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Genetics

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  • Prof. Mark Reimers covers the best ways to design and interpret microarray gene expression experiments, including experiment design, pre-processing, exploratory analysis, normalization and statistical testing.
  • 25 years of p53 research 2005, Springer
  • 2D PAGE v. 1-2, 2008., Springer Protocols
    v. 2, 2008 Springer Protocols
    Isolation of mitochondria from plant cell culture / Etienne H. Meyer and A. Harvey Millar -- Isolation and preparation of choroplasts from Arabidopsis thaliana plants / Sybille E. Kubis, Kathryn S. Lilley, and Paul Jarvis -- Isolation of plant cell wall proteins / Elisabeth Jamet ... [et al.] -- Isolation and fractionation of the endoplasmic reticulum from castor bean (Ricinius communis) endosperm for proteomic analyses / William J. Simon, Daniel J. Maltman, and Antoni R. Slabas -- Cell wall fractionation for yeast and fungal proteomics / Aida Pitarch, Césa Nombela, and Concha Gil -- Sample preparation procedure for cellular fungi / Alois Harder -- Isolation and enrichment of secreted proteins from filamentous fungi / Martha L. Medina and Wilson A. Frnacisco -- Isolation and solubilization of cellular membrane proteins from bacteria / Kheir Zuobi-Hasona and L. Jeannine Brady -- Isolation and solubilization of gram-positive bacterial cell wall-associated proteins / Jason N. Cole, Steven P. Djordjevic, and Mark J. Walker -- Cell fractionation of parasitic protozoa / Wanderley de Souza, José Andrés-Morgado-Diaz, and Narcisa L. Cunha-e-SilvaVolume 2. Application of fluorescence dye saturation labeling for differential proteome analysis of 1,000 microdissected cells from pancreatic ductal adenocarcinoma precursoe lesions / Barbara Sitek ... [et al.] -- Albumin and immunoglobulin depletion of human plasma / Rosalind e. Jenkins ... [et al.] -- Multi-component immunoaffinity subtraction and reversed-phase chromatography of human serum / James Martosella and Nina Zolotarjova -- Immunoaffinity fractionation of plasma proteins by chicken IgY antibodies / Lei Huang and Xiangming Fang -- Proteomics of cerebrospinal fluid methods for sample processing / John E. Hale ... [et al.] -- Sample preparation of bronchoalveolar lavage fluid / Baptiste Leroy, Paul Falmagne, and Ruddy Wattiez -- Preparation of nasal secretions for peoteome analysis / Begona Casado, Paolo Iadarola, and Lewis K. Pannell -- Preparation of urine samples for proteomic analysis / Rembert Pieper -- Isolation of cytoplasmatic proteins from cultures cells for two-dimensional gel electrophoresis / Ying Wang, Jen-Fu Chiu, and Qing-Yu He -- Sample preparation of culture medium from Madin-Darby Canine Kidney cells / Daniel Ambort, Daniel Lottaz, and Erwin Sterchi -- Sample preparation for mass spectrometry analysis of formalin-fixed paraffin-embedded tissue proteomic analysis of formalin-fixed tissue / Nicolas A. Stewart and Timothy D. Veenstra -- Metalloproteomics in the molecular study of cell physiology and disease / Hermann-Josef Thierse, Stefanie Helm, and Patrick Pankert -- Protein extraction from green plant tissue / Ragnar Flengsrud -- The terminator a device for high-throughput extraction of plant material / B. M. van den Berg --Volume 1. Mechanical/physical methods of cell disruption and tissue homogenization / Stanley Goldberg -- Bacteria and yeast cell disruption using lytic enzymes / Oriana Salazar -- Sample solublization buffers for two-dimensional electrophoresis / Walter Weiss and Angelika Görg -- Quantitation of protein in samples prepared for 2-D electrophoresis / Tom Berkelman -- Removal of interfering substances in samples prepared for two-dimensional (2-D) electrophoresis / Tom Berkelman -- Protein concentration by hydrophilic interaction chromatography combined with solid phase extraction / Ulrich Schneider -- Difference gel electrophoresis based on lys/cys tagging / Reiner Westermeier and Burghardt Scheibe -- Isotope-coded two-dimensional maps: tagging with deuterated acrylamide and 2-vinylpyridine / Pier Giorgio Righetti, Roberto Sebastiano, and Attilio Citterio.
  • ADAR proteins : structure and catalytic mechanism /Rena A. Goodman, Mark R. Macbeth and Peter A. Beal --ADAR proteins : double-stranded RNA and Z-DNA binding domains /Pierre Barraud and Frédéric H.-T. Allain --Editing of neurotransmitter receptor and ion channel RNAs in the nervous system /Jennifer L. Hood and Ronald B. Emeson --Modulation of microRNA expression and function by ADARs /Bjorn-Erik Wulff and Kazuko Nishikura --Nuclear editing of mRNA 3'-UTRs /Ling-Ling Chen and Gordon G. Carmichael --Control of ADAR1 editing of hepatitis delta virus RNAs /John L. Casey --Bioinformatic approaches for identification of A-to-I editing sites /Eli Eisenberg --ADARs : viruses and innate immunity /Charles E. Samuel --Role of ADARs in mouse development /Carl R. Walkley, Brian Liddicoat and Jochen C. Hartner --Regulation and functions of ADAR in Drosophila /Simona Paro, Xianghua Li, Mary A. O'Connell and Liam P. Keegan.
  • Advanced bacterial genetics 2007, ScienceDirect
    Strain collections and genetic nomenclature / S.R. Maloy ... [et al.] -- Use of antibiotic-resistant transposons for mutagenesis / S.R. Maloy -- In vivo mutagenesis using EZ-Tn5 / J.R. Kirby -- Identification of essential genes in bacteria / D.R. Hillyard ... [et al.] -- Isolation of transposon insertions / S.R. Maloy -- Localized mutagenesis / S.R. Maloy -- Generation of deletions and duplications using transposons as portable regions of homology with emphasis on Mud and Tn10 transposons / K.T. Hughes -- Target-directed proteolysis in vivo / M. Eser ... [et al.] -- Sets of transposon-generated sequence-tagged mutants for structure-function analysis and engineering / B. Traxler ... [et al.] -- Using genomic microarrays to study insertional/transposon mutant libraries / D.N. Baldwin ... [et al.] -- Screening transposon mutant libraries using full-genome oligonucleotide microarrays / K. M. Winterberg ... [et al.] -- Creating recombination-activated genes and sequence-defined mutant libraries using transposons / L. Gallagher ... [et al.] -- Use of operon and gene fusions to study gene regulation in Salmonella / K.T. Hughes ... [et al.] -- Genomic screening for regulatory genes using the T-POP transposon / C. Lee ... [et al.] -- Recombineering: In vivo genetic engineering in E. coli, S. enterica, and beyond / J.A. Sawitzke ... [et al.] -- [lambda]-red genetic engineering in Salmonella enterica serovar Typhimurium / J.E. Karlinsey -- Probing nucleoid structure in bacteria using phage lambda integrase-mediated chromosome rearrangements / N. Garcia-Russell ... [et al.] -- Dissecting nucleic acid-protein interactions using challenge phage / S.R. Maloy ... [et al.] -- Mud-P22 / J.A. Crain ... [et al.] -- Phage metagenomics / V. Casas ... [et al.].
  • Intended as a companion to the Fundamentals of Forensic DNA Typing volume published in 2009, Advanced Topics in Forensic DNA Typing: Methodology contains 18 chapters with 4 appendices providing up-to-date coverage of essential topics in this important field and citation to more than 2800 articles and internet resources. The book builds upon the previous two editions of John Butler's internationally acclaimed Forensic DNA Typing textbook with forensic DNA analysts as its primary audience. This book provides the most detailed information written to-date on DNA databases, low-level DNA, validation, and numerous other topics including a new chapter on legal aspects of DNA testing to prepare scientists for expert witness testimony. Over half of the content is new compared to previous editions. A forthcoming companion volume will cover interpretation issues. Contains the latest information - hot-topics and new technologies Well edited, attractively laid out, and makes productive use of its four-color format Author John Butler is ranked as the number one "high-impact author in legal medicine and forensic science, 2001 to 2011" by ScienceWatch.com.
  • Repair of DNA Interstrand Cross-links Produced by Cancer Chemotherapeutic Drugs /Anderson T. Wang, Peter J. McHugh --DNA-PK, a Pharmacological Target in Cancer Chemotherapy and Radiotherapy? /Bernard Salles D.V.M., Ph.D. --Growth Factor Receptor Signaling, DNA Damage Response, and Cancer Cell Susceptibility to Chemotherapy and Relapses /Moulay Alaoui-Jamali, Amine Saad, Gerald Batist --The Relationship Between DNA-Repair Genes, Cellular Radiosensitivity, and the Response of Tumors and Normal Tissues to Radiotherapy /David Murray, Matthew Parliament --Important Roles of ERCC1 in DNA Repair and Targeted Therapy /Jennifer J. Hu, Joseph de la Garza --The Role of BRCA1 and BRCA2 in Anticancer Drug Therapy /Andrew Y. Shuen, Jorge S. Reis-Filho --DNA-PK in CLL Chemotherapy /L. Amrein, D. Davidson, R. Aloyz, L. Panasci --Poly(ADP) Ribose Polymerase at the Interface of DNA Damage Signaling and DNA Repair /Jana Krietsch, Michele Rouleau, Michel Lebel --Cellular Protection Against the Antitumor Drug Bleomycin /Dindial Ramotar Ph.D., Mustapha Aouida Ph.D. --ATR as a Therapeutic Target /Fiona K. Middleton, Nicola J. Curtin --Telomeres, Telomerase, and DNA Damage Response in Cancer Therapy /Raina A. Tamakawa, Helen B. Fleisig --RAD51 Is a Key Protein of DNA Repair and Homologous Recombination in Humans /Alexander V. Mazin Ph.D., Olga M. Mazina.
  • Microarrays in Gene Expression Studies, p. 1-29 -- Cleaning and Normalization, p. 31-59 -- Some Cluster Analysis Methods, p. 61-97 -- Clustering of Tissue Samples, p. 99-131 -- Screening and Clustering of Genes, p. 133-183 -- Discriminant Analysis, p. 185-220 -- Supervised Classification of Tissue Samples, p. 221-251 -- Linking Microarray Data with Survival Analysis, p. 253-266.
  • Recent studies demonstrated a key role of the androgen receptor in the development of castration-recurrent or -resistant prostate cancer (CRPC), which is deadly and in urgent need of more effective therapies. Understanding the functions of androgen-responsive genes and their regulation and deregulation in prostate cancer progression may lead to new approaches to prevent and treat prostate cancer patients. This book provides an up-to-date review of the overall androgen-responsive gene expression program and the regulation, function, and clinical relevance of both protein coding and non-coding androgen-responsive genes. Experts in the field of androgen action and prostate cancer research discussed the importance of DNA elements, chromatin structure, cellular signaling, and cell-cell interactions in the regulation of androgen-responsive genes in the context of prostate cancer progression, including the development of CRPC. This book is intended for individuals interested in cancer endocrinology and medical and healthcare professionals involved in prostate cancer research.
  • Omics & microarrays revisited -- The commercial microarrays -- Supports & surface chemistries -- The arraying processes -- Gene expression microarray-based applications -- Protein microarray applications -- Multiplex assays.
  • Bacterial artificial chromosomes v. 1-2, 2004., Springer Protocols
    v. 2, 2004 Springer Protocols
    v. 1. Library construction, physical mapping, and sequencing -- v. 2. Functional studies.
  • Bacterial chromatin 2010, Springer
  • Microbial genomes / Voon Loong Chan -- Evolution and origin of virulence isolates / Voon Loong Chan, Philip M. Sherman, and Billy Bourke -- Genomic approach to understanding of infectious disease mechanisms / Voon Loong Chan, Philip M. Sherman, and Billy Bourke -- Knockout and disease models in toll-like receptor-mediated immunity / Huey-Lan Huang and Wen-Chen Yeh -- Campylobacter from glycome to pathogenesis / John Kelly ... [et al.] -- Genomics of helicobacter species / Zhongming Ge and David B. Schauer -- The organization of leptospira at a genomic level / Dieter M. Bulach ... [et al.] -- Listeria monocytogenes / Keith Ireton -- Mycobacterial genomes / David C. Alexander and Jun Liu -- Mycoplasma / Yuko Sasaki -- Genome comparisons of diverse staphylococcus aureus strains / Martin J. McGavin -- Type III secretion, systems in yersinia pestis, and yersinia pseudotuberculosis / James B. Bliska, Michelle B. Ryndak, and Jens P. Grabenstein -- Genomics and the evolution of pathogenic vibrio cholerae / William S. Jermyn ... [et al.] -- Future directions of infectious disease research / Philip M. Sherman, Billy Bourke, and Voon Loong Chan -- Index.
  • Chapter 1. Estimation and Testing in Time-Course Microarray Experiments -- Chapter 2. Classification for Differential Gene Expression Using Bayesian Hierarchical Models -- Chapter 3. Applications of MOSS for Discrete Multi-Way Data -- Chapter 4. Nonparametric Bayesian Bioinformatics -- Chapter 5. Measurement Error and Survival Model for cDNA Microarrays -- Chapter 6. Bayesian Robust Inference for Differential Gene Expression -- Chapter 7. Bayesian Hidden Markov Modeling of Array CGH Data -- Chapter 8. Bayesian Approaches to Phylogenetic Analysis -- Chapter 9. Gene Selection for the Identification of Biomarkers in High-Throughput Data -- Chapter 10. Sparsity Priors for Protein - Protein Interaction Predictions -- Chapter 11. Learning Bayesian Networks for Gene Expression Data -- Chapter 12. In-Vitro to In-Vivo Factor Profiling in Expression Genomics -- Chapter 13. In-Vitro to In-Vivo Factor Profiling in Expression Genomics Machines -- Chapter 14. A Bayesian Mixture Model for Protein Biomarker Discovery -- Chapter 15. Bayesian Methods for Detecting Differentially Expressed Genes -- Chapter 16. Bayes and Empirical Bayes Methods for Spotted Microarray Data Analysis -- Chapter 17. Bayesian Classification Method for QTL Mapping.
  • Behavioral neurogenetics 2012, Springer
  • The regulation of gene expression -- The regulation of enzyme activity -- Structure and function of signal pathways -- Signaling by nuclear receptors -- G protein-coupled signal transmission pathways -- Intracellular messenger substance : second messengers -- Ser/Thr-specific protein kinases and protein phosphates -- Signal transmission via transmembrane receptors with tyrosine-specific protein kinase activity -- Signal transmission via ras proteins -- Intracellular signal transduction : the protein cascades of the MAP kinase pathways -- Membrane receptors with associated tyrosine kinase activity -- Other receptor classes -- Regulation of the cell cycle -- Malfunction of signaling pathways and tumorigenesis : oncogenes and tumor suppressor genes -- Apoptosis.
  • Similarity searching using BLAST / Kit J. Menlove, Mark Clement, and Keith A. Crandall -- Gene orthology assessment with OrthologID / Mary Egan ... [et al.] -- Multiple alignment of DNA sequences with MAFFT / Kazutaka Katoh, George Asimenos, and Hiroyuki Toh -- SeqVis : a tool for detecting compositional heterogeneity among aligned nucleotide sequences / Lars Sommer Jermiin ... [et al.] -- Selection of models of DNA evolution with jModelTest / David Posada -- Estimating maximum likelihood phylogenies with PhyML / Stéphane Guindon ... [et al.] -- Trees from trees : construction of phylogenetic supertrees using clann / Christopher J. Creevey and James O. McInerney -- Detecting signatures of selection from DNA sequences using datamonkey / Art F.Y. Poon, Simon D.W. Frost, and Sergei L. Kosakovsky Pond -- Recombination detection and analysis using RDP3 / Darren P. Martin -- CodonExplorer : an interactive online database for the analysis of codon usage and sequence composition / Jesse Zaneveld ... [et al.] -- Genetic code prediction for metazoan mitochondria with GenDecoder / Federico Abascal, Rafael Zardoya, and David Posada -- Computational gene annotation in new genome assemblies using GeneID / Enrique Blanco and Josep F. Abril -- Promoter analysis : gene regulatory motif identification with A-GLAM / Leonardo Mariño-Ramírez ... [et al.] -- Analysis of genomic DNA with the UCSC Genome Browser / Jonathan Pevsner -- Mining for SNPs and SSRs using SNPServer, dbSNP and SSR taxonomy tree / Jacqueline Batley and David Edwards -- Analysis of transposable element sequences using CENSOR and RepeatMasker / Ahsan Huda and I. King Jordan -- DNA sequence polymorphism analysis using DnaSP / Julio Rozas.
  • Preface xi -- Acknowledgments xiii -- 1 Introduction I -- 1.1 Hybridization 1 -- 1.2 Affymetrix GeneChip Technology 3 -- 1.3 Spotted Arrays 6 -- 1.4 Serial Analysis of Gene Expression (SAGE) 8 -- 1.5 Example: Affymetrix vs. Spotted Arrays 9 -- 1.6 Summary 11 -- 1.7 Further Reading 13 -- 2 Overview of Data Analysis 15 -- 3 Basic Data Analysis 17 -- 3.1 Absolute Measurements 17 -- 3.2 Scaling 18 -- 3.2.1 Example: Linear and Nonlinear Scaling 20 -- 3.3 Detection of Outliers 20 -- 3.4 Fold Change 21 -- 3.5 Significance 22 -- 3.5.1 Nonparametric Tests 24 -- 3.5.2 Correction for Multiple Testing 24 -- 3.5.3 Example I: t-Test and ANOVA 25 -- 3.5.4 Example II: Number of Replicates 26 -- 3.6 Summary 28 -- 3.7 Further Reading 29 -- 4 Visualization by Reduction of Dimensionality 33 -- 4.1 Principal Component Analysis 33 -- 4.2 Example 1: PCA on Small Data Matrix 35 -- 4.3 Example 2: PCA on Real Data 37 -- 4.4 Summary 37 -- 4.5 Further Reading 39 -- 5 Cluster Analysis 41 -- 5.1 Hierarchical Clustering 41 -- 5.2 K-means Clustering 43 -- 5.3 Self-Organizing Maps 44 -- 5.4 Distance Measures 45 -- 5.4.1 Example: Comparison of Distance Measures 47 -- 5.5 Normalization 49 -- 5.6 Visualization of Clusters 50 -- 5.6.1 Example: Visualization of Gene Clusters in -- Bladder Cancer 50 -- 5.7 Summary 50 -- 5.8 Further Reading 52 -- 6 Beyond Cluster Analysis 55 -- 6.1 Function Prediction 55 -- 6.2 Discovery of Regulatory Elements in Promoter -- Regions 56 -- 6.2.1 Example 1: Discovery of Proteasomal Element 57 -- 6.2.2 Example 2: Rediscovery of Mlu Cell Cycle -- Box (MCB) 57 -- 6.3 Integration of data 58 -- 6.4 Summary 59 -- 6.5 Further Reading 59 -- 7 Reverse Engineering of Regulatory Networks 63 -- 7.1 The Time-Series Approach 63 -- 7.2 The Steady-State Approach 64 -- 7.3 Limitations of Network Modeling 65 -- 7.4 Example 1: Steady-State Model 65 -- 7.5 Example 2: Steady-State Model on Real Data 66 -- 7.6 Example 3: Steady-State Model on Real Data 68 -- 7.7 Example 4: Linear Time-Series Model 68 -- 7.8 Further Reading 71 -- 8 Molecular Classifiers 75 -- 8.1 Classification Schemes 76 -- 8.1.1 Nearest Neighbor 76 -- 8.1.2 Neural Networks 76 -- 8.1.3 Support Vector Machine 76 -- 8.2 Example I: Classification of Cancer Subtypes 77 -- 8.3 Example II: Classification of Cancer Subtypes 78 -- 8.4 Summary 79 -- 8.5 Further Reading 79 -- 9 Selection of Genes for Spotting on Arrays 81 -- 9.1 Gene Finding 82 -- 9.2 Selection of Regions Within Genes 82 -- 9.3 Selection of Primers for PCR 83 -- 9.4 Selection of Unique Oligomer Probes 83 -- 9.4.1 Example: Finding PCR Primers for Gene -- AF105374 83 -- 9.5 Experimental Design 84 -- 9.6 Further Reading 84 -- 10 Limitations of Expression Analysis 87 -- 10.1 Relative VersusAbsoluteRNA Quantification 88 -- 10.2 Further Reading 88 -- 11 Genotyping Chips 91 -- 11.1 Example: NeuralNetworksfor GeneChipprediction 91 -- 11.2 Further Reading 93 -- 12 Software Issues and Data Formats 95 -- 12.1 Standardization Efforts 96 -- 12.2 Standard File Format 97 -- 12.2.1 Example: Small Scripts in Awk 97 -- 12.3 Software for Clustering 98 -- 12.3.1 Example: Clustering with ClustArray 99 -- 12.4 Software for Statistical Analysis 99 -- 12.4.1 Example: StatisticalAnalysis with R 99 -- 12.4.2 The affyR Software Package 103 -- 12.4.3 Commercial Statistics Packages 103 -- 12.5 Summary 103 -- 12.6 Further Reading 104 -- 13 Commercial Software Packages 105 -- 14 Bibliography 109 -- Index 123.
  • When quantum mechanics was first proposed a century ago, nobody could have anticipated how deeply it would affect our lives. Today, we are connected and powered through devices whose existence is predicated on the basic principles of this strange physics. Not even the biological sciences have escaped its reach. As scientists query the deepest mysteries of the living world, the physical scales probed and the types of questions asked are increasingly blurring the lines between biology and physics. The hybrid field of biophysics represents the new frontier of the 21st century. The ribosome has been at the heart of three Nobel Prizes. Understanding its essential nature and how it interacts with other proteins and nucleic acids to control protein synthesis has been one of the central foundations in our understanding of the biology at the molecular level. With the advent of atomic scale structures, methods to visualize and separate individual molecules, and the computational power to model the complex interactions of over a million atoms at once, our understanding of how gene expression is controlled at the level of protein translation is now deeply ensconced in the biophysical realm. This book provides a premier resource to a wide audience, whether it be the general reader seeking a broad view of the field, a clinician interested in the role of protein translation in human disease, the bench researcher looking for state-of-the-art technologies, or computational scientists involved in cutting edge molecular modeling.
  • "Genes and environment. Biology and behavior. Nature and nurture. The terminology may be clear-cut, but the processes themselves are far from simple: unlike the direct cause-and-effect dichotomies of past frameworks, researchers now recognize these family-based connections as multifaceted, transactional, and emergent. [This book] aims at illuminating a multiplicity of approaches and methodologies for studying family dynamics, to match the complex interplay of physiological factors, environmental challenges, and behavioral adaptations that characterize family life and development. Chapters illustrate physical and social influences on parenting, childhood, adolescence, fertility, and family formation, providing analytical frameworks for understanding key areas such as family behavior, health, development, and adaptation to contextual stressors."--Book jacket.
  • Identification of fungal pathogenicity genes by Agrobacterium tumefaciens-mediated transformation / Karunakaran Maruthachalam ... [et al.] -- The genetics and molecular biology of carotenoid biosynthesis in mucorales / Catalina Sanz, Mahdi Shahriari, and Arturo P. Eslava -- Induction and repression of carbohydrate degrading enzymes in fungi with special reference to their coding genes / Pauline Walsh, Alan Hernon, and Anthonia O'Donovan -- Involvement of ADH1, IPT1, and PMT genes in Candida albicans pathogenesis / Mahmoud Rouabhia and Mahmoud Ghannoum -- Enhanced resistance to fungal pathogens in plants through selective utilization of useful fungal genes / B.K. Sarma ... [et al.] -- Genes encoding penicillin and cephalosporin biosinthesis in Acremonium chrysogenum : two separate clusters are required for cephalosporin production / Juan-Francisco Martøn, Carlos Garcia-Estrada, and Ricardo V. Ullon -- A review of the fungal B-galactosidase gene and its biotechnological applications / Anne G. Lydon -- Trichoderma genes involved in interactions with fungi and plants / Mala Mukherjee -- Use of luciferases as a tool to analyze fungal physiology in association with gene transcription / David M. Arana and Jess Pla --Fungal genes and their respective enzymes in industrial food, bio-based, and pharma applications / Marco van den Berg ... [et al.] -- Fungal metacaspases : an overview / Anthonia O'Donovan, Finola E. Cliffe, and Mary C. Shier -- Signaling molecules in the Arbuscular mycorrhizal fungi / Mohammad Miransari -- Role of pathogenic genes of Fusarium oxysporum, coding cell wall degrading enzymes during wilt infection in plants / Vijai Kumar Gupta, Maria Tuohy, and A. Manimaran -- Engineering fungal expression systems : recombinant expression of two class I alpha-1, 2-mannosidases from the filamentous fungus Aspergillus nidulans / C. Joshua Eades and William E. Hintz -- PCR-diagnostic of Septoria nodorum berk : aggresivenes in wheat tissue / I.V. Maksimov and A.Sh. Valeev -- Detection of toxigeneic and pathogenic fungi targeting metabolic pathway genes / Venkataramana Mudili ... [et al.] -- Pathogenicity genes in entomopathogenic fungia used as biopesticides / K. Uma Devi ... [et al.].
  • Executive summary -- Report of the working-group meeting / Christos Louis and Bart G.J. Knols -- Review of previous applications of genetics to vector control / Chris F. Curtis -- Genomics and expected benefits for vector entomology / Christos Louis -- Genetic approaches for malaria control / Marcelo Jacobs-Lorena -- Current thoughts about the integration of field and laboratory sciences in genetic control of disease vectors / Thomas W. Scott -- Genetic approaches in Aedes aegypti for control of dengue: an overview / Kenneth Olson .... [et al.] -- Malaria and dengue vector biology and control in West and Central Africa / Didier Fontenille and Pierre Carnevale -- Malaria and dengue vector biology and control in Southern and Eastern Africa / Maureen Coetzee -- Malaria and dengue vector biology and control in Southeast Asia / Pattamaporn Kittayapong -- Malaria and dengue vector biology and control in Latin America / Mario H. Rodriguez -- Transition from the laboratory to the field and effective interplay / Christos Louis -- Evaluation of drive mechanisms (including transgenes and drivers) in different environmental conditions and genetic backgrounds / Anthony A. James ... [et al.] -- Tools for monitoring the genetic structure and stability of mosquito populations / Gregory C. Lanzaro, Sergey Nuzhdin and Frederic Tripet -- What are relevant assays for refractoriness / George K. Christophides ... [et al.] -- Fitness studies: developing a consensus methodology / Thomas W. Scott ... [et al.] --Mosquito mating behaviour / Willem Takken ... [et al.] -- Pathogen evolution issues in genetically modified mosquito vector strategies / Mario H. Rodriquez -- Models to investigate some issues regarding the feasibility of driving refractoriness genes into mosquito vector populations / Chris F. Curtis -- Identification and characterization of field sites for genetic control of disease vectors / Bart G.J. Knols and Hervé Bossin -- Application of genetically modified mosquitoes in national vector control programmes: thoughts on integrated control / Abraham Mnzava ... [et al.] -- Entomological correlates of epidemiological impacts: how do we know it is working? / Andrew Githeko -- Ethical, legal and social issues in the use of genetically modified vectors for disease control / Yeya T. Touré and Lucien Manga.
  • Brutes or angels 2013, ebrary
    A guide to the rapidly progressing Age of Biotechnology, Brutes or Angels provides basic information on a wide array of new technologies in the life sciences, along with the ethical issues raised by each. With stem cell research, Dolly the cloned sheep, in vitro fertilization, age retardation, and pharmaceutical mind enhancement, humankind is now faced with decisions that it has never before had to consider. The thoughtfulness, or lack of it, that we bring to those decisions will largely determine the future character of the living world.
  • C. elegans 2006, Springer Protocols
    An overview of C. elegans biology / Kevin Strange -- Comparative genomics in C. elegans, C. briggsae, and other Caenorhabditis species / Avril Coghlan, Jason E. Stajich, and Todd W. Harris -- WormBase: methods for data mining and coparative genomics / Todd W. Harris and Lincoln D. Stein -- C. elegans deletion mutant screening / Robert J. Barstead and Donald G. Moerman -- Insertional mutagenesis in C. elegans using the drosophila transposon Mos1: a method for the rapid identification of mutated genes / Jean-Louis Bessereau -- Single nucleotide polymorphism mapping / M. Wayne Davis and Marc Hammarlund -- Creation of transgenic lines using microparticle bombardment methods / Vida Praitis -- Construction of plasmids for RNA interference and in vitro transcription of double-stranded RNA / Lisa Timmons -- Delivery methods for RNA interference in C. elegans / Lisa Timmons -- Functional genomic approaches in C. elegans / Todd Lamitina -- Assays for toxicity studies in C. elegans with Bt crystal proteins / Larry J. Bischof, Danielle L. Huffman, and Raffi V. Aroian -- Fluorescent reporter methods / Harald Hutter -- Electrophysiological analysis of neuronal and muscle function in C. elegans / Michael M. Francis and Andres Villu Maricq -- Sperm and oocyte isolation methods for biochemical and proteomic analysis / Michael A. Miller -- Preservation of C. elegans tissue via high-pressure freezing and freeze-substitution for ultrastructural analysis and immunocytochemistry / Robby M. Weimer -- Intracellular pH measurements in vivo using green fluorescent protein variants / Keith Nehrke -- Automated imaging of C. elegans behavior / Christopher J. Cronin, Zhaoyang Feng, and William R. Schafer -- Intracellular Ca2+ imaging in C. elegans / Rex A. Kerr and William R. Schafer -- In vitro culture of C. elegans somatic cells / Kevin Strange and Rebecca Morrison -- Techniques for analysis, sorting, and dispensing of C. elegans on the COPAS flow-sorting system / Rock Pulak.
  • Caenorhabditis elegans. 2nd ed. 2011, ScienceDirect
    Pt.I Genetics and functional genomics :Mapping mutations in C. elegans /Eric J. Lambie --Specialized chromosomes and their uses in caenorhabditis elegans /Martin R. Jones,Zoe Lohn,Ann M. Rose --Genome engineering by transgene-instructed gene conversion in C. elegans /Valérie J.P. Robert,Jean-Louis Bessereau --RNAi methods and screening : RNAi based high-throughput genetic interaction screening /Patricia G. Cipriani,Fabio Piano --Dissection of genetic pathways in C. elegans /Zheng Wang,David R. Sherwood --Pt.II Molecular biology and biochemistry :Transgenesis in C. elegans /Vida Praitis,Morris F. Maduro --RNA processing in C. elegans /J. Jason Morton,Thomas Blumenthal --Analysis of microRNA expression and function /Priscilla M. Van Wynsberghe,Shih-Peng Chan,Frank J. Slack,Amy E. Pasquinelli --In situ hybridization of embryos with antisense RNA probes /Gina Broitman-Maduro,Morris F. Maduro --Gene-centered regulatory network mapping /Albertha J.M. Walhout --Affinity purification of protein complexes in C. elegans /Esther Zanin,Julien Dumont,RetoGassmann,Iain Cheeseman,Paul Maddox,Shirin Bahmanyar,Ana Carvalho,Sherry Niessen,John R. Yates III,Karen Oegema,Arshad Desai --Pt.III Development :Cell indentification and cell lineage analysis /Claudiu A. Giurumescu,Andrew D. Chisholm --Thegenetics and cell biology of fertilization /Brian D. Geldziler,Mathew R. Marcello,Diane C. Shakes,Andrew Singson --Imaging embryonic morphogenesis in C. elegans /Jeff Hardin --Molecular and genetic approaches for the analysis of C. elegans neuronal development /Dong Yan,Yishi Jin --Methods for evaluating the caenorhabditis elegans dauer state : standard dauer-formation assay using synthetic daumones and proteomic analysis of O-GIcNAc modifications /Jeeyong Lee,Kwang-Youl Kim,Kyoe-Jin Joo,Keekyeong Kim,Pan-Young Jeong,Young-Ki Paik.
  • Cancer genomics 2013, Springer
    Genomic Pathology of Lung Cancer /Kenneth J. Craddock, Shirley Tam, Chang-Qi Zhu, Ming-Sound Tsao --Understanding Melanoma Progression by Gene Expression Signatures /J. Tímár, T. Barbai, B. Győrffy, E. Rásó --Prognostic Testing in Uveal Melanoma /Michael Zeschnigk, Dietmar R. Lohmann --Capturing and Deciphering the Molecular Signatures of Head and Neck Cancer /Thomas J. Belbin, Roberto A. Lleras, Richard V. Smith --Predictive and Prognostic Biomarkers for Colorectal Cancer /Lara Lipton, Michael Christie, Oliver Sieber --Expression Profiling of Hepatocellular Carcinoma /Rosina Maria Critelli, Elisabetta Cariani, Erica Villa --Kidney Cancer Genomics: Paving the Road to a New Paradigm of Personalized Medicine /George M. Yousef, Nicole M. A. White, Andrew H. Girgis --Pancreatic Cancer Genomics /Vincenzo Corbo, Andrea Mafficini, Eliana Amato, Aldo Scarpa --Breast Cancer Genomics: From Portraits to Landscapes /Ulrich Pfeffer, Valentina Mirisola, Alessia Isabella Esposito --Genomic Landscape of Ovarian Cancer /Delia Mezzanzanica, Loris De Cecco, Marina Bagnoli, Patrizia Pinciroli --Genetics of Endometrial Carcinoma /M. Angeles López-García, Begoña Vieites, M. Angeles Castilla --Usefulness of Molecular Biology in Follicular-Derived Thyroid Tumors: From Translational Research to Clinical Practice /Alexandre Bozec, Marius Ilie, Paul Hofman --Sarcomas Genetics: From Point Mutation to Complex Karyotype, from Diagnosis to Therapies /Frédéric Chibon, Alain Aurias, Jean-Michel Coindre --Novel Molecular Acquisitions in Leukemias /Sabina Chiaretti, Robin Foà --Where Do We Stand in the Genomics of Lymphomas? /Francesco Bertoni, Zhi-Ming Li, Emanuele Zucca --The Genomics of Multiple Myeloma and Its Relevance in the Molecular Classification and Risk Stratification of the Disease /Antonino Neri, Luca Agnelli --Genome-Wide Analysis and Gene Expression Profiling of Neuroblastoma: What Contribution Did They Give to the Tumor Treatment? /Gian Paolo Tonini.
  • Cancer genomics 2014, ScienceDirect
    Cancer Genomics addresses how recent technological advances in genomics are shaping how we diagnose and treat cancer. Built on the historical context of cancer genetics over the past 30 years, the book provides a snapshot of the current issues and state-of-the-art technologies used in cancer genomics. Subsequent chapters highlight how these approaches have informed our understanding of hereditary cancer syndromes and the diagnosis, treatment and outcome in a variety of adult and pediatric solid tumors and hematologic malignancies. The dramatic increase in cancer genomics research and ever-increasing availability of genomic testing are not without significant ethical issues, which are addressed in the context of the return of research results and the legal considerations underlying the commercialization of genomic discoveries. Finally, the book concludes with "Future Directions", examining the next great challenges to face the field of cancer genomics, namely the contribution of non-coding RNAs to disease pathogenesis and the interaction of the human genome with the environment. Tools such as sidebars, key concept summaries, a glossary, and acronym and abbreviation definitions make this book highly accessible to researchers from several fields associated with cancer genomics.Contributions from thought leaders provide valuable historical perspective to relate the advances in the field to current technologies and literature.
  • Cancer genomics and proteomics 2007, Springer Protocols
    Reciprocal subtraction differential RNA display (RSDD) : an efficient technology for cloning differentially expressed genes / Devanand Sarkar, Dong-chul Kang, and Paul B. Fisher -- Cloning differentially expressed genes using rapid subtraction hybridization (RaSH) / Habib Boukerche ... [et al.] -- The application of differential display as a gene profiling tool / Ken Chien-Neng Chang ... [et al.] -- Serial analysis of gene expression (SAGE) / Fred van Ruissen and Frank Baas -- Gene expression profile analysis of tumors / Katia Basso and Riccardo Dalla-Favera -- cDNA microarray and bioinformatic analysis of nuclear factor [kappa]B related genes in squamous cell carcinoma / Zhong Chen ... [et al.] -- Gene profiling uncovers retinoid target genes / Yan Ma ... [et al.] -- Complete open reading frame (C-ORF) technique : rapid and efficient method for obtaining complete protein coding sequences / Dong-chul Kang and Paul B. Fisher -- Chromatin immunoprecipitation assays : molecular analysis of chromatin modification and gene regulation / Piyali Dasgupta and Srikumar P. Chellappan -- Manipulating genes and gene copy number by bacterial artificial chromosome transfection / Stephanie F. Phelps, Sharon Illenye, and Nicholas H. Heintz -- Molecular cytogenetic applications in analysis of the cancer genome / Pulivarthi H. Rao, Subhadra V. Nandula, and Vundavalli V. Murty -- Monitoring methylation and gene expression in cancer / Hetty Carraway and James Herman -- The use of phage display peptide libraries for basic and translational research / Renee Brissette and Neil I. Goldstein -- Yeast and mammalian two-hybrid systems for studying protein-protein interactions / Shu-ichi Matsuzawa and John C. Reed -- Ribonomic and short hairpin RNA gene silencing methods to explore functional gene programs associated with tumor growth arrest / Timothy E. Baroni ... [et al.] -- Surface-epitope masking (SEM) : an immunological subtraction approach for developing monoclonal antibodies targeting surface-expressed molecules / Neil I. Goldstein and Paul B. Fisher -- Approaches for monitoring signal transduction changes in normal and cancer cells / Paul Dent ... [et al.] -- PKR in innate immunity, cancer, and viral oncolysis / Siddharth Balachandran and Glen N. Barber -- Analysis of transformation and tumorigenicity using mouse embryonic fibroblast cells / Hong Sun and Reshma Taneja -- Analysis of growth properties and cell cycle regulation using mouse embryonic fibroblast cells / Hong Sun, Neriman Tuba Gulbagci, and Reshma Taneja -- Reverse phase protein microarrays for monitoring biological responses / Virginia Espina ... [et al.] -- Protein crystallization / Champion Deivanayagam, William J. Cook, and Mark R. Walter.
  • The ouput of eukaryotic genomes is much more complex than expected. Genes produce different variants of RNAs from multiple promoters. One of the ultimate targets of biological analysis is to establish a relationship between the messenger RNAs that are transcribed from the genome and the genomic regions that control their expression - the promoters - in order to decipher the networks that regulate gene expression and the transcription factors that act as master regulators of transcriptional control. Novel technologies have recently appeared that allow deciphering of transcriptional network, based on the identification of the starting site of gene transcription, with the simultaneous measurement of expression level and identification of the promoter elements. These tagging technologies (including cap-analysis gene expression - CAGE - and others) are further boosted from the development of the novel generation of sequencing instruments, which allow transcriptional profiling by sequencing at the cost of microarray experiments. This book is a guide for users of new technologies, as it includes accurately proven protocols, allowing readers to prepare their samples for experiments. Additionally, it provides a guide for the bioinformatics tools that are available for the analysis of the obtained tags, including the design of the software, the sources and web information where they can be downloaded. Finally, the book provides examples of the application of these technologies to identify promoters, annotate genomes, identify new RNAs and reconstruct models of transcriptional control. Although examples mainly regard mammalians, the discussion expands to other groups of eukaryotes, where these approaches are complementing genome sequencing.
  • 1. A Recent Breakthrough in the CCN Field: Functional Interactions Between CCN2 and CCN3 are Uncovered / Bernard Perbal -- 2. Report on the Fifth International Workshop on the CCN Family of Genes / A. E. Irvine, B. Perbal, and H. Yeger -- 3. Asking the Right Questions: What Can the Structure of the CCN Protein Domains Tell Us? / Kenneth P. Holbourn, Bernard Perbal, and K. Ravi Acharya -- 4. Nucleophosmin/B23: A Multifunctional Regulator that Determines the Fate of CCN2 mRNA / Satoshi Kubota, Yoshiki Mukudai, Harumi Kawaki, Seiji Kondo, Takanori Eguchi, Kumi Sumiyoshi, Toshihiro Ohgawara, Tsuyoshi Shimo, and Masaharu Takigawa -- 5. The CCN Genes as the “Master” Regulators of Angiogenesis, Vasculogenesis, Fibrogenesis and Cell Differentiation/Fate Specification in Mechanical Force-Driven Developmental Processes and Pathological Events / Mary Hanna and Brahim Chaqour -- 6. A Monoclonal Antibody Approach to CCN5 Domain Analysis / Lan Wei, Frank McKeon, Joshua W. Russo, Joan Lemire, and John Castellot -- 7. Matricellular Protein CCN2 Produced by Tubular Epithelial Cells Plays a Pivotal Role in Renal Fibrogenesis / Hirokazu Okada, Tsutomu Inoue, and Hiromichi Suzuki -- 8. Cooperative Regulation of Cell Proliferation and Differentiation by CCN2 and CCN3 / Masaharu Takigawa, Harumi Kawaki, Satoshi Kubota, Karen M. Lyons, and Bernard Perbal -- 9. The Role of CCN3 in Mesenchymal Stem Cells / Ken-Ichi Katsube -- 10. Role of Connective Tissue Growth Factor in Cardiac Fibrosis / Daiji Kawanami, Saptarsi M. Haldar, and Mukesh K. Jain -- 11. Gene Expression of CCN Family Members in Young and Aged Human Skin In Vivo / Taihao Quan, Sharon Shin, Zhaoping Qin, and Gary J. Fisher -- 12. Global Expression Profiling Reveals a Role for CTGF/CCN2 in Lactogenic Differentiation of Mouse Mammary Epithelial Cells / Weihan Wang, Cynthia Jose, Nicholas Kenney, Bethanie Morrison, and Mary Lou Cutler -- 13. CCN3 (NOV): A Negative Regulator of CCN2 (CTGF) Activity and an Endogenous Inhibitor of Fibrosis in Experimental Diabetic Nephropathy / Bruce. L. Riser, Feridoon Najmabadi, Bernard Perbal, Jo Ann Rambow, Melisa L. Riser, Ernest Sukowski, Herman Yeger, Sarah C. Riser, and Darryl R. Peterson -- 14. Inhibitors of Connective Tissue Growth Factor (CCN2)-Mediated Fibrogenesis: Underlying Mechanisms and Prospects for Anti-fibrotic Therapy / David R. Brigstock -- 15. CCN3 Promotes Melanoma Progression by Regulating Integrin Expression, Adhesion and Apoptosis Induced by Cytotoxic Drugs / Viviana Vallacchi, Maria Daniotti, Annamaria De Filippo, Licia Rivoltini, Bernard Perbal, and Monica Rodolfo -- 16. CCN3: A NOVel Growth Factor in Leukaemia / Lynn McCallum and Alexandra E Irvine -- 17. Prognostic Relevance of CCN3 in Bone Sarcomas / Bernard Perbal, Noureddine Lazar, Diana Zambelli, Monia Zuntini, Massimo Serra, Jose Antonio Lopez-Guerrero, Antonio Llombart-Bosch, Piero Picci, and Katia Scotlandi -- 18. CCN6 Regulates Breast Cancer Growth and Invasion Through Modulation of IGF Signaling and Epithelial to Mesenchymal Transition / Anupama Pal, Wei Huang, and Celina G. Kleer -- 19. Novel Transcriptional Regulation of CCN2/CTGF by Nuclear Translocation of MMP3 / Takanori Eguchi, Satoshi Kubota, Kazumi Kawata, Yoshiki Mukudai, Junji Uehara, Toshihiro Ohgawara, Soichiro Ibaragi, Akira Sasaki, Takuo Kuboki, and Masaharu Takigawa -- Fifth International Workshop on the CCN Family of Genes: Abstracts and Posters October 18-22, 2008.
  • Cell line development 2009, Springer
    Mammalian cell lines command an effective monopoly for the production of therapeutic proteins that require post-translational modifications. This book deals with the methodology involved in the development of cell lines and the cell engineering approach that can be employed to enhance productivity and improve cell function.
  • Cell-based microarrays 2011, Springer Protocols
    Cell-Based Microarrays: Overview / Ella Palmer -- Cell-Based Co-transfection Microarrays for Use with HEK293T Cells on a Poly d-Lysine-Coated Polystyrene Microplate / Meenal Soni, Fang Lai -- Large-Scale Cell-Based Microarrays and Their Use with HEK293T Cells and Downstream Apoptotic Assays / Ella Palmer, Tom C. Freeman -- A Novel Fluorescent Transcriptional Reporter for Cell-Based Microarray Assays / Tanya M. Redmond, Michael D. Uhler -- High-Throughput Subcellular Protein Localization Using Transfected-Cell Arrays: Subcellular Protein Localization Using Cell Arrays / Yuhui Hu, Michal Janitz -- Cell Arrays for the Measurement of Organelle Dynamics in Living Cells / Holger Erfle, Tautvydas Lisauskas, Christoph Claas, Jürgen Reymann, Vytaute Starkuviene -- High-Throughput Immunofluorescence Microscopy Using Yeast Spheroplast Cell-Based Microarrays / Wei Niu, G. Traver Hart, Edward M. Marcotte -- Cell-Based Microarrays of Infectious Adenovirus Encoding Short Hairpin RNA (shRNA) / Hansjürgen Volkmer, Frank Weise -- Reverse Transfected Cell Microarrays in Infectious Disease Research / Andreas Konrad, Ramona Jochmann, Elisabeth Kuhn, Elisabeth Naschberger, Priya Chudasama, Michael Stürzl -- Transfected Cell Microarrays for the Expression of Membrane-Displayed Single-Chain Antibodies / Baochuan Lin, James B. Delehanty -- Blood Cell Capture on Antibody Microarrays and Monitoring of the Cell Capture Using Surface Plasmon Resonance Imaging / Yoann Roupioz, Sarah Milgram, André Roget, Thierry Livache -- Immobilized Culture and Transfection Microarray of Non-adherent Cells / Satoshi Yamaguchi, Erika Matsunuma, Teruyuki Nagamune -- Plasma Polymer and PEG-Based Coatings for DNA, Protein and Cell Microarrays / Andrew L. Hook, Nicolas H. Voelcker, Helmut Thissen -- Polymer Microarrays for Cellular High-Content Screening / Salvatore Pernagallo, Juan J. Diaz-Mochon -- High-Throughput Analyses of Gene Functions on a Cell Chip by Electroporation / Koichi Kato, Hiroo Iwata -- Microfluidic Image Cytometry / Ken-ichiro Kamei, Jing Sun, Hsian-Rong Tseng, Robert Damoiseaux.
  • Chemical genomics 2006, Springer
  • Chemical genomics 2005, Springer Protocols
  • Ch. 1. Utilizing small molecules in chemical genomics : toward high-throughput (HT) approaches / György Dormán and Ferenc Darvas -- ch. 2. Development and application of novel analytical methods in lipidomics / Yuqin Wang ... [et al.] -- ch. 3. From chemical genomics to chemical proteomics : the power of microarray technology / Sándor Spisák and András Guttman -- ch. 4. Genomic and proteomic biomarkers in the drug R&D process / László Takács, Anna Debreceni, and István Kurucz -- ch. 5. Quo vadis biomedical sciences in the omics era : toward computational biology and medicine / András Falus ... [et al.] -- ch. 6. Novel chemogenomic approaches to drug design / Didier Rognan.
  • Chromosomal mutagenesis 2008, Springer Protocols
    Biallelic gene knockouts in Chinese hamster ovary cells / Naoko Yamane-Ohnuki, Kazuya Yamano, and Mitsuo Satoh -- Highly proficient gene targeting by homologous recombination in the human pre-B cell line Nalm-6 / Noritaka Adachi, Aya Kurosawa, and Hideki Koyama -- Robust cell line development using meganucleases / Jean-Pierre Cabaniols and Frédéric Pâques -- Design and testing of zinc finger nucleases for use in mammalian cells / Matthew Porteus -- Gene targeting in Drosophila and Caenorhabditis elegans with zinc-finger nucleases / Dana Carroll ... [et al.] -- Orpheus recombination : a comprehensive bacteriophage system for murine targeting vector construction by transplacement / Knut Woltjen ... [et al.] -- Transposition -mediated mutagenesis in somatic cells : identification of transposon-genomic DNA junctions / David A. Largaespada and Lara S. Collier -- Insertional mutagenesis of the mouse germline with sleeping beauty transposition / Junji Takeda, Zsuzsanna Izsvák, and Zoltán Ivics -- Conditional gene trapping using the FLEx system / Thomas Floss and Frank Schnütgen -- Steps toward targeted insertional mutagenesis with class II transposable elements / Sareina Chiung-Yuan wu ... [et al.] -- Targeting integration of the Saccharomyces Ty5 retrotransposon / Troy L. Brady, Clarice L. Schmidt, and Daniel F. Voytas -- Site-specific chromosomal integration mediated by [phi]C31 integrase / Annahita Keravala and Michele P. Calos-- Triplex-mediated gene modification / Erica B. Schleifman, Joanna Y.Chin, and Peter M. Glazer -- Allelic exchange of unmarked mutations in Mycobacterium tuberculosis / Martin S. Pavelka, Jr. -- Mycobacterial recombineering Julia C. van Kessel and Graham F. Hatfull -- Chromosomal engineering of Clostridium perfringens using group II introns / Phalguni Gupta and Yue Chen.
  • Mechanical approaches to elucidate mechanisms of chromosome condensation at the nano- and microlevels / Kazushige Kawabata ... [et al.] -- Development of novel AFM probes for chromosome manipulation / Masato Saito, Gen Hashiguchi and Eiichi Tamiya -- Microchamber array-based sequence-specific DNA detection from a single chromosome via trace volume PCR / Masato Saito and Eiichi Tamiya -- On-chip chromosome sorter using electric and magnetic fields / Takahito Inoue ... [et al.] -- Fluorescence microscopy for analysis of chromosome dynamics / Sachihiro Matsunaga -- Fluorescence in situ hybridization (FISH) as a tool for comparative genomics: application of FISH to studies of chromosome evolution in vertebrates / Yoichi Matsuda ... [et al.] -- Immunocytochemistry for analyzing chromosomes / Osamu Hoshi ... [et al.] --Proteome analysis of human metaphase chromosomes / Kiichi Fukui and Susumu Uchiyama -- Antipeptide antibodies for examining the conformation and molecular assembly of an intracellular protein / Masatoshi Nakagawa ... [et al.] -- Structure and interactions of the imitation SWI-type chromatin-remodeling complex, ATP-dependent chromatin-assembly facter / Tadayasu Ohkubo ... [et al.] -- Dynamic and functional analysis of chromosomal proteins / Nobuko Ohmido ... [et al.] -- Development of a sustainable chromosome imaging database / Kenji Taniguchi ... [et al.] -- Image database and image analysis of chromosome information / Shin-ichi Toyabe ... [et al.].Transmission and scanning electron microscopy of mammalian metaphase chromosomes / Sumire Inaga, Keiichi Tanaka and Tatsuo Ushiki -- Atomic force microscopy of human chromosomes in relation to their higher-order structure / Osamu Hoshi, Daisuke Fukushi and Tatsuo Ushiki -- Mechanism of higher-order chromatin folding revealed by AFM observation of in vitro reconstituted chromatin / Kohji Hizume ... [et al.] -- Scanning near-field optical/atomic force microscopy as a tool for simultaneous specification of chromosome topography and particular gene location on the nanometer scale / Motoharu Shichiri ... [et al.] -- Isolation of human and plant chromosomes as nanomaterials / Susumu Uchiyama, Tomoyuki Doi and Kiichi Fukui --
  • Circadian rhythms are such an innate part of our lives that we rarely pause to speculate why they even exist. Perhaps this is the reason why in the medical practice the circadian variability of hormones, metabolites, physiological behaviors or the relevance of time in the presence or absence of different pathologies, have been practically ignored in the past. Some studies have suggested that the disruption of the circadian system may be cause for obesity and manifestations of Metabolic Syndrome (MetS). Shift-work, sleep-deprivation and bright-light-exposure at night are related to increased adiposity (obesity) and prevalence of MetS. Chronobiology and Obesity examines recent advances that have led to researchers to find the relevant link which exists between chronobiology and obesity, but, as it is emphasized throughout the book, there is much more that needs to be explored between the connection.
  • Clinical applications of PCR. 2nd ed. 2006, Springer Protocols
    Clinical applications of plasma Epstein-Barr virus DNA analysis and protocols for the quantitative analysis of the size of circulating Epstein-Barr virus DNA / K.C. Allen Chan and Y.M. Dennis Lo -- Molecular analysis of circulating RNA in plasma / Nancy B.Y. Tsui, Enders K.O. Ng, and Y.M. Dennis Lo -- Molecular analysis of mitochondrial DNA point mutations by polymerase chain reaction / Lee-Jun C. Wong, Bryan R. Cobb, and Tian-Jian Chen -- Novel applications of polymerase chain reaction to urinary nucleic acid analysis / Anatoly V. Lichtenstein ... [et al.] -- Detection and quantitation of circulating plasmodium falciparum DNA by polymerase chain reaction / Shira Gal and James S. Wainscoat -- Molecular diagnosis of severe acute respiratory syndrome / Enders K.O. Ng and Y.M. Dennis Lo -- Genomic sequencing of the severe acute respiratory syndrome-coronavirus / Stephen S.C. Chim, Rossa W.K. Chiu, and Y.M. Dennis Lo.Introduction to the polymerase chain reaction / Y.M. Dennis Lo and K.C. Allen Chan -- Setting up a polymerase chain reaction laboratory / Y.M. Dennis Lo and K.C. Allen Chan -- Real-time polymerase chain reaction and melting curve analysis / Robert J. Pryor and Carl T. Wittwer -- Qualitative and quantitative polymerase chain reaction-based methods for DNA methylation analyses / Ivy H.N. Wong -- In-cell polymerase chain reaction: strategy and diagnostic applications / T. Vauvert Hviid -- Qualitative and quantitative DNA and RNA analysis by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry / Chunming Ding -- Analysis of polymerase chain reaction products by denaturing high-performance liquid chromatography / Ching-Wan Lam -- Use of real-time polymerase chain reaction for the detection of fetal aneuploidies / Bernhard Zimmermann ... [et al.] -- Noninvasive prenatal diagnosis by analysis of fetal DNA in maternal plasma / Rossa W. K. Chiu and Y. M. Dennis Lo --
  • Codes of life 2008, Springer
    Codes of biosequences / Edward N. Trifonov -- The mechanisms of evolution : natural selection and natural conventions / Marcello Barbieri -- Catalytic propensity of amino acids and the origins of the genetic code and proteins / Ádám Kun ... [et al.] -- Why the genetic code originated : implications for the origin of protein synthesis / Massimo Di Giulio -- Self-referential formation of the genetic system / Romeu Cardoso Guimarães, Carlos Henrique Costa Moreira, and Sávio Torres de Farias -- The mathematical structure of the genetic code / Diego L. Gonzalez -- The arithmetical origin of the genetic code / Vladimir shCherbak -- Protein linguistics and the modular code of the cytoskeleton / Mario Gimona -- A lipid-based code in nuclear signaling / Nadir M. Maraldi -- Biological information transfer beyond the genetic code : the sugar code / Hans-Joachim Gabius -- The immune self code : from correspondence to complexity / Yair Neuman -- Signal transduction codes and cell fate / Marcella Faria -- Towards an understanding of language origins / Eörs Szathmáry -- The codes of language : turtles all the way up? / Stephen J. Cowley -- Code and context in gene expression, cognition, and consciousness / Seán Ó Nualláin -- Neural coding in the neuroheuristic perspective / Alessandro E.P. Villa -- Error detection and correction codes / Diego L. Gonzalez -- The musical code between nature and nurture : ecosemiotic and neurobiological claims / Mark Reybrouck.
  • Introduction -- Chronology -- Fundamentals -- Prologue -- Molecular basis of genetics -- Analysis of DNA -- Variability of DNA -- Processing of DNA -- Eukaryotic cells -- Formal genetics -- Chromosomes -- Regulation of gene function -- Epigenetic modifications -- Genetic signal pathways -- Genes in embryonic development -- Genomics -- Genetics and medicine -- Imbalanced homeostasis -- Metabolic disorders -- Immune system -- Origins of cancer -- Impaired cell and tissue structure -- Hemoglobin disorders -- Sex determination and differentiation -- Atypical patternns of genetic transmission -- Sensory perception -- Karyotype-phenotype relationnship -- A grief guide to genetic diagnosis -- Morbid anatomy of the human genome - chromosomal locations - alphabetic list -- Appendix -- Supplementary data.
  • Comparative genomics 2006, Springer
  • Comparative genomics v. 1-2, 2007, Springer Protocols
    v. 2, 2007 Springer Protocols
    v. 1. Genome visualization and annotation ; Sequence alignments ; Identification of conserved sequences and biases in codon usage ; Identification and structural characterization of noncoding RNAs -- v. 2. Comparative analysis of domain and protein families ; Orthologs, synteny, and genome evolution ; Experimental analysis of whole genomes : analysis of copy number and sequence polymorphisms.
  • Comparative genomics 2008, CRCnetBASE
    Introduction : the broad horizons of comparative genomics / James R. Brown -- Advances in next-generation DNA sequencing technologies / Michael L. Metzker -- Large scale phylogenetic reconstruction / Bernard M.E. Moret -- Comparative genomics of viruses using bioinformatics tools / Chris Upton and Elliot J. Lefkowitz -- Archaebacteria and the prokaryote-to-eukaryote transition (and the role of mitochondria therein) / William Martin, Tal Dagan, and Katrin Henze -- Comparative genomics of invertebrates / Takeshi Kawashima ... [et al.] -- Comparative vertebrate genomics / James W. Thomas -- Gaining insight into human population-specific selection pressure / Michael R. Barnes -- Comparative genomics in drug discovery / James R. Brown -- Comparative genomics and the development of novel antimicrobials / Diarmaid Hughes -- Comparative genomics and the development of antimalarial and antiparasitic therapeutics / Emilio F. Merino, Steven A. Sullivan, and Jane M. Carlton -- Comparative genomics in AIDS research / Philippe Lemey, Koen Deforche, and Anne-Mieke Vandamme -- Detailed comparisons of cancer genomes / Timon P.H. Buys ... [et al.] -- Comparative cancer epigenomics / Alice N.C. Kuo ... [et al.] -- G protein-coupled receptors and comparative genomics / Steven M. Foord -- Comparative toxicogenomics in mechanistic and predictive toxicology / Joshua C. Kwekel, Lyle D. Burgoon, and Tim R. Zacharewski -- Comparative genomics and crop improvement / Michael Francki and Rudi Appels -- Domestic animals : a treasure trove for comparative genomics / Leif Andersson.
  • Comparative genomics 2013, Springer
    This book provides an evolutionary conceptual framework for comparative genomics, with the ultimate objective of understanding the loss and gain of genes during evolution, the interactions among gene products, and the relationship between genotype, phenotype and the environment. The many examples in the book have been carefully chosen from primary research literature based on two criteria: their biological insight and their pedagogical merit. The phylogeny-based comparative methods, involving both continuous and discrete variables, often represent a stumbling block for many students entering the field of comparative genomics. They are numerically illustrated and explained in great detail. The book is intended for researchers new to the field, i.e., advanced undergraduate students, postgraduates and postdoctoral fellows, although professional researchers who are not in the area of comparative genomics will also find the book informative.
  • Computational chemogenomics 2013, CRCnetBASE
    This book focuses on applications of compound library design and virtual screening to expand the bioactive chemical space, to target hopping of chemotypes to identify synergies within related drug discovery projects or to repurpose known drugs, to propose mechanism of action of compounds, or to identify off-target effects by cross-reactivity analysis. Both ligand-based and structure-based in silico approaches, as reviewed in this book, play important roles for all these applications. Computational chemogenomics is expected to increase the quality and productivity of drug discovery and lead.
  • Computational biology: are we there yet? / Gary Peltz -- Statistical theory in QTL mapping / Benjamin Yakir, Anne PisanteÃÅ, and Ariel Darvasi -- Haplotype-based computational genetic analysis in mice / Jianmei Wang and Gary Peltz -- Haplotype structure of the mouse genome / Jianmei Wang ... [et al.] -- SNP discovery and genotyping: methods and applications / Jun Wang ... [et al.] -- Genetic and genomic approaches to complex lung disease using mouse models / Michael J. Holtzman, Edy Y. Kim, and Jeffrey D. Morton -- Murine models of osteoporosis / Robert F. Klein -- Murine models of substance and alcohol dependence: unraveling genetic complexities / Kim Cronise and John C. Crabbe -- Murine models of alcoholism: from QTL to gene / Chris Downing, Beth Bennett, and Thomas E. Johnson -- HLA polymorphism and disease susceptibility / -- Henry A. Erlich -- Asthma genetics: a case study / William Cookson.
  • Recent advances in development of sequencing technology has resulted in a deluge of genomic data. In order to make sense of this data, there is an urgent need for algorithms for data processing and quantitative reasoning. An emerging in silico approach, called computational genomic signatures, addresses this need by representing global species-specific features of genomes using simple mathematical models. This text introduces the general concept of computational genomic signatures, and it reviews some of the DNA sequence models which can be used as computational genomic signatures. The text takes the position that a practical computational genomic signature consists of both a model and a measure for computing the distance or similarity between models. Therefore, a discussion of sequence similarity/distance measurement in the context of computational genomic signatures is presented. The remainder of the text covers various applications of computational genomic signatures in the areas of metagenomics, phylogenetics and the detection of horizontal gene transfer.
  • Conditional mutagenesis 2007, Springer
    Conditional somatic mutagenesis in the mouse using site-specific recombinases -- Cre/loxP-mediated chromosome engineering of the mouse genome -- Tetracycline-controlled genetic switches -- Novel gene switches -- Improved embryonic stem cell technologies -- Gene trap mutagenesis -- RNA interference in mice -- Viral vectors: a wide range of choices and high levels of service -- Conditional mutagenesis by cell-permeable proteins: potential, limitations and prospects -- Analysis of mouse development with conditional mutagenesis -- Conditional mouse models of cancer -- Conditional mutagenesis reveals immunological functions of widely expressed genes: activation thresholds, homeostatic mechanisms and disease models -- Conditional transgenesis and recombination to study the molecular mechanisms of brain plasticity and memory -- A novel conditional knockout strategy applied to serotonin receptors -- Conditional mouse models for Friedreich Ataxia, a neurodegenerative disorder associating cardiomyopathy -- Animal models in cardiovascular diseases: new insights from conditional models -- Conditional animal models for the study of lipid metabolism and lipid disorders -- Conditional mouse models to study developmental and pathophysiological gene function in muscle -- Analysis of calcuim channels by conditional mutagenesis -- Conditional mutagenesis of G-protein coupled receptors and G-proteins -- Contribution of targeted conditional somatic mutagenesis to deciphering retinoid X receptor functions and to generating mouse models of human diseases.
  • CRISPR-Cas systems 2013, Springer
    CRISPR-Cas is a recently discovered defense system which protects bacteria and archaea against invasion by mobile genetic elements such as viruses and plasmids. A wide spectrum of distinct CRISPR-Cas immune systems has been identified in at least half of the available prokaryotic genomes. On-going biochemical and functional analyses have resulted in substantial insight into the functions and possible applications of these fascinating systems, although many secrets remain to be uncovered. In this book, experts summarize the state of the art of this exciting field.
  • ch. 1. Genetic Mapping -- ch. 2. Genotyping -- ch. 3. Somatic Cell Hybrids -- ch. 4. Cytogenetics -- ch. 5. Strategies for Large-Insert Cloning and Analysis -- ch. 6. Identifying Candidate Genes in Genomic DNA -- ch. 7. Searching Candidate Genes for Mutations -- ch. 8. Clinical Cytogenetics -- ch. 9. Clinical Molecular Genetics -- ch. 10. Cancer Genetics -- ch. 11. Transcriptional Profiling -- ch. 12. Vectors for Gene Therapy -- ch. 13. Delivery Systems for Gene Therapy -- ch. 14. Forensic Genetics -- ch. 15. Model Systems for the Analysis of Human Disease -- ch. 16. Automation and Robotics in Genetic Analysis -- ch. 17. Biochemical Genetics --ch. 18. High-Throughput Sequencing -- ch. 19. Mitochondrial Genetics -- ch. 20. Epigenetics -- Appendix 1. Abbreviations and Useful Data -- Appendix 2. Laboratory Guidelines, Equipment, and Stock Solutions -- Appendix 3. Commonly Used Techniques -- Appendix 4. Chromosome Karyotyping and Idiograms -- Appendix 5. Genetic Linkage Reference Maps: Access to Internet-Based Resources -- Appendix 6. Human-Mouse Comparative Maps -- Appendix. Suppliers.
  • Data mining in proteomics 2011, Springer Protocols
    Instruments and methods in proteomics -- In-depth protein characterization by mass spectrometry -- Analysis of phosphoproteomics data -- The origin and early reception of sequence databases -- Laboratory data and sample management for proteomics -- PRIDE and "Database on demand" As valuable tools for computational proteomics -- Analysing proteomics identifications in the context of functional and structural protein annotation: Integrating annotation using PICR, DAS, and BioMart -- Tranche distributed repository and proteomecommons.Org -- Data standardization by the HUPO-PSI: How has the community benefitted? -- mzIdentML: An open community-built standard format for the results of proteomics spectrum identification algorithms -- Spectra, chromatograms, metadata: mzML-the standard data format for mass spectrometer output -- imzML: Imaging mass spectrometry markup language: A common data format for mass spectrometry imaging -- Tandem mass spectrometry spectral libraries and library searching -- Inter-lab proteomics: Data mining in collaborative projects on the basis of the HUPO brain proteome project's pilot studies -- Data management and data integration in the HUPO plasma proteome project -- Statistics in experimental design, preprocessing, and analysis of proteomics data -- The evolution of protein interaction networks -- Cytoscape: Software for visualization and analysis of biological networks -- Text mining for systems modeling -- Identification of alternatively spliced transcripts using a proteomic informatics approach -- Distributions of ion series in ETD and CID spectra: Making a comparison -- Evaluation of peak-picking algorithms for protein mass spectrometry -- OpenMS and TOPP: Open source software for LC-MS data analysis -- LC/MS data processing for label-free quantitative analysis -- Spectral properties of correlation matrices - towards enhanced spectral clustering -- Standards, databases, and modeling tools in systems biology -- Modeling of cellular processes: Methods, data, and requirements.
  • Dictyostelium discoideum protocols 2006, Springer Protocols
  • Global analysis of gene expression by differential display : a mathematical model / Shitao Yang and Peng Liang -- Automation of fluorescent differential display with digital readout / Jonathan D. Meade ... [et al.] -- Ordered differential display / Mikhail V. Matz and Ella A. Meleshkevitch -- GeneCalling : transcript profiling coupled to a gene database query / Richard A. Shimkets -- High-density sampling differential display of prokaryotic mRNAs with RAP-PCR / Dana M. Walters and Pierre E. Rouviere -- Vertical arrays : microarrays of complex mixtures of nucleic acids / Rosana Risques ... [et al.] -- Automated pattern ranking in differential display data analysis / Tero Aittokallio ... [et al.] -- Linking cDNA-AFLP-based gene expression patterns and ESTs / Ling Qin, Pjotr Prins, and Johannes Helder -- Differentially expressed genes associated with hepatitis B virus HBx and MHBs protein function in hepatocellular carcinoma / Dae-Ghon Kim -- Identification of disease markers by differential display : prion disease / Michael Clinton ... [et al.] -- Saturation screening for p53 target genes by digital fluorescent differential display / Yong-Jig Cho ... [et al.] -- Identification of p53-regulated genes by the method of differential display / Yunping Lin, Roger P. Leng, and Samuel Benchimol --Identification by differential display of IL-24 autocrine loop activated by ras oncogenes / Zhongjia Tan, Mai Wang, and Peng Liang -- Comprehensive analysis of ovarian gene expression during ovulation using differential display / Lawrence L. Espey -- Functional analysis of nocturnin : a circadian clock-regulated gene identified by differential display / Julie E. Baggs and Carla B. Green -- Isolation and characterization of anthocyanin 5-0-glucosyltransferase in perilla frutescens var. crispa by differential display / Mami Yamasaki and Kazuki Saito -- Identification of target genes of a yeast transcriptional repressor / Bernard Mai and Linda L. Breeden -- Detection of an mRNA polymorphism by differential display / Shan Liang ... [et al.] -- Silencing in yeast : identification of CLr4 targets / Sergey V. Ivanov and Alla V. Ivanova -- Identification of mRNA bound to RNA binding proteins by differential display / Anne Carr-Schmid, Xinfu Jiao, and Megerditch Kiledjian.
  • ch. 1. Introduction, p. 1-3 / Kai Johnsson and Susanne Brakmann, p. 1-3 -- ch. 2. Evolutionary Biotechnology - From Ideas and Concepts to Experiments and Computer Simulations / Peter Schuster, p. 5-28 -- ch. 3. Using Evolutionary Strategies to Investigate the Structure and Function of Chorismate Mutases / Donald Hilvert, Sean V. Taylor and Peter Kast, p. 29-62 -- ch. 4. Construction of Environmental Libraries for Functional Screening of Enzyme Activity / Rolf Daniel, p. 63-78 -- ch. 5. Investigation of Phage Display for the Directed Evolution of Enzymes / Patrice Soumillion and Jacques Fastrez, p. 79-110 -- ch. 6. Directed Evolution of Binding Proteins by Cell Surface Display: Analysis of the Screening Process / K. Dane Wittrup, p. 111-126 -- ch. 7. Yeast n-Hybrid Systems for Molecular Evolution / Brian T. Carter, Hening Lin and Virginia W. Cornish, p. 127-158 -- ch. 8. Advanced Screening Strategies for Biocatalyst Discovery / Andreas Schwienhorst, p. 159-175 -- ch. 9. Engineering Protein Evolution / Stefan Lutz and Stephen J. Benkovic, p. 177-213 -- ch. 10. Exploring the Diversity of Heme Enzymes through Directed Evolution / Patrick C. Cirino and Frances H. Arnold, p. 215-243 -- ch. 11. Directed Evolution as a Means to Create Enantioselective Enzymes for Use in Organic Chemistry / Manfred T. Reetz and Karl-Erich Jaeger, p. 245-279 -- ch. 12. Applied Molecular Evolution of Enzymes Involved in Synthesis and Repair of DNA / John F. Davidson, Jon Anderson, Haiwei Guo, Daniel Landis and Lawrence A. Loeb, p. 281-307 -- ch. 13. Evolutionary Generation Versus Rational Design of Restriction Endonucleases with Novel Specificity / Thomas Lanio, Albert Jeltsch and Alfred Pingoud, p. 309-327 -- ch. 14. Evolutionary Generation of Enzymes with Novel Substrate Specificities / Uwe T. Bornscheuer, p. 329-341.
  • Lynch syndrome (LS) is the most common cause of inherited colorectal cancer, a disease with a high mortality rate. An estimated 37,000 of diagnosed colorectal cancer cases worldwide are attributed to Lynch syndrome each year. Intensive cancer screening, with early initiation and frequent follow-up, can reduce colorectal cancer incidence and mortality in LS patients. This book provides an up-to-date overview on the genetic and epigenetic basis of Lynch syndrome. It evaluates clinical features of the disease and critically comments on molecular tools available for identifying mutations responsible for Lynch syndrome; in addition the importance of functional assays that can help clarify the clinical nature of identified mutations is also discussed. The book also focuses on challenges in genetic counselling of at-risk individuals and discusses related ethical issues. The purpose of the book is to give a concise knowledge base for the broader scientific and medical community, including genetic counselors, in order to improve awareness on the potential impact that the diagnosis of LS has on treatment, management and surveillance of LS patients.
  • DNA and RNA profiling in human blood 2009, Springer Protocols
    PCR-ELISA for high-throughput blood group genotyping / Maryse St-Louis -- Single base extension in multiplex blood group genotyping / Gregory A. Denomme -- Real-time PCR assays for high-throughput blood group genotyping / Fernando Araujo -- Real-time PCR assays for high-throughput human platelet antigen typing / Simon E. McBride -- Multiplex ABO genotyping by minisequencing / Gianmarco Ferri and Susi Pelotti -- Multiplex genotyping for thrombophilia-associated SNPs by universal bead arrays / Susan Bortolin -- Pyrosequencing of toll-like receptor polymorphisms of functional relevance / Parviz Ahmad-Nejad -- Multiplex HLA-typing by pyrosequencing / Ying Lu ... [et al.] -- High-throughput multiplex HLA-typing by ligase detection reaction (LDR) and universal array (UA) approach / Clarissa Consolandi -- Medium- to high-throughput SNP genotyping using VeraCode microbeads / Charles H. Lin ... [et al.] -- The use of maternal plasma for prenatal RhD blood group genotyping / Kirstin Finning, Pete Martin, and Geoff Daniels -- Nanoliter high-throughput PCR for DNA and RNA profiling / Colin J.H. Brenan, Douglas Roberts, and James Hurley -- RNA stabilization of peripheral blood and profiling by bead chip analysis / Svenja Debey-Pascher, Daniela Eggle, and Joachim L. Schultze -- RNA profiling in peripheral blood cells by fluorescent differential display PCR / Martin Steinau and Mangalathu S. Rajeevan -- cDNA amplification by SMART-PCR and suppression subtractive hybridization (SSH)-PCR / Andrew Hillmann, Eimear Dunne, and Dermot Kenny -- Transcript profiling of human platelets using microarray and serial analysis of gene expression (SAGE) / Dmitri V. Gnatenko ... [et al.] -- Genome-wide platelet RNA profiling in clinical samples / Angelika Schedel and Nina Rolf -- PCR-based amplification of platelet mRNA sequences obtained from small-scale platelet samples / Jutta M. Rox, Jens Müller, and Bernd Pötzsch -- MicroRNA profiling of megakaryocytes / Ramiro Garzon -- Serial analysis of gene expression adapted for downsized extracts / SAGE/SADE) analysis in reticulocytes / Béatrice Bonafoux and Thérèse Commes -- Real-time PCR analysis for blood cell lineage specific markers / Louise Edvardsson and Tor Olofsson -- Monitoring the immune response using real-time PCR / Patrick Stordeur.
  • DNA arrays 2002, CRCnetBASE
  • DNA: alternative conformations and biology / Vladimir N. Potaman and Richard R. Sinden -- Sequence-dependent variability of B-DNA: an update on bending and curvature / Victor B. Zhurkin ... [et al.] -- Curved DNA and prokaryotic promoters: a mechanism for activation of transcription / Munehiko Asayama and Takashi Ohyama -- Repression of transcription by curved DNA and nucleoid protein H-NS: a mode of bacterial gene regulation / Cynthia L. Pon, Stefano Stella and Claudio O. Gualerzi -- Curved DNA and transcription in eukaryotes / Takashi Ohyama -- Putative roles of kin17, a mammalian protein binding -- Curved DNA, in transcription / Jaime F. Angulo ... [et al.] -- Roles for Z- and double-stranded RNA in transcription: encoding genetic information by shape rather than by sequence / Alan Herbert -- Do DNA triple helices or quadruplexes have a role in transcription? / Michael W. Van Dyke -- Nucleic acid structures and the transcription defects in fragile X syndrome and Friedreich's ataxia / Karen Usdin -- Possible roles of DNA supercoiling in transcription / Susumu Hirose and Kuniharu Matsumoto -- Gene regulation by HMGA and HMGB chromosomal proteins and related architectural DNA-binding proteins / Andrew A. Travers -- Molecular mechanisms of male sex determination: the enigma of SRY / Michael A. Weiss -- The role of unusual DNA structures in chromatin organization for transcription / Takashi Ohyama -- DNA bendability and nucleosome positioning in transcriptional regulation / Mensur Dlaki, David W. Ussery and Sren Brunak.
  • In situ detection of apoptosis by the TUNEL assay: An overview of techniques -- Combination of TUNEL assay with immunohistochemistry for simultaneous detection of DNA fragmentation and oxidative cell damage -- EM-ISEL: A useful tool to visualize DNA damage at the ultrastructural level -- In situ labeling of DNA breaks and apoptosis by T7 DNA polymerase -- In situ ligation: A decade and a half of experience -- In situ ligation simplified: Using PCR fragments for detection of double-strand DNA breaks in tissue sections -- 5'OH DNA breaks in apoptosis and their labeling by topoisomerase-based approach -- Detection of DNA strand breaks in apoptotic cells by flow- and image-cytometry -- Fluorochrome-labeled inhibitors of caspases: Convenient in vitro and in vivo markers of apoptotic cells for cytometric analysis -- Combining fluorescent in situ hybridization with the comet assay for targeted examination of DNA damage and repair -- Simultaneous labeling of single- and double-strand DNA breaks by DNA breakage detection-FISH (DBD-FISH) -- Co-localization of DNA repair proteins with UV-induced DNA damage in locally irradiated cells -- Ultrasound imaging of apoptosis: Spectroscopic detection of DNA-damage effects at high and low frequencies -- Quantifying etheno-DNA adducts in human tissues, white blood cells, and urine by ultrasensitive (32)P-postlabeling and immunohistochemistry -- ELISpot assay as a tool to study oxidative stress in peripheral blood mononuclear cells -- Cytokinesis-block micronucleus cytome assay in lymphocytes -- Buccal micronucleus cytome assay -- [Gamma]-H2AX detection in peripheral blood lymphocytes, splenocytes, bone marrow, xenografts, and skin -- Immunologic detection of benzo(a)pyrene-DNA adducts -- Non-invasive assessment of oxidatively damaged DNA: Liquid chromatography-tandem mass spectrometry analysis of urinary 8-oxo-7,8-dihydro-2'-deoxyguanosine -- Assessing sperm DNA fragmentation with the sperm chromatin dispersion test.
  • DNA damage recognition 2005, CRCnetBASE
  • DNA methylation : three decades in search of function / Aharon Razin -- Epigenetic mechanisms of gene regulation : relationships between DNA methylation, histone modification, and chromatin structure / Keith D. Robertson -- DNA hypo- vs. hypermethylation in cancer : tumor specificity, tumor progression, and therapeutic implications / Melanie Ehrlich and Guanchao Jiang -- DNA methylation in urological cancers / Wolfgang A. Schulz and Hans-Helge Seifert -- DNA methylation in colorectal cancer / Jeremy R. Jass ... [et al.] -- CpG island hypermethylation of tumor suppressor genes in human cancer : concepts, methodologies and uses / Michel Herranz and Manel Esteller -- The loss of methyl groups in DNA of tumor cells and tissues : the immunochemical approach / Alain Niveleau ... [et al.] -- Identifying clinicopathological association of DNA hypermethylation in cancers using CpG island microarrays / Susan H. Wei ... [et al.] -- Methylation analysis in cancer : (epi)genomic fast track from discovery to clinical routine / Carolina Haefliger, Sabine Maier and Alexander Olek --Regulation of DNA methyltransferases in cancer / Nancy Detich and Moshe Szyf -- Inhibition of poly(ADP-ribosyl)ation allows DNA hypermethylation / Anna Reale ... [et al.] -- The role of active demethylation in cancer and its therapeutic potential / Moshe Szyf ... [et al.] -- Purine analogues and their role in methylation and cancer chemotherapy / Katherine L. Seley and Sylvester L. Mosley -- DNA methyltransferase inhibitors : paving the way for epigenetic cancer therapeutics / Gregory K. Reid and A. Robert MacLeod -- Preclinical and clinical studies on 5-aza-2'-deoxycytidine, a potent inhibitor of DNA methylation, in cancer therapy / Richard L. Momparler -- Anticancer gene therapy by in vivo DNA electrotransfer of MBD2 antisense / Pascal Bigey and Daniel Scherman.
  • DNA methylation microarrays 2008, CRCnetBASE
  • Regulation of chromatin and DNA-methylation patterns in blood cell development / C. Bonifer, P. Lefevre, and H. Tagoh -- Methylation dynamics in the early mammalian embryo : implications of genome reprogramming defects for development / T. Haaf -- Epigenetic regulation in drosophila / F. Lyko ... [et.al.] -- Epimutations in human disease / B. Horsthemke -- Epigenotypes of latent herpesvirus genomes / J. Minarovits -- Epigenetics of complex diseases : from general theory to laboratory experiments / A. Schumacher and A. Petronis -- MSL proteins and the regulation of gene expression / S. Rea and A. Akhtar -- DNA methylation profiles of female steroid hormone-driven human malignancies / M. Campan, D.J. Weisenberger, and P.W. Laird -- Genome-wide analysis of DNA methylation changes in human malignancies / C. Plass and D.J. Smiraglia -- Decreased fidelity in replicating DNA methylation patterns in cancer cells leads to dense methylation of a CpG island / N. Watanabe ... [et.al.] -- Methylation of endogenous human retroelements in health and disease / W. A. Schulz, C. Steinhoff, and A.R. Florl -- Cancer-linked DNA hypomethylation and its relationship to hypermethylation / M. Ehrlich.
  • DNA microarrays. Part A-B pt. A-B, 2006., ScienceDirect
    pt. B, 2006 ScienceDirect
    Pt. A. Array platforms and wet-bench protocols -- pt. B. Databases and statistics.
  • Biochemical assays for the characterization of DNA helicases / Robert M. Brosh Jr. and Sudha Sharma -- Repair synthesis assay for nucleotide excision repair activity using fractionated cell extracts and UV-damaged plasmid DNA / Maureen Biggerstaff and Richard D. Wood -- Assaying for the dual incisions of nucleotide excision repair using DNA with a lesion at a specific site / Mahmud K.K. Shivji ... [et al.] -- Analysis of proliferating cell nuclear antigen (PCNA) associated with DNA excision repair sites in mammalian cells / A. Ivana Scovassi and Ennio Prosperi -- Analysis of DNA repair and chromatin assembly in vitro using immobilized damaged DNA substrates / Jill A. Mello, Jonathan G. Moggs, and Geneviève Almouzni.Cytometric assessment of histone H2AX phosphorylation: a reporter of DNA damage / Xuan Huang and Zbigniew Darzynkiewicz -- Detection of DNA strand breaks by flow and laser scanning cytometry in studies of apoptosis and cell proliferation (DNA replication) / Zbigniew Darzynkiewicz, Xuan Huang, and Masaki Okafuji -- In vitro rejoining of double-strand breaks in genomic DNA / George Iliakis and Nge Cheong -- Detection of DNA double-strand breaks and chromosome translocations using ligation-mediated PCR and inverse PCR / Michael J. Villalobos, Christopher J. Betti, and Andrew T.M. Vaughan -- Plasmid-based assays for DNA end-joining in vitro / George Iliakis ... [et al.] -- Use of gene targeting to study recombination in mammalian cell DNA repair mutants / Rodney S. Nairn and Gerald M. Adair --Gene-specific and mitochondrial repair of oxidative DNA damage / R. Michael Anson, Penelope A. Mason, and Vilhelm A. Bohr -- Quantitative PCR-based measurement of nuclear and mitochondrial DNA damage and repair in mammalian cells / Janine H. Santos ... [et al.] -- Measuring the formation and repair of DNA damage by ligation-mediated PCR / Gerd P. Pfeifer -- Immunochemical detection of UV-induced DNA damage and repair / Marcus S. Cooke and Alistair Robson -- A dot-blot immunoassay for measuring repair of ultraviolet photoproducts / Shirley McCready -- Quantification of photoproducts in mammalian cell DNA using radioimmunoassay / David L. Mitchell -- DNA damage quantitation by alkaline gel electrophoresis / Betsy M. Sutherland, Paula V. Bennett, and John C. Sutherland --Isolation of mutagen-sensitive Chinese hamster cell lines by replica plating / Malgorzata Z. Zdzienicka -- Complementation assays adapted for DNA repair-deficient keratinocytes / Mathilde Fréchet ... [et al.] -- Cytogenetic challenge assays for assessment of DNA repair capacities / William W. Au and Salama A. Salama -- Evaluating the delayed effects of cellular exposure to ionizing radiation / Shruti Nagar, James J. Corcoran, and William F. Morgan -- Inhibition of DNA synthesis by ionizing radiation: a marker for an S-phase checkpoint / Nicolaas G.J. Jaspers and Malgorzata Z. Zdzienicka -- Analysis of inhibition of DNA replication in irradiated cells using the SV40-based in vitro assay of DNA replication / George Iliakis, Ya Wang, and Hong Yan Wang --The comet assay: a sensitive genotoxicity test for the detection of DNA damage and repair / Günter Speit and Andreas Hartmann -- Fast micromethod DNA single-strand-break assay / Heinz C. Schröder ... [et al.] -- ³²P-postlabeling DNA-damage assays: PAGE, TLC, and HPLC / Shinya Shibutani, Sung Yeon Kim, and Naomi Suzuki -- Electrophoretic mobility shift assays to study protein binding to damaged DNA / Vaughn Smider, Byung Joon Hwang, and Gilbert Chu -- Construction of MMR plasmid substrates and analysis of MMR error correction and excision / Huixian Wang and John B. Hays -- Characterization of enzymes that initiate base excision repair at abasic sites / Walter A. Deutsch and Vijay Hegde -- Base excision repair in mammalian cells / Yoshihiro Matsumoto -- In vitro base excision repair assay using mammalian cell extracts / Guido Frosina ... [et al.] --
  • DNA repair. Part A-B pt. A-B, 2006., ScienceDirect
    pt. B, 2006 ScienceDirect
  • Drosophila cytogenetics protocols 2004, Springer Protocols
  • dsRNA genetic elements 2002, CRCnetBASE
  • E. coli gene expression protocols 2002, Springer Protocols
  • Ecological genomics : 2014, Springer
    "Researchers in the field of ecological genomics aim to determine how a genome or a population of genomes interacts with its environment across ecological and evolutionary timescales. Ecological genomics is trans-disciplinary by nature. Ecologists have turned to genomics to be able to elucidate the mechanistic bases of the biodiversity their research tries to understand. Genomicists have turned to ecology in order to better explain the functional cellular and molecular variation they observed in their model organisms. Ecological genomics covers 3 fields of research that have most benefited from the recent technological and conceptual developments in the field of ecological genomics: the study of life-history evolution and its impact of genome architectures; the study of the genomic bases of phenotypic plasticity and the study of the genomic bases of adaptation and speciation"-- Publisher's description.
  • v. 1. Genetics -- v. 2. Genetics -- v. 3. Genomics -- v. 4. Genomics -- v. 5. Proteomics -- v. 6. Proteomics -- v. 7. Bioinformatics -- v. 8. Bioinformatics.
  • v. 1. A-L -- v. 2. M-Z.
  • Multiple endocrine neoplasia type 1 / Agarwal, S.K. -- Multiple endocrine neoplasia type 2 / Lodish, M. -- Von Hippel-Lindau syndrome / Chou, A. ... [et al.] -- Carney complex -- Espiard, S., Bertherat, J. -- Multiple endocrine neoplasia type 4 / Lee, M., Pellegata, N.S. -- Novel hereditary forms of pheochromocytomas and paragangliomas / Dahia, P.L.M. -- Carney triad / Carney, J.A. -- Genetics of pituitary adenomas / Gadelha, M.R. ... [et al.] -- Clinical behavior and genetics of nonsyndromic, familial nonmedullary thyroid cancer / Bauer, A.J. -- Genetic defects associated with familial and sporadic hyperparathyroidism / Hendy, G.N., Cole, D.E.C. -- Endocrine tumors associated with neurofibromatosis type 1, Peutz-Jeghers syndrome, and other familial neoplasia syndromes / Kalkan, E., Waguespack, S.G.
  • The capacity of the epigenome to interpret both internal and external stimuli and alter expression programs is a critical component in normal development, aging, and disease pathogenesis. In the past decade, we have witnessed an explosion of unprecedented research on and support for epigenetics, epigenomics, and their interface with human health and disease. In this volume, Environmental Epigenomics in Health and Disease - Epigenetics and Complex Diseases, a number of leading investigators in the field of epigenetics discuss patterns of epigenomic modifications in normal cells, and how environmentally-induced changes in them are associated with disease pathogenesis. The authors comprehensively review the epigenetic adaptations that occur in human embryonic stem cells, as well as in differentiating cells and organs such as the brain when exposed to environmental factors, and discuss the legal and ethical implications of such alterations. The overall purpose of this volume and its companion, Environmental Epigenomics in Health and Disease - Epigenetics and Disease Origins, is to give readers an overview of how environmental exposures during early development can influence disease formation by disrupting epigenetic programming.
  • Exposure to environmental toxicants is associated with changes in DNA methylation and gene expression profiles that together can contribute to increased disease susceptibility. The chapters in this volume, Environmental Epigenomics in Health and Disease - Epigenetics and Disease Origins, address a wide range of environmental exposures, such as airborne particulates, cocaine, radiation, tobacco smoke, and xenoestrogens. Particular emphasis is placed on the consequences of environmental exposures during development on epigenetic reprogramming that influences adult disease pathogenesis. Health outcomes associated with these exposures include autoimmune disorders, neurodevelopmental disorders, and cancer. Importantly, dietary supplements and drugs can modify the epigenetic effects induced by these agents, thereby reducing their toxicological impact. The overall purpose of this volume and its companion, Environmental Epigenomics in Health and Disease - Epigenetics and Complex Diseases, is to give readers an overview of how environmental exposures during early development can influence disease formation by disrupting epigenetic processes and developmental programming.
  • Environmental genomics 2007, Springer Protocols
    Preface --Contributors --Pt. 1.Gene expression profiling --1.High-throughput whole mount in situ hybridization of zebrafish embryos for analysis of tissue-specific gene expression changes after environmental perturbation /Louise E. Coverdale, Lindsay E. Burton, and C. Cristofre Martin --2.Fluorescent RNA arbitrarily primed polymerase chain reaction /Doug Crump ... [et al.] --3.Isolation of O₃-response genes from Arabidopsis thaliana using cDNA macroarray /Masanori Tamaoki --4.Use of cDNA macroarrays and gene profiling for detection of effects of environmental toxicants /Jason L. Blum ... [et al.] --5.Constructing and screening a cDNA library /Kevin Larade and Kenneth B. Storey --6.Comparative molecular physiological genomics /Sean F. Eddy and Kenneth B. Storey --7.Proteomic analysis of neuroendocrine peptidergic system disruption using the AtT20 pituitary cell line as a model /Fumin Dong ... [et al.] --8.Proteomics-based method for risk assessment of peroxisome proliferating pollutants in the marine environment /Susana Cristobal --9.Environmental metabolomics using ¹H-NMR spectroscopy /Mark R. Viant --Pt. 2.Detection of whole genome mutation --10.Restriction landmark genome scanning for the detection of mutations /Jun-ichi Asakawa --11.Use of the comet assay in environmental toxicology /Loren D. Knopper and James P. McNamee --12.The micronucleus assay determination of chromosomal level DNA damage /Michael Fenech --13.Fluorescence in situ hybridization for the detection of chromosome aberrations and aneuploidy induced by environmental toxicants /Francesca Pacchierotti and Antonella Sgura --14.Laboratory methods for the detection of chromosomal structural aberrations in human and mouse sperm by fluorescence in situ hybridization /Francesco Marchetti, Debby Cabreros, and Andrew J. Wyrobek --Pt. 3.Determination of species diversity --15.Assembling DNA barcodes /Jeremy R. deWaard ... [et al.] --16.Application of suppressive subtractive hybridization to uncover the metagenomic diversity of environmental samples /Elizabeth A. Galbraith, Dionysios A. Antonopoulos, and Bryan A. White --17.16S rRNA targeted DGGE fingerprinting of microbial communities /Vesela A. Tzeneva ... [et al.] --18.An emulsion polymerase chain reaction-based method for molecular haplotyping /James G. Wetmur and Jia Chen --Index.
  • Introduction --Immune System and Atopic Disorders --Epigenetics --Epigenetics, Environment, and Allergic Diseases --Conclusions and Future Perspectives.
  • Behavioral Epigenetics is the study of how environmental factors affect alterations in behavior, addressing the fundamental mechanisms that shape development and individual vulnerability/resilience to adverse behavioral outcome. With an understanding of the molecular mechanisms involved in epigenetic modulation, researchers believe it will be possible to develop targeted therapies for those individuals in whom it malfunctions. This volume will address current understanding of the roles of epigenetic processes at the molecular/cellular level, their impact on neural development and behavior.
  • Epigenetic risks of cloning 2006, CRCnetBASE
  • Epigenetics 2004, Cold Spring Harb Lab Press
    Epigenetic reprogramming and genomic imprinting -- Chromosome inactivation -- DNA methylation -- Histone modification and nucleosome structure -- Chromatin structure and dynamics -- Polycomb and related silencing mechanisms -- Nuclear organization and dynamics -- Heterochromatin and transposon silencing -- RNA interference and related mechanisms -- Epigenetic regulation of phenotypes.
  • Epigenetics and cancer 2013, Springer
    Systems and Network Biology to Investigate Epigenetic De-regulatory Mechanisms of MicroRNAs in Pancreatic Cancer /Irfana Muqbil, Fazlul H. Sarkar, Ramzi M. Mohammad --Role of MicroRNAs in Cancer Epigenetics /Kishore B. Challagundla, Petra Wise, Muller Fabbri --Epigenetic Regulation of EZH2 and Its Targeted MicroRNAs /Sandy Leung-Kuen Au, Irene Oi-Lin Ng, Chun-Ming Wong --Epigenetics and MicroRNAs in Renal Cancer /Shahana Majid ... [et al.] --Epigenetic Regulation of MicroRNA in Colon Cancer /Qiong Zhang, Mukesh Verma, Sharad Khare --Epigenetic Regulation of miRNAs in Breast Cancer Formation and Progression /Zhiqian Zhang ... [et al.] --Epigenetic Variations of Stem Cell Markers in Cancer /Sripathi M. Sureban, Dongfeng Qu, Courtney W. Houchen --Recent Updates on Epigenetic Biomarkers for Prostate Cancer /Karen Chiam, Tanya Kate Day, Tina Bianco-Miotto --Epigenetics and Racial Disparities in Prostate Cancer /Benjamin A. Rybicki --Epigenetic Signatures of Breast Cancer Genes /Shrikant Anant, Animesh Dhar, Satish Ramalingam --Exploiting Epigenetic Modifiers to Circumvent Melanoma Dual Resistance to TCR-Engineered Immunotherapy- and BRAF V⁶⁰⁰E-Kinase Inhibitor /Ali R. Jazirehi CLS, --The Role of Epigenetics in Radiation Therapy and the DNA Damage Response /Steven P. Zielske --Plant Polyphenols as Epigenetic Modulators of Glutathione S-Transferase P1 Activity /Vijay S. Thakur, Sanjay Gupta --Epigenetic Regulations of mRNAs and miRNAs by Nutraceuticals /Yiwei Li ... [et al.] --Towards Curative Cancer Therapy with Maspin: A Unique Window of Opportunity to Target Cancer Dormancy /Alexander Kaplun, M. Margarida Bernardo, Sijana Dzinic.
  • Chromatin remodeling factors and DNA replication -- Epigenetic inheritance of chromatin states mediated by polycomb and trithorax group proteins in drosophila -- How to pack the genome for a safe trip -- Chromatin modifications on the inactive x chromosome -- Chromatin mechanisms in drosophila dosage compensation -- DNA methylation in epigenetic control of gene expression -- The epigenetic breakdown of cancer cells: from DNA methylation to histone modifications -- Developmental regulation of the beta-globin gene locus -- Epigenetic regulation of mammalian imprinted genes: from primary to functional imprints -- Seed development and genomic imprinting in plants.
  • Epigenetics and disease 2011, Springer
  • Epigenetics and cancer: DNA methylation / Santiago Ropero and Manel Esteller -- Epigenetics and cancer: histone modifications / Mario F. Fraga and Manel Esteller -- Epigenetic drugs: DNA demethylating agents / Ehab Atallah, Guillermo Garcia-Manero -- Epigenetic drugs: histone deacetylase inhibitors / Melissa Peart, Ricky W. Johnstone -- Sirtuins in biology and disease / Alejandro Vaquero, Danny Reinberg -- MicroRNAs in cell biology and disease / Muller Fabbri, Carlo M. Croce, George A. Calin -- Chromatin modifications by polycomb complexes / Miguel Vidal -- Epigenetics and its genetic syndromes / Richard J. Gibbons -- Epigenetics and immunity / Esteban Ballestar and Bruce C. Richardson -- Aetiology of major psychosis: why do we need epigenetics? / Gabriel Oh and Arturas Petronis -- Epigenetics and cardiovascular disease / Gertrund Lund and Silvio Zaina -- Epigenetics and plant biology / Luis Valledor ... [et al.] -- Epigenetics, environment, and evolution / Douglas M. Ruden, Parsa Rasouli, Xiangyi Lu -- Epigenetics and epigenomics / Jose Ignacio Martin-Subero, Reiner Siebert.
  • Epigenetics of aging 2010, Springer
  • Epigenetics protocols 2004, Springer Protocols
    Methods of epigenetic analysis / Trygve O. Tollefsbol -- Chromatin immunoprecipitation assays / Yan Yan, Haobin Chen, and Max Costa -- Native chromatin immunoprecipitation / Alan W. Thorne, Fiona A. Myers, and Tim R. Hebbes -- Q-PCR in combination with ChIP assays to detect changes in chromatin acetylation / Ryan A. Irvine and Chin-Lin Hsieh -- Restriction endonuclease accessibility as a determinant of altered chromatin structure / William M. Hempel and Pierre Ferrier -- Measuring changes in chromatin using micrococcal nuclease / Nicolas Steward and Hiroshi Sano -- DNasel hypersensitivity analysis of chromatin structure / Qianjin Lu and Bruce Richardson -- Inhibition of histone deacetylases / Cheng Liu and Dawei Xu -- Site-specific analysis of histone methylation and acetylation / David Umlauf, Yuji Goto, and Robert Feil -- Analysis of mammalian telomere position effect / Joseph A. Baur, Woodring E. Wright, and Jerry W. Shay -- Activity assays for poly-ADP ribose polymerase 1 / Eva Kirsten ... [et al.] -- Multigenerational selection and detection of altered histone acetylation and methylation patterns: toward a quantitative epigenetics in Drosophila / Mark D. Garfinkel ... [et al.] --Profiling DNA methylation by bisulfite genomic sequencing: problems and solutions / Liang Liu ... [et al.] -- Methylation-sensitive single-strand conformation analysis: a rapid method to screen for and analyze DNA methylation / Jean Benhattar and Geneviève Clément -- SIRPH analysis, SNuPE with IP-RP-HPLC for quantitative measurements of DNA methylation at specific CpG sites / Osman El-Maarri -- Real-time PCR-based assay for quantitative determination of methylation status / Ulrich Lehmann and Hans Kreipe -- Denaturing gradient gel electrophoresis to detect methylation changes in DNA / Masahiko Shiraishi -- Photocrosslinking oligonucleotide hybridization assay for concurrent gene dosage and CpG methylation analysis / Risa Peoples, Michael Wood, and Reuel Van Atta -- Methylation-specific oligonucleotide microarray / Pearlly S. Yan, Susan H. Wei, and Tim Hui-Ming Huang -- Methylation-specific PCR in situ hybridization / Gerard J. Nuovo -- Relative quantitation of DNA methyltransferase mRNA by real-time RT-PCR assay / John Attwood and Bruce Richardson -- DMB (DNMT-magnetic beads) assay: measuring DNA methyltransferase activity in vitro / Tomoki Yokochi and Keith D. Robertson.
  • "What lies at the heart of neuronal plasticity? Accumulating evidence points to epigenetics. This word originally indicated potentially heritable modifications in gene expression that do not involve changes in DNA sequence. Today this definition is much less strict, and epigenetic control is thought to include DNA methylation, histone modifications, histone variants, microRNA metabolic pathways and non-histone proteins modifications. Thus, while neuronal plasticity is rightly thought to be intimately associated to genomic control, it is critical to appreciate that there is much more to the genome than DNA sequence. Recent years have seen spectacular advances in the field of epigenetics. These have attracted the interest of researchers in many fields and evidence connecting epigenetic regulation to brain functions has been accumulating. Neurons daily convert a variety of external stimuli into rapid or long-lasting changes in gene expression. A variety of studies have centered on the molecular mechanisms implicated in epigenetic control and how these may operate in concert. It will be critical to unravel how specificity is achieved. Importantly, specific modifications seem to mediate both developmental processes and adult brain functions, such as synaptic plasticity and memory. Many aspects of the research in neurosciences and endocrinology during the upcoming decade will be dominated by the deciphering of epigenetic control. This book constitutes a compendium of the most updated views in the field"--Publisher.
  • Essential concepts in toxicogenomics 2008, Springer Protocols
    Toxicogenomics and classical toxicology, how to improve prediction and mechanistic understanding of human toxicity / Donna L. Mendrick -- Use of traditional endpoints and gene dysregulation to understand mechanisms of toxicity / Wayne R. Buck, Jeffrey F. Waring, Eric A. Blomme -- Quality control of microarray assays for toxicogenomic and in vitro diagnostic applications / Karol L. Thompson and Joseph Hackett -- Role of statistics in toxicogenomics / Michael Elashoff -- Predictive toxicogenomics in preclinical discovery / Scott A. Barros and Rory B. Martin -- In vivo predictive toxicogenomics / Mark W. Porter -- Bioinformatics, databasing and gene annotation / Lyle D. Burgoon and Timothy R. Zacharewski -- Microarray probe mapping and annotation in cross - species comparative toxicogenomics / John N Calley, William B Mattes, Timothy P. Ryan -- Toxicogenomics in biomarker discovery -- Marc F. DeCristofaro, Kellye K. Daniels -- From pharmacogenomics to translational biomarkers / Donna L. Mendrick -- Public consortium efforts in toxicogenomics / William B. Mattes -- Applications of toxicogenomics to nonclinical drug development / Frank D. Sistare, Joseph J. DeGeorge.
  • Evolution of the genome 2005, ScienceDirect
    Genome size evolution in animals /T. Ryan Gregory --Genome size evolution in plants /Michael D. Bennett and Ilia J. Leitch --Transposable elements /Margaret G. Kidwell --B chromosomes /Juan Pedro M. Camacho --Small-scale gene duplications /John S. Taylor and Jeroen Raes --Large-scale gene and ancient genome duplications /Yves Van de Peer and Axel Meyer --Polyploidy in plants /Jennifer A. Tate, Douglas E. Soltis, and Pamela S. Soltis --Polyploidy in animals /T. Ryan Gregory and Barbara K. Mable --Comparative genomics in eukaryotes /Alan Filipski and Sudhir Kumar --Comparative genomics in prokaryotes /T. Ryan Gregory and Rob DeSalle --Macroevolution and the genome /T. Ryan Gregory.
  • History of investigations -- The role of species concepts -- Testing the hypothesis -- Barriers to gene flow -- Hybrid fitness -- Gene duplication -- Origin of new evolutionary lineages -- Implications for endangered taxa -- Humans and associated lineages -- Emergent properties.
  • An introduction to bioinformatics for computer scientists / David W. Corne and Gary B. Fogel -- An introduction to evolutionary computation for biologists / Gary B. Fogel and David W. Corne -- Determining genome sequences from experimental data using evolutionary computation / Jacek Blazewicz and Marta Kasprzak -- Protein structure alignment using evolutionary computation / Joseph D. Szustakowski and Zhiping Weng -- Using genetic algorithms for pairwise and multiple sequence alignments / Cédric Notredame -- On the evolutionary search for solutions to the protein folding problem / Garrison W. Greenwood and Jae-Min Shin -- Toward effective polypeptide structure prediction with parallel fast messy genetic algorithms / Gary B. Lamont and Laurence D. Merkle -- Application of evolutionary computation to protein folding with specialized operators / Steffen Schulze-Kremer -- Identification of coding regions in DNA sequences using evolved neural networks / Gary B. Fogel, Kumar Chellapilla and David B. Fogel -- Clustering microarray data with evolutionary algorithms / Emanuel Falkenauer and Arnaud Marchand -- Evolutionary computation and fractal visualization of sequence data / Dan Ashlock and Jim Golden -- Identifying metabolic pathways and gene regulation networks with evolutionary algorithms / Junji Kitagawa and Hitoshi Iba --Evolutionary computational support for the characterization of biological systems / Bogdan Filipič and Janez Štrancar -- Discovery of genetic and environmental interactions in disease data using evolutionary computation / Laetitia Jourdan, Clarisse Dhaenens-Flipo and El-Ghazali Talbi -- Feature selection methods based on genetic algorithms for in silico drug design / Mark J. Embrechts, Muhsin Ozdemir, Larry Lockwood, Curt Breneman, Kristin Bennett, Dirk Devogelaere and Marcel Rijckaert --Interpreting analytical spectra with evolutionary computation / Jem J. Rowland.
  • Expressed sequence tags (ESTs) 2009, Springer Protocols
    Expressed sequence tags : an overview / John Parkinson and Mark Blaxter --Strategies for undertaking expressed sequence tag (EST) projects / Sandra W. Clifton and Makedonka Mitreva -- Construction of cDNA libraries : focus on protists and fungi / Naiara Rodríguez-Ezpeleta ... [et al.] -- Generation of full-length cDNA libraries : focus on plants / Motoaki Seki ... [et al.] -- Preparation of full-length cDNA libraries : focus on metazoans / Masako Harada and Yoshihide Hayashizaki -- Expressed sequence tags : normalization and subtraction of cDNA libraries / Marcelo Bento Soares ... [et al.] -- Generating EST libraries : trans-spliced cDNAs / Cecilia Fernández and Rick M. Maizels -- Large-scale sequencing and analytical processing of ESTs / Makedonka Mitreva and Elaine R. Mardis -- EST processing : from trace to sequence / Ralf Schmid and Mark Blaxter -- Obtaining accurate translations from expressed sequence tags / James Wasmuth and Mark Blaxter -- EST databases and web tools for EST projects /Yao-Qing Shen ... [et al.] -- Phylogenomic analysis of EST datasets / José M. Peregrín-Alvarez and John Parkinson -- Statistical analysis of expressed sequence tags / Edward Susko and Andrew J. Roger -- Application of ESTs in microarray analysis / Weizhong Li ... [et al.] -- Exploiting ESTs in human health / Sandro José de Souza.
  • Fanconi anemia 2007, Karger
    Why, what, and how can we learn from a rare disease like Fanconi anemia? / Schroeder-Kurth, T. -- Fanconi anemia: a disease with many faces / Dietrich, R., Velleuer, E. -- Milestones in Fanconi anemia research / Digweed, M., Hoehn, H., Sperling K. -- Fanconi anemia genes: structure, mutations, and genotype-phenotype correlations / Kalb, R. ... [et al.] -- Cancer in Fanconi anemia and Fanconi anemia genes in cancer / Neveling, K., Kalb, R., Schindler, D. -- Clonal chromosomal aberrations in bone marrow cells of Fanconi anemia patients: results and implications / Neitzel H. ... [et al.] -- Interphase FISH-assay for the detection of MDS- and AML-associated chromosomal imbalances in native bone marrow and peripheral blood cells / Tönnies, H. ... [et al.] -- Applications of cell cycle testing in Fanconi anemia / Schindler, D. ... [et al.] -- Prenatal diagnosis of Fanconi anemia: functional and molecular testing / Bechtold, A. ... [et al.] -- Revertant mosaicism in Fanconi anemia: natural gene therapy at work / Hoehn, H. ... [et al.] -- Stem cell transplantation in Fanconi anemia, recent advances with alternative donors / Eyrich, M., Winkler, B., Schlegel, P.G. -- Fanconi anemia genes in vertebrates: evolutionary conservation, sex-linkage, and embryonic expression of FANCC and FANCG in avian cells / Nanda, I. ... [et al.] -- Studying homologous recombination in Fanconi anemia / Demuth, I., Digweed, M. -- Functional knock-down of human RAD51 for testing the Fanconi anemia-BRCA connection / Rio, P., Hanenberg, H.
  • Forensic DNA typing protocols 2004, Springer Protocols
    Forensic DNA-typing technologies: a review / Angel Carracedo and Paula Sánchez-Diz -- DNA extraction and quantitation of forensic samples using the phenol-chloroform method and real-time PCR / Silvano Köchl, Harald Niederstätter, and Walther Parson -- A real-time PCR protocol to determine the number of amelogenine (X-Y) gene copies from forensic DNA samples / Antonio Alonso and Pablo Martín -- Species determination: the role and use of the cytochrome b gene / Adrian Linacre and James Chun-l Lee -- Constructing STR multiplex assays / John M. Butler -- Y chromosome STR typing / Leonor Gusma̋o and Cíntia Alves -- Using online databases for developing SNP markers of forensic interest / Christopher Phillips -- SNP typing in forensic genetics: a review / Beatriz Sobrino and Angel Carracedo -- Genotyping SNPs with the LightCycler / María Victoria Lareu and Clara Ruiz-Ponte -- Universal tag arrays in forensic SNP analysis / Marie Allen and Anna-Maria Divne --SNP typing on the nanochip electronic microarray / Claus Børsting, Juan J. Sanchez, and Niels Morling -- Genotyping SNPs using a UV-photocleavable oligonucleotide in MALDI-TOF MS / Peter M. Vallone, Kristina Fahr, and Markus Kostrzewa -- Mitochondrial D-loop and coding sequence analysis using pyrosequencing / Marie Allen and Hanna Andréasson -- SNaPshot typing of mitochondrial DNA coding region variants / Antonio Salas, Beatriz Quintáns, and Vanesa Álvarez-Iglesias -- Typing of Y chromosome SNPs with multiplex PCR methods / Juan J. Sanchez, Claus Børsting, and Niels Morling -- Y chromosome SNP analysis using the single-base extension: a hierarchical multiplex design / María Brión -- SNaPshot for pharmacogenetics by minisequencing / Klaus Bender -- Methods for the study of ancient DNA /Christine Keyser-Tracqui and Bertrand Ludes -- Protocols for ancient DNAtyping / Cristian Capelli and Frank Tschentscher.
  • Machine generated contents note: Introduction -- Worthy N. Martin and William M. Spears -- Overcoming Fitness Barriers in Multi-Modal Search Spaces 5 -- Martin J. Oates and David Come -- N iches in N K -Landscapes 27 -- Keith E. Mathia, Larry J. Eshelman, and J. David Schaffer -- New Methods for Tunable, Random Landscapes 47 -- R. E. Smith and J. E. Smith -- Analysis of Recombinative Algorithms on a Non-Separable Building-Block Problem 69 -- Richard A. Watson -- Direct Statistical Estimation of GA Landscape Properties 91 -- Colin R. Reeves -- Comparing Population Mean Curves 109 -- B. Naudts and I. Landrieu -- Local Performance of the ((/(I, () -ES in a Noisy Environment 127 -- Dirk V Arnold and Hans-Georg Beyer -- Recursive Conditional Scheme Theorem, Convergence and -- Population Sizing in Genetic Algorithms 143 -- Riccardo Poli -- Towards a Theory of Strong Overgeneral Classifiers 165 -- Tim Kovacs -- Evolutionary Optimization through PAC Learning 185 -- Forbes J. Burkowski -- Continuous Dynamical System Models of Steady-State Genetic Algorithms 209 -- Alden H. Wright and Jonathan E. Rowe -- Mutation-Selection Algorithm: A Large Deviation Approach 227 -- Paul Albuquerque and Christian Mazza -- The Equilibrium and Transient Behavior of Mutation and Recombination 241 -- William M. Spears -- The Mixing Rate of Different Crossover Operators 261 -- Adam Prigel-Bennett -- Dynamic Parameter Control in Simple Evolutionary Algorithms 275 -- Stefan Droste, Thomas Jansen, and Ingo Wegener -- Local Search and High Precision Gray Codes: Convergence Results and Neighborhoods 295 -- Darrell Whitley, Laura Barbulescu, and Jean-Paul Watson -- Burden and Benefits of Redundancy 313 -- Karsten Weicker and Nicole Weicker -- Author Index 335 -- Key Word Index 337.
  • Clinical Neurological Phenotype of FXTAS / Maureen A. Leehey, Elizabeth Berry-Kravis, Christopher G. Goetz and Randi J. Hagerman -- The Epidemiology of FXTAS / Deborah A. Hall and Sebastien Jacquemont -- FXTAS: Neuropsychological/Neuropsychiatric Phenotypes / Jim Grigsby, Angela G. Brega, Andreea L. Seritan and James A. Bourgeois -- Radiological Findings in FXTAS / Susan M. Rivera, Glenn T. Stebbins and Jim Grigsby -- The Pathology of FXTAS / Claudia M. Greco, Michael R. Hunsaker and Robert F. Berman -- The Molecular Biology of FXTAS / Flora Tassone and Paul J. Hagerman -- Genotype/Phenotype Relationships in FXTAS / Emily Allen, Maureen A. Leehey, Flora Tassone and Stephanie Sherman -- Animal Models for FXTAS / Rob Willemsen, Yujing Li, Robert F. Berman, Judith R. Brouwer and Ben A. Oostra, et al. -- Treatment and Management of FXTAS / Elizabeth Berry-Kravis, Deborah A. Hall, Maureen A. Leehey and Randi J. Hagerman -- Genetic Counseling for FXTAS and FMR1-Associated Disorders / Louise W. Gane, Katherine Howard and Liane Abrams.
  • Functional genomics 2003, Springer Protocols
  • Functional microbial genomics 2002, ScienceDirect
  • Emerging evidence indicates that the Gadd45 family of genes play a unique and critical role as sensors of stress, including genotoxic, physiological and oncogenic stress. The stress response Gadd45 family of genes (Gadd45a, Gadd45b & Gadd45g), discovered by Dr. Liebermann and other researchers, encode for small (18 kd) nuclear/cytoplasmic proteins).These genes are rapidly induced by a wide variety of endogenous and exogenous stress stimuli. In spite of marked similarities, Gadd45 genes are regulated differently & exhibit functional diversity. Gadd45 are implicated in cell cycle arrest, DNA demethylation & repair, apoptosis, cell survival, genomic stability, inflammation, & in response to physiological and oncogenic stress. Functions of Gadd45 genes are mediated by protein-protein interactions that modulate structure/function of other cellular proteins implicated in cell cycle regulation and the response of cells to stress; these interactions vary depending upon the biological setting including cell type, developmental stage and stress/stimulus. Protein partners include cdc2/cyclinB1, p21, the p38/JNK stress induced kinase pathways, and PCNA/histones. The purpose of this book is to provide a comprehensive picture of the unique global role Gadd45 genes play as stress sensors & the molecular pathways involved.
  • Coevolution within and between genes / Galtier, N.; Dutheil, J. -- Evolution of protein-protein interaction network / Makino, T.; Gojobori, T. -- Bacterial flagella and type III secretion: case studies in the evolution of complexity / Pallen, M.J.; Gophna, U. -- Comparative genomics and evolutionary trajectories of viral ATP dependent DNA-packaging systems / Burroughs, A.M.; Iyer, L.M.; Aravind, L. -- General trends in the evolution of prokaryotic transcriptional regulatory networks / Madan Babu, M.; Balaji, S.; Aravind, L. -- Divergence of regulatory sequences in duplicated fish genes / Van Hellemont, R. ... [et al.] -- Evolution of gene function on the X chromosome versus the autosomes / Singh, N.D.; Petrov, D.A. -- Amino acid repeats and the structure and evolution of proteins / Albà, M.M.; Tompa, P.; Veitia, R.A. -- Origination of chimeric genes through DNA-level recombination / Arguello, J.R. ... [et al.] -- Exaptation of protein coding sequences from transposable elements / Bowen, N.J.; Jordan, I.K. -- Modulation of host genes by mammalian transposable elements / Makalowski, W.; Toda, Y. -- Modern genomes with retro-look: retrotransposed elements, retroposition and the origin of new genes / Volff, J.-N.; Brosius, J.
  • "The third edition of this popular reference covers a variety of techniques related to gene manipulation, including DNA isolation, preparation, screening, and analysis. Topics range from very basic methods to current and sophisticated technologies, including methodologies created and tested by the authors. Other topics include approaches to grant funding and SiRNA technology. The authors offer detailed, step-by-step explanations of protocols and helpful troubleshooting guides. This edition features new techniques for every chapter, as well as several new chapters"--Provided by publisher.
  • Gene delivery to mammalian cells 2003, Springer Protocols
    v. 2 Springer Protocols
    v. 1. Nonviral gene transfer techniques -- v. 2. Viral gene transfer techniques.
  • Gene expression profiling 2004, Springer Protocols
  • "Gene expression studies merge three disciplines with different historical backgrounds: molecular biology, bioinformatics, and biostatistics. This book tears down the omnipresent language barriers among researchers of these different backgrounds by explaining the entire process of a gene expression study from conception to interpretation. It covers important technical and statistical pitfalls and problems, helping not only to explain concepts outside the domain of researchers, but to provide additional guidance in their field of expertise. The book also describes technical and statistical methods conceptually with illustrative examples, enabling those inexperienced with gene expression studies to grasp the basic principles"--Provided by publisher.
  • Gene function analysis 2007, Springer Protocols
    Gene function inference from gene expression of deletion mutants / Ghislain Bidaut -- Association analysis for large-scale gene set data / Stefan A. Kirov, Bing Zhang, and Jay R. Snoddy -- Estimating gene function with least squares nonnegative matrix factorization / Guoli Wang and Michael F. Ochs -- From promoter analysis to transcriptional regulatory network prediction using PAINT / Gregory E. Gonye ... [et al.] -- Prediction of intrinsic disorder and its use in functional proteomics / Vladimir N. Uversky ... [et al.] -- Sybil : methods and software for multiple genome comparison and visualization / Jonathan Crabtree ... [et al.] -- Estimating protein function using protein-protein relationships / Shailesh V. Date -- Bioinformatics tools for modeling transcription factor target genes and epigenetic changes / Ramana V. Dvuluri -- Mining biomedical data using MetaMap Transfer (MMTx) and the Unified Medical Language System (UMLS) / John D. Osborne ... [et al.] -- Statistical methods for identifying differentially expressed gene combinations / Yen-Yi Ho ... [et al.] -- Gene function analysis using the chicken B-cell line DT40 / Randolph B. Caldwell ... [et al.] -- Design and application of a shRNA-based gene replacement retrovirus / Rugang Zhang, Peter D. Adams, and Xiaofen Ye -- Construction of simple and efficient DNA vector-based short hairpin RNA expression systems for specific gene silencing in mammalian cells / Tsung-Lin Cheng and Wen-Tsan Chang -- Selection of recombinant antibodies from antibody gene libraries / Michael Hust, Stefan Dübel, and Thomas Schirrmann -- A bacterial/yeast merged two-hybrid system : protocol for yeast screening with single of parallel baits / Nadezhda Y. Tikhmyanova ... [et al.] -- A bacterial/yeast merged two-hybrid system : protocol for bacterial screening / Ilya G. Serebriiskii, Nadia Milech, and Erica A. Golemis -- Engineering Cys2His2 zinc finger domains using a bacterial cell-based two-hybrid selection system / Stacey Thibodeau-Beganny and J. Keith Joung.
  • Gene knockout protocols. 2nd ed. 2009, Springer Protocols
    Overview on mouse mutagenesis / Ralf Kühn and Wolfgang Wurst -- Construction of gene-targeting vectors by recombineering / Song-Choon Lee, Wei Wang, and Pentao Liu -- Gene-trap vectors and mutagenesis / Silke De-Zolt ... [et al.] -- Chromosome engineering in ES cells / Louise vander Weyden, Charles Shaw-Smith, and Allan Bradley -- Gene modification in embryonic stem cells by single-stranded DNA oligonucleotides / Marieke Aarts ... [et al.] -- Generation of shRNA transgenic mice / Christiane Hitz ... [et al.] -- Mutagenesis of mouse embryonic stem cells with ethylmethanesulfonate / Robert Munroe and John Schimenti -- Gene targeting in mouse embryonic stem cells / Lino Tessarollo ... [et al.] -- Manipulating mouse embryonic stem cells / Eileen Southon and Lino Tessarollo -- ES cell line establishment / Heidrun Kern and Branko Zevnik -- Generation of double-knockout embryonic stem cells / Eva Wielders, Marleen Dekker, and Hein te Riele -- Differentiation analysis of pluripotent mouse embryonic stem (ES) cells in vitro / Insa S. Schroeder ... [et al.] -- Cloning of ES cells and mice by nuclear transfer / Sayaka Wakayama, Satoshi Kishigami, and Teruhiko Wakayama -- Isolation, microinjection, and transfer of mouse blastocysts / Susan W. Reid and Lino Tessarollo -- Aggregation chimeras : combining ES cells, diploid, and tetraploid embryos / Mika Tanaka ... [et al.] -- VelociMouse : fully ES cell-derived F0-generation mice obtained from the injection of ES cells into eight-cell-stage embryos / Thomas M. DeChiara ... [et al.] -- Generation of Cre recombinase-expressing transgenic mice using bacterial artificial chromosomes / Jan Rodriguez Parkitna, David Engblom, and Günther Schütz -- Inducible Cre mice / Susanne Feil, Nadejda Valtcheva, and Robert Feil -- Creation and use of a Cre recombinase transgenic database / Andras Nagy, Lynn Mar, and Graham Watts -- Transposon mutagenesis in mice / David A. Largaespada -- Lentiviral transgenesis / Alexander Pfeifer and Andreas Hofmann -- Sperm cryopreservation and in vitro fertilization / Susan Marschall, Auke Boersma, and Martin Hrabé de Angelis -- Influence of genetic background on genetically engineered mouse phenotypes / Thomas Doetschman -- Pathologic phenotyping of mutant mice / Roderick T. Bronson -- Systemic first-line phenotyping / Valérie Gailus-Durner ... [et al.]
  • Gene mapping, discovery, and expression 2006, Springer Protocols
    Analysis of allele-specific gene expression / Julian C. Knight -- Construction of microRNA-containing vectors for expression in mammalian cells / Yoko Fukuda, Hiroaki Kawasaki, and Kazunari Taira -- Mining microarray data at NCBI's gene expression omnibus (GEO) / Tanya Barrett and Ron Edgar -- The Stanford microarray database: a user's guide / Jeremy Gollub, Catherine A. Ball, and Gavin Sherlock -- Detecting nucleosome ladders on unique DNA sequences in mouse liver nuclei / Tomara J. Fleury, Alfred Cioffi, and Arnold Stein -- DNA methyltransferase probing of DNA-protein interactions / Scott A. Hoose and Michael P. Kladde -- Protein binding microarrays (PBMS) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteins / Michael F. Berger and Martha L. Bulyk -- Quantitative profiling of protein-DNA binding on microarrays / Jiannis Ragoussis, Simon Field, and Irina A. Udalova -- Analysis of protein-DNA binding by streptavidin-agarose pulldown / Kenneth K. Wu -- Isolation and mass spectrometry of specific DNA binding proteins / Mariana Yaneva and Paul Tempst -- Isolation of transcription factor complexes by in vivo biotinylation tagging and direct binding to streptavidin beads / Patrick Rodriguez ... [et al.].Use of genome browsers to locate your favorite genes / Minou Bina -- Methods for identifying and mapping recent segmental and gene duplications in eukaryotic genomes / Razi Khaja ... [et al.] -- Identification and mapping of paralogous genes on a known genomic DNA sequence / Minou Bina -- Quantitative DNA fiber mapping in genome research and construction of physical maps / Heinz-Ulrich G. Weier and Lisa W. Chu -- PRINS for mapping single copy genes / Avirachan T. Tharapel and Stephen S. Wachtel -- VISTA family of computational tools for comparative analysis of DNA sequences and whole genomes / Inna Dubchak and Dmitriy V. Ryaboy -- Computational prediction of cis-Regulatory modules from multispecies alignments using galaxy, table browser, and GALA / Laura Elnitski, David King, and Ross C. Hardison -- Comparative promoter analysis in vertebrate genomes with the CORG workbench / Christoph Dieterich and Martin Vingron -- cis-Regulatory region analysis using BEARR / Vinsensius Berlian Vega -- A database of 9-Mers from promoter region of human protein-coding genes / Minou Bina, Phillip Wyss, and Syed Rehan Shah -- A program toolkit for the analysis of regulatory regions of genes / Phillip Wyss, Sheryl A. Lazarus, and Minou Bina --
  • A perspective on the future clinical impact of genetic diagnosis and gene-based drug therapies for patient health / Julian W. Tang -- Virally-encoded microRNA (miRNA): candidates for gene silencing / Ralph A. Tripp ... [et al.] -- Development of gene profile-responsive antisense agents / Sergei A. Kazakov and Brian H. Johnston -- Gene profiles in drug development: applications in target identification, biomarker discovery, and compound characterization / Eric A.G. Blomme and Dimitri Semizarov -- Gene profiles and cancer / Beverly A. Teicher -- RNA viruses and RNA-based drugs: a perfect match for RNA delivery and the identification of candidate therapeutic target inflammatory molecules / Brett A. Lidbury ... [et al.] -- Ethical considerations for a genetic future in diagnosis and drug development / Lexie Brans and Brett A. Lidbury.
  • Gene therapy 2010, Springer
  • Gene therapy protocols. 3rd ed. v. 1-, 2008-, Springer Protocols
    v. 1. Production and in vivo applications of gene transfer vectors. Preparation and quantification of pseudotyped retroviral vector / Hong Yu and Young Jik Kwon. Production of retroviral vectors for clinical use / Kenneth Cornetta, Lilith Reeves, and Scott Cross. Methods for the production of helper-dependent adenoviral vectors / Donna J. Palmer and Philip Ng. Methods for the production of first generation adenoviral vectors / Donna J. Palmer and Philip Ng. Large-scale production of recombinant adeno-associated viral vectors / Alejandro Negrete and Robert M. Kotin. Construction and production of recombinant herpes simplex virus vectors / William F. Goins ... [et al.] Plasmid-based gene transfer in mouse skeletal muscle by electroporation / Jonathan D. Schertzer and Goron S. Lynch. Chitosan nanoparticle-mediated gene transfer / Dongwon Lee and Shyam S. Mohapatra. PEG-PEI copolymers for oligonucleotide delivery to cells and tissues / Gordon J. Lutz, Shashank R. Sirsi, and Jason H. Williams. Non-viral gene delivery with cationic liposome-DNA complexes / Kai K. Ewert ... [et al.] Applications of lentiviral vectors in noninvasive molecular imaging / Abhijit De ... [et al.] Retroviral modification of mesenchymal stem cells for gene therapy of hemophilia A / Christopher B. Doering. Transduction of murine hematopoietic stem cells and in vivo selection of gene-modified cells / Lucienne M. Ide, Elisabeth Javazon, and H. Trent Spencer. Assessment of CFTR function after gene transfer in vitro and in vivo / Uta Griesenbach ... [et al.] Oncolytic adenoviruses for cancer gene therapy / Ta-Chiang Liu, Stephen H. Thorne, and David H. Kirn. Design of trans-splicing adeno-associated viral vectors for Duchenne muscular dystrophy gene therapy / Yi Lai ... [et al.] Prevention of type 1 diabetes in NOD mice by genetic engineering of hematopoietic stem cells / Jessamyn Bagley, Charoui Tian, and John Iacomini. Lentiviral vector delivery of siRNA and shRNA encoding genes into cultured and primary hematopoietic cells / Mingjie Li and John J. Rossi. Nanoparticle-mediated gene delivery to the lung / Rajagopal Ramesh. Retroviral-mediated gene therapy for the differentiation of primary cells into a mineralizing osteoblastic phenotype / Jennifer E. Phillips and Andrés J. García. In vivo siRNA delivery to the mouse hypothalamus shows a role of the co-chaperone XAP2 in regulating TRH transcription / Stéphanie Decherf, Zahra Hassani, and Barbara A. Demeneix. Efficient retroviral gene transfer to epidermal stem cells / Pedro Lei and Stelios T. Andreadis.
  • Generation of cDNA libraries 2003, Springer Protocols
  • GeneReviews NCBI Bookshelf
  • pt. 1. Genes and the heart -- pt. 2. Development and gender -- pt. 3. Mitochondrial diseases -- pt. 4. Ischemic heart disease -- pt. 5. Hypertension and arrhythmias -- pt. 6. Hypertrophy and failure.
  • Genes and mental illness -- How does stress work? the role of memes in epigenesis -- Culture and mental illness -- Genetic-memetic model of mental illness-migration and natural disasters as illustrations -- What do we inherit from our parents and ancestors? -- Genes -- Evolution -- Learning, imitation, and memes -- Storage and evolution of memes in the brain -- External storage of memes: culture, media, cyberspace -- Culture and the individual -- What is mental health -- What is mental illness? -- Psychiatric diagnosis: toward a memetic-epigenetic multiaxial model -- Memetic diagnosis, memetic assessment and biopsychosocial epigenetic formulation -- Principles of memetic therapy -- Broad-spectrum memetic therapy -- Specific memetic therapies -- Genetic-memetic prevention -- Overview of specific syndromes -- Attention-cognition spectrum syndromes: delirium, dementia, impulse control syndromes, ADHD, antisocial personality, obsessive-compulsive personality traits, obsessive-compulsive syndrome -- Anxiety-mood spectrum syndromes: anxiety, panic, phobias, ASD, PTSD, borderline syndrome, dependent and avoidant personalities, social phobia, bipolarity and mania, depression-neurotic and syndromic, adjustment disorders -- Reality perception spectrum syndromes (imagination, dissociation, conversion, somatoform, misattribution somatization, psychosis) -- Pleasure spectrum syndromes (substance use/abuse, additions to substances and beliefs, fanaticism) -- Primary memetic syndromes: eating disorders, factitious disorders, malingering, meme-directed destructive behaviors -- Challenges for the future.
  • This state-of-the-art book is written by a group of international experts to provide insight into the newest breakthroughs from basic pathogenesis to clinical aspects of multiple myeloma. The book provides a comprehensive overview of the genetic and molecular epidemiology of multiple myeloma in order to get a more refined and conclusive understanding of this disease. Areas, which are covered include the characterization of different myeloma entities by genomics and proteomics, notch signaling and targeting protein translation as a new treatment for multiple myeloma, cell cycle control of plasma cell differentiation, the role of bone disease in the pathogenesis of multiple myeloma as well as the molecular interaction of multiple myeloma with a microenvironment. Genetic and Molecular Epidemiology of Multiple Myeloma is a valuable resource for cancer researchers, medical, surgical, and radiation oncologists.
  • The early earth / Oliver Botta and Jeffrey L. Bada -- Reconstructing the universal tree of life / James R. Brown -- The nature of the last common ancestor / Luis Delaye, Arturo Becerra, and Antonio Lazcano -- Ribozyme-catalyzed genetics / Donald H. Burke -- The scope of selection / Michael Yarus and Rob Knight -- The evolutionary history of the translation machinery / George E. Fox and Ashwinikumar K. Naik -- Functional evolution of ribosomes / C. Briones and R. Amils -- Aminoacyl-tRNA synthetases as clues to establishment of the genetic code / Lluis Ribas de Pouplana and Paul Schimmel -- The relation between function, structure, and evolution of elongation factors Tu / Mathias Sprinzl -- Origin and evolution of DNA and DNA replication machineries / Patrick Forterre, Jonathan Filée, and Hannu Myllykallio -- Early evolution of DNA repair mechanisms / Jocelyne DiRuggiero and Frank T. Robb -- Extant variations in the genetic code / Manuel A.S. Santos and Mick F. Tuite -- Adaptive evolution of the genetic code / Rob D. Knight, S.J. Freeland, and Laura F. Landweber -- Expanding the genetic code in vitro and in vivo / Thomas J. Magliery and David R. Liu.
  • Genetic democracy 2008, Springer
    Introduction : the scope and importance of genetic democracy /Veikko Launis --The prerequisites for genetic democracy /Helena Siipi --Ethical expertise in democratic societies /Eerik Lagerspetz --Towards global bioethics : the UNESCO universal declaration on bioethics and human rights /Henk ten Have --Autonomy and genetic privacy /Juha Räikkä --Values, rights and GMO : against radicalism --The precautionary principle and the risks of modern agri-biotechnology /Marko Ahteensuu --Population databanks and democracy in light of the Icelandic experience /Vilhjálmur Árnason and Stefán Hjörleifsson --Equality and community in public deliberation : genetic democracy in Taiwan /Terence Hua Tai and Wen-Tsong Chiou --Genetic resources, genetic democracy and genetic equity /Keekok Lee --Moral constraints on permissible genetic design /Thomas Pogge.
  • Genetic engineering v. 27-28, 2006-2007., Springer
    v. 28, 2007 Springer
  • Genetic epidemiology 2009, Springer Protocols
    Molecular Genetics and Genetic Variation / Mohammed-Elfatih Twfieg, M. Dawn Teare -- Terminology, Concepts, and Models in Genetic Epidemiology / M. Dawn Teare, Mauro F. Koref -- An Introduction to Epidemiology / Cother Hajat -- Genetic Distance and Markers Used in Linkage Mapping / Kristina Allen-Brady, Nicola J. Camp -- Approaches to Genetic Linkage Analysis / M. Dawn Teare -- Fine-Scale Structure of the Genome and Markers Used in Association Mapping / Karen Curtin, Nicola J. Camp -- Genome-Wide Association Studies / Mark M. Iles -- Candidate Gene Association Studies / M. Dawn Teare -- Family-Based Association Studies / Frank Dudbridge -- Genome Variation: A Review of Web Resources / Andrew Collins, William J. Tapper -- Advanced Methods in Twin Studies / Jaakko Kaprio, Karri Silventoinen -- Mendelian Randomisation: A Tool for Assessing Causality in Observational Epidemiology / Nuala A. Sheehan, Sha Meng, Vanessa Didelez -- Copy Number Variation / Louise V. Wain, Martin D. Tobin -- Epigenetic Variation / Kevin Walters -- Modeling the Effect of Susceptibility Factors (HLA and PTPN22) in Rheumatoid Arthritis / Hervé Perdry, Françoise Clerget-Darpoux -- Coronary Artery Disease: An Example Case Study / Jennifer H. Barrett -- The Genetic Epidemiology of Obesity: A Case Study / Laura M. Johnson.
  • Genetic landscape of diabetes 2004, NCBI Bookshelf
  • Genetic recombination 2004, Springer Protocols
    Determination of mitotic recombination rates by fluctuation analysis in Saccharomyces cerevisiae / Rachelle Miller Spell and Sue Jinks-Robertson -- Determination of intrachromosomal recombination rates in cultured mammalian cells / Jason A. Smith and Alan S. Waldman -- Intrachromosomal homologous recombination in Arabidopsis thaliana / Waltraud Schmidt-Puchta, Nadiya Orel, Anzhela Kyryk, and Holger Puchta -- Analysis of recombinational repair of DNA double-strand breaks in mammalian cells with I-SceI nuclease / Jac A. Nickoloff and Mark A. Brenneman -- Transformation of monomorphic and pleomorphic Trypanosoma brucei / Richard McCulloch, Erik Vassella, Peter Burton, Michael Boshart, and J. David Barry -- Forward genetic screens for meiotic and mitotic recombination-defective mutants in mice / Laura Reinholdt, Terry Ashley, John Schimenti, and Naoko Shima -- Detecting carcinogens with the yeast DEL assay / Richard J. Brennan and Robert H. Schiestl --In vivo DNA deletion assay to detect environmental and genetic predisposition to cancer / Ramune Reliene, Alexander J. R. Bishop, Jiri Aubrecht, and Robert H. Schiestl -- Gene targeting at the chromosomal immunoglobulin locus: a model system for the study of mammalian homologous recombination mechanisms / Mark D. Baker -- DNA fragment transplacement in Saccharomyces cerevisiae: some genetic considerations / Glenn M. Manthey, Michelle S. Navarro, and Adam M. Bailis -- Targeted gene modification using triplex-forming oligonucleotides / Jean Y. Kuan and Peter M. Glazer -- Using nucleases to stimulate homologous recombination / Dana Carroll -- Enhancement of in vivo targeted nucleotide exchange by nonspecific carrier DNA / Katie K. Maguire and Eric B. Kmiec -- The use of the chromatin immunoprecipitation to investigate protein-DNA interactions during recombination / Tamara Goldfarb and Eric Alani -- Holliday junction branch migration and resolution assays / Angelos Constantinou and Stephen C. West.
  • Part 1.Application and Perspectives --ch. 1.Transgenic Modification of Production Traits in Farm Animals /Mathias Müller and Gottfried Brem --ch. 2.Genetically Modified Plants /Susanne Stirn and Horst Lörz --ch. 3.Fermented Food Production using Genetically Modified Yeast and Filamentous Fungi /Anke Niederhaus and Ulf Stahl --ch. 4.Production of Food Additives using Filamentous Fungi /Carsten M. Hjort --ch. 5.Perspectives of Genetic Engineering of Bacteria used in Food Fermentations /Arnold Geis --Part II.Legislation in Europe --ch. 6.The Legal Situation for Genetically Engineered Food in Europe /Rudolf Streinz and Lars O. Fuchs --Part III.Methods of Detection --ch. 7.Detection of Genetic Modifications: Some Basic Considerations /Knut J. Heller --ch. 8.DNA-based Methods for Detection of Genetic Modifications /Ralf Einspanier and Stephanie Rief --ch. 9.Genetic Engineering of Fishes and Methods for Detection /Hartmut Rehbein --ch. 10.Detection Methods for Genetically Modified Crops /Rolf Meyer --ch. 11.Methods to Detect the Application of Genetic Engineering in Composed and Processed Foods /Karl-Heinz Engel and Francisco Moreano --ch. 12.Mutations in Lactococcus lactis, and their Detection /Jan Kok and Bertus van den Burg --ch. 13.Detection Methods for Genetically Modified Microorganisms used in Food Fermentation /Walter P. Hammes, Christian Hertel and Torsten Bauer.
  • Part I. Application and Perspectives -- ch. 1. Transgenic modification of production traits in farm animals / Gottfried Brem, Mathias Müller -- ch. 2. Genetically modified plants / Susanne Stirn, Horst Lörz -- ch. 3. Fermentation of food by means of genetically modified yeast and filamentous fungi / Rena Leisegang, Elke Nevoigt, Anja Spielvogel, Georg Kristan, Anke Niederhaus, Ulf Stahl -- ch. 4. Production of food additives using filamentous fungi / Carsten M. Hjort -- ch. 5. Genetic engineering of bacteria used in food fermentation / Arnold Geis -- Part II. Legislation in Europe -- ch. 6. The Legal situation for genetically engineered food in Europe / Rudolf Streinz, Jan Kalbheim -- Part III. Methods of Detection -- ch. 7. Detection of genetic modifications : some basic considerations / Knut J. Heller -- ch. 8. DNA-based methods for detection of genetic modifications / Ralf Einspanier -- ch. 9. Genetic engineering of fish, and methods of detection / Hartmut Rehbein -- ch. 10. Detection methods for genetically modified crops / Rolf Meyer -- ch. 11. Methods for detection of genetically modified organisms in composite and processed foods / Karl-Heinz Engel, Francisco Moreano, Alexandra Ehlert -- ch. 12. Mutations in Lactococcus lactis and their detection / Jan Kok, Bertus van den Burg -- ch. 13. Methods for detection of genetically modified microorganisms used in food fermentation processes / Walter P. Hammes, Christian Hertel, Torsten Bauer.
  • Genetically modified organisms : concepts and methods -- Restriction enzymes : from their discovery to their applications -- Transforming growth factor-beta superfamily : animal models for development and disease -- Transfection of human neuroblastoma cells with Alzheimer's Disease brain hallmarks as a promising strategy to investigate the role of neurosteroidogenesis in neuroprotection -- Investigating therapeutic strategies for Fragile X syndrome in mice -- Innovative therapeutic perspectives in neuromuscular diseases -- Gene therapy for cancer treatment : state of the art -- Manipulating the mitochondrial genetic system.
  • Genetics and randomness 2010, CRCnetBASE
    Limits and uncertainty in nature and logic -- Quantum fluctuations, mutations, and "fixation" of uncertainty -- Recombination and randomness -- Uncertainty of development -- Organized randomness -- Random genetic drift and "deterministic" selection -- Life : making uncertainty certain.
  • Genetics and sports 2009, Karger
    Key concepts in human genetics : understanding the complex phenotype / W.T. Gibson -- Nature versus nurture in determining athletic ability / T.D. Brutsaert, E.J. Parra -- Genetics and sports : an overview of the pre-molecular biology era / M.W. Peeters ... [et al.] -- Genes, athlete status, and training : an overview / I.I. Ahmetov, V.A. Rogozkin -- Angiotensin : converting enzyme, renin-angiotensin system and human performance / D. Woods -- Actinin-3 and performance / N. yang, F. Garton, K. North -- East African runners : their genetics, lifestyle, and athletic prowess / V.O. Onywera -- Gene-lifestyle interactions and their consequences on human health / J. Pomeroy, A.M. Söderberg, P.W. Franks -- Genetic risk factors for musculoskeletal soft tissue injuries / M. Collins, S.M. Raleigh -- Innovative strategies for treatment of soft tissue injuries in human and animal athletes / A. Hoffmann, G. Gross -- Gene doping : possibilities and practicalities / D.J. Wells -- Genetic testing of athletes / A.G. Williams, H. Wackerhage -- The future of genetic research in exercise science and sports medicine / R.J. Trent, B. Yu.
  • Genetics for surgeons 2005, NCBI Bookshelf
  • Genetics of bacteria 2013, Springer
    Described as the earliest, simplest life forms, with unlimited metabolic versatility, bacteria are ideally suited to answer some very fundamental questions on life and its processes. They have been employed in almost all fields of biological studies, including Genetics. The whole edifice of science of Genetics centers around three processes: the generation, expression, and transmission of biological variation, and bacteria offer immediate advantages in studying all the three aspects of heredity. Being haploid and structurally simple, it becomes easy to isolate mutations of various kinds and relate them to a function. The availability of such mutants and their detailed genetic and biochemical analyses lead to a gamut of information on gene expression and its regulation. While studying the transmission of biological variation, it is clear that unlike their eukaryotic counterpart, a more genetic approach needs to be employed. Transmission of genetic information in most eukaryotic organisms rests on sexual reproduction that allows the generation of genetically variable offspring through the process of gene recombination. Even though bacteria show an apparent preference for asexual reproduction, they too have evolved mechanisms to trade their genetic material. In fact, bacteria not only could acquire many genes from close relatives, but also from entirely distant members through the process of horizontal gene transfer. Their success story of long evolutionary existence will stand testimony to these mechanisms. While teaching a course on Microbial Genetics to the post-graduate students at Delhi University, it was realized that a book devoted to bacterial genetics may be very handy to the students, researchers, and teachers alike. A strong foundation in genetics also helps in comprehending more modern concepts of molecular biology and recombinant DNA technology, always a favorite with the students and researchers. Planning the format of the book, emphasis has been laid on the generation and transmission of biological variability. The omission of expression part is indeed intentional because lots of information is available on this aspect in any modern biology book. The contents are spread over seven chapters and the text is supported with figures/tables wherever possible. The endeavor has been to induce the readers to appreciate the strength of bacterial genetics and realize the contribution of these tiny organisms to the growth of biological sciences as a whole and genetics in particular.
  • Genome dynamics and stability v. 1-, 2007-, Springer
  • Honeybee / D. Schlipalius, P.R. Ebert, G.J. Hunt -- Bumblebee / L. Wilfert, P. Schmid-Hempel, J. Gadau -- The jewel wasp - Nasonia / J. Gadau ... [et al.] -- Silkworm / Y. Yasukochi, H. Fujii, M.R. Goldsmith -- Pea aphid / J.A. Brisson, G.K. Davis -- Mosquito / D.W. Severson -- Hessian fly / J.J. Stuart, M.-S. Chen, M.O. Harris -- Tick / A.J. Ullmann, J.J. Stuart, C.A. Hill.
  • Genomics in the sea urchin : new perspectives on a perennial model system / Katherine M. Buckley amd Jonathan P. Rast -- Genome mapping and genomics of Caenorhabditis elegans / Jonathan Hodgkin, Michael Paulini, and mary Ann Tuli -- Genome mapping and genomics in Drosophila / Boris Adryan and Steven Russell -- Genome structure, functional genomics, and proteomics in ascidians / Yasunori Sasakura, Nicolas Sierro, Kenta Nakai, Kazuo Inaba, and takehiro G. Kusakabe -- Punching above their weight : the compact genomes of pufferfishes / Brian Cusack and Hugues Roest Crollius -- Medaka genomics and the methods and resources for decoding genomic functions / Tetsuaki Kimura, Yasuhiro Kamei, Yusuke Takehana, Takao Sasado, and Kiyoshi Naruse -- Xenopus genomics and genetics : progress and prospects / Amy K. Sater and Michael J. Gilchrist -- Mouse genome mapping and genomics / Paul Denny -- Rat genome mapping and genetics / Claude Szpirer and Göran Levan.
  • Introduction -- From genomes to protein functions -- Co-evolutionary signals within genome sequences reflect functional dependence of proteins -- Chromosomal proximity of genes as an indicator of functional linkage -- Analyses of complex genome-scale biological networks -- Application of protein interaction networks.
  • Genomes. 2nd ed. 2002, NCBI Bookshelf
  • Genomic imprinting 2008, Springer
    DNA methylation reprogramming in the germ line / Diane J. Lees-Murdock and Colum P. Walsh -- Control of imprinting at the GNAS cluster / Jo Peters and Christine M. Williamson -- The GNAS locus and pseudohypoparathyroidism / Murat Bastepe -- Imprinted genes, postnatal adaptations, and enduring effects on energy homeostasis / Margalida Frontera ... [et al.] -- What are imprinted genes doing in the brain? / William Davies ... [et al.] --Genomic imprinting and human psychology : cognition, behavior, and pathology / Lisa M. Goos and Gillian Ragsdale -- Genomic imprinting in plants / Olivier Garnier, Sylvia Laouiellé-Duprat, and Charles Spillane -- Imprinted genes and human disease : an evolutionary perspective / Francisco Úbeda and Jon F. Wilkins -- Evolutionary theories of imprinting ; enough already! / Tom Moore and Walter Mills.
  • Part I: Mouse models of human diseases and gene transcription. 1. Genetic modifiers in rodent models of obesity / Yun Wang, Patsy M. Nishina, and Jurgen K. Naggert -- 2. Quantitative trait loci in obesity and type II diabetes in rodents / Jung Han Kim -- 3. The human sweet tooth and its relationship to obesity / Amanda H. McDaniel and Danielle R. Reed -- 4. The adipose renin-angiotensin system: genetics, regulation, and physiologic function / Brynn H. Voy ... [et al.] -- 5. Regulation of fat synthesis and adipogenesis / Kee-Hong Kim ... [et al.] -- 6. Transcriptional regulation of energy metabolism in liver / Manabu T. Nakamura. Part II: Genomics: large-scale analysis of gene expression by microarray. 7. Design and analysis of microarray studies for obesity research / Marie-Pierre St.-Onge ... [et al.] -- 8. Solving clinical problems in nutrition research with microarrays / Steven R. Smith ... [et al.] -- 9. Genomic approaches to understanding vitamin D action / James C. Fleet -- 10. Gene expression profiling in adipose tissue / Naima Moustaid-Moussa ... [et al.] -- 11. Phytochemicals and gene expression / Orsolya Mezei and Neil F. Shay --12. Gene expression profiling of immune cells: application for understanding aging of immune cells / Sung Nim Han and Simin Nikbin Meydani -- 13. Improving the nutritional value of cereal grains using a genomic approach / Liang Shi and Tong Zhu. Part III: Proteomics: large-scale analysis of protein expression and regulation. 14. Proteomics and genomics to detail responses to extracellular stimuli / James A. Carroll and Clayton E. Mathews -- 15. 2D gel proteomics studies on leukocytes / Ivan C. Gerling and Michael J. Pabst -- 16. Proteomics: tools for nutrition research in the postgenomic era / Arthur Grider -- 17. Proteomic analysis of the adipocyte secretome / Nieves Ibarrola, Akhilesh Pandey, and Chaerkady Raghothama -- 18. Mass spectrometry strategies for proteomic studies / Maya Belghazi and Helene Rogniaux -- Bioinformatics tools / Simon M. Lin, Kimberly F. Johnson, and Seth W. Kullman -- 20. Statistical principles for analysis of array experiments / Arnold M. Saxton and E. Barry Moser.
  • Genomics protocols. 2nd ed. 2008, Springer Protocols
    Protein profiling based on two-dimensional difference gel electrophoresis / Gert Van den Bergh and Lutgarde Arckens -- Quantitative protein profiling by mass spectrometry using isotope-coded affinity tags / Arsalan S. Haqqani, John F. Kelly, and Danica B. Stanimirovic -- Quantitative protein profiling by mass spectrometry using label-free proteomics / Arsala S. Haqqani, John F. Kelly, and Danica B. Stanimirovic -- Using 2D-LC-MS/MS to identify Francisella tularensis peptides in extracts from an infected mouse macrophage cell line / John F. Kelly and Wen Ding -- Baculovirus expression vector system : an emerging host for high-throughput eukaryotic protein expression / Binesh Shrestha, Carol Smee, and Opher Gileadi -- Coimmunoprecipitation and proteomic analyses / S. Fabio Falsone, Bernd Gesslbauer, and Andreas J. Kungl -- Tandem affinity purification combined with mass spectrometry to identify components of protein complexes / Peter Kaiser ... [et al.] -- Mammalian two-hybrid assay for detecting protein-protein interactioins in vivo / Runtao He and Xuguang Li -- Detection of protein-protein interactions in live cells and animals with split firefly luciferase protein fragment complementation / Victor Villalobos, Snehal Naik, and David Piwnica-Worms -- Subcellular localization of intracellular human proteins by construction of tagged fusion proteins and transient expression in COS-7 cells / John E. Collins -- GeneFAS : a tool for the prediction of gene function using multiple sources of data / Trupti Joshi ... [et al.] --Comparative genomics-based prediction of protein function / Toni Gabaldón -- Design, manufacture, and assay of the efficacy of siRNAs for gene silencing / Louise A. Dawson and Badar A. Usmani.Whole genome amplification with Phi29 DNA polymerase to enable genetic or genomic analysis of samples of low DNA yield / Kaisa Silander and Janna Saarela -- Scanning for DNA variants by denaturant capillary electrophoresis / Per O. Ekstrøm -- Identification of SNPs, or mutations in sequence chromatograms / Nicole Draper -- BeadArray-based genotyping / Helen Butler and Jiannis Ragoussis -- Microsattelite-based candidate gene linkage analysis studies / Cathryn Mellersh -- Full complexity genomic hybridization on 60-mer oligonucleotide microarrays for array comparative genomic hybridization (aCGH) / Alexei Protopopov, Bin Feng, and Lynda Chin -- Detection of copy number changes at multiple loci in DNA prepared from formalin-fixed, paraffin-embedded tissue by multiplex ligation -dependent probe amplification / Minoru Takata -- Application of microarrays for DNA methylation profiling / Axel Schumacher, Andreas Weinhäusl, and Arturas Petronis -- Genomewide identification of protein binding locations using chromatin immunoprecipitation coupled with microarray / Byung-Kwan Cho, Eric M. Knight, and Bernhard Ø. Palsson -- Transcriptional profiling of small samples in the central nervous system / Stephen D. Ginsberg -- Quantitative expression profiling of RNA from formalin-fixed, paraffin-embedded tissues using randomly assembled bead arrays / Marina Bibikova ... [et al.] -- Expression profiling of microRNAs in cancer cells : technical considerations / Mouldy Sioud and Lina Cekaite -- Identification of disease biomarkers by profiling of serum proteins using SELDI-TOF mass spectrometry / Sigrun Langbein -- The applicability of a cluster of differentiation monoclonal antibody microarray to the diagnosis of human disease / Peter Ellmark ... [et al.] --
  • Germ cell protocols v. 1-2, 2004, Springer Protocols
    v. 2, 2004 Springer Protocols
    v. 1. Sperm and oocyte analysis -- v. 2. Molecular embryo analysis, live imaging, transgenesis, and cloning.
  • Introduction to DNA Microarray Technology, p. 1-22 -- Overview of Data Analysis, p. 23-24 -- Image Analysis, p. 25-31 -- Basic Data Analysis, p. 33-53 -- Visualization by Reduction of Dimensionality, p. 55-62 -- Cluster Analysis, p. 63-76 -- Beyond Cluster Analysis, p. 77-82 -- Automated Analysis, Integrated Analysis, and Systems Biology, p. 83-88 -- Reverse Engineering of Regulatory Networks, p. 89-100 -- Molecular Classifiers, p. 101-110 -- The Design of Probes for Arrays, p. 111-117 -- Genotyping and Resequencing Chips, p. 119-122 -- Experiment Design and Interpretation of Results, p. 123-129 -- Software Issues and Data Formats, p. 131-140 -- Appendix A. Web Resources: Commercial Software Packages, p. 141-143.
  • Handbook of glycomics. 1st ed. 2009, ScienceDirect
  • Part I. RNA Synthesis - Enzymatic RNA Synthesis, Ligation and Modification -- Chapter 1. Enzymatic RNA Synthesis using Bacteriophage T7 RNA Polymerase / Heike Gruegelsiepe, Astrid Schön, Leif A. Kirsebom and Roland K. Hartmann, p. 3-21 -- Chapter 2. Production of RNAs with Homogeneous 5' and 3' Ends / Mario Mörl, Esther Lizano, Dagmar K. Willkomm and Roland K. Hartmann, p. 22-35 -- Chapter 3. RNA Ligation using T4 DNA Ligase / Mikko J. Frilander and Janne J. Turunen, p. 36-52 -- Chapter 4. T4 RNA Ligase / Tina Persson, Dagmar K. Willkomm and Roland K. Hartmann, p. 53-74 -- Chapter 5. Co- and Post-Transcriptional Incorporation of Specific Modifications Including Photoreactive Groups into RNA Molecules / Nathan H. Zahler and Michael E. Harris, p. 75-85 -- Chapter 6. 3'-Terminal Attachment of Fluorescent Dyes and Biotin / Dagmar K. Willkomm and Roland K. Hartmann, p. 86-94 -- Part I. RNA Synthesis - Chemical RNA Synthesis -- Chapter 7. Chemical RNA Synthesis, Purification and Analysis / Brian S. Sproat, p. 95-111 -- Chapter 8. Modified RNAs as Tools in RNA Biochemistry / Thomas E. Edwards and Snorri T. H. Sigurdsson, p. 112-129 -- Part II. Structure Determination - Molecular Biology Methods -- Chapter 9. Direct Determination of RNA Sequence and Modification by Radiolabeling Methods / Olaf Gimple and Astrid Schön, p. 132-150 -- Chapter 10. Probing RNA Structures with Enzymes and Chemicals In Vitro and In Vivo / Eric Huntzinger, Maria Possedko, Flore Winter, Hervé Moine, Chantal Ehresmann and Pascale Romby, p. 151-171 -- Chapter 11. Study of RNA-Protein Interactions and RNA Structure in Ribonucleoprotein Particles / Virginie Marchand, Annie Mougin, Agnès Méreau and Christiane Branlant, p. 172-204 -- Chapter 12. Terbium(III) Footprinting as a Probe of RNA Structure and Metal-binding Sites / Dinari A. Harris and Nils G. Walter, p. 205-213 -- Chapter 13. Pb²⁺-induced Cleavage of RNA / Leif A. Kirsebom and Jerzy Ciesiolka, p. 214-228 -- Chapter 14. In Vivo Determination of RNA Structure by Dimethylsulfate / Christina Waldsich and Renée Schroeder, p. 229-237 -- Chapter 15. Probing Structure and Binding Sites on RNA by Fenton Cleavage / Gesine Bauer and Christian Berens, p. 238-249 -- Chapter 16. Measuring the Stoichiometry of Magnesium Ions Bound to RNA / A. J. Andrews and Carol Fierke, p. 250-258 -- Chapter 17. Nucleotide Analog Interference Mapping and Suppression: Specific Applications in Studies of RNA Tertiary Structure, Dynamic Helicase Mechanism and RNA-Protein Interactions, p. 259-293 / Olga Fedorova, Marc Boudvillain, Jane Kawaoka and Anna Marie Pyle -- Chapter 18. Nucleotide Analog Interference Mapping: Application to the RNase P System / Simona Cuzic and Roland K. Hartmann, p. 294-318 -- Chapter 19. Identification and Characterization of Metal Ion Binding by Thiophilic Metal Ion Rescue / Eric L. Christian, p. 319-344 -- Chapter 20. Identification of Divalent Metal Ion Binding Sites in RNA/DNA-metabolizing Enzymes by Fe(II)-mediated Hydroxyl Radical Cleavage / Yan-Guo Ren, Niklas Henriksson and Anders Virtanen, p. 345-353 -- Chapter 21. Protein-RNA Crosslinking in Native Ribonucleoprotein Particles / Henning Urlaub, Klaus Hartmuth and Reinhard Lührmann, p. 354-373 -- Chapter 22. Probing RNA Structure by Photoaffinity Crosslinking with 4-Thiouridine and 6-Thioguanosine / Michael E. Harris and Eric L. Christian, p. 374-384 -- Part II. Structure Determination - Biophysical Methods -- Chapter 23. Structural Analysis of RNA and RNA-Protein Complexes by Small-angle X-ray Scattering / Tao Pan and Tobin R. Sosnick, p. 385-397 -- Chapter 24. Temperature-Gradient Gel Electrophoresis of RNA / Detlev Riesner and Gerhard Steger, p. 398-414 -- Chapter 25. UV Melting, Native Gels and RNA Conformation / Andreas Werner, p. 415-427 -- Chapter 26. Sedimentation Analysis of Ribonucleoprotein Complexes / Jan Medenbach, Andrey Damianov, Silke Schreiner and Albrecht Bindereif, p. 428-437 -- Chapter 27. Preparation and Handling of RNA Crystals / Boris François, Aurélie Lescoute-Phillips, Andreas Werner and Benoît Masquida, p. 438-452 -- Part II. Structure Determination - Fluorescence and Single Molecule Studies -- Chapter 28. Fluorescence Labeling of RNA for Single Molecule Studies / Filipp Oesterhelt, Enno Schweinberger and Claus Seidel, p. 453-474 -- Chapter 29. Scanning Force Microscopy and Scanning Force Spectroscopy of RNA / Wolfgang Nellen, p. 475-487 -- Part III. RNA Genomics and Bioinformatics - Fluorescence and Single Molecule Studies -- Chapter 30. Comparative Analysis of RNA Secondary Structure: 6S RNA / James W. Brow and J. Christopher Ellis, p. 490-512 -- Chapter 31. Secondary Structure Prediction / Gerhard Steger, p. 513-535 -- Chapter 32. Modeling the Architecture of Structured RNAs within a Modular and Hierarchical Framework, p. 536-545 / Benoît Masquida and Eric Westhof -- Chapter 33. Modeling Large RNA Assemblies using a Reduced Representation, p. 546-559 / Jason A. Mears, Scott M. Stagg and Stephen C. Harvey -- Chapter 34. Molecular Dynamics Simulations of RNA Systems / Pascal Auffinger and Andrea C. Vaiana, p. 560-576 -- Chapter 35. Seeking RNA Motifs in Genomic Sequences / Matthieu Legendre and Daniel Gautheret, p. 577-594 -- Chapter 36. Approaches to Identify Novel Non-messenger RNAs in Bacteria and to Investigate their Biological Functions: RNA Mining / Jörg Vogel, E. Gerhart and H. Wagner, p. 595-613 -- Chapter 37. Approaches to Identify Novel Non-messenger RNAs in Bacteria and to Investigate their Biological Functions: Functional Analysis of Identified Non-mRNAs / E. Gerhart, H. Wagner and Jörg Vogel, p. 614-642 -- Chapter 38. Experimental RNomics: A Global Approach to Identify Non-coding RNAs in Model Organisms / Alexander Hüttenhofer, p. 643-654 -- Chapter 39. Large-scale Analysis of mRNA Splice Variants by Microarray / Young-Soo Kwon, Hai-Ri Li and Xiang-Dong Fu, p. 655-663 -- Part IV. Analysis of RNA Function 665 - RNA-Protein Interactions in vitro -- Chapter 40. RNA-Protein Interactions in vitro / Steffen Schiffer, Sylvia Rösch, Bettina Späth, Markus Englert, Hildburg Beier and Anita Marchfelder, p. 666-675 -- Chapter 41. Biotin-based Affinity Purification of RNA-Protein Complexes / Zsofia Palfi, Jingyi Hui and Albrecht Bindereif, p. 676-693 -- Chapter 42. Immunoaffinity Purification of Spliceosomal and Small Nuclear Ribonucleoprotein Complexes / Cindy L. Will, Evgeny M. Makarov, Olga V. Makarova and Reinhard Lührmann, p. 694-709 -- Chapter 43. Northwestern Techniques for the Identification of RNA-binding Proteins from cDNA Expression Libraries and the Analysis of RNA-Protein Interactions / Ángel Emilio Martínez De Alba, Michela Alessandra Denti and Martin Tabler, p. 710-728 -- Part IV. Analysis of RNA Function 665 - RNA-Protein Interactions in vivo -- Chapter 44. Fluorescent Detection of Nascent Transcripts and RNA-binding Proteins in Cell Nuclei, p. 729-736 / Jennifer A. Geiger and Karla M. Neugebauer -- Chapter 45. Identification and Characterization of RNA-binding Proteins through Three-hybrid Analysis / Felicia Scott and David R. Engelke, p. 737-754 -- Chapter 46. Analysis of Alternative Splicing In Vivo using Minigenes / Yesheng Tang, Tatyana Novoyatleva, Natalya Benderska, Shivendra Kishore, Alphonse Thanaraj and Stefan Stamm, p. 755-782 -- Part IV. Analysis of RNA Function 665 - SELEX -- Chapter 47. Artificial Selection: Finding Function amongst Randomized Sequences / Ico de Zwart, Catherine Lozupone, Rob Knight, Amanda Birmingham, Mali Illangasekare, Vasant Jadhav, Michal Legiewicz, Irene Majerfeld, Jeremy Widmann and Michael Yarus, p. 783-806 -- Chapter 48. Aptamer Selection against Biological Macromolecules: Proteins and Carbohydrates / C. Stefan Vörtler and Maria Milovnikova, p. 807-839 -- Chapter 49. In Vivo SELEX Strategies / Thomas A. Cooper, p. 840-852 -- Chapter 50. In Vitro Selection against Small Targets / Dirk Eulberg, Christian Maasch, Werner G. Purschke and Sven Klussmann, p. 853-877 -- Chapter 51. SELEX Strategies to Identify Antisense and Protein Target Sites in RNA or Heterogeneous Nuclear Ribonucleoprotein Complexes / Martin Lützelberger, Martin R. Jakobsen and Jørgen Kjems, p. 878-894 -- Chapter 52. Gene Silencing Methods for Mammalian Cells: Application of Synthetic Short Interfering RNAs / Matthias John, Anke Geick, Philipp Hadwiger, Hans-Peter Vomlocher and Olaf Heidenreich, p. 896-909 -- Appendix. UV Spectroscopy for the Quantitation of RNA, p. 910-913.
  • Hedgehog signaling protocols 2007, Springer Protocols
    Purifying the hedgehog protein and its variants / Darren P. Baker, Frederick R. Taylor, and R. Blake Pepinsky -- Application of sonic hedgehog to the developing chick limb / Eva Tieck and Cheryll Tickle -- Manipulation of hedgehog signaling in Xenopus by means of embryo microinjection and application of chemical inhibitors / Thomas Hollemann .. [et al.] -- Isolation of rat telencephalic neural explants to assay Shh GABAergic interneuron differentiation-inducing activity / Rina Mady and Jhumku D. Kohtz -- Genetic analysis of the vertebrate hedgehog-signaling pathway using muscle cell fate specification in the zebrafish embryo / Sudipto Roy -- Efficient manipulation of hedgehog/GLI signaling using retroviral expression systems / Maria Kasper ... [et al.] -- Cell surface marker and cell cycle analysis, hedgehog signaling, and flow cytometry / Krsting Detmer and Ronald E. Garner -- Detecting tagged hedgehog with intracellular and extracellular immunocytochemistry for functional analysis / Ainhoa Callejo, Luis Quijada, and Isabel Guerrero -- Confocal analysis of hedgehog morphogenetic gradient coupled with fluorescent in situ hybridization of hedgehog target genes / Armel Gallet and Pascal P. Thérond -- RNA in the hedgehog signaling pathway : pFRiPE, a vector for temporally and spatially controlled RNAi in Drosophila / Eric Marois and Suzanne Eaton -- Germline clone analysis for maternally acting Drosophila hedgehog components / Erica M. Selva and Beth E. Stronach -- Clone analysis of hedgehog signaling in Drosophila somatic tissues / Christing M. Bankers and Joan E. Hooper -- GAL4/UAS targeted gene expression for studying Drosophila hedgehog signaling / Denise Bussona nd Anne-Marie Pret -- Biochemical fractionation of Drosophila cells / Melanie Stegman and David Robbins -- Using immunoprecipitation to study protein-protein interactions in the hedgehog-signaling pathway / Chao Ton and Jin Jiang -- Sequence analyses to study the evolutionary history and cis-regulatory elements of hedgehog genes / Ferenc Müller and Anne-Gaelle Borycki.
  • Colorectal cancer is the third most commonly diagnosed cancer in the US and the third most recently linked to cancer deaths. The national annual incidence rate of colorectal cancer is approximately 148,000+, striking slightly more females than males. The lifetime risk of colorectal cancer is 5-6percent, however patients with a familial risk (with two or more first or second degree relatives) make up 20percent of the patients. Persons who carry genetic mutations linked to hereditary colorectal cancer are the most likely to develop the disease.
  • Horizontal gene transfer 2009, Springer Protocols
    Gene transfer: who benefits? / L. Olendzenski and J.P. Gogarten -- Defining the mobilome / J.L. Siefert -- The interplay of homologous recombination and horizontal gene transfer in bacterial speciation / J.G. Lawrence and A.C. Retchless -- Epistemological impacts of horizontal gene transfer on classification in microbiology / E. Bapteste and Y. Boucher -- Persistence mechanisms of conjugative plasmids / M.I. Bahl, L.H. Hansen and S.J. Sorensen -- The integron/gene cassette system: an active player in bacterial adaptation / M. Labbate, R.J. Case and H.W. Stokes -- Ancient gene transfer as a tool in phylogenetic reconstruction / J. Huang and J.P. Gogarten -- The tree of life viewed through the contents of genomes / C.H. House -- Horizontal gene transfer and the evolution of methanogenic pathways / G. Fournier -- Genome acquisition in horizontal gene transfer: symbiogenesis and macromolecular sequence analysis / L. Margulis -- Detection and quantitative assessment of horizontal gene transfer / O. Zhaxybayeva -- Composition-based methods to identify horizontal gene transfer / D. Cortez ... [et al.] -- Testing phylogenetic methods to identify horizontal gene transfer / M. Poptsova -- Untangling hybrid phylogenetic signals: horizontal gene transfer and artifacts of phylogenetic reconstruction / R.G. Beiko and M.A. Ragan -- Construction and use of flow cytometry optimized plasmid-sensor strains / M.I. Bahl ... [et al.] -- Experimental evolution of an essential Bacillus gene in an E. coli host / M. Larios-Sanz and M. Travisano -- Mass action models describing extant horizontal transfer of plasmids: inferences and parameter sensitivities / B.F. Smets and L. Lardon -- Interdomain transfers of sugar transporters overcome barriers to gene expression / K.M. Noll and K. Thirangoon --The role of horizontal gene transfer in photosynthesis, oxygen production, and oxygen tolerance / J. Raymond -- Horizontal gene transfer in cyanobacterial signature genes / S. Yerrapragada, J.L. Siefert and G.E. Fox -- Population genomics and the bacterial species concept / M.A. Riley and M. Lizotte-Waniewski -- A critique of prokaryotic species concepts / R.T. Papke -- What antimicrobial resistance has taught us about horizontal gene transfer / M. Barlow -- Potential for horizontal gene transfer in microbial communities of the terrestrial subsurface / J.M. Coombs -- Horizontal gene transfer and mobile genetic elements in marine systems / P.A. Sobecky and T.H. Hazen -- Horizontal gene transfer in metal and radionuclide contaminated soils / P.A. Sobecky and J.M. Coombs -- Horizontal gene transfer between microbial eukaryotes / J.O. Andersson -- Horizontal gene transfer in eukaryotic parasites: a case study of Entamoeba histolytica and Trichomonas vaginalis / U.C. Alsmark ... [et al.] -- Role of horizontal gene transfer in the evolution of photosynthetic eukaryotes and their plastids / P.J. Keeling -- Role of horizontal gene transfer in the evolution of plant parasitism among nematodes / M. Mitreva, G. Smant and J. Helder.
  • HOX gene expression 2007, Springer
  • Hox genes 2012, Springer
    Regulation of hox activity : insights from protein motifs / Samir Merabet ... [et al.] -- Cis-regulation in the drosophila : bithorax complex / Robert K. Maeda and François Karch -- Maintenance of hox gene expression patterns / Samantha Beck ... [et al.] -- Control of vertebrate hox clusters by remote and global cis-acting regulatory sequences / François Spitz -- The early evolution of hox genes : a battle of belief? / Bernd Schierwater and Kai Kamm -- Evolution of hox complexes / David E.K. Ferrier -- The nematode story : hox gene loss and rapid evolution / Aziz Aboobaker and Mark Blaxter -- Are the deuterostome posterior hox genes a fast-evolving class? / Robert Lanfear -- Hox genes and the body plans of chelicerates and pycnogonids / Wim G.M. Damen -- Hox3/zen and the evolution of extraembryonic epithelia in insects / Urs Schmidt-Ott, Ab. Matteen Rafiqi and Steffen Lemke -- Hox genes and brain development in drosophila / Heinrich Reichert and Bruno Bello -- Homeosis and beyond : what is the function of the hox genes? / Jean S. Deutsch.
  • Introduction to ABC protein and gene organization -- Nomenclature -- Overview of human ABC gene subfamilies -- ABC genes and human genetic disease -- Mouse knockouts -- Multidrug resistance and cancer therapy -- Phylogenetic analysis of human ABC genes -- Mouse ABC genes -- Drosophila ABC genes -- ABCA genes -- ABCB genes -- ABCC genes -- ABCD genes -- ABCE genes -- ABCF genes -- ABCG genes.
  • pt. 1. Human chromosome methods and nomenclature -- pt. 2. Chromosome heteromorphism (summaries) -- pt. 3. Fragile sites -- pt. 4. Copy number vairiants.
  • Human genes and genomes 2012, ScienceDirect
    In the nearly 60 years since Watson and Crick proposed the double helical structure of DNA, the molecule of heredity, waves of discoveries have made genetics the most thrilling field in the sciences. The study of genes and genomics today explores all aspects of the life with relevance in the lab, in the doctor's office, in the courtroom and even in social relationships. In this helpful guidebook, one of the most respected and accomplished human geneticists of our time communicates the importance of genes and genomics studies in all aspects of life. With the use of core concepts and the integration of extensive references, this book provides students and professionals alike with the most in-depth view of the current state of the science and its relevance across disciplines. Bridges the gap between basic human genetic understanding and one of the most promising avenues for advances in the diagnosis, prevention and treatment of human disease. Includes the latest information on diagnostic testing, population screening, predicting disease susceptibility, pharmacogenomics and moreExplores ethical, legal, regulatory and economic aspects of genomics in medicine. Integrates historical (classical) genetics approach with the latest discoveries in structural and functional genomics.
  • Human genome. 3rd ed. / 2011, ScienceDirect
    As genetic issues play a growing role in health practice and public policy, new knowledge in this field will continue to have significant implications for individuals and society. Written to communicate sound and modern science in an accessible way for professionals and students with various levels of scientific background, this thoroughly revised edition of The Human Genome contributes to creating a genetically literate research and clinical population. With case studies and introductory vignettes which illustrate a wide range of perspectives on complex topics in genetics and updated material on the latest research on disease-specific topics, this book serves as a valuable resource for students and working professionals alike. Full-color illustrations enhance and reinforce key concepts and themes * Chapters include interest boxes that focus on human health and disease, chapter-opening case studies, and concept statements to engage non-specialist readers.
  • Immunomics reviews v. 2-, 2009-, Springer
  • In situ detection of DNA damage 2002, Springer Protocols
  • In vitro mutagenesis protocols. 3rd ed. 2010, Springer Protocols
    Mutagenesis protocols in Saccharomyces cerevisiae by in vivo overlap extension / Mibuel Alcalde -- In vitro mutagenesis of Brucella species / Thomas A. Ficht, Jianwu Pei, and Melissa Kahl-McDonagh -- Random mutagenesis strategies for Campylobacter and Helicobacter species / Duncan J.H. Gaskin and Arnoud H.M. van Vliet -- Mutagenesis of the repeat regions of herpesviruses cloned as bacterial artificial chromosomes / Yuguang Zhao and Venugopal Nair -- An efficient protocol for VZV BAC-based mutagenesis / Zhen Zhang, Ying Huang, and Hua Zhu -- A method for rapid genetic integration into Plasmodium falciparum utilizing mycobacteriophage Bxb1 integrase / Sophie H. Adjalley, Marcus C.S. Lee, and David A. Fidock -- Random mutagenesis by error-prone PCR / Elizabeth O. McCullum ... [et al.] -- A rapid and versatile PCR-based site-directed mutagenesis protocol for generation of mutations along the entire length of a cloned cDNA / Vincent Dammai -- Rapid sequence scanning mutagenesis using in silico oligo design and the megaprimer PCR of whole plasmid method (MegaWhop) / Urich Krauss, Karl-Erich Jaeger, and Thorsten Eggert -- Insertion and deletion mutagenesis by overlap extension PCR / Jehan Lee ... [et al.] -- Targeted amplification of mutant strands for efficient site-directed mutagenesis and mutant screening / Lei Young and Qihan Dong -- A modified inverse PCR procedure for insertion, deletion, or replacement of a DNA fragment in a target sequence and its application in the ligand interaction scan method for generation of ligand-regulated proteins / Oran Erster and Moti Liscovitch -- Amplification of orthologous genes using degererate primers / Samya Chakravorty and jim O. Vigoreaux -- Computational evaluation of protein stability change upon mutations / Shuangye Yin, Feng Ding, and Nikolay V. Dokholyan -- Approaches for using animal models to identify loci that genetically interact with human disease-causing point mutations / Josef D. Franke -- Using peptide loop insertion mutagenesis for the evolution of proteins / Christian Heinis and Kai Johnsson -- Massive mutagenesis : high-throughput combinatorial site-directed mutagenesis / Julien Sylvestre -- Directed in vitro evolution of reporter genes based on semi-rational design and high-throughput screening / Ai-Sheng Xiong ... [et al.] -- Ribosome display for rapid protein evolution by consecutive rounds of mutation and selection / Hayato Yanagida, Tomoaki Matsuura, and Tetsuya Yomo -- Fine-tuning enzyme activity through saturation mutagenesis / Holly H. Hogrefe -- Characterization of structural determinants of type 1 corticotropin releasing hormone (CRH) receptor signalling properties / Danijela Markovic and Dimitris K. Grammatopoulos -- Site-directed mutagenesis for improving biophysical properties of Vh domains / Mehdi Arbabi-Ghahroudi, Roger MacKenzie, and Jamshid Tanha -- Phenotype based functional gene screening using retrovirus-mediated gene trapping in quasi-haploid RAW 264.7 cells / Sung Ouk Kim and Soon-Duck Ha -- Site-directed disulfide cross-linking to probe conformational changes of a transporter during its functional cycle : Escherichia coli AcrB multidrug exporter as an example / Yumiko Takatsuka and Hiroshi Nikaido -- Site-specific incorporation of extra components into RNA by transcription using unnatural base pair systems / Michiko Kimoto and Ichiro Hirao -- Mutagen : a random mutagenesis method providing a complementary diversity generated by human error-prone DNA polymerases / Philippe Mondon ... [et al.] -- Random-scanning mutagenesis / Robert A. Smith -- Easy two-step method for randomizing and cloning gene fragments / Vivan Q. Zhang and Holly H. Hogrefe -- Random mutagenesis using a mutator strain / Ghazala Muteeb and Ranjan Sen -- En passant mutagenesis : a two step markerless red recombination system / B. Karsten Tischer, Gregory A. Smith, and Nikolaus Osterrieder.
  • Energy systems for ATP regeneration in cell-free protein synthesis reactions / Kara A. Calhoun and James R. Swartz -- Continuous-exchange protein-synthesizing systems / Vladimir A. Shirokov ... [et al.] -- Cell-free production of integral membrane proteins on a preparative scale / Christian Klammt ... [et al.] -- SIMPLEX : a novel method for high-throughput construction and screening of protein libraries / Suang Rungpragayphan, Tsuneo Yamane, and Hideo Nakano -- Methods for high-throughput materialization of genetic information based on the wheat germ cell-free expression system / Tatsuya Sawasaki ... [et al.] -- Exogenous protein expression in Xenopus oocytes : basic procedures / Elena Bossi ... [et al.] -- In vitro translation to study HIV protease activity / Zene Matsuda ... [et al.] --The protein truncation test in mutation detection and molecular diagnosis / Oliver Hauss and Oliver Muller -- Creation of novel enantioselective lipases by SIMPLEX / Yuichi Koga, Tsuneo Yamane, and Hideo Nakano -- In vitro transcription and translation coupled with two-dimensional electrophoresis for bacterial proteome analysis / Nathalie Norais ... [et al.] -- In vitro screen of bioinformatically selected Bacillus anthracis vaccine candidates by coupled transcription, translation, and immunoprecipitation analysis / Orit Gat, Haim Grosfeld, and Avigdor Shafferman -- Functional expression of Type 1 rat GABA transporter in microinjected Xenopus laevis oocytes / Stefano Giovannardi ... [et al.] -- Production of protein for nuclear magnetic resonance study using the wheat germ cell-free system / Toshiyuki Kohno and Yaeta Endo.
  • Diagnosis and treatment: general principles -- Disorders of carbohydrate metabolism -- Disorders of mitochondrial energy metabolism -- Disorders of amino acid metabolism and transport -- Vitamin-responsive disorders -- Neurotransmitter and small peptide disorders -- Disorders of lipid and bile acid metabolism -- Disorders of nucleic acid and heme metabolism -- Disorders of metal transport -- Organelle-related disorders: lysosomes, peroxisomes, and Golgi and pre-Golgi systems.
  • Pt. 1. Genetics and the life sciences -- Pt. 2. Genetics and philosophy of science: the reductionism debate and beyond -- Pt. 3. Genetics and the ethical, legal and sociological debate.
  • Review of organic chemistry -- Energy considerations in biochemical reactions -- Proteins -- DNA -- Transcription and translation -- Chromosomes and gene regulation -- Genetic variation -- DNA technology -- Cell division -- Cell cycle control, cell death, and cancer -- Expression microarrays -- Classification -- Clustering -- Genetic regulatory networks -- Intervention -- External intervention based on optimal control theory.
  • Molecular characterization and phenotypic expression of mutations in genes for gonadotropins and their receptors in humans / Salvi, R., Pralong, F.P -- Role of kisspeptin/GPR54 system in human reproductive axis / Silveira, L.F.G. ... [et al.] -- Biology of kisspeptins / Hameed, S., Dhillo, W.S. -- Role of fibroblast growth factor signaling in gonadotropin-releasing hormone neuronal system development / Chung, W.C.J., Tsai, P.-S. -- FGFR1 mutations in Kallmann syndrome / Villanueva, C., de Roux, N. -- Biology of KAL1 and its orthologs : implications for x-linked Kallmann syndrome and the search for novel candidate genes / MacColl, G.S., Quinton, R., Bülow, H.E. -- Biological actions and interactions of anosmin-1 / Choy, C., Kim, S.H. -- Genotype and phenotype of patients with gonadotropin-releasing hormone receptor mutations / Kim, H.-G. ... [et al.] -- Hypogonadotropic hypogonadism and GNRH1 mutations in mice and humans / Bouligand, J. ... [et al.] -- Kallmann syndrome caused by mutations in the PROK2 and PROKR2 genes : pathophysiology and genotype-phenotype correlations / Sarfati, J., Dodé, C., Young, J. -- Neurokinin B and its receptor in hypogonadotropic hypogonadism / Semple, R.K., Topaloglu, A.K. -- Complex genetics in idiopathic hypogonadotropic hypogonadism / Pitteloud, N. ... [et al.] -- Rarer syndromes characterized by hypogonadotropic hypogonadism / Aminzadeh, M. ... [et al.].
  • Laser capture microdissection 2004, Springer Protocols
    An introduction to laser-based tissue microdissection techniques / Stephanie Curran and Graeme I. Murray -- Methacarn fixation for genomic DNA analysis in microdissected cells / Makoto Shibutani and Chikako Uneyama -- Multiplex quantitative real-time PCR of laser microdissected tissue / Patrick H. Rooney -- Comparative genomic hybridization using DNA from laser capture microdissected tissue / Grace Callagy, Lucy Jackson, and Carlos Caldas -- Detection of Ki-ras and p53 mutations by laser capture microdissection/PCR/SSCP / Deborah Dillon ... [et al.] -- Whole-genome allelotyping using laser microdissected tissue / Colleen M. Feltmate and Samuel C. Mok -- Microdissection for detecting genetic aberrations in early and advanced human urinary bladder cancer / Arndt Hartmann ... [et al.] -- Laser microdissection for microsatellite analysis in colon and breast cancer / Peter J. Wild ... [et al.] -- Assessment of RET/PTC oncogene activation in thyroid nodules utilizing laser microdissection followed by nested RT-PCR / Giovanni Tallini and Guilherme Brandao -- Combined laser-assisted microdissection and short tandem repeat analysis for detection of in situ microchimerism after solid organ transplantation / Ulrich Lehmann, Anne Versmold, and Hans Kreipe --Genetic analysis of HIV by in situ PCR-directed laser capture microscopy of infected cells / Daniele Marras -- Use of laser capture microdissection together with in situ hybridization and real-time PCR to study the distribution of latent herpes simplex virus genomes in mouse trigeminal ganglion / Xiao-Ping Chen, Marina Mata, and David J. Fink -- Laser capture microdissection and PCR for analysis of human papilloma virus infection / Kheng Chew ... [et al.] -- Laser capture microdissection of hepatic stages of the human parasite plasmodium falciparum for molecular analysis / Jean-Philippe Semblat ... [et al.].Laser-assisted microdissection of membrane-mounted tissue sections / Lise Mette Gjerdrum and Stephen Hamilton-Dutoit -- Laser-assisted microdissection of membrane-mounted sections following immunohistochemistry and in situ hybridization / Lise Mette Gjerdrum and Stephen Hamilton-Dutoit -- Laser-assisted cell microdissection using the PALM system / Patrick Micke ... [et al.] -- Laser microdissection and RNA analysis / Ludger Fink and Rainer Maria Bohle -- Gene expression profiling of primary tumor cell populations using laser capture microdissection, RNA transcript amplification, and GeneChip® microarrays / Veronica I. Luzzi, Victoria Holtschlag, and Mark A. Watson -- Quantification of gene expression in mouse and human renal proximal tubules / Jun-ya Kaimori, Masaru Takenaka, and Kousaku Okubo -- Laser capture microdissection for analysis of macrophage gene expression from atherosclerotic lesions / Eugene Trogan and Edward A. Fisher -- Analysis of pituitary cells by laser capture microdissection / Ricardo V. Lloyd, ... [et al.] -- Laser capture microdissection and colorectal cancer proteomics / Laura C. Lawrie and Stephanie Curran -- Proteomic analysis of human bladder tissue using SELDI® approach following microdissection techniques / Rene C. Krieg ... [et al.] --
  • Learning Basic Genetics with Interactive Computer Programs is a comprehensive and interactive learning program that focuses on chromosome simulation and model building. It is intended to assist students in learning more about genetics with ease. The 11 modules of this program form an integrated system for learning the basic concepts of genetics. The program innovation lies in its unique content design that incorporates cognitive feedback and experiential learning through the novel use of interactive applications. Each of the modules is designed to enhance learning by simultaneously employing "eyes-on," "minds-on," and "hands-on" activities. Topics are motivated by questions, information is presented in simple terms, and concepts are clarified by interactive prompts. Used as a supplement to traditional lectures and textbook assignments, the program not only serves as a foundation upon which to build more complex and detailed topics, but as a tutor to clarify and guide when there is confusion. The software that accompanies this book has been shown to be an ideal tool for learning about genetics, which requires a combination of understanding, conceptualization, and practical experience.
  • Lentivirus gene engineering protocols 2003, Springer Protocols
  • Long non-coding RNAs 2011, Springer
    Transcriptional and posttranscriptional programming by long noncoding RNAs / Radha Raman Pandey and Chandrasekhar Kanduri -- Long noncoding RNA as a regulator for transcription / Riki Kurokawa -- Long noncoding RNAs and X chromosome inactivation / Cristina Gontan, Iris Jonkers, and Joost Gribnau -- TERRA : long noncoding RNA at eukaryotic telomeres / Rajika Arora, Catherine M.C. Brun, and Claus M. Azzalin -- Transcription of satellite DNAs in mammals / Claire Vourc'h and Giuseppe Biamonti -- Multiple roles of Alu-related noncoding RNAs / Audrey Berger and Katharina Strub -- roX RNAs and genome regulation in Drosophila melanogaster / S. Kiran Koya and Victoria H. Meller -- Transcription of satellite DNAs in insects / Željka Pezer ... [et al.] -- Long nonprotein-coding RNAs in plants / Virginie Jouannet and Martin Crespi.
  • Mechanisms of morphogenesis 2013, ScienceDirect
    Morphogenesis is the set of processes that generate shape and form in the embryo--an important area within developmental biology. An exciting and up-to-the-minute account of the very latest research into the factors that create biological form, Mechanisms of Morphogenesis, second edition is a text reference on the mechanisms of cell and tissue morphogenesis in a diverse array of organisms, including prokaryotes, animals, plants and fungi. By combining hard data with computer modeling, Mechanisms of Morphogenesis, second edition equips readers with a much broader understanding of the scope of modern research than is otherwise available. The book focuses on the ways in which the genetic program is translated to generate cell shape, to direct cell migration, and to produce the shape, form and rates of growth of the various tissues. Each topic is illustrated with experimental data from real systems, with particular reference to gaps in current knowledge and pointers to future. Includes over 200 four-color figures. Offers an integrated view of theoretical developmental biology and computer modelling with laboratory-based discoveries. Covers experimental techniques as a guide to the reader. Organized around principles and mechanisms, using them to integrate discoveries from a range of organisms and systems.
  • Fulltext Springer Protocols
    Basic techniques in molecular biology / Ralph Rapley -- Probe design, production, and applications / Marilena Aquino de Muro -- Restriction enzymes: tools in clinical research / Gareth J.S. Jenkins -- Southern blotting as a diagnostic method / Bronwen Harvey and Pirkko Soundy -- Western blotting as a diagnostic method / Pirkko Soundy and Bronwen Harvey -- Principles and medical applications of the polymerase chain reaction / Bimal D. M. Theophilus -- Single strand conformation polymorphism (SSCP) analysis / Igor Vorechovsky -- Denaturing gradient gel electrophoresis (DGGE) / Jeroen H. Roelfsema and Dorien J.M. Peters -- Quantitative analysis of DNA sequences by PCR and solid phase sequencing / Anu Suomalainen and Ann-Christine Syvänen -- Introduction to capillary electrophoresis of DNA: biomedical applications / Beatriz Sanchez-Vega -- Mapping techniques / Simon G. Gregory --Dideoxyfingerprinting for mutation detection / Ioannis Bossis, Antonios Voutetakis, and Constantine A. Stratakis -- Conformation sensitive gel electrophoresis / Marian Hill -- Amplification refractory mutation system and molecular diagnostics / Richard Kitching and Arun Seth -- Ligase chain reaction / Carla Osiowy -- Chemical cleavage of mismatch: theory and clinical applications / Neil V. Whittock and Louise Izatt -- The protein truncation test / Johan T. den Dunnen -- Linkage, allele sharing, and association / Mara Giordano -- Single nucleotide polymorphisms: technology and applications / Cyril Mamotte, Frank Christiansen, and Lyle J. Palmer -- cDNA microarrays / Philip G. Febbo -- Nucleic acid sequence-based amplification / Katherine Loens, D. Ursi, H. Goosens, and M. Ieven -- The oligonucleotide ligation assay / Faye A. Eggerding --Quantitative taqman real-time PCR: diagnostic and scientific applications / Jörg Dötsch, Ellen Schoof, and Wolfgang Rascher -- Use of denaturing high-performance liquid chromatography in molecular medicine / Elizabeth L. Rugg and Gareth J. Magee -- Quantitative PCR / David Sugden -- Liquid chromatography-mass spectrometry of nucleic acids / Herbert Oberacher and Walther Parson -- Comparative genomic hybridization in clinical and medical research / Peng-Hui Wang, Yann-Jang Chen, and Chi-Hung Lin -- Bioinformatics tools for gene and protein sequence analysis / Bernd H.A. Rehm and Frank Reinecke -- In situ hybridization / Amanda D. Watters -- Enzyme-linked immunosorbent assay / William J. Jordan -- Protein therapeutics: mouse, humanized, and human antibodies / Benny K.C. Lo -- Karyotyping / Avery A. Sandberg, John F. Stone, and Zhong Chen --Microsatellite analysis / Rachel E. Ibbotson and Anton E. Parker -- Analysis of chromosomal translocations / Andreas Hochhaus -- Differential display: theory and applications / Irina Gromova, Pavel Gromov, and Julio E. Celis -- Techniques for gene expression profiling / Mark P. Richards -- Capillary electrophoresis in clinical analysis / Margaret A. Jenkins and Sujiva Ratnaike -- Flow cytometry in the biomedical arena / James L. Weaver and Maryalice Stetler-Stevenson -- Immunocytochemistry / Patricia A. Fetsch -- Ribotyping in clinical microbiology / Patricia Severino and Sylvain Brisse -- Diagnostic applications of protein microarrays / Samir Hanash -- The human genome project / Rahul Chodhari and Eddie Chung -- Prenatal diagnosis of inborn errors of metabolism / Guy T.N. Besley -- Gene therapy: methods and application / Stella B. Somiari.
  • Meiosis 2009., Karger
    The meiotic recombination hotspots of Schizosaccharomyces pombe / Pryce, D.W.; McFarlane, R.J. -- Meiotic recombination and crossovers in plants / De Muyt, A. ... [et al.] -- Meiosis in cereal crops : the grasses are back / Martinez-Perez, E. -- Homologue pairing, recombination and segregation in Caenorhabditis elegans / Zetka, M. -- Homolog pairing and segregation in Drosophila meiosis / McKee, B.D. -- The mammalian synaptonemal complex : a scaffold and beyond / Yang, F.; Wang, P.J. --The dance floor of meiosis : evolutionary conservation of nuclear envelope attachment and dynamics of meiotic telomeres / Alsheimer, M. -- Cohesin complexes and sister chromatid cohesion in mammalian meiosis / Suja, J.A.; Barbero, J.L. -- Variation in patterns of human meiotic recombination / Khil, P.P.; Camerini-Otero, R.D. -- Maternal origin of the human aneuploidies are homolog synapsis and recombination to blame? Notes (learned) from the underbelly / Garcia-Cruz, R.; Roig, I.; Garcia Caldés, M. -- Inverted meiosis : the true bugs as a model to study / Viera, A.; Page, J.; Rufas, J.S.The meiotic recombination hotspots of Schizosaccharomyces pombe / D.W. Pryce, R.J. McFarlane -- Meiotic recombination and crossovers in plants / A. De Muyt ... [et al.] -- Meiosis in cereal crops : the grasses are back / E. Martinez-Perez -- Homologue pairing, recombination, and segregation in Caenorhabditis elegans / M. Zetka -- Homolog pairing and segregation in Drosophila meiosis / B.D. McKee -- The mammalian synaptonemal complex : a scaffold and beyond / F. Yang, P.J. Wang --The dance floor of meiosis : evolutionary conservation of nuclear envelope attachment and dynamics of meiotic telomeres / M. Alsheimer -- Cohesin complexes and sister chromatid cohesion in mammalian meiosis / J.A. Suja, J.L. Barbero -- Variation in patterns of human meiotic recombination / P.P. Khil, R.D. Camerini-Otero -- Maternal origin of the human aneuploidies are homolog : synapsis and recombination to blame? notes (learned) from the underbelly / R. Garcia-Cruz, I. Roig, M. Garcia Caldes -- Inverted meiosis : the true bugs as a model to study / A. Viera, J. Page, J.S. Rufas.
  • Membrane proteomics 2009, Springer Protocols
    Online tools for predicting integral membrane proteins / H. Bigelow and B. Rost -- In silico identification of novel G protein coupled receptors / M.N. Davies and D.R. Flower -- Transcriptome-based identification of candidate membrane proteins / E.J. Evans ... [et al.] -- Separation of thylakoid membrane proteins by sucrose gradient ultracentrifugation or blue native-SDS-PAGE two-dimensional electrophoresis / G.M. D'Amici, C.G. Huber and L. Zolla -- Extraction of yeast mitochondrial membrane proteins by solubilization and detergent/polymer aqueous two-phase partitioning / H. Everberg, N. Gustavsson and F. Tjerneld -- 16-BAC/SDS-PAGE analysis of membrane proteins of yeast mitochondria purified by free flow electrophoresis / R.J. Braun ... [et al.] -- Sequential detergent extraction prior to mass spectrometry analysis / F.M. McCarthy, A.M. Cooksey and S.C. Burgess -- Enrichment of brain plasma membranes by affinity two-phase partitioning / J. Schindler and H.G. Nothwang -- Protocol to enrich and analyze plasma membrane proteins / R.J. Wisniewski -- Proteomic analysis of the lymphocyte plasma membrane using cell surface biotinylation and solution-phase isoelectric focusing / M.J. Peirce, A.P. Cope and R. Wait -- Identification of target membrane proteins as detected by phage antibodies / C.A. Geuijen, A.Q. Bakker and J. de Kruif -- Membrane protease degradomics: proteomic identification and quantification of cell surface protease substrates / G.S. Butler ... [et al.] -- Purification of basolateral integral membrane proteins by cationic colloidal silica-based apical membrane subtraction / R.J. Goode and R.J. Simpson -- Moving closer to the lipid raft proteome using quantitative proteomics / L.J. Foster -- Use of sequential chemical extractions to purify nuclear membrane proteins for proteomics identification / N. Korfali ... [et al.] -- Isolation of extracellular membranous vesicles for proteomic analysis / R.A. Mathias ... [et al.] -- Enrichment of human platelet membranes for proteomic analysis / D.W. Greening ... [et al.] -- Detergents and chaotropes for protein solubilization before two-dimensional electrophoresis / T. Rabilloud -- Two-dimensional separation of membrane proteins by 16-BAC-SDS-PAGE / H.G. Nothwang and J. Schindler -- MudPIT analysis: application to human heart tissue / K.G. Kline and C.C. Wu -- Liquid chromatography MALDI MS/MS for membrane proteome analysis / N. Wang, J.B. Young and L. Li -- Cysteinyl-tagging of integral membrane proteins for proteomic analysis using liquid chromatography-tandem mass spectrometry / S.K. Mitra and M.B. Goshe -- Quantitative proteomics analysis of pancreatic zymogen granule membrane proteins / X. Chen and P.C. Andrews.
  • Pt. 0. Introductory Material -- 1. brief introduction to meta-analysis, genetics, and genomics / Darlene R. Goldstein and Rudy Guerra -- Pt I. Similar Data Types I: Genotype Data -- 2. Combining information across genome-wide linkage scans / Carol J. Etzel and Tracy J. Costello -- 3. Genome search meta-analysis (GSMA): a nonparametric method for meta-analysis of genome-wide linkage studies / Cathryn M. Lewis -- 4. Heterogeneity in meta-analysis of quantitative trait linkage studies / Hans C. van Houwelingen and Jeremie J. P. Lebrec -- 5. empirical Bayesian framework for QTL genome-wide scans / Kui Zhang ... [et al.] -- Pt. II. Similar Data Types II: Gene Expression Data -- 6. Composite hypothesis testing: an approach built on intersection-union tests and Bayesian posterior probabilities / Stephen Erickson, Kyoungmi Kim and David B. Allison -- 7. Frequentist and Bayesian error pooling methods for enhancing statistical power in small sample microarray data analysis / Jae K. Lee, Hyung Jun Cho and Michael O'Connell -- 8. Significance testing for small microarray experiments / Charles Kooperberg ... [et al.] -- 9. Comparison of meta-analysis to combined analysis of a replicated microarray study / Darlene R. Goldstein ... [et al.] -- 10. Alternative probe set definitions for combining microarray data across studies using different versions of Affymetrix oligonucleotide arrays / Jeffrey S. Morris ... [et al.] -- 11. Gene ontology-based meta-analysis of genome-scale experiments / Chad A. Shaw -- Pt. III. Combining Different Data Types -- 12. Combining genomic data in human studies / Debashis Ghosh, Daniel Rhodes and Arul Chinnaiyan -- 13. overview of statistical approaches for expression trait loci mapping / Christina Kendziorski and Meng Chen -- 14. Incorporating GO annotation information in expression trait loci mapping / J. Blair Christian and Rudy Guerra -- 15. misclassification model for inferring transcriptional regulatory networks / Ning Sun and Hongyu Zhao -- 16. Data integration for the study of protein interactions / Fengzhu Sun ... [et al.] -- 17. Gene trees, species trees, and species networks / Luay Nakhleh, Derek Ruths and Hideki Innan.
  • Metagenomics 2010, Springer Protocols
    Molecular Methods to Study Complex Microbial Communities / José M. Vieites, María-Eugenia Guazzaroni, Ana Beloqui, Peter N. Golyshin, and Manuel Ferrer -- Construction of Small-Insert and Large-Insert Metagenomic Libraries / Carola Simon and Rolf Daniel -- Construction and Screening of Marine Metagenomic Libraries / Nancy Weiland, Carolin Löscher, Rebekka Metzger, and Ruth Schmitz -- Metagenomic Analysis of Isotopically Enriched DNA / Yin Chen, Josh D. Neufeld, Marc G. Dumont, Michael W. Friedrich, and J. Colin Murrell -- Wide Host-Range Cloning for Functional Metagenomics / Margaret Wexler and Andrew W.B. Johnston -- Cloning and Expression Vectors for a Gram-Positive Host, Streptomyces lividans / Kristof Vrancken, Lieve Van Mellaert, and Jozef Anné -- Heterologous Gene Expression in the Hyperthermophilic Archaeon Sulfolobus solfataricus / Angel Angelov and Wolfgang Liebl -- Novel Tools for the Functional Expression of Metagenomic DNA / Sonja Christina Troeschel, Thomas Drepper, Christian Leggewie, Wolfgang R. Streit, and Karl-Erich Jaeger -- Screening of Functional Promoter from Metagenomic DNA for Practical Use in Expression Systems / So-Youn Park and Geun-Joong Kim -- Substrate-Induced Gene Expression Screening: A Method for High-Throughput Screening of Metagenome Libraries / Taku Uchiyama and Kentaro Miyazaki -- Screens for Active and Stereoselective Hydrolytic Enzymes / Dominique Böttcher, Marlen Schmidt, and Uwe T. Bornscheuer.Screening for Cellulase-Encoding Clones in Metagenomic Libraries / Nele Ilmberger and Wolfgang R. Streit -- Screening Metagenomic Libraries for Laccase Activities / Manuel Ferrer, Ana Beloqui, and Peter N. Golyshin -- Screening for N-AHSL-Based-Signaling Interfering Enzymes / Phil M. Oger and Stéphane Uroz -- Identification of Molecular Markers to Follow Up the Bioremediation of Sites Contaminated with Chlorinated Compounds / Massimo Marzorati, Annalisa Balloi, Francesca De Ferra, and Daniele Daffonchio -- Methods for the Isolation of Genes Encoding Novel PHB Cycle Enzymes from Complex Microbial Communities / Ricardo F. Nordeste, Maria A. Trainer, and Trevor C. Charles -- Metagenomic Approaches to Identify and Isolate Bioactive Natural Products from Microbiota of Marine Sponges / Cristian Gurgui and Jörn Piel -- Screening for Novel Antibiotic Resistance Genes / Mindy G. Brown, Elizabeth H. Mitchell, and David L. Balkwill -- Novel Metal Resistance Genes from Microorganisms: A Functional Metagenomic Approach / José E. González-Pastor and Salvador Mirete -- Retrieval of Full-Length Functional Genes Using Subtractive Hybridization Magnetic Bead Capture / Tracy Meiring, Inonge Mulako, Marla I. Tuffin, Quinton Meyer, and Donald A. Cowan -- Detection and Isolation of Selected Genes of Interest from Metagenomic Libraries by a DNA Microarray Approach / Gopal P. Pathak and Wolfgang Gärtner -- Application of DNA Microarray for Screening Metagenome Library Clones / Soo-Je Park, Jong-Chan Chae, and Sung-Keun Rhee -- MetaGenomeThreader: A Software Tool for Predicting Genes in DNA-Sequences of Metagenome Projects / David J. Schmitz-Hübsch and Stefan Kurtz.
  • Acid mine drainage biofilm -- Waseca County farm soil -- Whale fall community -- Methane-oxidizing archaea -- Human fecal virus -- Sargasso Sea marine microbial metagenome -- Human distal gut microbiome -- Enhanced biological phosphorus removal (EBPR) sludge community -- Mouse gut microbiota metagenome.
  • A comprehensive analysis of the effect of microarray data preprocessing methods on differentially expressed transcript selection -- Differentiation detection in microarray normalization -- Preprocessing and normalization for Affymetrix GeneChip expression microarrays -- Spatial detrending and normalization methods for two-channel DNA and protein microarray data -- A survey of cDNA microarray normalization and a comparison by k-NN classification -- Technical variation in modeling the joint expression of several genes -- Biological interpretation for microarray normalization selection -- Methodology of functional analysis for omics data normalization -- Exon array analysis for the detection of alternative splicing -- Normalization of array CGH data -- SNP array-based analysis for the detection of chromosomal aberrations and copy number variations.
  • DNA microarray technology. Introduction / J.R. Pollack -- Comparative genomic hybridization on BAC arrays / B.P. Coe ... [et al.] -- Comparative genomic hybridization on spotted oligonucleotide microarrays / Y.H. Kim and J.R. Pollack -- Comparative genomic hybridization by representational oligonucleotide microarray analysis / R. Lucito and J. Byrnes -- Application of oligonucleotides arrays for coincident comparative genomic hybridization, ploidy status and loss of heterozygosity studies in human cancers / J.K. Cowell and K.C. Lo -- Molecular inversion probe assay for allelic quantitation / H. Ji and K. Welch -- A whole-genome amplification protocol for a wide variety of DNAs, including those from formalin-fixed and paraffin-embedded tissue / P.L. Paris -- Algorithms for calling gains and losses in array CGH data / P. Wang -- Methylation analysis by microarray / D.E. Deatherage ... [et al.] -- Methylation analysis by DNA immunoprecipitation (MeDIP) / E.A. Vucic ... [et al.] -- Combining chromatin immunoprecipitation and oligonucleotide tiling arrays (ChIP-Chip) for functional genomic studies / J. Eeckhoute, M. Lupien and M. Brown -- ChIP-Chip: algorithms for calling binding sites / X.S. Liu and C.A. Meyer -- Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip) / Y. Shibata and G.E. Crawford -- Microarray analysis of DNA replication timing / N. Karnani, C.M. Taylor and A. Dutta -- Integration of diverse microarray data types / K. Salari and J.R. Pollack.
  • Microarray data analysis 2007, Springer Protocols
  • Microarray image analysis 2010, CRCnetBASE
  • Introduction to microarray technologies / Robert S. Matson -- Nucleic acid sample preparation / Robert S. Matson -- Solid-phase substrates for nucleic acid microarrays / Robert S. Matson -- Protein sample preparation for microarrays / Robert S. Matson -- Solid-phase chemistries for protein microarrays / Robert S. Matson -- Protein microarrays : the link between genomics and proteomics / Persis P. Wadia and David B. Miklos -- Bead arrays : an introduction to multiplexed bead-based assays for proteins / Yong Song -- Carbohydrate arrays / Denong Wang -- Lectin microarrays / Masao Yamada -- Printing methods / Todd Martinsky.
  • Manufacturing of microarrays -- Technological platforms for microarray gene expression profiling -- Principles of gene microarray data analysis -- Gaining weights ... and feeling good about it! -- Complementary techniques -- Microarrays for cancer diagnosis and classification -- Gene profiling for the prediction of tumor response to treatment: the case of immunotherapy -- Identification of molecular determinants of tumor sensitivity and resistance to anticancer drugs -- SNP and mutation analysis -- Cancer development and progression -- Gene expression profiling in malignant lymphomas -- Tumor immunology.
  • Microarrays. 2nd ed. v. 1-2, 2007., Springer Protocols
    v.2, 2009 Springer Protocols
    v. 1. Synthesis methods -- v. 2. Applications and data analysis.
  • Microbial gene essentiality 2008, Springer Protocols
    Overview of whole-genome essentiality analysis / Karen Joy Shaw -- Pt. I. Experimental protocols. IA. Populational genome-wide essentiality screens. Transposon-based strategies for the identification of essential bacterial genes / William S. Reznikoff and Kelly M. Winterberg -- Identification and analysis of essential genes in Haemophilus influenzae / Sandy M.S. Wong and Brian J. Akerley -- Transposon site hybridization in Mycobacterium tuberculosis / Jeffrey P. Murry ... [et al.] -- Essential genes in the infection model of Pseudomonas aeruginosa PCR-based signature-tagged mutagenesis / François Sanschagrin, Irena Kukavica-Ibrulj, and Roger C. Levesque -- Whole-genome detection of conditionally essential and dispensable genes in Escherichia coli via genetic footprinting / Michael D. Scholle and Svetlana Y. Gerdes -- Generating a collection of insertion mutations in the Staphylococcus aureus genome using bursa aurealis / Taeok Bae ... [et al.] -- Multipurpose transposon insertion libraries for large-scale analysis of gene function in yeast / Anuj Kumar --IB. Systematic collections of knockout mutants. How to make a defined near-saturation mutant library. Case 1: Pseudomonas aeruginosa PAO1 / Michael A. Jacobs -- Comparing insertion libraries in two Pseudomonas aeruginosa strains to assess gene essentiality / Nicole T. Liberati ... [et al.] -- The construction of systematic in-frame, single-gene knockout mutant collection in Escherichia coli K-12 / Tomoya Baba and Hirotada Mori -- The applications of systematic in-frame, single-gene knockout mutant collection of Escherichia coli K-12 / Tomoya Baba ... [et al.] -- A novel, simple, high-throughput method for isolation of genome-wide transposon insertion mutants of Escherichia coli K-12 / Takeyoshi Miki, Yoshihiro Yamamoto, and Hideo Matsuda -- High-throughput creation of a whole-genome collection of yeast knockout strains / Angela M. Chu and Ronald W. Davis -- Analysis of genetic interactions on a genome-wide scale in budding yeast: diploid-based synthetic lethality analysis by microarray / Pamela B. Meluh ... [et al.] --IC. Genome minimization. Scarless engineering of the Escherichia coli genome / Tamás Fehér ... [et al.] -- Minimization of the Escherichia coli genome using the Tn5-targeted Cre/loxP excision system / Byung Jo Yu and Sun Chang Kim -- Construction of long chromosomal deletion mutants of Escherichia coli and minimization of the genome / Jun-ichi Kato and Masayuki Hashimoto -- ID. Conditional knockouts. Identification of essential genes in Staphylococcus aureus by construction and screening of conditional mutant library / Dezhong Yin and Yinduo Ji -- Techniques for the isolation and use of conditionally expressed antisense RNA to achieve essential gene knockdowns in Staphylococcus aureus / Allyn Forsyth and Liangsu Wang -- Introduction of conditional lethal amber mutations in Escherichia coli / Christopher D. Herring -- Pt. II. Bioinformatics. IIA. Statistics. Statistical methods for building random transposon mutagenesis libraries / Oliver Will -- Statistical evaluation of genetic footprinting data / Gábor Balázsi -- Modeling competitive outgrowth of mutant populations : why do essentiality screens yield divergent results? / Alexander I. Grenov and Svetlana Y. Gerdes --Statistical analysis of fitness data determined by TAG hybridization on microarrays / Brian D. Peyser, Rafael Irizarry, and Forrest A. Spencer -- IIB. Data integration and modeling. Profiling of Escherichia coli chromosome database / Yukiko Yamazaki, Hironori Niki, and Jun-ichi Kato -- Gene essentiality analysis based on DEG, a database of essential genes / Chun-Ting Zhang and Ren Zhang -- Detection of essential genes in Streptococcus pneumoniae using bioinformatics and allelic replacement mutagenesis / Jae-Hoon Song and Kwan Soo Ko -- Design and application of genome-scale reconstructed metabolic models / Isabel Rocha, Jochen Förster, and Jens Nielsen -- Predicting gene essentiality using genome-scale in silico models / Andrew R. Joyce and Bernhard Ø. Palsson -- Comparative approach to analysis of gene essentiality / Andrei L. Osterman and Svetlana Y. Gerdes.
  • Genome comparison of bacterial pathogens / Wassenaar, T.M. ... [et al.] -- In silico reconstruction of the metabolic and pathogenic potential of bacterial genomes using subsystems / McNeil, L.K., Aziz, R.K. -- The bacterial pan-genome and reverse vaccinology / Tettelin, H. -- 'Guilty by association' : protein-protein interactions (PPIS) in bacterial pathogens / Schauer, K., Stingl, K -- Helicobacter pylori sequences reflect past human migrations / Moodley, Y., Linz, B. -- Helicobacter pylori genome plasticity / Baltrus, D.A., Blaser, M.A., Guillemin, K. -- Genomics of Thermophilic campylobacter species / Gaskin, D.J.H. ... [et al.] -- Adaptation of pathogenic E. coli to various niches : genome flexibility is the key / Brzuszkiewicz, E. ... [et al.] -- Role of horizontal gene transfer in the evolution of Pseudomonas aeruginosa virulence / Qiu, X., Kulasekara, B.R., Lory, S. -- The genus Burkholderia : analysis of 56 genomic sequences / Ussery, D.W. ... [et al.] -- Genomics of host-restricted pathogens of the genus Bartonella / Engel, P., Dehio, C. -- Legionella pneumophila - host interactions : insights gained from comparative genomics and cell biology / Lomma, M. ... [et al.] -- A proteomics view of virulence factors of Staphylococcus aureus / Engelmann, S., Hecker, M. -- Pathogenomics of mycobacteria / Gutierrez, M.C., Supply, P., Brosch, R.
  • MicroRNA and Cancer 2011, Springer Protocols
    MicroRNA Biogenesis and Cancer / Julia Winter, Sven Diederichs -- Computational Identification of miRNAs Involved in Cancer / Anastasis Oulas, Nestoras Karathanasis, Panayiota Poirazi -- The Principles of MiRNA-Masking Antisense Oligonucleotides Technology / Zhiguo Wang -- The Concept of Multiple-Target Anti-miRNA Antisense Oligonucleotide Technology / Zhiguo Wang -- Modulation of MicroRNAs for Potential Cancer Therapeutics / Wei Wu -- Detection of MicroRNAs in Cultured Cells and Paraffin-Embedded Tissue Specimens by In Situ Hybridization / Ashim Gupta, Yin-Yuan Mo -- MicroRNA Northern Blotting, Precursor Cloning, and Ago2-Improved RNA Interference / Julia Winter, Sven Diederichs -- miRNA Profiling on High-Throughput OpenArray System / Elena V. Grigorenko, Elen Ortenberg, James Hurley, Andrew Bond, Kevin Munnelly -- Silicon Nanowire Biosensor for Ultrasensitive and Label-Free Direct Detection of miRNAs / Guo-Jun Zhang -- High-Throughput and Reliable Protocols for Animal MicroRNA Library Cloning / Caide Xiao -- MicroRNA Regulation of Growth Factor Receptor Signaling in Human Cancer Cells / Keith M. Giles, Andrew Barker, Priscilla M. Zhang, Michael R. Epis, Peter J. Leedman -- Epigenetic Regulation of MicroRNA Expression in Cancer / Hani Choudhry, James W. Catto -- In Vitro Functional Study of miR-126 in Leukemia / Zejuan Li, Jianjun Chen -- Prediction of the Biological Effect of Polymorphisms Within MicroRNA Binding Sites / Debora Landi, Roberto Barale, Federica Gemignani, Stefano Landi -- The Guideline of the Design and Validation of MiRNA Mimics / Zhiguo Wang -- Analysis of Targets and Functions Coregulated by MicroRNAs / Shu-Jen Chen, Hua-Chien Chen -- Utilization of SSCprofiler to Predict a New miRNA Gene / Anastasis Oulas, Panayiota Poirazi -- MicroRNA Profiling Using Fluorescence-Labeled Beads: Data Acquisition and Processing / Thomas Streichert, Benjamin Otto, Ulrich Lehmann.
  • MicroRNA methods 2007, ScienceDirect
  • MicroRNA protocols 2006, Springer Protocols
  • MicroRNAs and the immune system 2010, Springer Protocols
    A rapid, quantitative assay for direct detection of microRNAs and other small RNAs using splinted ligation -- Normalization of microRNA quantitative RT-PCR data in reduced scale experimental designs -- MicroRNA detection in bone marrow cells by LNA-FISH -- Measuring microRNA expression in size-limited facs-sorted and microdissected samples -- MicroRNA cloning from cells of the immune system -- High-throughput profiling in the hematopoietic system -- Construction of small RNA cDNA libraries for deep sequencing -- MicroRNA-profiling in formalin-fixed paraffin-embedded specimens -- Expression of miRNAs in lymphocytes : A review -- Mouse models for miRNA expression: The ROSA26 locus -- Regulation of monocytopoiesis by microRNAs -- MicroRNA activity in B lymphocytes -- Isolation and characterization of microRNAs of human mature erythrocytes -- Stable overexpression of miRNAs in bone marrow-derived murine mast cells using lentiviral expression vectors -- Monitoring microRNA activity and validating microRNA targets by reporter-based approaches -- Lentivirus-mediated antagomir expression -- Solution structure of miRNA:mRNA complex -- MiRNA editing -- Computational prediction of microRNA targets -- Large-scale integration of microRNA and gene expression data for identification of enriched microRNA-mRNA associations in biological systems -- Identification and validation of the cellular targets of virus-encoded microRNAs.
  • Mitochondrial DNA 2002, Springer Protocols
  • Mobile genetic elements 2004, Springer Protocols
  • Modern genome annotation 2008, Springer
  • Molecular cytogenetics 2002, Springer Protocols
  • Molecular diagnostics 2014, Springer
    Molecular Diagnostics: 12 Tests That Changed Everything focuses on specific laboratory tests and emphasizes how the availability of these tests has altered how clinicians treat their patients. Presented as a standard outline, each chapter focuses on a specific molecular test and provides background on the test and its clinical applications. Continuing with some discussion on how the test is done, interpreted, and used clinically, each chapter then concludes with a discussion of how that test has changed the way medicine is practiced with respect to the disease or condition in question. Authored by renowned experts in the field, Molecular Diagnostics: 12 Tests That Changed Everything is a valuable resource for pathologists, pathology residents, laboratory directors, development personnel, lab medicine fellows and those working in the broad area of oncology, infectious disease and genetics.
  • Identification of the gene involved in 4q25-linked Axenfeld-Rieger syndrome, PITX2 / Elena V. Semina -- Winged helix/forkhead transcription factors and Rieger syndrome / Darryl Y. Nishimura and Ruth E. Swiderski -- Rieger syndrome and PAX6 deletion / Ruth Riise -- The molecular and biochemical basis of Axenfeld-Rieger syndrome / Brad A. Amendt -- Role of PITX2 in the pituitary gland / Hoonkyo Suh ... [et al.] -- Expression and function of PITX2 in chick heart looping / Xueyan Yu, Shusheng Wang, and YiPing Chen -- The multiple roles of PITX2 in heart development / James F. Martin -- The role of PITX2 in tooth development / Brad A. Amendt -- PITX genes and ocular development / Elena V. Semina -- An overview of Axenfeld-Rieger syndrome and the anterior segment developmental disorders / Brad A. Amendt.
  • Molecular toxicology protocols 2004, Springer Protocols
    Analysis of K-RAS and P53 mutations in sputum samples / Weimin Gao and Phouthone Keohavong -- Allele-specific competitive blocker-PCR detection of rare base substitution / Barbara L. Parsons, Page B. McKinzie, and Robert H. Heflich -- Gel-based nonradioactive single-strand conformational polymorphism and mutation detection: limitations and solutions / Vibhuti Gupta ... [et al.] -- Detection and characterization of oncogene mutations in preneoplastic and early neoplastic lesions / Toshinari Minamoto -- Detection of DNA double-strand breaks and chromosome translocations using ligation-mediated PCR and inverse PCR / Michael J. Villalobos, Christopher J. Betti, and Andrew T.M. Vaughan -- Microsatellite instability: an indirect assay to detect defects in the cellular mismatch repair machinery / Anjana Saha, Narendra K. Bairwa, and Ramesh Bamezai -- Unscheduled DNA synthesis: a functional assay for global genomic nucleotide excision repair / Crystal M. Kelly and Jean J. Latimer -- Analysis of DNA repair using transfection-based host cell reactivation / Jennifer M. Johnson and Jean J. Latimer -- An immunoassay for measuring repair of ultraviolet photoproducts / Shirley McCready -- Analysis of DNA double-strand break repair by nonhomologous end joining in cell-free extracts from mammalian cells / Petra Pfeiffer ... [et al.] --The comet-FISH technique: a tool for detection of specific DNA damage and repair / Alexander Rapp, Michael Hausmann, and Karl Otto Greulich -- DNA double-strand break damage and repair assessed by pulsed-field gel electrophoresis / Nina Joshi and Stephen G. Grant -- Analysis of in vivo mutation in the Hprt and Tk genes of mouse lymphocytes / Vasily N. Dobrovolsky, Joseph G. Shaddock, and Robert H. Heflich -- Quantifying in vivo somatic mutations using transgenic mouse model systems / Roy R. Swiger -- Methods for detecting somatic mutations in vitro: the human T-cell cloning assay selecting for HPRT mutants / Sai-Mei Hou -- Molecular analysis of mutations in the human HPRT gene / Phouthone Keohavong, Liqiang Xi, and Stephen G. Grant -- Simultaneous quantification of t(14;18) and HPRT exon 2/3 deletions in human lymphocytes / James C. Fuscoe -- The GPA in vivo somatic mutation assay / Stephen G. Grant -- Flow cytometric measurement of mutant T cells with altered expression of TCR: detecting somatic mutations in humans and mice / Seishi Kyoizumi, Yoichiro Kusunoki, and Tomonori Hayashi -- Mutation screening of the TP53 gene by temporal temperature gradient gel electrophoresis / Therese Sørlie ... [et al.] --³²P-postlabeling analysis of DNA adducts / David H. Phillips, Alan Hewer, and Volker M. Arlt -- Modification of the ³²P-postlabeling method to detect a single adduct as a single spot / Masako Ochiai, Takashi Sugimura, and Minako Nagao -- DNA isolation and sample preparation for quantification of adduct levels by accelerator mass spectrometry / Karen H. Dingley ... [et al.] -- Fluoroimaging-based immunoassay of DNA photoproducts in ultraviolet-B-irradiated tadpoles / Iovanna Pandelova, Stephen R. Hewitt, and John B. Hays -- Analysis of DNA strand cleavage at abasic sites / Walter A. Deutsch and Vijay Hegde -- Premature chromosome condensation in human resting peripheral blood lymphocytes for chromosome aberration analysis using specific whole-chromosome DNA hybridization probes / Pataje G.S. Prasanna and William F. Blakely -- Mutagen-induced chromatid breakage as a marker of cancer risk / Xifeng Wu, Yun-Ling Zheng, and T.C. Hsu -- Flow cytometric analysis of micronuclei in erythrocytes / Jan Grawé -- The comet assay: a sensitive genotoxicity test for the detection of DNA damage / Günter Speit and Andreas Hartmann -- Computerized image analysis software for the comet assay / R.C. Chaubey --Measuring recombination proficiency in mouse embryonic stem cells / Andrew J. Pierce and Maria Jasin -- Strategies for measurement of biotransformation enzyme gene expression / Marjorie Romkes and Shama C. Buch -- Genotyping technologies: application to biotransformation enzyme genetic polymorphism screening / Marjorie Romkes and Shama C. Buch -- TaqMan® fluorogenic detection system to analyze gene transcription in autopsy material / Kaori Shintani-Ishida, Bao-Li Zhu, and Hitoshi Maeda -- Development of quantitative reverse transcriptase PCR assays for measuring gene expression / Tony E. Godfrey and Lori A. Kelly -- Quantification of selective phosphatidylserine oxidation during apoptosis / James P. Fabisiak ... [et al.] -- Quantitative method of measuring of phosphatidylserine externalization during apoptosis using electron paramagnetic resonance spectroscopy and annexin-conjugated iron / James P. Fabisiak, Grigory G. Borisenko, and Valerian E. Kagan -- Detection of programmed cell death in cells exposed to genotoxic agents using a caspase activation assay / Michael E. Gehring and Patrick P. Koty.
  • From destiny to freedom? : on human nature and liberal eugenics in the age of genetic manipulation /Michela Betta --Diagnostic knowledge in the genetic economy and commerce /Michela Betta --Body talk : genetic screening as a device of crime regulation /Richard Hil, Richard Hindmarsh --Genetic testing and human genetic databases /Astrid H. Gesche --Theimperative of the "new genetics" : challenges for ethics, law, and social policy /David Weisbrot --Insurance and genetics : regulating a private market in the public interest /David Weisbrot, Brian Opeskin --Thesocial imperative for community genetic screening : an Australian perspective /MaryAnne Aitken, Sylvia Metcalfe --Genetically transformed healthcare : healthy children and parents /Enzo A. Palombo, Mrinal Bhave --TheAustralian law reform inquiry into genetic commission testing - a worker's perspective /Susan Pennicuik --Genetic information and the Australian labour movement /Suzanne Jamieson --Protecting the vulnerable : genetic testing and screening for parentage, immigration, and aboriginality /Astrid H. Gesche --Essentially whose? : genetic testing and the ownership of genetic information /Lyn Turney --Self-knowledge and self-care in the age of genetic manipulation /Michela Betta.
  • mRNA processing and metabolism 2004, Springer Protocols
    Gene expression analysis of messenger RNP complexes / Luiz O.F. Penalva, Scott A. Tenenbaum, and Jack D. Keene -- Using the lambdaN peptide to tether proteins to RNAs / Julie Baron-Benhamou ... [et al.] -- An efficient system for cap- and poly(A)-dependent translation in vitro / Yuri V. Svitkin and Nahum Sonenberg -- A poly(A) tail-responsive in vitro system for cap- or IRES-driven translation from HeLa cells / Christian Thoma, Antje Ostareck-Lederer and Matthias W. Hentze -- Assessing messenger RNA decapping in cellular extracts / Naomi Bergman ... [et al.] -- Analysis of RNA exonucleolytic activities in cellular extracts / Devi Mukherjee ... [et al.] -- Application of ligation-mediated reverse transcription polymerase chain reaction to the identification of in vivo endonuclease-generated messenger RNA decay intermediates / Mark N. Hanson and Daniel R. Schoenberg -- Biochemical dissection of RNA silencing in plants / Guiliang Tang and Phillip D. Zamore -- RNA interference of mRNA processing factors in drosophila S2 cells / Alicia M. Celotto and Brenton R. Graveley -- RNA interference by short hairpin RNAs expressed in vertebrate cells / Gregory J. Hannon and Douglas S. Conklin.Using chromatin immunoprecipitation to map cotranscriptional mRNA processing in saccharomyces cerevisiae / Michael-Christopher Keogh and Stephen Buratowski -- Identifying phosphoCTD-associating proteins / Hemali P. Phatnani and Arno L. Greenleaf -- Imaging alternative splicing in living cells / Eric J. Wagner ... [et al.] -- Tobramycin affinity tag purification of spliceosomes / Klaus Hartmuth, Hans-Peter Vornlocher and Reinhard Lührmann -- Using single-strand conformational polymorphism gel electrophoresis to analyze mutually exclusive alternative splicing / Alicia M. Celotto and Brenton R. Graveley -- Methods for the analysis of adenosine-to-inosine editing in RNA / Zuo Zhang and Gordon G. Carmichael -- Assaying nuclear messenger RNA export in human cells / Bryan R. Cullen -- RNA unwinding assay for DExD/H-Box RNA helicases / Stephanie S. Tseng-Rogenski and Tien-Hsien Chang -- Approaches for monitoring nuclear translation / Francisco J. Iborra, Dean A. Jackson, and Peter R. Cook -- Immunopurification and analysis of protein and RNA components of mRNP in mammalian cells / Fabrice Lejeune and Lynne E. Maquat --
  • In theoretical terms, sex differences in brain and behavior offer the possibility of fascinating scientific studies on a range of molecular phenomena such as DNA methylation, chromatin protein modification, non-coding DNA, resulting in important neuroanatomical and neurochemical effects. However, this general subject has been treated with much hyperbole. Historically, sex differences were assumed to be present where they did not really exist, e.g. with respect to mathematics, executive leadership, etc. etc. Under what circumstances do we really care about sex differences in brain and behavior? These circumstances concern human maladies whose diagnoses are much different between boys and girls, or between women and men. Prominent examples to be discussed today will include autism, attention deficit hyperactivity disorders and congenital adrenal hyperplasia. The meeting will end with a consideration of effects of estrogenic hormones on the injured brain, and their roles as protective agents.
  • Chapter 1. A History of Behavior Genetics / Stephen C. Maxson -- Chapter 2. Developmental Neurobehavioral Genetics: Development as Explanation / Gilbert Gottlieb -- Chapter 3. Some Basics, Mendelian Traits, Polygenic Traits, Complex Traits / Byron C. Jones -- Chapter 4. An Introduction to Quantitative Genetics / Wim E. Crusio -- Chapter 5. From QTL Detection to Gene Identification / Marie-Pierre Moisan -- Chapter 6. Gene Expression / Richard A. Radcliffe -- Chapter 7. Bioinformatics of Behavior / Elissa J. Chesler -- Chapter 8. Congenic and Consomic Strains / Lorraine Flaherty and Valerie Bolivar -- Chapter 9. Animal Resources in Behavioral Neurogenetics / Jean-Michel Lassalle -- Chapter 10. Sample Size Requirements for Experiments on Laboratory Animals / Douglas Wahlsten -- Chapter 11. The Role of Association Studies in Psychiatric Disorders / Nicolas Ramoz and Philip Gorwood -- Chapter 12. Family and Twin Methods / Keith E. Whitfield and Tracy L. Nelson -- Chapter 13. Gene-Environment Interactions / Byron C. Jones and Leslie C. Jones -- Chapter 14. And Now it Starts to Get Interesting: Gene-Gene Interactions / Yamima Osher -- Chapter 15. Schizophrenia: Study of a Genetically Complex Phenotype / Michael F. Pogue-Geile and Irving I. Gottesman -- Chapter 16. Genetics of Major Affective Disorders / Wade Berrettini -- Chapter 17. Pedigree Analyses and the Study of Chimpanzee (Pan troglodytes) Personality and Subjective Well-Being / Alexander Weiss and James E. King -- Chapter 18. The Elusive World of Personality Genes: Cherchez le Phenotype / Richard P. Ebstein, Rachel Bachner-Melman, Jonathan Benjamin, and Robert H. Belmaker -- Chapter 19. Aggression: Concepts and Methods Relevant to Genetic Analyses in Mice and Humans / Stephen C. Maxson and Andrew Canastar -- Chapter 20. Genetic Analysis of Emotional Behaviors Using Animal Models / André Ramos and Pierre Mormède -- Chapter 21. Genetic Analysis of Food Search Behavior in the Fruit Fly (Drosophila melanogaster) / Amsale T. Belay and Marla B. Sokolowski -- Chapter 22. Genetic and Molecular Analyses of Drosophila
  • This book gives an overview of the current knowledge on the most common neurodegenerative diseases, including Alzheimer's disease, frontotemporal lobar degeneration, amyotrophic lateral sclerosis, and additional neurodegenerative diseases. Different aspects of each disease are reviewed, including clinical issues, treatments, basic discoveries (genetics and molecular biology), and translation of basic research into biomarkers for early diagnosis. In addition, emerging data indicate that neurodegeneration seems to also be present in classically non-degenerative disorders. Therefore, a chapter about overlapping mechanisms between dementias and psychiatric disorders is included, as well as a description of the role of neurodegeneration in multiple sclerosis. Neurodegenerative Diseases is aimed at clinicians, particularly those working in academic hospitals. This multidisciplinary book will also be of interest to basic researchers in medical fields.
  • Neurofibromatosis type 1 2012, Springer
    Neurofibromatosis type 1 (NF1), caused by mutational inactivation of the NF1 tumour suppressor gene, is one of the most common dominantly inherited human disorders, affecting 1 in 3000 individuals worldwide. This book presents in concise fashion, but as comprehensively as possible, our current state of knowledge on the molecular genetics, molecular biology and cellular biology of this tumour predisposition syndrome. Written by internationally recognized experts in the field, the 44 chapters that constitute this edited volume provide the reader with a broad overview of the clinical features of the disease, the structure and expression of the NF1 gene, its germ line and somatic mutational spectra and genotype-phenotype relationships, the structure and function of its protein product (neurofibromin), NF1 modifying loci, the molecular pathology of NF1-associated tumours, animal models of the disease, psycho-social aspects and future prospects for therapeutic treatment.Neurofibromatosis Type 1: Molecular and Cellular Biology will be of great value to medical geneticists, molecular and cellular biologists, oncologists, dermatologists, neurologists, genetic counsellors and general practitioners alike.
  • Neurogenetics 2006, CRCnetBASE
  • Part I Approach to neuromuscular diseases: principles and basics -- Clinical assessment in neuromuscular disorders -- Nerve and muscle: basic concepts -- Part II Approach to neuromuscular diseases: neuromuscular investigations -- Serum muscle enzymes in neuromuscular disease -- Autoantibody testing in peripheral neuropathy -- Autoantibody testing in autoimmune neuromuscular junction, hyperexcitability, and muscle disorders -- Forearm exercise testing -- Clinical electromyography (neve conduction studies and needle electromyography) -- Single-fiber EMG -- Quantitative EMG analysis -- Testing of autonomic function -- Quantitative sensory testing -- Nerve and muscle biopsies -- Skin biopsy -- Molecular diagnosis and genetic testing -- Part III Approach to neuromuscular diseases: assessment and treatment of neurologica disorders -- Outcome measures and clinical assessment instruments in neuromuscular disease -- Physical management of patients with neuromuscular diseases -- Immunotherapy in the treatment of autoimmune neuromuscular diseases -- Critical and respiratory care in neuromuscular disorders -- Part IV Neuromuscular disorders: neuronopathies (motor neuron and dorsal root ganglion disorders) -- Poliomyelitis and post-poliomyelitis syndrome -- Amyotrophic lateral sclerosis -- Spinal muscular atrophies -- Atypical motor neuron disorders -- Dorsal root ganglion disorders -- Part V Neuromuscular disorders: Peripheral neuropatahies -- Approach to peripheral nerve disorders -- Approach to small fiber neuropathy -- Charcot-Marie-Tooth diseases -- Inherited metabolic neruopathies -- Guillain-Barre Syndrome and related disorders -- Chronic inflammatory demyelinating polyradiculoneuropathy and related disorders -- Diabetic neuropathies -- Nutritional and alcoholic neuropathies -- Metabolic and endocrine neuropathies -- Environmental toxic neuropathies --Drug-induced toxic neuropathies -- Vasculitic neuropathies and neuropathies of connective tissue disease -- Nonvasculitic ischemic neuropathies -- Infectious and granulomatous peripheral neuropathies -- Peripheral nerve injury -- Compressive and entrapment neuropathies of the upper extremity -- Compressive and entrapment neuropathies of the lower extremity -- Cranial nerve palsies -- Peripheral nerve tumors -- Cervical radiculopathy -- Lumbosacral and thoracic radiculopathies -- Brachial plexopathies -- Lumbosacral plexopathies -- Part VI Neuromuscular disorders: neuromuscular junction disorders -- Myasthenia Gravis -- Lambert-Eaton Myasthenic Syndrome -- Botulism -- Toxic neuromuscular transmission disorders -- Part VII Neuromuscular disorders: muscle ion channel disorders -- Disorders of skeletal muscle membrane excitability: myotonia congenita, paramyotonia congenita, periodic paralysis, and related syndromes -- Malignant hyperthermia -- Part VIII Neuromuscular disorders: myopathies -- Approach to myopathies -- Dystrophinopathies -- Limb-girdle muscular dystrophies -- Facioscapulohumeral muscular dystrophy -- The myotonic dystrophies -- Oculpharyngeal muscular dystrophy -- Emery-Dreifuss muscular dystrophy -- Congenital myopathies -- Metabolic myopathies -- Mitochondrial myopathies -- Inflammatory myopathies -- Paraspinous myopathies: the dropped head and bent spine syndromes -- Endocrine myopathies -- Toxic myopathies -- Infectious and granulomatous myopathies -- Part IX Neuromuscular disorders: miscellaneous neuromuscular disorders and syndromes -- Myokymia and neuromyotonia -- Muscle cramps and fasciculations -- Stiff-man syndrome -- Tetanus -- Neuroleptic malignant syndrome -- Paraneoplastic neuromuscular disorders -- Acute neuromuscular weakness in the intensive care unit -- Floppy infant -- Rhabdomyolysis and myoglobinuria -- Eosinophilia-myalgia syndrome, eosinophilic fascitiitis, and related fasciitis disorders -- Neuropathis pain and other chronic musculoskeletal pain conditions.
  • Overview: developments in DNA sequencing / Keith R. Mitchelson ... [et al.] -- Chip capillary electrophoresis and total genetic analysis systems / Quiang Xiong and Jing Cheng -- Comparative sequence analysis by MALDI-TOF mass spectrometry: utilizing the known to discover the new / Mathias Ehrich, Franz Hillenkamp, and Dirk van den Boom -- Advances in dye-nucleotide conjugate chemistry for DNA sequencing / Shiv Kumar and Carl W. Fuller -- The 454 life sciences picoliter sequencing system / Marcel Margulies ... [et al.] -- An integrated system for DNA sequencing by synthesis / John R. Edwards, Dae Hyun Kim, and Jingyue Ju -- Single-molecule fluorescence microscopy and its applications to single-molecule sequencing by cyclic synthesis / Benedict Hebert and Ido Braslavsky -- Rapid DNA sequencing by direct nanoscale reading of nucleotide bases on individual DNA chains / James Weifu Lee and Amit Meller -- A single molecule system for whole genome analysis / Shiguo Zhou, Jill Herschleb, and David C. Schwartz -- Sequencing aided by mutagenesis facilitates the de novo sequencing of megabase DNA fragments by short read lengths / Jonathan M. Keith ... [et al.] -- Genome sequencing and assembly / Annette McGrath -- Valid recovery of nucleic acid sequence information from high contamination risk samples: ancient DNA and environmental DNA / George A. Kowalchuk ... [et al.].
  • Overview.History of DNA Sequencing Technologies /Lisa D. White --Clinical Molecular Diagnostic Techniques: A Brief Review /Megan L. Landsverk, Lee-Jun C. Wong --The Technologies and Bioinformatics.Methods of Gene Enrichment and Massively Parallel Sequencing Technologies /Hong Cui --Sequence Alignment, Analysis, and Bioinformatic Pipelines /Fuli Yu, Cristian Coarfa --Protein Structural Based Analysis for Interpretation of Missense Variants at the Genomics Era: Using MNGIE Disease as an Example /Victor Wei Zhang --Algorithms and Guidelines for Interpretation of DNA Variants /Jing Wang, Megan Landsverk --Application to Clinical Diagnosis.NGS-Based Clinical Diagnosis of Genetically Heterogeneous Disorders /C. A. Valencia, T. A. Sivakumaran, B. T. Tinkle --Molecular Diagnosis of Congenital Disorders of Glycosylation (CDG) /Melanie Jones, Madhuri Hegde --NGS Improves the Diagnosis of X-Linked Intellectual Disability (XLID) /Michael J. Friez, Monica J. Basehore --NGS Analysis of Heterogeneous Retinitis Pigmentosa /Rui Chen, Feng Wang --Next-Generation Sequencing Analyses of the Whole Mitochondrial Genome /Lee-Jun C. Wong --Application of Next-Generation Sequencing of Nuclear Genes for Mitochondrial Disorders /Valeria Vasta, Si Houn Hahn --Noninvasive Prenatal Diagnosis Using Next-Generation Sequencing /Nancy Bo Yin Tsui, Yuk Ming Dennis Lo --Compliance with CAP/CLIA Regulations.Guidelines and Approaches to Compliance with Regulatory and Clinical Standards: Quality Control Procedures and Quality Assurance /Ira M. Lubin, Lisa Kalman, Amy S. Gargis --Validation of NGS-Based DNA Testing and Implementation of Quality Control Procedures /Victor Wei Zhang, Lee-Jun C. Wong --Frequently Asked Questions About the Clinical Utility of Next-Generation Sequencing in Molecular Diagnosis of Human Genetic Diseases /Ephrem L. H. Chin, Victor Wei Zhang, Jing Wang, Margherita Milone, Susan Pacheco.
  • Nonhuman DNA typing 2008, CRCnetBASE
    Introduction to forensic science and DNA / Heather Miller Coyle -- Collection and preservation of biological evidence from the crime scene / Henry C. Lee -- Techniques of DNA fingerprinting / John Schienman -- Forensic canine STR analysis / Burkhard Berger, Cordula Eichmann, Walther Parson -- STR based forensic analysis of field samples from domestic and exotic cats / Marilyn A. Menotti-Raymond, Victor A. David, Stephen J. O'Brien -- Overview of insect evidence in forensic science / Heather Miller Coyle -- Use of forensic DNA typing in wildlife investigations / Richard M. Jobin -- DNA testing of animal evidence : case examples and method development / En-Uei Jiang, W. A. van Haeringen, L. H. P. van de Goor, Pero Dimsoski, Heather Miller Coyle -- Basics of forensic fungi /; Khudooma Said Al Na'imi -- Soil DNA typing in forensic science / Jonathan Hill, Linda Strausbaugh, Joerg Graf -- DNA profiling : the ability to predict an image from a DNA profile / Holly Long -- Appendix A: Brief history of forensic serology and DNA / Peter Bilous.
  • ch. 1. DNA Structure, p. 1-17 -- ch. 2. DNA Dynamics, p. 19-39 -- ch. 3. DNA Function, p. 41-48 -- ch. 4. Linear Theory of DNA, p. 49-79 -- ch. 5. Nonlinear Theory of DNA: Ideal Dynamical Models, p. 81-114 -- ch. 6. Nonlinear Theory of DNA: Non-Ideal Models, p. 115-132 -- ch. 7. Nonlinear Theory of DNA: Statistics of Nonlinear Excitations, p. 133-150 -- ch. 8. Experimental Tests of DNA Nonlinearity, p. 151-158 -- ch. 9. Nonlinearity and Function, p. 159-167.
  • Nuclear organization and function 2010, Cold Spring Harb Lab Press
    Chromatin modifications and gene expressions -- Transcription and beyond -- DNA replication and genome integrity -- Reprogramming and differentiation -- Heterochromatin formation and gene silencing -- Nuclear bodies and RNA biology -- Chromosome structure and mitosis -- Chromatin structure and organization -- Nuclear periphery.
  • Nuclear transfer protocols 2006, Springer Protocols
    Cloning of exotic/endangered species: (desert bighorn sheep) / James "Buck" Williams ... [et al.] -- Handmade somatic cell cloning in cattle / Gábor Vatja, Ian M. Lewis, and R. Tayfur Tecirlioglu -- Genetic modification of sheep by nuclear transfer with gene-targeted somatic cells / A. John Clark, Sarah Burl, and Chris Denning -- Transgenesis using nuclear transfer in goats / Anthoula Lazaris ... [et al.] -- Nuclear reprogramming : an overview / Takashi Tada -- Expression of imprinted genes in cloned mice / Takashi Kohda, Fumitoshi Ishino, and Atsuo Ogura -- Nuclear remodeling assay in xenopus egg extract / Koichi Gonda and Nobuaki Kikyo -- In vitro reprogramming of nuclei and cells / Anne-Mari Håkelien ... [et al.] -- Techniques for nuclear transfer to mouse embryonic stem cells / Danielè Pralong and Paul J. Verma -- Gene expression and methylation patterns in cloned embryos / Christine Wrenzycki ... [et al.] -- Are there any normal clones? / Ian Wilmut -- Future and applications of cloning / Alan O. Trounson.Origin and progress of nuclear transfer in nonmammalian animals / Marie A. Di Berardino -- In vitro maturation and embryo production in cattle / Marc-André Sirard and Karine Coenen -- Activation of oocytes after nuclear transfer / Zoltán Macháty -- Culture medium preferences of pre-implantation cloned mouse embryos / Björn Heindryckx, Josiane Van der Elst, and Marc Dhont -- Maintenance of pregnancy in pigs with limited viable embryos / Tim King and Paul A. De Sousa -- Health and neonatal care of bovine clones / Jacqui T. Forsyth and David N. Wells -- Optimization of procedures for cloning by somatic cell nuclear transfer in mice / Young Gie Chung, Shaorong Gao, and Keith E. Latham -- Production of cloned calves using roscovitine-treated adult somatic cells as donors / Kazuchika Miyoshi, Sezen Arat, and Steven L. Stice -- A double nuclear transfer technique for cloning pigs / Irina A. Polejaeva, Shawn Walker, and Keith Campbell -- Nuclear transfer in nonhuman primates / Shoukhrat M. Mitalipov and Don P. Wolf --
  • Nutrigenomics 2005, CRCnetBASE
  • Oligonucleotide synthesis 2004, Springer Protocols
    Synthesis of DNA using a new two-step cycle / Douglas J. Dellinger ... [et al.] -- RNA synthesis using 2'-O-(tert-butyldimethylsilyl) protection / Brian S. Sproat -- RNA oligonucleotide synthesis via 5'-silyl-2'-orthoester chemistry / Stephanie A. Hartsel... [et al.] -- Dimethylthiarum disulfide: new sulfur transfer reagent in phosphorothioates oligonucleotide synthesis -- Zhiwei Wang, Quanlai Song, and Yogesh H. Sanghvi -- Assay for evaluating ribonuclease H-mediated degradation of RNA-antisense oligonucleotide duplexes / Annie Galarneau ... [et al.] -- Di- and oligonucleotide synthesis using H-phosphonate chemistry / Jacek Stawinski and Roger Strömberg -- Solid-phase synthesis of circular oligonucleotides / Enrique Pedroso ... [et al.] -- Locked nucleic acid synthesis / Henrik M. Pfundheller ... [et al.] -- Synthesis of DNA mimics representing HypNA-pPNA hetero-oligomers / Vladimir A. Efimov and Oksana G. Chakhmakhcheva -- Base-modified oligonucleotides with increased duplex stability: pyrazolo[3,4-d] pyrimidines replacing purines / Frank Seela ... [et al.] --Introduction of hypermodified nucleotides in RNA / Darrell R. Davis and Ashok C. Bajji -- Chemical methods for peptide-oligonucleotide conjugate synthesis / Dmitry A. Stetsenko and Michael J. Gait -- Biotin labeled oligonucleotides with extraordinarily long tethering arms / A. Michael Morocho ... [et al.] -- Universal labeling chemistry for nucleic acid detection on DNA chips / Ali Laayoun ... [et al.] -- Postsynthetic functionalization of triple helix-forming oligonucleotides / Alexandre S. Boutorine and Jian-Sheng Sun -- Fluorescence-based on-line detection as an analytical tool in RNA electrophoresis / Ute Scheffer and Michael Göbel -- Design and optimization of molecular beacon real-time polymerase chain reaction assays / Jacqueline A. M. Vet and Salvatore A. E. Marras -- High-thoughput production of optimized primers (fimers) for whole-genome direct sequencing / Nikolai Polushin ... [et al.] -- Nonenzymatic template directed RNA synthesis / Marcus Hey and Michael Göbel -- DNAse I footprinting of small molecule binding sites on DNA / Christian Bailly ... [et al.] --Gene targeting using peptide nucleic acid / Peter E. Nielsen -- Nucleic acid library construction using synthetic DNA constructs / Hani S. Zaher and Peter J. Unrau -- In vitro selection from combinatorial nucleic acid libraries / Andres Jäschke -- In vitro selection procedures for identifying DNA and RNA aptamers targeted to nucleic acids and proteins / Eric Dausse ... [et al.] -- Short double-stranded ribonucleic acid as inhibitor of gene expression by the interference mechanism / Jean-Rémi Bertrand, Andrei Maksimenko, and Claude Malvy.
  • Oncogenomics handbook 2005, Springer
  • Organelle genetics 2012, Springer
  • Origin of group identity 2009, Springer
    An overview : identity from bacteria to belief -- The prokaryotes : viruses, hyperparasites and the origin of group identity -- Sensory systems (light, odor, pheromones) in communities of oceanic microbes -- Subjugation of the individual : prokaryotic group living : blooms, slime and mats -- Animal group identity : from slime to worms, emergence of the brain -- Group identity in aquatic animals : learning to belong -- Development of tetrapod group identity, the smell of self -- Origin of primate group identity : vision and the great ERV invasion -- Human group identity : language and a social mind.
  • Our genes, our choices. 1st ed. 2012, ScienceDirect
    Neurogenetic origins of behavior -- Jinn in the genome -- 2B or not 2B? -- Stephen Mobley and his X-chromosome -- Dial multifactorial for murder : the intersection of genes and culture -- Distorted capacity I : the measure of the impaired will -- Distorted capacity II: neuropsychiatric diseases and the impaired will -- Inheritance of behavior and genes for behavior : gene wars -- Scientific and historic bases of genethics: who watches the geneticists and by what principles? -- World is double helical -- DNA, RNA, and proteins in a few easy pieces -- Stochastic brain : from DNA blueprint to behavior -- Reintroducing genes and behavior -- Warriors and worriers -- How many genes does it take to make a behavior? -- Genesis and genetics of sexual behavior -- Gene by environment interaction -- Epigenetic revolution : finding the imprint of the environment on the genome -- DNA on trial -- Parents and children : neurogenetic determinism and neurogenetic individuality -- Summing up genetic predictors of behavior.
  • A brief overview of molecular genetics -- An overview of information theory -- More on molecular genetics -- More on information theory -- An outline of error-correcting codes -- DNA is an ephemeral memory -- A toy living world -- Subsidiary hypothesis, nested system -- Soft codes -- Biological reality conforms to the hypotheses -- Identification of genomic codes.
  • p53 2011, Springer
    TP53 mutations in human cancers : selection versus mutagenesis / Magali Olivier, Audrey Petitjean, Claude Caron de Fromentel, and Pierre Hainaut -- Lessons on p53 from mouse models / Dadi Jiang and Laura D. Attardi -- TP63, TP73 : the guardian's elder brothers / Stephanie Courtois, Pierre Hainaut and Claude Caron de Fromentel -- The regulation of p53 protein function by phosphorylation / Nicola J. Maclaine and Theodore Hupp -- The p53-Mdm2 loop : a critical juncture of stress response / Yaara Levav-Cohen, Zehavit Goldberg, Osnat Alsheich Bartok, Valentina Zuckerman, Sue Haupt and Ygal Haupt -- Cooperation between MDM2 and MDMX in the regulation of p53 / Jeremy Blaydes -- Regulation and function of the original p53-inducible p21 gene / Jennifer A. Fraser -- p53 localization / Carl G. Maki -- Modes of p53 interactions with DNA in the chromatin context / Vladana Vukojevic, Tatiana Yakovleva, and Georgy Bakalkin -- p53's dilemma in transcription : analysis by microarrays / Karuppiah Kannan, Gideon Rechavi and David Givol -- Tumor viruses and p53 / Nobuo Horikoshi -- p53 and immunity / Vikram Narayan, Sarah E. Meek and Kathryn L. Ball.
  • Paramecium 2008, CRCnetBASE
    Mating types in paramecium -- General description of the protista and of paramecium -- Methods of studying genetic processes in organisms of the paramecium Aurelia species group -- The determination of mating types in paramecium -- Symbionts and mitochondria of paramecium -- Determination of i-antigens -- Micronuclei and macronuclei -- Ribosomal RNA and DNA -- Cortical morphogenesis -- Behavior -- Epigenetics.
  • Pasteurella multocida 2012, Springer
    Pasteurella multocida: Diseases and Pathogenesis /I. W. Wilkie, M. Harper, J. D. Boyce and B. Adler --Pathogenomics of Pasteurella multocida /J. D. Boyce, T. Seemann, B. Adler and M. Harper --The Key Surface Components of Pasteurella multocida: Capsule and Lipopolysaccharide /Marina Harper, John D. Boyce and Ben Adler --Pasteurella multocida and Immune Cells /Katharina F. Kubatzky --Molecular Biology of Pasteurella multocida Toxin /Joachim H. C. Orth and Klaus Aktories --Pasteurella multocida Toxin Interaction with Host Cells: Entry and Cellular Effects /Brenda A. Wilson and Mengfei Ho --Swine Atrophic Rhinitis Caused by Pasteurella multocida Toxin and Bordetella Dermonecrotic Toxin /Yasuhiko Horiguchi --The Pasteurella multocida Toxin: A New Paradigm for the Link Between Bacterial Infection and Cancer /Alistair Lax.
  • PCR mutation detection protocols 2002, Springer Protocols
  • Conformation-Sensitive Capillary Electrophoresis / Emma Jane Ashton -- Conformation Sensitive Gel Electrophoresis / Marian Hill -- Denaturing HPLC for Mutation Screening / Mike Mitchell, Jacqueline Cutler -- In Situ Detection of Human Papillomavirus DNA After PCR-Amplification / Gerard J. Nuovo -- LATE-PCR and Allied Technologies: Real-Time Detection Strategies for Rapid, Reliable Diagnosis from Single Cells / Kenneth E. Pierce, Lawrence J. Wangh -- Long-PCR Amplification of Human Genomic DNA / Stephen Keeney -- Human Papilloma Virus Strain Detection Utilising Custom-Designed Oligonucleotide Microarrays / Duncan Ayers, Mark Platt, Farzad Javad, Philip J. Day -- Multiplex Ligation-Dependent Probe Amplification (MLPA®) for the Detection of Copy Number Variation in Genomic Sequences / Petra G. Os, Jan P. Schouten -- Screening for Genomic Rearrangements by Multiplex PCR/Liquid Chromatography / Claude Houdayer, Catherine Dehainault, Marion Gauthier-Villars, Dominique Stoppa-Lyonnet -- Mutation Surveyor: Software for DNA Sequence Analysis / Jayne A. Minton, Sarah E. Flanagan, Sian Ellard -- Non-invasive Prenatal Diagnosis / Cathy Meaney, Gail Norbury -- Automated DNA Sequencing / Yvonne Wallis, Natalie Morrell -- Phylogenetic Microarrays for Cultivation-Independent Identification and Metabolic Characterization of Microorganisms in Complex Samples / Alexander Loy, Michael Pester, Doris Steger -- Prenatal Detection of Chromosome Aneuploidy by Quantitative-Fluorescence PCR / Kathy Mann, Erwin Petek, Barbara Pertl -- Use of Robotics in High-Throughput DNA Sequencing / Stephen Keeney -- Detection of Factor V Leiden and Prothrombin c.20210G>A Allele by Roche Diagnostics LightCycler® / Peter C. Cooper -- RT-PCR for the Detection of Translocations in Bone and Soft Tissue Tumours in Formalin-Fixed Paraffin-Embedded Tissues / Ann Williams, D. Chas Mangham -- Detection of Minimal Residual Disease in Leukaemia by RT-PCR / Joanne Mason, Mike Griffiths -- Mutation Detection by Southern Blotting / Gillian Mellars, Keith Gomez.
  • PCR protocols. 3rd ed. 2011, Springer Protocols
    Setup of a PCR Laboratory / Zaheer Khan -- Long-Range PCR with a DNA Polymerase Fusion / Holly H. Hogrefe, Michael C. Borns -- Isolation of Genomic Insertion Sites of Proviruses Using Splinkerette-PCR-Based Procedures / Bin Yin -- Lariat-Dependent Nested PCR for Flanking Sequence Determination / Daniel J. Park -- CODEHOP PCR and CODEHOP PCR Primer Design / Jeannette P. Staheli, Richard Boyce, Dina Kovarik, Timothy M. Rose -- Sequencing of Difficult DNA Regions by SAM Sequencing / Keith R. Mitchelson -- A Global Single-Cell cDNA Amplification Method for Quantitative Microarray Analysis / Kazuki Kurimoto, Mitinori Saitou -- Quantitation of MicroRNAs by Real-Time RT-qPCR / Caifu Chen, Ruoying Tan, Linda Wong, Richard Fekete, Jason Halsey -- High-Throughput SuperSAGE / Hideo Matsumura, Kentaro Yoshida, Shujun Luo, Detlev H. Krüger, Günter Kahl, Gary P. Schroth, Ryohei Terauchi -- Deep Cap Analysis of Gene Expression / Junpei Kurosawa, Hiromi Nishiyori, Yoshihide Hayashizaki -- Linking Emulsion PCR Haplotype Analysis / James G. Wetmur, Jia Chen -- PAP-LMPCR: An Improved, Sequence-Selective Method for the In Vivo Analysis of Transcription Factor Occupancy and Chromatin Fine Structure / Richard Ingram, Arthur Riggs, Constanze Bonifer -- The Many Faces of MLPA / Thomas Ohnesorg, Erin Turbitt, Stefan J. White -- Assessing Gene-Specific Methylation Using HRM-Based Analysis / Ee Ming Wong, Alexander Dobrovic -- Alu PCR / Maurizio Cardelli -- Asynchronous PCR / Caifu Chen, David Ruff, Jason Halsey -- Novel Applications of PCR Through the Use of DNA Substrates / Stuart M. Wilson -- Enhanced Solid Phase PCR for Increased Loading of Amplicon onto Solid Support / Daniel J. Park -- Application of Blocking Oligonucleotides to Improve Signal-to-Noise Ratio in a PCR / Hege Vestheim, Bruce E. Deagle, Simon N. Jarman -- Asymmetric Overlap Extension PCR Method for Site-Directed Mutagenesis / Yue-Hua Xiao, Yan Pei -- Ribosome Display: A Technology for Selecting and Evolving Proteins from Large Libraries / Birgit Dreier, Andreas Plückthun -- GLOBE: Analysis of DNA-Protein Interaction Analysis / Takaaki Kojima, Hideo Nakano -- PCR DNA-Array Profiling of DNA-Binding Transcription Factor Activities in Adult Mouse Tissues / Yimin Sun, Jing Cheng, Keith R. Mitchelson -- Nucleotide Exchange and Excision Technology DNA Shuffling and Directed Evolution / Janina Speck, Sabine C. Stebel, Katja M. Arndt, Kristian M. Müller.
  • Pharmacogenomics 2005, Springer Protocols
  • Challenges, opportunities, and evolving landscapes in pharmacogenomics and personalized medicine : an industry perspective / Nadine Cohen and Theresa Frangiosa -- Implementation of pharmacogenomic sample collection in clinical trials / Deborah Sokol Ricci and Monique Franc -- Pharmacogenomics : the regulatory environment and labeling implications / Myong-Jin Kim ... [et al.] -- Applications of pharmacogenomics in drug discovery / Duncan McHale -- Applications of pharmacogenomics in clinical trials / Monique Franc -- Pharmacogenomics applications in drug metabolism : from genotyping to drug label-challenges? / Ann K. Daly -- The genetics of adverse drug reactions : promises and problems / Martin Armstrong -- Strategies and resources for marker selection and genotyping in genetic association studies / Nicole Soranzo, Dong-Jing Fu, and Qingqin S. Li -- Study design and statistical issues in pharmacogenetics research : from candidate genes to genome-wide screens / Nicholas J. Schork, Nathalie Malo, and Eric J. Topol -- Holy SNP, Batman! / Reyna Favis -- Predictive biomarker classifiers in the design of pivotal clinical trials / Richard Simon -- Translation of biomarkers into clinical utility / William L. Trepicchio and George Mulligan -- Pharmacogenomic study feasibility assessment and pharmaceutical business decision-making / Monique Franc and Theresa Frangiosa -- Co-development of drugs and pharmacogenomics-based diagnostics in oncology / Jeffrey S. Ross -- Pharmacogenomics applications in epilepsy / Chantal Depondt -- Pharmacogenomics in Alzheimer's disease / Ramón Cacabelos -- Pharmacogenomics applications in psychiatric disorders / Todd Lencz and Anil K. Malhotra -- Pharmacogenomics in HIV disease / Amalio Telenti -- Pharmacogenomics and cardiovascular drugs / Gérard Siest ... [et al.] -- Pharmacogenomic applications in children / Susan F.A. Grant and Hakon Hakonarson -- Pharmacogenomics of rare and monogenic disorders / Paul D. Maher.
  • Phospho-proteomics 2009, Springer Protocols
    A high-resolution two dimensional gel- and pro-Q DPS-based proteomics workflow for phosphoprotein identification and quantitative profiling / Ganesh K. Agrawal and Jay J. Thelen -- Differential phosphoprotein labelling (DIPPL) using ³²P and ³³P / Aviva M. Tolkovsky and Andreas Wyttenbach -- Identification of oxidative stress-induced tyrosine phosphorylated proteins by immunoprecipitation and mass spectrometry / Ma Carmen Duran, Hong-Lin Chan, and John F. Timms -- Enrichment and characterization of phosphopeptides by immobilized metal affinity chromatography (IMAC) and mass spectrometry / Tine E. Thingholm and Ole N. Jensen -- The use of titanium dioxide micro-columns to selectively isolate phosphopeptides from proteolytic digests / Tine E. Thingholm and Martin R. Larsen -- Enrichment and separation of mono- and multiply phosphorylated peptides using sequential elution from IMAC prior to mass spectrometric analysis / Tine E. Thingholm , Ole N. Jensen, and Martin R. Larsen -- Use of stable isotope labeling by amino acids in cell culture (SILAC) for phophotyrosine protein identification and quantitation / Guoan Zhang and Thomas A. Neubert -- Hydrophilic interaction chromatography for fractionation and enrichment of the phosphoproteome / Dean E. McNulty and Roland S. Annan -- SILAC for global phosphoproteomic analysis / Genaro Pimienta, Raghothama Chaerkady, and Akhilesh Pandey -- Quantitative phospho-proteomics based on soluble nanopolymers / Anton Iliuk and W. Andy Tao -- Profiling the tyrosine phosphorylation state using SH2 domains / Kevin Dierck ... [et al.] -- An overview of the qualitative analysis of phosphoproteins by mass spectrometry / Philip R. Gafken -- The analysis of phosphoproteomes by selective labelling and advanced mass spectrometric techniques / Angela Amoresano ... [et al.] -- On-line liquid chromatography electron capture dissociation for the characterization of phosphorylation sites in proteins / Steve M.M. Sweet and Helen J. Cooper -- Quantification of protein phosphorylation by [mu]LC-ICP-MS / Ralf Krüger, Nico Zinn, and Wolf D. Lehmann -- Reverse-phase diagonal chromatography for phosphoproteome research / Kris Gevaert and Joël Vandekerckhove -- Chemical tagging strategies for mass spectrometry-based phospho-proteomics / Alexander Leitner and Wolfgang Lindner -- Antibody array platform to monitor protein tyrosine phosphorylation in mammalian cells / Alicia S. Chung and Y. Eugene Chin -- Protein tyrosine kinase characterization based on fully automated synthesis of (phospho)peptide arrays in microplates / W. Carl Saxinger -- Kinome profiling using peptide arrays in eukaryotic cells / Kaushal Parikh, Maikel P. Peppelenbosch, and Tita Ritsema -- ProMoST : a tool for calculating the pI and molecular mass of phosphorylated and modified proteins on two-dimensional gels / Brian D. Halligan -- Kinase-specific preiction of protein phosphorylation sites / Martin L. Miller and Nikolaj Blom -- Reconstructing regulatory kinase pathways from phosphopeptide data : a bioinformatics approach / Lawrence G. Puente, Robin E.C. Lee, and Lynn A. Megeney.
  • Phylogenomics 2008, Springer Protocols
    From gene-scale to genome-scale phylogenetics : the data flood in, but the challenges remain / Antonis Rokas and Stylianos Chatzimanolis -- Phylogenomic analysis of chromosome sorting and painting / Roscoe Stanyon and Gary Stone -- FISH for mapping single copy genes / Terje Raudsepp and Bhanu P. Chowdhary -- Construction of radiation hybrid panels / John E. Page and William J. Murphy -- Survey sequencing and radiation hybrid mapping to construct comparative maps / Christophe Hitte ... [et al.] -- Construction of high-resolution comparative maps in mammals using BAC-end sequences / Denis M. Larkin and Harris A. Lewin -- Amniote phylogenomics : testing evolutionary hypotheses with BAC library scanning and targeted clone analysis of large-scale sequences from reptiles / Andrew M. Shedlock, Daniel E. Janes, and Scott V. Edwards -- Comparative physical mapping : universal overgo hybridization probe design and BAC library hybridization / James W. Thomas -- Phylogenomic resources at the UCSC Genome Browser / Kate Rosenbloom ... [et al.] -- Computational tools for the analysis of rearrangements in mammalian genomes / Glenn Tesler and Guillaume Bourque -- Computational reconstruction of ancestral DNA sequences / Mathieu Blanchette ... [et al.] -- Sequencing and phylogenomic analysis of whole mitochondrial genomes of animals / Rafael Zardoya and Mónica Suárez -- Retroposons : genetic footrpints on the evolutionary paths of life / Hidenori Nishihara and Norihiro Okada -- LINE-1 elements : analysis by FISH and nucleotide sequences / Paul D. Waters ... [et al.] -- Identification of cryptic sex chromosomes and isolation of X- and Y-borne genes / Paul D. Waters ... [et al.]
  • Phytochemicals 2006, CRCnetBASE
  • Pichia protocols. 2nd ed. 2007, Springer Protocols
    Introduction : distinction between Pichia pastoris and other expression systems / James M. Cregg -- Vectors and strains for expression / Joan Lin-Cereghino and Geoff P. Lin-Cereghino -- DNA-mediated transformation / James M. Cregg -- Rational design and optimization of fed-batch and continuous fermentation / Wenhui Zhag, Mehmet Inan, and Michael M. Meagher -- Saturation of the secretory pathway by overexpression of a hookworm (Necator americanus) protein (Na-ASP1) / Mehmet Inan ... [et al.] -- Purification of the N- and C-terminal subdomains of recombinant heavy chain fragment C of botulinum neurotoxin serotype C / Jicai Huang ... [et al.] -- Rapid screening of chromatography resins for the purification of proteins / Sandra E. Ríos, Erin M. Giaccone, and Tillman U. Gerngross -- Characterization of O-linked saccharides on glycoproteins / Roger K. Bretthauer -- Modification of the N-glycosylation pathway to produce homogeneous human-like glycans using glycoswitch plasmids / Wouter Vervecken ... [et al.] -- N-linked glycan characterization of heterologous proteins / Huijan Li ... [et al.] -- Heavy labeling of recombinant proteins / Eric Rodriguez -- Selenomethionine labeling of recombinant proteins / Anna M. Larsson and T. Alwyn Jones -- Selective isotopic labeling of recombinant proteins using amino acid auxotroph strains / James W. Whittaker -- Classical genetics / Ilya Tolstorukov and James M. Cregg -- Identification of pexophagy genes by restriction enzyme-mediated integration / Laura A. Schroder, Benjamin S. Glick, and William A. Dunn, Jr. -- Characterization of protein-protein interactions : application to the understanding of peroxisome biogenesis / Sebastien Leon ... [et al.] -- Localization of proteins and organelles using fluorescence microscopy / Jean-Claude Farre ... [et al.] -- Fluorescence microscopy and thin-section electron microscopy / Benjamin S. Glick.
  • Plant chromosome engineering 2011, Springer Protocols
    Recent advances in plant transformation -- Engineering the plastid genome of nicotiana sylvestris, a diploid model species for plastid genetics -- Homologous recombination in plants : An antireview -- Chromosome painting for plant biotechnology -- Plant B chromosomes -- Telomere truncation in plants -- Engineered plant minichromosomes -- Method for bxb1-mediated site-specific integration in planta -- Targeted mutagenesis in arabidopsis using zinc-finger nucleases -- Vectors and methods for hairpin RNA and artificial microRNA-mediated gene silencing in plants -- Recombinant protein expression in nicotiana -- Chromosome analysis and sorting using flow cytometry -- Super-stretched pachytene chromosomes for plant molecular cytogenetic mapping -- Cytological dissection of the triticeae chromosomes by the gametocidal system -- Development and use of oat-maize chromosome additions and radiation hybrids -- Enhancer trapping in plants -- Chromatin beacons : Global sampling of chromatin physical properties using chromatin charting lines -- Transposable elements as catalysts for chromosome rearrangements.
  • Plant genomes 2008, Karger
    Paleopolyploidy and its impact on the structure and function of modern plant genomes / A.H. Paterson -- Genomic history and gene family evolution in angiosperms: challenges and opportunities / J. Sampedro, D. Cosgrove -- The evolutionary position of subfunctionalization, downgraded / M. Freeling -- Grass genome structure and evolution / J. Messing, J.L. Bennetzen -- Phylogenetic insights into the pace and pattern of plant genome size evolution / C.E. Grover, J.S. Hawkins, J.F. Wendel -- Plant transposable elements / J.M. Deragon, J.M. Casacuberta, O. Panaud -- Plant sex chromosomes / D. Charlesworth -- Plant centromeres / J.C. Lamb ... [et al.] -- MiRNAs in the plant genome: all things great and small / B.C. Meyers, P.J. Green, C. Lu -- Recent insights into the evolution of genetic diversity of maize / A. Rafalski, S. Tingey -- The rice genome structure as a trail from the past to beyond / T. Sasaki.
  • Plant genomics 2009, Springer Protocols
    Role of model plant species / Richard Flavell -- New technologies for ultra-high throughput genotyping in plants / Nikki Appleby, David Edwards, and Jacqueline Batley -- Genetic maps and the use of synteny / Chris Duran, David Edwards, and Jacqueline Batley -- A simple TAE-based method to generate large insert BAC libraries from plant species / Bu-Jun Shi, J. Perry Gustafson, and Peter Langridge -- Transcript profiling and expression level mapping / Elena Potokina, Arnis Druka, and Michael J. Kearsey -- Methods for functional proteomic analyses / Christof Rampitsch and Natalia V. Bykova -- Stable transformation of plants / Huw D. Jones and Caroline A. Sparks -- Transient transformation of plants / Huw D. Jones, Angela Doherty, and Caroline A. Sparks -- Bridging the gene-to-function knowledge gap through functional genomics / Stephen J. Robinson and Isobel A.P. Parkin -- Heterologous and cell-free protein expression systems / Naser Farrokhi ... [et al.] -- Functional genomics and structural biology in the definition of gene function / Maria Hrmova and Geoffrey B. Fincher -- In situ analysis of gene expression in plants / Sinéad Drea ... [et al.] -- Plant and crop databases / David E. Matthews, Gerard R. Lazo, and Olin D. Anderson -- Plant genome annotation methods / Shu Ouyang ... [et al.] -- Molecular plant breeding : methodology and achievements / Rajeev K. Varshney ... [et l.] -- Practical delivery of genes to the marketplace / David A. Fischhoff and Molly N. Cline -- Ecological genomics of natural plant populations : the Israeli perspective / Eviatar Nevo -- Genome sequencing approaches and successes / Michael Imelfort ... [et al.]
  • 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 2013, Springer
    Terms and Concepts --History of the Key Disciplines --Enviromics --Genomics --Epigenomics --Molecular Phenomics --Systems Phenomics --Cohorts --Challenges --Personalized Preventive Medicine.
  • Post-transcriptional gene regulation 2008, Springer Protocols
    Bioinformatics approaches for studying untranslated regions of mRNAs / Paramjeet S. Bagga -- Identification of mRNA polyadenylation sites in genomes using cDNA sequences, expressed sequence tags, and trace / Ju Youn Lee, Ji Yeon Park, and Bin Tian -- Bioinformatic tools for studying post-transcriptional gene regulation : the UAlbany TUTR Collection and other informatic resources / Francis Doyle ... [et al.] -- In-line probing analysis of riboswitches / Elizabeth E. Regulski and Ronald R. Breaker -- Ribotrap : targeted purification of RNA-specific RNPs from cell lysates through immunoaffinity precipitation to identify regulatory proteins and RNAs / Dale L. Beach and Jack D. Keene -- Advances in RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray profiling / Timothy E. Baroni ... [et al.] -- Biosensors for RNA aptamers-protein interaction / Sara Tombelli, Maria Minunni, and Marco Mascini -- A tethering approach to study proteins that activate mRNA turnover in human cells / Sandra L. Clement and Jens Lykke-Andersen -- RNA analysis by biosynthetic tagging using a 4-thiouracil and uracil phosphoribosyltransferase / Gusti M. Zeiner ... [et al.] -- Efficient 5' cap-dependent RNA purification : use in identifying and studying subsets of RNA / Edyta Z. Bajak and Curt H. Hagedorn -- Enrichment of alternatively spliced isoforms / Julian P. Venables --In vivo methods to assess polyadenylation efficiency / Lisa K. Hague, Tyra Hall-Pogar, and Carol S. Lutz -- Monitoring the temporal and spatial distribution of RNA in living yeast cells / Roy M. Long and Carl R. Urbinati -- Analysis of mRNA partitioning between the cytosol and endoplasmic reticulum compartments of mammalian cells / Samuel B. Stephens ... [et al.] -- In vivo and in vitro analysis of poly(A) length effects on mRNA translation / Jing Peng, Elizabeth L. Murray, and Daniel R. Schoenberg -- A ribosomal density-mapping procedure to explore ribosome positions along translating mRNAs / Naama Eldad and Yoav Arava -- Identification of changes in gene expression by quantitation of mRNA levels / Wendy M. Olivas -- Application of the Invader® RNA assay to the polarity of vertebrate mRNA decay / Elizabeth L. Murray and Daniel R. Schoenberg -- Development of an in vitro mRNA decay system in insect cells / Kevin Sokoloski, John R. Anderson, and Jeffrey Wilusz -- Using synthetic precursor and inhibitor miRNAs to understand miRNA function / Lance P. Ford and Angie Cheng -- A step-by-step procedure to analyze the efficacy of siRNA using real-time PCR / Angie Cheng, Charles L. Johnson, and Lance P. Ford.
  • Primary Prevention of Genetic Disorders and Place of Preimplantation Diagnosis --Approaches to Preimplantation Diagnosis --Preimplation Diagnosis for Single-Gene Disorders --PGD for HLA Typing --Preimplantation Diagnosis for Chromosomal Disorders --Clinical Outcome of Preimplantation Genetic Diagnosis --Preimplantation Diagnosis and Establishment of Disease and Individual Specific Human Embryonic Stem Cell Lines --Social, Ethical, and Legal Aspects.
  • 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 2002, ScienceDirect
    Historical perspective / Robert H. Foote -- Activation of mammalian oocytes / Rafael A. Fissore, Jeremy Smyth, Manabu Kurokawa and Philippe Collas -- The nucleus / Fyodor D. Urnov and Alan P. Wolffe -- Nuclear reprogramming : biological and technological constraints / Kevin Eggan and Rudolf Jaenisch -- Plasticity of somatic nucleus by epigenetic reprogramming via cell hybridization / Takashi Tada, Masako Tada and M. Azim Surani -- Determinants of pluripotency in mammals / Michele Boiani and Hans R. Schöler -- Micromanipulation techniques for cloning / Raymond L. Page -- Microinsemination and nuclear transfer with male germ cells / Atsuo Ogura, Narumi Ogonuki and Kimiko Inoue -- Development of viable mammalian embryos in vitro : evolution of sequential media / David K. Gardner and Michelle Lane -- Genetic and phenotypic similarity among members of mammalian clonal sets / George E. Seidel, Jr. -- Genetic modification and cloning in mammals / Patrick W. Dunne and Jorge A. Piedrahita -- Pregnancy and neonatal care of cloned animals / Jonathan R. Hill and Pascale Chavatte-Palmer -- Donor cell type and cloning efficiency in mammals / Y. Tsunoda and Y. Kato -- Cloning of amphibians / J.B. Gurdon and J.A. Byrne -- Cloning of fish / Yuko Wakamatsu and Kenjiro Ozato -- Cloning of mice / Teruhiko Wakayama and Anthony C.F. Perry -- Cloning of rabbits / András Dinnyés, X. Cindy Tian and Xiangzhong Yang -- Nuclear transfer in swine / Randall S. Prather -- Cloning of cattle / Neal L. First, Zeki Beyhan and Jennifer D. Ambroggio -- Cell cycle regulation in cloning / Keith H.S. Campbell -- Cloning of rats / Philip Iannaccone, Michael Bader and Vasiliy Galat -- Cloning in nonhuman primates / Tanja Dominko, Calvin Simerly, Crista Martinovich and Gerald Schatten -- Nuclear transfer for stem cells / Alan Trounson -- Current research and commercial applications of cloning technology / Steven L. Stice -- Transgenic cloned goats and the production of therapeutic proteins / Esmail Behboodi, LiHow Chen, Margaret M. Destrempes, Harry M. Meade and Yann Echelard -- Ethical implications of cloning / Ronald M. Green -- Mammalian cloning : challenges for the future / R.L. Gardner.
  • 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 2004, ScienceDirect
  • Protein engineering 2009, Springer
    Understanding enzyme mechanism through protein chimeragenesis / N.M. Goodey and S.J. Benkovic -- Chemical protein engineering : synthetic and semisynthetic peptides and proteins / L. Merkel, L. Moroder, and N. Budisa -- Native chemical ligation: Semisynthesis of post-translationally modified proteins and biological probes / E. Vogel Taylor and B. Imperiali -- Chemical methods for mimicking post-translational modifications / S.I. van Kasteren, P. Garnier and B.G. Davis -- Noncanonical amino acids in protein science and engineering / K.E. Beatty and D.A. Tirrell -- Fidelity mechanisms of the aminoacyl-tRNA synthetases / A.P. Mascarenhas ... [et al.] -- Specialized components of the translational machinery for unnatural amino acid mutagenesis : tRNAs, aminoacyl-tRNA synthetases, and ribosomes / C. Köhrer and U.L. RajBhandary -- In vivo studies of receptors and ion channels with unnatural amino acids / D.A. Dougherty -- Synthesis of modified proteins using misacylated tRNAs / S.M. Hecht -- Cell-free synthesis of proteins with unnatural amino acids. The pure system and expansion of the genetic code / I. Hirao, T. Kanamori and T. Ueda -- Engineering nucleobases and polymerases for an expanded genetic alphabet / A.M. Leconte and F.E. Romesberg -- Understanding membrane proteins. How to design inhibitors of transmembrane protein-protein interactions / J.S. Slusky, H. Yin and W.F. DeGrado.
  • Protein engineering protocols 2006, Springer 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.
  • Genomic DNA isolation from different biological materials / Duckchul Park -- Extraction of plant RNA / Elspeth MacRae -- Overview on hybridization and detection techniques / Elena Hilario -- Checkerboard DNA/DNA hybridization technology : using DIG detection / Lisa S. Gellen, Glenn Wall-Manning, and Chris H. Sissons -- Nonradioactive northern and southern analyses from plant samples / Christoph Peterhaensel, Dagmar Weier, and Thomas Lahaye -- Screening a BAC library with nonradioactive overlapping oligonucleotide (overgo) probes / Elena Hilario, Tiffany F. Bennell, and Erik Rikkerink -- Direct in-gel hybridization of DNA with digoxigenin-labeled probes / Saeed A. Khan and Mohamed S. Nawaz --In situ hybridization of termite microbes / Shigeharu Moriya ... [et al.] -- RNA electrophoretic mobility shift assay using a fluorescent DNA sequencer / Yukinori Eguchi -- Comparative quantitation of mRNA expression in the central nervous system using fluorescence in situ hybridization / Darren J. Day, Eli M. Mrkusich, and John H. Miller -- Visualization of gene expression by fluorescent multiplex real-time PCR amplification / Maria Rosa Ponce ... [et al.] -- Fluorescence in situ hybridization for the identification of environmental microbes / Annelie Pernthaler and Jakob Pernthaler -- Introduction to kinetic (real-time) PCR / John Mackay -- Validation of siRNA knockdowns by quantitative real-time PCR / Sukru Tuzmen --Real-time quantitative PCR as an alternative to southern blot or fluorescence in situ hybridization for detection -- Of gene-copy number changes / Jasmien Hoebeeck, Frank Speleman, and Jo Vandesompele -- Design and work-up of a new molecular diagnostic assay based on real-time PCR / Harald Kessler -- Real-time PCR fluorescent chemistries / John Mackay and Olfert Landt -- Microarrays : an overview / Norman H. Lee and Alexander I. Saeed -- Oligonucleotide microarrays for the study of coastal microbial communities / Gaspar Taroncher-Oldenburg and Bess B. Ward.
  • Pyrosequencing protocols 2006, Springer Protocols
    The history of pyrosequencing / Pol Nyron -- Pyrosequencing applications / Sharon Marsh -- Web-based primer design software for genome-scale genotyping by pyrosequencing / Steven Ringquist ... [et al.] -- Pyrosequencing : a simple method for accurate genotyping / Cristi R. King and Tiffany Scott-Horton -- Universal primer applications for pyrosequencing / Dong-Chuan Guo and Dianna M. Milewicz -- Allele quantification and DNA pooling methods / Jonathon Wasson -- Multiplex pyrosequencing for DNA variation analysis / Pritesh Patel, Yih-Horng Shiao, and Paolo Fortina -- Analysis of gene-specific DNA methylation patterns by the pyrosequencing technology / Jørg Tost and Ivo Glynne Gut -- Detecting mutations that confer oxazolidinone resistance in gram-positive bacteria / Neil Woodford, Sarah E. North, and Matthew J. Ellington -- Pyrosequencing-based strategies for improved allele typing of HLA loci / Steven Ringquist ... [et al.] -- Pyrosequencing of phage display libraries for the identification of cell-specific targeting ligands / Ahad A. Rahim -- Gene copy number detection in animal studies / Gerli Pielberg and Leif Andersson -- Detection of allelic imbalance in gene expression using pyrosequencing / Hua Wang and Steven C. Elbein -- Pyrosequencing genotype storage techniques / Derek J. Van Booven.
  • Quantitative trait loci 2002, Springer Protocols
  • Recoding 2010, Springer
    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.
  • Recombinant gene expression. 2nd ed. 2004, Springer Protocols
    Copy-control tightly regulated expression vectors based on pBAC/oriV / Jadwiga Wild and Waclaw Szybalski -- Cell-free protein synthesis with prokaryotic combined transcription-translation / James R. Swartz, Michael C. Jewett, and Kim A. Woodrow -- Genetic tools for the manipulation of moderately halophilic bacteria of the family Halomonadaceae / Carmen Vargas and Joaquín J. Nieto -- Gene transfer and expression of Recombinant proteins in moderately halophilic bacteria / Amalia S. Afendra ... [et al.] -- Recombinant protein production in antarctic gram-negative bacteria / Angela Duilio, Maria Luisa Tutino, and Gennaro Marino -- Recombinant protein production in yeasts / Danilo Porro and Diethard Mattanovich -- Controlled expression of homologous genes by genomic promoter replacement in the yeast Saccharomyces cerevisiae / Kevin J. Vestrepen and Johan M. Thevelein -- High-throughput expression in microplate format in Saccharomyces cerevisiae / Caterina Holz and Christine Lang -- High-throughput expression in microplate format in Pichia pastoris / Mewes Böttner and Christine Lang -- Multiple gene expression by chromosomal integration and CRE-loxP-mediated marker recycling in Saccharomyces cerevisiae / Björn Johansson and Bärbel Hahn-Hägerdal --Flp-mediated integration of expression cassettes into FRT-tagged chromosomal loci in mammalian cells / Dagmar Wirth and Hansjörg Hauser -- Generation of high-recombinant protein-producing Chinese hamster ovary (CHO) cells / Jean-Louis Goergen and Lucía Monaco -- Preparation of recombinant proteins in milk / Louis-Marie Houdebine.Host cell compatibility in protein expression / James J. Greene -- Production of Recombinant proteins: challenges and solutions / Laura A. Palomares, Sandino Estrada-Moncada and Octavio T. Ramírez -- Folding promoting agents in Recombinant protein production / Beatrix Fahnert -- Back to basics: pBR322 and protein expression systems in e. coli / Paulina Balbás and Francisco Bolívar -- alpha-complementation enabled T7 expression vectors and their use for the expression of recombinant polypeptides for protein transduction experiments / Mikhail F. Alexeyev ... [et al.] -- Expression of recombinant alkaline phosphatase conjugates in Escherichia coli / Jean-Claude Boulain and Frédéric Ducancel -- Overexpression of chromosomal genes in Escherichia coli / Fernando Valle and Noemí Flores -- Chromosomal expression of foreign and native genes from regulatable promoters in Escherichia coli / Lu Zhou, Ke Zhang, and Barry L. Wanner -- Plasmid vectors for marker-free chromosomal insertion of genetic material in Escherichai coli / Sylvie Le Borgne, Francisco Bolívar, and Guillermo Gosset -- Copy-control pBAC/oriV vectors for genomic cloning / Jadwiga Wild and Waclaw Szybalski --Three decades of fungal transformation: key concepts and applications / Vianey Olmedo-Monfil, Carlos Cortés-Penagos, and Alfredo Herrera-Estrella -- Three decades of fungal transformation: novel technologies / Sergio Casas-Flores, Teresa Rosales-Saavedra, and Alfredo Herrera-Estrella -- Gene transfer and expression in plants / Argelia Lorence and Robert Verpoorte -- Production of Recombinant proteins by hairy roots cultured in plastic sleeve bioreactors / Fabricio Medina-Bolívar and Carole Cramer -- Engineering the chloroplasts genome for hyperexpression of human therapeutic proteins and vaccine antigens / Shashi Kumar and Henry Daniell -- New selection marker for plant transformation / Barbara Leyman ... [et al.] -- Enhancer detection and gene trapping as tools for functional genomics in plants / Gerardo Acosta-García, Daphné Autran, and Jean-Philippe Vielle-Calzada -- Gene transfer and expression in mammalian cell lines and transgenic animals / Félix Recillas-Targa -- Sustained heterologous transgene expression in mammalian and avian cell lines / Héctor Rincón-Arano and Félix Recillas-Targa -- Inducible gene expression in mammalian cells and mice / Wilfried Webber and Martin Fussenegger --
  • "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.
  • Fulltext (pt. B) ScienceDirect
  • Micro mining : computational approaches to miRNA discovery / Adam Grundhoff -- Animal microRNA gene prediction / Ola Snv?e and Pa<U+030a>l St?rom -- A suite of resources for the study of miRNA ontology and function / Praveen Sethupathy, Molly Megraw, and Artemis G. Hatzigeorgiou -- Regulation of translation and mRNA stability by Hfq-binding small RNAs in Escherichia coli / Hiroji Aiba -- Mechanisms by which microRNAs regulate gene expression in animal cells / Yang Yu and Timothy W. Nilsen -- The microRNAs of C. elegans / Mona J. Nolde and Frank J. Slack -- Isolation and characterization of small RNAs in C. elegans / Chisato Ushida and Yusuke Hokii -- MicroRNA tales in fly development / Utpal Bhadra ... [et al.] -- RNA interference and miRNAs in zebrafish / Alex S. Flynt, Elizabeth J. Thatcher, and James G. Patton -- Biogenesis and function of plant microRNAs / Zoltan Havelda -- Endogenous small RNA pathways in Arabidopsis / Manu Agarwal, Julien Curaba, and Xuemei Chen.How to assay miRNA expression : a technology guide / Mirco Castoldi, Vladimir Benes, and Martina U. Muckenthaler -- Methods to quantify microRNA gene expression / Lori A. Neely -- Regulation of alternative splicing by microRNAs / Rajesh K. Gaur -- Recent progress in polymerase II-mediated intronic microRNA expression systems / Shi-Lung Lin and Shao-Yao Ying -- MicroRNA-based RNA polymerase II expression vectors for RNA interference in mammalian cells / Anne B. Vojtek ... [et al.] -- Transgenic RNAi : a fast and low-cost approach to reverse genetics in mammals / Linghua Qiu and Zuoshang Xu -- Symphony of AIDS : an miRNA-based therapy / Yoichi R. Fujii -- MicroRNAs and cancer : connecting the dots / Sumedha D. Jayasena -- Mammalian transcriptional gene silencing by small RNAs / Daniel H. Kim and John J. Rossi -- Regulation of gene expression by RNA mediated transcriptional gene silencing / Kevin V. Morris.
  • Regulation of microRNAs 2011, Springer
    MicroRNA biogenesis and function : an overview / Rene F. Ketting -- Regulation of pri-miRNA processing through Smads / Akiko Hata and Brandi N. Davis -- Stimulation of pri-miR-18a processing by hnRNP A1 / Gracjan Michlewski, Sonia Guil, and Javier F. Cáceres -- KSRP promotes the maturation of a group of miRNA precursors / Michele Trabucchi ... [et al.] -- Hormonal repression of miRNA biosynthesis through a nuclear steroid hormone receptor / Sally Fujiyama-Nakamura, Kaoru Yamagata, and Shigeaki Kato -- Autoregulatory mechanisms controlling the microprocessor / Robinson Triboulet and Richard I. Gregory -- Regulation of pre-miRNA processing / Nicolas J. Lehrbach and Eric A. Miska -- The effect of RNA editing and ADARs on miRNA biogenesis and function / Bret S.E. Heale, Liam P. Keegan, and Mary A. O'Connell -- MiRNAs need a trim regulation of miRNA activity by trim-NHL proteins / F. Gregory Wulczyn ... [et al.] -- Properties of the regulatory RNA-binding protein HuR and its role in controlling miRNA repression / Nicole-Claudia Meisner and Witold Filipowicz -- Turnover of mature miRNAs and siRNAs in plants and algae / Heriberto Cerutti and Fadia Ibrahim -- MicroRNases and the regulated degradation of mature animal miRNAs / Helge Grosshans and Saibal Chatterjee.
  • Regulatory genome 2006, ScienceDirect
  • Regulatory RNAs 2006, Cold Spring Harb Lab Press
    Mechanism and biology of RNAi -- Genome-wide approaches -- Small RNAs in development -- Telomeres and cancer -- End regulation of transcripts -- RNPs and RNA editing -- Biology of short RNAs -- Control of gene expression by noncoding RNAs -- Heterochromatin -- Quality control, messenger RNA turnover, and translational control.
  • Regulatory RNAs 2012, Springer
    pt. 1. Basics -- pt. 2. Methods -- pt. 3. Applications.
  • This book provides a comprehensive and up-to-date collection of review articles focusing on RNA-mediated regulation in prokaryotes. The various modes of action include the direct interaction with proteins, direct sensing of metabolites or of physical parameters, and the interaction with RNAs to stimulate or prevent binding of ribosomes or to stimulate degradation. Written by leading experts in the field, the book covers small RNA functions, RNA thermometers, riboswitches, the diversity of small RNA-guided CRISPR-Cas defense systems and selected RNA chaperons in both prokaryotic domains, bacteria and archaea. Recent advances towards the computational identification of regulatory RNAs and their targets are included and particular attention is paid to small RNA in pathogenic bacteria. This volume is the only one exclusively covering regulatory RNAs in the prokaryotic domains to date, making it essential literature for anyone interested in RNA function and gene regulation and a valuable resource for teaching these concepts.
  • Repetitive DNA 2012, Karger
    The Repetitive DNA Content of Eukaryotic Genomes / López-Flores, I.; Garrido-Ramos, M.A. -- Telomere Dynamics in Mammals / Silvestre, D.C.; Londoño-Vallejo, A. -- Drosophila Telomeres: an Example of Co-Evolution with Transposable Elements / Silva-Sousa, R.; López-Panadès, E.; Casacuberta, E. -- The Evolutionary Dynamics of Transposable Elements in Eukaryote Genomes / Tollis, M.; Boissinot, S. -- SINEs as Driving Forces in Genome Evolution / Schmitz, J. -- Unstable Microsatellite Repeats Facilitate Rapid Evolution of Coding and Regulatory Sequences / Jansen, A.; Gemayel, R.; Verstrepen, K.J. -- Satellite DNA Evolution / Plohl, M.; Meštrović, N.; Mravinac, B. -- Satellite DNA-Mediated Effects on Genome Regulation / Pezer, Ž.; Brajković, J.; Feliciello, I.; Ugarković, Đ. -- The Birth-and-Death Evolution of Multigene Families Revisited / Eirín-López, J.M.; Rebordinos, L.; Rooney, A.P.; Rozas, J. -- Chromosomal Distribution and Evolution of Repetitive DNAs in Fish / Cioffi, M.B.; Bertollo, L.A.C..
  • Reporter genes 2007, Springer Protocols
    Methodologies for staining and visualization of [beta]-galactosidase in mouse embryos and tissues / Siobhan Loughna and Deborah Henderson -- Immunohistochemical detection of [beta]-galactosidase or green fluorescent protein on tissue sections / Philip A. Seymour and Maike Sander -- Detection of reporter gene expression in murine airways / Maria Limberis, Peter Bell, and James M. Wilson -- Three-dimensional analysis of molecular signals with episcopic imaging techniques / Wolfgang J. Weninger and Timothy J. Mohun -- Fluorescent proteins for cell biology / George H. Patterson -- Detection of GFP during nervous system development in Drosophila melanogaster / Karin Edoff, James S. Dods, and Andrea H. Brand -- Autofluorescent proteins for flow cytometry / Charles G. Bailey and John E. J. Rasko -- Fluorescent protein reporter systems for single-cell measurements / Steven K. Dower, Eva E. Qwarnstrom, and Endre Kiss-Toth -- Subcellular imaging of cancer cells in live mice / Robert M. Hoffman -- Noninvasive imaging of molecular events with bioluminescent reporter genes in living subjects / Pritha Ray and Sanjiv Sam Gambhir -- Green fluorescent protein as a tracer in chimeric tissues : the power of vapor fixation / Harald Jockusch and Daniel Eberhard.
  • Ch. 1. DT40 gene disruptions: a how-to for the design and the construction of targeting vectors / Hiroshi Arakawa and Jean-Marie Buerstedde -- Ch. 2. Immunoglobulin gene conversion or hypermutation: That's the question / Jean-Marie Buerstedde and Hiroshi Arakawa -- Ch. 3. Genome resources for the DT40 community / Randolph B Caldwell and Andrzej M. Kierzek -- Ch. 4. Chromosome engineering in DT40 cells and mammalian centromere function / William R.A. Brown ... [et al.] -- Ch. 5. Function of recQ family helicase in genome stability / Masayuki Seki, Shusuke Tada and Takemi Enomoto -- Ch. 6. Genetic analysis of apoptotic execution / Sandrine Ruchaud ... [et al.] -- Ch. 7. The DT40 system as a tool for analyzing kinetochore assembly / Masahiro Okada, Tesuya Hori and Tatsuo Fukagawa -- Ch. 8. Analysing the DNA damage and replication checkpoints in DT40 cells / Michael D Rainey, George Zachos, and David AF Gillespie -- Ch. 9. Using DT40 to study clathrin function / Frank R. Wettey and Antony P. Jackson -- Ch. 10. Genetic analysis OF B cell signaling / Hisaaki Shinohara and Tomohiro Kurosaki --Ch. 11. DT40 mutants: a model to study transcriptional regulation of B cell development and function / Jukka Alinikula, Olli Lassila and Kalle-Pekka Nera -- Ch. 12. Transcription and RNA processing factors play complex roles IN DT40 cells / Stephanie Bush and James L. Manley -- Ch. 13. Participation of histones, histone modifying enzymes and histone chaperones in vertebrate cell functions / Hidehiko Kikuchi ... [et al.] -- Ch. 14. Analysis of gene expression, copy number and palindrome formation with a DT40 enriched cDNA Microarray / Paul E. Neima ... [et al.] -- Ch. 15. Analysis of DNA replication damage bypass and its role in immunoglobulin repertoire development / Julian E. Sale, Anna-Laura Ross and Laura J. Simpson -- Ch. 16. The fanconi anemia pathway promotes homologous recombination repair in DT40 cell line / Julian E. Sale, Anna-Laura Ross and Laura J. Simpson -- Ch. 17. Calcium signaling, ion channels and more / Anne-Laure Perraud, Carsten Schmitz, Andrew M. Scharenberg -- Ch. 18. Phenotypic analysis of cellular responses to DNA damage / Helfrid Hochegger and Shunichu Takeda -- Ch. 19. ATM, a paradigm for a stress-responsive signal transducer in higher vertebrate cells / Ken-ichi Yamamoto, Masahiko Kobayashi and Hiroko Shimizu --METHOD 1. Stable transfection of DT40 / Julian E. Sale -- METHOD 2. Basic cell culture conditions / Huseyin Saribasak and Hiroshi Arakawa -- METHOD 3. Excision of floxed-DNA sequences by transient induction of Mer-Cre-Mer / Hiroshi Arakawa -- METHOD 4. Immunoglobulin gene conversion and hypermutation assay by FACS / Hiroshi Arakawa -- METHOD 5. Target screening by PCR / Hiroshi Arakawa -- METHOD 6. Mitotic index determination by flow cytometry / David AF Gillespie and Mark Walker -- METHOD 7. Centrifugal elutriation as a means of cell cycle phase separation and synchronization / David AF Gillespie and Catarina Henriques -- METHOD 8. Preparation of genomic DNA for microarray-based comparative genome hybridization / Robert Kimmel, Amalia Icreverzi, Paul Neiman -- METHOD 9. Analysis of cellular Mg2+ in DT40 cells / Anne-Laure Perraud, Carsten Schmitz, Andrew M. Scharenberg -- METHOD 10. Transient transfection of DT40 / Roger Franklin & Julian E. Sale -- METHOD 11. Retroviral transduction of DT40 / Felix Randow & Julian E. Sale -- METHOD 12. Colony survival assay / Laura. J. Simpson & Julian E. Sale -- METHOD 13. Subcloning DT40 by limiting dilution / Jean-Marie Buerstedde --METHOD 14. Subnuclear immunofluorescence / Dávid Szüts & Julian E. Sale -- METHOD 15. Sister chromatid exchange assay / Laura J. Simpson & Julian E. Sale -- METHOD 16. 2D cell cycle analysis / Roger Franklin & Julian E. Sale -- METHOD 17. Purification of tap-tagged proteins by two-step pull down from DT40 cells / Hiroyuki Kitao and Minoru Takata -- METHOD 18. Synchronization of cells / Eiichiro Sonoda -- METHOD 19. Tranfection of DT40 cells / Huseyin Saribasak and Hiroshi Arakawa -- METHOD 20. Luciferase reporter assay / Frank R. Wettey and Antony P. Jackson -- METHOD 21. Indirect immunofluorescence microscopy / Frank R. Wettey and Antony P. Jackson -- METHOD 22. Quantification of receptor-mediated endocytosis / Frank R. Wettey and Antony P. Jackson -- METHOD 23. Measurement of DNA synthesis and strand breaks using alkaline sucrose density gradient centrifugation / Kouichi Yamada and Jun Takezawa -- METHOD 24. Fractionation of nuclear and cytoplasmic proteins from DT40 cell lines / Yan-Dong Wang and Randolph B Caldwell.
  • Ribozymes and siRNA protocols. 2nd ed. 2004, Springer Protocols
  • RNA 2001, ScienceDirect
  • RNA 2008, Springer Protocols
    The transcriptional landscape -- Working with RNA -- Synthesis of RNA by in vitro transcription -- Efficient poly(A)+ RNA selection using LNA oligo(T) capture -- Genome browsers -- Web-based tools for studying RNA structure and function -- Northern blotting analysis -- Rapid amplification of cDNA ends (RACE) -- Fractionation of mRNA based on the length of the poly(A) tail -- Analysis of mutations that influence pre-mRNA splicing -- S1 nuclease analysis of alternatively spliced mRNA -- Promises and challenges in developing RNAi as a research tool and therapy -- Inhibition of gene function in mammalian cells using short-hairpin RNA (shRNA) -- Validation of RNAi by real time PCR -- Profiling RNA polymerase II using the fast chromatin immunoprecipitation method -- The post-transcriptional operon -- RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray (chip) profiling -- Isolation of RNP granules -- Electrophoretic mobility shift assay for characterizing RNA-protein interaction -- Polysome analysis and RNA purification from sucrose gradients -- Prediction of targets for microRNAs -- Outsourcing of experimental work.
  • Introduction /Michael Levitt --Modeling RNA Molecules /Neocles Leontis and Eric Westhof --Methods for Predicting RNA Secondary Structure /Kornelia Aigner, Fabian Dre€en and Gerhard Steger --Why Can't We Predict RNA Structure At Atomic Resolution? /Parin Sripakdeevong, Kyle Beauchamp and Rhiju Das --Template-Based and Template-Free Modeling of RNA 3D Structure: Inspirations from Protein Structure Modeling /Kristian Rother, Magdalena Rother, Michał Boniecki, Tomasz Puton and Konrad Tomala, et al. --The RNA Folding Problems: Different Levels of sRNA Structure Prediction /Fredrick Sijenyi, Pirro Saro, Zheng Ouyang, Kelly Damm-Ganamet and Marcus Wood, et al. --Computational Prediction and Modeling Aid in the Discovery of a Conformational Switch Controlling Replication and Translation in a Plus-Strand RNA Virus /Wojciech K. Kasprzak and Bruce A. Shapiro --Methods for Building and Refining 3D Models of RNA /Samuel C. Flores, Magdalena Jonikas, Christopher Bruns, Joy P. Ku and Jeanette Schmidt, et al. --Multiscale Modeling of RNA Structure and Dynamics /Feng Ding and Nikolay V. Dokholyan --Statistical Mechanical Modeling of RNA Folding: From Free Energy Landscape to Tertiary Structural Prediction /Song Cao and Shi-Jie Chen --Simulating Dynamics in RNA-Protein Complexes /John Eargle and Zaida Luthey-Schulten --Quantum Chemical Studies of Recurrent Interactions in RNA 3D Motifs /Jiří Šponer, Judit E. Šponer and Neocles B. Leontis --Nonredundant 3D Structure Datasets for RNA Knowledge Extraction and Benchmarking /Neocles B. Leontis and Craig L. Zirbel --Ions in Molecular Dynamics Simulations of RNA Systems /Pascal Auffinger --Modeling RNA Folding Pathways and Intermediates Using Time-Resolved Hydroxyl Radical Footprinting Data /Joshua S. Martin, Paul Mitiguy and Alain Laederach --A Top-Down Approach to Determining Global RNA Structures in Solution Using NMR and Small-Angle X-ray Scattering Measurements /Yun-Xing Wang, Jinbu Wang and Xiaobing Zuo --RNA Structure Determination by Structural Probing and Mass Spectrometry: MS3D /A. E. Hawkins and D. Fabris.
  • RNA editing 2007, ScienceDirect
  • RNA editing 2008, Springer
    Editing reactions from the perspective of RNA structure / Matthias Homann -- Editing of tRNA for structure and function / Juan D. Alfonzo -- RNA editing by adenosine deaminases that act on RNA (ADARs) / Michael F. Jantsch and Marie Öhman -- Insertion/deletion editing in Physarum polycephalum / Jonatha M. Gott and Amy C. Rhee -- RNA editing in plant mitochondria / Mizuki Takenaka ... [et al.] -- RNA editing in chloroplasts / Masahiro Sugiura -- Working together : the RNA editing machinery in Trypanosoma brucei / Jason Carnes and Kenneth Stuart -- RNA editing accessory factors : the example of mHel61p / H. Ulrich Göringer ... [et al.] -- The function of RNA editing in trypanosomes / Torsten Ochsenreiter and Stephen Hajduk -- Evolutionary aspects of RNA editing / Dave Speijer.
  • RNA exosome 2011, Springer
    "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.
  • The RNA infrastructure : an introduction to ncRNA networks / Lesley J. Collins -- RNA interactions / Manja Marz and Peter F. Stadler -- Plant RNA silencing in viral defence / Vitantonio Pantaleo -- Micrornas as post-transcriptional machines and their interplay with cellular networks / Sarath Chandra Janga and Swathi Vallabhaneni -- Spatiotemporal aspects of microRNA-mediated gene regulation / Joris Pothof and Dik C. van Gent -- Spliceosomal RNA infrastructure : the network of splicing components and their regulation by miRNAs / Lesley J. Collins -- Construction, structure, and dynamics of post-transcriptional regulatory network directed by RNA binding proteins / Sarath Chandra Janga and Nitish Mittal -- Safe keeping the message : mRNP complexes tweaking after transcription / Said Hafidh, Věra Čapková, and David Honys -- Unexpected functions of tRNA and tRNA processing enzymes / Rebecca L. Hurto -- Programmed DNA elimination in tetrahymena : a small RNA mediated genome surveillance mechanism / Kensuke Kataoka and Kazufumi Mochizuki -- Long noncoding RNA and epigenomics / Chandrasekhar Kanduri -- Promoter associated long noncoding RNAs repress transcription through a RNA binding protein TLS / Riki Kurokawa -- RNA networks in prokaryotes I :CRISPRs and riboswitches / Patrick J. Biggs and Lesley J. Collins -- RNA networks in prokaryotes II : tRNA processing and small RNAs / Lesley J. Collins and Patrick J. Biggs -- Localization of the bacterial RNA infrastructure / Kenneth C. Keiler -- Small RNA discovery and characterisation in eukaryotes using high throughput approaches / Helio Pais ... [et al.] -- How old are RNA networks? / Toni Daly, X. Sylvia Chen, and David Penny.
  • RNA interference 2005, ScienceDirect
  • The Nobel Prize winning discovery that small interfering RNA can be utilised to control cellular gene expression has propelled the field of RNA interference (RNAi) to the forefront of biomedical science as a potential molecular medicine set to revolutionalise disease treatment. Harnessing the molecular mechanisms of RNAi and development of delivery technologies is crucial for its transformation into a therapeutic modality, this dependency is the focus of "RNA Interference from Biology to Therapeutics" that gives a comprehensive overview of RNAi biology and state-of-the-art delivery methods relevant to clinical translation of RNAi therapeutics. Key players and shapers in the fields of RNAi and delivery science have been assembled in a single volume to produce a truly unique interdisciplinary text, making it a "must-read" for both students and experts in, and at the interface of, RNAi, pharmaceutical science and medicine. An attractive feature is the "future perspectives" section within each chapter that allows global leaders the opportunity to express their views on the direction the field is moving. Topics covered in the book include miRNA biology and therapeutic exploitation, exosome delivery and clinical translation."RNA Interference from Biology to Therapeutics" is an up-to-the-minute, highly informative and invaluable text for those actively involved or interested in this fascinating and high-impact field.
  • RNA interference technology 2005, MyiLibrary
    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.
  • 1. RNA polymerases and transcription factors of trypanosomes / Arthur Günzl -- 2. SL RNA biogenesis in kinetoplastids: a long and winding road / Nancy R. Sturm, Jesse R. Zamudio, and David A. Campbell -- 3. Pre-mRNA splicing in trypanosoma brucei: factors, mechanisms, and regulation / Christian Preusser, Nicolas Jaé, Arthur Günzl, and Albrecht Bindereif -- 4. mRNA turnover in trypanosomes / Christine Clayton -- 5. tRNA biogenesis and processing / Jessica L. Spears, Mary Anne T. Rubio, Paul J. Sample, and Juan D. Alfonzo -- 6. rRNA biogensis in trypanosomes / Shulamit Michaeli -- 7. RNA editing in African trypanosomes: a U-ser's G-U-ide / H. Ulrich Göringer -- 8. The RNA interference pathway in trypanosoma brucei / Elisabetta Ullu, Nikolay G. Kolev, Rebecca L. Barnes, and Christian Tschudi -- 9. Translation in trypanosomatids -- 10. Mitochondrial translation in trypanosomatids / Dmitri A. Maslov and Rajendra K. Agrawal -- 11. RNA-Seq analysis of the transcriptome of trypanosoma brucei / Jan Mani, Kapila Gunasekera, and Isabel Roditi.
  • RNA methodologies. 4th ed. 2010, ScienceDirect
    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 modification 2007, ScienceDirect
  • pt. D ScienceDirect
  • RNA silencing 2005, Springer Protocols
    Detection of microRNAs and assays to monitor microRNA activities in vivo and in vitro / Marianthi Kiriakidou ... [et al.] -- High-throughput analysis of microRNA gene expression using sensitive probes / Mouldy Sioud and Øystein Røsok -- Modification of human U1 snRNA for inhibition of gene expression at the level of pre-mRNA / Peng Liu ... [et al.].Identification of components of RNAi pathways using the tandem affinity purification method / Mikiko C. Siomi and Haruhiko Siomi -- Separation of Drosophila RNA silencing complexes by native gel electrophoresis / John W. Pham and Erik J. Sontheimer -- Preparation and analysis of drosha / Yoontae Lee and V. Narry Kim -- RNA interference in Caenorhabditis elegans / Nathaniel R. Dudley and Bob Goldstein -- Down-regulating gene expression by RNA interference in Trypanosoma brucei / Christine E. Clayton ... [et al.] -- Analysis of double-stranded RNA and small RNAs involved in RNA-mediated transcriptional gene silencing / M. Florian Mette ... [et al.] -- Strategies for the design of random siRNA libraries and the selection of anti-GFP siRNAs / Mouldy Sioud and Sébastien Wälchli -- Silencing gene expression with dicer-generated siRNA pools / Jason W. Myers and James E. Ferrell Jr. --Inhibition of gene expression in vivo using multiplex siRNA / Sung-Suk Chae and Timothy Hla -- Gene silencing by a DNA vector based RNAi technology / Guangchao Sui and Yang Shi -- Plasmid-based RNA interference: construction of small-hairpin RNA expression vectors / Scott Q. Harper and Beverly L. Davidson -- SiRNA delivery in vivo / Mouldy Sioud -- Peptide-based strategy for siRNA delivery into mammalian cells / Federica Simeoni ... [et al.] -- Lentiviral vector delivery of siRNA and shRNA encoding genes into cultured and primary hematopoietic cells / Mingjie Li and John J. Rossi -- Exon-specific RNA interference: a tool to determine the functional relevance of proteins encoded by alternatively spliced mRNAs / Alicia M. Celotto, Joo-Won Lee, and Brenton R. Graveley -- Immunoprecipitation of microRNPs and directional cloning of microRNAs / Elisavet Maniataki, Maria Dels Angels De Planell Saguer, and Zissimos Mourelatos --
  • The key features of RNA silencing / Kuniaki Saito ... [et al.] -- Selected strategies for the delivery of siRNA in vitro and in vivo / Sandra D. Laufer ... [et al.] -- RNAi suppression and its application / Xiaoping Yi, Rui Lu -- Strategies to prevent siRNA-triggered cellular toxicity / Matthias Bauer -- RNAi in malignant brain tumors: relevance to molecular and translational research / Mitsutoshi Nakada ... [et al.] -- Silencing Huntington's disease gene with RNAi / Yu Zhang, Robert M. Friedlander -- Application of Dicer-substrate siRNA in pain research / Philippe Sarret ... [et al.] -- RNAi treatment of HIV-1 infection / Karin J. von Eije, Ben Berkhout -- Application of RNA interference to treat conditions associated with dysregulation of transient receptor potential vanilloid 1 channel / Vickram Ramkumar ... [et al.] -- Harnessing RNAi-based functional genomics to unravel the molecular complexity underlying skin pigment variation / Hsiang Ho ... [et al.] --mRNA structure and its effects on posttranscriptional gene silencing / Stephen I. Rudnick, Veenu Aishwarya, Alan M. Gewirtz -- Antisense RNA-mediated regulation of the p53 tumor suppressor / Marianne Farnebo, Klas G. Wiman -- Antisense oligonucleotides: insights from preclinical studies and clinical trials / Doreen Kunze, Kai Kraemer, Susanne Fuessel -- What can the new hammerhead ribozyme structures teach us about design? / William G. Scott -- microRNA biogenesis and its impact on RNA interference / Stefanie Grund, Sven Diederichs -- MicroRNAs in epithelial antimicrobial immunity / Jun Liu ... [et al.] -- Emerging roles of long noncoding RNAs in gene expression and intracellular organization / Tetsuro Hirose -- Noncoding RNAs as therapeutic targets / Maciej Szymański, Jan Barciszewski -- Noncoding RNAs at H19/IGF2 locus: role in imprinting, gene expression, and associated pathologies / Nahalie Berteaux, Nathalie Spruyt, Eric Adriaenssens.
  • RNA turnover in eukaryotes 2008, ScienceDirect
  • RNAi 2008, Springer Protocols
  • Root genomics 2011, Springer
    With the predicted increase of the human population and the subsequent need for larger food supplies, root health in crop plants could play a major role in providing sustainable highly productive crops that can cope with global climate changes. While the essentiality of roots and their relation to plant performance is broadly recognized, less is known about their role in plant growth and development. "Root Genomics" examines how various new genomic technologies are rapidly being applied to the study of roots, including high-throughput sequencing and genotyping, Tilling, transcription.
  • RT-PCR protocols 2002, Springer Protocols
  • Sequence comparison 2009, Springer
  • SAGE and LongSAGE / Annabeth Laursen Høgh and Kåre Lehmann Nielsen -- Robust-LongSAGE (RL-SAGE) : an improved LongSAGE method for high-throughput transcriptome analysis / Malali Gowda and Guo-Liang Wang -- aRNA LongSAGE : SAGE with antisense RNA / Anna M. Heidenblut -- SuperSAGE / Hideo Matsumura ... [et al.] -- Low-cost-medium throughput Sanger dideoxy sequencing / Kåre Lehmann Nielsen -- DeepSAGE : higher sensitivity and multiplexing of samples using a simpler experimental protocol / Kåre Lehmann Nielsen -- High-resolution, genome-wide mapping of chromatin modifications by GMAT / Tae-Young Roh and Keji Zhao -- 5'- and 3'-RACEfrom LongSAGE tags / Kåre Lehmann Nielsen -- Extraction and annotation of SAGE tags using sequence quality values / Jeppe Emmersen -- Correction of technology-related artifacts in serial analysis of gene expression / Viatcheslav R. Akmaev -- Duplicate ditag analysis in LongSAGE / Jeppe Emmersen -- Statistical comparison of two or more SAGE libraries : one tag at a time / Gerben J. Schaaf ... [et al.] -- Scaling of gene expression data allowing the comparison of different gene expression platforms / Fred van Ruissen ... [et al.] -- Clustering analysis of SAGE transcription profiles using a Poisson approach / Haiyan Huang, Li Cai, and Wing H. Wong -- Identifying nonspecific SAGE tags by context of gene expression / Xijin Ge and San Ming Wang.
  • Single cell diagnostics 2007, Springer Protocols
    Noninvasive metabolic assessment of single cells / David K. Gardner -- Laser capture microdissection for analysis of single cells / Nobuki Nakamura ... [et al.] -- Fluorescence in situ hybridization (FISH) on single cells (sex determination and chromosome rearrangements) / Paul N. Scriven and Caroline Mackie Ogilvie -- Single cell PCR for PGD : methods, strategies, and limitations / Karen Sermon and Martine De Rycke -- Real-time quantitative PCR measurement of male fetal DNA in maternal plasma / Bernhard Zimmermann ... [et al.] -- Cell-free fetal DNA plasma extraction and real-time PCR quantification / Jill L. Maron, Kirby L. Johnson, and Diana W. Bianchi -- LATE-PCR and allied technologies : real-time detection strategies for rapid, reliable diagnosis from single cells / Kenneth E. Pierce and Lawrence J. Wangh -- Efficient isothermal amplification of the entire genome from single cells / Karen V. Schowalter, Jolene R. Fredrickson, and Alan R Thornhill -- Comparative genomic hybridization on single cells / Lucille Voullaire and Leeanda Wilton -- Generation of amplified RNAs and cDNA libraries from single mammalian cells / James Adjaye -- Real-time PCR to measure gene expression in single cells / Dagan Wells -- Gender determination and detection of aneuploidy in single cells using DNA array-based comparative genomic hybridization (array CGH) / Dong Gui Hui, Xin Yuan Guan, and Nicole Hussey -- Microarray technology for mutation analysis of low template DNA samples / Chelsea Salvado and David Cram.
  • Single nucleotide polymorphisms 2002, Springer Protocols
  • Small RNAs 2006, Springer
  • Nuclear remodeling and nuclear reprogramming for making transgenic pigs by nuclear transfer / Randall S. Prather -- Somatic cell nuclei in cloning : strangers traveling in a foreign land / Keith E. Latham, Shaorong Gao, and Zhiming Han -- Cloning cattle : the methods in the madness / Bjørn Oback and David N. Wells -- Centrosome inheritance after fertilization and nuclear transfer in mammals / Qing-Yuan Sun and Heide Schatten -- Developmental, behavioral, and physiological phenotype of cloned mice / Kellie L.K. Tamashiro ... [et al.] -- Nucleolar remodeling in nuclear transfer embryos / Jozef Laurincik and Poul Maddox-Hyttel -- Somatic cell nuclear transfer (SCNT) in mammals : the cytoplast and its reprogramming activities / Josef Fulka, Jr. and Helena Fulka -- Mitochondrial DNA inheritance after SCNT / Stefan Hiendleder -- Activation of fertilized and nuclear transfer eggs / Christopher Malcuit and Rafael A. Fissore.
  • 1. Stress-induced mutagenesis in bacteria / Ivan Matic -- 2. Mutagenesis associated with repair of DNA double-strand breaks under stress / Chandan Shee, P.J. Hastings, and Suman M. Rosenberg -- 3. Transcription-mediated mutagenic processes / Eduardo Robleto, Holly A. Martin, Carmen Vallin, Mario Pedraza-Reyes and Ronald Yasbin -- 4. Transposon mutagenesis in disease, drug discovery, and bacterial evolution / Zhongge Zhang, Jing Wang, Maksim A. Shlykov, and Milton H. Saier, Jr. -- 5. Hsp90 as a capacitor of both genetic and epigenetic changes in the genome during cancer progression and evolution / Xiangyi Lu, Luan Wang, Vincent E. Sollars, Mark D. Garfinkel, and Douglas M. Ruden -- 6. Inheritance of stress-induced epigenetic changes mediated by the ATF-2 family of transcription factors / Ki-Hyeon Seong, Toshio Maekawa and Shunsuke Ishii -- 7. Microsatellite repeats: canaries in the coalmine / Nimrat Chatterjee, Beatriz A. Santillan and John H. Wilson -- 8. Genetic instability induced by hypoxic stress / Susan E. Scanlon and Peter M. Glazer -- 9. Radiation-induced delayed genome instability and hypermutation in mammalian cells / Christopher P. Allen, Akira Fujimori, Ryuichi Okayasu and Jac A. Nickoloff -- 10. Radiation-induced bystander effects and stress-induced mutagenesis / Carmel Mothersill and Colin Seymour -- 11. Stress induced mutagenesis, genetic diversification, and cell survival via anastais, the reversal of late stage apoptosis / Ho Lam Tang, Ho Man Tang and Denise J. Mitchell -- 12. The transgenerational effects of parental exposure to mutagens in mammals / Yuri E. Dubrova -- 13. Revisiting mutagenesis in the age of High-throughput sequencing / Subhajyoti De and R. Matthew Ward.
  • Stroke genomics 2005, Springer Protocols
    Introduction to stroke genomics / Simon J. Read and Frank C. Barone -- Choice, methodology, and characterization of focal ischemic stroke models: the search for clinical relevance / David Virley -- Mutant animal models of stroke and gene expression: the stroke-prone spontaneously hypertensive rat / Hilary V. O. Carswell ... [et al.] -- Gene therapy in neurological disease / Midori A. Yenari and Robert M. Sapolsky -- Stem cell transplantation after middle cerebral artery occlusion / Paul Stroemer and Helen Hodges -- Endogenous brain protection: models, gene expression, and mechanisms / Frank C. Barone -- Production of transgenic and mutant mouse models / Alex Harper --3-nitropropionic acid model of metabolic stress: assessment by magnetic resonance imaging / Toby John Roberts -- Practicalities of genetic studies in human stroke / Ahamad Hassan and Hugh S. Markus -- Evaluation of the interactions of common genetic mutations in stroke / Zoltán Szolnoki -- Technologies of disease-related gene discovery using preclinical models of stroke / Xinkang Wang -- Quantitative analysis of gene transcription in stroke models using real-time RT-PCR / David C. Harrison and Brian C. Bond -- Effective analysis of genomic data / Paul R. Nelson, Andrew B. Goulter, and Richard J. Davis -- Bioinformatic approaches to assigning protein function from novel sequence data / David Michalovich and Richard Fagan -- Pragmatic target discovery from novel gene to functionally defined drug target: the interleukin-1 story / Stuart McRae Allen.
  • 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.
  • Bioinformatics in membrane protein analysis / Bengt Persson -- Prokaryotic membrane transport proteins / Joanne Clough ... [et al.] -- Membrane protein production strategies for structural genomics / Said Eshaghi and Par Nordlund -- Refolding of membrane proteins for large-scale production / Hans Kiefer, Thomas Ostermann, Monika Bahner -- Crystallization of membrane proteins / Alastair T. Gardiner, June Southall, and Richard J. Cogdell -- Signaling through membrane proteins / J. Robert Bostwick and Deborah S. Hartman -- Expression of membrane proteins in yeasts / Christoph Reinhart, Christoph Krettler -- Expression of functional membrane proteins in the baculovirus-insect cell system / Giel J.C.G.M. Bosman and Willem J. de Grip -- Expression of membrane proteins in mammalian cells / Kenneth Lundstrom -- Solubilization and purification of membrane proteins / Bernadette Byrne and Mika Jormakka -- Fluorescent labelling of membrane proteins in living cells / Ruud Hovius ... [et al.] -- Membrane protein NMR / Xiang-Qun (Sean) Xie -- Miniaturization of structural biology technologies--from expression to biophysical analyses / Enrique Abola, Peter Kuhn, and Raymond C. Stevens -- Electron microscopy and atomic force microscopy of reconstituted membrane proteins / Andreas Engel -- -- Structural genomics networks for membrane proteins / Kenneth Lundstrom -- Molecular modelling of membrane proteins / Slawomir Filipek and Anna Modzelewska -- Towards structural bases for GPCR ligand-binding / Sabrina A. Beretta ... [et al.].
  • Surrogate tissue analysis 2006, CRCnetBASE
  • "Understanding the genetic architecture underlying complex multigene disorders is one of the major goals of human genetics in the upcoming decades. Advances in whole genome sequencing and the success of high throughput functional genomics allow supplementing conventional reductionist biology with systems-level approaches to human heredity and health as systems of interacting genetic, epigenetic, and environmental factors. This integrative approach holds the promise of unveiling yet unexplored levels of molecular organization and biological complexity. It may also hold the key to deciphering the multigene patterns of disease inheritance"--Publisher's description.
  • Macrophage pattern recognition receptors in immunity, homeostasis, and self tolerance / Subhankar Mukhopadhyay, Annette Plüddemann, and Siamon Gordon -- Pattern recognition by toll-like receptors / Stefan Bauer, Thomas Müller, and Svetlana Hamm -- Nod-like receptors : pivotal guardians of the immunological integrity of barrier organs / Philip Rosenstiel and Stefan Schreiber -- Toll-like receptors and nod-like receptors : domain architecture and cellular signalling / Tanja Langefeld ... [et al.] -- Humoral pattern recognition molecules : mannan-binding lectin and ficolins / Steffen Thiel and Mihaela Gadjeva --Lung surfactant proteins A and D as pattern recognition proteins / Patrick Waters ... [et al.] -- Pattern recognition by pentraxins / Alok Agrawal ... [et al.] -- Target pattern recognition by complement proteins of the classical and alternative pathways / Yu-hoi Kang ... [et al.] -- Pattern recognition in phagocytic clearance of altered self / Yoshinobu Nakanishi, Peter M. Henson and Akiko Shiratsuchi -- Structural basis of pattern recognition by innate immune molecules / Eamon P. McGreal -- Lessons from the fly : pattern recognition in Drosophila melanogaster / Subhamoy Pal and Louisa P. Wu -- Immune recognition of plasmodium-infected erythrocytes / Damien V. Cordery and Britta C. Urban -- Innate immune recognition in tuberculosis infection / Anthony G. Tsolaki.
  • Basics of Personalized Medicine -- Molecular Diagnostics as Basis of Personalized Medicine -- Role of Biomarkers in Personalized Medicine -- Pharmacogenetics -- Pharmacogenomics -- Role of Pharmacoproteomics -- Role of Metabolomics in Personalized Medicine -- Personalized Biological Therapies -- Development of Personalized Medicine -- Personalized Therapy for Cancer -- Personalized Management of Neurological Disorders -- Personalized Therapy of Cardiovascular Diseases -- Personalized Management of Miscellaneous Disorders -- Personalized Preventive Medicine -- Organization of Personalized Medicine -- Ethical and Regulatory Aspects of Personalized Medicine -- Economics of Personalized Medicine -- Future of Personalized Medicine.
  • The thymus is an evolutionarily ancient primary lymphoid organ common to all vertebrates in which T cell development takes place. Failing thymus function is associated with immunodeficiency and/or autoimmunity. In this volume, leading experts provide a comprehensive overview of recent advances in thymopoiesis research. The chapters cover the development of the thymic epithelial microenvironment, address the formation of a diverse and self-tolerant repertoire of T cell receptors as the basis for cellular immunity, discuss the mechanisms by which progenitor cells colonize the thymus and detail the molecular basis for T lineage decisions. The reviews illustrate the important role of the multifaceted process of thymopoiesis for adaptive immunity.
  • Introduction: strategies for developing genetically modified mice / Marten H. Hofker -- Genetic modification of the mouse: general technology - pronuclear and blastocyst injection / Jan Willem Voncken -- Generation of chimeras by aggregation of embryonic stem cells with diploid or tetraploid mouse embryos / Jérôme Artus and Anna-Katerina Hadjantonakis -- Cryopreservation of mouse spermatozoa and in vitro fertilization / Naomi Nakagata -- Autopsy and histological analysis of the transgenic mouse / Marion J.J. Gijbels and Menno P.J. de Winther -- Transgene design / Bart van de Sluis and Jan Willem Voncken -- Inducible transgenic mouse models / Thomas L. Saunders -- Lentiviral transgenesis / Terunaga Nakagawa and Casper C. Hoogenraad -- Transgenesis in mouse embryonic stem cells / Janine van Ree, Wei Zhou, Ming Li, and Jan M. van Deursen -- Engineering BAC reporter gene constructs for mouse transgenesis / Yu Fu and Peter Maye -- Targeting vector construction through recombineering / Liviu A. Malureanu -- Generating conditional knockout mice / Roland H. Friedel, Wolfgang Wurst, Benedikt Wefers, and Ralf Kühm -- Hypomorphic mice / Darren J. Baker -- MICER targeting vectors for manipulating the mouse genome / Chunbong Liu, Paul F. Szurek, and Y. Eugene Yu -- Knock-in approaches / Anton J.M. Roebroek, Philip L.S.M. Gordts, and Sara Reekmans -- Generation of a series of knock-in alleles using RMCE in ES cells / Anton J.M. Roebroek, Philip L.S.M. Gordts, and Sara Reekmans -- Selection of targeting mutants from a library of randomly mutagenized ES cells / Kyoji Horie, George Gaitanaris, and Alexander Gragerov -- Generation of genetically modified rodents using random ENU mutagenesis / Ruben van Boxtel and Edwin Cuppen -- Bone marrow transplantations of study gene function in hematopoietic cells / Menno P.J. de Winther and Peter Heeringa -- Adenovirus-mediated gene transfer / Ko Willems van Dijk, Kyriakos E. Kyreos, Frits J. Fallaux, and Jurre Hageman.
  • Transgenic plants 2004, Springer Protocols
  • Transgenic wheat, barley and oats 2009, Springer Protocols
    Transgenic wheat, barley and oats : production and characterization / Paul A. Lazzeri and Huw D. Jones -- Selection of transformed plants / Huw D. Jones and Caroline A. Sparks -- Reporter genes / Alison Huttly -- Biolistics transformation of wheat / Caroline A. Sparks and Huw D. Jones -- Agrobacterium-mediated transformation of bread and durum wheat using freshly isolated immature embryos / Huixia Wu, Angela Doherty and Huw D. Jones -- Floral transformation of wheat / Sujata Agarwal ... [et al.] -- Highly efficient agrobacterium-mediated transformation of wheat via in planta inoculation / Thierry Risacher ... [et al.] -- Barley transformation using biolistic techniques / Wendy A. Harwood and Mark A. Smedley -- Barley transformation using agrobacterium-mediated techniques / Wendy A. Harwood ... [et al.] -- Transformation of oats and its application to improving osmotic stress tolerance / Shahina B. Maqbool ... [et al.] -- Promoter sequences for defining transgene expression / Huw D. Jones and Caroline A. Sparks -- Down-regulation of gene expression by RNA-induced gene silencing / Silvia Travella and Beat Keller -- Gene insertion patterns and sites / Philippe Vain and Vera Thole -- Fluorescent in situ hybridization to detect transgene integration into plant genomes / Trude Schwarzacher -- Establishing substantial equivalence : transcriptomics / María Marcela Baudo ... [et al.] -- Establishing substantial equivalence : proteomics / Alison Lovegrove, Louise Salt, and Peter R. Shewry -- Establishing substantial equivalence : metabolomics / Michael H. Beale, Jane L. Ward, and John M. Baker -- Design and management of field trials of transgenic cereals / Zoltán Bedő, Mariann Rakszegi, and László Láng -- GM risk assessment / Penny A.C. Sparrow -- Transgenic wheat, barley and oats : future prospects / Jim M. Dunwell.
  • Translation initiation 2007, ScienceDirect
    Transient kinetics, flourescence, and FRET in studies of initiation and translation in bacteria / Pohl Milon ... [et al.] -- Binding of mRNA to the bacterial translation initiation complex / Sean M. Studer and Simpson Joseph -- Real-time dynamics of ribosome-ligand interaction by time-resolved chemical probing methods / Attilio Fabbretti ... [et al] -- Overexpression and purification of mammalian mitochondrial translational initiation factor 2 and initiation factor 3 / Domenick G. Grasso ... [et al.] -- In vitro studies of archaeal translational initiation / Dario Benelli and Paola Londei -- Reconstitution of yeast translation initiation / Michael G. Acker ... [et al.] -- Assembly and analysis of eukaryotic translation initiation complexes / Andrey V. Pisarev -- Reconstitution of mammalian 48S ribosomal translation initiation complex / Romit Majumdar, Jayanta Chaudhuri, and Umadas Maitra -- Biophysical approach to studies of Cap-elF4E interaction by synthetic cap analogs / Anna Niedzwiecka ... [et al.] -- Biophysical studies of the translation initiation pathway with immobilized mRNA analogs / John E. G. McCarthy, Steven Marsden, and Tobias von der Haar -- Protection-based assays to measure aminoacyl-tRNA binding to translation initiation factors / Yves Mechulam ... [et al.] -- NMR methods for studying protein-protein interactions involved in translation initiation / Assen Marintchev, Dominique Frueh, and Gerhard Wagner -- Structural methods for studying IRES function / Jeffrey S. Kieft ... [et al.].
  • Translation initiation 2007, ScienceDirect
    Purification of FLAG-tagged eukaryotic initation factor 2B complexes, subcomplexes, and fragments from Saccharomyces cerevisiae / Sarah S. Mohammad-Qureshi ... [et al.] -- In vivo deletion analysis of the architecture of a multiprotein complex of translation initiation factors / Klaus H. Nielsen and Leos̆ Valás̆ek -- An approach to studying the localization and dynamics of eukaryotic translation factors in live yeast cells / Susan G. Campbell and Mark P. Ashe -- In vitro and tissue culture methods for analysis of translation initiation on the endoplasmic reticulum / Samuel B. Stephens and Christopher V. Nicchitta -- Mammalian stress granules and processing bodies / Nancy Kedersha and Paul Anderson -- Methods to analyze micro-RNA-mediated control of mRNA translation / Jennifer L. Clancy ... [et al.] -- Methods for studying signal-dependent regulation of translation factor activity / Xuemin Wang and Christopher G. Proud -- Analysis of mRNA translation in cultured hippocampal neurons / Yi-Shuian Huang and Joel D. Richter -- Detecting ribosomal association with the 5' leader of mRNAs by ribosome density mapping (RDM) / Naama Eldad and Yoav Arava -- Genome-wide analysis of mRNA polysomal profiles with spotted DNA microarrays / Danial Melamed and Yoad Arava -- Synthesis of anti-reverse cap analogs (ARCAs) and their applications in mRNA translation and stability / Ewa Grudzien-Nogalska ... [et al.] -- Methods for identifying compounds that specifically target translation / Letizia Brandi ... [et al.] -- Identifying small molecule inhibitors of eukaryotic translation initiation / Regina Cencic, Francis Robert, and Jerry Pelletier -- Isolation and identification of eukaryotic initiation factor 4A as a molecular target for the marine natural product pateamine A / Woon-Kai Low ... [et al.].
  • Translation initiation 2007, ScienceDirect
    Use of reticulocyte lysates for mechanistic studies of eukaryotic translation initiation / William C. Merrick and Diane Barth-Baus -- Studying translational control in Drosophila cell-free systems / Fátima Gebauer and Matthias W. Hentze -- Use of in vitro translation extract depleted in specific initiation factors for the investigation of translational regulation / Daniel R. Gallie -- A highly efficient and robust in vitro translation system for expression of picornavirus and hepatitis C virus in RNA genomes / Yuri V. Svitkin and Nahum Sonenberg -- A practical approach to isolate 48S complexes : affinity purification and analyses / Nicolas Locker and Peter J. Lukavsky -- Yeast phenotypic assays on translational control / Bumjun Lee ... [et al.] -- Localization and characterization of protein-protein interaction sites / Chingakham Ranjit Singh and Katsura Asano -- In vivo stabilization of preinitiation complexes by formaldehyde cross-linking / Leos Valás̆ek ... [et al.] -- Molecular genetic structure-function analysis of translation initiation factor elF5B / Byung-Sik Shin and Thomas E. Dever -- The use of fungal in vitro systems for studying translational regulation / Cheng Wu ... [et al.] -- Investigating translation initiation using drosophila molecular genetics / Gritta Tettweiler and Paul Lasko -- Analysis of RNA:protein interactions in vivo : identification of RNA-binding partners of nuclear factor 90 / Andrew M. Parrott, Melissa R. Walsh, and Michael B. Mathews -- Approaches for analyzing the differential activities and functions of elF4E family members / Robert E. Rhoads, Tzvetanka D. Dinkova, and Rosemary Jagus -- Tethered function assays : an adaptable approach to study RNA regulatory proteins / Jeff Coller and Marv Wickens -- Analysis of ribosomal shunting during translation initiation in eukaryotic mRNAs / Vincent P. Mauro, Stephen A. Chappell and John Dresios.
  • Lifestyle and Medical Approaches to Cancer Prevention / Peter Greenwald, p. 1-15 -- Application of Genetics to the Prevention of Colorectal Cancer / John Hopper, p. 17-33 -- Genetics and Prevention of Oesophageal Adenocarcinoma / Rebecca Fitzgerald, p. 35-46 -- Preclinical Models Relevant to Diet, Exercise, and Cancer Risk R. James Barnard and William Aronson, p. 47-62 -- Individualizing Interventions for Cancer Prevention / Michael Pollak, p. 63-70 -- Can Animal Models Help Us Select Specific Compounds for Cancer Prevention Trials? / Ernest Hawk, Asad Umar, Ronald Lubet, Levy Kopelovich and Jaye Viner, p. 71-88 -- Problems with Using Biomarkers as Surrogate End Points for Cancer: A Cautionary Tale / Arthur Schatzkin, p. 89-98 -- Can a Marker Be a Surrogate for Development of Cancer, and Would We Know It if It Exists? / William Armstrong, Thomas Taylor and Frank Meyskens, p. 99-112 -- How Should We Move the Field of Chemopreventive Agent Development Forward in a Productive Manner? / Frank Meyskens and Eva Szabo, p. 113-124 -- The Problems with Risk Selection; Scientific and Psychosocial Aspects / Anne-Renée Hartman, p. 125-144 -- Chemoprevention of Lung Cancer / Stéphane Vignot, Jean-Philippe Spano, Sylvie Lantuejoul, Fabrice André, Thierry Le Chevalier and Jean-Charles Soria, p. 145-165 -- Anti-nicotine Vaccination: Where Are We? / T. Cerny, p. 167-175 -- Primary Prevention of Colorectal Cancer: Lifestyle, Nutrition, Exercise / María Martínez, p. 177-211 -- Chemoprevention of Colorectal Cancer: Ready for Routine Use? / Nadir Arber and Bernard Levin, p. 213-230 -- Screening of Colorectal Cancer: Progress and Problems Sidney Winawer, p. 231-244 -- The Role of Endogenous Hormones in the Etiology and Prevention of Breast Cancer: The Epidemiological Evidence / Paola Muti, p. 245-256 -- Innovative Agents in Cancer Prevention / Margaret Manson, Peter Farmer, Andreas Gescher and William Steward, p. 257-275 -- The IARC Commitment to Cancer Prevention: The Example of Papillomavirus and Cervical Cancer / Silvia Franceschi, p. 277-297 -- Health Economics in the Genomic Age / Thomas Szucs, p. 299-313 -- Screening for Cancer: Are Resources Being Used Wisely? / Robert Kaplan, p. 315-334.
  • Understanding DNA. 3rd ed. 2004, ScienceDirect
    An introduction to molecular biology for non-scientiest -- Why a helix? -- Different kinds of double helix -- Twisting and curving -- Curving in three dimensions -- DNA supercoiling -- The assembly of DNA into chromosomes -- Specific DNA-protein interactions -- Methods used to study the structure of DNA -- DNA in disease, diagnostics, and medicine -- Cytosine methylation and DNA epigenetics.
  • V(D)J recombination 2009, Springer
    Early steps of V(D)J rearrangement : insights from biochemical studies of RAG-RSS complexes / Patrick C. Swanson, Sushil Kumar, and Prafulla Raval -- Regulation of RAG transposition / Adam G.W. Matthews and Marjorie A. Oettinger -- Recent insights into the formation of RAG-induced chromosomal translocations / Vicky L. Brandt and David B. Roth -- V(D)J recombination deficiencies / Jean-Pierre de Villartay -- Large-scale chromatin remodeling at the immunoglobulin heavy chain locus : a paradigm for multigene regulation / Daniel J. Bolland, Andrew L. Wood, and Anne E. Corcoran -- Genetic and epigenetic control of V gene rearrangement frequency / Ann J. Feeney -- Dynamic aspects of TCRa gene recombination : qualitative and quantitative assessments of the TCRa chain repertoire in man and mouse / Evelyne Jouvin-Marche, Patrizia Fuschiotti, and Patrice Noël Marche -- Germline transcription : a key regulator of accessibility and recombination / Iratxe Abarrategui and Michael S. Krangel --Dynamic regulation of antigen receptor gene assembly / Lance R. Thomas, Robin Milley Cobb, and Eugene M. Oltz -- Molecular genetics at the T-cell receptor b locus : insights into the regulation of V(D)J recombination / Marie Bonnet, Pierre Ferrier, and Salvatore Spicuglia -- Molecular pathways and mechanisms regulating the recombination of immunoglobulin genes during B-lymphocyte development / Kristen Johnson, Karen L. Reddy, and Harinder Singh -- Regulation of V(D)J recombinationby E-protein transcription factors / Mary Elizabeth Jones and Yuan Zhuang -- Temporal and spatial regulation of V(D)J recombination : interactions of extrinsic factors with the RAG complex / Yun Liu, Li Zhang, and Stephen Desiderio -- V(D)J recombination : of mice and sharks / Ellen Hsu -- Normal and pathological V(D)J recombination : contribution to the understanding of human lymphoid malignancies / Saïda Dadi ... [et al.].
  • Variation 2005, ScienceDirect
    Variation and variability : central concepts in biology / Benedikt Hallgrímsson and Brian K. Hall -- Variation from Darwin to the modern synthesis / Peter J. Bowler -- The statistics of variation / Leigh Van Valen -- Landmark morphometrics and the analysis of variation / Joan T. Richtsmeier, Subhash R. Lele, and Theodore M. Cole III -- Variation in ontogeny / Donna Carlson Jones and Rebecca Z. German -- Constraints on variation from genotype through phenotype to fitness / Lauren Ancel Meyers -- Developmental origins of variation / Ellen Larsen -- Canalization, cryptic variation, and developmental buffering : a critical examination and analytical perspective / Ian Dworkin -- Mutation and phenotypic variation : where is the connection? : capacitators, stressors, phenotypic variability, and evolutionary change / Ary A. Hoffmann and John A. McKenzie -- Within individual variation : developmental noise versus developmental stability / Katherine E. Willmore and Benedikt Hallgrímsson -- Developmental constraints, modules, and evolvability / Christian Peter Klingenberg -- Developmental regulation of variability / Miriam Leah Zelditch -- Role of stress in evolution : from individual adaptability to evolutionary adaptation / Alexander V. Badyaev -- Environmentally contingent variation : phenotypic plasticity and norms of reaction / Sonia E. Sultan and Stephen C. Stearns -- Variation and life-history evolution / Derek A. Roff -- Antisymmetry / A. Richard Palmer -- Variation in structure and its relationship to function : correlation, explanation, and extrapolation / Anthony P. Russell and Aaron M. Bauer -- A universal generative tendency toward increased organismal complexity / Daniel W. McShea -- Variation and versatility in macroevolution / V. Louise Roth -- Variation and developmental biology : prospects for the future / David M. Parichy -- Phenogenetics : genotypes, phenotypes, and variation / Samuel Sholtis and Kenneth M. Weiss -- The study of phenotypic variability : an emerging research agenda for understanding the developmental-genetic architecture underlying phenotypic variation / Benedikt Halgrímsson, Jevon James Yardley Brown, and Brian K. Hall.
  • Vertebrate genomes 2006., Karger
    The human genome and its upcoming dynamics / M. Platzer -- Primate genomes / H. Herlyn, H. Zischler -- The mouse genome / S.D.M. Brown, J.M. Hancock -- The dog genome / F. Galibert, C. André -- The feline genome / W.J. Murphy -- The bovine genome / J.E. Womack -- The sheep genome / N.E. Cockett -- Cracking the genomic piggy bank : identifying secrets of the pig genome / B.E. Mote, M.F. Rothschild -- The horse genome / B.P. Chowdhary, T. Raudsepp -- Marsupial and monotreme genomes / E. Koina, J. Fong, J.A. Marshall Graves -- The chicken genome / D.W. Burt -- Insights from Xenopus genomes / N. Pollet, A. Mazabraud -- The Tetraodon genome / H. Roest Crollius -- The medaka genome : why we need multiple fish models in vertebrate functional genomics / H. Mitani ... [et al.] -- The zebrafish genome : a review and msx gene case study / J.H. Postlethwait -- Urochordate genomes / N. Satoh ... [et al.].
  • Viruses 2012, Springer
    "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 NCBI 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. 2006, Springer Protocols
    Markers, selection, and media in yeast artificial chromosomes cloning / David Markie -- Construction of yeast artificial chromosome libraries from pathogens and nonmodel organisms / Cecilia P. Sanchez and Michael Lanzer -- Analysis and screening of yeast artificial chromosome libraries by filter hybridization / Cecilia P. Sanchez and Michael Lanzer -- Analysis of Yeast Artificial Chromosome DNA by restriction digestion, southern blotting nucleic acid hybridization and polymerase chain reaction / Sylvia Vasiliou and John Peter Quinn -- Postgenomic bioinformatic analysis of yeast artificial chromosome sequence / Kerry Miller, Scott Davidson, and Alasdair MacKenzie -- Transformation of yeast using bioactive beads with surface-immobilized yeast artificial chromosomes / Shigeki Kawakami ... [et al.] --Modification and amplification of yeast artificial chromosomes / Sanbing Shen, Anthony Harmar, and Nick Hastie -- Modifying yeast artificial chromosomes to generate Cre/LoxP and FLP/FRT site-specific deletions and inversions / Gabriela G. Loots -- Selective isolation of large chromosomal regions by transformation-associated recombination cloning for structural and functional analysis of mammalian genomes / Natalay Kouprina, Vladimir N. Noskov, and Vladimir Larionov -- A polymerase chain reaction-mediated yeast artificial chromosome-splitting technology for generating targeted yeast artificial chromosomes subclones / Yeon-Hee Kim ... [et al.] -- Genomic reconstruction by serial mitotic recombination of yeast artificial chromosomes / David Markie, Emma Jones, and Jiannis Ragoussis -- Targeting vector construction by yeast artificial chromosome modification / Peter J. Murray --Production of yeast artificial chromosomes transgenic mice by pronuclear injection of one-cell embryos / Alasdair MacKenzie -- Generation of yeast artificial chromosomes transgenic mice by intracytoplasmic sperm injection / Pedro N. Moreira ... [et al.] -- Establishment of cell lines that exhibit correct ontogenic stage-specific gene expression profiles from tissues of yeast artificial chromosome transgenic mice using chemically induced growth signals / C. Anthony Blau and Kenneth R. Peterson -- Application of yeast artificial chromosomes in fluorescence in situ hybridization / Thomas Liehr -- Contribution of yeast artificial chromosome-based physical maps to the final assembly of the trypanosoma cruzi genome / Marcia R.M. Santos ... [et al.].
  • Yeast gene analysis. 2nd ed. 2007, ScienceDirect
  • Pt.1 Forward and reverse genetics :Generating conditional mutations in zebrafish using gene-trap mutagenesis /Lisette A. Maddison,Jianjun Lu,Wenbiao Chen --Tol2-mediated transgenesis, gene trapping, enhancer trapping, and the Gal4-UAS system /Gembu Abe,Maximilliano L. Suster,Koichi Kawakami --Engineering zinc finger nucleases for targeted mutagenesis of zebrafish /Jeffry D. Sander,J.-R. Joanna Yeh,Randall T. Peterson,J. Keith Joung --Retroviral-mediated insertional mutagenesis in zebrafish /Adam Amsterdam,Gaurav Kumar Varshney,Shawn Michael Burgess --Genetic screens for mutations affecting adult traits and parental-effect genes /Francisco Pelegri,Mary C. Mullins --High-throughput target-selected gene inactivation in zebrafish /Ross N.W. Kettleborough,Ewart de Bruijn,Freek van Eeden,Edwin Cuppen,Derek L. Stemple --Genetic suppressor screens in haploids /Xiaoying Bai,Zhongan Yang,Hong Jiang,Shuo Lin,Leonard I. Zon --Transgenic zebrafish using transposable elements /Karl J. Clark,Mark D. Urban,Kimberly J. Skuster,Stephen C. Ekker --Spatiotemporal control of embryonic gene expression using caged morpholinos /Ilya A. Shestopalov,James K. Chen --Pt.2 Transgenesis :Advanced zebrafish transgenesis with Tol2 and application for Cre/lox recombination experiments /Christian Mosimann,Leonard I. Zion --Use of phage PhiC31 integrase as a tool for zebrafish genome manipulation /James A. Lister --Method for somatic cell nuclear transfer in zebrafish /Kannika Siripattarapravat,Jose B. Cibelli --Pt.3 The zebrafish genome and mapping technologies :Single nucleotide polymorphism (SNP) panels for rapid positional cloning in zebrafish /Matthew D. Clark,Victor Guryev,Ewart de Bruijn,Isaac J. Nijman,Masazumi Tada,Catherine Wilson,Panos Deloukas,John H. Postlethwait,Edwin Cuppen,Derek L. Stemple --Molecular cytogenetic methodologies and a BAC probe panel resource for genomic analyses in the zebrafish /Kimberly P. Dobrinski,Kim H. Brown,Jennifer L. Freeman,Charles Lee --Conserved synteny and the zebrafish genome /Julian M. Catchen,Ingo Braasch,John H. Postlethwait --Thezon 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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There are 120 high level MeSH Subject Headings under which all MeSH terms fall. Choose a subject heading to see the journals Lane offers in that subject area.

 

[print] 2014

New Book

Authored by
Stanford Alumni - Jeremy M. Berg
and
Michelle L. Kienholz

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