Download or read book The Complex Transcriptional Landscape of Caulobacter Crescentus written by Bo Zhou and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: One of the central aspects of the biological program that guide the development of an organism is embedded in the regulated and sequential expression of genes as development progresses. A large part of this regulation is achieved through the temporal activation and repression of transcriptional initiation by the selective binding of regulatory proteins, such as transcription factors, to promoters during specific stages of development. Thus, being able to globally and precisely identify these processes are important steps in gaining a systems-level insight and understanding of the developmental program. The cell cycle of Caulobacter crescentus, an alpha-proteobacteria that undergoes cell differentiation and asymmetric cell division, has been used extensively as a model organism to study bacterial development. A cyclical and integrated genetic circuit involving five master regulatory proteins, including DnaA, GcrA, CtrA, and SciP, and the DNA methyl-transferase CcrM, whose presence and activities oscillate in space and time, orchestrate the many facets of the Caulobacter cell cycle including DNA replication, DNA methylation, organelle biogenesis, and cytokinesis. This genetic circuit is at the core of the Caulobacter developmental program. While microarrays have shown 19% of mRNAs undergo changes in RNA level during the cell cycle and development, it is unclear exactly which regulatory factors of the core circuit drive the changes in transcription at each specific locus, and how these regulatory factors act combinatorially to effect transcriptional outcomes has not been systematically dissected. In order to achieve these goals and to further define the transcriptional regulatory landscape that guides the cell cycle, a thorough and global analysis of Caulobacter transcription as a function of the cell cycle and developmental progression is needed. In this thesis, I devised a novel protocol combining 5' rapid amplification of cDNA ends (5' RACE) and high-throughput sequencing to globally map the precise locations of transcriptional start sites (TSSs) in the Caulobacter genome, measured their transcription levels at multiple times in the cell cycle, and identified their transcription factor binding sites. Using the TSSs identified and a RNA sequencing dataset, I made a functional annotation of operons and other transcriptional units in the genome. A large number of antisense transcripts were identified, and many of them are within essential cell cycle-regulated genes, including two master regulators, a previous unknown feature of the core cell cycle control circuit. Many critical genes and operons have multiple promoters, and these promoters are often independently regulated. Furthermore, approximately 25% of the cell cycle-regulated promoters are co-regulated by two or more master regulatory proteins of the core genetic circuit. These results revealed surprising transcriptional complexity and uncovered multiple new layers of transcriptional control mediating the bacterial cell cycle and development and represent the first in-depth analysis of TSS control in as a function bacterial cell cycle and developmental progression.
Download or read book Computational Methods in Systems Biology written by Ashutosh Gupta and published by Springer. This book was released on 2013-09-18 with total page 299 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the proceedings of the 11th International Conference on Computational Methods in Systems Biology, CMSB 2013, held in Klosterneuburg, Austria, in September 2013. The 15 regular papers included in this volume were carefully reviewed and selected from 27 submissions. They deal with computational models for all levels, from molecular and cellular, to organs and entire organisms.
Download or read book Molecular Microbiology of Heavy Metals written by Dietrich H. Nies and published by Springer Science & Business Media. This book was released on 2007-03-24 with total page 455 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers allocation of metals in cells, metal transporter, storage and metalloregulatory proteins, cellular responses to metal ion stress, transcription of genes involved in metal ion homeostasis, uptake of essential metals, metal efflux and other detoxification mechanisms. The book also discusses metal bioreporters for the nanomolar range of concentration and tools to address the metallome. In addition, coverage details specific metals.
Download or read book Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria written by Frans J. de Bruijn and published by John Wiley & Sons. This book was released on 2016-07-13 with total page 1472 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bacteria in various habitats are subject to continuously changing environmental conditions, such as nutrient deprivation, heat and cold stress, UV radiation, oxidative stress, dessication, acid stress, nitrosative stress, cell envelope stress, heavy metal exposure, osmotic stress, and others. In order to survive, they have to respond to these conditions by adapting their physiology through sometimes drastic changes in gene expression. In addition they may adapt by changing their morphology, forming biofilms, fruiting bodies or spores, filaments, Viable But Not Culturable (VBNC) cells or moving away from stress compounds via chemotaxis. Changes in gene expression constitute the main component of the bacterial response to stress and environmental changes, and involve a myriad of different mechanisms, including (alternative) sigma factors, bi- or tri-component regulatory systems, small non-coding RNA’s, chaperones, CHRIS-Cas systems, DNA repair, toxin-antitoxin systems, the stringent response, efflux pumps, alarmones, and modulation of the cell envelope or membranes, to name a few. Many regulatory elements are conserved in different bacteria; however there are endless variations on the theme and novel elements of gene regulation in bacteria inhabiting particular environments are constantly being discovered. Especially in (pathogenic) bacteria colonizing the human body a plethora of bacterial responses to innate stresses such as pH, reactive nitrogen and oxygen species and antibiotic stress are being described. An attempt is made to not only cover model systems but give a broad overview of the stress-responsive regulatory systems in a variety of bacteria, including medically important bacteria, where elucidation of certain aspects of these systems could lead to treatment strategies of the pathogens. Many of the regulatory systems being uncovered are specific, but there is also considerable “cross-talk” between different circuits. Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria is a comprehensive two-volume work bringing together both review and original research articles on key topics in stress and environmental control of gene expression in bacteria. Volume One contains key overview chapters, as well as content on one/two/three component regulatory systems and stress responses, sigma factors and stress responses, small non-coding RNAs and stress responses, toxin-antitoxin systems and stress responses, stringent response to stress, responses to UV irradiation, SOS and double stranded systems repair systems and stress, adaptation to both oxidative and osmotic stress, and desiccation tolerance and drought stress. Volume Two covers heat shock responses, chaperonins and stress, cold shock responses, adaptation to acid stress, nitrosative stress, and envelope stress, as well as iron homeostasis, metal resistance, quorum sensing, chemotaxis and biofilm formation, and viable but not culturable (VBNC) cells. Covering the full breadth of current stress and environmental control of gene expression studies and expanding it towards future advances in the field, these two volumes are a one-stop reference for (non) medical molecular geneticists interested in gene regulation under stress.
Download or read book RNA Infrastructure and Networks written by Lesley J. Collins and published by Springer Science & Business Media. This book was released on 2011-09-15 with total page 297 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNAs form complexes with proteins and other RNAs. The RNA‐infrastructure represents the spatiotemporal interaction of these proteins and RNAs in a cell‐wide network. RNA Infrastructure and Networks brings together these ideas to illustrate the scope of RNA‐based biology, and how connecting RNA mechanisms is a powerful tool to investigate regulatory pathways. This book is but a taste of the wide range of RNA‐based mechanisms that connect in the RNA infrastructure.
Download or read book The Perfect Slime written by Hans-Curt Flemming and published by IWA Publishing. This book was released on 2016-09-15 with total page 336 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Perfect Slime presents the latest state of knowledge and all aspects of the Extracellular Polymeric Substances, (EPS) matrix – from the ecological and health to the antifouling perspectives. The book brings together all the current material in order to expand our understanding of the functions, properties and characteristics of the matrix as well as the possibilities to strengthen or weaken it. The EPS matrix represents the immediate environment in which biofilm organisms live. From their point of view, this matrix has paramount advantages. It allows them to stay together for extended periods and form synergistic microconsortia, it retains extracellular enzymes and turns the matrix into an external digestion system and it is a universal recycling yard, it protects them against desiccation, it allows for intense communication and represents a huge genetic archive. They can remodel their matrix, break free and eventually, they can use it as a nutrient source. The EPS matrix can be considered as one of the emergent properties of biofilms and are a major reason for the success of this form of life. Nevertheless, they have been termed the “black matter of biofilms” for good reasons. First of all: the isolation methods define the results. In most cases, only water soluble EPS components are investigated; insoluble ones such as cellulose or amyloids are much less included. In particular in environmental biofilms with many species, it is difficult to impossible isolate, separate the various EPS molecules they are encased in and to define which species produced which EPS. The regulation and the factors which trigger or inhibit EPS production are still very poorly understood. Furthermore: bacteria are not the only microorganisms to produce EPS. Archaea, Fungi and algae can also form EPS. This book investigates the questions, What is their composition, function, dynamics and regulation? What do they all have in common?
Download or read book Microbial Biofilms written by Mahmoud Ghannoum and published by John Wiley & Sons. This book was released on 2015-10-01 with total page 608 pages. Available in PDF, EPUB and Kindle. Book excerpt: An examination of the research and translational application to prevent and treat biofilm-associated diseases In the decade since the first edition of Microbial Biofilms was published, the interest in this field has expanded, spurring breakthrough research that has advanced the treatment of biofilm-associated diseases. This second edition takes the reader on an exciting, extensive review of bacterial and fungal biofilms, ranging from basic molecular interactions to innovative therapies, with particular emphasis on the division of labor in biofilms, new approaches to combat the threat of microbial biofilms, and how biofilms evade the host defense. Chapters written by established investigators cover recent findings, and contributions from investigators new to the field provide unique and fresh insights. Specifically, Microbial Biofilms provides state-of-the-art research in the field of bacterial and fungal biofilms detailed descriptions of the in vitro and in vivo models available to evaluate microbial biofilms future areas of research and their translational and clinical applications Microbial Biofilms is a useful reference for researchers and clinicians. It will also provide insight in the dynamic field of microbial biofilms for graduate and postgraduate students.
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 Lasso Peptides written by Yanyan Li and published by Springer. This book was released on 2014-10-21 with total page 113 pages. Available in PDF, EPUB and Kindle. Book excerpt: Lasso peptides form a growing family of fascinating ribosomally-synthesized and post-translationally modified peptides produced by bacteria. They contain 15 to 24 residues and share a unique interlocked topology that involves an N-terminal 7 to 9-residue macrolactam ring where the C-terminal tail is threaded and irreversibly trapped. The ring results from the condensation of the N-terminal amino group with a side-chain carboxylate of a glutamate at position 8 or 9, or an aspartate at position 7, 8 or 9. The trapping of the tail involves bulky amino acids located in the tail below and above the ring and/or disulfide bridges connecting the ring and the tail. Lasso peptides are subdivided into three subtypes depending on the absence (class II) or presence of one (class III) or two (class I) disulfide bridges. The lasso topology results in highly compact structures that give to lasso peptides an extraordinary stability towards both protease degradation and denaturing conditions. Lasso peptides are generally receptor antagonists, enzyme inhibitors and/or antibacterial or antiviral (anti-HIV) agents. The lasso scaffold and the associated biological activities shown by lasso peptides on different key targets make them promising molecules with high therapeutic potential. Their application in drug design has been exemplified by the development of an integrin antagonist based on a lasso peptide scaffold. The biosynthesis machinery of lasso peptides is therefore of high biotechnological interest, especially since such highly compact and stable structures have to date revealed inaccessible by peptide synthesis. Lasso peptides are produced from a linear precursor LasA, which undergoes a maturation process involving several steps, in particular cleavage of the leader peptide and cyclization. The post-translational modifications are ensured by a dedicated enzymatic machinery, which is composed of an ATP-dependent cysteine protease (LasB) and a lactam synthetase (LasC) that form an enzymatic complex called lasso synthetase. Microcin J25, produced by Escherichia coli AY25, is the archetype of lasso peptides and the most extensively studied. To date only around forty lasso peptides have been isolated, but genome mining approaches have revealed that they are widely distributed among Proteobacteria and Actinobacteria, particularly in Streptomyces, making available a rich resource of novel lasso peptides and enzyme machineries towards lasso topologies.
Download or read book Physical Biology of the Cell written by Rob Phillips and published by Garland Science. This book was released on 2012-10-29 with total page 1089 pages. Available in PDF, EPUB and Kindle. Book excerpt: Physical Biology of the Cell is a textbook for a first course in physical biology or biophysics for undergraduate or graduate students. It maps the huge and complex landscape of cell and molecular biology from the distinct perspective of physical biology. As a key organizing principle, the proximity of topics is based on the physical concepts that
Download or read book Next Generation Sequencing written by Jerzy Kulski and published by BoD – Books on Demand. This book was released on 2016-01-14 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: Next generation sequencing (NGS) has surpassed the traditional Sanger sequencing method to become the main choice for large-scale, genome-wide sequencing studies with ultra-high-throughput production and a huge reduction in costs. The NGS technologies have had enormous impact on the studies of structural and functional genomics in all the life sciences. In this book, Next Generation Sequencing Advances, Applications and Challenges, the sixteen chapters written by experts cover various aspects of NGS including genomics, transcriptomics and methylomics, the sequencing platforms, and the bioinformatics challenges in processing and analysing huge amounts of sequencing data. Following an overview of the evolution of NGS in the brave new world of omics, the book examines the advances and challenges of NGS applications in basic and applied research on microorganisms, agricultural plants and humans. This book is of value to all who are interested in DNA sequencing and bioinformatics across all fields of the life sciences.
Download or read book DNA Methyltransferases Role and Function written by Albert Jeltsch and published by Springer. This book was released on 2016-11-08 with total page 537 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA methyltransferases are important enzymes in a broad range of organisms. Dysfunction of DNA methyltransferases in humans leads to many severe diseases, including cancer. This book focuses on the biochemical properties of these enzymes, describing their structures and mechanisms in bacteria, humans and other species, including plants, and also explains the biological processes of reading of DNA methylation and DNA demethylation. It covers many emerging aspects of the biological roles of DNA methylation functioning as an essential epigenetic mark and describes the role of DNA methylation in diseases. Moreover, the book explains modern technologies, like targeted rewriting of DNA methylation by designed DNA methyltransferases, as well as technological applications of DNA methyltransferases in DNA labelling. Finally, the book summarizes recent methods for the analysis of DNA methylation in human DNA. Overall, this book represents a comprehensive state-of-the-art- work and is a must-have for advanced researchers in the field of DNA methylation and epigenetics.
Download or read book Manipulating the Mouse Embryo written by Andras Nagy and published by Cold Spring Harbor, N.Y. : Cold Spring Harbor Laboratory Press. This book was released on 2003 with total page 784 pages. Available in PDF, EPUB and Kindle. Book excerpt: Provides background information and detailed protocols for developing a mouse colony and using the animals in transgenic and gene-targeting experiments. The protocols list the animals, equipment, and reagents required and step-by-step procedures. Topics include in vitro culture of preimplantation embryos, surgical procedures, the production of chimeras, and the analysis of genome alterations. The third edition adds protocols for cloning mice, modifying embryonic stem cells, intracytoplasmic sperm injection, and cryopreservation of embryos.
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 Hi C Data Analysis written by Silvio Bicciato and published by Humana. This book was released on 2022-09-04 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume details a comprehensive set of methods and tools for Hi-C data processing, analysis, and interpretation. Chapters cover applications of Hi-C to address a variety of biological problems, with a specific focus on state-of-the-art computational procedures adopted for the data analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Hi-C Data Analysis: Methods and Protocols aims to help computational and molecular biologists working in the field of chromatin 3D architecture and transcription regulation.
Download or read book Minimal Cells Design Construction Biotechnological Applications written by Alvaro R. Lara and published by Springer Nature. This book was released on 2019-12-04 with total page 233 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a comprehensive overview of the design, generation and characterization of minimal cell systems. Written by leading experts, it presents an in-depth analysis of the current issues and challenges in the field, including recent advances in the generation and characterization of reduced-genome strains generated from model organisms with relevance in biotechnology, and basic research such as Escherichia coli, Corynebacterium glutamicum and yeast. It also discusses methodologies, such as bottom-up and top-down genome minimization strategies, as well as novel analytical and experimental approaches to characterize and generate minimal cells. Lastly, it presents the latest research related to minimal cells of serveral microorganisms, e.g. Bacillus subtilis. The design of biological systems for biotechnological purposes employs strategies aimed at optimizing specific tasks. This approach is based on enhancing certain biological functions while reducing other capacities that are not required or that could be detrimental to the desired objective. A highly optimized cell factory would be expected to have only the capacity for reproduction and for performing the expected task. Such a hypothetical organism would be considered a minimal cell. At present, numerous research groups in academia and industry are exploring the theoretical and practical implications of constructing and using minimal cells and are providing valuable fundamental insights into the characteristics of minimal genomes, leading to an understanding of the essential gene set. In addition, research in this field is providing valuable information on the physiology of minimal cells and their utilization as a biological chassis to which useful biotechnological functions can be added.
Download or read book Symbiosis Cellular Molecular Medical and Evolutionary Aspects written by Malgorzata Kloc and published by Springer Nature. This book was released on 2020-12-02 with total page 616 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents a comprehensive overview of the latest developments in symbiosis research. It covers molecular, organellar, cellular, immunologic, genetic and evolutionary aspects of symbiotic interactions in humans and other model systems. The book also highlights new approaches to interdisciplinary research and therapeutic applications. Symbiosis refers to any mutually beneficial interaction between different organisms. The symbiotic origin of cellular organelles and the exchange of genetic material between hosts and their bacterial and viral symbionts have helped shaped the current diversity of life. Recently, symbiosis has gained a new level of recognition, due to the realization that all organisms function as a holobiome and that any kind of interference with the hosts influences their symbionts and vice versa, and can have profound consequences for the survival of both. For example, in humans, the microbiome, i.e., the entirety of all the microorganisms living in association with the intestines, oral cavity, urogenital system and skin, is partially inherited during pregnancy and influences the maturation and functioning of the human immune system, protects against pathogens and regulates metabolism. Symbionts also regulate cancer development, wound healing, tissue regeneration and stem cell function. The medical applications of this new realization are vast and largely uncharted. The composition and robustness of human symbionts could make them a valuable diagnostic tool for predicting impending diseases, and the manipulation of symbionts could yield new strategies for the treatment of incurable diseases.
