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Book Synopsis The Evolving Chromatin and Transcriptional Landscapes – Emerging Methods, Tools and Techniques by : Jean-Philippe Lambert
Download or read book The Evolving Chromatin and Transcriptional Landscapes – Emerging Methods, Tools and Techniques written by Jean-Philippe Lambert and published by Frontiers Media SA. This book was released on 2022-01-03 with total page 157 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Chromatin organization plays a major role in gene regulation and can affect the function and evolution of new transcriptional programs. Here, we present the first multi-species comparative genomic analysis of the relationship between chromatin organization and gene expression by measuring mRNA abundance and nucleosome positions genome-wide in 13 Ascomycota yeast species. Our work introduces a host of new computational tools for studying chromatin structure, function, and evolution. We improved on existing methods for detecting nucleosome positions and developed a new approach for identifying nucleosome-free regions (NFRs) and characterizing chromatin organization at gene promoters. We used a general statistical approach for studying the evolution of chromatin and gene regulation at a functional level. We also introduced a new technique for discovering the DNA binding motifs of transacting General Regulatory Factors (GRFs) and developed a new technique for quantifying the relative contribution of intrinsic sequence, GRFs, and transcription to establishing NFRs. And finally, we built a computational framework to quantify the evolutionary interplay between nucleosome positions, transcription factor binding sites, and gene expression. Through our analysis, we found large conservation of global and functional chromatin organization. Chromatin organization has also substantially diverged in both global quantitative features and in functional groups of genes. We find that global usage of intrinsic anti-nucleosomal sequences such as PolyA varies over this phylogeny, and uncover that PolyG tracts also intrinsically repel nucleosomes. The specific sequences bound by GRFs are also highly plastic; we experimentally validate an evolutionary handover from Cbfl in pre-WGD yeasts to Rebi in post-WGD yeast. We also identify five mechanisms that couple chromatin organization to evolution of gene regulation, including (i) compensatory evolution of alternative modifiers associated with conserved chromatin organization; (ii) a gradual transition from constitutive to transregulated NFRs; (iii) a loss of intrinsic anti-nucleosomal sequences accompanying changes in chromatin organization and gene expression, (iv) repositioning of motifs from NFRs to nucleosome-occluded regions; and (v) the expanded use of NFRs by paralogous activator-repressor pairs. Our multi-species dataset and general computational framework provide a foundation for future studies on how chromatin structure changes over time and in evolution.
Book Synopsis Evolution of Nucleosome Positioning and Gene Regulation in Yeasts by : Alex Tsankov
Download or read book Evolution of Nucleosome Positioning and Gene Regulation in Yeasts written by Alex Tsankov and published by . This book was released on 2010 with total page 111 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chromatin organization plays a major role in gene regulation and can affect the function and evolution of new transcriptional programs. Here, we present the first multi-species comparative genomic analysis of the relationship between chromatin organization and gene expression by measuring mRNA abundance and nucleosome positions genome-wide in 13 Ascomycota yeast species. Our work introduces a host of new computational tools for studying chromatin structure, function, and evolution. We improved on existing methods for detecting nucleosome positions and developed a new approach for identifying nucleosome-free regions (NFRs) and characterizing chromatin organization at gene promoters. We used a general statistical approach for studying the evolution of chromatin and gene regulation at a functional level. We also introduced a new technique for discovering the DNA binding motifs of transacting General Regulatory Factors (GRFs) and developed a new technique for quantifying the relative contribution of intrinsic sequence, GRFs, and transcription to establishing NFRs. And finally, we built a computational framework to quantify the evolutionary interplay between nucleosome positions, transcription factor binding sites, and gene expression. Through our analysis, we found large conservation of global and functional chromatin organization. Chromatin organization has also substantially diverged in both global quantitative features and in functional groups of genes. We find that global usage of intrinsic anti-nucleosomal sequences such as PolyA varies over this phylogeny, and uncover that PolyG tracts also intrinsically repel nucleosomes. The specific sequences bound by GRFs are also highly plastic; we experimentally validate an evolutionary handover from Cbfl in pre-WGD yeasts to Rebi in post-WGD yeast. We also identify five mechanisms that couple chromatin organization to evolution of gene regulation, including (i) compensatory evolution of alternative modifiers associated with conserved chromatin organization; (ii) a gradual transition from constitutive to transregulated NFRs; (iii) a loss of intrinsic anti-nucleosomal sequences accompanying changes in chromatin organization and gene expression, (iv) repositioning of motifs from NFRs to nucleosome-occluded regions; and (v) the expanded use of NFRs by paralogous activator-repressor pairs. Our multi-species dataset and general computational framework provide a foundation for future studies on how chromatin structure changes over time and in evolution.
Topic Editors Dr. Paola Bianchi and Dr. Richard Van Wijk provide consultancy to Agios Pharmaceuticals. Dr. Richard Van Wijk has research support from RR Mechatronics and Agios Pharmaceuticals.
Book Synopsis New Methods for Red Blood Cell Research and Diagnosis by : Richard Van Wijk
Download or read book New Methods for Red Blood Cell Research and Diagnosis written by Richard Van Wijk and published by Frontiers Media SA. This book was released on 2021-11-26 with total page 167 pages. Available in PDF, EPUB and Kindle. Book excerpt: Topic Editors Dr. Paola Bianchi and Dr. Richard Van Wijk provide consultancy to Agios Pharmaceuticals. Dr. Richard Van Wijk has research support from RR Mechatronics and Agios Pharmaceuticals.
Book Synopsis Innate lymphocytes in tumor surveillance by : Dagmar Stoiber
Download or read book Innate lymphocytes in tumor surveillance written by Dagmar Stoiber and published by Frontiers Media SA. This book was released on 2022-12-27 with total page 121 pages. Available in PDF, EPUB and Kindle. Book excerpt:
American Association for Cancer Research 2019 Proceedings: Abstracts 2749-5314 - Part B
Book Synopsis AACR 2019 Proceedings: Abstracts 2749-5314 by : American Association for Cancer Research
Download or read book AACR 2019 Proceedings: Abstracts 2749-5314 written by American Association for Cancer Research and published by Coe Truman International, LLC. This book was released on 2019-03-08 with total page 3012 pages. Available in PDF, EPUB and Kindle. Book excerpt: American Association for Cancer Research 2019 Proceedings: Abstracts 2749-5314 - Part B
Animal evolution has always been at the core of Biology, but even today many fundamental questions remain open. The field of animal ‘evo-devo’ is leveraging recent technical and conceptual advances in development, paleontology, genomics and transcriptomics to propose radically different answers to traditional evolutionary controversies. This book is divided into four parts, each of which approaches animal evolution from a different perspective. The first part (chapters 2 and 3) investigates how new sources of evidence have changed conventional views of animal origins, while the second (chapters 4–8) addresses the connection between embryogenesis and evolution, and the genesis of cellular, tissue and morphological diversity. The third part (chapters 9 and 10) investigates how big data in molecular biology is transforming our understanding of the mechanisms governing morphological change in animals. In closing, the fourth part (chapters 11–13) explores new theoretical and conceptual approaches to animal evolution. ‘Old questions and young approaches to animal evolution’ offers a comprehensive and updated view of animal evolutionary biology that will serve both as a first step into this fascinating field for students and university educators, and as a review of complementary approaches for researchers.
Book Synopsis Old Questions and Young Approaches to Animal Evolution by : José M. Martín-Durán
Download or read book Old Questions and Young Approaches to Animal Evolution written by José M. Martín-Durán and published by Springer. This book was released on 2019-07-22 with total page 284 pages. Available in PDF, EPUB and Kindle. Book excerpt: Animal evolution has always been at the core of Biology, but even today many fundamental questions remain open. The field of animal ‘evo-devo’ is leveraging recent technical and conceptual advances in development, paleontology, genomics and transcriptomics to propose radically different answers to traditional evolutionary controversies. This book is divided into four parts, each of which approaches animal evolution from a different perspective. The first part (chapters 2 and 3) investigates how new sources of evidence have changed conventional views of animal origins, while the second (chapters 4–8) addresses the connection between embryogenesis and evolution, and the genesis of cellular, tissue and morphological diversity. The third part (chapters 9 and 10) investigates how big data in molecular biology is transforming our understanding of the mechanisms governing morphological change in animals. In closing, the fourth part (chapters 11–13) explores new theoretical and conceptual approaches to animal evolution. ‘Old questions and young approaches to animal evolution’ offers a comprehensive and updated view of animal evolutionary biology that will serve both as a first step into this fascinating field for students and university educators, and as a review of complementary approaches for researchers.
The endometrium goes through cyclical changes under the influence of hormones, and immune effectors in the endometrium change their populations cyclically as well. Dynamic changes in immune effectors determine endometrial cytokine and chemokine milieus and, consequently, the endometrial immune response. Endometrial immune responses have been shown to be important for trophoblast invasion and early pregnancy. Indeed, dysregulated endometrial inflammatory immune responses are associated with reproductive failures, such as recurrent pregnancy losses, repeated implantation failure, and gynecological diseases with oncogenic potential. Hence, the investigation of endometrial gene expression may predict infertility, gynecological and oncological conditions. This book presents the state of the art in endometrial gene expression as well as recent developmental findings relating to reproduction and reproductive disorders. It begins with a review of the genetic regulation of urogenital tract formation and molecular mechanism underlying the physiology of menstrual cycle before moving on to the current and emerging technological advances in molecular biology. Endometrial gene expressions of immune inflammatory conditions, viral infection, metabolic and nutritional conditions, and reproductive disorders are then presented in following chapters. Examples of the use and interpretation of gene expression in clinical scenarios including recurrent pregnancy losses, infertility and multiple implantation failures are presented with currently available endometrial gene analysis. Utilizing the latest evidence and clinical guidelines, Endometrial Gene Expression will be a cutting-edge resource for gynecologist, reproductive immunologist, reproductive endocrinologists, obstetrician, maternal fetal medicine specialist and other health care providers in the field of reproductive medicine.
Book Synopsis Endometrial Gene Expression by : Joanne Kwak-Kim
Download or read book Endometrial Gene Expression written by Joanne Kwak-Kim and published by Springer Nature. This book was released on 2019-11-08 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt: The endometrium goes through cyclical changes under the influence of hormones, and immune effectors in the endometrium change their populations cyclically as well. Dynamic changes in immune effectors determine endometrial cytokine and chemokine milieus and, consequently, the endometrial immune response. Endometrial immune responses have been shown to be important for trophoblast invasion and early pregnancy. Indeed, dysregulated endometrial inflammatory immune responses are associated with reproductive failures, such as recurrent pregnancy losses, repeated implantation failure, and gynecological diseases with oncogenic potential. Hence, the investigation of endometrial gene expression may predict infertility, gynecological and oncological conditions. This book presents the state of the art in endometrial gene expression as well as recent developmental findings relating to reproduction and reproductive disorders. It begins with a review of the genetic regulation of urogenital tract formation and molecular mechanism underlying the physiology of menstrual cycle before moving on to the current and emerging technological advances in molecular biology. Endometrial gene expressions of immune inflammatory conditions, viral infection, metabolic and nutritional conditions, and reproductive disorders are then presented in following chapters. Examples of the use and interpretation of gene expression in clinical scenarios including recurrent pregnancy losses, infertility and multiple implantation failures are presented with currently available endometrial gene analysis. Utilizing the latest evidence and clinical guidelines, Endometrial Gene Expression will be a cutting-edge resource for gynecologist, reproductive immunologist, reproductive endocrinologists, obstetrician, maternal fetal medicine specialist and other health care providers in the field of reproductive medicine.
Book Synopsis Applications and Methods in Genomic Networks by : Kimberly Glass
Download or read book Applications and Methods in Genomic Networks written by Kimberly Glass and published by Frontiers Media SA. This book was released on 2022-07-01 with total page 234 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Advances in Animal Genomics provides an outstanding collection of integrated strategies involving traditional and modern - omics (structural, functional, comparative and epigenomics) approaches and genomics-assisted breeding methods which animal biotechnologists can utilize to dissect and decode the molecular and gene regulatory networks involved in the complex quantitative yield and stress tolerance traits in livestock. Written by international experts on animal genomics, this book explores the recent advances in high-throughput, next-generation whole genome and transcriptome sequencing, array-based genotyping, and modern bioinformatics approaches which have enabled to produce huge genomic and transcriptomic resources globally on a genome-wide scale. This book is an important resource for researchers, students, educators and professionals in agriculture, veterinary and biotechnology sciences that enables them to solve problems regarding sustainable development with the help of current innovative biotechnologies. Integrates basic and advanced concepts of animal biotechnology and presents future developments Describes current high-throughput next-generation whole genome and transcriptome sequencing, array-based genotyping, and modern bioinformatics approaches for sustainable livestock production Illustrates integrated strategies to dissect and decode the molecular and gene regulatory networks involved in complex quantitative yield and stress tolerance traits in livestock Ensures readers will gain a strong grasp of biotechnology for sustainable livestock production with its well-illustrated discussion
Book Synopsis Advances in Animal Genomics by : Sukanta Mondal
Download or read book Advances in Animal Genomics written by Sukanta Mondal and published by Academic Press. This book was released on 2020-11-25 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Animal Genomics provides an outstanding collection of integrated strategies involving traditional and modern - omics (structural, functional, comparative and epigenomics) approaches and genomics-assisted breeding methods which animal biotechnologists can utilize to dissect and decode the molecular and gene regulatory networks involved in the complex quantitative yield and stress tolerance traits in livestock. Written by international experts on animal genomics, this book explores the recent advances in high-throughput, next-generation whole genome and transcriptome sequencing, array-based genotyping, and modern bioinformatics approaches which have enabled to produce huge genomic and transcriptomic resources globally on a genome-wide scale. This book is an important resource for researchers, students, educators and professionals in agriculture, veterinary and biotechnology sciences that enables them to solve problems regarding sustainable development with the help of current innovative biotechnologies. Integrates basic and advanced concepts of animal biotechnology and presents future developments Describes current high-throughput next-generation whole genome and transcriptome sequencing, array-based genotyping, and modern bioinformatics approaches for sustainable livestock production Illustrates integrated strategies to dissect and decode the molecular and gene regulatory networks involved in complex quantitative yield and stress tolerance traits in livestock Ensures readers will gain a strong grasp of biotechnology for sustainable livestock production with its well-illustrated discussion
Integrative Omics: Concepts, Methodology and Applications provides a holistic and integrated view of defining and applying network approaches, integrative tools, and methods to solve problems for the rationalization of genotype to phenotype relationships. The reference includes a range of chapters in a systemic ‘step by step’ manner, which begins with the basic concepts from Omic to Multi Integrative Omics approaches, followed by their full range of approaches, applications, emerging trends, and future trends. All key areas of Omics are covered including biological databases, sequence alignment, pharmacogenomics, nutrigenomics and microbial omics, integrated omics for Food Science and Identification of genes associated with disease, clinical data integration and data warehousing, translational omics as well as omics technology policy and society research. Integrative Omics: Concepts, Methodology and Applications highlights the recent concepts, methodologies, advancements in technologies and is also well-suited for researchers from both academic and industry background, undergraduate and graduate students who are mainly working in the area of computational systems biology, integrative omics and translational science. The book bridges the gap between biological sciences, physical sciences, computer science, statistics, data science, information technology and mathematics by presenting content specifically dedicated to mathematical models of biological systems. Provides a holistic, integrated view of a defining and applying network approach, integrative tools, and methods to solve problems for rationalization of genotype to phenotype relationships Offers an interdisciplinary approach to Databases, data analytics techniques, biological tools, network construction, analysis, modeling, prediction and simulation of biological systems leading to ‘translational research’, i.e., drug discovery, drug target prediction, and precision medicine Covers worldwide methods, concepts, databases, and tools used in the construction of integrated pathways
Book Synopsis Integrative Omics by : Manish Kumar Gupta
Download or read book Integrative Omics written by Manish Kumar Gupta and published by Elsevier. This book was released on 2024-05-10 with total page 434 pages. Available in PDF, EPUB and Kindle. Book excerpt: Integrative Omics: Concepts, Methodology and Applications provides a holistic and integrated view of defining and applying network approaches, integrative tools, and methods to solve problems for the rationalization of genotype to phenotype relationships. The reference includes a range of chapters in a systemic ‘step by step’ manner, which begins with the basic concepts from Omic to Multi Integrative Omics approaches, followed by their full range of approaches, applications, emerging trends, and future trends. All key areas of Omics are covered including biological databases, sequence alignment, pharmacogenomics, nutrigenomics and microbial omics, integrated omics for Food Science and Identification of genes associated with disease, clinical data integration and data warehousing, translational omics as well as omics technology policy and society research. Integrative Omics: Concepts, Methodology and Applications highlights the recent concepts, methodologies, advancements in technologies and is also well-suited for researchers from both academic and industry background, undergraduate and graduate students who are mainly working in the area of computational systems biology, integrative omics and translational science. The book bridges the gap between biological sciences, physical sciences, computer science, statistics, data science, information technology and mathematics by presenting content specifically dedicated to mathematical models of biological systems. Provides a holistic, integrated view of a defining and applying network approach, integrative tools, and methods to solve problems for rationalization of genotype to phenotype relationships Offers an interdisciplinary approach to Databases, data analytics techniques, biological tools, network construction, analysis, modeling, prediction and simulation of biological systems leading to ‘translational research’, i.e., drug discovery, drug target prediction, and precision medicine Covers worldwide methods, concepts, databases, and tools used in the construction of integrated pathways
