recombination -- In Ovo Electroporation of miRNA-Based-Plasmids to Investigate Gene Function in the Developing Neural Tube -- Proteomic Strategies: SILAC and 2D-DIGE--Powerful Tool to Investigate Cellular Alterations -- Conditional Gene-Trap Mutagenesis in Zebrafish.
  • 2007 Springer Protocols
    Ochs, Michael F.
    Gene function inference from gene expression of deletion mutants / Ghislain Bidaut -- Association analysis for large-scale gene set data / Stefan A. Kirov, Bing Zhang, and Jay R. Snoddy -- Estimating gene function with least squares nonnegative matrix factorization / Guoli Wang and Michael F. Ochs -- From promoter analysis to transcriptional regulatory network prediction using PAINT / Gregory E. Gonye ... [et al.] -- Prediction of intrinsic disorder and its use in functional proteomics / Vladimir N. Uversky ... [et al.] -- Sybil : methods and software for multiple genome comparison and visualization / Jonathan Crabtree ... [et al.] -- Estimating protein function using protein-protein relationships / Shailesh V. Date -- Bioinformatics tools for modeling transcription factor target genes and epigenetic changes / Ramana V. Dvuluri -- Mining biomedical data using MetaMap Transfer (MMTx) and the Unified Medical Language System (UMLS) / John D. Osborne ... [et al.] -- Statistical methods for identifying differentially expressed gene combinations / Yen-Yi Ho ... [et al.] -- Gene function analysis using the chicken B-cell line DT40 / Randolph B. Caldwell ... [et al.] -- Design and application of a shRNA-based gene replacement retrovirus / Rugang Zhang, Peter D. Adams, and Xiaofen Ye -- Construction of simple and efficient DNA vector-based short hairpin RNA expression systems for specific gene silencing in mammalian cells / Tsung-Lin Cheng and Wen-Tsan Chang -- Selection of recombinant antibodies from antibody gene libraries / Michael Hust, Stefan Dübel, and Thomas Schirrmann -- A bacterial/yeast merged two-hybrid system : protocol for yeast screening with single of parallel baits / Nadezhda Y. Tikhmyanova ... [et al.] -- A bacterial/yeast merged two-hybrid system : protocol for bacterial screening / Ilya G. Serebriiskii, Nadia Milech, and Erica A. Golemis -- Engineering Cys2His2 zinc finger domains using a bacterial cell-based two-hybrid selection system / Stacey Thibodeau-Beganny and J. Keith Joung.
  • 2009 Springer Protocols
    Kühn, Ralf; Wurst, Wolfgang.
    Overview on mouse mutagenesis / Ralf Kühn and Wolfgang Wurst -- Construction of gene-targeting vectors by recombineering / Song-Choon Lee, Wei Wang, and Pentao Liu -- Gene-trap vectors and mutagenesis / Silke De-Zolt ... [et al.] -- Chromosome engineering in ES cells / Louise vander Weyden, Charles Shaw-Smith, and Allan Bradley -- Gene modification in embryonic stem cells by single-stranded DNA oligonucleotides / Marieke Aarts ... [et al.] -- Generation of shRNA transgenic mice / Christiane Hitz ... [et al.] -- Mutagenesis of mouse embryonic stem cells with ethylmethanesulfonate / Robert Munroe and John Schimenti -- Gene targeting in mouse embryonic stem cells / Lino Tessarollo ... [et al.] -- Manipulating mouse embryonic stem cells / Eileen Southon and Lino Tessarollo -- ES cell line establishment / Heidrun Kern and Branko Zevnik -- Generation of double-knockout embryonic stem cells / Eva Wielders, Marleen Dekker, and Hein te Riele -- Differentiation analysis of pluripotent mouse embryonic stem (ES) cells in vitro / Insa S. Schroeder ... [et al.] -- Cloning of ES cells and mice by nuclear transfer / Sayaka Wakayama, Satoshi Kishigami, and Teruhiko Wakayama -- Isolation, microinjection, and transfer of mouse blastocysts / Susan W. Reid and Lino Tessarollo -- Aggregation chimeras : combining ES cells, diploid, and tetraploid embryos / Mika Tanaka ... [et al.] -- VelociMouse : fully ES cell-derived F0-generation mice obtained from the injection of ES cells into eight-cell-stage embryos / Thomas M. DeChiara ... [et al.] -- Generation of Cre recombinase-expressing transgenic mice using bacterial artificial chromosomes / Jan Rodriguez Parkitna, David Engblom, and Günther Schütz -- Inducible Cre mice / Susanne Feil, Nadejda Valtcheva, and Robert Feil -- Creation and use of a Cre recombinase transgenic database / Andras Nagy, Lynn Mar, and Graham Watts -- Transposon mutagenesis in mice / David A. Largaespada -- Lentiviral transgenesis / Alexander Pfeifer and Andreas Hofmann -- Sperm cryopreservation and in vitro fertilization / Susan Marschall, Auke Boersma, and Martin Hrabé de Angelis -- Influence of genetic background on genetically engineered mouse phenotypes / Thomas Doetschman -- Pathologic phenotyping of mutant mice / Roderick T. Bronson -- Systemic first-line phenotyping / Valérie Gailus-Durner ... [et al.]
  • 2006 Springer Protocols
    Bina, Minou.
    Analysis of allele-specific gene expression / Julian C. Knight -- Construction of microRNA-containing vectors for expression in mammalian cells / Yoko Fukuda, Hiroaki Kawasaki, and Kazunari Taira -- Mining microarray data at NCBI's gene expression omnibus (GEO) / Tanya Barrett and Ron Edgar -- The Stanford microarray database: a user's guide / Jeremy Gollub, Catherine A. Ball, and Gavin Sherlock -- Detecting nucleosome ladders on unique DNA sequences in mouse liver nuclei / Tomara J. Fleury, Alfred Cioffi, and Arnold Stein -- DNA methyltransferase probing of DNA-protein interactions / Scott A. Hoose and Michael P. Kladde -- Protein binding microarrays (PBMS) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteins / Michael F. Berger and Martha L. Bulyk -- Quantitative profiling of protein-DNA binding on microarrays / Jiannis Ragoussis, Simon Field, and Irina A. Udalova -- Analysis of protein-DNA binding by streptavidin-agarose pulldown / Kenneth K. Wu -- Isolation and mass spectrometry of specific DNA binding proteins / Mariana Yaneva and Paul Tempst -- Isolation of transcription factor complexes by in vivo biotinylation tagging and direct binding to streptavidin beads / Patrick Rodriguez ... [et al.]. Use of genome browsers to locate your favorite genes / Minou Bina -- Methods for identifying and mapping recent segmental and gene duplications in eukaryotic genomes / Razi Khaja ... [et al.] -- Identification and mapping of paralogous genes on a known genomic DNA sequence / Minou Bina -- Quantitative DNA fiber mapping in genome research and construction of physical maps / Heinz-Ulrich G. Weier and Lisa W. Chu -- PRINS for mapping single copy genes / Avirachan T. Tharapel and Stephen S. Wachtel -- VISTA family of computational tools for comparative analysis of DNA sequences and whole genomes / Inna Dubchak and Dmitriy V. Ryaboy -- Computational prediction of cis-Regulatory modules from multispecies alignments using galaxy, table browser, and GALA / Laura Elnitski, David King, and Ross C. Hardison -- Comparative promoter analysis in vertebrate genomes with the CORG workbench / Christoph Dieterich and Martin Vingron -- cis-Regulatory region analysis using BEARR / Vinsensius Berlian Vega -- A database of 9-Mers from promoter region of human protein-coding genes / Minou Bina, Phillip Wyss, and Syed Rehan Shah -- A program toolkit for the analysis of regulatory regions of genes / Phillip Wyss, Sheryl A. Lazarus, and Minou Bina --
  • 2008 CRCnetBASE
    Lidbury, Brett A.; Mahalingam, Suresh.
    A perspective on the future clinical impact of genetic diagnosis and gene-based drug therapies for patient health / Julian W. Tang -- Virally-encoded microRNA (miRNA): candidates for gene silencing / Ralph A. Tripp ... [et al.] -- Development of gene profile-responsive antisense agents / Sergei A. Kazakov and Brian H. Johnston -- Gene profiles in drug development: applications in target identification, biomarker discovery, and compound characterization / Eric A.G. Blomme and Dimitri Semizarov -- Gene profiles and cancer / Beverly A. Teicher -- RNA viruses and RNA-based drugs: a perfect match for RNA delivery and the identification of candidate therapeutic target inflammatory molecules / Brett A. Lidbury ... [et al.] -- Ethical considerations for a genetic future in diagnosis and drug development / Lexie Brans and Brett A. Lidbury.
  • 2013 Springer Protocols
    Bina, Minou.
    1. Gene regulation / Minou Bina -- 2. Isolation of nuclei for use in genome-wide DNase hypersensitivity assays to probe chromatin structure / Guoyu Ling and David J. Waxman -- 3. DNase I digestion of isolated nuclei for genome-wide mapping of Denise hypersensitivity sites in chromatin / Guoyu Ling and David J. Waxman -- 4. Isolation and analysis of DNA derived from nucleosome-free regions / Matthew Murtha, Yatong Wang, Claudio Basilico, and Lisa Dailey -- 5. Acquisition of high quality DNA for massive parallel sequencing by in vivo chromatin immunoprecipitation / M. van den Boogaard, L.Y.E. Wong, V.M. Christoffels and P. Barnett -- 6. Luciferase assay to study the activity of a cloned promoter DNA fragment / Nina Solberg and Stefan Krauss -- 7. Promoter deletion analysis using a dual-luciferase reporter system / Yong Zhong Xu, Cynthia Kanagaratham, Sylwia Jancik and Danuta Radzioch -- 8. Application of mRNA display for in vitro selection of DNA-binding transcription factor complexes / Seiji Tateyama and Hiroshi Yanagawa -- 9. Isolation of intracellular protein -- DNA complexes using HaloCHIP an antibody-free alternative to chromatin immunoprecipitation / Danette L. Daniels and Marjeta Urh -- 10. Modified yeast one-hybrid system for genome-wide identification of transcription factor binding sites / Kazuyuki Yanai -- 11. Identifying specific protein-DNA interactions using SILAC-based quantitative proteomics / Cornelia G. Spruijt, H. Irem Baymaz, and Michiel Vermeulen -- 12. Electrophoretic mobility-shift and super-shift assays for studies and characterization of protein-DNA complexes / Elsie I. Pares-Matos -- 13. Combination of native and denaturing PAGE for the detection of protein binding regions in long fragments of genomic DNA / Kristel Kaer and Mart Speek -- 14. Quantitative nanoproteomics approach for protein complex (QNanoPX) using gold nanoparticle-based DNA probe / Shu-Hui Chen and Mei-Yin Lin -- 15. Chromatin assembly and in vitro transcription analyses for evaluation of individual protein activities in multicomponent transcriptional complexes / Takayuki Furumatsu and Hiroshi Asahara -- 16. Using FRET to monitor protein-induced DNA bending : the TBP-TATA complex as a model system / Rebecca H. Blair, James A. Goodrich, and Jennifer F. Kugel -- 17. Promoter independent abortive transcription assays unravel functional interactions between TFIIB and RNA polymerase / Simone C. Wiesler, Finn Werner, and Robert O.J. Weinzierl -- 18. Fluorescence cross-correlation spectroscopy (FCCS) to observe dimerization of transcription factors in living cells / Hisayo Sadamoto and Hideki Muto -- 19. Nuclear recruitment assay as a tool to validate transcription factor interactions in mammalian cells / C.J.J. Boogerd, V.M. Christoffels, and P. Barnett -- 20. Preparation of cell lines for single-cell analysis of transcriptional activation dynamics / Ilona U. Rafalska-Metcalf and Susan M. Janicki -- 21. Peptide microarrays for profiling of serine/threonine kinase activity of recombinant kinases and lysates of cells and tissue samples / Riet Hilhorst, Liesbeth Houkes, Monique Mommersteeg, Joyce Musch, Adriënne van den Berg and Rob Ruijtenbeck -- 22. Immunoaffinity purification of protein complexes from mammalian cells / Chieri Tomomori-Sato, Shigeo Sato, Ronald C. Conaway and Joan W. Conaway -- 23. Simple and efficient identification of chromatin modifying complexes and characterization of complex composition / Jeong-Heon Lee and David Skalnik -- 24. Heavy methyl-SILAC labeling coupled with liquid chromatography and high-resolution mass spectrometry to study the dynamics of site-specific histone methylation / Xing-Jun Cao, Barry M. Zee, and Benjamin A. Garcia -- 25. Analysis of p300 occupancy at the early stage of stem cell differentiation by chromatin immunoprecipitation / Melanie Le May and Qiao Li -- 26. Mammalian two-hybrid assays for studies of interaction of p300 with transcription factors / Daniela B. Mendonnc̦a, Gustavo Mendonc̦a, and Lyndon F. Cooper -- 27. Fluorescence anisotropy microplate assay to investigate the interaction of full-length steroid receptor coactivator-1a with steroid receptors / Chen Zhang, Steven K. Nordeen, and David J. Shapiro -- 28. Use of histone deacetylase inhibitors to examine the roles of bromodomain and histone acetylation in p300-dependent gene expression / Jihong Chen and Qiao Li -- 29. Histone deacetylase inhibitor valproic acid as a small molecule inducer to direct the differentiation of pluripotent stem cells / Jihong Chen, Natascha Lacroix, and Qiao Li -- 30. Sedimentation and immunoprecipitation assays for analyzing complexes that repress transcription / Ping Lu, Bruce S. Hostager, Paul B. Rothman, and John D. Colgan -- 31. Methods for studies of protein interactions with different DNA methyltransferases / Jianchang Yang.
  • 2012 Springer Protocols
    Deplancke, Bart; Gheldof, Nele.
    pt. I. Regulatory state components. 1. How do you find transcription factors? Computational approaches to compile and annotate repertoires of regulators for any genome / Juan M. Vaquerizas, Sarah A. Teichmann, and Nicholas M. Luscombe. 2. Expression pattern analysis of regulatory transcription factors in Caenorhabditis elegans / Huiyun Feng, Hannah L. Craig, and Ian A. Hope. 3. High-throughput SELEX determination of DNA sequences bound by transcription factors in vitro / Nobuo Ogawa and Mark D. Biggin. 4. Convenient determination of protein-binding DNA sequences using quadruple 9-mer-based microarray and DsRed-monomer fusion protein / Min-Jeong Kim, Pil Joong Chung, Tae-Ho Lee, Tae-Hoon Kim, Baek Hie Nahm, and Yeon-Ki Kim. 5. Analysis of specific protein-DNA interactions by bacterial one-hybrid assay / Marcus B. Noyes. 6. MITOMI : a microfluidic platform for in vitro characterization of transcription factor-DNA interaction / Sylvie Rockel, Marcel Geertz, and Sebastian J. Maerkl. 7. Detecting protein-protein interactions with the split-ubiquitin sensor / Alexander Dünkler, Judith Müller, and Nils Johnsson. 8. Genome-wide dissection of posttranscriptional and posttranslational interactions / Mukesh Bansal and Andrea Califano. 9. Linking cellular signalling to gene expression using EXT-encoded reporter libraries / Anna Botvinik and Moritz J. Rossner. 10. Sample preparation for small RNA massive parallel sequencing / Willemijn M. Gommans and Eugene Berezikov -- pt. II. Genomic components. 11. CAGE (cap analysis of gene expression) : a protocol for the detection of promoter and transcriptional networks / Hazuki Takahashi, Sachi Kato, Mitsuyoshi Murata, and Piero Carninci. 12. Detecting DNaseI-hypersensitivity sites with MLPA / Thomas Ohnesorg, Stefanie Eggers, and Stefan J. White. 13. Detecting long-range chromatin interactions using the chromosome conformation capture sequencing (4C-seq) method / Nele Gheldof, Marion Leleu, Daan Noordermeer, Jacques Rougemont, and Alexandre Reymond -- pt. III. Mapping protein-DNA interactions. 14. Analyzing transcription factor occupancy during embryo development using ChIP-seq / Yad Ghavi-Helm and Eileen E.M. Furlong. 15. Genome-wide profiling of DNA-binding proteins using barcode-based multiplex solexa sequencing / Sunil Kumar Raghav and Bart Deplancke. 16. Computational analysis of protein-DNA interactions from ChIP-seq data / Jacques Rougemont and Felix Naef. 17. Using a yeast inverse one-hybrid system to identify functional binding sites of transcription factors / Jizhou Yan and Shawn M. Burgess. 18. Using cisTargetX to predict transcriptional targets and networks in Drosophila / Delphine Potier, Zeynep Kalender Atak, Marina Naval Sanchez, Carl Herrmann, and Stein Aerts. 19. Proteomic methodologies to study transcription factor function / Harry W. Jarrett. 20. High-throughput gateway-compatible yeast one-hybrid screen to detect protein-DNA interactions / Korneel Hens, Jean-Daniel Feuz, and Bart Deplancke -- pt. IV. Visualization GRNs. 21. BioTapestry : a tool to visualize the dynamic properties of gene regulatory networks / William J.R. Longabaugh -- pt. V. Modeling of GRNs. 22. Implicit methods for qualitative modeling of gene regulatory networks / Abhishek Garg, Kartik Mohanram, Giovanni De Micheli, and Ioannis Xenarios.
  • 2005 CRCnetBASE
    Sohail, Muhammad.
  • 2012 Springer Protocols
    Peccoud, Jean.
    Part I. Assembly of oligonucleotides in synthons. Building block synthesis using the polymerase chain assembly method / Julie A. Marchand and Jean Peccoud. Oligonucleotide assembly in yeast to produce synthetic DNA fragments / Daniel G. Gibson. Topdown real-time gene synthesis / Mo Chao Huang [and others] De novo DNA synthesis using single-molecule PCR / Tuval Ben Yehezekel, Gregory Linshiz, and Ehud Shapiro -- Part II. Synthon assembly. SLIC : a method for sequence- and ligation-independent cloning / Mamie Z. Li and Stephen J. Elledge. Assembly of standardized DNA parts using bioBrick ends in E. coli / Olivia Ho-Shing [and others] Assembling DNA fragments by USER fusion / Narayana Annaluru [and others] Fusion PCR via novel overlap sequences / Kamonchai Cha-aim [and others] Using recombineering to generate point mutations : the oligonucleotide-based "Hit and Fix" method / Suhwan Chang, Stacey Stauffer, and Shyam K. Sharan. Using recombineering to generate point mutations : galK-based positive-negative selection method / Kajal Biswas, Stacey Stauffer, and Shyam K. Sharan. Assembling large DNA segments in yeast / Héloïse Muller [and others] Recursive construction of perfect DNA molecules and libraries from imperfect oligonucleotides / Gregory Linshiz, Tuval Ben Yehezkel, and Ehud Shapiro. Cloning whole bacterial genomes in yeast / Gwynedd A. Benders. Production of infectious poliovirus from synthetic viral genomes / Jeronimo Cello and Steffen Muller -- Part III. Software for gene synthesis. In silico design of functional DNA constructs / Alan Villalobos, Mark Welch, and Jeremy Minshull. Using DNAworks in designing oligonucleotides for PCR-based gene synthesis / David Hoover. De novo gene synthesis design using TmPrime software / Mo-Huang Li [and others] Design-a-gene with GeneDesign / Sarah M. Richardson [and others] -- Part IV. Education and security. Leading a successful iGEM team / Wayne Materi. The Build-a-Genome course / Eric M. Cooper [and others] DNA synthesis security / Ali Nouri and Christopher F. Chyba.
  • 2010 Springer
    Giacca, Mauro.
  • 2015 ScienceDirect
    Arbuthnot, Patrick.
    Essentials of viruses and their suitability for treatment ssing gene therapy -- Harnessing RNAi to silence viral gene expression -- Engineering sequence-specific DNA binding proteins for antiviral gene editing -- Viral vectors for delivery of antiviral sequences -- Delivery of antiviral nucleic acids with nonviral vectors -- Gene therapy for chronic hepatitis B virus infection -- Gene therapy for hepatitis C virus infection -- Gene therapy for HIV-1 infection -- Gene therapy for respiratory viral infections -- Gene therapy for infection with hemorrhagic fever viruses -- Gene transfer for prophylaxis and therapy of viral infections -- Antiviral gene therapy : summary and perspectives.
  • 2013 ClinicalKey
    Gerson, Stanton L.; Lattime, Edmund C.
    Ex Vivo Gene Therapy: Utilization of Genetic Vectors for the Generation of Genetically Modified Cell Products for Therapy -- Targeting Tumor Vasculature Using Adeno-Associated Virus Phage Vectors Coding Tumor Necrosis Factor-a -- Viral Insertion Site Detection and Analysis in Cancer Gene Therapy -- Targeted Systemic Delivery of Therapeutic siRNA -- Bacterial Delivery of RNAi Effectors -- Gene-Directed Enzyme Prodrug Cancer Therapy -- Electroporation Gene Therapy -- Toxin-Based Cancer Gene Therapy: Under the Control of Oncofetal H19 Regulatory Sequences -- Gene Therapy in Radiotherapy of Cancer -- Advances in Oncolytic Virotherapy for Brain Tumors -- Oncolytic Adenoviruses in the Treatment of Cancer in Humans -- Selectively Replicating Oncolytic Adenoviruses Combined with Chemotherapy, Radiotherapy, or Molecular Targeted Therapy for Treatment of Human Cancers -- Reoviral Therapy for Cancer: Strategies for Improving Antitumor Efficacy Using Radio- and Chemotherapy -- Selectively Replicating Herpes Simplex Viral Vectors -- Modified Oncolytic Herpesviruses for Gene Therapy of Cancer -- The Lister Strain of Vaccinia Virus as an Anticancer Therapeutic Agent -- Poxvirus-Based Strategies for Combined Vaccine and Tumor Microenvironment Manipulation -- Genetically Engineered (T Cell Receptor) T Cells for AdoptiveTherapy -- Genetically Modified Dendritic Cell Vaccines for Solid Tumors -- Dendritic Cell Vaccination -- Chemokine Gene-Modified Dendritic Cells for Cancer Therapy -- The Use of T Cell Costimulation to Enhance the Immunogenicity of Tumors -- Clinical Application of Plasmid-Based Cancer Vaccines -- Lentivector Vaccines -- Therapeutic Efficacy and Systemic Antitumor T Cell Immunity Induced by RheoSwitch-Regulated IL-12 Expression after Intratumoral Injection of Adenovirus Vector or Vector-Transduced Dendritic Cells -- Clinical Trials Using LV-P₁₄₀K-MGMT for Gliomas -- RNA Interference Therapeutics for Tumor Therapy: Promising Work in Progress -- MGMT Stem Cell Selection and Protection: Preclinical Large Animal and Clinical Studies -- Cytidine Deaminase in Myeloprotective Gene Therapy -- Genetically Engineered Salmonella typhimurium for Targeted Cancer Therapy -- Imaging of Oncolytic Virus Gene Expression -- Lentiviral-Encoded Sodium Iodide Symporter-Mediated Cancer Gene Therapy -- Bacteriophage: From Bacteria to a Successful Targeted Systemic Gene Delivery for Cancer -- Issues in Moving Gene Therapy Approaches to Early Clinical Trials -- The FDA Review Process for Cancer Gene Therapy -- Ethics in Translational Gene Transfer Research.
  • 2015 Springer Protocols
    Stein, Ulrike; Walther, Wolfgang.
    Aptamer targeting the ERBB2 receptor tyrosine kinase for applications in tumor therapy / Georg Mahlknecht, Michael Sela, and Yosef Yarden -- Gene gun her2/neu DNA vaccination : evaluation of vaccine efficacy in a syngeneic her2/neu mouse tumor model / Tam Nguyen-Hoai, Antonio Pezzutto, and Jörg Westermann -- MIDGE technology for the production of a fourfold gene-modified, allogenic cell-based vaccine for cancer therapy / Manuel Schmidt, Barbara Volz, Patrick Grossmann, Kerstin Heinrich, and Burghardt Wittig -- Evaluation of bystander cell killing effects in suicide gene therapy of cancer : engineered thymidylate kinase (TMPK)/AZT enzyme-prodrug axis / Takeya Sato, Anton Neschadim, Ryo Nakagawa, Teruyuki Yanagisawa, and Jeffrey A. Medin -- Oncoleaking : use of the pore-forming Clostridium perfringens enterotoxin (CPE) for suicide gene therapy / Jessica Pahle, Jutta Aumann, Dennis Kobelt, and Wolfgang Walther -- iCaspase 9 suicide gene system / Xiaoou Zhou, Antonio Di Stasi, and Malcolm K. Brenner -- p53-encoding pDNA purification by affinity chromatography for cancer therapy / Ângela Sousa, João A. Queiroz, and Fani Sousa -- Phase 2, open-label, randomized study of pexa-vec (JX-594) administered by intratumoral injection in patients with unresectable primary hepatocellular carcinoma / Caroline J. Breitbach, Anne Moon, James Burke, Tae-Ho Hwang, and David H. Kirn -- Antiangiogenic metargidin peptide (AMEP) tene therapy in disseminated melanoma / Iben Spanggaard and Julie Gehl -- Clinical evaluation of ErbB-targeted CAR T-cells, rollowing intracavity delivery in patients with ErbB-expressing solid tumors / Sophie Papa, May van Schalkwyk, and John Maher.
  • v. 1-, 2008- Springer Protocols
    Le Doux, Joseph M.
    v. 1. Production and in vivo applications of gene transfer vectors. Preparation and quantification of pseudotyped retroviral vector / Hong Yu and Young Jik Kwon. Production of retroviral vectors for clinical use / Kenneth Cornetta, Lilith Reeves, and Scott Cross. Methods for the production of helper-dependent adenoviral vectors / Donna J. Palmer and Philip Ng. Methods for the production of first generation adenoviral vectors / Donna J. Palmer and Philip Ng. Large-scale production of recombinant adeno-associated viral vectors / Alejandro Negrete and Robert M. Kotin. Construction and production of recombinant herpes simplex virus vectors / William F. Goins ... [et al.] Plasmid-based gene transfer in mouse skeletal muscle by electroporation / Jonathan D. Schertzer and Goron S. Lynch. Chitosan nanoparticle-mediated gene transfer / Dongwon Lee and Shyam S. Mohapatra. PEG-PEI copolymers for oligonucleotide delivery to cells and tissues / Gordon J. Lutz, Shashank R. Sirsi, and Jason H. Williams. Non-viral gene delivery with cationic liposome-DNA complexes / Kai K. Ewert ... [et al.] Applications of lentiviral vectors in noninvasive molecular imaging / Abhijit De ... [et al.] Retroviral modification of mesenchymal stem cells for gene therapy of hemophilia A / Christopher B. Doering. Transduction of murine hematopoietic stem cells and in vivo selection of gene-modified cells / Lucienne M. Ide, Elisabeth Javazon, and H. Trent Spencer. Assessment of CFTR function after gene transfer in vitro and in vivo / Uta Griesenbach ... [et al.] Oncolytic adenoviruses for cancer gene therapy / Ta-Chiang Liu, Stephen H. Thorne, and David H. Kirn. Design of trans-splicing adeno-associated viral vectors for Duchenne muscular dystrophy gene therapy / Yi Lai ... [et al.] Prevention of type 1 diabetes in NOD mice by genetic engineering of hematopoietic stem cells / Jessamyn Bagley, Charoui Tian, and John Iacomini. Lentiviral vector delivery of siRNA and shRNA encoding genes into cultured and primary hematopoietic cells / Mingjie Li and John J. Rossi. Nanoparticle-mediated gene delivery to the lung / Rajagopal Ramesh. Retroviral-mediated gene therapy for the differentiation of primary cells into a mineralizing osteoblastic phenotype / Jennifer E. Phillips and Andrés J. García. In vivo siRNA delivery to the mouse hypothalamus shows a role of the co-chaperone XAP2 in regulating TRH transcription / Stéphanie Decherf, Zahra Hassani, and Barbara A. Demeneix. Efficient retroviral gene transfer to epidermal stem cells / Pedro Lei and Stelios T. Andreadis.
  • 2003 ScienceDirect
    Makrides, Savvas C.
    Also available: Print – 2003
  • 2003 Springer Protocols
    Ying, Shao-Yao.
    Complementary DNA libraries: an overview / Shao-Yao Ying -- Rapid amplification of cDNA ends / Yue Zhang -- cDNA generation on paramagnetic beads / Zhaohui Wang and Michael G.K. Jones -- Construction of a normalized cDNA library by mRNA-cDNA hybridization and subtraction / Ye-Guang Chen -- Amplification of cDNA ends using PCR suppression effect and step-out PCR / Mikhail V. Matz [and others] -- Use of inverse PCR to clone cDNA ends / Sheng-He Huang, Steven H.M. Chen, and Ambrose Y. Jong -- Construction of size-fractionated cDNA library assisted by an in vitro recombination reaction / Osamu Ohara -- Construction of a full-length enriched and 5'-end enriched cDNA library using the oligo-capping method / Yutaka Suzuki and Sumio Sugano -- cDNA library construction using in vitro transcriptional amplification / Shi-Lung Lin and Henry Ji -- Amplification of representative cDNA pools from microscopic amounts of animal tissue / Mikhail V. Matz -- Single cell cDNA library construction using cycling aRNA amplification / Shi-Lung Lin -- mRNA/cDNA library construction using RNA-polymerase cycling reaction / Shi-Lung Lin and Shao-Yao Ying -- Quality assessment of cDNA libraries / Hans-Jürgen Fülle -- Assessment of the quality of mRNA libraries by agarose gel electrophoresis / Tsen-Yin Lin and Shao-Yao Ying -- PACS RT-PCR: a method for the generation and measurement of any poly(A)-containing mRNA not affected by contaminating genomic DNA / Igor Nepluev and Rodney J. Folz -- Single-cell mRNA library analysis by northern blot hybridization / Shi-Lung Lin -- Generation of cDNA libraries for profiling gene expression of given tissues or cells / Xin Zhang, Qiu-Hua Huang, and Ze-Guang Han -- Screening poly (dA/dT( -- )) cDNA for gene identification / San Ming Wang [and others] -- Generation of longer cDNA fragments from SAGE tags for gene identification / Jian-Jun Chen [and others] -- Generation of full-length cDNA libraries enriched for differentiatlly expressed genes / Bakhyt Zhumabayeva [and others] -- Subtractive hybridization for the identification of differentially expressed genes using uracil-DNA glycosylase and mung-bean nuclease / Tsen-Yin Lin and Shao-Yao Ying -- Subtractive cloning of differential genes using RNA-PCR / Shao-Yao Ying and Shi-Lung Lin -- Strategy for construction of a cDNA encoding a repetitive amino acid sequence / Masahiro Asada and Toru Imamura -- Preparing lambda libraries for expression of proteins in prokaryotes or eukaryotes / Rebecca L. Mullinax and Joseph A. Sorge -- Peptide library construction from RNA-PCR-derived RNAs / Shi-Lung Lin -- Identifying interacting proteins in an Escherichia coli-based two-hybrid system / Bonnie Wu, Rebecca L. Mullinax, and Joseph A. Sorge -- Future perspectives / Shao-Yao Ying.
  • NCBI Bookshelf
  • 2011 Springer
    Dhalla, Naranjan S.; Nagano, Makoto; Ošt̕ádal, Bohuslav.
    pt. 1. Genes and the heart -- pt. 2. Development and gender -- pt. 3. Mitochondrial diseases -- pt. 4. Ischemic heart disease -- pt. 5. Hypertension and arrhythmias -- pt. 6. Hypertrophy and failure.
  • 2007 Springer
    Lewis, Edward B.; Lipshitz, Howard D.
  • 2010 Springer
    Leigh, Hoyle.
    Genes and mental illness -- How does stress work? the role of memes in epigenesis -- Culture and mental illness -- Genetic-memetic model of mental illness-migration and natural disasters as illustrations -- What do we inherit from our parents and ancestors? -- Genes -- Evolution -- Learning, imitation, and memes -- Storage and evolution of memes in the brain -- External storage of memes: culture, media, cyberspace -- Culture and the individual -- What is mental health -- What is mental illness? -- Psychiatric diagnosis: toward a memetic-epigenetic multiaxial model -- Memetic diagnosis, memetic assessment and biopsychosocial epigenetic formulation -- Principles of memetic therapy -- Broad-spectrum memetic therapy -- Specific memetic therapies -- Genetic-memetic prevention -- Overview of specific syndromes -- Attention-cognition spectrum syndromes: delirium, dementia, impulse control syndromes, ADHD, antisocial personality, obsessive-compulsive personality traits, obsessive-compulsive syndrome -- Anxiety-mood spectrum syndromes: anxiety, panic, phobias, ASD, PTSD, borderline syndrome, dependent and avoidant personalities, social phobia, bipolarity and mania, depression-neurotic and syndromic, adjustment disorders -- Reality perception spectrum syndromes (imagination, dissociation, conversion, somatoform, misattribution somatization, psychosis) -- Pleasure spectrum syndromes (substance use/abuse, additions to substances and beliefs, fanaticism) -- Primary memetic syndromes: eating disorders, factitious disorders, malingering, meme-directed destructive behaviors -- Challenges for the future.
  • 2013 Springer
    Lentzsch, Suzanne.
    This state-of-the-art book is written by a group of international experts to provide insight into the newest breakthroughs from basic pathogenesis to clinical aspects of multiple myeloma. The book provides a comprehensive overview of the genetic and molecular epidemiology of multiple myeloma in order to get a more refined and conclusive understanding of this disease. Areas, which are covered include the characterization of different myeloma entities by genomics and proteomics, notch signaling and targeting protein translation as a new treatment for multiple myeloma, cell cycle control of plasma cell differentiation, the role of bone disease in the pathogenesis of multiple myeloma as well as the molecular interaction of multiple myeloma with a microenvironment. Genetic and Molecular Epidemiology of Multiple Myeloma is a valuable resource for cancer researchers, medical, surgical, and radiation oncologists.
  • 2007 Springer
    Meyer, Gundela.
  • 2014 Oxford Medicine Online
    MacFarlane, Ian M.; LeRoy, Bonnie; Veach, Patricia McCarthy.
    Developing research questions -- Finding sources -- Writing a review of literature -- Ethics in research -- Choosing a paradigm -- Designing a quantitative study -- Quantitative data analysis : I've got data, how do I get answers? -- Conducting qualitative genetic counseling research -- Preparing a manuscript for publication -- Guidelines for directing research.
  • 2008 Springer
    Launis, Veikko; Räikkä, Juha.
    Introduction : the scope and importance of genetic democracy / Veikko Launis -- The prerequisites for genetic democracy / Helena Siipi -- Ethical expertise in democratic societies / Eerik Lagerspetz -- Towards global bioethics : the UNESCO universal declaration on bioethics and human rights / Henk ten Have -- Autonomy and genetic privacy / Juha Räikkä -- Values, rights and GMO : against radicalism -- The precautionary principle and the risks of modern agri-biotechnology / Marko Ahteensuu -- Population databanks and democracy in light of the Icelandic experience / Vilhjálmur Árnason and Stefán Hjörleifsson -- Equality and community in public deliberation : genetic democracy in Taiwan / Terence Hua Tai and Wen-Tsong Chiou -- Genetic resources, genetic democracy and genetic equity / Keekok Lee -- Moral constraints on permissible genetic design / Thomas Pogge.
  • 2010 Springer
    Teebi, Ahmad S.
  • v. 27-28, 2006-2007. Springer
    v. 28, 2007 Springer
    Hollaender, Alexander; Setlow, Jane K.
  • 2006 Springer
    Nolta, Jan A.
    Also available: Print – 2006
  • 2009 Springer Protocols
    Teare, M. Dawn.
    Molecular Genetics and Genetic Variation / Mohammed-Elfatih Twfieg, M. Dawn Teare -- Terminology, Concepts, and Models in Genetic Epidemiology / M. Dawn Teare, Mauro F. Koref -- An Introduction to Epidemiology / Cother Hajat -- Genetic Distance and Markers Used in Linkage Mapping / Kristina Allen-Brady, Nicola J. Camp -- Approaches to Genetic Linkage Analysis / M. Dawn Teare -- Fine-Scale Structure of the Genome and Markers Used in Association Mapping / Karen Curtin, Nicola J. Camp -- Genome-Wide Association Studies / Mark M. Iles -- Candidate Gene Association Studies / M. Dawn Teare -- Family-Based Association Studies / Frank Dudbridge -- Genome Variation: A Review of Web Resources / Andrew Collins, William J. Tapper -- Advanced Methods in Twin Studies / Jaakko Kaprio, Karri Silventoinen -- Mendelian Randomisation: A Tool for Assessing Causality in Observational Epidemiology / Nuala A. Sheehan, Sha Meng, Vanessa Didelez -- Copy Number Variation / Louise V. Wain, Martin D. Tobin -- Epigenetic Variation / Kevin Walters -- Modeling the Effect of Susceptibility Factors (HLA and PTPN22) in Rheumatoid Arthritis / Hervé Perdry, Françoise Clerget-Darpoux -- Coronary Artery Disease: An Example Case Study / Jennifer H. Barrett -- The Genetic Epidemiology of Obesity: A Case Study / Laura M. Johnson.
  • 2004 NCBI Bookshelf
    Dean, Laura; McEntyre, Johanna.
  • 2016 Springer Protocols
    Bose, Jeffrey L.
    Understanding staphylococcal nomenclature / Christina N. Krute and Jeffrey L. Bose -- Restriction-modification systems as a barrier for genetic manipulation of Staphylococcus aureus / Marat R. Sadykov -- Complementation plasmids, inducible gene-expression systems, and reporters for Staphylococci / Ralph Bertram -- De novo assembly of plasmids using yeast recombinational cloning / Ameya A. Mashruwala and Jeffrey M. Boyd -- Splicing by overlap extension PCR to obtain hybrid DNA products / Justin A. Thornton -- Method for preparation and electroporation of S. aureus and S. epidermidis / Melinda R. Grosser and Anthony R. Richardson -- Rapid isolation of DNA from staphylococcus / Kelsey L. Krausz and Jeffrey L. Bose -- Bacteriophage transduction in Staphylococcus aureus : broth-based method / Kelsey L. Krausz and Jeffrey L. Bose -- Bacteriophage transduction in Staphylococcus aureus / Michael E. Olson -- Batch transduction of transposon mutant libraries for rapid phenotype screening in staphylococcus / Katherine L. Maliszewski -- Conjugative transfer in Staphylococcus aureus / Cortney R. Halsey and Paul D. Fey -- Allelic exchange / McKenzie K. Lehman, Jeffrey L. Bose, and Kenneth W. Bayles -- Creation of staphylococcal mutant libraries using transposon Tn917 / Kelly C. Rice -- Generation of a transposon mutant library in Staphylococcus aureus and staphylococcus epidermidis using bursa aurealis / Vijaya Kumar Yajjala ... [et al.] -- Chemical and UV mutagenesis / Jeffrey L. Bose -- Pulse field gel electrophoresis / Batu K. Sharma-Kuinkel, Thomas H. Rude, and Vance G. Fowler Jr. -- RNA-sequencing of Staphylococcus aureus messenger RNA / Ronan K. Carroll, Andy Weiss, and Lindsey N. Shaw -- Quantitative real-time PCR (qPCR) workflow for analyzing Staphylococcus aureus gene expression / April M. Lewis and Kelly C. Rice -- Electrophoretic mobility shiftaAssays / Sarah E. Rowe and James P. O'Gara -- Rapid amplification of cDNA ends for RNA transcript sequencing in staphylococcus / Eric Miller.
  • 2012 Cambridge
    Chapman, Audrey R.
    "The manner in which genetic research associated with addiction is conducted, interpreted and translated into clinical practice and policy initiatives raises important social, ethical and legal issues. Genetic Research on Addiction fulfils two key aims; the first is to identify the ethical issues and requirements arising when carrying out genetically-based addiction research, and the second is to explore the ethical, legal and public policy implications of interpreting, translating and applying this research. The book describes research guidelines on human protection issues such as improving the informed consent process, protecting privacy, responsibilities to minors and determining whether to accept industry funding. The broader public health policy implications of the research are explored and guidelines offered for developing effective social interventions. Highly relevant for clinicians, researchers, academics and policy-makers in the fields of addiction, mental health and public policy"--Provided by publisher.
  • 2011
    Bustamante, Erika Liliana; Clandinin, Thomas R.; Fuller, Margaret T.; Kim, Seung K.; Tsao, Philip.
    In humans, the hormones insulin and glucagon are the principal regulators of blood sugar homeostasis. In the fruit fly, Drosophila melanogaster, the regulation of circulating sugar levels is similarly controlled by insulin-like and glucagon-like factors. Insulin signaling in Drosophila has been studied intensively; by contrast, relatively little is known about the genetic regulation of Drosophila Adipokinetic hormone (Akh), the polypeptide with glucagon-like functions, and the corpora cardiaca (CC) cells that produce Akh. Here I describe the use of an enhancer trap screen that led to the identification of a novel regulator of CC function, the homeodomain transcription factor unplugged (unpg). Knocking down unpg in the CC cells results in decreased Akh transcript levels and reduced circulating glucose and trehalose. I also describe the identification of a number of enhancer traps that are capable of driving GFP expression in the CC cells, suggesting a role for the associated genes in CC cell function. As in human diabetes, insulin deficiency in the fruit fly elevates circulating glucose levels and impairs triglyceride regulation. Reduced insulin signaling in Drosophila also increases expression of the adipokine Akh, a phenotype reminiscent of the excessive glucagon signaling that accompanies human diabetes. Thus, it remains unclear if insulin deficiency or adipokine excess is the primary basis for diabetic phenotypes in flies lacking insulin-producing cells. Here I show that simultaneous targeted ablation of cells producing Drosophila insulin and adipokinetic hormone results in hypoglycemia. Mutation of the gene encoding the Akh receptor (Akhr) reduces circulating glucose levels in adult Drosophila lacking insulin, arguing that excessive Akh signaling is the basis for hyperglycemia in insulin-deficient flies. Simultaneous attenuation of insulin and Akh synthesis also produced hypoglycemic flies. Similar approaches revealed triglyceride imbalance from insulin deficiency requires Akh. Thus adipokines like Akh, not insulin, may be the principal hormonal regulators of glucose and lipid balance in some non-mammalian animal classes and states of insulin deficiency.
  • 2013 Springer
    Carrasquillo, Minerva M.; Morgan, Kevin.
    Since 2009, a revolution has been witnessed in Alzheimer's Disease genetics. New genetic links are being discovered at an unprecedented pace and our understanding of the molecular mechanisms of neurodegeneration have taken a quantum leap forward. This book provides a thorough description of the genes that have been implicated in the aetiology of late-onset Alzheimer's disease (LOAD) based on evidence of genetic association. These "AD susceptibility genes" are described both in their genomic and cellular context, as well as with respect to their known or suspected molecular functions. Although these genes are not sufficient to explain all of the genetic contributions to LOAD, they represent the best replicated set of genes to date. Undoubtedly the list will grow as more advanced genomic approaches towards the identification of novel LOAD genes progresses.
  • 2012 Springer Protocols
    Martin, Jean-René.
    In vivo functional brain imaging using a genetically encoded Ca2+-scensitive bioluminescence reporter, GFP-Aequorin / Jean-Rene Martin -- Ca2+ imaging in brain slices using bioluminescent reporters / Ludovic Tricoire, Estelle Drobac, and Bertrand Lambolez -- Calcium imaging of neural activity in the olfactory system of drosophila / Antonia Strutz [and others] -- Functional imaging of antennal lobe neurons in drosophila with synapto-pHluorin / Dinghui Yu and Ronald L. Davis -- Performing electrophysiology and two-photon calcium imaging in the adult drosophila central brain during walking behavior / M. Eugenia Chiappe and Vivek Jayaraman -- In Vivo optical recording of brain interneuron activities from a drosophila male on a treadmill / Soh Kohatsu, Masayuki Koganezawa, and Daisuke Yamamoto -- Two-photon imaging of population activity with genetically encoded calcium indicators in living flies / Robert A.A. Campbell [and others] -- Engineering and application of genetically encoded calcium indicators / Jasper Akerboom [and others] -- Imaging cAMP dynamics in the drosophila brain with the genetically encoded sensor Epac1-Camps / Katherine R. Lelito and Orie T. Shafer.
  • 2003 Wiley
    Heller, Knut.
    Part 1. Application and Perspectives -- ch. 1. Transgenic Modification of Production Traits in Farm Animals / Mathias Müller and Gottfried Brem -- ch. 2. Genetically Modified Plants / Susanne Stirn and Horst Lörz -- ch. 3. Fermented Food Production using Genetically Modified Yeast and Filamentous Fungi / Anke Niederhaus and Ulf Stahl -- ch. 4. Production of Food Additives using Filamentous Fungi / Carsten M. Hjort -- ch. 5. Perspectives of Genetic Engineering of Bacteria used in Food Fermentations / Arnold Geis -- Part II. Legislation in Europe -- ch. 6. The Legal Situation for Genetically Engineered Food in Europe / Rudolf Streinz and Lars O. Fuchs -- Part III. Methods of Detection -- ch. 7. Detection of Genetic Modifications: Some Basic Considerations / Knut J. Heller -- ch. 8. DNA-based Methods for Detection of Genetic Modifications / Ralf Einspanier and Stephanie Rief -- ch. 9. Genetic Engineering of Fishes and Methods for Detection / Hartmut Rehbein -- ch. 10. Detection Methods for Genetically Modified Crops / Rolf Meyer -- ch. 11. Methods to Detect the Application of Genetic Engineering in Composed and Processed Foods / Karl-Heinz Engel and Francisco Moreano -- ch. 12. Mutations in Lactococcus lactis, and their Detection / Jan Kok and Bertus van den Burg -- ch. 13. Detection Methods for Genetically Modified Microorganisms used in Food Fermentation / Walter P. Hammes, Christian Hertel and Torsten Bauer.
  • 2006 Wiley
    Heller, Knut.
    Part I. Application and Perspectives -- ch. 1. Transgenic modification of production traits in farm animals / Gottfried Brem, Mathias Müller -- ch. 2. Genetically modified plants / Susanne Stirn, Horst Lörz -- ch. 3. Fermentation of food by means of genetically modified yeast and filamentous fungi / Rena Leisegang, Elke Nevoigt, Anja Spielvogel, Georg Kristan, Anke Niederhaus, Ulf Stahl -- ch. 4. Production of food additives using filamentous fungi / Carsten M. Hjort -- ch. 5. Genetic engineering of bacteria used in food fermentation / Arnold Geis -- Part II. Legislation in Europe -- ch. 6. The Legal situation for genetically engineered food in Europe / Rudolf Streinz, Jan Kalbheim -- Part III. Methods of Detection -- ch. 7. Detection of genetic modifications : some basic considerations / Knut J. Heller -- ch. 8. DNA-based methods for detection of genetic modifications / Ralf Einspanier -- ch. 9. Genetic engineering of fish, and methods of detection / Hartmut Rehbein -- ch. 10. Detection methods for genetically modified crops / Rolf Meyer -- ch. 11. Methods for detection of genetically modified organisms in composite and processed foods / Karl-Heinz Engel, Francisco Moreano, Alexandra Ehlert -- ch. 12. Mutations in Lactococcus lactis and their detection / Jan Kok, Bertus van den Burg -- ch. 13. Methods for detection of genetically modified microorganisms used in food fermentation processes / Walter P. Hammes, Christian Hertel, Torsten Bauer.
  • 2002 CRCnetBASE
    Burrows, Beth Elpern; Letourneau, Deborah Kay.
  • 2012 Karger
    Piguet, Pascale; Poindron, Philippe.
    Genetically modified organisms : concepts and methods -- Restriction enzymes : from their discovery to their applications -- Transforming growth factor-beta superfamily : animal models for development and disease -- Transfection of human neuroblastoma cells with Alzheimer's Disease brain hallmarks as a promising strategy to investigate the role of neurosteroidogenesis in neuroprotection -- Investigating therapeutic strategies for Fragile X syndrome in mice -- Innovative therapeutic perspectives in neuromuscular diseases -- Gene therapy for cancer treatment : state of the art -- Manipulating the mitochondrial genetic system.
  • 2009
    Hartl, Daniel L.; Jones, Elizabeth W.
    Status: Not Checked OutLane Catalog Record
    Genes, genomes, and genetic analysis -- DNA structure and genetic variation -- Transmission genetics : the principle of segregation -- Chromosomes and sex-chromosome inheritance -- Genetic linkage and chromosome mapping -- Molecular biology of DNA replication and recombination -- Molecular organization of chromosomes -- Human karyotypes and chromosome behavior -- Genetics of bacteria and their viruses -- Molecular biology of gene expression -- Molecular mechanisms of gene regulation -- Genomics, proteomics, and transgenics -- Genetic control of development -- Molecular mechanisms of mutation and DNA repair -- Molecular genetics of the cell cycle and cancer -- Mitochondrial DNA and extranuclear inheritance -- Molecular evolution and population genetics -- The genetic basis of complex traits.
  • 2008
    Hartwell, Leland.
    Status: Not Checked OutLane Catalog Record
    Genetics: the study of biological information -- Mendel's breakthrough: patterns, particles, and principles of heredity -- Extensions to mendel: complexities in relating genotype to phenotype -- The chromosome theory of inheritance -- Linkage, recombination, and the the mapping of genes on chromosomes -- DNA: how the molecule of heredity carries, replicates, and recombines information -- Anatomy and function of a gene: dissection through mutation -- Gene expression: the flow of genetic information from DNA to RNA to protein -- Deconstructing the genome: DNA at high resolution -- Reconstructing the genome through genetic and molecular analysis -- The direct detection of genotype distinguishes individual genomes -- Systems biology and proteomics -- The eukaryotic chromosome: an organelle for packaging and managing DNA -- Chromosomal rearrangements and changes in chromosome number reshape eukaryotic genomes -- The prokaryotic chromosome: genetic analysis in bacteria -- The chromosomes of organelles outside the nucleus exhibit non-mendelian patterns of inheritance -- Gene regulation in prokaryotes -- Gene regulation in eukaryotes -- Cell-cycle regulation and the genetics of cancer -- Using genetics to study development -- The genetic analysis of populations and how they evolve -- Evolution at the molecular level.
  • 2010 CRCnetBASE
    Ruvinsky, Anatoly.
    Limits and uncertainty in nature and logic -- Quantum fluctuations, mutations, and "fixation" of uncertainty -- Recombination and randomness -- Uncertainty of development -- Organized randomness -- Random genetic drift and "deterministic" selection -- Life : making uncertainty certain.
  • 2009 Karger
    Collins, Malcolm.
    Key concepts in human genetics : understanding the complex phenotype / W.T. Gibson -- Nature versus nurture in determining athletic ability / T.D. Brutsaert, E.J. Parra -- Genetics and sports : an overview of the pre-molecular biology era / M.W. Peeters ... [et al.] -- Genes, athlete status, and training : an overview / I.I. Ahmetov, V.A. Rogozkin -- Angiotensin : converting enzyme, renin-angiotensin system and human performance / D. Woods -- Actinin-3 and performance / N. yang, F. Garton, K. North -- East African runners : their genetics, lifestyle, and athletic prowess / V.O. Onywera -- Gene-lifestyle interactions and their consequences on human health / J. Pomeroy, A.M. Söderberg, P.W. Franks -- Genetic risk factors for musculoskeletal soft tissue injuries / M. Collins, S.M. Raleigh -- Innovative strategies for treatment of soft tissue injuries in human and animal athletes / A. Hoffmann, G. Gross -- Gene doping : possibilities and practicalities / D.J. Wells -- Genetic testing of athletes / A.G. Williams, H. Wackerhage -- The future of genetic research in exercise science and sports medicine / R.J. Trent, B. Yu.
  • 2005 NCBI Bookshelf
    Morrison, Patrick J.; Spence, Roy A. J.
  • 2013 Springer
    Srivastava, Sheela.
    Described as the earliest, simplest life forms, with unlimited metabolic versatility, bacteria are ideally suited to answer some very fundamental questions on life and its processes. They have been employed in almost all fields of biological studies, including Genetics. The whole edifice of science of Genetics centers around three processes: the generation, expression, and transmission of biological variation, and bacteria offer immediate advantages in studying all the three aspects of heredity. Being haploid and structurally simple, it becomes easy to isolate mutations of various kinds and relate them to a function. The availability of such mutants and their detailed genetic and biochemical analyses lead to a gamut of information on gene expression and its regulation. While studying the transmission of biological variation, it is clear that unlike their eukaryotic counterpart, a more genetic approach needs to be employed. Transmission of genetic information in most eukaryotic organisms rests on sexual reproduction that allows the generation of genetically variable offspring through the process of gene recombination. Even though bacteria show an apparent preference for asexual reproduction, they too have evolved mechanisms to trade their genetic material. In fact, bacteria not only could acquire many genes from close relatives, but also from entirely distant members through the process of horizontal gene transfer. Their success story of long evolutionary existence will stand testimony to these mechanisms. While teaching a course on Microbial Genetics to the post-graduate students at Delhi University, it was realized that a book devoted to bacterial genetics may be very handy to the students, researchers, and teachers alike. A strong foundation in genetics also helps in comprehending more modern concepts of molecular biology and recombinant DNA technology, always a favorite with the students and researchers. Planning the format of the book, emphasis has been laid on the generation and transmission of biological variability. The omission of expression part is indeed intentional because lots of information is available on this aspect in any modern biology book. The contents are spread over seven chapters and the text is supported with figures/tables wherever possible. The endeavor has been to induce the readers to appreciate the strength of bacterial genetics and realize the contribution of these tiny organisms to the growth of biological sciences as a whole and genetics in particular.
  • 2013
    Thakker, R. V.
    Status: Not Checked OutLane Catalog Record
    This book identifies and analyzes the genetic basis of bone disorders in humans and demonstrates the utility of mouse models in furthering the knowledge of mechanisms and evaluations of treatments. The book is aimed at all students of bone biology and genetics, and with this in mind, it includes general introductory chapters on genetics and bone biology and more specific disease-orientated chapters, which comprehensively summarize the clinical, genetic, molecular genetic, animal model, functional and molecular pathology, diagnostic, counselling and treatment aspects of each disorder. Saves academic, medical, and pharma researchers time in quickly accessing the very latest details on a broad range of genetic bone issues, as opposed to searching through thousands of journal articles. Provides a common language for bone biologists and geneticists to discuss the development of bone cells and genetics and their interactions in the development of disease. Researchers in all areas bone biology and genetics will gain insight into how clinical observations and practices can feed back into the research cycle and will, therefore, be able to develop more targeted genomic and proteomic assays. For those clinical researchers who are also MDs, correct diagnosis (and therefore correct treatment) of bone diseases depends on a strong understanding of the molecular basis for the disease.
  • 2009 Springer
    Lindor, Noralane M.; Potter, John D.
  • 2016 Karger
    Haaf, Thomas; Vona, Barbara.
    Genetics and deafness : a view from the inside / Blankmeyer Burke, T. Snoddon, K., Wilkinson, E. -- Hearing loss in older age and its effect on the individuals, their families, and the community / McMahon, C.M -- Audiological assessment and management in the era of precision medicine / Munro, K.J., Newton, V.E., Moore, D.R -- Next-generation newborn hearing screening / Shen, J., Morton, C.C -- Clinical challenges in diagnosing the genetic etiology of hearing loss / Birkeland, A.C., Lesperance, M.M. -- Genetic elucidation of nonsyndromic hearing loss in the high-throughput sequencing era / Vona, B., Hofrichter, M.A.H., Chioza, B.A., Crosby, A.H., Nanda, I., Haaf, T. -- Genetic modifiers of hearing loss / Yousaf, R., Friedman, T.B., Riazuddin, S. -- Genetics of age-related hearing loss / Dawes, P., Payton, A. -- Genetic modifiers of hearing loss in mice : the case of phenotypic modification in homozygous cdh23ahl age-related hearing loss / Kikkawa, Y., Miyasaka, Y. -- Using zebrafish to study human deafness and hearing regeneration / Varshney, G.K., Pei, W., Burgess, S.M. -- Current understanding and potential of gene therapy for hearing restoration in humans / Akil, O., Lustig, L.
  • 2014 Springer
    Grant, Struan F. A.
    In the past four years, many genetic loci have been implicated for BMI from the outcomes of genome-wide association studies (GWAS), primarily in adults. Insulin-induced gene 2 (INSIG2) was the first locus to be reported by this method to have a role in obesity, but replication attempts have yielded inconsistent outcomes. The identification of the second locus, the fat mass- and obesity-associated gene (FTO), has been more robustly observed by others. Studies from both FTO knock out and FTO over expression mouse model support the fact that FTO is directly involved in the regulation of energy intake and metabolism in mice, where the lack of FTO expression leads to leanness while enhanced expression of FTO leads to obesity. Along with numerous other studies, a number of genetic variants have been established robustly in the context of obesity, giving us fresh insights into the pathogenesis of the disease. This book provides a comprehensive overview of efforts aimed at uncovering genetic variants associated with obesity, which have been particularly successful in the past 5 years with the advent of genome-wide association studies (GWAS). The Genetics of Obesity covers this state of the art technology and its application to obesity in great detail. Topics include genetics of childhood obesity, genetics of syndromic obesity, copy number variants and extreme obesity, co-morbidities of obesity genetics, and functional follow-up of genetic variants.
  • 2007
    Hickey, G. I.; Fletcher, H.; Winter, P.
    Status: Not Checked OutLane Catalog Record
  • v. 1-, 2007- Springer
  • 2016 Springer
    Cathomen, Toni; Hirsch, Matthew; Porteus, Matthew H.
  • 2005 Springer
    Nigg, Erich A.
    Also available: Print – 2005
  • 2011
    Markova-Raina, Penka Vassileva; Batzoglou, Serafim; Feldman, Marcus W.; Petrov, Dmitri A.
    Recent advances in technology have unleashed a breathtaking amount of genome sequence data. My doctoral research builds on the resulting opportunities of whole genome sequence data and analysis in a quest for gaining new insights into molecular evolution, and in particular molecular evolution and adaptation of proteins. Chapter One of my dissertation is focused on methodology, specifically the impact that the choice of multiple sequence alignment procedure has on the inference of positive selection. I find that selection inference is highly dependent on the choice of alignment procedure. Furthermore, in the case of the 12 Drosophila genomes proteins and commonly used alignment programs, most of the inferences are false positives, caused by misaligned codons. These results put into question the reliability of some of the previously reported conclusions on adaptation in these proteins, as well as in similar studies of other species. The second chapter relates these alignment errors to specific regions in the proteins, the so-called intrinsically disordered protein regions. Disordered protein regions do not have a stable fold in native physiological conditions, and therefore do not fit the standard assumptions made in codon-based evolutionary analyses about structure and folding constraints. My findings indicate that in the case of the false-positively inferred positively selected sites, as well as in general throughout the alignments, most alignment errors and ambiguities originate in disordered regions. Indels in the alignments also appear predominantly in those regions. Examination of widely used alignment benchmarks indicates that disordered regions have mostly been excluded from the benchmarks. I discuss implications of these findings for both evolutionary research and development of alignment software. The last chapter of my dissertation characterizes the evolution of disordered regions in Drosophila. I survey protein substitution and polymorphism patterns in D. melanogaster and D. simulans, and find that relative to structured regions, disordered ones have multiple-fold higher rates of replacement polymorphisms and substitutions, as well as fewer rare polymorphisms. Structured regions appear to be significantly more impacted by both positive and purifying selection, contrary to indications from previous reports where within-species data was not incorporated in the analysis.
  • 2009 Springer
    Kole, Chittaranjan; Nene, Vishvanath.
  • 2008 Springer
    Hunter, Wayne; Kole, Chittaranjan.
    Honeybee / D. Schlipalius, P.R. Ebert, G.J. Hunt -- Bumblebee / L. Wilfert, P. Schmid-Hempel, J. Gadau -- The jewel wasp - Nasonia / J. Gadau ... [et al.] -- Silkworm / Y. Yasukochi, H. Fujii, M.R. Goldsmith -- Pea aphid / J.A. Brisson, G.K. Davis -- Mosquito / D.W. Severson -- Hessian fly / J.J. Stuart, M.-S. Chen, M.O. Harris -- Tick / A.J. Ullmann, J.J. Stuart, C.A. Hill.
  • 2008 Springer
    Kocher, Thomas D.; Kole, Chittaranjan.
  • 2012 Springer
    Denny, Paul; Kole, Chittaranjan.
    Genomics in the sea urchin : new perspectives on a perennial model system / Katherine M. Buckley amd Jonathan P. Rast -- Genome mapping and genomics of Caenorhabditis elegans / Jonathan Hodgkin, Michael Paulini, and mary Ann Tuli -- Genome mapping and genomics in Drosophila / Boris Adryan and Steven Russell -- Genome structure, functional genomics, and proteomics in ascidians / Yasunori Sasakura, Nicolas Sierro, Kenta Nakai, Kazuo Inaba, and takehiro G. Kusakabe -- Punching above their weight : the compact genomes of pufferfishes / Brian Cusack and Hugues Roest Crollius -- Medaka genomics and the methods and resources for decoding genomic functions / Tetsuaki Kimura, Yasuhiro Kamei, Yusuke Takehana, Takao Sasado, and Kiyoshi Naruse -- Xenopus genomics and genetics : progress and prospects / Amy K. Sater and Michael J. Gilchrist -- Mouse genome mapping and genomics / Paul Denny -- Rat genome mapping and genetics / Claude Szpirer and Göran Levan.
  • 2005 Springer
    Newton, William E.; Palacios, Rafael.
  • 2002 NCBI Bookshelf
    Brown, T. A.
  • 2013 Springer
    Muley, Vijaykumar Yogesh; Acharya, Vishal.
    Introduction -- From genomes to protein functions -- Co-evolutionary signals within genome sequences reflect functional dependence of proteins -- Chromosomal proximity of genes as an indicator of functional linkage -- Analyses of complex genome-scale biological networks -- Application of protein interaction networks.
  • 2010
    Paulsen, Renee Darlene; Cimprich, Karlene; Meyer, Tobias; Wang, Clifford; Wysocka, Joanna.
    Genome instability has long been known to be a hallmark of cancerous cells, but the cellular causes and consequences of such instability are still not fully understood. Mutations, translocations, DNA rearrangements, as well as chromosomal loss can all result in the loss of genomic integrity. To prevent the disruption of cellular homeostasis due to DNA damage accumulation, cells contain pathways to sense and respond to DNA damage including cell cycle checkpoints and numerous DNA repair processes, collectively known as the DNA damage response (DDR). Mutations in many of the genes involved in the DDR are linked to several diseases, including premature aging, neurodegeneration and cancer. These signaling pathways are especially critical during DNA replication when the DNA is unwound and vulnerable to processing. Here, the cell relies on the S-phase checkpoint to sense DNA damage at the sites of replication forks and to facilitate a number of downstream pathways to maintain genomic stability. These processes include blocking further origin firing, facilitating DNA repair, preventing cell cycle progression, and stabilizing stalled replication forks. Here, two genome-wide siRNA screens were employed to identify additional genes involved in genome stabilization by monitoring phosphorylation of the histone variant H2AX, an early mark of DNA damage. The first screen looked at H2AX phosphorylation that occurred simply by individual protein depletion, and the second screen used a low level of a replication inhibitor, aphidicolin, to specifically identify genes that were needed to prevent DNA damage during S-phase, potentially due to the loss of replication fork stabilization mechanisms. While the results from the second screen are still undergoing further characterization, we did discover hundreds of genes whose down-regulation led to elevated levels of H2AX phosphorylation in the absence of any external stress. From this gene set, we identified many gene networks that were significantly enriched amongst our screening hits as well as several intriguing individual genes that were chosen for follow up study. These included genes involved in mRNA processing, the pathology of Charcot-Marie-Tooth syndrome, and the histone methyl transferase protein, Set8.
  • 2008 Springer
    Wilkins, Jon F.
    DNA methylation reprogramming in the germ line / Diane J. Lees-Murdock and Colum P. Walsh -- Control of imprinting at the GNAS cluster / Jo Peters and Christine M. Williamson -- The GNAS locus and pseudohypoparathyroidism / Murat Bastepe -- Imprinted genes, postnatal adaptations, and enduring effects on energy homeostasis / Margalida Frontera ... [et al.] -- What are imprinted genes doing in the brain? / William Davies ... [et al.] -- Genomic imprinting and human psychology : cognition, behavior, and pathology / Lisa M. Goos and Gillian Ragsdale -- Genomic imprinting in plants / Olivier Garnier, Sylvia Laouiellé-Duprat, and Charles Spillane -- Imprinted genes and human disease : an evolutionary perspective / Francisco Úbeda and Jon F. Wilkins -- Evolutionary theories of imprinting ; enough already! / Tom Moore and Walter Mills.
    Also available: Print – 2008
  • 2012 Springer Protocols
    Engel, Nora.
    Uniparental embryos in the study of genomic imprinting / Yong Cheng, Dasari Amarnath, and Keith E. Latham -- Derivation of induced pluripotent stem cells by retroviral gene transduction in mammalian species / Masanori Imamura [and others] -- Generation of trophoblast stem cells / Michael C. Golding -- Immunomagnetic purification of murine primordial germ cells / Emily Y. Smith and James L. Resnick -- Whole genome methylation profiling by immunoprecipitation of methylated DNA / Andrew J. Sharp -- Identification of imprinted loci by transcriptome sequencing / Tomas Babak -- Data mining as a discovery tool for imprinted genes / Chelsea Brideau and Paul Soloway -- Engineering of large deletions and duplications in vivo / Louis Lefebvre -- Methylated DNA immunoprecipitation (MeDIP) from low amounts of cells / Julie Borgel, Sylvain Guibert, and Michael Weber -- Chromatin immunoprecipitation to characterize the epigenetic profiles of imprinted domains / Purnima Singh and Piroska E. Szabo -- Quantitative chromosome conformation capture / Raffaella Nativio, Yoko Ito, and Adele Murrell -- Genome-wide analysis of DNA methylation in low cell numbers by reduced representation bisulfite sequencing / Sebastien A. Smallwood and Gavin Kelsey -- Isolation of RNA and DNA from single preimplantation embryos and a small number of mammalian oocytes for Imprinting Studies / Sarah Rose Huffman, Md Almamun, and Rocio Melissa Rivera -- Generation of cDNA libraries from RNP-derived regulatory noncoding RNAs / Mathieu Rederstorff -- Co-immunoprecipitation of long noncoding RNAs / Victoria A. Moran, Courtney N. Niland, and Ahmad M. Khalil -- Specialized technologies for epigenetics in plants / Wenyan Xiao -- Computational studies of imprinted genes / Martina Paulsen -- Insights on imprinting from beyond mice and men / Andrew Pask -- Nonmammalian parent-of-origin effects / Elena de la Casa-Esperon.
  • 2012 Springer Protocols
    Feuk, Lars.
    What have studies of genomic disorders taught us about our genome / Alexandra D. Simmons, Claudia M.B. Carvalho, and James R. Lupski -- Microdeletion and microduplication syndromes / Lisenka E.L.M. Vissers and Paweł Stankiewicz -- Structural genomic variation in intellectual disability / Rolph Pfundt and Joris A. Veltman -- Copy number variation and psychiatric disease risk / Rebecca J. Levy [and others] -- Detection and characterization of copy number variation in autism spectrum disorder / Christian R. Marshall and Stephen W. Scherer -- Structural variation in subtelomeres / M. Katharine Rudd -- Array-based approaches in prenatal diagnosis / Paul D. Brady [and others] -- Structural variation and its effect on expression / Louise Harewood, Evelyne Chaignat, and Alexandre Reymond -- Challenges of studying complex and dynamic regions of the human genome / Edward J. Hollox -- Population genetic nature of copy number variation / Per Sjodin and Mattias Jakobsson -- Detection and interpretation of genomic structural variation in mammals / Ira M. Hall and Aaron R. Quinlan -- Structural genetic variation in the context of somatic mosaicism / Jan P. Dumanski and Arkadiusz Piotrowski -- Online resources for genomic structural variation / Tam P. Sneddon and Deanna M. Church -- Algorithm implementation for CNV discovery using affymetrix and illumina SNP array data / Laura Winchester and Jiannis Ragoussis -- Targeted screening and validation of copy number variations / Shana Ceulemans, Karlijn van der Ven, and Jurgen Del-Favero -- High-resolution copy number profiling by array CGH using DNA isolated from formalin-fixed, paraffin-embedded tissues / Hendrik F. van Essen and Bauke Ylstra -- Characterizing and interpreting genetic variation from personal genome sequencing / Anna C.V. Johansson and Lars Feuk -- Massively parallel sequencing approaches for characterization of structural variation / Daniel C. Koboldt [and others].
  • 2014 Springer
    Marko-Varga, György A.
    This book offers a valuable resource that allows students, researchers, educators and the general public to learn about proteomics and genomics. Chromosomes form the basis for our genetic heritage and are the code for protein synthesis. The Human Genome Map was presented in 2002, and the Proteome Sequence Map is currently being created by a global consortia initiative. Proteome and genome building blocks already form the basis of scientific research areas and shape major areas of the pharmaceutical and biomedical industries. The book provides background information on and our current understanding of these gene and protein areas, and explains in detail how cutting-edge science is using these resources to develop new medicines and new diagnostics for patient treatment and care. The book will benefit all students and researchers who need a good understanding of genomics and proteomics within the clinical field. Its content is also suitable for a broad readership, including those not specialized in this field. Dr. Marko-Varga is head of Div. Clinical Protein Science & Imaging at the Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University. He's also Professor at the 1st Department of Surgery, Tokyo Medical University, Tokyo, Japan.
  • 2013 Springer
    Kutikhin, Anton G.; Yuzhalin, Arseniy E.
    The Biology of Toll-like Receptors and NOD-like Receptors: Toggles of Inflammation -- Pattern Recognition Receptors, Gene Polymorphisms, and Cancer: A Double-Edged Sword -- Structural Genomic Variation in Toll-Like Receptor 4 and Cancer -- Structural Genomic Variation in Other Toll-like Receptors and Cancer -- Structural Genomic Variation in Toll-Like Receptor Signaling Pathway and Cancer -- Structural Genomic Variation in Toll-like Receptor Pathway and Prostate Cancer -- Structural Genomic Variation in NOD-Like Receptors and Cancer -- Structural Genomic Variation in Pattern Recognition Receptors and Cardiovascular Diseases -- Hot Spots In the Field: Where Should We Go.
  • 2008 Springer Protocols
    Elaswarapu, Ramnath; Starkey, Michael P.
    Protein profiling based on two-dimensional difference gel electrophoresis / Gert Van den Bergh and Lutgarde Arckens -- Quantitative protein profiling by mass spectrometry using isotope-coded affinity tags / Arsalan S. Haqqani, John F. Kelly, and Danica B. Stanimirovic -- Quantitative protein profiling by mass spectrometry using label-free proteomics / Arsala S. Haqqani, John F. Kelly, and Danica B. Stanimirovic -- Using 2D-LC-MS/MS to identify Francisella tularensis peptides in extracts from an infected mouse macrophage cell line / John F. Kelly and Wen Ding -- Baculovirus expression vector system : an emerging host for high-throughput eukaryotic protein expression / Binesh Shrestha, Carol Smee, and Opher Gileadi -- Coimmunoprecipitation and proteomic analyses / S. Fabio Falsone, Bernd Gesslbauer, and Andreas J. Kungl -- Tandem affinity purification combined with mass spectrometry to identify components of protein complexes / Peter Kaiser ... [et al.] -- Mammalian two-hybrid assay for detecting protein-protein interactioins in vivo / Runtao He and Xuguang Li -- Detection of protein-protein interactions in live cells and animals with split firefly luciferase protein fragment complementation / Victor Villalobos, Snehal Naik, and David Piwnica-Worms -- Subcellular localization of intracellular human proteins by construction of tagged fusion proteins and transient expression in COS-7 cells / John E. Collins -- GeneFAS : a tool for the prediction of gene function using multiple sources of data / Trupti Joshi ... [et al.] --Comparative genomics-based prediction of protein function / Toni Gabaldón -- Design, manufacture, and assay of the efficacy of siRNAs for gene silencing / Louise A. Dawson and Badar A. Usmani. Whole genome amplification with Phi29 DNA polymerase to enable genetic or genomic analysis of samples of low DNA yield / Kaisa Silander and Janna Saarela -- Scanning for DNA variants by denaturant capillary electrophoresis / Per O. Ekstrøm -- Identification of SNPs, or mutations in sequence chromatograms / Nicole Draper -- BeadArray-based genotyping / Helen Butler and Jiannis Ragoussis -- Microsattelite-based candidate gene linkage analysis studies / Cathryn Mellersh -- Full complexity genomic hybridization on 60-mer oligonucleotide microarrays for array comparative genomic hybridization (aCGH) / Alexei Protopopov, Bin Feng, and Lynda Chin -- Detection of copy number changes at multiple loci in DNA prepared from formalin-fixed, paraffin-embedded tissue by multiplex ligation -dependent probe amplification / Minoru Takata -- Application of microarrays for DNA methylation profiling / Axel Schumacher, Andreas Weinhäusl, and Arturas Petronis -- Genomewide identification of protein binding locations using chromatin immunoprecipitation coupled with microarray / Byung-Kwan Cho, Eric M. Knight, and Bernhard Ø. Palsson -- Transcriptional profiling of small samples in the central nervous system / Stephen D. Ginsberg -- Quantitative expression profiling of RNA from formalin-fixed, paraffin-embedded tissues using randomly assembled bead arrays / Marina Bibikova ... [et al.] -- Expression profiling of microRNAs in cancer cells : technical considerations / Mouldy Sioud and Lina Cekaite -- Identification of disease biomarkers by profiling of serum proteins using SELDI-TOF mass spectrometry / Sigrun Langbein -- The applicability of a cluster of differentiation monoclonal antibody microarray to the diagnosis of human disease / Peter Ellmark ... [et al.] --
  • 2014 Springer Protocols
    Gaivão, Isabel; Sierra, L. María.
    Genotoxicity and DNA Repair: A Practical Approach provides a key reference for determining how to analyze the genotoxic activity of molecules or materials and, at the same time, serves as a useful tool for researchers in the Environmental Mutagenesis and DNA Repair fields. Focused on genotoxicity assays recommended by the "OECD guidelines for the testing of chemicals", this volume also covers other useful assays, such as some gene mutation assays, the comet assay in different species and applications, and the SMART assays of Drosophila. For all the assays, the book presents brief theoretical introductions to the topics and updated standard and modified step-by-step protocols to perform them. Special emphasis is placed on the analysis of nanoparticles, including an integrative approach analysis. The DNA Repair section includes several assays that provide information on repair activity in vitro and in vivo, as well as recent applications to study DNA repair in humans, cell cultures, and animal models. As a volume in the Methods in Pharmacology and Toxicology series, the chapters contain the kind of detail and key implementation advice that ensures reproducible results in the lab.
  • 2013 Springer Protocols
    Bajpayee, Mahima; Dhawan, Alok.
    Genetic toxicology is recognized by geneticists and researchers concerned with the genetic impact of man-made chemicals.In Genotoxicity Assessment: Methods and Protocols, expert researchers in the field provide comprehensive genetictoxicology protocols. These include in vitro and in vivo protocols on mutation assays, cytogenetic techniques, and primary DNA damage, assays in alternate to animal models, and updated ICH guidelines. Written in the highly successfulMethods in Molecular Biology series format, the chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, as well as key tips ontroubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Genotoxicity Assessment: Methods and Protocols seeks to aid research students and scientists working in regulatory toxicology as well as biomedical, biochemical and pharmaceutical sciences.
  • 2013 Springer
    Schedl, Tim.
    Also available: Print – 2013
  • 2010 ScienceDirect
    Soriano, Philippe M.; Wassarman, Paul M.
    Also available: Print – 2010
  • 2014 Wiley
    Goodnow, Robert A.
    Just enough knowledge? -- A brief history of the development of combinatorial chemistry and the emerging need for DNA-encoded chemistry -- A history of DNA-encoding -- DNA-compatible chemistry -- Foundations of a DNA-encoded library (DEL) -- Practices for synthesizing DNA-encoded libraries -- Chemical gene design for DNA-encoded libraries -- Analytical challenges for DNA-encoded library systems -- Information technology: functionality and architectures for DNA-encoding -- Theoretical considerations of the application of DNA-encoded libraries to drug discovery -- Begin with the end in mind : the hit-to-lead process -- Enumeration and visualization of large combinatorial chemical libraries -- Screening large compound collections -- Reported applications of DNA-encoded library chemistry -- Dual-pharmacophore DNA-encoded chemical libraries -- Hit identification and hit follow-up -- Using DNA to program chemical synthesis, discover new reactions, and detect ligand binding -- An outlook and the changing feasibility and economics of chemical diversity exploration with DNA-encoded combinatorial approaches -- Keeping the promise? an outlook on dna chemical library technology.
  • 2009 Springer
    Kim, Yong-Kyu.
  • v. 1-5, 1974-75.
    King, Robert C.
    Status: Not Checked OutLane Catalog Record
    v. 1. Bacteria, bacteriophages and fungi.--v. 2. Plants, plant viruses, and protists.--v. 3.Invertebrates of genetic interest.--v. 4. Vertebrates of genetic interest.--v. 5. Molecular genetics.
  • 2010 Springer
    Tercyak, Kenneth P.
  • 2009 ScienceDirect
    Cummings, Richard D.; Pierce, J. Michael.
  • 2005 Wiley
    Hartmann, Roland K.
    Part I. RNA Synthesis - Enzymatic RNA Synthesis, Ligation and Modification -- Chapter 1. Enzymatic RNA Synthesis using Bacteriophage T7 RNA Polymerase / Heike Gruegelsiepe, Astrid Schön, Leif A. Kirsebom and Roland K. Hartmann, p. 3-21 -- Chapter 2. Production of RNAs with Homogeneous 5' and 3' Ends / Mario Mörl, Esther Lizano, Dagmar K. Willkomm and Roland K. Hartmann, p. 22-35 -- Chapter 3. RNA Ligation using T4 DNA Ligase / Mikko J. Frilander and Janne J. Turunen, p. 36-52 -- Chapter 4. T4 RNA Ligase / Tina Persson, Dagmar K. Willkomm and Roland K. Hartmann, p. 53-74 -- Chapter 5. Co- and Post-Transcriptional Incorporation of Specific Modifications Including Photoreactive Groups into RNA Molecules / Nathan H. Zahler and Michael E. Harris, p. 75-85 -- Chapter 6. 3'-Terminal Attachment of Fluorescent Dyes and Biotin / Dagmar K. Willkomm and Roland K. Hartmann, p. 86-94 -- Part I. RNA Synthesis - Chemical RNA Synthesis -- Chapter 7. Chemical RNA Synthesis, Purification and Analysis / Brian S. Sproat, p. 95-111 -- Chapter 8. Modified RNAs as Tools in RNA Biochemistry / Thomas E. Edwards and Snorri T. H. Sigurdsson, p. 112-129 -- Part II. Structure Determination - Molecular Biology Methods -- Chapter 9. Direct Determination of RNA Sequence and Modification by Radiolabeling Methods / Olaf Gimple and Astrid Schön, p. 132-150 -- Chapter 10. Probing RNA Structures with Enzymes and Chemicals In Vitro and In Vivo / Eric Huntzinger, Maria Possedko, Flore Winter, Hervé Moine, Chantal Ehresmann and Pascale Romby, p. 151-171 -- Chapter 11. Study of RNA-Protein Interactions and RNA Structure in Ribonucleoprotein Particles / Virginie Marchand, Annie Mougin, Agnès Méreau and Christiane Branlant, p. 172-204 -- Chapter 12. Terbium(III) Footprinting as a Probe of RNA Structure and Metal-binding Sites / Dinari A. Harris and Nils G. Walter, p. 205-213 -- Chapter 13. Pb²⁺-induced Cleavage of RNA / Leif A. Kirsebom and Jerzy Ciesiolka, p. 214-228 -- Chapter 14. In Vivo Determination of RNA Structure by Dimethylsulfate / Christina Waldsich and Renée Schroeder, p. 229-237 -- Chapter 15. Probing Structure and Binding Sites on RNA by Fenton Cleavage / Gesine Bauer and Christian Berens, p. 238-249 -- Chapter 16. Measuring the Stoichiometry of Magnesium Ions Bound to RNA / A. J. Andrews and Carol Fierke, p. 250-258 -- Chapter 17. Nucleotide Analog Interference Mapping and Suppression: Specific Applications in Studies of RNA Tertiary Structure, Dynamic Helicase Mechanism and RNA-Protein Interactions, p. 259-293 / Olga Fedorova, Marc Boudvillain, Jane Kawaoka and Anna Marie Pyle -- Chapter 18. Nucleotide Analog Interference Mapping: Application to the RNase P System / Simona Cuzic and Roland K. Hartmann, p. 294-318 -- Chapter 19. Identification and Characterization of Metal Ion Binding by Thiophilic Metal Ion Rescue / Eric L. Christian, p. 319-344 -- Chapter 20. Identification of Divalent Metal Ion Binding Sites in RNA/DNA-metabolizing Enzymes by Fe(II)-mediated Hydroxyl Radical Cleavage / Yan-Guo Ren, Niklas Henriksson and Anders Virtanen, p. 345-353 -- Chapter 21. Protein-RNA Crosslinking in Native Ribonucleoprotein Particles / Henning Urlaub, Klaus Hartmuth and Reinhard Lührmann, p. 354-373 -- Chapter 22. Probing RNA Structure by Photoaffinity Crosslinking with 4-Thiouridine and 6-Thioguanosine / Michael E. Harris and Eric L. Christian, p. 374-384 -- Part II. Structure Determination - Biophysical Methods -- Chapter 23. Structural Analysis of RNA and RNA-Protein Complexes by Small-angle X-ray Scattering / Tao Pan and Tobin R. Sosnick, p. 385-397 -- Chapter 24. Temperature-Gradient Gel Electrophoresis of RNA / Detlev Riesner and Gerhard Steger, p. 398-414 -- Chapter 25. UV Melting, Native Gels and RNA Conformation / Andreas Werner, p. 415-427 -- Chapter 26. Sedimentation Analysis of Ribonucleoprotein Complexes / Jan Medenbach, Andrey Damianov, Silke Schreiner and Albrecht Bindereif, p. 428-437 -- Chapter 27. Preparation and Handling of RNA Crystals / Boris François, Aurélie Lescoute-Phillips, Andreas Werner and Benoît Masquida, p. 438-452 -- Part II. Structure Determination - Fluorescence and Single Molecule Studies -- Chapter 28. Fluorescence Labeling of RNA for Single Molecule Studies / Filipp Oesterhelt, Enno Schweinberger and Claus Seidel, p. 453-474 -- Chapter 29. Scanning Force Microscopy and Scanning Force Spectroscopy of RNA / Wolfgang Nellen, p. 475-487 -- Part III. RNA Genomics and Bioinformatics - Fluorescence and Single Molecule Studies -- Chapter 30. Comparative Analysis of RNA Secondary Structure: 6S RNA / James W. Brow and J. Christopher Ellis, p. 490-512 -- Chapter 31. Secondary Structure Prediction / Gerhard Steger, p. 513-535 -- Chapter 32. Modeling the Architecture of Structured RNAs within a Modular and Hierarchical Framework, p. 536-545 / Benoît Masquida and Eric Westhof -- Chapter 33. Modeling Large RNA Assemblies using a Reduced Representation, p. 546-559 / Jason A. Mears, Scott M. Stagg and Stephen C. Harvey -- Chapter 34. Molecular Dynamics Simulations of RNA Systems / Pascal Auffinger and Andrea C. Vaiana, p. 560-576 -- Chapter 35. Seeking RNA Motifs in Genomic Sequences / Matthieu Legendre and Daniel Gautheret, p. 577-594 -- Chapter 36. Approaches to Identify Novel Non-messenger RNAs in Bacteria and to Investigate their Biological Functions: RNA Mining / Jörg Vogel, E. Gerhart and H. Wagner, p. 595-613 -- Chapter 37. Approaches to Identify Novel Non-messenger RNAs in Bacteria and to Investigate their Biological Functions: Functional Analysis of Identified Non-mRNAs / E. Gerhart, H. Wagner and Jörg Vogel, p. 614-642 -- Chapter 38. Experimental RNomics: A Global Approach to Identify Non-coding RNAs in Model Organisms / Alexander Hüttenhofer, p. 643-654 -- Chapter 39. Large-scale Analysis of mRNA Splice Variants by Microarray / Young-Soo Kwon, Hai-Ri Li and Xiang-Dong Fu, p. 655-663 -- Part IV. Analysis of RNA Function 665 - RNA-Protein Interactions in vitro -- Chapter 40. RNA-Protein Interactions in vitro / Steffen Schiffer, Sylvia Rösch, Bettina Späth, Markus Englert, Hildburg Beier and Anita Marchfelder, p. 666-675 -- Chapter 41. Biotin-based Affinity Purification of RNA-Protein Complexes / Zsofia Palfi, Jingyi Hui and Albrecht Bindereif, p. 676-693 -- Chapter 42. Immunoaffinity Purification of Spliceosomal and Small Nuclear Ribonucleoprotein Complexes / Cindy L. Will, Evgeny M. Makarov, Olga V. Makarova and Reinhard Lührmann, p. 694-709 -- Chapter 43. Northwestern Techniques for the Identification of RNA-binding Proteins from cDNA Expression Libraries and the Analysis of RNA-Protein Interactions / Ángel Emilio Martínez De Alba, Michela Alessandra Denti and Martin Tabler, p. 710-728 -- Part IV. Analysis of RNA Function 665 - RNA-Protein Interactions in vivo -- Chapter 44. Fluorescent Detection of Nascent Transcripts and RNA-binding Proteins in Cell Nuclei, p. 729-736 / Jennifer A. Geiger and Karla M. Neugebauer -- Chapter 45. Identification and Characterization of RNA-binding Proteins through Three-hybrid Analysis / Felicia Scott and David R. Engelke, p. 737-754 -- Chapter 46. Analysis of Alternative Splicing In Vivo using Minigenes / Yesheng Tang, Tatyana Novoyatleva, Natalya Benderska, Shivendra Kishore, Alphonse Thanaraj and Stefan Stamm, p. 755-782 -- Part IV. Analysis of RNA Function 665 - SELEX -- Chapter 47. Artificial Selection: Finding Function amongst Randomized Sequences / Ico de Zwart, Catherine Lozupone, Rob Knight, Amanda Birmingham, Mali Illangasekare, Vasant Jadhav, Michal Legiewicz, Irene Majerfeld, Jeremy Widmann and Michael Yarus, p. 783-806 -- Chapter 48. Aptamer Selection against Biological Macromolecules: Proteins and Carbohydrates / C. Stefan Vörtler and Maria Milovnikova, p. 807-839 -- Chapter 49. In Vivo SELEX Strategies / Thomas A. Cooper, p. 840-852 -- Chapter 50. In Vitro Selection against Small Targets / Dirk Eulberg, Christian Maasch, Werner G. Purschke and Sven Klussmann, p. 853-877 -- Chapter 51. SELEX Strategies to Identify Antisense and Protein Target Sites in RNA or Heterogeneous Nuclear Ribonucleoprotein Complexes / Martin Lützelberger, Martin R. Jakobsen and Jørgen Kjems, p. 878-894 -- Chapter 52. Gene Silencing Methods for Mammalian Cells: Application of Synthetic Short Interfering RNAs / Matthias John, Anke Geick, Philipp Hadwiger, Hans-Peter Vomlocher and Olaf Heidenreich, p. 896-909 -- Appendix. UV Spectroscopy for the Quantitation of RNA, p. 910-913.
  • v. 1-2, 2007 Wiley
    Balding, D. J.; Bishop, M. J.; Cannings, C.
    Also available: Print – v. 1-2., 2007
  • 2007 CRCnetBASE
    Ghosh, Sankar.
  • 2010 Springer
    Lin, Shili; Zhao, Hongyu.
  • 2015 Springer Protocols
    Riobo, Natalia A.
    Luciferase reporter assays to study transcriptional activity of hedgehog signaling in normal and cancer cells / Silvia Pandolfi and Barbara Stecca -- Measuring expression levels of endogenous gli genes by immunoblotting and real-time PCR / Pawel Niewiadomski and Rajat Rohatgi -- Quantitative immunoblotting of endogenous hedgehog pathway components / Shohreh F. Farzan and David J. Robbins -- Measuring Gli2 phosphorylation by selected reaction monitoring mass spectrometry / Robert Ahrends, Pawel Niewiadomski, Mary N. Teruel, and Rajat Rohatgi -- Rapid screening of Gli2/3 mutants using the Flp-In system / Pawel Niewiadomski and Rajat Rohatgi -- Insights into gli factors ubiquitylation methods / Paola Infante, Romina Alfonsi, and Lucia Di Marcotullio -- Determination of acetylation of the gli transcription factors / Sonia Coni, Laura Di Magno, and Gianluca Canettieri -- Efficient detection of indian hedgehog during endochondral ossification by whole-mount immunofluorescence / João Francisco Botelho, Daniel Smith-Paredes, and Veronica Palma A. -- Methods for detection of Ptc1-driven LacZ expression in adult mouse skin / Donna M. Brennan-Crispi, My G. Mahoney, and Natalia A. Riobo -- Determination and analysis of cellular metabolic changes by noncanonical hedgehog signaling / Raffaele Teperino and John Andrew Pospisilik.
  • 2007 Springer Protocols
    Horabin, Jamila I.
    Purifying the hedgehog protein and its variants / Darren P. Baker, Frederick R. Taylor, and R. Blake Pepinsky -- Application of sonic hedgehog to the developing chick limb / Eva Tieck and Cheryll Tickle -- Manipulation of hedgehog signaling in Xenopus by means of embryo microinjection and application of chemical inhibitors / Thomas Hollemann .. [et al.] -- Isolation of rat telencephalic neural explants to assay Shh GABAergic interneuron differentiation-inducing activity / Rina Mady and Jhumku D. Kohtz -- Genetic analysis of the vertebrate hedgehog-signaling pathway using muscle cell fate specification in the zebrafish embryo / Sudipto Roy -- Efficient manipulation of hedgehog/GLI signaling using retroviral expression systems / Maria Kasper ... [et al.] -- Cell surface marker and cell cycle analysis, hedgehog signaling, and flow cytometry / Krsting Detmer and Ronald E. Garner -- Detecting tagged hedgehog with intracellular and extracellular immunocytochemistry for functional analysis / Ainhoa Callejo, Luis Quijada, and Isabel Guerrero -- Confocal analysis of hedgehog morphogenetic gradient coupled with fluorescent in situ hybridization of hedgehog target genes / Armel Gallet and Pascal P. Thérond -- RNA in the hedgehog signaling pathway : pFRiPE, a vector for temporally and spatially controlled RNAi in Drosophila / Eric Marois and Suzanne Eaton -- Germline clone analysis for maternally acting Drosophila hedgehog components / Erica M. Selva and Beth E. Stronach -- Clone analysis of hedgehog signaling in Drosophila somatic tissues / Christing M. Bankers and Joan E. Hooper -- GAL4/UAS targeted gene expression for studying Drosophila hedgehog signaling / Denise Bussona nd Anne-Marie Pret -- Biochemical fractionation of Drosophila cells / Melanie Stegman and David Robbins -- Using immunoprecipitation to study protein-protein interactions in the hedgehog-signaling pathway / Chao Ton and Jin Jiang -- Sequence analyses to study the evolutionary history and cis-regulatory elements of hedgehog genes / Ferenc Müller and Anne-Gaelle Borycki.
  • 2010 Springer
    Rodriguez-Bigas, Miguel A.
    Colorectal cancer is the third most commonly diagnosed cancer in the US and the third most recently linked to cancer deaths. The national annual incidence rate of colorectal cancer is approximately 148,000+, striking slightly more females than males. The lifetime risk of colorectal cancer is 5-6percent, however patients with a familial risk (with two or more first or second degree relatives) make up 20percent of the patients. Persons who carry genetic mutations linked to hereditary colorectal cancer are the most likely to develop the disease.
  • 2011 Springer Protocols
    Kwon, Young Min; Ricke, Steven C.
    [Publisher-supplied data] Due to their novel concepts and extraordinary high-throughput sequencing capacity, the next generation sequencing methods allow scientists to grasp system-wide landscapes of the complex molecular events taking place in various biological systems, including microorganisms and microbial communities. These methods are now being recognized as essential tools for a more comprehensive and deeper understanding of the mechanisms underlying many biological processes. In High-Throughput Next Generation Sequencing: Methods and Applications, experts in the field explore the most recent advances in the applications of next generation sequencing technologies with an emphasis on microorganisms and their communities; however, the methods described in this book will also offer general applications relevant to the study of any living organisms. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, High-Throughput Next Generation Sequencing: Methods and Applications is an excellent collection of chapters to aid all scientists who wish to apply these innovative research tools to enhance their own pursuits in microbiology and also biology in general.
  • 2012 Wellcome Trust
    Reynolds, L. A.; Tansey, E. M.
  • 2014 Springer Protocols
    Edgell, David R.
    Homing endonucleases : from genetic anomalies to programmable genomic clippers / Marlene Belfort and Richard P. Bonocora -- Bioinformatic identification of homing endonucleases and their target sites / Eyal Privman -- PCR-based bioprospecting for homing endonucleases in fungal mitochondrial rRNA genes / Mohamed Hafez [and four others.] -- Mapping homing endonuclease cleavage sites using in vitro generated protein / Richard P. Bonocora and Marlene Belfort -- Mapping free-standing homing endonuclease promoters using 5'RLM-RACE / Ewan A. Gibb -- PCR analysis of chloroplast double-strand break (DSB) repair products induced by I-CreII in chlamydomonas and arabidopsis / Taegun Kwon [and three others ] -- A two-plasmid bacterial selection system for characterization and engineering of homing endonucleases / Ning Sun and Huimin Zhao -- Rapid screening of endonuclease target site preference using a modified bacterial two-plasmid selection / Jason M. Wolfs, Benjamin P. Kleinstiver, and David R. Edgell -- A yeast-based recombination assay for homing endonuclease activity / Jean-Charles Epinat -- Rapid determination of homing endonuclease DNA binding specificity profile / Lei Zhao and Barry L. Stoddard -- Quantifying the information content of homing endonuclease target sites by single base pair profiling / Joshua I. Friedman, Hui Li, and Raymond J. Monnat, Jr. -- Homing endonuclease target site specificity defined by sequential enrichment and next-generation sequencing of highly complex target site libraries/ Hui Li and Raymond J. Monnat Jr. -- Homing endonuclease target determination Using SELEX adapted for yeast surface display / Kyle Jacoby and Andrew M. Scharenberg -- Engineering and flow-cytometric analysis of chimeric LAGLIDADG homing endonucleases from homologous I-OnuI-family enzymes / Sarah K. Baxter, Andrew M. Scharenberg, and Abigail R. Lambert -- Bioinformatics identification of coevolving residues / Russell J. Dickson and Gregory B. Gloor -- Identification and analysis of genomic homing endonuclease target sites / Stefan Pellenz and Raymond J. Monnat Jr. -- Redesigning the specificity of protein-DNA interactions with Rosetta / Summer Thyme and David Baker.
  • 2009 Springer Protocols
    Gogarten, J. Peter; Gogarten, Maria Boekels; Olendzenski, Lorraine.
    Gene transfer: who benefits? / L. Olendzenski and J.P. Gogarten -- Defining the mobilome / J.L. Siefert -- The interplay of homologous recombination and horizontal gene transfer in bacterial speciation / J.G. Lawrence and A.C. Retchless -- Epistemological impacts of horizontal gene transfer on classification in microbiology / E. Bapteste and Y. Boucher -- Persistence mechanisms of conjugative plasmids / M.I. Bahl, L.H. Hansen and S.J. Sorensen -- The integron/gene cassette system: an active player in bacterial adaptation / M. Labbate, R.J. Case and H.W. Stokes -- Ancient gene transfer as a tool in phylogenetic reconstruction / J. Huang and J.P. Gogarten -- The tree of life viewed through the contents of genomes / C.H. House -- Horizontal gene transfer and the evolution of methanogenic pathways / G. Fournier -- Genome acquisition in horizontal gene transfer: symbiogenesis and macromolecular sequence analysis / L. Margulis -- Detection and quantitative assessment of horizontal gene transfer / O. Zhaxybayeva -- Composition-based methods to identify horizontal gene transfer / D. Cortez ... [et al.] -- Testing phylogenetic methods to identify horizontal gene transfer / M. Poptsova -- Untangling hybrid phylogenetic signals: horizontal gene transfer and artifacts of phylogenetic reconstruction / R.G. Beiko and M.A. Ragan -- Construction and use of flow cytometry optimized plasmid-sensor strains / M.I. Bahl ... [et al.] -- Experimental evolution of an essential Bacillus gene in an E. coli host / M. Larios-Sanz and M. Travisano -- Mass action models describing extant horizontal transfer of plasmids: inferences and parameter sensitivities / B.F. Smets and L. Lardon -- Interdomain transfers of sugar transporters overcome barriers to gene expression / K.M. Noll and K. Thirangoon -- The role of horizontal gene transfer in photosynthesis, oxygen production, and oxygen tolerance / J. Raymond -- Horizontal gene transfer in cyanobacterial signature genes / S. Yerrapragada, J.L. Siefert and G.E. Fox -- Population genomics and the bacterial species concept / M.A. Riley and M. Lizotte-Waniewski -- A critique of prokaryotic species concepts / R.T. Papke -- What antimicrobial resistance has taught us about horizontal gene transfer / M. Barlow -- Potential for horizontal gene transfer in microbial communities of the terrestrial subsurface / J.M. Coombs -- Horizontal gene transfer and mobile genetic elements in marine systems / P.A. Sobecky and T.H. Hazen -- Horizontal gene transfer in metal and radionuclide contaminated soils / P.A. Sobecky and J.M. Coombs -- Horizontal gene transfer between microbial eukaryotes / J.O. Andersson -- Horizontal gene transfer in eukaryotic parasites: a case study of Entamoeba histolytica and Trichomonas vaginalis / U.C. Alsmark ... [et al.] -- Role of horizontal gene transfer in the evolution of photosynthetic eukaryotes and their plastids / P.J. Keeling -- Role of horizontal gene transfer in the evolution of plant parasitism among nematodes / M. Mitreva, G. Smant and J. Helder.
  • 2002 ScienceDirect
    Kado, Clarence I.; Syvanen, Michael.
    Also available: Print – 2002
  • 2007 Springer
    Papageorgiou, Spyros.
  • 2014 Springer Protocols
    Graba, Yacine; Rezsöhazy, René.
    Discovery and classification of homeobox genes in animal genomes / Ferdinand Marlétaz, Jordi Paps, Ignacio Maeso, and Peter W. H. Holland -- How to study hox gene expression and function in mammalian oocytes and early embryos / Delphine Paul, Caroline Sauvegarde, René Rezsohazy, and Isabelle Donnay -- Genetic lineage tracing analysis of anterior hox expressing cells / Brigitte Laforest, Nicolas Bertrand, and Stéphane Zaffran -- A genetic strategy to obtain P-Gal4 elements in the Drosophila hox genes / Luis de Navas, David Foronda, Delia del Saz, and Ernesto Sánchez-Herrero -- Hox complex analysis through BAC recombineering / Mark Parrish, Youngwook Ahn, Christof Nolte, Bony De Kumar and Robb Krumlauf -- The genetics of murine Hox loci : TAMERE, STRING, and PANTHERE to engineer chromosome variants / Patrick Tschopp and Denis Duboule -- Topological organization of Drosophila hox genes using DNA fluorescent in situ hybridization / Frédéric Bantignies and Giacomo Cavalli -- Mining the Cis-regulatory elements of hox clusters / Navneet Kaur Matharu and Rakesh K. Mishra -- Functional analysis of hox genes in Zebrafish / Franck Ladam and Charles G. Sagerström -- Transgenesis in non-model organisms : the case of Parhyale / Zacharias Kontarakis and Anastasios Pavlopoulos -- Tissue specific RNA isolation in Drosophila embryos : a strategy to analyze context dependent transcriptome landscapes using FACS / Arnaud Defaye and Laurent Perrin -- Hox transcriptomics in Drosophila embryos / Maria Polychronidou and Ingrid Lohmann -- Measuring hox-DNA binding by electrophoretic mobility / Kelly Churion [and four others] -- Chromatin immunoprecipitation and chromatin immunoprecipitation with massively parallel sequencing on mouse embryonic tissue / Shilu Amin and Nicoletta Bobola -- chIP for hox proteins from Drosophila imaginal discs / Pavan Agrawal and L. S. Shashidhara -- SELEX-seq : a method for characterizing the compete repertoire of binding site preferences for transcription factor complexes / Todd R. Riley [and six others] -- DamID as an approach to studyinhg long-distance chromatin iteractions / Fabienne Cléard, François Karch, and oRbert K. Maeda -- cgCHIP : a cell type- and gene-specific method for chromatin analysis / Marios Agelopoulos, Daniel J. McKay, and Ricahrd S. Mann -- Bimolecular fluorescence complementation (biFC) in live Drosophila embryos / Marilyne Duffraisse, Bruno Hudry, and Samir Merabet -- Rational drug repurposing using sscMap analysis in a HOX-TALE model of leukemia / Laura M. Kettyle, Fabio G. Liberante, and Alexander Thompson.
  • 2012 Springer
    Deutsch, Jean S.
    Regulation of hox activity : insights from protein motifs / Samir Merabet ... [et al.] -- Cis-regulation in the drosophila : bithorax complex / Robert K. Maeda and François Karch -- Maintenance of hox gene expression patterns / Samantha Beck ... [et al.] -- Control of vertebrate hox clusters by remote and global cis-acting regulatory sequences / François Spitz -- The early evolution of hox genes : a battle of belief? / Bernd Schierwater and Kai Kamm -- Evolution of hox complexes / David E.K. Ferrier -- The nematode story : hox gene loss and rapid evolution / Aziz Aboobaker and Mark Blaxter -- Are the deuterostome posterior hox genes a fast-evolving class? / Robert Lanfear -- Hox genes and the body plans of chelicerates and pycnogonids / Wim G.M. Damen -- Hox3/zen and the evolution of extraembryonic epithelia in insects / Urs Schmidt-Ott, Ab. Matteen Rafiqi and Steffen Lemke -- Hox genes and brain development in drosophila / Heinrich Reichert and Bruno Bello -- Homeosis and beyond : what is the function of the hox genes? / Jean S. Deutsch.
    Also available: Print – 2010
  • 2002 NCBI Bookshelf
    Dean, Michael Carlton.
    Introduction to ABC protein and gene organization -- Nomenclature -- Overview of human ABC gene subfamilies -- ABC genes and human genetic disease -- Mouse knockouts -- Multidrug resistance and cancer therapy -- Phylogenetic analysis of human ABC genes -- Mouse ABC genes -- Drosophila ABC genes -- ABCA genes -- ABCB genes -- ABCC genes -- ABCD genes -- ABCE genes -- ABCF genes -- ABCG genes.
  • 2012 Springer
    Wyandt, Herman Edwin; Tonk, Vijay S.
    pt. 1. Human chromosome methods and nomenclature -- pt. 2. Chromosome heteromorphism (summaries) -- pt. 3. Fragile sites -- pt. 4. Copy number vairiants.
  • 2012 ScienceDirect
    Rosenberg, Leon E.; Rosenberg, Diane Drobnis.
    In the nearly 60 years since Watson and Crick proposed the double helical structure of DNA, the molecule of heredity, waves of discoveries have made genetics the most thrilling field in the sciences. The study of genes and genomics today explores all aspects of the life with relevance in the lab, in the doctor's office, in the courtroom and even in social relationships. In this helpful guidebook, one of the most respected and accomplished human geneticists of our time communicates the importance of genes and genomics studies in all aspects of life. With the use of core concepts and the integration of extensive references, this book provides students and professionals alike with the most in-depth view of the current state of the science and its relevance across disciplines. Bridges the gap between basic human genetic understanding and one of the most promising avenues for advances in the diagnosis, prevention and treatment of human disease. Includes the latest information on diagnostic testing, population screening, predicting disease susceptibility, pharmacogenomics and moreExplores ethical, legal, regulatory and economic aspects of genomics in medicine. Integrates historical (classical) genetics approach with the latest discoveries in structural and functional genomics.
  • 2011 ScienceDirect
    Richards, Julia E.; Hawley, R. Scott.
    As genetic issues play a growing role in health practice and public policy, new knowledge in this field will continue to have significant implications for individuals and society. Written to communicate sound and modern science in an accessible way for professionals and students with various levels of scientific background, this thoroughly revised edition of The Human Genome contributes to creating a genetically literate research and clinical population. With case studies and introductory vignettes which illustrate a wide range of perspectives on complex topics in genetics and updated material on the latest research on disease-specific topics, this book serves as a valuable resource for students and working professionals alike. Full-color illustrations enhance and reinforce key concepts and themes * Chapters include interest boxes that focus on human health and disease, chapter-opening case studies, and concept statements to engage non-specialist readers.
  • 2013 Springer
    I︠u︡rov, I︠u︡riĭ Borisovich.
  • 2006 Springer
    Bandelt, Hans-Jürgen; Macaulay, Vincent; Richards, Martin.
  • 2011
    Riordan, Daniel Patrick; Brown, Patrick O.; Fire, Andrew Z.; Herschlag, Daniel; Sidow, Arend; Stearns, Tim.
    The unique post-transcriptional behavior of each mRNA is thought to be largely determined by features present in its molecular sequence, representing a type of RNA regulatory code. However, the details by which distinct regulatory outcomes are programmed into the sequences of different transcripts are mostly unknown. We set out to identify features of yeast mRNAs that influence their post-transcriptional fates. Using bioinformatic and in vitro selection approaches, we characterized several RNA recognition elements involved in mediating specific interactions with individual yeast RNA-binding proteins (RBPs). Most of the RNA elements we uncovered were associated with significant mRNA expression changes and were phylogenetically conserved in related yeasts, providing insights into the function and evolution of the corresponding interactions. We also analyzed RNA-protein interaction sites for the yeast Puf3 RBP by high-throughput sequencing under different growth conditions. These results provided high-resolution experimental evidence for Puf3 binding at consensus RNA elements in the transcriptome, and enabled detailed comparisons of individual interaction sites. Finally, we developed complementary methods for transcriptome-wide mapping of potential sites of RNA 2'-O-methylation. Application of these methods to the yeast transcriptome successfully recovered known sites of RNA modification and suggested that ribose methylation of functionally-related transcripts may occur and influence the regulation of endogenous yeast mRNAs. Overall, these results contribute to understanding of how RNA sequence features help to specify global differences in gene expression characteristics.
  • 2013 Springer Protocols
    Shav-Tal, Yaron.
    As imaging technologies and approaches have evolved, the scope of certain imaging techniques has moved far beyond the production of purely illustrative images or appealing time-lapse movies to providing the scientist with a rich range of ways to measure and quantify the biological process and outcome of gene expression. In Imaging Gene Expression: Methods and Protocols, expert authors offer up-to-date approaches and protocols that scientists in the field have developed, which would benefit the broader scientific community. Divided in three convenient parts, this detailed book covers the output of a gene, namely the RNA molecules that are transcribed from the gene and the way by which these molecules can be tracked or quantified in fixed or living cells, protocols that focus on the gene, DNA, or chromatin, as well as a variety of ways by which nuclear processes intertwined with gene expression can be followed and quantified in living cells as well as approaches for studying several sub-nuclear structures found in eukaryotic cells. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective subjects, lists of materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, Imaging Gene Expression: Methods and Protocols will serve researchers working toward imaging in the context of complete organisms.
  • 2002 ScienceDirect
    Kaczmarek, L.; Robertson, Harold A.
    Also available: Print – 2002
  • 2006 Springer
    Pinaud, Raphael; Tremere, Liisa A.
    Also available: Print – 2006
  • 2012 Springer Protocols
    Christiansen, Frank T.; Tait, Brian D.
    Major histocompatibility complex : a paradigm for studies of the human genome / Richard J.N. Allcock -- HLA typing by SSO and SSP methods / Heather Dunckley -- Methods for diagnostic HLA typing in disease association and drug hypersensitivity / Michael D. Varney [and others] -- HLA typing using bead-based methods / Daniel Trajanoski and Samantha J. Fidler -- HLA Typing by Direct DNA Sequencing / Linda K. Smith -- Data analysis of HLA sequencing using assign-SBT v3.6+ from conexio / Carla Wirtz and David Sayer -- Simple methods for the detection of HLA-G variants in coding and non-coding regions / Holger Nuckel [and others] -- Molecular typing of HLA-E / Nina Lauterbach [and others] -- Molecular analysis of complement component C4 gene copy number / Alison S.L. Castley and O. Patricia Martinez -- Genotyping of single nucleotide polymorphisms by 5' nuclease allelic discrimination / Mari Malkki and Effie W. Petersdorf -- High resolution MICA genotyping by sequence-based typing (SBT) / Yizhou Zou and Peter Stastny -- Standard methods for the management of immunogenetic data / Pierre-Antoine Gourraud [and others] -- Analytical methods for immunogenetic population data / Steven J. Mack [and others] -- Analytical methods for disease association studies with immunogenetic data / Jill A. Hollenbach [and others] -- Impact of HLA matching and HLA antibodies in organ transplantation : a collaborative transplant study view / Caner Susal and Gerhard Opelz -- Screening for antibodies against MICA by luminex flow cytometry / Yizhou Zou and Peter Stastny -- HLA antibody detection and characterization by solid phase immunoassays : methods and pitfalls / Andrea A. Zachary [and others] -- Detection and characterisation of alloreactive T cells / Mandvi Bharadwaj, Nicole A. Mifsud, and James McCluskey -- Detection of allo-HLA cross-reactivity by virus-specific memory T-cell clones using single HLA-transfected K562 cells / Lloyd J. D'Orsogna [and others] -- Separation and cryopreservation of lymphocytes from spleen and lymph node / Gabriella Tassone and Samantha J. Fidler -- Crossmatching by Complement-Dependent Lymphocytotoxicity / Samantha J. Fidler -- Lymphocyte crossmatch by flow cytometry for Kidney Transplantation / Jonathan Downing -- Overview of the killer cell immunoglobulin-like receptor system / Raja Rajalingam -- KIR typing by non-sequencing methods : polymerase-chain reaction with sequence-specific primers / David Ordonez [and others] -- Killer cell immunoglobulin-like receptors (KIR) typing by DNA sequencing / Lihua Hou [and others] -- Overview of methods required to evaluate donor NK cell alloreactivity for haploidentical haemopoietic stem cell transplantation / Andrea Velardi -- Detection of NK cell alloreactivity by flow cytometric CD107a assay / Dianne De Santis [and others] -- Clinical production and therapeutic applications of alloreactive natural killer cells / David H. McKenna [and others] -- Minor histocompatibility antigen typing by DNA sequencing for clinical practice in hematopoietic stem-cell transplantation / Eric Spierings and Els Goulmy -- Donor registries and search strategies / Carolyn K. Hurley, Machteld Oudshoorn, and Michelle Setterholm -- Cytokine gene polymorphisms : methods of detection and biological significance / Gurvinder Kaur and Narinder Mehra -- IMGT® tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations : IMGT/V-QUEST and IMGT/HighV-QUEST for NGS / Eltaf Alamyar -- IMGT/DomainGapAlign : the IMGT® tool for the analysis of IG, TR, MH, IgSF, and MhSF domain amino acid polymorphism / Francois Ehrenmann and Marie-Paule Lefranc -- Human Gm, Km, and Am allotypes and their molecular characterization : a remarkable demonstration of polymorphism / Marie-Paule Lefranc and Gerard Lefranc.
  • v. 2-, 2009- Springer
  • 2014 CRCnetBASE
    Aggarwal, Bharat B.; Heber, David.
    Chapter 1. Evolution of innate and adaptive immunity / David Heber and Bharat B. Aggarwal -- chapter 2. Cellular mechanisms of cytokine activation / David Heber and Bharat B. Aggarwal -- chapter 3. Cellular lipids and inflammation / David Heber and Susanne Henning -- chapter 4. Biomarkers of inflammation and the Western diet / David Heber and Susanne Henning -- chapter 5. Phytochemicals and immune function / David Heber -- chapter 6. Genetic and environmental modifiers of immune function / David Heber -- chapter 7. Cancer and inflammation / David Heber -- chapter 8. Abdominal obesity : pathophysiology and related metabolic complications / Ana F.T.A. Junqueria and Caroline M. Apovian -- chapter 9. Type 2 diabetes and inflammation / Zhaoping Li and David Heber -- chapter 10. Heart disease and inflammation / Kaveh Daniel Navab -- chapter 11. Chronic kidney disease and inflammation / Karl J. Neff and Carel Le Roux -- chapter 12. Alzheimer's disease and inflammation / Stephen T. Chen and Gary W. Small -- chapter 13. Nutrition in autoimmunity : a focus on systemic lupus erythematosus and rheumatoid arthritis / Maureen McMahon -- chapter 14. Asthma and inflammation / Andre Nel and David Heber -- chapter 15. Muscle and immune function / Anthony Thomas and David Heber -- chapter 16. Approaches to reducing abdominal obesity / Zhaoping Li and David Heber -- chapter 17. Barriers to fruit and vegetable consumption and practical strategies for increasing fruit and vegetable intake / Susan Bowerman -- chapter 18. Healthy fats and oils : balancing omega-3 and omega-6 acids in tissues / Bill Lands -- chapter 19. Spices and dietary supplements with anti-inflammatory activity / Bharat B. Aggarwal and David Heber.
  • 2005 NAP
    Hernandez, Lyla M.
  • 2011 Springer Protocols
    Hinchcliffe, Marcus; Yu, Bing.
    Accessing and selecting genetic markers from available resources / Christopher G. Bell -- Linkage analysis / Jennifer H. Barrett and M. Dawn Teare -- Association mapping / Jodie N. Painter, Dale R. Nyholt, and Grant W. Montgomery -- The ForeSee (4C) approach for integrative analysis in gene discovery / Yike Guo, Robin E.J. Munro, Dimitrios Kalaitzopoulos, and Anita Grigoriadis -- R statistical tools for gene discovery / Andrea S. Foulkes and Kinman Au -- In silico PCR analysis / Bing Yu and Changbin Zhang -- In silico analysis of the exome for gene discovery / Marcus Hinchcliffe and Paul Webster -- In silico knowledge and content tracking / Herman van Haagen and Barend Mons -- Application of gene ontology to gene identification / Hugo P. Bastos . [and others] -- Phenotype mining for functional genomics and gene discovery / Philip Groth, Ulf Leser, and Bertram Weiss -- Conceptual thinking for in silico prioritization of candidate disease genes / Nicki Tiffin -- Web tools for the prioritization of candidate disease genes / Martin Oti, Sara Ballouz, and Merridee A. Wouters -- Comparative view of in silico DNA sequencing analysis tools / Sissades Tongsima [and others] -- Mutation surveyor : an in Silico tool for sequencing analysis / Chongmei Dong and Bing Yu -- In silico searching for disease -- associated functional DNA variants / Rao Sethumadhavan, C. George Priya Doss, and R. Rajasekaran -- In silico prediction of transcriptional factor-binding sites / Dmitry Y. Oshchepkov and Victor G. Levitsky -- In silico prediction of splice-affecting nucleotide variants / Claude Houdayer -- In silico tools for qPCR assay design and data analysis / Stephen Bustin, Anders Bergkvist, and Tania Nolan -- RNA structure prediction / Stephan H. Bernhart -- In silico prediction of post-translational modifications / Chunmei Liu and Hui Li -- In silico protein motif discovery and structural analysis / Catherine Mooney [and others].
  • 2002 Springer Protocols
    Didenko, Vladimir V.
  • 2010 Springer Protocols
    Braman, Jeff.
    Mutagenesis protocols in Saccharomyces cerevisiae by in vivo overlap extension / Mibuel Alcalde -- In vitro mutagenesis of Brucella species / Thomas A. Ficht, Jianwu Pei, and Melissa Kahl-McDonagh -- Random mutagenesis strategies for Campylobacter and Helicobacter species / Duncan J.H. Gaskin and Arnoud H.M. van Vliet -- Mutagenesis of the repeat regions of herpesviruses cloned as bacterial artificial chromosomes / Yuguang Zhao and Venugopal Nair -- An efficient protocol for VZV BAC-based mutagenesis / Zhen Zhang, Ying Huang, and Hua Zhu -- A method for rapid genetic integration into Plasmodium falciparum utilizing mycobacteriophage Bxb1 integrase / Sophie H. Adjalley, Marcus C.S. Lee, and David A. Fidock -- Random mutagenesis by error-prone PCR / Elizabeth O. McCullum ... [et al.] -- A rapid and versatile PCR-based site-directed mutagenesis protocol for generation of mutations along the entire length of a cloned cDNA / Vincent Dammai -- Rapid sequence scanning mutagenesis using in silico oligo design and the megaprimer PCR of whole plasmid method (MegaWhop) / Urich Krauss, Karl-Erich Jaeger, and Thorsten Eggert -- Insertion and deletion mutagenesis by overlap extension PCR / Jehan Lee ... [et al.] -- Targeted amplification of mutant strands for efficient site-directed mutagenesis and mutant screening / Lei Young and Qihan Dong -- A modified inverse PCR procedure for insertion, deletion, or replacement of a DNA fragment in a target sequence and its application in the ligand interaction scan method for generation of ligand-regulated proteins / Oran Erster and Moti Liscovitch -- Amplification of orthologous genes using degererate primers / Samya Chakravorty and jim O. Vigoreaux -- Computational evaluation of protein stability change upon mutations / Shuangye Yin, Feng Ding, and Nikolay V. Dokholyan -- Approaches for using animal models to identify loci that genetically interact with human disease-causing point mutations / Josef D. Franke -- Using peptide loop insertion mutagenesis for the evolution of proteins / Christian Heinis and Kai Johnsson -- Massive mutagenesis : high-throughput combinatorial site-directed mutagenesis / Julien Sylvestre -- Directed in vitro evolution of reporter genes based on semi-rational design and high-throughput screening / Ai-Sheng Xiong ... [et al.] -- Ribosome display for rapid protein evolution by consecutive rounds of mutation and selection / Hayato Yanagida, Tomoaki Matsuura, and Tetsuya Yomo -- Fine-tuning enzyme activity through saturation mutagenesis / Holly H. Hogrefe -- Characterization of structural determinants of type 1 corticotropin releasing hormone (CRH) receptor signalling properties / Danijela Markovic and Dimitris K. Grammatopoulos -- Site-directed mutagenesis for improving biophysical properties of Vh domains / Mehdi Arbabi-Ghahroudi, Roger MacKenzie, and Jamshid Tanha -- Phenotype based functional gene screening using retrovirus-mediated gene trapping in quasi-haploid RAW 264.7 cells / Sung Ouk Kim and Soon-Duck Ha -- Site-directed disulfide cross-linking to probe conformational changes of a transporter during its functional cycle : Escherichia coli AcrB multidrug exporter as an example / Yumiko Takatsuka and Hiroshi Nikaido -- Site-specific incorporation of extra components into RNA by transcription using unnatural base pair systems / Michiko Kimoto and Ichiro Hirao -- Mutagen : a random mutagenesis method providing a complementary diversity generated by human error-prone DNA polymerases / Philippe Mondon ... [et al.] -- Random-scanning mutagenesis / Robert A. Smith -- Easy two-step method for randomizing and cloning gene fragments / Vivan Q. Zhang and Holly H. Hogrefe -- Random mutagenesis using a mutator strain / Ghazala Muteeb and Ranjan Sen -- En passant mutagenesis : a two step markerless red recombination system / B. Karsten Tischer, Gregory A. Smith, and Nikolaus Osterrieder.
  • 2007 Springer Protocols
    Grandi, Guido.
    Energy systems for ATP regeneration in cell-free protein synthesis reactions / Kara A. Calhoun and James R. Swartz -- Continuous-exchange protein-synthesizing systems / Vladimir A. Shirokov ... [et al.] -- Cell-free production of integral membrane proteins on a preparative scale / Christian Klammt ... [et al.] -- SIMPLEX : a novel method for high-throughput construction and screening of protein libraries / Suang Rungpragayphan, Tsuneo Yamane, and Hideo Nakano -- Methods for high-throughput materialization of genetic information based on the wheat germ cell-free expression system / Tatsuya Sawasaki ... [et al.] -- Exogenous protein expression in Xenopus oocytes : basic procedures / Elena Bossi ... [et al.] -- In vitro translation to study HIV protease activity / Zene Matsuda ... [et al.] -- The protein truncation test in mutation detection and molecular diagnosis / Oliver Hauss and Oliver Muller -- Creation of novel enantioselective lipases by SIMPLEX / Yuichi Koga, Tsuneo Yamane, and Hideo Nakano -- In vitro transcription and translation coupled with two-dimensional electrophoresis for bacterial proteome analysis / Nathalie Norais ... [et al.] -- In vitro screen of bioinformatically selected Bacillus anthracis vaccine candidates by coupled transcription, translation, and immunoprecipitation analysis / Orit Gat, Haim Grosfeld, and Avigdor Shafferman -- Functional expression of Type 1 rat GABA transporter in microinjected Xenopus laevis oocytes / Stefano Giovannardi ... [et al.] -- Production of protein for nuclear magnetic resonance study using the wheat germ cell-free system / Toshiyuki Kohno and Yaeta Endo.
  • 2006 Springer
    Fernandes, J.
    Diagnosis and treatment: general principles -- Disorders of carbohydrate metabolism -- Disorders of mitochondrial energy metabolism -- Disorders of amino acid metabolism and transport -- Vitamin-responsive disorders -- Neurotransmitter and small peptide disorders -- Disorders of lipid and bile acid metabolism -- Disorders of nucleic acid and heme metabolism -- Disorders of metal transport -- Organelle-related disorders: lysosomes, peroxisomes, and Golgi and pre-Golgi systems.
  • 2010
    Glazer, Dariya Sergiuivna; Altman, Russ B.; Cherry, Joe H.; Levitt, Michael; Sherlock, Gavin.
    Structural Genomics consortia aim to determine the structure of proteins with novel folds. In order to interpret their biological significance, it is critical to annotate the functions of these structures. Most structures are solved by X-ray crystallography experiments and represent static snapshots of the molecules. Structure-based function prediction methods do not perform well when the snapshots fail to display the relevant functional conformations. We show that coupling structure-based function prediction methods to molecular dynamics simulations considerably improves their performance in locating calcium binding sites. Our approach can be easily extended to other functions of interest. In particular, we generated short- to medium- scale molecular simulation trajectories (1ns -- 10ns) using GROMACS, a software suite developed for creating molecular dynamics simulations. Gromos 43a5, Gromos 53a6, AMBER '96, AMBER '99SB, AMBER '03, and OPLS-AA force fields were used to generate trajectories for 11 pairs of PDB structures, HOLO and APO form for the presence of calcium ions in the structures (22 structrures in total). Extracting structures at various time points over the course of the simulations we created structural ensembles which inform about the dynamic nature of each of the simulation systems. Using FEATURE, a machine learning algorithm that evaluates the presence of enriched physico-chemical properties around a site of interest, we analyzed the structural ensembles for the presence of calcium binding sites. We devised a clustering algorithm which allowed for definitive determination of the similarity of the local environments around the points identified by FEATURE as potential calcium binding site centers in different structural ensembles for each of the 22 PDB structures. Our results indicate that short scale simulations with 2 or 3 different force fields generate sufficient structural diversity to allow for improved identification of calcium binding sites. Furthermore, inclusion of calcium ions in the simulation systems does not significantly improve the performance of FEATURE. This result highlights the need for improved force fields, such that the dynamic nature of calcium binding sites can be accurately reproduced.
  • 2007 Springer
    Fagot-Largeault, Anne; Rahman, Shahid; Torres, Juan Manuel.
    Pt. 1. Genetics and the life sciences -- Pt. 2. Genetics and philosophy of science: the reductionism debate and beyond -- Pt. 3. Genetics and the ethical, legal and sociological debate.
  • 2014 Springer
    De Laey, J. J.; Holder, Graham E.; Puech, Bernard.
    Introduction to Molecular Genetics and Genetic Testing for Retinal Dystrophies -- Electrophysiological Testing -- Dark Adaptation -- Fluorescein Angiography -- Indocyanine Green Angiography -- Fundus Autofluorescence Imaging in Retinal Dystrophies -- Spectral-Domain Optical Coherence Tomography in Hereditary Retinal Dystrophies -- Inherited Stationary Disorders of the Retina -- Retinitis Pigmentosa and Allied Disorders -- Leber Congenital Amaurosis and Early-Onset Retinal Dystrophy -- Retinitis Punctata Albescens -- Usher Syndromes -- Cone and Cone-Rod Dystrophies -- Enhanced S-Cone Syndrome -- Chorioretinopathies: Choroideraemia and Gyrate Atrophy -- Late-Onset Retinal Dystrophy (LORD) -- Stargardt Disease -- The Bestrophinopathies -- Retinal Dystrophies Associated with the PRPH2 Gene -- Alström Syndrome -- Bardet-Biedl Syndrome -- Cohen Syndrome -- Juvenile Neuronal Ceroid Lipofuscinoses (JNCL) -- Adult Refsum Disease (ARD) -- Abetalipoproteinemia -- LCHAD Deficiency -- Jalili Syndrome -- Spinocerebellar Ataxia 7 -- Dominant Cystoid Macular Dystrophy -- Autosomal Dominant Stargardt-Like Macular Dystrophy (ELOVL4) -- Spastic Paraplegia and Retinal Degeneration: Kjellin Syndrome -- Autosomal Dominant Drusen -- Cuticular Drusen -- Extensive Macular Atrophy with Pseudodrusen-Like Appearance -- Congenital Hypotrichosis with Juvenile Macular Dystrophy -- Mitochondrial Retinopathies -- Sorsby Fundus Dystrophy -- Bietti Crystalline Corneoretinal Dystrophy -- Cystinosis -- Primary Oxalosis -- Alport Syndrome -- X-Linked Retinoschisis -- Paramacular Choriocapillaris Atrophy -- Exudative Vitreoretinopathy -- Stickler Syndrome -- Wagner Syndrome -- Incontinentia Pigmenti Type II (IP2) -- Ganglion Cell Diseases -- Pseudoxanthoma Elasticum -- Aicardi Syndrome -- Microcephaly and Chorioretinopathy With or Without Mental Retardation and Lymphedema -- Alagille Syndrome -- Future Therapies for Retinitis Pigmentosa.
  • 2014 Springer Protocols
    Anders, Hans-Joachim; Migliorini, Adriana.
    Detection of RNA modifications by HPLC analysis and competitive ELISA / Gernot Nees, Andreas Kaufmann, and Stefan Bauer -- Enzymatic synthesis and purification of a defined RIG-I ligand / Marion Goldeck ... [et al.] -- Crystallization of mouse RIG-I ATPase domain : in situ proteolysis / Filiz Civril and Karl-Peter Hopfner -- Isolation of RIG-I-associated RNAs from virus-infected cells / Andreas Schmidt ... [et al.] -- Structure modeling of Toll-Like Receptors / Jing Gong and Tiandi Wei -- Nucleic acid recognition in dendritic cells / Alexander Heiseke, Katharina Eisenächer, and Anne Krug -- Viral nucleic acid recognition in human nonimmune cells : in vitro systems / Andrea Ribeiro and Markus Wörnle -- Analysis of nucleic acid-induced nonimmune cell death in vitro / Simone Romoli and Adriana Migliorini -- In vitro analysis of nucleic acid recognition in B lymphocytes / Saskia Ziegler and Isabelle Bekeredjian-Ding -- Mapping of optimal CD8 T cell epitopes / Julia Roider, Thomas Vollbrecht, and Rika Draenert -- Modular approach to suppression assays : TLR ligands, conditioned medium, and viral infection / Viktor H. Koelzer and David Anz -- MicroRNA methodology : advances in miRNA technologies/ Theresa Kaeuferle ... [et al.] -- Expression profiling by real-time quantitative polymerase chain reaction (RT-qPCR) / Maciej Lech and Hans-Joachim Anders -- Evaluating the role of nucleic acid antigens in murine models of systemic lupus erythematosus / Amanda A. Watkins, Ramon G. B. Bonegio, and Ian R. Rifkin -- Induction and analysis of nephrotoxic serum nephritis in mice / John M. Hoppe and Volker Vielhauer -- Isolation of intratumoral leukocytes of TLR-stimulated tumor-bearing mice / Moritz Rapp, David Anz, and Max Schnurr -- Bifunctional siRNAs for tumor therapy / Fanny Matheis and Robert Besch.
  • 2005 Springer
    Altukhov, I︠U︡. P.
  • 2006 Springer
    Haubold, Bernhard; Wiehe, Thomas.
  • 2007 CRCnetBASE
    Datta, Aniruddha; Dougherty, Edward R.
    Review of organic chemistry -- Energy considerations in biochemical reactions -- Proteins -- DNA -- Transcription and translation -- Chromosomes and gene regulation -- Genetic variation -- DNA technology -- Cell division -- Cell cycle control, cell death, and cancer -- Expression microarrays -- Classification -- Clustering -- Genetic regulatory networks -- Intervention -- External intervention based on optimal control theory.
  • 2003 CRCnetBASE
    Burczynski, Michael E.
  • 2014 CRCnetBASE
    Eckwahl, Matthew.
    Part 1. Cell polarity, growth, and cell cycle -- part 2. Yeast regulatory circuits -- part 3. Gene expression and trait locus analysis -- part 4. Comparative genomics.
  • 2010 Karger
    Quinton, Richard.
    Molecular characterization and phenotypic expression of mutations in genes for gonadotropins and their receptors in humans / Salvi, R., Pralong, F.P -- Role of kisspeptin/GPR54 system in human reproductive axis / Silveira, L.F.G. ... [et al.] -- Biology of kisspeptins / Hameed, S., Dhillo, W.S. -- Role of fibroblast growth factor signaling in gonadotropin-releasing hormone neuronal system development / Chung, W.C.J., Tsai, P.-S. -- FGFR1 mutations in Kallmann syndrome / Villanueva, C., de Roux, N. -- Biology of KAL1 and its orthologs : implications for x-linked Kallmann syndrome and the search for novel candidate genes / MacColl, G.S., Quinton, R., Bülow, H.E. -- Biological actions and interactions of anosmin-1 / Choy, C., Kim, S.H. -- Genotype and phenotype of patients with gonadotropin-releasing hormone receptor mutations / Kim, H.-G. ... [et al.] -- Hypogonadotropic hypogonadism and GNRH1 mutations in mice and humans / Bouligand, J. ... [et al.] -- Kallmann syndrome caused by mutations in the PROK2 and PROKR2 genes : pathophysiology and genotype-phenotype correlations / Sarfati, J., Dodé, C., Young, J. -- Neurokinin B and its receptor in hypogonadotropic hypogonadism / Semple, R.K., Topaloglu, A.K. -- Complex genetics in idiopathic hypogonadotropic hypogonadism / Pitteloud, N. ... [et al.] -- Rarer syndromes characterized by hypogonadotropic hypogonadism / Aminzadeh, M. ... [et al.].
  • 2008 Springer
    Blau, N.; Duran, Marinus; Gibson, K. Michael.
  • 2011 Springer Protocols
    Murray, Graeme I.
    Laser capture microdissection : methods and applications / Kristen DeCarlo . [and others] -- Laser microdissection for gene expression profiling / Lori A. Field [and others] -- Gene expression using the PALM system / Jian-Xin Lu and Cheuk-Chun Szeto -- Immunoguided microdissection techniques / Michael A. Tangrea [and others] -- Optimized RNA extraction from non-deparaffinized laser-microdissected material / Danny Jonigk [and others] -- Laser capture microdissection for analysis of gene expression in formalin-fixed paraffin-embedded Tissue / Ru Jiang, Rona S. Scott, and Lindsey M. Hutt-Fletcher -- MicroRNA profiling using RNA from microdissected immunostained tissue / Clemens L. Bockmeyer [and others] -- Profiling solid tumor heterogeneity by LCM and biological MS of fresh-frozen tissue sections / Donald J. Johann [and others] -- Amplification testing in breast cancer by multiplex ligation-dependent probe amplification of microdissected tissue / Cathy B. Moelans, Roel A. de Weger, and Paul J. van Diest -- Detection and quantification of MicroRNAs in laser-microdissected formalin-fixed paraffin-embedded breast cancer tissues / Sarkawt M. Khoshnaw [and others] -- Laser capture microdissection applications in breast cancer proteomics / Rene B.H. Braakman [and others] -- Proteomic analysis of laser microdissected ovarian cancer tissue with SELDI-TOF MS / Isabelle Cadron [and others] -- LCM Assisted biomarker discovery from archival neoplastic gastrointestinal tissues / Patricia A. Meitner and Murray B. Resnick -- Purification of diseased cells from Barrett's esophagus and related lesions by laser capture microdissection / Masood A. Shammas and Manjula Y. Rao -- Laser microdissection of intestinal epithelial cells and downstream analysis / Benjamin Funke -- Application of laser microdissection and quantitative PCR to assess the response of esophageal cancer to neoadjuvant chemo-radiotherapy / Claus Hann von Weyhern and Bjorn L.D.M. Brucher -- Oligonucleotide microarray expression profiling of contrasting invasive phenotypes in colorectal cancer / Christopher C. Thorn, Deborah Williams, and Thomas C. Freeman -- Evaluation of gastrointestinal mtDNA depletion in mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) / Carla Giordano and Giulia d'Amati -- Laser microdissection for gene expression study of hepatocellular carcinomas arising in cirrhotic and non-cirrhotic livers / Maria Tretiakova and John Hart -- Laser capture microdissection of pancreatic ductal adeno-carcinoma cells to analyze EzH2 by western blot analysis / Aamer M. Qazi [and others] -- Laser-capture microdissection of renal tubule cells and linear amplification of RNA for microarray profiling and real-time PCR / Susie-Jane Noppert, Susanne Eder, and Michael Rudnicki -- Subcellular renal proximal tubular mitochondrial toxicity with tenofovir treatment / James J. Kohler and Seyed H. Hosseini -- Application of laser-capture microdissection to study renal carcinogenesis / Kerstin Stemmer and Daniel R. Dietrich -- Laser-capture microdissection and transcriptional profiling in archival FFPE tissue in prostate cancer / Ajay Joseph and Vincent J. Gnanapragasam -- Quantitative analysis of the enzymes associated with 5-Fluorouracil metabolism in prostate cancer biopsies / Tomoaki Tanaka -- Microdissection of gonadal tissues for gene expression analyses / Anne Jørgensen, Marlene Danner Dalgaard, and Si Brask Sonne -- Duplex real-time PCR assay for quantifying mitochondrial DNA deletions in laser microdissected single spiral ganglion cells / Adam Markaryan, Erik G. Nelson, and Raul Hinojosa -- Neuronal type-specific gene expression profiling and laser-capture microdissection / Charmaine Y. Pietersen . [et al.] -- Region-specific in situ hybridization-guided laser-capture microdissection on postmortem human brain tissue coupled with gene expression quantification / Rene Bernard, Sharon Burke, and Ilan A. Kerman -- UV-laser microdissection and mRNA expression analysis of individual neurons from postmortem Parkinson's disease brains / Jan Grundemann, Falk Schlaudraff, and Birgit Liss -- Transcriptome profiling of murine spinal neurulation using laser capture microdissection and high-density oligonucleotide microarrays / Shoufeng Cao, Boon-Huat Bay, and George W. Yip -- Probing the CNS microvascular endothelium by immune-guided laser-capture microdissection coupled to quantitative RT-PCR / Nivetha Murugesan [and others] -- Laser-capture microdissection for factor VIII-expressing endothelial cells in cancer tissues / Tomoatsu Kaneko [and others] -- Laser-capture microdissection and analysis of liver endothelial cells from patients with Budd-Chiari syndrome / Selcuk Sozer and Ronald Hoffman -- Laser-capture microdissection of hyperlipidemic/ApoE-/- mouse aorta atherosclerosis / Michael Beer [and others] -- Gene expression profiling in laser-microdissected bone marrow megakaryocytes / Kais Hussein -- Specific RNA collection from the rat endolymphatic sac by laser-capture microdissection (LCM) : LCM of a very small organ surrounded by bony tissues / Kosuke Akiyama [and others] -- Use of laser capture microdissection on adult human articular cartilage for gene expression analysis / Naoshi Fukui, Yasuko Ikeda, and Nobuho Tanaka -- Laser-capture microdissection of developing barley seeds and cDNA array analysis of selected tissues / Johannes Thiel, Diana Weier, and Winfriede Weschke -- Quantitative RT-PCR gene expression analysis of a laser microdissected placenta : an approach to study preeclampsia / Yuditiya Purwosunu [and others].
  • 2013 Springer
    Gophna, Uri.
    "Although the phenomenon of lateral gene transfer has been known since the 1940s, it was the genomics era that has really revealed the extent and many facets of this evolutionary/genetic phenomenon. Even in the early 2000s with but a handful of genomes available, it became clear that the nature of microorganisms is full of genetic exchange between lineages that are sometimes far apart. The years following this saw an explosion of genomic data, which shook the "tree of life" and also raised doubts about the most appropriate species concepts for prokaryotes. This book represents the manyfold contributions of LGT to the evolution of micro and, to an extent, macroorganisms by focusing on the areas where it has the largest impact: metabolic innovations and adaptations and speciation." Back cover.
  • 2014 Springer
    Tseng, Charles C.; Yang, Xiaoli.
    Learning Basic Genetics with Interactive Computer Programs is a comprehensive and interactive learning program that focuses on chromosome simulation and model building. It is intended to assist students in learning more about genetics with ease. The 11 modules of this program form an integrated system for learning the basic concepts of genetics. The program innovation lies in its unique content design that incorporates cognitive feedback and experiential learning through the novel use of interactive applications. Each of the modules is designed to enhance learning by simultaneously employing "eyes-on," "minds-on," and "hands-on" activities. Topics are motivated by questions, information is presented in simple terms, and concepts are clarified by interactive prompts. Used as a supplement to traditional lectures and textbook assignments, the program not only serves as a foundation upon which to build more complex and detailed topics, but as a tutor to clarify and guide when there is confusion. The software that accompanies this book has been shown to be an ideal tool for learning about genetics, which requires a combination of understanding, conceptualization, and practical experience.
  • 2013 Springer Protocols
    Rose, Ray J.
    Featuring current resources used to discover new legume family genes and to understand genes and their interactions, Legume Genomics: Methods and Protocols provides techniques from expert researchers to study these plants that are so vitally important for food, feed, human nutrition, bioenergy, and industrial purposes. This detailed volume covers genome characterization and analysis, transcriptome analysis and miRNA identification/analysis, forward and reverse genetics, molecular markers, as well as transformation strategies used to investigate gene function and many other topics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and useful, Legume Genomics: Methods and Protocols aims to serve plant molecular biologists, molecular breeders, plant physiologists and biochemists, developmental biologists, and those interested in plant-microbe interactions.
  • 2003 Springer Protocols
    Federico, Maurizio.
    From lentiviruses to lentivirus vectors / M. Federico -- The choice of a suitable lentivirus vector: Transcriptional targeting / F. Lotti and F. Mavilio -- Choice and use of appropriate packaging cell types / A.L. Pacchia, S. Mukherjee and J.P. Dougherty -- Small- to large-scale production of lentivirus vectors / M.P. Marino, M.J. Luce and J. Reiser -- Detection and titration of lentivirus vector preparations / J. Gatlin, M. Islas-Ohlmayer and J.V. Garcia -- Detection and selection of lentiviral vector-transduced cells / Y. Cui and L.J. Chang -- Detection of replication-competent lentiviral particles / H. Segall and R.E. Sutton -- Lymphocytes / D. Chinnasamy and F. Candotti -- Monocyte/macrophages and dendritic cells / H. Segall and R.E. Sutton -- Hematopoietic stem and progenitor cells / R.E. Donahue and I.S. Chen -- Mesenchymal stem cells / X.Y. Zhang, V.F. La Russa and J. Reiser -- Hippocampal neurons / J.L. Nadeau -- Dorsal root ganglia sensory neurons / J. Fleming, S.L. Ginn and I.E. Alexander -- Cardiomyocytes / D. Bonci, M.V. Latronico and G. Condorelli -- Airway epithelia / L.G. Johnson, S.H. Randell and J.C. Olsen -- Corneal cells / B. Appukuttan, T. McFarland and J.T. Stout -- Retinal tissue / T. McFarland, B. Appukuttan and J.T. Stout -- Hiv-2 vectors / S.K. Arya, J.E. Cho and S.H. Chang -- Siv vectors / A. Ruggieri, D. Negre and F.L. Cosset -- Fiv vectors / N. Loewen [and others] -- Hybrid lentivirus vectors / V. Planelles -- Cells of respiratory epithelium / P.L. Sinn and P.B. McCray, Jr. -- Cells of the nervous system / C. Rosenblad and C. Lundberg.
  • 2011 Springer
    Ugarković, Đurđica.
    Transcriptional and posttranscriptional programming by long noncoding RNAs / Radha Raman Pandey and Chandrasekhar Kanduri -- Long noncoding RNA as a regulator for transcription / Riki Kurokawa -- Long noncoding RNAs and X chromosome inactivation / Cristina Gontan, Iris Jonkers, and Joost Gribnau -- TERRA : long noncoding RNA at eukaryotic telomeres / Rajika Arora, Catherine M.C. Brun, and Claus M. Azzalin -- Transcription of satellite DNAs in mammals / Claire Vourc'h and Giuseppe Biamonti -- Multiple roles of Alu-related noncoding RNAs / Audrey Berger and Katharina Strub -- roX RNAs and genome regulation in Drosophila melanogaster / S. Kiran Koya and Victoria H. Meller -- Transcription of satellite DNAs in insects / Željka Pezer ... [et al.] -- Long nonprotein-coding RNAs in plants / Virginie Jouannet and Martin Crespi.
  • 2015 Springer
    Atzmon, Gil.
    The release of the complete version of the human genome sequence in 2003 has paved the way for defining gene function and genetic background for phenotypic variation in humans and allowed us to study the aging process in a new light. This new volume results from that research and focuses on the genetic and epigenetic process of aging. While the interpretation of the genome data is still in its initial stages, this new volume looks at the evolving understanding of molecular mechanisms involved in cellular processes, gene function associated with complex traits, epigenetic components involve in gene control and the creation of hypothesis-free genome-wide approaches. Longevity Genes: A Blueprint for Aging explores the genetic and genomic elements that can maintain a long life such as DNA damage mechanisms, epigenetics and the way we can use this knowledge to generate customized treatments. It touches on some of the multidisciplinary approaches as well as genomic-wide association technology used to analyze complex traits. This book describes the hunt for genes affecting complex traits using a high throughput technology, with adequate consideration for the selection of an appropriate population, applications of statistical genetics and computational biology, and most importantly, considering phenotype-genotype association studies. Longevity Genes provides coverage of not only established aspects of genetics and aging, but also new approaches and perceptions in this important area of research.
    Also available: Print – 2015
  • 2006 Springer
    Lois, Carlos; Pease, Shirley.
  • 2011 Springer Protocols
    Hadlaczky, Gyula.
    [Publisher-supplied data] The rapid progression of genetics and molecular biology has turned chromosomal engineering from science fiction to reality, with the successful production of transgenic animals with engineered chromosomes and chromosomes developed for pharmaceutical protein production which are now ready for the medical industry. Mammalian Chromosome Engineering: Methods and Protocols provides the reader with up-to date information on this rapidly evolving field and strives to take the reader into the exciting realm of chromosomal engineering from the basic principles to the practical applications of these new technologies. The five overview and ten protocol chapters cover the engineering of chromosomes with extrachromosomal vectors and transposon systems, the manipulation of naturally occurred minichromosomes, the generation and engineering of synthetic artificial chromosomes, and the induced de novo platform artificial chromosome system. Written in the highly successful Methods in Molecular Biology series format, protocols chapters contain brief introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Mammalian Chromosome Engineering: Methods and Protocols serves as a bench-side resource for current protocols and aims to help scientists to explore the many prospects for future research and vital applications.
  • 2013 ScienceDirect
    Davies, Jamie A.
    Morphogenesis is the set of processes that generate shape and form in the embryo--an important area within developmental biology. An exciting and up-to-the-minute account of the very latest research into the factors that create biological form, Mechanisms of Morphogenesis, second edition is a text reference on the mechanisms of cell and tissue morphogenesis in a diverse array of organisms, including prokaryotes, animals, plants and fungi. By combining hard data with computer modeling, Mechanisms of Morphogenesis, second edition equips readers with a much broader understanding of the scope of modern research than is otherwise available. The book focuses on the ways in which the genetic program is translated to generate cell shape, to direct cell migration, and to produce the shape, form and rates of growth of the various tissues. Each topic is illustrated with experimental data from real systems, with particular reference to gaps in current knowledge and pointers to future. Includes over 200 four-color figures. Offers an integrated view of theoretical developmental biology and computer modelling with laboratory-based discoveries. Covers experimental techniques as a guide to the reader. Organized around principles and mechanisms, using them to integrate discoveries from a range of organisms and systems.
  • 2005 Springer
    2005 Springer Protocols
    Rapley, Ralph; Walker, John M.
    Basic techniques in molecular biology / Ralph Rapley -- Probe design, production, and applications / Marilena Aquino de Muro -- Restriction enzymes: tools in clinical research / Gareth J.S. Jenkins -- Southern blotting as a diagnostic method / Bronwen Harvey and Pirkko Soundy -- Western blotting as a diagnostic method / Pirkko Soundy and Bronwen Harvey -- Principles and medical applications of the polymerase chain reaction / Bimal D. M. Theophilus -- Single strand conformation polymorphism (SSCP) analysis / Igor Vorechovsky -- Denaturing gradient gel electrophoresis (DGGE) / Jeroen H. Roelfsema and Dorien J.M. Peters -- Quantitative analysis of DNA sequences by PCR and solid phase sequencing / Anu Suomalainen and Ann-Christine Syvänen -- Introduction to capillary electrophoresis of DNA: biomedical applications / Beatriz Sanchez-Vega -- Mapping techniques / Simon G. Gregory -- Dideoxyfingerprinting for mutation detection / Ioannis Bossis, Antonios Voutetakis, and Constantine A. Stratakis -- Conformation sensitive gel electrophoresis / Marian Hill -- Amplification refractory mutation system and molecular diagnostics / Richard Kitching and Arun Seth -- Ligase chain reaction / Carla Osiowy -- Chemical cleavage of mismatch: theory and clinical applications / Neil V. Whittock and Louise Izatt -- The protein truncation test / Johan T. den Dunnen -- Linkage, allele sharing, and association / Mara Giordano -- Single nucleotide polymorphisms: technology and applications / Cyril Mamotte, Frank Christiansen, and Lyle J. Palmer -- cDNA microarrays / Philip G. Febbo -- Nucleic acid sequence-based amplification / Katherine Loens, D. Ursi, H. Goosens, and M. Ieven -- The oligonucleotide ligation assay / Faye A. Eggerding -- Quantitative taqman real-time PCR: diagnostic and scientific applications / Jörg Dötsch, Ellen Schoof, and Wolfgang Rascher -- Use of denaturing high-performance liquid chromatography in molecular medicine / Elizabeth L. Rugg and Gareth J. Magee -- Quantitative PCR / David Sugden -- Liquid chromatography-mass spectrometry of nucleic acids / Herbert Oberacher and Walther Parson -- Comparative genomic hybridization in clinical and medical research / Peng-Hui Wang, Yann-Jang Chen, and Chi-Hung Lin -- Bioinformatics tools for gene and protein sequence analysis / Bernd H.A. Rehm and Frank Reinecke -- In situ hybridization / Amanda D. Watters -- Enzyme-linked immunosorbent assay / William J. Jordan -- Protein therapeutics: mouse, humanized, and human antibodies / Benny K.C. Lo -- Karyotyping / Avery A. Sandberg, John F. Stone, and Zhong Chen -- Microsatellite analysis / Rachel E. Ibbotson and Anton E. Parker -- Analysis of chromosomal translocations / Andreas Hochhaus -- Differential display: theory and applications / Irina Gromova, Pavel Gromov, and Julio E. Celis -- Techniques for gene expression profiling / Mark P. Richards -- Capillary electrophoresis in clinical analysis / Margaret A. Jenkins and Sujiva Ratnaike -- Flow cytometry in the biomedical arena / James L. Weaver and Maryalice Stetler-Stevenson -- Immunocytochemistry / Patricia A. Fetsch -- Ribotyping in clinical microbiology / Patricia Severino and Sylvain Brisse -- Diagnostic applications of protein microarrays / Samir Hanash -- The human genome project / Rahul Chodhari and Eddie Chung -- Prenatal diagnosis of inborn errors of metabolism / Guy T.N. Besley -- Gene therapy: methods and application / Stella B. Somiari.
  • 2009. Karger
    Benavente, Ricardo; Volff, Jean-Nicolas.
    The meiotic recombination hotspots of Schizosaccharomyces pombe / Pryce, D.W.; McFarlane, R.J. -- Meiotic recombination and crossovers in plants / De Muyt, A. ... [et al.] -- Meiosis in cereal crops : the grasses are back / Martinez-Perez, E. -- Homologue pairing, recombination and segregation in Caenorhabditis elegans / Zetka, M. -- Homolog pairing and segregation in Drosophila meiosis / McKee, B.D. -- The mammalian synaptonemal complex : a scaffold and beyond / Yang, F.; Wang, P.J. -- The dance floor of meiosis : evolutionary conservation of nuclear envelope attachment and dynamics of meiotic telomeres / Alsheimer, M. -- Cohesin complexes and sister chromatid cohesion in mammalian meiosis / Suja, J.A.; Barbero, J.L. -- Variation in patterns of human meiotic recombination / Khil, P.P.; Camerini-Otero, R.D. -- Maternal origin of the human aneuploidies are homolog synapsis and recombination to blame? Notes (learned) from the underbelly / Garcia-Cruz, R.; Roig, I.; Garcia Caldés, M. -- Inverted meiosis : the true bugs as a model to study / Viera, A.; Page, J.; Rufas, J.S. The meiotic recombination hotspots of Schizosaccharomyces pombe / D.W. Pryce, R.J. McFarlane -- Meiotic recombination and crossovers in plants / A. De Muyt ... [et al.] -- Meiosis in cereal crops : the grasses are back / E. Martinez-Perez -- Homologue pairing, recombination, and segregation in Caenorhabditis elegans / M. Zetka -- Homolog pairing and segregation in Drosophila meiosis / B.D. McKee -- The mammalian synaptonemal complex : a scaffold and beyond / F. Yang, P.J. Wang -- The dance floor of meiosis : evolutionary conservation of nuclear envelope attachment and dynamics of meiotic telomeres / M. Alsheimer -- Cohesin complexes and sister chromatid cohesion in mammalian meiosis / J.A. Suja, J.L. Barbero -- Variation in patterns of human meiotic recombination / P.P. Khil, R.D. Camerini-Otero -- Maternal origin of the human aneuploidies are homolog : synapsis and recombination to blame? notes (learned) from the underbelly / R. Garcia-Cruz, I. Roig, M. Garcia Caldes -- Inverted meiosis : the true bugs as a model to study / A. Viera, J. Page, J.S. Rufas.
  • 2009 Springer Protocols
    Peirce, Matthew J.; Wait, Robin.
    Online tools for predicting integral membrane proteins / H. Bigelow and B. Rost -- In silico identification of novel G protein coupled receptors / M.N. Davies and D.R. Flower -- Transcriptome-based identification of candidate membrane proteins / E.J. Evans ... [et al.] -- Separation of thylakoid membrane proteins by sucrose gradient ultracentrifugation or blue native-SDS-PAGE two-dimensional electrophoresis / G.M. D'Amici, C.G. Huber and L. Zolla -- Extraction of yeast mitochondrial membrane proteins by solubilization and detergent/polymer aqueous two-phase partitioning / H. Everberg, N. Gustavsson and F. Tjerneld -- 16-BAC/SDS-PAGE analysis of membrane proteins of yeast mitochondria purified by free flow electrophoresis / R.J. Braun ... [et al.] -- Sequential detergent extraction prior to mass spectrometry analysis / F.M. McCarthy, A.M. Cooksey and S.C. Burgess -- Enrichment of brain plasma membranes by affinity two-phase partitioning / J. Schindler and H.G. Nothwang -- Protocol to enrich and analyze plasma membrane proteins / R.J. Wisniewski -- Proteomic analysis of the lymphocyte plasma membrane using cell surface biotinylation and solution-phase isoelectric focusing / M.J. Peirce, A.P. Cope and R. Wait -- Identification of target membrane proteins as detected by phage antibodies / C.A. Geuijen, A.Q. Bakker and J. de Kruif -- Membrane protease degradomics: proteomic identification and quantification of cell surface protease substrates / G.S. Butler ... [et al.] -- Purification of basolateral integral membrane proteins by cationic colloidal silica-based apical membrane subtraction / R.J. Goode and R.J. Simpson -- Moving closer to the lipid raft proteome using quantitative proteomics / L.J. Foster -- Use of sequential chemical extractions to purify nuclear membrane proteins for proteomics identification / N. Korfali ... [et al.] -- Isolation of extracellular membranous vesicles for proteomic analysis / R.A. Mathias ... [et al.] -- Enrichment of human platelet membranes for proteomic analysis / D.W. Greening ... [et al.] -- Detergents and chaotropes for protein solubilization before two-dimensional electrophoresis / T. Rabilloud -- Two-dimensional separation of membrane proteins by 16-BAC-SDS-PAGE / H.G. Nothwang and J. Schindler -- MudPIT analysis: application to human heart tissue / K.G. Kline and C.C. Wu -- Liquid chromatography MALDI MS/MS for membrane proteome analysis / N. Wang, J.B. Young and L. Li -- Cysteinyl-tagging of integral membrane proteins for proteomic analysis using liquid chromatography-tandem mass spectrometry / S.K. Mitra and M.B. Goshe -- Quantitative proteomics analysis of pancreatic zymogen granule membrane proteins / X. Chen and P.C. Andrews.
  • 2010 CRCnetBASE
    Goldstein, Darlene Renee; Guerra, Rudy.
    Pt. 0. Introductory Material -- 1. brief introduction to meta-analysis, genetics, and genomics / Darlene R. Goldstein and Rudy Guerra -- Pt I. Similar Data Types I: Genotype Data -- 2. Combining information across genome-wide linkage scans / Carol J. Etzel and Tracy J. Costello -- 3. Genome search meta-analysis (GSMA): a nonparametric method for meta-analysis of genome-wide linkage studies / Cathryn M. Lewis -- 4. Heterogeneity in meta-analysis of quantitative trait linkage studies / Hans C. van Houwelingen and Jeremie J. P. Lebrec -- 5. empirical Bayesian framework for QTL genome-wide scans / Kui Zhang ... [et al.] -- Pt. II. Similar Data Types II: Gene Expression Data -- 6. Composite hypothesis testing: an approach built on intersection-union tests and Bayesian posterior probabilities / Stephen Erickson, Kyoungmi Kim and David B. Allison -- 7. Frequentist and Bayesian error pooling methods for enhancing statistical power in small sample microarray data analysis / Jae K. Lee, Hyung Jun Cho and Michael O'Connell -- 8. Significance testing for small microarray experiments / Charles Kooperberg ... [et al.] -- 9. Comparison of meta-analysis to combined analysis of a replicated microarray study / Darlene R. Goldstein ... [et al.] -- 10. Alternative probe set definitions for combining microarray data across studies using different versions of Affymetrix oligonucleotide arrays / Jeffrey S. Morris ... [et al.] -- 11. Gene ontology-based meta-analysis of genome-scale experiments / Chad A. Shaw -- Pt. III. Combining Different Data Types -- 12. Combining genomic data in human studies / Debashis Ghosh, Daniel Rhodes and Arul Chinnaiyan -- 13. overview of statistical approaches for expression trait loci mapping / Christina Kendziorski and Meng Chen -- 14. Incorporating GO annotation information in expression trait loci mapping / J. Blair Christian and Rudy Guerra -- 15. misclassification model for inferring transcriptional regulatory networks / Ning Sun and Hongyu Zhao -- 16. Data integration for the study of protein interactions / Fengzhu Sun ... [et al.] -- 17. Gene trees, species trees, and species networks / Luay Nakhleh, Derek Ruths and Hideki Innan.
  • 2010 Springer Protocols
    Daniel, Rolf; Streit, Wolfgang.
    Molecular Methods to Study Complex Microbial Communities / José M. Vieites, María-Eugenia Guazzaroni, Ana Beloqui, Peter N. Golyshin, and Manuel Ferrer -- Construction of Small-Insert and Large-Insert Metagenomic Libraries / Carola Simon and Rolf Daniel -- Construction and Screening of Marine Metagenomic Libraries / Nancy Weiland, Carolin Löscher, Rebekka Metzger, and Ruth Schmitz -- Metagenomic Analysis of Isotopically Enriched DNA / Yin Chen, Josh D. Neufeld, Marc G. Dumont, Michael W. Friedrich, and J. Colin Murrell -- Wide Host-Range Cloning for Functional Metagenomics / Margaret Wexler and Andrew W.B. Johnston -- Cloning and Expression Vectors for a Gram-Positive Host, Streptomyces lividans / Kristof Vrancken, Lieve Van Mellaert, and Jozef Anné -- Heterologous Gene Expression in the Hyperthermophilic Archaeon Sulfolobus solfataricus / Angel Angelov and Wolfgang Liebl -- Novel Tools for the Functional Expression of Metagenomic DNA / Sonja Christina Troeschel, Thomas Drepper, Christian Leggewie, Wolfgang R. Streit, and Karl-Erich Jaeger -- Screening of Functional Promoter from Metagenomic DNA for Practical Use in Expression Systems / So-Youn Park and Geun-Joong Kim -- Substrate-Induced Gene Expression Screening: A Method for High-Throughput Screening of Metagenome Libraries / Taku Uchiyama and Kentaro Miyazaki -- Screens for Active and Stereoselective Hydrolytic Enzymes / Dominique Böttcher, Marlen Schmidt, and Uwe T. Bornscheuer. Screening for Cellulase-Encoding Clones in Metagenomic Libraries / Nele Ilmberger and Wolfgang R. Streit -- Screening Metagenomic Libraries for Laccase Activities / Manuel Ferrer, Ana Beloqui, and Peter N. Golyshin -- Screening for N-AHSL-Based-Signaling Interfering Enzymes / Phil M. Oger and Stéphane Uroz -- Identification of Molecular Markers to Follow Up the Bioremediation of Sites Contaminated with Chlorinated Compounds / Massimo Marzorati, Annalisa Balloi, Francesca De Ferra, and Daniele Daffonchio -- Methods for the Isolation of Genes Encoding Novel PHB Cycle Enzymes from Complex Microbial Communities / Ricardo F. Nordeste, Maria A. Trainer, and Trevor C. Charles -- Metagenomic Approaches to Identify and Isolate Bioactive Natural Products from Microbiota of Marine Sponges / Cristian Gurgui and Jörn Piel -- Screening for Novel Antibiotic Resistance Genes / Mindy G. Brown, Elizabeth H. Mitchell, and David L. Balkwill -- Novel Metal Resistance Genes from Microorganisms: A Functional Metagenomic Approach / José E. González-Pastor and Salvador Mirete -- Retrieval of Full-Length Functional Genes Using Subtractive Hybridization Magnetic Bead Capture / Tracy Meiring, Inonge Mulako, Marla I. Tuffin, Quinton Meyer, and Donald A. Cowan -- Detection and Isolation of Selected Genes of Interest from Metagenomic Libraries by a DNA Microarray Approach / Gopal P. Pathak and Wolfgang Gärtner -- Application of DNA Microarray for Screening Metagenome Library Clones / Soo-Je Park, Jong-Chan Chae, and Sung-Keun Rhee -- MetaGenomeThreader: A Software Tool for Predicting Genes in DNA-Sequences of Metagenome Projects / David J. Schmitz-Hübsch and Stefan Kurtz.
  • 2011 Springer
    Nelson, Karen E.
    1.The human genome, microbiomes, and disease -- 2. Host genotype and the effect on microbial communities -- 3. The human microbiome and host-pathogen interactions -- 4. The human virome -- 5. Selection and sequencing of strains as references for human microbiome studies -- 6. The human vaginal microbiome -- 7. The human lung microbiome -- 8. The human skin microbiome in health and skin diseases -- 9. The human oral microbiome -- 10. Retraction: the human and his microbiome risk factors for infections -- 11. Retraction: infectogenomics: aspect of host responses to microbes in digestive tract -- 12. Autoimmune disease and human metagenome -- 13. Metagenomic applications and the potential for understanding chronic liver disease -- 14. Symbiotic gut microbiota and the modulation of human metabolic phenotypes -- 15. MetaHIT: the European Union project on metagenomics of the human intestinal tract -- 16. Implications of human microbiome research for the developing world -- Index.
  • 2006 NCBI Bookshelf
    Acid mine drainage biofilm -- Waseca County farm soil -- Whale fall community -- Methane-oxidizing archaea -- Human fecal virus -- Sargasso Sea marine microbial metagenome -- Human distal gut microbiome -- Enhanced biological phosphorus removal (EBPR) sludge community -- Mouse gut microbiota metagenome.
  • 2008 CRCnetBASE
    Stafford, Phillip.
    A comprehensive analysis of the effect of microarray data preprocessing methods on differentially expressed transcript selection -- Differentiation detection in microarray normalization -- Preprocessing and normalization for Affymetrix GeneChip expression microarrays -- Spatial detrending and normalization methods for two-channel DNA and protein microarray data -- A survey of cDNA microarray normalization and a comparison by k-NN classification -- Technical variation in modeling the joint expression of several genes -- Biological interpretation for microarray normalization selection -- Methodology of functional analysis for omics data normalization -- Exon array analysis for the detection of alternative splicing -- Normalization of array CGH data -- SNP array-based analysis for the detection of chromosomal aberrations and copy number variations.
    Also available: Print – 2008
  • 2009 Springer
    Pollack, Jonathan R.
    DNA microarray technology. Introduction / J.R. Pollack -- Comparative genomic hybridization on BAC arrays / B.P. Coe ... [et al.] -- Comparative genomic hybridization on spotted oligonucleotide microarrays / Y.H. Kim and J.R. Pollack -- Comparative genomic hybridization by representational oligonucleotide microarray analysis / R. Lucito and J. Byrnes -- Application of oligonucleotides arrays for coincident comparative genomic hybridization, ploidy status and loss of heterozygosity studies in human cancers / J.K. Cowell and K.C. Lo -- Molecular inversion probe assay for allelic quantitation / H. Ji and K. Welch -- A whole-genome amplification protocol for a wide variety of DNAs, including those from formalin-fixed and paraffin-embedded tissue / P.L. Paris -- Algorithms for calling gains and losses in array CGH data / P. Wang -- Methylation analysis by microarray / D.E. Deatherage ... [et al.] -- Methylation analysis by DNA immunoprecipitation (MeDIP) / E.A. Vucic ... [et al.] -- Combining chromatin immunoprecipitation and oligonucleotide tiling arrays (ChIP-Chip) for functional genomic studies / J. Eeckhoute, M. Lupien and M. Brown -- ChIP-Chip: algorithms for calling binding sites / X.S. Liu and C.A. Meyer -- Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip) / Y. Shibata and G.E. Crawford -- Microarray analysis of DNA replication timing / N. Karnani, C.M. Taylor and A. Dutta -- Integration of diverse microarray data types / K. Salari and J.R. Pollack.
    Also available: Print – 2009
  • 2007 Springer Protocols
    Korenberg, Michael J.
  • 2010 CRCnetBASE
    Fraser, Karl; Liu, Xiaohui; Wang, Zidong.
  • 2009 CRCnetBASE
    Matson, Robert S.
    Introduction to microarray technologies / Robert S. Matson -- Nucleic acid sample preparation / Robert S. Matson -- Solid-phase substrates for nucleic acid microarrays / Robert S. Matson -- Protein sample preparation for microarrays / Robert S. Matson -- Solid-phase chemistries for protein microarrays / Robert S. Matson -- Protein microarrays : the link between genomics and proteomics / Persis P. Wadia and David B. Miklos -- Bead arrays : an introduction to multiplexed bead-based assays for proteins / Yong Song -- Carbohydrate arrays / Denong Wang -- Lectin microarrays / Masao Yamada -- Printing methods / Todd Martinsky.
  • 2006 Springer
    Mocellin, Simone.
    Manufacturing of microarrays -- Technological platforms for microarray gene expression profiling -- Principles of gene microarray data analysis -- Gaining weights ... and feeling good about it! -- Complementary techniques -- Microarrays for cancer diagnosis and classification -- Gene profiling for the prediction of tumor response to treatment: the case of immunotherapy -- Identification of molecular determinants of tumor sensitivity and resistance to anticancer drugs -- SNP and mutation analysis -- Cancer development and progression -- Gene expression profiling in malignant lymphomas -- Tumor immunology.
    Also available: Print – 2006
  • v. 1-2, 2007. Springer Protocols
    v.2, 2009 Springer Protocols
    Rampal, Jang B.
    v. 1. Synthesis methods -- v. 2. Applications and data analysis.
  • 2008 Springer Protocols
    Gerdes, Svetlana Y.; Osterman, Andrei L.
    Overview of whole-genome essentiality analysis / Karen Joy Shaw -- Pt. I. Experimental protocols. IA. Populational genome-wide essentiality screens. Transposon-based strategies for the identification of essential bacterial genes / William S. Reznikoff and Kelly M. Winterberg -- Identification and analysis of essential genes in Haemophilus influenzae / Sandy M.S. Wong and Brian J. Akerley -- Transposon site hybridization in Mycobacterium tuberculosis / Jeffrey P. Murry ... [et al.] -- Essential genes in the infection model of Pseudomonas aeruginosa PCR-based signature-tagged mutagenesis / François Sanschagrin, Irena Kukavica-Ibrulj, and Roger C. Levesque -- Whole-genome detection of conditionally essential and dispensable genes in Escherichia coli via genetic footprinting / Michael D. Scholle and Svetlana Y. Gerdes -- Generating a collection of insertion mutations in the Staphylococcus aureus genome using bursa aurealis / Taeok Bae ... [et al.] -- Multipurpose transposon insertion libraries for large-scale analysis of gene function in yeast / Anuj Kumar -- IB. Systematic collections of knockout mutants. How to make a defined near-saturation mutant library. Case 1: Pseudomonas aeruginosa PAO1 / Michael A. Jacobs -- Comparing insertion libraries in two Pseudomonas aeruginosa strains to assess gene essentiality / Nicole T. Liberati ... [et al.] -- The construction of systematic in-frame, single-gene knockout mutant collection in Escherichia coli K-12 / Tomoya Baba and Hirotada Mori -- The applications of systematic in-frame, single-gene knockout mutant collection of Escherichia coli K-12 / Tomoya Baba ... [et al.] -- A novel, simple, high-throughput method for isolation of genome-wide transposon insertion mutants of Escherichia coli K-12 / Takeyoshi Miki, Yoshihiro Yamamoto, and Hideo Matsuda -- High-throughput creation of a whole-genome collection of yeast knockout strains / Angela M. Chu and Ronald W. Davis -- Analysis of genetic interactions on a genome-wide scale in budding yeast: diploid-based synthetic lethality analysis by microarray / Pamela B. Meluh ... [et al.] -- IC. Genome minimization. Scarless engineering of the Escherichia coli genome / Tamás Fehér ... [et al.] -- Minimization of the Escherichia coli genome using the Tn5-targeted Cre/loxP excision system / Byung Jo Yu and Sun Chang Kim -- Construction of long chromosomal deletion mutants of Escherichia coli and minimization of the genome / Jun-ichi Kato and Masayuki Hashimoto -- ID. Conditional knockouts. Identification of essential genes in Staphylococcus aureus by construction and screening of conditional mutant library / Dezhong Yin and Yinduo Ji -- Techniques for the isolation and use of conditionally expressed antisense RNA to achieve essential gene knockdowns in Staphylococcus aureus / Allyn Forsyth and Liangsu Wang -- Introduction of conditional lethal amber mutations in Escherichia coli / Christopher D. Herring -- Pt. II. Bioinformatics. IIA. Statistics. Statistical methods for building random transposon mutagenesis libraries / Oliver Will -- Statistical evaluation of genetic footprinting data / Gábor Balázsi -- Modeling competitive outgrowth of mutant populations : why do essentiality screens yield divergent results? / Alexander I. Grenov and Svetlana Y. Gerdes -- Statistical analysis of fitness data determined by TAG hybridization on microarrays / Brian D. Peyser, Rafael Irizarry, and Forrest A. Spencer -- IIB. Data integration and modeling. Profiling of Escherichia coli chromosome database / Yukiko Yamazaki, Hironori Niki, and Jun-ichi Kato -- Gene essentiality analysis based on DEG, a database of essential genes / Chun-Ting Zhang and Ren Zhang -- Detection of essential genes in Streptococcus pneumoniae using bioinformatics and allelic replacement mutagenesis / Jae-Hoon Song and Kwan Soo Ko -- Design and application of genome-scale reconstructed metabolic models / Isabel Rocha, Jochen Förster, and Jens Nielsen -- Predicting gene essentiality using genome-scale in silico models / Andrew R. Joyce and Bernhard Ø. Palsson -- Comparative approach to analysis of gene essentiality / Andrei L. Osterman and Svetlana Y. Gerdes.
  • 2003 CRCnetBASE
    Dougherty, Thomas J.; Projan, Steven J.
    Also available: Print – 2003
  • 2009. Karger
    Bereswill, Stefan; Reuse, Hilde de.
    Genome comparison of bacterial pathogens / Wassenaar, T.M. ... [et al.] -- In silico reconstruction of the metabolic and pathogenic potential of bacterial genomes using subsystems / McNeil, L.K., Aziz, R.K. -- The bacterial pan-genome and reverse vaccinology / Tettelin, H. -- 'Guilty by association' : protein-protein interactions (PPIS) in bacterial pathogens / Schauer, K., Stingl, K -- Helicobacter pylori sequences reflect past human migrations / Moodley, Y., Linz, B. -- Helicobacter pylori genome plasticity / Baltrus, D.A., Blaser, M.A., Guillemin, K. -- Genomics of Thermophilic campylobacter species / Gaskin, D.J.H. ... [et al.] -- Adaptation of pathogenic E. coli to various niches : genome flexibility is the key / Brzuszkiewicz, E. ... [et al.] -- Role of horizontal gene transfer in the evolution of Pseudomonas aeruginosa virulence / Qiu, X., Kulasekara, B.R., Lory, S. -- The genus Burkholderia : analysis of 56 genomic sequences / Ussery, D.W. ... [et al.] -- Genomics of host-restricted pathogens of the genus Bartonella / Engel, P., Dehio, C. -- Legionella pneumophila - host interactions : insights gained from comparative genomics and cell biology / Lomma, M. ... [et al.] -- A proteomics view of virulence factors of Staphylococcus aureus / Engelmann, S., Hecker, M. -- Pathogenomics of mycobacteria / Gutierrez, M.C., Supply, P., Brosch, R.
  • 2006 Wiley
    Hecker, M.; Humphery-Smith, Ian.
    "Discover important lessons learned about whole organism biology via microbial proteomics This text provides an exhaustive analysis and presentation of current research in the field of microbial proteomics, with an emphasis on new developments and applications and future directions in research. The editors and authors show how and why the relative simplicity of microbes has made them attractive targets for extensive experimental manipulation in a quest for both improved disease prevention and treatment and an improved understanding of whole organism functional biology. In particular, the text demonstrates how microbial proteomic analyses can aid in drug discovery, including identification of new targets, novel diagnostic markers, and lead optimization. Each chapter is written by one or more leading experts in the field and carefully edited to ensure a consistent and thorough approach throughout. Methods, technologies, and tools associated with the most promising approaches are stressed."--Publisher's website.
    Also available: Print – 2006
  • 2011 Springer Protocols
    Wu, Wei.
    MicroRNA Biogenesis and Cancer / Julia Winter, Sven Diederichs -- Computational Identification of miRNAs Involved in Cancer / Anastasis Oulas, Nestoras Karathanasis, Panayiota Poirazi -- The Principles of MiRNA-Masking Antisense Oligonucleotides Technology / Zhiguo Wang -- The Concept of Multiple-Target Anti-miRNA Antisense Oligonucleotide Technology / Zhiguo Wang -- Modulation of MicroRNAs for Potential Cancer Therapeutics / Wei Wu -- Detection of MicroRNAs in Cultured Cells and Paraffin-Embedded Tissue Specimens by In Situ Hybridization / Ashim Gupta, Yin-Yuan Mo -- MicroRNA Northern Blotting, Precursor Cloning, and Ago2-Improved RNA Interference / Julia Winter, Sven Diederichs -- miRNA Profiling on High-Throughput OpenArray System / Elena V. Grigorenko, Elen Ortenberg, James Hurley, Andrew Bond, Kevin Munnelly -- Silicon Nanowire Biosensor for Ultrasensitive and Label-Free Direct Detection of miRNAs / Guo-Jun Zhang -- High-Throughput and Reliable Protocols for Animal MicroRNA Library Cloning / Caide Xiao -- MicroRNA Regulation of Growth Factor Receptor Signaling in Human Cancer Cells / Keith M. Giles, Andrew Barker, Priscilla M. Zhang, Michael R. Epis, Peter J. Leedman -- Epigenetic Regulation of MicroRNA Expression in Cancer / Hani Choudhry, James W. Catto -- In Vitro Functional Study of miR-126 in Leukemia / Zejuan Li, Jianjun Chen -- Prediction of the Biological Effect of Polymorphisms Within MicroRNA Binding Sites / Debora Landi, Roberto Barale, Federica Gemignani, Stefano Landi -- The Guideline of the Design and Validation of MiRNA Mimics / Zhiguo Wang -- Analysis of Targets and Functions Coregulated by MicroRNAs / Shu-Jen Chen, Hua-Chien Chen -- Utilization of SSCprofiler to Predict a New miRNA Gene / Anastasis Oulas, Panayiota Poirazi -- MicroRNA Profiling Using Fluorescence-Labeled Beads: Data Acquisition and Processing / Thomas Streichert, Benjamin Otto, Ulrich Lehmann.
  • 2015 Springer
    Santulli, Gaetano.
    microRNAs in the malignant transformation process / Anne E. Sarver, Lihua Li, Reena V. Kartha, Subbaya Subramanian -- microRNA and chronic lymphocytic leukemia / Dana Elena Giza, George A. Calin -- microRNA in malignant lymphoma / Hiroyuki Tagawa -- MicroRNAs and gastrointestinal stromal tumor / Pinar Akçakaya, Weng-Onn Lui -- Insights into the role of microRNAs in pancreatic cancer pathogenesis: potential for diagnosis, prognosis, and therapy / Mohammad Aslam Khan [and others] -- microRNAs and colorectal cancer / Anna Lena Ress, Samantha Perakis, Martin Pichler -- microRNAs and prostate cancer / Sajni Josson, Leland W. K. Chung, Murali Gururajan -- microRNA and ovarian cancer / Ream Langhe -- microRNA and lung cancer / Valerio Del Vescovo, Michela A. Denti -- microRNAs and soft tissue sarcomas / Tomohiro Fujiwara, Toshiyuki Kunisada, Ken Takeda, Toshifumi Ozaki -- microRNA and bone cancer / Mary Nugent.
    Also available: Print – 2015
  • 2015 Springer
    Santulli, Gaetano.
    Exploiting microRNA specificity and selectivity: paving a sustainable path towards precision medicine / Gaetano Santulli -- microRNAs and personalized medicine: evaluating their potential as cancer biomarkers / Anne Saumet and Charles-Henri Lecellier -- microRNA and pain / Atsushi Sakai and Hidenori Suzuki -- microRNA and epilepsy / Cristina R. Reschke and David C. Henshall -- microRNA and autism / Ayyappan Anitha and Ismail Thanseem -- microRNAs and neurogenerative diseases / Lifeng Qiu, Eng King Tan, and Li Zeng -- microRNAs and Fragile X Syndrome / Shi-Lung Lin -- The emerging role of mitomiRs in the pathophysiology of human disease / Filipe V. Duarte, Carlos M. Palmeira, and Anabela P. Rolo -- microRNAs in cerebrovascualar disease / Ondřej Volný, Linda Kašičková, Dominika Coufalová, Petra Cimflová, and Jan Novák -- microRNAs and cardiovascular remodeling / Koh Ono -- microRNAs in essential hypertension and blood pressure regulation / Francine Z. Marques and Fadi J. Charchar -- microRNA and pulmonary hypertension / Olivier Boucherat, François Potus, and Sébastien Bonnet -- microRNAs in diabetic kidney disease / Arthur C.K. Chung -- microRNA and kidney transplantation / Kíra Jelencsics and Rainer Oberbauer -- microRNA and wound healing / Jaideep Banerjee and Chandan K. Sen -- Essential role of microRNA in skin physiology and disease / Damjan Glavač and Metka Ravnik-Glavač -- microRNA and allergy / Ana Rebane -- microRNA in human reproduction / Iris Eisenberg, Noora Kotaja, Debra Goldman-Wohl, and Tal Imbar -- microRNAs and hepatitis B / Yutaka Naito, Yasuhito Tanaka, and Takahiro Ochiya -- Circulating microRNAs: the future of biomarkers in anti-doping field / Nicolas Leuenberger and Martial Saugy -- microRNA expression profiling: technologies, insights, and prospects / Christine Roden, Stephen Mastriano, Nayi Wang, and Jun Lu.
    Also available: Print – 2015
  • 2007 ScienceDirect
    Hannon, Gregory J.; Rossi, John J.
    Also available: Print – 2007
  • 2012 Springer Protocols
    Ying, Shao-Yao.
    MicroRNA / Shao-Yao Ying, Donald C. Chang, and Shi-Lung Lin -- Analysis of MicroRNA length variety generated by recombinant human dicer / Julia Starega-Roslan and Wlodzimierz J. Krzyzosiak -- User-friendly computational workflow for the analysis of MicroRNA deep sequencing data / Anna Majer, Kyle A. Caligiuri, and Stephanie A. Booth -- RNA gene information : retroelement-MicroRNA entangling as the RNA quantum code / Yoichi Robertus Fujii -- Setting up an intronic miRNA database / Ludwig Christian Hinske [and others] -- Identify intronic MicroRNA with bioinformatics / Chih-Hao Kuo [and others] -- Experimental miRNA target validation / Jens Heyn [and others] -- Enrichment analysis of miRNA targets / Jianzhen Xu and Chi-Wai Wong -- MicroRNA expression profiling during neural differentiation of mouse embryonic carcinoma P19 cells / Botao Zhao [and others] -- Evaluating the MicroRNA targeting sites by luciferase reporter gene assay / Yi Jin [and others] -- Expression pattern analysis of MicroRNAs in Caenorhabditis elegans / Meltem Isik and Eugene Berezikov -- Use of viral systems to study miRNA-mediated regulation of gene expression in human cells / Eleonora Forte and Micah A. Luftig -- Cloning, expression, and functional analysis of genomic miRNA using retroviral system in cancer cells / Abdol Hossein Rezaeian, Yuan Gao, and Hui-Kuan Lin -- Preparing synaptoneurosomes from adult mouse forebrain / Giovanni Lugli and Neil R. Smalheiser -- Isolation of total RNA and detection procedures for miRNA present in bovine-cultured adipocytes and adipose tissues / Scott L. Pratt [and others] -- miRNA and shRNA expression vectors based on mRNA and miRNA processing / Ping Wu [and others] -- Gene silencing in vitro and in vivo using intronic MicroRNAs / Shi-Lung Lin and Shao-Yao Ying -- Vector-free methods for manipulating miRNA activity in vitro and in vivo / Angeliki Pantazi and Athanasios Zovoilis -- MicroRNA expression profiling of human-induced pluripotent and embryonic stem cells / Amit Sharma and Joseph C. Wu -- MicroRNA expression during neuronal differentiation of human teratocarcinoma NTera2D1 and mouse embryonic carcinoma P19 cells / Hirohiko Hohjoh -- Isolation and identification of gene-specific MicroRNAs / Shi-Lung Lin, Donald C. Chang, and Shao-Yao Ying -- Transgene-like animal models using intronic MicroRNAs / Shi-Lung Lin, Shin-Ju E. Chang, and Shao-Yao Ying -- Mechanism and method for generating tumor-free iPS cells using intronic MicroRNA miR-302 induction / Shi-Lung Lin and Shao-Yao Ying -- Salivary MicroRNAs and oral cancer detection / Janice M. Yoshizawa and David T.W. Wong -- Application of intronic MicroRNA agents in cosmetics / Jack S.K. Chen and David T.S. Wu -- MicroRNAs in skin and wound healing / Jaideep Banerjee and Chandan K. Sen -- MiRNA targets of prostate cancer / Jia Han Deng [and others].
  • 2006 Springer Protocols
    Ying, Shao-Yao.
  • 2010 Springer Protocols
    Monticelli, Silvia.
    A rapid, quantitative assay for direct detection of microRNAs and other small RNAs using splinted ligation -- Normalization of microRNA quantitative RT-PCR data in reduced scale experimental designs -- MicroRNA detection in bone marrow cells by LNA-FISH -- Measuring microRNA expression in size-limited facs-sorted and microdissected samples -- MicroRNA cloning from cells of the immune system -- High-throughput profiling in the hematopoietic system -- Construction of small RNA cDNA libraries for deep sequencing -- MicroRNA-profiling in formalin-fixed paraffin-embedded specimens -- Expression of miRNAs in lymphocytes : A review -- Mouse models for miRNA expression: The ROSA26 locus -- Regulation of monocytopoiesis by microRNAs -- MicroRNA activity in B lymphocytes -- Isolation and characterization of microRNAs of human mature erythrocytes -- Stable overexpression of miRNAs in bone marrow-derived murine mast cells using lentiviral expression vectors -- Monitoring microRNA activity and validating microRNA targets by reporter-based approaches -- Lentivirus-mediated antagomir expression -- Solution structure of miRNA:mRNA complex -- MiRNA editing -- Computational prediction of microRNA targets -- Large-scale integration of microRNA and gene expression data for identification of enriched microRNA-mRNA associations in biological systems -- Identification and validation of the cellular targets of virus-encoded microRNAs.
  • 2011 Springer
    Cho, William C. S.
    1 -- MicroRNAs in Cancer (An Overview) -- 2. The Role of MicroRNAs in Lung Cancer Development, Progression, and Metastasis -- 3. MicroRNAs in Breast Cancer -- 4. MicroRNAs in Colorectal Cancer -- 5. MicroRNAs in Gastric Cancer -- 6. MicroRNAs in Prostate Cancer: A Possible Role as Novel Biomarkers and Therapeutic Targets?- 7. MicroRNAs in Hepatocellular Carcinoma -- 8. MicroRNAs in Cervical Carcinoma -- 9. MicroRNAs in Esophageal Cancer -- 10. MicroRNAs in Bladder Cancer -- 11. MicroRNAs in Lymphoma -- 12. MicroRNAs in Leukemia -- 13. MicroRNAs in Pancreatic Cancer: Potential Interests as Biomarkers and Therapeutic Tools -- 14. MicroRNAs in Epithelial Ovarian Cancer -- 15. MicroRNAs in Brain Tumors -- 16. MicroRNAs and Cancer Stem Cells -- 17. MicroRNAs in Cancer Invasion and Metastasis -- 18. MicroRNAs in Predicting Radiotherapy and Chemotherapy Response -- 19. Role of MicroRNAs in Anti-cancer Drug Resistance -- 20. MicroRNAs and Cancer Metabolism -- 21. MicroRNAs as Blood-based Biomarkers of Cancer -- 22. RNAi-based Approaches to the Treatment of Brain Tumors.
  • 2011 Springer Protocols
    Dalmay, Tamas.
    In situ detection of microRNAs in animals / Dylan Sweetman -- Detection of microRNAs in plants by in situ hybridisation / Eva Varallyay and Zoltan Havelda -- Detecting sRNAs by northern blotting / Sara Lopez-Gomollon -- Profiling microRNAs by real-time PCR / Nanna Jacobsen, Ditte Andreasen, and Peter Mouritzen -- Detection of small RNAs and microRNAs using deep sequencing technology / Ericka R. Havecker -- Detection of microRNAs in prostate cancer cells by mircoRNA array / Xiaoqing Tang [and others] -- MicroRNA knock down by cholesterol-conjugated antisence oligos in mouse organ culture / Sharon Kredo-Russo and Eran Hornstein -- Protocols for use of homologous recombination gene targeting to produce microRNA mutants in drosophila / Ya-Wen Chen, Ruifen Weng, and Stephen M. Cohen -- Engineering elements for gene silencing : the artificial microRNAs technology / Pablo Andres Manavella and Ignacio Rubio-Somoza -- Mimicry technology : suppressing small RNA activity in plants / Ignacio Rubio-Somoza and Pablo Andres Manavella -- Experimental validation of microRNA targets using a luciferase reporter system / Francisco E. Nicolas -- Experimental identification of microRNA targets by immunoprecipitation of argonaute protein complexes / Michaela Beitzinger and Gunter Meister -- Comprehensive identification of miRNA target sites in live animals / Dimitrios G. Zisoulis, Gene W. Yeo, and Amy E. Pasquinelli -- Target validation of plant microRNAs / Cesar Llave [and others] -- High-throughput sequencing-based methodology to identify all uncapped and cleaved RNA molecules in eukaryotic genomes / Matthew W. Endres, Rebecca T. Cook, and Brian D. Gregory.
  • 2013 Springer Protocols
    Kantartzi, Stella K.
    Microsatellites or simple sequence repeats (SSRs) have become the markers of choice for a variety of molecular studies because of their versatility, operational flexibility, and lower cost than other marker systems. Microsatellites: Methods and Protocols brings together experts in the field to cover this significant area of research. Broken in to four convenient parts, this volume delves into classical and modern methods for the discovery and development of microsatellite markers, descriptions of amplification and visualization of SSRs, automated capillary sequencers that are widely used for fragment analysis, as well as a variety of methods for the analysis of data obtained by the use of microsatellites. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and invaluable, Microsatellites: Methods and Protocols aims at researchers that need detailed protocols for incorporating microsatellite markers into their projects and expert scientists looking to expand their knowledge of SSRs discovery, use, and analysis.
  • 2014 Springer Protocols
    Arenz, Christoph.
    Part I. Reviews -- Pathway of miRNA maturation / Michael Sand -- MicroRNA maturation and human disease / Marlen Hesse and Christoph Arenz -- Approaches to the modulation of miRNA maturation / Valerie T. Tripp, Jaclyn R. McKenna, and Douglas D. Young -- Part II. Methods -- Expression profiling of components of the miRNA maturation machinery / Michael Sand and Marina Skrygan -- Primary MicroRNA processing assay reconstituted using recombinant Drosha and DGCR8 / Ian Barr and Feng Guo -- In vivo processing assay based on a dual-luciferase reporter system to evaluate DROSHA enzymatic activity / Vera Bilan, Danilo Allegra, Florian Kuchenbauer, and Daniel Mertens -- Assaying dicer-mediated miRNA maturation by means of fluorescent substrates / Marlen Hesse, Brian P. Davies, and Christoph Arenz -- Fluorescence correlation spectroscopy-based enzyme assay for human dicer / Eileen Magbanua and Ulrich Hahn -- Detection of microRNA maturation using unmodified pre-microRNA and branched rolling circle amplification / Saskia Neubacher and Christoph Arenz -- Quantitative RT-PCR specific for precursor and mature miRNAs / Hannah Zöllner, Stephan A. Hahn, and Abdelouahid Maghnouj -- Cellular microRNA sensors based on luciferase reporters / Colleen M. Connelly and Alexander Deiters -- Identification of inhibitors of microRNA function from small molecule screens / Colleen M. Connelly and Alexander Deiters -- Inhibition of miRNA maturation by peptide nucleic acids / Concetta Avitabile, Enrica Fabbri, Nicoletta Bianchi, Roberto Gambari, and Alessandra Romanelli -- Molecular methods for validation of the biological activity of peptide nucleic acids targeting microRNAs / Eleonora Brognara, Enrica Fabbri, Nicoletta Bianchi, Alessia Finotti, Roberto Corradini, and Roberto Gambari -- Lentiviral overexpression of miRNAs / Hannah Zöllner, Stephan A. Hahn, and Abdelouahid Maghnouj.
  • 2009 Springer Protocols
    Stuart, Jeffrey A.
    Biochemical isolation of mtDNA nucleoids from animal cells / D.F. Bogenhagen -- Analysis of mitochondrial DNA by two-dimensional agarose gel electrophoresis / A. Reyes [and others] -- Comparative purification strategies for Drosophila and human mitochondrial DNA replication proteins: DNA polymerase gamma and mitochondrial single-stranded DNA-binding protein / M.T. Oliveira and L.S. Kaguni -- Functional analysis of mutant mitochondrial DNA polymerase proteins involved in human disease / S.S. Chan and W.C. Copeland -- Preparation of human mitochondrial single-stranded DNA-binding protein / M.J. Longley, L.A. Smith and W.C. Copeland -- Methods for assessing binding of mitochondrial transcription factor A (TFAM) to DNA / A. Fukuoh and D. Kang -- Inducible expression in human cells, purification, and in vitro assays for the mitochondrial DNA helicase Twinkle / S. Goffart and H. Spelbrink -- Purification strategy for recombinant forms of the human mitochondrial DNA helicase / T.D. Ziebarth and L.S. Kaguni -- Methods for studying mitochondrial transcription termination with isolated components / P.L. Polosa [and others] -- Oxidative phosphorylation: synthesis of mitochondrially encoded proteins and assembly of individual structural subunits into functional holoenzyme complexes / S.C. Leary and F. Sasarman -- Reactive oxygen species production by mitochondria / A.J. Lambert and M.D. Brand -- Measuring mtDNA damage using a supercoiling-sensitive qPCR approach / S.W. Chan and J.Z. Chen -- Quantitative analysis of oxidized guanine, 8-oxoguanine, in mitochondrial DNA by immunofluorescence method / M. Ohno, S. Oka and Y. Nakabeppu -- In vitro measurement of DNA base excision repair in isolated mitochondria / M.M. Page and J.A. Stuart -- Targeting repair proteins to the mitochondria of mammalian cells through stable transfection, transient transfection, viral transduction, and TAT-mediated protein transduction / C.A. Koczor [and others] -- Construction and characterization of a cell line deficient in repair of mitochondrial, but not nuclear, oxidative DNA damage / S. Oka, M. Ohno and Y. Nakabeppu -- Mitochondrial DNA oxidative damage and mutagenesis in Saccharomyces cerevisiae / L.M. Griffiths [and others] -- Determination of DNA mutation load in human tissues using denaturing HPLC-based heteroduplex analysis / K.S. Lim, R.K. Naviaux and R.H. Haas -- Rapid identification of unknown heteroplasmic mitochondrial DNA mutations with mismatch-specific surveyor nuclease / S. Bannwarth, V. Procaccio and V. Paquis-Flucklinger -- Collection of isolated cells for studying mitochondrial DNA mutations within individual cells / Y. Kraytsberg [and others] -- Quantitative analysis of somatic mitochondrial DNA mutations by single-cell single-molecule PCR / Y. Kraytsberg [and others] -- Measuring DNA precursor pools in mitochondria / C.K. Mathews and L.J. Wheeler -- Establishment of human cell lines lacking mitochondrial DNA / K. Hashiguchi and Q.M. Zhang-Akiyama.
  • 2016 Springer Protocols
    McKenzie, Matthew.
    Part I. Detection of mitochondrial DNA mutations and mitochondrial DNA damage -- Part II. Visualization of mitochondrial DNA and mitochondrial DNA nucleoids -- Part III. Analysis of mitochondrial DNA replication, mitochondrial DNA-encoded protein translation and mitochondrial DNA copy number -- Part IV. Modification of mitochondrial DNA -- Part V. Purification of proteins involved in mitochondrial DNA replication and transcription -- Index.
  • 2010 Springer
    Dakubo, Gabriel D.
    1. Basic mitochondrial genetics, bioenergetics, and biogenesis -- 2. The Warburg phenomenon and other metabolic alterations of cancer cells -- 3. Mitochondrial control of apoptosis and cancer -- 4. Mitochondrial-to-nuclear communications in cancer -- 5. Types of mitochondrial genetic alterations in cancer -- 6. Mitochondrial genetic alterations in cancer I: skin, head and neck, salivary glands, thyroid, breast, lung, esophageal, gastric, colorectal, pancreatic, liver and gallbladder cancers -- 7. Mitochondrial genetic alterations in cancer II: renal, urinary bladder, prostate, ovarian, endometrial, cervical, nervous system, hemoatologic and connective tissue cancers -- 8. Mitochondrial genome rearrangement and copy number changes in cancer -- 9. Functional importance of mitochondrial genetic alterations in cancer -- 10. The role of mitochondrial reactive oxygen species in cancer -- 11. Mitochondrial DNA measurement in exfoliated cells for cancer detection and monitoring: the copy number advantage -- 12. Early cancer detection and monitoring using changes in the mitochondrial genome as biosensors -- 13. Analysis of mitochondrial genome alterations in cancer -- 14. "Mitocans": agents targeting mitochondria to kill cancer cells -- Index.
  • 2012 Springer Protocols
    Bigot, Yves.
    Transposable elements as tools for reshaping the genome : it is a huge world after all! / Solenne Bire and Florence Rouleaux-Bonnin -- Using and understanding RepeatMasker / Sébastien Tempel -- Roadmap for annotating transposable elements in eukaryote genomes / Emmanuelle Permal, Timothée Flutre, and Hadi Quesneville -- To detect and analyze sequence repeats whatever be their origin / Jacques Nicolas -- Exploring bacterial insertion sequences with ISfinder : objectives, uses, and future developments / P. Siguier [and others] -- Methods and software in NGS for TE analysis / Cristian Chaparro and Francois Sabot -- The application of LTR retrotransposons as molecular markers in plants / Alan H. Schulman [and others] -- Individual analysis of transposon polymorphisms by AFLP / Susanta K. Behura -- Construction of a library of random mutants in the spirochete Leptospira biflexa using a mariner transposon / Leyla Slamti and Mathieu Picardeau -- Ac-Ds solutions for rice insertion mutagenesis / Emmanuel Guiderdoni and Pascal Gantet -- Engineering the Caenorhabditis elegans genome by Mos1-induced transgene-instructed gene conversion / Valérie J.P. Robert -- Genome-wide manipulations of Drosophila melanogaster with transposons, Flp recombinase, and [phi]C31 integrase / Koen J.T. Venken and Hugo J. Bellen -- The Sleeping Beauty transposon toolbox / Ismahen Ammar, Zsuzsanna Izsvák, and Zoltán Ivics -- PiggyBac toolbox / Mario Di Matteo [and others] -- Insertion site pattern : global approach by linear amplification-mediated PCR and mass sequencing / Cynthia C. Bartholomae [and others] -- Comprehensive DNA methylation profiling of human repetitive DNA elements using an MeDIP-on-RepArray assay / Eric Gilson and Béatrice Hovard -- Novel approach for the development of new antibodies directed against transposase-derived proteins encoded by human neogenes / Ahmed Arnaoty [and others].
  • 2008 Springer
    Frishman, Dmitrij; Valencia, Alfonso.
  • 2013 ClinicalKey
    Clark, David P.; Pazdernik, Nanette Jean.
    Unit 1. Basic Chemical and Biological Principles -- Unit 2. The Genome -- Unit 3. The Central Dogma of Molecular Biology -- Unit 4. Regulating Gene Expression -- Unit 5. Subcellular Life Forms -- Unit 6. Changing the DNA Blueprint.
  • 2002 Springer Protocols
    Fan, Yao-Shan.
  • 2005 Springer
    Viljoen, Gerrit J.; Crowther, John R.; Nel, L. H.
  • 2014 Springer
    Highsmith, W. Edward.
    Molecular Diagnostics: 12 Tests That Changed Everything focuses on specific laboratory tests and emphasizes how the availability of these tests has altered how clinicians treat their patients. Presented as a standard outline, each chapter focuses on a specific molecular test and provides background on the test and its clinical applications. Continuing with some discussion on how the test is done, interpreted, and used clinically, each chapter then concludes with a discussion of how that test has changed the way medicine is practiced with respect to the disease or condition in question. Authored by renowned experts in the field, Molecular Diagnostics: 12 Tests That Changed Everything is a valuable resource for pathologists, pathology residents, laboratory directors, development personnel, lab medicine fellows and those working in the broad area of oncology, infectious disease and genetics.
  • 2013 Springer
    Kango-Singh, Madhuri; Singh, Amit.
    Undoubtedly, Drosophila melanogaster, fruit fly, has proven to be one of the most popular invertebrate model organisms, and the work horse for modern day biologists. Drosophila, a highly versatile model with a genetic legacy of more than a century, provides powerful genetic, cellular, biochemical and molecular biology tools to address many questions extending from basic biology to human diseases. One of the most important questions in biology focuses on: how does a multi-cellular organism develop from a single-celled embryo? The discovery of the genes responsible for pattern formation has helped refine this question. Drosophila eye model has been extensively used to study molecular genetic mechanisms involved in patterning and growth. Since the genetic machinery involved in the Drosophila eye is similar to humans, it has been used to model human diseases and homology to eyes in other taxa. This book will discuss molecular genetic mechanisms of pattern formation, axial patterning, growth regulation in Drosophila eye, and more.
  • 2013 Springer
    D'Amato, Mauro; Rioux, John D.
    Inflammatory bowel disease (IBD) affects 1% of people worldwide. This condition is partly inherited, and genetic research has made enormous progress during the last few years, providing important insight into disease pathogenesis. This book provides a concise but complete overview of existing knowledge, with particular focus on the molecular and genetic mechanisms at the basis of IBD. Invited experts, at the frontline of IBD research, introduce basic concepts in the pathophysiology of IBD and its two major forms Crohn?s disease and ulcerative colitis, provide a historical perspective and highlight latest discoveries of IBD genetic research, describe how this information has helped to unravel novel pathogenetic pathways, and formulate a vision for future investigations and their clinical application in IBD. State-of-the-art information contained in this book is an exceptional resource for all those in the biomedical field with a specific interest in IBD, including basic scientists, gastroenterologists, GI specialist doctors and research nurses, but also medical and biomedical students.
  • 1987 ScienceDirect
    Gottesman, Michael M.
    Also available: Print – 1987
  • 2007 Springer
    Aguilera, Andrés; Rothstein, Rodney.
    Also available: Print – 2007
  • 2005 Springer
    Amendt, Brad A.
    Identification of the gene involved in 4q25-linked Axenfeld-Rieger syndrome, PITX2 / Elena V. Semina -- Winged helix/forkhead transcription factors and Rieger syndrome / Darryl Y. Nishimura and Ruth E. Swiderski -- Rieger syndrome and PAX6 deletion / Ruth Riise -- The molecular and biochemical basis of Axenfeld-Rieger syndrome / Brad A. Amendt -- Role of PITX2 in the pituitary gland / Hoonkyo Suh ... [et al.] -- Expression and function of PITX2 in chick heart looping / Xueyan Yu, Shusheng Wang, and YiPing Chen -- The multiple roles of PITX2 in heart development / James F. Martin -- The role of PITX2 in tooth development / Brad A. Amendt -- PITX genes and ocular development / Elena V. Semina -- An overview of Axenfeld-Rieger syndrome and the anterior segment developmental disorders / Brad A. Amendt.
  • 2011 Springer Protocols
    Orgogozo, Virginie; Rockman, Matthew V.
    Characterizing the genome. Genome size determination using flow cytometry of propidium iodide-stained nuclei / Emily E. Hare and J. Spencer Johnston. Chromosome analysis in invertebrates and vertebrates / David M. Rowell, Shu Ly Lim, and Frank Grutzner. Genomic libraries : I. Constuction and screening of fosmid genomic libraries / Mike A. Quail [and others] Genomic libraries : II. Subcloning, sequencing, and assembling large-insert genomic DNA clones / Mike A. Quail [and others] -- Targeting regions of the genome. Reduced representation methods for subgenomic enrichment and next-generation sequencing / Jeffrey M. Good. Accessing the transcriptome : how to normalize mRNA pools / Heiko Vogel and Christopher W. Wheat. Transcriptome sequencing goals, assembly, and assessment / Christopher W. Wheat and Heiko Vogel. Rapid retrieval of DNA target sequences by primer extension capture / Adrian W. Briggs -- Measuring genetic diversity. SNP discovery and genotyping for evolutionary genetics using RAD sequencing / Paul D. Etter [and others] DNA microarray-based mutation discovery and genotyping / David Gresham. Genotyping with Sequenom / Martina Bradić, João Costa, and Ivo M. Chelo. Isolating microsatellite loci : looking back, looking ahead / José A. Andrés and Steven M. Bogdanowicz. Design of custom oligonucleotide microarrays for single species or interspecies hybrids using array olico selector / Amy A. Caudy -- Obtaining candidate gene sequences. Identification of homologous gene sequences by PCR with degenerate primers / Michael Lang and Virginie Orgogozo -- Characterizing cDNA ends by circular RACE / Patrick T. McGrath. Identification of DNA sequences that flank a known region by inverse PCR / Anastasios Pavlopoulos -- Analyzing candidate gene transcripts. Quantification of transcript levels with quantitative RT-PCR / Karen L. Carleton. Using pyrosequencing to measure allele-specific mRNA abundance and infer the effects of cis- and trans-regulatory differences / Patricia J. Wittkopp. Whole-mount in situ hybridization of sectioned tissues of species hybrids to detect cis-regulatory changes in gene expression pattern / Ryo Futahashi. Identifying fluorescently labeled single molecules in image stacks using machine learning / Scott A. Rifkin -- Testing candidate genes and candidate mutations. Experimental approaches to evaluate the contributions of candidate cis-regulatory mutations to phenotypic evolution / Mark Rebeiz and Thomas M. Williams. Experimental approaches to evaluate the contributions of candidate protein-coding mutations to pheotypic evolution / Jay F. Storz and Anthony J. Zera. Making reporter gene constructs to analyze cis-regulatory elements / José Bessa and José Luis Gómez-Skarmeta. PCR directed in vivo plasmid construction using homologous recombination in baker's yeast / Erik C. Andersen. Production of fosmid genomic libraries optimized for liquid culture recombineering and cross-species transgenesis / Radoslaw Kamil Ejsmont [and others] Recombination-mediated genetic engineering of large genomic DNA transgenes / Radoslaw Kamil Ejsmont [and others] Overlap extension PCR : an efficient method for transgene construction / Matthew D. Nelson and David H.A. Fitch. Gene knockdown analysis by double-stranded RNA injection / Benjamin N. Philip and Yoshinori Tomoyasu.
  • 2012 Future Med
    Rosell Costa, R.
    Integrating molecular knowledge in clinical decision-making for personalized cancer management -- Gastrointestinal stromal tumors -- Metastatic melanoma -- Ovarian cancer -- Triple-negative breast cancer -- Gastric cancer -- Pleural mesothelioma -- Lung adenocarcinoma.
  • 2006 Springer
    Betta, Michela.
    From destiny to freedom? : on human nature and liberal eugenics in the age of genetic manipulation / Michela Betta -- Diagnostic knowledge in the genetic economy and commerce / Michela Betta -- Body talk : genetic screening as a device of crime regulation / Richard Hil, Richard Hindmarsh -- Genetic testing and human genetic databases / Astrid H. Gesche -- The imperative of the "new genetics" : challenges for ethics, law, and social policy / David Weisbrot -- Insurance and genetics : regulating a private market in the public interest / David Weisbrot, Brian Opeskin -- The social imperative for community genetic screening : an Australian perspective / MaryAnne Aitken, Sylvia Metcalfe -- Genetically transformed healthcare : healthy children and parents / Enzo A. Palombo, Mrinal Bhave -- The Australian law reform inquiry into genetic commission testing - a worker's perspective / Susan Pennicuik -- Genetic information and the Australian labour movement / Suzanne Jamieson -- Protecting the vulnerable : genetic testing and screening for parentage, immigration, and aboriginality / Astrid H. Gesche -- Essentially whose? : genetic testing and the ownership of genetic information / Lyn Turney -- Self-knowledge and self-care in the age of genetic manipulation / Michela Betta.
  • 2010
    Naam, Ramez.
    Status: Not Checked OutLane Catalog Record
    Introduction. Healing and enhancing -- 1. Designer bodies -- 2. Designer minds -- 3. Created equal -- 4. Methuselah's genes -- 5. Designer lifespans -- 8. Methuselah's world -- 7. A child of one's own -- 8. Designer children -- 9. The wired brain -- 10. World wide mind -- 11. Life without limits.
  • 2012 Springer
    Di Pietro, Antonio; Pérez-Martín, José.
    This book combines state-of-the-art expertise from a variety of diverse pathogen model systems to provide an update to our current understanding of the regulation of fungal morphogenesis as a key determinant of pathogenicity in fungi.
  • 2002 CRCnetBASE
    Forey, Peter L.; MacLeod, Norman.
  • 2014 Springer Protocols
    Coppola, Vincenzo; Singh, Shree Ram.
  • 2015 Springer
    Brás, José M. Tomás; Schneider, Susanne A.
    This book covers recent developments and possible pitfalls in the diagnosis of genetic movement disorders and related conditions. It is divided into three sections: technical and scientific aspects; clinical aspects with guidance towards work-up; and ethical and legal aspects of genetic testing in a clinical and research setting. The first section includes chapters on genetic analysis and counselling with critical discussion of potential problems when interpreting the results. Clinical chapters summarize genetic forms of movement disorders including parkinsonism, tics and dystonia with algorithms for hands-on daily practice. Related conditions such as RLS, ataxias and dementias are also covered. Finally, chapters on ethical and legal aspects of genetic testing are included. Movement Disorder Genetics is aimed at clinicians and scientists working in the field of movement disorders and related conditions. .
  • 2006 Springer
    Bent, Elizabeth; Tuzun, Sadik.
  • 2013 Springer
    Christen, Yves; Pfaff, Donald W.
    In theoretical terms, sex differences in brain and behavior offer the possibility of fascinating scientific studies on a range of molecular phenomena such as DNA methylation, chromatin protein modification, non-coding DNA, resulting in important neuroanatomical and neurochemical effects. However, this general subject has been treated with much hyperbole. Historically, sex differences were assumed to be present where they did not really exist, e.g. with respect to mathematics, executive leadership, etc. etc. Under what circumstances do we really care about sex differences in brain and behavior? These circumstances concern human maladies whose diagnoses are much different between boys and girls, or between women and men. Prominent examples to be discussed today will include autism, attention deficit hyperactivity disorders and congenital adrenal hyperplasia. The meeting will end with a consideration of effects of estrogenic hormones on the injured brain, and their roles as protective agents.
  • 2008 Springer
    Dudoit, Sandrine; Laan, M. J. van der.
  • 2011
    Wenger, Jared William; Pringle, John R.; Sherlock, Gavin; Spormann, Alfred M.; Stearns, Tim.
    The processes by which the budding yeast Saccharomyces cerevisiae metabolizes carbon sources by both fermentation and respiration have been studied for more than a century. Yeast metabolism has been used both industrially, for the production of important molecules such as ethanol, and as a model for basic scientific research. Applied scientists have studied yeast metabolism to create and optimize novel metabolic phenotypes not naturally found in Saccharomyces yeasts. In parallel, basic scientists have used yeast as a model to understand fundamental processes such as evolutionary adaptation, as well as the pathways of carbon metabolism themselves. There are many unanswered questions in both of these fields, some of which I have addressed in this work. With respect to the industrial importance of yeast, I asked whether there are naturally existing Saccharomyces yeasts that can metabolize the five-carbon sugars important for lignocellulosic ethanol production (such as xylose), and, if so, what is the genetic basis for their phenotypes? Having characterized natural genetic variation in xylose metabolism, I also wanted to understand something more fundamental about how carbon metabolism can adapt, including the molecular nature of adaptations to selection on a limiting carbon source. Specifically, I asked what is the niche breadth of, and are there genetic trade-offs in, yeast that have been evolved under glucose-limitation? I have used a combination of classical genetics, physiology, and high-throughput genomics to answer these two questions. I have discovered novel xylose-utilizing Saccharomyces yeasts and have shed considerable light on the genetic basis for their phenotypes. In addition, I have discovered at least one trade-off for adaptation to limiting glucose, namely that amplification of the hexose-transporter genes HXT6 and HXT7 causes reduced fitness in carbon-rich environments. These two projects highlight two major spheres of Saccharomyces research, and they provide key answers to outstanding questions in both fields.
  • 2013- NCBI Bookshelf
    Beck, Jeff.
    "The NCBI Handbook 2nd Edition is geared towards advanced users of NCBI resources to provide an understanding of how bioinformatics resources at NCBI work. It is not a step-by-step user manual but complements NCBI user guides, tutorials, help information, and other existing documentation. It is our intent that the handbook will reflect, to the extent possible, the current state of databases, resources, and tools at NCBI, with information updated periodically"--Resource home page.
  • 2007 CRCnetBASE
    Jones, Byron C.; Mormède, Pierre.
    Chapter 1. A History of Behavior Genetics / Stephen C. Maxson -- Chapter 2. Developmental Neurobehavioral Genetics: Development as Explanation / Gilbert Gottlieb -- Chapter 3. Some Basics, Mendelian Traits, Polygenic Traits, Complex Traits / Byron C. Jones -- Chapter 4. An Introduction to Quantitative Genetics / Wim E. Crusio -- Chapter 5. From QTL Detection to Gene Identification / Marie-Pierre Moisan -- Chapter 6. Gene Expression / Richard A. Radcliffe -- Chapter 7. Bioinformatics of Behavior / Elissa J. Chesler -- Chapter 8. Congenic and Consomic Strains / Lorraine Flaherty and Valerie Bolivar -- Chapter 9. Animal Resources in Behavioral Neurogenetics / Jean-Michel Lassalle -- Chapter 10. Sample Size Requirements for Experiments on Laboratory Animals / Douglas Wahlsten -- Chapter 11. The Role of Association Studies in Psychiatric Disorders / Nicolas Ramoz and Philip Gorwood -- Chapter 12. Family and Twin Methods / Keith E. Whitfield and Tracy L. Nelson -- Chapter 13. Gene-Environment Interactions / Byron C. Jones and Leslie C. Jones -- Chapter 14. And Now it Starts to Get Interesting: Gene-Gene Interactions / Yamima Osher -- Chapter 15. Schizophrenia: Study of a Genetically Complex Phenotype / Michael F. Pogue-Geile and Irving I. Gottesman -- Chapter 16. Genetics of Major Affective Disorders / Wade Berrettini -- Chapter 17. Pedigree Analyses and the Study of Chimpanzee (Pan troglodytes) Personality and Subjective Well-Being / Alexander Weiss and James E. King -- Chapter 18. The Elusive World of Personality Genes: Cherchez le Phenotype / Richard P. Ebstein, Rachel Bachner-Melman, Jonathan Benjamin, and Robert H. Belmaker -- Chapter 19. Aggression: Concepts and Methods Relevant to Genetic Analyses in Mice and Humans / Stephen C. Maxson and Andrew Canastar -- Chapter 20. Genetic Analysis of Emotional Behaviors Using Animal Models / André Ramos and Pierre Mormède -- Chapter 21. Genetic Analysis of Food Search Behavior in the Fruit Fly (Drosophila melanogaster) / Amsale T. Belay and Marla B. Sokolowski -- Chapter 22. Genetic and Molecular Analyses of Drosophila
  • 2014 Springer
    Galimberti, Daniela; Scarpini, E.
    This book gives an overview of the current knowledge on the most common neurodegenerative diseases, including Alzheimer's disease, frontotemporal lobar degeneration, amyotrophic lateral sclerosis, and additional neurodegenerative diseases. Different aspects of each disease are reviewed, including clinical issues, treatments, basic discoveries (genetics and molecular biology), and translation of basic research into biomarkers for early diagnosis. In addition, emerging data indicate that neurodegeneration seems to also be present in classically non-degenerative disorders. Therefore, a chapter about overlapping mechanisms between dementias and psychiatric disorders is included, as well as a description of the role of neurodegeneration in multiple sclerosis. Neurodegenerative Diseases is aimed at clinicians, particularly those working in academic hospitals. This multidisciplinary book will also be of interest to basic researchers in medical fields.
  • 2012 Springer
    Cooper, David N.; Upadhyaya, M.
    Neurofibromatosis type 1 (NF1), caused by mutational inactivation of the NF1 tumour suppressor gene, is one of the most common dominantly inherited human disorders, affecting 1 in 3000 individuals worldwide. This book presents in concise fashion, but as comprehensively as possible, our current state of knowledge on the molecular genetics, molecular biology and cellular biology of this tumour predisposition syndrome. Written by internationally recognized experts in the field, the 44 chapters that constitute this edited volume provide the reader with a broad overview of the clinical features of the disease, the structure and expression of the NF1 gene, its germ line and somatic mutational spectra and genotype-phenotype relationships, the structure and function of its protein product (neurofibromin), NF1 modifying loci, the molecular pathology of NF1-associated tumours, animal models of the disease, psycho-social aspects and future prospects for therapeutic treatment.Neurofibromatosis Type 1: Molecular and Cellular Biology will be of great value to medical geneticists, molecular and cellular biologists, oncologists, dermatologists, neurologists, genetic counsellors and general practitioners alike.
  • 2006 CRCnetBASE
    Farmer, Jennifer M.; Lynch, David R.
  • 2014 Springer
    Kaminski, Henry J.; Katirji, Bashar; Ruff, Robert L.
    Part I Approach to neuromuscular diseases: principles and basics -- Clinical assessment in neuromuscular disorders -- Nerve and muscle: basic concepts -- Part II Approach to neuromuscular diseases: neuromuscular investigations -- Serum muscle enzymes in neuromuscular disease -- Autoantibody testing in peripheral neuropathy -- Autoantibody testing in autoimmune neuromuscular junction, hyperexcitability, and muscle disorders -- Forearm exercise testing -- Clinical electromyography (neve conduction studies and needle electromyography) -- Single-fiber EMG -- Quantitative EMG analysis -- Testing of autonomic function -- Quantitative sensory testing -- Nerve and muscle biopsies -- Skin biopsy -- Molecular diagnosis and genetic testing -- Part III Approach to neuromuscular diseases: assessment and treatment of neurologica disorders -- Outcome measures and clinical assessment instruments in neuromuscular disease -- Physical management of patients with neuromuscular diseases -- Immunotherapy in the treatment of autoimmune neuromuscular diseases -- Critical and respiratory care in neuromuscular disorders -- Part IV Neuromuscular disorders: neuronopathies (motor neuron and dorsal root ganglion disorders) -- Poliomyelitis and post-poliomyelitis syndrome -- Amyotrophic lateral sclerosis -- Spinal muscular atrophies -- Atypical motor neuron disorders -- Dorsal root ganglion disorders -- Part V Neuromuscular disorders: Peripheral neuropatahies -- Approach to peripheral nerve disorders -- Approach to small fiber neuropathy -- Charcot-Marie-Tooth diseases -- Inherited metabolic neruopathies -- Guillain-Barre Syndrome and related disorders -- Chronic inflammatory demyelinating polyradiculoneuropathy and related disorders -- Diabetic neuropathies -- Nutritional and alcoholic neuropathies -- Metabolic and endocrine neuropathies -- Environmental toxic neuropathies -- Drug-induced toxic neuropathies -- Vasculitic neuropathies and neuropathies of connective tissue disease -- Nonvasculitic ischemic neuropathies -- Infectious and granulomatous peripheral neuropathies -- Peripheral nerve injury -- Compressive and entrapment neuropathies of the upper extremity -- Compressive and entrapment neuropathies of the lower extremity -- Cranial nerve palsies -- Peripheral nerve tumors -- Cervical radiculopathy -- Lumbosacral and thoracic radiculopathies -- Brachial plexopathies -- Lumbosacral plexopathies -- Part VI Neuromuscular disorders: neuromuscular junction disorders -- Myasthenia Gravis -- Lambert-Eaton Myasthenic Syndrome -- Botulism -- Toxic neuromuscular transmission disorders -- Part VII Neuromuscular disorders: muscle ion channel disorders -- Disorders of skeletal muscle membrane excitability: myotonia congenita, paramyotonia congenita, periodic paralysis, and related syndromes -- Malignant hyperthermia -- Part VIII Neuromuscular disorders: myopathies -- Approach to myopathies -- Dystrophinopathies -- Limb-girdle muscular dystrophies -- Facioscapulohumeral muscular dystrophy -- The myotonic dystrophies -- Oculpharyngeal muscular dystrophy -- Emery-Dreifuss muscular dystrophy -- Congenital myopathies -- Metabolic myopathies -- Mitochondrial myopathies -- Inflammatory myopathies -- Paraspinous myopathies: the dropped head and bent spine syndromes -- Endocrine myopathies -- Toxic myopathies -- Infectious and granulomatous myopathies -- Part IX Neuromuscular disorders: miscellaneous neuromuscular disorders and syndromes -- Myokymia and neuromyotonia -- Muscle cramps and fasciculations -- Stiff-man syndrome -- Tetanus -- Neuroleptic malignant syndrome -- Paraneoplastic neuromuscular disorders -- Acute neuromuscular weakness in the intensive care unit -- Floppy infant -- Rhabdomyolysis and myoglobinuria -- Eosinophilia-myalgia syndrome, eosinophilic fascitiitis, and related fasciitis disorders -- Neuropathis pain and other chronic musculoskeletal pain conditions.
  • 2007 ScienceDirect
    Mitchelson, Keith R.
    Overview: developments in DNA sequencing / Keith R. Mitchelson ... [et al.] -- Chip capillary electrophoresis and total genetic analysis systems / Quiang Xiong and Jing Cheng -- Comparative sequence analysis by MALDI-TOF mass spectrometry: utilizing the known to discover the new / Mathias Ehrich, Franz Hillenkamp, and Dirk van den Boom -- Advances in dye-nucleotide conjugate chemistry for DNA sequencing / Shiv Kumar and Carl W. Fuller -- The 454 life sciences picoliter sequencing system / Marcel Margulies ... [et al.] -- An integrated system for DNA sequencing by synthesis / John R. Edwards, Dae Hyun Kim, and Jingyue Ju -- Single-molecule fluorescence microscopy and its applications to single-molecule sequencing by cyclic synthesis / Benedict Hebert and Ido Braslavsky -- Rapid DNA sequencing by direct nanoscale reading of nucleotide bases on individual DNA chains / James Weifu Lee and Amit Meller -- A single molecule system for whole genome analysis / Shiguo Zhou, Jill Herschleb, and David C. Schwartz -- Sequencing aided by mutagenesis facilitates the de novo sequencing of megabase DNA fragments by short read lengths / Jonathan M. Keith ... [et al.] -- Genome sequencing and assembly / Annette McGrath -- Valid recovery of nucleic acid sequence information from high contamination risk samples: ancient DNA and environmental DNA / George A. Kowalchuk ... [et al.].
  • 2013 Springer
    Wong, Lee-Jun C.
    Overview. History of DNA Sequencing Technologies / Lisa D. White -- Clinical Molecular Diagnostic Techniques: A Brief Review / Megan L. Landsverk, Lee-Jun C. Wong -- The Technologies and Bioinformatics. Methods of Gene Enrichment and Massively Parallel Sequencing Technologies / Hong Cui -- Sequence Alignment, Analysis, and Bioinformatic Pipelines / Fuli Yu, Cristian Coarfa -- Protein Structural Based Analysis for Interpretation of Missense Variants at the Genomics Era: Using MNGIE Disease as an Example / Victor Wei Zhang -- Algorithms and Guidelines for Interpretation of DNA Variants / Jing Wang, Megan Landsverk -- Application to Clinical Diagnosis. NGS-Based Clinical Diagnosis of Genetically Heterogeneous Disorders / C. A. Valencia, T. A. Sivakumaran, B. T. Tinkle -- Molecular Diagnosis of Congenital Disorders of Glycosylation (CDG) / Melanie Jones, Madhuri Hegde -- NGS Improves the Diagnosis of X-Linked Intellectual Disability (XLID) / Michael J. Friez, Monica J. Basehore -- NGS Analysis of Heterogeneous Retinitis Pigmentosa / Rui Chen, Feng Wang -- Next-Generation Sequencing Analyses of the Whole Mitochondrial Genome / Lee-Jun C. Wong -- Application of Next-Generation Sequencing of Nuclear Genes for Mitochondrial Disorders / Valeria Vasta, Si Houn Hahn -- Noninvasive Prenatal Diagnosis Using Next-Generation Sequencing / Nancy Bo Yin Tsui, Yuk Ming Dennis Lo -- Compliance with CAP/CLIA Regulations. Guidelines and Approaches to Compliance with Regulatory and Clinical Standards: Quality Control Procedures and Quality Assurance / Ira M. Lubin, Lisa Kalman, Amy S. Gargis -- Validation of NGS-Based DNA Testing and Implementation of Quality Control Procedures / Victor Wei Zhang, Lee-Jun C. Wong -- Frequently Asked Questions About the Clinical Utility of Next-Generation Sequencing in Molecular Diagnosis of Human Genetic Diseases / Ephrem L. H. Chin, Victor Wei Zhang, Jing Wang, Margherita Milone, Susan Pacheco.
  • 2013 Springer
    Masoudi-Nejad, Ali; Hosseinkhan, Nazanin; Narimani, Zahra.
    Preface -- Next generation sequencing methodologies -- Emergence of next generation sequencing -- Assembly of sequencing data -- De novo assembly algorithms -- Index.
  • 2013 Springer
    Choudhry, Hani; Wu, Wei.
    Introduction: next generation sequencing technology and cancer research -- The majority of total nuclear-encoded non-ribosomal RNA in a human cell is dark matter unannotated RNA -- Total RNA-seq of breast cancer in hypoxia -- Altered antisense-to-sense transcript ratios in breast cancer -- Identification of piRNAs in Hela cells by massive parallel sequencing -- Discovery of new microRNAs by small RNAome deep sequencing in childhood acute lymphoblastic leukemia -- Whole-Exome Sequencing Identifies FAM20A Mutations as a Cause of Amelogenesis Imperfecta and Gingival Hyperplasia Syndrome -- Whole-exome sequencing in CIC and IDH1/2 contributing to human oligodendroglioma -- Genetic and structural variation in the gastric cancer kinome revealed through targeted deep sequencing -- Tumour evolution inferred by single-cell sequencing -- Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq -- Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNASeq analysis -- Whole genome DNA methylation analysis based on high throughput sequencing technology -- Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors -- High-resolution genome-wide mapping of HIF-binding sites by ChIP-seq -- MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action -- Genome-wide identification of polycomb-associated RNAs by RIP-seq -- Single-molecule sequencing: sequence methods to enable accurate quantisation -- Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells -- Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA -- The genome information process for cancer research: the challenge and perspective.
  • 2012 Springer Protocols
    Fan, Jian-Bing.
    Controlling miRNA regulation in disease / Willemijn M. Gommans and Eugene Berezikov -- Introduction to miRNA profiling technologies and cross-platform comparison / Sarah Aldridge and James Hadfield -- Stem-loop RT-qPCR for microRNA expression profiling / James Hurley [and others] -- Poly(T) adaptor RT-PCR / Rui-Shi [and others] -- MicroRNA in situ hybridization / Boye Schnack Nielsen -- Agilent microRNA microarray profiling system / Petula N. D'Andrade and Stephanie Fulmer-Smentek -- MiRNA expression profiling using Illumina Universal BeadChips / Jing Chen, Craig S. April, and Jian-Bing Fan -- MicroRNA expression analysis using the Affymetrix platform / Suzanne Dee and robert C. Getts -- Individualized miRNA assay panels using optically encoded beads / Keld Sorensen -- Microfluidic primer extension assay / Markus Beier and Valesca Boisguérin -- MicroRNA profiling using [mu]Paraflo microfluidic array technology / Xiaochuan Zhou [and others] -- MicroRNA expression analysis using the Illumina microRNA-Seq platform / Shujun Luo -- Next-generation sequencing of miRNAs with Roche 454 GS-FLX technology : steps for a successful application / Ana Raquel Soares, Patrícia M. Pereira, and Manuel A.S. Santos -- Methods for small RNA preparation for digital gene expression profiling by next-generation sequencing / Sam E.V. Linsen and Edwin Cuppen -- Profiling of short RNAs using Helicos single-molecule sequencing / Philipp Kapranov, Fatih Ozsolak, and Patrice M. Milos -- DeepBASE : annotation and discovery of microRNAs and other noncoding RNAs from deep-sequencing data / Jian-Hua Yang and Liang-Hu Qu -- PhenomiR : microRNAs in human diseases and biological processes / Andreas Ruepp, Andreas Kowarsch, and Fabian Theis -- MiRNA expression profiling : from reference genes to global mean normalization / Barbara D'haene [and others] -- MiRNA data analysis : next-gen sequencing / Preethi H. Gunaratne [and others] -- Integrated miRNA expression analysis and target prediction / William Ritchie and John E.J. Rasko -- MiRNAs in human cancer / Xiaomin Zhong, George Coukos, and Lin Zhang -- Blood-based miRNA preparation for noninvasive biomarker development / Svenja Debey-Pascher [and others].
  • 2006 CRCnetBASE
    Cadenas, Enrique; Lamas, Santiago.
  • 2016 Springer
    Bernard, Pascal; Wilhelm, Dagmar.
    1. The reproductive system -- 2. Non-coding RNAs: an introduction -- 3. How many non-coding RNAs does it take to compensate male/female genetic imbalance? -- 4. The piRNA pathway guards the germline genome against transposable elements -- 5. Non-coding RNA in spermatogenesis and epididymal maturation -- 7. Non-coding RNAs in mammary gland development and disease -- 8. Non-coding RNAs in prostate cancer: from discovery to clinical applications -- 9. Non-coding RNAs in uterine development, function and disease -- Index.
    Also available: Print – 2016
  • 2014 Springer
    Fabbri, Muller.
    Introduction / Muller Gabbri -- Biogenesis and physiology of microRNAs / Carlos A. Melo and Sonia A. Melo -- Detecting noncoding RNA expression : from arrays to next-generation sequencing / Catalina Perdomo, Joshua Campbell, and Frank Schembri -- MicroRNAs in solid tumors / Jin Wang and Subrata Sen -- MicroRNAs in hematologic malignancies / Johannes Bloehdorn ... [et al.] -- miRNAs as cancer biomarkers / Edward R. Sauter -- Unraveling the complex network of interactions between noncoding RNAs and epigenetics in cancer / Veronica Davalos and Manel Esteller -- MicroRNA SNPs in cancer / Yujing LI and Peng Jin -- Bioinformatics approaches to the study of MircoRNAs / Ravi Gupta and Ramana V. Davuluri -- Beyond miRNAs : role of other noncoding RNAs in cancer / Roxana S. Redis and George A. Calin -- Translational implication for noncoding RNA in cancer / Duaa Dakhallah, Melissa Piper, and S. Patrick Nana-Sinkam.
  • 2008 CRCnetBASE
    Coyle, Heather Miller.
    Introduction to forensic science and DNA / Heather Miller Coyle -- Collection and preservation of biological evidence from the crime scene / Henry C. Lee -- Techniques of DNA fingerprinting / John Schienman -- Forensic canine STR analysis / Burkhard Berger, Cordula Eichmann, Walther Parson -- STR based forensic analysis of field samples from domestic and exotic cats / Marilyn A. Menotti-Raymond, Victor A. David, Stephen J. O'Brien -- Overview of insect evidence in forensic science / Heather Miller Coyle -- Use of forensic DNA typing in wildlife investigations / Richard M. Jobin -- DNA testing of animal evidence : case examples and method development / En-Uei Jiang, W. A. van Haeringen, L. H. P. van de Goor, Pero Dimsoski, Heather Miller Coyle -- Basics of forensic fungi /; Khudooma Said Al Na'imi -- Soil DNA typing in forensic science / Jonathan Hill, Linda Strausbaugh, Joerg Graf -- DNA profiling : the ability to predict an image from a DNA profile / Holly Long -- Appendix A: Brief history of forensic serology and DNA / Peter Bilous.
  • 2011
    AlQuraishi, Mohammed Nazar; Altman, Russ B.; McAdams, Harley; Sherlock, Gavin; Sidow, Arend.
    The foundation of molecular analyses of chemical and biological phenomena is the energy potential, a mathematical description of the energy of every possible interaction in a molecular system. The accuracy of computational and laboratory studies of phenomena ranging from pharmaceutical drug interactions and protein folding to material phase transitions and thin film growth is often limited by the accuracy of these energy potentials. Currently, energy potentials are inferred using a mixture of theoretical modeling and experimental data. So-called "physical potentials" rely on theoretical models to specify the potential's mathematical form and use experimental data to fit few model parameters. In contrast, "statistical potentials", also known as knowledge-based potentials, fit many parameters to experimental data and use theoretical models for the expected statistics of interactions under randomness to infer a potential. In both approaches, theoretical models shape and constrain the inferred potential, resulting in a so-called parametric model. There are several drawbacks to this: (i) The a priori assumptions underlying the inferred potentials may be inaccurate. (ii) Substantial domain knowledge is required (often exceeding what is known). (iii) Potential modeling is lengthy and technically difficult. The theoretical development of some potentials has taken decades. To overcome these problems, potentials could in principle be determined strictly from experimental data without recourse to theoretical modeling by experimentally measuring the energies of all distinct interactions, resulting in a "de novo" energy potential. In practice, direct measurement of interatomic potentials has only been possible for the simplest systems, due to a combinatorial explosion in the number of possible interactions that renders experiment-based inference intractable. In this thesis, we develop a tractable methodology for the inference of de novo potentials that circumvents the experimental intractability barrier. Our methodology overcomes this barrier by synthesizing concepts from structural biology, statistical mechanics, and recent discoveries in information theory known as compressed sensing. The result is a non-parametric potential that does not require an a priori assumption of a theoretical model, overcoming a fundamental limitation of both physical and statistical potentials. To explore the utility and role that this new methodology can play in molecular analysis, we focus on an important and long-standing problem in biology: the sequence specificity of DNA-binding proteins to their DNA targets. We develop a method that uses energy potentials to predict the DNA binding sites of proteins. In the first part of the thesis, we use existing statistical potentials. We develop three novel enhancements of statistical potentials tailored specifically for the protein-DNA binding application. These enhancements exploit certain molecular features of protein-DNA binding, as well as the unique experimental data sets available in this domain, to improve the performance of statistical potentials in predicting protein-DNA binding. In the second part of the thesis, we introduce the notion of a de novo potential, i.e. an energy potential derived exclusively from experimental data, without relying on any theoretical modeling. We discuss previous challenges that have prevented the development of such non-parametric potentials, and then introduce our methodology for inferring de novo potentials. We first present a general methodology that is applicable to any domain of molecular interactions, then specialize our general methodology to the specific application of protein-DNA interactions. Using this specialized version, we infer a number of different protein-DNA energy potentials, and apply them to the problem of predicting the DNA binding sites of proteins. We show that our new method achieves near experimental accuracy for over half of the tests performed, significantly outperforming the state of the art in this field.
  • 2011
    Abeliuk Acuna, Eduardo; Dill, David; McAdams, Harley; Osgood, Brad; Shapiro, Lucy.
    In the last decade remarkable technologies, such as high-density tiling arrays and high-throughput DNA sequencing have enabled whole-genome studies at an unprecedented scale and resolution. In this work I describe how we used these technologies to map novel genetic elements as well as regulatory features of the bacterium Caulobacter crescentus, a model species used for understanding the prokaryotic cell-cycle. I describe a dynamic programming algorithm I used to determine the location of 27 novel small RNA transcripts (sRNAs), several novel antisense RNA transcripts, as well as the accurate mapping of mRNA transcripts. Many of these predictions were validated biochemically. In addition, I describe how we coupled high-throughput transposon mutagenesis with statistical analysis to map all the essential genetic elements in the Caulobacter crescentus genome to 8 base-pair accuracy. We found that 480 out of the 3960 genes contained in Caulobacter's genome are essential for cell viability, as well as 3 out of the 27 novel sRNA that we had identified. Interestingly, there are 90 essential small intergenic DNA segments of unknown function. Finally, I describe the operon organization of Caulobacter's genome.
  • 2015 Springer Protocols
    Hirose, Tetsuro; Nakagawa, Shinichi.
    Visualization of lncRNA by single-molecule fluorescence in situ hybridization / Margaret Dunagin , Moran N. Cabili , John Rinn , and Arjun Raj -- Super-resolution imaging of nuclear bodies by STED microscopy / Yasushi Okada and Shinichi Nakagawa -- High-resolution 3D DNA FISH using plasmid probes and computational correction of optical aberrations to study chromatin structure at the sub-megabase scale / Luca Giorgetti, Tristan Piolot, and Edith Heard -- Time-lapse imaging of nuclear bodies / Saskia Hutten, Samuel Swift, and Angus I. Lamond -- Visualization of nucleic acids with synthetic exciton-controlled fluorescent oligonucleotide probes / Dan Ohtan Wang and Akimitsu Okamoto -- Live CLEM imaging to analyze nuclear structures at high resolution / Tokuko Haraguchi, Hiroko Osakada, and Takako Koujin -- Ultrastructural analysis of nuclear bodies using electron microscopy / Sylvie Souquere and Gérard Pierron -- Analyses of nuclear proteins and nucleic acid structures using atomic force microscopy / Jamie L. Gilmore [and eight others] -- Genome-wide co-localization screening of nuclear body components using a fluorescently tagged FLJ cDNA clone library / Tetsuro Hirose and Naoki Goshima -- Purification of specific chromatin regions using oligonucleotides : capture hybridization analysis of RNA targets (CHART) / Christopher P. Davis and Jason A. West -- RNA antisense purification (RAP) for mapping RNA interactions with chromatin / Jesse Engreitz, Eric S. Lander, and Mitchell Guttman -- In situ dissection of RNA functional subunits by domain-specific chromatin isolation by RNA purification (dChIRP) / Jeffrey J. Quinn and Howard Y. Chang -- Extracting, enriching, and identifying nuclear body sub-complexes using label-based quantitative mass spectrometry / Archa Fox [and three othrs] -- Studying RNA-binding protein interactions with target mRNAs in eukaryotic cells : native ribonucleoprotein immunoprecipitation (RIP) assays / Joseph A. Cozzitorto [and eight others] -- Cross-linking and immunoprecipitation of nuclear RNA-binding proteins / Quan Li , Yuri Uemura , and Yukio Kawahara -- Purification of noncoding RNA and bound proteins using FLAG peptide-conjugated antisense-oligonucleotides / Shungo Adachi and Tohru Natsume -- MMCT-mediated chromosome engineering technique applicable to functional analysis of lncRNA and nuclear dynamics / Makiko Meguro-Horike and Shin-ichi Horike -- Reconstitution of nucleocytoplasmic transport using digitonin-permeabilized cells / Shingo Kose, Tomoko Funakoshi, and Naoko Imamoto -- Genome-wide analysis of long noncoding RNA turnover / Hidenori Tani [and eight others] -- Knockdown of nuclear-retained long noncoding RNAs using modified DNA antisense oligonucleotides / Xinying Zong [and six others] -- siRNA screening of nuclear proteins / Yuko Hasegawa and Shinichi Nakagawa.
  • 2010 Cold Spring Harb Lab Press
    Grodzicker, Terri.
    Chromatin modifications and gene expressions -- Transcription and beyond -- DNA replication and genome integrity -- Reprogramming and differentiation -- Heterochromatin formation and gene silencing -- Nuclear bodies and RNA biology -- Chromosome structure and mitosis -- Chromatin structure and organization -- Nuclear periphery.
  • 2008 Springer
    Golovkin, Maxim; Reddy, Anireddy S. N.
    Spliceosomal proteins in plants / Y. Ru, B.B. Wang and V. Brendel -- Analysis of alternative splicing in plants with bioinformatics tools / B.J. Haas -- Splice site requirements and switches in plants / M.A. Schuler -- U12-dependent intron splicing in plants / C.G. Simpson and J.W. Brown -- Plant SR proteins and their functions / A. Barta, M. Kalyna and Z.J. Lorkovic -- Spatiotemporal organization of pre-mRNA splicing proteins in plants / G.S. Ali and A.S. Reddy -- Regulation of splicing by protein phosphorylation / R. Fluhr -- mRNA cap binding proteins: effects on abscisic acid signal transduction, mRNA processing, and microarray analyses / J.M. Kuhn, V. Hugouvieux and J.I. Schroeder -- Messenger RNA 3' end formation in plants / A.G. Hunt -- State of decay: an update on plant mRNA turnover / D.A. Belostotsky -- Regulation of flowering time by RNA processing / L.C. Terzi and G.G. Simpson -- Alternative splicing in plant defense / W. Gassmann -- Nuclear RNA export and its importance in abiotic stress responses of plants / V. Chinnusamy, Z. Gong and J.K. Zhu -- Regulation of alternative splicing of pre-mRNAs by stresses / G.S. Ali and A.S. Reddy -- Intron-mediated regulation of gene expression / A.B. Rose -- The role of the plant nucleolus in pre-mRNA processing / J.W. Brown and P.J. Shaw.
    Also available: Print – 2008
  • 2006 Springer Protocols
    Trounson, Alan; Verma, Paul J.
    Cloning of exotic/endangered species: (desert bighorn sheep) / James "Buck" Williams ... [et al.] -- Handmade somatic cell cloning in cattle / Gábor Vatja, Ian M. Lewis, and R. Tayfur Tecirlioglu -- Genetic modification of sheep by nuclear transfer with gene-targeted somatic cells / A. John Clark, Sarah Burl, and Chris Denning -- Transgenesis using nuclear transfer in goats / Anthoula Lazaris ... [et al.] -- Nuclear reprogramming : an overview / Takashi Tada -- Expression of imprinted genes in cloned mice / Takashi Kohda, Fumitoshi Ishino, and Atsuo Ogura -- Nuclear remodeling assay in xenopus egg extract / Koichi Gonda and Nobuaki Kikyo -- In vitro reprogramming of nuclei and cells / Anne-Mari Håkelien ... [et al.] -- Techniques for nuclear transfer to mouse embryonic stem cells / Danielè Pralong and Paul J. Verma -- Gene expression and methylation patterns in cloned embryos / Christine Wrenzycki ... [et al.] -- Are there any normal clones? / Ian Wilmut -- Future and applications of cloning / Alan O. Trounson. Origin and progress of nuclear transfer in nonmammalian animals / Marie A. Di Berardino -- In vitro maturation and embryo production in cattle / Marc-André Sirard and Karine Coenen -- Activation of oocytes after nuclear transfer / Zoltán Macháty -- Culture medium preferences of pre-implantation cloned mouse embryos / Björn Heindryckx, Josiane Van der Elst, and Marc Dhont -- Maintenance of pregnancy in pigs with limited viable embryos / Tim King and Paul A. De Sousa -- Health and neonatal care of bovine clones / Jacqui T. Forsyth and David N. Wells -- Optimization of procedures for cloning by somatic cell nuclear transfer in mice / Young Gie Chung, Shaorong Gao, and Keith E. Latham -- Production of cloned calves using roscovitine-treated adult somatic cells as donors / Kazuchika Miyoshi, Sezen Arat, and Steven L. Stice -- A double nuclear transfer technique for cloning pigs / Irina A. Polejaeva, Shawn Walker, and Keith Campbell -- Nuclear transfer in nonhuman primates / Shoukhrat M. Mitalipov and Don P. Wolf --
  • 2016 Springer Protocols
    Mayer, Günter.
    Selection of aptamers for metabolite sensing and construction of optical nanosensors / Yi Long ... [et al.] -- SELEX of cell-specific RNA aptamers / Katharina Berg, Eileen Magbanua, and Ulrich Hahn -- Developing aptamers by cell-based SELEX / Silvia Catuogno, Carla Lucia Esposito, and Vittorio de Franciscis -- DNA aptamer generation by genetic alphabet expansion SELEX (ExSELEX) using an unnatural base pair system / Michiko Kimoto, Ken-ichiro Matsunaga, and Ichiro Hirao -- Capillary electrophoresis for the selection of DNA aptamers recognizing activated protein C / Nasim Shahidi Hamedani and Jens Müller -- Preparation of SELEX samples for next-generation sequencing / Fabian Tolle and Günter Mayer -- Next-generation analysis of deep sequencing data : bringing light into the black box of SELEX experiments / Michael Blank -- Aptamer binding studies using MicroScale thermophoresis / Dennis Breitsprecher ... [et al.] -- Label-free determination of the dissociation constant of small molecule-aptamer interaction by isothermal titration calorimetry / Marc Vogel and Beatrix Suess -- Applications of aptamers in flow and imaging cytometry / Isis C. Nascimento ... [et al.] -- In vitro and in vivo imaging of fluorescent aptamers / Ioanna Théodorou ... [et al.] -- Crystallographic pursuit of a protein-RNA aptamer complex / John J. G. Tesmer -- Voltammetric aptasensor based on magnetic beads assay for detection of human activated protein C / Arzum Erdem, Gulsah Congur, and Ece Eksin -- Apta-PCR / Alessandro Pinto ... [et al.] -- Aptamer-based enzyme capture assay for measurement of plasma thrombin levels / Jens Müller ... [et al.] -- Application of aptamers in histopathology / Sarah Shigdar ... [et al.] -- Aptamer stainings for super-resolution microscopy / Maria Angela Gomes de Castro, Burkhard Rammner, and Felipe Opazo -- Synthesis and characterization of aptamer-targeted SNALPs for the delivery of siRNA / Samantha E. Wilner and Matthew Levy -- Screening of genetic switches based on the twister ribozyme motif / Michele Felletti, Benedikt Klauser, and Jörg S. Hartig.
  • 2014 Springer
    Murakami, Katsuhiko S.; Trakselis, Michael A.
    This book provides a review of the multitude of nucleic acid polymerases, including DNA and RNA polymerases from Archea, Bacteria and Eukaryota, mitochondrial and viral polymerases, and other specialized polymerases such as telomerase, template-independent terminal nucleotidyl transferase and RNA self-replication ribozyme. Although many books cover several different types of polymerases, no book so far has attempted to catalog all nucleic acid polymerases. The goal of this book is to be the top reference work for postgraduate students, postdocs, and principle investigators who study polymerase.
  • 2006 CRCnetBASE
    Lorincz, Attila T.
  • 2007 Springer
    Buzdin, Anton; Lukyanov, Sergey.
  • 2006 CRCnetBASE
    Choi, Sang-Woon; Friso, Simonetta.
  • 2005 CRCnetBASE
    Fuchs, Jürgen; Packer, Lester; Rimbach, Gerald.
  • 2014 CRCnetBASE
    Ferguson, Lynnette R.
    Nutrigenetics and nutrigenomics : importance for functional foods and personalized nutrition / Lynnette R. Ferguson -- Variations in solute transporter genes affecting micronutrient solute transport and human health / Peter Eck -- Genetic variants in the omega-6 and omega-3 fatty acid metabolic pathways : their role in the determination of nutritional requirements and chronic disease risk / Artemis P. Simopoulos -- Nutrigenomic approaches to unravelling the physiological effects of complex foods / Peter J. Gillies and John P. Vanden Heuvel -- Modulating the risk of cardiovascular disease through nutrigenetics / Antonio Garcia-Rios ... [et al.] -- Modulating the risk of obesity and diabetes through nutrigenetics / Helen M. Roche and Catherine Phillips -- Nutrigenetics and Crohn's disease -- / Lynnette R. Ferguson -- Microbiome and host interactions in inflammatory bowel diseases : relevance for personalized nutrition / Wayne Young, Bianca Knoch, and Nicole C. Roy -- The importance of cell-specific gene expression patterns for understanding nutrient and gene interactions in inflammatory bowel diseases / Anna Russ ... [et al.] -- Data mining and network analysis : potential importance in nutrigenomics research / Varma Vijayalakshmi and Jim Kaput -- Metabolomics : an important tool for assessing state of health and risk of disease in nutrigenomics research / Hui Ming Lin and Daryl Rowan -- Epigenetics : what role could this play in functional foods and personalised nutrition? / Matthew P.G. Barnett, Shalom A. Bassett, and Emma Bermingham -- Foodomics to study efficacy of human dietary interventions : proof of principle study / Stephanie Ellett ... [et al.] -- Considerations in estimating genotype in nutrigenetic studies / Angharad R. Morgan -- Bringing nutrigenomics to the food industry : industry-academia partnerships as an important challenge / Ralf C. Schlothauer and Joerg Kistler -- Commercialisation of nutrigenetics and nutrigenomics / Virginia Parslow and Lynnette R. Ferguson -- Bringing nutrigenomics to the public : Is direct-to-consumer testing the future of nutritional genomics? / David Castle -- Nutritional genomics in practice : interaction with health professionals in bringing nutritional genomics to the public / Colleen Fogarty Draper -- Harvesting normative potential for nutrigenomic research / Bart Penders and Michiel Korthals -- Public health context for nutrigenomics and personalized nutrition / Elizabeth H. Marchlewicz, Karen E. Peterson, and Filbert S. Omenn -- Nutrigenomics and public health / Maria Agelli and John Milner.
  • 2011 CRCnetBASE
    Maulik, Gautam; Maulik, Nilanjana.
    "Extensive research on nutrigenomics has unveiled numerous epigenetic mechanisms that are influenced by our dietary signature. This book illustrates how nutrition can influence epigenetic inheritance and the mechanisms that underlie modification of the metabolic imprint of an individual. The text discusses the basics of nutrigenomics and epigenetic regulation, types of nutrition influencing genetic imprinting, and the role of nutrition in modulating an individual's predisposition to disease. It also covers epigenetic variation, genomic imprinting, maternal nutrition, neonatal nutrition, as well as epigenetics and nutrition relating to cancer, heart disease, and obesity"--Provided by publisher.
    Also available: Print – 2011
  • 2014 Springer
    Barh, Debmalya.
    Breast cancer is the most common cancer in females that accounts for highest cancer specific deaths worldwide. In the last few decades research has proven that breast cancer can be treated if diagnosed at early stages and proper therapeutic strategy is adopted. Omics-based recent approaches have unveiled the molecular mechanism behind the breast tumorigenesis and aid in identification of next-generation molecular markers for early diagnosis, prognosis, and even the effective targeted therapy. Significant development has taken place in the field of omics in breast cancer in the last decade. The most promising omics approaches and their outcomes in breast cancer have been presented in this book for the first time. The book covers omics technologies and budding fields such as breast cancer miRNA, lipidomics, epigenomics, proteomics, nutrigenomics, stem cell, pharmacogenomics and personalized medicine, and many more along with conventional topics such as breast cancer management etc. It is a research-based reference book useful for clinician-scientists, researchers, geneticists and health care industries involved in various aspects of breast cancer. The book will also be useful for students of biomedicine, pathology, and pharmacy.
  • 2013 Springer
    Barh, Debmalya; Dhawan, Dipali; Ganguly, N. K.
    Omics for Personalized Medicine will give to its prospective readers the insight of both the current developments and the future potential of personalized medicine. The book brings into light how the pharmacogenomics and omics technologies are bringing a revolution in transforming the medicine and the health care sector for the better. Students of biomedical research and medicine along with medical professionals will benefit tremendously from the book by gaining from the diverse fields of knowledge of new age personalized medicine presented in the highly detailed chapters of the book. The book chapters are divided into two sections for convenient reading with the first section covering the general aspects of pharmaocogenomic technology that includes latest research and development in omics technologies. The first section also highlights the role of omics in modern clinical trials and even discusses the ethical consideration in pharmocogenomics. The second section is focusing on the development of personalized medicine in several areas of human health. The topics covered range from metabolic and neurological disorders to non-communicable as well as infectious diseases, and even explores the role of pharmacogenomics in cell therapy and transplantation technology. Thirty-four chapters of the book cover several aspects of pharmacogenomics and personalized medicine and have taken into consideration the varied interest of the readers from different fields of biomedical research and medicine. Advent of pharmacogenomics is the future of modern medicine, which has resulted from culmination of decades of research and now is showing the way forward. The book is an honest endeavour of researchers from all over the world to disseminate the latest knowledge and knowhow in personalized medicine to the community health researchers in particular and the educated public in general.
  • 2014 CRCnetBASE
    Liu, Yu.
    Part 1. Omics and human disease -- part 2. Translational and personalized medicine -- part 3. Molecular and genetic markers -- part 4. Omics and pathogens -- part 5. Companion diagnostics.
  • 2010 Springer
    Cho, William C. S.
  • 2005 Springer
    LaRochelle, William J.; Shimkets, Richard A.
    Also available: Print – 2005
  • 2008
    Reimers, Mark.
    Prof. Mark Reimers covers the best ways to design and interpret microarray gene expression experiments, including experiment design, pre-processing, exploratory analysis, normalization and statistical testing.
  • 2012 Springer
    Bullerwell, Charles E.
    pt. 1. Origins of organelle genomes -- pt. 2. Organelle genome evolution -- pt. 3. Mechanisms of organelle gene loss -- pt. 4. Origins of organelle proteomes -- pt. 5. Evolution of organelle transcription -- pt. 6. Evolution of organelle RNA processing -- pt. 7. Evolution of organelle translation, tRNAs and the genetic code.
  • 2009 Springer
    Villarreal, Luis P.
    An overview : identity from bacteria to belief -- The prokaryotes : viruses, hyperparasites and the origin of group identity -- Sensory systems (light, odor, pheromones) in communities of oceanic microbes -- Subjugation of the individual : prokaryotic group living : blooms, slime and mats -- Animal group identity : from slime to worms, emergence of the brain -- Group identity in aquatic animals : learning to belong -- Development of tetrapod group identity, the smell of self -- Origin of primate group identity : vision and the great ERV invasion -- Human group identity : language and a social mind.
  • 2012 ScienceDirect
    Goldman, David.
    Neurogenetic origins of behavior -- Jinn in the genome -- 2B or not 2B? -- Stephen Mobley and his X-chromosome -- Dial multifactorial for murder : the intersection of genes and culture -- Distorted capacity I : the measure of the impaired will -- Distorted capacity II: neuropsychiatric diseases and the impaired will -- Inheritance of behavior and genes for behavior : gene wars -- Scientific and historic bases of genethics: who watches the geneticists and by what principles? -- World is double helical -- DNA, RNA, and proteins in a few easy pieces -- Stochastic brain : from DNA blueprint to behavior -- Reintroducing genes and behavior -- Warriors and worriers -- How many genes does it take to make a behavior? -- Genesis and genetics of sexual behavior -- Gene by environment interaction -- Epigenetic revolution : finding the imprint of the environment on the genome -- DNA on trial -- Parents and children : neurogenetic determinism and neurogenetic individuality -- Summing up genetic predictors of behavior.
  • 2008
    Battail, Gérard.
    A brief overview of molecular genetics -- An overview of information theory -- More on molecular genetics -- More on information theory -- An outline of error-correcting codes -- DNA is an ephemeral memory -- A toy living world -- Subsidiary hypothesis, nested system -- Soft codes -- Biological reality conforms to the hypotheses -- Identification of genomic codes.
  • 2011 Springer
    Ayed, Ayeda; Hupp, Theodore.
    TP53 mutations in human cancers : selection versus mutagenesis / Magali Olivier, Audrey Petitjean, Claude Caron de Fromentel, and Pierre Hainaut -- Lessons on p53 from mouse models / Dadi Jiang and Laura D. Attardi -- TP63, TP73 : the guardian's elder brothers / Stephanie Courtois, Pierre Hainaut and Claude Caron de Fromentel -- The regulation of p53 protein function by phosphorylation / Nicola J. Maclaine and Theodore Hupp -- The p53-Mdm2 loop : a critical juncture of stress response / Yaara Levav-Cohen, Zehavit Goldberg, Osnat Alsheich Bartok, Valentina Zuckerman, Sue Haupt and Ygal Haupt -- Cooperation between MDM2 and MDMX in the regulation of p53 / Jeremy Blaydes -- Regulation and function of the original p53-inducible p21 gene / Jennifer A. Fraser -- p53 localization / Carl G. Maki -- Modes of p53 interactions with DNA in the chromatin context / Vladana Vukojevic, Tatiana Yakovleva, and Georgy Bakalkin -- p53's dilemma in transcription : analysis by microarrays / Karuppiah Kannan, Gideon Rechavi and David Givol -- Tumor viruses and p53 / Nobuo Horikoshi -- p53 and immunity / Vikram Narayan, Sarah E. Meek and Kathryn L. Ball.
  • 2013 Springer Protocols
    Su, Gloria H.
    Identification and analysis of precursors to invasive pancreatic cancer / Hanno Matthaei, Marco Dal Molin, and Anirban Maitra -- Tissue microarrays : construction and use / Helen Remotti -- Immunohistochemistry of pancreatic neoplasia / Sukhwinder Kaur ... [et al.] -- Method for conducting highly sensitive MicroRNA in situ hybridization and immunohistochemical analysis in pancreatic cancer / Lorenzo F. Sempere and Murray Korc -- Optimal molecular profiling of tissue and tissue components : defining the best processing and microdissection methods for biomedical applications / Jaime Rodriguez-Canales -- Considerations for sequencing analyses of pancreatic cancer progression and metastasis / Alvin Makohon-Moore and Christine A. Iacobuzio-Donahue -- DNA methylation analysis in human cancer / Eileen O'Sullivan and Michael Goggins -- Quantitative real-time PCR expression analysis of peripheral blood mononuclear cells in pancreatic cancer patients / Michael J. Baine, Kavita Mallya, and Surinder K. Batra -- Development of a cytokine-modified allogeneic whole cell pancreatic cancer vaccine / Dan Laheru, Barbara Biedrzycki, and Elizabeth M. Jaffee -- Prevention and genetics of pancreatic cancer : a programmatic approach / Aimee L. Lucas ... [et al.] -- Development of orthotopic pancreatic tumor mouse models / Wanglong Qiu and Gloria H. Su -- Evaluating Dietary Compounds in Pancreatic Cancer Modeling Systems / Emman Mascarinas, Guido Eibl, and Paul J. Grippo -- Quantification of murine pancreatic tumors by high-resolution ultrasound / Stephen A. Sastra and Kenneth P. Olive -- Microdissection and culture of murine pancreatic ductal epithelial cells / Yuliya Pylayeva-Gupta, Kyoung Eun Lee, and Dafna Bar-Sagi -- Sphere-forming assays for assessment of benign and malignant pancreatic stem cells / Yue J. Wang ... [et al.] -- Analysis of transplanted bone marrow-derived cells in chronic pancreatitis / Christoph B. Westphalen, Frederic Marrache, and Timothy C. Wang -- Analysis of the potential for pancreatic cancer metastasis in vitro and in vivo / Chen Huang and Keping Xie -- Use of fluorescent probes in the study of reactive oxygen species in pancreatic cancer cells / Richard D. Dinnen, Yuehua Mao, and Robert L. Fine -- Analysis of tumor-associated mucin glycotopes by western transfer methods / Vinayaga S. Gnanapragassam, Maneesh Jain, and Surinder K. Batra -- Evaluating tumor angiogenesis / Minji K. Uh, Jessica Kandel, and Jan Kitajewski -- Pooled shRNA screenings : experimental approach / Ruth Rodriguez-Barrueco, Netonia Marshall, and Jose M. Silva -- Pooled ShRNA screenings : computational analysis / Jiyang Yu ... [et al.].
  • 2008 CRCnetBASE
    Beale, Geoffrey; Preer, John R.
    Mating types in paramecium -- General description of the protista and of paramecium -- Methods of studying genetic processes in organisms of the paramecium Aurelia species group -- The determination of mating types in paramecium -- Symbionts and mitochondria of paramecium -- Determination of i-antigens -- Micronuclei and macronuclei -- Ribosomal RNA and DNA -- Cortical morphogenesis -- Behavior -- Epigenetics.
  • 2012 Springer
    Adler, Ben; Aktories, K.; Orth, Joachim H. C.
    Pasteurella multocida: Diseases and Pathogenesis / I. W. Wilkie, M. Harper, J. D. Boyce and B. Adler -- Pathogenomics of Pasteurella multocida / J. D. Boyce, T. Seemann, B. Adler and M. Harper -- The Key Surface Components of Pasteurella multocida: Capsule and Lipopolysaccharide / Marina Harper, John D. Boyce and Ben Adler -- Pasteurella multocida and Immune Cells / Katharina F. Kubatzky -- Molecular Biology of Pasteurella multocida Toxin / Joachim H. C. Orth and Klaus Aktories -- Pasteurella multocida Toxin Interaction with Host Cells: Entry and Cellular Effects / Brenda A. Wilson and Mengfei Ho -- Swine Atrophic Rhinitis Caused by Pasteurella multocida Toxin and Bordetella Dermonecrotic Toxin / Yasuhiko Horiguchi -- The Pasteurella multocida Toxin: A New Paradigm for the Link Between Bacterial Infection and Cancer / Alistair Lax.
  • 2012 Springer
    Minarovits, Janos; Niller, Hans Helmut.
    The Impact of Foreign DNA Integration on Tumor Biology and Evolution via Epigenetic Alterations / Walter Doerfler -- The Role of DNMT3B Mutations in the Pathogenesis of ICF Syndrome / Sole Gatto, Maurizio D'Esposito and Maria R. Matarazzo -- Dysfunction of the Methyl-CpG-Binding Protein MeCP2 in Rett Syndrome / Gaston Calfa, Alan K. Percy and Lucas Pozzo-Miller -- Epigenetic Alterations in Glioblastoma Multiforme / John K. Wiencke -- Aberrant Epigenetic Regulation in Breast Cancer / Amanda Ewart Toland -- The Impact of Epigenetic Alterations on Diagnosis, Prediction, and Therapy of Prostate Cancer / Christian Arsov, Wolfgang Goering and Wolfgang A. Schulz -- Epigenetic Reprogramming in Lung Carcinomas / András Kádár and Tibor A. Rauch -- Epigenetic Changes in Virus-Associated Neoplasms / Hans Helmut Niller, Ferenc Banati, Eva Ay and Janos Minarovits -- Genetic and Epigenetic Determinants of Aggression / Barbara Klausz, József Haller, Áron Tulogdi and Dóra Zelena -- Co-Regulation and Epigenetic Dysregulation in Schizophrenia and Bipolar Disorder / Dóra Zelena -- Disruption of Epigenetic Mechanisms in Autoimmune Syndromes / Lorenzo de la Rica and Esteban Ballestar -- Imprinting Disorders / Thomas Eggermann -- Epigenetics and Atherosclerosis / Einari Aavik, Mikko P. Turunen and Seppo Ylä-Herttuala -- Microbe-Induced Epigenetic Alterations / Hans Helmut Niller, Ferenc Banati, Eva Ay and Janos Minarovits.
  • 2016 Springer
    Minarovits, Janos; Niller, Hans Helmut.
    1. Epigenetic regulation -- 2. HIV-induced epigenetic alterations in host cells -- 3. Epigenetic alterations in Epstein-Barr virus-associated diseases -- 4. Epigenetic dysregulation in virus-associated neoplasms -- 5. Epigenetic alterations induced by bacterial lipopolysaccharides -- 6. Patho-epigenetics of infectious diseases caused by intracellular bacteria -- Index.
    Also available: Print – 2016
  • 2002 Springer Protocols
    Rapley, Ralph; Theophilus, Bimal D. M.
    Agarose and polyacrylamide gel electrophoresis / Andrea M. Guilliatt -- Internal labeling of DNA probes / Ralph Rapley -- End-labeling of DNA probes / Adrian J. Harwood -- Southern blotting of agarose gels bu capillary transfer / Ralph Rapley -- Restriction fragment length polymorphism / Mohammad S. Enayat -- PCR: principles, procedures, and parameters / Nicola Louise Jones -- Allele-specific oligonucleotide PCR / Elaine K. Green -- Long-range PCR / Peter A. Davies -- Analysis of nucleotide sequence variations by solid-phase minisequencing / Anu Wartiovaara -- Cycle sequencing of PCR products / G.K. Surdhar -- Fluorescent in situ hybridization / Sara A. Dyer -- The protein truncation test / Carol A. Hardy -- Mutation detection in factor vii cDNA from lymphocytes of hemophilia A patients by solid phase fluorescent chemical cleavage of mismatch / Naushin H. Waseem -- Denaturing gradient gel electrophoresis / Yvonee Wallis -- Conformation-sensitive gel electrophoresis / Ian J. Williams -- SSCp/heteroduplex analysis -- Cleavase fragment length polymorphism analysis for genotyping and mutation detection / Laura Heisler -- Automated genotyping using the DNA MassArray technology / Christian Jurinke -- An introduction to bioinformatics / Henry Brzeski.
  • 2011 Springer Protocols
    Rapley, Ralph; Theophilus, Bimal D. M.
    Conformation-Sensitive Capillary Electrophoresis / Emma Jane Ashton -- Conformation Sensitive Gel Electrophoresis / Marian Hill -- Denaturing HPLC for Mutation Screening / Mike Mitchell, Jacqueline Cutler -- In Situ Detection of Human Papillomavirus DNA After PCR-Amplification / Gerard J. Nuovo -- LATE-PCR and Allied Technologies: Real-Time Detection Strategies for Rapid, Reliable Diagnosis from Single Cells / Kenneth E. Pierce, Lawrence J. Wangh -- Long-PCR Amplification of Human Genomic DNA / Stephen Keeney -- Human Papilloma Virus Strain Detection Utilising Custom-Designed Oligonucleotide Microarrays / Duncan Ayers, Mark Platt, Farzad Javad, Philip J. Day -- Multiplex Ligation-Dependent Probe Amplification (MLPA®) for the Detection of Copy Number Variation in Genomic Sequences / Petra G. Os, Jan P. Schouten -- Screening for Genomic Rearrangements by Multiplex PCR/Liquid Chromatography / Claude Houdayer, Catherine Dehainault, Marion Gauthier-Villars, Dominique Stoppa-Lyonnet -- Mutation Surveyor: Software for DNA Sequence Analysis / Jayne A. Minton, Sarah E. Flanagan, Sian Ellard -- Non-invasive Prenatal Diagnosis / Cathy Meaney, Gail Norbury -- Automated DNA Sequencing / Yvonne Wallis, Natalie Morrell -- Phylogenetic Microarrays for Cultivation-Independent Identification and Metabolic Characterization of Microorganisms in Complex Samples / Alexander Loy, Michael Pester, Doris Steger -- Prenatal Detection of Chromosome Aneuploidy by Quantitative-Fluorescence PCR / Kathy Mann, Erwin Petek, Barbara Pertl -- Use of Robotics in High-Throughput DNA Sequencing / Stephen Keeney -- Detection of Factor V Leiden and Prothrombin c.20210G>A Allele by Roche Diagnostics LightCycler® / Peter C. Cooper -- RT-PCR for the Detection of Translocations in Bone and Soft Tissue Tumours in Formalin-Fixed Paraffin-Embedded Tissues / Ann Williams, D. Chas Mangham -- Detection of Minimal Residual Disease in Leukaemia by RT-PCR / Joanne Mason, Mike Griffiths -- Mutation Detection by Southern Blotting / Gillian Mellars, Keith Gomez.
  • 2015 Springer Protocols
    Basu, Chhandak.
    "This volume provides an overview on design PCR primers for successful DNA amplification. Chapters focus on primer design strategies for quantitative PCR, in silico PCR primer design , and primer design using software. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls." -- Provided by publisher.
  • Springer Protocols
    Yuryev, Anton.
  • 2011 Springer Protocols
    Park, Daniel J.
    Setup of a PCR Laboratory / Zaheer Khan -- Long-Range PCR with a DNA Polymerase Fusion / Holly H. Hogrefe, Michael C. Borns -- Isolation of Genomic Insertion Sites of Proviruses Using Splinkerette-PCR-Based Procedures / Bin Yin -- Lariat-Dependent Nested PCR for Flanking Sequence Determination / Daniel J. Park -- CODEHOP PCR and CODEHOP PCR Primer Design / Jeannette P. Staheli, Richard Boyce, Dina Kovarik, Timothy M. Rose -- Sequencing of Difficult DNA Regions by SAM Sequencing / Keith R. Mitchelson -- A Global Single-Cell cDNA Amplification Method for Quantitative Microarray Analysis / Kazuki Kurimoto, Mitinori Saitou -- Quantitation of MicroRNAs by Real-Time RT-qPCR / Caifu Chen, Ruoying Tan, Linda Wong, Richard Fekete, Jason Halsey -- High-Throughput SuperSAGE / Hideo Matsumura, Kentaro Yoshida, Shujun Luo, Detlev H. Krüger, Günter Kahl, Gary P. Schroth, Ryohei Terauchi -- Deep Cap Analysis of Gene Expression / Junpei Kurosawa, Hiromi Nishiyori, Yoshihide Hayashizaki -- Linking Emulsion PCR Haplotype Analysis / James G. Wetmur, Jia Chen -- PAP-LMPCR: An Improved, Sequence-Selective Method for the In Vivo Analysis of Transcription Factor Occupancy and Chromatin Fine Structure / Richard Ingram, Arthur Riggs, Constanze Bonifer -- The Many Faces of MLPA / Thomas Ohnesorg, Erin Turbitt, Stefan J. White -- Assessing Gene-Specific Methylation Using HRM-Based Analysis / Ee Ming Wong, Alexander Dobrovic -- Alu PCR / Maurizio Cardelli -- Asynchronous PCR / Caifu Chen, David Ruff, Jason Halsey -- Novel Applications of PCR Through the Use of DNA Substrates / Stuart M. Wilson -- Enhanced Solid Phase PCR for Increased Loading of Amplicon onto Solid Support / Daniel J. Park -- Application of Blocking Oligonucleotides to Improve Signal-to-Noise Ratio in a PCR / Hege Vestheim, Bruce E. Deagle, Simon N. Jarman -- Asymmetric Overlap Extension PCR Method for Site-Directed Mutagenesis / Yue-Hua Xiao, Yan Pei -- Ribosome Display: A Technology for Selecting and Evolving Proteins from Large Libraries / Birgit Dreier, Andreas Plückthun -- GLOBE: Analysis of DNA-Protein Interaction Analysis / Takaaki Kojima, Hideo Nakano -- PCR DNA-Array Profiling of DNA-Binding Transcription Factor Activities in Adult Mouse Tissues / Yimin Sun, Jing Cheng, Keith R. Mitchelson -- Nucleotide Exchange and Excision Technology DNA Shuffling and Directed Evolution / Janina Speck, Sabine C. Stebel, Katja M. Arndt, Kristian M. Müller.
  • 2014 Springer
    Houser, Christine M.
    Often, information in review books can raise as many questions as it answers. This interferes with the study process, because the learner must either look up additional information or skip ahead without truly comprehending what he or she has read. As an alternative, Pediatric Genetics and Inborn Errors of Metabolism: A Practically Painless Review presents bite-size chunks of information that can be read and processed rapidly, helping learners to stay active while studying and to pick up new information the first time they read it. This book's question and answer format allows for self-testing or study with a partner or a group. The format also facilitates dipping into the book during a few minutes of downtime at the hospital or office. Pediatric Genetics and Inborn Errors of Metabolism: A Practically Painless Review is a quick and easy way to master these tricky topics and is suitable for those studying for the pediatric board exam, practicing physicians brushing up their skills, and any busy clinician who wants to learn more about these topics while on the go.
  • 2015 CRCnetBASE
    Lee, Heewon.
  • 2008 Springer Protocols
    Cohen, Nadine.
    Challenges, opportunities, and evolving landscapes in pharmacogenomics and personalized medicine : an industry perspective / Nadine Cohen and Theresa Frangiosa -- Implementation of pharmacogenomic sample collection in clinical trials / Deborah Sokol Ricci and Monique Franc -- Pharmacogenomics : the regulatory environment and labeling implications / Myong-Jin Kim ... [et al.] -- Applications of pharmacogenomics in drug discovery / Duncan McHale -- Applications of pharmacogenomics in clinical trials / Monique Franc -- Pharmacogenomics applications in drug metabolism : from genotyping to drug label-challenges? / Ann K. Daly -- The genetics of adverse drug reactions : promises and problems / Martin Armstrong -- Strategies and resources for marker selection and genotyping in genetic association studies / Nicole Soranzo, Dong-Jing Fu, and Qingqin S. Li -- Study design and statistical issues in pharmacogenetics research : from candidate genes to genome-wide screens / Nicholas J. Schork, Nathalie Malo, and Eric J. Topol -- Holy SNP, Batman! / Reyna Favis -- Predictive biomarker classifiers in the design of pivotal clinical trials / Richard Simon -- Translation of biomarkers into clinical utility / William L. Trepicchio and George Mulligan -- Pharmacogenomic study feasibility assessment and pharmaceutical business decision-making / Monique Franc and Theresa Frangiosa -- Co-development of drugs and pharmacogenomics-based diagnostics in oncology / Jeffrey S. Ross -- Pharmacogenomics applications in epilepsy / Chantal Depondt -- Pharmacogenomics in Alzheimer's disease / Ramón Cacabelos -- Pharmacogenomics applications in psychiatric disorders / Todd Lencz and Anil K. Malhotra -- Pharmacogenomics in HIV disease / Amalio Telenti -- Pharmacogenomics and cardiovascular drugs / Gérard Siest ... [et al.] -- Pharmacogenomic applications in children / Susan F.A. Grant and Hakon Hakonarson -- Pharmacogenomics of rare and monogenic disorders / Paul D. Maher.
  • 2008 Springer Protocols
    Yan, Qing.
  • 2009 Springer Protocols
    Graauw, Marjo de.
    A high-resolution two dimensional gel- and pro-Q DPS-based proteomics workflow for phosphoprotein identification and quantitative profiling / Ganesh K. Agrawal and Jay J. Thelen -- Differential phosphoprotein labelling (DIPPL) using ³²P and ³³P / Aviva M. Tolkovsky and Andreas Wyttenbach -- Identification of oxidative stress-induced tyrosine phosphorylated proteins by immunoprecipitation and mass spectrometry / Ma Carmen Duran, Hong-Lin Chan, and John F. Timms -- Enrichment and characterization of phosphopeptides by immobilized metal affinity chromatography (IMAC) and mass spectrometry / Tine E. Thingholm and Ole N. Jensen -- The use of titanium dioxide micro-columns to selectively isolate phosphopeptides from proteolytic digests / Tine E. Thingholm and Martin R. Larsen -- Enrichment and separation of mono- and multiply phosphorylated peptides using sequential elution from IMAC prior to mass spectrometric analysis / Tine E. Thingholm , Ole N. Jensen, and Martin R. Larsen -- Use of stable isotope labeling by amino acids in cell culture (SILAC) for phophotyrosine protein identification and quantitation / Guoan Zhang and Thomas A. Neubert -- Hydrophilic interaction chromatography for fractionation and enrichment of the phosphoproteome / Dean E. McNulty and Roland S. Annan -- SILAC for global phosphoproteomic analysis / Genaro Pimienta, Raghothama Chaerkady, and Akhilesh Pandey -- Quantitative phospho-proteomics based on soluble nanopolymers / Anton Iliuk and W. Andy Tao -- Profiling the tyrosine phosphorylation state using SH2 domains / Kevin Dierck ... [et al.] -- An overview of the qualitative analysis of phosphoproteins by mass spectrometry / Philip R. Gafken -- The analysis of phosphoproteomes by selective labelling and advanced mass spectrometric techniques / Angela Amoresano ... [et al.] -- On-line liquid chromatography electron capture dissociation for the characterization of phosphorylation sites in proteins / Steve M.M. Sweet and Helen J. Cooper -- Quantification of protein phosphorylation by [mu]LC-ICP-MS / Ralf Krüger, Nico Zinn, and Wolf D. Lehmann -- Reverse-phase diagonal chromatography for phosphoproteome research / Kris Gevaert and Joël Vandekerckhove -- Chemical tagging strategies for mass spectrometry-based phospho-proteomics / Alexander Leitner and Wolfgang Lindner -- Antibody array platform to monitor protein tyrosine phosphorylation in mammalian cells / Alicia S. Chung and Y. Eugene Chin -- Protein tyrosine kinase characterization based on fully automated synthesis of (phospho)peptide arrays in microplates / W. Carl Saxinger -- Kinome profiling using peptide arrays in eukaryotic cells / Kaushal Parikh, Maikel P. Peppelenbosch, and Tita Ritsema -- ProMoST : a tool for calculating the pI and molecular mass of phosphorylated and modified proteins on two-dimensional gels / Brian D. Halligan -- Kinase-specific preiction of protein phosphorylation sites / Martin L. Miller and Nikolaj Blom -- Reconstructing regulatory kinase pathways from phosphopeptide data : a bioinformatics approach / Lawrence G. Puente, Robin E.C. Lee, and Lynn A. Megeney.
  • 2008 Springer Protocols
    Murphy, William J.
    From gene-scale to genome-scale phylogenetics : the data flood in, but the challenges remain / Antonis Rokas and Stylianos Chatzimanolis -- Phylogenomic analysis of chromosome sorting and painting / Roscoe Stanyon and Gary Stone -- FISH for mapping single copy genes / Terje Raudsepp and Bhanu P. Chowdhary -- Construction of radiation hybrid panels / John E. Page and William J. Murphy -- Survey sequencing and radiation hybrid mapping to construct comparative maps / Christophe Hitte ... [et al.] -- Construction of high-resolution comparative maps in mammals using BAC-end sequences / Denis M. Larkin and Harris A. Lewin -- Amniote phylogenomics : testing evolutionary hypotheses with BAC library scanning and targeted clone analysis of large-scale sequences from reptiles / Andrew M. Shedlock, Daniel E. Janes, and Scott V. Edwards -- Comparative physical mapping : universal overgo hybridization probe design and BAC library hybridization / James W. Thomas -- Phylogenomic resources at the UCSC Genome Browser / Kate Rosenbloom ... [et al.] -- Computational tools for the analysis of rearrangements in mammalian genomes / Glenn Tesler and Guillaume Bourque -- Computational reconstruction of ancestral DNA sequences / Mathieu Blanchette ... [et al.] -- Sequencing and phylogenomic analysis of whole mitochondrial genomes of animals / Rafael Zardoya and Mónica Suárez -- Retroposons : genetic footrpints on the evolutionary paths of life / Hidenori Nishihara and Norihiro Okada -- LINE-1 elements : analysis by FISH and nucleotide sequences / Paul D. Waters ... [et al.] -- Identification of cryptic sex chromosomes and isolation of X- and Y-borne genes / Paul D. Waters ... [et al.]
  • 2014 Springer
    Blau, N.; Dionisi-Vici, Carlo; Duran, Marinus; Gibson, K. Michael.
    Introductory Chapters -- Amino acids -- Organic acids -- Vitamins and neurotransmitter -- Energy metabolism -- Organelles -- Selected disorder -- Biochemical phenotypes of questionable clinical significance -- Profiles.
  • 2006 CRCnetBASE
    Bidlack, Wayne R.; Meskin, Mark S.; Randolph, R. Keith.
  • 2002 ScienceDirect
    Dixon, Richard A.; Romeo, John T.
  • 2007 Springer Protocols
    Cregg, James M.
    Introduction : distinction between Pichia pastoris and other expression systems / James M. Cregg -- Vectors and strains for expression / Joan Lin-Cereghino and Geoff P. Lin-Cereghino -- DNA-mediated transformation / James M. Cregg -- Rational design and optimization of fed-batch and continuous fermentation / Wenhui Zhag, Mehmet Inan, and Michael M. Meagher -- Saturation of the secretory pathway by overexpression of a hookworm (Necator americanus) protein (Na-ASP1) / Mehmet Inan ... [et al.] -- Purification of the N- and C-terminal subdomains of recombinant heavy chain fragment C of botulinum neurotoxin serotype C / Jicai Huang ... [et al.] -- Rapid screening of chromatography resins for the purification of proteins / Sandra E. Ríos, Erin M. Giaccone, and Tillman U. Gerngross -- Characterization of O-linked saccharides on glycoproteins / Roger K. Bretthauer -- Modification of the N-glycosylation pathway to produce homogeneous human-like glycans using glycoswitch plasmids / Wouter Vervecken ... [et al.] -- N-linked glycan characterization of heterologous proteins / Huijan Li ... [et al.] -- Heavy labeling of recombinant proteins / Eric Rodriguez -- Selenomethionine labeling of recombinant proteins / Anna M. Larsson and T. Alwyn Jones -- Selective isotopic labeling of recombinant proteins using amino acid auxotroph strains / James W. Whittaker -- Classical genetics / Ilya Tolstorukov and James M. Cregg -- Identification of pexophagy genes by restriction enzyme-mediated integration / Laura A. Schroder, Benjamin S. Glick, and William A. Dunn, Jr. -- Characterization of protein-protein interactions : application to the understanding of peroxisome biogenesis / Sebastien Leon ... [et al.] -- Localization of proteins and organelles using fluorescence microscopy / Jean-Claude Farre ... [et al.] -- Fluorescence microscopy and thin-section electron microscopy / Benjamin S. Glick.
  • 2014 Springer Protocols
    Siomi, Mikiko C.
    Chromatin Immunoprecipitation Assay of Piwi in Drosophila / Hang Yin and Haifan Lin -- Drosophila Germline Stem Cells for In Vitro Analyses of PIWI-Mediated RNAi / Yuzo Niki, Takuya Sato, Takafumi Yamaguchi, Ayaka Saisho, Hiroshi Uetake, and Hidenori Watanabe -- RNAi and Overexpression of Genes in Ovarian Somatic Cells / Kuniaki Saito -- Making piRNAs In Vitro / Shinpei Kawaoka, Susumu Katsuma, and Yukihide Tomari -- A Framework for piRNA Cluster Manipulation / Ivan Olovnikov, Adrien Le Thomas, and Alexei A. Aravin -- Biochemical and Mass Spectrometric Analysis of 3ʹ-End Methylation of piRNAs / Takeo Suzuki, Kenjyo Miyauchi, Yuriko Sakaguchi, and Tsutomu Suzuki -- HITS-CLIP (CLIP-Seq) for Mouse Piwi Proteins / Anastassios Vourekas and Zissimos Mourelatos -- DNA Methylation in Mouse Testes / Satomi Kuramochi-Miyagawa, Kanako Kita-Kojima, Yusuke Shiromoto, Daisuke Ito, Hirotaka Koshima, and Toru Nakano -- Analysis of Small RNA-Guided Endonuclease Activity in Endogenous Piwi Protein Complexes from Mouse Testes / Michael Reuter and Ramesh S. Pillai -- Small RNA Library Construction from Minute Biological Samples / Jessica A. Matts, Yuliya Sytnikova, Gung-wei Chirn, Gabor L. Igloi, and Nelson C. Lau -- Analysis of sDMA Modifications of PIWI Proteins / Shozo Honda, Yoriko Kirino, and Yohei Kirino -- Analyses of piRNA-Mediated Transcriptional Transposon Silencing in Drosophila: Nuclear Run-On Assay on Ovaries / Sergey Shpiz and Alla Kalmykova -- Combined RNA/DNA Fluorescence In Situ Hybridization on Whole-Mount Drosophila Ovaries / Shpiz, Sergey Lavrov, and Alla Kalmykova -- Fast and Accurate Method to Purify Small Noncoding RNAs from Drosophila Ovaries / Thomas Grentzinger and Séverine Chambeyron -- Isolation of Zebrafish Gonads for RNA Isolation / Hsin-Yi Huang and René F. Ketting -- Small RNA Library Construction for High-Throughput Sequencing / Jon McGinn and Benjamin Czech -- Analysis of Piwi-Loaded Small RNAs in Terahymena / Tomoko Noto, Henriette M. Kurth, and Kazufumi Mochizuki -- Effective Gene Knockdown in the Drosophila Germline by Artificial miRNA-Mimicking siRNAs / Hailong Wang, Haidong Huang, and Dahua Chen -- Isolation and Bioinformatic Analyses of Small RNAs Interacting with Germ Cell-Specific Argonaute in Rice / Reina Komiya and Ken-Ichi Nonomura.
  • 2014 Springer Protocols
    Hicks, Glenn R.; Robert, Stéphanie.
    Fully-automated Compound Screening in Arabidopsis thaliana Seedlings -- Time-profiling Fluorescent Reporters in the Arabidopsis Root -- Screening for Bioactive Small Molecules by in vivo Monitoring of Luciferase-based Reporter Gene Expression in Arabidopsis thaliana -- Application of Yeast-two Hybrid Assay to Chemical Genomic Screens: A High-throughput System to Identify Novel Molecules Modulating Plant Hormone Receptor Complexes -- High-throughput Screening of Small Molecule Libraries for Inducers of Plant Defense Responses -- Using a Reverse Genetics Approach to Investigate Small Molecule Activity -- Investigating the Phytohormone Ethylene Response Pathway by Chemical Genetics -- Screening for Inhibitors of Chloroplast Galactolipid Synthesis Acting in membrano and in Planta -- Forward Chemical Screening of Small RNA Pathways -- Identification and Use of Fluorescent Dyes for Plant Cell Wall Imaging Using High-Throughput Screening -- High-throughput Identification of Chemical Endomembrane Cycling Disruptors Utilizing Tobacco Pollen -- Plant Chemical Genomics: Gravity Sensing and Response -- Screening Chemical Libraries for Compounds that Affect Protein Sorting to the Yeast Vacuole -- The use of Multi-drug Approach to Uncover New Players of the Endomembrane System Trafficking Machinery -- Cheminformatic Analysis of High-Throughput Compound Screens -- Endomembrane Dissection Using Chemically-Induced Bioactive Clusters -- Statistical Molecular Design: A Tool to Follow Up Hits From Small Molecule Screening -- Early Stage Hit Triage for Plant Chemical Genetic Screens and Target Site Identification -- Screening for Gene Function using the FOX (Full-length cDNA OvereXpressor gene) Hunting System -- Quantification of Stable Isotope Label in Metabolites via Mass Spectrometry -- 1H NMR Based Metabolomics Methods for Chemical Genomics Experiments -- Determination of Auxin Transport Parameters on the Cellular Level -- Analyzing the in vivo Status of Exogenously Applied Auxins: A HPLC-based Method to Characterize the Intracellularly Localized Auxin Transporters.
  • 2011 Springer Protocols
    Birchler, James A.
    Recent advances in plant transformation -- Engineering the plastid genome of nicotiana sylvestris, a diploid model species for plastid genetics -- Homologous recombination in plants : An antireview -- Chromosome painting for plant biotechnology -- Plant B chromosomes -- Telomere truncation in plants -- Engineered plant minichromosomes -- Method for bxb1-mediated site-specific integration in planta -- Targeted mutagenesis in arabidopsis using zinc-finger nucleases -- Vectors and methods for hairpin RNA and artificial microRNA-mediated gene silencing in plants -- Recombinant protein expression in nicotiana -- Chromosome analysis and sorting using flow cytometry -- Super-stretched pachytene chromosomes for plant molecular cytogenetic mapping -- Cytological dissection of the triticeae chromosomes by the gametocidal system -- Development and use of oat-maize chromosome additions and radiation hybrids -- Enhancer trapping in plants -- Chromatin beacons : Global sampling of chromatin physical properties using chromatin charting lines -- Transposable elements as catalysts for chromosome rearrangements.
  • 2012 Springer Protocols
    Carles, Maria C.; Hennell, James R.; Sucher, Nikolaus J.
    A taxonomist's view on genomic authentication -- DNA fingerprinting, DNA barcoding, and next generation sequencing technology in plants -- Challenges in the DNA barcoding of plant material -- Plant genetics for forensic applications -- DNA purification from multiple sources in plant research with homemade silica resins -- Random amplified marker technique for plants rich in polyphenols -- Amplified fragment length polymorphism: An invaluable fingerprinting technique for genomic, transcriptomic, and epigenetic studies -- Restriction fragment length polymorphism of the 5s-rRNA-NTS region: A rapid and precise method for plant identification -- ISSR: A reliable and cost-effective technique for detection of DNA polymorphism -- Development of sequence characterized amplified region from random amplified polymorphic DNA amplicons -- Authentication of medicinal plants by SNP-based multiplex PCR -- Multiplex PCR method to discriminate artemisia iwayomogi from other artemisia plants -- Loop-mediated isothermal amplification for the detection of plant pathogens -- Genomic DNA extraction and barcoding of endophytic fungi -- Using GenBank(R) for genomic authentication: a tutorial.
  • 2014 Springer Protocols
    McKeown, Peter C.; Spillane, Charlie.
    1. Landscaping plant epigenetics / Peter C. McKeown and Charles Spillane -- 2. The gene balance hypothesis: dosage effects in plants / James A. Birchler and Reiner A. Veitia -- 3. High-throughput RNA-seq for allelic or locus-specific expression analysis in Arabidopsis-related species, hybrids, and allotetraploids / Danny W.-K. Ng, Xiaoli Shi, Gyoungju Nah and Z. Jeffrey Chen -- 4. Inference of allele-specific expression from RNA-seq data / Paul K. Korir and Cathal Seoighe -- 5. Screening for imprinted genes using high-resolution melting analysis of PCR amplicons / Robert Day and Richard Macknight -- 6. Analysis of genomic imprinting by quantitative allele-specific expression by pyrosequencing® / Peter C. McKeown, Antoine Fort and Charles Spilane -- 7. Endosperm-specific chromatin profiling by fluorence-activated nuclei sorting and chip-on-chip / Isabelle Weinhofer and Claudia Köhler -- 8. Imaging sexual reproduction in Arabidopsis using fluorescent markers / Mathieu Ingouff -- 9. Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip / Sandra Cortijo, René Wardenaar, Maria Colomé-Tatché, Frank Johannes and Vincent Colot -- 10. Methylation-sensitive amplified polymorphism (MSAP) marker to investigate drought-stress response in montepulciano and sangiovese grape cultivars / Emidio Albertini and Gianpiero Marconi -- 11. Detecting histone modifications inplants / Jie Song, Bas Rutjens and Caroline Dean -- 12. Quantitatively profiling genome-wide patterns of histone modifications in Arabidopsis thaliana using a chIP-seq / Chongyuan Luo and Eric Lam -- 13. Analysis of retrotransposon activity in plants / Christopher DeFraia and R. Keith Slotkin -- 14. Detecting epigenetic effects of transposable elements in plants / Christian Parisod, Armel Salmon, Malika Ainouche and Marie-Angèle Grandbastieu -- 15. Detection and investigation of transitive gene silencing in plants / Leen Vermeersch, Nancy De Winne and And Depicker.
  • 2015 Springer Protocols
    Mysore, Kirankumar S.; Senthil-Kumar, Muthappa.
    Advances in plant gene silencing methods / Prachi Pandey, Muthappa Senthil-Kumar, and Kirankumar S. Mysore -- Strategies for altering plant traits using virus-induced gene silencing technologies / Christophe Lacomme -- Bioinformatics tools for achieving better gene silencing in plants / Firoz Ahmed, Xinbin Dai, and Patrick Xuechun Zhao -- Profiling of small RNAs involved in plant-pathogen interactions / Dongdong Niu ... [et al.] -- RNAi-mediated resistance to viruses in genetically engineered plants / Abdulrazak B. Ibrahim and Francisco J. L. Aragão -- Simplifying transgene locus structure through Cre-lox recombination / Vibha Srivastava and David W. Ow -- Transgene-induced gene silencing in plants / Yun Jin and Hui-Shan Guo -- Gene silencing by DNA interference in fern gametophytes / Masamitsu Wada and Hidenori Tsuboi -- Induction of stable epigenetic gene silencing in plants using a virus vector / Akira Kanazawa and Megumi Kasai -- Method for validating microRNAs in plants by miR-RACE / Jinggui Fang and Xin Sun -- MR VIGS : microRNA-based virus-induced gene silencing in plants / Weiwei Chen ... [et al.] -- High-throughput RNA interference (RNAi)-based approach using hairy roots for the study of plant-rhizobia interactions / Senjuti Sinharoy, Catalina I. Pislariu, and Michael K. Udvardi -- Functional genomics method for assaying gene function in phytopathogenic fungi through host-induced gene silencing mediated by agroinfiltration / Vinay Panwar, Brent McCallum, and Guus Bakkeren -- Effective and convenient method for the delivery of apple latent spherical virus (ALSV)-based vectors into plant cells by agroinoculation / Tatsuya Kon and Nubuyuki Yoshikawa -- Virus-induced gene silencing (VIGS) for functional genomics in rice using Rice tungro bacilliform virus (RTBV) as a vector / Ravi Kant, Shweta Sharma, and Indranil Dasgupta -- Virus-induced gene silencing of fiber-related genes in cotton / John R. Tuttle, Candace H. Haigler, and Dominique (Niki) Robertson -- Establishment of an efficient virus-induced gene silencing (VIGS) assay in Arabidopsis by agrobacterium-mediated rubbing infection / Ana Marcia E. de A. Manhães, Marcos V. V. de Oliveira, and Libo Shan -- Virus-induced gene silencing as a scalable tool to study drought tolerance in plants / Gavin M. George, Michael E. Ruckle, and James R. Lloyd -- VIGS for dissecting mechanisms involved in the symbiotic interaction of microbes with plants / Mette Grønlund -- Construction of a cotton VIGS library for functional Genomics study / Maoying Li, Fangjun Li, and Ping He -- Synthetic gene complementation to determine off-target silencing / Dhirendra Kumar -- Construction of mismatched inverted repeat (IR) silencing vectors for maximizing IR stability and effective gene silencing in plants / M. E. Chrissie Rey ... [et al.].
  • 2008 Karger
    Volff, Jean-Nicolas.
    Paleopolyploidy and its impact on the structure and function of modern plant genomes / A.H. Paterson -- Genomic history and gene family evolution in angiosperms: challenges and opportunities / J. Sampedro, D. Cosgrove -- The evolutionary position of subfunctionalization, downgraded / M. Freeling -- Grass genome structure and evolution / J. Messing, J.L. Bennetzen -- Phylogenetic insights into the pace and pattern of plant genome size evolution / C.E. Grover, J.S. Hawkins, J.F. Wendel -- Plant transposable elements / J.M. Deragon, J.M. Casacuberta, O. Panaud -- Plant sex chromosomes / D. Charlesworth -- Plant centromeres / J.C. Lamb ... [et al.] -- MiRNAs in the plant genome: all things great and small / B.C. Meyers, P.J. Green, C. Lu -- Recent insights into the evolution of genetic diversity of maize / A. Rafalski, S. Tingey -- The rice genome structure as a trail from the past to beyond / T. Sasaki.
  • 2009 Springer Protocols
    Gustafson, J. P.; Langridge, Peter; Somers, Daryl J.
    Role of model plant species / Richard Flavell -- New technologies for ultra-high throughput genotyping in plants / Nikki Appleby, David Edwards, and Jacqueline Batley -- Genetic maps and the use of synteny / Chris Duran, David Edwards, and Jacqueline Batley -- A simple TAE-based method to generate large insert BAC libraries from plant species / Bu-Jun Shi, J. Perry Gustafson, and Peter Langridge -- Transcript profiling and expression level mapping / Elena Potokina, Arnis Druka, and Michael J. Kearsey -- Methods for functional proteomic analyses / Christof Rampitsch and Natalia V. Bykova -- Stable transformation of plants / Huw D. Jones and Caroline A. Sparks -- Transient transformation of plants / Huw D. Jones, Angela Doherty, and Caroline A. Sparks -- Bridging the gene-to-function knowledge gap through functional genomics / Stephen J. Robinson and Isobel A.P. Parkin -- Heterologous and cell-free protein expression systems / Naser Farrokhi ... [et al.] -- Functional genomics and structural biology in the definition of gene function / Maria Hrmova and Geoffrey B. Fincher -- In situ analysis of gene expression in plants / Sinéad Drea ... [et al.] -- Plant and crop databases / David E. Matthews, Gerard R. Lazo, and Olin D. Anderson -- Plant genome annotation methods / Shu Ouyang ... [et al.] -- Molecular plant breeding : methodology and achievements / Rajeev K. Varshney ... [et l.] -- Practical delivery of genes to the marketplace / David A. Fischhoff and Molly N. Cline -- Ecological genomics of natural plant populations : the Israeli perspective / Eviatar Nevo -- Genome sequencing approaches and successes / Michael Imelfort ... [et al.]
  • 2015 Springer Protocols
    Batley, Jacqueline.
    Advances in plant genotyping : where the future will take us / Dhwani A. Patel [and three others] -- Molecular marker applications in plants / Alice C. Hayward [and three others] -- Bioinformatics : identification of markers from next-generation sequence data / Pradeep Ruperao and David Edwards -- Molecular marker databases / Kaitao Lai, Michał Tadeusz Lorenc, and David Edwards -- Plant genotyping using flourescently tagged inter-simple sequence repeats (ISSRs) : basic principles and methodology / Linda M. Prince -- SSR genotyping / Annaliese S. Mason -- Genotyping analysis using an RFLP assay / Shutao Dai and Yan Long -- DNA barcoding for plants / Natasha de Vere [ and three others] -- Multiplexed digital gene expression analysis for gentical genomics in large plant populations / Christian Obermeier [and three others] -- SNP genotyping by heteroduplex analysis / Norma Paniego [and three others] -- Application of the high-resolution melting technique for gene mapping and SNP detection in plants / David Chagné -- Challenges of genotyping polyploid species / Annaliese S. Mason -- Genomic reduction assisted single nucleotide polymorphism discovery using 454-pyrosequencing / Peter J. Maughan, Joshua A. Udall, and Eric N. Jellen -- Inter-SINE amplified polymorphism (ISAP) for rapid and robust plant genotyping / Torsten Wenke [and four others] -- Screening of mutations by TILLING in plants / Nian Wang and Lei Shi -- Gene analysis using mass spectrometric cleaved amplified polymorphic sequence (MS-CAPS) with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF) / Hideyuki Kajiwara -- Quantitative SNP genotyping of polyploids with MassARRAY and other platforms / Marcelo Mollinari and Oliver Serang -- SNP genotyping using KASPar assays / Scott M. Smith and Peter J. Maughan -- Skim-based genotyping by sequncing / Agnieszka A. Gilicz, Philipp E. Bayer, and David Edwards -- The restriction enzyme target approach to genotyping by sequencing (GBS) / Elena Hilario -- Methods for the design, implementation, and analysis of Illumina Infinium [trademark] SNP assays in plants / David Chagné [and four others] -- Use of the Illumina GoldenGate assay for single nuccleotide polymorphism (SNP) genotyping in cereal crops / Shiaoman Chao and Cindy Lawley.
  • 2015 Springer Protocols
    Murcha, Monika W.; Whelan, James.
    Isolation of intact mitochondria from the model plant species Arabidopsis thaliana and Oryza sativa / Monika W. Murcha and James Whelan -- Determining mitochondrial transcript termini for the study of transcription start sites and transcript 5' end maturation / Stefan Binder and Kristina Kühn -- Mitochondrial run-on transcription assay using biotin labeling / Kristina Kühn -- In vitro RNA uptake studies in plant mitochondria / Szymon Kubiszewski-Jakubiak [and five others] -- In vitro and in vivo protein uptake studies in plant mitochondria / Owen Duncan [and three others] -- Plant mitochondrial proteomics / Nicolas L. Taylor and A. Harvey Millar -- Identification of lysine-acetylated mitochondrial proteins and their acetylation sites / Markus Hartl, Ann-Christine König, and Iris Finkemeier -- Flowchart to analyze protease activity in plant mitochondria / Pedro F. Teixeira [and three others] -- Activity measurements of mitochondrial enzymes in native gels / Peter Schertl and Hans-Peter Braun -- Activity assay for plant mitochondrial enzymes / Shaobai Huang, Chun Pong Lee, and A. Harvey Millar -- Analysis of type II NAD(P)H dehydrogenases / Kathleen L. Soole and Chevaun A. Smith -- Assessment of respiration in isolated plant mitochondria using clark-type electrodes / Richard P. Jacoby, A. Harvey Millar, and Nicolas L. Taylor -- Micro-respiratory measurements in plants / Yun Shin Sew, A. Harvey Millar, and Elke Stroeher -- Improvements to define mitochondrial metabolomics using nonaqueous fractionation / Richard Fly [and four others] -- Mitochondrial markers of programmed cell death in Arabidopsis thaliana / Theresa J. Reape ... [et al.] -- Imaging and analysis of mitochondrial dynamics in living cells / Sanjaya B. Ekanayake [and four others] -- Analysis of plant mitochondrial function using fluorescent protein sensors / Stephan Wagner [and six others] -- In planta analysis of leaf mitochondrial superoxide and nitric oxide / Marina Cvetkovska and Greg C. Vanlerberghe -- Databases and informatics resources for analysis of plant mitochondria / Reena Narsai -- Expression and crystallization of the plant alternative oxidase / Benjamin May [and six others].
  • 2011 Springer Protocols
    Perry, Sharyn E.; Yuan, Ling.
    1. MADS and more: transcription factors that shape the plant / Rainer Melzer and Günter Thei€en -- 2. In silico mining and PCR-based approaches to transcription factor discovery in non-model plants: gene diversity of the WRKY transcription factors in conifers / Jun-Jun Liu and Yu Xiang -- 3. Isolation of plant transcription factors using a yeast one-hybrid system / Tatiana Pyvovarenko and Sergiy Lopato -- 4. A transposon-based activation tagging system for gene function discovery in arabidopsis / Nayelli Marsch-Martinez -- 5. CRWA-T, an effective gene silencing system utilizing chimeric repressors / Nobutaka Mitsuda, Kyoko Matsui, Miho Ikeda, Masaru Nakata, Yoshimi Oshima, Yukari Nagatoshi, and Masaru Ohme-Takagi -- 6. Analysis of a transcription factor using transient assay in arabidopsis protoplasts / Yuji Iwata, Mi-Hyun Lee, and Nozomu Koizumi -- 7. Microarray-based identification of transcription factor target genes / Maartje Gorte, Anneke Horstman, Robert B. Page, Renze Heidstra, Arnold Stromberg and Kim Boutilier -- 8. Yeast protein-protein interaction assays and screens / Stefan de Folter and Richard G.H. Immink -- 9. Mapping functional domains of transcription factors / Ling Zhu and Enamul Huq -- 10. Biomolecular fluorescence complementation as a tool to study interactions of regulatory proteins in plant protoplasts / Sitakanta Pattanaik, Joshua R. Werkman, and Ling Yuan -- 11. Isolation of transcription factor complexes from arabidopsis cell suspension cultures by tandem affinity purification / Jelle Van Leene, Dominique Eeckhout, Geert Persiau, Eveline Van De Slijke, Jan Geerinck, Gert Van Isterdael, Erwin Witters, and Geert De Jaeger -- 12. Assaying transcription factor stability / Jasmina Kurepa and Jan A. Smalle -- 13. How to access the intercellular trafficking of transcription factors / Munawar Ahmad, Won Kyong Cho, Yeonggil Rim, Lijun Huang, and Jae-Yean Kim -- 14. SELEX (systematic evolution of ligands by exponential enrichment), as a powerful tool for deciphering the protein-DNA interaction space / Chenglin Chai, Zidian Xie, and Erich Grotewold -- 15. Footprinting and missing nucleoside analysis of transcription factor-DNA complexes / Ivana L. Viola and Daniel H. Gonzalez -- 16. Chromatin immunoprecipitation to verify or to identify in vivo protein-DNA interactions / Yumei Zheng and Sharyn E. Perry -- 17. Visualizing and characterizing invivo DNA-binding events and direct target genes of plant transcription factors / Jose M. Muiño, Gerco C. Angenent, and Kerstin Kaufmann -- 18. Mapping in vivo protein-DNA interactions in plants by DamID, a DNA adenine methylation-based method / Sophie Germann and Valérie Gaudin -- 19. Directed evolution through DNA shuffling for the improvement and understanding of genes and promoters / Joshua R. Werkman, Sitakanta Pattanaik, and Ling Yuan.
  • 2012 Springer
    Casacuberta, Josep M.; Grandbastien, Marie-Angèle.
    Transposable elements are DNA sequences with the capacity to move within a genome. Although their presence and impact has long been known, the recent genome-wide analysis of many eukaryotic genomes has uncovered their major role in genome dynamics and function. The present book explains how to recognize and study transposable elements, e.g. by using state-of-the-art strategies based on new-generation sequencing. Moreover, the impact of transposable elements on plant genome structure and function is reviewed in detail and illustrated in examples and case studies. The book is intended both for readers familiar with the field and for newcomers. With large-scale sequencing becoming increasingly available, more and more people will come across transposable element sequences in their data, and this volume will hopefully help to convince them that transposable elements are not just "junk" DNA, and may actually be the most interesting and fun part of their data!
  • 2013 Springer Protocols
    Peterson, Thomas.
    Historical overview of transposable element research / P.A. Peterson -- Distinguishing variable phenotypes from variegation caused by transposon activities / V. Walbot -- Using transposons for genetic mosaic analysis of plant development / P.W. Becraft -- Survey of natural and transgenic gene markers used to monitor transposon activity / L. Krishnaswamy and T. Peterson -- Molecular biology of maize Ac/Ds elements: An overview / K. Lazarow, M.L. Doll and R. Kunze -- Gene tagging with engineered Ds elements in maize / Y. Li, G. Segal, Q. Wangm H.K. Donner -- Plant regeneration methods for rapid generation of a large scale Ds transposant population in rice / Y.H. Xuan [and nine others] -- Isolation of sequences flanking Ac insertion sites by Ac casting / D. Wang and T. Peterson -- Regulation of the mutator system of transposons in maize / D. Lisch -- Using MuDR/Mu transposons in directed tagging strategies / V. Walbot and J. Questa -- Genetic and molecular analyses of UniformMu transposon insertion lines / D.R. McCarty, M. Suzuki, C. Hunter, J. Collins, W.T. Avigne, K.E. Koch -- Digestion-ligation-amplification (DLA): A simple genome walking method to amplify unknown sequences flanking mutator (Mu) transposons and thereby facilitate gene cloning / S. Liu, A.P. Hsia and P.S. Schnable -- Molecular genetics and epigenetics of CACTA elements / N.V. Fedoroff -- Activation tagging using the maize En-I transposon system for the identification of abiotic stress resistance genes in arabidopsis / A. Harb and A. Pereira -- Reverse genetics in rice using Tos17 / D. Mieulet, A. Dievart, G. Droc, N. Lanau, E. Guiderdoni -- Identification and applications of the Petunia Class II Act1/dTph1 transposable element system / T. Gerats, J. Zethof and M. Vandenbussche -- Transposon display: A versatile method for transposon tagging / M. Vandenbussche, J. Zethof and T. Gerats -- Massive indexed parallel identification of transposon flanking sequences / M. Vandenbussche, J. Zethof and T. Gerats -- Use of next generation sequencing (NGS) technologies for the genome-wide detection of transposition / M. Elbaidouri, C. Chaparro and O. Panaud -- Overview of repeat annotation and de novo repeat identification / N. Jiang -- Computational methods for identification of DNA transposons / N. Jiang -- Tenest 2.0: Computational annotation and visualization of nested transposable elements / B.A. Kronmiller and R.P. Wise.
  • 2014 Springer Protocols
    Bobrowicz, Agnieszka J.; Rorbach, Joanna.
  • 2015 Springer Protocols
    Hunt, Arthur G.; Li, Qingshun Quinn.
    Computational analysis of plant polyadenylation signals / Xiaohui Wu , Guoli Ji , and Qingshun Quinn Li -- Prediction of plant mRNA polyadenylation sites / Xiaohui Wu , Guoli Ji , and Qingshun Quinn Li -- Extraction of poly(A) sites from large-scale RNA-seq data / Min Dong ... [et al.] -- Poly(A)-tag deep sequencing data processing to extract poly(A) sites / Xiaohui Wu, Guoli Ji, and Qingshun Quinn Li -- Analysis of poly(A) site choice using a java-based clustering algorithm / Patrick E. Thomas -- RADPRE : a computational program for identification of differential mRNA processing including alternative polyadenylation / Denghui Xing and Qingshun Quinn Li -- Characterization of plant polyadenylation complexes by using tandem affinity purification / Hongwei Zhao, Xinfu Ye, and Qingshun Quinn Li -- In vitro analysis of cleavage and polyadenylation in Arabidopsis / Hongwei Zhao and Qingshun Quinn Li -- Production, purification, and assay of recombinant proteins for in vitro biochemical analyses of the plant polyadenylation complex / Stephen A. Bell and Balasubrahmanyam Addepalli -- Detection of disulfide linkage by chemical derivatization and mass spectrometry / Balasubrahmanyam Addepalli -- Transient expression using agroinfiltration to study polyadenylation in plants / Carol Von Lanken and Arthur G. Hunt -- 3' RACE protocol to confirm polyadenylation sites / Liuyin Ma and Arthur G. Hunt -- Phage display library screening for identification of interacting protein partners / Balasubrahmanyam Addepalli, Suryadevara Rao, and Arthur G. Hunt -- Genome- wide determination of poly(A) site choice in plants / Pratap Kumar Pati, Liuyin Ma, and Arthur G. Hunt -- DNA/RNA hybrid primer mediated poly(A) tag library construction for illumina sequencing / Man Liu, Xiaohui Wu, and Qingshun Quinn Li -- Poly(A) tag library construction from 10 ng total RNA / Jingyi Cao and Qingshun Quinn Li -- Rapid, simple, and inexpensive method for the preparation of strand-specific RNA-seq libraries / Arthur G. Hunt -- Genome-wide analysis of distribution of RNA polymerase II isoforms using ChIP-Seq / Laura de Lorenzo.
  • 2013 Springer
    Paus, Tomáš.
    Terms and Concepts -- History of the Key Disciplines -- Enviromics -- Genomics -- Epigenomics -- Molecular Phenomics -- Systems Phenomics -- Cohorts -- Challenges -- Personalized Preventive Medicine.
  • 2016 Springer Protocols
    Dassi, Erik.
    Regulation of gene expression / Alessandro Quattrone and Erik Dassi -- Computational approach for the discovery of protein-RNA networks / Domenica Marchese, Carmen Maria Livi, and Gian Gaetano Tartaglia -- Transcriptional regulation with CRISPR/Cas9 effectors in mammalian cells / Hannah Pham, Nicola A. Kearns, and René Maehr -- Studying the translatome with polysome profiling / Paola Zuccotti and Angelika Modelska -- Exploring ribosome positioning on translating transcripts with ribosome profiling / Pieter Spealman ... [et al.] -- Studying isoform-specific mRNA recruitment to polyribosomes with Frac-seq / Rocio T. Martinez-Nunez and Jeremy R. Sanford -- Use of the pBUTR reporter system for scalable analysis of 3' UTR-mediated gene regulation / Arindam Chaudhury and Joel R. Neilson -- Comprehensive identification of RNA-binding proteins by RNA interactome capture / Alfredo Castello ... [et al.] -- Identifying RBP targets with RIP-seq / Hans-Herman Wessels ... [et al.] -- PAR-CLIP : a method for transcriptome-wide identification of RNA binding protein interaction sites / Charles Danan, Sudhir Manickavel, and Markus Hafner -- Profiling the binding sites of RNA-binding proteins with nucleotide resolution using iCLIP / FX Reymond Sutandy, Andrea Hildebrandt, and Julian König -- Pipeline for PAR-CLIP data analysis / Marvin Jens -- Capture and identification of miRNA targets by biotin pulldown and RNA-seq / Shen Mynn Tan and Judy Lieberman -- Identification of miRNA-target RNA interactions using CLASH / Aleksandra Helwak and David Tollervey -- Genome-wide analysis of A-to-I RNA editing / Yiannis A. Savva, Georges St. Laurent, and Robert A. Reenan -- Nucleotide-level profiling of m5C RNA methylation / Tennille Sibbritt ... [et al.] -- Probing N 6-methyladenosine (m6A) RNA modification in total RNA with SCARLET / Nian Liu and Tao Pan -- Genome-wide identification of alternative polyadenylation events using 3'T-fill / Stefan Wilkening, Vicent Pelechano, and Lars M. Steinmetz -- Genome-wide profiling of alternative translation initiation sites / Xiangwei Gao, Ji Wan, and Shu-Bing Qian -- Genome-wide study of mRNA isoform half-lives / Joseph V. Geisberg and Zarmik Moqtaderi -- Visualizing mRNA dynamics in live neurons and brain tissues / Hye Yoon Park and Minho Song -- Single-molecule live-cell visualization of pre-mRNA splicing / Robert M. Martin ... [et al.].
  • 2008 Springer Protocols
    Wilusz, Jeffrey.
    Bioinformatics approaches for studying untranslated regions of mRNAs / Paramjeet S. Bagga -- Identification of mRNA polyadenylation sites in genomes using cDNA sequences, expressed sequence tags, and trace / Ju Youn Lee, Ji Yeon Park, and Bin Tian -- Bioinformatic tools for studying post-transcriptional gene regulation : the UAlbany TUTR Collection and other informatic resources / Francis Doyle ... [et al.] -- In-line probing analysis of riboswitches / Elizabeth E. Regulski and Ronald R. Breaker -- Ribotrap : targeted purification of RNA-specific RNPs from cell lysates through immunoaffinity precipitation to identify regulatory proteins and RNAs / Dale L. Beach and Jack D. Keene -- Advances in RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray profiling / Timothy E. Baroni ... [et al.] -- Biosensors for RNA aptamers-protein interaction / Sara Tombelli, Maria Minunni, and Marco Mascini -- A tethering approach to study proteins that activate mRNA turnover in human cells / Sandra L. Clement and Jens Lykke-Andersen -- RNA analysis by biosynthetic tagging using a 4-thiouracil and uracil phosphoribosyltransferase / Gusti M. Zeiner ... [et al.] -- Efficient 5' cap-dependent RNA purification : use in identifying and studying subsets of RNA / Edyta Z. Bajak and Curt H. Hagedorn -- Enrichment of alternatively spliced isoforms / Julian P. Venables -- In vivo methods to assess polyadenylation efficiency / Lisa K. Hague, Tyra Hall-Pogar, and Carol S. Lutz -- Monitoring the temporal and spatial distribution of RNA in living yeast cells / Roy M. Long and Carl R. Urbinati -- Analysis of mRNA partitioning between the cytosol and endoplasmic reticulum compartments of mammalian cells / Samuel B. Stephens ... [et al.] -- In vivo and in vitro analysis of poly(A) length effects on mRNA translation / Jing Peng, Elizabeth L. Murray, and Daniel R. Schoenberg -- A ribosomal density-mapping procedure to explore ribosome positions along translating mRNAs / Naama Eldad and Yoav Arava -- Identification of changes in gene expression by quantitation of mRNA levels / Wendy M. Olivas -- Application of the Invader® RNA assay to the polarity of vertebrate mRNA decay / Elizabeth L. Murray and Daniel R. Schoenberg -- Development of an in vitro mRNA decay system in insect cells / Kevin Sokoloski, John R. Anderson, and Jeffrey Wilusz -- Using synthetic precursor and inhibitor miRNAs to understand miRNA function / Lance P. Ford and Angie Cheng -- A step-by-step procedure to analyze the efficacy of siRNA using real-time PCR / Angie Cheng, Charles L. Johnson, and Lance P. Ford.
  • 2012 Springer
    Kuliev, Anver.
    Primary Prevention of Genetic Disorders and Place of Preimplantation Diagnosis -- Approaches to Preimplantation Diagnosis -- Preimplation Diagnosis for Single-Gene Disorders -- PGD for HLA Typing -- Preimplantation Diagnosis for Chromosomal Disorders -- Clinical Outcome of Preimplantation Genetic Diagnosis -- Preimplantation Diagnosis and Establishment of Disease and Individual Specific Human Embryonic Stem Cell Lines -- Social, Ethical, and Legal Aspects.
  • 2014 Springer
    Braude, Peter R.; El-Toukhy, Tarek.
    This unique book offers a comprehensive yet practical user-friendly guide to preimplantation genetic diagnosis (PGD). It provides understanding of and insight into the complete procedure, its recent clinical and laboratory developments and its future prospects, whilst offering an easy point of reference for patient enquiries. Concluding with perspectives on the ethical and social issues often encountered by healthcare professionals counselling patients with regards to PGD. Each chapter within Preimplantation Genetic Diagnosis in Clinical Practice is written by established authorities in their fields. An essential resource for PGD specialists and non-specialists, and for all practitioners working within the disciplines of fertility, reproductive medicine and medical genetics.
  • 2015 Springer
    Grech, Godfrey; Grossman, Iris.
    Introduction -- Preventive and predictive genetics: a perspective -- Roadmap to drug development enabled by pharmacogenetics -- Pharmacogenetics, statistical considerations -- Pharmacokinetics and pharmacogenetics: bringing the magic bullet closer to reality -- Pharmacogenetics of adverse drug reactions -- Pharmacogenomics for haemoglobinopathies therapeutics -- Pharmacogenetics of neurodegenerative disorders -- Pharmacogenetics of asthma -- Pharmacogenetics and antineoplastic therapies -- Pharmacogenetics of coumarin anticoagulant therapy -- Implementation of genomic medicine: tools and challenges -- Ethical considerations in the genomic era -- Index.
  • 2008 Springer
    Bunz, Fred.
  • 2013 Springer
    Gersen, Steven L.; Keagle, Martha B.
    Part I. Basic Concepts and Background. History of Clinical Cytogenetics / Steven L. Gersen -- DNA, Chromosomes, and Cell Division / Martha B. Keagle -- Human Chromosome Nomenclature: An Overview and Definition of Terms / Marilyn L. Slovak, Aaron Theisen, Lisa G. Shaffer -- Part II. Examining and Analyzing Chromosomes. Basic Cytogenetics Laboratory Procedures / Martha B. Keagle, Steven L. Gersen -- The Essentials of Light Microscopy / Nathan S. Claxton, Stephen T. Ross -- Quality Control and Quality Assurance / Martha B. Keagle -- Instrumentation in the Cytogenetics Laboratory / Steven L. Gersen -- Part III. Clinical Cytogenetics. Autosomal Aneuploidy / Jin-Chen C. Wang -- Structural Chromosome Rearrangements / Kathleen Kaiser-Rogers, Kathleen W. Rao -- Sex Chromosomes, Sex Chromosome Disorders, and Disorders of Sex Development / Cynthia M. Powell -- The Cytogenetics of Infertility / Linda Marie Randolph -- Prenatal Cytogenetics / Linda Marie Randolph -- The Cytogenetics of Spontaneous Abortion / Solveig M. V. Pflueger, -- Chromosome Instability / Xiao-Xiang Zhang, -- Part IV. Cancer Cytogenetics. The Cytogenetics of Hematologic Neoplasms / Aurelia Meloni-Ehrig -- The Cytogenetics of Solid Tumors / Linda D. Cooley, Kathleen S. Wilson -- Part V. Adjunct Technologies -- Fluorescence In Situ Hybridization (FISH) / Daynna J. Wolff -- Microarray-Based Cytogenetics / Lisa G. Shaffer -- Part VI. Beyond Chromosomes. Fragile X--A Family of Disorders: Changing Phenotype and Molecular Genetics / Elaine B. Spector -- Genomic Imprinting and Uniparental Disomy / Jin-Chen C. Wang -- Genetic Counseling / Sarah Hutchings Clark.
  • 2014 ScienceDirect
    Cibelli, Jose B.
    Principles of Cloning, Second Edition is the fully revised edition of the authoritative book on the science of cloning. The book presents the basic biological mechanisms of how cloning works and progresses to discuss current and potential applications in basic biology, agriculture, biotechnology, and medicine. Beginning with the history and theory behind cloning, the book goes on to examine methods of micromanipulation, nuclear transfer, genetic modification, and pregnancy and neonatal care of cloned animals. The cloning of various species-including mice, sheep, cattle, and non-mammals-is considered as well.
  • 2006 Springer
    Patterson, Cam; Runge, Marschall Stevens.
    Also available: Print – 2006
  • 2006 Springer Protocols
    Pellestor, Franck.
  • 2014 Springer
    Halper, Jaroslava.
    This volume is a reference handbook focusing on diseases like Marfan syndrome, Ehlers-Danlos syndrome, Loeys-Dietz syndrome and other heritable soft connective tissue diseases. The book presents detailed information for both basic scientists and for clinicians seeing patients. It is also a stepping stone for new investigations and studies that goes beyond the facts about the composition and biochemistry of the connective tissue and extracellular matrix, as the authors connect individual components to specific aspects of various soft tissue disorders and to the actual or potential treatment of them. Progress in Heritable Soft Connective Tissue Diseases features very prominent physicians and scientists as contributors who bring their most recent discoveries to the benefit of readers. Their expertise will help clinicians with proper diagnosis of sometimes elusive and uncommon heritable diseases of soft connective tissues. This book also offers an update on the pathophysiology of these diseases, including an emphasis on unifying aspects such as connections between embryonic development of the different types of connective tissues and systems, and the role of TGF-beta in development and physiology of soft tissues. This new set of data explains, at least in part, why many of these disorders are interconnected, though the primary pathophysiological events, such as gene mutations, may be different for each disorder.
    Also available: Print – 2014
  • 2009 Springer
    Köhrer, Caroline; RajBhandary, Uttam.
    Understanding enzyme mechanism through protein chimeragenesis / N.M. Goodey and S.J. Benkovic -- Chemical protein engineering : synthetic and semisynthetic peptides and proteins / L. Merkel, L. Moroder, and N. Budisa -- Native chemical ligation: Semisynthesis of post-translationally modified proteins and biological probes / E. Vogel Taylor and B. Imperiali -- Chemical methods for mimicking post-translational modifications / S.I. van Kasteren, P. Garnier and B.G. Davis -- Noncanonical amino acids in protein science and engineering / K.E. Beatty and D.A. Tirrell -- Fidelity mechanisms of the aminoacyl-tRNA synthetases / A.P. Mascarenhas ... [et al.] -- Specialized components of the translational machinery for unnatural amino acid mutagenesis : tRNAs, aminoacyl-tRNA synthetases, and ribosomes / C. Köhrer and U.L. RajBhandary -- In vivo studies of receptors and ion channels with unnatural amino acids / D.A. Dougherty -- Synthesis of modified proteins using misacylated tRNAs / S.M. Hecht -- Cell-free synthesis of proteins with unnatural amino acids. The pure system and expansion of the genetic code / I. Hirao, T. Kanamori and T. Ueda -- Engineering nucleobases and polymerases for an expanded genetic alphabet / A.M. Leconte and F.E. Romesberg -- Understanding membrane proteins. How to design inhibitors of transmembrane protein-protein interactions / J.S. Slusky, H. Yin and W.F. DeGrado.
  • 2006 Springer Protocols
    Arndt, Katja M.; Müller, Kristian M.
  • 2014 Springer
    Santos, Andre L. S.
    This book contains a collection of critical reviews on the expression of biologically functional proteins in Leishmania and Trypanosoma, which was written by renowned researchers on this field. Species belonging to these trypanosomatids genera are etiological agents of leishmaniasis, Chagas' disease and sleeping sickness that are extremely debilitating human infection diseases, which remain a major health problem especially in countries from Latin America, Africa and Middle East. Substantiating the problem, the currently accepted drugs for these diseases are quite unsatisfying due to their low efficacy and high toxicity. In order to solve these real problems, several research groups around the world have become involved in the study and identification of novel potential targets in the trypanosomatid cell. Since proteins are key macromolecules involved in crucial metabolic processes of all living cells, studies have focused on the expression of specific proteins produced by Leishmania and Trypanosoma by means of different biochemical, molecular and proteomic approaches in order to explore them as targets for understanding the parasite life cycle and developing new strategies against trypanosomiasis. With these proposals in mind, the book "Proteins and Proteome of Leishmania and Trypanosoma" encompasses (i) an integrated view about the biochemistry of parasites belonging to the Leishmania and Trypanosoma genera; (ii) an updated review on the expression of biologically relevant proteins by human pathogenic trypanosomatids and their possible role in the interaction with host cells/molecules as well as a target for development of both alternative chemotherapies and vaccine; and (iii) several pictures, diagrams and tables that can be used to illustrate both undergraduate and postgraduate teaching as well as scientific lectures, being a useful resource for students and researchers.
  • 2006 Springer Protocols
    Hilario, Elena; Mackay, John.
    Genomic DNA isolation from different biological materials / Duckchul Park -- Extraction of plant RNA / Elspeth MacRae -- Overview on hybridization and detection techniques / Elena Hilario -- Checkerboard DNA/DNA hybridization technology : using DIG detection / Lisa S. Gellen, Glenn Wall-Manning, and Chris H. Sissons -- Nonradioactive northern and southern analyses from plant samples / Christoph Peterhaensel, Dagmar Weier, and Thomas Lahaye -- Screening a BAC library with nonradioactive overlapping oligonucleotide (overgo) probes / Elena Hilario, Tiffany F. Bennell, and Erik Rikkerink -- Direct in-gel hybridization of DNA with digoxigenin-labeled probes / Saeed A. Khan and Mohamed S. Nawaz -- In situ hybridization of termite microbes / Shigeharu Moriya ... [et al.] -- RNA electrophoretic mobility shift assay using a fluorescent DNA sequencer / Yukinori Eguchi -- Comparative quantitation of mRNA expression in the central nervous system using fluorescence in situ hybridization / Darren J. Day, Eli M. Mrkusich, and John H. Miller -- Visualization of gene expression by fluorescent multiplex real-time PCR amplification / Maria Rosa Ponce ... [et al.] -- Fluorescence in situ hybridization for the identification of environmental microbes / Annelie Pernthaler and Jakob Pernthaler -- Introduction to kinetic (real-time) PCR / John Mackay -- Validation of siRNA knockdowns by quantitative real-time PCR / Sukru Tuzmen -- Real-time quantitative PCR as an alternative to southern blot or fluorescence in situ hybridization for detection -- Of gene-copy number changes / Jasmien Hoebeeck, Frank Speleman, and Jo Vandesompele -- Design and work-up of a new molecular diagnostic assay based on real-time PCR / Harald Kessler -- Real-time PCR fluorescent chemistries / John Mackay and Olfert Landt -- Microarrays : an overview / Norman H. Lee and Alexander I. Saeed -- Oligonucleotide microarrays for the study of coastal microbial communities / Gaspar Taroncher-Oldenburg and Bess B. Ward.
  • 2014 Springer Protocols
    Poliseno, Laura.
    Pseudogene redux with new biological significance / Leonardo Salmena -- Contribution of pseudogenes to sequence diversity / Mauno Vihinen -- Computational methods for pseudogene annotation based on sequence homology / Paul M. Harrison -- Computational methods of identification of pseudogenes based on functionality : entropy and GC content / Evgeniy S. Balakirev ... [et al.] -- Methods of identification of pseudogenes based on functionality : hybridization of 18S rRNA and mRNA during translation / Chuanhua Xing -- Whole-genome identification of neutrally evolving pseudogenes using the evolutionary measure dN/dS / Lise Olivia Andrieux and David Torrents Arenales -- Methods to study the occurrence and the evolution of pseudogenes through a phylogenetic approach / Jacques Dainat and Pierre Pontarotti -- Methods for detecting transcribed pseudogenes : PCR on regions of high sequence similarity followed by cloning and sequencing / Wenyong Ding and Jianwu Dai -- RNA amplification for pseudogene detection using RNA-Seq / Stephen C. M. Tsoi and Michael K. Dyck -- GENCODE pseudogenes / Adam Frankish and Jennifer Harrow -- Methods to detect transcribed pseudogenes : RNA-Seq discovery allows learning through features / Camilo Valdes and Enrico Capobianco -- Proteomics techniques for the detection of translated pseudogenes / Nadia Ucciferri and Silvia Rocchiccioli -- Pseudogenes as competitive endogenous RNAs : target prediction and validation / Florian A. Karreth ... [et al.] -- Pseudogenes : a novel source of trans-acting antisense RNAs / Per Johnsson, Kevin V. Morris, and Dan Grandér -- Pseudogene-derived endogenous siRNAs and their function / Wen-Ling Chan and Jan-Gowth Chang -- Methods to study translated pseudogenes : in vitro translation, fusion with a tag/reporter gene, and complementation assay / Anne Parle-McDermott
  • 2006 Springer Protocols
    Marsh, Sharon.
    The history of pyrosequencing / Pol Nyron -- Pyrosequencing applications / Sharon Marsh -- Web-based primer design software for genome-scale genotyping by pyrosequencing / Steven Ringquist ... [et al.] -- Pyrosequencing : a simple method for accurate genotyping / Cristi R. King and Tiffany Scott-Horton -- Universal primer applications for pyrosequencing / Dong-Chuan Guo and Dianna M. Milewicz -- Allele quantification and DNA pooling methods / Jonathon Wasson -- Multiplex pyrosequencing for DNA variation analysis / Pritesh Patel, Yih-Horng Shiao, and Paolo Fortina -- Analysis of gene-specific DNA methylation patterns by the pyrosequencing technology / Jørg Tost and Ivo Glynne Gut -- Detecting mutations that confer oxazolidinone resistance in gram-positive bacteria / Neil Woodford, Sarah E. North, and Matthew J. Ellington -- Pyrosequencing-based strategies for improved allele typing of HLA loci / Steven Ringquist ... [et al.] -- Pyrosequencing of phage display libraries for the identification of cell-specific targeting ligands / Ahad A. Rahim -- Gene copy number detection in animal studies / Gerli Pielberg and Leif Andersson -- Detection of allelic imbalance in gene expression using pyrosequencing / Hua Wang and Steven C. Elbein -- Pyrosequencing genotype storage techniques / Derek J. Van Booven.
  • 2011
    Hong, Sun-Hae; Doniach, S.; McAdams, Harley; Shapiro, Lucy.
    Replication and segregation of the chromosome in the bacterium Caulobacter crescentus takes place simultaneously. Although it is known that each arm of the circular chromosome is on average linearly positioned along the cell length, the detailed configuration of the DNA in the cell is not well understood. Furthermore, in replicating bacterial cells, the centromere is segregated by a ParA-dependent mechanism and anchored at the pole, but the segregation mechanism for the rest of the chromosome is not known. To address these questions, I tracked the position and motion of multiple chromosomal loci both in non-replicating and replicating cells. By characterizing compaction of the DNA in non-replicating cells, I show that the DNA in the Caulobacter cells has the mean end-to-end distance that scale as (contour length)0.22, which suggests that compaction of the bacterial DNA is primarily driven by supercoiling. Analysis of the replication/segregation dynamics revealed that Caulobacter chromosome segregation is bimodal: Centromere-proximal DNA is segregated with the centromere at a slow pace whereas the rest of the DNA is segregated much faster. The dynamics of the centromere-distal DNA are consistent with a model where continuous compaction pulls the DNA toward the pole. The results provide a new perspective on the physical configuration of the non-replicating DNA and on the movement and compaction of newly replicated DNA immediately after replication and during its transport from the replisome to the cell poles.
  • 2014 Springer Protocols
    Biassoni, Roberto; Raso, Alessandro.
    Twenty years of qPCR: A mature technology? -- Minimum information necessary for quantitative real-time PCR experiments -- Selection of reliable reference genes for RT-qPCR analysis -- Introduction to digital PCR -- mRNA and microRNA purity and integrity: The key to success in expression profiling -- Mediator probe PCR: Detection of real-time PCR by label-free probes and a universal fluorogenic reporter -- Absolute quantification of viral DNA: The quest for perfection -- A multiplex real-time PCR-platform integrated into automated extraction method for the rapid detection and measurement of oncogenic HPV type-specific viral DNA load from cervical samples -- Real-time PCR detection of mycoplasma pneumoniae in the diagnosis of community-acquired pneumonia -- A sensible technique to detect mollicutes impurities in human cells cultured in GMP condition -- Real-time quantification assay to monitor BCR-ABL1 transcripts in chronic myeloid leukemia -- A reliable assay for rapidly defining transplacental metastasis using quantitative PCR -- Circulating cell-free DNA in cancer -- Gene expression analysis by qPCR in clinical kidney transplantation -- Posttranscriptional regulatory networks: From expression profiling to integrative analysis of mRNA and microRNA data -- Clinical applications using digital PCR -- Developing noninvasive diagnosis for single-gene disorders: the role of digital PCR.
  • 2002 Springer Protocols
    Camp, Nicola J.; Cox, Angela.
    pt. 1. Mapping quantitative trait loci in humans -- Association studies / Jennifer H. Barrett -- Parametric linkage analysis / Lyle J. Palmer -- Nonparametric linkage analysis: I. Haseman-Elston / Chad P. Garner -- Nonparametric linkage analysis: II. Variance components / Angela J. Marlow -- Linkage and association: the transmission/disequilibrium test for QTLs / Mark M. Iles -- Joint linkage and segregation analysis using Markov chain Monte Carlo methods / Ellen M. Wijsman -- pt. 2. Mapping quantitative trait loci in rodents -- Approaches to the analysis of QTL data in mice, using the nonobese diabetic mouse as an example / Heather J. Cordell -- Experimental designs for QTL fine mapping in rodents / Anne Shalom -- Approaches to the analysis of complex quantitative phenotypes and marker map construction based on the analysis of rat models of hypertension / Dominique Gauguier -- A case study of QTL analysis in a mouse model of asthma / Youming Zhang -- pt. 3. Mapping quantitative trait loci in agricultural settings -- QTL analysis in plants / Shizhong Xu -- QTL analysis in livestock / Joao L. Rocha.
  • 2012 Springer Protocols
    Rifkin, Scott A.
    Backcross populations and near isogenic lines / Rik Kooke, Erik Wijnker, and Joost J.B. Keurentjes -- F₂ designs for QTL analysis / Yuan-Ming Zhang -- Design and construction of recombinant inbred lines / Daniel A. Pollard -- Two flavors of bulk segregant analysis in yeast / Maitreya J. Dunham -- Selecting markers and evaluating coverage / Matthew A. Cleveland and Nader Deeb -- Composite interval mapping and multiple interval mapping : procedures and guidelines for using windows QTL cartographer / Luciano Da Costa E. Silva, Shengchu Wang, and Zhao-Bang Zeng -- Design database for quantitative trait loci (QTL) data warehouse, data mining, and meta-analysis / Zhi-Liang Hu, James M. Reecy, and Xiao-Lin Wu -- Meta-analysis of QTL mapping experiments / Xiao-Lin Wu and Zhi-Liang Hu -- Using eQTLs to reconstruct gene regulatory networks / Lin S. Chen -- Estimation and interpretation of genetic effects with epistasis using the NOIA model / Jose M. Alvarez-Castro, Orjan Carlborg, and Lars Ronnegard -- Identifying QTL for multiple complex traits in experimental crosses / Samprit Banerjee and Nengjun Yi -- Functional mapping of developmental processes : theory, applications, and prospects / Kiranmoy Das [and others] -- Statistical models for genetic mapping in polyploids : challenges and opportunities / Jiahan Li [and others] -- eQTL / Lun Li, Xianghua Zhang, and Hongyu Zhao -- Genetic mapping of quantitative trait loci for disease -- related phenotypes / Marcella Devoto and Mario Falchi -- Quantitative trait locus analysis in haplodiploid hymenoptera / Jssurgen Gadau, Christof Pietsch, and Leo W. Beukeboom.
  • 2013 Springer
    Leszczynski, Dariusz.
    Methods of proteomics have been shown to be powerful tools in search of target proteins - proteins that respond in cells to an internal or an external stimulus. Proteomics is widely used in biomedical research. However, in radiation biology research, following exposures of living matter to low doses of either ionizing or non-ionizing radiation, proteomics approach is only very slowly gaining support. This book, by presenting the current status of the use of proteomics in radiation biology, will help to attract attention to the field of radiation proteomics.
    Also available: Print – 2013
    Also available: Print – 2013
  • 2010 Springer
    Atkins, John F.; Gesteland, Raymond F.
    Part I. Redefinition -- 1. Selenocysteine Biosynthesis, Selenoproteins, and Selenoproteomes / Vadim N. Gladyshev and Dolph L. Hatfield -- 2. Reprogramming the Ribosome for Selenoprotein Expression: RNA Elements and Protein Factors / Marla J. Berry and Michael T. Howard -- 3. Translation of UAG as Pyrrolysine / Joseph A. Krzycki -- 4. Specification of Standard Amino Acids by Stop Codons / Olivier Namy and Jean-Pierre Rousset -- 5. Ribosome “Skipping”: “Stop-Carry On” or “StopGo” Translation / Jeremy D. Brown and Martin D. Ryan -- 6. Recoding Therapies for Genetic Diseases / Kim M. Keeling and David M. Bedwell -- Part II. Frameshifting - Redirection of Linear Readout -- 7. Pseudoknot-Dependent Programmed -1 Ribosomal Frameshifting: Structures, Mechanisms and Models / Ian Brierley, Robert J.C. Gilbert, and Simon Pennell -- 8. Programmed -1 Ribosomal Frameshift in the Human Immunodeficiency Virus of Type 1 / Léa Brakier-Gingras and Dominic Dulude -- 9. Ribosomal Frameshifting in Decoding Plant Viral RNAs / W. Allen Miller and David P. Giedroc -- 10. Programmed Frameshifting in Budding Yeast / Philip J. Farabaugh -- 11. Recoding in Bacteriophages / Roger W. Hendrix -- 12. Programmed Ribosomal -1 Frameshifting as a Tradition: The Bacterial Transposable Elements of the IS3 Family / Olivier Fayet and Marie-Françoise Prère -- 13. Autoregulatory Frameshifting in Antizyme Gene Expression Governs Polyamine Levels from Yeast to Mammals / Ivaylo P. Ivanov and Senya Matsufuji -- 14. Sequences Promoting Recoding Are Singular Genomic Elements / Pavel V. Baranov and Olga Gurvich -- 15. Mutants That Affect Recoding / Jonathan D. Dinman and Michael O'Connor -- 16. The E Site and Its Importance for Improving Accuracy and Preventing Frameshifts / Markus Pech, Oliver Vesper, Hiroshi Yamamoto, Daniel N. Wilson, and Knud H. Nierhaus -- Part III. Discontiguity -- 17. Translational Bypassing - Peptidyl-tRNA Re-pairing at Non-overlapping Sites / Norma M. Wills -- 18. trans-Translation / Kenneth C. Keiler and Dennis M. Lee -- Part IV. Transcription Slippage -- 19. Transcript Slippage and Recoding / Michael Anikin, Vadim Molodtsov, Dmitry Temiakov, and William T. McAllister -- Part V. Appendix -- 20. Computational Resources for Studying Recoding / Andrew E. Firth, Michaël Bekaert, and Pavel V. Baranov.
  • 2012 Springer Protocols
    Conn, Graeme L.
    Purification of RNA expressed in vivo inserted in a tRNA scaffold / Luc Ponchon and Frederic Dardel -- Selective RNase H cleavage of target RNAs from a tRNA scaffold / Luc Ponchon [and others] -- Preparation of long templates for RNA in vitro transcription by recursive PCR / Jessica C. Bowman [and others] -- General protocols for preparation of plasmid DNA template, RNA in vitro transcription, and RNA purification by denaturing PAGE / Jo L. Linpinsel and Graeme L. Conn -- Preparation of short RNA by in vitro transcription / Cheng Lu and Pingwei Li -- Native RNA purification by gel filtration chromatography / Evan P. Booy, Hui Meng, and Sean A. McKenna -- Cis-acting ribozymes for the production of RNA in vitro transcripts with defined 5ʹ and 3ʹ ends / Johanna M. Avis, Graeme L. Conn, and Scott C. Walker -- Trans-acting antigenomic HDV ribozyme for production of in vitro transcripts with homogenous 3ʹ ends / Milena Szafraniec [and others] -- Rapid preparation of RNA samples using DNA-affinity chromatography and DNAzyme methods / Hae-Kap Cheong, Eunha Hwang, and Chaejoon Cheong -- Preparation of lN-GST fusion protein for affinity immobilization of RNA / Genevieve Di Tomasso [and others] -- Affinity purification of RNA using an ARiBo tag / Genevieve Di Tomasso [and others] -- Plasmid template design and in vitro transcription of short RNAs within a "structure cassette" for structure probing experiments / Virginia K. Vachon and Graeme L. Conn -- In vitro transcription of modified RNAs / Stephanie L. Moon and Jeffrey Wilusz -- End-labeling oligonucleotides with chemical tags after synthesis / N. Ruth Zearfoss and Sean P. Ryder -- High-purity enzymatic synthesis of site-specifically modified tRNA / Ya-Ming Hou -- Se-derivatized RNAs for x-ray crystallography / Lina Lin and Zhen Huang -- Biosynthetic preparation of 13C/15N-labeled rNTPs for high-resolution NMR studies of RNAs / Luigi Martino and Maria R. Conte -- Preparative separation of ribonucleoside monophosphates by ion-pair reverse-phase HPLC / Pierre Dagenais and Pascale Legault -- Splint ligation of RNA with T4 DNA ligase / Christopher J. Kershaw and Raymond T. O'Keefe.
  • 2012 Springer Protocols
    Lorence, Argelia.
    Using folding promoting agents in recombinant protein production : a review / Beatrix Fahnert -- Routine identity confirmation of recombinant proteins by MALDI-TOF mass spectrometry / Brett J. Savary and Prasanna Vasu -- A matter of packaging : influence of nucleosome positioning on heterologous gene expression / María de la Cruz Muñoz-Centeno, Gonzalo Millán-Zambrano, and Sebastián Chávez -- Tools of the trade : developing antibody-based detection capabilities for recombinant proteins / Maureen C. Dolan [and others] -- Heat-shock protein fusion vectors for improved expression of soluble recombinant proteins in Escherichia coli / Christos A. Kyratsous and Christos A. Panagiotidis -- The use of a flagellar export signal for the secretion of recombinant proteins in salmonella / Ferenc Vonderviszt [and others] -- Optimization of purification protocols based on the step-by-step monitoring of the protein aggregates in soluble fractions / Ario de Marco -- Heterologous protein expression by Lactococcus lactis / Julio Villator-Hernández [and others] -- An extended suite of genetic tools for use in bacteria of the halomonadaceae : an overview / Montserrat Argandoña [and others] -- Regulated recombinant protein production in the antarctic bacterium Pseudoalteromonas haloplanktis TAC125 / Valentina Rippa [and others] -- A novel strategy for the construction of genomic mutants of the antarctic bacterium Pseudoalteromonas haloplanktis TAC125 / Maria Giuliani [and others] -- A new bacterial co-expression system for over-expressing soluble protein and validating protein-protein interaction / Jumei Zeng and Zheng-Guo He -- Heterologous high-level gene expression in the photosynthetic bacterium Rhodobacter capsulatus / Nadine Katzke [and others] -- Plasmid DNA production for therapeutic applications / Alvaro R. Lara and Octavio T. Ramírez -- Recombinant protein production in the eukaryotic protozoan parasite Leishmania tarentolae : a review / Tomoaki Niimi -- Expression of multisubunit proteins in Leishmania tarentolae / Marisa Sugino and Tomoaki Niimi -- Recombinant protein production in yeasts / Diethard Mattanovich [and others] -- Yeasts as a tool for heterologous gene expression / Raja Mokdad-Gargouri [and others] -- The Cre/Lox system : a practical tool to efficiently eliminate selectable markers in fungal endophytes / Simona Florea [and others] -- Aptamer-regulated expression of essential genes in yeast / Beatrix Suess [and others] -- Cloning and expression of hemicellulases from Aspergillus nidulans in Pichia pastoris / Prasanna Vasu, Stefan Bauer, and Brett J. Savary -- A thiamine-regulatable epitope-tagged protein expression system in fission yeast / Tiina Tamm -- Heterologous gene expression by chromosomal integration in fission yeast / Akihisa Matsuyama and Minoru Yoshida -- Genetic engineering of industrial strains of Saccharomyces cerevisiae / Sylvie le Borgne -- Recombinant protein production in plants : challenges and solutions / Elizabeth E. Hood and Deborah V. Vicuna Requesens -- A novel plant cell bioproduction platform for high-yield secretion of recombinant proteins / Jianfeng Xu and Marcia J. Kieliszewski -- Super-promoter :TEV, a powerful gene expression system for tobacco hairy roots / Luis Ñopo [and others] -- Bioseparation of recombinant proteins from plant extract with hydrophobin fusion technology / Jussi J. Joensuu [and others] -- Quality assessment of recombinant proteins produced in plants / Giuliana Medrano [and others] -- Cell-free protein synthesis as a promising expression system for recombinant proteins / Xumeng Ge and Jianfeng Xu -- The use of bacterial artificial chromosomes for recombinant protein production in mammalian cell lines / Leander Blaas [and others] -- Engineering the chaperone network of CHO cells for optimal recombinant protein production and authenticity / Lyne Jossé, C. Mark Smales, and Mick F. Tuite -- High-throughput baculovirus expression in insect cells / Richard B. Hitchman, Robert D. Possee, and Linda A. King -- Recombinant protein expression in milk of livestock species / Zsuzsanna Bösze and László Hiripi.
  • 2012 Springer Protocols
    Bill, Roslyn M.
    Optimising yeast as a host for recombinant protein production (review) / Nicklas Bonander and Roslyn M. Bill -- Which yeast species shall I choose? : Saccharomyces cerevisiae versus Pichia pastoris (review) / Richard A.J. Darby [and others] -- Preparation of Pichia pastoris expression plasmids / Christel Logez [and others] -- Preparation of Saccharomyces cerevisiae expression plasmids / David Drew and Hyun Kim -- Codon optimisation for heterologous gene expression in yeast / Kristina Hedfalk -- Yeast transformation to generate high-yielding clones / Mohammed Jamshad and Richard A.J. Darby -- Screening for high-yielding Pichia pastoris clones : the production of G protein-coupled receptors as a case study / Shweta Singh [and others] -- Screening for high-yielding Saccharomyces cerevisiae clones: using a green fluorescent protein fusion strategy in the production of membrane proteins / David Drew and Hyun Kim -- The effect of antifoam addition on protein production yields / Sarah J. Routledge and Roslyn M. Bill -- Setting up a bioreactor for recombinant protein production in yeast / Sarah J. Routlledge and Michelle Clare -- The implementation of a design of experiments strategy to increase recombinant protein yields in yeast (review) / Nagamani Bora [and others] -- Online analysis and process control in recombinant protein production (review) / Shane M. Palmer and Edmund R.S. Kunji -- Monitoring the biomass accumulation of recombinant yeast cultures : offline estimations of dry cell mass and cell counts / Shane M. Palmer and Edmund R.S. Kunji -- Online monitoring of biomass accumulation in recombinant yeast cultures / Shane M. Palmer and Edmund R.S. Kunji -- Optimising Pichia pastoris induction / Zharain Bawa and Richard A.J. Darby -- Optimizing Saccharomyces cerevisiae induction regimes / David Drew and Hyun Kim -- Large-scale production of membrane proteins in Pichia pastoris : the production of G protein-coupled receptors as a case study / Shweta Singh [and others] -- Large-scale production of secreted proteins in Pichia pastoris / Nagamani Bora -- Disruption of yeast cells to isolate recombinant proteins / Mohammed Jamshad and Richard A.J. Darby.
  • 2008 Springer
    Egel, Richard; Lankenau, Dirk-Henner.
    "Once per life cycle, mitotic nuclear divisions are replaced by meiosis I and II - reducing chromosome number from the diploid level to a haploid genome, reshuffling the homologous chromosomes by their centromeres, and recombining chromosome arms by crossing-over. In animals, including humans, all this happens during the germ cell formation of eggs and sperm. Due to the reign of meiosis, no child is a true genetic copy of either parent. Questions still open primarily concern the placement of and mutual coordination between neighboring crossover events. The current book addresses these processes and mechanisms in multicellular eukaryotes, such as Drosophila, Anibidopsis, mice and humans. The pioneering model systems of yeasts, as well as evolutionary aspects, will be addressed in a forthcoming volume."--Jacket.
  • 2008 Springer
    Egel, Richard; Lankenau, Dirk-Henner.
    Once per life cycle, mitotic nuclear divisions are replaced by meiosis I and II - reducing chromosome number from the diploid level to a haploid genome and recombining chromosome arms by crossing-over. In animals, all this happens during formation of eggs and sperm - in yeasts before spore formation. The mechanisms of reciprocal exchange at crossover/chiasma sites are central to mainstream meiosis. To initiate the meiotic exchange of DNA, surgical cuts are made as a form of calculated damage that subsequently is repaired by homologous recombination. These key events are accompanied by ancillar.
  • pt. A-B, 2002. ScienceDirect
    pt. B ScienceDirect
    Packer, Lester; Sen, Chandan K.
    Also available: Print – pt. A-B, 2002.
  • 2012
    Church, George M.; Regis, Edward.
    Status: Not Checked OutLane Catalog Record
    From bioplastics to H. sapiens 2.0 -- -3,800 Myr, Late Hadean : at the inorganic/organic interface -- -3,500 Myr, Archean : reading the most ancient texts and the future of living software -- -500 Myr, Cambrian : the mirror world and the explosion of diversity ; How fast can evolution go and how diverse can it be? -- -360 Myr, Carboniferous : "the best substitute for petroleum is petroleum" -- -60 Myr, Paleocene : emergence of mammalian immune system ; Solving the health care crisis through genome engineering -- -30,000 Yr, Pleistocene Park : engineering extinct genomes -- -10,000 Yr, Neolithic : industrial revolutions ; The agricultural revolution and synthetic genomics ; The BioFab Manifesto -- -100 Yr, Anthropocene : the third industrial revolution ; iGEM -- -1 Yr, Holocene : from personal genomes to immortal human components -- Epigenetic epilogue. +1 Yr, the end of the beginning, transhumanism, and the Panspermia Era : societal risks and countermeasures.
  • 2009 CRCnetBASE
    Gaur, Rajesh K.; Rossi, John J.
    Micro mining : computational approaches to miRNA discovery / Adam Grundhoff -- Animal microRNA gene prediction / Ola Snv?e and Pa<U+030a>l St?rom -- A suite of resources for the study of miRNA ontology and function / Praveen Sethupathy, Molly Megraw, and Artemis G. Hatzigeorgiou -- Regulation of translation and mRNA stability by Hfq-binding small RNAs in Escherichia coli / Hiroji Aiba -- Mechanisms by which microRNAs regulate gene expression in animal cells / Yang Yu and Timothy W. Nilsen -- The microRNAs of C. elegans / Mona J. Nolde and Frank J. Slack -- Isolation and characterization of small RNAs in C. elegans / Chisato Ushida and Yusuke Hokii -- MicroRNA tales in fly development / Utpal Bhadra ... [et al.] -- RNA interference and miRNAs in zebrafish / Alex S. Flynt, Elizabeth J. Thatcher, and James G. Patton -- Biogenesis and function of plant microRNAs / Zoltan Havelda -- Endogenous small RNA pathways in Arabidopsis / Manu Agarwal, Julien Curaba, and Xuemei Chen. How to assay miRNA expression : a technology guide / Mirco Castoldi, Vladimir Benes, and Martina U. Muckenthaler -- Methods to quantify microRNA gene expression / Lori A. Neely -- Regulation of alternative splicing by microRNAs / Rajesh K. Gaur -- Recent progress in polymerase II-mediated intronic microRNA expression systems / Shi-Lung Lin and Shao-Yao Ying -- MicroRNA-based RNA polymerase II expression vectors for RNA interference in mammalian cells / Anne B. Vojtek ... [et al.] -- Transgenic RNAi : a fast and low-cost approach to reverse genetics in mammals / Linghua Qiu and Zuoshang Xu -- Symphony of AIDS : an miRNA-based therapy / Yoichi R. Fujii -- MicroRNAs and cancer : connecting the dots / Sumedha D. Jayasena -- Mammalian transcriptional gene silencing by small RNAs / Daniel H. Kim and John J. Rossi -- Regulation of gene expression by RNA mediated transcriptional gene silencing / Kevin V. Morris.
  • 2007 Springer
    Bassett, Carole Leavel.
  • 2011 Springer
    Grosshans, Helge.
    MicroRNA biogenesis and function : an overview / Rene F. Ketting -- Regulation of pri-miRNA processing through Smads / Akiko Hata and Brandi N. Davis -- Stimulation of pri-miR-18a processing by hnRNP A1 / Gracjan Michlewski, Sonia Guil, and Javier F. Cáceres -- KSRP promotes the maturation of a group of miRNA precursors / Michele Trabucchi ... [et al.] -- Hormonal repression of miRNA biosynthesis through a nuclear steroid hormone receptor / Sally Fujiyama-Nakamura, Kaoru Yamagata, and Shigeaki Kato -- Autoregulatory mechanisms controlling the microprocessor / Robinson Triboulet and Richard I. Gregory -- Regulation of pre-miRNA processing / Nicolas J. Lehrbach and Eric A. Miska -- The effect of RNA editing and ADARs on miRNA biogenesis and function / Bret S.E. Heale, Liam P. Keegan, and Mary A. O'Connell -- MiRNAs need a trim regulation of miRNA activity by trim-NHL proteins / F. Gregory Wulczyn ... [et al.] -- Properties of the regulatory RNA-binding protein HuR and its role in controlling miRNA repression / Nicole-Claudia Meisner and Witold Filipowicz -- Turnover of mature miRNAs and siRNAs in plants and algae / Heriberto Cerutti and Fadia Ibrahim -- MicroRNases and the regulated degradation of mature animal miRNAs / Helge Grosshans and Saibal Chatterjee.
    Also available: Print – 2010
  • 2001 ScienceDirect
    Matthews, Benjamin F.; Romeo, John T.; Saunders, James A.
  • 2010
    Liu, Gwen; Blau, Helen M.; Chen, Chang-Zheng; Fire, Andrew Z.; Sarnow, P.
    MicroRNA (miRNA) genes, which encode an abundant class of ~22-nucleotide (nt), evolutionarily conserved small RNAs, control a fundamental layer of genetic programs at the post-transcriptional level. However, little is known about how the activity of miRNA genes is regulated and how the regulatory information controlling their activity is encoded. Interestingly, mature miRNAs can often be classified into large families consisting of members with identical seeds (nucleotides 2 through 8 of the mature miRNAs) and highly homologous ~22-nt mature miRNA sequences, but with divergent sequences and structural elements beyond their mature miRNAs. Here we investigated whether members of a miRNA gene family that encode identical or nearly identical mature miRNAs are functionally interchangeable in vivo and if not, why? We compare the activities of the mir-181 gene family in promoting double positive T cell development and show that miRNA genes that encode identical to nearly identical mature miRNAs can have distinct activities. The differences in activity between mir-181a-1 and mir-181c are largely determined by their unique primary/precursor-miRNA (pri/pre-miRNA) loop nucleotides, and the differences in activity between mir-181a-1 and mir-181b-1 are determined by both the pri/pre-miRNA loop and stem. Furthermore, the organization of mir-181a-1/b-1 in a cluster is important for its full activity. We also show that mir-181 family members can differentially regulate target genes quantitatively, and that some target genes can be upregulated. Taken together, we have demonstrated that regulatory information encoded in a miRNA gene beyond the mature miRNA plays a critical role in controlling the activity of the miRNA gene, suggesting that miRNA family members could have evolved different functions through their divergent miRNA gene sequences and structural elements beyond their mature miRNAs. Although, proteins may have evolved to recognize the structural and sequence elements of the pri/pre-miRNAs, we suggest that the regulatory information encoded in the structured pri/pre-miRNA may be directly interpreted through target and pri/pre-miRNA interactions.
  • 2006 ScienceDirect
    Davidson, Eric H.
  • 2015 Springer Protocols
    2014 Springer Protocols
    Carmichael, Gordon G.
    Diverse functions and mechanisms of mammalian long noncoding RNAs -- Sequence-defined oligoaminoamides for the delivery of siRNAs -- A biochemical approach to identify direct microRNA targets -- Native gel analysis for mammalian microRNPs assembled from pre-microRNAs -- Identification and validation of miRNA target sites within nontraditional miRNA targets -- Fractionation of non-polyadenylated and ribosomal-free RNAs from mammalian cells -- Affinity purification of long noncoding RNA-protein complexes from formaldehyde cross-linked mammalian cells -- RNA pulldown protocol for in vitro detection and identification of RNA-associated proteins -- nRIP-seq: A technique to identify RNA targets of an RNA binding protein on a genome-wide scale -- Analysis of the subcellular distribution of RNA by fluorescence in situ hybridization -- RNA fluorescence in situ hybridization in cultured mammalian cells -- Locating RNAs in situ with FISH-STIC probes -- Rapid and efficient elimination of specific nuclear noncoding RNAs in mammalian cells with antisense oligonucleotides -- On using magnesium and potassium ions in RNA experiments -- Studying the affinity, kinetic stability, and specificity of RNA/protein interactions: SINE ncRNA/Pol II complexes as a model system
  • 2006 Cold Spring Harb Lab Press
    SU Catalog (SearchWorks) Click LINK above for Print location/circulation status.
    Stewart, David J.; Stillman, Bruce.
    Mechanism and biology of RNAi -- Genome-wide approaches -- Small RNAs in development -- Telomeres and cancer -- End regulation of transcripts -- RNPs and RNA editing -- Biology of short RNAs -- Control of gene expression by noncoding RNAs -- Heterochromatin -- Quality control, messenger RNA turnover, and translational control.
  • 2012 Springer
    Ghosh, Zhumur; Mallick, Bibekanand.
    pt. 1. Basics -- pt. 2. Methods -- pt. 3. Applications.
  • 2012 Springer
    Hess, Wolfgang R.; Marchfelder, Anita.
    This book provides a comprehensive and up-to-date collection of review articles focusing on RNA-mediated regulation in prokaryotes. The various modes of action include the direct interaction with proteins, direct sensing of metabolites or of physical parameters, and the interaction with RNAs to stimulate or prevent binding of ribosomes or to stimulate degradation. Written by leading experts in the field, the book covers small RNA functions, RNA thermometers, riboswitches, the diversity of small RNA-guided CRISPR-Cas defense systems and selected RNA chaperons in both prokaryotic domains, bacteria and archaea. Recent advances towards the computational identification of regulatory RNAs and their targets are included and particular attention is paid to small RNA in pathogenic bacteria. This volume is the only one exclusively covering regulatory RNAs in the prokaryotic domains to date, making it essential literature for anyone interested in RNA function and gene regulation and a valuable resource for teaching these concepts.
  • 2012 Karger
    Garrido-Ramos, Manuel A.
    The Repetitive DNA Content of Eukaryotic Genomes / López-Flores, I.; Garrido-Ramos, M.A. -- Telomere Dynamics in Mammals / Silvestre, D.C.; Londoño-Vallejo, A. -- Drosophila Telomeres: an Example of Co-Evolution with Transposable Elements / Silva-Sousa, R.; López-Panadès, E.; Casacuberta, E. -- The Evolutionary Dynamics of Transposable Elements in Eukaryote Genomes / Tollis, M.; Boissinot, S. -- SINEs as Driving Forces in Genome Evolution / Schmitz, J. -- Unstable Microsatellite Repeats Facilitate Rapid Evolution of Coding and Regulatory Sequences / Jansen, A.; Gemayel, R.; Verstrepen, K.J. -- Satellite DNA Evolution / Plohl, M.; Meštrović, N.; Mravinac, B. -- Satellite DNA-Mediated Effects on Genome Regulation / Pezer, Ž.; Brajković, J.; Feliciello, I.; Ugarković, Đ. -- The Birth-and-Death Evolution of Multigene Families Revisited / Eirín-López, J.M.; Rebordinos, L.; Rooney, A.P.; Rozas, J. -- Chromosomal Distribution and Evolution of Repetitive DNAs in Fish / Cioffi, M.B.; Bertollo, L.A.C..
  • 2007 Springer Protocols
    Anson, Donald S.
    Methodologies for staining and visualization of [beta]-galactosidase in mouse embryos and tissues / Siobhan Loughna and Deborah Henderson -- Immunohistochemical detection of [beta]-galactosidase or green fluorescent protein on tissue sections / Philip A. Seymour and Maike Sander -- Detection of reporter gene expression in murine airways / Maria Limberis, Peter Bell, and James M. Wilson -- Three-dimensional analysis of molecular signals with episcopic imaging techniques / Wolfgang J. Weninger and Timothy J. Mohun -- Fluorescent proteins for cell biology / George H. Patterson -- Detection of GFP during nervous system development in Drosophila melanogaster / Karin Edoff, James S. Dods, and Andrea H. Brand -- Autofluorescent proteins for flow cytometry / Charles G. Bailey and John E. J. Rasko -- Fluorescent protein reporter systems for single-cell measurements / Steven K. Dower, Eva E. Qwarnstrom, and Endre Kiss-Toth -- Subcellular imaging of cancer cells in live mice / Robert M. Hoffman -- Noninvasive imaging of molecular events with bioluminescent reporter genes in living subjects / Pritha Ray and Sanjiv Sam Gambhir -- Green fluorescent protein as a tracer in chimeric tissues : the power of vapor fixation / Harald Jockusch and Daniel Eberhard.
  • Springer, 2005
    Istrail, Sorin; Kasif, Simon; Mesirov, Jill; Miyano, Satoru; Pevzner, Pavel; Waterman, Michael S.
  • Springer, 2007
    Huang, Haiyan; Speed, T. P.
  • 2008 Springer
    Christen, Yves; Gage, F.
  • 2006 Springer
    Buerstedde, Jean-Marie; Takeda, Shunichi.
    Ch. 1. DT40 gene disruptions: a how-to for the design and the construction of targeting vectors / Hiroshi Arakawa and Jean-Marie Buerstedde -- Ch. 2. Immunoglobulin gene conversion or hypermutation: That's the question / Jean-Marie Buerstedde and Hiroshi Arakawa -- Ch. 3. Genome resources for the DT40 community / Randolph B Caldwell and Andrzej M. Kierzek -- Ch. 4. Chromosome engineering in DT40 cells and mammalian centromere function / William R.A. Brown ... [et al.] -- Ch. 5. Function of recQ family helicase in genome stability / Masayuki Seki, Shusuke Tada and Takemi Enomoto -- Ch. 6. Genetic analysis of apoptotic execution / Sandrine Ruchaud ... [et al.] -- Ch. 7. The DT40 system as a tool for analyzing kinetochore assembly / Masahiro Okada, Tesuya Hori and Tatsuo Fukagawa -- Ch. 8. Analysing the DNA damage and replication checkpoints in DT40 cells / Michael D Rainey, George Zachos, and David AF Gillespie -- Ch. 9. Using DT40 to study clathrin function / Frank R. Wettey and Antony P. Jackson -- Ch. 10. Genetic analysis OF B cell signaling / Hisaaki Shinohara and Tomohiro Kurosaki -- Ch. 11. DT40 mutants: a model to study transcriptional regulation of B cell development and function / Jukka Alinikula, Olli Lassila and Kalle-Pekka Nera -- Ch. 12. Transcription and RNA processing factors play complex roles IN DT40 cells / Stephanie Bush and James L. Manley -- Ch. 13. Participation of histones, histone modifying enzymes and histone chaperones in vertebrate cell functions / Hidehiko Kikuchi ... [et al.] -- Ch. 14. Analysis of gene expression, copy number and palindrome formation with a DT40 enriched cDNA Microarray / Paul E. Neima ... [et al.] -- Ch. 15. Analysis of DNA replication damage bypass and its role in immunoglobulin repertoire development / Julian E. Sale, Anna-Laura Ross and Laura J. Simpson -- Ch. 16. The fanconi anemia pathway promotes homologous recombination repair in DT40 cell line / Julian E. Sale, Anna-Laura Ross and Laura J. Simpson -- Ch. 17. Calcium signaling, ion channels and more / Anne-Laure Perraud, Carsten Schmitz, Andrew M. Scharenberg -- Ch. 18. Phenotypic analysis of cellular responses to DNA damage / Helfrid Hochegger and Shunichu Takeda -- Ch. 19. ATM, a paradigm for a stress-responsive signal transducer in higher vertebrate cells / Ken-ichi Yamamoto, Masahiko Kobayashi and Hiroko Shimizu -- METHOD 1. Stable transfection of DT40 / Julian E. Sale -- METHOD 2. Basic cell culture conditions / Huseyin Saribasak and Hiroshi Arakawa -- METHOD 3. Excision of floxed-DNA sequences by transient induction of Mer-Cre-Mer / Hiroshi Arakawa -- METHOD 4. Immunoglobulin gene conversion and hypermutation assay by FACS / Hiroshi Arakawa -- METHOD 5. Target screening by PCR / Hiroshi Arakawa -- METHOD 6. Mitotic index determination by flow cytometry / David AF Gillespie and Mark Walker -- METHOD 7. Centrifugal elutriation as a means of cell cycle phase separation and synchronization / David AF Gillespie and Catarina Henriques -- METHOD 8. Preparation of genomic DNA for microarray-based comparative genome hybridization / Robert Kimmel, Amalia Icreverzi, Paul Neiman -- METHOD 9. Analysis of cellular Mg2+ in DT40 cells / Anne-Laure Perraud, Carsten Schmitz, Andrew M. Scharenberg -- METHOD 10. Transient transfection of DT40 / Roger Franklin & Julian E. Sale -- METHOD 11. Retroviral transduction of DT40 / Felix Randow & Julian E. Sale -- METHOD 12. Colony survival assay / Laura. J. Simpson & Julian E. Sale -- METHOD 13. Subcloning DT40 by limiting dilution / Jean-Marie Buerstedde -- METHOD 14. Subnuclear immunofluorescence / Dávid Szüts & Julian E. Sale -- METHOD 15. Sister chromatid exchange assay / Laura J. Simpson & Julian E. Sale -- METHOD 16. 2D cell cycle analysis / Roger Franklin & Julian E. Sale -- METHOD 17. Purification of tap-tagged proteins by two-step pull down from DT40 cells / Hiroyuki Kitao and Minoru Takata -- METHOD 18. Synchronization of cells / Eiichiro Sonoda -- METHOD 19. Tranfection of DT40 cells / Huseyin Saribasak and Hiroshi Arakawa -- METHOD 20. Luciferase reporter assay / Frank R. Wettey and Antony P. Jackson -- METHOD 21. Indirect immunofluorescence microscopy / Frank R. Wettey and Antony P. Jackson -- METHOD 22. Quantification of receptor-mediated endocytosis / Frank R. Wettey and Antony P. Jackson -- METHOD 23. Measurement of DNA synthesis and strand breaks using alkaline sucrose density gradient centrifugation / Kouichi Yamada and Jun Takezawa -- METHOD 24. Fractionation of nuclear and cytoplasmic proteins from DT40 cell lines / Yan-Dong Wang and Randolph B Caldwell.
  • 2012 Springer Protocols
    Douthwaite, Julie A.; Jackson, Ronald H.
    Ribosome display : a perspective / Andreas Plückthun -- Preparation and testing of E. coli S30 in vitro transcirption translation extracts / James F. Zawada -- Eurkaryotic ribosome display selection using rabbit reticulocyte lysate / Julie A Douthwaite -- Stabilized ribosome display for in vitro selection / Shuta Hara [and others] -- Eukaryotic ribosome display with in situ DNA recovery / Mingyue He [and others] -- mRNA display using covalent coupling of mRNA to translated proteins / Rong Wang, Steve W. Cotten, and Rihe Liu -- SNAP display : in vitro rotein evolution in microdroplets / Miriam Kaltenbach and Florian Hollfelder -- cDNA display : rapid stabilization of mRNA display / Shingo Ueno and Naoto Nemoto -- Optimisation of antibody affinity by ribosome display using error-prone or site-directed mutagenesis / Leeanne Lewis and Chris Lloyd -- Affinity maturation of phage display antibody populations using ribosome display / Maria A. Groves and Adrian A. Nickson -- Evolution of protein stability using ribosome display / Andrew Buchanan -- Selection of lead antibodies from naive ribosome display antibody libraries / Peter Ravn -- Evolution of disulfide-rich peptide aptamers using cDNA display / Yuki Mochizuki and Naoto Nemoto -- Peptide screening using PURE ribosome display / Hiroyuki Ohashi [and others] -- Rapid selection of high-affinity binders using ribosome display / Birgit Dreier and Andreas Plückthun -- mRNA display-based selections using synthetic peptide and natural protein libraries / Steve W. Cotten [and others] -- Identification of candidate vaccine genes using ribosome display / Liancheng Lei -- Ribosome display for the selection of Sac7d scaffolds / Barbara Mouratou [and others] -- Charging of tRNAs using ribozymes and selection of cyclic peptides containing thioethers / Patrick C. Reid [and others] -- Update on pure translation display with unnatural amino acid incorporation / R. Edward Watts and Anthony C. Forster -- In vitro selection of unnatural cyclic peptide libraries via mRNA display / Zhong Ma and Matthew C.T. Hartman -- Optimization of CAT-354, a therapeutic antibody directed against interleukin-13, using ribosome display / George Thom and Ralph Minter -- Affinity maturation and functional dissection of a humanised anti-RAGE monoclonal antibody by ribosome display / Simon E. Hufton.
  • 2013 Springer Protocols
    Yang, Yinong.
    Rice artificial hybridization for genetic analysis / Xueyan Sha -- Fluorescence in situ hybridization techniques for cytogenetic and genomic analyses / Jason G. Walling, Wenli Zhang, and Jiming Jiang -- Generation of rice mutants by chemical mutagenesis / Thomas H. Tai -- TILLING and ecotilling for rice / Jennifer L. Cooper [and others] -- Functional characterization of rice genes using a gene-indexed T-DNA insertional mutant population / Ki-Hong Jung and Gynheung An -- QTL analysis and map-based cloning of salt tolerance gene in rice / Ji-Ping Gao and Hong-Xuan Lin -- Site-specific gene integration in rice / Vibha Srivastava -- Transcriptome profiling analysis using rice oligonucleotide microarrays / Ki-Hong Jung and Pamela C. Ronald -- Cloning of small RNAs for the discovery of novel microRNAs in plants / Guru Jagadeeswaran and Ramanjulu Sunkar -- Global identification of small RNA targets in plants by sequencing sliced ends of messenger RNAs / Yong-Fang Li and Ramanjulu Sunkar -- Artificial microRNAs for specific gene silencing in rice / Norman Warthmann [and others] -- Rice proteomic analysis : sample preparation for protein identification / Ganesh Kumar Agrawal [and others] -- Quantification of jasmonic and salicylic acids in rice seedling leaves / Kyoungwon Cho [and others] -- Analysis of insect-induced volatiles from rice / Nan Zhao [and others] -- Phenotypic and physiological evaluation for drought and salinity stress responses in rice / Utlwang Batlang [and others] -- Phenotypic, physiological, and molecular evaluation of rice chilling stress response at the vegetative stage / Benildo G. de los Reyes [and others] -- Analysis of rice root hair morphology using cryo-scanning electron microscopy / Zhiming Yu -- Inoculation and virulence assay for bacterial blight and bacterial leaf streak of rice / Bing Yang and Adam Bogdanove -- Inoculation and scoring methods for rice sheath blight disease / Yulin Jia [and others] -- Molecular approaches to improve rice abiotic stress tolerance / Junya Mizoi and Kazuko Yamaguchi-Shinozaki -- Molecular strategies to improve rice disease resistance / Emily E. Helliwell and Yinong Yang -- Molecular strategies to engineer transgenic rice seed compartments for large-scale production of plant-made pharmaceuticals / Trevor Greenham and Illimar Altosaar.
  • 2001 ScienceDirect
    Moore, Peter; Nishimura, Susumu; Söll, Dieter.
  • 2008 Springer Protocols
    Nielsen, Henrik.
    The transcriptional landscape -- Working with RNA -- Synthesis of RNA by in vitro transcription -- Efficient poly(A)+ RNA selection using LNA oligo(T) capture -- Genome browsers -- Web-based tools for studying RNA structure and function -- Northern blotting analysis -- Rapid amplification of cDNA ends (RACE) -- Fractionation of mRNA based on the length of the poly(A) tail -- Analysis of mutations that influence pre-mRNA splicing -- S1 nuclease analysis of alternatively spliced mRNA -- Promises and challenges in developing RNAi as a research tool and therapy -- Inhibition of gene function in mammalian cells using short-hairpin RNA (shRNA) -- Validation of RNAi by real time PCR -- Profiling RNA polymerase II using the fast chromatin immunoprecipitation method -- The post-transcriptional operon -- RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray (chip) profiling -- Isolation of RNP granules -- Electrophoretic mobility shift assay for characterizing RNA-protein interaction -- Polysome analysis and RNA purification from sucrose gradients -- Prediction of targets for microRNAs -- Outsourcing of experimental work.
  • 2012 Springer Protocols
    Gassmann, Walter; Jin, Hailing.
    SuperSAGE : powerful serial analysis of gene expression / Hideo Matsumura [and others] -- Northern blot analysis for expression profiling of mRNAs and small RNAs / Ankur R. Bhardwaj [and others] -- Construction of RNA-seq libraries from large and microscopic tissues for the illumina sequencing platform / Hagop S. Atamian and Isgouhi Kaloshian -- Strand-specific RNA-seq applied to malaria samples / Nadia Ponts, Duk-Won D. Chung, and Karine G. Le Roch -- RNA in situ hybridization in Arabidopsis / Miin-Feng Wu and Doris Wagner -- Laser microdissection of cells and isolation of high-quality RNA after cryosectioning / Marta Barcala, Carmen Fenoll, and Carolina Escobar -- Detection and quantification of alternative splicing variants using RNA-seq / Douglas W. Bryant Jr, Henry D. Priest, and Todd C. Mockler -- Separating and analyzing sulfur-containing RNAs with Organomercury Gels / Elisa Biondi and Donald H. Burke -- RNAse mapping and quantitation of RNA isoforms / Lakshminarayan K. Venkatesh, Olufemi Fasina, and David J. Pintel -- Detection and quantification of viral and satellite RNAs in plant hosts / Sun-Jung Kwon, Jang-Kyun Seo, and A.L.N. Rao -- In situ detection of mature miRNAs in plants using LNA-modified DNA probes / Xiaozhen Yao, Hai Huang, and Lin Xu -- Small RNA isolation and library construction for expression profiling of small RNAs from neurospora and fusarium using illumina high-throughput deep sequencing / Gyungsoon Park and Katherine A. Borkovich -- Isolation and profiling of protein-associated small RNAs / Hongwei Zhao [and others] -- New virus discovery by deep sequencing of small RNAs / Kashmir Singh, Ravneet Kaur, and Wenping Qiu -- Global assembly of expressed sequence tags / Foo Cheung -- Computational analysis of RNA-seq / Scott A. Givan, Christopher A. Bottoms, and William G. Spollen -- Identification of microRNAs and natural antisense transcript-originated endogenous siRNAs from small-RNA deep sequencing data / Weixiong Zhang [and others].
  • 2011 Springer Protocols
    Aphasizhev, Ruslan.
    Three-dimensional reconstruction of trypanosoma brucei editosomes using single-particle electron microscopy / H.U. Goringer ... [et al.] -- Icoda: RNAi-based inducible knock-in system in trypanosoma brucei / G.E. Ringpis, R.H. Lathrop and R. Aphasizhev -- Perturbing a-to-i RNA editing using genetics and homologous recombination / C.J. Staber ... [et al.] -- Laser microdissection and pressure catapulting of single human motor neurons for RNA editing analysis / H. Sun ... [et al.] -- Biochemical identification of A-to-I RNA editing sites by the inosine chemical erasing (ice) method / M. Sakurai and T. Suzuki -- Identifying mRNA editing deaminase targets by RNA-seq / B.R. Rosenberg, S. Dewell and F.N. Papavasiliou -- Mouse and other rodent models of C to U RNA editing / V. Blanc and N.O. Davidson -- In vivo analysis of RNA editing in plastids / S. Ruf and R. Bock -- Identifying specific trans-factors of RNA editing in plant mitochondria by multiplex single base extension typing / M. Takenaka -- Complementation of mutants in plant mitochondrial RNA editing by protoplast transfection / M. Takenaka and A. Zehrmann -- A high-throughput assay for DNA deaminases / M. Wang, C. Rada and M.S. Neuberger -- Biochemical fractionation and purification of high-molecular-mass apobec3g complexes / Y.L. Chiu -- Analysis of tRNA editing in native and synthetic substrates / J.L. Spears, K.W. Gaston and J.D. Alfonzo -- Post-transcriptional modification of RNAs by artificial box h/aca and box c/d rnps / C. Huang, J. Karijolich and Y.T. Yu -- Functional analysis of noncoding RNAs in trypanosomes: RNA walk, a novel approach to study RNA-RNA interactions between small RNA and its target / C. Wachtel and S. Michaeli -- A post-labeling approach for the characterization and quantification of RNA modifications based on site-directed cleavage by dnazymes / M. Meusburger, M. Hengesbach and M. Helm.
  • 2015 Springer Protocols
    Picardi, Ernesto.
    Free energy minimization to predict RNA secondary structures and computational RNA design / Alexander Churkin, Lina Weinbrand, and Danny Barash -- RNA secondary structure prediction from multi-aligned sequences / Michiaki Hamada -- Simple protocol for the inference of RNA global pairwise alignments / Eugenio Mattei, Manuela Helmer-Citterich, and Fabrizio Ferrè -- De novo secondary structure motif discovery using RNA profile / Federico Zambelli and Giulio Pavesi -- Drawing and editing the secondary structure(s) of RNA / Yann Ponty and Fabrice Leclerc -- Modeling and predicting RNA three-dimensional structures / Jérôme Waldispühl and Vladimir Reinharz -- Fast prediction of RNA-RNA interaction using heuristic algorithm / Soheila Montaseri -- Quality control of RNA-Seq experiments / Xing Li ... [and 3 others] -- Accurate mapping of RNA-Seq data / Kin Fai Au -- Quantifying entire transcriptomes by aligned RNA-Seq data / Raffaele A. Calogero and Francesca Zolezzi -- Transcriptome assembly and alternative splicing analysis / Paola Bonizzoni ... [and 5 others] -- Detection of post-transcriptional RNA editing events / Ernesto Picardi ... [and 3 others] -- Prediction of miRNA targets / Anastasis Oulas ... [and 6 others] -- Using deep sequencing data for identification of editing sites in mature miRNAs / Shahar Alon and Eli Eisenberg -- NGS-trex : an automatic analysis workflow for RNA-seq data / Ilenia Boria ... [and 3 others] -- e-DNA meta-barcoding : from NGS raw data to taxonomic profiling / Fosso Bruno, Marzano Marinella, and Monica Santamaria -- Deciphering metatranscriptomic data / Evguenia Kopylova ... [and 6 others] -- RIP-seq data analysis to determine RNA-protein associations / Federico Zambelli and Giulio Pavesi -- ViennaRNA eeb services / Andreas R. Gruber, Stephan H. Bernhart, and Ronny Lorenz -- Exploring the RNA editing potential of RNA-Seq data by ExpEdit / Mattia D'Antonio ... [and 4 others] -- Guideline for the annotation of UTR regulatory elements in the UTRsite collection / Matteo Giulietti ... [and 3 others] -- Rfam : annotating families of non-coding RNA sequences / Jennifer Daub ... [and 3 others] -- ASPicDB : a database web tool for alternative splicing analysis / Mattia D'Antonio ... [and 5 others] -- Analysis of alternative splicing events in custom gene datasets by AStalavista / Sylvain Foissac and Michael Sammeth -- Computational design of artificial RNA molecules for gene regulation / Alessandro Laganà ... [and 6 others].
  • 2012 Springer
    Leontis, Neocles B.; Westhof, Eric.
    Introduction / Michael Levitt -- Modeling RNA Molecules / Neocles Leontis and Eric Westhof -- Methods for Predicting RNA Secondary Structure / Kornelia Aigner, Fabian Dre€en and Gerhard Steger -- Why Can't We Predict RNA Structure At Atomic Resolution? / Parin Sripakdeevong, Kyle Beauchamp and Rhiju Das -- Template-Based and Template-Free Modeling of RNA 3D Structure: Inspirations from Protein Structure Modeling / Kristian Rother, Magdalena Rother, Michał Boniecki, Tomasz Puton and Konrad Tomala, et al. -- The RNA Folding Problems: Different Levels of sRNA Structure Prediction / Fredrick Sijenyi, Pirro Saro, Zheng Ouyang, Kelly Damm-Ganamet and Marcus Wood, et al. -- Computational Prediction and Modeling Aid in the Discovery of a Conformational Switch Controlling Replication and Translation in a Plus-Strand RNA Virus / Wojciech K. Kasprzak and Bruce A. Shapiro -- Methods for Building and Refining 3D Models of RNA / Samuel C. Flores, Magdalena Jonikas, Christopher Bruns, Joy P. Ku and Jeanette Schmidt, et al. -- Multiscale Modeling of RNA Structure and Dynamics / Feng Ding and Nikolay V. Dokholyan -- Statistical Mechanical Modeling of RNA Folding: From Free Energy Landscape to Tertiary Structural Prediction / Song Cao and Shi-Jie Chen -- Simulating Dynamics in RNA-Protein Complexes / John Eargle and Zaida Luthey-Schulten -- Quantum Chemical Studies of Recurrent Interactions in RNA 3D Motifs / Jiří Šponer, Judit E. Šponer and Neocles B. Leontis -- Nonredundant 3D Structure Datasets for RNA Knowledge Extraction and Benchmarking / Neocles B. Leontis and Craig L. Zirbel -- Ions in Molecular Dynamics Simulations of RNA Systems / Pascal Auffinger -- Modeling RNA Folding Pathways and Intermediates Using Time-Resolved Hydroxyl Radical Footprinting Data / Joshua S. Martin, Paul Mitiguy and Alain Laederach -- A Top-Down Approach to Determining Global RNA Structures in Solution Using NMR and Small-Angle X-ray Scattering Measurements / Yun-Xing Wang, Jinbu Wang and Xiaobing Zuo -- RNA Structure Determination by Structural Probing and Mass Spectrometry: MS3D / A. E. Hawkins and D. Fabris.
  • 2011 Springer Protocols
    Gerst, Jeffrey E.
    Single molecule imaging of RNA in situ / Mona Batish, Arjun Raj, and Sanjay Tyagi -- FISH and immunofluorescence staining in Chlamydomonas / James Uniacke, Daniel Colón-Ramos, and William Zerges -- High resolution fluorescent in situ hybridization in Drosophila / Eric Lécuyer -- Localization and anchorage of maternal mRNAs to cortical structures of ascidian eggs and embryos using high resolution in situ hybridization / Alexandre Paix, Janet Chenevert, and Christian Sardet -- Visualization of mRNA localization in Xenopus oocytes / James A. Gagnon and Kimberly L. Mowry -- Visualization of mRNA expression in the zebrafish embryo / Yossy Machluf and Gil Levkowitz -- High-resolution fluorescence in situ hybridization to detect mRNAs in neuronal compartments in vitro and in vivo / Sharon A. Swanger, Gary J. Bassell, and Christina Gross -- Localization of mRNA in vertebrate axonal compartments by in situ hybridization / José Roberto Sotelo-Silveira ... [et al.] -- Tiny molecular beacons for in vivo mRNA detection / Diana P. Bratu, Irina E. Catrina, and Salvatore A.E. Marras -- Delivery of molecular beacons for live-cell imaging and analysis of RNA / Antony K. Chen ... [et al.] -- Genetically-encoded fluorescent probes for imaging endogenous mRNA in living cells / Takeaki Ozawa and Yoshio Umezawa -- Visualization of induced RNA in single bacterial cells / Azra Borogovac and Natalia E. Broude -- Visualizing mRNAs in fixed and living yeast cells / Franck Gallardo and Pascal Chartrand -- In vivo visualization of RNA using the U1A-based tagged RNA system / Sunglan Chung and Peter A. Takizawa -- Visualizing endogenous mRNAs in living yeast using m-TAG, a PCR-based RNA aptamer integration method, and fluorescence microscopy / Liora Haim-Vilmovsky and Jeffrey E. Gerst -- Imaging mRNAs in living mammalian cells / Sharon Yunger and Yaron Shav-Tal -- Using the mRNA-MS2/MS2CP-FP system to study mRNA transport during Drosophila oogenesis / Katsiarina Belaya and Daniel St Johnston -- Genome-wide analysis of RNA extracted from isolated mitochondria / Erez Eliyahu, Daniel Melamed and Yoav Arava -- Analyzing mRNA localization to the endoplasmic reticulum via cell fractionation / Sujatha Jagannathan, Christine Nwosu and Christopher V. Nicchitta -- Isolation of mRNAs encoding peroxisomal proteins from yeast using a combined cell fractionation and affinity purification procedure / Gadi Zipor, Cecile Brocard and Jeffrey E. Gerst -- Profiling axonal mRNA transport / Dianna E. Willis and Jeffery L. Twiss -- RNA purification from tumor cell protrusions using porous polycarbonate filters / Jay Shankar and Ivan R. Nabi -- RNA-binding protein immunopurification-microarray (RIP-chip) analysis to profile localized RNAs / Alessia Galgano and André P. Gerber -- RaPID : an aptamer-based mRNA affinity purification technique for the identification of RNA and protein factors present in ribonucleoprotein complexes / Boris Slobodin and Jeffrey E. Gerst -- RIP : an mRNA localization technique / Sabarinath Jayaseelan ... [et al.] -- The dual use of RNA aptamer sequences for affinity purification and localization studies of RNAs and RNA-protein complexes / Scott C. Walker ... [et al.] -- Identifying and searching for conserved RNA localisation signals / Russell S. Hamilton and Ilan Davis -- Computational prediction of RNA structural motifs involved in post-transcriptional regulatory processes / Michal Rabani, Michael Kertesz, and Eran Segal.
  • 2007 ScienceDirect
    Gott, Jonatha M.
    Also available: Print – 2007
  • 2008 Springer
    Göringer, H. Ulrich.
    Editing reactions from the perspective of RNA structure / Matthias Homann -- Editing of tRNA for structure and function / Juan D. Alfonzo -- RNA editing by adenosine deaminases that act on RNA (ADARs) / Michael F. Jantsch and Marie Öhman -- Insertion/deletion editing in Physarum polycephalum / Jonatha M. Gott and Amy C. Rhee -- RNA editing in plant mitochondria / Mizuki Takenaka ... [et al.] -- RNA editing in chloroplasts / Masahiro Sugiura -- Working together : the RNA editing machinery in Trypanosoma brucei / Jason Carnes and Kenneth Stuart -- RNA editing accessory factors : the example of mHel61p / H. Ulrich Göringer ... [et al.] -- The function of RNA editing in trypanosomes / Torsten Ochsenreiter and Stephen Hajduk -- Evolutionary aspects of RNA editing / Dave Speijer.
  • 2011 Springer
    Jensen, Torben Heick.
    "The diversity of RNAs inside living cells is amazing. We have known of the more "classic" RNA species: mRNA, tRNA, rRNA, snRNA and snoRNA for some time now, but in a steady stream new types of molecules are being described as it is becoming clear that most of the genomic information of cells ends up in RNA. To deal with the enormous load of resulting RNA processing and degradation reactions, cells need adequate and efficient molecular machines. The RNA exosome is arising as a major facilitator to this effect. Structural and functional data gathered over the last decade have illustrated the biochemical importance of this multimeric complex and its many co-factors, revealing its enormous regulatory power. By gathering some of the most prominent researchers in the exosome field, it is the aim of the book to introduce this fascinating protein complex and to give a timely and rich account of its many functions"--Provided by publisher.
    Also available: Print – 2011
  • 2014 Springer Protocols
    Waldsich, Christina.
    Predicting RNA Structure: Advances and Limitations -- Cis-Acting 5' Hammerhead Optimization for In Vitro Transcription of Highly Structured RNAs -- RNA Structural Analysis by Enzymatic Digestion -- A Mutate-and-Map Protocol for Inferring Base Pairs in Structured RNA -- Mapping RNA Structure In Vitro Using Nucleobase-Specific Probes -- Massively Parallel RNA Chemical Mapping with a Reduced Bias MAP-Seq Protocol -- Probing RNA Folding by Hydroxyl Radical Footprinting -- Monitoring Global Structural Changes and Specific Metal Binding Sites in RNA by In-Line Probing and Tb(III) Cleavage -- Chemical Probing of RNA in Living Cells -- A Chemogenetic Approach to Study the Structural Basis of Protein-Facilitated RNA Folding -- Applying UV Crosslinking to Study RNA-Protein Interactions in Multicomponent Ribonucleoprotein Complexes -- The Kinetics of Ribozyme Cleavage: A Tool to Analyze RNA Folding as a Function of Catalysis -- RNA Catalytic Activity as a Probe of Chaperone-Mediated RNA Folding -- Evaluation of RNA Chaperone Activity In Vivo and In Vitro Using Misfolded Group I Ribozymes -- RNA Conformational Changes Analyzed by Comparative Gel Electrophoresis -- Detecting RNA Tertiary Folding by Sedimentation Velocity Analytical Ultracentrifugation -- RNA Folding Dynamics Using Laser Assisted Single-Molecule Refolding -- RNA Refolding Studied by Light-Coupled NMR Spectroscopy -- Exploring RNA Oligomerization and Ligand Binding by Fluorescence Correlation Spectroscopy and Small Angle X-Ray Scattering.
  • 2011 Springer
    Collins, Lesley J.
    The RNA infrastructure : an introduction to ncRNA networks / Lesley J. Collins -- RNA interactions / Manja Marz and Peter F. Stadler -- Plant RNA silencing in viral defence / Vitantonio Pantaleo -- Micrornas as post-transcriptional machines and their interplay with cellular networks / Sarath Chandra Janga and Swathi Vallabhaneni -- Spatiotemporal aspects of microRNA-mediated gene regulation / Joris Pothof and Dik C. van Gent -- Spliceosomal RNA infrastructure : the network of splicing components and their regulation by miRNAs / Lesley J. Collins -- Construction, structure, and dynamics of post-transcriptional regulatory network directed by RNA binding proteins / Sarath Chandra Janga and Nitish Mittal -- Safe keeping the message : mRNP complexes tweaking after transcription / Said Hafidh, Věra Čapková, and David Honys -- Unexpected functions of tRNA and tRNA processing enzymes / Rebecca L. Hurto -- Programmed DNA elimination in tetrahymena : a small RNA mediated genome surveillance mechanism / Kensuke Kataoka and Kazufumi Mochizuki -- Long noncoding RNA and epigenomics / Chandrasekhar Kanduri -- Promoter associated long noncoding RNAs repress transcription through a RNA binding protein TLS / Riki Kurokawa -- RNA networks in prokaryotes I :CRISPRs and riboswitches / Patrick J. Biggs and Lesley J. Collins -- RNA networks in prokaryotes II : tRNA processing and small RNAs / Lesley J. Collins and Patrick J. Biggs -- Localization of the bacterial RNA infrastructure / Kenneth C. Keiler -- Small RNA discovery and characterisation in eukaryotes using high throughput approaches / Helio Pais ... [et al.] -- How old are RNA networks? / Toni Daly, X. Sylvia Chen, and David Penny.
  • 2005 ScienceDirect
    Engelke, David R.; Rossi, John J.
    Also available: Print – 2005
  • 2015 Springer Protocols
    Sioud, Mouldy.
    RNA interference : mechanisms, technical challenges, and therapeutic opportunities / Mouldy Sioud -- Nanostructured RNAs for RNA interference / Yuko Nakashima [and others] -- One long oligonucleotide or two short oligonucleotides based shRNA construction and expression / Xue-jun Wang and Sheng-qi Wang -- PLGA microspheres encapsulating siRNA / Giuseppe De Rosa and Giuseppina Salzano -- Magnetic nanoparticle and magnetic field assisted siRNA delivery in vitro / Olga Mykhaylyk [and others] -- Cytoplasmic delivery of siRNAs to monocytes and dendritic cells via electroporation / Mouldy Sioud -- Delivery of siRNAs to cancer cells via bacteria / Omar Ahmed, Andrea Krühn, and Hermann Lage -- Microwell array-mediated delivery of lipoplexes containing nucleic acids for enhanced therapeutic efficacy / Yun Wu, Daniel Gallego-Perez, and L. James Lee -- Modulating the tumor microenvironment with RNA interference as a cancer treatment strategy / Karin Zins [and others] -- Targeted in vivo delivery of siRNA and an endosome- releasing agent to hepatocytes / Magdolna G. Sebestyén [and others] -- Cell-internalization SELEX : method for identifying cell- internalizing RNA aptamers for delivering siRNAs to target cells / William H. Thiel [and others] -- Strategies for siRNA navigation to desired cells / Mouldy Sioud -- Use of guanidinopropyl-modified siRNAs to silence gene expression / Maximilian C.R. Buff [and others] -- Therapy of respiratory viral infections with intranasal siRNAs / Sailen Barik and Patrick Lu -- Engineering therapeutic cancer vaccines that activate antitumor immunity / Per Ole Iversen and Mouldy Sioud -- Immunosuppressive factor blockade in dendritic cells via siRNAs results in objective clinical responses / Mouldy Sioud, Anne Mobergslien, and Stein Sæbøe-Larssen -- Targeting bcr-abl transcripts with siRNAs in an imatinib- resistant chronic myeloid leukemia patient : challenges and future directions / Michael Koldehoff -- Facile method for interfering with off-target silencing mediated by the sense strand / Anne Mobergslien and Mouldy Sioud -- Overcoming the challenges of siRNA activation of innate immunity : design better therapeutic siRNAs / Mouldy Sioud -- Gene silencing in vitro and in vivo using intronic microRNAs / Jia Han Deng [and others] -- In silico identification of novel endo-siRNAs / Andrew Schuster [and others] -- Computer-assisted annotation of small RNA transcriptomes / Nicole Ortogero [and others] -- miR-CATCH : microRNA capture affinity technology / Sebastian Vencken [and others] -- Roles of MicroRNAs in cancers and development / Shigeru Takasaki -- Targeting microRNAs to withstand cancer metastasis / Valentina Profumo [and others] -- Urinary microRNAs as a new class of noninvasive biomarkers in oncology, nephrology, and cardiology / Hana Mlcochova [and others] -- Magnetic bead-based isolation of exosomes / Morten P. Oksvold, Axl Neurauter, and Ketil W. Pedersen -- Modified 2'-ribose small RNAs function as toll-like receptor-7/8 antagonists / Mouldy Sioud.
  • 2013 Springer
    Howard, Kenneth A.
    The Nobel Prize winning discovery that small interfering RNA can be utilised to control cellular gene expression has propelled the field of RNA interference (RNAi) to the forefront of biomedical science as a potential molecular medicine set to revolutionalise disease treatment. Harnessing the molecular mechanisms of RNAi and development of delivery technologies is crucial for its transformation into a therapeutic modality, this dependency is the focus of "RNA Interference from Biology to Therapeutics" that gives a comprehensive overview of RNAi biology and state-of-the-art delivery methods relevant to clinical translation of RNAi therapeutics. Key players and shapers in the fields of RNAi and delivery science have been assembled in a single volume to produce a truly unique interdisciplinary text, making it a "must-read" for both students and experts in, and at the interface of, RNAi, pharmaceutical science and medicine. An attractive feature is the "future perspectives" section within each chapter that allows global leaders the opportunity to express their views on the direction the field is moving. Topics covered in the book include miRNA biology and therapeutic exploitation, exosome delivery and clinical translation."RNA Interference from Biology to Therapeutics" is an up-to-the-minute, highly informative and invaluable text for those actively involved or interested in this fascinating and high-impact field.
  • 2011 Springer Protocols
    Harper, Scott Q.
    Designing hairpin-based RNAi shuttles / Yu Shen -- Rapid cloning and validation of microRNA shuttle vectors : a practical guide / Ryan L. Boudreau [and others] -- Use of small noncoding RNAs to silence transcription in human cells / Kevin V. Morris -- Delivery strategies for RNAi to the nervous system / Kevin D. Foust and Brian K. Kaspar -- Cloning small RNAs / Eric J. Devor and Lingyan Huang -- Profiling the miRNome : detecting global miRNA expression levels with DNA microarrays / Peter White -- High-throughput profiling of mature microRNA by real-time PCR / Jinmai Jiang [and others] -- In situ detection of microRNAs in paraffin-embedded, formalin-fixed tissues : different methodologies and co-localization with possible targets / Gerard J. Nuovo [and others] -- Tracing of siRNAs inside cells by FRET imaging / Markus Hirsch [and others] -- Application of RIP-chip for the identification of miRNA targets / Lu Ping Tan, Anke van den Berg, and Joost L. Kluiver.
  • 2005 MyiLibrary
    Appasani, Krishnarao; Fire, Andrew Z.; Nirenberg, Marshall W.
    Chemical modifications to achieve increased stability and sensitive detection of siRNA -- RNA interference in postimplantation mouse embryos -- In ovo RNAi opens new possibilities for functional genomics in vertebrates -- Sect. 4. Gene silencing in model organisms. Practical applications of RNAi in C. elegans -- Inducible RNAi as a forward genetic tool in Trypanosoma brucei -- RNA-mediated gene silencing in fission yeast -- RNA silencing in filamentous fungi: Mucor ciccinelloides as a model organism -- RNAi and gene silencing phenomena mediated by viral suppressors in plants -- Sect. 1. Basic RNAi, siRNA, microRNAs and gene-silencing mechanisms. RNAi beginnings. Overview of the pathway in C. elegans -- Dicer in RNAi: its roles in vivo and utility in vitro -- Genes required for RNA interference -- MicroRNAs: a small contribution from worms -- miRNAs in the brain and the application of RNAi to neurons -- Sect. 2. Design, synthesis of siRNAs. Degign and synthesis of small interfering RNA (siRNA) -- Automated design and high throughput chemical synthesis of siRNA -- Rational design of siRNAs with the Sfold software -- Enzymatic production of small interfering RNAs -- Sect. 3. Vector development and in vivo, in vitro and in ovo delivery methods. Six methods of inducing RNAi in mammalian cells -- Viral delivery of shRNA -- siRNA delivery by lentiviral vectors: design and applications -- Liposomal delivery of siRNAs in mice -- Sect. 5. Drug target validation. Delivering siRNA in vivo for functional genomics and novel therapeutics -- The role of RNA interference in drug target validation: application to Hepatitis C -- RNAi in the drug discovery process -- RNA interference technology in the discovery and validation of druggable targets -- Sect. 6. Therapeutic and drug development. RNAi-mediated silencing of viral gene expression and replication -- RNAi in drug development: practical considerations -- RNA interference studies in liver failure -- RNAi applications in living animal systems -- Sect. 7. High-throughput genome-wide RNAi analysis. High-throughput RNAi by soaking in Caenorhabtis elegans -- Tools for integrative genomics: genome-wide RNAi and expression profiling in Drosophila -- Microarray analysis and RNA silencing to determine genes functionally important in mesothelioma -- High-throughput RNA interference -- Generation of highly specific vector-based shRNAi libraries directed against the entire human genome.
    Also available: Print – 2005
  • 2014 Springer Protocols
    Alvarez, M. Lucrecia; Nourbakhsh, Mahtab.
    Part I Structural RNA mapping -- Full-length characterization of transcribed genomic region -- Rapid mapping of RNA 3 and 5 ends -- Single nucleotide mapping of RNA 5 and 3 ends -- Analysis of RNA secondary structure -- Tertiary structure mapping of the Pri-miRNA miR-17-92 -- In situ hybridization detection of miRNA using LNA [trademark] oligonucleotides -- Quantification of miRNAs by a simple and specific qPCR method -- RNA isolation for small RNA next-generation sequencing from acellular biofluids -- Sequencing small RNA : introduction and data analysis fundamentals -- Measuring expression levels of small regulatory RNA molecules from body fluids and formalin-fixed, paraffin-embedded samples -- MicroRNA profiling in plasma or serum using quantitative RT-PCR -- MicroRNA profiling of exosomes isolated from biofluids and conditioned media -- Isolation of urinary exosomes for RNA biomarker discovery using a simple, fast, and highly scalable method -- Part II Functional RNA mapping -- Identification of actively translated mRNAs -- Mapping of internal ribosome entry sites (IRES) -- Mapping of protein binding RNA elements -- Purification of RNA-binding proteins -- De novo approach to classify protein-coding and noncoding transcripts based on sequence composition -- Computational methods to predict long noncoding RNA functions based on co-expression network -- MicroRNA biogenesis : dicing assay -- Faster experimental validation of microRNA targets using cold fusion cloning and a dual firefly-Renilla luciferase reporter assay -- Experimental validation of predicted mammalian microRNAs of mirtron origin -- A guide for miRNA target prediction and analysis using web-based applications -- Tapping microRNA regulation networks through integrated analysis of microRNA-mRNA high-throughput profiles -- miRWalk database for miRNA-target interactions -- A schematic workflow for collecting information about the interaction between copy number variants and microRNAs using existing resources -- SYBR green and TaqMan quantitative PCR arrays : expression profile of genes relevant to a pathway or a disease state -- Comprehensive meta-analysis of microRNA expression using a robust rank aggregation approach.
  • 2010 ScienceDirect
    Farrell, Robert E.
    RNA and the cellular biochemistry revisited -- RNA isolation strategies -- The truth about tissues -- Going green : RNA and the molecular biology of plants -- Isolation of polyadenylated RNA -- Quality control for RNA preparations -- Resilient ribonucleases -- Stringency : conditions that influence nucleic acid structure -- Electrophoresis of RNA -- Photodocumentation and image analysis -- Northern analysis -- Nucleic acid probe technology -- Practical nucleic acid hybridization -- Principles of detection -- Quantifications of specific mRNAs by nuclease protection -- Analysis of nuclear RNA -- cDNA synthesis -- RT-PCR : a science and an art form -- Quantitative PCR techniques -- Functional genomics and transcript profiling -- High-throughput analysis of gene expression -- Non-array methods for global analysis of gene expression -- RNAi : take a RISC-role the dicer -- Genomes, transcriptomes, proteomes, and bioinformatics -- An RNA paradigm.
  • 2007 ScienceDirect
    Gott, Jonatha M.
    Also available: Print – 2007
  • 2015 ScienceDirect
    He, Chuan.
    Methodology for the high-throughput identification and characterization of tRNA variants that are substrates for a tRNA decay pathway -- Nucleoside analysis by hydrophilic interaction liquid chromatography coupled with mass spectrometry -- A platform for discovery and quantification of modified ribonucleosides in RNA: application to stress-induced reprogramming of tRNA modifications -- Recogniion of specified RNA modifications by the innate immune system -- Kinetic analysis of tRNA methyltransferases -- Preparation of human nuclear RNA m6A methyltransferases and demethylases and biochemical characterization of their catalytic activity -- Transcriptome-wide mapping of N6-methyladenosine by m6A-Seq -- Probing RNA modification status at single-nucleotide resolution in total RNA -- High-resolution mapping of N6-methyladenosine in transcriptome and genome using a photo-crosslinking-assisted strategy -- Pseudouridine in mRNA: incorporation, detection, and recoding -- Pseudo-Seq: genome-wide detection of pseudouridine modifications in RNA -- Pseudouridine chemical labeling and profiling -- Experimental approaches for target profiling of RNA cytosine methyltranferases -- RNA 5-methylcytosine analysis by bisulfite sequencing -- Biochemical and transcriptome-wide identification of A-to-I RNA editing sites by ICE-Seq -- Radical SAM-mediated methylation of ribosomal RNA.
  • pt. C-D, 2003. ScienceDirect
    pt. D ScienceDirect
    Adhya, Sankar Lal; Garges, Susan.
    Also available: Print – pt. C-D, 2003.
  • 2005 Springer Protocols
    Carmichael, Gordon G.
    Detection of microRNAs and assays to monitor microRNA activities in vivo and in vitro / Marianthi Kiriakidou ... [et al.] -- High-throughput analysis of microRNA gene expression using sensitive probes / Mouldy Sioud and Øystein Røsok -- Modification of human U1 snRNA for inhibition of gene expression at the level of pre-mRNA / Peng Liu ... [et al.]. Identification of components of RNAi pathways using the tandem affinity purification method / Mikiko C. Siomi and Haruhiko Siomi -- Separation of Drosophila RNA silencing complexes by native gel electrophoresis / John W. Pham and Erik J. Sontheimer -- Preparation and analysis of drosha / Yoontae Lee and V. Narry Kim -- RNA interference in Caenorhabditis elegans / Nathaniel R. Dudley and Bob Goldstein -- Down-regulating gene expression by RNA interference in Trypanosoma brucei / Christine E. Clayton ... [et al.] -- Analysis of double-stranded RNA and small RNAs involved in RNA-mediated transcriptional gene silencing / M. Florian Mette ... [et al.] -- Strategies for the design of random siRNA libraries and the selection of anti-GFP siRNAs / Mouldy Sioud and Sébastien Wälchli -- Silencing gene expression with dicer-generated siRNA pools / Jason W. Myers and James E. Ferrell Jr. -- Inhibition of gene expression in vivo using multiplex siRNA / Sung-Suk Chae and Timothy Hla -- Gene silencing by a DNA vector based RNAi technology / Guangchao Sui and Yang Shi -- Plasmid-based RNA interference: construction of small-hairpin RNA expression vectors / Scott Q. Harper and Beverly L. Davidson -- SiRNA delivery in vivo / Mouldy Sioud -- Peptide-based strategy for siRNA delivery into mammalian cells / Federica Simeoni ... [et al.] -- Lentiviral vector delivery of siRNA and shRNA encoding genes into cultured and primary hematopoietic cells / Mingjie Li and John J. Rossi -- Exon-specific RNA interference: a tool to determine the functional relevance of proteins encoded by alternatively spliced mRNAs / Alicia M. Celotto, Joo-Won Lee, and Brenton R. Graveley -- Immunoprecipitation of microRNPs and directional cloning of microRNAs / Elisavet Maniataki, Maria Dels Angels De Planell Saguer, and Zissimos Mourelatos --
  • 2010 Springer
    Barciszewski, Jan; Erdmann, V. A.
    The key features of RNA silencing / Kuniaki Saito ... [et al.] -- Selected strategies for the delivery of siRNA in vitro and in vivo / Sandra D. Laufer ... [et al.] -- RNAi suppression and its application / Xiaoping Yi, Rui Lu -- Strategies to prevent siRNA-triggered cellular toxicity / Matthias Bauer -- RNAi in malignant brain tumors: relevance to molecular and translational research / Mitsutoshi Nakada ... [et al.] -- Silencing Huntington's disease gene with RNAi / Yu Zhang, Robert M. Friedlander -- Application of Dicer-substrate siRNA in pain research / Philippe Sarret ... [et al.] -- RNAi treatment of HIV-1 infection / Karin J. von Eije, Ben Berkhout -- Application of RNA interference to treat conditions associated with dysregulation of transient receptor potential vanilloid 1 channel / Vickram Ramkumar ... [et al.] -- Harnessing RNAi-based functional genomics to unravel the molecular complexity underlying skin pigment variation / Hsiang Ho ... [et al.] -- mRNA structure and its effects on posttranscriptional gene silencing / Stephen I. Rudnick, Veenu Aishwarya, Alan M. Gewirtz -- Antisense RNA-mediated regulation of the p53 tumor suppressor / Marianne Farnebo, Klas G. Wiman -- Antisense oligonucleotides: insights from preclinical studies and clinical trials / Doreen Kunze, Kai Kraemer, Susanne Fuessel -- What can the new hammerhead ribozyme structures teach us about design? / William G. Scott -- microRNA biogenesis and its impact on RNA interference / Stefanie Grund, Sven Diederichs -- MicroRNAs in epithelial antimicrobial immunity / Jun Liu ... [et al.] -- Emerging roles of long noncoding RNAs in gene expression and intracellular organization / Tetsuro Hirose -- Noncoding RNAs as therapeutic targets / Maciej Szymański, Jan Barciszewski -- Noncoding RNAs at H19/IGF2 locus: role in imprinting, gene expression, and associated pathologies / Nahalie Berteaux, Nathalie Spruyt, Eric Adriaenssens.
  • 2008 ScienceDirect
    Arraiano, Cecilia; Maquat, Lynne.
    Also available: Print – 2008
  • 2008 ScienceDirect
    Kiledjian, Megerditch; Maquat, Lynne.
    Also available: Print – 2008
  • Atkins, John F.; Cech, Thomas R.; Gesteland, Raymond F.
  • 2008 Springer Protocols
    Barik, Sailen.
  • 2011 Springer Protocols
    Kodama, Hiroaki; Komamine, Atsushi.
    Overview of plant RNAi / Yuichiro Watanabe -- Caveat of RNAi in plants : the off-target effect / Muthappa Senthil-Kumar and Kirankumar S. Mysore -- Plant gateway vectors for RNAi as a tool for functional genomic studies / Toshiya Muranaka -- Heat-inducible RNAi for gene functional analysis in plants / Frederic Masclaux and Jean-Philippe Galaud -- Gene function analysis by artificial microRNAs in Physcomitrella patens / Basel Khraiwesh [and others] -- Virus-induced gene silencing in ornamental plants / Cai-Zhong Jiang, Jen-Chih Chen, and Michael Reid -- Local RNA silencing mediated by agroinfiltration / Jutta Maria Helm, Elena Dadami, and Kriton Kalantidis -- Direct transfer of synthetic double-stranded RNA into protoplasts of Arabidopsis thaliana / Ha-il Jung, Zhiyang Zhai, and Olena K. Vatamaniuk -- Detection of long and short double-stranded RNAs / Toshiyuki Fukuhara [and others] -- Quantitative stem-loop RT-PCR for detection of microRNAs / Erika Varkonyi-Gasic and Roger P. Hellens -- Large-scale sequencing of plant small RNAs / William P. Donovan, Yuanji Zhang, and Miya D. Howell -- Computational prediction of plant miRNA targets / Ying-Hsuan Sun [and others] -- Bisulfite sequencing for cytosine-methylation analysis in plants / Nazmul Haque and Masamichi Nishiguchi -- Using nuclear run-on transcription assays in RNAi studies / Basel Khraiwesh -- Proteomic analysis of RNA interference induced knockdown plant / Sang Yeol Lee and Kyun Oh Lee -- Comparative analysis of phosphoprotein expression using 2D-DIGE / Tomoya Asano and Takumi Nishiuchi.
  • 2011 CRCnetBASE
    Gaur, Rajarshi Kumar.
    "RNA interference (RNAi) is a system within living cells that helps to control active genes and their activity level. Two types of small RNA molecules--microRNA (miRNA) and small interfering RNA (siRNA)--are central to RNA interference. The discovery of RNAi was preceded first by observations of transcriptional inhibition by antisense RNA expressed in transgenic plants and more directly by reports of unexpected outcomes in experiments performed by plant scientists in the U.S. and The Netherlands in the early 1990s. RNAi technology are used for large-scale screens that systematically shut down each gene in the cell, which can help identify the components necessary for a particular cellular process or an event such as cell division. Exploitation of the pathway is also a promising tool in biotechnology and medicine. This book reviews the selective and robust effect of RNAi on gene expression which makes it a valuable research tool, both in cell culture and in living organisms because synthetic dsRNA introduced into cells can induce suppression of specific genes of interest. This book will introduce new technology in the study of RNA interference in microorganisms, plants and animals."--Provided by publisher.
  • 2015 Springer Protocols
    Schmidt, Frank J.
    Identifying RNA recombination events and non-covalent RNA-RNA interactions with the molecular colony technique / Helena V. Chetverina and Alexander B. Chetverin -- RNA-directed recombination of RNA in vitro / Niles Lehman, Nilesh Vaidya, and Jessica A.M. Yeates -- RNA-RNA SELEX / B. Cho -- Identification of antisense RNA stem-loops that inhibit RNA-protein interactions using a bacterial reporter system / Kazuo Harada -- Transactivation of large ribozymes / Matthew B. Martin, Thomas L. Leeper, and Frank J. Schmidt -- Native purification and labeling of RNA for single molecule fluorescence studies / Arlie J. Rinaldi, Krishna C. Suddala, and Nils G. Walter -- Single molecule studies of RNA-RNA interactions / Dongmei Yu, Peiwu Qin, and Peter V. Cornish -- Modification interference analysis of the ribosome / Simpson Joseph -- Assessing intermolecular RNA:RNA interactions within a ribonucleoprotein complex using heavy metal cleavage mapping / Keith T. Gagnon and E. Stuart Maxwell -- Electrophoretic mobility shift assays : analysis of tRNA binding to the T box riboswitch antiterminator RNA / R. Anupam, S. Zhou, and J.V. Hines -- Fluorescence anisotropy : analysis of tRNA binding to the T box riboswitch antiterminator RNA / S. Zhou, R. Anupam, and J.V. Hines -- Electrophoretic mobility shift assay of RNA-RNA complexes / Geunu Bak [and three others] -- Structural studies of a double-stranded RNA from trypanosome RNA editing by small-angle X-ray scattering / Angela Criswell and Blaine H.M. Mooers -- Fusion RNAs in crystallographic studies of double-stranded RNA from trypanosome RNA editing / Blaine H.M. Mooers.
  • 2011 Springer
    Oliveira, António Costa de; Varshney, R. K.
    With the predicted increase of the human population and the subsequent need for larger food supplies, root health in crop plants could play a major role in providing sustainable highly productive crops that can cope with global climate changes. While the essentiality of roots and their relation to plant performance is broadly recognized, less is known about their role in plant growth and development. "Root Genomics" examines how various new genomic technologies are rapidly being applied to the study of roots, including high-throughput sequencing and genotyping, Tilling, transcription.
  • 2002 Springer Protocols
    O'Connell, Joe.
    RT-PCR in biomedicine. Opportunities arising from the new accessibility of mrna / J. O'Connell -- The basics of RT-PCR. Some practical considerations / J. O'Connell -- Using the quantitative competitive RT-PCR technique to analyze minute amounts of different mrnas in small tissue samples / S. Greber-Platzer [and others] -- Detection of mrna expression and alternative splicing in a single cell / T. Kumazaki -- Nested RT-PCR. Sensitivity controls are essential to determine the biological significance of detected mrna / T. Goode [and others] -- Quantitative RT-PCR. A review of current methodologies / C. Joyce -- Rapid development of a quantitative-competitive (qc) RT-PCR assay using a composite primer approach / J. O'Connell [and others] -- Quantitation of gene expression by RT-PCR and hplc analysis of pcr products / F. Bachmair, C.G. Huber and G. Daxenbichler -- Time-resolved fluorometric detection of cytokine mrnas amplified by RT-PCR / K. Nieminen [and others] -- Mimic-based RT-PCR quantitation of substance p mrna in human mononuclear phagocytes and lymphocytes / J.P. Lai, S.D. Douglas and W.Z. Ho -- Detection and quantification of the hepatitis c viral genome / L.J. Fanning -- Semi-quantitative detection of hepatitis c virus rna by "real-time" RT-PCR / J.F. Schlaak -- RT-PCR for the assessment of genetically heterogenous populations of the hepatitis c virus / B. Mullan [and others] -- In situ immuno-pcr. A newly developed method for highly sensitive antigen detection in situ / Y. Cao -- RT-PCR from laser-capture microdissected samples / T. Crnogorac-Jurcevic, T.O. Nielsen and N.R. Lemoine -- Mycobacterium paratuberculosis detected by nested pcr in intestinal granulomas isolated by lcm in cases of crohn's disease / P. Ryan [and others] -- RT-PCR-based approaches to generate probes for mrna detection by in situ hybridization / J. O'Connell -- Amplified rna for gene array hybridizations / V.I. Shustova and S.J. Meltzer -- Semi-quantitative determination of differential gene expression in primary tumors and matched metastases by RT-PCR. Comparison with other methods / B. Mann and C. Hanski -- Detection of single nucleotide polymorphisms using a non-isotopic rnase cleavage assay / F. Waldron-Lynch [and others] -- Detection of clonally expanded t-cells by RT-PCR-sscp and nucleotide sequencing of t-cell receptor beta-cdr3 regions / M.S. Kurokawa, K. Nishioka and T. Kato -- Generation of scfv from a phage display mini-library derived from tumor-infiltrating b-cells / N. Gruel [and others] -- Generation of murine scfv intrabodies from b-cell hybridomas / C.H. Nam, S. Moutel and J.L. Teillaud -- Quantitation of mrna levels by RT-PCR in cells purified by facs. Application to peripheral cannabinoid receptors in leukocyte subsets / J. Marchand and P. Carayon -- Detection of anti-sense rna transcripts by anti-sense RT-PCR / M.C. Yeung and A.S. Lau -- RT-PCR in cdna library construction / V. Healy -- An RT-PCR-based protocol for the rapid generation of large, representative cdna libraries for expression screening / J. O'Connell.
  • 2015 Springer
    Sills, E. Scott.
    The Development of PGD -- Elements of Informed Consent for Preimplantation Genetic Diagnosis -- Follicular Recruitment & Oocyte Recovery in Assisted Reproduction -- Biomarker-based Flow-Cytometric Semen Analysis for Male Infertility Diagnostics and Clinical Decision Making in ART -- Comparison of Methods for Assessment of Sperm DNA Damage (Fragmentation) and Implications for the Assisted Reproductive Technologies -- Tweaking ICSI for a PGD program -- Comprehensive Chromosomal Screening from Polar Body Biopsy to Blastocyst Trophectoderm Sampling: Evidence and Considerations -- Polar Body Diagnosis -- An Alternative and Addition to Preimplantation Diagnosis -- Efficiency of Polar Body Biopsy for Aneuploidy Screening by DNA Microarray for Single Embryo Transfer -- Prediction of Embryo Viability by Morphokinetic Evaluation to Facilitate Single Transfer -- Comparison of PCR Techniques for Embryo Screening and Single Embryo Transfer -- Array CGH and Partial Genome Sequencing for Rapidly Karyotyping IVF Blastocysts Before Transfer -- Single Embryo Transfers Enabled by aCGH -- Current and Future Methodologies -- SNP array, qPCR, and next-generation sequencing based comprehensive chromosome screening -- Expanding PGD Applications to Non-traditional Genetic and Non-Genetic Conditions -- Should molecular cytogenetic techniques be applied to facilitate single embryo transfer in egg donation cases? Assessment of frequency and distribution of embryo aneuploidy after anonymous donor oocyte IVF -- Selecting the Single Embryo for Transfer in Mitochondrial Disorders -- Single Embryo Transfer: The Significance of the Embryo Transfer Technique -- The Vitrification Component: An Integral Part of a Successful eSET Program -- A Review of Luteal Support Protocols for Single Embryo Transfers -- Fresh and Frozen -- Cost effectiveness of single embryo transfers relative to higher embryo transfer policies in clinical practice: A population based analysis -- The Quebec experience -- One plus one equals two at once: Presenting cumulative pregnancy rates as the ideal outcome in elective SET programs -- Single Embryo Transfer in a State-Sponsored IVF Context: Current Experience from Israel -- Single Embryo Transfer: the Quebec Experience -- Regulatory Aspects of Embryo Testing: An American View -- Regulatory Challenges in Assisted Reproduction: A European Perspective -- Preimplantation Genetic Screen