Epigenetics Methods
Epigenetics Methods

Author: Trygve O Tollefsbol

Publisher: Academic Press

Published: 2020-07-08

Total Pages: 740

ISBN-13: 0128194154

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In recent years, the field of epigenetics has grown significantly, driving new understanding of human developmental processes and disease expression, as well as advances in diagnostics and therapeutics. As the field of epigenetics continues to grow, methods and technologies have multiplied, resulting in a wide range of approaches and tools researchers might employ. Epigenetics Methods offers comprehensive instruction in methods, protocols, and experimental approaches applied in field of epigenetics. Here, across thirty-five chapters, specialists offer step-by-step overviews of methods used to study various epigenetic mechanisms, as employed in basic and translational research. Leading the reader from fundamental to more advanced methods, the book begins with thorough instruction in DNA methylation techniques and gene or locus-specific methylation analyses, followed by histone modification methods, chromatin evaluation, enzyme analyses of histone methylation, and studies of non-coding RNAs as epigenetic modulators. Recently developed techniques and technologies discussed include single-cell epigenomics, epigenetic editing, computational epigenetics, systems biology epigenetic methods, and forensic epigenetic approaches. Epigenetics methods currently in-development, and their implication for future research, are also considered in-depth. In addition, as with the wider life sciences, reproducibility across experiments, labs, and subdisciplines is a growing issue for epigenetics researchers. This volume provides consensus-driven methods instruction and overviews. Tollefsbol and contributing authors survey the range of existing methods; identify best practices, common themes, and challenges; and bring unity of approach to a diverse and ever-evolving field. - Includes contributions by leading international investigators involved in epigenetic research and clinical and therapeutic application - Integrates technology and translation with fundamental chapters on epigenetics methods, as well as chapters on more novel and advanced epigenetics methods - Written at verbal and technical levels that can be understood by scientists and students alike - Includes chapters on state-of-the-art techniques such as single-cell epigenomics, use of CRISPR/Cas9 for epigenetic editing, and epigenetics methods applied to forensics

Footprinting of Nucleic Acid-Protein Complexes
Footprinting of Nucleic Acid-Protein Complexes

Author:

Publisher: Academic Press

Published: 2014-05-19

Total Pages: 216

ISBN-13: 148329501X

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Footprinting of Nucleic Acid-Protein Complexes provides protocols for studying the stoichiometry, binding site size and location, and structural changes in nucleic acids caused by their interaction with proteins. The methods are central to studying key biological processes, such as transcription and translation. The techniques are important to experiments in vivoand in vitro, in eukaryotes and in prokaryotes, at qualitative and quantitative levels,and across many disciplines.This book is a laboratory manual of footprinting techniques for studying nucleic acid-protein interactions. It contains clear and concise descriptions of the most important methodologies, and includes in vivo as well as in vitro applications. It is aimed at bench scientists from graduate students on, and should be of value in industrial labs as well as in academic settings. Use of different footprinting approaches can provide unique insights into DNA-protein systems. The protocols containedin this handbook are written to be"user-friendly,"and thus should be conducive to extending the use of footprinting to new systems. The section on quantitative analysis of DNAse I footprints should prove especially useful for in depth evaluation of cooperative interactions.(For the End User)Provides clear exposition of footprinting techniques for characterizing DNA-protein interactionsCovers both protection methods for identifying sites of protein binding and interference methods for determining points of contact between DNA and proteinIncludes approaches for both in vitro and in vivo measurementsHigh quality, timely, and of lasting practical value in the laboratory

Methods in Plant Cell Biology
Methods in Plant Cell Biology

Author: David W. Galbraith

Publisher: Academic Press

Published: 1995

Total Pages: 605

ISBN-13: 0125641516

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Methods in Plant Cell Biology provides in two volumes a comprehensive collection of analytical methods essential for researchers and students in the plant sciences. Individual chapters, written by experts in the field, provide an introductory overview, followed by a step-by-step technical description of the methods. Key Features * Written by experts, many of whom have developed the individual methods described * Contains most, if not all, the methods needed for modern research in plant cell biology * Up-to-date and comprehensive * Full references * Allows quick access to relevant journal articles and to the sources of chemicals required for the procedures * Selective concentration on higher plant methods allows for particular emphasis on those problems specific to plants.

DNA'Protein Interactions
DNA'Protein Interactions

Author: Tom Moss

Publisher: Springer Science & Business Media

Published: 2008-02-02

Total Pages: 633

ISBN-13: 1592592082

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Dr. Tom Moss assembles the new standard collection of cutting-edge techniques to identify key protein-DNA interactions and define their components, their manner of interaction, and their manner of function, both in the cell and in the test tube. The techniques span a wide range, from factor identification to atomic detail, and include multiple DNA footprinting analyses, including in vivo strategies, gel shift (EMSA) optimization, SELEX, surface plasmon resonance, site-specific DNA-protein crosslinking, and UV laser crosslinking. Comprehensive and broad ranging, DNA-Protein Interactions: Principles and Protocols, 2nd Edition, offers a stellar array of over 100 up-to-date and readily reproducible techniques that biochemists and molecular, cellular, and developmental biologists can use successfully today to understand DNA-protein interactions.

Mass Spectrometry-Based Chemical Proteomics
Mass Spectrometry-Based Chemical Proteomics

Author: W. Andy Tao

Publisher: John Wiley & Sons

Published: 2019-07-10

Total Pages: 449

ISBN-13: 1118970217

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PROVIDES STRATEGIES AND CONCEPTS FOR UNDERSTANDING CHEMICAL PROTEOMICS, AND ANALYZING PROTEIN FUNCTIONS, MODIFICATIONS, AND INTERACTIONS—EMPHASIZING MASS SPECTROMETRY THROUGHOUT Covering mass spectrometry for chemical proteomics, this book helps readers understand analytical strategies behind protein functions, their modifications and interactions, and applications in drug discovery. It provides a basic overview and presents concepts in chemical proteomics through three angles: Strategies, Technical Advances, and Applications. Chapters cover those many technical advances and applications in drug discovery, from target identification to validation and potential treatments. The first section of Mass Spectrometry-Based Chemical Proteomics starts by reviewing basic methods and recent advances in mass spectrometry for proteomics, including shotgun proteomics, quantitative proteomics, and data analyses. The next section covers a variety of techniques and strategies coupling chemical probes to MS-based proteomics to provide functional insights into the proteome. In the last section, it focuses on using chemical strategies to study protein post-translational modifications and high-order structures. Summarizes chemical proteomics, up-to-date concepts, analysis, and target validation Covers fundamentals and strategies, including the profiling of enzyme activities and protein-drug interactions Explains technical advances in the field and describes on shotgun proteomics, quantitative proteomics, and corresponding methods of software and database usage for proteomics Includes a wide variety of applications in drug discovery, from kinase inhibitors and intracellular drug targets to the chemoproteomics analysis of natural products Addresses an important tool in small molecule drug discovery, appealing to both academia and the pharmaceutical industry Mass Spectrometry-Based Chemical Proteomics is an excellent source of information for readers in both academia and industry in a variety of fields, including pharmaceutical sciences, drug discovery, molecular biology, bioinformatics, and analytical sciences.

An Introduction to Biotechnology
An Introduction to Biotechnology

Author: W.T. Godbey

Publisher: Elsevier

Published: 2014-12-08

Total Pages: 435

ISBN-13: 1908818484

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An Introduction to Biotechnology is a biotechnology textbook aimed at undergraduates. It covers the basics of cell biology, biochemistry and molecular biology, and introduces laboratory techniques specific to the technologies addressed in the book; it addresses specific biotechnologies at both the theoretical and application levels.Biotechnology is a field that encompasses both basic science and engineering. There are currently few, if any, biotechnology textbooks that adequately address both areas. Engineering books are equation-heavy and are written in a manner that is very difficult for the non-engineer to understand. Numerous other attempts to present biotechnology are written in a flowery manner with little substance. The author holds one of the first PhDs granted in both biosciences and bioengineering. He is more than an author enamoured with the wow-factor associated with biotechnology; he is a practicing researcher in gene therapy, cell/tissue engineering, and other areas and has been involved with emerging technologies for over a decade. Having made the assertion that there is no acceptable text for teaching a course to introduce biotechnology to both scientists and engineers, the author committed himself to resolving the issue by writing his own. - The book is of interest to a wide audience because it includes the necessary background for understanding how a technology works. - Engineering principles are addressed, but in such a way that an instructor can skip the sections without hurting course content - The author has been involved with many biotechnologies through his own direct research experiences. The text is more than a compendium of information - it is an integrated work written by an author who has experienced first-hand the nuances associated with many of the major biotechnologies of general interest today.

In VIVO Footprinting
In VIVO Footprinting

Author: I.L. Cartwright

Publisher: Elsevier Science

Published: 1997-08-22

Total Pages: 0

ISBN-13: 9780762301454

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The revolution in biological research initiated by the demonstration that particular DNA molecules could be isolated, recombined in novel ways, and conveniently replicated to high copy number in vivo for further study, that is, the recombinant DNA era, has spawned many additional advances, both methodological and intellectual, that have enhanced our understanding of cellular processes to an astonishing degree. As part of the subsequent outpouring of information, research exploring the mechanisms of gene regulation, both in prokaryotes and eukaryotes (but particularly the latter), has been particularly well represented. Although no one technical approach can be said to have brought the filed to its current level of sophistication, the ability to map the interactions of trans-acting factors with their DNA recognition sequences to a high level of precision has certainly been one of the more important advances. This "footprinting" approach has become almost ubiquitous in gene regulatory studies; however, it is in its "in vivo" application that ambiguities, confusions, and inconsistencies that may arise from a purely "in vitro"-based approach can often be resolved and placed in their proper perspective. Put more simply, that an interaction can be demonstrated to occur between purified factors and a particular piece of DNA in a test tube does not, of course, say anything regarding whether such interactions are occurring in vivo. The ability to probe for such interactions as they occur inside cells, with due attention paid to the relevant developmental stage, or to the tissue specificity of the interaction being probed, has made in vivo footprinting approach an invaluable adjunct to the "gene jockey's" arsenal of weapons.

A Handbook of Transcription Factors
A Handbook of Transcription Factors

Author: Timothy R. Hughes

Publisher: Springer Science & Business Media

Published: 2011-05-10

Total Pages: 310

ISBN-13: 904819069X

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Transcription factors are the molecules that the cell uses to interpret the genome: they possess sequence-specific DNA-binding activity, and either directly or indirectly influence the transcription of genes. In aggregate, transcription factors control gene expression and genome organization, and play a pivotal role in many aspects of physiology and evolution. This book provides a reference for major aspects of transcription factor function, encompassing a general catalogue of known transcription factor classes, origins and evolution of specific transcription factor types, methods for studying transcription factor binding sites in vitro, in vivo, and in silico, and mechanisms of interaction with chromatin and RNA polymerase.