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- (Opinionated) guide to microarray data analysis — Epigenetics of aging (103)
- Epigenetics, brain, and behavior — In vitro mutagenesis protocols. 3rd ed. (103)
- In vitro transcription and translation protocols. 2nd ed. — Phylogenomics (103)
- Physician's guide to the diagnosis, treatment, and follow-up of inherited metabolic diseases — Zebrafish : genetics, genomics and informatics. 3rd ed. (103)
- Physician's guide to the diagnosis, treatment, and follow-up of inherited metabolic diseases 2014SpringerIntroductory Chapters -- Amino acids -- Organic acids -- Vitamins and neurotransmitter -- Energy metabolism -- Organelles -- Selected disorder -- Biochemical phenotypes of questionable clinical significance -- Profiles.
- Phytochemicals nutrient-gene interactions 2006CRCnetBASE
- Phytochemistry in the genomics and post-genomics eras. 1st ed. 2002ScienceDirect
- Pichia protocols. 2nd ed. 2007Springer ProtocolsIntroduction : distinction between Pichia pastoris and other expression systems / James M. Cregg -- Vectors and strains for expression / Joan Lin-Cereghino and Geoff P. Lin-Cereghino -- DNA-mediated transformation / James M. Cregg -- Rational design and optimization of fed-batch and continuous fermentation / Wenhui Zhag, Mehmet Inan, and Michael M. Meagher -- Saturation of the secretory pathway by overexpression of a hookworm (Necator americanus) protein (Na-ASP1) / Mehmet Inan ... [et al.] -- Purification of the N- and C-terminal subdomains of recombinant heavy chain fragment C of botulinum neurotoxin serotype C / Jicai Huang ... [et al.] -- Rapid screening of chromatography resins for the purification of proteins / Sandra E. Ríos, Erin M. Giaccone, and Tillman U. Gerngross -- Characterization of O-linked saccharides on glycoproteins / Roger K. Bretthauer -- Modification of the N-glycosylation pathway to produce homogeneous human-like glycans using glycoswitch plasmids / Wouter Vervecken ... [et al.] -- N-linked glycan characterization of heterologous proteins / Huijan Li ... [et al.] -- Heavy labeling of recombinant proteins / Eric Rodriguez -- Selenomethionine labeling of recombinant proteins / Anna M. Larsson and T. Alwyn Jones -- Selective isotopic labeling of recombinant proteins using amino acid auxotroph strains / James W. Whittaker -- Classical genetics / Ilya Tolstorukov and James M. Cregg -- Identification of pexophagy genes by restriction enzyme-mediated integration / Laura A. Schroder, Benjamin S. Glick, and William A. Dunn, Jr. -- Characterization of protein-protein interactions : application to the understanding of peroxisome biogenesis / Sebastien Leon ... [et al.] -- Localization of proteins and organelles using fluorescence microscopy / Jean-Claude Farre ... [et al.] -- Fluorescence microscopy and thin-section electron microscopy / Benjamin S. Glick.
- Plant chromosome engineering 2011Springer ProtocolsRecent advances in plant transformation -- Engineering the plastid genome of nicotiana sylvestris, a diploid model species for plastid genetics -- Homologous recombination in plants : An antireview -- Chromosome painting for plant biotechnology -- Plant B chromosomes -- Telomere truncation in plants -- Engineered plant minichromosomes -- Method for bxb1-mediated site-specific integration in planta -- Targeted mutagenesis in arabidopsis using zinc-finger nucleases -- Vectors and methods for hairpin RNA and artificial microRNA-mediated gene silencing in plants -- Recombinant protein expression in nicotiana -- Chromosome analysis and sorting using flow cytometry -- Super-stretched pachytene chromosomes for plant molecular cytogenetic mapping -- Cytological dissection of the triticeae chromosomes by the gametocidal system -- Development and use of oat-maize chromosome additions and radiation hybrids -- Enhancer trapping in plants -- Chromatin beacons : Global sampling of chromatin physical properties using chromatin charting lines -- Transposable elements as catalysts for chromosome rearrangements.
- Plant genomes 2008KargerPaleopolyploidy and its impact on the structure and function of modern plant genomes / A.H. Paterson -- Genomic history and gene family evolution in angiosperms: challenges and opportunities / J. Sampedro, D. Cosgrove -- The evolutionary position of subfunctionalization, downgraded / M. Freeling -- Grass genome structure and evolution / J. Messing, J.L. Bennetzen -- Phylogenetic insights into the pace and pattern of plant genome size evolution / C.E. Grover, J.S. Hawkins, J.F. Wendel -- Plant transposable elements / J.M. Deragon, J.M. Casacuberta, O. Panaud -- Plant sex chromosomes / D. Charlesworth -- Plant centromeres / J.C. Lamb ... [et al.] -- MiRNAs in the plant genome: all things great and small / B.C. Meyers, P.J. Green, C. Lu -- Recent insights into the evolution of genetic diversity of maize / A. Rafalski, S. Tingey -- The rice genome structure as a trail from the past to beyond / T. Sasaki.
- Plant genomics methods and protocols 2009Springer ProtocolsRole of model plant species / Richard Flavell -- New technologies for ultra-high throughput genotyping in plants / Nikki Appleby, David Edwards, and Jacqueline Batley -- Genetic maps and the use of synteny / Chris Duran, David Edwards, and Jacqueline Batley -- A simple TAE-based method to generate large insert BAC libraries from plant species / Bu-Jun Shi, J. Perry Gustafson, and Peter Langridge -- Transcript profiling and expression level mapping / Elena Potokina, Arnis Druka, and Michael J. Kearsey -- Methods for functional proteomic analyses / Christof Rampitsch and Natalia V. Bykova -- Stable transformation of plants / Huw D. Jones and Caroline A. Sparks -- Transient transformation of plants / Huw D. Jones, Angela Doherty, and Caroline A. Sparks -- Bridging the gene-to-function knowledge gap through functional genomics / Stephen J. Robinson and Isobel A.P. Parkin -- Heterologous and cell-free protein expression systems / Naser Farrokhi ... [et al.] -- Functional genomics and structural biology in the definition of gene function / Maria Hrmova and Geoffrey B. Fincher -- In situ analysis of gene expression in plants / Sinéad Drea ... [et al.] -- Plant and crop databases / David E. Matthews, Gerard R. Lazo, and Olin D. Anderson -- Plant genome annotation methods / Shu Ouyang ... [et al.] -- Molecular plant breeding : methodology and achievements / Rajeev K. Varshney ... [et l.] -- Practical delivery of genes to the marketplace / David A. Fischhoff and Molly N. Cline -- Ecological genomics of natural plant populations : the Israeli perspective / Eviatar Nevo -- Genome sequencing approaches and successes / Michael Imelfort ... [et al.]
- 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!
- Population neuroscience 2013SpringerTerms and Concepts -- History of the Key Disciplines -- Enviromics -- Genomics -- Epigenomics -- Molecular Phenomics -- Systems Phenomics -- Cohorts -- Challenges -- Personalized Preventive Medicine.
- Post-transcriptional gene regulation 2008Springer ProtocolsBioinformatics 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.
- Practical preimplantation genetic diagnosis. 2nd ed. 2012SpringerPrimary 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.
- 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.
- 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.
- Principles of cancer genetics 2008Springer
- 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.
- Principles of cloning. Second edition. [2nd ed.] 2014ScienceDirectPrinciples 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.
- Principles of molecular medicine. 2nd ed. 2006Springer
- PRINS and in situ PCR protocols. 2nd ed. 2006Springer Protocols
- 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.
- Protein engineering 2009SpringerUnderstanding 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.
- Protein engineering protocols 2006Springer Protocols
- 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.
- Protocols for nucleic acid analysis by nonradioactive probes. 2nd ed. 2006Springer ProtocolsGenomic 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.
- Pyrosequencing protocols 2006Springer ProtocolsThe 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.
- Quantitative trait loci methods and protocols 2002Springer Protocols
- 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.
- "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.
- 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.
- Redox cell biology and genetics. Part A-B pt. A-B, 2002.ScienceDirectpt. B ScienceDirect
- Regulation of gene expression by small RNAs 2009CRCnetBASEMicro 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.
- Regulation of gene expression in plants the role of transcript structure and processing 2007Springer
- Regulation of microRNAs 2011SpringerMicroRNA 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.
- Regulation of phytochemicals by molecular techniques. 1st ed. 2001ScienceDirect
- Regulatory genome gene regulatory networks in development and evolution 2006ScienceDirect
- Regulatory RNAs 2006Cold Spring Harb Lab PressMechanism 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.
- Regulatory RNAs basics, methods, and applications 2012Springerpt. 1. Basics -- pt. 2. Methods -- pt. 3. Applications.
- Regulatory RNAs in prokaryotes 2012SpringerThis 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.
- Repetitive DNA 2012KargerThe 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..
- Reporter genes a practical guide 2007Springer ProtocolsMethodologies 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 11th annual international conference, RECOMB 2007, Oakland, CA, USA, April 21-25, 2007 : proceedingsSpringer, 2007
- Research in computational molecular biology 9th annual International Conference, RECOMB 2005, Cambridge, MA, USA, May 14-18, 2005 : proceedingsSpringer, 2005
- Retrotransposition, diversity, and the brain 2008Springer
- Reviews and protocols in DT40 research 2006SpringerCh. 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.
- RNA 2001ScienceDirect
- RNA 3D structure analysis and prediction 2012SpringerIntroduction / 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.
- RNA editing 2008SpringerEditing 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.
- RNA editing 2007ScienceDirect
- RNA exosome 2011Springer"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.
- RNA infrastructure and networks 2011SpringerThe 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.
- RNA interference 2005ScienceDirect
- RNA interference from biology to therapeutics 2013SpringerThe 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.
- 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.
- 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.
- RNA methods and protocols 2008Springer ProtocolsThe 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.
- RNA modification 2007ScienceDirect
- RNA polymerases and associated factors. Part C-D pt. C-D, 2003.ScienceDirectpt. D ScienceDirect
- RNA silencing methods and protocols 2005Springer ProtocolsDetection 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 --
- RNA technologies and their applications 2010SpringerThe 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.
- RNA turnover in bacteria, archaea and organelles 2008ScienceDirect
- RNA turnover in eukaryotes analysis of specialized and quality control RNA decay pathways 2008ScienceDirect
- RNAi design and application 2008Springer Protocols
- RNAi technology 2011CRCnetBASE"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.
- Root genomics 2011SpringerWith 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.
- RT-PCR protocols 2002Springer Protocols
- Sequence comparison theory and methods 2009Springer
- Serial analysis of gene expression (SAGE) methods and protocols 2008Springer ProtocolsSAGE 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.
- Single cell diagnostics methods and protocols 2007Springer ProtocolsNoninvasive 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.
- Single nucleotide polymorphisms methods and protocols 2002Springer Protocols
- Small RNAs analysis and regulatory functions 2006Springer
- Somatic cell nuclear transfer 2006SpringerNuclear 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.
- Statistics of gene mapping 2007Springer
- Stem cell therapy in lysosomal storage diseases 2013Springer1. Lysosomal diseases and therapeutic options: an overview / Eveline J. Langereis and Frits A. Wijburg -- 2. Alternative treatment options: enzyme replacement and small molecule therapies / James Edmond Wraith and Simon Jones -- 3. Hematopoietic cell transplantation in inborn errors of metabolism / Jaap J. Boelens, Paul Szaboles, and Rob Wynn -- 4. Leukodystrophies and lysosomal storage disorders / Maria L. Escolar and Mieke Aldenhoven -- 5. Hematopoietic stem cell gene therapy for lysosomal storage disorders: expected benefits and limitations / Alessandra Biffi and Ilaria Visigalli -- 6. Alternative future therapies for lysosomal storage diseases: embryonic stem cell- and induced pluripotent stem cell therapy / Arie Koen Braat, Paul J. Coffer, and Niels Geijsen -- 7. Concluding comments and future directions / Robert Wynn and Jaap Jan Boelens.
- Stress-induced mutagenesis 2013Springer1. 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.
- Stroke genomics methods and reviews 2005Springer ProtocolsIntroduction 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.
- 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.
- Structural genomics on membrane proteins 2006CRCnetBASEBioinformatics 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.].
- Synthetic nucleic acids as inhibitors of gene expression mechanisms, applications, and therapeutics implications 2005CRCnetBASE
- Target pattern recognition in innate immunity 2009SpringerMacrophage 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.
- Telomeres and telomerase in aging, disease, and cancer molecular mechanisms of adult stem cell ageing 2008Springer
- Textbook of personalized medicine 2009SpringerBasics 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.
- Thymic development and selection of T Lymphocytes 2014SpringerThe 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.
- Transgenic mouse methods and protocols. 2nd ed. 2011Springer ProtocolsIntroduction: 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.
- Transgenic wheat, barley and oats production and characterization protocols 2009Springer ProtocolsTransgenic 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.
- Translation initiation cell biology, high-throughput methods, and chemical-based approaches 2007ScienceDirectPurification 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.].
- Translation initiation extract systems and molecular genetics 2007ScienceDirectUse 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.
- Translation initiation reconstituted systems and biophysical methods 2007ScienceDirectTransient 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.].
- Transposons and the dynamic genome 2009Springer
- Tumor prevention and genetics III 2005SpringerLifestyle 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.
- Untranslated gene regions and other non-coding elements regulation of eukaryotic gene expression 2013SpringerThere 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.
- 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.
- V(D)J recombination 2009SpringerEarly 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.].
- Variation 2005ScienceDirectVariation 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.
- Vertebrate genomes 2006.KargerThe 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.].
- Viruses essential agents of life 2012Springer"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.
- 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.
- WormBook the online review of C. elegans biologyNCBI Bookshelf"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."
- YAC protocols. 2nd ed. 2006Springer ProtocolsMarkers, 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.].
- Yeast gene analysis. 2nd ed. 2007ScienceDirect
- Zebrafish : genetics, genomics and informatics. 3rd ed. 2011ScienceDirectPt.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.
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