Download or read book Systems Evaluation of Regulatory Components in Bacterial Transcription Initiation written by Donghyuk Kim and published by . This book was released on 2014 with total page 138 pages. Available in PDF, EPUB and Kindle. Book excerpt: In bacterial transcription, transcription initiation is arguably the most important regulatory point, because transcribing unnecessary genes into RNA could be a waste of energy, time and resources. There are multiple components which are involved in bacterial transcription initiation: RNA polymerase, [sigma]-factors, transcription factors, and transcription start sites. Each component has been intensively investigated, however in a limited scope and mostly with low-throughput methods. New technologies, such as hybridization on microarray and deep-sequencing, enabled researchers to study each component in a systems level, in a combination of two or more components, and in comparison between different species. In order to facilitate the analysis, integration, and comparison, software, MetaScope, was developed to accommodate multiple genome-scale datasets to visualize, analyze, integrate, and compare. TSS-seq, modified 5'-RACE with deep-sequencing, gave a genome-scale landscape of transcription start sites, and comparison of TSSs of conserved genes between closely-related species, E. coli and K. pneumoniae, showed significantly different usage of promoters, which implies different regulation of orthologous genes. To further investigate properties of promoters which were identified by TSS-seq, ChIP-chip experiments were performed for [sigma]-factors in E. coli to determine [sigma]-factor regulons. From the reconstructed [sigma]-factor network, extensive overlaps between regulons were observed. [sigma]70 and [sigma]38 share the largest set of genes in E. coli, and additional experiments revealed that those [sigma]-factors work in competition and utilize the negative regulation by [sigma]38 . ChIP-exo, which applies exonuclease to present better resolution of DNA-binding, and RNA-seq implemented more detailed identification of Fur regulon in E. coli. Reconstruction of Fur regulon completed the previous knowledge of bacterial response to iron change, and also enabled its role over iron metabolism. In order to understand how bacteria respond to nitrogen limitation, the same methods were used under conditions that were predicted from model-based prediction, and resulted in reconstruction of regulons for major transcription factors, NtrC and Nac. Determination of those regulons expanded the current knowledge of nitrogen metabolism and how it is regulated in bacteria. Thus, systems approaches enabled a genome-scale assessment of regulatory components in multiple levels, and contributed to expansion of the current knowledge of bacterial transcription initiation.
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
Download or read book Biology for AP Courses written by Julianne Zedalis and published by . This book was released on 2017-10-16 with total page 1923 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biology for AP® courses covers the scope and sequence requirements of a typical two-semester Advanced Placement® biology course. The text provides comprehensive coverage of foundational research and core biology concepts through an evolutionary lens. Biology for AP® Courses was designed to meet and exceed the requirements of the College Board’s AP® Biology framework while allowing significant flexibility for instructors. Each section of the book includes an introduction based on the AP® curriculum and includes rich features that engage students in scientific practice and AP® test preparation; it also highlights careers and research opportunities in biological sciences.
Download or read book Molecular Biology of the Cell written by and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Prokaryotic Metabolism and Physiology written by Byung Hong Kim and published by Cambridge University Press. This book was released on 2019-05-16 with total page 509 pages. Available in PDF, EPUB and Kindle. Book excerpt: Extensive and up-to-date review of key metabolic processes in bacteria and archaea and how metabolism is regulated under various conditions.
Download or read book Genes Signals written by Mark Ptashne and published by CSHL Press. This book was released on 2002 with total page 212 pages. Available in PDF, EPUB and Kindle. Book excerpt: P. 103.
Download or read book Bacteriophage T4 written by Christopher K. Mathews and published by . This book was released on 1983 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Gene Regulation and Metabolism written by Julio Collado-Vides and published by MIT Press. This book was released on 2002 with total page 326 pages. Available in PDF, EPUB and Kindle. Book excerpt: An overview of current computational approaches to metabolism and gene regulation.
Download or read book Techniques in Molecular Biology written by J.M. Walker and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: The last few years have seen the rapid development of new methodology in the field of molecular biology. New techniques have been regularly introduced and the sensitivity of older techniques greatly improved upon. Developments in the field of genetic engineering in particular have contributed a wide range of new techniques. The purpose of this book therefore is to introduce the reader to a selection of the more advanced analytical and preparative techniques which the editors consider to be frequently used by research workers in the field of molecular biology. In choosing techniques for this book we have obviously had to be selective, and for the sake of brevity a knowledge of certain basic biochemical techniques and terminology has been assumed. However, since many areas of molecular biology are developing at a formidable rate and constantly generating new terminology, a glossary of terms has been included. The techniques chosen for this book are essentially based on those used in a series of workshops on 'techniques in molecular biology' that have been held at The Hatfield Polytechnic in recent years. In choosing these chapters we have taken into account many useful suggestions and observations made by participants at these workshops. Each chapter aims to describe both the theory and relevant practical details for a given technique, and to identify both the potential and limitations of the technique. Each chapter is written by authors who regularly use the technique in their own laboratories.
Download or read book Molecular Mechanisms of Microbial Evolution written by Pabulo H. Rampelotto and published by Springer. This book was released on 2018-10-12 with total page 452 pages. Available in PDF, EPUB and Kindle. Book excerpt: One of the most profound paradigms that have transformed our understanding about life over the last decades was the acknowledgement that microorganisms play a central role in shaping the past and present environments on Earth and the nature of all life forms. Each organism is the product of its history and all extant life traces back to common ancestors, which were microorganisms. Nowadays, microorganisms represent the vast majority of biodiversity on Earth and have survived nearly 4 billion years of evolutionary change. Microbial evolution occurred and continues to take place in a great variety of environmental conditions. However, we still know little about the processes of evolution as applied to microorganisms and microbial populations. In addition, the molecular mechanisms by which microorganisms communicate/interact with each other and with multicellular organisms remains poorly understood. Such patterns of microbe-host interaction are essential to understand the evolution of microbial symbiosis and pathogenesis.Recent advances in DNA sequencing, high-throughput technologies, and genetic manipulation systems have enabled studies that directly characterize the molecular and genomic bases of evolution, producing data that are making us change our view of the microbial world. The notion that mutations in the coding regions of genomes are, in combination with selective forces, the main contributors to biodiversity needs to be re-examined as evidence accumulates, indicating that many non-coding regions that contain regulatory signals show a high rate of variation even among closely related organisms. Comparative analyses of an increasing number of closely related microbial genomes have yielded exciting insight into the sources of microbial genome variability with respect to gene content, gene order and evolution of genes with unknown functions. Furthermore, laboratory studies (i.e. experimental microbial evolution) are providing fundamental biological insight through direct observation of the evolution process. They not only enable testing evolutionary theory and principles, but also have applications to metabolic engineering and human health. Overall, these studies ranging from viruses to Bacteria to microbial Eukaryotes are illuminating the mechanisms of evolution at a resolution that Darwin, Delbruck and Dobzhansky could barely have imagined. Consequently, it is timely to review and highlight the progress so far as well as discuss what remains unknown and requires future research. This book explores the current state of knowledge on the molecular mechanisms of microbial evolution with a collection of papers written by authors who are leading experts in the field.
Download or read book Bacillus Subtilis and Its Closest Relatives written by A. L. Sonenshein and published by . This book was released on 2002 with total page 664 pages. Available in PDF, EPUB and Kindle. Book excerpt: Focusing on issues of gene organization, regulation, and evolution in the context of the whole life of the cell, this new volume complements the editors' classic 1993 volume Bacillus subtilis and Other Gram-Positive Bacteria. Building upon the previous edition, Bacillus subtilis and Its Closest Relatives contains an updated annotation of the complete B. subtilis genome and includes a unique compilation of major pathways of metabolism and macromolecular synthesis, correlating genes and proteins and assigning new functions to many genes. It also provides clear explanations of the major regulatory mechanisms that are unique to gram-positive bacteria as well as an overview of their special properties. This essential reference offers detailed, current information and is valuable reading for microbiologists, biotechnologists, and students.
Download or read book Gene Transfer to Plants written by Ingo Potrykus and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 370 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Toxin Antitoxin Systems in Pathogenic Bacteria written by Juan Carlos Alonso and published by Mdpi AG. This book was released on 2021-06-17 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bacterial toxin-antitoxin (TA) systems, which are ubiquitously present in bacterial genomes, are not essential for normal cell proliferation. The TA systems regulate fundamental cellular processes, facilitate survival under stress conditions, have essential roles in virulence and represent potential therapeutic targets. These genetic TA loci are also shown to be involved in the maintenance of successful multidrug-resistant mobile genetic elements. The TA systems are classified as types I to VI, according to the nature of the antitoxin and to the mode of toxin inhibition. Type II TA systems encode a labile antitoxin and its stable toxin; degradation of the antitoxin renders a free toxin, which is bacteriostatic by nature. A free toxin generates a reversible state with low metabolic activity (quiescence) by affecting important functions of bacterial cells such as transcription, translation, DNA replication, replication and cell-wall synthesis, biofilm formation, phage predation, the regulation of nucleotide pool, etc., whereas antitoxins are toxin inhibitors. Under stress conditions, the TA systems might form networks. To understand the basis of the unique response of TA systems to stress, the prime causes of the emergence of drug-resistant strains, and their contribution to therapy failure and the development of chronic and recurrent infections, must be known in order to grasp how TA systems contribute to the mechanisms of phenotypic heterogeneity and pathogenesis that will enable the rational development of new treatments for infections caused by pathogens.
Download or read book Bacterial Physiology and Metabolism written by Byung Hong Kim and published by Cambridge University Press. This book was released on 2008-02-21 with total page 934 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent determination of genome sequences for a wide range of bacteria has made in-depth knowledge of prokaryotic metabolic function essential in order to give biochemical, physiological, and ecological meaning to the genomic information. Clearly describing the important metabolic processes that occur in prokaryotes under different conditions and in different environments, this advanced text provides an overview of the key cellular processes that determine bacterial roles in the environment, biotechnology, and human health. Prokaryotic structure is described as well as the means by which nutrients are transported into cells across membranes. Glucose metabolism through glycolysis and the TCA cycle are discussed, as well as other trophic variations found in prokaryotes, including the use of organic compounds, anaerobic fermentation, anaerobic respiratory processes, and photosynthesis. The regulation of metabolism through control of gene expression and control of the activity of enzymes is also covered, as well as survival mechanisms used under starvation conditions.
Download or read book Ubiquitin and the Biology of the Cell written by Jan-Michael Peters and published by Springer Science & Business Media. This book was released on 1998-05-31 with total page 498 pages. Available in PDF, EPUB and Kindle. Book excerpt: The last several years have been a landmark period in the ubiquitin field. The breadth of ubiquitin's roles in cell biology was first sketched, and the importance of ubiquitin-dependent proteolysis as a regulatory mechanism gained general acceptance. The many strands of work that led to this new perception are re counted in this book. A consequence of this progress is that the field has grown dramatically since the first book on ubiquitin was published almost a decade ago [M. Rechsteiner (ed. ), Ubiquitin, Plenum Press, 1988]. In this span, students of the cell cycle, transcription, signal transduction, protein sorting, neuropathology, cancer, virology, and immunology have attempted to chart the role of ubi quit in in their particular experimental systems, and this integration of the field into cell biology as a whole continues at a remarkable pace. We hope that for active researchers in the field as well as for newcomers and those on the fence, this book will prove helpful for its breadth, historical perspective, and practical tips. Structural data are now available on many of the components of the ubiquitin pathway. The structures have provided basic insights into the unusual biochemical mechanisms of ubiquitination and proteasome-mediated proteolysis. Because high-speed computer graphics can convey structures more effectively than print media, we have supplemented the figures of the book with a Worldwide Web site that can display the structures in a flexible, viewer-controlled format.
Download or read book Gene Regulatory Sequences and Human Disease written by Nadav Ahituv and published by Springer Science & Business Media. This book was released on 2012-05-30 with total page 289 pages. Available in PDF, EPUB and Kindle. Book excerpt: In Gene Regulatory Sequences and Human Disease, the Editor will introduce the different technological advances that led to this breakthrough. In addition, several examples will be provided of nucleotide variants in noncoding sequences that have been shown to be associated with various human diseases.
Download or read book Two component Signal Transduction written by James A. Hoch and published by Amer Society for Microbiology. This book was released on 1995 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: The human enteroviruses, particularly the polio viruses, have had a significant role in the history of medicine and microbiology; and continue to cause clinical problems, as well as provide targets for molecular investigation. This book offers a link between the basic science and clinical medicine.
