Download or read book Development of Computational Tools and Resources for Systems Biology of Bacterial Pathogens written by Ranjit Kumar and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Bacterial pathogens are a major cause of diseases in human, agricultural plants and farm animals. Even after decades of research they remain a challenge to health care as they are known to rapidly evolve and develop resistance to the existing drugs. Systems biology is an emerging area of research where all of the components of the system, their interactions, and the dynamics can be studied in a comprehensive, quantitative, and integrative fashion to generate predictive models. When applied to bacterial pathogenesis, systems biology approaches will help identify potential novel molecular targets for drug discovery. A pre-requisite for conducting systems analysis is the identification of the building blocks of the system i.e. individual components of the system (structural annotation), identification of their functions (functional annotation) and identification of the interactions among the individual components (interaction prediction). In the context of bacterial pathogenesis, it is necessary to identify the host-pathogen interactions. This dissertation work describes computational resources that enable comprehensive systems level study of host pathogen system to enhance our understanding of bacterial pathogenesis. It specifically focuses on improving the structural and functional annotation of pathogen genomes as well as identifying host-pathogen interactions at a genome scale. The novel contributions of this dissertation towards systems biology of bacterial pathogens include three computational tools/resources. "TAAPP" (Tiling array analysis pipeline for prokaryotes) is a web based tool for the analysis of whole genome tiling array data for bacterial pathogens. TAAPP helps improve the structural annotation of bacterial genomes. "ISO-IEA" (Inferred from sequence orthology - Inferred from electronic annotation) is a tool that can be used for the functional annotation of any sequenced genome. "HPIDB" (Host pathogen interaction database) is developed with data a mining capability that includes host-pathogen interaction prediction. The new knowledge gained due to the implementation of these tools is the description of the non coding RNA as well as a computationally predicted host-pathogen interaction network for the human respiratory pathogen Streptococcus pneumoniae. In summary, the computation tools and resources developed in this dissertation study will enable building systems biology models of bacterial pathogens.
Download or read book Computational Systems Biology of Pathogen Host Interactions written by Saliha Durmuş and published by Frontiers Media SA. This book was released on 2016-05-30 with total page 200 pages. Available in PDF, EPUB and Kindle. Book excerpt: A thorough understanding of pathogenic microorganisms and their interactions with host organisms is crucial to prevent infectious threats due to the fact that Pathogen-Host Interactions (PHIs) have critical roles in initiating and sustaining infections. Therefore, the analysis of infection mechanisms through PHIs is indispensable to identify diagnostic biomarkers and next-generation drug targets and then to develop strategic novel solutions against drug-resistance and for personalized therapy. Traditional approaches are limited in capturing mechanisms of infection since they investigate hosts or pathogens individually. On the other hand, the systems biology approach focuses on the whole PHI system, and is more promising in capturing infection mechanisms. Here, we bring together studies on the below listed sections to present the current picture of the research on Computational Systems Biology of Pathogen-Host Interactions: - Computational Inference of PHI Networks using Omics Data - Computational Prediction of PHIs - Text Mining of PHI Data from the Literature - Mathematical Modeling and Bioinformatic Analysis of PHIs Computational Inference of PHI Networks using Omics Data Gene regulatory, metabolic and protein-protein networks of PHI systems are crucial for a thorough understanding of infection mechanisms. Great advances in molecular biology and biotechnology have allowed the production of related omics data experimentally. Many computational methods are emerging to infer molecular interaction networks of PHI systems from the corresponding omics data. Computational Prediction of PHIs Due to the lack of experimentally-found PHI data, many computational methods have been developed for the prediction of pathogen-host protein-protein interactions. Despite being emerging, currently available experimental PHI data are far from complete for a systems view of infection mechanisms through PHIs. Therefore, computational methods are the main tools to predict new PHIs. To this end, the development of new computational methods is of great interest. Text Mining of PHI Data from Literature Despite the recent development of many PHI-specific databases, most data relevant to PHIs are still buried in the biomedical literature, which demands for the use of text mining techniques to unravel PHIs hidden in the literature. Only some rare efforts have been performed to achieve this aim. Therefore, the development of novel text mining methods specific for PHI data retrieval is of key importance for efficient use of the available literature. Mathematical Modeling and Bioinformatic Analysis of PHIs After the reconstruction of PHI networks experimentally and/or computationally, their mathematical modeling and detailed computational analysis is required using bioinformatics tools to get insights on infection mechanisms. Bioinformatics methods are increasingly applied to analyze the increasing amount of experimentally-found and computationally-predicted PHI data.
Download or read book Biodefense in the Age of Synthetic Biology written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2019-01-05 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt: Scientific advances over the past several decades have accelerated the ability to engineer existing organisms and to potentially create novel ones not found in nature. Synthetic biology, which collectively refers to concepts, approaches, and tools that enable the modification or creation of biological organisms, is being pursued overwhelmingly for beneficial purposes ranging from reducing the burden of disease to improving agricultural yields to remediating pollution. Although the contributions synthetic biology can make in these and other areas hold great promise, it is also possible to imagine malicious uses that could threaten U.S. citizens and military personnel. Making informed decisions about how to address such concerns requires a realistic assessment of the capabilities that could be misused. Biodefense in the Age of Synthetic Biology explores and envisions potential misuses of synthetic biology. This report develops a framework to guide an assessment of the security concerns related to advances in synthetic biology, assesses the levels of concern warranted for such advances, and identifies options that could help mitigate those concerns.
Download or read book Computational Systems Biology of Pathogen Host Interactions written by and published by . This book was released on 2016 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: A thorough understanding of pathogenic microorganisms and their interactions with host organisms is crucial to prevent infectious threats due to the fact that Pathogen-Host Interactions (PHIs) have critical roles in initiating and sustaining infections. Therefore, the analysis of infection mechanisms through PHIs is indispensable to identify diagnostic biomarkers and next-generation drug targets and then to develop strategic novel solutions against drug-resistance and for personalized therapy. Traditional approaches are limited in capturing mechanisms of infection since they investigate hosts or pathogens individually. On the other hand, the systems biology approach focuses on the whole PHI system, and is more promising in capturing infection mechanisms. Here, we bring together studies on the below listed sections to present the current picture of the research on Computational Systems Biology of Pathogen-Host Interactions: - Computational Inference of PHI Networks using Omics Data - Computational Prediction of PHIs - Text Mining of PHI Data from the Literature - Mathematical Modeling and Bioinformatic Analysis of PHIs Computational Inference of PHI Networks using Omics Data Gene regulatory, metabolic and protein-protein networks of PHI systems are crucial for a thorough understanding of infection mechanisms. Great advances in molecular biology and biotechnology have allowed the production of related omics data experimentally. Many computational methods are emerging to infer molecular interaction networks of PHI systems from the corresponding omics data. Computational Prediction of PHIs Due to the lack of experimentally-found PHI data, many computational methods have been developed for the prediction of pathogen-host protein-protein interactions. Despite being emerging, currently available experimental PHI data are far from complete for a systems view of infection mechanisms through PHIs. Therefore, computational methods are the main tools to predict new PHIs. To this end, the development of new computational methods is of great interest. Text Mining of PHI Data from Literature Despite the recent development of many PHI-specific databases, most data relevant to PHIs are still buried in the biomedical literature, which demands for the use of text mining techniques to unravel PHIs hidden in the literature. Only some rare efforts have been performed to achieve this aim. Therefore, the development of novel text mining methods specific for PHI data retrieval is of key importance for efficient use of the available literature. Mathematical Modeling and Bioinformatic Analysis of PHIs After the reconstruction of PHI networks experimentally and/or computationally, their mathematical modeling and detailed computational analysis is required using bioinformatics tools to get insights on infection mechanisms. Bioinformatics methods are increasingly applied to analyze the increasing amount of experimentally-found and computationally-predicted PHI data. Acknowledgements: We, editors of this e-book, acknowledge Emrah Nikerel (Yeditepe University, Turkey) and Arzucan Özgür (Bogaaziçi University, Turkey) for their contributions during the initiation of the Research Topic.
Download or read book Systems Microbiology written by Brian Douglas Robertson and published by Caister Academic Press Limited. This book was released on 2012 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems biology is the study of the dynamic interactions of more than one component in a biological system in order to understand and predict the behavior of the system as a whole. Systems biology is a rapidly expanding discipline fuelled by the 'omics' era and new technological advances that have increased the precision of data. A focus on simple single cell organisms, such as bacteria, aids tractability and means that systems microbiology is a rapidly maturing science. Recommended for all microbiology laboratories, this book contains cutting-edge reviews by world-leading experts on the systems biology of microorganisms. As well as covering theoretical approaches and mathematical modeling, the book includes case studies on single microbial species of bacteria and archaea, and it explores the systems analysis of microbial phenomena, such as chemotaxis and phagocytosis. The topics covered include: the mathematical models for systems biology * systems biology of Escherichia coli metabolism * bacterial chemotaxis * systems biology of infection * host-microbe interactions * phagocytosis * system-level study of metabolism in Mycobacterium tuberculosis * systems biology of Sulfolobus.
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 Handbook of Research on Computational and Systems Biology written by Limin Angela Liu and published by IGI Global. This book was released on 2011 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This book offers information on the state-of-the-art development in the fields of computational biology and systems biology, presenting methods, tools, and applications of these fields by many leading experts around the globe"--Provided by publisher.
Download or read book Bioinformatics and Systems Biology written by Frederick Marcus and published by Springer Science & Business Media. This book was released on 2008-07-22 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt: Collaborative research in bioinformatics and systems biology is a key element of modern biology and health research. This book highlights and provides access to many of the methods, environments, results and resources involved, including integral laboratory data generation and experimentation and clinical activities. Collaborative projects embody a research paradigm that connects many of the top scientists, institutions, their resources and research worldwide, resulting in first-class contributions to bioinformatics and systems biology. Central themes include describing processes and results in collaborative research projects using computational biology and providing a guide for researchers to access them. The book is also a practical guide on how science is managed. It shows how collaborative researchers are putting results together in a way accessible to the entire biomedical community.
Download or read book Evolutionary Systems Biology written by Orkun S. Soyer and published by Springer Science & Business Media. This book was released on 2012-07-23 with total page 459 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book aims to introduce the reader to the emerging field of Evolutionary Systems Biology, which approaches classical systems biology questions within an evolutionary framework. An evolutionary approach might allow understanding the significance of observed diversity, uncover “evolutionary design principles” and extend predictions made in model organisms to others. In addition, evolutionary systems biology can generate new insights into the adaptive landscape by combining molecular systems biology models and evolutionary simulations. This insight can enable the development of more detailed mechanistic evolutionary hypotheses.
Download or read book The New Science of Metagenomics written by National Research Council and published by National Academies Press. This book was released on 2007-06-24 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: Although we can't usually see them, microbes are essential for every part of human life-indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying-one at a time-the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.
Download or read book Bioinformatics written by David Edwards and published by Springer. This book was released on 2010-04-29 with total page 451 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioinformatics is a relatively new field of research. It evolved from the requirement to process, characterize, and apply the information being produced by DNA sequencing technology. The production of DNA sequence data continues to grow exponentially. At the same time, improved bioinformatics such as faster DNA sequence search methods have been combined with increasingly powerful computer systems to process this information. Methods are being developed for the ever more detailed quantification of gene expression, providing an insight into the function of the newly discovered genes, while molecular genetic tools provide a link between these genes and heritable traits. Genetic tests are now available to determine the likelihood of suffering specific ailments and can predict how plant cultivars may respond to the environment. The steps in the translation of the genetic blueprint to the observed phenotype is being increasingly understood through proteome, metabolome and phenome analysis, all underpinned by advances in bioinformatics. Bioinformatics is becoming increasingly central to the study of biology, and a day at a computer can often save a year or more in the laboratory. The volume is intended for graduate-level biology students as well as researchers who wish to gain a better understanding of applied bioinformatics and who wish to use bioinformatics technologies to assist in their research. The volume would also be of value to bioinformatics developers, particularly those from a computing background, who would like to understand the application of computational tools for biological research. Each chapter would include a comprehensive introduction giving an overview of the fundamentals, aimed at introducing graduate students and researchers from diverse backgrounds to the field and bring them up-to-date on the current state of knowledge. To accommodate the broad range of topics in applied bioinformatics, chapters have been grouped into themes: gene and genome analysis, molecular genetic analysis, gene expression analysis, protein and proteome analysis, metabolome analysis, phenome data analysis, literature mining and bioinformatics tool development. Each chapter and theme provides an introduction to the biology behind the data describes the requirements for data processing and details some of the methods applied to the data to enhance biological understanding.
Download or read book Microbiome Host Interactions written by D. Dhanasekaran and published by CRC Press. This book was released on 2021-04-01 with total page 863 pages. Available in PDF, EPUB and Kindle. Book excerpt: Microbiota are a promising and fascinating subject in biology because they integrate the microbial communities in humans, animals, plants, and the environment. In humans, microbiota are associated with the gut, skin, and genital, oral, and respiratory organs. The plant microbial community is referred to as "holobiont," and it is influential in the maintenance and health of plants, which themselves play a role in animal health and the environment. The contents of Microbiome-Host Interactions cover all areas as well as new research trends in the fields of plant, animal, human, and environmental microbiome interactions. The book covers microbiota in polar soil environments, in health and disease, in Caenorhabditis elegans, and in agroecosystems, as well as in rice root and actinorhizal root nodules, speleothems, and marine shallow-water hydrothermal vents. Moreover, this book provides comprehensive accounts of advanced next-generation DNA sequencing, metagenomic techniques, high-throughput 16S rRNA sequencing, and understanding nucleic acid sequence data from fungal, algal, viral, bacterial, cyanobacterial, actinobacterial, and archaeal communities using QIIME software (Quantitative Insights into Microbial Ecology). FEATURES Summarizes recent insight in microbiota and host interactions in distinct habitats, including Antarctic, hydrothermal vents, speleothems, oral, skin, gut, feces, reproductive tract, soil, root, root nodules, forests, and mangroves Illustrates the high-throughput amplicon sequencing, computational techniques involved in the microbiota analysis, downstream analysis and visualization, and multivariate analysis commonly used for microbiome analysis Describes probiotics and prebiotics in the composition of the gut microbiota, skin microbiome impact in dermatologic disease prevention, and microbial communities in the reproductive tract of humans and animals Presents information in a reachable way for students, teachers, researchers, microbiologists, computational biologists, and other professionals who are interested in strengthening or enlarging their knowledge about microbiome analysis with next-generation DNA sequencing in the different branches of the sciences
Download or read book The Social Biology of Microbial Communities written by Institute of Medicine and published by National Academies Press. This book was released on 2013-01-10 with total page 633 pages. Available in PDF, EPUB and Kindle. Book excerpt: Beginning with the germ theory of disease in the 19th century and extending through most of the 20th century, microbes were believed to live their lives as solitary, unicellular, disease-causing organisms . This perception stemmed from the focus of most investigators on organisms that could be grown in the laboratory as cellular monocultures, often dispersed in liquid, and under ambient conditions of temperature, lighting, and humidity. Most such inquiries were designed to identify microbial pathogens by satisfying Koch's postulates.3 This pathogen-centric approach to the study of microorganisms produced a metaphorical "war" against these microbial invaders waged with antibiotic therapies, while simultaneously obscuring the dynamic relationships that exist among and between host organisms and their associated microorganisms-only a tiny fraction of which act as pathogens. Despite their obvious importance, very little is actually known about the processes and factors that influence the assembly, function, and stability of microbial communities. Gaining this knowledge will require a seismic shift away from the study of individual microbes in isolation to inquiries into the nature of diverse and often complex microbial communities, the forces that shape them, and their relationships with other communities and organisms, including their multicellular hosts. On March 6 and 7, 2012, the Institute of Medicine's (IOM's) Forum on Microbial Threats hosted a public workshop to explore the emerging science of the "social biology" of microbial communities. Workshop presentations and discussions embraced a wide spectrum of topics, experimental systems, and theoretical perspectives representative of the current, multifaceted exploration of the microbial frontier. Participants discussed ecological, evolutionary, and genetic factors contributing to the assembly, function, and stability of microbial communities; how microbial communities adapt and respond to environmental stimuli; theoretical and experimental approaches to advance this nascent field; and potential applications of knowledge gained from the study of microbial communities for the improvement of human, animal, plant, and ecosystem health and toward a deeper understanding of microbial diversity and evolution. The Social Biology of Microbial Communities: Workshop Summary further explains the happenings of the workshop.
Download or read book Bacterial Pathogenesis written by Brenda A. Wilson and published by John Wiley & Sons. This book was released on 2020-08-11 with total page 683 pages. Available in PDF, EPUB and Kindle. Book excerpt: This highly anticipated update of the acclaimed textbook draws on the latest research to give students the knowledge and tools to explore the mechanisms by which bacterial pathogens cause infections in humans and animals. Written in an approachable and engaging style, the book uses illustrative examples and thought-provoking exercises to inspire students with the potential excitement and fun of scientific discovery. Completely revised and updated, and for the first time in stunning full-color, Bacterial Pathogenesis: A Molecular Approach, Fourth Edition, builds on the core principles and foundations of its predecessors while expanding into new concepts, key findings, and cutting-edge research, including new developments in the areas of the microbiome and CRISPR as well as the growing challenges of antimicrobial resistance. All-new detailed illustrations help students clearly understand important concepts and mechanisms of the complex interplay between bacterial pathogens and their hosts. Study questions at the end of each chapter challenge students to delve more deeply into the topics covered, and hone their skills in reading, interpreting, and analyzing data, as well as devising their own experiments. A detailed glossary defines and expands on key terms highlighted throughout the book. Written for advanced undergraduate, graduate, and professional students in microbiology, bacteriology, and pathogenesis, this text is a must-have for anyone looking for a greater understanding of virulence mechanisms across the breadth of bacterial pathogens.
Download or read book Microbial Biofilms written by Hilary M. Lappin-Scott and published by Cambridge University Press. This book was released on 2003-09-18 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biochemistry and ecology of biofilms from industrial, medical and other viewpoints.
Download or read book The Pangenome written by Hervé Tettelin and published by Springer Nature. This book was released on 2020-04-30 with total page 311 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book’s respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.
Download or read book Protein Secretion in Bacteria written by Maria Sandkvist and published by John Wiley & Sons. This book was released on 2020-07-02 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein transport into and across membranes is a fundamental process in bacteria that touches upon and unites many areas of microbiology, including bacterial cell physiology, adhesion and motility, nutrient scavenging, intrabacterial signaling and social behavior, toxin deployment, interbacterial antagonism and collaboration, host invasion and disruption, and immune evasion. A broad repertoire of mechanisms and macromolecular machines are required to deliver protein substrates across bacterial cell membranes for intended effects. Some machines are common to most, if not all bacteria, whereas others are specific to Gram-negative or Gram-positive species or species with unique cell envelope properties such as members of Actinobacteria and Spirochetes. Protein Secretion in Bacteria, authored and edited by an international team of experts, draws together the many distinct functions and mechanisms involved in protein translocation in one concise tome. This comprehensive book presents updated information on all aspects of bacterial protein secretion encompassing: Individual secretory systems–Sec, Tat, and T1SS through the newly discovered T9SS Mechanisms, structures, and functions of bacterial secretion systems Lipoprotein sorting pathways, outer membrane vesicles, and the sortase system Structures and roles of surface organelles, including flagella, pili, and curli Emerging technologies and translational implications Protein Secretion in Bacteria serves as both an introductory guide for students and postdocs and a ready reference for seasoned researchers whose work touches on protein export and secretion. This volume synthesizes the diversity of mechanisms of bacterial secretion across the microbial world into a digestible resource to stimulate new research, inspire continued identification and characterization of novel systems, and bring about new ways to manipulate these systems for biotechnological, preventative, and therapeutic applications.
