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Organism And Disease Specific Atlases Of Transcription Start Sites Using Cap Analysis Of Gene Expression Cage
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Book Synopsis Organism- and Disease-specific Atlases of Transcription Start Sites Using Cap Analysis of Gene Expression (CAGE) by :
Download or read book Organism- and Disease-specific Atlases of Transcription Start Sites Using Cap Analysis of Gene Expression (CAGE) written by and published by . This book was released on 2018 with total page 185 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Efficient Global Mapping and Analysis of Transcription Start Sites with STRIPE-seq and TSRexploreR by : Robert Anthony Policastro
Download or read book Efficient Global Mapping and Analysis of Transcription Start Sites with STRIPE-seq and TSRexploreR written by Robert Anthony Policastro and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Heterogeneity in transcription initiation has important consequences for transcript stability and translation, and shifts in transcription start site (TSS) usage are prevalent in various disease and developmental contexts. Thus, accurate mapping of transcription start sites (TSSs) is key for understanding transcriptional regulation. However, current protocols for genome-wide TSS profiling are laborious and/or expensive. We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid, and cost-effective protocol for sequencing capped RNA 5' ends from as little as 50 ng total RNA. Including depletion of uncapped RNA and reaction cleanups, a STRIPE-seq library can be constructed in about 5 h. We show application of STRIPE-seq to TSS profiling in yeast and human cells and show that it can also be effectively used for quantification of transcript levels and analysis of differential gene expression. In parallel to our development of STRIPE-seq, we built TSRexploreR, an R package for end-to-end analysis of TSS mapping data. TSRexploreR provides functions for TSS and TSR detection, normalization, correlation, visualization, and differential TSS/TSR analysis. TSRexploreR is highly interoperable, accepting the data structures of TSS and TSR sets generated by several existing tools for processing and alignment of TSS mapping data, such as CAGEr for Cap Analysis of Gene Expression (CAGE) data. Lastly, TSRexploreR implements a novel approach for the detection of shifts in TSS distribution.
Book Synopsis Enhancers and Promoters by : Tilman Borggrefe
Download or read book Enhancers and Promoters written by Tilman Borggrefe and published by Humana. This book was released on 2021-09-09 with total page 376 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains cutting-edge techniques to study the function of enhancers and promoters in depth. Chapters are divided into six sections and describe enhancer-promoter transcripts, nucleosome occupancy, DNA accessibility, chromatin interactions, protein-DNA interactions, functional analyses, and DNA methylation assays. Written in the Methods in Molecular Biology series format, chapters include comprehensive introductions, lists of the necessary materials and reagents, step-by-step laboratory protocols, and useful suggestions for troubleshooting. Authoritative and cutting-edge, Enhancers and Promoters: Methods and Protocols is a useful guide for future experiments.
Book Synopsis Gene Quantification by : Francois Ferre
Download or read book Gene Quantification written by Francois Ferre and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 379 pages. Available in PDF, EPUB and Kindle. Book excerpt: Geneticists and molecular biologists have been interested in quantifying genes and their products for many years and for various reasons (Bishop, 1974). Early molecular methods were based on molecular hybridization, and were devised shortly after Marmur and Doty (1961) first showed that denaturation of the double helix could be reversed - that the process of molecular reassociation was exquisitely sequence dependent. Gillespie and Spiegelman (1965) developed a way of using the method to titrate the number of copies of a probe within a target sequence in which the target sequence was fixed to a membrane support prior to hybridization with the probe - typically a RNA. Thus, this was a precursor to many of the methods still in use, and indeed under development, today. Early examples of the application of these methods included the measurement of the copy numbers in gene families such as the ribosomal genes and the immunoglo bulin family. Amplification of genes in tumors and in response to drug treatment was discovered by this method. In the same period, methods were invented for estimating gene num bers based on the kinetics of the reassociation process - the so-called Cot analysis. This method, which exploits the dependence of the rate of reassociation on the concentration of the two strands, revealed the presence of repeated sequences in the DNA of higher eukaryotes (Britten and Kohne, 1968). An adaptation to RNA, Rot analysis (Melli and Bishop, 1969), was used to measure the abundance of RNAs in a mixed population.
Book Synopsis Epigenetics Methods by : Trygve Tollefsbol
Download or read book Epigenetics Methods written by Trygve Tollefsbol and published by Academic Press. This book was released on 2020-07-08 with total page 736 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Book Synopsis Genomics, Circuits, and Pathways in Clinical Neuropsychiatry by : Thomas Lehner
Download or read book Genomics, Circuits, and Pathways in Clinical Neuropsychiatry written by Thomas Lehner and published by Academic Press. This book was released on 2016-06-07 with total page 798 pages. Available in PDF, EPUB and Kindle. Book excerpt: This foundational work comprehensively examines the current state of the genetics, genomics and brain circuitry of psychiatric and neurological disorders. It consolidates discoveries of specific genes and genomic regions associated with these conditions, the genetic and anatomic architecture of these syndromes, and addresses how recent advances in genomics are leading to a reappraisal of the biology underlying clinical neuroscience. In doing so, it critically examines the promise and limitations of these discoveries toward treatment, and to the interdisciplinary nature of understanding brain and behavior. Coverage includes new discoveries regarding autism, epilepsy, intellectual disability, dementias, movement disorders, language impairment, disorders of attention, schizophrenia, and bipolar disorder. Genomics, Circuits, and Pathways in Clinical Neuropsychiatry focuses on key concepts, challenges, findings, and methods in genetics, genomics, molecular pathways, brain circuitry, and related neurobiology of neurologic and psychiatric disorders. Provides interdisciplinary appeal in psychiatry, neurology, neuroscience, and genetics Identifies key concepts, methods, and findings Includes coverage of multiple disorders from autism to schizophrenia Reviews specific genes associated with disorders Discusses the genetic architecture of these syndromes Explains how recent findings are influencing the understanding of biology Clarifies the promise of these findings for future treatment
Author :National Academies of Sciences, Engineering, and Medicine Publisher :National Academies Press ISBN 13 :0309437873 Total Pages :231 pages Book Rating :4.3/5 (94 download)
Book Synopsis Gene Drives on the Horizon by : National Academies of Sciences, Engineering, and Medicine
Download or read book Gene Drives on the Horizon written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2016-08-28 with total page 231 pages. Available in PDF, EPUB and Kindle. Book excerpt: Research on gene drive systems is rapidly advancing. Many proposed applications of gene drive research aim to solve environmental and public health challenges, including the reduction of poverty and the burden of vector-borne diseases, such as malaria and dengue, which disproportionately impact low and middle income countries. However, due to their intrinsic qualities of rapid spread and irreversibility, gene drive systems raise many questions with respect to their safety relative to public and environmental health. Because gene drive systems are designed to alter the environments we share in ways that will be hard to anticipate and impossible to completely roll back, questions about the ethics surrounding use of this research are complex and will require very careful exploration. Gene Drives on the Horizon outlines the state of knowledge relative to the science, ethics, public engagement, and risk assessment as they pertain to research directions of gene drive systems and governance of the research process. This report offers principles for responsible practices of gene drive research and related applications for use by investigators, their institutions, the research funders, and regulators.
Book Synopsis Molecular Biology by : David P. Clark
Download or read book Molecular Biology written by David P. Clark and published by Elsevier. This book was released on 2012-03-20 with total page 924 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Biology, Second Edition, examines the basic concepts of molecular biology while incorporating primary literature from today’s leading researchers. This updated edition includes Focuses on Relevant Research sections that integrate primary literature from Cell Press and focus on helping the student learn how to read and understand research to prepare them for the scientific world. The new Academic Cell Study Guide features all the articles from the text with concurrent case studies to help students build foundations in the content while allowing them to make the appropriate connections to the text. Animations provided deal with topics such as protein purification, transcription, splicing reactions, cell division and DNA replication and SDS-PAGE. The text also includes updated chapters on Genomics and Systems Biology, Proteomics, Bacterial Genetics and Molecular Evolution and RNA. An updated ancillary package includes flashcards, online self quizzing, references with links to outside content and PowerPoint slides with images. This text is designed for undergraduate students taking a course in Molecular Biology and upper-level students studying Cell Biology, Microbiology, Genetics, Biology, Pharmacology, Biotechnology, Biochemistry, and Agriculture. NEW: "Focus On Relevant Research" sections integrate primary literature from Cell Press and focus on helping the student learn how to read and understand research to prepare them for the scientific world NEW: Academic Cell Study Guide features all articles from the text with concurrent case studies to help students build foundations in the content while allowing them to make the appropriate connections to the text NEW: Animations provided include topics in protein purification, transcription, splicing reactions, cell division and DNA replication and SDS-PAGE Updated chapters on Genomics and Systems Biology, Proteomics, Bacterial Genetics and Molecular Evolution and RNA Updated ancillary package includes flashcards, online self quizzing, references with links to outside content and PowerPoint slides with images Fully revised art program
Book Synopsis The Cell Biology of Stem Cells by : Eran Meshorer
Download or read book The Cell Biology of Stem Cells written by Eran Meshorer and published by Springer Science & Business Media. This book was released on 2011-01-11 with total page 246 pages. Available in PDF, EPUB and Kindle. Book excerpt: Stem cells have been gaining a lot of attention in recent years. Their unique potential to self-renew and differentiate has turned them into an attractive model for the study of basic biological questions such as cell division, replication, transcription, cell fate decisions, and more. With embryonic stem (ES) cells that can generate each cell type in the mammalian body and adult stem cells that are able to give rise to the cells within a given lineage, basic questions at different developmental stages can be addressed. Importantly, both adult and embryonic stem cells provide an excellent tool for cell therapy, making stem cell research ever more pertinent to regenerative medicine. As the title The Cell Biology of Stem Cells suggests, our book deals with multiple aspects of stem cell biology, ranging from their basic molecular characteristics to the in vivo stem cell trafficking of adult stem cells and the adult stem-cell niche, and ends with a visit to regeneration and cell fate reprogramming. In the first chapter, “Early embryonic cell fate decisions in the mouse”, Amy Ralson and Yojiro Yamanaka describe the mechanisms that support early developmental decisions in the mouse pre-implantation embryo and the current understanding of the source of the most immature stem cell types, which includes ES cells, trophoblast stem (TS) cells and extraembryonic endoderm stem (XEN) cells.
Book Synopsis Transcription and Splicing by : B. D. Hames
Download or read book Transcription and Splicing written by B. D. Hames and published by Oxford University Press, USA. This book was released on 1988 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book gives a co-ordinated review of our present knowledge of eukaryotic RNA synthesis.
Download or read book Oral Health in America written by and published by . This book was released on 2000 with total page 32 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Lateral DNA Transfer by : Frederic Bushman
Download or read book Lateral DNA Transfer written by Frederic Bushman and published by CSHL Press. This book was released on 2002 with total page 472 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is about mobile genes—the transfer of DNA between unrelated cells. It discusses the machinery of gene transfer and its wide-ranging biological and health consequences. Mobile DNA makes possible the development of antibiotic resistance in microbes, the conversion of harmless to pathogenic bacteria, and the triggering of cancerous growth in cells. It also contributes to human evolution. This well-illustrated volume contains an up-to-date account of a topic now seen as increasingly important, and will be invaluable for both working scientists and as a textbook for advanced courses.
Book Synopsis Mechanisms of Gene Regulation by : Carsten Carlberg
Download or read book Mechanisms of Gene Regulation written by Carsten Carlberg and published by Springer. This book was released on 2016-06-06 with total page 219 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook aims to describe the fascinating area of eukaryotic gene regulation for graduate students in all areas of the biomedical sciences. Gene expression is essential in shaping the various phenotypes of cells and tissues and as such, regulation of gene expression is a fundamental aspect of nearly all processes in physiology, both in healthy and in diseased states. This pivotal role for the regulation of gene expression makes this textbook essential reading for students of all the biomedical sciences, in order to be better prepared for their specialized disciplines. A complete understanding of transcription factors and the processes that alter their activity is a major goal of modern life science research. The availability of the whole human genome sequence (and that of other eukaryotic genomes) and the consequent development of next-generation sequencing technologies have significantly changed nearly all areas of the biological sciences. For example, the genome-wide location of histone modifications and transcription factor binding sites, such as provided by the ENCODE consortium, has greatly improved our understanding of gene regulation. Therefore, the focus of this book is the description of the post-genome understanding of gene regulation. The purpose of this book is to provide, in a condensed form, an overview on the present understanding of the mechanisms of gene regulation. The authors are not aiming to compete with comprehensive treatises, but rather focus on the essentials. Therefore, the authors have favored a high figure-to-text ratio following the rule stating that “a picture tells more than thousand words”. The content of the book is based on the lecture course, which is given by Prof. Carlberg since 2001 at the University of Eastern Finland in Kuopio. The book is subdivided into 4 sections and 13 chapters. Following the Introduction there are three sections, which take a view on gene regulation from the perspective of transcription factors, chromatin and non-coding RNA, respectively. Besides its value as a textbook, Mechanisms of Gene Regulation will be a useful reference for individuals working in biomedical laboratories.
Book Synopsis Genomic “dark matter”: implications for understanding human disease mechanisms, diagnostics, and cures by : Philipp Kapranov
Download or read book Genomic “dark matter”: implications for understanding human disease mechanisms, diagnostics, and cures written by Philipp Kapranov and published by Frontiers E-books. This book was released on with total page 106 pages. Available in PDF, EPUB and Kindle. Book excerpt: The vast majority of the human genome has been historically ignored from the point of view of molecular mechanisms of disease, diagnostics and potential therapeutic targets. The predominant focus of disease research has traditionally been placed on the protein-coding regions of the human genome, which account for only ~4-5% of its total sequence complexity. This bias has an obvious underlying reason: protein-coding regions encode a crucial class of molecules in a cell, whose function and importance are well established. Furthermore, proteins are the predominant class of cellular molecules against which effective therapeutics can be designed. This bias pervades the design of analytical tools made to measure DNA, DNA-protein interactions, as well as procedures used to measure and annotate transcriptome expression. Microarrays for example, are often biased to the regions of genome known to encode exons or promoters of protein-coding mRNAs. Other aspects of our approach towards measuring expression of RNAs such as the typical choice of polyA+ RNA selection, enriched in mRNAs, for next generation sequencing also reinforces this bias. In summary, the 2-3% of the genome and RNAs made from it has dominated the conceptual thinking of academic and medical communities as well as industries that make devices that measure nucleic acids for research or diagnostic purposes and the pharmaceutical industry. However, during the last decade a tide of data has gained sufficient momentum to suggest that the cell actually uses the remaining 97-98% of the genome to produce stable RNAs – the so-called “dark matter” RNA. The first reports to suggest this were based on tiling array technology and sequencing of ESTs, which while powerful, had their limitations: tiling arrays could not estimate the relative mass of the RNAs produced from the non-protein coding regions in a cell and the EST sequencing methods were not deep enough. The advent of next-generation sequencing, in particular, single-molecule sequencing has allowed us not only confirm the previous observations but also for the first time to estimate not only from where, but also how much non-exonic RNA is produced. Its fraction of the total transcriptome is quite significant, up to 2/3 of all RNA made in a human cell (http://www.biomedcentral.com/1741-7007/8/149 ). Moreover, the non-exonic RNAs are differentially expressed in disease: for example, between the primary tumors and metastatic derivatives. We believe that the logical next step from these observations is to ask three questions, perhaps some of the most important questions of our time in biomedical science: (1) do “dark matter” RNAs underlie mechanisms of human disease?; (2) Can they be used for diagnostics?; and (3) Can they be used as targets for therapeutics?. We thus would like to propose a Research Topic in the Frontiers in Genetics/Frontiers in Non-Coding RNAs that is specifically dedicated to publishing manuscripts addressing these three questions.
Book Synopsis Next Generation Sequencing by : Jerzy Kulski
Download or read book Next Generation Sequencing written by Jerzy Kulski and published by BoD – Books on Demand. This book was released on 2016-01-14 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: Next generation sequencing (NGS) has surpassed the traditional Sanger sequencing method to become the main choice for large-scale, genome-wide sequencing studies with ultra-high-throughput production and a huge reduction in costs. The NGS technologies have had enormous impact on the studies of structural and functional genomics in all the life sciences. In this book, Next Generation Sequencing Advances, Applications and Challenges, the sixteen chapters written by experts cover various aspects of NGS including genomics, transcriptomics and methylomics, the sequencing platforms, and the bioinformatics challenges in processing and analysing huge amounts of sequencing data. Following an overview of the evolution of NGS in the brave new world of omics, the book examines the advances and challenges of NGS applications in basic and applied research on microorganisms, agricultural plants and humans. This book is of value to all who are interested in DNA sequencing and bioinformatics across all fields of the life sciences.
Book Synopsis Handbook of Marine Model Organisms in Experimental Biology by : Agnes Boutet
Download or read book Handbook of Marine Model Organisms in Experimental Biology written by Agnes Boutet and published by CRC Press. This book was released on 2021-12-13 with total page 964 pages. Available in PDF, EPUB and Kindle. Book excerpt: The importance of molecular approaches for comparative biology and the rapid development of new molecular tools is unprecedented. The extraordinary molecular progress belies the need for understanding the development and basic biology of whole organisms. Vigorous international efforts to train the next-generation of experimental biologists must combine both levels – next generation molecular approaches and traditional organismal biology. This book provides cutting-edge chapters regarding the growing list of marine model organisms. Access to and practical advice on these model organisms have become a conditio sine qua non for a modern education of advanced undergraduate students, graduate students and postdocs working on marine model systems. Model organisms are not only tools they are also bridges between fields – from behavior, development and physiology to functional genomics. Key Features Offers deep insights into cutting-edge model system science Provides in-depth overviews of all prominent marine model organisms Illustrates challenging experimental approaches to model system research Serves as a reference book also for next-generation functional genomics applications Fills an urgent need for students Related Titles Jarret, R. L. & K. McCluskey, eds. The Biological Resources of Model Organisms (ISBN 978-1-1382-9461-5) Kim, S.-K. Healthcare Using Marine Organisms (ISBN 978-1-1382-9538-4) Mudher, A. & T. Newman, eds. Drosophila: A Toolbox for the Study of Neurodegenerative Disease (ISBN 978-0-4154-1185-1) Green, S. L. The Laboratory Xenopus sp. (ISBN 978-1-4200-9109-0)
Book Synopsis Harpers Illustrated Biochemistry 29th Edition by : Robert Murray
Download or read book Harpers Illustrated Biochemistry 29th Edition written by Robert Murray and published by McGraw Hill Professional. This book was released on 2012-02-28 with total page 832 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gain a thorough understanding of the principles of biochemistry and molecular biology as they relate to modern medicine. Includes 16 case histories. Clear, concise, and in full color, Harper's This book unrivaled the ability to clarify the link between biochemistry and the molecular basis of disease. Combining outstanding full-color illustrations with integrated coverage of biochemical diseases and clinical information, Harper's offers an organization and careful balance of detail and brevity not found in any other text on the subject. New to this edition: New chapters on Aging, Cancer, and Clinical Chemistry. Every chapter has been updated to reflect the latest advances in knowledge and technology. Each chapter now begins with a statement of objectives, followed by a brief discussion of the biomedical importance of topics discussed within the chapter. There are 250 multiple-choice questions to test your knowledge and comprehension. Increased number of tables that encapsulate important information, such as vitamin and mineral requirements.
