Download or read book Systematic Mutagenesis of Escherichia Coli Genome and Genome wide Expression Analysis Indicates that FNR of E Coli K12 Regulates a Large Number of Genes of Unknown Function written by Yisheng Kang and published by . This book was released on 2005 with total page 144 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Integrating Genome wide Analyses to Investigate the Regulatory Role of FNR and IscR in Response to Anaerobiosis in Escherichia Coli written by and published by . This book was released on 2013 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Escherichia coli contains multiple O2-sensing transcription factors, including FNR and IscR. FNR is predominantly active under anaerobic conditions, where it ligates an O20́3labile [4Fe0́34S] cluster for dimerization and DNA binding. Ligation of a [2Fe0́32S] cluster by IscR broadens its DNA binding specificity from binding only a Type 2 site to binding both Type 1 and Type 2 sites. Fe0́3S occupancy of IscR is regulated by O2 availability and a complex pattern of gene expression results under aerobic and anaerobic conditions. We studied the FNR and IscR regulons on a genome0́3scale and found little overlap between the two regulons. FNR occupancy at many sites was strongly influenced by nucleoid0́3associated proteins (NAPs). While only a subset of predicted FNR binding sites were bound in vivo, many sites appeared to be masked by the NAPs H0́3NS, IHF, and Fis. Cells lacking H0́3NS and its paralog StpA showed increased FNR occupancy at sites normally bound by H0́3NS, indicating that the genome is not readily accessible for FNR binding. Correlation of FNR ChIP0́3seq peaks with transcriptomic data showed that less than half of the FNR regulated operons could be attributed to direct FNR binding. FNR bound some promoters without regulating expression, presumably requiring additional condition specific transcription factors. ChIP0́3chip analysis of IscR binding revealed that IscR primarily binds Type 2 sites under aerobic and anaerobic conditions. Correlation of IscR binding regions containing a Type 1 or Type 2 site with the transcriptomic data revealed 33 operons directly regulated by IscR under aerobic or anaerobic conditions. The four previously reported promoters containing Type 1 sites and both known and novel promoters containing Type 2 sites were identified. The previous finding that promoters with Type 2 sites are also regulated by IscR primarily under aerobic conditions extended to newly identified operons. Further analyses suggested that multiple mechanisms prevent IscR regulation of Type 2 sites under anaerobic conditions including action of other global transcription factors FNR, ArcA, and Fur. In summary, this work expands our knowledge of the FNR and IscR regulons and the role of combinatorial regulation in the E. coli response to changes in O2 concentration.
Download or read book Microarray based Escherichia Coli Functional Genomic Studies written by Yu Qiu and published by . This book was released on 2006 with total page 204 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Sequence Evolution Function written by Eugene V. Koonin and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.
Download or read book Dissertation Abstracts International written by and published by . This book was released on 2008 with total page 980 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 The Yeast Two hybrid System written by Paul L. Bartel and published by Oxford University Press, USA. This book was released on 1997 with total page 362 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume, part of the Advances in Molecular Biology series, presents work by pioneers in the field and is the first publication devoted solely to the yeast two-hybrid system. It includes detailed protocols, practical advice on troubleshooting, and suggestions for future development. In addition, it illustrates how to construct an activation domain hybrid library, how to identify mutations that disrupt an interaction, and how to use the system in mammalian cells. Many of the contributors have developed new applications and variations of the technique.
Download or read book Molecular Biology and Pathogenicity of Mycoplasmas written by Shmuel Razin and published by Springer Science & Business Media. This book was released on 2007-05-08 with total page 574 pages. Available in PDF, EPUB and Kindle. Book excerpt: was the result of the efforts of Robert Cleverdon. The rapidly developing discipline of molecular biology and the rapidly expanding knowledge of the PPLO were brought together at this meeting. In addition to the PPLO specialists, the conference invited Julius Marmur to compare PPLO DNA to DNA of other organisms; David Garfinkel, who was one of the first to develop computer models of metabolism; Cyrus Levinthal to talk about coding; and Henry Quastler to discuss information theory constraints on very small cells. The conference was an announcement of the role of PPLO in the fundamental understanding of molecular biology. Looking back 40-some years to the Connecticut meeting, it was a rather bold enterprise. The meeting was international and inter-disciplinary and began a series of important collaborations with influences resonating down to the present. If I may be allowed a personal remark, it was where I first met Shmuel Razin, who has been a leading figure in the emerging mycoplasma research and a good friend. This present volume is in some ways the fulfillment of the promise of that early meeting. It is an example of the collaborative work of scientists in building an understanding of fundamental aspects of biology.
Download or read book Biological Sequence Analysis written by Richard Durbin and published by Cambridge University Press. This book was released on 1998-04-23 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Probabilistic models are becoming increasingly important in analysing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analysing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it aims to be accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time present the state-of-the-art in this new and highly important field.
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 Microbial Production of L Amino Acids written by Robert Faurie and published by Springer Science & Business Media. This book was released on 2003-01-17 with total page 195 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume deals with "Microbial Production of L-Amino Acids" and presents five comprehensive, expert and actual review articles on the modern production of Amino Acids by application of biotechnologically optimized microorganisms. This includes not only the modern techniques of enzyme, metabolic and transport engineering but also sophisticated analytical methods like metabolic flux analysis and subsequent pathway modeling. A general review about industrial processes of Amino Acid production provides a comprehensive overview about recent strain development as well as fermentation technologies. It was our special interest to focus the other articles on the most important and best selling amino acids on the world market i.e. L-Glutamate, L-Lysine and L-Threonine. The authors of this special volume have contributed significantly to the progress of Amino Acid biotechnology in the last decades and earn our special gratitude and admiration for their expert review articles.
Download or read book The Genus Yersinia written by Robert D. Perry and published by Springer Science & Business Media. This book was released on 2007-09-25 with total page 454 pages. Available in PDF, EPUB and Kindle. Book excerpt: The 9th International Symposium on Yersinia was held in Lexington, Kentucky, USA on October 10-14, 2006. Over 250 Yersinia researchers from 18 countries gathered to present and discuss their research. In addition to 37 oral presentations, there were 150 poster presentations. This Symposium volume is based on selected presentations from the meeting and contains both reviews and research articles. It is divided into six topic areas: 1) genomics; 2) structure and metabolism; 3) regulatory mechanisms; 4) pathogenesis and host interactions; 5) molecular epidemiology and detection; and 6) vaccine and antimicrobial therapy development. Consequently, this volume covers a wide range of current research areas in the Yersinia field.
Download or read book Stress Induced Mutagenesis written by David Mittelman and published by Springer Science & Business Media. This book was released on 2013-03-12 with total page 284 pages. Available in PDF, EPUB and Kindle. Book excerpt: The discovery of stress-induced mutagenesis has changed ideas about mutation and evolution, and revealed mutagenic programs that differ from standard spontaneous mutagenesis in rapidly proliferating cells. The stress-induced mutations occur during growth-limiting stress, and can include adaptive mutations that allow growth in the otherwise growth-limiting environment. The stress responses increase mutagenesis specifically when cells are maladapted to their environments, i.e. are stressed, potentially accelerating evolution then. The mutation mechanism also includes temporary suspension of post-synthesis mismatch repair, resembling mutagenesis characteristic of some cancers. Stress-induced mutation mechanisms may provide important models for genome instability underlying some cancers and genetic diseases, resistance to chemotherapeutic and antibiotic drugs, pathogenicity of microbes, and many other important evolutionary processes. This book covers pathways of stress-induced mutagenesis in all systems. The principle focus is mammalian systems, but much of what is known of these pathways comes from non-mammalian systems.
Download or read book The Minimal Cell written by Pier Luigi Luisi and published by Springer Science & Business Media. This book was released on 2010-11-01 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the last ten years there has been a considerable increase of interest on the notion of the minimal cell. With this term we usually mean a cell-like structure containing the minimal and sufficient number of components to be defined as alive, or at least capable of displaying some of the fundamental functions of a living cell. In fact, when we look at extant living cells we realize that thousands of molecules are organized spatially and functionally in order to realize what we call cellular life. This fact elicits the question whether such huge complexity is a necessary condition for life, or a simpler molecular system can also be defined as alive. Obviously, the concept of minimal cell encompasses entire families of cells, from totally synthetic cells, to semi-synthetic ones, to primitive cell models, to simple biomimetic cellular systems. Typically, in the experimental approach to the construction of minimal the main ingredient is the compartment. Lipid vesicles (liposomes) are used to host simple and complex molecular transformations, from single or multiple enzymic reactions, to polymerase chain reactions, to gene expression. Today this research is seen as part of the broader scenario of synthetic biology but it is rooted in origins of life studies, because the construction of a minimal cell might provide biophysical insights into the origins of primitive cells, and the emergence of life on earth. The volume provides an overview of physical, biochemical and functional studies on minimal cells, with emphasis to experimental approaches. 15 International experts report on their innovative contributions to the construction of minimal cells.
Download or read book Functional Metagenomics Tools and Applications written by Trevor C. Charles and published by Springer. This book was released on 2017-10-09 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this book, the latest tools available for functional metagenomics research are described.This research enables scientists to directly access the genomes from diverse microbial genomes at one time and study these “metagenomes”. Using the modern tools of genome sequencing and cloning, researchers have now been able to harness this astounding metagenomic diversity to understand and exploit the diverse functions of microorganisms. Leading scientists from around the world demonstrate how these approaches have been applied in many different settings, including aquatic and terrestrial habitats, microbiomes, and many more environments. This is a highly informative and carefully presented book, providing microbiologists with a summary of the latest functional metagenomics literature on all specific habitats.
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 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.
