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Microbial Functional Genomics by Jizhong Zhou,Dorothea K. Thompson,Ying Xu,James M. Tiedje Pdf
Microbial Functional Genomics offers a timely summary of the principles, approaches, and applications. It presents a comprehensive review of microbial functional genomics, covering microbial diversity, microbial genome sequencing, genomic technologies, genome-wide functional analysis, applied functional genomics, and future directions. An introduction will offer a definition of the field and an overview of the historical and comparative genomics aspects.
Functional Microbial Genomics by Brendan Wren,Nick Dorrell Pdf
Functional Microbial Genomics, edited by two leading experts in the field, provides the researcher with an up-to-date collection of articles on post-genome technologies central to studying the function of microorganisms.Since the release of the first complete genome sequence of a free-living organ
Functional Metagenomics: Tools and Applications by Trevor C. Charles,Mark R. Liles,Angela Sessitsch Pdf
In this book, the latest tools available for functional metagenomics research are described.This research enables scientists to directly access the genomes from diverse microbial genomes at one time and study these “metagenomes”. Using the modern tools of genome sequencing and cloning, researchers have now been able to harness this astounding metagenomic diversity to understand and exploit the diverse functions of microorganisms. Leading scientists from around the world demonstrate how these approaches have been applied in many different settings, including aquatic and terrestrial habitats, microbiomes, and many more environments. This is a highly informative and carefully presented book, providing microbiologists with a summary of the latest functional metagenomics literature on all specific habitats.
Microbial Genomics in Sustainable Agroecosystems by Vijay Tripathi,Pradeep Kumar,Pooja Tripathi,Amit Kishore Pdf
In recent decades, significant advances in new methodologies like DNA sequencing and high-throughput sequencing have been used to identify microorganisms and monitor their interactions with different environments. Microbial genomics techniques are opening new approaches to microbiology by revealing how microorganisms affect human beings and the environment. This book covers four major areas: 1) Environmental microbial genomics, 2) Microbial genomics in human health, 3) Microbial genomics in crop improvement and plant health protection, and 4) Genome analysis of microbial pathogens. Within these areas, the topics addressed include: microbial genome diversity, evolution, and microbial genome sequencing; bioinformatics and microarray-based genomic technologies; functional genomics of bioremediation of soil and water from organic and inorganic pollutants and carbon management; functional genomics of microbial pathogens and relevant microorganisms; functional genomics of model microorganisms; and applied functional genomics. Given its scope, the book offers a comprehensive source of information on the latest applications of microorganisms and microbial genomics to enhance the sustainability of agriculture and the environment.
National Research Council,Division on Earth and Life Studies,Board on Life Sciences,Committee on Metagenomics: Challenges and Functional Applications
Author : National Research Council,Division on Earth and Life Studies,Board on Life Sciences,Committee on Metagenomics: Challenges and Functional Applications Publisher : National Academies Press Page : 170 pages File Size : 43,6 Mb Release : 2007-06-24 Category : Science ISBN : 9780309106764
The New Science of Metagenomics by National Research Council,Division on Earth and Life Studies,Board on Life Sciences,Committee on Metagenomics: Challenges and Functional Applications Pdf
Although we can't usually see them, microbes are essential for every part of human life-indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying-one at a time-the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.
Functional Microbial Genomics, edited by two leading experts in the field, provides the researcher with an up-to-date collection of articles on post-genome technologies central to studying the function of microorganisms.Since the release of the first complete genome sequence of a free-living organism in 1995, over 100 microbial genomes have been completely sequenced. The advent of new technologies for post-genomic analyses has allowed the rapid exploitation of this genome sequence information, heralding a golden era in microbial research. Functional Microbial Genomics provides in-depth accounts from scientists working with these new technologies explaining both the techniques and the ways in which they have been applied to the study of gene function in different microbial species.Methods in Microbiology is the most prestigious series devoted to techniques and methodology in the field. Established for over 30 years, Methods in Microbiology will continue to provide you with tried and tested, cutting edge protocols to directly benefit your research.
Microbial Diversity in the Genomic Era by Surajit Das,Hirak Ranjan Dash Pdf
Microbial Diversity in the Genomic Era, Second Edition presents techniques used for microbial taxonomy and phylogeny, along with their applications and respective strengths and challenges. Though many advanced techniques for the identification of unknown bacterium are available in the genomic era, a far fewer number of the total microbial species have been discovered and identified to date. With that in mind, this book incorporates recently developed biosystematics methods and approaches to assess microbial taxonomy, with suitable recommendations for where to apply them across the range of bacterial identification and infectious disease research. Here, international researchers in the field first provide a broad overview of microbial genomics research and microbiome directed medicine, followed by sections on molecular tools for microbial diversity research, extremophilic microbial diversity, functional microbial diversity across application areas, microbial diversity and infectious disease research, and future directions for research. Step-by-step methodologies are provided for key techniques, along with applied case studies breaking down recent research studies into the practical components, illuminating pathways for new studies across the field. This new edition has been fully updated to address advances in the field of microbiome directed medicine, and whole genome sequencing for studying microbial diversity, considering both recent technological advances and new applications areas, from extremophile studies to the latest approaches in human microbiome analysis. Instructs in techniques used for microbial taxonomy and phylogeny, with discussions of their applications and respective pros and cons Reviews the evolving field of microbial typing and the genomic technologies that enable comparative metagenomic analysis of complex microbial environments Covers microbiome directed translational research, as well as whole genome sequencing for studying microbial diversity, with newly added research protocols and case studies Reviews future applications in the field of microbiome directed medicine Features chapter contributions from global experts in the field
Functional Genomics and Evolution of Photosynthetic Systems by Robert Burnap,Wim Vermaas Pdf
New possibilities have been brought about by the stunning number of genomic sequences becoming available for photosynthetic organisms. This new world of whole genome sequence data spans the phyla from photosynthetic microbes to algae to higher plants. These whole genome projects are intrinsically interesting, but also inform the variety of other molecular sequence databases including the recent 'meta-genomic' sequencing efforts that analyze entire communities of organisms. As impressive as they are, are obviously only the beginning of the effort to decipher the biological meaning encoded within them. This book aims to highlight progress in this direction. This book aims toward a genome-level understanding of the structure, function, and evolution of photosynthetic systems and the advantages accrued from the availability of phyletically diverse sets of gene sequences for the major components of the photosynthetic apparatus. While not meant to be fully comprehensive in terms of the topics covered, it does provide detailed views of specific cases and thereby illustrates important new directions that are being taken in this fast-moving field—a field that involves the integration of bioinformatics, molecular biology, physiology, and ecology.
Structure and Function of the Bacterial Genome by Charles J. Dorman Pdf
Presents an integrated view of the expression of bacterial genetic information, genome architecture and function, and bacterial physiology and pathogenesis This book blends information from the very latest research on bacterial chromosome and nucleoid architecture, whole-genome analysis, cell signaling, and gene expression control with well-known gene regulation paradigms from model organisms (including pathogens) to give readers a picture of how information flows from the environment to the gene, modulating its expression and influencing the competitive fitness of the microbe. Structure and Function of the Bacterial Genome explores the governance of the expression of the genes that make a bacterium what it is, and updates the basics of gene expression control with information about transcription promoter structure and function, the role of DNA as a regulatory factor (in addition to its role as a carrier of genetic information), small RNAs, RNAs that sense chemical signals, ribosomes and translation, posttranslational modification of proteins, and protein secretion. It looks at the forces driving the conservation and the evolution of the dynamic genome and offers chapters that cover DNA replication, DNA repair, plasmid biology, recombination, transposition, the roles of repetitive DNA sequences, horizontal gene transfer, the defense of the genome by CRISPR-Cas, restriction enzymes, Argonaute proteins and BREX systems. The book finishes with a chapter that gives an integrated overview of genome structure and function. Blends knowledge of gene regulatory mechanisms with a consideration of nucleoid structure and dynamics Offers a 'DNA-centric' approach to considering transcription control Views horizontal gene transfer from a gene regulation perspective Assesses the opportunities and limitations of designing synthetic microbes or rewiring existing ones Structure and Function of the Bacterial Genome is an ideal book for graduate and undergraduate students studying microbial cell biology, bacterial pathogenesis, gene regulation, and molecular microbiology. It will also appeal to principal investigators conducting research on these and related topics and researchers in synthetic biology and other arms of biotechnology.
Microbial Environmental Genomics (MEG) by Francis Martin,Stephane Uroz Pdf
This volume guides researchers on how to characterize, image rare, and hitherto unknown taxa and their interactions, to identify new functions and biomolecules and to understand how environmental changes condition the activity and the response of the organisms living with us and in our environment. Chapters cover different organism types (i.e., archaea, bacteria, fungi, protest, microfauna and microeukaryotes) and propose detailed protocols to produce high quality DNA, to analyse active microbial communities directly involved in complex interactions or processes through stable isotope probing, to identify and characterize of new functional genes, to image in situ interactions and to apply bioinformatics analysis tools to complex metagenomic or RNAseq sequence data. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Microbial Environmental Genomics (MEG): Methods and Protocols, Second Edition aims to serve as a primary research reference for researchers in microbiology working to in the expanding field of molecular ecology and environmental genomics.
Computing for Comparative Microbial Genomics by David Wayne Ussery,Trudy M. Wassenaar,Stefano Borini Pdf
Overview and Goals This book describes how to visualize and compare bacterial genomes. Sequencing technologies are becoming so inexpensive that soon going for a cup of coffee will be more expensive than sequencing a bacterial genome. Thus, there is a very real and pressing need for high-throughput computational methods to compare hundreds and thousands of bacterial genomes. It is a long road from molecular biology to systems biology, and in a sense this text can be thought of as a path bridging these ? elds. The goal of this book is to p- vide a coherent set of tools and a methodological framework for starting with raw DNA sequences and producing fully annotated genome sequences, and then using these to build up and test models about groups of interacting organisms within an environment or ecological niche. Organization and Features The text is divided into four main parts: Introduction, Comparative Genomics, Transcriptomics and Proteomics, and ? nally Microbial Communities. The ? rst ? ve chapters are introductions of various sorts. Each of these chapters represents an introduction to a speci? c scienti? c ? eld, to bring all readers up to the same basic level before proceeding on to the methods of comparing genomes. First, a brief overview of molecular biology and of the concept of sequences as biological inf- mation are given.
Sequence — Evolution — Function by Eugene V. Koonin,Michael Galperin Pdf
Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.
National Academies of Sciences, Engineering, and Medicine,Division on Earth and Life Studies,Board on Life Sciences
Author : National Academies of Sciences, Engineering, and Medicine,Division on Earth and Life Studies,Board on Life Sciences Publisher : National Academies Press Page : 201 pages File Size : 41,8 Mb Release : 2020-12-18 Category : Science ISBN : 9780309676731
Next Steps for Functional Genomics by National Academies of Sciences, Engineering, and Medicine,Division on Earth and Life Studies,Board on Life Sciences Pdf
One of the holy grails in biology is the ability to predict functional characteristics from an organism's genetic sequence. Despite decades of research since the first sequencing of an organism in 1995, scientists still do not understand exactly how the information in genes is converted into an organism's phenotype, its physical characteristics. Functional genomics attempts to make use of the vast wealth of data from "-omics" screens and projects to describe gene and protein functions and interactions. A February 2020 workshop was held to determine research needs to advance the field of functional genomics over the next 10-20 years. Speakers and participants discussed goals, strategies, and technical needs to allow functional genomics to contribute to the advancement of basic knowledge and its applications that would benefit society. This publication summarizes the presentations and discussions from the workshop.
National Research Council,Division on Earth and Life Studies,Board on Life Sciences,Committee on Metagenomics: Challenges and Functional Applications
Author : National Research Council,Division on Earth and Life Studies,Board on Life Sciences,Committee on Metagenomics: Challenges and Functional Applications Publisher : National Academies Press Page : 170 pages File Size : 53,5 Mb Release : 2007-05-24 Category : Science ISBN : 9780309185752
The New Science of Metagenomics by National Research Council,Division on Earth and Life Studies,Board on Life Sciences,Committee on Metagenomics: Challenges and Functional Applications Pdf
Although we can't usually see them, microbes are essential for every part of human life-indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying-one at a time-the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.
Microbial Genomics in Sustainable Agroecosystems by Vijay Tripathi,Pradeep Kumar,Pooja Tripathi,Amit Kishore,Madhu Kamle Pdf
Today, microbiology is a rapidly growing discipline in the life sciences, and the technologies are evolving on a virtually daily basis. Next-generation sequencing technologies have revolutionized microbial analysis, and can help us understand the biology and genomic diversity of various bacterial species with significant impacts on agro-ecosystems. In addition, advances in molecular biology and microbiology techniques hold the potential to improve the productivity and sustainability of agriculture and forestry. This new volume addresses the role of microbial genomics in understanding the living systems that exist in the soil and their interactions with plants, an aspect that is also important for crop improvement. The topics covered focus on a deeper and clearer understanding of how microbes cause diseases, the genome-based development of novel antibacterial agents and vaccines, and the role of microbial genomics in crop improvement and agroforestry. Given its scope, the book offers a valuable resource for researchers and students of agriculture and infectious biology.
