The Individual Microbe Single Cell Analysis And Agent Based Modelling

Author : Johan H. J. Leveau,Ferdi L. Hellweger,Jan-Ulrich Kreft,Clara Prats,Weiwen Zhang
Publisher : Frontiers Media SA
Page : 187 pages
File Size : 54,6 Mb
Release : 2019-02-19
Category : Electronic
ISBN : 9782889457496

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The Individual Microbe: Single-Cell Analysis and Agent-Based Modelling by Johan H. J. Leveau,Ferdi L. Hellweger,Jan-Ulrich Kreft,Clara Prats,Weiwen Zhang Pdf

Recent technological advances in single-cell microbiology, using flow cytometry, microfluidics, x-ray fluorescence microprobes, and single-cell -omics, allow for the observation of individuals within populations. Simultaneously, individual-based models (or more generally agent-based models) allow for individual microbes to be simulated. Bridging these techniques forms the foundation of individual-based ecology of microbes (µIBE). µIBE has elucidated genetic and phenotypic heterogeneity that has important consequences for a number of human interests, including antibiotic or biocide resistance, the productivity and stability of industrial fermentations, the efficacy of food preservatives, and the potential of pathogens to cause disease. Individual-based models can help us to understand how these sets of traits of individual microbes influence the above. This eBook compiles all publications from a recent Research Topic in Frontiers in Microbiology. It features recent research where individual observational and/or modelling techniques are applied to gain unique insights into the ecology of microorganisms. The Research Topic “The Individual Microbe: Single-Cell Analysis and Agent-Based Modelling” arose from the 2016 @ASM conference of the same name hosted by the American Society for Microbiology at its headquarters in Washington, D.C. We are grateful to ASM for funding and hosting this conference.

Author : Susann Müller,Thomas Bley
Publisher : Springer
Page : 242 pages
File Size : 54,5 Mb
Release : 2011-03-02
Category : Science
ISBN : 9783642168871

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High Resolution Microbial Single Cell Analytics by Susann Müller,Thomas Bley Pdf

Light Microscopic Analysis of Mitochondrial Heterogeneity in Cell Populations and Within Single Cells, by S. Jakobs, S. Stoldt, and D. Neumann * Advanced Microscopy of Microbial Cells, by J. A. J. Haagensen, B. Regenberg, and C. Sternberg * Algebraic and Geometric Understanding of Cells, Epigenetic Inheritance of Phenotypes Between Generations, by K. Yasuda * Measuring the Mechanical Properties of Single Microbial Cells, by C. R. Thomas, J. D. Stenson, and Z. Zhang * Single Cell Analytics: Pushing the Limits of the Doable, by H. Kortmann, L.M. Blank, and A. Schmid * Cultivation-Independent Assessment of Bacterial Viability, by F. Hammes, M. Berney, and T. Egli * Resolution of Natural Microbial Community Dynamics by Community Fingerprinting, Flow Cytometry and Trend Interpretation Analysis, by P. Bombach, T. Hübschmann, I. Fetzer, S. Kleinsteuber, R. Geyer, H. Harms, and S. Müller *Multivariate Data Analysis Methods for the Interpretation of Microbial Flow Cytometric Data, by H.M. Davey, and C.L. Davey * From Single Cells to Microbial Population Dynamics: Modelling in Biotechnology Based on Measurements of Individual Cells, by T. Bley

Author : Anonim
Publisher : Academic Press
Page : 394 pages
File Size : 48,5 Mb
Release : 2020-02-21
Category : Medical
ISBN : 9780128172827

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Microbiomics by Anonim Pdf

Microbiomics: Dimensions, Applications, and Translational Implications of Human and Environmental Microbiome Research describes a new, holistic approach to microbiomics. International experts provide in-depth discussion of current research methods for studying human, environmental, viral and fungal microbiomes, as well as the implications of new discoveries for human health, nutrition, disease, cancer research, probiotics and in the food and agricultural industries. Distinct chapters covering culturomics and sub-microbiomes, such as the viriome and mycetobiome, provide an integrative framework for the expansion of microbiomics into new areas of application, as well as crosspollination between research areas. Detailed case studies include the use of microbiomics to develop natural products with antimicrobial properties, microbiomic enhancements in food and beverage technology, microbes for bioprotection and biopreservation, microbial tools to reduce antibiotic resistance, and maintenance and cultivation of human microbial communities. Provides an integrated approach for realizing the potential of microbiomics across the life, environmental, food and agricultural sciences Includes thorough analysis of human, environmental, viral and mycetol microbiomes, as well as methods and technology for identifying microbiotes Features chapter contributions from international leaders in microbiomic methods, technology and applications

Author : Peter Deines,Brendan J. M. Bohannan,Posy Elizabeth Busby,Steven Earl Lindow,Kyle Matthew Meyer,Zhong Wei
Publisher : Frontiers Media SA
Page : 152 pages
File Size : 51,8 Mb
Release : 2022-11-22
Category : Science
ISBN : 9782832506790

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The Role of Dispersal and Transmission in Structuring Microbial Communities by Peter Deines,Brendan J. M. Bohannan,Posy Elizabeth Busby,Steven Earl Lindow,Kyle Matthew Meyer,Zhong Wei Pdf

Author : Stanley Brul,Suzanne Van Gerwen,Marcel Zwietering
Publisher : Elsevier
Page : 309 pages
File Size : 51,8 Mb
Release : 2007-03-12
Category : Technology & Engineering
ISBN : 9781845692940

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Modelling Microorganisms in Food by Stanley Brul,Suzanne Van Gerwen,Marcel Zwietering Pdf

Predicting the growth and behaviour of microorganisms in food has long been an aim in food microbiology research. In recent years, microbial models have evolved to become more exact and the discipline of quantitative microbial ecology has gained increasing importance for food safety management, particularly as minimal processing techniques have become more widely used. These processing methods operate closer to microbial death, survival and growth boundaries and therefore require even more precise models. Written by a team of leading experts in the field, Modelling microorganims in food assesses the latest developments and provides an outlook for the future of microbial modelling. Part one discusses general issues involved in building models of microbial growth and inactivation in foods, with chapters on the historical background of the field, experimental design, data processing and model fitting, the problem of uncertainty and variability in models and modelling lag-time. Further chapters review the use of quantitative microbiology tools in predictive microbiology and the use of predictive microbiology in risk assessment. The second part of the book focuses on new approaches in specific areas of microbial modelling, with chapters discussing the implications of microbial variability in predictive modelling and the importance of taking into account microbial interactions in foods. Predicting microbial inactivation under high pressure and the use of mechanistic models are also covered. The final chapters outline the possibility of incorporating systems biology approaches into food microbiology. Modelling microorganisms in food is a standard reference for all those in the field of food microbiology. Assesses the latest developments in microbial modelling Discusses the issues involved in building models of microbial growth Chapters review the use of quantitative microbiology tools in predictive microbiology

Author : Matthew W. Chang
Publisher : John Wiley & Sons
Page : 340 pages
File Size : 51,9 Mb
Release : 2022-05-03
Category : Science
ISBN : 9783527825486

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Principles in Microbiome Engineering by Matthew W. Chang Pdf

Principles in Microbiome Engineering Provides an overview of the techniques and applications insight into the complex composition and interactions of microbiomes Microbiomes, the communities of microorganisms that inhabit specific ecosystems or organisms, can be engineered to modify the structure of microbiota and reestablish ecological balance. In recent years, a better understanding of microbial composition and host-microbe interactions has led to the development of new applications for improving human health and increasing agricultural productivity and quality. Principles in Microbiome Engineering introduces readers to the tools and applications involved in manipulating the composition of a microbial community to improve the function of an eco-system. Covering a range of key topics, this up-to-date volume discusses current research in areas such as microbiome-based therapeutics for human diseases, crop plant breeding, animal husbandry, soil engineering, food and beverage applications, and more. Divided into three sections, the text first describes the critical roles of systems biology, synthetic biology, computer modelling, and machine learning in microbiome engineering. Next, the volume explores various state-of-the-art applications, including cancer immunotherapy and prevention of diseases associated with the human microbiome, followed by a concluding section offering perspectives on the future of microbiome engineering and potential applications. Introduces a variety of applications of microbiome engineering in the fields of medicine, agriculture, and food and beverage products Presents current research into the complex interactions and relationships between microbiomes and biotic and abiotic elements of their environments Examines the use of technologies such as Artificial Intelligence (AI), Machine Learning (ML), and Big Data analytics to advance understanding of microbiomes Discusses the engineering of microbiomes to address human health conditions such as neuro psychiatric disorders and autoimmune and inflammatory diseases Edited and authored by leading researchers in the rapidly evolving field, Principles in Microbiome Engineering is an essential resource for biotechnologists, biochemists, microbiologists, pharmacologists, and practitioners working in the biotechnology and pharmaceutical industries.

Author : IWA Task Group on Biofilm Modeling
Publisher : IWA Publishing
Page : 194 pages
File Size : 50,8 Mb
Release : 2006-04-30
Category : Science
ISBN : 9781843390879

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Mathematical Modeling of Biofilms by IWA Task Group on Biofilm Modeling Pdf

Over 90% of bacterial biomass exists in the form of biofilms. The ability of bacteria to attach to surfaces and to form biofilms often is an important competitive advantage for them over bacteria growing in suspension. Some biofilms are "good" in natural and engineered systems; they are responsible for nutrient cycling in nature and are used to purify waters in engineering processes. Other biofilms are "bad" when they cause fouling and infections of humans and plants. Whether we want to promote good biofilms or eliminate bad biofilms, we need to understand how they work and what works to control them. Mathematical Modeling of Biofilms provides guidelines for the selection and use of mathematical models of biofilms. The whole range of existing models - from simple analytical expressions to complex numerical models - is covered. The application of the models for the solution of typical problems is demonstrated, and the performance of the models is tested in comparative studies. With the dramatic evolution of the computational capacity still going on, modeling tools for research and practice will become more and more significant in the next few years. This report provides the foundation to understand the models and to select the most appropriate one for a given use. Mathematical Modeling of Biofilms gives a state-of-the-art overview that is especially valuable for educating students, new biofilm researchers, and design engineers. Through a series of three benchmark problems, the report demonstrates how to use the different models and indicates when simple or highly complex models are most appropriate. This is the first report to give a quantitative comparison of existing biofilm models. The report supports model-based design of biofilm reactors. The report can be used as basis for teaching biofilm-system modeling. The report provides the foundation for researchers seeking to use biofilm modeling or to develop new biofilm models. Scientific and Technical Report No.18

Author : Bruce Alberts
Publisher : Unknown
Page : 0 pages
File Size : 50,5 Mb
Release : 2002
Category : Cytology
ISBN : 0815332181

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Molecular Biology of The Cell by Bruce Alberts Pdf

Author : Luis Diambra,Pau Formosa-Jordan,David M. Holloway
Publisher : Frontiers Media SA
Page : 157 pages
File Size : 49,9 Mb
Release : 2023-06-07
Category : Science
ISBN : 9782832525685

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Pattern formation in biology by Luis Diambra,Pau Formosa-Jordan,David M. Holloway Pdf

Author : Saliha Durmuş,Tunahan Çakır,Reinhard Guthke,Emrah Nikerel,Arzucan Özgür
Publisher : Frontiers Media SA
Page : 200 pages
File Size : 47,5 Mb
Release : 2016-05-30
Category : Electronic book
ISBN : 9782889198214

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Computational Systems Biology of Pathogen-Host Interactions by Saliha Durmuş,Tunahan Çakır,Reinhard Guthke,Emrah Nikerel,Arzucan Özgür Pdf

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.

Author : Darren D.R. Flower,Jon Timmis
Publisher : Springer Science & Business Media
Page : 453 pages
File Size : 44,5 Mb
Release : 2007-04-16
Category : Medical
ISBN : 9780387392417

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In Silico Immunology by Darren D.R. Flower,Jon Timmis Pdf

This book outlines three emergent disciplines, which are now poised to engineer a paradigm shift from hypothesis- to data-driven research: theoretical immunology, immunoinformatics, and Artificial Immune Systems. It details how these disciplines will enable new understanding to emerge from the analysis of complex datasets. Coverage shows how these three are set to transform immunological science and the future of health care.

Author : Hyun-Seob Song
Publisher : MDPI
Page : 295 pages
File Size : 44,9 Mb
Release : 2018-07-04
Category : Electronic
ISBN : 9783038429753

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Microbial Community Modeling: Prediction of Microbial Interactions and Community Dynamics by Hyun-Seob Song Pdf

This book is a printed edition of the Special Issue "Microbial Community Modeling: Prediction of Microbial Interactions and Community Dynamics" that was published in Processes

Author : Reinhard Guthke,Jörg Linde,Marc Thilo Figge,Franziska Mech
Publisher : Frontiers E-books
Page : 139 pages
File Size : 47,8 Mb
Release : 2024-07-01
Category : Electronic
ISBN : 9782889190607

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Systems Biology of Microbial Infection by Reinhard Guthke,Jörg Linde,Marc Thilo Figge,Franziska Mech Pdf

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.

Author : Eberhard Voit
Publisher : Garland Science
Page : 480 pages
File Size : 47,6 Mb
Release : 2017-09-05
Category : Computers
ISBN : 9781351332941

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A First Course in Systems Biology by Eberhard Voit Pdf

A First Course in Systems Biology is an introduction for advanced undergraduate and graduate students to the growing field of systems biology. Its main focus is the development of computational models and their applications to diverse biological systems. The book begins with the fundamentals of modeling, then reviews features of the molecular inventories that bring biological systems to life and discusses case studies that represent some of the frontiers in systems biology and synthetic biology. In this way, it provides the reader with a comprehensive background and access to methods for executing standard systems biology tasks, understanding the modern literature, and launching into specialized courses or projects that address biological questions using theoretical and computational means. New topics in this edition include: default modules for model design, limit cycles and chaos, parameter estimation in Excel, model representations of gene regulation through transcription factors, derivation of the Michaelis-Menten rate law from the original conceptual model, different types of inhibition, hysteresis, a model of differentiation, system adaptation to persistent signals, nonlinear nullclines, PBPK models, and elementary modes. The format is a combination of instructional text and references to primary literature, complemented by sets of small-scale exercises that enable hands-on experience, and large-scale, often open-ended questions for further reflection.

Author : Anonim
Publisher : Academic Press
Page : 1571 pages
File Size : 43,7 Mb
Release : 2020-08-24
Category : Science
ISBN : 9780128160787

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Systems Medicine by Anonim Pdf

Technological advances in generated molecular and cell biological data are transforming biomedical research. Sequencing, multi-omics and imaging technologies are likely to have deep impact on the future of medical practice. In parallel to technological developments, methodologies to gather, integrate, visualize and analyze heterogeneous and large-scale data sets are needed to develop new approaches for diagnosis, prognosis and therapy. Systems Medicine: Integrative, Qualitative and Computational Approaches is an innovative, interdisciplinary and integrative approach that extends the concept of systems biology and the unprecedented insights that computational methods and mathematical modeling offer of the interactions and network behavior of complex biological systems, to novel clinically relevant applications for the design of more successful prognostic, diagnostic and therapeutic approaches. This 3 volume work features 132 entries from renowned experts in the fields and covers the tools, methods, algorithms and data analysis workflows used for integrating and analyzing multi-dimensional data routinely generated in clinical settings with the aim of providing medical practitioners with robust clinical decision support systems. Importantly the work delves into the applications of systems medicine in areas such as tumor systems biology, metabolic and cardiovascular diseases as well as immunology and infectious diseases amongst others. This is a fundamental resource for biomedical students and researchers as well as medical practitioners who need to need to adopt advances in computational tools and methods into the clinical practice. Encyclopedic coverage: ‘one-stop’ resource for access to information written by world-leading scholars in the field of Systems Biology and Systems Medicine, with easy cross-referencing of related articles to promote understanding and further research Authoritative: the whole work is authored and edited by recognized experts in the field, with a range of different expertise, ensuring a high quality standard Digitally innovative: Hyperlinked references and further readings, cross-references and diagrams/images will allow readers to easily navigate a wealth of information