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Chemical Biology Of The Genome

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Chemical Biology of the Genome

Chemical Biology of the Genome Book
Author : Siddhartha Roy,Tapas K. Kundu
Publisher : Academic Press
Release : 2021-05-14
ISBN : 0128176458
Language : En, Es, Fr & De

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Book Description :

Chemical Biology of the Genome provides a comprehensive overview of essential concepts and principles of genomic and epigenomics dynamics as explored through the lens of chemical biology. Key examples and case studies illustrate chemical biology methods for study and analysis of the genome and epigenome, with an emphasis on relevance to physiological and pathophysiological processes and drug discovery. Authors and international leaders in biochemical studies of the genome, Drs. Siddhartha Roy and Tapas Kundu, adopt an integrated, interdisciplinary approach throughout, demonstrating how fast evolving chemical and mass-scale sequencing tools are increasingly used to interpret biochemical processes of the genome. Later sections discuss chemical modifications of the genome, DNA sequence recognition by proteins and gene regulation, GWAS and EpiGWAS studies, 3D architecture of the genome, and functional genome architecture. In-depth, discovery focused chapters examine intervention in gene networks using SiRNA/ShRNA, miRNA, and anti-miR, small molecule modulation of iPS, drug resistance pathways altered DNA methylation as drug targets, anti-miR as therapeutics, and nanodelivery of drugs. Offers an interdisciplinary discussion of the chemical biology of the genome and epigenome, employing illustrative case studies in both physiological and pathophysiological contexts Supports researchers in employing chemical and mass-scale sequencing approaches to interpret genomic and epigenomic dynamics Highlights innovative pathways and molecular targets for new disease study and drug discovery

Advancing Development of Synthetic Gene Regulators

Advancing Development of Synthetic Gene Regulators Book
Author : Anandhakumar Chandran
Publisher : Springer
Release : 2017-09-19
ISBN : 9811065470
Language : En, Es, Fr & De

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Book Description :

This book focuses on an “outside the box” notion by utilizing the powerful applications of next-generation sequencing (NGS) technologies in the interface of chemistry and biology. In personalized medicine, developing small molecules targeting a specific genomic sequence is an attractive goal. N-methylpyrrole (P)–N-methylimidazole (I) polyamides (PIPs) are a class of small molecule that can bind to the DNA minor groove. First, a cost-effective NGS (ion torrent platform)-based Bind-n-Seq was developed to identify the binding specificity of PIP conjugates in a randomized DNA library. Their biological influences rely primarily on selective DNA binding affinity, so it is important to analyze their genome-wide binding preferences. However, it is demanding to enrich specifically the small-molecule-bound DNA without chemical cross-linking or covalent binding in chromatinized genomes. Herein is described a method that was developed using high-throughput sequencing to map the differential binding sites and relative enriched regions of non-cross-linked SAHA-PIPs throughout the complex human genome. SAHA-PIPs binding motifs were identified and the genome-level mapping of SAHA-PIPs-enriched regions provided evidence for the differential activation of the gene network. A method using high-throughput sequencing to map the binding sites and relative enriched regions of alkylating PIP throughout the human genome was also developed. The genome-level mapping of alkylating the PIP-enriched region and the binding sites on the human genome identifies significant genomic targets of breast cancer. It is anticipated that this pioneering low-cost, high through-put investigation at the sequence-specific level will be helpful in understanding the binding specificity of various DNA-binding small molecules, which in turn will be beneficial for the development of small-molecule-based drugs targeting a genome-level sequence.

Chemical Genomics

Chemical Genomics Book
Author : Haian Fu
Publisher : Cambridge University Press
Release : 2012-02-13
ISBN : 1107377587
Language : En, Es, Fr & De

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Book Description :

Advances in chemistry, biology and genomics coupled with laboratory automation and computational technologies have led to the rapid emergence of the multidisciplinary field of chemical genomics. This edited text, with contributions from experts in the field, discusses the new techniques and applications that help further the study of chemical genomics. The beginning chapters provide an overview of the basic principles of chemical biology and chemical genomics. This is followed by a technical section that describes the sources of small-molecule chemicals; the basics of high-throughput screening technologies; and various bioassays for biochemical-, cellular- and organism-based screens. The final chapters connect the chemical genomics field with personalized medicine and the druggable genome for future discovery of new therapeutics. This book will be valuable to researchers, professionals and graduate students in many fields, including biology, biomedicine and chemistry.

Chemical Biology of Natural Products

Chemical Biology of Natural Products Book
Author : David J. Newman,Gordon M. Cragg,Paul Grothaus
Publisher : CRC Press
Release : 2017-09-22
ISBN : 1351643282
Language : En, Es, Fr & De

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Book Description :

Chemical Biology of Natural Products This unique, long-awaited volume is designed to address contemporary aspects of natural product chemistry and its influence on biological systems, not solely on human interactions. The subjects covered include discovery, isolation and characterization, biosynthesis, biosynthetic engineering, pharmaceutical, and other applications of these compounds. Each chapter begins with a brief and simple introduction to the subject matter, and then proceeds to guide the reader towards the more contemporary, cutting-edge research in the field, with the contributing authors presenting current examples from their own work in order to exemplify key themes. Topics covered in the text include genome mining, heterologous expression, natural product synthesis, biosynthesis, glycosylation, chemical ecology, and therapeutic applications of natural products, both current and potential.

Chemical Genomics

Chemical Genomics Book
Author : Stefan Jaroch,Hilmar Weinmann
Publisher : Springer Science & Business Media
Release : 2007-05-26
ISBN : 3540376356
Language : En, Es, Fr & De

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Book Description :

Chemical genomics is a highly interdisciplinary and very exciting field of research both in academics and in the life sciences industry. The Ernst Schering Research Foundation Workshop 58 was organized to bring together scientific leaders in the field to discuss the implications of chemical genomics for drug discovery. Various aspects of the interface between chemistry and biology are covered in this volume, such as chemogenomics efforts in the pharmaceutical industry, diversity-oriented synthesis, chemogenomic approaches to the study of cell function, screening technologies, and natural products as tools in chemical biology.

The Chemical Biology of Long Noncoding RNAs

The Chemical Biology of Long Noncoding RNAs Book
Author : Stefan Jurga,Jan Barciszewski
Publisher : Springer Nature
Release : 2020-10-01
ISBN : 303044743X
Language : En, Es, Fr & De

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Book Description :

This book offers a comprehensive and detailed overview of various aspects of long non-coding RNAs. It discusses their emerging significance in molecular medicine, ranging from human cancers to cardiovascular and metabolic diseases. Transcriptomic studies have demonstrated that the majority of genomes found in complex organisms are expressed in highly dynamic and cell-specific patterns, producing huge numbers of intergenic, antisense and intronic long non-protein-coding RNAs (lncRNAs). Thousands of lncRNAs have been identified, and unlike mRNA, they have no protein-coding capacity. A large repertoire of ncRNAs, actively transcribed from the mammalian genome, control diverse cellular processes, both in terms of development and diseases, through a variety of gene regulatory mechanisms. IncRNAs have emerged as a new paradigm in epigenetic regulation of the genome. Given its scope, the book will be of particular interest to molecular, chemical, cell and developmental biologists, as well as specialists in translational medicine involved in disease-oriented research. It also offers a valuable resource for in silico experts seeking a deeper understanding of lncRNA expression and function through computational analysis of the NGS data.

Chemical and Functional Genomic Approaches to Stem Cell Biology and Regenerative Medicine

Chemical and Functional Genomic Approaches to Stem Cell Biology and Regenerative Medicine Book
Author : Sheng Ding
Publisher : John Wiley & Sons
Release : 2008-02-08
ISBN : 0470199121
Language : En, Es, Fr & De

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Book Description :

Scientists believe that stem cells have the potential to revolutionize the treatment of numerous diseases and conditions. This guide covers recent advances in technologies and their applications in stem cell biology, addressing the use of both embryonic and adult stem cells and discussing diverse technologies, including genome-wide expression analysis, informatics, chemical genomics, and more. Applications covered encompass self-renewal, differentiation, reprogramming, and regeneration in model organisms. This is a premier reference for practicing professionals involved in stem cell research and students.

Chemical Synthetic Biology

Chemical Synthetic Biology Book
Author : Pier Luigi Luisi,Cristiano Chiarabelli
Publisher : John Wiley & Sons
Release : 2011-02-10
ISBN : 9781119990307
Language : En, Es, Fr & De

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Book Description :

Chemistry plays a very important role in the emerging field of synthetic biology. In particular, chemical synthetic biology is concerned with the synthesis of chemical structures, such as proteins, that do not exist in nature. With contributions from leading international experts, Chemical Synthetic Biology shows how chemistry underpins synthetic biology. The book is an essential guide to this fascinating new field, and will find a place on the bookshelves of researchers and students working in synthetic chemistry, synthetic and molecular biology, bioengineering, systems biology, computational genomics, and bioinformatics.

Computational Chemogenomics

Computational Chemogenomics Book
Author : Edgar Jacoby
Publisher : CRC Press
Release : 2013-12-03
ISBN : 981441140X
Language : En, Es, Fr & De

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Book Description :

This book focuses on applications of compound library design and virtual screening to expand the bioactive chemical space, to target hopping of chemotypes to identify synergies within related drug discovery projects or to repurpose known drugs, to propose mechanism of action of compounds, or to identify off-target effects by cross-reactivity analysis. Both ligand-based and structure-based in silico approaches, as reviewed in this book, play important roles for all these applications. Computational chemogenomics is expected to increase the quality and productivity of drug discovery and lead to the discovery of new medicines.

Drug Discovery from Natural Products

Drug Discovery from Natural Products Book
Author : Olga Genilloud,Francisca Vicente
Publisher : Royal Society of Chemistry
Release : 2012-08-21
ISBN : 184973495X
Language : En, Es, Fr & De

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Book Description :

This book offers an integrated review of the most recent trends in natural products drug discovery and key lead candidates that are outstanding for their chemistry and biology as a starting point in novel drug development. The authors focus on different trends that are and will continue to be impacting multiples stages of modern drug discovery from NPs that have not been included in other works. This is complemented with a series of case studies from leading experts from industry and academia on key molecules and derivatives that have been chosen for their novelty in chemistry, biology and clinical applications. The book intends to reflect the current confluence of different disciplines in chemical biology and synthetic chemistry supported by a more profound knowledge of systems biology that ensures the concurrency and synergisms of expertise from different research fields that impact in the discovery of novel molecules. In the first section the chapters reflect recent approaches to exploit the biosynthetic potential of microbial resources (including genome mining, metagenomic and epigenetic approaches), as well as biosynthetic chemistry tools to respond to product supply and novel screening alternatives that have lead to the discovery of novel chemistry. The second part reviews, in the form of case studies, some examples of bioactive molecules in the important therapeutic areas of antiinfectives, oncology and antiparasitics.

Data Mining in Drug Discovery

Data Mining in Drug Discovery Book
Author : Rémy D. Hoffmann,Arnaud Gohier,Pavel Pospisil
Publisher : John Wiley & Sons
Release : 2013-09-25
ISBN : 3527656006
Language : En, Es, Fr & De

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Book Description :

Written for drug developers rather than computer scientists, this monograph adopts a systematic approach to mining scientifi c data sources, covering all key steps in rational drug discovery, from compound screening to lead compound selection and personalized medicine. Clearly divided into four sections, the first part discusses the different data sources available, both commercial and non-commercial, while the next section looks at the role and value of data mining in drug discovery. The third part compares the most common applications and strategies for polypharmacology, where data mining can substantially enhance the research effort. The final section of the book is devoted to systems biology approaches for compound testing. Throughout the book, industrial and academic drug discovery strategies are addressed, with contributors coming from both areas, enabling an informed decision on when and which data mining tools to use for one's own drug discovery project.

The DNA Replication Repair Interface

The DNA Replication Repair Interface Book
Author : Anonim
Publisher : Academic Press
Release : 2021-11-12
ISBN : 0323907342
Language : En, Es, Fr & De

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Book Description :

Replication-Coupled Repair, Volume 661 in the Methods in Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters on a variety of timely topics, including the Repair of replication-born DNA breaks by sister chromatid recombination, High resolution and high throughput DNA cyclization measurements to interrogate DNA bendability, A programmable detection method for genomic signatures: from disease diagnosis to genome editing, Characterization of the telomerase modulating activities of yeast DNA helicases, Eukaryotic DNA replication with purified budding yeast proteins, Single molecule studies of yeast Rad51 paralogs, Light activation and deactivation of Cas9 for DNA repair studies, and more. Other chapters explore MIDAS: Direct sequencing to map mitotic DNA synthesis and common fragile sites at high precision, Studying the DNA damage response in embryonic systems, GLASS-ChIP to map Mre11 cleavage sites in the human genome, New chemical biology approaches to trap reaction intermediates in living cells, Single-molecule imaging approaches for monitoring replication fork conflicts at genomic DNA G4 structures and R-loops in human cells, Monitoring the replication of structured DNA through heritable epigenetic change, Visualizing replication fork encounters with DNA interstrand crosslinks, and much more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in Methods in Enzymology series Includes the latest information on replication-coupled repair

Chemogenomics and Chemical Genetics

Chemogenomics and Chemical Genetics Book
Author : ERIC MARECHAL,Sylvaine Roy,Laurence Lafanechère
Publisher : Springer Science & Business Media
Release : 2011-06-21
ISBN : 3642196152
Language : En, Es, Fr & De

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Book Description :

Biological and chemical sciences have undergone an unprecedented transformation, reflected by the huge use of parallel and automated technologies in key fields such as genome sequencing, DNA chips, nanoscale functional biology or combinatorial chemistry. It is now possible to generate and store from tens of thousands to millions of new small molecules, based on enhanced chemical synthesis strategies. Automated screening of small molecules is one of the technologies that has revolutionized biology, first developed for the pharmaceutical industry and recently introduced in academic laboratories. High-throughput and high-content screening allow the identification of bioactive compounds in collections of molecules (chemical libraries), being effective on biological targets defined at various organisational scales, from proteins to cells to complete organisms. These bioactive molecules can be therapeutic drug candidates, molecules for biotech, diagnostic or agronomic applications, or tools for basic research. Handling a large number of biological (genomic and post-genomic), chemical and experimental information, screening approaches cannot be envisaged without any electronic storage and mathematical treatment of the data. “Chemogenomics and Chemical Genetics” is an introductory manual presenting methods and concepts making up the basis for this recent discipline. This book is dedicated to biologists, chemists and computer scientist beginners. It is organized in brief, illustrated chapters with practical examples. Clear definitions of biological, chemical and IT concepts are given in a glossary section to help readers who are not familiar with one of these disciplines. "Chemogenomics and Chemical Genetics" should therefore be helpful for students (from Bachelor's degree level), technological platform engineers, and researchers in biology, chemistry, bioinformatics, cheminformatics, both in biotech and academic laboratories.

High Throughput Screening Methods

High Throughput Screening Methods Book
Author : Joshua A. Bittker,Nathan T. Ross
Publisher : Royal Society of Chemistry
Release : 2016-12-08
ISBN : 1782624716
Language : En, Es, Fr & De

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Book Description :

High throughput screening remains a key part of early stage drug and tool compound discovery, and methods and technologies have seen many fundamental improvements and innovations over the past 20 years. This comprehensive book provides a historical survey of the field up to the current state-of-the-art. In addition to the specific methods, this book also considers cultural and organizational questions that represent opportunities for future success. Following thought-provoking foreword and introduction from Professor Stuart Schreiber and the editors, chapters from leading experts across academia and industry cover initial considerations for screening, methods appropriate for different goals in small molecule discovery, newer technologies that provide alternative approaches to traditional miniaturization procedures, and practical aspects such as cost and resourcing. Within the context of their historical development, authors explain common pitfalls and their solutions. This book will serve as both a practical reference and a thoughtful guide to the philosophy underlying technological change in such a fast-moving area for postgraduates and researchers in academia and industry, particularly in the areas of chemical biology, pharmacology, structural biology and assay development.

Chemical Biology of Nucleic Acids

Chemical Biology of Nucleic Acids Book
Author : Volker A. Erdmann,Wojciech T. Markiewicz,Jan Barciszewski
Publisher : Springer Science & Business
Release : 2014-04-22
ISBN : 3642544525
Language : En, Es, Fr & De

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Book Description :

This volume contains 29 engrossing chapters contributed by worldwide, leading research groups in the field of chemical biology. Topics include pre-biology; the establishment of the genetic code; isomerization of RNA; damage of nucleobases in RNA; the dynamic structure of nucleic acids and their analogs in DNA replication, extra- and intra-cellular transport; molecular crowding by the use of ionic liquids; new technologies enabling the modification of gene expression via editing of therapeutic genes; the use of riboswitches; the modification of mRNA cap regions; new approaches to detect appropriately modified RNAs with EPR spectroscopy and the use of parallel and high-throughput techniques for the analysis of the structure and new functions of nucleic acids. This volume discusses how chemistry can add new frontiers to the field of nucleic acids in molecular medicine, biotechnology and nanotechnology and is not only an invaluable source of information to chemists, biochemists and life scientists but will also stimulate future research.

Molecular Biology

Molecular Biology Book
Author : Nancy Lynn Craig
Publisher : Unknown
Release : 2010-08-19
ISBN : 0199562067
Language : En, Es, Fr & De

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Book Description :

Molecular Biology: Principles of Genome Function offers a fresh, distinctive approach to the teaching of molecular biology. With its focus on key principles, its emphasis on the commonalities that exist between the three kingdoms of life, and its integrated approach throughout, it is the perfect companion to any molecular biology course.

RNA Modification

RNA Modification Book
Author : Anonim
Publisher : Academic Press
Release : 2015-12-11
ISBN : 0128023317
Language : En, Es, Fr & De

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Book Description :

RNA Modification provides a useful examination of the science and its role in biological regulation, the current frontier of life science research, and includes various RNA modications and their role in gene expression. It represents the most up-to-date knowledge and protocols available today. Dynamic RNA modifications and their roles in biological regulation are the current frontier of life science research This volume of Methods in Enzymology represents up to date knowledge and protocols

Wiley Encyclopedia of Chemical Biology Volume 4

Wiley Encyclopedia of Chemical Biology  Volume 4 Book
Author : Tadhg P. Begley
Publisher : Wiley-Blackwell
Release : 2009-02-03
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

The first major reference at the interface of chemistry, biology, and medicine Chemical biology is a rapidly developing field that uses the principles, tools, and language of chemistry to answer important questions in the life sciences. It has enabled researchers to gather critical information about the molecular biology of the cell and is the fundamental science of drug discovery, playing a key role in the development of novel agents for the prevention, diagnosis, and treatment of disease. Now students and researchers across the range of disciplines that use chemical biology techniques have a single resource that encapsulates what is known in the field. It is an excellent place to begin any chemical biology investigation. Major topics addressed in the encyclopedia include: Applications of chemical biology Biomolecules within the cell Chemical views of biology Chemistry of biological processes and systems Synthetic molecules as tools for chemical biology Technologies and techniques in chemical biology Some 300 articles range from pure basic research to areas that have immediate applications in fields such as drug discovery, sensor technology, and catalysis. Novices in the field can turn to articles that introduce them to the basics, whereas experienced researchers have access to articles exploring the cutting edge of the science. Each article ends with a list of references to facilitate further investigation. With contributions from leading researchers and pioneers in the field, the Wiley Encyclopedia of Chemical Biology builds on Wiley's unparalleled reputation for helping students and researchers understand the crucial role of chemistry and chemical techniques in the life sciences.

Enzyme Technologies

Enzyme Technologies Book
Author : Wu-Kuang Yeh,Hsiu-Chiung Yang,James R. McCarthy
Publisher : John Wiley and Sons
Release : 2011-05-04
ISBN : 1118125037
Language : En, Es, Fr & De

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Book Description :

An authoritative review of the latest developments in thechemical biology of enzymes In the first decade of the twenty-first century, enzymes andtheir multiple applications have played a critical role in thediscovery and development of many new therapeutic agents.This bookis a coordinated compilation of research expertise and currentopinion uniquely focused on enzymes and their properties andapplications. Compiled by editors with a combined pharmaceutical experience ofover sixty years, the text provides in-depth reviews of recentdevelopments in selective topics on biosynthesis, biocatalysis, andchemical biology of enzymes as it applies to drug discovery,development, and manufacture. The first in a multi-part series on enzymes, this volumefeatures three sections: New Approaches to Find and Modify Enzymes describes the emergingfield of metagenomics, presents the practical applications ofdirected evolution to enzymes and pathways, and explores approachesfor the discovery and design of biocatalysts Biocatalytic Applications reviews specific applications ofdifferent reactions in producing active pharmaceutical ingredientsand surveys recent developments employing enzymes in organicsynthesis Biosynthetic Applications goes over successful drug discoveriesand developments by combinatorial biosynthesis and reviews theapplication of combinatorial biosynthesis among multiple compatiblehosts These timely discussions, which cover everything from chemicalbiology of enzymes, to the redesign of binding and catalyticspecificities of enzymes, make this volume a valuable tool forkeeping up to date. As such, it is an important read forresearchers, students, and professors in the study ofbiotechnology, life sciences, biochemistry, enzymology, medicinalchemistry, and natural products.

Medicinal Plants

Medicinal Plants Book
Author : Hao Da,Xiao Jie Gu,Pei Gen Xiao
Publisher : Woodhead Publishing
Release : 2015-06-29
ISBN : 0081001037
Language : En, Es, Fr & De

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Book Description :

Medicinal Plants: Chemistry, Biology and Omics reviews the phytochemistry, chemotaxonomy, molecular biology, and phylogeny of selected medicinal plant tribes and genera, and their relevance to drug efficacy. Medicinal plants provide a myriad of pharmaceutically active components, which have been commonly used in traditional Chinese medicine and worldwide for thousands of years. Increasing interest in plant-based medicinal resources has led to additional discoveries of many novel compounds, in various angiosperm and gymnosperm species, and investigations on their chemotaxonomy, molecular phylogeny and pharmacology. Chapters in this book explore the interrelationship within traditional Chinese medicinal plant groups and between Chinese species and species outside of China. Chapters also discuss the incongruence between chemotaxonomy and molecular phylogeny, concluding with chapters on systems biology and “-omics technologies (genomics, transcriptomics, proteomics, and metabolomics), and how they will play an increasingly important role in future pharmaceutical research. Reviews best practice and essential developments in medicinal plant chemistry and biology Discusses the principles and applications of various techniques used to discover medicinal compounds Explores the analysis and classification of novel plant-based medicinal compounds Includes case studies on pharmaphylogeny Compares and integrates traditional knowledge and current perception of worldwide medicinal plants