Library Science

For both volumes: Expert investigators describe not only the classic methods, but also the many novel techniques they have perfected for the transfer of large DNAs into the cells of both microbes and animals via large-insert recombinant DNAs. Volume 1 presents readily reproducible techniques for library construction, physical mapping, and sequencing.. An accompanying volume, Volume 2: Functional Studies, provides a wide variety of methods and applications for functional analysis of the DNA-transformed organisms. Besides protocols, each chapter includes scientific reviews, software tools, database resources, genome sequencing strategies, and illustrative case studies.

Authors: Zhao, Shaying; Stodolsky, Marvin

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For both volumes: Expert investigators describe not only the classic methods, but also the many novel techniques they have perfected for the transfer of large DNAs into the cells of both microbes and animals via large-insert recombinant DNAs. Volume 1 presents readily reproducible techniques for library construction, physical mapping, and sequencing.. An accompanying volume, Volume 2: Functional Studies, provides a wide variety of methods and applications for functional analysis of the DNA-transformed organisms. Besides protocols, each chapter includes scientific reviews, software tools, database resources, genome sequencing strategies, and illustrative case studies.

Authors: Zhao, Shaying; Stodolsky, Marvin

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A collection of readily reproducible techniques for the study of mRNA processing and metabolism. These cutting-edge techniques range from cotranscriptional processing events that occur while the mNA is engaged with elongating RNA polymerase II, to in vivo and in vitro splicing and its biochemical analysis, and alternative splicing. Additional methods cover mRNA export, the recovery and analysis of mRNP complexes, cytoplasmic translation, mRNA degradation in vivo and in vitro, and the controversial concept of nuclear translation. Each proven protocol is described in step-by-step detail and contains a background introduction outlining the principle behind the technique, lists of equipment and reagents, and tips on troubleshooting and avoiding know pitfalls.

Authors: Schoenberg, Daniel R.

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This new edition combines updates of key chapters from the first edition with a large number of new key methodologies that have emerged more recently for studying G protein-coupled receptors (GPCRs) and events immediately downstream of their activation. The methods are focused primarily on events at the receptor level, including ligand binding, the genetic manipulation of receptors, the generation of model cell lines in which to study them, and the interaction and activation of G-proteins. Additional methods concentrate on receptor expression and localization, receptor internalization and post-translational modification, GPCR–protein interactions, and the use of knock-out and knock-in strategies for determining the physiological roles of receptors.

Authors: Willars, Gary B.; Challiss, R. A. John

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Leading experts describe in step-by-step detail their most productive transposon-based methods and strategies for studying genome structure, function, and evolution. These readily reproducible techniques cover a wide range, including mutagenesis, transgenesis, gene silencing, and molecular systematics. Among the highlights are a series of DNA hybridization methods for analyzing the distribution and dynamics of mobile DNA at the hosts’ genomic level, techniques for studying LTR retrotransposons in heterologous host systems, and mutagenesis protocols for investigating gene functions in a broad range of organisms. These cutting-edge methods offer investigators powerful genetic tools for dissecting the function of a specific gene, elaborating on the mechanisms leading to genetic change and diversity, and studying the evolutionary impact of mobile DNA on the biology and evolution of organisms.

Authors: Miller, Wolfgang J.; Capy, Pierre

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Genetic recombination is any process in which DNA sequences interact and undergo a transfer of information, producing new “recombinant” sequences that contain information from each of the original molecules. This book presents leading peer-reviewed protocols to carry out recombinant investigations in the lab. Part I provides approaches and model systems for studying several aspects of recombination in a variety of eukaryotic organisms and in mammalian parasites. Part II describes approaches for using recombination as a reporter of genomic instability in lower and higher eukaryotes. Part III discusses various methods and approaches for targeted genomic manipulation in higher and lower eukaryotes, while the final part presents biochemical analyses useful for furthering the understanding of recombination mechanisms, thus making this an invaluable book for both the novice and the established researcher in the field of recombination.

Authors: Waldman, Alan S.

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This thoroughly revised and updated edition of a widely used practical guide to flow cytometry describes in step-by-step detail an array of time proven and cutting-edge techniques much needed in today’s advanced laboratories. These readily reproducible methods deploy emerging flow cytometry technologies in many new applications, especially in the field of stem cells, functional genomics and proteomics, and microbiology. Here, the aspiring investigator will find methods for the characterization of stem/progenitor cells by monitoring the efflux of fluorescent dyes and the elucidation of signal transduction pathways using phospho-specific antibodies. There are also techniques for monitoring gene transfer and expression using fluorescent protein technology, high throughput screening for discovery of novel protein interactions, phenotypic and functional characterization of T cell subsets and precursors, and microbial flow cytometry, to highlight but some of the many useful procedures.

Authors: Hawley, Teresa S.; Hawley, Robert G.

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A diverse collection of unique methodologies to synthesize and construct protein arrays for basic and clinical research in a high-throughput manner. These readily reproducible techniques can be applied to such applications as quantifying specific proteins of interest and discovering novel proteins, as well as to a variety of affinity substances, including antibodies, peptides, proteins, aptamers, and chemicals. The techniques can be used for biomarkers discovery, assay development, clinical sample testing, and building the next generation of molecular tools.

Authors: Fung, Eric

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In Crystallographic Methods and Protocols leading specialists in the application of X-ray crystallography to biological problems provide a basic and comprehensive guide to its successful use in obtaining detailed three-dimensional structures of proteins, nucleic acids, and their complexes. These deeply experienced researchers describe in clear practical terms their proven methods for preparing samples, crystallizing them, obtaining preliminary characterizations, acquiring and analyzing data, and solving and refining structures. Their step-by-step instructions give biologically trained workers immediate access to a powerful technique essential to solving many biologically relevant problems.

Authors: Jones, Christopher; Mulloy, Barbara; Sanderson, Mark R.

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Yeast Protocols contains many key techniques for studying the biology of yeasts at both the cellular and molecular levels. Working primarily from Saccharomyces cerevisiae, the expert contributors explain step-by-step how to successfully isolate, identify, and culture yeasts; the secrets of meiotic mapping; how to use PFGE in karyotyping and gene localization; the methods for purification and analysis of various cell components; and the construction and exploitation of genomic DNA clone banks. They also cover the latest methods for chromosome engineering, insertional mutagenesis by Ty elements, mRNA abundance and half-life measurements, the use of reporter gene systems, genotoxicity testing, and more. Yeast Protocols follows the widely applauded Humana Methods in Molecular Biology style: brief introductions putting the particular method in context, comprehensive lists of materials, cookbook style instructions, and troubleshooting notes to avoid common pitfalls and solve problems. The techniques can be used with confidence and success by both inexperienced newcomers and established researchers.

Authors: Baniahmad, Aria

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Capillary Electrophoresis Guidebook offers both newcomers and experienced research workers hands-on guidance to performing capillary electrophoresis. It provides sufficient practical advice to permit you to develop and optimize your own separations, along with extensive troubleshooting sections to overcome practical difficulties. The book contains operating instructions for standard commercially available instruments and includes guidelines for activities such as changing capillaries, method development, quantitative procedures, optimizing sensitivity, and the validation of methods. Review chapters written by leading experts discuss micellar electrokinetic capillary chromatography, capillary gel electrophoresis, advanced sampling techniques, and electrochromatography. Important application areas such as the analysis of proteins, peptides, amino acids, pharmaceuticals, chiral compounds, and nucleic acids are also treated.

Authors: Altria, Kevin D.

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