Books by Subject
- Adeno-associated virus : methods and protocols — Epigenetics protocols. 2nd ed. (137)
- Epistasis : methods and protocols — Inborn metabolic diseases : diagnosis and treatment. 4th, rev. ed. (137)
- Incorporating the dynamic nature of molecules improves performance of structure-based function prediction methods — Plant transcription factors : methods and protocols (137)
- Plant transposable elements-- impact on genome structure and function — Zebrafish : genetics, genomics and informatics. 3rd ed. (135)
- 2012 SpringerCasacuberta, Josep M.; Grandbastien, Marie-Angèle.Transposable elements are DNA sequences with the capacity to move within a genome. Although their presence and impact has long been known, the recent genome-wide analysis of many eukaryotic genomes has uncovered their major role in genome dynamics and function. The present book explains how to recognize and study transposable elements, e.g. by using state-of-the-art strategies based on new-generation sequencing. Moreover, the impact of transposable elements on plant genome structure and function is reviewed in detail and illustrated in examples and case studies. The book is intended both for readers familiar with the field and for newcomers. With large-scale sequencing becoming increasingly available, more and more people will come across transposable element sequences in their data, and this volume will hopefully help to convince them that transposable elements are not just "junk" DNA, and may actually be the most interesting and fun part of their data!
- 2013 Springer ProtocolsPeterson, Thomas.Historical overview of transposable element research / P.A. Peterson -- Distinguishing variable phenotypes from variegation caused by transposon activities / V. Walbot -- Using transposons for genetic mosaic analysis of plant development / P.W. Becraft -- Survey of natural and transgenic gene markers used to monitor transposon activity / L. Krishnaswamy and T. Peterson -- Molecular biology of maize Ac/Ds elements: An overview / K. Lazarow, M.L. Doll and R. Kunze -- Gene tagging with engineered Ds elements in maize / Y. Li, G. Segal, Q. Wangm H.K. Donner -- Plant regeneration methods for rapid generation of a large scale Ds transposant population in rice / Y.H. Xuan [and nine others] -- Isolation of sequences flanking Ac insertion sites by Ac casting / D. Wang and T. Peterson -- Regulation of the mutator system of transposons in maize / D. Lisch -- Using MuDR/Mu transposons in directed tagging strategies / V. Walbot and J. Questa -- Genetic and molecular analyses of UniformMu transposon insertion lines / D.R. McCarty, M. Suzuki, C. Hunter, J. Collins, W.T. Avigne, K.E. Koch -- Digestion-ligation-amplification (DLA): A simple genome walking method to amplify unknown sequences flanking mutator (Mu) transposons and thereby facilitate gene cloning / S. Liu, A.P. Hsia and P.S. Schnable -- Molecular genetics and epigenetics of CACTA elements / N.V. Fedoroff -- Activation tagging using the maize En-I transposon system for the identification of abiotic stress resistance genes in arabidopsis / A. Harb and A. Pereira -- Reverse genetics in rice using Tos17 / D. Mieulet, A. Dievart, G. Droc, N. Lanau, E. Guiderdoni -- Identification and applications of the Petunia Class II Act1/dTph1 transposable element system / T. Gerats, J. Zethof and M. Vandenbussche -- Transposon display: A versatile method for transposon tagging / M. Vandenbussche, J. Zethof and T. Gerats -- Massive indexed parallel identification of transposon flanking sequences / M. Vandenbussche, J. Zethof and T. Gerats -- Use of next generation sequencing (NGS) technologies for the genome-wide detection of transposition / M. Elbaidouri, C. Chaparro and O. Panaud -- Overview of repeat annotation and de novo repeat identification / N. Jiang -- Computational methods for identification of DNA transposons / N. Jiang -- Tenest 2.0: Computational annotation and visualization of nested transposable elements / B.A. Kronmiller and R.P. Wise.
- 2015 Springer ProtocolsHunt, Arthur G.; Li, Qingshun Quinn.Computational analysis of plant polyadenylation signals / Xiaohui Wu , Guoli Ji , and Qingshun Quinn Li -- Prediction of plant mRNA polyadenylation sites / Xiaohui Wu , Guoli Ji , and Qingshun Quinn Li -- Extraction of poly(A) sites from large-scale RNA-seq data / Min Dong ... [et al.] -- Poly(A)-tag deep sequencing data processing to extract poly(A) sites / Xiaohui Wu, Guoli Ji, and Qingshun Quinn Li -- Analysis of poly(A) site choice using a java-based clustering algorithm / Patrick E. Thomas -- RADPRE : a computational program for identification of differential mRNA processing including alternative polyadenylation / Denghui Xing and Qingshun Quinn Li -- Characterization of plant polyadenylation complexes by using tandem affinity purification / Hongwei Zhao, Xinfu Ye, and Qingshun Quinn Li -- In vitro analysis of cleavage and polyadenylation in Arabidopsis / Hongwei Zhao and Qingshun Quinn Li -- Production, purification, and assay of recombinant proteins for in vitro biochemical analyses of the plant polyadenylation complex / Stephen A. Bell and Balasubrahmanyam Addepalli -- Detection of disulfide linkage by chemical derivatization and mass spectrometry / Balasubrahmanyam Addepalli -- Transient expression using agroinfiltration to study polyadenylation in plants / Carol Von Lanken and Arthur G. Hunt -- 3' RACE protocol to confirm polyadenylation sites / Liuyin Ma and Arthur G. Hunt -- Phage display library screening for identification of interacting protein partners / Balasubrahmanyam Addepalli, Suryadevara Rao, and Arthur G. Hunt -- Genome- wide determination of poly(A) site choice in plants / Pratap Kumar Pati, Liuyin Ma, and Arthur G. Hunt -- DNA/RNA hybrid primer mediated poly(A) tag library construction for illumina sequencing / Man Liu, Xiaohui Wu, and Qingshun Quinn Li -- Poly(A) tag library construction from 10 ng total RNA / Jingyi Cao and Qingshun Quinn Li -- Rapid, simple, and inexpensive method for the preparation of strand-specific RNA-seq libraries / Arthur G. Hunt -- Genome-wide analysis of distribution of RNA polymerase II isoforms using ChIP-Seq / Laura de Lorenzo.
- 2013 SpringerPaus, Tomáš.Terms and Concepts -- History of the Key Disciplines -- Enviromics -- Genomics -- Epigenomics -- Molecular Phenomics -- Systems Phenomics -- Cohorts -- Challenges -- Personalized Preventive Medicine.
- 2016 Springer ProtocolsDassi, Erik.Regulation of gene expression / Alessandro Quattrone and Erik Dassi -- Computational approach for the discovery of protein-RNA networks / Domenica Marchese, Carmen Maria Livi, and Gian Gaetano Tartaglia -- Transcriptional regulation with CRISPR/Cas9 effectors in mammalian cells / Hannah Pham, Nicola A. Kearns, and René Maehr -- Studying the translatome with polysome profiling / Paola Zuccotti and Angelika Modelska -- Exploring ribosome positioning on translating transcripts with ribosome profiling / Pieter Spealman ... [et al.] -- Studying isoform-specific mRNA recruitment to polyribosomes with Frac-seq / Rocio T. Martinez-Nunez and Jeremy R. Sanford -- Use of the pBUTR reporter system for scalable analysis of 3' UTR-mediated gene regulation / Arindam Chaudhury and Joel R. Neilson -- Comprehensive identification of RNA-binding proteins by RNA interactome capture / Alfredo Castello ... [et al.] -- Identifying RBP targets with RIP-seq / Hans-Herman Wessels ... [et al.] -- PAR-CLIP : a method for transcriptome-wide identification of RNA binding protein interaction sites / Charles Danan, Sudhir Manickavel, and Markus Hafner -- Profiling the binding sites of RNA-binding proteins with nucleotide resolution using iCLIP / FX Reymond Sutandy, Andrea Hildebrandt, and Julian König -- Pipeline for PAR-CLIP data analysis / Marvin Jens -- Capture and identification of miRNA targets by biotin pulldown and RNA-seq / Shen Mynn Tan and Judy Lieberman -- Identification of miRNA-target RNA interactions using CLASH / Aleksandra Helwak and David Tollervey -- Genome-wide analysis of A-to-I RNA editing / Yiannis A. Savva, Georges St. Laurent, and Robert A. Reenan -- Nucleotide-level profiling of m5C RNA methylation / Tennille Sibbritt ... [et al.] -- Probing N 6-methyladenosine (m6A) RNA modification in total RNA with SCARLET / Nian Liu and Tao Pan -- Genome-wide identification of alternative polyadenylation events using 3'T-fill / Stefan Wilkening, Vicent Pelechano, and Lars M. Steinmetz -- Genome-wide profiling of alternative translation initiation sites / Xiangwei Gao, Ji Wan, and Shu-Bing Qian -- Genome-wide study of mRNA isoform half-lives / Joseph V. Geisberg and Zarmik Moqtaderi -- Visualizing mRNA dynamics in live neurons and brain tissues / Hye Yoon Park and Minho Song -- Single-molecule live-cell visualization of pre-mRNA splicing / Robert M. Martin ... [et al.].
- 2008 Springer ProtocolsWilusz, Jeffrey.Bioinformatics approaches for studying untranslated regions of mRNAs / Paramjeet S. Bagga -- Identification of mRNA polyadenylation sites in genomes using cDNA sequences, expressed sequence tags, and trace / Ju Youn Lee, Ji Yeon Park, and Bin Tian -- Bioinformatic tools for studying post-transcriptional gene regulation : the UAlbany TUTR Collection and other informatic resources / Francis Doyle ... [et al.] -- In-line probing analysis of riboswitches / Elizabeth E. Regulski and Ronald R. Breaker -- Ribotrap : targeted purification of RNA-specific RNPs from cell lysates through immunoaffinity precipitation to identify regulatory proteins and RNAs / Dale L. Beach and Jack D. Keene -- Advances in RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray profiling / Timothy E. Baroni ... [et al.] -- Biosensors for RNA aptamers-protein interaction / Sara Tombelli, Maria Minunni, and Marco Mascini -- A tethering approach to study proteins that activate mRNA turnover in human cells / Sandra L. Clement and Jens Lykke-Andersen -- RNA analysis by biosynthetic tagging using a 4-thiouracil and uracil phosphoribosyltransferase / Gusti M. Zeiner ... [et al.] -- Efficient 5' cap-dependent RNA purification : use in identifying and studying subsets of RNA / Edyta Z. Bajak and Curt H. Hagedorn -- Enrichment of alternatively spliced isoforms / Julian P. Venables -- In vivo methods to assess polyadenylation efficiency / Lisa K. Hague, Tyra Hall-Pogar, and Carol S. Lutz -- Monitoring the temporal and spatial distribution of RNA in living yeast cells / Roy M. Long and Carl R. Urbinati -- Analysis of mRNA partitioning between the cytosol and endoplasmic reticulum compartments of mammalian cells / Samuel B. Stephens ... [et al.] -- In vivo and in vitro analysis of poly(A) length effects on mRNA translation / Jing Peng, Elizabeth L. Murray, and Daniel R. Schoenberg -- A ribosomal density-mapping procedure to explore ribosome positions along translating mRNAs / Naama Eldad and Yoav Arava -- Identification of changes in gene expression by quantitation of mRNA levels / Wendy M. Olivas -- Application of the Invader® RNA assay to the polarity of vertebrate mRNA decay / Elizabeth L. Murray and Daniel R. Schoenberg -- Development of an in vitro mRNA decay system in insect cells / Kevin Sokoloski, John R. Anderson, and Jeffrey Wilusz -- Using synthetic precursor and inhibitor miRNAs to understand miRNA function / Lance P. Ford and Angie Cheng -- A step-by-step procedure to analyze the efficacy of siRNA using real-time PCR / Angie Cheng, Charles L. Johnson, and Lance P. Ford.
- 2012 SpringerKuliev, Anver.Primary Prevention of Genetic Disorders and Place of Preimplantation Diagnosis -- Approaches to Preimplantation Diagnosis -- Preimplation Diagnosis for Single-Gene Disorders -- PGD for HLA Typing -- Preimplantation Diagnosis for Chromosomal Disorders -- Clinical Outcome of Preimplantation Genetic Diagnosis -- Preimplantation Diagnosis and Establishment of Disease and Individual Specific Human Embryonic Stem Cell Lines -- Social, Ethical, and Legal Aspects.
- 2014 SpringerBraude, Peter R.; El-Toukhy, Tarek.This unique book offers a comprehensive yet practical user-friendly guide to preimplantation genetic diagnosis (PGD). It provides understanding of and insight into the complete procedure, its recent clinical and laboratory developments and its future prospects, whilst offering an easy point of reference for patient enquiries. Concluding with perspectives on the ethical and social issues often encountered by healthcare professionals counselling patients with regards to PGD. Each chapter within Preimplantation Genetic Diagnosis in Clinical Practice is written by established authorities in their fields. An essential resource for PGD specialists and non-specialists, and for all practitioners working within the disciplines of fertility, reproductive medicine and medical genetics.
- 2015 SpringerGrech, Godfrey; Grossman, Iris.Introduction -- Preventive and predictive genetics: a perspective -- Roadmap to drug development enabled by pharmacogenetics -- Pharmacogenetics, statistical considerations -- Pharmacokinetics and pharmacogenetics: bringing the magic bullet closer to reality -- Pharmacogenetics of adverse drug reactions -- Pharmacogenomics for haemoglobinopathies therapeutics -- Pharmacogenetics of neurodegenerative disorders -- Pharmacogenetics of asthma -- Pharmacogenetics and antineoplastic therapies -- Pharmacogenetics of coumarin anticoagulant therapy -- Implementation of genomic medicine: tools and challenges -- Ethical considerations in the genomic era -- Index.
- 2008 SpringerBunz, Fred.
- 2013 SpringerGersen, Steven L.; Keagle, Martha B.Part I. Basic Concepts and Background. History of Clinical Cytogenetics / Steven L. Gersen -- DNA, Chromosomes, and Cell Division / Martha B. Keagle -- Human Chromosome Nomenclature: An Overview and Definition of Terms / Marilyn L. Slovak, Aaron Theisen, Lisa G. Shaffer -- Part II. Examining and Analyzing Chromosomes. Basic Cytogenetics Laboratory Procedures / Martha B. Keagle, Steven L. Gersen -- The Essentials of Light Microscopy / Nathan S. Claxton, Stephen T. Ross -- Quality Control and Quality Assurance / Martha B. Keagle -- Instrumentation in the Cytogenetics Laboratory / Steven L. Gersen -- Part III. Clinical Cytogenetics. Autosomal Aneuploidy / Jin-Chen C. Wang -- Structural Chromosome Rearrangements / Kathleen Kaiser-Rogers, Kathleen W. Rao -- Sex Chromosomes, Sex Chromosome Disorders, and Disorders of Sex Development / Cynthia M. Powell -- The Cytogenetics of Infertility / Linda Marie Randolph -- Prenatal Cytogenetics / Linda Marie Randolph -- The Cytogenetics of Spontaneous Abortion / Solveig M. V. Pflueger, -- Chromosome Instability / Xiao-Xiang Zhang, -- Part IV. Cancer Cytogenetics. The Cytogenetics of Hematologic Neoplasms / Aurelia Meloni-Ehrig -- The Cytogenetics of Solid Tumors / Linda D. Cooley, Kathleen S. Wilson -- Part V. Adjunct Technologies -- Fluorescence In Situ Hybridization (FISH) / Daynna J. Wolff -- Microarray-Based Cytogenetics / Lisa G. Shaffer -- Part VI. Beyond Chromosomes. Fragile X--A Family of Disorders: Changing Phenotype and Molecular Genetics / Elaine B. Spector -- Genomic Imprinting and Uniparental Disomy / Jin-Chen C. Wang -- Genetic Counseling / Sarah Hutchings Clark.
- 2014 ScienceDirectCibelli, Jose B.Principles of Cloning, Second Edition is the fully revised edition of the authoritative book on the science of cloning. The book presents the basic biological mechanisms of how cloning works and progresses to discuss current and potential applications in basic biology, agriculture, biotechnology, and medicine. Beginning with the history and theory behind cloning, the book goes on to examine methods of micromanipulation, nuclear transfer, genetic modification, and pregnancy and neonatal care of cloned animals. The cloning of various species-including mice, sheep, cattle, and non-mammals-is considered as well.
- 2006 SpringerPatterson, Cam; Runge, Marschall Stevens.Also available: Print – 2006
- 2006 Springer ProtocolsPellestor, Franck.
- 2014 SpringerHalper, Jaroslava.This volume is a reference handbook focusing on diseases like Marfan syndrome, Ehlers-Danlos syndrome, Loeys-Dietz syndrome and other heritable soft connective tissue diseases. The book presents detailed information for both basic scientists and for clinicians seeing patients. It is also a stepping stone for new investigations and studies that goes beyond the facts about the composition and biochemistry of the connective tissue and extracellular matrix, as the authors connect individual components to specific aspects of various soft tissue disorders and to the actual or potential treatment of them. Progress in Heritable Soft Connective Tissue Diseases features very prominent physicians and scientists as contributors who bring their most recent discoveries to the benefit of readers. Their expertise will help clinicians with proper diagnosis of sometimes elusive and uncommon heritable diseases of soft connective tissues. This book also offers an update on the pathophysiology of these diseases, including an emphasis on unifying aspects such as connections between embryonic development of the different types of connective tissues and systems, and the role of TGF-beta in development and physiology of soft tissues. This new set of data explains, at least in part, why many of these disorders are interconnected, though the primary pathophysiological events, such as gene mutations, may be different for each disorder.Also available: Print – 2014
- 2009 SpringerKöhrer, Caroline; RajBhandary, Uttam.Understanding enzyme mechanism through protein chimeragenesis / N.M. Goodey and S.J. Benkovic -- Chemical protein engineering : synthetic and semisynthetic peptides and proteins / L. Merkel, L. Moroder, and N. Budisa -- Native chemical ligation: Semisynthesis of post-translationally modified proteins and biological probes / E. Vogel Taylor and B. Imperiali -- Chemical methods for mimicking post-translational modifications / S.I. van Kasteren, P. Garnier and B.G. Davis -- Noncanonical amino acids in protein science and engineering / K.E. Beatty and D.A. Tirrell -- Fidelity mechanisms of the aminoacyl-tRNA synthetases / A.P. Mascarenhas ... [et al.] -- Specialized components of the translational machinery for unnatural amino acid mutagenesis : tRNAs, aminoacyl-tRNA synthetases, and ribosomes / C. Köhrer and U.L. RajBhandary -- In vivo studies of receptors and ion channels with unnatural amino acids / D.A. Dougherty -- Synthesis of modified proteins using misacylated tRNAs / S.M. Hecht -- Cell-free synthesis of proteins with unnatural amino acids. The pure system and expansion of the genetic code / I. Hirao, T. Kanamori and T. Ueda -- Engineering nucleobases and polymerases for an expanded genetic alphabet / A.M. Leconte and F.E. Romesberg -- Understanding membrane proteins. How to design inhibitors of transmembrane protein-protein interactions / J.S. Slusky, H. Yin and W.F. DeGrado.
- 2006 Springer ProtocolsArndt, Katja M.; Müller, Kristian M.
- 2014 SpringerSantos, Andre L. S.This book contains a collection of critical reviews on the expression of biologically functional proteins in Leishmania and Trypanosoma, which was written by renowned researchers on this field. Species belonging to these trypanosomatids genera are etiological agents of leishmaniasis, Chagas' disease and sleeping sickness that are extremely debilitating human infection diseases, which remain a major health problem especially in countries from Latin America, Africa and Middle East. Substantiating the problem, the currently accepted drugs for these diseases are quite unsatisfying due to their low efficacy and high toxicity. In order to solve these real problems, several research groups around the world have become involved in the study and identification of novel potential targets in the trypanosomatid cell. Since proteins are key macromolecules involved in crucial metabolic processes of all living cells, studies have focused on the expression of specific proteins produced by Leishmania and Trypanosoma by means of different biochemical, molecular and proteomic approaches in order to explore them as targets for understanding the parasite life cycle and developing new strategies against trypanosomiasis. With these proposals in mind, the book "Proteins and Proteome of Leishmania and Trypanosoma" encompasses (i) an integrated view about the biochemistry of parasites belonging to the Leishmania and Trypanosoma genera; (ii) an updated review on the expression of biologically relevant proteins by human pathogenic trypanosomatids and their possible role in the interaction with host cells/molecules as well as a target for development of both alternative chemotherapies and vaccine; and (iii) several pictures, diagrams and tables that can be used to illustrate both undergraduate and postgraduate teaching as well as scientific lectures, being a useful resource for students and researchers.
- 2006 Springer ProtocolsHilario, Elena; Mackay, John.Genomic DNA isolation from different biological materials / Duckchul Park -- Extraction of plant RNA / Elspeth MacRae -- Overview on hybridization and detection techniques / Elena Hilario -- Checkerboard DNA/DNA hybridization technology : using DIG detection / Lisa S. Gellen, Glenn Wall-Manning, and Chris H. Sissons -- Nonradioactive northern and southern analyses from plant samples / Christoph Peterhaensel, Dagmar Weier, and Thomas Lahaye -- Screening a BAC library with nonradioactive overlapping oligonucleotide (overgo) probes / Elena Hilario, Tiffany F. Bennell, and Erik Rikkerink -- Direct in-gel hybridization of DNA with digoxigenin-labeled probes / Saeed A. Khan and Mohamed S. Nawaz -- In situ hybridization of termite microbes / Shigeharu Moriya ... [et al.] -- RNA electrophoretic mobility shift assay using a fluorescent DNA sequencer / Yukinori Eguchi -- Comparative quantitation of mRNA expression in the central nervous system using fluorescence in situ hybridization / Darren J. Day, Eli M. Mrkusich, and John H. Miller -- Visualization of gene expression by fluorescent multiplex real-time PCR amplification / Maria Rosa Ponce ... [et al.] -- Fluorescence in situ hybridization for the identification of environmental microbes / Annelie Pernthaler and Jakob Pernthaler -- Introduction to kinetic (real-time) PCR / John Mackay -- Validation of siRNA knockdowns by quantitative real-time PCR / Sukru Tuzmen -- Real-time quantitative PCR as an alternative to southern blot or fluorescence in situ hybridization for detection -- Of gene-copy number changes / Jasmien Hoebeeck, Frank Speleman, and Jo Vandesompele -- Design and work-up of a new molecular diagnostic assay based on real-time PCR / Harald Kessler -- Real-time PCR fluorescent chemistries / John Mackay and Olfert Landt -- Microarrays : an overview / Norman H. Lee and Alexander I. Saeed -- Oligonucleotide microarrays for the study of coastal microbial communities / Gaspar Taroncher-Oldenburg and Bess B. Ward.
- 2006 Springer ProtocolsMarsh, Sharon.The history of pyrosequencing / Pol Nyron -- Pyrosequencing applications / Sharon Marsh -- Web-based primer design software for genome-scale genotyping by pyrosequencing / Steven Ringquist ... [et al.] -- Pyrosequencing : a simple method for accurate genotyping / Cristi R. King and Tiffany Scott-Horton -- Universal primer applications for pyrosequencing / Dong-Chuan Guo and Dianna M. Milewicz -- Allele quantification and DNA pooling methods / Jonathon Wasson -- Multiplex pyrosequencing for DNA variation analysis / Pritesh Patel, Yih-Horng Shiao, and Paolo Fortina -- Analysis of gene-specific DNA methylation patterns by the pyrosequencing technology / Jørg Tost and Ivo Glynne Gut -- Detecting mutations that confer oxazolidinone resistance in gram-positive bacteria / Neil Woodford, Sarah E. North, and Matthew J. Ellington -- Pyrosequencing-based strategies for improved allele typing of HLA loci / Steven Ringquist ... [et al.] -- Pyrosequencing of phage display libraries for the identification of cell-specific targeting ligands / Ahad A. Rahim -- Gene copy number detection in animal studies / Gerli Pielberg and Leif Andersson -- Detection of allelic imbalance in gene expression using pyrosequencing / Hua Wang and Steven C. Elbein -- Pyrosequencing genotype storage techniques / Derek J. Van Booven.
- 2014 Springer ProtocolsBiassoni, Roberto; Raso, Alessandro.Twenty years of qPCR: A mature technology? -- Minimum information necessary for quantitative real-time PCR experiments -- Selection of reliable reference genes for RT-qPCR analysis -- Introduction to digital PCR -- mRNA and microRNA purity and integrity: The key to success in expression profiling -- Mediator probe PCR: Detection of real-time PCR by label-free probes and a universal fluorogenic reporter -- Absolute quantification of viral DNA: The quest for perfection -- A multiplex real-time PCR-platform integrated into automated extraction method for the rapid detection and measurement of oncogenic HPV type-specific viral DNA load from cervical samples -- Real-time PCR detection of mycoplasma pneumoniae in the diagnosis of community-acquired pneumonia -- A sensible technique to detect mollicutes impurities in human cells cultured in GMP condition -- Real-time quantification assay to monitor BCR-ABL1 transcripts in chronic myeloid leukemia -- A reliable assay for rapidly defining transplacental metastasis using quantitative PCR -- Circulating cell-free DNA in cancer -- Gene expression analysis by qPCR in clinical kidney transplantation -- Posttranscriptional regulatory networks: From expression profiling to integrative analysis of mRNA and microRNA data -- Clinical applications using digital PCR -- Developing noninvasive diagnosis for single-gene disorders: the role of digital PCR.
- 2002 Springer ProtocolsCamp, Nicola J.; Cox, Angela.pt. 1. Mapping quantitative trait loci in humans -- Association studies / Jennifer H. Barrett -- Parametric linkage analysis / Lyle J. Palmer -- Nonparametric linkage analysis: I. Haseman-Elston / Chad P. Garner -- Nonparametric linkage analysis: II. Variance components / Angela J. Marlow -- Linkage and association: the transmission/disequilibrium test for QTLs / Mark M. Iles -- Joint linkage and segregation analysis using Markov chain Monte Carlo methods / Ellen M. Wijsman -- pt. 2. Mapping quantitative trait loci in rodents -- Approaches to the analysis of QTL data in mice, using the nonobese diabetic mouse as an example / Heather J. Cordell -- Experimental designs for QTL fine mapping in rodents / Anne Shalom -- Approaches to the analysis of complex quantitative phenotypes and marker map construction based on the analysis of rat models of hypertension / Dominique Gauguier -- A case study of QTL analysis in a mouse model of asthma / Youming Zhang -- pt. 3. Mapping quantitative trait loci in agricultural settings -- QTL analysis in plants / Shizhong Xu -- QTL analysis in livestock / Joao L. Rocha.
- 2013 SpringerLeszczynski, Dariusz.Methods of proteomics have been shown to be powerful tools in search of target proteins - proteins that respond in cells to an internal or an external stimulus. Proteomics is widely used in biomedical research. However, in radiation biology research, following exposures of living matter to low doses of either ionizing or non-ionizing radiation, proteomics approach is only very slowly gaining support. This book, by presenting the current status of the use of proteomics in radiation biology, will help to attract attention to the field of radiation proteomics.Also available: Print – 2013Also available: Print – 2013
- 2010 SpringerAtkins, John F.; Gesteland, Raymond F.Part I. Redefinition -- 1. Selenocysteine Biosynthesis, Selenoproteins, and Selenoproteomes / Vadim N. Gladyshev and Dolph L. Hatfield -- 2. Reprogramming the Ribosome for Selenoprotein Expression: RNA Elements and Protein Factors / Marla J. Berry and Michael T. Howard -- 3. Translation of UAG as Pyrrolysine / Joseph A. Krzycki -- 4. Specification of Standard Amino Acids by Stop Codons / Olivier Namy and Jean-Pierre Rousset -- 5. Ribosome “Skipping”: “Stop-Carry On” or “StopGo” Translation / Jeremy D. Brown and Martin D. Ryan -- 6. Recoding Therapies for Genetic Diseases / Kim M. Keeling and David M. Bedwell -- Part II. Frameshifting - Redirection of Linear Readout -- 7. Pseudoknot-Dependent Programmed -1 Ribosomal Frameshifting: Structures, Mechanisms and Models / Ian Brierley, Robert J.C. Gilbert, and Simon Pennell -- 8. Programmed -1 Ribosomal Frameshift in the Human Immunodeficiency Virus of Type 1 / Léa Brakier-Gingras and Dominic Dulude -- 9. Ribosomal Frameshifting in Decoding Plant Viral RNAs / W. Allen Miller and David P. Giedroc -- 10. Programmed Frameshifting in Budding Yeast / Philip J. Farabaugh -- 11. Recoding in Bacteriophages / Roger W. Hendrix -- 12. Programmed Ribosomal -1 Frameshifting as a Tradition: The Bacterial Transposable Elements of the IS3 Family / Olivier Fayet and Marie-Françoise Prère -- 13. Autoregulatory Frameshifting in Antizyme Gene Expression Governs Polyamine Levels from Yeast to Mammals / Ivaylo P. Ivanov and Senya Matsufuji -- 14. Sequences Promoting Recoding Are Singular Genomic Elements / Pavel V. Baranov and Olga Gurvich -- 15. Mutants That Affect Recoding / Jonathan D. Dinman and Michael O'Connor -- 16. The E Site and Its Importance for Improving Accuracy and Preventing Frameshifts / Markus Pech, Oliver Vesper, Hiroshi Yamamoto, Daniel N. Wilson, and Knud H. Nierhaus -- Part III. Discontiguity -- 17. Translational Bypassing - Peptidyl-tRNA Re-pairing at Non-overlapping Sites / Norma M. Wills -- 18. trans-Translation / Kenneth C. Keiler and Dennis M. Lee -- Part IV. Transcription Slippage -- 19. Transcript Slippage and Recoding / Michael Anikin, Vadim Molodtsov, Dmitry Temiakov, and William T. McAllister -- Part V. Appendix -- 20. Computational Resources for Studying Recoding / Andrew E. Firth, Michaël Bekaert, and Pavel V. Baranov.
- 2012 Springer ProtocolsLorence, Argelia.Using folding promoting agents in recombinant protein production : a review / Beatrix Fahnert -- Routine identity confirmation of recombinant proteins by MALDI-TOF mass spectrometry / Brett J. Savary and Prasanna Vasu -- A matter of packaging : influence of nucleosome positioning on heterologous gene expression / María de la Cruz Muñoz-Centeno, Gonzalo Millán-Zambrano, and Sebastián Chávez -- Tools of the trade : developing antibody-based detection capabilities for recombinant proteins / Maureen C. Dolan [and others] -- Heat-shock protein fusion vectors for improved expression of soluble recombinant proteins in Escherichia coli / Christos A. Kyratsous and Christos A. Panagiotidis -- The use of a flagellar export signal for the secretion of recombinant proteins in salmonella / Ferenc Vonderviszt [and others] -- Optimization of purification protocols based on the step-by-step monitoring of the protein aggregates in soluble fractions / Ario de Marco -- Heterologous protein expression by Lactococcus lactis / Julio Villator-Hernández [and others] -- An extended suite of genetic tools for use in bacteria of the halomonadaceae : an overview / Montserrat Argandoña [and others] -- Regulated recombinant protein production in the antarctic bacterium Pseudoalteromonas haloplanktis TAC125 / Valentina Rippa [and others] -- A novel strategy for the construction of genomic mutants of the antarctic bacterium Pseudoalteromonas haloplanktis TAC125 / Maria Giuliani [and others] -- A new bacterial co-expression system for over-expressing soluble protein and validating protein-protein interaction / Jumei Zeng and Zheng-Guo He -- Heterologous high-level gene expression in the photosynthetic bacterium Rhodobacter capsulatus / Nadine Katzke [and others] -- Plasmid DNA production for therapeutic applications / Alvaro R. Lara and Octavio T. Ramírez -- Recombinant protein production in the eukaryotic protozoan parasite Leishmania tarentolae : a review / Tomoaki Niimi -- Expression of multisubunit proteins in Leishmania tarentolae / Marisa Sugino and Tomoaki Niimi -- Recombinant protein production in yeasts / Diethard Mattanovich [and others] -- Yeasts as a tool for heterologous gene expression / Raja Mokdad-Gargouri [and others] -- The Cre/Lox system : a practical tool to efficiently eliminate selectable markers in fungal endophytes / Simona Florea [and others] -- Aptamer-regulated expression of essential genes in yeast / Beatrix Suess [and others] -- Cloning and expression of hemicellulases from Aspergillus nidulans in Pichia pastoris / Prasanna Vasu, Stefan Bauer, and Brett J. Savary -- A thiamine-regulatable epitope-tagged protein expression system in fission yeast / Tiina Tamm -- Heterologous gene expression by chromosomal integration in fission yeast / Akihisa Matsuyama and Minoru Yoshida -- Genetic engineering of industrial strains of Saccharomyces cerevisiae / Sylvie le Borgne -- Recombinant protein production in plants : challenges and solutions / Elizabeth E. Hood and Deborah V. Vicuna Requesens -- A novel plant cell bioproduction platform for high-yield secretion of recombinant proteins / Jianfeng Xu and Marcia J. Kieliszewski -- Super-promoter :TEV, a powerful gene expression system for tobacco hairy roots / Luis Ñopo [and others] -- Bioseparation of recombinant proteins from plant extract with hydrophobin fusion technology / Jussi J. Joensuu [and others] -- Quality assessment of recombinant proteins produced in plants / Giuliana Medrano [and others] -- Cell-free protein synthesis as a promising expression system for recombinant proteins / Xumeng Ge and Jianfeng Xu -- The use of bacterial artificial chromosomes for recombinant protein production in mammalian cell lines / Leander Blaas [and others] -- Engineering the chaperone network of CHO cells for optimal recombinant protein production and authenticity / Lyne Jossé, C. Mark Smales, and Mick F. Tuite -- High-throughput baculovirus expression in insect cells / Richard B. Hitchman, Robert D. Possee, and Linda A. King -- Recombinant protein expression in milk of livestock species / Zsuzsanna Bösze and László Hiripi.
- 2008 SpringerEgel, Richard; Lankenau, Dirk-Henner."Once per life cycle, mitotic nuclear divisions are replaced by meiosis I and II - reducing chromosome number from the diploid level to a haploid genome, reshuffling the homologous chromosomes by their centromeres, and recombining chromosome arms by crossing-over. In animals, including humans, all this happens during the germ cell formation of eggs and sperm. Due to the reign of meiosis, no child is a true genetic copy of either parent. Questions still open primarily concern the placement of and mutual coordination between neighboring crossover events. The current book addresses these processes and mechanisms in multicellular eukaryotes, such as Drosophila, Anibidopsis, mice and humans. The pioneering model systems of yeasts, as well as evolutionary aspects, will be addressed in a forthcoming volume."--Jacket.
- 2008 SpringerEgel, Richard; Lankenau, Dirk-Henner.Once per life cycle, mitotic nuclear divisions are replaced by meiosis I and II - reducing chromosome number from the diploid level to a haploid genome and recombining chromosome arms by crossing-over. In animals, all this happens during formation of eggs and sperm - in yeasts before spore formation. The mechanisms of reciprocal exchange at crossover/chiasma sites are central to mainstream meiosis. To initiate the meiotic exchange of DNA, surgical cuts are made as a form of calculated damage that subsequently is repaired by homologous recombination. These key events are accompanied by ancillar.
- pt. A-B, 2002. ScienceDirectpt. B ScienceDirectPacker, Lester; Sen, Chandan K.Also available: Print – pt. A-B, 2002.
- 2012Church, George M.; Regis, Edward.PrintStatus: Not Checked OutLane Catalog RecordFrom bioplastics to H. sapiens 2.0 -- -3,800 Myr, Late Hadean : at the inorganic/organic interface -- -3,500 Myr, Archean : reading the most ancient texts and the future of living software -- -500 Myr, Cambrian : the mirror world and the explosion of diversity ; How fast can evolution go and how diverse can it be? -- -360 Myr, Carboniferous : "the best substitute for petroleum is petroleum" -- -60 Myr, Paleocene : emergence of mammalian immune system ; Solving the health care crisis through genome engineering -- -30,000 Yr, Pleistocene Park : engineering extinct genomes -- -10,000 Yr, Neolithic : industrial revolutions ; The agricultural revolution and synthetic genomics ; The BioFab Manifesto -- -100 Yr, Anthropocene : the third industrial revolution ; iGEM -- -1 Yr, Holocene : from personal genomes to immortal human components -- Epigenetic epilogue. +1 Yr, the end of the beginning, transhumanism, and the Panspermia Era : societal risks and countermeasures.
- 2009 CRCnetBASEGaur, Rajesh K.; Rossi, John J.Micro mining : computational approaches to miRNA discovery / Adam Grundhoff -- Animal microRNA gene prediction / Ola Snv?e and Pa<U+030a>l St?rom -- A suite of resources for the study of miRNA ontology and function / Praveen Sethupathy, Molly Megraw, and Artemis G. Hatzigeorgiou -- Regulation of translation and mRNA stability by Hfq-binding small RNAs in Escherichia coli / Hiroji Aiba -- Mechanisms by which microRNAs regulate gene expression in animal cells / Yang Yu and Timothy W. Nilsen -- The microRNAs of C. elegans / Mona J. Nolde and Frank J. Slack -- Isolation and characterization of small RNAs in C. elegans / Chisato Ushida and Yusuke Hokii -- MicroRNA tales in fly development / Utpal Bhadra ... [et al.] -- RNA interference and miRNAs in zebrafish / Alex S. Flynt, Elizabeth J. Thatcher, and James G. Patton -- Biogenesis and function of plant microRNAs / Zoltan Havelda -- Endogenous small RNA pathways in Arabidopsis / Manu Agarwal, Julien Curaba, and Xuemei Chen. How to assay miRNA expression : a technology guide / Mirco Castoldi, Vladimir Benes, and Martina U. Muckenthaler -- Methods to quantify microRNA gene expression / Lori A. Neely -- Regulation of alternative splicing by microRNAs / Rajesh K. Gaur -- Recent progress in polymerase II-mediated intronic microRNA expression systems / Shi-Lung Lin and Shao-Yao Ying -- MicroRNA-based RNA polymerase II expression vectors for RNA interference in mammalian cells / Anne B. Vojtek ... [et al.] -- Transgenic RNAi : a fast and low-cost approach to reverse genetics in mammals / Linghua Qiu and Zuoshang Xu -- Symphony of AIDS : an miRNA-based therapy / Yoichi R. Fujii -- MicroRNAs and cancer : connecting the dots / Sumedha D. Jayasena -- Mammalian transcriptional gene silencing by small RNAs / Daniel H. Kim and John J. Rossi -- Regulation of gene expression by RNA mediated transcriptional gene silencing / Kevin V. Morris.
- 2007 SpringerBassett, Carole Leavel.
- 2011 SpringerGrosshans, Helge.MicroRNA biogenesis and function : an overview / Rene F. Ketting -- Regulation of pri-miRNA processing through Smads / Akiko Hata and Brandi N. Davis -- Stimulation of pri-miR-18a processing by hnRNP A1 / Gracjan Michlewski, Sonia Guil, and Javier F. Cáceres -- KSRP promotes the maturation of a group of miRNA precursors / Michele Trabucchi ... [et al.] -- Hormonal repression of miRNA biosynthesis through a nuclear steroid hormone receptor / Sally Fujiyama-Nakamura, Kaoru Yamagata, and Shigeaki Kato -- Autoregulatory mechanisms controlling the microprocessor / Robinson Triboulet and Richard I. Gregory -- Regulation of pre-miRNA processing / Nicolas J. Lehrbach and Eric A. Miska -- The effect of RNA editing and ADARs on miRNA biogenesis and function / Bret S.E. Heale, Liam P. Keegan, and Mary A. O'Connell -- MiRNAs need a trim regulation of miRNA activity by trim-NHL proteins / F. Gregory Wulczyn ... [et al.] -- Properties of the regulatory RNA-binding protein HuR and its role in controlling miRNA repression / Nicole-Claudia Meisner and Witold Filipowicz -- Turnover of mature miRNAs and siRNAs in plants and algae / Heriberto Cerutti and Fadia Ibrahim -- MicroRNases and the regulated degradation of mature animal miRNAs / Helge Grosshans and Saibal Chatterjee.Also available: Print – 2010
- 2001 ScienceDirectMatthews, Benjamin F.; Romeo, John T.; Saunders, James A.
- 2010Liu, Gwen; Blau, Helen M.; Chen, Chang-Zheng; Fire, Andrew Z.; Sarnow, P.MicroRNA (miRNA) genes, which encode an abundant class of ~22-nucleotide (nt), evolutionarily conserved small RNAs, control a fundamental layer of genetic programs at the post-transcriptional level. However, little is known about how the activity of miRNA genes is regulated and how the regulatory information controlling their activity is encoded. Interestingly, mature miRNAs can often be classified into large families consisting of members with identical seeds (nucleotides 2 through 8 of the mature miRNAs) and highly homologous ~22-nt mature miRNA sequences, but with divergent sequences and structural elements beyond their mature miRNAs. Here we investigated whether members of a miRNA gene family that encode identical or nearly identical mature miRNAs are functionally interchangeable in vivo and if not, why? We compare the activities of the mir-181 gene family in promoting double positive T cell development and show that miRNA genes that encode identical to nearly identical mature miRNAs can have distinct activities. The differences in activity between mir-181a-1 and mir-181c are largely determined by their unique primary/precursor-miRNA (pri/pre-miRNA) loop nucleotides, and the differences in activity between mir-181a-1 and mir-181b-1 are determined by both the pri/pre-miRNA loop and stem. Furthermore, the organization of mir-181a-1/b-1 in a cluster is important for its full activity. We also show that mir-181 family members can differentially regulate target genes quantitatively, and that some target genes can be upregulated. Taken together, we have demonstrated that regulatory information encoded in a miRNA gene beyond the mature miRNA plays a critical role in controlling the activity of the miRNA gene, suggesting that miRNA family members could have evolved different functions through their divergent miRNA gene sequences and structural elements beyond their mature miRNAs. Although, proteins may have evolved to recognize the structural and sequence elements of the pri/pre-miRNAs, we suggest that the regulatory information encoded in the structured pri/pre-miRNA may be directly interpreted through target and pri/pre-miRNA interactions.
- 2006 ScienceDirectDavidson, Eric H.
- 2006 Cold Spring Harb Lab PressSU Catalog (SearchWorks) Click LINK above for Print location/circulation status.Stewart, David J.; Stillman, Bruce.Mechanism and biology of RNAi -- Genome-wide approaches -- Small RNAs in development -- Telomeres and cancer -- End regulation of transcripts -- RNPs and RNA editing -- Biology of short RNAs -- Control of gene expression by noncoding RNAs -- Heterochromatin -- Quality control, messenger RNA turnover, and translational control.
- 2012 SpringerGhosh, Zhumur; Mallick, Bibekanand.pt. 1. Basics -- pt. 2. Methods -- pt. 3. Applications.
- 2012 SpringerHess, Wolfgang R.; Marchfelder, Anita.This book provides a comprehensive and up-to-date collection of review articles focusing on RNA-mediated regulation in prokaryotes. The various modes of action include the direct interaction with proteins, direct sensing of metabolites or of physical parameters, and the interaction with RNAs to stimulate or prevent binding of ribosomes or to stimulate degradation. Written by leading experts in the field, the book covers small RNA functions, RNA thermometers, riboswitches, the diversity of small RNA-guided CRISPR-Cas defense systems and selected RNA chaperons in both prokaryotic domains, bacteria and archaea. Recent advances towards the computational identification of regulatory RNAs and their targets are included and particular attention is paid to small RNA in pathogenic bacteria. This volume is the only one exclusively covering regulatory RNAs in the prokaryotic domains to date, making it essential literature for anyone interested in RNA function and gene regulation and a valuable resource for teaching these concepts.
- 2012 KargerGarrido-Ramos, Manuel A.The Repetitive DNA Content of Eukaryotic Genomes / López-Flores, I.; Garrido-Ramos, M.A. -- Telomere Dynamics in Mammals / Silvestre, D.C.; Londoño-Vallejo, A. -- Drosophila Telomeres: an Example of Co-Evolution with Transposable Elements / Silva-Sousa, R.; López-Panadès, E.; Casacuberta, E. -- The Evolutionary Dynamics of Transposable Elements in Eukaryote Genomes / Tollis, M.; Boissinot, S. -- SINEs as Driving Forces in Genome Evolution / Schmitz, J. -- Unstable Microsatellite Repeats Facilitate Rapid Evolution of Coding and Regulatory Sequences / Jansen, A.; Gemayel, R.; Verstrepen, K.J. -- Satellite DNA Evolution / Plohl, M.; Meštrović, N.; Mravinac, B. -- Satellite DNA-Mediated Effects on Genome Regulation / Pezer, Ž.; Brajković, J.; Feliciello, I.; Ugarković, Đ. -- The Birth-and-Death Evolution of Multigene Families Revisited / Eirín-López, J.M.; Rebordinos, L.; Rooney, A.P.; Rozas, J. -- Chromosomal Distribution and Evolution of Repetitive DNAs in Fish / Cioffi, M.B.; Bertollo, L.A.C..
- 2007 Springer ProtocolsAnson, Donald S.Methodologies for staining and visualization of [beta]-galactosidase in mouse embryos and tissues / Siobhan Loughna and Deborah Henderson -- Immunohistochemical detection of [beta]-galactosidase or green fluorescent protein on tissue sections / Philip A. Seymour and Maike Sander -- Detection of reporter gene expression in murine airways / Maria Limberis, Peter Bell, and James M. Wilson -- Three-dimensional analysis of molecular signals with episcopic imaging techniques / Wolfgang J. Weninger and Timothy J. Mohun -- Fluorescent proteins for cell biology / George H. Patterson -- Detection of GFP during nervous system development in Drosophila melanogaster / Karin Edoff, James S. Dods, and Andrea H. Brand -- Autofluorescent proteins for flow cytometry / Charles G. Bailey and John E. J. Rasko -- Fluorescent protein reporter systems for single-cell measurements / Steven K. Dower, Eva E. Qwarnstrom, and Endre Kiss-Toth -- Subcellular imaging of cancer cells in live mice / Robert M. Hoffman -- Noninvasive imaging of molecular events with bioluminescent reporter genes in living subjects / Pritha Ray and Sanjiv Sam Gambhir -- Green fluorescent protein as a tracer in chimeric tissues : the power of vapor fixation / Harald Jockusch and Daniel Eberhard.
- Research in computational molecular biology : 9th annual International Conference, RECOMB 2005, Cambridge, MA, USA, May 14-18, 2005 : proceedingsSpringer, 2005Istrail, Sorin; Kasif, Simon; Mesirov, Jill; Miyano, Satoru; Pevzner, Pavel; Waterman, Michael S.
- Research in computational molecular biology : 11th annual international conference, RECOMB 2007, Oakland, CA, USA, April 21-25, 2007 : proceedingsSpringer, 2007Huang, Haiyan; Speed, T. P.
- 2008 SpringerChristen, Yves; Gage, F.
- 2006 SpringerBuerstedde, Jean-Marie; Takeda, Shunichi.Ch. 1. DT40 gene disruptions: a how-to for the design and the construction of targeting vectors / Hiroshi Arakawa and Jean-Marie Buerstedde -- Ch. 2. Immunoglobulin gene conversion or hypermutation: That's the question / Jean-Marie Buerstedde and Hiroshi Arakawa -- Ch. 3. Genome resources for the DT40 community / Randolph B Caldwell and Andrzej M. Kierzek -- Ch. 4. Chromosome engineering in DT40 cells and mammalian centromere function / William R.A. Brown ... [et al.] -- Ch. 5. Function of recQ family helicase in genome stability / Masayuki Seki, Shusuke Tada and Takemi Enomoto -- Ch. 6. Genetic analysis of apoptotic execution / Sandrine Ruchaud ... [et al.] -- Ch. 7. The DT40 system as a tool for analyzing kinetochore assembly / Masahiro Okada, Tesuya Hori and Tatsuo Fukagawa -- Ch. 8. Analysing the DNA damage and replication checkpoints in DT40 cells / Michael D Rainey, George Zachos, and David AF Gillespie -- Ch. 9. Using DT40 to study clathrin function / Frank R. Wettey and Antony P. Jackson -- Ch. 10. Genetic analysis OF B cell signaling / Hisaaki Shinohara and Tomohiro Kurosaki -- Ch. 11. DT40 mutants: a model to study transcriptional regulation of B cell development and function / Jukka Alinikula, Olli Lassila and Kalle-Pekka Nera -- Ch. 12. Transcription and RNA processing factors play complex roles IN DT40 cells / Stephanie Bush and James L. Manley -- Ch. 13. Participation of histones, histone modifying enzymes and histone chaperones in vertebrate cell functions / Hidehiko Kikuchi ... [et al.] -- Ch. 14. Analysis of gene expression, copy number and palindrome formation with a DT40 enriched cDNA Microarray / Paul E. Neima ... [et al.] -- Ch. 15. Analysis of DNA replication damage bypass and its role in immunoglobulin repertoire development / Julian E. Sale, Anna-Laura Ross and Laura J. Simpson -- Ch. 16. The fanconi anemia pathway promotes homologous recombination repair in DT40 cell line / Julian E. Sale, Anna-Laura Ross and Laura J. Simpson -- Ch. 17. Calcium signaling, ion channels and more / Anne-Laure Perraud, Carsten Schmitz, Andrew M. Scharenberg -- Ch. 18. Phenotypic analysis of cellular responses to DNA damage / Helfrid Hochegger and Shunichu Takeda -- Ch. 19. ATM, a paradigm for a stress-responsive signal transducer in higher vertebrate cells / Ken-ichi Yamamoto, Masahiko Kobayashi and Hiroko Shimizu -- METHOD 1. Stable transfection of DT40 / Julian E. Sale -- METHOD 2. Basic cell culture conditions / Huseyin Saribasak and Hiroshi Arakawa -- METHOD 3. Excision of floxed-DNA sequences by transient induction of Mer-Cre-Mer / Hiroshi Arakawa -- METHOD 4. Immunoglobulin gene conversion and hypermutation assay by FACS / Hiroshi Arakawa -- METHOD 5. Target screening by PCR / Hiroshi Arakawa -- METHOD 6. Mitotic index determination by flow cytometry / David AF Gillespie and Mark Walker -- METHOD 7. Centrifugal elutriation as a means of cell cycle phase separation and synchronization / David AF Gillespie and Catarina Henriques -- METHOD 8. Preparation of genomic DNA for microarray-based comparative genome hybridization / Robert Kimmel, Amalia Icreverzi, Paul Neiman -- METHOD 9. Analysis of cellular Mg2+ in DT40 cells / Anne-Laure Perraud, Carsten Schmitz, Andrew M. Scharenberg -- METHOD 10. Transient transfection of DT40 / Roger Franklin & Julian E. Sale -- METHOD 11. Retroviral transduction of DT40 / Felix Randow & Julian E. Sale -- METHOD 12. Colony survival assay / Laura. J. Simpson & Julian E. Sale -- METHOD 13. Subcloning DT40 by limiting dilution / Jean-Marie Buerstedde -- METHOD 14. Subnuclear immunofluorescence / Dávid Szüts & Julian E. Sale -- METHOD 15. Sister chromatid exchange assay / Laura J. Simpson & Julian E. Sale -- METHOD 16. 2D cell cycle analysis / Roger Franklin & Julian E. Sale -- METHOD 17. Purification of tap-tagged proteins by two-step pull down from DT40 cells / Hiroyuki Kitao and Minoru Takata -- METHOD 18. Synchronization of cells / Eiichiro Sonoda -- METHOD 19. Tranfection of DT40 cells / Huseyin Saribasak and Hiroshi Arakawa -- METHOD 20. Luciferase reporter assay / Frank R. Wettey and Antony P. Jackson -- METHOD 21. Indirect immunofluorescence microscopy / Frank R. Wettey and Antony P. Jackson -- METHOD 22. Quantification of receptor-mediated endocytosis / Frank R. Wettey and Antony P. Jackson -- METHOD 23. Measurement of DNA synthesis and strand breaks using alkaline sucrose density gradient centrifugation / Kouichi Yamada and Jun Takezawa -- METHOD 24. Fractionation of nuclear and cytoplasmic proteins from DT40 cell lines / Yan-Dong Wang and Randolph B Caldwell.
- 2012 Springer ProtocolsDouthwaite, Julie A.; Jackson, Ronald H.Ribosome display : a perspective / Andreas Plückthun -- Preparation and testing of E. coli S30 in vitro transcirption translation extracts / James F. Zawada -- Eurkaryotic ribosome display selection using rabbit reticulocyte lysate / Julie A Douthwaite -- Stabilized ribosome display for in vitro selection / Shuta Hara [and others] -- Eukaryotic ribosome display with in situ DNA recovery / Mingyue He [and others] -- mRNA display using covalent coupling of mRNA to translated proteins / Rong Wang, Steve W. Cotten, and Rihe Liu -- SNAP display : in vitro rotein evolution in microdroplets / Miriam Kaltenbach and Florian Hollfelder -- cDNA display : rapid stabilization of mRNA display / Shingo Ueno and Naoto Nemoto -- Optimisation of antibody affinity by ribosome display using error-prone or site-directed mutagenesis / Leeanne Lewis and Chris Lloyd -- Affinity maturation of phage display antibody populations using ribosome display / Maria A. Groves and Adrian A. Nickson -- Evolution of protein stability using ribosome display / Andrew Buchanan -- Selection of lead antibodies from naive ribosome display antibody libraries / Peter Ravn -- Evolution of disulfide-rich peptide aptamers using cDNA display / Yuki Mochizuki and Naoto Nemoto -- Peptide screening using PURE ribosome display / Hiroyuki Ohashi [and others] -- Rapid selection of high-affinity binders using ribosome display / Birgit Dreier and Andreas Plückthun -- mRNA display-based selections using synthetic peptide and natural protein libraries / Steve W. Cotten [and others] -- Identification of candidate vaccine genes using ribosome display / Liancheng Lei -- Ribosome display for the selection of Sac7d scaffolds / Barbara Mouratou [and others] -- Charging of tRNAs using ribozymes and selection of cyclic peptides containing thioethers / Patrick C. Reid [and others] -- Update on pure translation display with unnatural amino acid incorporation / R. Edward Watts and Anthony C. Forster -- In vitro selection of unnatural cyclic peptide libraries via mRNA display / Zhong Ma and Matthew C.T. Hartman -- Optimization of CAT-354, a therapeutic antibody directed against interleukin-13, using ribosome display / George Thom and Ralph Minter -- Affinity maturation and functional dissection of a humanised anti-RAGE monoclonal antibody by ribosome display / Simon E. Hufton.
- 2013 Springer ProtocolsYang, Yinong.Rice artificial hybridization for genetic analysis / Xueyan Sha -- Fluorescence in situ hybridization techniques for cytogenetic and genomic analyses / Jason G. Walling, Wenli Zhang, and Jiming Jiang -- Generation of rice mutants by chemical mutagenesis / Thomas H. Tai -- TILLING and ecotilling for rice / Jennifer L. Cooper [and others] -- Functional characterization of rice genes using a gene-indexed T-DNA insertional mutant population / Ki-Hong Jung and Gynheung An -- QTL analysis and map-based cloning of salt tolerance gene in rice / Ji-Ping Gao and Hong-Xuan Lin -- Site-specific gene integration in rice / Vibha Srivastava -- Transcriptome profiling analysis using rice oligonucleotide microarrays / Ki-Hong Jung and Pamela C. Ronald -- Cloning of small RNAs for the discovery of novel microRNAs in plants / Guru Jagadeeswaran and Ramanjulu Sunkar -- Global identification of small RNA targets in plants by sequencing sliced ends of messenger RNAs / Yong-Fang Li and Ramanjulu Sunkar -- Artificial microRNAs for specific gene silencing in rice / Norman Warthmann [and others] -- Rice proteomic analysis : sample preparation for protein identification / Ganesh Kumar Agrawal [and others] -- Quantification of jasmonic and salicylic acids in rice seedling leaves / Kyoungwon Cho [and others] -- Analysis of insect-induced volatiles from rice / Nan Zhao [and others] -- Phenotypic and physiological evaluation for drought and salinity stress responses in rice / Utlwang Batlang [and others] -- Phenotypic, physiological, and molecular evaluation of rice chilling stress response at the vegetative stage / Benildo G. de los Reyes [and others] -- Analysis of rice root hair morphology using cryo-scanning electron microscopy / Zhiming Yu -- Inoculation and virulence assay for bacterial blight and bacterial leaf streak of rice / Bing Yang and Adam Bogdanove -- Inoculation and scoring methods for rice sheath blight disease / Yulin Jia [and others] -- Molecular approaches to improve rice abiotic stress tolerance / Junya Mizoi and Kazuko Yamaguchi-Shinozaki -- Molecular strategies to improve rice disease resistance / Emily E. Helliwell and Yinong Yang -- Molecular strategies to engineer transgenic rice seed compartments for large-scale production of plant-made pharmaceuticals / Trevor Greenham and Illimar Altosaar.
- 2001 ScienceDirectMoore, Peter; Nishimura, Susumu; Söll, Dieter.
- 2008 Springer ProtocolsNielsen, Henrik.The transcriptional landscape -- Working with RNA -- Synthesis of RNA by in vitro transcription -- Efficient poly(A)+ RNA selection using LNA oligo(T) capture -- Genome browsers -- Web-based tools for studying RNA structure and function -- Northern blotting analysis -- Rapid amplification of cDNA ends (RACE) -- Fractionation of mRNA based on the length of the poly(A) tail -- Analysis of mutations that influence pre-mRNA splicing -- S1 nuclease analysis of alternatively spliced mRNA -- Promises and challenges in developing RNAi as a research tool and therapy -- Inhibition of gene function in mammalian cells using short-hairpin RNA (shRNA) -- Validation of RNAi by real time PCR -- Profiling RNA polymerase II using the fast chromatin immunoprecipitation method -- The post-transcriptional operon -- RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray (chip) profiling -- Isolation of RNP granules -- Electrophoretic mobility shift assay for characterizing RNA-protein interaction -- Polysome analysis and RNA purification from sucrose gradients -- Prediction of targets for microRNAs -- Outsourcing of experimental work.
- 2011 Springer ProtocolsAphasizhev, Ruslan.Three-dimensional reconstruction of trypanosoma brucei editosomes using single-particle electron microscopy / H.U. Goringer ... [et al.] -- Icoda: RNAi-based inducible knock-in system in trypanosoma brucei / G.E. Ringpis, R.H. Lathrop and R. Aphasizhev -- Perturbing a-to-i RNA editing using genetics and homologous recombination / C.J. Staber ... [et al.] -- Laser microdissection and pressure catapulting of single human motor neurons for RNA editing analysis / H. Sun ... [et al.] -- Biochemical identification of A-to-I RNA editing sites by the inosine chemical erasing (ice) method / M. Sakurai and T. Suzuki -- Identifying mRNA editing deaminase targets by RNA-seq / B.R. Rosenberg, S. Dewell and F.N. Papavasiliou -- Mouse and other rodent models of C to U RNA editing / V. Blanc and N.O. Davidson -- In vivo analysis of RNA editing in plastids / S. Ruf and R. Bock -- Identifying specific trans-factors of RNA editing in plant mitochondria by multiplex single base extension typing / M. Takenaka -- Complementation of mutants in plant mitochondrial RNA editing by protoplast transfection / M. Takenaka and A. Zehrmann -- A high-throughput assay for DNA deaminases / M. Wang, C. Rada and M.S. Neuberger -- Biochemical fractionation and purification of high-molecular-mass apobec3g complexes / Y.L. Chiu -- Analysis of tRNA editing in native and synthetic substrates / J.L. Spears, K.W. Gaston and J.D. Alfonzo -- Post-transcriptional modification of RNAs by artificial box h/aca and box c/d rnps / C. Huang, J. Karijolich and Y.T. Yu -- Functional analysis of noncoding RNAs in trypanosomes: RNA walk, a novel approach to study RNA-RNA interactions between small RNA and its target / C. Wachtel and S. Michaeli -- A post-labeling approach for the characterization and quantification of RNA modifications based on site-directed cleavage by dnazymes / M. Meusburger, M. Hengesbach and M. Helm.
- 2015 Springer ProtocolsPicardi, Ernesto.Free energy minimization to predict RNA secondary structures and computational RNA design / Alexander Churkin, Lina Weinbrand, and Danny Barash -- RNA secondary structure prediction from multi-aligned sequences / Michiaki Hamada -- Simple protocol for the inference of RNA global pairwise alignments / Eugenio Mattei, Manuela Helmer-Citterich, and Fabrizio Ferrè -- De novo secondary structure motif discovery using RNA profile / Federico Zambelli and Giulio Pavesi -- Drawing and editing the secondary structure(s) of RNA / Yann Ponty and Fabrice Leclerc -- Modeling and predicting RNA three-dimensional structures / Jérôme Waldispühl and Vladimir Reinharz -- Fast prediction of RNA-RNA interaction using heuristic algorithm / Soheila Montaseri -- Quality control of RNA-Seq experiments / Xing Li ... [and 3 others] -- Accurate mapping of RNA-Seq data / Kin Fai Au -- Quantifying entire transcriptomes by aligned RNA-Seq data / Raffaele A. Calogero and Francesca Zolezzi -- Transcriptome assembly and alternative splicing analysis / Paola Bonizzoni ... [and 5 others] -- Detection of post-transcriptional RNA editing events / Ernesto Picardi ... [and 3 others] -- Prediction of miRNA targets / Anastasis Oulas ... [and 6 others] -- Using deep sequencing data for identification of editing sites in mature miRNAs / Shahar Alon and Eli Eisenberg -- NGS-trex : an automatic analysis workflow for RNA-seq data / Ilenia Boria ... [and 3 others] -- e-DNA meta-barcoding : from NGS raw data to taxonomic profiling / Fosso Bruno, Marzano Marinella, and Monica Santamaria -- Deciphering metatranscriptomic data / Evguenia Kopylova ... [and 6 others] -- RIP-seq data analysis to determine RNA-protein associations / Federico Zambelli and Giulio Pavesi -- ViennaRNA eeb services / Andreas R. Gruber, Stephan H. Bernhart, and Ronny Lorenz -- Exploring the RNA editing potential of RNA-Seq data by ExpEdit / Mattia D'Antonio ... [and 4 others] -- Guideline for the annotation of UTR regulatory elements in the UTRsite collection / Matteo Giulietti ... [and 3 others] -- Rfam : annotating families of non-coding RNA sequences / Jennifer Daub ... [and 3 others] -- ASPicDB : a database web tool for alternative splicing analysis / Mattia D'Antonio ... [and 5 others] -- Analysis of alternative splicing events in custom gene datasets by AStalavista / Sylvain Foissac and Michael Sammeth -- Computational design of artificial RNA molecules for gene regulation / Alessandro Laganà ... [and 6 others].
- 2012 SpringerLeontis, Neocles B.; Westhof, Eric.Introduction / Michael Levitt -- Modeling RNA Molecules / Neocles Leontis and Eric Westhof -- Methods for Predicting RNA Secondary Structure / Kornelia Aigner, Fabian Dre€en and Gerhard Steger -- Why Can't We Predict RNA Structure At Atomic Resolution? / Parin Sripakdeevong, Kyle Beauchamp and Rhiju Das -- Template-Based and Template-Free Modeling of RNA 3D Structure: Inspirations from Protein Structure Modeling / Kristian Rother, Magdalena Rother, Michał Boniecki, Tomasz Puton and Konrad Tomala, et al. -- The RNA Folding Problems: Different Levels of sRNA Structure Prediction / Fredrick Sijenyi, Pirro Saro, Zheng Ouyang, Kelly Damm-Ganamet and Marcus Wood, et al. -- Computational Prediction and Modeling Aid in the Discovery of a Conformational Switch Controlling Replication and Translation in a Plus-Strand RNA Virus / Wojciech K. Kasprzak and Bruce A. Shapiro -- Methods for Building and Refining 3D Models of RNA / Samuel C. Flores, Magdalena Jonikas, Christopher Bruns, Joy P. Ku and Jeanette Schmidt, et al. -- Multiscale Modeling of RNA Structure and Dynamics / Feng Ding and Nikolay V. Dokholyan -- Statistical Mechanical Modeling of RNA Folding: From Free Energy Landscape to Tertiary Structural Prediction / Song Cao and Shi-Jie Chen -- Simulating Dynamics in RNA-Protein Complexes / John Eargle and Zaida Luthey-Schulten -- Quantum Chemical Studies of Recurrent Interactions in RNA 3D Motifs / Jiří Šponer, Judit E. Šponer and Neocles B. Leontis -- Nonredundant 3D Structure Datasets for RNA Knowledge Extraction and Benchmarking / Neocles B. Leontis and Craig L. Zirbel -- Ions in Molecular Dynamics Simulations of RNA Systems / Pascal Auffinger -- Modeling RNA Folding Pathways and Intermediates Using Time-Resolved Hydroxyl Radical Footprinting Data / Joshua S. Martin, Paul Mitiguy and Alain Laederach -- A Top-Down Approach to Determining Global RNA Structures in Solution Using NMR and Small-Angle X-ray Scattering Measurements / Yun-Xing Wang, Jinbu Wang and Xiaobing Zuo -- RNA Structure Determination by Structural Probing and Mass Spectrometry: MS3D / A. E. Hawkins and D. Fabris.
- 2011 Springer ProtocolsGerst, Jeffrey E.Single molecule imaging of RNA in situ / Mona Batish, Arjun Raj, and Sanjay Tyagi -- FISH and immunofluorescence staining in Chlamydomonas / James Uniacke, Daniel Colón-Ramos, and William Zerges -- High resolution fluorescent in situ hybridization in Drosophila / Eric Lécuyer -- Localization and anchorage of maternal mRNAs to cortical structures of ascidian eggs and embryos using high resolution in situ hybridization / Alexandre Paix, Janet Chenevert, and Christian Sardet -- Visualization of mRNA localization in Xenopus oocytes / James A. Gagnon and Kimberly L. Mowry -- Visualization of mRNA expression in the zebrafish embryo / Yossy Machluf and Gil Levkowitz -- High-resolution fluorescence in situ hybridization to detect mRNAs in neuronal compartments in vitro and in vivo / Sharon A. Swanger, Gary J. Bassell, and Christina Gross -- Localization of mRNA in vertebrate axonal compartments by in situ hybridization / José Roberto Sotelo-Silveira ... [et al.] -- Tiny molecular beacons for in vivo mRNA detection / Diana P. Bratu, Irina E. Catrina, and Salvatore A.E. Marras -- Delivery of molecular beacons for live-cell imaging and analysis of RNA / Antony K. Chen ... [et al.] -- Genetically-encoded fluorescent probes for imaging endogenous mRNA in living cells / Takeaki Ozawa and Yoshio Umezawa -- Visualization of induced RNA in single bacterial cells / Azra Borogovac and Natalia E. Broude -- Visualizing mRNAs in fixed and living yeast cells / Franck Gallardo and Pascal Chartrand -- In vivo visualization of RNA using the U1A-based tagged RNA system / Sunglan Chung and Peter A. Takizawa -- Visualizing endogenous mRNAs in living yeast using m-TAG, a PCR-based RNA aptamer integration method, and fluorescence microscopy / Liora Haim-Vilmovsky and Jeffrey E. Gerst -- Imaging mRNAs in living mammalian cells / Sharon Yunger and Yaron Shav-Tal -- Using the mRNA-MS2/MS2CP-FP system to study mRNA transport during Drosophila oogenesis / Katsiarina Belaya and Daniel St Johnston -- Genome-wide analysis of RNA extracted from isolated mitochondria / Erez Eliyahu, Daniel Melamed and Yoav Arava -- Analyzing mRNA localization to the endoplasmic reticulum via cell fractionation / Sujatha Jagannathan, Christine Nwosu and Christopher V. Nicchitta -- Isolation of mRNAs encoding peroxisomal proteins from yeast using a combined cell fractionation and affinity purification procedure / Gadi Zipor, Cecile Brocard and Jeffrey E. Gerst -- Profiling axonal mRNA transport / Dianna E. Willis and Jeffery L. Twiss -- RNA purification from tumor cell protrusions using porous polycarbonate filters / Jay Shankar and Ivan R. Nabi -- RNA-binding protein immunopurification-microarray (RIP-chip) analysis to profile localized RNAs / Alessia Galgano and André P. Gerber -- RaPID : an aptamer-based mRNA affinity purification technique for the identification of RNA and protein factors present in ribonucleoprotein complexes / Boris Slobodin and Jeffrey E. Gerst -- RIP : an mRNA localization technique / Sabarinath Jayaseelan ... [et al.] -- The dual use of RNA aptamer sequences for affinity purification and localization studies of RNAs and RNA-protein complexes / Scott C. Walker ... [et al.] -- Identifying and searching for conserved RNA localisation signals / Russell S. Hamilton and Ilan Davis -- Computational prediction of RNA structural motifs involved in post-transcriptional regulatory processes / Michal Rabani, Michael Kertesz, and Eran Segal.
- 2008 SpringerGöringer, H. Ulrich.Editing reactions from the perspective of RNA structure / Matthias Homann -- Editing of tRNA for structure and function / Juan D. Alfonzo -- RNA editing by adenosine deaminases that act on RNA (ADARs) / Michael F. Jantsch and Marie Öhman -- Insertion/deletion editing in Physarum polycephalum / Jonatha M. Gott and Amy C. Rhee -- RNA editing in plant mitochondria / Mizuki Takenaka ... [et al.] -- RNA editing in chloroplasts / Masahiro Sugiura -- Working together : the RNA editing machinery in Trypanosoma brucei / Jason Carnes and Kenneth Stuart -- RNA editing accessory factors : the example of mHel61p / H. Ulrich Göringer ... [et al.] -- The function of RNA editing in trypanosomes / Torsten Ochsenreiter and Stephen Hajduk -- Evolutionary aspects of RNA editing / Dave Speijer.
- 2007 ScienceDirectGott, Jonatha M.
- 2011 SpringerJensen, Torben Heick."The diversity of RNAs inside living cells is amazing. We have known of the more "classic" RNA species: mRNA, tRNA, rRNA, snRNA and snoRNA for some time now, but in a steady stream new types of molecules are being described as it is becoming clear that most of the genomic information of cells ends up in RNA. To deal with the enormous load of resulting RNA processing and degradation reactions, cells need adequate and efficient molecular machines. The RNA exosome is arising as a major facilitator to this effect. Structural and functional data gathered over the last decade have illustrated the biochemical importance of this multimeric complex and its many co-factors, revealing its enormous regulatory power. By gathering some of the most prominent researchers in the exosome field, it is the aim of the book to introduce this fascinating protein complex and to give a timely and rich account of its many functions"--Provided by publisher.Also available: Print – 2011
- 2014 Springer ProtocolsWaldsich, Christina.Predicting RNA Structure: Advances and Limitations -- Cis-Acting 5' Hammerhead Optimization for In Vitro Transcription of Highly Structured RNAs -- RNA Structural Analysis by Enzymatic Digestion -- A Mutate-and-Map Protocol for Inferring Base Pairs in Structured RNA -- Mapping RNA Structure In Vitro Using Nucleobase-Specific Probes -- Massively Parallel RNA Chemical Mapping with a Reduced Bias MAP-Seq Protocol -- Probing RNA Folding by Hydroxyl Radical Footprinting -- Monitoring Global Structural Changes and Specific Metal Binding Sites in RNA by In-Line Probing and Tb(III) Cleavage -- Chemical Probing of RNA in Living Cells -- A Chemogenetic Approach to Study the Structural Basis of Protein-Facilitated RNA Folding -- Applying UV Crosslinking to Study RNA-Protein Interactions in Multicomponent Ribonucleoprotein Complexes -- The Kinetics of Ribozyme Cleavage: A Tool to Analyze RNA Folding as a Function of Catalysis -- RNA Catalytic Activity as a Probe of Chaperone-Mediated RNA Folding -- Evaluation of RNA Chaperone Activity In Vivo and In Vitro Using Misfolded Group I Ribozymes -- RNA Conformational Changes Analyzed by Comparative Gel Electrophoresis -- Detecting RNA Tertiary Folding by Sedimentation Velocity Analytical Ultracentrifugation -- RNA Folding Dynamics Using Laser Assisted Single-Molecule Refolding -- RNA Refolding Studied by Light-Coupled NMR Spectroscopy -- Exploring RNA Oligomerization and Ligand Binding by Fluorescence Correlation Spectroscopy and Small Angle X-Ray Scattering.
- 2011 SpringerCollins, Lesley J.The RNA infrastructure : an introduction to ncRNA networks / Lesley J. Collins -- RNA interactions / Manja Marz and Peter F. Stadler -- Plant RNA silencing in viral defence / Vitantonio Pantaleo -- Micrornas as post-transcriptional machines and their interplay with cellular networks / Sarath Chandra Janga and Swathi Vallabhaneni -- Spatiotemporal aspects of microRNA-mediated gene regulation / Joris Pothof and Dik C. van Gent -- Spliceosomal RNA infrastructure : the network of splicing components and their regulation by miRNAs / Lesley J. Collins -- Construction, structure, and dynamics of post-transcriptional regulatory network directed by RNA binding proteins / Sarath Chandra Janga and Nitish Mittal -- Safe keeping the message : mRNP complexes tweaking after transcription / Said Hafidh, Věra Čapková, and David Honys -- Unexpected functions of tRNA and tRNA processing enzymes / Rebecca L. Hurto -- Programmed DNA elimination in tetrahymena : a small RNA mediated genome surveillance mechanism / Kensuke Kataoka and Kazufumi Mochizuki -- Long noncoding RNA and epigenomics / Chandrasekhar Kanduri -- Promoter associated long noncoding RNAs repress transcription through a RNA binding protein TLS / Riki Kurokawa -- RNA networks in prokaryotes I :CRISPRs and riboswitches / Patrick J. Biggs and Lesley J. Collins -- RNA networks in prokaryotes II : tRNA processing and small RNAs / Lesley J. Collins and Patrick J. Biggs -- Localization of the bacterial RNA infrastructure / Kenneth C. Keiler -- Small RNA discovery and characterisation in eukaryotes using high throughput approaches / Helio Pais ... [et al.] -- How old are RNA networks? / Toni Daly, X. Sylvia Chen, and David Penny.
- 2005 ScienceDirectEngelke, David R.; Rossi, John J.
- 2013 SpringerHoward, Kenneth A.The Nobel Prize winning discovery that small interfering RNA can be utilised to control cellular gene expression has propelled the field of RNA interference (RNAi) to the forefront of biomedical science as a potential molecular medicine set to revolutionalise disease treatment. Harnessing the molecular mechanisms of RNAi and development of delivery technologies is crucial for its transformation into a therapeutic modality, this dependency is the focus of "RNA Interference from Biology to Therapeutics" that gives a comprehensive overview of RNAi biology and state-of-the-art delivery methods relevant to clinical translation of RNAi therapeutics. Key players and shapers in the fields of RNAi and delivery science have been assembled in a single volume to produce a truly unique interdisciplinary text, making it a "must-read" for both students and experts in, and at the interface of, RNAi, pharmaceutical science and medicine. An attractive feature is the "future perspectives" section within each chapter that allows global leaders the opportunity to express their views on the direction the field is moving. Topics covered in the book include miRNA biology and therapeutic exploitation, exosome delivery and clinical translation."RNA Interference from Biology to Therapeutics" is an up-to-the-minute, highly informative and invaluable text for those actively involved or interested in this fascinating and high-impact field.
- 2011 Springer ProtocolsHarper, Scott Q.Designing hairpin-based RNAi shuttles / Yu Shen -- Rapid cloning and validation of microRNA shuttle vectors : a practical guide / Ryan L. Boudreau [and others] -- Use of small noncoding RNAs to silence transcription in human cells / Kevin V. Morris -- Delivery strategies for RNAi to the nervous system / Kevin D. Foust and Brian K. Kaspar -- Cloning small RNAs / Eric J. Devor and Lingyan Huang -- Profiling the miRNome : detecting global miRNA expression levels with DNA microarrays / Peter White -- High-throughput profiling of mature microRNA by real-time PCR / Jinmai Jiang [and others] -- In situ detection of microRNAs in paraffin-embedded, formalin-fixed tissues : different methodologies and co-localization with possible targets / Gerard J. Nuovo [and others] -- Tracing of siRNAs inside cells by FRET imaging / Markus Hirsch [and others] -- Application of RIP-chip for the identification of miRNA targets / Lu Ping Tan, Anke van den Berg, and Joost L. Kluiver.
- 2005 MyiLibraryAppasani, Krishnarao; Fire, Andrew Z.; Nirenberg, Marshall W.Chemical modifications to achieve increased stability and sensitive detection of siRNA -- RNA interference in postimplantation mouse embryos -- In ovo RNAi opens new possibilities for functional genomics in vertebrates -- Sect. 4. Gene silencing in model organisms. Practical applications of RNAi in C. elegans -- Inducible RNAi as a forward genetic tool in Trypanosoma brucei -- RNA-mediated gene silencing in fission yeast -- RNA silencing in filamentous fungi: Mucor ciccinelloides as a model organism -- RNAi and gene silencing phenomena mediated by viral suppressors in plants -- Sect. 1. Basic RNAi, siRNA, microRNAs and gene-silencing mechanisms. RNAi beginnings. Overview of the pathway in C. elegans -- Dicer in RNAi: its roles in vivo and utility in vitro -- Genes required for RNA interference -- MicroRNAs: a small contribution from worms -- miRNAs in the brain and the application of RNAi to neurons -- Sect. 2. Design, synthesis of siRNAs. Degign and synthesis of small interfering RNA (siRNA) -- Automated design and high throughput chemical synthesis of siRNA -- Rational design of siRNAs with the Sfold software -- Enzymatic production of small interfering RNAs -- Sect. 3. Vector development and in vivo, in vitro and in ovo delivery methods. Six methods of inducing RNAi in mammalian cells -- Viral delivery of shRNA -- siRNA delivery by lentiviral vectors: design and applications -- Liposomal delivery of siRNAs in mice -- Sect. 5. Drug target validation. Delivering siRNA in vivo for functional genomics and novel therapeutics -- The role of RNA interference in drug target validation: application to Hepatitis C -- RNAi in the drug discovery process -- RNA interference technology in the discovery and validation of druggable targets -- Sect. 6. Therapeutic and drug development. RNAi-mediated silencing of viral gene expression and replication -- RNAi in drug development: practical considerations -- RNA interference studies in liver failure -- RNAi applications in living animal systems -- Sect. 7. High-throughput genome-wide RNAi analysis. High-throughput RNAi by soaking in Caenorhabtis elegans -- Tools for integrative genomics: genome-wide RNAi and expression profiling in Drosophila -- Microarray analysis and RNA silencing to determine genes functionally important in mesothelioma -- High-throughput RNA interference -- Generation of highly specific vector-based shRNAi libraries directed against the entire human genome.
- 2010 ScienceDirectFarrell, Robert E.RNA and the cellular biochemistry revisited -- RNA isolation strategies -- The truth about tissues -- Going green : RNA and the molecular biology of plants -- Isolation of polyadenylated RNA -- Quality control for RNA preparations -- Resilient ribonucleases -- Stringency : conditions that influence nucleic acid structure -- Electrophoresis of RNA -- Photodocumentation and image analysis -- Northern analysis -- Nucleic acid probe technology -- Practical nucleic acid hybridization -- Principles of detection -- Quantifications of specific mRNAs by nuclease protection -- Analysis of nuclear RNA -- cDNA synthesis -- RT-PCR : a science and an art form -- Quantitative PCR techniques -- Functional genomics and transcript profiling -- High-throughput analysis of gene expression -- Non-array methods for global analysis of gene expression -- RNAi : take a RISC-role the dicer -- Genomes, transcriptomes, proteomes, and bioinformatics -- An RNA paradigm.
- 2015 ScienceDirectHe, Chuan.Methodology for the high-throughput identification and characterization of tRNA variants that are substrates for a tRNA decay pathway -- Nucleoside analysis by hydrophilic interaction liquid chromatography coupled with mass spectrometry -- A platform for discovery and quantification of modified ribonucleosides in RNA: application to stress-induced reprogramming of tRNA modifications -- Recogniion of specified RNA modifications by the innate immune system -- Kinetic analysis of tRNA methyltransferases -- Preparation of human nuclear RNA m6A methyltransferases and demethylases and biochemical characterization of their catalytic activity -- Transcriptome-wide mapping of N6-methyladenosine by m6A-Seq -- Probing RNA modification status at single-nucleotide resolution in total RNA -- High-resolution mapping of N6-methyladenosine in transcriptome and genome using a photo-crosslinking-assisted strategy -- Pseudouridine in mRNA: incorporation, detection, and recoding -- Pseudo-Seq: genome-wide detection of pseudouridine modifications in RNA -- Pseudouridine chemical labeling and profiling -- Experimental approaches for target profiling of RNA cytosine methyltranferases -- RNA 5-methylcytosine analysis by bisulfite sequencing -- Biochemical and transcriptome-wide identification of A-to-I RNA editing sites by ICE-Seq -- Radical SAM-mediated methylation of ribosomal RNA.
- 2007 ScienceDirectGott, Jonatha M.
- pt. C-D, 2003. ScienceDirectpt. D ScienceDirectAdhya, Sankar Lal; Garges, Susan.Also available: Print – pt. C-D, 2003.
- 2005 Springer ProtocolsCarmichael, Gordon G.Detection of microRNAs and assays to monitor microRNA activities in vivo and in vitro / Marianthi Kiriakidou ... [et al.] -- High-throughput analysis of microRNA gene expression using sensitive probes / Mouldy Sioud and Øystein Røsok -- Modification of human U1 snRNA for inhibition of gene expression at the level of pre-mRNA / Peng Liu ... [et al.]. Identification of components of RNAi pathways using the tandem affinity purification method / Mikiko C. Siomi and Haruhiko Siomi -- Separation of Drosophila RNA silencing complexes by native gel electrophoresis / John W. Pham and Erik J. Sontheimer -- Preparation and analysis of drosha / Yoontae Lee and V. Narry Kim -- RNA interference in Caenorhabditis elegans / Nathaniel R. Dudley and Bob Goldstein -- Down-regulating gene expression by RNA interference in Trypanosoma brucei / Christine E. Clayton ... [et al.] -- Analysis of double-stranded RNA and small RNAs involved in RNA-mediated transcriptional gene silencing / M. Florian Mette ... [et al.] -- Strategies for the design of random siRNA libraries and the selection of anti-GFP siRNAs / Mouldy Sioud and Sébastien Wälchli -- Silencing gene expression with dicer-generated siRNA pools / Jason W. Myers and James E. Ferrell Jr. -- Inhibition of gene expression in vivo using multiplex siRNA / Sung-Suk Chae and Timothy Hla -- Gene silencing by a DNA vector based RNAi technology / Guangchao Sui and Yang Shi -- Plasmid-based RNA interference: construction of small-hairpin RNA expression vectors / Scott Q. Harper and Beverly L. Davidson -- SiRNA delivery in vivo / Mouldy Sioud -- Peptide-based strategy for siRNA delivery into mammalian cells / Federica Simeoni ... [et al.] -- Lentiviral vector delivery of siRNA and shRNA encoding genes into cultured and primary hematopoietic cells / Mingjie Li and John J. Rossi -- Exon-specific RNA interference: a tool to determine the functional relevance of proteins encoded by alternatively spliced mRNAs / Alicia M. Celotto, Joo-Won Lee, and Brenton R. Graveley -- Immunoprecipitation of microRNPs and directional cloning of microRNAs / Elisavet Maniataki, Maria Dels Angels De Planell Saguer, and Zissimos Mourelatos --
- 2010 SpringerBarciszewski, Jan; Erdmann, V. A.The key features of RNA silencing / Kuniaki Saito ... [et al.] -- Selected strategies for the delivery of siRNA in vitro and in vivo / Sandra D. Laufer ... [et al.] -- RNAi suppression and its application / Xiaoping Yi, Rui Lu -- Strategies to prevent siRNA-triggered cellular toxicity / Matthias Bauer -- RNAi in malignant brain tumors: relevance to molecular and translational research / Mitsutoshi Nakada ... [et al.] -- Silencing Huntington's disease gene with RNAi / Yu Zhang, Robert M. Friedlander -- Application of Dicer-substrate siRNA in pain research / Philippe Sarret ... [et al.] -- RNAi treatment of HIV-1 infection / Karin J. von Eije, Ben Berkhout -- Application of RNA interference to treat conditions associated with dysregulation of transient receptor potential vanilloid 1 channel / Vickram Ramkumar ... [et al.] -- Harnessing RNAi-based functional genomics to unravel the molecular complexity underlying skin pigment variation / Hsiang Ho ... [et al.] -- mRNA structure and its effects on posttranscriptional gene silencing / Stephen I. Rudnick, Veenu Aishwarya, Alan M. Gewirtz -- Antisense RNA-mediated regulation of the p53 tumor suppressor / Marianne Farnebo, Klas G. Wiman -- Antisense oligonucleotides: insights from preclinical studies and clinical trials / Doreen Kunze, Kai Kraemer, Susanne Fuessel -- What can the new hammerhead ribozyme structures teach us about design? / William G. Scott -- microRNA biogenesis and its impact on RNA interference / Stefanie Grund, Sven Diederichs -- MicroRNAs in epithelial antimicrobial immunity / Jun Liu ... [et al.] -- Emerging roles of long noncoding RNAs in gene expression and intracellular organization / Tetsuro Hirose -- Noncoding RNAs as therapeutic targets / Maciej Szymański, Jan Barciszewski -- Noncoding RNAs at H19/IGF2 locus: role in imprinting, gene expression, and associated pathologies / Nahalie Berteaux, Nathalie Spruyt, Eric Adriaenssens.
- 2008 ScienceDirectArraiano, Cecilia; Maquat, Lynne.Also available: Print – 2008
- 2008 ScienceDirectKiledjian, Megerditch; Maquat, Lynne.Also available: Print – 2008
- Atkins, John F.; Cech, Thomas R.; Gesteland, Raymond F.PrintLane Catalog Record
- 2008 Springer ProtocolsBarik, Sailen.
- 2011 Springer ProtocolsKodama, Hiroaki; Komamine, Atsushi.Overview of plant RNAi / Yuichiro Watanabe -- Caveat of RNAi in plants : the off-target effect / Muthappa Senthil-Kumar and Kirankumar S. Mysore -- Plant gateway vectors for RNAi as a tool for functional genomic studies / Toshiya Muranaka -- Heat-inducible RNAi for gene functional analysis in plants / Frederic Masclaux and Jean-Philippe Galaud -- Gene function analysis by artificial microRNAs in Physcomitrella patens / Basel Khraiwesh [and others] -- Virus-induced gene silencing in ornamental plants / Cai-Zhong Jiang, Jen-Chih Chen, and Michael Reid -- Local RNA silencing mediated by agroinfiltration / Jutta Maria Helm, Elena Dadami, and Kriton Kalantidis -- Direct transfer of synthetic double-stranded RNA into protoplasts of Arabidopsis thaliana / Ha-il Jung, Zhiyang Zhai, and Olena K. Vatamaniuk -- Detection of long and short double-stranded RNAs / Toshiyuki Fukuhara [and others] -- Quantitative stem-loop RT-PCR for detection of microRNAs / Erika Varkonyi-Gasic and Roger P. Hellens -- Large-scale sequencing of plant small RNAs / William P. Donovan, Yuanji Zhang, and Miya D. Howell -- Computational prediction of plant miRNA targets / Ying-Hsuan Sun [and others] -- Bisulfite sequencing for cytosine-methylation analysis in plants / Nazmul Haque and Masamichi Nishiguchi -- Using nuclear run-on transcription assays in RNAi studies / Basel Khraiwesh -- Proteomic analysis of RNA interference induced knockdown plant / Sang Yeol Lee and Kyun Oh Lee -- Comparative analysis of phosphoprotein expression using 2D-DIGE / Tomoya Asano and Takumi Nishiuchi.
- 2011 CRCnetBASEGaur, Rajarshi Kumar."RNA interference (RNAi) is a system within living cells that helps to control active genes and their activity level. Two types of small RNA molecules--microRNA (miRNA) and small interfering RNA (siRNA)--are central to RNA interference. The discovery of RNAi was preceded first by observations of transcriptional inhibition by antisense RNA expressed in transgenic plants and more directly by reports of unexpected outcomes in experiments performed by plant scientists in the U.S. and The Netherlands in the early 1990s. RNAi technology are used for large-scale screens that systematically shut down each gene in the cell, which can help identify the components necessary for a particular cellular process or an event such as cell division. Exploitation of the pathway is also a promising tool in biotechnology and medicine. This book reviews the selective and robust effect of RNAi on gene expression which makes it a valuable research tool, both in cell culture and in living organisms because synthetic dsRNA introduced into cells can induce suppression of specific genes of interest. This book will introduce new technology in the study of RNA interference in microorganisms, plants and animals."--Provided by publisher.
- 2015 Springer ProtocolsSchmidt, Frank J.Identifying RNA recombination events and non-covalent RNA-RNA interactions with the molecular colony technique / Helena V. Chetverina and Alexander B. Chetverin -- RNA-directed recombination of RNA in vitro / Niles Lehman, Nilesh Vaidya, and Jessica A.M. Yeates -- RNA-RNA SELEX / B. Cho -- Identification of antisense RNA stem-loops that inhibit RNA-protein interactions using a bacterial reporter system / Kazuo Harada -- Transactivation of large ribozymes / Matthew B. Martin, Thomas L. Leeper, and Frank J. Schmidt -- Native purification and labeling of RNA for single molecule fluorescence studies / Arlie J. Rinaldi, Krishna C. Suddala, and Nils G. Walter -- Single molecule studies of RNA-RNA interactions / Dongmei Yu, Peiwu Qin, and Peter V. Cornish -- Modification interference analysis of the ribosome / Simpson Joseph -- Assessing intermolecular RNA:RNA interactions within a ribonucleoprotein complex using heavy metal cleavage mapping / Keith T. Gagnon and E. Stuart Maxwell -- Electrophoretic mobility shift assays : analysis of tRNA binding to the T box riboswitch antiterminator RNA / R. Anupam, S. Zhou, and J.V. Hines -- Fluorescence anisotropy : analysis of tRNA binding to the T box riboswitch antiterminator RNA / S. Zhou, R. Anupam, and J.V. Hines -- Electrophoretic mobility shift assay of RNA-RNA complexes / Geunu Bak [and three others] -- Structural studies of a double-stranded RNA from trypanosome RNA editing by small-angle X-ray scattering / Angela Criswell and Blaine H.M. Mooers -- Fusion RNAs in crystallographic studies of double-stranded RNA from trypanosome RNA editing / Blaine H.M. Mooers.
- 2011 SpringerOliveira, António Costa de; Varshney, R. K.With the predicted increase of the human population and the subsequent need for larger food supplies, root health in crop plants could play a major role in providing sustainable highly productive crops that can cope with global climate changes. While the essentiality of roots and their relation to plant performance is broadly recognized, less is known about their role in plant growth and development. "Root Genomics" examines how various new genomic technologies are rapidly being applied to the study of roots, including high-throughput sequencing and genotyping, Tilling, transcription.
- 2002 Springer ProtocolsO'Connell, Joe.RT-PCR in biomedicine. Opportunities arising from the new accessibility of mrna / J. O'Connell -- The basics of RT-PCR. Some practical considerations / J. O'Connell -- Using the quantitative competitive RT-PCR technique to analyze minute amounts of different mrnas in small tissue samples / S. Greber-Platzer [and others] -- Detection of mrna expression and alternative splicing in a single cell / T. Kumazaki -- Nested RT-PCR. Sensitivity controls are essential to determine the biological significance of detected mrna / T. Goode [and others] -- Quantitative RT-PCR. A review of current methodologies / C. Joyce -- Rapid development of a quantitative-competitive (qc) RT-PCR assay using a composite primer approach / J. O'Connell [and others] -- Quantitation of gene expression by RT-PCR and hplc analysis of pcr products / F. Bachmair, C.G. Huber and G. Daxenbichler -- Time-resolved fluorometric detection of cytokine mrnas amplified by RT-PCR / K. Nieminen [and others] -- Mimic-based RT-PCR quantitation of substance p mrna in human mononuclear phagocytes and lymphocytes / J.P. Lai, S.D. Douglas and W.Z. Ho -- Detection and quantification of the hepatitis c viral genome / L.J. Fanning -- Semi-quantitative detection of hepatitis c virus rna by "real-time" RT-PCR / J.F. Schlaak -- RT-PCR for the assessment of genetically heterogenous populations of the hepatitis c virus / B. Mullan [and others] -- In situ immuno-pcr. A newly developed method for highly sensitive antigen detection in situ / Y. Cao -- RT-PCR from laser-capture microdissected samples / T. Crnogorac-Jurcevic, T.O. Nielsen and N.R. Lemoine -- Mycobacterium paratuberculosis detected by nested pcr in intestinal granulomas isolated by lcm in cases of crohn's disease / P. Ryan [and others] -- RT-PCR-based approaches to generate probes for mrna detection by in situ hybridization / J. O'Connell -- Amplified rna for gene array hybridizations / V.I. Shustova and S.J. Meltzer -- Semi-quantitative determination of differential gene expression in primary tumors and matched metastases by RT-PCR. Comparison with other methods / B. Mann and C. Hanski -- Detection of single nucleotide polymorphisms using a non-isotopic rnase cleavage assay / F. Waldron-Lynch [and others] -- Detection of clonally expanded t-cells by RT-PCR-sscp and nucleotide sequencing of t-cell receptor beta-cdr3 regions / M.S. Kurokawa, K. Nishioka and T. Kato -- Generation of scfv from a phage display mini-library derived from tumor-infiltrating b-cells / N. Gruel [and others] -- Generation of murine scfv intrabodies from b-cell hybridomas / C.H. Nam, S. Moutel and J.L. Teillaud -- Quantitation of mrna levels by RT-PCR in cells purified by facs. Application to peripheral cannabinoid receptors in leukocyte subsets / J. Marchand and P. Carayon -- Detection of anti-sense rna transcripts by anti-sense RT-PCR / M.C. Yeung and A.S. Lau -- RT-PCR in cdna library construction / V. Healy -- An RT-PCR-based protocol for the rapid generation of large, representative cdna libraries for expression screening / J. O'Connell.
- 2003. NLMKoonin, Eugene V.; Galperin, Michael Y.
- 2009 SpringerChao, Kun-Mao; Zhang, Louxin.
- 2008 Springer ProtocolsNielsen, Kåre Lehmann.SAGE and LongSAGE / Annabeth Laursen Høgh and Kåre Lehmann Nielsen -- Robust-LongSAGE (RL-SAGE) : an improved LongSAGE method for high-throughput transcriptome analysis / Malali Gowda and Guo-Liang Wang -- aRNA LongSAGE : SAGE with antisense RNA / Anna M. Heidenblut -- SuperSAGE / Hideo Matsumura ... [et al.] -- Low-cost-medium throughput Sanger dideoxy sequencing / Kåre Lehmann Nielsen -- DeepSAGE : higher sensitivity and multiplexing of samples using a simpler experimental protocol / Kåre Lehmann Nielsen -- High-resolution, genome-wide mapping of chromatin modifications by GMAT / Tae-Young Roh and Keji Zhao -- 5'- and 3'-RACEfrom LongSAGE tags / Kåre Lehmann Nielsen -- Extraction and annotation of SAGE tags using sequence quality values / Jeppe Emmersen -- Correction of technology-related artifacts in serial analysis of gene expression / Viatcheslav R. Akmaev -- Duplicate ditag analysis in LongSAGE / Jeppe Emmersen -- Statistical comparison of two or more SAGE libraries : one tag at a time / Gerben J. Schaaf ... [et al.] -- Scaling of gene expression data allowing the comparison of different gene expression platforms / Fred van Ruissen ... [et al.] -- Clustering analysis of SAGE transcription profiles using a Poisson approach / Haiyan Huang, Li Cai, and Wing H. Wong -- Identifying nonspecific SAGE tags by context of gene expression / Xijin Ge and San Ming Wang.
- 2007 Springer ProtocolsThornhill, Alan.Noninvasive metabolic assessment of single cells / David K. Gardner -- Laser capture microdissection for analysis of single cells / Nobuki Nakamura ... [et al.] -- Fluorescence in situ hybridization (FISH) on single cells (sex determination and chromosome rearrangements) / Paul N. Scriven and Caroline Mackie Ogilvie -- Single cell PCR for PGD : methods, strategies, and limitations / Karen Sermon and Martine De Rycke -- Real-time quantitative PCR measurement of male fetal DNA in maternal plasma / Bernhard Zimmermann ... [et al.] -- Cell-free fetal DNA plasma extraction and real-time PCR quantification / Jill L. Maron, Kirby L. Johnson, and Diana W. Bianchi -- LATE-PCR and allied technologies : real-time detection strategies for rapid, reliable diagnosis from single cells / Kenneth E. Pierce and Lawrence J. Wangh -- Efficient isothermal amplification of the entire genome from single cells / Karen V. Schowalter, Jolene R. Fredrickson, and Alan R Thornhill -- Comparative genomic hybridization on single cells / Lucille Voullaire and Leeanda Wilton -- Generation of amplified RNAs and cDNA libraries from single mammalian cells / James Adjaye -- Real-time PCR to measure gene expression in single cells / Dagan Wells -- Gender determination and detection of aneuploidy in single cells using DNA array-based comparative genomic hybridization (array CGH) / Dong Gui Hui, Xin Yuan Guan, and Nicole Hussey -- Microarray technology for mutation analysis of low template DNA samples / Chelsea Salvado and David Cram.
- 2002 Springer ProtocolsKwok, Pui-Yan.SNPs: why do we care? / Lisa D. Brooks -- Denaturing high-performance liquid chromatography / Andreas Premstaller and Peter J. Oefner -- SNP detection and allele frequency determination by SSCP / Tomoko Tahira [and others] -- Conformation-sensitive gel electrophoresis / Arupa Ganguly -- Detection of mutations in DNA by solid-phase chemical cleavage method: a simplified assay / Chinh T. Bui [and others] -- SNP discovery by direct DNA sequencing / Pui-Yan Kwok and Shenghui Duan -- Computational SNP discovery in DNA sequence data / Gabor T. Marth -- Genotyping SNPs with molecular beacons / Salvatore A.E. Marras, Fred Russell Kramer, and Sanjay Tyagi -- SNP genotyping by the 51-nuclease reaction / Kenneth J. Livak -- Genotyping SNPs by minisequencing primer extension using oligonucliotide microarrays / Katarina Lindroos, Ulrika Liljedahl, and Ann-Christine Syvänen -- Quantitative analysis of SNPs in pooled DNA samples by solid-phase minisequencing / Charlotta Olsson, Ulrika Liljedahl, and Ann-Christine Syvänen -- Homogeneous primer extension assay with fluorescence polarization detection / Tony M. Hsu and Pui-Yan Kwok -- Pyrosequencing for SNP genotyping / Mostafa Ronaghi -- Homogeneous allele-specific PCR in SNP genotyping / Søren Germer and Russell Higuchi -- Oligonucleotide ligation assay / Jonas Jarvius, Mats Nilsson, and Ulf Landegren -- Invader assay for SNP genotyping / Victor Lyamichev and Bruce Neri -- MALDI-TOF mass spectrometry-based SNP genotyping / Niels Storm [and others].
- 2016 Springer ProtocolsRossi, John J.; Shum, Kato.Synthesis and conjugation of small interfering ribonucleic neutral SiRNNs / Alexander S. Hamil and Steven F. Dowdy - - Liver-targeted SiRNA delivery using biodegradable poly(amide) polymer conjugates / Stephanie E. Barrett and Erin N. Guidry -- PepFect6 mediated SiRNA delivery into organotypic cultures / Suvarna Dash-Wagh, Ülo Langel, and Mats Ulfendahl -- Highly efficient SiRNA delivery mediated by cationic helical polypeptides and polypeptide-based nanosystems / Lichen Yin, Nan Zheng, and Jianjun Cheng -- Disulfide-bridged cleavable PEGylation of poly- L -lysine for SiRNA delivery / Min Tang ... [et al.] -- Preparation of a cyclic RGD : modified liposomal SiRNA formulation for use in active targeting to tumor and tumor endothelial cells / Yu Sakurai, Tomoya Hada, and Hideyoshi Harashima -- Multifunctional envelope-type nano device containing a pH-sensitive cationic lipid for efficient delivery of short interfering RNA to hepatocytes in vivo / Yusuke Sato, Hideyoshi Harashima, and Michinori Kohara -- Bioreducible poly (beta-amino ester)s for intracellular delivery of SiRNA / Kristen L. Kozielski and Jordan J. Green -- Preparation of polyion complex micelles using block copolymers for SiRNA delivery / Hyun Jin Kim ... [et al.] -- Delivery of small interfering RNAs to cells via exosomes / Jessica Wahlgren ... [et al.] -- Dendrimer nanovectors for SiRNA delivery / Xiaoxuan Liu and Ling Peng -- Chitosan nanoparticles for SiRNA delivery in vitro / Héloïse Ragelle ... [et al.] -- Non-covalently functionalized of single-walled carbon nanotubes by DSPE-PEG-PEI for SiRNA delivery / King Sun Siu ... [et al.] -- SiRNA in vivo-targeted delivery to murine dendritic cells by oral administration of recombinant yeast / Kun Xu ... [et al.] -- TLR9-targeted SiRNA delivery in vivo / Dewan Md Sakib Hossain ... [et al.] -- Aptamer-MiRNA conjugates for cancer cell-targeted delivery / Carla L. Esposito, Silvia Catuogno, and Vittorio de Franciscis -- Method for confirming cytoplasmic delivery of RNA aptamers / David D. Dickey ... [et al.] -- Hapten-binding bispecific antibodies for the targeted delivery of SiRNA and SiRNA-containing nanoparticles / Irmgard S. Thorey ... [et al.] -- Stable delivery of CCR5-directed shRNA into human primary peripheral blood mononuclear cells and hematopoietic stem/progenitor cells via a lentiviral vector / Saki Shimizu, Swati Seth Yadav, and Dong Sung An -- Hepatic delivery of artificial micro RNAs using helper- dependent adenoviral vectors / Carol Crowther, Betty Mowa, and Patrick Arbuthnot -- Intravascular AAV9 administration for delivering RNA silencing constructs to the CNS and periphery / Brett D. Dufour and Jodi L. McBride -- Efficient gene suppression in dorsal root ganglia and spinal cord using adeno-associated virus vectors encoding short-hairpin RNA / Mitsuhiro Enomoto ... [et al.] -- Synthetic SiRNA delivery : progress and prospects / Thomas C. Roberts ... [et al.].
- 2013 Springer ProtocolsHirschey, Matthew D.Introduction: sirtuins in aging and diseases / Leonard Guarente -- Sirtuins in yeast: phenotypes and tools / Scott Tsuchiyama [and four others] -- C. elegans sirtuins / Mohan Viswanathan and Heidi A. Tissenbaum -- Genetic and biochemical tools for investigating sirtuin function in Drosophila melanogaster / Jason G. Wood, Rachel Whitaker, and Stephen L. Helfand -- Generating mammalian sirtuin tools for protein-interaction analysis / Kathleen A. Hershberger [and three others] -- Mass spectrometry-based detection of protein acetylation / Yu Li [and three others] -- SILAC-based quantification of Sirt1-responsive lysine acetylome / Yue Chen, Gozde Colak, and Yingming Zhao -- Targeted quantitation of acetylated lysine peptides by selected reaction monitoring mass spectrometry / Matthew J. Rardin, Jason M. Held, and Bradford W. Gibson -- Identification of deacetylase substrates with the biotin switch approach / J. Will Thompson, Alex Robeson, and Joshua L. Andersen -- Assaying chromatin sirtuins / Lei Zhong [and four others] -- Measurement of sirtuin enzyme activity using a substrate-agnostic fluorometric nicotinamide assay / Basil P. Hubbard and David A. Sinclair -- Detecting sirtuin-catalyzed deacylation reactions using 32P-labeled NAD and thin-layer chromatography / Anita Zhu, Xiaoyang Su, and Hening Lin -- Chemical acetylation and deacetylation / Kristofer S. Fritz -- Accurate measurement of nicotinamide adenine dinucleotide (NAD+) with high-performance liquid chromatography / Jun Yoshino and Shin-ichiro Imai -- In vivo measurement of the acetylation state of sirtuin substrates as a proxy for sirtuin activity / John Dominy, Pere Puigserver, and Carles Cantó -- Oxygen flux analysis to understand the biological function of sirtuins / Dongning Wang [and three others] -- The emerging links between sirtuins and autophagy / In Hye Lee, Jeanho Yun, and Toren Finkel -- Methods to study the role of sirtuins in genome stability / Paloma Martínez-Redondo and Alejandro Vaquero -- Circadian measurements of sirtuin biology / Kathryn Moynihan Ramsey [and five others] -- Utilizing calorie restriction to evaluate the role of sirtuins in healthspan and lifespan of mice / Jessica Curtis and Rafael de Cabo.
- 2015 Springer ProtocolsRederstorff, Mathieu.Small non-coding RNAs : a quick look in the rearview mirror / Guillaume Clerget, Yoann Abel, and Mathieu Rederstorff -- Alcoholic precipitation of small non-coding RNAs / Guillaume Clerget, Valérie Bourguignon-Igel, and Mathieu Rederstorff -- Quantification and quality control of a small non-coding RNA preparation / Virginie Marchand and Christiane Branlant -- Impact of RNA isolation protocols on RNA detection by Northern blotting / Katrin Damm [and seven others] -- Improved Northern blot detection of small RNAs using EDC crosslinking and DNA/LNA probes / Katrin Damm [and seven others] -- Direct cloning of double-stranded RNAs / Manli Shen [and three others] -- Detection and labeling of small non-coding RNAs by splinted ligation / Gabrielle Bourgeois [and three others] -- Fluorescence in situ hybridization of small non-coding RNAs / Valentin Vautrot [and three others] -- RT-qPCR-based quantification of small non-coding RNAs / Fjoralba Zeka, Pieter Mestdagh, and Jo Vandesompele -- Stem-loop RT-PCR based quantification of small non-coding RNAs / Véronique Salone and Mathieu Rederstorff -- miR-RACE : an effective approach to accurately determine the sequence of computationally identified miRNAs / Chen Wang and Jinggui Fang -- Probing small non-coding RNAs structures / Jean-Vincent Philippe [and three others] -- cDNA library generation for the analysis of small RNAs by high-throughput sequencing / Jennifer Gebetsberger, Roger Fricker, and Norbert Polacek -- CLIP-Seq to discover transcriptome-wide imprinting of RNA binding proteins in living cells / Jérôme Saulière and Hervé Le Hir -- Microarray analysis of small non-coding RNAs / Michael Karbiener and Marcel Scheideler -- RML-RACE, PPM-RACE, and qRT-PCR : an integrated strategy to accurately validate miRNA target genes / Chen Wang and Jinggui Fang -- Dual luciferase gene reporter assays to study miRNA function / Thomas Clément, Véronique Salone, and Mathieu Rederstorff -- Gene expression knockdown by transfection of siRNAs into mammalian cells / Yoann Abel and Mathieu Rederstorff -- Efficient and selective knockdown of small non-coding RNAs / Xue-Hai Liang, Wen Shen, and Stanley T. Crooke -- Cell-SELEX : in vitro selection of synthetic small specific ligands / Helena Dickinson [and three others] -- Small non-coding RNAs and aptamers in diagnostics and therapeutics / Marissa Leonard, Yijuan Zhang, and Xiaoting Zhang.
- 2006 SpringerHammann, Christian; Nellen, Wolfgang.
- 2006 SpringerSutovsky, Peter.Nuclear remodeling and nuclear reprogramming for making transgenic pigs by nuclear transfer / Randall S. Prather -- Somatic cell nuclei in cloning : strangers traveling in a foreign land / Keith E. Latham, Shaorong Gao, and Zhiming Han -- Cloning cattle : the methods in the madness / Bjørn Oback and David N. Wells -- Centrosome inheritance after fertilization and nuclear transfer in mammals / Qing-Yuan Sun and Heide Schatten -- Developmental, behavioral, and physiological phenotype of cloned mice / Kellie L.K. Tamashiro ... [et al.] -- Nucleolar remodeling in nuclear transfer embryos / Jozef Laurincik and Poul Maddox-Hyttel -- Somatic cell nuclear transfer (SCNT) in mammals : the cytoplast and its reprogramming activities / Josef Fulka, Jr. and Helena Fulka -- Mitochondrial DNA inheritance after SCNT / Stefan Hiendleder -- Activation of fertilized and nuclear transfer eggs / Christopher Malcuit and Rafael A. Fissore.Also available: Print – 2006
- 2014 CRCnetBASEAyyanathan, Kasirajan.This new volume on gene expression and epigenetics discusses environmental effects related to specific gene expression. The book also shows methods for bioinformatic analysis of the epigenome. The book is broken into two sections: the first looks at eukaryotic DNA methylation and the second addresses how to integrate genomic medicine into clinical practice. The book includes chapters on these topics: Gene expression in colon cancer tissue Epigenetics in human acute kidney injury Embryologically relevant candidate genes in MRKH patients DNA methylation in common skeletal disorders Causal relat.
- 2013 Springer ProtocolsGaile, Daniel; Klebanov, L. B.; Yakovlev, Andrej Yu.What statisticians should know about microarray gene expression technology / Stephen Welle -- Where statistics and molecular microarray experiments biology meet / Diana M. Kelmansky -- Multiple hypothesis testing : a methodological overview / Anthony Almudevar -- Gene selection with the [delta]-sequence method / Xing Qiu and Lev Klebanov -- Using of normalizations for gene expression analysis / Peter Bubeliny -- Constructing multivariate prognostic gene signatures with censored survival data / Derick R. Peterson -- Clustering of gene expression data via normal mixture models / G.J. McLachlan [and others] -- Network-based analysis of multivariate gene expression data / Wei Zhi [and others] -- Genomic outlier detection in high-throughput data analysis / Debashis Ghosh -- Impact of experimental noise and annotation imprecision on data quality in microarray experiments / Andreas Scherer, Manhong Dai, and Fan Meng -- Aggregation effect in microarray data analysis / Linlin Chen, Anthony Almudevar, and Lev Klebanov -- Test for normality of the gene expression data / Bobosharif Shokirov.
- 2007 SpringerSiegmund, David; Yakir, Benjamin.
- 2011 Springer ProtocolsWilliams, James A.Bacterial genome reengineering / Jindan Zhou and Kenneth E. Rudd -- Targeted chromosomal gene knockout using PCR fragments / Kenan C. Murphy -- Scarless chromosomal gene knockout methods / Bong Hyun Sung, Jun Hyoung Lee, and Sun Chang Kim -- Random chromosomal gene disruption in vivo using transposomes / Les M. Hoffman -- Genome engineering using targeted oligonucleotide libraries and functional selection / Elie J. Diner, Fernando Garza-Sanchez, and Christopher S. Hayes -- Microarray-based genetic footprinting strategy to identify strain improvement genes after competitive selection of transposon libraries / Alison K. Hottes and Saeed Tavazoie -- Optimization of synthetic operons using libraries of post-transcriptional regulatory elements / Daniel E. Agnew and Brian F. Pfleger -- Marker-free chromosomal expression of foreign and native genes in Escherichia coli / Chung-Jen Chiang [and others] -- Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli / Mohan Babu [and others] -- Assembling new Escherichia coli strains by transduction using phage P1 / Sean D. Moore -- Yeast bioinformatics and strain engineering resources / Audrey L. Atkin -- Delete and repeat : a comprehensive toolkit for sequential gene knockout in the budding yeast Saccharomyces cerevisiae / Johannes H. Hegemann and Sven Boris Heick -- Genome-wide transposon mutagenesis in Saccharomyces cerevisiae and Candida albicans / Tao Xu, Nike Bharucha, and Anuj Kumar -- Signature-tagged mutagenesis to characterize genes through competitive selection of bar-coded genome libraries / Julia Oh and Corey Nislow -- Global strain engineering by mutant transcription factors / Amanda M. Lanza and Hal S. Alper -- Genomic promoter replacement cassettes to alter gene expression in the yeast Saccharomyces cerevisiae / Andreas Kaufmann and Michael Knop -- Microbial genome analysis and comparisons : web-based protocols and resources / Medha Bhagwat and Arvind A. Bhagwat -- Plasmid artificial modification : a novel method for efficient DNA transfer into bacteria / Tohru Suzuki and Kazumasa Yasui -- Broad-host-range plasmid vectors for gene expression in bacteria / Rahmi Lale, Trygve Brautaset, and Svein Valla -- Simple method for Introducing marker-free deletions in the Bacillus subtilis genome / Takuya Morimoto [and others] -- Transposon-mediated random mutagenesis of Bacillus subtilis / Adam C. Wilson and Hendrik Szurmant -- Integrative food grade expression system for lactic acid bacteria / Grace L. Douglas, Yong Jun Goh, and Todd R. Klaenhammer -- Clostron-mediated engineering of Clostridium / Sarah A. Kuehne [and others] -- High-throughput transposon mutagenesis of Corynebacterium glutamicum / Nobuaki Suzuki, Masayuki Inui, and Hideaki Yukawa -- Mini-mu transposon mutagenesis of ethanologenic Zymomonas mobilis / Katherine M. Pappas -- Engineering thermoacidophilic archaea using linear DNA recombination / Yukari Maezato, Karl Dana, and Paul Blum -- Targeted gene disruption in koji mold Aspergillus oryzae / Jun-ichi Maruyama and Katsuhiko Kitamoto -- Selectable and inheritable gene silencing through RNA interference in the unicellular alga Chlamydomonas reinhardtii / Karin van Dijk and Nandita Sarkar.
- 2013 SpringerMittelman, David A.1. Stress-induced mutagenesis in bacteria / Ivan Matic -- 2. Mutagenesis associated with repair of DNA double-strand breaks under stress / Chandan Shee, P.J. Hastings, and Suman M. Rosenberg -- 3. Transcription-mediated mutagenic processes / Eduardo Robleto, Holly A. Martin, Carmen Vallin, Mario Pedraza-Reyes and Ronald Yasbin -- 4. Transposon mutagenesis in disease, drug discovery, and bacterial evolution / Zhongge Zhang, Jing Wang, Maksim A. Shlykov, and Milton H. Saier, Jr. -- 5. Hsp90 as a capacitor of both genetic and epigenetic changes in the genome during cancer progression and evolution / Xiangyi Lu, Luan Wang, Vincent E. Sollars, Mark D. Garfinkel, and Douglas M. Ruden -- 6. Inheritance of stress-induced epigenetic changes mediated by the ATF-2 family of transcription factors / Ki-Hyeon Seong, Toshio Maekawa and Shunsuke Ishii -- 7. Microsatellite repeats: canaries in the coalmine / Nimrat Chatterjee, Beatriz A. Santillan and John H. Wilson -- 8. Genetic instability induced by hypoxic stress / Susan E. Scanlon and Peter M. Glazer -- 9. Radiation-induced delayed genome instability and hypermutation in mammalian cells / Christopher P. Allen, Akira Fujimori, Ryuichi Okayasu and Jac A. Nickoloff -- 10. Radiation-induced bystander effects and stress-induced mutagenesis / Carmel Mothersill and Colin Seymour -- 11. Stress induced mutagenesis, genetic diversification, and cell survival via anastais, the reversal of late stage apoptosis / Ho Lam Tang, Ho Man Tang and Denise J. Mitchell -- 12. The transgenerational effects of parental exposure to mutagens in mammals / Yuri E. Dubrova -- 13. Revisiting mutagenesis in the age of High-throughput sequencing / Subhajyoti De and R. Matthew Ward.
- 2005 Springer ProtocolsRead, Simon J.; Virley, David.Introduction to stroke genomics / Simon J. Read and Frank C. Barone -- Choice, methodology, and characterization of focal ischemic stroke models: the search for clinical relevance / David Virley -- Mutant animal models of stroke and gene expression: the stroke-prone spontaneously hypertensive rat / Hilary V. O. Carswell ... [et al.] -- Gene therapy in neurological disease / Midori A. Yenari and Robert M. Sapolsky -- Stem cell transplantation after middle cerebral artery occlusion / Paul Stroemer and Helen Hodges -- Endogenous brain protection: models, gene expression, and mechanisms / Frank C. Barone -- Production of transgenic and mutant mouse models / Alex Harper -- 3-nitropropionic acid model of metabolic stress: assessment by magnetic resonance imaging / Toby John Roberts -- Practicalities of genetic studies in human stroke / Ahamad Hassan and Hugh S. Markus -- Evaluation of the interactions of common genetic mutations in stroke / Zoltán Szolnoki -- Technologies of disease-related gene discovery using preclinical models of stroke / Xinkang Wang -- Quantitative analysis of gene transcription in stroke models using real-time RT-PCR / David C. Harrison and Brian C. Bond -- Effective analysis of genomic data / Paul R. Nelson, Andrew B. Goulter, and Richard J. Davis -- Bioinformatic approaches to assigning protein function from novel sequence data / David Michalovich and Richard Fagan -- Pragmatic target discovery from novel gene to functionally defined drug target: the interleukin-1 story / Stuart McRae Allen.
- 2007 SpringerBastolla, U.Modeling conformational flexibility and evolution of structure : RNA as an example / P. Schuster and P.F. Stadler -- Gene3D and understanding proteome evolution / J.G. Ranea ... [et al.] -- The evolution of the globins : we thought we understood it / A.M. Lesk -- The structurally constrained neutral model of protein evolution / U. Bastolla ... [et al.] -- Towards unifying protein evolution theory / N.V. Dokholyan and E.I. Shakhnovich -- A twenty-first century view of evolution : genome system architecture, repetitive DNA, and natural genetic engineering / J.A. Shapiro -- Genomic changes in bacteria : from free-living to endosymbiotic life / F.J. Silva ... [et al.] -- Molecular phylogenetics : mathematical framework and unsolved problems / X. Xia -- Phylogenetics and computational biology of multigene families / P. Liò, M. Brilli and R. Fani -- SeqinR 1.0-2 : a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis / D. Charif and J.R. Lobry -- Evolutionary genomics of gene expression / I.K. Jordan and L. Mariño-Ramírez -- From biophysics to evolutionary genetics : statistical aspects of gene regulation / M. Lässig -- Drift and selection in evolving interacting systems / T. Ohta -- Adaptation in simple and complex fitness landscapes / K. Jain and J. Krug -- Genetic variability in RNA viruses : consequences in epidemiology and in the development of new strategies for the extinction of infectivity / E. Lázaro.
- 2014 Springer ProtocolsChen, Yu Wai.1. DisMeta : a meta server for construct design and optimization / Yuanpeng Janet Huang, Thomas B. Acton, and Gaetano T. Montelione -- 2. Stable expression clones and auto-induction for protein production in E. coli / F. William Studier -- 3. High-throughput expression screening and purification of recombinant proteins in E. coli / Natalie J. Saez and Renaud Vincentelli -- 4. Medium-throughput production of recombinant human proteins : ligation-independent cloning / Claire Strain-Damerell, Pravin Mahajam, Opher Gileadi and Nicola A. Burgess-Brown -- 5. Medium-throughput production of recombinant human proteins : protein production in E. coli / Nicola A. Burgess-Brown, Pravin Mahajan, Claire Strain-Damerell, Opher Gileadi and Susanne Gräslund -- 6. Medium-throughput production of recombinant human proteins : protein production in insect cells / Pravin Mahajan , Claire Strain-Damerell, Opher Gileadi and Nicola A. Burgess-Brown -- 7. OmniBac : universal multigene transfer plasmids for baculovirus expression vectors systems / Deepak B. Thimiri Govinda Raj, Lakshmi S. Vijayachandran, and Imre Berger -- 8. Multiprotein complex production in insect cells by using polyproteins / Yan Nie, Itxaso Bellon-Echeverria, Simon Trowitzch, Christoph Bieniossek and Imre Berger -- 9. Expression screening in mammalian suspension cells / Susan D. Chapple and Michael R. Dyson -- 10. Cell-free expression of protein complexes for structural biology / Takaho Terada, Takehi Murata, Mikako Shirouzu and Shigeyuki Yokoyama -- 11. Cell-free protein synthesis for functional and structural studies / Shin-ichi Makino, Emily T. Beebe, John L. Markley and Brian G. Fox -- 13. Insoluble protein purification with sarkosyl : facts and precautions / Ben Chisnall, Courtney Johnson, Yavuz Kulaberoglu and Yu Wai Chen -- 13. Estimation of crystallization likelihood through a fluorimetric thermal stability assay / Vincent Mariaule, Florine Dupeux, and José A. Márquez -- 14. CrystalDirect : a novel approach for automated crystal harvesting based on photoablation of thin films / José A. Márquez and Florent Cipriani -- 15. Methods to refine macromolecular structures in cases of severe diffraction anisotropy / Michael R. Sawaya -- 16. Applications of NMR-based PRE and EPR-based DEER spectroscopy to homodimer chain exchange characterization and structure determination / Yunhuang Yang, Theresa A. Ramelot, Shuisong Ni, Robert M. McCarrick and Michael A. Kennedy -- 17. Cost-effective protocol for the parallel production of libraries of 13CH3-specifically labeled mutants for NMR studies of high molecular weight proteins / Elodie Crublet, Rime Kerfah, Guillaume Mas, Marjolaine Noirclerc-Savoye, Violaine Lantez, Thierry Vernet and Jerome Boisbouvier -- 18. High-throughput SAXS for the characterization of biomolecules in solution : a practical approach / Kevin N. Dyer, Michael Hammel, Robert P. Rambo, Susan E. Tsutakawa, Ivan Rodic, Scott Classen, John A. Tainer and Greg L. Hura -- 19. Measuring spatial restraints on native protein complexes using isotope-tagged chemical cross-linking and mass spectrometry / Franz Herzog -- 20. Modeling of proteins and their assemblies with the integrative modeling platform / Benjamin Webb, Keren Lasker, Javier Velázquez-Muriel, Dina Schneidman-Duhovny, Riccardo Pellarin, Massimiliano Bonomi, Charles Greenberg, Barak Raveh, Elina Tjioe, Daniel Russel and Andrej Sali -- 21. Quality and validation of structures from structural genomics / Marcin J. Domagalski, Heping Zheng, Matthew D. Zimmerman, Zhigniew Dauter, Alexander Wlodawer and Wladek Minor -- 22. Navigating the global protein-protein interaction landscape using iRefWeb / Andrei L. Turinsky, Sabry Razick, Brian Turner, Ian M. Donaldson and Shoshana J. Wodak -- 23. Mespeus-a database of metal interactions with proteins / Marjorie M. Harding and Kun-Yi Hsin -- 24. High-quality macromolecular graphics on mobile devices : a quick starter's guide / Chin-Pang Benny Yiu and Yu Wai Chen.
- 2006 CRCnetBASELundstrom, Kenneth H.Bioinformatics in membrane protein analysis / Bengt Persson -- Prokaryotic membrane transport proteins / Joanne Clough ... [et al.] -- Membrane protein production strategies for structural genomics / Said Eshaghi and Par Nordlund -- Refolding of membrane proteins for large-scale production / Hans Kiefer, Thomas Ostermann, Monika Bahner -- Crystallization of membrane proteins / Alastair T. Gardiner, June Southall, and Richard J. Cogdell -- Signaling through membrane proteins / J. Robert Bostwick and Deborah S. Hartman -- Expression of membrane proteins in yeasts / Christoph Reinhart, Christoph Krettler -- Expression of functional membrane proteins in the baculovirus-insect cell system / Giel J.C.G.M. Bosman and Willem J. de Grip -- Expression of membrane proteins in mammalian cells / Kenneth Lundstrom -- Solubilization and purification of membrane proteins / Bernadette Byrne and Mika Jormakka -- Fluorescent labelling of membrane proteins in living cells / Ruud Hovius ... [et al.] -- Membrane protein NMR / Xiang-Qun (Sean) Xie -- Miniaturization of structural biology technologies--from expression to biophysical analyses / Enrique Abola, Peter Kuhn, and Raymond C. Stevens -- Electron microscopy and atomic force microscopy of reconstituted membrane proteins / Andreas Engel -- -- Structural genomics networks for membrane proteins / Kenneth Lundstrom -- Molecular modelling of membrane proteins / Slawomir Filipek and Anna Modzelewska -- Towards structural bases for GPCR ligand-binding / Sabrina A. Beretta ... [et al.].
- 2006 CRCnetBASEBurczynski, Michael E.; Rockett, John C.
- 2014 CRCnetBASEChen, Bor-Sen; Wang, Yu-Chao.Mathematical models and design specifications in synthetic gene networks -- Robust synthetic biology designs based on system dynamic models -- Robust synthetic biology designs based on network evolutionary methods -- Construction of promoter and promoter-RBS libraries for synthesis of gene networks -- Robust synthetic gene network designs based on library-search method -- Robust design of synthetic biological filter and transistor based on promoter-RBS libraries -- Communication and synchronization of a population of coupled synthetic gene networks.
- 2013 Springer ProtocolsRabinovich, Peter M.Cell engineering with synthetic messenger RNA / Peter M. Rabinovich and Sherman M. Weissman -- In vitro transcription of long RNA containing modified nucleosides / Norbert Pardi [and others] -- HPLC purification of in vitro transcribed long RNA / Drew Weissman [and others] -- Synthetic mRNAs with superior translation and stability properties / Ewa Grudzien-Nogalska [and others] -- Nonviral, cationic lipid-mediated delivery of mRNA / James G. Hecker -- Light-induced mRNA transfection / Sigurd Leinæs Bøe and Eivind Hovig -- Engineering B cells with mRNA / Jaewoo Lee, David Boczkowski, and Smita Nair -- Programming human dendritic cells with mRNA / Jaewoo Lee, David Boczkowski, and Smita Nair -- Large volume flow electroporation of mRNA : clinical scale process / Linhong Li [and others] -- Retrovirus-based mRNA transfer for transient cell manipulation / Melanie Galla, Axel Schambach, and Christopher Baum -- mRNA delivery to human dendritic cells by recombinant yeast and activation of antigen-specific memory T cells / Frank Breinig, Tanja Breinig, and Manfred J. Schmitt -- Nonviral RNA transfection to transiently modify T cells with chimeric antigen receptors for adoptive therapy / Tobias Riet [and others] -- Natural killer cell reprogramming with chimeric immune receptors / Noriko Shimasaki and Dario Campana -- Reprogramming to pluripotency and differentiation of cells with synthetic mRNA / Peizhe Wang and Jie Na -- Antitumor vaccination with synthetic mRNA : strategies for in vitro and in vivo preclinical studies / Mustafa Diken [and others] -- Mannosylated and histidylated LPR technology for vaccination with tumor antigen mRNA / Chantal Pichon and Patrick Midoux -- Analysis of survivin-specific T cells in breast cancer patients using human DCs engineered with survivin mRNA / Ozcan Met and Inge Marie Svane -- mRNA electroporation as a tool for immunomonitoring / Nathalie Cools [and others] -- mRNA PCR-based epitope chase method / Jean-Daniel Doucet, Dominique Gauchat, and Rejean Lapointe.
- Synthetic nucleic acids as inhibitors of gene expression : mechanisms, applications, and therapeutics implications2005 CRCnetBASEKhachigian, Levon Michael.
- 2007 MyiLibraryRigoutsos, Isidore; Stephanopoulos, Gregory N.
- 2015 Springer ProtocolsKühn, Ralf; Wefers, Benedikt; Wurst, Wolfgang.Xanthomonas and the TAL effectors: nature's molecular biologist -- TAL effector DNA-binding principles and specificity -- The development of TALE nucleases for biotechnology -- Online tools for TALEN design -- Assembly of customized TAL effectors through advanced ultimate system -- Engineering customized TALENs using the platinum gate TALEN kit -- Design, assembly, and characterization of TALE-based transcriptional activators and repressors -- A new approach to dissect nuclear organization: TALE-mediated genome visualization (TGV) -- TALEN-induced translocations in human cells -- Mutagenesis in newts: Protocol for Iberian ribbed newts -- Targeted mutagenesis in Bombyx mori using TALENs -- Geneknockout by targeted mutagenesis in a hemimetabolous insect, the two-spotted cricket Gryllus bimaculatus, using TALENs -- Methods for talen evaluation, use, and mutation detection in the mosquito Aedes aegypti -- Methods for TALEN-mediated genomic manipulations in drosophila -- Targeted mutagenesis in zebrafish by TALENs -- Mutagenesis in xenopus and zebrafish using TALENs -- Genome editing in mice using TALE nucleases -- Genome editing in rats using tale nucleases -- Designer nuclease-mediated generation of knockout THP1 cells.
- 2009 SpringerKishore, Uday.Macrophage pattern recognition receptors in immunity, homeostasis, and self tolerance / Subhankar Mukhopadhyay, Annette Plüddemann, and Siamon Gordon -- Pattern recognition by toll-like receptors / Stefan Bauer, Thomas Müller, and Svetlana Hamm -- Nod-like receptors : pivotal guardians of the immunological integrity of barrier organs / Philip Rosenstiel and Stefan Schreiber -- Toll-like receptors and nod-like receptors : domain architecture and cellular signalling / Tanja Langefeld ... [et al.] -- Humoral pattern recognition molecules : mannan-binding lectin and ficolins / Steffen Thiel and Mihaela Gadjeva -- Lung surfactant proteins A and D as pattern recognition proteins / Patrick Waters ... [et al.] -- Pattern recognition by pentraxins / Alok Agrawal ... [et al.] -- Target pattern recognition by complement proteins of the classical and alternative pathways / Yu-hoi Kang ... [et al.] -- Pattern recognition in phagocytic clearance of altered self / Yoshinobu Nakanishi, Peter M. Henson and Akiko Shiratsuchi -- Structural basis of pattern recognition by innate immune molecules / Eamon P. McGreal -- Lessons from the fly : pattern recognition in Drosophila melanogaster / Subhamoy Pal and Louisa P. Wu -- Immune recognition of plasmodium-infected erythrocytes / Damien V. Cordery and Britta C. Urban -- Innate immune recognition in tuberculosis infection / Anthony G. Tsolaki.Also available: Print – 2009
- 2011 Springer ProtocolsZhou, Songyang.Introduction to telomeres and telomerase / Z. Songyang -- Analysis of average telomere length in cultured human cells / D. Liu -- Telomere length analysis by quantitative fluorescent in situ hybridization (Q-FISH) / I. Ourliac-Garnier and A. Londono-Vallejo -- Telomere strand-specific length analysis by fluorescent in situ hybridization (Q-CO-FISH) / I. Ourliac-Garnier and A. Londono-Vallejo -- Telomere G-overhang length measurement method 1: The DSN method / Y. Zhao, J.W. Shay and W.E. Wright -- Telomere G-overhang length measurement method 2: G-tail telomere HPA / H. Tahara -- Telomere terminal G/C strand synthesis: Measuring telomerase action and C-RICH fill-in / Y. Zhao, J.W. Shay and W.E. Wright -- G-quadruplex structures and G-quadruplex-interactive compounds / R.I. Mathad and D. Yang -- Analysis of yeast telomerase by primer extension assays / M. Hsu and N.F. Lue -- Telomeric repeat amplification protocol: Measuring the activity of the telomerase / H. Xin -- CO-FISH, COD-FISH, ReD-FISH, SKY-FISH / E.S. Williams [and others] -- Visualization of human telomerase localization by fluorescence microscopy techniques / E. Abreu, R.M. Terns and M.P. Terns -- Cytogenetic analysis of telomere dysfunction / A.S. Multani and S. Chang -- Probing the telomere damage response / R. Rai and S. Chang -- Analysis of telomere proteins by chromatin immunoprecipitation (CHIP) / W. Ma -- Studying of telomeric protein-protein interactions by bi-molecular fluorescence complementation (BIFC) and peptide array-based assays / W. Ma, H. Kim and Z. Songyang -- Human telomere POT1-TPP1 complex and its role in telomerase activity regulation / F. Wang and M. Lei.
- Telomeres and telomerase in aging, disease, and cancer : molecular mechanisms of adult stem cell ageing2008 SpringerRudolph, K. Lenhard.
- 2009 SpringerJain, K. K.Basics of Personalized Medicine -- Molecular Diagnostics as Basis of Personalized Medicine -- Role of Biomarkers in Personalized Medicine -- Pharmacogenetics -- Pharmacogenomics -- Role of Pharmacoproteomics -- Role of Metabolomics in Personalized Medicine -- Personalized Biological Therapies -- Development of Personalized Medicine -- Personalized Therapy for Cancer -- Personalized Management of Neurological Disorders -- Personalized Therapy of Cardiovascular Diseases -- Personalized Management of Miscellaneous Disorders -- Personalized Preventive Medicine -- Organization of Personalized Medicine -- Ethical and Regulatory Aspects of Personalized Medicine -- Economics of Personalized Medicine -- Future of Personalized Medicine.
- 2014 SpringerBoehm, T. L. J.; Takahama, Yousuke.The thymus is an evolutionarily ancient primary lymphoid organ common to all vertebrates in which T cell development takes place. Failing thymus function is associated with immunodeficiency and/or autoimmunity. In this volume, leading experts provide a comprehensive overview of recent advances in thymopoiesis research. The chapters cover the development of the thymic epithelial microenvironment, address the formation of a diverse and self-tolerant repertoire of T cell receptors as the basis for cellular immunity, discuss the mechanisms by which progenitor cells colonize the thymus and detail the molecular basis for T lineage decisions. The reviews illustrate the important role of the multifaceted process of thymopoiesis for adaptive immunity.
- 2013 Springer ProtocolsLee, Tin-Lap; Luk, Alfred Chun Shui.A Brief Introduction to Tiling Microarrays: Principles, Concepts, and Applications -- Design of Tiling Arrays and their Application to Bacterial Transcriptome Analysis -- Transcript Profiling in Arabidopsis with Genome Tiling Microarrays -- Genome-wide Analysis of Transcription Factor Binding Sites in Skeletal Muscle Cells using ChIP-seq -- Analysis of Allele-Specific Gene Expression Using a Target-Oriented Tiling Microarray Assay -- Detection of Epigenetic Alterations Using Tiling Arrays -- Investigating Gene Promoter Methylation in a Mouse Model of Status Epilepticus -- Integrative Analysis of ChIP-chip and ChIP-seq Dataset -- HAT: A Novel Statistical Approach to Discover Functional Regions in the Genome -- Inference of Alternative Splicing from Tiling Array Data -- Analysis of in vivo Occupancy of Aebp1, a Transcription Factor, using High Resolution Tiling Array -- Application of the Simple and Efficient MPeak Modeling in Binding Peak Identification in CHIP-CHIP Studies -- Evaluation of MeDIP-chip in the Context of Whole Genome Bisulphite Sequencing (WGBS-seq) in Arabidopsis -- Mapping Genomic Features of Tiling Microarray Data by TileMapper.
- 2008 SpringerDudek, Serena M.
- 2012 Springer ProtocolsVancura, Ales.Genome-wide in vivo cross-linking of sequence-specific transcription factors / Xiao-Yong li and Mark D. Biggin -- Characterization of complex regulatory networks and identification of promoter regulatory elements in yeast : "in silico" And "wet-lab" approaches / Nuno P. Mira, Miguel C. Teixeira, and Isabel Sá-Correia -- Electrophoretic mobility shift assay analysis of NF[kappa]B transcriptional regulation by nuclear I[kappa]B[alpha] / Ashish Juvekar [and others] -- Probing endogenous RNA polymerase II pre-initiation complexes by electrophoretic mobility shift assay / Emmanuelle Wilhelm, Christopher Takacs, and Brendan Bell -- Elucidating protein : DNA complex by oligonucleotide DNA affinity purification / Teddy T.C. Yang and Chi-Wing Chow -- Chromatin immunoprecipitation assay as a tool for analyzing transcription factor activity / Padmaja Gade and Dhan V. Kalvakolanu -- Two-step cross-linking for analysis of protein-chromatin interactions / Bing Tian, Jun Yan, and Allan R. Brasier -- Chromatin immunoprecipitation analysis of NF[kappa]B transcriptional regulation by nuclear I[kappa]B[alpha] in human macrophages / Sitharam Ramaswami [and others] -- In vivo ChIP for the analysis of microdissected tissue samples / Chris Murgatroyd, Anke Hoffmann, and Dietmar Spengler -- Quantification of protein-DNA interactions by in vivo chromatin immunoprecipitation in yeast / Amparo Pascual-Ahuir and Markus Proft -- Mapping protein-DNA interactions using ChIP-sequencing / Charles E. Massie and Ian G. Mils -- ChIP and re-ChIP assays : investigating interactions between regulatory proteins, histone modifications, and the DNA sequences to which they bind / Agnieszka D. Truax and Susanna F. Greer -- Transcriptional regulation of genes via hypoxia-inducible factor / Olga Roche and Michael Ohh -- Exchange protein directly activated by cyclic AMP-1-regulated recruitment of CCAAT/enhancer-binding proteins to the suppressor of cytokine signaling-3 promoter / William A. Sands [and others] -- Computational analysis of promoter elements and chromatin features in yeast / John J. Wyrick -- Chromatin affinity purification / Ryoko Harada and Alain Nepveu -- Determination of histone acetylation status by chromatin immunoprecipitation / Luciano Galdieri, John Moon, and Ales Vancura -- Immunostaining of Drosophila polytene chromosomes to investigate recruitment of chromatin-binding proteins / Magdalena Murawska and Alexander Brehm -- Detection of transcriptional activators, co-activators, and chromatin remodeling by chromatin immunoprecipitation coupled with real-time PCR / Tamara Y. Erkina and Alexandre M. Erkine -- Chromatin endogenous cleavage and psoralen crosslinking assays to analyze rRNA gene chromatin in vivo / Joachim Griesenbeck [and others] -- UV-induced DNA damage and DNA repair in ribosomal genes chromatin / Julie Pelloux [and others] -- Analysis of SUC2 promoter structure by nucleosome scanning / Jennifer Chang and Ales Vancura -- Chromatin immunoprecipitation of mouse embryos / Anne K. Voss [and others] -- Chromatin immunoprecipitation in mouse hippocampal cells and tissues / Badi Sri Sailaja, Takumi Takizawa, and Eran Meshorer -- Approaches for studying nucleosome movement by ATP-dependent chromatin remodeling complexes / Swetansu K. Hota and Blaine Bartholomew -- Mapping protein-DNA and protein-protein interactions of ATP-dependent chromatin remodelers / Swetansu K. Hota [and others] -- Evaluation of histone-modifying enzymes in stem cell populations / Leanne Stalker and Christopher Wynder -- Purification of multiprotein histone acetyltransferase complexes / Yuan-Liang Wang, Francesco Faiola, and Ernest Martinez -- Reconstitution of active and stoichiometric multisubunit lysine acetyltransferase complexes in insect cells / Kezhi Yan [and others] -- Affinity purification of MLL3/MLL4 histone H3K4 methyltransferase complex / Young-Wook Cho, SunHwa Hong, and Kai Ge -- Methods for analyzing histone citrullination in chromatin structure and gene regulation / Pingxin Li, Jing Hu, and Yanming Wang -- Analysis of mRNA abundance and stability by ribonuclease protection assay / Cristina Romero-López [and others] -- Array-based nuclear run-on analysis / Jinshui Fan [and others] -- In vivo run-on assays to monitor nascent precursor RNA transcripts / Piergiorgio Percipalle and Emilie Louvet -- Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET) / Xiaoan Ruan and Yijun Ruan -- Analysis of co-transcriptional RNA processing by RNA- ChIP assay / Danielle Bittencourt and Didier Auboeuf -- Quantitative analysis of transcription elongation by RNA polymerase I in vitro / David Alan Schneider -- Detection and characterization of transcription termination / Ghada Ghazal, Jules Gagnon, and Sherif Abou Elela -- Promoter-associated noncoding RNA from the CCND1 promoter / Xiaoyuan Song [and others].
- 2013 Springer ProtocolsZhang, Baohong.Transgenic cotton : from biotransformation methods to agricultural application / Baohong Zhang -- Genetically modified cotton in India and detection strategies / Gurinder Jit Randhawa and Rashmi Chhabra -- Agrobacterium-mediated transformation of cotton / Baohong Zhang -- Biolistic transformation of cotton zygotic embryo meristem / Kanniah Rajasekaran -- Biolistic transformation of cotton embryogenic cell suspension cultures / Kanniah Rajasekaran -- Cotton transformation via pollen tube pathway / Min Wang, Baohong Zhang, and Qinglian Wang -- Silicon carbide whisker-mediated transformation of cotton (Gossypium hirsutum L.) / Muhammad Arshad, Yusuf Zafar, and Shaheen Asad -- Investigating transgene integration and organization in cotton (Gossypium hirsutum L.) genome / Jun Zhang and Yan Hong -- Estimating the copy number of transgenes in transformed cotton by real-time quantitative PCR / Chengxin Yi and Yan Hong -- Development of enzyme-linked immunosorbent assay for the detection of Bt protein in transgenic cotton / Suchitra Kamle, Abhishek Ojha, and Arvind Kumar -- DNA-based diagnostics for genetically modified cotton : decaplex PCR assay to Differentiate MON531 and MON15985 Bt cotton events / Gurinder Jit Randhawa, Monika Singh, and Rashmi Chhabra -- Simple and rapid method for determining transgenic cotton plants / Baohong Zhang [and others] -- Efficient grafting technique for recovery of transgenic cotton plants / Min Wang, Qinglian Wang, and Baohong Zhang -- Inheritance of transgenes in transgenic Bt lines resistance to Helicoerpa armigera in upland cotton / Baolong Zhang, Wangzhen Guo, and Tianzhen Zhang -- Agrobacterium rhizogenes-induced cotton hairy root culture as an alternative tool for cotton functional genomics / Hee Jin Kim -- Overexpression of miR 156 in cotton via Agrobacterium-mediated transformation / Baohong Zhang [and others] -- Development of transgenic CryIA(c) + GNA cotton plants via pollen tube pathway method confers resistance to Helicoverpa armigera and Aphis gossypii Glover / Zhi Liu, Zhen Zhu, and Tianzhen Zhang -- Agrobacterium-mediated transformation of cotton (Gossypium hirsutum) shoot apex with a fungal phytase gene improves phosphorus acquisition / Zhiying Ma, Jianfeng Liu, and Xingfen Wang -- Genetic transformation of cotton with a harpin-encoding gene hpaXoo confers an enhanced defense response against Verticillium dahliae kleb / Weiguo Miao and Jingsheng Wang -- Development of insect-resistant transgenic cotton with chimeric TVip3A* accumulating in chloroplasts / Jiahe Wu and Yingchuan Tian -- Determining gene flow in transgenic cotton / Xiaoping Pan.
- 2011 Springer ProtocolsDeursen, Jan van; Hofker, Marten H.Introduction: strategies for developing genetically modified mice / Marten H. Hofker -- Genetic modification of the mouse: general technology - pronuclear and blastocyst injection / Jan Willem Voncken -- Generation of chimeras by aggregation of embryonic stem cells with diploid or tetraploid mouse embryos / Jérôme Artus and Anna-Katerina Hadjantonakis -- Cryopreservation of mouse spermatozoa and in vitro fertilization / Naomi Nakagata -- Autopsy and histological analysis of the transgenic mouse / Marion J.J. Gijbels and Menno P.J. de Winther -- Transgene design / Bart van de Sluis and Jan Willem Voncken -- Inducible transgenic mouse models / Thomas L. Saunders -- Lentiviral transgenesis / Terunaga Nakagawa and Casper C. Hoogenraad -- Transgenesis in mouse embryonic stem cells / Janine van Ree, Wei Zhou, Ming Li, and Jan M. van Deursen -- Engineering BAC reporter gene constructs for mouse transgenesis / Yu Fu and Peter Maye -- Targeting vector construction through recombineering / Liviu A. Malureanu -- Generating conditional knockout mice / Roland H. Friedel, Wolfgang Wurst, Benedikt Wefers, and Ralf Kühm -- Hypomorphic mice / Darren J. Baker -- MICER targeting vectors for manipulating the mouse genome / Chunbong Liu, Paul F. Szurek, and Y. Eugene Yu -- Knock-in approaches / Anton J.M. Roebroek, Philip L.S.M. Gordts, and Sara Reekmans -- Generation of a series of knock-in alleles using RMCE in ES cells / Anton J.M. Roebroek, Philip L.S.M. Gordts, and Sara Reekmans -- Selection of targeting mutants from a library of randomly mutagenized ES cells / Kyoji Horie, George Gaitanaris, and Alexander Gragerov -- Generation of genetically modified rodents using random ENU mutagenesis / Ruben van Boxtel and Edwin Cuppen -- Bone marrow transplantations of study gene function in hematopoietic cells / Menno P.J. de Winther and Peter Heeringa -- Adenovirus-mediated gene transfer / Ko Willems van Dijk, Kyriakos E. Kyreos, Frits J. Fallaux, and Jurre Hageman.
- 2009 Springer ProtocolsJones, Huw D.; Shewry, P. R.Transgenic wheat, barley and oats : production and characterization / Paul A. Lazzeri and Huw D. Jones -- Selection of transformed plants / Huw D. Jones and Caroline A. Sparks -- Reporter genes / Alison Huttly -- Biolistics transformation of wheat / Caroline A. Sparks and Huw D. Jones -- Agrobacterium-mediated transformation of bread and durum wheat using freshly isolated immature embryos / Huixia Wu, Angela Doherty and Huw D. Jones -- Floral transformation of wheat / Sujata Agarwal ... [et al.] -- Highly efficient agrobacterium-mediated transformation of wheat via in planta inoculation / Thierry Risacher ... [et al.] -- Barley transformation using biolistic techniques / Wendy A. Harwood and Mark A. Smedley -- Barley transformation using agrobacterium-mediated techniques / Wendy A. Harwood ... [et al.] -- Transformation of oats and its application to improving osmotic stress tolerance / Shahina B. Maqbool ... [et al.] -- Promoter sequences for defining transgene expression / Huw D. Jones and Caroline A. Sparks -- Down-regulation of gene expression by RNA-induced gene silencing / Silvia Travella and Beat Keller -- Gene insertion patterns and sites / Philippe Vain and Vera Thole -- Fluorescent in situ hybridization to detect transgene integration into plant genomes / Trude Schwarzacher -- Establishing substantial equivalence : transcriptomics / María Marcela Baudo ... [et al.] -- Establishing substantial equivalence : proteomics / Alison Lovegrove, Louise Salt, and Peter R. Shewry -- Establishing substantial equivalence : metabolomics / Michael H. Beale, Jane L. Ward, and John M. Baker -- Design and management of field trials of transgenic cereals / Zoltán Bedő, Mariann Rakszegi, and László Láng -- GM risk assessment / Penny A.C. Sparrow -- Transgenic wheat, barley and oats : future prospects / Jim M. Dunwell.
- 2007 ScienceDirectLorsch, Jon.Purification of FLAG-tagged eukaryotic initation factor 2B complexes, subcomplexes, and fragments from Saccharomyces cerevisiae / Sarah S. Mohammad-Qureshi ... [et al.] -- In vivo deletion analysis of the architecture of a multiprotein complex of translation initiation factors / Klaus H. Nielsen and Leos̆ Valás̆ek -- An approach to studying the localization and dynamics of eukaryotic translation factors in live yeast cells / Susan G. Campbell and Mark P. Ashe -- In vitro and tissue culture methods for analysis of translation initiation on the endoplasmic reticulum / Samuel B. Stephens and Christopher V. Nicchitta -- Mammalian stress granules and processing bodies / Nancy Kedersha and Paul Anderson -- Methods to analyze micro-RNA-mediated control of mRNA translation / Jennifer L. Clancy ... [et al.] -- Methods for studying signal-dependent regulation of translation factor activity / Xuemin Wang and Christopher G. Proud -- Analysis of mRNA translation in cultured hippocampal neurons / Yi-Shuian Huang and Joel D. Richter -- Detecting ribosomal association with the 5' leader of mRNAs by ribosome density mapping (RDM) / Naama Eldad and Yoav Arava -- Genome-wide analysis of mRNA polysomal profiles with spotted DNA microarrays / Danial Melamed and Yoad Arava -- Synthesis of anti-reverse cap analogs (ARCAs) and their applications in mRNA translation and stability / Ewa Grudzien-Nogalska ... [et al.] -- Methods for identifying compounds that specifically target translation / Letizia Brandi ... [et al.] -- Identifying small molecule inhibitors of eukaryotic translation initiation / Regina Cencic, Francis Robert, and Jerry Pelletier -- Isolation and identification of eukaryotic initiation factor 4A as a molecular target for the marine natural product pateamine A / Woon-Kai Low ... [et al.].
- 2007 ScienceDirectLorsch, Jon.Use of reticulocyte lysates for mechanistic studies of eukaryotic translation initiation / William C. Merrick and Diane Barth-Baus -- Studying translational control in Drosophila cell-free systems / Fátima Gebauer and Matthias W. Hentze -- Use of in vitro translation extract depleted in specific initiation factors for the investigation of translational regulation / Daniel R. Gallie -- A highly efficient and robust in vitro translation system for expression of picornavirus and hepatitis C virus in RNA genomes / Yuri V. Svitkin and Nahum Sonenberg -- A practical approach to isolate 48S complexes : affinity purification and analyses / Nicolas Locker and Peter J. Lukavsky -- Yeast phenotypic assays on translational control / Bumjun Lee ... [et al.] -- Localization and characterization of protein-protein interaction sites / Chingakham Ranjit Singh and Katsura Asano -- In vivo stabilization of preinitiation complexes by formaldehyde cross-linking / Leos Valás̆ek ... [et al.] -- Molecular genetic structure-function analysis of translation initiation factor elF5B / Byung-Sik Shin and Thomas E. Dever -- The use of fungal in vitro systems for studying translational regulation / Cheng Wu ... [et al.] -- Investigating translation initiation using drosophila molecular genetics / Gritta Tettweiler and Paul Lasko -- Analysis of RNA:protein interactions in vivo : identification of RNA-binding partners of nuclear factor 90 / Andrew M. Parrott, Melissa R. Walsh, and Michael B. Mathews -- Approaches for analyzing the differential activities and functions of elF4E family members / Robert E. Rhoads, Tzvetanka D. Dinkova, and Rosemary Jagus -- Tethered function assays : an adaptable approach to study RNA regulatory proteins / Jeff Coller and Marv Wickens -- Analysis of ribosomal shunting during translation initiation in eukaryotic mRNAs / Vincent P. Mauro, Stephen A. Chappell and John Dresios.
- 2007 ScienceDirectLorsch, Jon.Transient kinetics, flourescence, and FRET in studies of initiation and translation in bacteria / Pohl Milon ... [et al.] -- Binding of mRNA to the bacterial translation initiation complex / Sean M. Studer and Simpson Joseph -- Real-time dynamics of ribosome-ligand interaction by time-resolved chemical probing methods / Attilio Fabbretti ... [et al] -- Overexpression and purification of mammalian mitochondrial translational initiation factor 2 and initiation factor 3 / Domenick G. Grasso ... [et al.] -- In vitro studies of archaeal translational initiation / Dario Benelli and Paola Londei -- Reconstitution of yeast translation initiation / Michael G. Acker ... [et al.] -- Assembly and analysis of eukaryotic translation initiation complexes / Andrey V. Pisarev -- Reconstitution of mammalian 48S ribosomal translation initiation complex / Romit Majumdar, Jayanta Chaudhuri, and Umadas Maitra -- Biophysical approach to studies of Cap-elF4E interaction by synthetic cap analogs / Anna Niedzwiecka ... [et al.] -- Biophysical studies of the translation initiation pathway with immobilized mRNA analogs / John E. G. McCarthy, Steven Marsden, and Tobias von der Haar -- Protection-based assays to measure aminoacyl-tRNA binding to translation initiation factors / Yves Mechulam ... [et al.] -- NMR methods for studying protein-protein interactions involved in translation initiation / Assen Marintchev, Dominique Frueh, and Gerhard Wagner -- Structural methods for studying IRES function / Jeffrey S. Kieft ... [et al.].
- 2009 SpringerLankenau, Dirk-Henner; Volff, Jean-Nicolas.
- 2005 SpringerMorant, R.; Senn, Hansjörg.Lifestyle and Medical Approaches to Cancer Prevention / Peter Greenwald, p. 1-15 -- Application of Genetics to the Prevention of Colorectal Cancer / John Hopper, p. 17-33 -- Genetics and Prevention of Oesophageal Adenocarcinoma / Rebecca Fitzgerald, p. 35-46 -- Preclinical Models Relevant to Diet, Exercise, and Cancer Risk R. James Barnard and William Aronson, p. 47-62 -- Individualizing Interventions for Cancer Prevention / Michael Pollak, p. 63-70 -- Can Animal Models Help Us Select Specific Compounds for Cancer Prevention Trials? / Ernest Hawk, Asad Umar, Ronald Lubet, Levy Kopelovich and Jaye Viner, p. 71-88 -- Problems with Using Biomarkers as Surrogate End Points for Cancer: A Cautionary Tale / Arthur Schatzkin, p. 89-98 -- Can a Marker Be a Surrogate for Development of Cancer, and Would We Know It if It Exists? / William Armstrong, Thomas Taylor and Frank Meyskens, p. 99-112 -- How Should We Move the Field of Chemopreventive Agent Development Forward in a Productive Manner? / Frank Meyskens and Eva Szabo, p. 113-124 -- The Problems with Risk Selection; Scientific and Psychosocial Aspects / Anne-Renée Hartman, p. 125-144 -- Chemoprevention of Lung Cancer / Stéphane Vignot, Jean-Philippe Spano, Sylvie Lantuejoul, Fabrice André, Thierry Le Chevalier and Jean-Charles Soria, p. 145-165 -- Anti-nicotine Vaccination: Where Are We? / T. Cerny, p. 167-175 -- Primary Prevention of Colorectal Cancer: Lifestyle, Nutrition, Exercise / María Martínez, p. 177-211 -- Chemoprevention of Colorectal Cancer: Ready for Routine Use? / Nadir Arber and Bernard Levin, p. 213-230 -- Screening of Colorectal Cancer: Progress and Problems Sidney Winawer, p. 231-244 -- The Role of Endogenous Hormones in the Etiology and Prevention of Breast Cancer: The Epidemiological Evidence / Paola Muti, p. 245-256 -- Innovative Agents in Cancer Prevention / Margaret Manson, Peter Farmer, Andreas Gescher and William Steward, p. 257-275 -- The IARC Commitment to Cancer Prevention: The Example of Papillomavirus and Cervical Cancer / Silvia Franceschi, p. 277-297 -- Health Economics in the Genomic Age / Thomas Szucs, p. 299-313 -- Screening for Cancer: Are Resources Being Used Wisely? / Robert Kaplan, p. 315-334.
- 2013 SpringerBarrett, Lucy W.; Fletcher, Sue; Wilton, Steve D.There is now compelling evidence that the complexity of higher organisms correlates with the relative amount of non-coding RNA rather than the number of protein-coding genes. Previously dismissed as ""junk DNA"", it is the non-coding regions of the genome that are responsible for regulation, facilitating complex temporal and spatial gene expression through the combinatorial effect of numerous mechanisms and interactions working together to fine-tune gene expression. The major regions involved in regulation of a particular gene are the 5' and 3' untranslated regions and introns.
- 2014 ScienceDirectDoudna, Jennifer A.; Sontheimer, Erik J.This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers recent research and methods development for changing the DNA sequence within the genomes of cells and organisms. Focusing on enzymes that generate double-strand breaks in DNA, the chapters describe use of molecular tools to introduce or delete genetic information at specific sites in the genomes of animal, plant and bacterial cells.
- 2005 ScienceDirectHall, Brian Keith; Hallgrímsson, Benedikt.Variation and variability : central concepts in biology / Benedikt Hallgrímsson and Brian K. Hall -- Variation from Darwin to the modern synthesis / Peter J. Bowler -- The statistics of variation / Leigh Van Valen -- Landmark morphometrics and the analysis of variation / Joan T. Richtsmeier, Subhash R. Lele, and Theodore M. Cole III -- Variation in ontogeny / Donna Carlson Jones and Rebecca Z. German -- Constraints on variation from genotype through phenotype to fitness / Lauren Ancel Meyers -- Developmental origins of variation / Ellen Larsen -- Canalization, cryptic variation, and developmental buffering : a critical examination and analytical perspective / Ian Dworkin -- Mutation and phenotypic variation : where is the connection? : capacitators, stressors, phenotypic variability, and evolutionary change / Ary A. Hoffmann and John A. McKenzie -- Within individual variation : developmental noise versus developmental stability / Katherine E. Willmore and Benedikt Hallgrímsson -- Developmental constraints, modules, and evolvability / Christian Peter Klingenberg -- Developmental regulation of variability / Miriam Leah Zelditch -- Role of stress in evolution : from individual adaptability to evolutionary adaptation / Alexander V. Badyaev -- Environmentally contingent variation : phenotypic plasticity and norms of reaction / Sonia E. Sultan and Stephen C. Stearns -- Variation and life-history evolution / Derek A. Roff -- Antisymmetry / A. Richard Palmer -- Variation in structure and its relationship to function : correlation, explanation, and extrapolation / Anthony P. Russell and Aaron M. Bauer -- A universal generative tendency toward increased organismal complexity / Daniel W. McShea -- Variation and versatility in macroevolution / V. Louise Roth -- Variation and developmental biology : prospects for the future / David M. Parichy -- Phenogenetics : genotypes, phenotypes, and variation / Samuel Sholtis and Kenneth M. Weiss -- The study of phenotypic variability : an emerging research agenda for understanding the developmental-genetic architecture underlying phenotypic variation / Benedikt Halgrímsson, Jevon James Yardley Brown, and Brian K. Hall.
- 2009 SpringerFerrier, Pierre.Early steps of V(D)J rearrangement : insights from biochemical studies of RAG-RSS complexes / Patrick C. Swanson, Sushil Kumar, and Prafulla Raval -- Regulation of RAG transposition / Adam G.W. Matthews and Marjorie A. Oettinger -- Recent insights into the formation of RAG-induced chromosomal translocations / Vicky L. Brandt and David B. Roth -- V(D)J recombination deficiencies / Jean-Pierre de Villartay -- Large-scale chromatin remodeling at the immunoglobulin heavy chain locus : a paradigm for multigene regulation / Daniel J. Bolland, Andrew L. Wood, and Anne E. Corcoran -- Genetic and epigenetic control of V gene rearrangement frequency / Ann J. Feeney -- Dynamic aspects of TCRa gene recombination : qualitative and quantitative assessments of the TCRa chain repertoire in man and mouse / Evelyne Jouvin-Marche, Patrizia Fuschiotti, and Patrice Noël Marche -- Germline transcription : a key regulator of accessibility and recombination / Iratxe Abarrategui and Michael S. Krangel -- Dynamic regulation of antigen receptor gene assembly / Lance R. Thomas, Robin Milley Cobb, and Eugene M. Oltz -- Molecular genetics at the T-cell receptor b locus : insights into the regulation of V(D)J recombination / Marie Bonnet, Pierre Ferrier, and Salvatore Spicuglia -- Molecular pathways and mechanisms regulating the recombination of immunoglobulin genes during B-lymphocyte development / Kristen Johnson, Karen L. Reddy, and Harinder Singh -- Regulation of V(D)J recombinationby E-protein transcription factors / Mary Elizabeth Jones and Yuan Zhuang -- Temporal and spatial regulation of V(D)J recombination : interactions of extrinsic factors with the RAG complex / Yun Liu, Li Zhang, and Stephen Desiderio -- V(D)J recombination : of mice and sharks / Ellen Hsu -- Normal and pathological V(D)J recombination : contribution to the understanding of human lymphoid malignancies / Saïda Dadi ... [et al.].Also available: Print – 2009
- 2006. KargerVolff, Jean-Nicolas.The human genome and its upcoming dynamics / M. Platzer -- Primate genomes / H. Herlyn, H. Zischler -- The mouse genome / S.D.M. Brown, J.M. Hancock -- The dog genome / F. Galibert, C. André -- The feline genome / W.J. Murphy -- The bovine genome / J.E. Womack -- The sheep genome / N.E. Cockett -- Cracking the genomic piggy bank : identifying secrets of the pig genome / B.E. Mote, M.F. Rothschild -- The horse genome / B.P. Chowdhary, T. Raudsepp -- Marsupial and monotreme genomes / E. Koina, J. Fong, J.A. Marshall Graves -- The chicken genome / D.W. Burt -- Insights from Xenopus genomes / N. Pollet, A. Mazabraud -- The Tetraodon genome / H. Roest Crollius -- The medaka genome : why we need multiple fish models in vertebrate functional genomics / H. Mitani ... [et al.] -- The zebrafish genome : a review and msx gene case study / J.H. Postlethwait -- Urochordate genomes / N. Satoh ... [et al.].
- 2013 Springer ProtocolsBrambilla, Riccardo.Lentiviral vectors as research tools in neurobiology: design and production / Alessandro Papale and Riccardo Brambilla -- Recombinant adenovirus in neurobiology / Qian Li and Tong-Chuan He -- Adeno-associated virus-based vectors / Nathalie Dutheil and Erwan Bezard -- Herpes simples virus 1 (HSV-1)-based vectors / Aldo Pourchet, Matias E. Melendez, Anna Greco, and Alberto L. Epstein -- Aphavirus-based vectors / Kenneth Lundstrom -- Viral vectors to study synaptic function / Hélène Marie -- Using viral vectors to study the memory trace in mice / Asim J. Rashid, Chen Yan, and Sheena A. Josselyn -- Development of cell-type-specific viral vectors to tease apart the neural circuitry that contributes to drug addiction / Susan M. Ferguson and John F. Neumaier -- Using viral-mediated gene transfer to study depressive-like behavior / Amy R. Furay and John F. Neumaier -- Gene therapy for parkinson's disease / Erika Elgstrand Wettergren, Luis Quintino, Giuseppe Manfré, and Cecilia Lundberg -- Lentiviral vectors in huntington's disease research and therapy / Aurélie Delzor, Noëlle Dufour, and Nicole Déglon -- Application of viral vectors to motor neuron disorders / Elisabeth Dirren and Bernard L. Schneider -- In vivo gene silencing by virally delivered MicroRNA / Eugenia V. Gurevich, Mohamed R. Ahmed, and Yonatan Carl -- Viral manipulation of neural stem/precursor cells / Nunzio Iraci, Giulia Elisabetta Tyzack, Chiara Cossetti, Clara Alfaro-Cervello, and Stefano Pluchino -- Viral vector-based techniques for optogenetic modulation in vivo / Mathias Mahn, Shiri Ron, and Ofer Yizhar -- Viral vectors for optogenetics of hypothalamic neuropeptides / H. Sophie Knobloch, Alexander Charlet, Ron Stoop, and Valery Grinevich -- Viral vectors in primate research: examples from parkinson's disease research / Grégory Porras, Benjamin Dehay, and Erwan Bezard.
- 2011 Springer ProtocolsAl-Rubeai, Mohamed; Merten, Otto-Wilhelm.Introduction to viral vectors -- Introduction to gene therapy : a clinical aftermath -- Host cells and cell banking -- Overview of current scalable methods for purification of viral vectors -- Methods to construct recombinant adenovirus vectors -- Manufacturing of adenovirus vectors : production and purification of helper dependent adenovirus -- Manufacturing of retroviruses -- Lentiviral vectors -- Adeno-associated viruses -- Manufacturing of adeno-associated viruses, for example: AAV2 -- Vector characterization methods for quality control testing of recombinant adeno-associated viruses -- Baculoviruses mediate efficient gene expression in a wide range of vertebrate cells -- Herpes simplex virus type 1-derived recombinant and amplicon vectors -- Manufacture of measles viruses -- In vivo gene delivery into hCD34+ cells in a humanized mouse model -- In vivo evaluation of gene transfer into mesenchymal cells (in view of cartilage repair) -- Ethical consideration -- Clinical trials of GMP products in the gene therapy field.
- 2012 SpringerWitzany, Günther."Viruses are now considered to play major roles in the evolution of life. Because they have genes that are not found in any cellular organism they seem to be remnants of early stages of life on earth. Besides their disease causing features and actions as genetic parasites viruses have lifestyles that are clearly symbiotic and even symbiogenetic. Increasing empirical data suggest that some viruses such as endogenous retroviruses and non-retroviral RNA viruses and even DNA viruses prefer cellular genomes as habitat. They determine genetic host (group) identity and genetic host features. Viruses and virus-related modules such as mobile genetic elements and other repeat sequences identified in intronic regions of host genomes play important roles in gene regulation and genetic content (re)arrangement. This book exemplifies some astonishing key features of viruses acting as essential agents of life."--Publisher.
- 2013 Springer ProtocolsBecker, Annette.Virus-induced gene silencing (VIGS) in plants : an overview of target species and the virus-derived vector systems -- Rationale for developing new virus vectors to analyze gene function in grasses through virus-induced gene silencing -- Virus-induced gene silencing for rice using agroinoculation -- Utilizing virus-induced gene silencing for the functional characterization of maize genes during infection with the fungal pathogen ustilago maydis -- Analysis of developmental control genes using virus-induced gene silencing -- Virus-induced gene silencing in the rapid cycling columbine aquilegia coerulea Origami -- Virus-induced gene silencing of the alkaloid-producing basal eudicot model plant eschscholzia californica (California poppy) -- Virus-induced gene silencing using artificial miRNAs in nicotiana benthamiana -- The use of vigs technology to study plant-herbivore interactions -- Virus-aided gene expression and silencing using TRV for functional analysis of floral scent-related genes -- Virus-induced gene silencing in soybean and common bean -- Functional genomic analysis of cotton genes with agrobacterium-mediated virus-induced gene silencing -- Highly efficient virus-induced gene silencing in apple and soybean by apple latent spherical virus vector and biolistic inoculation -- VIGS : a tool to study fruit development in Solanum lycopersicum -- A protocol for VIGS in arabidopsis thaliana using a one-step TYMV-derived vector -- Virus-induced gene silencing in strawberry fruit.
- 2011 SpringerHorvath, Steve.Networks and fundamental concepts -- Approximately factorizable networks -- Different types of network concepts -- Adjacency functions and their topological effects -- Correlation and gene co-expression networks -- Geometric interpretation of correlation networks using the singular value decomposition -- Constructing networks from matrices -- Clustering procedures and module detection -- Evaluating whether a module is preserved in another network -- Association measures and statistical significance measures -- Structural equation models and directed networks -- Integrated weighted correlation network analysis of mouse liver gene expression data -- Networks based on regression models and prediction methods -- Networks between categorical or discretized numeric variables -- Network based on the joint probability distribution of random varaibles.
- 2015 Springer ProtocolsKroneis, Thomas.Principles of whole-genome amplification / Zbigniew Tadeusz Czyz, Stefan Kirsch, and Bernhard Polzer -- Bias in whole genome amplification : causes and considerations / Jeffrey Sabina and John H. Leamon -- Single-cell lab or how to perform single-cell molecular analysis / Roland Kirchner and Marianna Alunni-Fabbroni -- Sample preparation methods following cellsearch approach compatible of single-cell whole-genome amplification : an overview / Joost F. Swennenhuis and Leon Terstappen -- Deterministic whole-genome amplification of single cells / Zbigniew Tadeusz Czyż and Christoph A. Klein -- Construction of a DNA library on microbeads using whole genome amplification / Takaaki Kojima, Bo Zhu, and Hideo Nakano -- Heat-induced fragmentation and adapter-assisted whole genome amplification using GenomePlex® single-cell whole genome amplification kit (WGA4) / Amin El-Heliebi, Shukun Chen , and Thomas Kroneis -- Whole genome amplification by isothermal multiple strand displacement using Phi29 DNA polymerase / Thomas Kroneis and Amin El-Heliebi -- Using multiplex PCR for assessing the quality of whole genome amplified DNA / Amin El-Heliebi, Shukun Chen, and Thomas Kroneis -- Quality control of isothermal amplified DNA based on short tandem repeat analysis / Thomas Kroneis and Amin El-Heliebi -- Laser microdissection of FFPE tissue areas and subsequent whole genome amplification by Ampli1 / Zbigniew Tadeusz Czyz, Nikolas H. Stoecklein, and Bernhard Polzer -- Whole genome amplification from blood spot samples / Karina Meden Sørensen -- Analysis of whole mitogenomes from ancient samples / Gloria Gonzales Fortes and Johanna L. A. Paijmans -- Copy number variation analysis by array analysis of single cells following whole genome amplification / Eftychia Dimitriadou, Masoud Zamani Esteki, and Joris Robert Vermeesch -- Whole genome amplification in genomic analysis of single circulating tumor cells / Christin Gasch, Klaus Pantel, and Sabine Riethdorf -- Whole genome amplification of labeled viable single cells suited for array-comparative genomic hybridization / Thomas Kroneis and Amin El-Heliebi -- Low-volume on-chip single-cell whole genome amplification for multiple subsequent analyses / Thomas Kroneis, Shukun Chen, and Amin El-Heliebi -- Detection and characterization of circulating tumor cells by the cellsearch approach / Frank Coumans and Leon Terstappen.
- Chalfie, Martin; Girard, Lisa."WormBook is a comprehensive online review of C. elegans biology, containing over 100 original, peer-reviewed chapters on a wide range of topics related to the biology of C. elegans and related nematodes; as well as WormMethods, a collection of laboratory methods and protocols useful for nematode researchers."
- 2006 Springer ProtocolsMacKenzie, Alasdair.Markers, selection, and media in yeast artificial chromosomes cloning / David Markie -- Construction of yeast artificial chromosome libraries from pathogens and nonmodel organisms / Cecilia P. Sanchez and Michael Lanzer -- Analysis and screening of yeast artificial chromosome libraries by filter hybridization / Cecilia P. Sanchez and Michael Lanzer -- Analysis of Yeast Artificial Chromosome DNA by restriction digestion, southern blotting nucleic acid hybridization and polymerase chain reaction / Sylvia Vasiliou and John Peter Quinn -- Postgenomic bioinformatic analysis of yeast artificial chromosome sequence / Kerry Miller, Scott Davidson, and Alasdair MacKenzie -- Transformation of yeast using bioactive beads with surface-immobilized yeast artificial chromosomes / Shigeki Kawakami ... [et al.] -- Modification and amplification of yeast artificial chromosomes / Sanbing Shen, Anthony Harmar, and Nick Hastie -- Modifying yeast artificial chromosomes to generate Cre/LoxP and FLP/FRT site-specific deletions and inversions / Gabriela G. Loots -- Selective isolation of large chromosomal regions by transformation-associated recombination cloning for structural and functional analysis of mammalian genomes / Natalay Kouprina, Vladimir N. Noskov, and Vladimir Larionov -- A polymerase chain reaction-mediated yeast artificial chromosome-splitting technology for generating targeted yeast artificial chromosomes subclones / Yeon-Hee Kim ... [et al.] -- Genomic reconstruction by serial mitotic recombination of yeast artificial chromosomes / David Markie, Emma Jones, and Jiannis Ragoussis -- Targeting vector construction by yeast artificial chromosome modification / Peter J. Murray -- Production of yeast artificial chromosomes transgenic mice by pronuclear injection of one-cell embryos / Alasdair MacKenzie -- Generation of yeast artificial chromosomes transgenic mice by intracytoplasmic sperm injection / Pedro N. Moreira ... [et al.] -- Establishment of cell lines that exhibit correct ontogenic stage-specific gene expression profiles from tissues of yeast artificial chromosome transgenic mice using chemically induced growth signals / C. Anthony Blau and Kenneth R. Peterson -- Application of yeast artificial chromosomes in fluorescence in situ hybridization / Thomas Liehr -- Contribution of yeast artificial chromosome-based physical maps to the final assembly of the trypanosoma cruzi genome / Marcia R.M. Santos ... [et al.].
- 2016 Springer ProtocolsPerez, Pilar; Sanchez-Diaz, Alberto.Time-lapse fluorescence microscopy of budding yeast cells / Arun Kumar and Manuel Mendoza -- Real-time visualization and quantification of contractile ring proteins in single living cells / Reshma Davidson ... [et al.] -- Fluorescence recovery after photo-bleaching (FRAP) and fluorescence loss in photo-bleaching (FLIP) experiments to study protein dynamics during budding yeast cell division / Alessio Bolognesi ... [et al.] -- High-speed super-resolution imaging of live fission yeast cells / Caroline Laplante ... [et al.] -- Monitoring chitin deposition during septum assembly in budding yeast / Irene Arcones and Cesar Roncero -- Imaging septum formation by fluorescence microscopy / Juan Carlos Ribas and Juan Carlos G. Cortés -- Visualization of cytokinesis events in budding yeast by transmission electron microscopy / Franz Meitinger and Gislene Pereira -- Visualization of fission yeast cells by transmission electron microscopy / Matthias Sipiczki -- Characterization of septin ultrastructure in budding yeast using electron tomography / Aurélie Bertin and Eva Nogales -- Isolation of cytokinetic actomyosin rings from Saccharomyces cerevisiae and Schizosaccharomyces pombe / Junqi Huang ... [et al.] -- Measurements of myosin-II motor activity during cytokinesis in fission yeast / Qing Tang, Luther W. Pollard, and Matthew Lord -- In vitro biochemical characterization of cytokinesis actin-binding proteins / Dennis Zimmermann ... [et al.] -- Characterization of cytokinetic F-BARs and other membrane-binding proteins / Nathan A. McDonald and Kathleen L. Gould -- Analysis of three-dimensional structures of exocyst components / Johannes Lesigang and Gang Dong -- Analysis of Rho-GTPase activity during budding yeast cytokinesis / Masayuki Onishi and John R. Pringle -- Detection of phosphorylation status of cytokinetic components / Franz Meitinger, Saravanan Palani, and Gislene Pereira -- Studying protein-protein interactions in budding yeast using co-immunoprecipitation / Magdalena Foltman and Alberto Sanchez-Diaz -- Conditional budding yeast mutants with temperature-sensitive and auxin-inducible degrons for screening of suppressor genes / Asli Devrekanli and Masato T. Kanemaki -- Synchronization of the budding yeast Saccharomyces cerevisiae / Magdalena Foltman, Iago Molist, and Alberto Sanchez-Diaz -- Fission yeast cell cycle synchronization methods / Marta Tormos-Pérez, Livia Pérez-Hidalgo, and Sergio Moreno -- Review of fluorescent proteins for use in yeast / Maja Bialecka-Fornal, Tatyana Makushok, and Susanne M. Rafelski -- Visualization and image analysis of yeast cells / Steve Bagley -- Toolbox for protein structure prediction / Daniel Barry Roche and Liam James McGuffin -- From structure to function : a comprehensive compendium of tools to unveil protein domains and understand their role in cytokinesis / Sergio A. Rincon and Anne Paoletti.
- 2015 Springer ProtocolsDevaux, Frédéric.Using RNA-seq for analysis of differential gene expression in fungal species / Can Wang ... [et al.] -- Enhancing structural annotation of yeast genomes with RNA-Seq data / Hugo Devillers, Nicolas Morin, and Cécile Neuvéglise -- Pathogen gene expression profiling during infection using a nanostring nCounter platform / Wenjie Xu ... [et al.] -- Comparative transcriptomics in yeasts / Dawn A. Thompson -- Mapping the transcriptome-wide landscape of RBP binding sites using gPAR-CLIP-seq : experimental procedures / Ting Han and John K. Kim -- Mapping the transcriptome-wide landscape of RBP binding sites using gPAR-CLIP-seq : bioinformatic analysis / Mallory A. Freeberg and John K. Kim -- Translation analysis at the genome scale by ribosome profiling / Agnès Baudin-Baillieu ... [et al. ] -- Biotin-genomic run-on (Bio-GRO) : a high-resolution method for the analysis of nascent transcription in yeast / Antonio Jordán-Pla ... [et al.] -- Genome-wide probing of RNA structures in vitro using nucleases and deep sequencing / Yue Wan ... [et al.] -- Genome-wide chromatin immunoprecipitation in Candida albicans and other yeasts / Matthew B. Lohse [et al.] -- ChIPseq in yeast species : from chromatin immunoprecipitation to high-throughput sequencing and bioinformatics data analyses / Gaëlle Lelandais, Corinne Blugeon, and Jawad Merhej -- Systematic determination of transcription factor DNA- binding specificities in yeast / Lourdes Peña-Castillo and Gwenael Badis -- Generation and analysis of chromosomal contact maps of yeast species / Axel Cournac ... [et al.] -- Versatile procedure to generate genome-wide spatiotemporal program of replication in yeast species / Nicolas Agier and Gilles Fischer -- Single-step affinity purification (ssAP) and mass spectrometry of macromolecular complexes in the yeast S. cerevisiae / Christian Trahan, Lisbeth-Carolina Aguilar, and Marlene Oeffinger -- Label-free quantitative proteomics in yeast / Thibaut Léger ... [et al.] -- Profiling of yeast lipids by shotgun lipidomics / Christian Klose and Kirill Tarasov -- Identification of links between cellular pathways by genetic interaction mapping (GIM) / Christophe Malabat and Cosmin Saveanu -- On the mapping of epistatic genetic interactions in natural isolates : combining classical genetics and genomics / Jing Hou and Joseph Schacherer -- Experimental evolution and resequencing analysis of yeast / Celia Payen and Maitreya J. Dunham -- Reconstruction and analysis of the evolution of modular transcriptional regulatory programs using arboretum / Sara A. Knaack, Dawn A. Thompson, and Sushmita Roy -- Predicting gene and genomic regulation in Saccharomyces cerevisiae, using the YEASTRACT database : a step-by-step guided analysis / Miguel C. Teixeira, Pedro T. Monteiro, and Isabel Sá-Correia.
- 2007 ScienceDirectStansfield, Ian; Stark, Michael J. R.
- 2011 Springer ProtocolsBecskei, Attila.Global estimation of mRNA stability in yeast / Julia Marin-Navarro [and others] -- Genomic-wide methods to evaluate transcription rates in yeast / Jose Garcia-Martinez, Vicent Pelechano, and Jose E. Perez-Ortin -- Construction of cis-regulatory input functions of yeast promoters / Prasuna Ratna and Attila Becskei -- Luminescence as a continuous real-time reporter of promoter activity in yeast undergoing respiratory oscillations or cell division rhythms / J. Brian Robertson and Carl Hirschie Johnson -- Linearizer gene circuits with negative feedback regulation / Dmitry Nevozhay, Rhys M. Adams, and Gabor Balazsi -- Measuring in vivo signaling kinetics in a mitogen-activated kinase pathway using dynamic input stimulation / Megan N. McClean, Pascal Hersen, and Sharad Ramanathan -- Stochastic analysis of gene expression / Xiu-Deng Zheng and Yi Tao -- Studying adaptation and homeostatic behaviors of kinetic networks by using MATLAB / Tormod Drengstig, Thomas Kjosmoen, and Peter Ruoff -- Biochemical systems analysis of signaling pathways to understand fungal pathogenicity / Jacqueline Garcia [and others] -- Clustering change patterns using fourier transformation with time-course gene expression data / Jaehee Kim -- Finding modulators of stochasticity levels by quantitative genetics / Steffen Fehrmann and Gael Yvert -- Functional mapping of expression quantitative trait loci that regulate oscillatory gene expression / Arthur Berg [and others] -- Evolutionary aspects of a genetic network : studying the lactose/galactose regulon of Kluyveromyces lactis / Alexander Anders and Karin D. Breunig -- Analysis of subtelomeric silencing in Candida glabrata / Alejandro Juarez-Reyes, Alejandro De Las Penas, and Irene Castano -- Morphological and molecular genetic analysis of epigenetic switching of the human fungal pathogen Candida albicans / Denes Hnisz, Michael Tscherner, and Karl Kuchler -- Quantitation of cellular components in Cryptococcus neoformans for system biology analysis / Arpita Singh, Asfia Qureshi, and Maurizio Del Poeta.
- 2011 ScienceDirectDetrich, H. William; Westerfield, Monte; Zon, Leonard I.Pt.1 Forward and reverse genetics : Generating conditional mutations in zebrafish using gene-trap mutagenesis / Lisette A. Maddison, Jianjun Lu, Wenbiao Chen -- Tol2-mediated transgenesis, gene trapping, enhancer trapping, and the Gal4-UAS system / Gembu Abe, Maximilliano L. Suster, Koichi Kawakami -- Engineering zinc finger nucleases for targeted mutagenesis of zebrafish / Jeffry D. Sander, J.-R. Joanna Yeh, Randall T. Peterson, J. Keith Joung -- Retroviral-mediated insertional mutagenesis in zebrafish / Adam Amsterdam, Gaurav Kumar Varshney, Shawn Michael Burgess -- Genetic screens for mutations affecting adult traits and parental-effect genes / Francisco Pelegri, Mary C. Mullins -- High-throughput target-selected gene inactivation in zebrafish / Ross N.W. Kettleborough, Ewart de Bruijn, Freek van Eeden, Edwin Cuppen, Derek L. Stemple -- Genetic suppressor screens in haploids / Xiaoying Bai, Zhongan Yang, Hong Jiang, Shuo Lin, Leonard I. Zon -- Transgenic zebrafish using transposable elements / Karl J. Clark, Mark D. Urban, Kimberly J. Skuster, Stephen C. Ekker -- Spatiotemporal control of embryonic gene expression using caged morpholinos / Ilya A. Shestopalov, James K. Chen -- Pt.2 Transgenesis : Advanced zebrafish transgenesis with Tol2 and application for Cre/lox recombination experiments / Christian Mosimann, Leonard I. Zion -- Use of phage PhiC31 integrase as a tool for zebrafish genome manipulation / James A. Lister -- Method for somatic cell nuclear transfer in zebrafish / Kannika Siripattarapravat, Jose B. Cibelli -- Pt.3 The zebrafish genome and mapping technologies : Single nucleotide polymorphism (SNP) panels for rapid positional cloning in zebrafish / Matthew D. Clark, Victor Guryev, Ewart de Bruijn, Isaac J. Nijman, Masazumi Tada, Catherine Wilson, Panos Deloukas, John H. Postlethwait, Edwin Cuppen, Derek L. Stemple -- Molecular cytogenetic methodologies and a BAC probe panel resource for genomic analyses in the zebrafish / Kimberly P. Dobrinski, Kim H. Brown, Jennifer L. Freeman, Charles Lee -- Conserved synteny and the zebrafish genome / Julian M. Catchen, Ingo Braasch, John H. Postlethwait -- The zon laboratory guide to positional cloning in zebrafish / Yi Zhou, Leonard I. Zon -- Pt.4 Informatics and comparative genomics : Data extraction, transformation, and dissemination through ZFIN / Douglas G. Howe, Ken Frazer, David Fashena, Leyla Ruzicka, Yvonne Bradford, Sridhar Ramachandran, Barbara J. Ruef, Ceri Van Slyke, Amy Singer, Monte Westerfield -- DNA methylation profiling in zebrafish / Shan-Fu Wu, Haiying Zhang, Saher Sue Hammond, Magdalena Potok, David A. Nix, David A. Jones, Bradley R. Cairns -- Chromatin immunoprecipitation in adult zebrafish red cells / Eirini Trompouki, Teresa Venezia Bowman, Anthony DiBiase, Yi Zhou, Leonard I. Zon -- Discerning different in vivo roles of microRNAs by experimental approaches in zebrafish / Luke Pase, Graham J. Lieschke -- Sequencing-based expression profiling in zebrafish / Jin Liang, Gabriel Renaud, Shawn M. Burgess -- Chromatin modification in zebrafish development / Jordi Cayuso Mas, Emily S. Noël, Elke A. Ober -- Pt.5 Infrastructure : Advances in zebrafish husbandry and management / Christian Lawrence -- Aquaculture and husbandry at the Zebrafish International Resource Center / Zoltán M. Varga.
- Adeno-associated virus : methods and protocols — Epigenetics protocols. 2nd ed. (137)
- Epistasis : methods and protocols — Inborn metabolic diseases : diagnosis and treatment. 4th, rev. ed. (137)
- Incorporating the dynamic nature of molecules improves performance of structure-based function prediction methods — Plant transcription factors : methods and protocols (137)
- Plant transposable elements-- impact on genome structure and function — Zebrafish : genetics, genomics and informatics. 3rd ed. (135)
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A repository of medical knowledge from internal medicine, cardiology, genetics, pharmacy, diagnosis and management, basic sciences, patient care, and more.
Continuously expanding, all databases in the repository contain the latest editions of selected medical titles.MicroMedex: Premier pharmaceutical information source containing multiple databases and drug reference tools. Of particular value is DRUGDEX Evaluations, one of the most comprehensive drug sources available.DynaMed is a clinical information resource used by physicians to answer clinical questions quickly and easily at the point of care. Topics are updated daily as new evidence becomes available.Scopus is the largest abstract and citation database of peer-reviewed literature: scientific journals, books and conference proceedings.A drug information resource containing: American Hospital Formulary System (AHFS), drug formulary for Lucile Packard Children's Hospital (LPCH) and Stanford Hospital & Clinics (SHC), Lexi-Drugs (adverse reactions, dosage and administration, mechanism of action, storage, use, and administration information), Lexi-Calc, Lexi-ID, Lexi-I.V. Compatibility (King Guide), Lexi-Interact, and Lexi-PALS.Cumulative Index to Nursing and Allied Health Literature (CINAHL) contains coverage of nursing and allied health literature.A knowledge database that provides access to topic reviews based on over 6000 clinically relevant articles. The evidence-based content, updated regularly, provides the latest practice guidelines in 59 medical specialtiesProvides critical assessments of systematic reviews compiled from a variety of medical journals.Selects from the biomedical literature original studies and systematic reviews that are immediately clinically relevant and then summarizes these articles in an enhanced abstract with expert commentary.
Multidisciplinary coverage of over 10,000 high-impact journals in the sciences, social sciences, and arts and humanities, as well as international proceedings coverage for over 120,000 conferences.
Includes cited reference searching, citation maps, and an analyze tool.
Features systematic reviews that summarize the effects of interventions and makes a determination whether the intervention is efficacious or not.
Cochrane reviews are created through a strict process of compiling and analyzing data from multiple randomized control trials to ensure comprehensiveness and reliability.Provides systematic coverage of the psychological literature from the 1800s to the present through articles, book chapters and dissertations.BMJ Clinical Evidence. A clinical information tool built around systematic reviews summarizing the current state of knowledge about prevention and treatment of clinical conditions.PIER (Physicians' Information and Education Resource) is a Web-based decision-support tool designed for rapid point-of-care delivery of up-to-date, evidence-based guidance for primary care physicians.Cochrane Central Register of Controlled Trials (CENTRAL) provides access to 300,000 controlled trials that have been identified the Cochrane Collaboration.Provides drug information targeted for patients.A continually updating drug monograph.The National Guideline Clearinghouse (NGC): A comprehensive database of evidence-based clinical practice guidelines and related documents.MedlinePlus: A repository of health information from the National Library of Medicine. Links are from trusted sites. No advertising, no endorsement of commercial companies or productsLPCH CareNotes via MicroMedex: Patient education handouts customized by LPCH clinical staffMicromedex Lab Advisor: Evidence based laboratory test informationA drug database organized by generic name, trade name and drug class.LPCH / Stanford Hospital Formulary.A goldmine of trusted consumer health information from the world's largest medical library.A trusted source of expert advice for and about kids, providing the information necessary to help patients and parents understand their unique needs.Provides patient handouts from the American Academy of Family Physician.Access to the Stanford Health Library for patients.Lane provides access to over 5,000 eBooks many of which provide helpful background material that will prepare you to better tackle primary literature.
Largest, broadest eBook package; covers all sciences, as well as technology (including software), medicine, and humanities.
In addition to covering Wiley and Springer, MyiLibrary is also the only provider for Oxford and Cambridge University Press titles. No seat restrictions.A collection of biomedical books that can be searched directly by concept, and linked to terms in PubMed abstracts.
A web-based, decision support system for infectious diseases, epidemiology, microbiology and antimicrobial chemotherapy. The database, updated weekly, currently includes 337 diseases, 224 countries, 1,147 microbial taxa and 306 antibacterial (-fungal, -parasitic, -viral) agents and vaccines.
Over 10,000 notes outline the status of specific infections within each country.
Provides online, full-text access to Springer's journal titles as well as journals from other publishers.
Subjects include: life sciences, chemical sciences, environmental sciences, geosciences, computer science, mathematics, medicine, physics and astronomy, engineering and economics. Also includes eBooks.Collection of over 8 thousand fulltext titles in engineering, math, and basic and applied biomedical research. Coverage is from 1967 to the present.A library of ebooks on a wide array of topics, digitized and made available online in conjunction with the original publishers.