Download or read book Decoding Transcriptional Regulatory Networks Activated During Stringent Response in Escherichia Coli written by Hemali Bharat Patel and published by . This book was released on 2009 with total page 392 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: The stringent response is a response network in bacteria that is triggered by nutrient limitation and involves a global reprogramming of gene transcription, orchestrated largely by a signaling molecule guanosine tetraphosphate (ppGpp). Despite decades of studies on individual genes perturbed during the stringent response in Escherichia coli, the characteristic transcriptional profile and the role of ppGpp in affecting global transcriptional changes during the stringent response had remained to be determined systematically. We provoked the stringent response, in the strain E. coli K-12, by multiple induction pathways and identified the core transcriptional profile that is characteristic of the cellular response to ppGpp accumulation. By comparison of wild type and ppGpp-deficient E. coli mutant strains, we identified the gene expression changes that are specifically dependent upon ppGpp. We found six transcriptional regulators that are recruited in the core stringent response. We show the regulatory targets of one of these six regulators, RpoS. Over 80% of transcriptional regulation was directly or indirectly dependent upon the general stress response sigma factor, RpoS, even in presence of ppGpp. Our findings suggest that ppGpp alone is not capable of mounting a global stringent response, and it relies heavily on transcriptional regulators such as RpoS. Existing regulatory models for ppGpp-mediated regulation suggest a global redistribution of RNA polymerase (RNAP), upon binding with ppGpp, during stringent response. We have shown evidence for such redistribution of RNAP in presence of ppGpp by conducting ChIP-chip analysis of ppGpp-rich and ppGpp-deficient cells with an antibody specific to the alpha-subunit of RNAP. We also correlated transcriptional changes with a phenotype of increased viability in acidic medium, and demonstrated that it was dependent upon both ppGpp and RpoS. We have shown that ppGpp enhances long-term survival, up to two hours, in acid. Our results reveal the significance of stringent response in development of phenotypes that facilitate adaptation in acidic host environments for E. coli.

Download or read book Dissertation Abstracts International written by and published by . This book was released on 2009 with total page 840 pages. Available in PDF, EPUB and Kindle. Book excerpt:

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.

Download or read book Genomic Signal Processing and Statistics written by Edward R. Dougherty and published by Hindawi Publishing Corporation. This book was released on 2005 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent advances in genomic studies have stimulated synergetic research and development in many cross-disciplinary areas. Processing the vast genomic data, especially the recent large-scale microarray gene expression data, to reveal the complex biological functionality, represents enormous challenges to signal processing and statistics. This perspective naturally leads to a new field, genomic signal processing (GSP), which studies the processing of genomic signals by integrating the theory of signal processing and statistics. Written by an international, interdisciplinary team of authors, this invaluable edited volume is accessible to students just entering this emergent field, and to researchers, both in academia and in industry, in the fields of molecular biology, engineering, statistics, and signal processing. The book provides tutorial-level overviews and addresses the specific needs of genomic signal processing students and researchers as a reference book. The book aims to address current genomic challenges by exploiting potential synergies between genomics, signal processing, and statistics, with special emphasis on signal processing and statistical tools for structural and functional understanding of genomic data. The first part of this book provides a brief history of genomic research and a background introduction from both biological and signal-processing/statistical perspectives, so that readers can easily follow the material presented in the rest of the book. In what follows, overviews of state-of-the-art techniques are provided. We start with a chapter on sequence analysis, and follow with chapters on feature selection, classification, and clustering of microarray data. We then discuss the modeling, analysis, and simulation of biological regulatory networks, especially gene regulatory networks based on Boolean and Bayesian approaches. Visualization and compression of gene data, and supercomputer implementation of genomic signal processing systems are also treated. Finally, we discuss systems biology and medical applications of genomic research as well as the future trends in genomic signal processing and statistics research.

Download or read book The Aminoacyl tRNA Synthetases written by Michael Ibba and published by CRC Press. This book was released on 2005-04-01 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: By virtue of their role as catalysts of the aminoacylation reaction, the aminoacyl-tRNA synthetases ensure that the first step of translation is performed quickly and accurately. In this volume of 36 separate chapters, the many facets of this ancient and ubiquitous family are reviewed, including their surprising structural diversity, enzymology, tRNA interaction properties, and curious alternative functions. These chapters illustrate the degree to which the aminoacyl-tRNA synthetases employ a variety of mechanisms to carry out both the standard functions related to the synthesis of aminoacylated tRNA for protein synthesis, as well as the surprising functions associated with amino acid biosynthesis, cytokine function, and even the processivity of DNA replication. Other chapters explore the regulation of their synthesis, their role in disease, and their prospects as targets for antibacterial therapeutics. This monograph will be a valuable resource for all scientists interested in the fundamentals of protein synthesis from both a basic research and clinical perspective, as well as the relation of translational components to the evolution of the genetic code.

Download or read book Bacterial Signaling written by Reinhard Krämer and published by John Wiley & Sons. This book was released on 2009-12-09 with total page 513 pages. Available in PDF, EPUB and Kindle. Book excerpt: Providing a comprehensive insight into cellular signaling processes in bacteria with a special focus on biotechnological implications, this is the first book to cover intercellular as well as intracellular signaling and its relevance for biofilm formation, host pathogen interactions, symbiotic relationships, and photo- and chemotaxis. In addition, it deals in detail with principal bacterial signaling mechanisms -- making this a valuable resource for all advanced students in microbiology. Dr. Krämer is a world-renowned expert in intracellular signaling and its implications for biotechnology processes, while Dr. Jung is an expert on intercellular signaling and its relevance for biomedicine and agriculture.

Download or read book Control of Macromolecular Synthesis written by Ole Maaløe and published by . This book was released on 1966 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Desk Encyclopedia of Microbiology written by Moselio Schaechter and published by Academic Press. This book was released on 2010-04-19 with total page 1277 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Desk Encyclopedia of Microbiology, Second Edition is a single-volume comprehensive guide to microbiology for the advanced reader. Derived from the six volume e-only Encyclopedia of Microbiology, Third Edition, it bridges the gap between introductory texts and specialized reviews. Covering topics ranging from the basic science of microbiology to the current "hot" topics in the field, it will be invaluable for obtaining background information on a broad range of microbiological topics, preparing lectures and preparing grant applications and reports. - The most comprehensive single-volume source providing an overview of microbiology to non-specialists - Bridges the gap between introductory texts and specialized reviews - Provides concise and general overviews of important topics within the field making it a helpful resource when preparing for lectures, writing reports, or drafting grant applications

Download or read book The Science and Applications of Synthetic and Systems Biology written by Institute of Medicine and published by National Academies Press. This book was released on 2011-12-30 with total page 570 pages. Available in PDF, EPUB and Kindle. Book excerpt: Many potential applications of synthetic and systems biology are relevant to the challenges associated with the detection, surveillance, and responses to emerging and re-emerging infectious diseases. On March 14 and 15, 2011, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to explore the current state of the science of synthetic biology, including its dependency on systems biology; discussed the different approaches that scientists are taking to engineer, or reengineer, biological systems; and discussed how the tools and approaches of synthetic and systems biology were being applied to mitigate the risks associated with emerging infectious diseases. The Science and Applications of Synthetic and Systems Biology is organized into sections as a topic-by-topic distillation of the presentations and discussions that took place at the workshop. Its purpose is to present information from relevant experience, to delineate a range of pivotal issues and their respective challenges, and to offer differing perspectives on the topic as discussed and described by the workshop participants. This report also includes a collection of individually authored papers and commentary.

Download or read book Abiotic Stress Response in Plants written by Arun Shanker and published by BoD – Books on Demand. This book was released on 2011-08-29 with total page 362 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plants, unlike animals, are sessile. This demands that adverse changes in their environment are quickly recognized, distinguished and responded to with suitable reactions. Drought, heat, cold and salinity are among the major abiotic stresses that adversely affect plant growth and productivity. In general, abiotic stress often causes a series of morphological, physiological, biochemical and molecular changes that unfavorably affect plant growth, development and productivity. Drought, salinity, extreme temperatures (cold and heat) and oxidative stress are often interrelated; these conditions singularly or in combination induce cellular damage. To cope with abiotic stresses, of paramount significance is to understand plant responses to abiotic stresses that disturb the homeostatic equilibrium at cellular and molecular level in order to identify a common mechanism for multiple stress tolerance. This multi authored edited compilation attempts to put forth an all-inclusive biochemical and molecular picture in a systems approach wherein mechanism and adaptation aspects of abiotic stress are dealt with. The chief objective of the book hence is to deliver state of the art information for comprehending the effects of abiotic stress in plants at the cellular level.

Download or read book Industrial Microorganisms written by Richard H. Baltz and published by ASM Press. This book was released on 1993 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is based on the proceedings of the 5th ASM Conference on the Genetics and Molecular Biology of Industrial Microorganisms held in Bloomington, Indiana in October 1992. The meeting focussed on prokaryotes and lower eukaryotes, with the programme balanced between streptomyces, fungi and yeasts, and other bacteria including Escherichia coli and emerging bacterial systems. The topics of the symposia reflect major trends in research that have immediate and future industrial applications

Download or read book Cryo EM Part A Sample Preparation and Data Collection written by and published by Academic Press. This book was released on 2010-09-30 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cryo-EM Part A: Sample Preparation and Data Collection is dedicated to a description of the instruments, samples, protocols, and analyses that belong to cryo-EM. It emphasizes the relatedness of the ideas, instrumentation, and methods underlying all cryo-EM approaches, which allow practitioners to easily move between them. Within each section, the articles are ordered according to the most common symmetry of the sample to which their methods are applied. - Includes time-tested core methods and new innovations applicable to any researcher - Methods included are useful to both established researchers and newcomers to the field - Relevant background and reference information given for procedures can be used as a guide

Download or read book Genome Mapping and Genomics in Animal Associated Microbes written by Vishvanath Nene and published by Springer Science & Business Media. This book was released on 2008-11-24 with total page 253 pages. Available in PDF, EPUB and Kindle. Book excerpt: Achievements and progress in genome mapping and the genomics of microbes supersede by far those for higher plants and animals, in part due to their enormous economic implication but also smaller genome size. In the post-genomic era, whole genome sequences of animal-associated microbes are providing clues to depicting the genetic basis of the complex host-pathogen relationships and the evolution of parasitism; and to improving methods of controlling pathogens. This volume focuses on a globally important group of intracellular prokaryotic pathogens which affect livestock animals. These include Brucella, Mycobacterium, Anaplasma and Ehrlichia, as well as the protozoan pathogens Cryptosporidium and Theileria, for which genome sequence data is available. Insights from comparative genomics of the microbes described provide clues to the adaptation involved in host-microbe interactions, as well as resources potentially useful for application in future research and product development.

Download or read book Feedback Control in Systems Biology written by Carlo Cosentino and published by CRC Press. This book was released on 2011-10-17 with total page 298 pages. Available in PDF, EPUB and Kindle. Book excerpt: Like engineering systems, biological systems must also operate effectively in the presence of internal and external uncertainty—such as genetic mutations or temperature changes, for example. It is not surprising, then, that evolution has resulted in the widespread use of feedback, and research in systems biology over the past decade has shown that feedback control systems are widely found in biology. As an increasing number of researchers in the life sciences become interested in control-theoretic ideas such as feedback, stability, noise and disturbance attenuation, and robustness, there is a need for a text that explains feedback control as it applies to biological systems. Written by established researchers in both control engineering and systems biology, Feedback Control in Systems Biology explains how feedback control concepts can be applied to systems biology. Filling the need for a text on control theory for systems biologists, it provides an overview of relevant ideas and methods from control engineering and illustrates their application to the analysis of biological systems with case studies in cellular and molecular biology. Control Theory for Systems Biologists The book focuses on the fundamental concepts used to analyze the effects of feedback in biological control systems, rather than the control system design methods that form the core of most control textbooks. In addition, the authors do not assume that readers are familiar with control theory. They focus on "control applications" such as metabolic and gene-regulatory networks rather than aircraft, robots, or engines, and on mathematical models derived from classical reaction kinetics rather than classical mechanics. Another significant feature of the book is that it discusses nonlinear systems, an understanding of which is crucial for systems biologists because of the highly nonlinear nature of biological systems. The authors cover tools and techniques for the analysis of linear and nonlinear systems; negative and positive feedback; robustness analysis methods; techniques for the reverse-engineering of biological interaction networks; and the analysis of stochastic biological control systems. They also identify new research directions for control theory inspired by the dynamic characteristics of biological systems. A valuable reference for researchers, this text offers a sound starting point for scientists entering this fascinating and rapidly developing field.

Download or read book Engineering the Genetic Code written by Nediljko Budisa and published by John Wiley & Sons. This book was released on 2006-05-12 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: The ability to introduce non-canonical amino acids in vivo has greatly expanded the repertoire of accessible proteins for basic research and biotechnological application. Here, the different methods and strategies to incorporate new or modified amino acids are explained in detail, including a lot of practical advice for first-time users of this powerful technique. Novel applications in protein biochemistry, genomics, biotechnology and biomedicine made possible by the expansion of the genetic code are discussed and numerous examples are given. Essential reading for all molecular life scientists who want to stay ahead in their research.

Download or read book Bacterial Resistance to Antibiotics written by Boyan B. Bonev and published by John Wiley & Sons. This book was released on 2019-06-10 with total page 288 pages. Available in PDF, EPUB and Kindle. Book excerpt: AN AUTHORITATIVE SURVEY OF CURRENT RESEARCH INTO CLINICALLY USEFUL CONVENTIONAL AND NONCONVENTIONAL ANTIBIOTIC THERAPEUTICS Pharmaceutically-active antibiotics revolutionized the treatment of infectious diseases, leading to decreased mortality and increased life expectancy. However, recent years have seen an alarming rise in the number and frequency of antibiotic-resistant "Superbugs." The Centers for Disease Control and Prevention (CDC) estimates that over two million antibiotic-resistant infections occur in the United States annually, resulting in approximately 23,000 deaths. Despite the danger to public health, a minimal number of new antibiotic drugs are currently in development or in clinical trials by major pharmaceutical companies. To prevent reverting back to the pre-antibiotic era—when diseases caused by parasites or infections were virtually untreatable and frequently resulted in death—new and innovative approaches are needed to combat the increasing resistance of pathogenic bacteria to antibiotics. Bacterial Resistance to Antibiotics – From Molecules to Man examines the current state and future direction of research into developing clinically-useful next-generation novel antibiotics. An internationally-recognized team of experts cover topics including glycopeptide antibiotic resistance, anti-tuberculosis agents, anti-virulence therapies, tetracyclines, the molecular and structural determinants of resistance, and more. Presents a multidisciplinary approach for the optimization of novel antibiotics for maximum potency, minimal toxicity, and appropriated degradability Highlights critical aspects that may relieve the problematic medical situation of antibiotic resistance Includes an overview of the genetic and molecular mechanisms of antibiotic resistance Addresses contemporary issues of global public health and longevity Includes full references, author remarks, and color illustrations, graphs, and charts Bacterial Resistance to Antibiotics – From Molecules to Man is a valuable source of up-to-date information for medical practitioners, researchers, academics, and professionals in public health, pharmaceuticals, microbiology, and related fields.

Download or read book Restriction Endonucleases written by Alfred Pingoud and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 462 pages. Available in PDF, EPUB and Kindle. Book excerpt: Restriction enzymes are highly specific nucleases which occur ubiquitously among prokaryotic organisms, where they serve to protect bacterial cells against foreign DNA. Many different types of restriction enzymes are known, among them multi-subunit enzymes which depend on ATP or GTP hydrolysis for target site location. The best known representatives, the orthodox type II restriction endonucleases, are homodimers which recognize palindromic sequences, 4 to 8 base pairs in length, and cleave the DNA within or immediately adjacent to the recognition site. In addition to their important biological role (up to 10 % of the genomes of prokaryotic organisms code for restriction/modification systems!), they are among the most important enzymes used for the analysis and recombination of DNA. In addition, they are model systems for the study of protein-nucleic acids interactions and, because of their ubiquitous occurence, also for the understanding of the mechanisms of evolution.