Download or read book Systems Biology Approaches for Host Pathogen Interaction Analysis written by Mohd. Tashfeen Ashraf and published by Elsevier. This book was released on 2024-02-16 with total page 317 pages. Available in PDF, EPUB and Kindle. Book excerpt: System Biology Approaches for Microbial Pathogenesis Interaction Analysis aids biological researchers to expand their research scope using piled up data generated through recent technological advancement. In addition, it also opens avenues for bioinformatics and computer science researchers to utilize their expertise in biological meaningful ways. It also covers network biology approaches to decipher complex multiple host-pathogen interactions in addition to giving valuable coverage of artificial intelligence. The host-pathogen interactions are generally considered as highly specific interactions leading to a variety of consequences. The utilization of data science approaches has revolutionized scientific research including host-pathogen interaction analyses. Data science approaches coupled with network biology has taken host-pathogen interaction analysis from specific interaction to a new paradigm of understanding consequences of these interaction in the biological network. Unfortunately, basic biological researchers are mostly unaware of these advancements. In contrast, data scientists are not familiar with biological aspects of such data. System Biology Approaches for Microbial Pathogenesis Interaction Analysis will bridge these gaps through a new paradigm of understanding consequences of interaction in biological networks. Covers network biology approaches to decipher complex multiple host-pathogen interactions Gives the biological researcher insights into artificial intelligence, providing an additional competitive edge Provides a new paradigm for understanding the consequences of interactions in biological networks

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 Systems Biology Approaches Prevention Diagnosis and Understanding Mechanisms of Complex Diseases written by Sanket Joshi and published by Springer Nature. This book was released on with total page 587 pages. Available in PDF, EPUB and Kindle. Book excerpt:

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 Biology of Tuberculosis written by Johnjoe McFadden and published by Springer Science & Business Media. This book was released on 2012-12-09 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book starts with a general introduction into the relevance of systems biology for understanding tuberculosis. This will be followed by several chapters which describe the application of systems biology to various aspects of the study of the pathogen, Mycobacterium tuberculosis, and its interaction with the host. The book provides the reader with an account of how the new science of systems biology is providing novel insights into the ancient scourge of tuberculosis. It will also describe how systems biology can be applied to the control of tuberculosis, including the development of new treatments, vaccines and diagnostics.

Download or read book A Systems Biology Approach to Investigating Host pathogen Interactions in Infection with Burkholderia Pseudomallei written by Deniz Cizmeci and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Host Pathogen Interactions written by Carlos Medina and published by . This book was released on 2018 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed volume explores numerous multidisciplinary approaches employed to analyze the role of different molecules or strategies used by different guests to survive inside hosts. Divided into several sections, the book delves into animal-pathogen interaction, microbe-microbe interaction, as well as plant-pathogen interaction. Written for the highly successful Methods in Molecular Biology series, chapters include brief 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.uthoritative and practical, Host-Pathogen Interactions: Methods and Protocols provides many molecular and bioinformatics techniques currently in use at reputed laboratories in countries all around the world, vital for many kinds of host-pathogen interactions studies.

Download or read book Systems Biology of Microbial Infection written by Reinhard Guthke and published by Frontiers E-books. This book was released on with total page 139 pages. Available in PDF, EPUB and Kindle. Book excerpt: The systems biology of microbial infections aims at describing and analysing the confrontation of the host with bacterial and fungal pathogens. It intends to understand and to model the interaction of the host, in particular the immune system of humans or animals, with components of pathogens. This comprises experimental studies that provide spatio-temporal data from monitoring the response of host and pathogenic cells to perturbations or when interacting with each other, as well as the integrative analysis of genome-wide data from both the host and the pathogen. In perspective, the host-pathogen interaction should be described by a combination of spatio-temporal models with interacting molecular networks of the host and the pathogen. The aim is to unravel the main mechanisms of pathogenicity, to identify diagnostic biomarkers and potential drug targets, and to explore novel strategies for personalized therapy by computer simulations. Some microorganisms are part of the normal microbial flora, existing either in a mutualistic or commensal relationship with the host. Microorganisms become pathogenic if they posses certain physiological characteristics and virulence determinants as well as capabilities for immune evasion. Despite the different pathogenesis of infections, there are several common traits: (1) Before infection, pathogens must be able to overcome (epithelial) barriers. The infection starts by adhesion and colonization and is followed by entering of the pathogen into the host through the mucosa or (injured) skin. (2) Next, infection arises if the pathogen multiplies and overgrows the normal microbial flora, either at the place of entrance or in deeper tissue layers or organs. (3) After the growth phase, the pathogen damages the host’s cells, tissues and organs by producing toxins or destructive enzymes. Thus, systems biology of microbial infection comprises all levels of the pathogen and the host’s immune system. The investigation may start with the pathogen, its adhesion and colonization at the host, its interaction with host cell types e.g. epithelia cells, dendritic cells, macrophages, neutrophils, natural killer cells, etc. Because infection diseases are mainly found in patients with a weakened immune system, e.g. reduced activities of immune effector cells or defects in the epithelial barriers, systems biology of infection can also start with modelling of the immune defence including innate and adaptive immunity. Systems biological studies comprise both experimental and theoretical approaches. The experimental studies may be dedicated to reveal the relevance of certain genes or proteins in the above mentioned processes on the side of the pathogen and/or the host by applying functional and biochemical analyses based on knock-out mutants and knock- down experiments. At the theoretical, i.e. mathematical and computational, side systems biology of microbial infection comprises: (1) modelling of molecular mechanisms of bacterial or fungal infections, (2) modelling of non-protective and protective immune defences against microbial pathogens to generate information for possible immune therapy approaches, (3) modelling of infection dynamics and identification of biomarkers for diagnosis and for individualized therapy, (4) identifying essential virulence determinants and thereby predicting potential drug targets.

Download or read book Recent Advances on Model Hosts written by Eleftherios Mylonakis and published by Springer Science & Business Media. This book was released on 2011-12-01 with total page 135 pages. Available in PDF, EPUB and Kindle. Book excerpt: Most studies of bacterial or fungal infectious diseases focus separately on the pathogenic microbe, the host response, or the characterization of therapeutic compounds. Compartmentalization of pathogenesis-related research into an analysis of the “pathogen”, the “host,” or the “antimicrobial compound” has largely been dictated by the lack of model systems in which all of these approaches can be used simultaneously, as well as by the traditional view that microbiology, immunology, and chemical biology and pharmacology are separate disciplines. An increasing number of workers from different fields have turned to insects, fish, worms and other model hosts as facile, ethically expedient, relatively simple, and inexpensive hosts to model a variety of human infectious diseases and to study host responses and innate immunity. Because many of these hosts are genetically tractable, they can be used in conjunction with an appropriate pathogen to facilitate the discovery of novel features of the host innate immune response. This book provides a series of reports from the 1st International Conference on Model Hosts. This first of its kind meeting focused on invertebrate, vertebrate and amoeboid systems used for the study of host-pathogen interactions, virulence and immunity, as well as on the relevance of these pathogenesis systems and mammalian models. Importantly, a common, fundamental set of molecular mechanisms is employed by a significant number of microbial pathogens against a widely divergent array of metazoan hosts. Moreover, the evolutionarily conserved immune responses of these model hosts have contributed important insights to our understanding of the innate immune response of mammals. This book provides a series of reports from the 1st International Conference on Model Hosts. This first of its kind meeting focused on invertebrate, vertebrate and amoeboid systems used for the study of host-pathogen interactions, virulence and immunity, as well as on the relevance of these pathogenesis systems and mammalian models. Importantly, a common, fundamental set of molecular mechanisms is employed by a significant number of microbial pathogens against a widely divergent array of metazoan hosts. Moreover, the evolutionarily conserved immune responses of these model hosts have contributed important insights to our understanding of the innate immune response of mammals.

Download or read book Systems Biology written by Michael G. Katze and published by Springer Science & Business Media. This book was released on 2013-01-04 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: First, systems biology is an inter-disciplinary approach, requiring the combined talents of biologists, mathematicians, and computer scientists. Second, systems biology is holistic, with the goal of obtaining a comprehensive understanding of the workings of biological systems. This is achieved through the acquisition of massive amounts of data by high-throughput technologies—oligonucleotide microarrays, mass spectrometry, and next-generation sequencing—and the analysis of this data through sophisticated mathematical algorithms. It is perhaps the use of mathematics, to integrate abundant and diverse types of data and to generate models of interconnected molecular networks, that best characterizes systems biology.

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 Microbial Interventions in Agriculture and Environment written by Dhananjaya Pratap Singh and published by Springer Nature. This book was released on 2019-11-09 with total page 491 pages. Available in PDF, EPUB and Kindle. Book excerpt: Microbial communities and their multi-functionalities play a crucial role in the management of soil and plant health, and thus help in managing agro-ecology, the environment and agriculture. Microorganisms are key players in N-fixation, nutrient acquisition, carbon sequestration, plant growth promotion, pathogen suppression, induced systemic resistance and tolerance against stresses, and these parameters are used as indicators of improved crop productivity and sustainable soil health. Beneficial belowground microbial interactions in the rhizosphere help plants combat abiotic challenges in the unfavourable environmental conditions of native soils. These microorganisms and their products offer potential solutions for agriculture in problematic areas since they are able to degrade xenobiotic compounds, pesticides and toxic chemicals and help remediate heavy metals in the rhizosphere and so make deteriorated soils suitable for crop production. This book compiles the latest research on the role of microbes in the rhizosphere and agro-ecology, covering interaction mechanisms, microbe-mediated crop production, plant and soil health management, food and nutrition, nutrient recycling, land reclamation, clean water systems, agro-waste management, biodegradation, bioremediation, biomass and bioenergy, sanitation and rural livelihood security. It is a comprehensive reference resource for agricultural activists, policymakers, environmentalists and advisors working for governments, non-governmental organizations and industries, helping them update their knowledge of this important, but often neglected, research area.

Download or read book Applications of RNA Seq in Biology and Medicine written by Irina Vlasova-St. Louis and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book evaluates and comprehensively summarizes the scientific findings that have been achieved through RNA-sequencing (RNA-Seq) technology. RNA-Seq transcriptome profiling of healthy and diseased tissues allows FOR understanding the alterations in cellular phenotypes through the expression of differentially spliced RNA isoforms. Assessment of gene expression by RNA-Seq provides new insight into host response to pathogens, drugs, allergens, and other environmental triggers. RNA-Seq allows us to accurately capture all subtypes of RNA molecules, in any sequenced organism or single-cell type, under different experimental conditions. Merging genomics and transcriptomic profiling provides novel information underlying causative DNA mutations. Combining RNA-Seq with immunoprecipitation and cross-linking techniques is a clever multi-omics strategy assessing transcriptional, post-transcriptional and post-translational levels of gene expression regulation.

Download or read book Fungal Diseases in Animals written by Arti Gupta and published by Springer Nature. This book was released on 2021-06-22 with total page 191 pages. Available in PDF, EPUB and Kindle. Book excerpt: The importance of fungal infections in both human and animals has increased over the last few decades. This book presents an overview of the different categories of fungal infections that can be encountered in animals (including lower vertebrates) originating from environmental sources with or without transmission to humans. In addition, the endemic infections with indirect transmission from the environment, the zoophilic fungal pathogens with near-direct transmission, the zoonotic fungi that can be directly transmitted from animals to humans, mycotoxicoses and antifungal resistance in animals will also be discussed. This book includes case studies and reviews the current state of knowledge on the mechanism of fungal attraction, recognition, infection, extracellular hydrolytic enzymes and pathogenesis of nematophagous fungi. The book also covers diagnostics, fungal formulations, as well as prevention methods. It discusses strategies to access the fungal pathogen groups, metagenomic analyses, genomics, secretomics, metabolomics, proteomics and transcriptomics. In addition, pathogen description, understanding, distribution and recent research results are provided.

Download or read book Molecular Biology of The Cell written by Bruce Alberts 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 Protein Protein Interaction Regulators written by Siddhartha Roy and published by Royal Society of Chemistry. This book was released on 2020-12-15 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: New genomic information has revealed the crucial role that protein-protein interactions (PPIs) play in regulating numerous cellular functions. Aberrant forms of these interactions are common in numerous diseases and thus PPIs have emerged as a vast class of critical drug targets. Despite the importance of PPIs in biology, it has been extremely challenging to convert targets into therapeutics and targeting PPIs had long been considered a very difficult task. However, over the past decade the field has advanced with increasing growth in the number of successful PPI regulators. Protein-Protein Interaction Regulators surveys the latest advances in the structural understanding of PPIs as well as recent developments in modulator discovery.

Download or read book Bacterial Evasion of Host Immune Responses written by Brian Henderson and published by Cambridge University Press. This book was released on 2003-04-28 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: Table of contents