Books by Subject
- Accurate methods for ancestry and relatedness inference — Epigenetics of aging (154)
- Epigenetics protocols. 2nd ed. — Introduction to genomic signal processing with control (154)
- Investigations in yeast functional genomics and molecular biology — Protein engineering protocols (154)
- Proteins and proteomics of Leishmania and Trypanosoma — Zebrafish-- genetics, genomics, and transcriptomics. Fourth edition. [4th ed.] (153)
- 2013Jesse M. Rodriguez.The predisposition to many diseases is strongly influenced by the genome of an individual. However, the association between the genome and most diseases is not fully understood, so there is an ongoing effort to characterize these associations. One way to characterize disease-genome associations is by studying the familial and ancestral origin of individuals in the context of disease. This kind of study relies on the fact that individuals with shared origins tend to have genomes and phenotypes that are similar to one another. Detailed information regarding familial and ancestral origin is often unknown, however, it can be inferred computationally by examining the genome. Therefore, it is important that we have accurate methods to infer this information in order to facilitate disease-genome associations. In this dissertation, I describe the contributions I have made to accurately inferring the ancestry and relatedness of individuals based on their genomes. First, I describe my work on ALLOY, a method to infer the ancestral origin of segments of the genome based on a factorial HMM. Next, I present PARENTE, a method to infer which individuals in a group are related to one another by detecting genomic segments that are identical-by-descent (IBD) using an embedded likelihood ratio test. Finally, I present PARENTE2, an extension of PARENTE that incorporates linkage disequilibrium information and results in significantly higher accuracy.
- 2013Julie Marie Granka.Organismic evolution involves both selective and neutral forces, although their relative contributions are often unknown. This thesis proposes novel statistical methods for analyzing genetic data from a variety of organisms, including yeast, Mycobacterium tuberculosis, and humans. The chapters of this thesis provide complimentary perspectives on the relative roles of selection and neutrality, from the molecular to the population level, and present various statistical tools for genetic data analysis. Chapter 2 proposes a maximum-likelihood based method with which to classify and identify interactions, or epistasis, between pairs of genes. Chapter 3 details a study of genetic data from Mycobacterium tuberculosis isolated from human Aboriginal Canadian communities; our analyses suggest that the bacterium spread to these communities via the Canadian fur trade in the 18th and 19th centuries. Chapter 4 discusses the detection of signatures of natural selection in the genomes of 12 diverse African human populations, and proposes novel considerations for identifying biological functions under selection and for comparing signals of selection between populations. Finally, Chapter 5 details the inference of the genetic basis and evolutionary history of light skin pigmentation and short stature in the genetically diverse [not equal to sign] Khomani Bushmen of the Kalahari Desert of South Africa, believed to be one of the world's most ancient human populations. These chapters emphasize that a more complete understanding of the evolutionary history of humans and other organisms requires not only the consideration of neutral and selective processes, but also both phenotypic and genetic information. The statistical methods and approaches presented in the following chapters have the potential to improve inferences of natural selection and demography from genetic data, as well as provide insight into the relative roles of both.
- 2011 Springer Protocolsedited by Richard O. Snyder, Philippe Moullier.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 SpringerCharles E. Samuel, editor.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 ScienceDirectedited by Kelly T. Hughes, Stanley R. Maloy.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.].
- 2012 ScienceDirectJohn M. Butler.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 SpringerLawrence Panasci, Raquel Aloyz, Moulay Alaoui-Jamali, editors.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 SpringerGuo-Liang Wang, Barbara Valent, editors.
- Analysis of the WntD signaling pathway in inhibition of dorsal activity and in embryonic primordial germ cell guidance2011Mark A. McElwain.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 Protocolsedited by Beth Shapiro, Michael Hofreiter.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 SpringerZhou Wang, editor.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 Protocolsedited by Andreas Werner.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 Protocolsedited by Ronald P. van Rij.[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 SpringerAndrea S. Foulkes.
- 2013 CRCnetBASERobert S. Matson.Omics & microarrays revisited -- The commercial microarrays -- Supports & surface chemistries -- The arraying processes -- Gene expression microarray-based applications -- Protein microarray applications -- Multiplex assays.
- 2013 Springer Protocolsedited by Diponkar Banerjee, Sohrab P. Shah.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 SpringerEdward A. Birge.
- 2015 Springer Protocolsedited by Kumaran Narayanan, Monash University Malaysia, Bandar Sunway, Malaysia, Icahn School of Medicine at Mount Sinai, New York, USA.
- 2010 SpringerRemus T. Dame, Charles J. Dorman, editors.
- 2006 Springeredited by Voon L. Chan, Philip M. Sherman, Billy Bourke.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.
- 2015 Springer Protocolsedited by Alessio Mengoni, Marco Galardini, Marco Fondi.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 Protocolsedited by Kenneth C. Keiler.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 Protocolsedited by Irina Artsimovitch, Thomas J. Santangelo.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 Protocolsedited by David W. Murhammer.
- 2015 Springer Protocolsedited by Susan K. Buchanan, Nicholas Noinaj.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 CRCnetBASEedited by Dipak K. Dey, Samiran Ghosh, Bani K. Mallick.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.
- BeadChip molecular immunohematology : toward routine donor and patient antigen profiling by DNA analysis2011 SpringerJoAnn M. Mould, Paul M. Ness, Steve R. Sloan, editors.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 SpringerJohn F. Cryan, Andreas Reif, editors.
- 2014 World ScientificErrol C Friedberg, University of Texas Southwestern Medical Center at Dallas, USA ; foreword by Sydney Brenner.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
- Bioinformatics-- the impact of accurate quantification on proteomic and genetic analysis and research2014 CRCnetBASEedited by Yu Liu, PhD.
- Bioinformatics and the cell : modern computational approaches in genomics, proteomics, and transcriptomics2007 Springerby Xuhua Xia.
- 2009 Springer Protocolsedited by David Posada.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.
- 2012 Springer Protocolsedited by Stephan Sudowe, Angelika B. Reske-Kunz.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].
- 2013 SpringerJonathan D. Dinman, editor.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 SpringerAlan Booth, Susan M. McHale, Nancy S. Landale, editors."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 CRCnetBASEeditor, V. K. Gupta ; co-editor, M. Ayyachamy.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 Springeredited by B.G.J. Knols and C. Louis.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 ProQuest Ebook CentralJames T. Bradley.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 Protocolsedited by David Biron, Gal Haspel.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.
- 2011 ScienceDirectedited by Joel H. Rothman, Andrew Singson.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 Protocolsby Lynda J. Campbell.[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 Protocolsedited by Mukesh Verma.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.
- 2013Craig Patrick Giacomini.Recurrent gene fusions and chromosomal translocations have long been recognized for their roles in oncogenesis. This dissertation employs genomic approaches to discover and characterize novel gene fusions in several cancer types. First we developed a "breakpoint analysis" pipeline for gene fusion discovery and applied this method to a collection of nearly 1,000 human cancer samples profiled on DNA microarrays. This approach led to the discovery and characterization of twelve new gene fusions in diverse cancer types including angiosarcoma, pancreatic cancer, and colon cancer. Separately, we performed RNA Sequencing on a series of 36 breast cancer specimens and used a suite of computational tools developed in-house to discover ~350 candidate gene rearrangements. Notably, we discovered recurrent fusions of the sterile 20 (STE20)-like kinase TAOK1, and functional studies suggest that these fusions encode potent oncoproteins that drive breast carcinogenesis. Many of the alterations discovered in this dissertation represent the first gene fusions reported to date in the corresponding cancer type, and many represent potentially druggable targets with therapeutic implications for patients.
- 2014 ScienceDirectedited by Graham Dellaire, Jason N. Berman, Robert J. Arceci.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 SpringerUlrich Pfeffer, editor.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 Protocolsedited by Narendra Wajapeyee.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 Protocolsedited by Paul B. Fisher.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 Springeredited by Igor Jurisica, Dennis A. Wigle, Bill Wong.
- 2010 CRCnetBASEeditor, Piero Carninci.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 Protocolsedited by Gary R. Skuse and Maureen C. Ferran.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.
- CCN proteins in health and disease : an overview of the fifth international workshop on the CCN family of genes2010 SpringerAnnick Perbal, Masaharu Takigawa, Bernard Perbal, editors.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.
- CD14-expressing bladder cancer cells establish tumor-promoting inflammation and drive tumor cell proliferation2013Ming Tatt Cheah.Keratin 14 (KRT14) expression marks the most primitive differentiation state in bladder cancer (BC) cells. However, the mechanisms by which KRT14-expressing cells promote tumorigenicity remain undefined. We found that KRT14-expressing cells express higher levels of CD14 and inflammatory factors such as IL6 and IL8. Using a syngeneic mouse BC model, we isolated CD14 high BC cells and show that this population is more tumorigenic compared to CD14 low cells and forms tumors that are more highly vascularized with higher myeloid cell infiltration. Inflammatory factors produced by CD14 high BC cells directly drive the recruitment and polarization of monocytes and macrophages to acquire immune-suppressive characteristics. In contrast, CD14 low BC cells have higher relative proliferation, which is markedly increased when stimulated by factors produced by CD14 high cells. Collectively, we demonstrate that CD14 high BC cells orchestrate tumor-promoting inflammation and drive tumor cell proliferation to promote tumor growth.
- 2011 Springer Protocolsedited by Chaofu Lu, John Browse, and James G. Wallis.
- 2011 Springer Protocolsedited by Ella Palmer.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.
- 2009 Springeredited by Mohamed Al-Rubeai.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.
- 2014 Springer Protocolsedited by Robert J. Henry, Agnelo Furtado.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.
- Characterizing multiple roles for ubiquitination and SUMOylation in the DNA damage tolerance pathways2013Michelle Kathryn Zeman.Accurate maintenance and transmission of DNA from one cell to another is crucial for the propagation of a species, as accumulation of random mutations can result in loss of critical cellular functions. During DNA replication, DNA lesions encountered by the replication machinery cannot be repaired, as unwinding of the parental DNA separates the damaged DNA from the undamaged template which would normally be used for repair. These replication-blocking lesions can be seriously detrimental to the cell, as stalled replication forks can collapse into double-stranded DNA breaks and lead to genomic rearrangements. To prevent the accumulation of stalled and collapsed forks, the cell uses DNA damage tolerance (DDT) pathways to bypass the DNA lesion and complete replication. There are two known DDT pathways -- translesion synthesis, which uses specialized translesion synthesis polymerases to replicate directly over a DNA lesion, and template switching, which promotes invasion into the sister chromatid and extrusion of the newly synthesized strand for use as a template. These processes rely on a series of E3 ubiquitin ligases in mammalian cells, including Rad18, SHPRH, and HLTF. As a result, we wished to examine the role of ubiquitin modification, and ubiquitin-related SUMO modification, on the control of DDT. Together, the data presented here provide important new insight into how cells control the response to DNA damage and, importantly, how this response is repressed in the absence of damage. As misregulation of Rad18 and SHPRH, as well as several other DDT components, has been implicated in cancer development and progression, knowing more about this regulation may help us understand how cells avoid the generation of mutations, and ultimately the development of disease.
- 2005 Springer Protocolsedited by Edward D. Zanders.Also available: Print – 2005
- 2006 SpringerS. Jaroch, H. Weinmann, editors.
- 2013 CRCnetBASEedited by Ferenc Darvas, Andras Guttman, Gyorgy Dorman.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 Protocolsedited by Randall H. Morse.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.
- 2013Chien-Jung Lin.During embryonic development, dynamic remodeling of the chromatin landscape is required for the transcriptional machinery to access the genomic DNA in a spatiotemporally controlled manner. This intricate level of regulation allows precise gene regulation, necessary for complex morphogenetic processes. The Brg1/Brm-associated factor (BAF) complex is a multisubunit, ATP-dependent chromatin remodeling complex. Among the subunits, Brg1 is an ATPase that is critical for the function of the complex. Here, we study the role of Brg1 in foregut and cardiac outflow tract development. In the foregut, Brg1 functions with HDAC proteins in the ventral epithelium to regulate Nkx2-1 expression, essential for foregut septation into trachea and esophagus. In the absence of Brg1, embryos develop a single-tube foregut, reminiscent of human patients with tracheoesophageal fistula. In the developing heart, Brg1 functions in the secondary heart field-derived myocardium to control Semaphorin 3c (Sema3c) expression, essential for the outflow tract to septate into pulmonary artery and aorta. Deletion of Brg1 in the secondary heart field results in decreased neural crest cell colonization of the outflow tract, leading to a phenotype similar to the persistent truncus arteriosus pathology. Brg1 cooperates with HDAC proteins and Chd7 in the outflow tract myocardium to control Sema3c expression. These studies demonstrate novel functions and molecular mechanisms of Brg1 in foregut and cardiovascular development.
- 2015 Springer Protocolsedited by Shondra M. Pruett-Miller.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 Protocolsedited by Gregory D. Davis, Kevin J. Kayser.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 CRCnetBASEedited by Kiichi Fukui, Tatsuo Ushiki.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 SpringerMarta Garaulet, Jose M. Ordovás, editors.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 SpringerPeter B. Gahan, editor.
- 2016 SpringerPeter B. Gahan, Michael Fleischhacker, Bernd Schmidt, editors.Circulating cell-free miR-373, miR-200a, miR-200b and miR-200c in patients with epithelial ovarian cancer / Xiaodan Meng, Volkmar Müller, Karin Milde-Langosch, Fabian Trillsch, Klaus Pantel [and others] -- Cell-free miRNA-141 and miRNA-205 as prostate cancer biomarkers / Ivan D. Osipov, Ivan A. Zaporozhchenko, Anna A. Bondar, Marat M. Zaripov [and others] -- Clinical utility of circulating tumor DNA for molecular assessment and precision medicine in pancreatic cancer / Erina Takai, Yasushi Totoki, Hiromi Nakamura, Mamoru Kato, Tatsuhiro Shibata [and others] -- An enquiry concerning the characteristics of cell-free DNA released by cultured cancer cells / Abel Jacobus Bronkhorst, Johannes F. Wentzel, Janine Aucamp, Etresia van Dyk [and others] -- Detection of p53 mutations in circulating DNA of transplanted hepatocellular carcinoma patients as a biomarker of tumor recurrence / N. García-Fernández, Hada C. Macher, Amalia Rubio, Pilar Jiménez-Arriscado [and others] -- Unbiased detection of somatic copy number aberrations in cfDNA of lung cancer cases and high-risk controls with low coverage whole genome sequencing / Fiona Taylor, James Bradford, Penella J. Woll, Dawn Teare, Angela Cox -- Liquid Profiling in Lung Cancer & Quantification of extracellular miRNAs in bronchial lavage / Bernd Schmidt, Grit Rehbein, Michael Fleischhacker -- Screening of KRAS mutation in pre- and post-surgery serum of patients suffering from colon cancer by COLD-PCR HRM / Elena Trujillo-Arribas, Hada C. Macher, Pilar Jiménez-Arriscado [and others] -- Non-dividing cell virtosomes affect in vitro and in vivo tumour cell replication / Mariano Garcia-Arranz, Damian Garcia-Olmo, Luz Vega-Clemente, Maurice Stroun [and others] -- Features of circulating DNA fragmentation in blood of healthy females and breast cancer patients / Svetlana N. Tamkovich, Natalia A. Kirushina, Vladimir E. Voytsitskiy [and others] -- Liquid profiling of circulating nucleic acids as a novel tool for the management of cancer patients / Stefan Holdenrieder -- Characterization of human pregnancy specific glycoprotein (PSG) gene copy number variations in pre-eclampsia patients / Chia Lin Chang, Chia Yu Chang, Da Xian Lee, Po Jen Cheng -- Non-invasive prenatal diagnosis of feto-maternal platelet incompatibility by cold high resolution melting analysis / Marta Ferro, Hada C. Macher, Pilar Noguerol, Pilar Jimenez-Arriscado [and others] -- Implementing non-invasive prenatal diagnosis (NIPD) in a National Health Service laboratory: from dominant to recessive disorders / Suzanne Drury, Sarah Mason, Fiona McKay, Kitty Lo, Christopher Boustred, Lucy Jenkins [and others] -- Comparative analysis of harmful physical factors effect on the cell genome / Irina N. Vasilyeva, Valery N. Zinkin, Vladimir G. Bespalov -- Heterochromatic tandem repeats in the extracellular DNA / Olga I. Podgornaya, Irina N. Vasilyeva, Vladimir G. Bespalov -- A historical and evolutionary perspective on circulating nucleic acids and extracellular vesicles: circulating nucleic acids as homeostatic genetic entities / Janine Aucamp, Abel Jacobus Bronkhorst, Piet J. Pretorius -- Comparison of microRNA content in plasma and urine indicates the existence of a transrenal passage of selected microRNAs / Eva Pazourkova, Sarka Pospisilova, Iveta Svobodova, Ales Horinek, Antonin Brisuda [and others] -- A quantitative assessment of cell-free DNA utilizing several housekeeping genes: measurements from four different cell lines / Janine Aucamp, Abel Jacobus Bronkhorst, Johannes F. Wentzel, Piet J. Pretorius -- Oligodeoxynucleotide analogues of circulating DNA inhibit dsRNA-induced immune response at the early stages of signal transduction cascade in a cell type-dependent manner / Anna V. Cherepanova, Zhanna K. Nazarkina, Pavel P. Laktionov -- Evaluation of the state of transplanted liver health by monitoring of organ-specific genomic marker in circulating DNA from receptor / Hada C. Macher, G. Suárez-Artacho, Pilar Jiménez-Arriscado, S. Álvarez-Gómez [and others] -- Vesicular and extra-vesicular RNAs of human blood plasma / Anna V. Savelyeva, Dmitriy N. Baryakin, Elena D. Chikova, Elena V. Kuligina [and others] -- Artificial analogues of circulating box C/D RNAs induce strong innate immune response and microRNA activation in human adenocarcinoma cells / Grigory A. Stepanov, Julia A. Filippova, Anna A. Nushtaeva, Elena V. Kuligina [and others] -- Multiple ways of cfDNA reception and following ROS production in endothelial cells / Anna Yu. Alekseeva, Larisa V. Kameneva, Svetlana V. Kostyuk, Natalia N. Veiko -- Protein content of circulating nucleoprotein complexes / Svetlana N. Tamkovich, Oleg S. Tutanov, Danil S. Serdukov, Maxim S. Belenikin [and others] -- Digital PCR of genomic rearrangements for monitoring circulating tumour DNA / Hongdo Do, Daniel Cameron, Ramyar Molania, Bibhusal Thapa, Gareth Rivalland [and others] -- mFast-SeqS as a monitoring and pre-screening tool for tumor-specific aneuploidy in plasma DNA / Jelena Belic, Marina Koch, Peter Ulz, Martina Auer, Teresa Gerhalter, Sumitra Mohan [and others] -- Methodological variables in the analysis of cell-free DNA / Abel Jacobus Bronkhorst, Janine Aucamp, Piet J. Pretorius -- Novel technology for enrichment of biomolecules from cell-free body fluids and subsequent DNA sizing / Vipulkumar Patel, Peter Celec, Magdalena Grunt, Heidi Schwarzenbach, Ingo Jenneckens [and others] -- A rapid and sensitive method for detection of the T790M mutation of EGFR in plasma DNA / Hideharu Kimura, Shingo Nishikawa, Hayato Koba, Taro Yoneda, Takashi Sone [and others] -- Evaluation of different blood collection tubes and blood storage conditions for the preservation and stability of cell-free circulating DNA for the analysis of the methylated mSEPT9 colorectal cancer screening marker / Jurgen Distler, Reimo Tetzner, Gunter Weiss, Thomas König, Anne Schlegel [and others] -- Purification of circulating cell-free DNA from plasma and urine using the automated large-volume extraction on the QIAsymphony® SP instrument / Alexander Wolf, Katharina Beller, Sebastian Groemminger, Wera Hofmann, Matthias Sachse [and others] -- Detection and quantification of KIT mutations in ctDNA by plasma Safe-SeqS / Johannes Fredebohm, Daniel H. Mehnert, Ann-Kathrin Löber, Frank Holtrup [and others] -- Lost in translation? Ethical challenges of implementing a new diagnostic procedure / Dagmar Schmitz -- Academia meets industry / Christian Schäfer, Tobias Paprotka, Ellen Heitzer, Mark Eccleston, Johannes Noe [and others].Also available: Print – 2016
- 2006 Springer Protocolsedited by Y.M. Dennis Lo, Rossa W.K. Chiu, K.C. Allen Chan.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.
- Clinical molecular genetics in the UK c.1975-c.2000 : the transcript of a witness seminar held by the History of Modern Biomedicine Research Group, Queen Mary, University of London, on 5 February 20132014 Wellcome Trustedited by E.M. Jones and E.M. Tansey.
- 2010Brian Patrick Grone.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 Springeredited by Marcello Barbieri.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 BookEberhard Passarge.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.
- v. 1-2, 2007 Springer Protocolsv. 2, 2007 Springer Protocolsedited by Nicholas H. Bergman.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.
- 2013 SpringerXuhua Xia.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.
- 2008 CRCnetBASEedited by James R. Brown.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 SpringerPer Sunnerhagen, Jure Piškur (eds.).
- 2014 CRCnetBASEedited by Azad K. Kaushik, and Yfke Pasman.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 ScienceDirectedited by Christer Hogstrand and Peter Kille.
- 2006 Springeredited by Wei Zhang and Ilya Shmulevich.
- 2015 SpringerAndrew E. Teschendorff, editor.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 CRCnetBASEedited by Edgar Jacoby.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 Springeredited by Gary Peltz.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 AtyponOzkan Ufuk Nalbantoglu and Khalid Sayood.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.
- 2010Samuel Gross.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 Springercontributors: A. Abuin ... [et al.] ; editors: Robert Feil and Daniel Metzger.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 SpringerGhazi M. Rayan, Joseph Upton III.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 Protocolsedited by Alexei Morozov.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.
- 2011Rayka Yokoo.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.
- 2013Alexander Fraser Lovejoy.While the presence of modified nucleotides in cellular RNA has been known about for over 60 years, it is only recently that such nucleotides have become studied and mapped in mRNAs. With recent transcriptome-wide maps of N6-methyladenosine and 5-methylcytosine showing widespread mRNA modification and evolutionary conservation of many sites, it is clear that site-specific mRNA modification may represent a new level of post-transcriptional regulation of gene expression. With this in mind, we set out to map other mRNA modifications to begin to get an idea of the role they may play in gene expression. We developed a high-throughput sequencing technique that identified the first known pseudouridines in mRNA. We were able to identify the enzymes that modified a few of the top hits, as well as show that modification of at least one of the top sites is conserved throughout the fungal lineage. We have made progress toward developing an improved high-throughput sequencing technique, which could allow elucidation of a transcriptome-wide map of pseudouridines. Adapting the same technique as was used to identify mRNA pseudouridylation, we also found a few dozen possible 2'-O-methylation sites in mRNA with an interesting functional theme, though these potential modifications still need to be validated. In addition, we attempted to map and find a functional role for N6-methyladenosines in yeast undergoing meiosis, and while this failed, it led to our discovery of a target set of bound mRNAs and role in gene expression of a meiosis-specific RNA binding protein, Rim4p. The work described in this thesis identifies the third known internal, site-specific modified nucleotide in mRNA, suggesting that mRNA modifications may be more common than previously thought and may play an important, under-explored role in post-transcriptional control of gene expression.
- 2013 SpringerRodolphe Barrangou, John van der Oost, editors.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- Wileyeditorial board, Nicholas C. Dracopoli ... [et al.].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 Protocolsv. 2, 2008 Springer Protocolsedited by Anton Posch.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 Protocolsedited by Michael Hamacher, Martin Eisenacher and Christian Stephan.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 Protocolsedited by François Pompanon and Aurélie Bonin.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-.opus a Luigi Gedda una cum aliis auctoibus.Status: Not Checked OutLane Catalog Record
- Developing Aiptasia pallida as a tractable model system for cnidarian-dinoflagellate symbiosis : identifying transferred metabolites and designing tools for analysis of ultra-high-throughput-sequencing data2011Matthew Strecker Burriesci.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.
- Developing the anemone Aiptasia as a tractable model for cnidarian-dinoflagellate symbiosis : generating transcriptomic resources and profiling gene expression2013Erik Michael Lehnert.Coral reefs are animal-built structures that provide habitats for a disproportionately large number of marine species relative to the small percentage of the ocean that they cover. Corals, and some other cnidarians such as anemones, host dinoflagellates within the cells of their gastrodermal tissue. The dinoflagellates fix carbon photosynthetically and transfer it to the host; the dinoflagellates can provide up to 90% of the hosts' metabolic requirements. The symbiosis between the cnidarian host and its dinoflagellate symbiont is therefore the trophic foundation on which coral reef are built. Despite its importance, the molecular mechanisms controlling symbiosis establishment, maintenance, and breakdown remain poorly understood. Our lab is working to further develop the small sea anemone, Aiptasia, as a model system for studying cnidarian-dinoflagellate symbiosis. To this end, I sequenced the transcriptome of aposymbiotic Aiptasia, of symbiotic Aiptasia, and of the dinoflagellate symbionts. I then used these resources to perform gene-expression analysis comparing symbiotic and aposymbiotic anemones, which provided numerous testable biological hypotheses about both the structural basis of the symbiosis and the downstream metabolic effects of metabolite transfer to the host. These resources should serve as the foundation for future experiments in our laboratory and more widely in the field of coral biology.
- 2011Ilya Anatoliy Shestopalov.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.
- 2012Ryan Ward Streble Peacock.Studying the effects of gene expression in biological systems has traditionally been undertaken by measuring phenotypic response at a limited number of expression levels. Typically the effects of gene expression are assayed at a high level of overexpression and compared to physiological levels of expression; however, many examples exist in which the level of gene expression greatly affects the resulting cellular phenotypes. Of particular interest for our purposes is the interplay between oncogenes in driving tumorigenesis and cancer progression. For example, oncogene H-Ras is capable of both enhancing cellular proliferation at intermediate levels expression levels (doses) and causing cell cycle arrest and senescence at high expression levels. In order to more thoroughly investigate such behavior we have created a set of tools for measuring dose-dependent effects of gene expression. These tools consist of promoter library to drive wide range gene expression, single-cell proliferation measurements, and data analysis methods to calculate correlation curves between gene expression level and phenotype response. The system is designed for cell-by-cell measuring of both expression level and phenotype response by flow cytometry. This approach allows for full dose experiments to be performed in a single heterogeneous culture with individual cells accessing different expression levels for a given phenotype. Because we are interested in studying the cell biology and genetics of tumor cells, measuring the phenotype of proliferation rate was of particular interest. To aid in further investigation of proliferation rate response to gene overexpression a genetic proliferation reporter was developed. This reporter utilizes the cell cycle-dependent activity of the E2F class of transcription factors, which are active during the G1/S transition. The highly stable fluorescent proteins EGFP and mCherry are expressed from both an E2F-responsive and constitutive promoter, respectively. The ratio of fluorescence levels correlates to proliferation rate in a variety of cell lines, matching predictions made initially by computational model. Finally, given a culture containing expression of a gene or combination of genes by the promoter library and phenotype measurement, the data collected from those cells must be analyzed to determine a correlation curve representing the dose response of the phenotype to level of expression of the genes of interest. In order to calculate this curve from the flow cytometry data several empirical analysis methods were evaluated. We determined the locally weighted scatter plot smoothing (LOWESS) curve fitting method to be best for our purposes of fitting the dose-response curves. As the LOWESS fits of flow cytometry data represented a technical hurdle to performing the dose-response experiments a custom software package was created to allow for easy implementation of the constitutive promoter library for studying dose-dependent behavior. The result is a set of biological and computational tools that allow for high throughput evaluation of gene dose effects. Further effort has been undertaken to move the system to evaluate multiple genes simultaneously, with the ultimate goal of being able to measure genetic cooperation.
- Development of genetic tools and techniques for controlling and quantitatively assessing gene-dosage profiles2013Joshua P. Ferreira.Cancer arises from the alteration of genes and the deregulation of the inherent control mechanisms existing with a cell. Cancer progression is the result of several of these genes or pathways being altered. Unfortunately, its analysis is not as straightforward as identifying a handful of discrete, independent mutational events occurring within a cell. Rather, these genes, pathways, and other regulatory elements are interconnected. Altering the expression level (dose) of one gene can have direct and indirect effects on many additional genes/pathways. Furthermore, combinations of genes can interact to have collaborative or antagonistic effects that are greater than or less than the sum of their individual contributions. It is not enough to study the effects of single genes/pathways at a few discrete expression levels. To this end, we have developed genetic tools that allow for controlling gene expression over a full range. Controlling gene expression at the level of transcription allowed for a 40-fold range of expression to be investigated. However, the range in expression of the transcriptionally controlled system varied across cell lines. Expanding beyond this system, we have turned to controlling gene expression at the level of translation. Using translational control elements, we were able to varying gene expression over a 200 -- 300-fold range. Furthermore, the translational control system was shown to be consistent across six different cell lines and with every transgene that has been tested to date. To address the fact that cancer progression is a multi-faceted event, we developed a system that would allow observation of the effects resulting from the interactions of multiple genes. By using retroviral vectors equipped with fluorescent protein fusions, we successfully derived a system that has the capacity to interrogate up to three genes of interest within a single culture of cells. This single culture makes it logistically feasible to study such large combinations of gene dosage levels. This single culture is heterogeneous in expression for each of the transgenes introduced; and by utilizing flow cytometry, the precise dosage level of each transgene can be correlated to measureable phenotypes at the single-cell level. To demonstrate how the tools we have developed can be utilized to quantitatively assess gene-dosage profiles, we ectopically controlled the expression of various mutant forms of the oncogenic version of H-Ras (H-RasG12V) in both murine fibroblast and pre-B cells. We chose to study proliferation as a measurable phenotypic read-out. In NIH/3T3 fibroblasts we observed a maximum in proliferation at low levels of expression of H-RasG12V. A mutant version, H-RasG12V T35S, which is only able to signal down the MAPK pathway, exhibited maximal proliferation at intermediate expression levels. Other H-Ras mutants did not exhibit any proliferation optima when expressed by themselves. In contrast, when the mutants were investigated in pairwise fashion, some cooperation could be observed between particular mutant pairs. Finally, the effect of these H-Ras mutants on proliferation was investigated in a murine pre-B cell line. By adding a reference population of cells to a culture of cells expressing H-Ras mutant oncogenes over a range of expression levels, we were able to track the population dynamics between these two subsets of cells. A simple mathematical approach will be detailed to demonstrate how we can calculate the net proliferation rate as a function of H-Ras expression level by tracking the distribution of these two cell populations over time.
- 2013Shoa Long Clarke.In this work, I present two studies of the evolution and function of developmental enhancers. In the first study, I describe the discovery of the first examples of cis-regulatory elements that are conserved across the two great clades of the bilaterian tree (deuterostomes and protostomes). These bilaterian conserved regulatory elements (Bicores) are developmental enhancers that respond to key signaling pathways and have been conserved for approximately 650 million years. In vertebrates, Bicores have neofunctionalized to drive expression in the central nervous system. In the second study, I present a genome-wide set of putative enhancers that function in the development of the mammalian neocortex. These elements, identified through ChIP-seq, are validated through both computational and experimental approaches. I show that many elements are anciently conserved beyond mammals, and we show that older elements are more likely to be pleiotropic. Pleiotropic elements most likely function in other aspects of central nervous system development, and elements that are conserved to zebrafish function in the developing zebrafish forebrain. I also provide evidence that specific repeat families have played a major role in the generation of enhancers that function in neocortex development. Finally, in the conclusion, I discuss how enhancer neofunctionalization and pleiotropy fit into a model of enhancer evolution and the evo-devo framework.
- 2013 Springer Protocolsedited by Ludwig Eichinger, Francisco Rivero.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].
- 2014 Springer Protocolsedited by Elizabeth M.J. Gillam, School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia, Janine N. Copp, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada, David F. Ackerley, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
- 2012Tiffany Hung.Recent advances in transcriptome analysis have revealed a large number of non-protein coding transcripts that have previously been uncharacterized. A subset of these molecules, termed long noncoding RNAs (lncRNAs), has been implicated in the regulation of chromatin states. Here, we detail a journey of lncRNA discovery and analysis, beginning from the de novo discovery of lncRNAs within the promoters of cell cycle genes, followed by the functional characterization of select candidates. We characterize two examples that regulate the p53-mediated DNA damage response. LncRNA PANDA blocks the apoptosis pathway by inhibiting the transcription factor NF-YA, and lncRNA DINO regulates the p53 transcriptional response by regulating SET7-mediated post-translational modification. Altogether, these studies support a model whereby pervasive lncRNA transcripts, previously discarded as transcriptional byproducts, function through diverse mechanisms as critical regulators of biological pathways.
- 2013Dustin Howard Hite.The central dogma of biology states that DNA, the genetic information, is transcribed into RNA, an information containing intermediate, which is then translated into proteins, actionable molecules which perform the majority of tasks required for life. To synthesize proteins, the cell employs a massive, macromolecular machine, the ribosome, and a myriad of protein factors to successfully translate an mRNA. My graduate studies have focused both on the ribosome and the protein translation factors that interact with the ribosome to facilitate translation initiation, elongation, and termination. First, utilizing recent advances in high throughput sequencing, we discovered that sequencing of ribosome protected fragments could illuminate in vivo dynamics of ribosome structural changes in Saccharomyces cerevisiae. We demonstrated that the ribosome protects two distinct sizes of fragments and assigned each fragment population to approximate stages of the translation elongation cycle where large structural rearrangements of the ribosome are known to occur. Once these assignments were made, we were able to model elongation speed and demonstrated that, contrary to previous reports, tRNA abundance and codon optimality were not the major determinants of elongation speed; surprisingly our data indicated that the polarity of the amino acid being decoded dictated elongation rates under these conditions, with polar amino acids acting to slow elongation rates. This study also implicated Dom34, a known NO GO decay factor, as a novel component of canonical translation termination and ribosome recycling. Second, we used another genome-wide assay of translation, "gradient encoding" microarray analysis, to interrogate the genome-wide effects of depleting five individual translation factors. Based on the current understanding of the molecular mechanisms of each translation factor, we hypothesized that the depletion of each factor would result in differential translation of mRNAs based on the physical properties of each mRNA species. However, we were startled to observe that the translational program of S. cerevisiae was relatively unperturbed by the depletion of three initiation factors, one elongation factor, and one termination factor. Further investigation revealed that yeast were actively compensating for the deficiency of each factor by either increasing or decreasing translation initiation rates such that the depleted factor was no longer limiting. This tuning was mediated by changes in eIF2[alpha] phosphorylation levels, a known modulator of translation initiation. Overall, we have leveraged high throughput technologies to provide novel understanding of in vivo structural dynamics of the ribosome and reveal a novel, unexpected robustness of the translational program in S. cerevisiae.
- 2013 SpringerMatjaž Vogelsang, editor.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 CRCnetBASEAmanda C Sozer, PhD.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 Protocolsedited by Peter Bugert.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.
- 2012 Springer Protocolsedited by W. John Kress and David L. Erickson.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 Protocolsedited by Svein Valla and Rahmi Lale.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.
- 2009 Springer Protocolsedited by Vladimir V. Didenko.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.
- 2013 Springer Protocolsedited by Svetlana Makovets.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 Protocolsedited by Antonio Alonso.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.
- 2006 SpringerW. Doerfler and P. Böhm, eds.
- 2006 SpringerW. Doerfler and P. Böhm (eds.).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.
- 2008 CRCnetBASESun-Chong Wang, Arturas Petronis.
- 2016 SpringerAlbert Jeltsch, Renata Z. Jurkowska, editors.Mechanisms and biological roles of DNA methyltransferases and DNA methylation: from past achievements to future challenges / Renata Z. Jurkowska, Albert Jeltsch -- DNA and RNA pyrimidine nucleobase alkylation at the carbon-5 position / Yuri Motorin, Salifu Seidu-Larry, Mark Helm -- Bacterial DNA methylation and methylomes / Josep Casadesús -- Domain structure of the Dnmt1, Dnmt3a, and Dnmt3b DNA methyltransferases / Shoji Tajima, Isao Suetake, Kohei Takeshita, Atsushi Nakagawa, Hironobu Kimura -- Enzymology of mammalian DNA methyltransferases / Renata Z. Jurkowska, Albert Jeltsch -- Genetic studies on mammalian DNA methyltransferases / Jiameng Dan, Taiping Chen -- The role of DNA methylation in cancer / Ranjani Lakshminarasimhan, Gangning Liang -- Structure and mechanism of plant DNA methyltransferases / Jiamu Du -- DNA methylation and gene regulation in honeybees: from genome-wide analyses to obligatory epialleles / Laura Wedd, Ryszard Maleszka -- N6-methyladenine: a conserved and dynamic DNA mark / Zach Klapholz O'Brown, Eric Lieberman Greer -- Pathways of DNA demethylation / Wendy Dean -- Structure and function of TET enzymes / Xiaotong Yin, Yanhui Xu -- Proteins that read DNA methylation / Takashi Shimbo, Paul A. Wade -- DNA base flipping: a general mechanism for writing, reading, and erasing DNA modifications / Samuel Hong, Xiaodong Cheng -- Current and emerging technologies for the analysis of the genome-wide and locus-specific DNA methylation patterns / J̲örg Tost -- DNA methyltransferase inhibitors: development and applications / Marie Lopez, Ludovic Halby, Paola B. Arimondo -- Rewriting DNA methylation signatures at will: the curable genome within reach? / Sabine Stolzenburg, Désirée Goubert, Marianne G. Rots -- Engineering and directed evolution of DNA methyltransferases / Paola Laurino, Liat Rockah-Shmuel, Dan S. Tawfik -- DNA labeling using DNA methyltransferases / MiglėTomkuvienė, Edita Kriukienė, Saulius Klimaašuskas.Also available: Print – 2016
- DNA microarrays and related genomics techniques : design, analysis, and interpretation of experiments2006 CRCnetBASEedited by David B. Allison ... [et al.].
- pt. A-B, 2006. ScienceDirectpt. B ScienceDirectedited by Alan Kimmel & Brian Oliver.Pt. A. Array platforms and wet-bench protocols -- pt. B. Databases and statistics.Also available: Print – pt. A-B, 2006.
- 2015 Springer Protocolsedited by Benoit P. Leblanc and Sebastien Rodrigue.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.
- 2011 Springer Protocolsedited by Hideo Tsubouchi.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. ScienceDirectpt. B ScienceDirectedited by Judith Campbell, Paul Modrich.Also available: Print – pt. A-B, 2006.
- 2012 Springer Protocolsedited by Lotte Bjergbæk.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.
- 2012Heather Briana DeBruhl.The Myb gene family plays a role in several types of human cancers. For example, high expression levels of c-Myb in colon cancer and B-Myb in breast cancer correlated with poor prognosis for the patient. B-Myb, the vertebrate homolog of invertebrate Myb, activates transcription of mitotic genes. In Drosophila, mutation of Myb reduced expression of mitotic genes, such as the regulatory kinase genes polo and ial (AurB). Previous studies revealed multiple mitotic defects in Myb mutant cells, including disrupted chromosome condensation and abnormal spindles. I now show that binucleate cells, the hallmark phenotype of cytokinesis failure, accumulate in Myb-null ovarian follicle cell and wing disc epithelia. Myb functions as an activator in the generally repressive Drosophila RBF, E2F2, and Myb (dREAM)/Myb-MuvB complex. Absence of the dREAM subunits Mip130 or E2F2 suppressed the Myb-null cytokinesis defect. While previous Myb-null mitotic phenotypes were difficult to quantitatively assay, the binucleate phenotype was binary, countable, and had a near zero background level in wild-type tissues. This offered a unique opportunity to use the Myb-null binucleate phenotype to study how the dREAM complex represses transcription. In the absence of Myb, repression by the dREAM complex was sensitive to the decreased dose of the subunits E2F2, Mip120, Caf1, and interestingly Lin-52, which was previously genetically implicated as an activator in the complex. Surprisingly, reducing the dose of His2Av also suppressed the Myb-null binucleate phenotype, suggesting a novel role for this variant histone in transcriptional repression by the dREAM complex.
- 2014 SpringerChristian R. Landry, Nadia Aubin-Horth, editors."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
- 2012Fouad Zakharia.The central theme of this work revolves around the genetics of admixed individuals---individuals who derive their ancestry from two or more different ancestral populations.The genomes of admixed individuals exhibit unique properties that make them both fascinating and challenging to study using existing statistical methods. Their uniqueness lies in their block-like structure, a feature that is the direct result of generations of recombination events. An important advance in the field of admixture genetics has been the development of algorithms capable of determining the ancestry of different regions in the admixed genome. As we will illustrate in this work, local ancestry information can readily be harnessed towards the investigation of subcontinental structure, by which we attempt to determine the specific ancestral populations that gave rise to the admixed genomes under study, and whether differences exist in the ancestral makeup of these admixed samples. The latter line of investigation is of particular relevance to genome-wide association studies, which are prone to confounding if structure in a population has not been explicitly corrected for. This work is thus divided into three parts. We first apply some straightforward multivariate statistical methods such as PCA to gain insights into the African ancestry of African Americans. To this end, we introduce a novel method for the study of specific components of admixture in admixed individuals. We then expand on this work to introduce more sophisticated algorithms for the study of admixed genomics. These methods entail the development of an improved method for local ancestry deconvolution, and the implementation of a PCA approach designed to handle large amounts of missing data. We illustrate the power of using these methods in conjunction with one another with the study of two Latino populations. Finally, we describe a novel phasing algorithm designed to incorporate sequencing information into the process of haplotype reconstruction---an important upstream step for many of the analyses described here.
- Electronic gene sequencing : a novel method for DNA sequencing based on direct heat or pH measurement2010Hesaam Esfandyarpour.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 Protocolsedited by Shulin Li, Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA, Jeffry Cutrera, Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA, Richard Heller, Old Dominion University, Frank Reidy Center for Biolectrics, Norfolk, VA, USA, Justin Teissie, Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biollogie structurale, Toulouse, France, Université de Toulouse, UPS, IPBS Toulouse, France.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.
- Elsevier's Encyclopaedic dictionary of medicine : in five languages, English, French, German, Italian, and Spanishpt. A-<D>, 1987-<90>compiled by A.F. Dorian.Status: Not Checked OutLane Catalog Recordpt. A. General medicine -- pt. B. Anatomy -- pt. C. Biology, genetics and biochemistry -- pt. D. Therapeutic substances.
- 2013Hyo Jei Choi.The genome is under constant threat by DNA damage arising from endogenous and exogenous sources, and it is particularly susceptible to damage during DNA replication. Using a genome-wide siRNA screen to identify proteins necessary for genome maintenance in the presence of replication stress, we identified NEK8/NPHP9, a ciliary protein kinase associated with two renal ciliopathies in humans and mice, nephronophthisis (NPHP) and polycystic kidney disease (PKD). Renal ciliopathies are a leading cause of kidney failure, but their exact etiology is poorly understood. Recent findings have shown that several genes linked to the DNA damage signaling are mutated in patients with NPHP or NPHP-like diseases. However, whether loss of the DNA damage response (DDR) itself played a causal role in NPHP is not clear, and the underlying mechanism linking these genes to NPHP is not addressed. This thesis work provides new mechanistic insight into the functions of the NIMA-related kinase, NEK8, in suppressing DNA damage arising from replication stress, and for the first time connects the replication stress response to cystic kidney diseases and renal ciliopathies. Here we directly demonstrate that replication stress, caused by the DNA polymerase inhibitor aphidicolin, as well as NEK8 loss, affects renal cell architecture in a 3D-culture system. Moreover, NEK8 mutation leads to replication stress and DNA damage in the pre-cystic kidney. We further establish that NEK8 is a crucial effector of the replication stress response and that it functions as part of the ATR-dependent signaling pathway, regulating replication fork dynamics and fork stability through effects on CDK activity. We also show NEK8's role in the replication stress response is compromised by ciliopathy-causing mutations. Thus, our study strongly suggests that excessive replication stress or a defect in the ability of cells to respond to replication stress leads to chronic damage in renal epithelial cells and kidney failure in ciliopathies. The major contributions of this dissertation are: (1) We validated NEK8 as a high confidence hit from a previously described unbiased siRNA screen designed to uncover genes that help maintain genome stability during DNA replication stress. (2) Cells lacking NEK8 form spontaneous DNA double-strand breaks (DSBs) which further accumulate when replication forks stall. (3) NEK8 acts at the replication fork to regulate fork dynamics and replication origin firing, particularly under conditions of replication stress. (4) NEK8 functions in the ATR pathway, interacting with ATR and other components of the replication checkpoint, and it suppresses S-phase CDK activity during replication to prevent premature origin firing. (5) NEK8 mutations, which produce kinase-inactive protein or juvenile cystic kidneys (jck), abolish the interaction of NEK8 with ATR and fail to prevent DNA damage accumulation in NEK8-deficient cells. (6) Disruption of NEK8, as well as replication stress induced by aphidicolin, perturbs both ciliogenesis and spheroid structure in a 3D assay that models renal kidney architecture and NPHP. This study therefore provides the first direct evidence that replication stress contributes to renal ciliopathies and mechanistic insight into how it does so. Furthermore, it identifies a new critical component of the replication stress response: NEK8.
- 2005 WileySU Catalog (SearchWorks) Click LINK above for Print location/circulation status.editor, Lynn B. Jorde.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 SpringerGeorge P. Rédei.v. 1. A-L -- v. 2. M-Z.
- 2013 Kargervolume editor, Constantine A. Stratakis.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.
- 2013Monica Elise Ortiz.Evolution has selected for organisms that benefit from genetically encoded cell-cell communication. We observe cell-cell communication throughout every scale in nature, from simple single-celled bacteria to complex multicellular mammals. Engineers have begun to repurpose elements of natural communication systems to coordinate their own population-level behaviors, including oscillations and programmed pattern formation. Existing engineered systems, however, rely on small, system-specific biomolecules to send messages among cells. However, such molecules are capable of sending only a single message, typically "regulate transcription.'' Thus, the information transmission capacity of such biological communication systems is fundamentally limited. Through this thesis, I demonstrated the decoupling of messages from a common communication channel via the autonomous transmission of numerous arbitrary genetic messages. To do so, I engineered a cell-cell communication platform using bacteriophage M13 gene products to autonomously package and deliver heterologous DNA messages of varying lengths and encoded functions. Further, I increased the range of engineered DNA messaging across semisolid media by coupling message transmission or receipt to active cellular chemotaxis. Through this coupling, I demonstrated that our system is adaptable to different contexts by creating simple patterns. Finally, using recombinase-mediated logic gates developed within the Endy laboratory, I demonstrated the ability to program bacteria by transmitting logic gates to surrounding cells. Overall, this work significantly enhances the suite of cell-cell communication tools available to engineers. I have shown that a variety of DNA messages can be transmitted among cells and have moved the field of synthetic biology closer to designing synthetic ecologies with more complex communication schemes and varied behaviors.
- 2013 SpringerRandy L. Jirtle, Frederick L. Tyson, editors.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 SpringerRandy L. Jirtle, Frederick L. Tyson, editors.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 Protocolsedited by C. Cristofre Martin.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 SpringerAdam R. Karpf, editor.Also available: Print – 2013
- 2013 SpringerMarién Pascual, Sergio Roa.Introduction -- Immune System and Atopic Disorders -- Epigenetics -- Epigenetics, Environment, and Allergic Diseases -- Conclusions and Future Perspectives.
- 2013 ScienceDirectedited by J. David Sweatt, Michael J. Meaney, Eric J. Nestler.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.
- 2013Kapa Lenkov.The ability of an animal to change quickly in response to its surroundings is essential to its survival and in some species, individuals respond by changing phenotype. The studies in this thesis focus on the molecular mechanisms through which environmental information can affect changes in phenotype in an African cichlid fish, Astatotilapia burtoni. This species is particularly useful for this study, as adult male burtoni assume one of two distinct, reversible, behavioral and physiological phenotypes. Dominant (D) males are brightly colored, reproductively capable and engage in mating and aggressive territorial behaviors while non-dominant (ND) males are drably colored, reproductively incapable, and are behaviorally passive. Importantly, the transition from ND to D or the reverse can occur in a matter of minutes and is triggered solely by external social cues. How such external information is translated into phenotypic changes on the molecular level is the focus of these experiments and my data suggest an epigenetic mechanism may regulate this transition. The specific epigenetic mechanism assessed here is DNA methylation, which is the covalent attachment of a methyl group to the cytosine nucleotide of DNA, which can lead to changes in expression. First, I showed that DNA methylation is present in A. burtoni, as not all animals utilize this mechanism. I used immunohistochemistry to demonstrate that high levels of global methylation are present in the nuclei of all cells examined, most likely bound with the highest frequency to heterochromatin, to suppress transcription of specific transcribed regions. However, there were no differences detected between behavioral states using these methods. Next I demonstrated that epigenetic mechanisms play a role during the determination of social status by treating juvenile males with epigenetic modifiers that either promote or interfere with DNA methyltransferase (DNMT). Animals injected with zebularine, which blocks the activity of DNMT, were statistically unlikely to ascend to D status, while those injected with methionine, which acts as a methyl donor, were statistically likely to become D males. Once a potential role for DNA methylation in social status determination was found, I surveyed potential sites of action on the GnRH1 gene, a key regulator of reproductive behavior, for variations in methylation on the single nucleotide level. I found that fully established Ds and NDs do not have differences in methylation levels in any on the individual nucleotides assayed on the GnRH1 promoter or coding region; however, juvenile males have lower levels of methylation than Ds at some sites on the promoter, while males transitioning to D status have lower average promoter methylation, but higher average coding region methylation than D males. Furthermore, ND animals injected with zebularine have higher average levels of methylation on both the promoter and coding region than control ND males. In order to better understand the context of the methylation changes during sexual maturation, methylation levels on the GnRH1 gene were measured during normal development. GnRH1 methylation levels remain constant between two and four weeks of age but increase significantly at several sites between 4 and 6 weeks of age. Furthermore, crowding mothers during the brooding stage and raising young in crowded tanks results in lower methylation levels at both 2 and 6 weeks of age, as well as causing delayed growth at the 6 week stage. Finally, I measured GnRH1 methylation in a non-reproductive context. Since GnRH agonists can interfere with short-term memory in humans, I measured changes in methylation in the GnRH1 gene during memory formation and storage. Animals who successfully learned a memory task showed a correlation with higher methylation at sites in the GnRH1 coding region than non-learners. Learners were successfully able to recall their training after three months; however, the increased methylation in the coding region was no longer present. In summary, DNA methylation is present in A. burtoni and increases on the GnRH1 gene promoter and coding sequence during transitions in development and sexual maturation. As GnRH1 expression levels are known to increase in these cases, increased methylation is not acting canonically as a repressor of expression on GnRH1. During short-term learning, higher methylation is limited to only the coding region of GnRH1, indicating that there may be several different epigenetic regulatory pathways involving this gene. Furthermore, the observation that there are no differences in GnRH1 methylation between stable D and ND males, or, in the long-term, between learners and non-learners, suggests that methylation in this location may be transitory and used as a short-term marker for other regulatory mechanisms.
- 2012 SpringerCornelis Murre, editor.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.
- Epigenetic regulation of olfactory receptor gene expression by the Drosophila Myb-MuvB/dREAM complex2012Choon Kiat Sim.In both mammals and insects an olfactory neuron will usually select a single olfactory receptor and repress remaining members of large receptor families. Here we show that a conserved multiprotein complex Myb-MuvB(MMB)/dREAM plays an important role in mediating neuron-specific expression of the CO2 receptor genes (Gr63a/Gr21a) in Drosophila. Activity of Myb in the complex is required for expression of Gr63a/Gr21a and it acts in opposition to the histone methyltransferase Su(var)3-9. Consistent with this, we observe repressive di-methylated H3K9 modifications at the receptor gene loci suggesting a mechanism for silencing receptor gene expression. Conversely, other complex members, Mip120 and E2F2, are required for repression of Gr63a in inappropriate neurons. Misexpression in mutants is accompanied by an increase in the H3K4me3 mark of active chromatin at the receptor gene locus. Nuclei of CO2 receptor-expressing neurons contain reduced levels of the repressive subunit Mip120 compared to surrounding neurons and increased levels of Myb, suggesting that activity of the complex can be regulated in a cell-specific manner. Our evidence suggests a model in which olfactory receptors are regulated epigenetically and the MMB/dREAM complex plays a critical role in specifying, maintaining and modulating the receptor-to-neuron map.
- 2006 CRCnetBASEedited by Akio Inui.
- 2014 SpringerMichael Lübbert, Peter A. Jones, editors.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 SpringerFazlul H. Sarkar, editor.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.
- 2013 SpringerAnna K. Naumova, Celia M. T. Greenwood, editors."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 Springeredited by Susan M. Gasser, En Li.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 SpringerSophie Rousseaux, Saadi Khochbin, editors.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 SpringerPaolo Sassone-Corsi, Yves Christen, editors."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.
- 2016 SpringerNathan A. Berger, editor.1. Epigenetics and Cancer -- 2. Epigenetics, Enhancers, and Cancer -- 3. Early Life: Epigenetic Effects on Obesity, Diabetes, and Cancer -- 4. Nutritional and Lifestyle Impact on Epigenetics and Cancer -- 5. Environmentally Induced Alterations in the Epigenome Affecting Obesity and Cancer in Minority Populations -- 6. Stress, Exercise, and Epigenetic Modulation of Cancer -- 7. Epigenetic Effects of Gut Microbiota on Obesity and Gastrointestinal Cancers -- 8. Epigenetics in Obesity and Esophageal Cancer -- 9. Epigenetics, Obesity, and Colon Cancer -- 10. Energy Balance, Epigenetics, and Prostate Cancer -- 11. Effects of Physical Activity on DNA Methylation and Associations with Breast Cancer -- Index.
- 2009 CRCnetBASEeditor, Manel Esteller.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 SpringerTrygve O. Tollefsbol, editor.
- Accurate methods for ancestry and relatedness inference — Epigenetics of aging (154)
- Epigenetics protocols. 2nd ed. — Introduction to genomic signal processing with control (154)
- Investigations in yeast functional genomics and molecular biology — Protein engineering protocols (154)
- Proteins and proteomics of Leishmania and Trypanosoma — Zebrafish-- genetics, genomics, and transcriptomics. Fourth edition. [4th ed.] (153)
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