Books by Subject
- Accurate methods for ancestry and relatedness inference — Epigenetics of aging (154)
- Epigenetics protocols. 2nd ed. — Introduction to genomic signal processing with control (154)
- Investigations in yeast functional genomics and molecular biology — Protein engineering protocols (154)
- Proteins and proteomics of Leishmania and Trypanosoma — Zebrafish-- genetics, genomics, and transcriptomics. Fourth edition. [4th ed.] (152)
- 2014 CRCnetBASEedited by Matthew Eckwahl, MPhil.Part 1. Cell polarity, growth, and cell cycle -- part 2. Yeast regulatory circuits -- part 3. Gene expression and trait locus analysis -- part 4. Comparative genomics.
- 2010 Kargervolume editor, Richard Quinton.Molecular characterization and phenotypic expression of mutations in genes for gonadotropins and their receptors in humans / Salvi, R., Pralong, F.P -- Role of kisspeptin/GPR54 system in human reproductive axis / Silveira, L.F.G. ... [et al.] -- Biology of kisspeptins / Hameed, S., Dhillo, W.S. -- Role of fibroblast growth factor signaling in gonadotropin-releasing hormone neuronal system development / Chung, W.C.J., Tsai, P.-S. -- FGFR1 mutations in Kallmann syndrome / Villanueva, C., de Roux, N. -- Biology of KAL1 and its orthologs : implications for x-linked Kallmann syndrome and the search for novel candidate genes / MacColl, G.S., Quinton, R., Bülow, H.E. -- Biological actions and interactions of anosmin-1 / Choy, C., Kim, S.H. -- Genotype and phenotype of patients with gonadotropin-releasing hormone receptor mutations / Kim, H.-G. ... [et al.] -- Hypogonadotropic hypogonadism and GNRH1 mutations in mice and humans / Bouligand, J. ... [et al.] -- Kallmann syndrome caused by mutations in the PROK2 and PROKR2 genes : pathophysiology and genotype-phenotype correlations / Sarfati, J., Dodé, C., Young, J. -- Neurokinin B and its receptor in hypogonadotropic hypogonadism / Semple, R.K., Topaloglu, A.K. -- Complex genetics in idiopathic hypogonadotropic hypogonadism / Pitteloud, N. ... [et al.] -- Rarer syndromes characterized by hypogonadotropic hypogonadism / Aminzadeh, M. ... [et al.].
- 2008 Springeredited by Nenad Blau, Marinus Duran and K. Michael Gibson.
- 2011 Springer Protocolsedited by Graeme I. Murray.Laser capture microdissection : methods and applications / Kristen DeCarlo . [and others] -- Laser microdissection for gene expression profiling / Lori A. Field [and others] -- Gene expression using the PALM system / Jian-Xin Lu and Cheuk-Chun Szeto -- Immunoguided microdissection techniques / Michael A. Tangrea [and others] -- Optimized RNA extraction from non-deparaffinized laser-microdissected material / Danny Jonigk [and others] -- Laser capture microdissection for analysis of gene expression in formalin-fixed paraffin-embedded Tissue / Ru Jiang, Rona S. Scott, and Lindsey M. Hutt-Fletcher -- MicroRNA profiling using RNA from microdissected immunostained tissue / Clemens L. Bockmeyer [and others] -- Profiling solid tumor heterogeneity by LCM and biological MS of fresh-frozen tissue sections / Donald J. Johann [and others] -- Amplification testing in breast cancer by multiplex ligation-dependent probe amplification of microdissected tissue / Cathy B. Moelans, Roel A. de Weger, and Paul J. van Diest -- Detection and quantification of MicroRNAs in laser-microdissected formalin-fixed paraffin-embedded breast cancer tissues / Sarkawt M. Khoshnaw [and others] -- Laser capture microdissection applications in breast cancer proteomics / Rene B.H. Braakman [and others] -- Proteomic analysis of laser microdissected ovarian cancer tissue with SELDI-TOF MS / Isabelle Cadron [and others] -- LCM Assisted biomarker discovery from archival neoplastic gastrointestinal tissues / Patricia A. Meitner and Murray B. Resnick -- Purification of diseased cells from Barrett's esophagus and related lesions by laser capture microdissection / Masood A. Shammas and Manjula Y. Rao -- Laser microdissection of intestinal epithelial cells and downstream analysis / Benjamin Funke -- Application of laser microdissection and quantitative PCR to assess the response of esophageal cancer to neoadjuvant chemo-radiotherapy / Claus Hann von Weyhern and Bjorn L.D.M. Brucher -- Oligonucleotide microarray expression profiling of contrasting invasive phenotypes in colorectal cancer / Christopher C. Thorn, Deborah Williams, and Thomas C. Freeman -- Evaluation of gastrointestinal mtDNA depletion in mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) / Carla Giordano and Giulia d'Amati -- Laser microdissection for gene expression study of hepatocellular carcinomas arising in cirrhotic and non-cirrhotic livers / Maria Tretiakova and John Hart -- Laser capture microdissection of pancreatic ductal adeno-carcinoma cells to analyze EzH2 by western blot analysis / Aamer M. Qazi [and others] -- Laser-capture microdissection of renal tubule cells and linear amplification of RNA for microarray profiling and real-time PCR / Susie-Jane Noppert, Susanne Eder, and Michael Rudnicki -- Subcellular renal proximal tubular mitochondrial toxicity with tenofovir treatment / James J. Kohler and Seyed H. Hosseini -- Application of laser-capture microdissection to study renal carcinogenesis / Kerstin Stemmer and Daniel R. Dietrich -- Laser-capture microdissection and transcriptional profiling in archival FFPE tissue in prostate cancer / Ajay Joseph and Vincent J. Gnanapragasam -- Quantitative analysis of the enzymes associated with 5-Fluorouracil metabolism in prostate cancer biopsies / Tomoaki Tanaka -- Microdissection of gonadal tissues for gene expression analyses / Anne Jørgensen, Marlene Danner Dalgaard, and Si Brask Sonne -- Duplex real-time PCR assay for quantifying mitochondrial DNA deletions in laser microdissected single spiral ganglion cells / Adam Markaryan, Erik G. Nelson, and Raul Hinojosa -- Neuronal type-specific gene expression profiling and laser-capture microdissection / Charmaine Y. Pietersen . [et al.] -- Region-specific in situ hybridization-guided laser-capture microdissection on postmortem human brain tissue coupled with gene expression quantification / Rene Bernard, Sharon Burke, and Ilan A. Kerman -- UV-laser microdissection and mRNA expression analysis of individual neurons from postmortem Parkinson's disease brains / Jan Grundemann, Falk Schlaudraff, and Birgit Liss -- Transcriptome profiling of murine spinal neurulation using laser capture microdissection and high-density oligonucleotide microarrays / Shoufeng Cao, Boon-Huat Bay, and George W. Yip -- Probing the CNS microvascular endothelium by immune-guided laser-capture microdissection coupled to quantitative RT-PCR / Nivetha Murugesan [and others] -- Laser-capture microdissection for factor VIII-expressing endothelial cells in cancer tissues / Tomoatsu Kaneko [and others] -- Laser-capture microdissection and analysis of liver endothelial cells from patients with Budd-Chiari syndrome / Selcuk Sozer and Ronald Hoffman -- Laser-capture microdissection of hyperlipidemic/ApoE-/- mouse aorta atherosclerosis / Michael Beer [and others] -- Gene expression profiling in laser-microdissected bone marrow megakaryocytes / Kais Hussein -- Specific RNA collection from the rat endolymphatic sac by laser-capture microdissection (LCM) : LCM of a very small organ surrounded by bony tissues / Kosuke Akiyama [and others] -- Use of laser capture microdissection on adult human articular cartilage for gene expression analysis / Naoshi Fukui, Yasuko Ikeda, and Nobuho Tanaka -- Laser-capture microdissection of developing barley seeds and cDNA array analysis of selected tissues / Johannes Thiel, Diana Weier, and Winfriede Weschke -- Quantitative RT-PCR gene expression analysis of a laser microdissected placenta : an approach to study preeclampsia / Yuditiya Purwosunu [and others].
- 2013 SpringerUri Gophna, editor."Although the phenomenon of lateral gene transfer has been known since the 1940s, it was the genomics era that has really revealed the extent and many facets of this evolutionary/genetic phenomenon. Even in the early 2000s with but a handful of genomes available, it became clear that the nature of microorganisms is full of genetic exchange between lineages that are sometimes far apart. The years following this saw an explosion of genomic data, which shook the "tree of life" and also raised doubts about the most appropriate species concepts for prokaryotes. This book represents the manyfold contributions of LGT to the evolution of micro and, to an extent, macroorganisms by focusing on the areas where it has the largest impact: metabolic innovations and adaptations and speciation." Back cover.
- 2014 SpringerCharles C. Tseng, Xiaoli Yang.Learning Basic Genetics with Interactive Computer Programs is a comprehensive and interactive learning program that focuses on chromosome simulation and model building. It is intended to assist students in learning more about genetics with ease. The 11 modules of this program form an integrated system for learning the basic concepts of genetics. The program innovation lies in its unique content design that incorporates cognitive feedback and experiential learning through the novel use of interactive applications. Each of the modules is designed to enhance learning by simultaneously employing "eyes-on," "minds-on," and "hands-on" activities. Topics are motivated by questions, information is presented in simple terms, and concepts are clarified by interactive prompts. Used as a supplement to traditional lectures and textbook assignments, the program not only serves as a foundation upon which to build more complex and detailed topics, but as a tutor to clarify and guide when there is confusion. The software that accompanies this book has been shown to be an ideal tool for learning about genetics, which requires a combination of understanding, conceptualization, and practical experience.
- 2013 Springer Protocolsedited by Ray J. Rose.Featuring current resources used to discover new legume family genes and to understand genes and their interactions, Legume Genomics: Methods and Protocols provides techniques from expert researchers to study these plants that are so vitally important for food, feed, human nutrition, bioenergy, and industrial purposes. This detailed volume covers genome characterization and analysis, transcriptome analysis and miRNA identification/analysis, forward and reverse genetics, molecular markers, as well as transformation strategies used to investigate gene function and many other topics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and useful, Legume Genomics: Methods and Protocols aims to serve plant molecular biologists, molecular breeders, plant physiologists and biochemists, developmental biologists, and those interested in plant-microbe interactions.
- 2011[edited by] Jocelyn E. Krebs, Elliott S. Goldstein, Stephen T. Kilpatrick.Status: Not Checked OutLane Catalog Record
- 2016 SpringerErwei Song, editor.Non-coding RNAs: New Players in Cancers -- The Working Modules of Long Non-coding RNAs in Cancer Cells -- Methods to Study Long Non-coding RNA Biology in Cancer -- Relationship between Non-coding RNA Dysregulation and Epigenetic Mechanisms in Cancer -- Non-coding RNAs in Growth and Death of Cancer Cells -- Non-coding RNAs in Cancer Cell Plasticity -- Non-coding RNAs in Regulation of Cancer Metabolic Reprogramming -- Non-coding RNAs in Tumor Angiogenesis -- Non-coding RNAs in Cancer Immunity -- Non-coding RNAs in Therapeutic Resistance of Cancer -- Non-coding RNAs Regulating Cancer Signaling Network -- Non-coding RNAs Regulating NFkB Signaling -- Non-coding RNAs Regulating p53 and c-Myc Signaling -- Viral Non-coding RNAs in Cancer Biology -- Non-coding RNAs in Cancer Diagnosis -- Therapeutic Potentials of Non-coding RNAs: Targeted Delivery of NcRNAs in Cancer Cells.
- 2011 SpringerĐurđica Ugarković, editor.Transcriptional and posttranscriptional programming by long noncoding RNAs / Radha Raman Pandey and Chandrasekhar Kanduri -- Long noncoding RNA as a regulator for transcription / Riki Kurokawa -- Long noncoding RNAs and X chromosome inactivation / Cristina Gontan, Iris Jonkers, and Joost Gribnau -- TERRA : long noncoding RNA at eukaryotic telomeres / Rajika Arora, Catherine M.C. Brun, and Claus M. Azzalin -- Transcription of satellite DNAs in mammals / Claire Vourc'h and Giuseppe Biamonti -- Multiple roles of Alu-related noncoding RNAs / Audrey Berger and Katharina Strub -- roX RNAs and genome regulation in Drosophila melanogaster / S. Kiran Koya and Victoria H. Meller -- Transcription of satellite DNAs in insects / Željka Pezer ... [et al.] -- Long nonprotein-coding RNAs in plants / Virginie Jouannet and Martin Crespi.
- 2015 SpringerGil Atzmon, PhD editor.The release of the complete version of the human genome sequence in 2003 has paved the way for defining gene function and genetic background for phenotypic variation in humans and allowed us to study the aging process in a new light. This new volume results from that research and focuses on the genetic and epigenetic process of aging. While the interpretation of the genome data is still in its initial stages, this new volume looks at the evolving understanding of molecular mechanisms involved in cellular processes, gene function associated with complex traits, epigenetic components involve in gene control and the creation of hypothesis-free genome-wide approaches. Longevity Genes: A Blueprint for Aging explores the genetic and genomic elements that can maintain a long life such as DNA damage mechanisms, epigenetics and the way we can use this knowledge to generate customized treatments. It touches on some of the multidisciplinary approaches as well as genomic-wide association technology used to analyze complex traits. This book describes the hunt for genes affecting complex traits using a high throughput technology, with adequate consideration for the selection of an appropriate population, applications of statistical genetics and computational biology, and most importantly, considering phenotype-genotype association studies. Longevity Genes provides coverage of not only established aspects of genetics and aging, but also new approaches and perceptions in this important area of research.
- 2006 SpringerShirley Pease, Carlos Lois (eds.).
- 2011 Springer Protocolsedited by Gyula Hadlaczky.[Publisher-supplied data] The rapid progression of genetics and molecular biology has turned chromosomal engineering from science fiction to reality, with the successful production of transgenic animals with engineered chromosomes and chromosomes developed for pharmaceutical protein production which are now ready for the medical industry. Mammalian Chromosome Engineering: Methods and Protocols provides the reader with up-to date information on this rapidly evolving field and strives to take the reader into the exciting realm of chromosomal engineering from the basic principles to the practical applications of these new technologies. The five overview and ten protocol chapters cover the engineering of chromosomes with extrachromosomal vectors and transposon systems, the manipulation of naturally occurred minichromosomes, the generation and engineering of synthetic artificial chromosomes, and the induced de novo platform artificial chromosome system. Written in the highly successful Methods in Molecular Biology series format, protocols chapters contain brief introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Mammalian Chromosome Engineering: Methods and Protocols serves as a bench-side resource for current protocols and aims to help scientists to explore the many prospects for future research and vital applications.
- 2013 ScienceDirectJamie A. Davies.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.
- 2009. Kargervolume editors, Ricardo Benavente, Jean-Nicolas Volff.The meiotic recombination hotspots of Schizosaccharomyces pombe / Pryce, D.W.; McFarlane, R.J. -- Meiotic recombination and crossovers in plants / De Muyt, A. ... [et al.] -- Meiosis in cereal crops : the grasses are back / Martinez-Perez, E. -- Homologue pairing, recombination and segregation in Caenorhabditis elegans / Zetka, M. -- Homolog pairing and segregation in Drosophila meiosis / McKee, B.D. -- The mammalian synaptonemal complex : a scaffold and beyond / Yang, F.; Wang, P.J. -- The dance floor of meiosis : evolutionary conservation of nuclear envelope attachment and dynamics of meiotic telomeres / Alsheimer, M. -- Cohesin complexes and sister chromatid cohesion in mammalian meiosis / Suja, J.A.; Barbero, J.L. -- Variation in patterns of human meiotic recombination / Khil, P.P.; Camerini-Otero, R.D. -- Maternal origin of the human aneuploidies are homolog synapsis and recombination to blame? Notes (learned) from the underbelly / Garcia-Cruz, R.; Roig, I.; Garcia Caldés, M. -- Inverted meiosis : the true bugs as a model to study / Viera, A.; Page, J.; Rufas, J.S. The meiotic recombination hotspots of Schizosaccharomyces pombe / D.W. Pryce, R.J. McFarlane -- Meiotic recombination and crossovers in plants / A. De Muyt ... [et al.] -- Meiosis in cereal crops : the grasses are back / E. Martinez-Perez -- Homologue pairing, recombination, and segregation in Caenorhabditis elegans / M. Zetka -- Homolog pairing and segregation in Drosophila meiosis / B.D. McKee -- The mammalian synaptonemal complex : a scaffold and beyond / F. Yang, P.J. Wang -- The dance floor of meiosis : evolutionary conservation of nuclear envelope attachment and dynamics of meiotic telomeres / M. Alsheimer -- Cohesin complexes and sister chromatid cohesion in mammalian meiosis / J.A. Suja, J.L. Barbero -- Variation in patterns of human meiotic recombination / P.P. Khil, R.D. Camerini-Otero -- Maternal origin of the human aneuploidies are homolog : synapsis and recombination to blame? notes (learned) from the underbelly / R. Garcia-Cruz, I. Roig, M. Garcia Caldes -- Inverted meiosis : the true bugs as a model to study / A. Viera, J. Page, J.S. Rufas.
- 2009 Springer Protocolsedited by Matthew J. Peirce and Robin Wait.Online tools for predicting integral membrane proteins / H. Bigelow and B. Rost -- In silico identification of novel G protein coupled receptors / M.N. Davies and D.R. Flower -- Transcriptome-based identification of candidate membrane proteins / E.J. Evans ... [et al.] -- Separation of thylakoid membrane proteins by sucrose gradient ultracentrifugation or blue native-SDS-PAGE two-dimensional electrophoresis / G.M. D'Amici, C.G. Huber and L. Zolla -- Extraction of yeast mitochondrial membrane proteins by solubilization and detergent/polymer aqueous two-phase partitioning / H. Everberg, N. Gustavsson and F. Tjerneld -- 16-BAC/SDS-PAGE analysis of membrane proteins of yeast mitochondria purified by free flow electrophoresis / R.J. Braun ... [et al.] -- Sequential detergent extraction prior to mass spectrometry analysis / F.M. McCarthy, A.M. Cooksey and S.C. Burgess -- Enrichment of brain plasma membranes by affinity two-phase partitioning / J. Schindler and H.G. Nothwang -- Protocol to enrich and analyze plasma membrane proteins / R.J. Wisniewski -- Proteomic analysis of the lymphocyte plasma membrane using cell surface biotinylation and solution-phase isoelectric focusing / M.J. Peirce, A.P. Cope and R. Wait -- Identification of target membrane proteins as detected by phage antibodies / C.A. Geuijen, A.Q. Bakker and J. de Kruif -- Membrane protease degradomics: proteomic identification and quantification of cell surface protease substrates / G.S. Butler ... [et al.] -- Purification of basolateral integral membrane proteins by cationic colloidal silica-based apical membrane subtraction / R.J. Goode and R.J. Simpson -- Moving closer to the lipid raft proteome using quantitative proteomics / L.J. Foster -- Use of sequential chemical extractions to purify nuclear membrane proteins for proteomics identification / N. Korfali ... [et al.] -- Isolation of extracellular membranous vesicles for proteomic analysis / R.A. Mathias ... [et al.] -- Enrichment of human platelet membranes for proteomic analysis / D.W. Greening ... [et al.] -- Detergents and chaotropes for protein solubilization before two-dimensional electrophoresis / T. Rabilloud -- Two-dimensional separation of membrane proteins by 16-BAC-SDS-PAGE / H.G. Nothwang and J. Schindler -- MudPIT analysis: application to human heart tissue / K.G. Kline and C.C. Wu -- Liquid chromatography MALDI MS/MS for membrane proteome analysis / N. Wang, J.B. Young and L. Li -- Cysteinyl-tagging of integral membrane proteins for proteomic analysis using liquid chromatography-tandem mass spectrometry / S.K. Mitra and M.B. Goshe -- Quantitative proteomics analysis of pancreatic zymogen granule membrane proteins / X. Chen and P.C. Andrews.
- 2010 CRCnetBASEedited by Rudy Guerra, Darlene R. Goldstein.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.
- 2006 NCBI BookshelfAcid 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.
- 2010 Springer ProtocolsWolfgang R. Streit, Rolf Daniel editors.Molecular Methods to Study Complex Microbial Communities / José M. Vieites, María-Eugenia Guazzaroni, Ana Beloqui, Peter N. Golyshin, and Manuel Ferrer -- Construction of Small-Insert and Large-Insert Metagenomic Libraries / Carola Simon and Rolf Daniel -- Construction and Screening of Marine Metagenomic Libraries / Nancy Weiland, Carolin Löscher, Rebekka Metzger, and Ruth Schmitz -- Metagenomic Analysis of Isotopically Enriched DNA / Yin Chen, Josh D. Neufeld, Marc G. Dumont, Michael W. Friedrich, and J. Colin Murrell -- Wide Host-Range Cloning for Functional Metagenomics / Margaret Wexler and Andrew W.B. Johnston -- Cloning and Expression Vectors for a Gram-Positive Host, Streptomyces lividans / Kristof Vrancken, Lieve Van Mellaert, and Jozef Anné -- Heterologous Gene Expression in the Hyperthermophilic Archaeon Sulfolobus solfataricus / Angel Angelov and Wolfgang Liebl -- Novel Tools for the Functional Expression of Metagenomic DNA / Sonja Christina Troeschel, Thomas Drepper, Christian Leggewie, Wolfgang R. Streit, and Karl-Erich Jaeger -- Screening of Functional Promoter from Metagenomic DNA for Practical Use in Expression Systems / So-Youn Park and Geun-Joong Kim -- Substrate-Induced Gene Expression Screening: A Method for High-Throughput Screening of Metagenome Libraries / Taku Uchiyama and Kentaro Miyazaki -- Screens for Active and Stereoselective Hydrolytic Enzymes / Dominique Böttcher, Marlen Schmidt, and Uwe T. Bornscheuer. Screening for Cellulase-Encoding Clones in Metagenomic Libraries / Nele Ilmberger and Wolfgang R. Streit -- Screening Metagenomic Libraries for Laccase Activities / Manuel Ferrer, Ana Beloqui, and Peter N. Golyshin -- Screening for N-AHSL-Based-Signaling Interfering Enzymes / Phil M. Oger and Stéphane Uroz -- Identification of Molecular Markers to Follow Up the Bioremediation of Sites Contaminated with Chlorinated Compounds / Massimo Marzorati, Annalisa Balloi, Francesca De Ferra, and Daniele Daffonchio -- Methods for the Isolation of Genes Encoding Novel PHB Cycle Enzymes from Complex Microbial Communities / Ricardo F. Nordeste, Maria A. Trainer, and Trevor C. Charles -- Metagenomic Approaches to Identify and Isolate Bioactive Natural Products from Microbiota of Marine Sponges / Cristian Gurgui and Jörn Piel -- Screening for Novel Antibiotic Resistance Genes / Mindy G. Brown, Elizabeth H. Mitchell, and David L. Balkwill -- Novel Metal Resistance Genes from Microorganisms: A Functional Metagenomic Approach / José E. González-Pastor and Salvador Mirete -- Retrieval of Full-Length Functional Genes Using Subtractive Hybridization Magnetic Bead Capture / Tracy Meiring, Inonge Mulako, Marla I. Tuffin, Quinton Meyer, and Donald A. Cowan -- Detection and Isolation of Selected Genes of Interest from Metagenomic Libraries by a DNA Microarray Approach / Gopal P. Pathak and Wolfgang Gärtner -- Application of DNA Microarray for Screening Metagenome Library Clones / Soo-Je Park, Jong-Chan Chae, and Sung-Keun Rhee -- MetaGenomeThreader: A Software Tool for Predicting Genes in DNA-Sequences of Metagenome Projects / David J. Schmitz-Hübsch and Stefan Kurtz.
- 2011 SpringerKaren E. Nelson, editor ; foreword by Jane L. Peterson and Susan Garges.1.The human genome, microbiomes, and disease -- 2. Host genotype and the effect on microbial communities -- 3. The human microbiome and host-pathogen interactions -- 4. The human virome -- 5. Selection and sequencing of strains as references for human microbiome studies -- 6. The human vaginal microbiome -- 7. The human lung microbiome -- 8. The human skin microbiome in health and skin diseases -- 9. The human oral microbiome -- 10. Retraction: the human and his microbiome risk factors for infections -- 11. Retraction: infectogenomics: aspect of host responses to microbes in digestive tract -- 12. Autoimmune disease and human metagenome -- 13. Metagenomic applications and the potential for understanding chronic liver disease -- 14. Symbiotic gut microbiota and the modulation of human metabolic phenotypes -- 15. MetaHIT: the European Union project on metagenomics of the human intestinal tract -- 16. Implications of human microbiome research for the developing world -- Index.
- 2013Konrad J. Karczewski.Most human variation lies outside of coding regions, where molecular functions are more difficult to determine than for variants in coding regions. As most disease-associated variants lie in non-coding regions, characterizing the role of regulatory variation is crucial to understanding the molecular mechanisms of these diseases and methods to do so are currently limited. Recently, a number of research efforts, including the ENCODE project, have produced a wealth of data on transcription factor binding sites and other regulatory information, in addition to increasingly available whole genome sequence and transcriptomics data. These data will crucial to understanding the molecular basis of many diseases, but their scale and disparate nature, as well as high levels of noise, require clever informatics methods to integrate and properly apply this information. In this thesis, I describe methods to address some of the major informatics challenges to characterize the role of regulatory variants in phenotypes and disease. In particular, I have shown that I can (1) detect cooperativity among transcription factors using human variation data, (2) associate transcription factors to functional modules and thus discover new TF interactions and disease associations, (3) provide molecular mechanisms for disease-associated non-coding variants, and (4) explore regulatory functional mechanisms using long-range interactions in the human genome.
- 2008 CRCnetBASEedited by Phillip Stafford.A comprehensive analysis of the effect of microarray data preprocessing methods on differentially expressed transcript selection -- Differentiation detection in microarray normalization -- Preprocessing and normalization for Affymetrix GeneChip expression microarrays -- Spatial detrending and normalization methods for two-channel DNA and protein microarray data -- A survey of cDNA microarray normalization and a comparison by k-NN classification -- Technical variation in modeling the joint expression of several genes -- Biological interpretation for microarray normalization selection -- Methodology of functional analysis for omics data normalization -- Exon array analysis for the detection of alternative splicing -- Normalization of array CGH data -- SNP array-based analysis for the detection of chromosomal aberrations and copy number variations.Also available: Print – 2008
- 2009 Springeredited by Jonathan R. Pollack.DNA microarray technology. Introduction / J.R. Pollack -- Comparative genomic hybridization on BAC arrays / B.P. Coe ... [et al.] -- Comparative genomic hybridization on spotted oligonucleotide microarrays / Y.H. Kim and J.R. Pollack -- Comparative genomic hybridization by representational oligonucleotide microarray analysis / R. Lucito and J. Byrnes -- Application of oligonucleotides arrays for coincident comparative genomic hybridization, ploidy status and loss of heterozygosity studies in human cancers / J.K. Cowell and K.C. Lo -- Molecular inversion probe assay for allelic quantitation / H. Ji and K. Welch -- A whole-genome amplification protocol for a wide variety of DNAs, including those from formalin-fixed and paraffin-embedded tissue / P.L. Paris -- Algorithms for calling gains and losses in array CGH data / P. Wang -- Methylation analysis by microarray / D.E. Deatherage ... [et al.] -- Methylation analysis by DNA immunoprecipitation (MeDIP) / E.A. Vucic ... [et al.] -- Combining chromatin immunoprecipitation and oligonucleotide tiling arrays (ChIP-Chip) for functional genomic studies / J. Eeckhoute, M. Lupien and M. Brown -- ChIP-Chip: algorithms for calling binding sites / X.S. Liu and C.A. Meyer -- Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip) / Y. Shibata and G.E. Crawford -- Microarray analysis of DNA replication timing / N. Karnani, C.M. Taylor and A. Dutta -- Integration of diverse microarray data types / K. Salari and J.R. Pollack.Also available: Print – 2009
- 2007 Springer Protocolsedited by Michael J. Korenberg.
- 2010 CRCnetBASEKarl Fraser, Zidong Wang, Xiaohui Liu.
- 2009 CRCnetBASE[edited by] Robert S. Matson.Introduction to microarray technologies / Robert S. Matson -- Nucleic acid sample preparation / Robert S. Matson -- Solid-phase substrates for nucleic acid microarrays / Robert S. Matson -- Protein sample preparation for microarrays / Robert S. Matson -- Solid-phase chemistries for protein microarrays / Robert S. Matson -- Protein microarrays : the link between genomics and proteomics / Persis P. Wadia and David B. Miklos -- Bead arrays : an introduction to multiplexed bead-based assays for proteins / Yong Song -- Carbohydrate arrays / Denong Wang -- Lectin microarrays / Masao Yamada -- Printing methods / Todd Martinsky.
- 2006 Springeredited by Simone Mocellin.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.
- v. 1-2, 2007. Springer Protocolsv.2, 2009 Springer Protocolsedited by Jang B. Rampal.v. 1. Synthesis methods -- v. 2. Applications and data analysis.
- 2008 Springer Protocolsedited by Andrei L. Osterman, Svetlana Y. Gerdes.Overview of whole-genome essentiality analysis / Karen Joy Shaw -- Pt. I. Experimental protocols. IA. Populational genome-wide essentiality screens. Transposon-based strategies for the identification of essential bacterial genes / William S. Reznikoff and Kelly M. Winterberg -- Identification and analysis of essential genes in Haemophilus influenzae / Sandy M.S. Wong and Brian J. Akerley -- Transposon site hybridization in Mycobacterium tuberculosis / Jeffrey P. Murry ... [et al.] -- Essential genes in the infection model of Pseudomonas aeruginosa PCR-based signature-tagged mutagenesis / François Sanschagrin, Irena Kukavica-Ibrulj, and Roger C. Levesque -- Whole-genome detection of conditionally essential and dispensable genes in Escherichia coli via genetic footprinting / Michael D. Scholle and Svetlana Y. Gerdes -- Generating a collection of insertion mutations in the Staphylococcus aureus genome using bursa aurealis / Taeok Bae ... [et al.] -- Multipurpose transposon insertion libraries for large-scale analysis of gene function in yeast / Anuj Kumar -- IB. Systematic collections of knockout mutants. How to make a defined near-saturation mutant library. Case 1: Pseudomonas aeruginosa PAO1 / Michael A. Jacobs -- Comparing insertion libraries in two Pseudomonas aeruginosa strains to assess gene essentiality / Nicole T. Liberati ... [et al.] -- The construction of systematic in-frame, single-gene knockout mutant collection in Escherichia coli K-12 / Tomoya Baba and Hirotada Mori -- The applications of systematic in-frame, single-gene knockout mutant collection of Escherichia coli K-12 / Tomoya Baba ... [et al.] -- A novel, simple, high-throughput method for isolation of genome-wide transposon insertion mutants of Escherichia coli K-12 / Takeyoshi Miki, Yoshihiro Yamamoto, and Hideo Matsuda -- High-throughput creation of a whole-genome collection of yeast knockout strains / Angela M. Chu and Ronald W. Davis -- Analysis of genetic interactions on a genome-wide scale in budding yeast: diploid-based synthetic lethality analysis by microarray / Pamela B. Meluh ... [et al.] -- IC. Genome minimization. Scarless engineering of the Escherichia coli genome / Tamás Fehér ... [et al.] -- Minimization of the Escherichia coli genome using the Tn5-targeted Cre/loxP excision system / Byung Jo Yu and Sun Chang Kim -- Construction of long chromosomal deletion mutants of Escherichia coli and minimization of the genome / Jun-ichi Kato and Masayuki Hashimoto -- ID. Conditional knockouts. Identification of essential genes in Staphylococcus aureus by construction and screening of conditional mutant library / Dezhong Yin and Yinduo Ji -- Techniques for the isolation and use of conditionally expressed antisense RNA to achieve essential gene knockdowns in Staphylococcus aureus / Allyn Forsyth and Liangsu Wang -- Introduction of conditional lethal amber mutations in Escherichia coli / Christopher D. Herring -- Pt. II. Bioinformatics. IIA. Statistics. Statistical methods for building random transposon mutagenesis libraries / Oliver Will -- Statistical evaluation of genetic footprinting data / Gábor Balázsi -- Modeling competitive outgrowth of mutant populations : why do essentiality screens yield divergent results? / Alexander I. Grenov and Svetlana Y. Gerdes -- Statistical analysis of fitness data determined by TAG hybridization on microarrays / Brian D. Peyser, Rafael Irizarry, and Forrest A. Spencer -- IIB. Data integration and modeling. Profiling of Escherichia coli chromosome database / Yukiko Yamazaki, Hironori Niki, and Jun-ichi Kato -- Gene essentiality analysis based on DEG, a database of essential genes / Chun-Ting Zhang and Ren Zhang -- Detection of essential genes in Streptococcus pneumoniae using bioinformatics and allelic replacement mutagenesis / Jae-Hoon Song and Kwan Soo Ko -- Design and application of genome-scale reconstructed metabolic models / Isabel Rocha, Jochen Förster, and Jens Nielsen -- Predicting gene essentiality using genome-scale in silico models / Andrew R. Joyce and Bernhard Ø. Palsson -- Comparative approach to analysis of gene essentiality / Andrei L. Osterman and Svetlana Y. Gerdes.
- 2003 CRCnetBASE[edited by] Thomas J. Dougherty, Steven J. Projan.Also available: Print – 2003
- 2009. Kargervolume editors, Hilde de Reuse, Stefan Bereswill.Genome comparison of bacterial pathogens / Wassenaar, T.M. ... [et al.] -- In silico reconstruction of the metabolic and pathogenic potential of bacterial genomes using subsystems / McNeil, L.K., Aziz, R.K. -- The bacterial pan-genome and reverse vaccinology / Tettelin, H. -- 'Guilty by association' : protein-protein interactions (PPIS) in bacterial pathogens / Schauer, K., Stingl, K -- Helicobacter pylori sequences reflect past human migrations / Moodley, Y., Linz, B. -- Helicobacter pylori genome plasticity / Baltrus, D.A., Blaser, M.A., Guillemin, K. -- Genomics of Thermophilic campylobacter species / Gaskin, D.J.H. ... [et al.] -- Adaptation of pathogenic E. coli to various niches : genome flexibility is the key / Brzuszkiewicz, E. ... [et al.] -- Role of horizontal gene transfer in the evolution of Pseudomonas aeruginosa virulence / Qiu, X., Kulasekara, B.R., Lory, S. -- The genus Burkholderia : analysis of 56 genomic sequences / Ussery, D.W. ... [et al.] -- Genomics of host-restricted pathogens of the genus Bartonella / Engel, P., Dehio, C. -- Legionella pneumophila - host interactions : insights gained from comparative genomics and cell biology / Lomma, M. ... [et al.] -- A proteomics view of virulence factors of Staphylococcus aureus / Engelmann, S., Hecker, M. -- Pathogenomics of mycobacteria / Gutierrez, M.C., Supply, P., Brosch, R.
- 2006 Wiley[edited by] Ian Humphery-Smith, Michael Hecker."Discover important lessons learned about whole organism biology via microbial proteomics This text provides an exhaustive analysis and presentation of current research in the field of microbial proteomics, with an emphasis on new developments and applications and future directions in research. The editors and authors show how and why the relative simplicity of microbes has made them attractive targets for extensive experimental manipulation in a quest for both improved disease prevention and treatment and an improved understanding of whole organism functional biology. In particular, the text demonstrates how microbial proteomic analyses can aid in drug discovery, including identification of new targets, novel diagnostic markers, and lead optimization. Each chapter is written by one or more leading experts in the field and carefully edited to ensure a consistent and thorough approach throughout. Methods, technologies, and tools associated with the most promising approaches are stressed."--Publisher's website.
- 2011 Springer Protocolsedited by Wei Wu.MicroRNA Biogenesis and Cancer / Julia Winter, Sven Diederichs -- Computational Identification of miRNAs Involved in Cancer / Anastasis Oulas, Nestoras Karathanasis, Panayiota Poirazi -- The Principles of MiRNA-Masking Antisense Oligonucleotides Technology / Zhiguo Wang -- The Concept of Multiple-Target Anti-miRNA Antisense Oligonucleotide Technology / Zhiguo Wang -- Modulation of MicroRNAs for Potential Cancer Therapeutics / Wei Wu -- Detection of MicroRNAs in Cultured Cells and Paraffin-Embedded Tissue Specimens by In Situ Hybridization / Ashim Gupta, Yin-Yuan Mo -- MicroRNA Northern Blotting, Precursor Cloning, and Ago2-Improved RNA Interference / Julia Winter, Sven Diederichs -- miRNA Profiling on High-Throughput OpenArray System / Elena V. Grigorenko, Elen Ortenberg, James Hurley, Andrew Bond, Kevin Munnelly -- Silicon Nanowire Biosensor for Ultrasensitive and Label-Free Direct Detection of miRNAs / Guo-Jun Zhang -- High-Throughput and Reliable Protocols for Animal MicroRNA Library Cloning / Caide Xiao -- MicroRNA Regulation of Growth Factor Receptor Signaling in Human Cancer Cells / Keith M. Giles, Andrew Barker, Priscilla M. Zhang, Michael R. Epis, Peter J. Leedman -- Epigenetic Regulation of MicroRNA Expression in Cancer / Hani Choudhry, James W. Catto -- In Vitro Functional Study of miR-126 in Leukemia / Zejuan Li, Jianjun Chen -- Prediction of the Biological Effect of Polymorphisms Within MicroRNA Binding Sites / Debora Landi, Roberto Barale, Federica Gemignani, Stefano Landi -- The Guideline of the Design and Validation of MiRNA Mimics / Zhiguo Wang -- Analysis of Targets and Functions Coregulated by MicroRNAs / Shu-Jen Chen, Hua-Chien Chen -- Utilization of SSCprofiler to Predict a New miRNA Gene / Anastasis Oulas, Panayiota Poirazi -- MicroRNA Profiling Using Fluorescence-Labeled Beads: Data Acquisition and Processing / Thomas Streichert, Benjamin Otto, Ulrich Lehmann.
- 2015 SpringerGaetano Santulli, editor.microRNAs in the malignant transformation process / Anne E. Sarver, Lihua Li, Reena V. Kartha, Subbaya Subramanian -- microRNA and chronic lymphocytic leukemia / Dana Elena Giza, George A. Calin -- microRNA in malignant lymphoma / Hiroyuki Tagawa -- MicroRNAs and gastrointestinal stromal tumor / Pinar Akçakaya, Weng-Onn Lui -- Insights into the role of microRNAs in pancreatic cancer pathogenesis: potential for diagnosis, prognosis, and therapy / Mohammad Aslam Khan [and others] -- microRNAs and colorectal cancer / Anna Lena Ress, Samantha Perakis, Martin Pichler -- microRNAs and prostate cancer / Sajni Josson, Leland W. K. Chung, Murali Gururajan -- microRNA and ovarian cancer / Ream Langhe -- microRNA and lung cancer / Valerio Del Vescovo, Michela A. Denti -- microRNAs and soft tissue sarcomas / Tomohiro Fujiwara, Toshiyuki Kunisada, Ken Takeda, Toshifumi Ozaki -- microRNA and bone cancer / Mary Nugent.
- 2012Xuyang Sun.Mammalian neurogenesis - an elagant process of producing extraodinarily diversified neuronal propulations - has been largely studied in the context of evoluationarily conserved signalling pathways and neurogenic transcription factors. Yet little is known about the roles of chromatin remodellers and regulatory RNAs, such as microRNAs, in the formation of neurons. We recently discovered that miR-9* and miR-124 instruct compositional changes of SWI/SNF-like BAF chromatin-remodelling complexes during murine nervous development, a process important for neuronal differentiation and function. Here I set out to directly test the neurogenic activity of these microRNAs in human non-neuronal cells. Together with Andrew Yoo, I showed that ectopic expression of miR-9/9* and miR-124 (miR-9/9*-124) in human dermal fibroblasts induces their conversion into neurons (chapter 2). Addition of neurogenic transcription factors such as NEUROD2, ASCL1 and MYT1L enhances the rate of conversion and the maturation of the converted neurons, whereas expression of these transcription factors alone without miR-9/9*-124 appeared ineffective. As a step closer to cell replacement therapy, I next showed that these microRNAs could directly convert human astrocytes into neurons, of which the subtype identity can be further biased by specfic neurogenic factors (chapeter 3). Collectively, these studies indicate that the genetic circuitry involving miR-9/9*-124 and BAF chromatin remodelling complex can have an instructive role in neuronal fate determination, and may form a neuronal ground state that can be further specified by different transciption factors and/or signalling pathways.
- 2015 SpringerGaetano Santulli, editor.Exploiting microRNA specificity and selectivity: paving a sustainable path towards precision medicine / Gaetano Santulli -- microRNAs and personalized medicine: evaluating their potential as cancer biomarkers / Anne Saumet and Charles-Henri Lecellier -- microRNA and pain / Atsushi Sakai and Hidenori Suzuki -- microRNA and epilepsy / Cristina R. Reschke and David C. Henshall -- microRNA and autism / Ayyappan Anitha and Ismail Thanseem -- microRNAs and neurogenerative diseases / Lifeng Qiu, Eng King Tan, and Li Zeng -- microRNAs and Fragile X Syndrome / Shi-Lung Lin -- The emerging role of mitomiRs in the pathophysiology of human disease / Filipe V. Duarte, Carlos M. Palmeira, and Anabela P. Rolo -- microRNAs in cerebrovascualar disease / Ondřej Volný, Linda Kašičková, Dominika Coufalová, Petra Cimflová, and Jan Novák -- microRNAs and cardiovascular remodeling / Koh Ono -- microRNAs in essential hypertension and blood pressure regulation / Francine Z. Marques and Fadi J. Charchar -- microRNA and pulmonary hypertension / Olivier Boucherat, François Potus, and Sébastien Bonnet -- microRNAs in diabetic kidney disease / Arthur C.K. Chung -- microRNA and kidney transplantation / Kíra Jelencsics and Rainer Oberbauer -- microRNA and wound healing / Jaideep Banerjee and Chandan K. Sen -- Essential role of microRNA in skin physiology and disease / Damjan Glavač and Metka Ravnik-Glavač -- microRNA and allergy / Ana Rebane -- microRNA in human reproduction / Iris Eisenberg, Noora Kotaja, Debra Goldman-Wohl, and Tal Imbar -- microRNAs and hepatitis B / Yutaka Naito, Yasuhito Tanaka, and Takahiro Ochiya -- Circulating microRNAs: the future of biomarkers in anti-doping field / Nicolas Leuenberger and Martial Saugy -- microRNA expression profiling: technologies, insights, and prospects / Christine Roden, Stephen Mastriano, Nayi Wang, and Jun Lu.
- 2007 ScienceDirectedited by John J. Rossi, Gregory J. Hannon.Also available: Print – 2007
- 2012 Springer Protocolsedited by Shao-Yao Ying.MicroRNA / Shao-Yao Ying, Donald C. Chang, and Shi-Lung Lin -- Analysis of MicroRNA length variety generated by recombinant human dicer / Julia Starega-Roslan and Wlodzimierz J. Krzyzosiak -- User-friendly computational workflow for the analysis of MicroRNA deep sequencing data / Anna Majer, Kyle A. Caligiuri, and Stephanie A. Booth -- RNA gene information : retroelement-MicroRNA entangling as the RNA quantum code / Yoichi Robertus Fujii -- Setting up an intronic miRNA database / Ludwig Christian Hinske [and others] -- Identify intronic MicroRNA with bioinformatics / Chih-Hao Kuo [and others] -- Experimental miRNA target validation / Jens Heyn [and others] -- Enrichment analysis of miRNA targets / Jianzhen Xu and Chi-Wai Wong -- MicroRNA expression profiling during neural differentiation of mouse embryonic carcinoma P19 cells / Botao Zhao [and others] -- Evaluating the MicroRNA targeting sites by luciferase reporter gene assay / Yi Jin [and others] -- Expression pattern analysis of MicroRNAs in Caenorhabditis elegans / Meltem Isik and Eugene Berezikov -- Use of viral systems to study miRNA-mediated regulation of gene expression in human cells / Eleonora Forte and Micah A. Luftig -- Cloning, expression, and functional analysis of genomic miRNA using retroviral system in cancer cells / Abdol Hossein Rezaeian, Yuan Gao, and Hui-Kuan Lin -- Preparing synaptoneurosomes from adult mouse forebrain / Giovanni Lugli and Neil R. Smalheiser -- Isolation of total RNA and detection procedures for miRNA present in bovine-cultured adipocytes and adipose tissues / Scott L. Pratt [and others] -- miRNA and shRNA expression vectors based on mRNA and miRNA processing / Ping Wu [and others] -- Gene silencing in vitro and in vivo using intronic MicroRNAs / Shi-Lung Lin and Shao-Yao Ying -- Vector-free methods for manipulating miRNA activity in vitro and in vivo / Angeliki Pantazi and Athanasios Zovoilis -- MicroRNA expression profiling of human-induced pluripotent and embryonic stem cells / Amit Sharma and Joseph C. Wu -- MicroRNA expression during neuronal differentiation of human teratocarcinoma NTera2D1 and mouse embryonic carcinoma P19 cells / Hirohiko Hohjoh -- Isolation and identification of gene-specific MicroRNAs / Shi-Lung Lin, Donald C. Chang, and Shao-Yao Ying -- Transgene-like animal models using intronic MicroRNAs / Shi-Lung Lin, Shin-Ju E. Chang, and Shao-Yao Ying -- Mechanism and method for generating tumor-free iPS cells using intronic MicroRNA miR-302 induction / Shi-Lung Lin and Shao-Yao Ying -- Salivary MicroRNAs and oral cancer detection / Janice M. Yoshizawa and David T.W. Wong -- Application of intronic MicroRNA agents in cosmetics / Jack S.K. Chen and David T.S. Wu -- MicroRNAs in skin and wound healing / Jaideep Banerjee and Chandan K. Sen -- MiRNA targets of prostate cancer / Jia Han Deng [and others].
- 2010 Springer Protocolsedited by Silvia Monticelli.A rapid, quantitative assay for direct detection of microRNAs and other small RNAs using splinted ligation -- Normalization of microRNA quantitative RT-PCR data in reduced scale experimental designs -- MicroRNA detection in bone marrow cells by LNA-FISH -- Measuring microRNA expression in size-limited facs-sorted and microdissected samples -- MicroRNA cloning from cells of the immune system -- High-throughput profiling in the hematopoietic system -- Construction of small RNA cDNA libraries for deep sequencing -- MicroRNA-profiling in formalin-fixed paraffin-embedded specimens -- Expression of miRNAs in lymphocytes : A review -- Mouse models for miRNA expression: The ROSA26 locus -- Regulation of monocytopoiesis by microRNAs -- MicroRNA activity in B lymphocytes -- Isolation and characterization of microRNAs of human mature erythrocytes -- Stable overexpression of miRNAs in bone marrow-derived murine mast cells using lentiviral expression vectors -- Monitoring microRNA activity and validating microRNA targets by reporter-based approaches -- Lentivirus-mediated antagomir expression -- Solution structure of miRNA:mRNA complex -- MiRNA editing -- Computational prediction of microRNA targets -- Large-scale integration of microRNA and gene expression data for identification of enriched microRNA-mRNA associations in biological systems -- Identification and validation of the cellular targets of virus-encoded microRNAs.
- 2011 SpringerWilliam C.S. Cho, editor.1 -- MicroRNAs in Cancer (An Overview) -- 2. The Role of MicroRNAs in Lung Cancer Development, Progression, and Metastasis -- 3. MicroRNAs in Breast Cancer -- 4. MicroRNAs in Colorectal Cancer -- 5. MicroRNAs in Gastric Cancer -- 6. MicroRNAs in Prostate Cancer: A Possible Role as Novel Biomarkers and Therapeutic Targets?- 7. MicroRNAs in Hepatocellular Carcinoma -- 8. MicroRNAs in Cervical Carcinoma -- 9. MicroRNAs in Esophageal Cancer -- 10. MicroRNAs in Bladder Cancer -- 11. MicroRNAs in Lymphoma -- 12. MicroRNAs in Leukemia -- 13. MicroRNAs in Pancreatic Cancer: Potential Interests as Biomarkers and Therapeutic Tools -- 14. MicroRNAs in Epithelial Ovarian Cancer -- 15. MicroRNAs in Brain Tumors -- 16. MicroRNAs and Cancer Stem Cells -- 17. MicroRNAs in Cancer Invasion and Metastasis -- 18. MicroRNAs in Predicting Radiotherapy and Chemotherapy Response -- 19. Role of MicroRNAs in Anti-cancer Drug Resistance -- 20. MicroRNAs and Cancer Metabolism -- 21. MicroRNAs as Blood-based Biomarkers of Cancer -- 22. RNAi-based Approaches to the Treatment of Brain Tumors.
- 2011 Springer Protocolsedited by Tamas Dalmay.In situ detection of microRNAs in animals / Dylan Sweetman -- Detection of microRNAs in plants by in situ hybridisation / Eva Varallyay and Zoltan Havelda -- Detecting sRNAs by northern blotting / Sara Lopez-Gomollon -- Profiling microRNAs by real-time PCR / Nanna Jacobsen, Ditte Andreasen, and Peter Mouritzen -- Detection of small RNAs and microRNAs using deep sequencing technology / Ericka R. Havecker -- Detection of microRNAs in prostate cancer cells by mircoRNA array / Xiaoqing Tang [and others] -- MicroRNA knock down by cholesterol-conjugated antisence oligos in mouse organ culture / Sharon Kredo-Russo and Eran Hornstein -- Protocols for use of homologous recombination gene targeting to produce microRNA mutants in drosophila / Ya-Wen Chen, Ruifen Weng, and Stephen M. Cohen -- Engineering elements for gene silencing : the artificial microRNAs technology / Pablo Andres Manavella and Ignacio Rubio-Somoza -- Mimicry technology : suppressing small RNA activity in plants / Ignacio Rubio-Somoza and Pablo Andres Manavella -- Experimental validation of microRNA targets using a luciferase reporter system / Francisco E. Nicolas -- Experimental identification of microRNA targets by immunoprecipitation of argonaute protein complexes / Michaela Beitzinger and Gunter Meister -- Comprehensive identification of miRNA target sites in live animals / Dimitrios G. Zisoulis, Gene W. Yeo, and Amy E. Pasquinelli -- Target validation of plant microRNAs / Cesar Llave [and others] -- High-throughput sequencing-based methodology to identify all uncapped and cleaved RNA molecules in eukaryotic genomes / Matthew W. Endres, Rebecca T. Cook, and Brian D. Gregory.
- MicroRNAs in malignant tumors of the skin : first steps of tiny players in the skin to a new world of genomic medicine2016 SpringerMichael Sand.
- 2013 Springer Protocolsedited by Stella K. Kantartzi.Microsatellites or simple sequence repeats (SSRs) have become the markers of choice for a variety of molecular studies because of their versatility, operational flexibility, and lower cost than other marker systems. Microsatellites: Methods and Protocols brings together experts in the field to cover this significant area of research. Broken in to four convenient parts, this volume delves into classical and modern methods for the discovery and development of microsatellite markers, descriptions of amplification and visualization of SSRs, automated capillary sequencers that are widely used for fragment analysis, as well as a variety of methods for the analysis of data obtained by the use of microsatellites. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and invaluable, Microsatellites: Methods and Protocols aims at researchers that need detailed protocols for incorporating microsatellite markers into their projects and expert scientists looking to expand their knowledge of SSRs discovery, use, and analysis.
- 2014 Springer Protocolsedited by Christoph Arenz.Part I. Reviews -- Pathway of miRNA maturation / Michael Sand -- MicroRNA maturation and human disease / Marlen Hesse and Christoph Arenz -- Approaches to the modulation of miRNA maturation / Valerie T. Tripp, Jaclyn R. McKenna, and Douglas D. Young -- Part II. Methods -- Expression profiling of components of the miRNA maturation machinery / Michael Sand and Marina Skrygan -- Primary MicroRNA processing assay reconstituted using recombinant Drosha and DGCR8 / Ian Barr and Feng Guo -- In vivo processing assay based on a dual-luciferase reporter system to evaluate DROSHA enzymatic activity / Vera Bilan, Danilo Allegra, Florian Kuchenbauer, and Daniel Mertens -- Assaying dicer-mediated miRNA maturation by means of fluorescent substrates / Marlen Hesse, Brian P. Davies, and Christoph Arenz -- Fluorescence correlation spectroscopy-based enzyme assay for human dicer / Eileen Magbanua and Ulrich Hahn -- Detection of microRNA maturation using unmodified pre-microRNA and branched rolling circle amplification / Saskia Neubacher and Christoph Arenz -- Quantitative RT-PCR specific for precursor and mature miRNAs / Hannah Zöllner, Stephan A. Hahn, and Abdelouahid Maghnouj -- Cellular microRNA sensors based on luciferase reporters / Colleen M. Connelly and Alexander Deiters -- Identification of inhibitors of microRNA function from small molecule screens / Colleen M. Connelly and Alexander Deiters -- Inhibition of miRNA maturation by peptide nucleic acids / Concetta Avitabile, Enrica Fabbri, Nicoletta Bianchi, Roberto Gambari, and Alessandra Romanelli -- Molecular methods for validation of the biological activity of peptide nucleic acids targeting microRNAs / Eleonora Brognara, Enrica Fabbri, Nicoletta Bianchi, Alessia Finotti, Roberto Corradini, and Roberto Gambari -- Lentiviral overexpression of miRNAs / Hannah Zöllner, Stephan A. Hahn, and Abdelouahid Maghnouj.
- 2009 Springer Protocolsedited by Jeffrey A. Stuart.Biochemical isolation of mtDNA nucleoids from animal cells / D.F. Bogenhagen -- Analysis of mitochondrial DNA by two-dimensional agarose gel electrophoresis / A. Reyes [and others] -- Comparative purification strategies for Drosophila and human mitochondrial DNA replication proteins: DNA polymerase gamma and mitochondrial single-stranded DNA-binding protein / M.T. Oliveira and L.S. Kaguni -- Functional analysis of mutant mitochondrial DNA polymerase proteins involved in human disease / S.S. Chan and W.C. Copeland -- Preparation of human mitochondrial single-stranded DNA-binding protein / M.J. Longley, L.A. Smith and W.C. Copeland -- Methods for assessing binding of mitochondrial transcription factor A (TFAM) to DNA / A. Fukuoh and D. Kang -- Inducible expression in human cells, purification, and in vitro assays for the mitochondrial DNA helicase Twinkle / S. Goffart and H. Spelbrink -- Purification strategy for recombinant forms of the human mitochondrial DNA helicase / T.D. Ziebarth and L.S. Kaguni -- Methods for studying mitochondrial transcription termination with isolated components / P.L. Polosa [and others] -- Oxidative phosphorylation: synthesis of mitochondrially encoded proteins and assembly of individual structural subunits into functional holoenzyme complexes / S.C. Leary and F. Sasarman -- Reactive oxygen species production by mitochondria / A.J. Lambert and M.D. Brand -- Measuring mtDNA damage using a supercoiling-sensitive qPCR approach / S.W. Chan and J.Z. Chen -- Quantitative analysis of oxidized guanine, 8-oxoguanine, in mitochondrial DNA by immunofluorescence method / M. Ohno, S. Oka and Y. Nakabeppu -- In vitro measurement of DNA base excision repair in isolated mitochondria / M.M. Page and J.A. Stuart -- Targeting repair proteins to the mitochondria of mammalian cells through stable transfection, transient transfection, viral transduction, and TAT-mediated protein transduction / C.A. Koczor [and others] -- Construction and characterization of a cell line deficient in repair of mitochondrial, but not nuclear, oxidative DNA damage / S. Oka, M. Ohno and Y. Nakabeppu -- Mitochondrial DNA oxidative damage and mutagenesis in Saccharomyces cerevisiae / L.M. Griffiths [and others] -- Determination of DNA mutation load in human tissues using denaturing HPLC-based heteroduplex analysis / K.S. Lim, R.K. Naviaux and R.H. Haas -- Rapid identification of unknown heteroplasmic mitochondrial DNA mutations with mismatch-specific surveyor nuclease / S. Bannwarth, V. Procaccio and V. Paquis-Flucklinger -- Collection of isolated cells for studying mitochondrial DNA mutations within individual cells / Y. Kraytsberg [and others] -- Quantitative analysis of somatic mitochondrial DNA mutations by single-cell single-molecule PCR / Y. Kraytsberg [and others] -- Measuring DNA precursor pools in mitochondria / C.K. Mathews and L.J. Wheeler -- Establishment of human cell lines lacking mitochondrial DNA / K. Hashiguchi and Q.M. Zhang-Akiyama.
- 2016 Springer Protocolsedited by Matthew McKenziePart I. Detection of mitochondrial DNA mutations and mitochondrial DNA damage -- Part II. Visualization of mitochondrial DNA and mitochondrial DNA nucleoids -- Part III. Analysis of mitochondrial DNA replication, mitochondrial DNA-encoded protein translation and mitochondrial DNA copy number -- Part IV. Modification of mitochondrial DNA -- Part V. Purification of proteins involved in mitochondrial DNA replication and transcription -- Index.
- 2010 SpringerGabriel D. Dakubo.1. Basic mitochondrial genetics, bioenergetics, and biogenesis -- 2. The Warburg phenomenon and other metabolic alterations of cancer cells -- 3. Mitochondrial control of apoptosis and cancer -- 4. Mitochondrial-to-nuclear communications in cancer -- 5. Types of mitochondrial genetic alterations in cancer -- 6. Mitochondrial genetic alterations in cancer I: skin, head and neck, salivary glands, thyroid, breast, lung, esophageal, gastric, colorectal, pancreatic, liver and gallbladder cancers -- 7. Mitochondrial genetic alterations in cancer II: renal, urinary bladder, prostate, ovarian, endometrial, cervical, nervous system, hemoatologic and connective tissue cancers -- 8. Mitochondrial genome rearrangement and copy number changes in cancer -- 9. Functional importance of mitochondrial genetic alterations in cancer -- 10. The role of mitochondrial reactive oxygen species in cancer -- 11. Mitochondrial DNA measurement in exfoliated cells for cancer detection and monitoring: the copy number advantage -- 12. Early cancer detection and monitoring using changes in the mitochondrial genome as biosensors -- 13. Analysis of mitochondrial genome alterations in cancer -- 14. "Mitocans": agents targeting mitochondria to kill cancer cells -- Index.
- 2012 Springer Protocolsedited by Yves Bigot.Transposable elements as tools for reshaping the genome : it is a huge world after all! / Solenne Bire and Florence Rouleaux-Bonnin -- Using and understanding RepeatMasker / Sébastien Tempel -- Roadmap for annotating transposable elements in eukaryote genomes / Emmanuelle Permal, Timothée Flutre, and Hadi Quesneville -- To detect and analyze sequence repeats whatever be their origin / Jacques Nicolas -- Exploring bacterial insertion sequences with ISfinder : objectives, uses, and future developments / P. Siguier [and others] -- Methods and software in NGS for TE analysis / Cristian Chaparro and Francois Sabot -- The application of LTR retrotransposons as molecular markers in plants / Alan H. Schulman [and others] -- Individual analysis of transposon polymorphisms by AFLP / Susanta K. Behura -- Construction of a library of random mutants in the spirochete Leptospira biflexa using a mariner transposon / Leyla Slamti and Mathieu Picardeau -- Ac-Ds solutions for rice insertion mutagenesis / Emmanuel Guiderdoni and Pascal Gantet -- Engineering the Caenorhabditis elegans genome by Mos1-induced transgene-instructed gene conversion / Valérie J.P. Robert -- Genome-wide manipulations of Drosophila melanogaster with transposons, Flp recombinase, and [phi]C31 integrase / Koen J.T. Venken and Hugo J. Bellen -- The Sleeping Beauty transposon toolbox / Ismahen Ammar, Zsuzsanna Izsvák, and Zoltán Ivics -- PiggyBac toolbox / Mario Di Matteo [and others] -- Insertion site pattern : global approach by linear amplification-mediated PCR and mass sequencing / Cynthia C. Bartholomae [and others] -- Comprehensive DNA methylation profiling of human repetitive DNA elements using an MeDIP-on-RepArray assay / Eric Gilson and Béatrice Hovard -- Novel approach for the development of new antibodies directed against transposase-derived proteins encoded by human neogenes / Ahmed Arnaoty [and others].
- 2008 SpringerDmitrij Frishman, Alfonso Valencia, editors.
- 2016 CambridgeJim Kozubek, Brigham and Womenʹs Hospital, staff scientist, Department of Neurology Broad Institute of MIT and Harvard.This book tells the dramatic story of Crispr and the potential impact of this gene-editing technology.
- 2012 Future Mededitor, Rafael Rosell.Integrating molecular knowledge in clinical decision-making for personalized cancer management -- Gastrointestinal stromal tumors -- Metastatic melanoma -- Ovarian cancer -- Triple-negative breast cancer -- Gastric cancer -- Pleural mesothelioma -- Lung adenocarcinoma.
- 2013 ClinicalKeyDavid P. Clark, Nanette J. Pazdernik.Unit 1. Basic Chemical and Biological Principles -- Unit 2. The Genome -- Unit 3. The Central Dogma of Molecular Biology -- Unit 4. Regulating Gene Expression -- Unit 5. Subcellular Life Forms -- Unit 6. Changing the DNA Blueprint.
- 2014 SpringerW. Edward Highsmith, Jr., editor.Molecular Diagnostics: 12 Tests That Changed Everything focuses on specific laboratory tests and emphasizes how the availability of these tests has altered how clinicians treat their patients. Presented as a standard outline, each chapter focuses on a specific molecular test and provides background on the test and its clinical applications. Continuing with some discussion on how the test is done, interpreted, and used clinically, each chapter then concludes with a discussion of how that test has changed the way medicine is practiced with respect to the disease or condition in question. Authored by renowned experts in the field, Molecular Diagnostics: 12 Tests That Changed Everything is a valuable resource for pathologists, pathology residents, laboratory directors, development personnel, lab medicine fellows and those working in the broad area of oncology, infectious disease and genetics.
- 2013 SpringerAmit Singh, Madhuri Kango-Singh, editors.Undoubtedly, Drosophila melanogaster, fruit fly, has proven to be one of the most popular invertebrate model organisms, and the work horse for modern day biologists. Drosophila, a highly versatile model with a genetic legacy of more than a century, provides powerful genetic, cellular, biochemical and molecular biology tools to address many questions extending from basic biology to human diseases. One of the most important questions in biology focuses on: how does a multi-cellular organism develop from a single-celled embryo? The discovery of the genes responsible for pattern formation has helped refine this question. Drosophila eye model has been extensively used to study molecular genetic mechanisms involved in patterning and growth. Since the genetic machinery involved in the Drosophila eye is similar to humans, it has been used to model human diseases and homology to eyes in other taxa. This book will discuss molecular genetic mechanisms of pattern formation, axial patterning, growth regulation in Drosophila eye, and more.
- 2013 SpringerMauro D'Amato, John D. Rioux, editors.Inflammatory bowel disease (IBD) affects 1% of people worldwide. This condition is partly inherited, and genetic research has made enormous progress during the last few years, providing important insight into disease pathogenesis. This book provides a concise but complete overview of existing knowledge, with particular focus on the molecular and genetic mechanisms at the basis of IBD. Invited experts, at the frontline of IBD research, introduce basic concepts in the pathophysiology of IBD and its two major forms Crohn?s disease and ulcerative colitis, provide a historical perspective and highlight latest discoveries of IBD genetic research, describe how this information has helped to unravel novel pathogenetic pathways, and formulate a vision for future investigations and their clinical application in IBD. State-of-the-art information contained in this book is an exceptional resource for all those in the biomedical field with a specific interest in IBD, including basic scientists, gastroenterologists, GI specialist doctors and research nurses, but also medical and biomedical students.
- 1987 ScienceDirectedited by Michael M. Gottesman.Also available: Print – 1987
- 2007 SpringerAndrés Aguilera, Rodney Rothstein, (eds.).Also available: Print – 2007
- 2011 Springer Protocolsedited by Virginie Orgogozo, Matthew V. Rockman.Characterizing the genome. Genome size determination using flow cytometry of propidium iodide-stained nuclei / Emily E. Hare and J. Spencer Johnston. Chromosome analysis in invertebrates and vertebrates / David M. Rowell, Shu Ly Lim, and Frank Grutzner. Genomic libraries : I. Constuction and screening of fosmid genomic libraries / Mike A. Quail [and others] Genomic libraries : II. Subcloning, sequencing, and assembling large-insert genomic DNA clones / Mike A. Quail [and others] -- Targeting regions of the genome. Reduced representation methods for subgenomic enrichment and next-generation sequencing / Jeffrey M. Good. Accessing the transcriptome : how to normalize mRNA pools / Heiko Vogel and Christopher W. Wheat. Transcriptome sequencing goals, assembly, and assessment / Christopher W. Wheat and Heiko Vogel. Rapid retrieval of DNA target sequences by primer extension capture / Adrian W. Briggs -- Measuring genetic diversity. SNP discovery and genotyping for evolutionary genetics using RAD sequencing / Paul D. Etter [and others] DNA microarray-based mutation discovery and genotyping / David Gresham. Genotyping with Sequenom / Martina Bradić, João Costa, and Ivo M. Chelo. Isolating microsatellite loci : looking back, looking ahead / José A. Andrés and Steven M. Bogdanowicz. Design of custom oligonucleotide microarrays for single species or interspecies hybrids using array olico selector / Amy A. Caudy -- Obtaining candidate gene sequences. Identification of homologous gene sequences by PCR with degenerate primers / Michael Lang and Virginie Orgogozo -- Characterizing cDNA ends by circular RACE / Patrick T. McGrath. Identification of DNA sequences that flank a known region by inverse PCR / Anastasios Pavlopoulos -- Analyzing candidate gene transcripts. Quantification of transcript levels with quantitative RT-PCR / Karen L. Carleton. Using pyrosequencing to measure allele-specific mRNA abundance and infer the effects of cis- and trans-regulatory differences / Patricia J. Wittkopp. Whole-mount in situ hybridization of sectioned tissues of species hybrids to detect cis-regulatory changes in gene expression pattern / Ryo Futahashi. Identifying fluorescently labeled single molecules in image stacks using machine learning / Scott A. Rifkin -- Testing candidate genes and candidate mutations. Experimental approaches to evaluate the contributions of candidate cis-regulatory mutations to phenotypic evolution / Mark Rebeiz and Thomas M. Williams. Experimental approaches to evaluate the contributions of candidate protein-coding mutations to pheotypic evolution / Jay F. Storz and Anthony J. Zera. Making reporter gene constructs to analyze cis-regulatory elements / José Bessa and José Luis Gómez-Skarmeta. PCR directed in vivo plasmid construction using homologous recombination in baker's yeast / Erik C. Andersen. Production of fosmid genomic libraries optimized for liquid culture recombineering and cross-species transgenesis / Radoslaw Kamil Ejsmont [and others] Recombination-mediated genetic engineering of large genomic DNA transgenes / Radoslaw Kamil Ejsmont [and others] Overlap extension PCR : an efficient method for transgene construction / Matthew D. Nelson and David H.A. Fitch. Gene knockdown analysis by double-stranded RNA injection / Benjamin N. Philip and Yoshinori Tomoyasu.
- 2006 Springeredited by Michaela Betta.From destiny to freedom? : on human nature and liberal eugenics in the age of genetic manipulation / Michela Betta -- Diagnostic knowledge in the genetic economy and commerce / Michela Betta -- Body talk : genetic screening as a device of crime regulation / Richard Hil, Richard Hindmarsh -- Genetic testing and human genetic databases / Astrid H. Gesche -- The imperative of the "new genetics" : challenges for ethics, law, and social policy / David Weisbrot -- Insurance and genetics : regulating a private market in the public interest / David Weisbrot, Brian Opeskin -- The social imperative for community genetic screening : an Australian perspective / MaryAnne Aitken, Sylvia Metcalfe -- Genetically transformed healthcare : healthy children and parents / Enzo A. Palombo, Mrinal Bhave -- The Australian law reform inquiry into genetic commission testing - a worker's perspective / Susan Pennicuik -- Genetic information and the Australian labour movement / Suzanne Jamieson -- Protecting the vulnerable : genetic testing and screening for parentage, immigration, and aboriginality / Astrid H. Gesche -- Essentially whose? : genetic testing and the ownership of genetic information / Lyn Turney -- Self-knowledge and self-care in the age of genetic manipulation / Michela Betta.
- 2010Ramez Naam.Status: Not Checked OutLane Catalog RecordIntroduction. Healing and enhancing -- 1. Designer bodies -- 2. Designer minds -- 3. Created equal -- 4. Methuselah's genes -- 5. Designer lifespans -- 8. Methuselah's world -- 7. A child of one's own -- 8. Designer children -- 9. The wired brain -- 10. World wide mind -- 11. Life without limits.
- 2012 Springer[edited by] José Pérez-Martín, Antonio Di Pietro.This book combines state-of-the-art expertise from a variety of diverse pathogen model systems to provide an update to our current understanding of the regulation of fungal morphogenesis as a key determinant of pathogenicity in fungi.
- 2014 Springer Protocolsedited by Shree Ram Singh, Vincenzo Coppola.
- 2015 SpringerSusanne A. Schneider, José M. Tomás Brás, editors.This book covers recent developments and possible pitfalls in the diagnosis of genetic movement disorders and related conditions. It is divided into three sections: technical and scientific aspects; clinical aspects with guidance towards work-up; and ethical and legal aspects of genetic testing in a clinical and research setting. The first section includes chapters on genetic analysis and counselling with critical discussion of potential problems when interpreting the results. Clinical chapters summarize genetic forms of movement disorders including parkinsonism, tics and dystonia with algorithms for hands-on daily practice. Related conditions such as RLS, ataxias and dementias are also covered. Finally, chapters on ethical and legal aspects of genetic testing are included. Movement Disorder Genetics is aimed at clinicians and scientists working in the field of movement disorders and related conditions. .
- 2006 SpringerSadik Tuzun, Elizabeth Bent, editors.
- 2013 SpringerDonald W. Pfaff, Yves Christen, editors.In theoretical terms, sex differences in brain and behavior offer the possibility of fascinating scientific studies on a range of molecular phenomena such as DNA methylation, chromatin protein modification, non-coding DNA, resulting in important neuroanatomical and neurochemical effects. However, this general subject has been treated with much hyperbole. Historically, sex differences were assumed to be present where they did not really exist, e.g. with respect to mathematics, executive leadership, etc. etc. Under what circumstances do we really care about sex differences in brain and behavior? These circumstances concern human maladies whose diagnoses are much different between boys and girls, or between women and men. Prominent examples to be discussed today will include autism, attention deficit hyperactivity disorders and congenital adrenal hyperplasia. The meeting will end with a consideration of effects of estrogenic hormones on the injured brain, and their roles as protective agents.
- 2008 SpringerSandrine Dudoit, Mark J. van der Laan.
- 2011Jared William Wenger.The processes by which the budding yeast Saccharomyces cerevisiae metabolizes carbon sources by both fermentation and respiration have been studied for more than a century. Yeast metabolism has been used both industrially, for the production of important molecules such as ethanol, and as a model for basic scientific research. Applied scientists have studied yeast metabolism to create and optimize novel metabolic phenotypes not naturally found in Saccharomyces yeasts. In parallel, basic scientists have used yeast as a model to understand fundamental processes such as evolutionary adaptation, as well as the pathways of carbon metabolism themselves. There are many unanswered questions in both of these fields, some of which I have addressed in this work. With respect to the industrial importance of yeast, I asked whether there are naturally existing Saccharomyces yeasts that can metabolize the five-carbon sugars important for lignocellulosic ethanol production (such as xylose), and, if so, what is the genetic basis for their phenotypes? Having characterized natural genetic variation in xylose metabolism, I also wanted to understand something more fundamental about how carbon metabolism can adapt, including the molecular nature of adaptations to selection on a limiting carbon source. Specifically, I asked what is the niche breadth of, and are there genetic trade-offs in, yeast that have been evolved under glucose-limitation? I have used a combination of classical genetics, physiology, and high-throughput genomics to answer these two questions. I have discovered novel xylose-utilizing Saccharomyces yeasts and have shed considerable light on the genetic basis for their phenotypes. In addition, I have discovered at least one trade-off for adaptation to limiting glucose, namely that amplification of the hexose-transporter genes HXT6 and HXT7 causes reduced fitness in carbon-rich environments. These two projects highlight two major spheres of Saccharomyces research, and they provide key answers to outstanding questions in both fields.
- 2013- NCBI Bookshelfeditors, Jeffrey Beck [and thirteen others] ; reviewers, Kathi Canese [and five others] ; copy-editor, Stacy Lathrop."The NCBI Handbook 2nd Edition is geared towards advanced users of NCBI resources to provide an understanding of how bioinformatics resources at NCBI work. It is not a step-by-step user manual but complements NCBI user guides, tutorials, help information, and other existing documentation. It is our intent that the handbook will reflect, to the extent possible, the current state of databases, resources, and tools at NCBI, with information updated periodically"--Resource home page.
- 2007 CRCnetBASEedited by Byron C. Jones, Pierre Mormède.Chapter 1. A History of Behavior Genetics / Stephen C. Maxson -- Chapter 2. Developmental Neurobehavioral Genetics: Development as Explanation / Gilbert Gottlieb -- Chapter 3. Some Basics, Mendelian Traits, Polygenic Traits, Complex Traits / Byron C. Jones -- Chapter 4. An Introduction to Quantitative Genetics / Wim E. Crusio -- Chapter 5. From QTL Detection to Gene Identification / Marie-Pierre Moisan -- Chapter 6. Gene Expression / Richard A. Radcliffe -- Chapter 7. Bioinformatics of Behavior / Elissa J. Chesler -- Chapter 8. Congenic and Consomic Strains / Lorraine Flaherty and Valerie Bolivar -- Chapter 9. Animal Resources in Behavioral Neurogenetics / Jean-Michel Lassalle -- Chapter 10. Sample Size Requirements for Experiments on Laboratory Animals / Douglas Wahlsten -- Chapter 11. The Role of Association Studies in Psychiatric Disorders / Nicolas Ramoz and Philip Gorwood -- Chapter 12. Family and Twin Methods / Keith E. Whitfield and Tracy L. Nelson -- Chapter 13. Gene-Environment Interactions / Byron C. Jones and Leslie C. Jones -- Chapter 14. And Now it Starts to Get Interesting: Gene-Gene Interactions / Yamima Osher -- Chapter 15. Schizophrenia: Study of a Genetically Complex Phenotype / Michael F. Pogue-Geile and Irving I. Gottesman -- Chapter 16. Genetics of Major Affective Disorders / Wade Berrettini -- Chapter 17. Pedigree Analyses and the Study of Chimpanzee (Pan troglodytes) Personality and Subjective Well-Being / Alexander Weiss and James E. King -- Chapter 18. The Elusive World of Personality Genes: Cherchez le Phenotype / Richard P. Ebstein, Rachel Bachner-Melman, Jonathan Benjamin, and Robert H. Belmaker -- Chapter 19. Aggression: Concepts and Methods Relevant to Genetic Analyses in Mice and Humans / Stephen C. Maxson and Andrew Canastar -- Chapter 20. Genetic Analysis of Emotional Behaviors Using Animal Models / André Ramos and Pierre Mormède -- Chapter 21. Genetic Analysis of Food Search Behavior in the Fruit Fly (Drosophila melanogaster) / Amsale T. Belay and Marla B. Sokolowski -- Chapter 22. Genetic and Molecular Analyses of Drosophila
- 2014 SpringerDaniela Galimberti, Elio Scarpini, editors.This book gives an overview of the current knowledge on the most common neurodegenerative diseases, including Alzheimer's disease, frontotemporal lobar degeneration, amyotrophic lateral sclerosis, and additional neurodegenerative diseases. Different aspects of each disease are reviewed, including clinical issues, treatments, basic discoveries (genetics and molecular biology), and translation of basic research into biomarkers for early diagnosis. In addition, emerging data indicate that neurodegeneration seems to also be present in classically non-degenerative disorders. Therefore, a chapter about overlapping mechanisms between dementias and psychiatric disorders is included, as well as a description of the role of neurodegeneration in multiple sclerosis. Neurodegenerative Diseases is aimed at clinicians, particularly those working in academic hospitals. This multidisciplinary book will also be of interest to basic researchers in medical fields.
- 2012 SpringerMeena Upadhyaya, David N. Cooper, editors.Neurofibromatosis type 1 (NF1), caused by mutational inactivation of the NF1 tumour suppressor gene, is one of the most common dominantly inherited human disorders, affecting 1 in 3000 individuals worldwide. This book presents in concise fashion, but as comprehensively as possible, our current state of knowledge on the molecular genetics, molecular biology and cellular biology of this tumour predisposition syndrome. Written by internationally recognized experts in the field, the 44 chapters that constitute this edited volume provide the reader with a broad overview of the clinical features of the disease, the structure and expression of the NF1 gene, its germ line and somatic mutational spectra and genotype-phenotype relationships, the structure and function of its protein product (neurofibromin), NF1 modifying loci, the molecular pathology of NF1-associated tumours, animal models of the disease, psycho-social aspects and future prospects for therapeutic treatment.Neurofibromatosis Type 1: Molecular and Cellular Biology will be of great value to medical geneticists, molecular and cellular biologists, oncologists, dermatologists, neurologists, genetic counsellors and general practitioners alike.
- 2006 CRCnetBASEedited by David R. Lynch ; associate editor Jennifer M. Farmer.
- 2014 Springeredited by Bashar Katirji, Henry J. Kaminski, Robert L. Ruff.Part I Approach to neuromuscular diseases: principles and basics -- Clinical assessment in neuromuscular disorders -- Nerve and muscle: basic concepts -- Part II Approach to neuromuscular diseases: neuromuscular investigations -- Serum muscle enzymes in neuromuscular disease -- Autoantibody testing in peripheral neuropathy -- Autoantibody testing in autoimmune neuromuscular junction, hyperexcitability, and muscle disorders -- Forearm exercise testing -- Clinical electromyography (neve conduction studies and needle electromyography) -- Single-fiber EMG -- Quantitative EMG analysis -- Testing of autonomic function -- Quantitative sensory testing -- Nerve and muscle biopsies -- Skin biopsy -- Molecular diagnosis and genetic testing -- Part III Approach to neuromuscular diseases: assessment and treatment of neurologica disorders -- Outcome measures and clinical assessment instruments in neuromuscular disease -- Physical management of patients with neuromuscular diseases -- Immunotherapy in the treatment of autoimmune neuromuscular diseases -- Critical and respiratory care in neuromuscular disorders -- Part IV Neuromuscular disorders: neuronopathies (motor neuron and dorsal root ganglion disorders) -- Poliomyelitis and post-poliomyelitis syndrome -- Amyotrophic lateral sclerosis -- Spinal muscular atrophies -- Atypical motor neuron disorders -- Dorsal root ganglion disorders -- Part V Neuromuscular disorders: Peripheral neuropatahies -- Approach to peripheral nerve disorders -- Approach to small fiber neuropathy -- Charcot-Marie-Tooth diseases -- Inherited metabolic neruopathies -- Guillain-Barre Syndrome and related disorders -- Chronic inflammatory demyelinating polyradiculoneuropathy and related disorders -- Diabetic neuropathies -- Nutritional and alcoholic neuropathies -- Metabolic and endocrine neuropathies -- Environmental toxic neuropathies -- Drug-induced toxic neuropathies -- Vasculitic neuropathies and neuropathies of connective tissue disease -- Nonvasculitic ischemic neuropathies -- Infectious and granulomatous peripheral neuropathies -- Peripheral nerve injury -- Compressive and entrapment neuropathies of the upper extremity -- Compressive and entrapment neuropathies of the lower extremity -- Cranial nerve palsies -- Peripheral nerve tumors -- Cervical radiculopathy -- Lumbosacral and thoracic radiculopathies -- Brachial plexopathies -- Lumbosacral plexopathies -- Part VI Neuromuscular disorders: neuromuscular junction disorders -- Myasthenia Gravis -- Lambert-Eaton Myasthenic Syndrome -- Botulism -- Toxic neuromuscular transmission disorders -- Part VII Neuromuscular disorders: muscle ion channel disorders -- Disorders of skeletal muscle membrane excitability: myotonia congenita, paramyotonia congenita, periodic paralysis, and related syndromes -- Malignant hyperthermia -- Part VIII Neuromuscular disorders: myopathies -- Approach to myopathies -- Dystrophinopathies -- Limb-girdle muscular dystrophies -- Facioscapulohumeral muscular dystrophy -- The myotonic dystrophies -- Oculpharyngeal muscular dystrophy -- Emery-Dreifuss muscular dystrophy -- Congenital myopathies -- Metabolic myopathies -- Mitochondrial myopathies -- Inflammatory myopathies -- Paraspinous myopathies: the dropped head and bent spine syndromes -- Endocrine myopathies -- Toxic myopathies -- Infectious and granulomatous myopathies -- Part IX Neuromuscular disorders: miscellaneous neuromuscular disorders and syndromes -- Myokymia and neuromyotonia -- Muscle cramps and fasciculations -- Stiff-man syndrome -- Tetanus -- Neuroleptic malignant syndrome -- Paraneoplastic neuromuscular disorders -- Acute neuromuscular weakness in the intensive care unit -- Floppy infant -- Rhabdomyolysis and myoglobinuria -- Eosinophilia-myalgia syndrome, eosinophilic fascitiitis, and related fasciitis disorders -- Neuropathis pain and other chronic musculoskeletal pain conditions.
- 2007 ScienceDirecteditor, Keith R. Mitchelson.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.].
- 2012 Springer Protocolsedited by Jian-Bing Fan.Controlling miRNA regulation in disease / Willemijn M. Gommans and Eugene Berezikov -- Introduction to miRNA profiling technologies and cross-platform comparison / Sarah Aldridge and James Hadfield -- Stem-loop RT-qPCR for microRNA expression profiling / James Hurley [and others] -- Poly(T) adaptor RT-PCR / Rui-Shi [and others] -- MicroRNA in situ hybridization / Boye Schnack Nielsen -- Agilent microRNA microarray profiling system / Petula N. D'Andrade and Stephanie Fulmer-Smentek -- MiRNA expression profiling using Illumina Universal BeadChips / Jing Chen, Craig S. April, and Jian-Bing Fan -- MicroRNA expression analysis using the Affymetrix platform / Suzanne Dee and robert C. Getts -- Individualized miRNA assay panels using optically encoded beads / Keld Sorensen -- Microfluidic primer extension assay / Markus Beier and Valesca Boisguérin -- MicroRNA profiling using [mu]Paraflo microfluidic array technology / Xiaochuan Zhou [and others] -- MicroRNA expression analysis using the Illumina microRNA-Seq platform / Shujun Luo -- Next-generation sequencing of miRNAs with Roche 454 GS-FLX technology : steps for a successful application / Ana Raquel Soares, Patrícia M. Pereira, and Manuel A.S. Santos -- Methods for small RNA preparation for digital gene expression profiling by next-generation sequencing / Sam E.V. Linsen and Edwin Cuppen -- Profiling of short RNAs using Helicos single-molecule sequencing / Philipp Kapranov, Fatih Ozsolak, and Patrice M. Milos -- DeepBASE : annotation and discovery of microRNAs and other noncoding RNAs from deep-sequencing data / Jian-Hua Yang and Liang-Hu Qu -- PhenomiR : microRNAs in human diseases and biological processes / Andreas Ruepp, Andreas Kowarsch, and Fabian Theis -- MiRNA expression profiling : from reference genes to global mean normalization / Barbara D'haene [and others] -- MiRNA data analysis : next-gen sequencing / Preethi H. Gunaratne [and others] -- Integrated miRNA expression analysis and target prediction / William Ritchie and John E.J. Rasko -- MiRNAs in human cancer / Xiaomin Zhong, George Coukos, and Lin Zhang -- Blood-based miRNA preparation for noninvasive biomarker development / Svenja Debey-Pascher [and others].
- 2013 SpringerLee-Jun C. Wong, editor.Overview. History of DNA Sequencing Technologies / Lisa D. White -- Clinical Molecular Diagnostic Techniques: A Brief Review / Megan L. Landsverk, Lee-Jun C. Wong -- The Technologies and Bioinformatics. Methods of Gene Enrichment and Massively Parallel Sequencing Technologies / Hong Cui -- Sequence Alignment, Analysis, and Bioinformatic Pipelines / Fuli Yu, Cristian Coarfa -- Protein Structural Based Analysis for Interpretation of Missense Variants at the Genomics Era: Using MNGIE Disease as an Example / Victor Wei Zhang -- Algorithms and Guidelines for Interpretation of DNA Variants / Jing Wang, Megan Landsverk -- Application to Clinical Diagnosis. NGS-Based Clinical Diagnosis of Genetically Heterogeneous Disorders / C. A. Valencia, T. A. Sivakumaran, B. T. Tinkle -- Molecular Diagnosis of Congenital Disorders of Glycosylation (CDG) / Melanie Jones, Madhuri Hegde -- NGS Improves the Diagnosis of X-Linked Intellectual Disability (XLID) / Michael J. Friez, Monica J. Basehore -- NGS Analysis of Heterogeneous Retinitis Pigmentosa / Rui Chen, Feng Wang -- Next-Generation Sequencing Analyses of the Whole Mitochondrial Genome / Lee-Jun C. Wong -- Application of Next-Generation Sequencing of Nuclear Genes for Mitochondrial Disorders / Valeria Vasta, Si Houn Hahn -- Noninvasive Prenatal Diagnosis Using Next-Generation Sequencing / Nancy Bo Yin Tsui, Yuk Ming Dennis Lo -- Compliance with CAP/CLIA Regulations. Guidelines and Approaches to Compliance with Regulatory and Clinical Standards: Quality Control Procedures and Quality Assurance / Ira M. Lubin, Lisa Kalman, Amy S. Gargis -- Validation of NGS-Based DNA Testing and Implementation of Quality Control Procedures / Victor Wei Zhang, Lee-Jun C. Wong -- Frequently Asked Questions About the Clinical Utility of Next-Generation Sequencing in Molecular Diagnosis of Human Genetic Diseases / Ephrem L. H. Chin, Victor Wei Zhang, Jing Wang, Margherita Milone, Susan Pacheco.
- 2013 SpringerAli Masoudi-Nejad, Zahra Narimani, Nazanin Hosseinkhan.Preface -- Next generation sequencing methodologies -- Emergence of next generation sequencing -- Assembly of sequencing data -- De novo assembly algorithms -- Index.
- 2013 SpringerWei Wu, Hani Choudhry, editors.Introduction: next generation sequencing technology and cancer research -- The majority of total nuclear-encoded non-ribosomal RNA in a human cell is dark matter unannotated RNA -- Total RNA-seq of breast cancer in hypoxia -- Altered antisense-to-sense transcript ratios in breast cancer -- Identification of piRNAs in Hela cells by massive parallel sequencing -- Discovery of new microRNAs by small RNAome deep sequencing in childhood acute lymphoblastic leukemia -- Whole-Exome Sequencing Identifies FAM20A Mutations as a Cause of Amelogenesis Imperfecta and Gingival Hyperplasia Syndrome -- Whole-exome sequencing in CIC and IDH1/2 contributing to human oligodendroglioma -- Genetic and structural variation in the gastric cancer kinome revealed through targeted deep sequencing -- Tumour evolution inferred by single-cell sequencing -- Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq -- Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNASeq analysis -- Whole genome DNA methylation analysis based on high throughput sequencing technology -- Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors -- High-resolution genome-wide mapping of HIF-binding sites by ChIP-seq -- MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action -- Genome-wide identification of polycomb-associated RNAs by RIP-seq -- Single-molecule sequencing: sequence methods to enable accurate quantisation -- Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells -- Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA -- The genome information process for cancer research: the challenge and perspective.
- 2006 CRCnetBASEedited by Santiago Lamas, Enrique Cadenas.
- Non-coding genome : lncRNA and enhancer function in epidermal homeostasis and melanoma drug resistance2013Dan E. Webster.Information encoded within the ~3 billion base pairs of the human genome is processed to coordinate diverse biological functions. While ~2% of the human genome is well characterized as coding for canonical proteins, the function of the vast majority of non-coding DNA is unknown (discussed further in Chapter 1). The central aim of this thesis has been to identify functional non-coding regions of the genome and determine their role in human epidermal biology. The epidermis, or skin, maintains a tight balance between its regenerative capacity and its function as a protective tissue barrier. Progenitor cells located in the basal layer of the epidermis continually self-renew, while epidermal cells that divide and migrate outwards engage a terminal differentiation program to form a barrier. Transcriptome profiling of this differentiation process led to the identification of the long non-coding RNA (lncRNA) ANCR, which was then shown to regulate progenitor function of the epidermis (Chapter 2). A novel technology was developed to investigate the protein-binding partners of RNAs (Chapter 3), and this technique was used to uncover the functional significance of a second discovered lncRNA, TINCR, that regulates terminal differentiation of the epidermis in part by binding the protein STAU1 (Chapter 4). The most deadly cancer derived from the epidermis is malignant melanoma. While treatments targeting the mutated BRAF oncogene are initially effective against a subset of melanomas, drug resistance rapidly develops. A region of non-coding DNA was discovered that acts as a lineage-specific enhancer for the drug resistance gene, MET, and disruption of this enhancer by genome editing of < 7bp of DNA within an MITF motif can selectively block drug-induced MET expression and innate resistance to BRAF inhibition (Chapter 5). Taken together, this work demonstrates a framework for identifying functional non-coding RNA and DNA that regulate a diverse set of biological processes.
- 2016 SpringerDagmar Wilhelm, Pascal Bernard, editors.1. The reproductive system -- 2. Non-coding RNAs: an introduction -- 3. How many non-coding RNAs does it take to compensate male/female genetic imbalance? -- 4. The piRNA pathway guards the germline genome against transposable elements -- 5. Non-coding RNA in spermatogenesis and epididymal maturation -- 7. Non-coding RNAs in mammary gland development and disease -- 8. Non-coding RNAs in prostate cancer: from discovery to clinical applications -- 9. Non-coding RNAs in uterine development, function and disease -- Index.
- 2014 SpringerMuller Fabbri, editor.Introduction / Muller Gabbri -- Biogenesis and physiology of microRNAs / Carlos A. Melo and Sonia A. Melo -- Detecting noncoding RNA expression : from arrays to next-generation sequencing / Catalina Perdomo, Joshua Campbell, and Frank Schembri -- MicroRNAs in solid tumors / Jin Wang and Subrata Sen -- MicroRNAs in hematologic malignancies / Johannes Bloehdorn ... [et al.] -- miRNAs as cancer biomarkers / Edward R. Sauter -- Unraveling the complex network of interactions between noncoding RNAs and epigenetics in cancer / Veronica Davalos and Manel Esteller -- MicroRNA SNPs in cancer / Yujing LI and Peng Jin -- Bioinformatics approaches to the study of MircoRNAs / Ravi Gupta and Ramana V. Davuluri -- Beyond miRNAs : role of other noncoding RNAs in cancer / Roxana S. Redis and George A. Calin -- Translational implication for noncoding RNA in cancer / Duaa Dakhallah, Melissa Piper, and S. Patrick Nana-Sinkam.
- 2011Mohammed Nazar AlQuraishi.The foundation of molecular analyses of chemical and biological phenomena is the energy potential, a mathematical description of the energy of every possible interaction in a molecular system. The accuracy of computational and laboratory studies of phenomena ranging from pharmaceutical drug interactions and protein folding to material phase transitions and thin film growth is often limited by the accuracy of these energy potentials. Currently, energy potentials are inferred using a mixture of theoretical modeling and experimental data. So-called "physical potentials" rely on theoretical models to specify the potential's mathematical form and use experimental data to fit few model parameters. In contrast, "statistical potentials", also known as knowledge-based potentials, fit many parameters to experimental data and use theoretical models for the expected statistics of interactions under randomness to infer a potential. In both approaches, theoretical models shape and constrain the inferred potential, resulting in a so-called parametric model. There are several drawbacks to this: (i) The a priori assumptions underlying the inferred potentials may be inaccurate. (ii) Substantial domain knowledge is required (often exceeding what is known). (iii) Potential modeling is lengthy and technically difficult. The theoretical development of some potentials has taken decades. To overcome these problems, potentials could in principle be determined strictly from experimental data without recourse to theoretical modeling by experimentally measuring the energies of all distinct interactions, resulting in a "de novo" energy potential. In practice, direct measurement of interatomic potentials has only been possible for the simplest systems, due to a combinatorial explosion in the number of possible interactions that renders experiment-based inference intractable. In this thesis, we develop a tractable methodology for the inference of de novo potentials that circumvents the experimental intractability barrier. Our methodology overcomes this barrier by synthesizing concepts from structural biology, statistical mechanics, and recent discoveries in information theory known as compressed sensing. The result is a non-parametric potential that does not require an a priori assumption of a theoretical model, overcoming a fundamental limitation of both physical and statistical potentials. To explore the utility and role that this new methodology can play in molecular analysis, we focus on an important and long-standing problem in biology: the sequence specificity of DNA-binding proteins to their DNA targets. We develop a method that uses energy potentials to predict the DNA binding sites of proteins. In the first part of the thesis, we use existing statistical potentials. We develop three novel enhancements of statistical potentials tailored specifically for the protein-DNA binding application. These enhancements exploit certain molecular features of protein-DNA binding, as well as the unique experimental data sets available in this domain, to improve the performance of statistical potentials in predicting protein-DNA binding. In the second part of the thesis, we introduce the notion of a de novo potential, i.e. an energy potential derived exclusively from experimental data, without relying on any theoretical modeling. We discuss previous challenges that have prevented the development of such non-parametric potentials, and then introduce our methodology for inferring de novo potentials. We first present a general methodology that is applicable to any domain of molecular interactions, then specialize our general methodology to the specific application of protein-DNA interactions. Using this specialized version, we infer a number of different protein-DNA energy potentials, and apply them to the problem of predicting the DNA binding sites of proteins. We show that our new method achieves near experimental accuracy for over half of the tests performed, significantly outperforming the state of the art in this field.
- 2008 CRCnetBASEedited by Heather Miller Coyle.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.
- 2011Eduardo Abeliuk.In the last decade remarkable technologies, such as high-density tiling arrays and high-throughput DNA sequencing have enabled whole-genome studies at an unprecedented scale and resolution. In this work I describe how we used these technologies to map novel genetic elements as well as regulatory features of the bacterium Caulobacter crescentus, a model species used for understanding the prokaryotic cell-cycle. I describe a dynamic programming algorithm I used to determine the location of 27 novel small RNA transcripts (sRNAs), several novel antisense RNA transcripts, as well as the accurate mapping of mRNA transcripts. Many of these predictions were validated biochemically. In addition, I describe how we coupled high-throughput transposon mutagenesis with statistical analysis to map all the essential genetic elements in the Caulobacter crescentus genome to 8 base-pair accuracy. We found that 480 out of the 3960 genes contained in Caulobacter's genome are essential for cell viability, as well as 3 out of the 27 novel sRNA that we had identified. Interestingly, there are 90 essential small intergenic DNA segments of unknown function. Finally, I describe the operon organization of Caulobacter's genome.
- 2012Badreddin Edris.Cancer is a disease that is characterized by uncontrolled cell proliferation and is the second leading cause of death in the industrialized world. Cancers can be broadly classified based on their cell type of origin: carcinomas arise from cells of the epithelium, leukemias and lymphomas arise from the cells of the hematopoietic system, and sarcomas arise from cells of the mesenchyme. Recent advances in the understanding of the biological mechanisms of cancer initiation, growth, and metastasis have led to a number of new therapeutic modalities with cancer-specific modes of action; these new biotherapeutic drugs have led to significant improvements in the clinical management of many tumor types. However, these advances have predominantly been directed towards the treatments of carcinomas, leukemias, and lymphomas. For sarcomas, there exist very few available targeted therapies, and the treatment of these tumors remains a significant unmet medical need. This dissertation concerns the identification and inhibition of novel therapeutic targets in sarcomas. In Chapter One, a brief introduction to the epidemiology, biology, and available treatments for cancer is presented. In Chapter Two, a relatively understudied receptor tyrosine kinase (RTK), ROR2, is shown to be a prognostic biomarker of patient outcome and to play a pro-tumorigenic role in two soft-tissue sarcomas, leiomyosarcoma (LMS) and gastrointestinal stromal tumor (GIST). In Chapter Three, a cell surface protein, CD47, is shown to prevent immune-mediated clearance of LMS tumors by macrophages, and anti-CD47 monoclonal antibody (mAb) drugs are demonstrated to have therapeutic efficacy against LMS tumors in vitro and in vivo. In Chapter Four, a mAb directed towards KIT, an RTK over-expressed and mutated in GIST, is shown to slow tumor growth in vitro and in vivo in GIST tumors that are both sensitive and resistant to treatment with the current standard of care drug, imatinib. In Chapter Five, a computational approach is taken to identify novel drugs for LMS by comparing gene expression profiles of these tumors to those of benign lesions arising from the same cell type; drugs identified by this analysis were then tested in vitro on LMS cells. Chapters Six and Seven contain discussions and concluding remarks on the results presented in earlier chapters. In sum, these results help further the identification and experimental validation of novel therapeutic targets in soft-tissue sarcomas. It is hoped that these studies will add to the scientific understanding of soft-tissue sarcoma biology and will help to enable further scientific and clinical advances to improve the lives of patients suffering from these cancers.
- 2015 Springer Protocolsedited by Shinichi Nakagawa, Tetsuro Hirose.Visualization of lncRNA by single-molecule fluorescence in situ hybridization / Margaret Dunagin , Moran N. Cabili , John Rinn , and Arjun Raj -- Super-resolution imaging of nuclear bodies by STED microscopy / Yasushi Okada and Shinichi Nakagawa -- High-resolution 3D DNA FISH using plasmid probes and computational correction of optical aberrations to study chromatin structure at the sub-megabase scale / Luca Giorgetti, Tristan Piolot, and Edith Heard -- Time-lapse imaging of nuclear bodies / Saskia Hutten, Samuel Swift, and Angus I. Lamond -- Visualization of nucleic acids with synthetic exciton-controlled fluorescent oligonucleotide probes / Dan Ohtan Wang and Akimitsu Okamoto -- Live CLEM imaging to analyze nuclear structures at high resolution / Tokuko Haraguchi, Hiroko Osakada, and Takako Koujin -- Ultrastructural analysis of nuclear bodies using electron microscopy / Sylvie Souquere and Gérard Pierron -- Analyses of nuclear proteins and nucleic acid structures using atomic force microscopy / Jamie L. Gilmore [and eight others] -- Genome-wide co-localization screening of nuclear body components using a fluorescently tagged FLJ cDNA clone library / Tetsuro Hirose and Naoki Goshima -- Purification of specific chromatin regions using oligonucleotides : capture hybridization analysis of RNA targets (CHART) / Christopher P. Davis and Jason A. West -- RNA antisense purification (RAP) for mapping RNA interactions with chromatin / Jesse Engreitz, Eric S. Lander, and Mitchell Guttman -- In situ dissection of RNA functional subunits by domain-specific chromatin isolation by RNA purification (dChIRP) / Jeffrey J. Quinn and Howard Y. Chang -- Extracting, enriching, and identifying nuclear body sub-complexes using label-based quantitative mass spectrometry / Archa Fox [and three othrs] -- Studying RNA-binding protein interactions with target mRNAs in eukaryotic cells : native ribonucleoprotein immunoprecipitation (RIP) assays / Joseph A. Cozzitorto [and eight others] -- Cross-linking and immunoprecipitation of nuclear RNA-binding proteins / Quan Li , Yuri Uemura , and Yukio Kawahara -- Purification of noncoding RNA and bound proteins using FLAG peptide-conjugated antisense-oligonucleotides / Shungo Adachi and Tohru Natsume -- MMCT-mediated chromosome engineering technique applicable to functional analysis of lncRNA and nuclear dynamics / Makiko Meguro-Horike and Shin-ichi Horike -- Reconstitution of nucleocytoplasmic transport using digitonin-permeabilized cells / Shingo Kose, Tomoko Funakoshi, and Naoko Imamoto -- Genome-wide analysis of long noncoding RNA turnover / Hidenori Tani [and eight others] -- Knockdown of nuclear-retained long noncoding RNAs using modified DNA antisense oligonucleotides / Xinying Zong [and six others] -- siRNA screening of nuclear proteins / Yuko Hasegawa and Shinichi Nakagawa.
- 2010 Cold Spring Harb Lab Pressmeeting organized by Terri Grodzicker, David Spector, David Stewart, and Bruce Stillman.Chromatin modifications and gene expressions -- Transcription and beyond -- DNA replication and genome integrity -- Reprogramming and differentiation -- Heterochromatin formation and gene silencing -- Nuclear bodies and RNA biology -- Chromosome structure and mitosis -- Chromatin structure and organization -- Nuclear periphery.
- 2008 SpringerAnireddy S.N. Reddy, Maxim Golovkin, editors.Spliceosomal proteins in plants / Y. Ru, B.B. Wang and V. Brendel -- Analysis of alternative splicing in plants with bioinformatics tools / B.J. Haas -- Splice site requirements and switches in plants / M.A. Schuler -- U12-dependent intron splicing in plants / C.G. Simpson and J.W. Brown -- Plant SR proteins and their functions / A. Barta, M. Kalyna and Z.J. Lorkovic -- Spatiotemporal organization of pre-mRNA splicing proteins in plants / G.S. Ali and A.S. Reddy -- Regulation of splicing by protein phosphorylation / R. Fluhr -- mRNA cap binding proteins: effects on abscisic acid signal transduction, mRNA processing, and microarray analyses / J.M. Kuhn, V. Hugouvieux and J.I. Schroeder -- Messenger RNA 3' end formation in plants / A.G. Hunt -- State of decay: an update on plant mRNA turnover / D.A. Belostotsky -- Regulation of flowering time by RNA processing / L.C. Terzi and G.G. Simpson -- Alternative splicing in plant defense / W. Gassmann -- Nuclear RNA export and its importance in abiotic stress responses of plants / V. Chinnusamy, Z. Gong and J.K. Zhu -- Regulation of alternative splicing of pre-mRNAs by stresses / G.S. Ali and A.S. Reddy -- Intron-mediated regulation of gene expression / A.B. Rose -- The role of the plant nucleolus in pre-mRNA processing / J.W. Brown and P.J. Shaw.Also available: Print – 2008
- 2006 Springer Protocolsedited by Paul J. Verma, Alan O. Trounson.Cloning of exotic/endangered species: (desert bighorn sheep) / James "Buck" Williams ... [et al.] -- Handmade somatic cell cloning in cattle / Gábor Vatja, Ian M. Lewis, and R. Tayfur Tecirlioglu -- Genetic modification of sheep by nuclear transfer with gene-targeted somatic cells / A. John Clark, Sarah Burl, and Chris Denning -- Transgenesis using nuclear transfer in goats / Anthoula Lazaris ... [et al.] -- Nuclear reprogramming : an overview / Takashi Tada -- Expression of imprinted genes in cloned mice / Takashi Kohda, Fumitoshi Ishino, and Atsuo Ogura -- Nuclear remodeling assay in xenopus egg extract / Koichi Gonda and Nobuaki Kikyo -- In vitro reprogramming of nuclei and cells / Anne-Mari Håkelien ... [et al.] -- Techniques for nuclear transfer to mouse embryonic stem cells / Danielè Pralong and Paul J. Verma -- Gene expression and methylation patterns in cloned embryos / Christine Wrenzycki ... [et al.] -- Are there any normal clones? / Ian Wilmut -- Future and applications of cloning / Alan O. Trounson. Origin and progress of nuclear transfer in nonmammalian animals / Marie A. Di Berardino -- In vitro maturation and embryo production in cattle / Marc-André Sirard and Karine Coenen -- Activation of oocytes after nuclear transfer / Zoltán Macháty -- Culture medium preferences of pre-implantation cloned mouse embryos / Björn Heindryckx, Josiane Van der Elst, and Marc Dhont -- Maintenance of pregnancy in pigs with limited viable embryos / Tim King and Paul A. De Sousa -- Health and neonatal care of bovine clones / Jacqui T. Forsyth and David N. Wells -- Optimization of procedures for cloning by somatic cell nuclear transfer in mice / Young Gie Chung, Shaorong Gao, and Keith E. Latham -- Production of cloned calves using roscovitine-treated adult somatic cells as donors / Kazuchika Miyoshi, Sezen Arat, and Steven L. Stice -- A double nuclear transfer technique for cloning pigs / Irina A. Polejaeva, Shawn Walker, and Keith Campbell -- Nuclear transfer in nonhuman primates / Shoukhrat M. Mitalipov and Don P. Wolf --
- 2016 Springer Protocolsedited by Gunter Mayer.Selection of aptamers for metabolite sensing and construction of optical nanosensors / Yi Long ... [et al.] -- SELEX of cell-specific RNA aptamers / Katharina Berg, Eileen Magbanua, and Ulrich Hahn -- Developing aptamers by cell-based SELEX / Silvia Catuogno, Carla Lucia Esposito, and Vittorio de Franciscis -- DNA aptamer generation by genetic alphabet expansion SELEX (ExSELEX) using an unnatural base pair system / Michiko Kimoto, Ken-ichiro Matsunaga, and Ichiro Hirao -- Capillary electrophoresis for the selection of DNA aptamers recognizing activated protein C / Nasim Shahidi Hamedani and Jens Müller -- Preparation of SELEX samples for next-generation sequencing / Fabian Tolle and Günter Mayer -- Next-generation analysis of deep sequencing data : bringing light into the black box of SELEX experiments / Michael Blank -- Aptamer binding studies using MicroScale thermophoresis / Dennis Breitsprecher ... [et al.] -- Label-free determination of the dissociation constant of small molecule-aptamer interaction by isothermal titration calorimetry / Marc Vogel and Beatrix Suess -- Applications of aptamers in flow and imaging cytometry / Isis C. Nascimento ... [et al.] -- In vitro and in vivo imaging of fluorescent aptamers / Ioanna Théodorou ... [et al.] -- Crystallographic pursuit of a protein-RNA aptamer complex / John J. G. Tesmer -- Voltammetric aptasensor based on magnetic beads assay for detection of human activated protein C / Arzum Erdem, Gulsah Congur, and Ece Eksin -- Apta-PCR / Alessandro Pinto ... [et al.] -- Aptamer-based enzyme capture assay for measurement of plasma thrombin levels / Jens Müller ... [et al.] -- Application of aptamers in histopathology / Sarah Shigdar ... [et al.] -- Aptamer stainings for super-resolution microscopy / Maria Angela Gomes de Castro, Burkhard Rammner, and Felipe Opazo -- Synthesis and characterization of aptamer-targeted SNALPs for the delivery of siRNA / Samantha E. Wilner and Matthew Levy -- Screening of genetic switches based on the twister ribozyme motif / Michele Felletti, Benedikt Klauser, and Jörg S. Hartig.
- 2014 SpringerKatsuhiko S. Murakami, Michael A. Trakselis, editors.This book provides a review of the multitude of nucleic acid polymerases, including DNA and RNA polymerases from Archea, Bacteria and Eukaryota, mitochondrial and viral polymerases, and other specialized polymerases such as telomerase, template-independent terminal nucleotidyl transferase and RNA self-replication ribozyme. Although many books cover several different types of polymerases, no book so far has attempted to catalog all nucleic acid polymerases. The goal of this book is to be the top reference work for postgraduate students, postdocs, and principle investigators who study polymerase.
- 2007 Springeredited by Anton Buzdin and Sergey Lukyanov.
- 2014 CRCnetBASE[edited by] Lynnette R. Ferguson.Nutrigenetics and nutrigenomics : importance for functional foods and personalized nutrition / Lynnette R. Ferguson -- Variations in solute transporter genes affecting micronutrient solute transport and human health / Peter Eck -- Genetic variants in the omega-6 and omega-3 fatty acid metabolic pathways : their role in the determination of nutritional requirements and chronic disease risk / Artemis P. Simopoulos -- Nutrigenomic approaches to unravelling the physiological effects of complex foods / Peter J. Gillies and John P. Vanden Heuvel -- Modulating the risk of cardiovascular disease through nutrigenetics / Antonio Garcia-Rios ... [et al.] -- Modulating the risk of obesity and diabetes through nutrigenetics / Helen M. Roche and Catherine Phillips -- Nutrigenetics and Crohn's disease -- / Lynnette R. Ferguson -- Microbiome and host interactions in inflammatory bowel diseases : relevance for personalized nutrition / Wayne Young, Bianca Knoch, and Nicole C. Roy -- The importance of cell-specific gene expression patterns for understanding nutrient and gene interactions in inflammatory bowel diseases / Anna Russ ... [et al.] -- Data mining and network analysis : potential importance in nutrigenomics research / Varma Vijayalakshmi and Jim Kaput -- Metabolomics : an important tool for assessing state of health and risk of disease in nutrigenomics research / Hui Ming Lin and Daryl Rowan -- Epigenetics : what role could this play in functional foods and personalised nutrition? / Matthew P.G. Barnett, Shalom A. Bassett, and Emma Bermingham -- Foodomics to study efficacy of human dietary interventions : proof of principle study / Stephanie Ellett ... [et al.] -- Considerations in estimating genotype in nutrigenetic studies / Angharad R. Morgan -- Bringing nutrigenomics to the food industry : industry-academia partnerships as an important challenge / Ralf C. Schlothauer and Joerg Kistler -- Commercialisation of nutrigenetics and nutrigenomics / Virginia Parslow and Lynnette R. Ferguson -- Bringing nutrigenomics to the public : Is direct-to-consumer testing the future of nutritional genomics? / David Castle -- Nutritional genomics in practice : interaction with health professionals in bringing nutritional genomics to the public / Colleen Fogarty Draper -- Harvesting normative potential for nutrigenomic research / Bart Penders and Michiel Korthals -- Public health context for nutrigenomics and personalized nutrition / Elizabeth H. Marchlewicz, Karen E. Peterson, and Filbert S. Omenn -- Nutrigenomics and public health / Maria Agelli and John Milner.
- 2011 CRCnetBASEedited by Nilanjana Maulik, Gautam Maulik."Extensive research on nutrigenomics has unveiled numerous epigenetic mechanisms that are influenced by our dietary signature. This book illustrates how nutrition can influence epigenetic inheritance and the mechanisms that underlie modification of the metabolic imprint of an individual. The text discusses the basics of nutrigenomics and epigenetic regulation, types of nutrition influencing genetic imprinting, and the role of nutrition in modulating an individual's predisposition to disease. It also covers epigenetic variation, genomic imprinting, maternal nutrition, neonatal nutrition, as well as epigenetics and nutrition relating to cancer, heart disease, and obesity"--Provided by publisher.Also available: Print – 2011
- 2014 SpringerDebmalya Barh, editor.Breast cancer is the most common cancer in females that accounts for highest cancer specific deaths worldwide. In the last few decades research has proven that breast cancer can be treated if diagnosed at early stages and proper therapeutic strategy is adopted. Omics-based recent approaches have unveiled the molecular mechanism behind the breast tumorigenesis and aid in identification of next-generation molecular markers for early diagnosis, prognosis, and even the effective targeted therapy. Significant development has taken place in the field of omics in breast cancer in the last decade. The most promising omics approaches and their outcomes in breast cancer have been presented in this book for the first time. The book covers omics technologies and budding fields such as breast cancer miRNA, lipidomics, epigenomics, proteomics, nutrigenomics, stem cell, pharmacogenomics and personalized medicine, and many more along with conventional topics such as breast cancer management etc. It is a research-based reference book useful for clinician-scientists, researchers, geneticists and health care industries involved in various aspects of breast cancer. The book will also be useful for students of biomedicine, pathology, and pharmacy.
- 2013 SpringerDebmalya Barh, Dipali Dhawan, Nirmal Kumar Ganguly, editors.Omics for Personalized Medicine will give to its prospective readers the insight of both the current developments and the future potential of personalized medicine. The book brings into light how the pharmacogenomics and omics technologies are bringing a revolution in transforming the medicine and the health care sector for the better. Students of biomedical research and medicine along with medical professionals will benefit tremendously from the book by gaining from the diverse fields of knowledge of new age personalized medicine presented in the highly detailed chapters of the book. The book chapters are divided into two sections for convenient reading with the first section covering the general aspects of pharmaocogenomic technology that includes latest research and development in omics technologies. The first section also highlights the role of omics in modern clinical trials and even discusses the ethical consideration in pharmocogenomics. The second section is focusing on the development of personalized medicine in several areas of human health. The topics covered range from metabolic and neurological disorders to non-communicable as well as infectious diseases, and even explores the role of pharmacogenomics in cell therapy and transplantation technology. Thirty-four chapters of the book cover several aspects of pharmacogenomics and personalized medicine and have taken into consideration the varied interest of the readers from different fields of biomedical research and medicine. Advent of pharmacogenomics is the future of modern medicine, which has resulted from culmination of decades of research and now is showing the way forward. The book is an honest endeavour of researchers from all over the world to disseminate the latest knowledge and knowhow in personalized medicine to the community health researchers in particular and the educated public in general.
- Omics in clinical practice : genomics, pharmacogenomics, proteomics, and transcriptomics in clinical research2014 CRCnetBASEedited by Yu Liu.Part 1. Omics and human disease -- part 2. Translational and personalized medicine -- part 3. Molecular and genetic markers -- part 4. Omics and pathogens -- part 5. Companion diagnostics.
- 2010 SpringerWilliam C.S. Cho, editor.
- 2005 Springeredited by William J. LaRochelle, Richard A. Shimkets.Also available: Print – 2005
- 2008Mark Reimers.Prof. Mark Reimers covers the best ways to design and interpret microarray gene expression experiments, including experiment design, pre-processing, exploratory analysis, normalization and statistical testing.
- 2012 SpringerCharles E. Bullerwell, editor.pt. 1. Origins of organelle genomes -- pt. 2. Organelle genome evolution -- pt. 3. Mechanisms of organelle gene loss -- pt. 4. Origins of organelle proteomes -- pt. 5. Evolution of organelle transcription -- pt. 6. Evolution of organelle RNA processing -- pt. 7. Evolution of organelle translation, tRNAs and the genetic code.
- 2009 SpringerLuis P. Villarreal.An overview : identity from bacteria to belief -- The prokaryotes : viruses, hyperparasites and the origin of group identity -- Sensory systems (light, odor, pheromones) in communities of oceanic microbes -- Subjugation of the individual : prokaryotic group living : blooms, slime and mats -- Animal group identity : from slime to worms, emergence of the brain -- Group identity in aquatic animals : learning to belong -- Development of tetrapod group identity, the smell of self -- Origin of primate group identity : vision and the great ERV invasion -- Human group identity : language and a social mind.
- 2012 ScienceDirectDavid Goldman.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.
- 2008Gérard Battail.A brief overview of molecular genetics -- An overview of information theory -- More on molecular genetics -- More on information theory -- An outline of error-correcting codes -- DNA is an ephemeral memory -- A toy living world -- Subsidiary hypothesis, nested system -- Soft codes -- Biological reality conforms to the hypotheses -- Identification of genomic codes.
- 2011 Springer[edited by] Ayeda Ayed, Theodore Hupp.TP53 mutations in human cancers : selection versus mutagenesis / Magali Olivier, Audrey Petitjean, Claude Caron de Fromentel, and Pierre Hainaut -- Lessons on p53 from mouse models / Dadi Jiang and Laura D. Attardi -- TP63, TP73 : the guardian's elder brothers / Stephanie Courtois, Pierre Hainaut and Claude Caron de Fromentel -- The regulation of p53 protein function by phosphorylation / Nicola J. Maclaine and Theodore Hupp -- The p53-Mdm2 loop : a critical juncture of stress response / Yaara Levav-Cohen, Zehavit Goldberg, Osnat Alsheich Bartok, Valentina Zuckerman, Sue Haupt and Ygal Haupt -- Cooperation between MDM2 and MDMX in the regulation of p53 / Jeremy Blaydes -- Regulation and function of the original p53-inducible p21 gene / Jennifer A. Fraser -- p53 localization / Carl G. Maki -- Modes of p53 interactions with DNA in the chromatin context / Vladana Vukojevic, Tatiana Yakovleva, and Georgy Bakalkin -- p53's dilemma in transcription : analysis by microarrays / Karuppiah Kannan, Gideon Rechavi and David Givol -- Tumor viruses and p53 / Nobuo Horikoshi -- p53 and immunity / Vikram Narayan, Sarah E. Meek and Kathryn L. Ball.
- 2013 Springer Protocolsedited by Gloria H. Su.Identification and analysis of precursors to invasive pancreatic cancer / Hanno Matthaei, Marco Dal Molin, and Anirban Maitra -- Tissue microarrays : construction and use / Helen Remotti -- Immunohistochemistry of pancreatic neoplasia / Sukhwinder Kaur ... [et al.] -- Method for conducting highly sensitive MicroRNA in situ hybridization and immunohistochemical analysis in pancreatic cancer / Lorenzo F. Sempere and Murray Korc -- Optimal molecular profiling of tissue and tissue components : defining the best processing and microdissection methods for biomedical applications / Jaime Rodriguez-Canales -- Considerations for sequencing analyses of pancreatic cancer progression and metastasis / Alvin Makohon-Moore and Christine A. Iacobuzio-Donahue -- DNA methylation analysis in human cancer / Eileen O'Sullivan and Michael Goggins -- Quantitative real-time PCR expression analysis of peripheral blood mononuclear cells in pancreatic cancer patients / Michael J. Baine, Kavita Mallya, and Surinder K. Batra -- Development of a cytokine-modified allogeneic whole cell pancreatic cancer vaccine / Dan Laheru, Barbara Biedrzycki, and Elizabeth M. Jaffee -- Prevention and genetics of pancreatic cancer : a programmatic approach / Aimee L. Lucas ... [et al.] -- Development of orthotopic pancreatic tumor mouse models / Wanglong Qiu and Gloria H. Su -- Evaluating Dietary Compounds in Pancreatic Cancer Modeling Systems / Emman Mascarinas, Guido Eibl, and Paul J. Grippo -- Quantification of murine pancreatic tumors by high-resolution ultrasound / Stephen A. Sastra and Kenneth P. Olive -- Microdissection and culture of murine pancreatic ductal epithelial cells / Yuliya Pylayeva-Gupta, Kyoung Eun Lee, and Dafna Bar-Sagi -- Sphere-forming assays for assessment of benign and malignant pancreatic stem cells / Yue J. Wang ... [et al.] -- Analysis of transplanted bone marrow-derived cells in chronic pancreatitis / Christoph B. Westphalen, Frederic Marrache, and Timothy C. Wang -- Analysis of the potential for pancreatic cancer metastasis in vitro and in vivo / Chen Huang and Keping Xie -- Use of fluorescent probes in the study of reactive oxygen species in pancreatic cancer cells / Richard D. Dinnen, Yuehua Mao, and Robert L. Fine -- Analysis of tumor-associated mucin glycotopes by western transfer methods / Vinayaga S. Gnanapragassam, Maneesh Jain, and Surinder K. Batra -- Evaluating tumor angiogenesis / Minji K. Uh, Jessica Kandel, and Jan Kitajewski -- Pooled shRNA screenings : experimental approach / Ruth Rodriguez-Barrueco, Netonia Marshall, and Jose M. Silva -- Pooled ShRNA screenings : computational analysis / Jiyang Yu ... [et al.].
- 2008 CRCnetBASEG.H. Beale, John R. Preer, Jr.Mating types in paramecium -- General description of the protista and of paramecium -- Methods of studying genetic processes in organisms of the paramecium Aurelia species group -- The determination of mating types in paramecium -- Symbionts and mitochondria of paramecium -- Determination of i-antigens -- Micronuclei and macronuclei -- Ribosomal RNA and DNA -- Cortical morphogenesis -- Behavior -- Epigenetics.
- 2012 SpringerKlaus Aktories, Joachim H.C. Orth, Ben Adler, editors.Pasteurella multocida: Diseases and Pathogenesis / I. W. Wilkie, M. Harper, J. D. Boyce and B. Adler -- Pathogenomics of Pasteurella multocida / J. D. Boyce, T. Seemann, B. Adler and M. Harper -- The Key Surface Components of Pasteurella multocida: Capsule and Lipopolysaccharide / Marina Harper, John D. Boyce and Ben Adler -- Pasteurella multocida and Immune Cells / Katharina F. Kubatzky -- Molecular Biology of Pasteurella multocida Toxin / Joachim H. C. Orth and Klaus Aktories -- Pasteurella multocida Toxin Interaction with Host Cells: Entry and Cellular Effects / Brenda A. Wilson and Mengfei Ho -- Swine Atrophic Rhinitis Caused by Pasteurella multocida Toxin and Bordetella Dermonecrotic Toxin / Yasuhiko Horiguchi -- The Pasteurella multocida Toxin: A New Paradigm for the Link Between Bacterial Infection and Cancer / Alistair Lax.
- 2012 SpringerJanos Minarovits, Hans Helmut Niller, editors.The Impact of Foreign DNA Integration on Tumor Biology and Evolution via Epigenetic Alterations / Walter Doerfler -- The Role of DNMT3B Mutations in the Pathogenesis of ICF Syndrome / Sole Gatto, Maurizio D'Esposito and Maria R. Matarazzo -- Dysfunction of the Methyl-CpG-Binding Protein MeCP2 in Rett Syndrome / Gaston Calfa, Alan K. Percy and Lucas Pozzo-Miller -- Epigenetic Alterations in Glioblastoma Multiforme / John K. Wiencke -- Aberrant Epigenetic Regulation in Breast Cancer / Amanda Ewart Toland -- The Impact of Epigenetic Alterations on Diagnosis, Prediction, and Therapy of Prostate Cancer / Christian Arsov, Wolfgang Goering and Wolfgang A. Schulz -- Epigenetic Reprogramming in Lung Carcinomas / András Kádár and Tibor A. Rauch -- Epigenetic Changes in Virus-Associated Neoplasms / Hans Helmut Niller, Ferenc Banati, Eva Ay and Janos Minarovits -- Genetic and Epigenetic Determinants of Aggression / Barbara Klausz, József Haller, Áron Tulogdi and Dóra Zelena -- Co-Regulation and Epigenetic Dysregulation in Schizophrenia and Bipolar Disorder / Dóra Zelena -- Disruption of Epigenetic Mechanisms in Autoimmune Syndromes / Lorenzo de la Rica and Esteban Ballestar -- Imprinting Disorders / Thomas Eggermann -- Epigenetics and Atherosclerosis / Einari Aavik, Mikko P. Turunen and Seppo Ylä-Herttuala -- Microbe-Induced Epigenetic Alterations / Hans Helmut Niller, Ferenc Banati, Eva Ay and Janos Minarovits.
- 2016 SpringerJanos Minarovits, Hans Helmut Niller, editors.1. Epigenetic regulation -- 2. HIV-induced epigenetic alterations in host cells -- 3. Epigenetic alterations in Epstein-Barr virus-associated diseases -- 4. Epigenetic dysregulation in virus-associated neoplasms -- 5. Epigenetic alterations induced by bacterial lipopolysaccharides -- 6. Patho-epigenetics of infectious diseases caused by intracellular bacteria -- Index.
- 2011 Springer Protocolsedited by Bimal D.M. Theophilus and Ralph Rapley.Conformation-Sensitive Capillary Electrophoresis / Emma Jane Ashton -- Conformation Sensitive Gel Electrophoresis / Marian Hill -- Denaturing HPLC for Mutation Screening / Mike Mitchell, Jacqueline Cutler -- In Situ Detection of Human Papillomavirus DNA After PCR-Amplification / Gerard J. Nuovo -- LATE-PCR and Allied Technologies: Real-Time Detection Strategies for Rapid, Reliable Diagnosis from Single Cells / Kenneth E. Pierce, Lawrence J. Wangh -- Long-PCR Amplification of Human Genomic DNA / Stephen Keeney -- Human Papilloma Virus Strain Detection Utilising Custom-Designed Oligonucleotide Microarrays / Duncan Ayers, Mark Platt, Farzad Javad, Philip J. Day -- Multiplex Ligation-Dependent Probe Amplification (MLPA®) for the Detection of Copy Number Variation in Genomic Sequences / Petra G. Os, Jan P. Schouten -- Screening for Genomic Rearrangements by Multiplex PCR/Liquid Chromatography / Claude Houdayer, Catherine Dehainault, Marion Gauthier-Villars, Dominique Stoppa-Lyonnet -- Mutation Surveyor: Software for DNA Sequence Analysis / Jayne A. Minton, Sarah E. Flanagan, Sian Ellard -- Non-invasive Prenatal Diagnosis / Cathy Meaney, Gail Norbury -- Automated DNA Sequencing / Yvonne Wallis, Natalie Morrell -- Phylogenetic Microarrays for Cultivation-Independent Identification and Metabolic Characterization of Microorganisms in Complex Samples / Alexander Loy, Michael Pester, Doris Steger -- Prenatal Detection of Chromosome Aneuploidy by Quantitative-Fluorescence PCR / Kathy Mann, Erwin Petek, Barbara Pertl -- Use of Robotics in High-Throughput DNA Sequencing / Stephen Keeney -- Detection of Factor V Leiden and Prothrombin c.20210G>A Allele by Roche Diagnostics LightCycler® / Peter C. Cooper -- RT-PCR for the Detection of Translocations in Bone and Soft Tissue Tumours in Formalin-Fixed Paraffin-Embedded Tissues / Ann Williams, D. Chas Mangham -- Detection of Minimal Residual Disease in Leukaemia by RT-PCR / Joanne Mason, Mike Griffiths -- Mutation Detection by Southern Blotting / Gillian Mellars, Keith Gomez.
- 2015 Springer Protocolsedited by Chhandak Basu."This volume provides an overview on design PCR primers for successful DNA amplification. Chapters focus on primer design strategies for quantitative PCR, in silico PCR primer design , and primer design using software. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls." -- Provided by publisher.
- edited by Anton Yuryev.
- 2011 Springer Protocolsedited by Daniel J. Park.Setup of a PCR Laboratory / Zaheer Khan -- Long-Range PCR with a DNA Polymerase Fusion / Holly H. Hogrefe, Michael C. Borns -- Isolation of Genomic Insertion Sites of Proviruses Using Splinkerette-PCR-Based Procedures / Bin Yin -- Lariat-Dependent Nested PCR for Flanking Sequence Determination / Daniel J. Park -- CODEHOP PCR and CODEHOP PCR Primer Design / Jeannette P. Staheli, Richard Boyce, Dina Kovarik, Timothy M. Rose -- Sequencing of Difficult DNA Regions by SAM Sequencing / Keith R. Mitchelson -- A Global Single-Cell cDNA Amplification Method for Quantitative Microarray Analysis / Kazuki Kurimoto, Mitinori Saitou -- Quantitation of MicroRNAs by Real-Time RT-qPCR / Caifu Chen, Ruoying Tan, Linda Wong, Richard Fekete, Jason Halsey -- High-Throughput SuperSAGE / Hideo Matsumura, Kentaro Yoshida, Shujun Luo, Detlev H. Krüger, Günter Kahl, Gary P. Schroth, Ryohei Terauchi -- Deep Cap Analysis of Gene Expression / Junpei Kurosawa, Hiromi Nishiyori, Yoshihide Hayashizaki -- Linking Emulsion PCR Haplotype Analysis / James G. Wetmur, Jia Chen -- PAP-LMPCR: An Improved, Sequence-Selective Method for the In Vivo Analysis of Transcription Factor Occupancy and Chromatin Fine Structure / Richard Ingram, Arthur Riggs, Constanze Bonifer -- The Many Faces of MLPA / Thomas Ohnesorg, Erin Turbitt, Stefan J. White -- Assessing Gene-Specific Methylation Using HRM-Based Analysis / Ee Ming Wong, Alexander Dobrovic -- Alu PCR / Maurizio Cardelli -- Asynchronous PCR / Caifu Chen, David Ruff, Jason Halsey -- Novel Applications of PCR Through the Use of DNA Substrates / Stuart M. Wilson -- Enhanced Solid Phase PCR for Increased Loading of Amplicon onto Solid Support / Daniel J. Park -- Application of Blocking Oligonucleotides to Improve Signal-to-Noise Ratio in a PCR / Hege Vestheim, Bruce E. Deagle, Simon N. Jarman -- Asymmetric Overlap Extension PCR Method for Site-Directed Mutagenesis / Yue-Hua Xiao, Yan Pei -- Ribosome Display: A Technology for Selecting and Evolving Proteins from Large Libraries / Birgit Dreier, Andreas Plückthun -- GLOBE: Analysis of DNA-Protein Interaction Analysis / Takaaki Kojima, Hideo Nakano -- PCR DNA-Array Profiling of DNA-Binding Transcription Factor Activities in Adult Mouse Tissues / Yimin Sun, Jing Cheng, Keith R. Mitchelson -- Nucleotide Exchange and Excision Technology DNA Shuffling and Directed Evolution / Janina Speck, Sabine C. Stebel, Katja M. Arndt, Kristian M. Müller.
- 2014 SpringerChristine M. Houser.Often, information in review books can raise as many questions as it answers. This interferes with the study process, because the learner must either look up additional information or skip ahead without truly comprehending what he or she has read. As an alternative, Pediatric Genetics and Inborn Errors of Metabolism: A Practically Painless Review presents bite-size chunks of information that can be read and processed rapidly, helping learners to stay active while studying and to pick up new information the first time they read it. This book's question and answer format allows for self-testing or study with a partner or a group. The format also facilitates dipping into the book during a few minutes of downtime at the hospital or office. Pediatric Genetics and Inborn Errors of Metabolism: A Practically Painless Review is a quick and easy way to master these tricky topics and is suitable for those studying for the pediatric board exam, practicing physicians brushing up their skills, and any busy clinician who wants to learn more about these topics while on the go.
- 2015 CRCnetBASEedited by Heewon Lee.
- 2008 Springer ProtocolsNadine Cohen, editor.Challenges, opportunities, and evolving landscapes in pharmacogenomics and personalized medicine : an industry perspective / Nadine Cohen and Theresa Frangiosa -- Implementation of pharmacogenomic sample collection in clinical trials / Deborah Sokol Ricci and Monique Franc -- Pharmacogenomics : the regulatory environment and labeling implications / Myong-Jin Kim ... [et al.] -- Applications of pharmacogenomics in drug discovery / Duncan McHale -- Applications of pharmacogenomics in clinical trials / Monique Franc -- Pharmacogenomics applications in drug metabolism : from genotyping to drug label-challenges? / Ann K. Daly -- The genetics of adverse drug reactions : promises and problems / Martin Armstrong -- Strategies and resources for marker selection and genotyping in genetic association studies / Nicole Soranzo, Dong-Jing Fu, and Qingqin S. Li -- Study design and statistical issues in pharmacogenetics research : from candidate genes to genome-wide screens / Nicholas J. Schork, Nathalie Malo, and Eric J. Topol -- Holy SNP, Batman! / Reyna Favis -- Predictive biomarker classifiers in the design of pivotal clinical trials / Richard Simon -- Translation of biomarkers into clinical utility / William L. Trepicchio and George Mulligan -- Pharmacogenomic study feasibility assessment and pharmaceutical business decision-making / Monique Franc and Theresa Frangiosa -- Co-development of drugs and pharmacogenomics-based diagnostics in oncology / Jeffrey S. Ross -- Pharmacogenomics applications in epilepsy / Chantal Depondt -- Pharmacogenomics in Alzheimer's disease / Ramón Cacabelos -- Pharmacogenomics applications in psychiatric disorders / Todd Lencz and Anil K. Malhotra -- Pharmacogenomics in HIV disease / Amalio Telenti -- Pharmacogenomics and cardiovascular drugs / Gérard Siest ... [et al.] -- Pharmacogenomic applications in children / Susan F.A. Grant and Hakon Hakonarson -- Pharmacogenomics of rare and monogenic disorders / Paul D. Maher.
- 2008 Springer Protocolsedited by Qing Yan.
- 2009 Springer Protocolsedited by Marjo de Graauw.A high-resolution two dimensional gel- and pro-Q DPS-based proteomics workflow for phosphoprotein identification and quantitative profiling / Ganesh K. Agrawal and Jay J. Thelen -- Differential phosphoprotein labelling (DIPPL) using 32P and 33P / Aviva M. Tolkovsky and Andreas Wyttenbach -- Identification of oxidative stress-induced tyrosine phosphorylated proteins by immunoprecipitation and mass spectrometry / Ma Carmen Duran, Hong-Lin Chan, and John F. Timms -- Enrichment and characterization of phosphopeptides by immobilized metal affinity chromatography (IMAC) and mass spectrometry / Tine E. Thingholm and Ole N. Jensen -- The use of titanium dioxide micro-columns to selectively isolate phosphopeptides from proteolytic digests / Tine E. Thingholm and Martin R. Larsen -- Enrichment and separation of mono- and multiply phosphorylated peptides using sequential elution from IMAC prior to mass spectrometric analysis / Tine E. Thingholm , Ole N. Jensen, and Martin R. Larsen -- Use of stable isotope labeling by amino acids in cell culture (SILAC) for phophotyrosine protein identification and quantitation / Guoan Zhang and Thomas A. Neubert -- Hydrophilic interaction chromatography for fractionation and enrichment of the phosphoproteome / Dean E. McNulty and Roland S. Annan -- SILAC for global phosphoproteomic analysis / Genaro Pimienta, Raghothama Chaerkady, and Akhilesh Pandey -- Quantitative phospho-proteomics based on soluble nanopolymers / Anton Iliuk and W. Andy Tao -- Profiling the tyrosine phosphorylation state using SH2 domains / Kevin Dierck ... [et al.] -- An overview of the qualitative analysis of phosphoproteins by mass spectrometry / Philip R. Gafken -- The analysis of phosphoproteomes by selective labelling and advanced mass spectrometric techniques / Angela Amoresano ... [et al.] -- On-line liquid chromatography electron capture dissociation for the characterization of phosphorylation sites in proteins / Steve M.M. Sweet and Helen J. Cooper -- Quantification of protein phosphorylation by [mu]LC-ICP-MS / Ralf Krüger, Nico Zinn, and Wolf D. Lehmann -- Reverse-phase diagonal chromatography for phosphoproteome research / Kris Gevaert and Joël Vandekerckhove -- Chemical tagging strategies for mass spectrometry-based phospho-proteomics / Alexander Leitner and Wolfgang Lindner -- Antibody array platform to monitor protein tyrosine phosphorylation in mammalian cells / Alicia S. Chung and Y. Eugene Chin -- Protein tyrosine kinase characterization based on fully automated synthesis of (phospho)peptide arrays in microplates / W. Carl Saxinger -- Kinome profiling using peptide arrays in eukaryotic cells / Kaushal Parikh, Maikel P. Peppelenbosch, and Tita Ritsema -- ProMoST : a tool for calculating the pI and molecular mass of phosphorylated and modified proteins on two-dimensional gels / Brian D. Halligan -- Kinase-specific preiction of protein phosphorylation sites / Martin L. Miller and Nikolaj Blom -- Reconstructing regulatory kinase pathways from phosphopeptide data : a bioinformatics approach / Lawrence G. Puente, Robin E.C. Lee, and Lynn A. Megeney.
- 2008 Springer Protocolsedited by William J. Murphy.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.]
- 2013Elena F. Koslover.The packaging and expression of the genome requires a cell to overcome elastic and entropic forces to form a highly compact structure that remains dynamically accessible to transcription machinery. The eukaryotic genome is packaged into a hierarchical structure collectively termed chromatin and the prokaryotic genome is also condensed and structured by the binding of architectural proteins along the DNA. We use a combination of analytic theory and computational techniques to study how the mechanical properties of DNA and associated proteins impact genome structure and dynamics across a wide range of length and time scales. We demonstrate that the elasticity of the DNA molecule can give rise to tension-mediated cooperative binding between DNA-bending proteins, allowing them to sense each other across a tunable length scale. At the lowest level of eukaryotic chromatin packing, DNA is wound around protein cores to form nucleosomes, which then condense into regular helical fibers under physiologic conditions. Using energy landscape optimization methods, we investigate the role of DNA mechanics in determining the structure of these compact chromatin fibers. We then proceed to examine how he statistical properties of DNA at long length scales are modulated by its interactions with proteins that modify its geometry. To this end, we develop a generalized approach for coarse-grained modeling of polymer systems by mapping to continuous and discrete elastic models. Moving into the realm of dynamics, we uncover an important role for force fluctuations in biomolecular kinetics, demonstrating how microsecond fluctuations can qualitatively alter nucleosomal transcription by RNA polymerase, an essential process for eukaryotic gene expression. Finally, we use a combination of analytic reaction-diffusion models and simulations to study the target site search process of DNA-binding proteins under a variety of conditions relevant to in vitro and in vivo systems, elucidating a key role for confinement and a surprising robustness to DNA configuration. These multi-scale studies further our fundamental understanding of how the complex hierarchy of genome packing and processing arises from the basic physical properties of DNA and interacting proteins.
- 2014 SpringerNenad Blau, Marinus Duran, K. Michael Gibson, Carlo Dionisi-Vici, editors.Introductory Chapters -- Amino acids -- Organic acids -- Vitamins and neurotransmitter -- Energy metabolism -- Organelles -- Selected disorder -- Biochemical phenotypes of questionable clinical significance -- Profiles.
- 2007 Springer Protocolsedited by James M. Cregg.Introduction : distinction between Pichia pastoris and other expression systems / James M. Cregg -- Vectors and strains for expression / Joan Lin-Cereghino and Geoff P. Lin-Cereghino -- DNA-mediated transformation / James M. Cregg -- Rational design and optimization of fed-batch and continuous fermentation / Wenhui Zhag, Mehmet Inan, and Michael M. Meagher -- Saturation of the secretory pathway by overexpression of a hookworm (Necator americanus) protein (Na-ASP1) / Mehmet Inan ... [et al.] -- Purification of the N- and C-terminal subdomains of recombinant heavy chain fragment C of botulinum neurotoxin serotype C / Jicai Huang ... [et al.] -- Rapid screening of chromatography resins for the purification of proteins / Sandra E. Ríos, Erin M. Giaccone, and Tillman U. Gerngross -- Characterization of O-linked saccharides on glycoproteins / Roger K. Bretthauer -- Modification of the N-glycosylation pathway to produce homogeneous human-like glycans using glycoswitch plasmids / Wouter Vervecken ... [et al.] -- N-linked glycan characterization of heterologous proteins / Huijan Li ... [et al.] -- Heavy labeling of recombinant proteins / Eric Rodriguez -- Selenomethionine labeling of recombinant proteins / Anna M. Larsson and T. Alwyn Jones -- Selective isotopic labeling of recombinant proteins using amino acid auxotroph strains / James W. Whittaker -- Classical genetics / Ilya Tolstorukov and James M. Cregg -- Identification of pexophagy genes by restriction enzyme-mediated integration / Laura A. Schroder, Benjamin S. Glick, and William A. Dunn, Jr. -- Characterization of protein-protein interactions : application to the understanding of peroxisome biogenesis / Sebastien Leon ... [et al.] -- Localization of proteins and organelles using fluorescence microscopy / Jean-Claude Farre ... [et al.] -- Fluorescence microscopy and thin-section electron microscopy / Benjamin S. Glick.
- 2014 Springer Protocolsedited by Mikiko C. Siomi.Chromatin Immunoprecipitation Assay of Piwi in Drosophila / Hang Yin and Haifan Lin -- Drosophila Germline Stem Cells for In Vitro Analyses of PIWI-Mediated RNAi / Yuzo Niki, Takuya Sato, Takafumi Yamaguchi, Ayaka Saisho, Hiroshi Uetake, and Hidenori Watanabe -- RNAi and Overexpression of Genes in Ovarian Somatic Cells / Kuniaki Saito -- Making piRNAs In Vitro / Shinpei Kawaoka, Susumu Katsuma, and Yukihide Tomari -- A Framework for piRNA Cluster Manipulation / Ivan Olovnikov, Adrien Le Thomas, and Alexei A. Aravin -- Biochemical and Mass Spectrometric Analysis of 3ʹ-End Methylation of piRNAs / Takeo Suzuki, Kenjyo Miyauchi, Yuriko Sakaguchi, and Tsutomu Suzuki -- HITS-CLIP (CLIP-Seq) for Mouse Piwi Proteins / Anastassios Vourekas and Zissimos Mourelatos -- DNA Methylation in Mouse Testes / Satomi Kuramochi-Miyagawa, Kanako Kita-Kojima, Yusuke Shiromoto, Daisuke Ito, Hirotaka Koshima, and Toru Nakano -- Analysis of Small RNA-Guided Endonuclease Activity in Endogenous Piwi Protein Complexes from Mouse Testes / Michael Reuter and Ramesh S. Pillai -- Small RNA Library Construction from Minute Biological Samples / Jessica A. Matts, Yuliya Sytnikova, Gung-wei Chirn, Gabor L. Igloi, and Nelson C. Lau -- Analysis of sDMA Modifications of PIWI Proteins / Shozo Honda, Yoriko Kirino, and Yohei Kirino -- Analyses of piRNA-Mediated Transcriptional Transposon Silencing in Drosophila: Nuclear Run-On Assay on Ovaries / Sergey Shpiz and Alla Kalmykova -- Combined RNA/DNA Fluorescence In Situ Hybridization on Whole-Mount Drosophila Ovaries / Shpiz, Sergey Lavrov, and Alla Kalmykova -- Fast and Accurate Method to Purify Small Noncoding RNAs from Drosophila Ovaries / Thomas Grentzinger and Séverine Chambeyron -- Isolation of Zebrafish Gonads for RNA Isolation / Hsin-Yi Huang and René F. Ketting -- Small RNA Library Construction for High-Throughput Sequencing / Jon McGinn and Benjamin Czech -- Analysis of Piwi-Loaded Small RNAs in Terahymena / Tomoko Noto, Henriette M. Kurth, and Kazufumi Mochizuki -- Effective Gene Knockdown in the Drosophila Germline by Artificial miRNA-Mimicking siRNAs / Hailong Wang, Haidong Huang, and Dahua Chen -- Isolation and Bioinformatic Analyses of Small RNAs Interacting with Germ Cell-Specific Argonaute in Rice / Reina Komiya and Ken-Ichi Nonomura.
- 2014 Springer Protocolsedited by Glenn R. Hicks, Stéphanie Robert.Fully-automated Compound Screening in Arabidopsis thaliana Seedlings -- Time-profiling Fluorescent Reporters in the Arabidopsis Root -- Screening for Bioactive Small Molecules by in vivo Monitoring of Luciferase-based Reporter Gene Expression in Arabidopsis thaliana -- Application of Yeast-two Hybrid Assay to Chemical Genomic Screens: A High-throughput System to Identify Novel Molecules Modulating Plant Hormone Receptor Complexes -- High-throughput Screening of Small Molecule Libraries for Inducers of Plant Defense Responses -- Using a Reverse Genetics Approach to Investigate Small Molecule Activity -- Investigating the Phytohormone Ethylene Response Pathway by Chemical Genetics -- Screening for Inhibitors of Chloroplast Galactolipid Synthesis Acting in membrano and in Planta -- Forward Chemical Screening of Small RNA Pathways -- Identification and Use of Fluorescent Dyes for Plant Cell Wall Imaging Using High-Throughput Screening -- High-throughput Identification of Chemical Endomembrane Cycling Disruptors Utilizing Tobacco Pollen -- Plant Chemical Genomics: Gravity Sensing and Response -- Screening Chemical Libraries for Compounds that Affect Protein Sorting to the Yeast Vacuole -- The use of Multi-drug Approach to Uncover New Players of the Endomembrane System Trafficking Machinery -- Cheminformatic Analysis of High-Throughput Compound Screens -- Endomembrane Dissection Using Chemically-Induced Bioactive Clusters -- Statistical Molecular Design: A Tool to Follow Up Hits From Small Molecule Screening -- Early Stage Hit Triage for Plant Chemical Genetic Screens and Target Site Identification -- Screening for Gene Function using the FOX (Full-length cDNA OvereXpressor gene) Hunting System -- Quantification of Stable Isotope Label in Metabolites via Mass Spectrometry -- 1H NMR Based Metabolomics Methods for Chemical Genomics Experiments -- Determination of Auxin Transport Parameters on the Cellular Level -- Analyzing the in vivo Status of Exogenously Applied Auxins: A HPLC-based Method to Characterize the Intracellularly Localized Auxin Transporters.
- 2011 Springer Protocolsedited by James A. Birchler.Recent advances in plant transformation -- Engineering the plastid genome of nicotiana sylvestris, a diploid model species for plastid genetics -- Homologous recombination in plants : An antireview -- Chromosome painting for plant biotechnology -- Plant B chromosomes -- Telomere truncation in plants -- Engineered plant minichromosomes -- Method for bxb1-mediated site-specific integration in planta -- Targeted mutagenesis in arabidopsis using zinc-finger nucleases -- Vectors and methods for hairpin RNA and artificial microRNA-mediated gene silencing in plants -- Recombinant protein expression in nicotiana -- Chromosome analysis and sorting using flow cytometry -- Super-stretched pachytene chromosomes for plant molecular cytogenetic mapping -- Cytological dissection of the triticeae chromosomes by the gametocidal system -- Development and use of oat-maize chromosome additions and radiation hybrids -- Enhancer trapping in plants -- Chromatin beacons : Global sampling of chromatin physical properties using chromatin charting lines -- Transposable elements as catalysts for chromosome rearrangements.
- 2012 Springer Protocolsedited by Nikolaus J. Sucher, James R. Hennell, Maria C. Carles.A taxonomist's view on genomic authentication -- DNA fingerprinting, DNA barcoding, and next generation sequencing technology in plants -- Challenges in the DNA barcoding of plant material -- Plant genetics for forensic applications -- DNA purification from multiple sources in plant research with homemade silica resins -- Random amplified marker technique for plants rich in polyphenols -- Amplified fragment length polymorphism: An invaluable fingerprinting technique for genomic, transcriptomic, and epigenetic studies -- Restriction fragment length polymorphism of the 5s-rRNA-NTS region: A rapid and precise method for plant identification -- ISSR: A reliable and cost-effective technique for detection of DNA polymorphism -- Development of sequence characterized amplified region from random amplified polymorphic DNA amplicons -- Authentication of medicinal plants by SNP-based multiplex PCR -- Multiplex PCR method to discriminate artemisia iwayomogi from other artemisia plants -- Loop-mediated isothermal amplification for the detection of plant pathogens -- Genomic DNA extraction and barcoding of endophytic fungi -- Using GenBank(R) for genomic authentication: a tutorial.
- 2014 Springer Protocolsedited by Charles Spillane, Peter C. McKeown.1. Landscaping plant epigenetics / Peter C. McKeown and Charles Spillane -- 2. The gene balance hypothesis: dosage effects in plants / James A. Birchler and Reiner A. Veitia -- 3. High-throughput RNA-seq for allelic or locus-specific expression analysis in Arabidopsis-related species, hybrids, and allotetraploids / Danny W.-K. Ng, Xiaoli Shi, Gyoungju Nah and Z. Jeffrey Chen -- 4. Inference of allele-specific expression from RNA-seq data / Paul K. Korir and Cathal Seoighe -- 5. Screening for imprinted genes using high-resolution melting analysis of PCR amplicons / Robert Day and Richard Macknight -- 6. Analysis of genomic imprinting by quantitative allele-specific expression by pyrosequencing® / Peter C. McKeown, Antoine Fort and Charles Spilane -- 7. Endosperm-specific chromatin profiling by fluorence-activated nuclei sorting and chip-on-chip / Isabelle Weinhofer and Claudia Köhler -- 8. Imaging sexual reproduction in Arabidopsis using fluorescent markers / Mathieu Ingouff -- 9. Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip / Sandra Cortijo, René Wardenaar, Maria Colomé-Tatché, Frank Johannes and Vincent Colot -- 10. Methylation-sensitive amplified polymorphism (MSAP) marker to investigate drought-stress response in montepulciano and sangiovese grape cultivars / Emidio Albertini and Gianpiero Marconi -- 11. Detecting histone modifications inplants / Jie Song, Bas Rutjens and Caroline Dean -- 12. Quantitatively profiling genome-wide patterns of histone modifications in Arabidopsis thaliana using a chIP-seq / Chongyuan Luo and Eric Lam -- 13. Analysis of retrotransposon activity in plants / Christopher DeFraia and R. Keith Slotkin -- 14. Detecting epigenetic effects of transposable elements in plants / Christian Parisod, Armel Salmon, Malika Ainouche and Marie-Angèle Grandbastieu -- 15. Detection and investigation of transitive gene silencing in plants / Leen Vermeersch, Nancy De Winne and And Depicker.
- 2015 Springer Protocolsedited by Kirankumar S. Mysore, Muthappa Senthil-Kumar.Advances in plant gene silencing methods / Prachi Pandey, Muthappa Senthil-Kumar, and Kirankumar S. Mysore -- Strategies for altering plant traits using virus-induced gene silencing technologies / Christophe Lacomme -- Bioinformatics tools for achieving better gene silencing in plants / Firoz Ahmed, Xinbin Dai, and Patrick Xuechun Zhao -- Profiling of small RNAs involved in plant-pathogen interactions / Dongdong Niu ... [et al.] -- RNAi-mediated resistance to viruses in genetically engineered plants / Abdulrazak B. Ibrahim and Francisco J. L. Aragão -- Simplifying transgene locus structure through Cre-lox recombination / Vibha Srivastava and David W. Ow -- Transgene-induced gene silencing in plants / Yun Jin and Hui-Shan Guo -- Gene silencing by DNA interference in fern gametophytes / Masamitsu Wada and Hidenori Tsuboi -- Induction of stable epigenetic gene silencing in plants using a virus vector / Akira Kanazawa and Megumi Kasai -- Method for validating microRNAs in plants by miR-RACE / Jinggui Fang and Xin Sun -- MR VIGS : microRNA-based virus-induced gene silencing in plants / Weiwei Chen ... [et al.] -- High-throughput RNA interference (RNAi)-based approach using hairy roots for the study of plant-rhizobia interactions / Senjuti Sinharoy, Catalina I. Pislariu, and Michael K. Udvardi -- Functional genomics method for assaying gene function in phytopathogenic fungi through host-induced gene silencing mediated by agroinfiltration / Vinay Panwar, Brent McCallum, and Guus Bakkeren -- Effective and convenient method for the delivery of apple latent spherical virus (ALSV)-based vectors into plant cells by agroinoculation / Tatsuya Kon and Nubuyuki Yoshikawa -- Virus-induced gene silencing (VIGS) for functional genomics in rice using Rice tungro bacilliform virus (RTBV) as a vector / Ravi Kant, Shweta Sharma, and Indranil Dasgupta -- Virus-induced gene silencing of fiber-related genes in cotton / John R. Tuttle, Candace H. Haigler, and Dominique (Niki) Robertson -- Establishment of an efficient virus-induced gene silencing (VIGS) assay in Arabidopsis by agrobacterium-mediated rubbing infection / Ana Marcia E. de A. Manhães, Marcos V. V. de Oliveira, and Libo Shan -- Virus-induced gene silencing as a scalable tool to study drought tolerance in plants / Gavin M. George, Michael E. Ruckle, and James R. Lloyd -- VIGS for dissecting mechanisms involved in the symbiotic interaction of microbes with plants / Mette Grønlund -- Construction of a cotton VIGS library for functional Genomics study / Maoying Li, Fangjun Li, and Ping He -- Synthetic gene complementation to determine off-target silencing / Dhirendra Kumar -- Construction of mismatched inverted repeat (IR) silencing vectors for maximizing IR stability and effective gene silencing in plants / M. E. Chrissie Rey ... [et al.].
- 2008 Kargervolume editor, Jean-Nicolas Volff.Paleopolyploidy and its impact on the structure and function of modern plant genomes / A.H. Paterson -- Genomic history and gene family evolution in angiosperms: challenges and opportunities / J. Sampedro, D. Cosgrove -- The evolutionary position of subfunctionalization, downgraded / M. Freeling -- Grass genome structure and evolution / J. Messing, J.L. Bennetzen -- Phylogenetic insights into the pace and pattern of plant genome size evolution / C.E. Grover, J.S. Hawkins, J.F. Wendel -- Plant transposable elements / J.M. Deragon, J.M. Casacuberta, O. Panaud -- Plant sex chromosomes / D. Charlesworth -- Plant centromeres / J.C. Lamb ... [et al.] -- MiRNAs in the plant genome: all things great and small / B.C. Meyers, P.J. Green, C. Lu -- Recent insights into the evolution of genetic diversity of maize / A. Rafalski, S. Tingey -- The rice genome structure as a trail from the past to beyond / T. Sasaki.
- 2009 Springer Protocolsedited by Daryl J. Somers, Peter Langridge, and J. Perry Gustafson.Role of model plant species / Richard Flavell -- New technologies for ultra-high throughput genotyping in plants / Nikki Appleby, David Edwards, and Jacqueline Batley -- Genetic maps and the use of synteny / Chris Duran, David Edwards, and Jacqueline Batley -- A simple TAE-based method to generate large insert BAC libraries from plant species / Bu-Jun Shi, J. Perry Gustafson, and Peter Langridge -- Transcript profiling and expression level mapping / Elena Potokina, Arnis Druka, and Michael J. Kearsey -- Methods for functional proteomic analyses / Christof Rampitsch and Natalia V. Bykova -- Stable transformation of plants / Huw D. Jones and Caroline A. Sparks -- Transient transformation of plants / Huw D. Jones, Angela Doherty, and Caroline A. Sparks -- Bridging the gene-to-function knowledge gap through functional genomics / Stephen J. Robinson and Isobel A.P. Parkin -- Heterologous and cell-free protein expression systems / Naser Farrokhi ... [et al.] -- Functional genomics and structural biology in the definition of gene function / Maria Hrmova and Geoffrey B. Fincher -- In situ analysis of gene expression in plants / Sinéad Drea ... [et al.] -- Plant and crop databases / David E. Matthews, Gerard R. Lazo, and Olin D. Anderson -- Plant genome annotation methods / Shu Ouyang ... [et al.] -- Molecular plant breeding : methodology and achievements / Rajeev K. Varshney ... [et l.] -- Practical delivery of genes to the marketplace / David A. Fischhoff and Molly N. Cline -- Ecological genomics of natural plant populations : the Israeli perspective / Eviatar Nevo -- Genome sequencing approaches and successes / Michael Imelfort ... [et al.]
- 2015 Springer Protocolsedited by Jacqueline Batley.Advances in plant genotyping : where the future will take us / Dhwani A. Patel [and three others] -- Molecular marker applications in plants / Alice C. Hayward [and three others] -- Bioinformatics : identification of markers from next-generation sequence data / Pradeep Ruperao and David Edwards -- Molecular marker databases / Kaitao Lai, Michał Tadeusz Lorenc, and David Edwards -- Plant genotyping using flourescently tagged inter-simple sequence repeats (ISSRs) : basic principles and methodology / Linda M. Prince -- SSR genotyping / Annaliese S. Mason -- Genotyping analysis using an RFLP assay / Shutao Dai and Yan Long -- DNA barcoding for plants / Natasha de Vere [ and three others] -- Multiplexed digital gene expression analysis for gentical genomics in large plant populations / Christian Obermeier [and three others] -- SNP genotyping by heteroduplex analysis / Norma Paniego [and three others] -- Application of the high-resolution melting technique for gene mapping and SNP detection in plants / David Chagné -- Challenges of genotyping polyploid species / Annaliese S. Mason -- Genomic reduction assisted single nucleotide polymorphism discovery using 454-pyrosequencing / Peter J. Maughan, Joshua A. Udall, and Eric N. Jellen -- Inter-SINE amplified polymorphism (ISAP) for rapid and robust plant genotyping / Torsten Wenke [and four others] -- Screening of mutations by TILLING in plants / Nian Wang and Lei Shi -- Gene analysis using mass spectrometric cleaved amplified polymorphic sequence (MS-CAPS) with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF) / Hideyuki Kajiwara -- Quantitative SNP genotyping of polyploids with MassARRAY and other platforms / Marcelo Mollinari and Oliver Serang -- SNP genotyping using KASPar assays / Scott M. Smith and Peter J. Maughan -- Skim-based genotyping by sequncing / Agnieszka A. Gilicz, Philipp E. Bayer, and David Edwards -- The restriction enzyme target approach to genotyping by sequencing (GBS) / Elena Hilario -- Methods for the design, implementation, and analysis of Illumina Infinium [trademark] SNP assays in plants / David Chagné [and four others] -- Use of the Illumina GoldenGate assay for single nuccleotide polymorphism (SNP) genotyping in cereal crops / Shiaoman Chao and Cindy Lawley.
- 2015 Springer Protocolsedited by James Whelan, Monika W. Murcha.Isolation of intact mitochondria from the model plant species Arabidopsis thaliana and Oryza sativa / Monika W. Murcha and James Whelan -- Determining mitochondrial transcript termini for the study of transcription start sites and transcript 5' end maturation / Stefan Binder and Kristina Kühn -- Mitochondrial run-on transcription assay using biotin labeling / Kristina Kühn -- In vitro RNA uptake studies in plant mitochondria / Szymon Kubiszewski-Jakubiak [and five others] -- In vitro and in vivo protein uptake studies in plant mitochondria / Owen Duncan [and three others] -- Plant mitochondrial proteomics / Nicolas L. Taylor and A. Harvey Millar -- Identification of lysine-acetylated mitochondrial proteins and their acetylation sites / Markus Hartl, Ann-Christine König, and Iris Finkemeier -- Flowchart to analyze protease activity in plant mitochondria / Pedro F. Teixeira [and three others] -- Activity measurements of mitochondrial enzymes in native gels / Peter Schertl and Hans-Peter Braun -- Activity assay for plant mitochondrial enzymes / Shaobai Huang, Chun Pong Lee, and A. Harvey Millar -- Analysis of type II NAD(P)H dehydrogenases / Kathleen L. Soole and Chevaun A. Smith -- Assessment of respiration in isolated plant mitochondria using clark-type electrodes / Richard P. Jacoby, A. Harvey Millar, and Nicolas L. Taylor -- Micro-respiratory measurements in plants / Yun Shin Sew, A. Harvey Millar, and Elke Stroeher -- Improvements to define mitochondrial metabolomics using nonaqueous fractionation / Richard Fly [and four others] -- Mitochondrial markers of programmed cell death in Arabidopsis thaliana / Theresa J. Reape ... [et al.] -- Imaging and analysis of mitochondrial dynamics in living cells / Sanjaya B. Ekanayake [and four others] -- Analysis of plant mitochondrial function using fluorescent protein sensors / Stephan Wagner [and six others] -- In planta analysis of leaf mitochondrial superoxide and nitric oxide / Marina Cvetkovska and Greg C. Vanlerberghe -- Databases and informatics resources for analysis of plant mitochondria / Reena Narsai -- Expression and crystallization of the plant alternative oxidase / Benjamin May [and six others].
- 2011 Springer Protocolsedited by Ling Yuan, Sharyn E. Perry.1. MADS and more: transcription factors that shape the plant / Rainer Melzer and Günter Thei€en -- 2. In silico mining and PCR-based approaches to transcription factor discovery in non-model plants: gene diversity of the WRKY transcription factors in conifers / Jun-Jun Liu and Yu Xiang -- 3. Isolation of plant transcription factors using a yeast one-hybrid system / Tatiana Pyvovarenko and Sergiy Lopato -- 4. A transposon-based activation tagging system for gene function discovery in arabidopsis / Nayelli Marsch-Martinez -- 5. CRWA-T, an effective gene silencing system utilizing chimeric repressors / Nobutaka Mitsuda, Kyoko Matsui, Miho Ikeda, Masaru Nakata, Yoshimi Oshima, Yukari Nagatoshi, and Masaru Ohme-Takagi -- 6. Analysis of a transcription factor using transient assay in arabidopsis protoplasts / Yuji Iwata, Mi-Hyun Lee, and Nozomu Koizumi -- 7. Microarray-based identification of transcription factor target genes / Maartje Gorte, Anneke Horstman, Robert B. Page, Renze Heidstra, Arnold Stromberg and Kim Boutilier -- 8. Yeast protein-protein interaction assays and screens / Stefan de Folter and Richard G.H. Immink -- 9. Mapping functional domains of transcription factors / Ling Zhu and Enamul Huq -- 10. Biomolecular fluorescence complementation as a tool to study interactions of regulatory proteins in plant protoplasts / Sitakanta Pattanaik, Joshua R. Werkman, and Ling Yuan -- 11. Isolation of transcription factor complexes from arabidopsis cell suspension cultures by tandem affinity purification / Jelle Van Leene, Dominique Eeckhout, Geert Persiau, Eveline Van De Slijke, Jan Geerinck, Gert Van Isterdael, Erwin Witters, and Geert De Jaeger -- 12. Assaying transcription factor stability / Jasmina Kurepa and Jan A. Smalle -- 13. How to access the intercellular trafficking of transcription factors / Munawar Ahmad, Won Kyong Cho, Yeonggil Rim, Lijun Huang, and Jae-Yean Kim -- 14. SELEX (systematic evolution of ligands by exponential enrichment), as a powerful tool for deciphering the protein-DNA interaction space / Chenglin Chai, Zidian Xie, and Erich Grotewold -- 15. Footprinting and missing nucleoside analysis of transcription factor-DNA complexes / Ivana L. Viola and Daniel H. Gonzalez -- 16. Chromatin immunoprecipitation to verify or to identify in vivo protein-DNA interactions / Yumei Zheng and Sharyn E. Perry -- 17. Visualizing and characterizing invivo DNA-binding events and direct target genes of plant transcription factors / Jose M. Muiño, Gerco C. Angenent, and Kerstin Kaufmann -- 18. Mapping in vivo protein-DNA interactions in plants by DamID, a DNA adenine methylation-based method / Sophie Germann and Valérie Gaudin -- 19. Directed evolution through DNA shuffling for the improvement and understanding of genes and promoters / Joshua R. Werkman, Sitakanta Pattanaik, and Ling Yuan.
- 2012 SpringerMarie-Angèle Grandbastien, Josep M. Casacuberta, editors.Transposable elements are DNA sequences with the capacity to move within a genome. Although their presence and impact has long been known, the recent genome-wide analysis of many eukaryotic genomes has uncovered their major role in genome dynamics and function. The present book explains how to recognize and study transposable elements, e.g. by using state-of-the-art strategies based on new-generation sequencing. Moreover, the impact of transposable elements on plant genome structure and function is reviewed in detail and illustrated in examples and case studies. The book is intended both for readers familiar with the field and for newcomers. With large-scale sequencing becoming increasingly available, more and more people will come across transposable element sequences in their data, and this volume will hopefully help to convince them that transposable elements are not just "junk" DNA, and may actually be the most interesting and fun part of their data!
- 2013 Springer Protocolsedited by Thomas Peterson.Historical overview of transposable element research / P.A. Peterson -- Distinguishing variable phenotypes from variegation caused by transposon activities / V. Walbot -- Using transposons for genetic mosaic analysis of plant development / P.W. Becraft -- Survey of natural and transgenic gene markers used to monitor transposon activity / L. Krishnaswamy and T. Peterson -- Molecular biology of maize Ac/Ds elements: An overview / K. Lazarow, M.L. Doll and R. Kunze -- Gene tagging with engineered Ds elements in maize / Y. Li, G. Segal, Q. Wangm H.K. Donner -- Plant regeneration methods for rapid generation of a large scale Ds transposant population in rice / Y.H. Xuan [and nine others] -- Isolation of sequences flanking Ac insertion sites by Ac casting / D. Wang and T. Peterson -- Regulation of the mutator system of transposons in maize / D. Lisch -- Using MuDR/Mu transposons in directed tagging strategies / V. Walbot and J. Questa -- Genetic and molecular analyses of UniformMu transposon insertion lines / D.R. McCarty, M. Suzuki, C. Hunter, J. Collins, W.T. Avigne, K.E. Koch -- Digestion-ligation-amplification (DLA): A simple genome walking method to amplify unknown sequences flanking mutator (Mu) transposons and thereby facilitate gene cloning / S. Liu, A.P. Hsia and P.S. Schnable -- Molecular genetics and epigenetics of CACTA elements / N.V. Fedoroff -- Activation tagging using the maize En-I transposon system for the identification of abiotic stress resistance genes in arabidopsis / A. Harb and A. Pereira -- Reverse genetics in rice using Tos17 / D. Mieulet, A. Dievart, G. Droc, N. Lanau, E. Guiderdoni -- Identification and applications of the Petunia Class II Act1/dTph1 transposable element system / T. Gerats, J. Zethof and M. Vandenbussche -- Transposon display: A versatile method for transposon tagging / M. Vandenbussche, J. Zethof and T. Gerats -- Massive indexed parallel identification of transposon flanking sequences / M. Vandenbussche, J. Zethof and T. Gerats -- Use of next generation sequencing (NGS) technologies for the genome-wide detection of transposition / M. Elbaidouri, C. Chaparro and O. Panaud -- Overview of repeat annotation and de novo repeat identification / N. Jiang -- Computational methods for identification of DNA transposons / N. Jiang -- Tenest 2.0: Computational annotation and visualization of nested transposable elements / B.A. Kronmiller and R.P. Wise.
- 2014 Springer Protocolsedited by Joanna Rorbach, Agnieszka J. Bobrowicz.
- 2015 Springer Protocolsedited by Arthur G. Hunt, Qingshun Quinn Li.Computational analysis of plant polyadenylation signals / Xiaohui Wu , Guoli Ji , and Qingshun Quinn Li -- Prediction of plant mRNA polyadenylation sites / Xiaohui Wu , Guoli Ji , and Qingshun Quinn Li -- Extraction of poly(A) sites from large-scale RNA-seq data / Min Dong ... [et al.] -- Poly(A)-tag deep sequencing data processing to extract poly(A) sites / Xiaohui Wu, Guoli Ji, and Qingshun Quinn Li -- Analysis of poly(A) site choice using a java-based clustering algorithm / Patrick E. Thomas -- RADPRE : a computational program for identification of differential mRNA processing including alternative polyadenylation / Denghui Xing and Qingshun Quinn Li -- Characterization of plant polyadenylation complexes by using tandem affinity purification / Hongwei Zhao, Xinfu Ye, and Qingshun Quinn Li -- In vitro analysis of cleavage and polyadenylation in Arabidopsis / Hongwei Zhao and Qingshun Quinn Li -- Production, purification, and assay of recombinant proteins for in vitro biochemical analyses of the plant polyadenylation complex / Stephen A. Bell and Balasubrahmanyam Addepalli -- Detection of disulfide linkage by chemical derivatization and mass spectrometry / Balasubrahmanyam Addepalli -- Transient expression using agroinfiltration to study polyadenylation in plants / Carol Von Lanken and Arthur G. Hunt -- 3' RACE protocol to confirm polyadenylation sites / Liuyin Ma and Arthur G. Hunt -- Phage display library screening for identification of interacting protein partners / Balasubrahmanyam Addepalli, Suryadevara Rao, and Arthur G. Hunt -- Genome- wide determination of poly(A) site choice in plants / Pratap Kumar Pati, Liuyin Ma, and Arthur G. Hunt -- DNA/RNA hybrid primer mediated poly(A) tag library construction for illumina sequencing / Man Liu, Xiaohui Wu, and Qingshun Quinn Li -- Poly(A) tag library construction from 10 ng total RNA / Jingyi Cao and Qingshun Quinn Li -- Rapid, simple, and inexpensive method for the preparation of strand-specific RNA-seq libraries / Arthur G. Hunt -- Genome-wide analysis of distribution of RNA polymerase II isoforms using ChIP-Seq / Laura de Lorenzo.
- 2013 SpringerTomáš Paus.Terms and Concepts -- History of the Key Disciplines -- Enviromics -- Genomics -- Epigenomics -- Molecular Phenomics -- Systems Phenomics -- Cohorts -- Challenges -- Personalized Preventive Medicine.
- 2016 Springer Protocolsedited by Erik Dassi.Regulation of gene expression / Alessandro Quattrone and Erik Dassi -- Computational approach for the discovery of protein-RNA networks / Domenica Marchese, Carmen Maria Livi, and Gian Gaetano Tartaglia -- Transcriptional regulation with CRISPR/Cas9 effectors in mammalian cells / Hannah Pham, Nicola A. Kearns, and René Maehr -- Studying the translatome with polysome profiling / Paola Zuccotti and Angelika Modelska -- Exploring ribosome positioning on translating transcripts with ribosome profiling / Pieter Spealman ... [et al.] -- Studying isoform-specific mRNA recruitment to polyribosomes with Frac-seq / Rocio T. Martinez-Nunez and Jeremy R. Sanford -- Use of the pBUTR reporter system for scalable analysis of 3' UTR-mediated gene regulation / Arindam Chaudhury and Joel R. Neilson -- Comprehensive identification of RNA-binding proteins by RNA interactome capture / Alfredo Castello ... [et al.] -- Identifying RBP targets with RIP-seq / Hans-Herman Wessels ... [et al.] -- PAR-CLIP : a method for transcriptome-wide identification of RNA binding protein interaction sites / Charles Danan, Sudhir Manickavel, and Markus Hafner -- Profiling the binding sites of RNA-binding proteins with nucleotide resolution using iCLIP / FX Reymond Sutandy, Andrea Hildebrandt, and Julian König -- Pipeline for PAR-CLIP data analysis / Marvin Jens -- Capture and identification of miRNA targets by biotin pulldown and RNA-seq / Shen Mynn Tan and Judy Lieberman -- Identification of miRNA-target RNA interactions using CLASH / Aleksandra Helwak and David Tollervey -- Genome-wide analysis of A-to-I RNA editing / Yiannis A. Savva, Georges St. Laurent, and Robert A. Reenan -- Nucleotide-level profiling of m5C RNA methylation / Tennille Sibbritt ... [et al.] -- Probing N 6-methyladenosine (m6A) RNA modification in total RNA with SCARLET / Nian Liu and Tao Pan -- Genome-wide identification of alternative polyadenylation events using 3'T-fill / Stefan Wilkening, Vicent Pelechano, and Lars M. Steinmetz -- Genome-wide profiling of alternative translation initiation sites / Xiangwei Gao, Ji Wan, and Shu-Bing Qian -- Genome-wide study of mRNA isoform half-lives / Joseph V. Geisberg and Zarmik Moqtaderi -- Visualizing mRNA dynamics in live neurons and brain tissues / Hye Yoon Park and Minho Song -- Single-molecule live-cell visualization of pre-mRNA splicing / Robert M. Martin ... [et al.].
- 2008 Springer Protocolsedited by Jeffrey Wilusz.Bioinformatics approaches for studying untranslated regions of mRNAs / Paramjeet S. Bagga -- Identification of mRNA polyadenylation sites in genomes using cDNA sequences, expressed sequence tags, and trace / Ju Youn Lee, Ji Yeon Park, and Bin Tian -- Bioinformatic tools for studying post-transcriptional gene regulation : the UAlbany TUTR Collection and other informatic resources / Francis Doyle ... [et al.] -- In-line probing analysis of riboswitches / Elizabeth E. Regulski and Ronald R. Breaker -- Ribotrap : targeted purification of RNA-specific RNPs from cell lysates through immunoaffinity precipitation to identify regulatory proteins and RNAs / Dale L. Beach and Jack D. Keene -- Advances in RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray profiling / Timothy E. Baroni ... [et al.] -- Biosensors for RNA aptamers-protein interaction / Sara Tombelli, Maria Minunni, and Marco Mascini -- A tethering approach to study proteins that activate mRNA turnover in human cells / Sandra L. Clement and Jens Lykke-Andersen -- RNA analysis by biosynthetic tagging using a 4-thiouracil and uracil phosphoribosyltransferase / Gusti M. Zeiner ... [et al.] -- Efficient 5' cap-dependent RNA purification : use in identifying and studying subsets of RNA / Edyta Z. Bajak and Curt H. Hagedorn -- Enrichment of alternatively spliced isoforms / Julian P. Venables -- In vivo methods to assess polyadenylation efficiency / Lisa K. Hague, Tyra Hall-Pogar, and Carol S. Lutz -- Monitoring the temporal and spatial distribution of RNA in living yeast cells / Roy M. Long and Carl R. Urbinati -- Analysis of mRNA partitioning between the cytosol and endoplasmic reticulum compartments of mammalian cells / Samuel B. Stephens ... [et al.] -- In vivo and in vitro analysis of poly(A) length effects on mRNA translation / Jing Peng, Elizabeth L. Murray, and Daniel R. Schoenberg -- A ribosomal density-mapping procedure to explore ribosome positions along translating mRNAs / Naama Eldad and Yoav Arava -- Identification of changes in gene expression by quantitation of mRNA levels / Wendy M. Olivas -- Application of the Invader® RNA assay to the polarity of vertebrate mRNA decay / Elizabeth L. Murray and Daniel R. Schoenberg -- Development of an in vitro mRNA decay system in insect cells / Kevin Sokoloski, John R. Anderson, and Jeffrey Wilusz -- Using synthetic precursor and inhibitor miRNAs to understand miRNA function / Lance P. Ford and Angie Cheng -- A step-by-step procedure to analyze the efficacy of siRNA using real-time PCR / Angie Cheng, Charles L. Johnson, and Lance P. Ford.
- 2012 SpringerAnver Kuliev.Primary Prevention of Genetic Disorders and Place of Preimplantation Diagnosis -- Approaches to Preimplantation Diagnosis -- Preimplation Diagnosis for Single-Gene Disorders -- PGD for HLA Typing -- Preimplantation Diagnosis for Chromosomal Disorders -- Clinical Outcome of Preimplantation Genetic Diagnosis -- Preimplantation Diagnosis and Establishment of Disease and Individual Specific Human Embryonic Stem Cell Lines -- Social, Ethical, and Legal Aspects.
- 2014 SpringerTarek El-Toukhy, Peter Braude, editors.This unique book offers a comprehensive yet practical user-friendly guide to preimplantation genetic diagnosis (PGD). It provides understanding of and insight into the complete procedure, its recent clinical and laboratory developments and its future prospects, whilst offering an easy point of reference for patient enquiries. Concluding with perspectives on the ethical and social issues often encountered by healthcare professionals counselling patients with regards to PGD. Each chapter within Preimplantation Genetic Diagnosis in Clinical Practice is written by established authorities in their fields. An essential resource for PGD specialists and non-specialists, and for all practitioners working within the disciplines of fertility, reproductive medicine and medical genetics.
- 2012 Springer Protocolsedited by Charles Coutelle, Simon N. Waddington.The concept of prenatal gene therapy -- Candidate diseases for prenatal gene therapy -- Vector systems for prenatal gene therapy: Choosing vectors for different applications -- Vector systems for prenatal gene therapy: Principles of adenovirus design and production -- Vector systems for prenatal gene therapy: Principles of retrovirus vector design and production -- Vector systems for prenatal gene therapy: Principles of adeno-associated virus vector design and production -- Vector systems for prenatal gene therapy: Principles of non-viral vector design and production -- Use of manipulated stem cells for prenatal therapy -- Animal models for prenatal gene therapy: Choosing the right model -- Animal models for prenatal gene therapy: Rodent models for prenatal gene therapy -- Animal models for prenatal gene therapy: The sheep model -- Animal models for prenatal gene therapy: The nonhuman primate model -- Choice of surrogate and physiological markers for prenatal gene therapy -- Monitoring for potential adverse effects of prenatal gene therapy: Use of large animal models with relevance to human application -- Monitoring for potential adverse effects of prenatal gene therapy: Mouse models for developmental aberrations and inadvertent germ line transmission -- Monitoring for potential adverse effects of prenatal gene therapy: Genotoxicity analysis in vitro and on small animal models ex vivo and in vivo -- Risks, benefits and ethical, legal, and societal considerations for translation of prenatal gene therapy to human application.
- 2015 SpringerGodrey Grech, Iris Grossman, editorsIntroduction -- Preventive and predictive genetics: a perspective -- Roadmap to drug development enabled by pharmacogenetics -- Pharmacogenetics, statistical considerations -- Pharmacokinetics and pharmacogenetics: bringing the magic bullet closer to reality -- Pharmacogenetics of adverse drug reactions -- Pharmacogenomics for haemoglobinopathies therapeutics -- Pharmacogenetics of neurodegenerative disorders -- Pharmacogenetics of asthma -- Pharmacogenetics and antineoplastic therapies -- Pharmacogenetics of coumarin anticoagulant therapy -- Implementation of genomic medicine: tools and challenges -- Ethical considerations in the genomic era -- Index.
- 2008 SpringerFred Bunz.
- 2013 SpringerSteven L. Gersen and Martha B. Keagle, editors.Part I. Basic Concepts and Background. History of Clinical Cytogenetics / Steven L. Gersen -- DNA, Chromosomes, and Cell Division / Martha B. Keagle -- Human Chromosome Nomenclature: An Overview and Definition of Terms / Marilyn L. Slovak, Aaron Theisen, Lisa G. Shaffer -- Part II. Examining and Analyzing Chromosomes. Basic Cytogenetics Laboratory Procedures / Martha B. Keagle, Steven L. Gersen -- The Essentials of Light Microscopy / Nathan S. Claxton, Stephen T. Ross -- Quality Control and Quality Assurance / Martha B. Keagle -- Instrumentation in the Cytogenetics Laboratory / Steven L. Gersen -- Part III. Clinical Cytogenetics. Autosomal Aneuploidy / Jin-Chen C. Wang -- Structural Chromosome Rearrangements / Kathleen Kaiser-Rogers, Kathleen W. Rao -- Sex Chromosomes, Sex Chromosome Disorders, and Disorders of Sex Development / Cynthia M. Powell -- The Cytogenetics of Infertility / Linda Marie Randolph -- Prenatal Cytogenetics / Linda Marie Randolph -- The Cytogenetics of Spontaneous Abortion / Solveig M. V. Pflueger, -- Chromosome Instability / Xiao-Xiang Zhang, -- Part IV. Cancer Cytogenetics. The Cytogenetics of Hematologic Neoplasms / Aurelia Meloni-Ehrig -- The Cytogenetics of Solid Tumors / Linda D. Cooley, Kathleen S. Wilson -- Part V. Adjunct Technologies -- Fluorescence In Situ Hybridization (FISH) / Daynna J. Wolff -- Microarray-Based Cytogenetics / Lisa G. Shaffer -- Part VI. Beyond Chromosomes. Fragile X--A Family of Disorders: Changing Phenotype and Molecular Genetics / Elaine B. Spector -- Genomic Imprinting and Uniparental Disomy / Jin-Chen C. Wang -- Genetic Counseling / Sarah Hutchings Clark.
- 2014 ScienceDirectedited by Jose Cibelli [and six others].Principles of Cloning, Second Edition is the fully revised edition of the authoritative book on the science of cloning. The book presents the basic biological mechanisms of how cloning works and progresses to discuss current and potential applications in basic biology, agriculture, biotechnology, and medicine. Beginning with the history and theory behind cloning, the book goes on to examine methods of micromanipulation, nuclear transfer, genetic modification, and pregnancy and neonatal care of cloned animals. The cloning of various species-including mice, sheep, cattle, and non-mammals-is considered as well.
- 2006 Springeredited by Marschall S. Runge, Cam Patterson ; foreword by Victor A. McKusick.
- 2006 Springer Protocolsedited by Franck Pellestor.
- 2014 SpringerJaroslava Halper, editor.This volume is a reference handbook focusing on diseases like Marfan syndrome, Ehlers-Danlos syndrome, Loeys-Dietz syndrome and other heritable soft connective tissue diseases. The book presents detailed information for both basic scientists and for clinicians seeing patients. It is also a stepping stone for new investigations and studies that goes beyond the facts about the composition and biochemistry of the connective tissue and extracellular matrix, as the authors connect individual components to specific aspects of various soft tissue disorders and to the actual or potential treatment of them. Progress in Heritable Soft Connective Tissue Diseases features very prominent physicians and scientists as contributors who bring their most recent discoveries to the benefit of readers. Their expertise will help clinicians with proper diagnosis of sometimes elusive and uncommon heritable diseases of soft connective tissues. This book also offers an update on the pathophysiology of these diseases, including an emphasis on unifying aspects such as connections between embryonic development of the different types of connective tissues and systems, and the role of TGF-beta in development and physiology of soft tissues. This new set of data explains, at least in part, why many of these disorders are interconnected, though the primary pathophysiological events, such as gene mutations, may be different for each disorder.Also available: Print – 2014
- 2009 SpringerCaroline Köhrer, Uttam L. RajBhandary (eds.).Understanding enzyme mechanism through protein chimeragenesis / N.M. Goodey and S.J. Benkovic -- Chemical protein engineering : synthetic and semisynthetic peptides and proteins / L. Merkel, L. Moroder, and N. Budisa -- Native chemical ligation: Semisynthesis of post-translationally modified proteins and biological probes / E. Vogel Taylor and B. Imperiali -- Chemical methods for mimicking post-translational modifications / S.I. van Kasteren, P. Garnier and B.G. Davis -- Noncanonical amino acids in protein science and engineering / K.E. Beatty and D.A. Tirrell -- Fidelity mechanisms of the aminoacyl-tRNA synthetases / A.P. Mascarenhas ... [et al.] -- Specialized components of the translational machinery for unnatural amino acid mutagenesis : tRNAs, aminoacyl-tRNA synthetases, and ribosomes / C. Köhrer and U.L. RajBhandary -- In vivo studies of receptors and ion channels with unnatural amino acids / D.A. Dougherty -- Synthesis of modified proteins using misacylated tRNAs / S.M. Hecht -- Cell-free synthesis of proteins with unnatural amino acids. The pure system and expansion of the genetic code / I. Hirao, T. Kanamori and T. Ueda -- Engineering nucleobases and polymerases for an expanded genetic alphabet / A.M. Leconte and F.E. Romesberg -- Understanding membrane proteins. How to design inhibitors of transmembrane protein-protein interactions / J.S. Slusky, H. Yin and W.F. DeGrado.
- 2006 Springer Protocolsedited by Katja M. Arndt, Kristian M. Müller.
- Accurate methods for ancestry and relatedness inference — Epigenetics of aging (154)
- Epigenetics protocols. 2nd ed. — Introduction to genomic signal processing with control (154)
- Investigations in yeast functional genomics and molecular biology — Protein engineering protocols (154)
- Proteins and proteomics of Leishmania and Trypanosoma — Zebrafish-- genetics, genomics, and transcriptomics. Fourth edition. [4th ed.] (152)
- Harrison's Principles of Internal Medicine
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- Surgical Exposures in Orthopaedics
- Mandell, Douglas, & Bennett's Principles & Practice of Infectious Diseases
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