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Developing Bind N Seq For Identification Of C2h2 Zinc Fingers And Other Proteins Dna Binding Properties
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Book Synopsis Developing Bind-n-Seq for Identification of C2H2 Zinc Fingers and Other Proteins DNA Binding Properties by : Artem Zykovich
Download or read book Developing Bind-n-Seq for Identification of C2H2 Zinc Fingers and Other Proteins DNA Binding Properties written by Artem Zykovich and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcription factors (TF) play a central role in the regulation of gene expression. Knowledge of TF-DNA binding preferences can significantly improve our understanding of global cellular processes such as differentiation and apoptosis as well as mechanisms that lead to abnormalities in cell fate like cancer. The C2H2 zinc finger is the most common DNA binding domain in the human genome. In addition to being so widespread, there is great interest in studying this domain because it has been successfully employed in targeted genome engineering. Despite years of research on amino acid-nucleotide binding preferences, there is no comprehensive recognition code. Therefore every new zinc finger protein must be tested to empirically determine its DNA binding properties. We developed a new high-throughput method, Bind-n-Seq, for the in vitro analysis of protein-DNA interactions using massively parallel sequencing. The procedure has three steps: (i) binding proteins to randomized oligonucleotide DNA targets, (ii) sequencing the bound oligonucleotides with next-generation technology and (iii) finding motifs among the sequences. There are several key features of Bind-n-Seq that provide advantages over extant methods. Three nucleotide barcodes allow pooling up to 64 binding reactions in a single sequencing run. Extensive library coverage in conjunction with massive sequencing output results in identification of thousands of protein-DNA interactions. The technique is simple and inexpensive. Proteins with long or cooperative binding sites can also be analyzed. We have developed a new motif finding algorithm, Merminator, specifically designed for Bind-n-Seq data. Merminator is based on differential k-mer compositions before and after protein binding. Merminator can be used online at the Bind-n-Seq Source website, where one can process and store data from Bind-n-Seq experiments. The combination of Bind-n-Seq and Merminator allows researchers to investigate protein-DNA interactions in unprecedented depth and breadth.
Book Synopsis Engineered Zinc Finger Proteins by : Joel P. Mackay
Download or read book Engineered Zinc Finger Proteins written by Joel P. Mackay and published by Humana Press. This book was released on 2011-08-24 with total page 440 pages. Available in PDF, EPUB and Kindle. Book excerpt: Among the many types of DNA binding domains, C2H2 zinc finger proteins (ZFPs) have proven to be the most malleable for creating custom DNA-binding proteins. In Engineered Zinc Finger Proteins: Methods and Protocols, expert researchers from some of the most active laboratories in this field present detailed methods, guidance, and perspectives. The volume contains sections covering the engineering of ZFPs, methods for the creation, evaluation, and delivery of artificial transcription factors (ATFs), methods for the creation and evaluation of zinc finger nucleases (ZFNs), and a collection of the several applications and assays beyond ATFs and ZFNs, including zinc finger transposases and ChIP-seq methodology amongst other subjects. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, Engineered Zinc Finger Proteins: Methods and Protocols aims to aid both seasoned practitioners and new investigators with its vital methods and insights as they seek to create the next generation of engineered ZFPs and applications.
Book Synopsis Tissue Specific Gene Expression by : Rainer Renkawitz
Download or read book Tissue Specific Gene Expression written by Rainer Renkawitz and published by John Wiley & Sons. This book was released on 1989 with total page 221 pages. Available in PDF, EPUB and Kindle. Book excerpt: This collection of review articles is a valuable contribution to current research in one of the most important areas of molecular biology. It summarizes the exciting results of research on regulatory mechanisms of a selected number of model genes (for example, immunoglobulin genes, human growth hormone gene, albumin gene). Written by international experts, it concentrates on * regulatory proteins * regulatory sequences * chromatin structure * tissue specific splicing By focusing on a few representative model genes, the book enables the reader to draw both detailed and general conclusions about the mechanisms of tissue specific gene regulation. Geneticists in research and medicine can thus acquire vital information without having to consider an otherwise overwhelming number of systems.
Book Synopsis Epigenetics: Development and Disease by : Tapas Kumar Kundu
Download or read book Epigenetics: Development and Disease written by Tapas Kumar Kundu and published by Springer Science & Business Media. This book was released on 2012-11-13 with total page 698 pages. Available in PDF, EPUB and Kindle. Book excerpt: Epigenetics fine-tunes the life processes dictated by DNA sequences, but also kick-starts pathophysiological processes including diabetes, AIDS and cancer. This volume tracks the latest research on epigenetics, including work on new-generation therapeutics.
Book Synopsis Molecular Evolution by : Roderick D.M. Page
Download or read book Molecular Evolution written by Roderick D.M. Page and published by John Wiley & Sons. This book was released on 2009-07-14 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of evolution at the molecular level has given the subject of evolutionary biology a new significance. Phylogenetic 'trees' of gene sequences are a powerful tool for recovering evolutionary relationships among species, and can be used to answer a broad range of evolutionary and ecological questions. They are also beginning to permeate the medical sciences. In this book, the authors approach the study of molecular evolution with the phylogenetic tree as a central metaphor. This will equip students and professionals with the ability to see both the evolutionary relevance of molecular data, and the significance evolutionary theory has for molecular studies. The book is accessible yet sufficiently detailed and explicit so that the student can learn the mechanics of the procedures discussed. The book is intended for senior undergraduate and graduate students taking courses in molecular evolution/phylogenetic reconstruction. It will also be a useful supplement for students taking wider courses in evolution, as well as a valuable resource for professionals. First student textbook of phylogenetic reconstruction which uses the tree as a central metaphor of evolution. Chapter summaries and annotated suggestions for further reading. Worked examples facilitate understanding of some of the more complex issues. Emphasis on clarity and accessibility.
Book Synopsis Systems Biology of RNA Binding Proteins by : Gene W. Yeo
Download or read book Systems Biology of RNA Binding Proteins written by Gene W. Yeo and published by Springer. This book was released on 2014-09-08 with total page 474 pages. Available in PDF, EPUB and Kindle. Book excerpt: After transcription in the nucleus, RNA binding proteins (RBPs) recognize cis-regulatory RNA elements within pre-mRNA sequence to form mRNA-protein (mRNP) complexes. Similarly to DNA binding proteins such as transcription factors that regulate gene expression by binding to DNA elements in the promoters of genes, RBPs regulate the fate of target RNAs by interacting with specific sequences or RNA secondary structural features within the transcribed RNA molecule. The set of functional RNA elements recognized by RBPs within target RNAs and which control the temporal, functional and spatial dynamics of the target RNA define a putative “mRNP code”. These cis-regulatory RNA elements can be found in the 5’ and 3’ untranslated regions (UTRs), introns, and exons of all protein-coding genes. RNA elements in 5’ and 3’ UTRs are frequently involved in targeting RNA to specific cellular compartments, affecting 3’ end formation, controlling RNA stability and regulating mRNA translation. RNA elements in introns and exons are known to function as splicing enhancers or silencers during the splicing process from pre-mRNA to mature mRNA. This book provides case studies of RNA binding proteins that regulate aspects of RNA processing that are important for fundamental understanding of diseases and development. Chapters include systems-level perspectives, mechanistic insights into RNA processing and RNA Binding proteins in genetic variation, development and disease. The content focuses on systems biology and genomics of RNA Binding proteins and their relation to human diseases.
Book Synopsis Pathogenesis of Idiopathic Scoliosis by : Masafumi Machida
Download or read book Pathogenesis of Idiopathic Scoliosis written by Masafumi Machida and published by Springer. This book was released on 2018-02-23 with total page 193 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides comprehensive coverage of current topics in idiopathic scoliosis (IS). A three-dimensional deformity of the spine, the condition is characterized by lateral curvature combined with vertebral rotation. The primary lesion, however, lies in the median sagittal plane, taking the form of a lordosis. Although the clinical manifestations of scoliosis have been well documented, its cause and pathogenesis have not yet been determined. Research into what causes IS has focused on the structural elements of the spine, spinal musculature, collagenous structures, the endocrine system, the central nervous system, and genetics. Results of these studies have brought about a new perception of IS epiphenomena, but the main cause of IS remains unknown. Recently, several investigators have produced new hypotheses regarding the cause of IS using the developing techniques of genetics, biochemistry, and neurology. This book is a review of the various causative factors thus far proposed for IS and an introduction to the directions in which research is heading to determine the primary cause of IS.
Book Synopsis Abiotic Stress-Mediated Sensing and Signaling in Plants: An Omics Perspective by : Sajad Majeed Zargar
Download or read book Abiotic Stress-Mediated Sensing and Signaling in Plants: An Omics Perspective written by Sajad Majeed Zargar and published by Springer. This book was released on 2018-02-20 with total page 358 pages. Available in PDF, EPUB and Kindle. Book excerpt: The natural environment for plants is composed of a complex set of abiotic and biotic stresses; plant responses to these stresses are equally complex. Systems biology allows us to identify regulatory hubs in complex networks. It also examines the molecular “parts” (transcripts, proteins and metabolites) of an organism and attempts to combine them into functional networks or models that effectively describe and predict the dynamic activities of that organism in different environments. This book focuses on research advances regarding plant responses to abiotic stresses, from the physiological level to the molecular level. It highlights new insights gained from the integration of omics datasets and identifies remaining gaps in our knowledge, outlining additional focus areas for future crop improvement research. Plants have evolved a wide range of mechanisms for coping with various abiotic stresses. In many crop plants, the molecular mechanisms involved in a single type of stress tolerance have since been identified; however, in order to arrive at a holistic understanding of major and common events concerning abiotic stresses, the signaling pathways involved must also be elucidated. To date several molecules, like transcription factors and kinases, have been identified as promising candidates that are involved in crosstalk between stress signalling pathways. However, there is a need to better understand the tolerance mechanisms for different abiotic stresses by thoroughly grasping the signalling and sensing mechanisms involved. Accordingly, this book covers a range of topics, including the impacts of different abiotic stresses on plants, the molecular mechanisms leading to tolerance for different abiotic stresses, signaling cascades revealing cross-talk among various abiotic stresses, and elucidation of major candidate molecules that may provide abiotic stress tolerance in plants.
Book Synopsis Introduction to Bioinformatics by : Arthur Lesk
Download or read book Introduction to Bioinformatics written by Arthur Lesk and published by . This book was released on 2019-05 with total page 433 pages. Available in PDF, EPUB and Kindle. Book excerpt: The ideal text for biology students encountering bioinformatics for the first time, Introduction to Bioinformatics describes how recent technological advances in the field can be used as a powerful set of tools for receiving and analyzing biological data.
Book Synopsis Molecular Approaches in Plant Biology and Environmental Challenges by : Sudhir P. Singh
Download or read book Molecular Approaches in Plant Biology and Environmental Challenges written by Sudhir P. Singh and published by Springer Nature. This book was released on 2019-10-01 with total page 507 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses molecular approaches in plant as response to environmental factors, such as variations in temperature, water availability, salinity, and metal stress. The book also covers the impact of increasing global population, urbanization, and industrialization on these molecular behaviors. It covers the natural tolerance mechanism which plants adopt to cope with adverse environments, as well as the novel molecular strategies for engineering the plants in human interest. This book will be of interest to researchers working on the impact of the changing environment on plant ecology, issues of crop yield, and nutrient quantity and quality in agricultural crops. The book will be of interest to researchers as well as policy makers in the environmental and agricultural domains.
Book Synopsis Grand Challenges in Fungal Biotechnology by : Helena Nevalainen
Download or read book Grand Challenges in Fungal Biotechnology written by Helena Nevalainen and published by Springer Nature. This book was released on 2020-01-08 with total page 535 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides a comprehensive overview of the major applications and potential of fungal biotechnology. The respective chapters report on the latest advances and opportunities in each topic area, proposing new and sustainable solutions to some of the major challenges faced by modern society. Aimed at researchers and biotechnologists in academia and industry, it represents essential reading for anyone interested in fungal biotechnology, as well as those working within the broader area of microbial biotechnology. Written in an accessible language, the book also offers a valuable reference resource for decision-makers in government and at non-governmental organizations who are involved in the development of cleaner technologies and the global bioeconomy. The 21st century is characterized by a number of critical challenges in terms of human health, developing a sustainable bioeconomy, facilitating agricultural production, and establishing practices that support a cleaner environment. While there are chemical solutions to some of these challenges, developing bio-based approaches is becoming increasingly important. Filamentous fungi, ‘the forgotten kingdom,’ are a group of unique organisms whose full potential has yet to be revealed. Some key properties, such as their exceptional capacity to secrete proteins into the external environment, have already been successfully harnessed for the production of industrial enzymes and cellulosic biofuels. Many further aspects discussed here –such as feeding the hungry with fungal protein, and the potential applications of the various small molecules produced by fungi –warrant further exploration. In turn, the book covers the use of fungal cell factories to produce foreign molecules, e.g. for therapeutics. Strategies including molecular approaches to strain improvement, and recent advances in high-throughput technologies, which are key to finding better products and producers, are also addressed. Lastly, the book discusses the advent of synthetic biology, which is destined to greatly expand the scope of fungal biotechnology. The chapter “Fungal Biotechnology in Space: Why and How?” is available open access under a Creative Commons Attribution 4.0 International License at link.springer.com.
Download or read book Plant Proteomics written by Jozef Samaj and published by Springer Science & Business Media. This book was released on 2007-09-09 with total page 397 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plant Proteomics highlights rapid progress in this field, with emphasis on recent work in model plant species, sub-cellular organelles, and specific aspects of the plant life cycle such as signaling, reproduction and stress physiology. Several chapters present a detailed look at diverse integrated approaches, including advanced proteomic techniques combined with functional genomics, bioinformatics, metabolomics and molecular cell biology, making this book a valuable resource for a broad spectrum of readers.
Book Synopsis Salinity Responses and Tolerance in Plants, Volume 1 by : Vinay Kumar
Download or read book Salinity Responses and Tolerance in Plants, Volume 1 written by Vinay Kumar and published by Springer. This book was released on 2018-04-05 with total page 408 pages. Available in PDF, EPUB and Kindle. Book excerpt: Soil salinity is a key abiotic-stress and poses serious threats to crop yields and quality of produce. Owing to the underlying complexity, conventional breeding programs have met with limited success. Even genetic engineering approaches, via transferring/overexpressing a single ‘direct action gene’ per event did not yield optimal results. Nevertheless, the biotechnological advents in last decade coupled with the availability of genomic sequences of major crops and model plants have opened new vistas for understanding salinity-responses and improving salinity tolerance in important glycophytic crops. Our goal is to summarize these findings for those who wish to understand and target the molecular mechanisms for producing salt-tolerant and high-yielding crops. Through this 2-volume book series, we critically assess the potential venues for imparting salt stress tolerance to major crops in the post-genomic era. Accordingly, perspectives on improving crop salinity tolerance by targeting the sensory, ion-transport and signaling mechanisms are presented here in volume 1. Volume 2 will focus on the potency of post-genomic era tools that include RNAi, genomic intervention, genome editing and systems biology approaches for producing salt tolerant crops.
Book Synopsis Molecular Exercise Physiology by : Adam Sharples
Download or read book Molecular Exercise Physiology written by Adam Sharples and published by Taylor & Francis. This book was released on 2022-05-11 with total page 359 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fully revised and expanded, the second edition of Molecular Exercise Physiology offers a student-friendly introduction. It introduces a history documenting the emergence of molecular biology techniques to investigate exercise physiology, the methodology used, exercise genetics and epigenetics, and the molecular mechanisms that lead to adaptation after different types of exercise, with explicit links to outcomes in sport performance, nutrition, physical activity and clinical exercise. Structured around key topics in sport and exercise science and featuring contributions from pioneering scientists, such as Nobel Prize winners, this edition includes new chapters based on cutting-edge research in epigenetics and muscle memory, satellite cells, exercise in cancer, at altitude, and in hot and cold climates. Chapters include learning objectives, structured guides to further reading, review questions, overviews of work by key researchers and box discussions from important pioneers in the field, making it a complete resource for any molecular exercise physiology course. The book includes cell and molecular biology laboratory methods for dissertation and research projects in molecular exercise physiology and muscle physiology. This book is essential reading for upper-level undergraduate or postgraduate courses in cellular and molecular exercise physiology and muscle physiology. It is a valuable resource for any student with an advanced interest in exercise physiology in both sport performance and clinical settings.
Book Synopsis Practical Bioinformatics by : Michael Agostino
Download or read book Practical Bioinformatics written by Michael Agostino and published by Garland Science. This book was released on 2012-09-26 with total page 392 pages. Available in PDF, EPUB and Kindle. Book excerpt: Practical Bioinformatics is specifically designed for biology majors, with a heavy emphasis on the steps required to perform bioinformatics analysis to answer biological questions. It is written for courses that have a practical, hands-on element and contains many exercises (for example, database searches, protein analysis, data interpretation) to
Download or read book Prostate Cancer written by Scott M. Dehm and published by Springer Nature. This book was released on 2020-01-03 with total page 483 pages. Available in PDF, EPUB and Kindle. Book excerpt: The purpose of this book is to provide a contemporary overview of the causes and consequences of prostate cancer from a cellular and genetic perspective. Written by experts in the fields of epidemiology, toxicology, cell biology, genetics, genomics, cell-cell interactions, cell signaling, hormone signaling, and transcriptional regulation, the text covers aspects of prostate cancer from disease initiation to metastasis. Chapters explore in depth the cells of origin for prostate cancer, its genomic subtypes, neural transcription factors in disease progression, epigenetic regulation of chromatin, and many other topics. This book distinguishes itself from other texts on prostate cancer by its focus on cellular and genetic mechanisms, as opposed to clinical diagnosis and management. As a result, this book will be of broad interest to basic and translational scientists with familiarity of these topics, as well as to trainees at earlier stages of their research careers.
Book Synopsis Chromosome Banding by : Adrian Thomas Sumner
Download or read book Chromosome Banding written by Adrian Thomas Sumner and published by Springer. This book was released on 1990-11-22 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt:
