Computational Modeling Of Virulence Genes Expression

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Computational Modeling Of Virulence Genes Expression

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Author : Shiny Martis Badiadka
language : en
Publisher:
Release Date : 2020

Computational Modeling Of Virulence Genes Expression written by Shiny Martis Badiadka and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020 with categories.

Plant pathogens are a major threat to food security all around the world. Virulence genes enable the pathogens to disease the host and pose threats. We study and computationally model the expression of virulence in pathogens. The pel genes, a major virulence factor in pectinolytic bacteria which infect plants and cause soft rot disease. The Pel enzymes released by the pathogen result in the maceration of tissue in crops and facilitate pathogenesis. We model the pel genes in our model organism Dickeya dadantii. We study pelD/E genes which encode proteins with similar enzymatic activities, but also share the same set of transcriptional regulators, thus raising the question of the benefit of this duplication and the specific role of these two genes. We model their expression with respect to the KdgR repressor and CRP activator. We develop a quantitative dynamic kinetic model of this process that reproduces the observed behavior of the two genes and explains their specific role in the infection. The regulatory part of the model is based on experimental values, and fitted kinetic parameters are subjected to systematic evaluation. The model is robust and has multiple applications for studying the pathogenesis of pectinolytic bacteria. In addition, we explore the instance of carbon catabolite repression observed during the regulation of virulence genes Dickeya dadantii. The novel antibiotic seconeolitsin is characterized in the gram negative model organism Dickeya dadantii. Growth kinetics and MIC studies are carried out. The variations in the level of supercoiling in the presence of seconeolitsin and novobiocin are quantified and analyzed. The effect of supercoiling on the expression of genes, especially the pelE gene is studied using the novel antibiotic seconeolitsin. The study explores the role of supercoiling as a gene regulator.

Microbial Biofilms

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Author : Hilary M. Lappin-Scott
language : en
Publisher: Cambridge University Press
Release Date : 2003-09-18

Microbial Biofilms written by Hilary M. Lappin-Scott and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2003-09-18 with Medical categories.

Biochemistry and ecology of biofilms from industrial, medical and other viewpoints.

The Pangenome

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Author : Hervé Tettelin
language : en
Publisher: Springer Nature
Release Date : 2020-04-30

The Pangenome written by Hervé Tettelin and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-04-30 with Science categories.

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.

Computational Systems Biology And Bioinformatics

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Author : Jonathan H. Chan
language : en
Publisher: Springer
Release Date : 2010-11-08

Computational Systems Biology And Bioinformatics written by Jonathan H. Chan and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-11-08 with Science categories.

Ussery.

Computational Methods To Analyze Rna Data For Human Diseases

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Author : Min Zeng
language : en
Publisher: Frontiers Media SA
Release Date : 2023-09-25

Computational Methods To Analyze Rna Data For Human Diseases written by Min Zeng and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-09-25 with Science categories.

Salmonella Host Pathogen Interactions

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Author : John S. Gunn
language : en
Publisher: Frontiers Media SA
Release Date : 2011-11-01

Salmonella Host Pathogen Interactions written by John S. Gunn and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-11-01 with categories.

This Research Topic provides updated information on several important areas of Salmonella host cell interaction. Articles begin on topics outside of the host cell, examining the transit to and interaction with the epithelium, including pattern recognition. Once inside the host cell, topics of manuscripts include examination of the Salmonella-containing vacuole, its ability to resist intracellular killing, and the bacterial gene induction within the host cells responsible for survival. Finally, knowledge concerning carriage in and transmission from the infected host are discussed.This Research Topic provides updated information on several important areas of Salmonella host cell interaction. Articles begin on topics outside of the host cell, examining the transit to and interaction with the epithelium, including pattern recognition. Once inside the host cell, topics of manuscripts include examination of the Salmonella-containing vacuole, its ability to resist intracellular killing, and the bacterial gene induction within the host cells responsible for survival. Finally, knowledge concerning carriage in and transmission from the infected host are discussed.

Computational Methods In Systems Biology

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Author : Ezio Bartocci
language : en
Publisher: Springer
Release Date : 2016-09-03

Computational Methods In Systems Biology written by Ezio Bartocci and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-09-03 with Computers categories.

This book constitutes the refereed proceedings of the 14th International Conference on Computational Methods in Systems Biology, CMSB 2016, held in Cambridge, UK, in September 2016. The 20 full papers, 3 tool papers and 9 posters presented were carefully reviewed and selected from 37 regular paper submissions. The topics include formalisms for modeling biological processes; models and their biological applications; frameworks for model verification, validation, analysis, and simulation of biological systems; high-performance computational systems biology and parallel implementations; model inference from experimental data; model integration from biological databases; multi-scale modeling and analysis methods; and computational approaches for synthetic biology.

Computational Systems Biology Of Pathogen Host Interactions

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Author : Saliha Durmuş
language : en
Publisher: Frontiers Media SA
Release Date : 2016-05-30

Computational Systems Biology Of Pathogen Host Interactions written by Saliha Durmuş and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-05-30 with Electronic book categories.

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.

Proceedings Of Integrated Intelligence Enable Networks And Computing

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Author : Krishan Kant Singh Mer
language : en
Publisher: Springer Nature
Release Date : 2021-04-23

Proceedings Of Integrated Intelligence Enable Networks And Computing written by Krishan Kant Singh Mer and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-04-23 with Technology & Engineering categories.

This book presents best selected research papers presented at the First International Conference on Integrated Intelligence Enable Networks and Computing (IIENC 2020), held from May 25 to May 27, 2020, at the Institute of Technology, Gopeshwar, India (Government Institute of Uttarakhand Government and affiliated to Uttarakhand Technical University). The book includes papers in the field of intelligent computing. The book covers the areas of machine learning and robotics, signal processing and Internet of things, big data and renewable energy sources.

Biothermodynamics Part D

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Author :
language : en
Publisher: Academic Press
Release Date : 2011-02-16

Biothermodynamics Part D written by and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-02-16 with Science categories.

The use of thermodynamics in biological research can be equated to an energy book-keeping system. While the structure and function of a molecule is important, it is equally important to know what drives the energy force. This volume presents sophisticated methods for estimating the thermodynamic parameters of specific protein-protein, protein-DNA and small molecule interactions. Elucidates the relationships between structure and energetics and their applications to molecular design, aiding researchers in the design of medically important molecules Provides a "must-have" methods volume that keeps MIE buyers and online subscribers up-to-date with the latest research Offers step-by-step lab instructions, including necessary equipment, from a global research community