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Investigation Of Combinatorial Gene Regulation In Saccharomyces Species
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Book Synopsis Investigation of Combinatorial Gene Regulation in Saccharomyces Species by : Aaron Taras Spivak
Download or read book Investigation of Combinatorial Gene Regulation in Saccharomyces Species written by Aaron Taras Spivak and published by . This book was released on 2012 with total page 174 pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcriptional control of gene expression is a result of complex interactions between the cis -regulatory elements (CRE) at gene promoters. To understand the regulatory logic of a cell, we need to identify the CRE combinations that regulate gene expression. This dissertation describes a sensitive computational method to identify phylogenetically conserved CRE combinations for any species of interest. In contrast to previous methods, I do not need to align genomes to identify these combinations. I applied the method in 7 sensu stricto and sensu lato Saccharomyces species. 80% of the predictions displayed some evidence of combinatorial transcriptional behavior in several existing datasets including (1) ChIP-chip data for co-localization of transcription factors, (2) gene expression data for co-expression of predicted regulatory targets, and (3) gene ontology databases for common pathway membership of predicted regulatory targets. To establish definitive evidence that these CRE interactions influence TF occupancy, I performed ChIP-Seq experiments on transcription factors in a wild-type strain and strains in which a predicted cofactor was deleted. These experiments showed that TF occupancy at the promoters of the CRE combination target genes depends on the predicted cofactor while occupancy of other promoters is independent of the predicted cofactor. In addition to identifying phylogenetically conserved CRE combinations, the method can annotate potential regulatory differences between species. Previous studies of cis -regulatory rewiring between species assume that CREs act independently and have found that promoter divergence does not necessarily explain expression divergence. By analyzing the S. cerevisiae and S. bayanus genomes, I identified differences in combinatorial cis -regulation between the species and showed that the predicted changes in gene regulation explain several of the species-specific differences seen in gene expression datasets. In some instances, the same CRE combinations appear to regulate genes involved in distinct biological processes in the two different species. The results of this research demonstrate (1) that combinatorial cis -regulation can be inferred from similarities between species and (2) that combinatorial cis -regulation can explain differences between species.
Book Synopsis Evolution of a Combinatorial Transcriptional Circuit: A Case Study in Yeasts by : Annie E. Tsong
Download or read book Evolution of a Combinatorial Transcriptional Circuit: A Case Study in Yeasts written by Annie E. Tsong and published by . This book was released on 2005 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: Developing new regulation of existing genes is a major source of evolutionary novelty. In this thesis, I examine evolution of transcriptional regulation by dissecting a combinatorial regulatory circuit that governs mating-type in the ascomycete branch of the fungal lineage. I first determine the means by which four conserved transcription factors regulate mating-type in the pathogenic yeast C. albicans. I then closely compare the C. albicans circuit to that of S. cerevisiae, identifying several classes of changes that have arisen since their divergence from a common ancestor. Among the many changes identified, I focus on a group of orthologs, the a-specific genes, that is positively regulated in C. albicans, but is negatively regulated in S. cerevisiae. I demonstrate that positive regulation represents the ancestral form, and that the S. cerevisiae mode of negative regulation is a recently derived innovation. By examining the regulation of asgs in a group of 16 modern yeasts that diverged at successively later times from a common ancestor, I deduce specific, sequential changes in both cis- and trans-regulatory elements that constitute the transition from positive to negative regulation.
Book Synopsis Molecular Biology of The Cell by : Bruce Alberts
Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Gene Regulation in Eukaryotes by : Edgar Wingender
Download or read book Gene Regulation in Eukaryotes written by Edgar Wingender and published by Wiley-Blackwell. This book was released on 1993 with total page 452 pages. Available in PDF, EPUB and Kindle. Book excerpt: A much-needed guide through the overwhelming amount of literature in the field. Comprehensive and detailed, this book combines background information with the most recentinsights. It introduces current concepts, emphasizing the transcriptional control of genetic information. Moreover, it links data on the structure of regulatory proteins with basic cellular processes. Both advanced students and experts will find answers to such intriguing questions as: - How are programs of specific gene repertoires activated and controlled? - Which genes drive and control morphogenesis? - Which genes govern tissue-specific tasks? - How do hormones control gene expression in coordinating the activities of different tissues? An abundant number of clearly presented glossary terms facilitates understanding of the biological background. Speacial feature: over 2200 (!) literature references.
Book Synopsis Untranslated Gene Regions and Other Non-coding Elements by : Lucy W. Barrett
Download or read book Untranslated Gene Regions and Other Non-coding Elements written by Lucy W. Barrett and published by Springer Science & Business Media. This book was released on 2013-06-26 with total page 63 pages. Available in PDF, EPUB and Kindle. Book excerpt: There is now compelling evidence that the complexity of higher organisms correlates with the relative amount of non-coding RNA rather than the number of protein-coding genes. Previously dismissed as “junk DNA”, it is the non-coding regions of the genome that are responsible for regulation, facilitating complex temporal and spatial gene expression through the combinatorial effect of numerous mechanisms and interactions working together to fine-tune gene expression. The major regions involved in regulation of a particular gene are the 5’ and 3’ untranslated regions and introns. In addition, pervasive transcription of complex genomes produces a variety of non-coding transcripts that interact with these regions and contribute to regulation. This book discusses recent insights into the regulatory roles of the untranslated gene regions and non-coding RNAs in the control of complex gene expression, as well as the implications of this in terms of organism complexity and evolution.
Book Synopsis A Handbook of Transcription Factors by : Timothy R. Hughes
Download or read book A Handbook of Transcription Factors written by Timothy R. Hughes and published by Springer Science & Business Media. This book was released on 2011-05-10 with total page 310 pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcription factors are the molecules that the cell uses to interpret the genome: they possess sequence-specific DNA-binding activity, and either directly or indirectly influence the transcription of genes. In aggregate, transcription factors control gene expression and genome organization, and play a pivotal role in many aspects of physiology and evolution. This book provides a reference for major aspects of transcription factor function, encompassing a general catalogue of known transcription factor classes, origins and evolution of specific transcription factor types, methods for studying transcription factor binding sites in vitro, in vivo, and in silico, and mechanisms of interaction with chromatin and RNA polymerase.
Author :Jacqueline M. Matthews Publisher :Springer Science & Business Media ISBN 13 :1461432294 Total Pages :184 pages Book Rating :4.4/5 (614 download)
Book Synopsis Protein Dimerization and Oligomerization in Biology by : Jacqueline M. Matthews
Download or read book Protein Dimerization and Oligomerization in Biology written by Jacqueline M. Matthews and published by Springer Science & Business Media. This book was released on 2012-09-04 with total page 184 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume has a strong focus on homo-oligomerization, which is surprisingly common. However, protein function is so often linked to both homo- and hetero-oligomerization and many heterologous interactions likely evolved from homologous interaction, so this volume also covers many aspects of hetero-oligomerization.
Book Synopsis Regulation of Gene Expression by Small RNAs by : Rajesh K. Gaur
Download or read book Regulation of Gene Expression by Small RNAs written by Rajesh K. Gaur and published by CRC Press. This book was released on 2009-04-27 with total page 440 pages. Available in PDF, EPUB and Kindle. Book excerpt: New Findings Revolutionize Concepts of Gene FunctionEndogenous small RNAs have been found in various organisms, including humans, mice, flies, worms, fungi, and bacteria. Furthermore, it's been shown that microRNAs acting as cellular rheostats have the ability to modulate gene expression. In higher eukaryotes, microRNAs may regulate as much as 50 p
Book Synopsis Investigations in Yeast Functional Genomics and Molecular Biology by : Matthew Eckwahl
Download or read book Investigations in Yeast Functional Genomics and Molecular Biology written by Matthew Eckwahl and published by CRC Press. This book was released on 2014-02-24 with total page 414 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book examines conserved pathways mediating cell cycle progression and cell polarity establishment. It includes examples of yeast, regulatory circuits, and feedback regulation, with emphasis on system-wide approaches. It also covers protein interaction networks and trait locus analysis and presents methods and challenges in comparative genomics analysis and evolutionary genetics.
Book Synopsis Genomic Regulatory Systems by : Eric H. Davidson
Download or read book Genomic Regulatory Systems written by Eric H. Davidson and published by Elsevier. This book was released on 2001-01-24 with total page 274 pages. Available in PDF, EPUB and Kindle. Book excerpt: The interaction between biology and evolution has been the subject of great interest in recent years. Because evolution is such a highly debated topic, a biologically oriented discussion will appeal not only to scientists and biologists but also to the interested lay person. This topic will always be a subject of controversy and therefore any breaking information regarding it is of great interest.The author is a recognized expert in the field of developmental biology and has been instrumental in elucidating the relationship between biology and evolution. The study of evolution is of interest to many different kinds of people and Genomic Regulatory Systems: In Development and Evolution is written at a level that is very easy to read and understand even for the nonscientist. * Contents Include* Regulatory Hardwiring: A Brief Overview of the Genomic Control Apparatus and Its Causal Role in Development and Evolution * Inside the Cis-Regulatory Module: Control Logic and How the Regulatory Environment Is Transduced into Spatial Patterns of Gene Expression* Regulation of Direct Cell-Type Specification in Early Development* The Secret of the Bilaterians: Abstract Regulatory Design in Building Adult Body Parts* Changes That Make New Forms: Gene Regulatory Systems and the Evolution of Body Plans
Book Synopsis Plant Promoters and Transcription Factors by : Lutz Nover
Download or read book Plant Promoters and Transcription Factors written by Lutz Nover and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 279 pages. Available in PDF, EPUB and Kindle. Book excerpt: The control of plant gene expression at the transcriptional level is the main subject of this volume. Genetics, molecular biology and gene technology have dramatically improved our knowledge of this event. The functional analysis of promoters and transcription factors provides more and more insights into the molecular anatomy of initiation complexes assembled from RNA polymerase and the multiplicity of helper and control proteins. Formation of specific DNA-protein complexes - activating or repressing transcription - is the crux of developmental or environmental control of gene expression. The book presents an up-to-date, critical overview of this rapidly advancing field.
Book Synopsis Introduction to Epigenetics by : Renato Paro
Download or read book Introduction to Epigenetics written by Renato Paro and published by Springer Nature. This book was released on 2021-03-23 with total page 215 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access textbook leads the reader from basic concepts of chromatin structure and function and RNA mechanisms to the understanding of epigenetics, imprinting, regeneration and reprogramming. The textbook treats epigenetic phenomena in animals, as well as plants. Written by four internationally known experts and senior lecturers in this field, it provides a valuable tool for Master- and PhD- students who need to comprehend the principles of epigenetics, or wish to gain a deeper knowledge in this field. After reading this book, the student will: Have an understanding of the basic toolbox of epigenetic regulation Know how genetic and epigenetic information layers are interconnected Be able to explain complex epigenetic phenomena by understanding the structures and principles of the underlying molecular mechanisms Understand how misregulated epigenetic mechanisms can lead to disease
Download or read book The Yeasts written by Cletus Kurtzman and published by Elsevier. This book was released on 2011-05-09 with total page 2362 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Yeasts: A Taxonomic Study is a three-volume book that covers the taxonomic aspect of yeasts. The main goal of this book is to provide important information about the identification of yeasts. It also discusses the growth tests that can be used to identify different species of yeasts, and it examines how the more important species of yeasts provide information for the selection of species needed for biotechnology. • Volume 1 discusses the identification, classification and importance of yeasts in the field of biotechnology. • Volume 2 focuses on the identification and classification of ascomycetous yeasts. • Volume 3 deals with the identification and classification of basidiomycetous yeasts, along with the genus Prototheca. High-quality photomicrographs and line drawings Detailed phylogenetic trees Up-to-date, clearly presented yeast taxonomy and systematic, easy-to-use reference sequence accession numbers to allow for correct identification
Book Synopsis Guide to Yeast Genetics and Molecular Biology by : Christine Guthrie
Download or read book Guide to Yeast Genetics and Molecular Biology written by Christine Guthrie and published by . This book was released on 1991-01-28 with total page 933 pages. Available in PDF, EPUB and Kindle. Book excerpt: Guide to Yeast Genetics and Molecular Biology presents, for the first time, a comprehensive compilation of the protocols and procedures that have made Saccharomyces cerevisiae such a facile system for all researchers in molecular and cell biology. Whether you are an established yeast biologist or a newcomer to the field, this volume contains all the up-to-date methods you will need to study "Your Favorite Gene" in yeast. Basic Methods in Yeast Genetics**Physical and genetic mapping**Making and recovering mutants**Cloning and Recombinant DNA Methods**High-efficiency transformation**Preparation of yeast artificial chromosome vectors**Basic Methods of Cell Biology**Immunomicroscopy**Protein targeting assays**Biochemistry of Gene Expression**Vectors for regulated expression**Isolation of labeled and unlabeled DNA, RNA, and protein
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 Yeast Metabolic Engineering by : Valeria Mapelli
Download or read book Yeast Metabolic Engineering written by Valeria Mapelli and published by Humana Press. This book was released on 2014-04-18 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Yeast Metabolic Engineering: Methods and Protocols provides the widely established basic tools used in yeast metabolic engineering, while describing in deeper detail novel and innovative methods that have valuable potential to improve metabolic engineering strategies in industrial biotechnology applications. Beginning with an extensive section on molecular tools and technology for yeast engineering, this detailed volume is not limited to methods for Saccharomyces cerevisiae, but describes tools and protocols for engineering other yeasts of biotechnological interest, such as Pichia pastoris, Hansenula polymorpha and Zygosaccharomyces bailii. Tools and technologies for the investigation and determination of yeast metabolic features are described in detail as well as metabolic models and their application for yeast metabolic engineering, while a chapter describing patenting and regulations with a special glance at yeast biotechnology closes the volume. Written in the highly successful Methods in Molecular Biology series format, most chapters include an introduction to their respective topic, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols and tips on troubleshooting and avoiding known pitfalls. Comprehensive and authoritative, Yeast Metabolic Engineering: Methods and Protocols aims to familiarize researchers with the current state of these vital and increasingly useful technologies.
Download or read book The Barley Genome written by Nils Stein and published by Springer. This book was released on 2018-08-18 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an overview of the state-of-the-art in barley genome analysis, covering all aspects of sequencing the genome and translating this important information into new knowledge in basic and applied crop plant biology and new tools for research and crop improvement. Unlimited access to a high-quality reference sequence is removing one of the major constraints in basic and applied research. This book summarizes the advanced knowledge of the composition of the barley genome, its genes and the much larger non-coding part of the genome, and how this information facilitates studying the specific characteristics of barley. One of the oldest domesticated crops, barley is the small grain cereal species that is best adapted to the highest altitudes and latitudes, and it exhibits the greatest tolerance to most abiotic stresses. With comprehensive access to the genome sequence, barley’s importance as a genetic model in comparative studies on crop species like wheat, rye, oats and even rice is likely to increase.
