The Individual Microbe Single Cell Analysis And Agent Based Modelling

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The Individual Microbe: Single-Cell Analysis and Agent-Based Modelling

Author : Johan H. J. Leveau
Publisher : Frontiers Media SA
ISBN 13 : 2889457494
Total Pages : 187 pages
Book Rating : 4.8/5 (894 download)

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Book Synopsis The Individual Microbe: Single-Cell Analysis and Agent-Based Modelling by : Johan H. J. Leveau

Download or read book The Individual Microbe: Single-Cell Analysis and Agent-Based Modelling written by Johan H. J. Leveau and published by Frontiers Media SA. This book was released on 2019-02-19 with total page 187 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Microbiomics

Author :
Publisher : Academic Press
ISBN 13 : 0128172827
Total Pages : 394 pages
Book Rating : 4.1/5 (281 download)

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Book Synopsis Microbiomics by :

Download or read book Microbiomics written by and published by Academic Press. This book was released on 2020-02-21 with total page 394 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Mathematical Modeling of Biofilms

Author : IWA Task Group on Biofilm Modeling
Publisher : IWA Publishing
ISBN 13 : 1843390876
Total Pages : 194 pages
Book Rating : 4.8/5 (433 download)

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Book Synopsis Mathematical Modeling of Biofilms by : IWA Task Group on Biofilm Modeling

Download or read book Mathematical Modeling of Biofilms written by IWA Task Group on Biofilm Modeling and published by IWA Publishing. This book was released on 2006-04-30 with total page 194 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

The Role of Dispersal and Transmission in Structuring Microbial Communities

Author : Peter Deines
Publisher : Frontiers Media SA
ISBN 13 : 2832506798
Total Pages : 152 pages
Book Rating : 4.8/5 (325 download)

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Book Synopsis The Role of Dispersal and Transmission in Structuring Microbial Communities by : Peter Deines

Download or read book The Role of Dispersal and Transmission in Structuring Microbial Communities written by Peter Deines and published by Frontiers Media SA. This book was released on 2022-11-22 with total page 152 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Microbial Biofilms

Author : Hilary M. Lappin-Scott
Publisher : Cambridge University Press
ISBN 13 : 9780521542128
Total Pages : 332 pages
Book Rating : 4.5/5 (421 download)

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Book Synopsis Microbial Biofilms by : Hilary M. Lappin-Scott

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.

Modelling Microorganisms in Food

Author : Stanley Brul
Publisher : Elsevier
ISBN 13 : 1845692942
Total Pages : 309 pages
Book Rating : 4.8/5 (456 download)

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Book Synopsis Modelling Microorganisms in Food by : Stanley Brul

Download or read book Modelling Microorganisms in Food written by Stanley Brul and published by Elsevier. This book was released on 2007-03-12 with total page 309 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Principles in Microbiome Engineering

Author : Matthew W. Chang
Publisher : John Wiley & Sons
ISBN 13 : 3527825487
Total Pages : 340 pages
Book Rating : 4.5/5 (278 download)

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Book Synopsis Principles in Microbiome Engineering by : Matthew W. Chang

Download or read book Principles in Microbiome Engineering written by Matthew W. Chang and published by John Wiley & Sons. This book was released on 2022-05-03 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Molecular Biology of the Cell

Author :
Publisher :
ISBN 13 : 9780815332183
Total Pages : 0 pages
Book Rating : 4.3/5 (321 download)

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Book Synopsis Molecular Biology of the Cell by :

Download or read book Molecular Biology of the Cell written by and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Pattern formation in biology

Author : Luis Diambra
Publisher : Frontiers Media SA
ISBN 13 : 2832525687
Total Pages : 157 pages
Book Rating : 4.8/5 (325 download)

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Book Synopsis Pattern formation in biology by : Luis Diambra

Download or read book Pattern formation in biology written by Luis Diambra and published by Frontiers Media SA. This book was released on 2023-06-07 with total page 157 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Computational Systems Biology of Pathogen-Host Interactions

Author : Saliha Durmuş
Publisher : Frontiers Media SA
ISBN 13 : 2889198219
Total Pages : 200 pages
Book Rating : 4.8/5 (891 download)

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Book Synopsis Computational Systems Biology of Pathogen-Host Interactions by : Saliha Durmuş

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.

In Silico Immunology

Author : Darren D.R. Flower
Publisher : Springer Science & Business Media
ISBN 13 : 0387392416
Total Pages : 453 pages
Book Rating : 4.3/5 (873 download)

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Book Synopsis In Silico Immunology by : Darren D.R. Flower

Download or read book In Silico Immunology written by Darren D.R. Flower and published by Springer Science & Business Media. This book was released on 2007-04-16 with total page 453 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Systems-Level Modelling of Microbial Communities

Author : Aarthi Ravikrishnan
Publisher : CRC Press
ISBN 13 : 0429946066
Total Pages : 77 pages
Book Rating : 4.4/5 (299 download)

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Book Synopsis Systems-Level Modelling of Microbial Communities by : Aarthi Ravikrishnan

Download or read book Systems-Level Modelling of Microbial Communities written by Aarthi Ravikrishnan and published by CRC Press. This book was released on 2018-09-06 with total page 77 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems-Level Modelling of Microbial Communities: Theory and Practice introduces various aspects of modelling microbial communities and presents a detailed overview of the computational methods which have been developed in this area. This book is aimed at researchers in the field of computational/systems biology as well as biologists/experimentalists studying microbial communities, who are keen on embracing the concepts of computational modelling. The primary focus of this book is on methods for modelling interactions between micro-organisms in a community, with special emphasis on constraint-based and network-based modelling techniques. A brief overview of population- and agent-based modelling is also presented. Lastly, it covers the experimental methods to understand microbial communities, and provides an outlook on how the field may evolve in the coming years.

Microbial Community Modeling: Prediction of Microbial Interactions and Community Dynamics

Author : Hyun-Seob Song
Publisher : MDPI
ISBN 13 : 3038429759
Total Pages : 295 pages
Book Rating : 4.0/5 (384 download)

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

Download or read book Microbial Community Modeling: Prediction of Microbial Interactions and Community Dynamics written by Hyun-Seob Song and published by MDPI. This book was released on 2018-07-04 with total page 295 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Individual-based Modeling and Ecology

Author : Volker Grimm
Publisher : Princeton University Press
ISBN 13 : 1400850622
Total Pages : 445 pages
Book Rating : 4.4/5 (8 download)

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Book Synopsis Individual-based Modeling and Ecology by : Volker Grimm

Download or read book Individual-based Modeling and Ecology written by Volker Grimm and published by Princeton University Press. This book was released on 2013-11-28 with total page 445 pages. Available in PDF, EPUB and Kindle. Book excerpt: Individual-based models are an exciting and widely used new tool for ecology. These computational models allow scientists to explore the mechanisms through which population and ecosystem ecology arises from how individuals interact with each other and their environment. This book provides the first in-depth treatment of individual-based modeling and its use to develop theoretical understanding of how ecological systems work, an approach the authors call "individual-based ecology.? Grimm and Railsback start with a general primer on modeling: how to design models that are as simple as possible while still allowing specific problems to be solved, and how to move efficiently through a cycle of pattern-oriented model design, implementation, and analysis. Next, they address the problems of theory and conceptual framework for individual-based ecology: What is "theory"? That is, how do we develop reusable models of how system dynamics arise from characteristics of individuals? What conceptual framework do we use when the classical differential equation framework no longer applies? An extensive review illustrates the ecological problems that have been addressed with individual-based models. The authors then identify how the mechanics of building and using individual-based models differ from those of traditional science, and provide guidance on formulating, programming, and analyzing models. This book will be helpful to ecologists interested in modeling, and to other scientists interested in agent-based modeling.

A First Course in Systems Biology

Author : Eberhard Voit
Publisher : Garland Science
ISBN 13 : 1351332945
Total Pages : 481 pages
Book Rating : 4.3/5 (513 download)

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Book Synopsis A First Course in Systems Biology by : Eberhard Voit

Download or read book A First Course in Systems Biology written by Eberhard Voit and published by Garland Science. This book was released on 2017-09-05 with total page 481 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Systems Biology of Microbial Infection

Author : Reinhard Guthke
Publisher : Frontiers E-books
ISBN 13 : 2889190609
Total Pages : 139 pages
Book Rating : 4.8/5 (891 download)

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Book Synopsis Systems Biology of Microbial Infection by : Reinhard Guthke

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.

Agent-based Modeling and Simulation

Author : S. Taylor
Publisher : Springer
ISBN 13 : 1137453648
Total Pages : 223 pages
Book Rating : 4.1/5 (374 download)

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Book Synopsis Agent-based Modeling and Simulation by : S. Taylor

Download or read book Agent-based Modeling and Simulation written by S. Taylor and published by Springer. This book was released on 2014-08-27 with total page 223 pages. Available in PDF, EPUB and Kindle. Book excerpt: Operational Research (OR) deals with the use of advanced analytical methods to support better decision-making. It is multidisciplinary with strong links to management science, decision science, computer science and many application areas such as engineering, manufacturing, commerce and healthcare. In the study of emergent behaviour in complex adaptive systems, Agent-based Modelling & Simulation (ABMS) is being used in many different domains such as healthcare, energy, evacuation, commerce, manufacturing and defense. This collection of articles presents a convenient introduction to ABMS with papers ranging from contemporary views to representative case studies. The OR Essentials series presents a unique cross-section of high quality research work fundamental to understanding contemporary issues and research across a range of Operational Research (OR) topics. It brings together some of the best research papers from the esteemed Operational Research Society and its associated journals, also published by Palgrave Macmillan.