Download or read book Microbial Gene Essentiality Protocols and Bioinformatics written by Andrei L. Osterman and published by Humana Press. This book was released on 2010-11-19 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book contains a comprehensive collection of experimental and computational strategies and techniques for microbial genome-scale essentiality studies, developed and presented by the leading groups in the field. It contains detailed description of the procedures, discussion of potential difficulties and failures. All protocols follow the successful Methods in Molecular BiologyTM series format.
Download or read book Microbial Gene Essentiality written by Svetlana Y. Gerdes and published by . This book was released on 2008 with total page 486 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Gene Essentiality written by Long Jason Lu and published by . This book was released on 2015-02-28 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume opens by covering two main types of approaches widely used to determine essential genes: single-gene knockouts and transposon mutagenesis, in both prokaryotes and Candida albicans. Given the significant advancement in the computational predictions of microbial essential genes, the second half of the book examines four main types of approaches: comparative genomics, supervised machine learning, constraint-based methods, and corrections of transposon mutagenesis data, as well as databases and servers that are often used in studying gene essentiality. Written in the highly successful Methods in Molecular Biology series format, chapters include an introduction 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. Authoritative and up-to-date, Gene Essentiality: Methods and Protocols will aid researchers who wish to further our knowledge in this vital field of study.
Download or read book Microbial Gene Essentiality Protocols and Bioinformatics written by Andrei L. Osterman and published by Humana Press. This book was released on 2008-02-04 with total page 486 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book contains a comprehensive collection of experimental and computational strategies and techniques for microbial genome-scale essentiality studies, developed and presented by the leading groups in the field. It contains detailed description of the procedures, discussion of potential difficulties and failures. All protocols follow the successful Methods in Molecular BiologyTM series format.
Download or read book The New Science of Metagenomics written by National Research Council and published by National Academies Press. This book was released on 2007-06-24 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Gene Essentiality written by Long Jason Lu and published by Humana. This book was released on 2016-10-05 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume opens by covering two main types of approaches widely used to determine essential genes: single-gene knockouts and transposon mutagenesis, in both prokaryotes and Candida albicans. Given the significant advancement in the computational predictions of microbial essential genes, the second half of the book examines four main types of approaches: comparative genomics, supervised machine learning, constraint-based methods, and corrections of transposon mutagenesis data, as well as databases and servers that are often used in studying gene essentiality. Written in the highly successful Methods in Molecular Biology series format, chapters include an introduction 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. Authoritative and up-to-date, Gene Essentiality: Methods and Protocols will aid researchers who wish to further our knowledge in this vital field of study.
Download or read book Predicting essentials Genes in Microbial Genomes written by Krishnaveni Palaniappan and published by . This book was released on 2010 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: Essential genes constitute the minimal gene set of an organism that is indispensable for its survival under most favorable conditions. The problem of accurately identifying and predicting genes essential for survival of an organism has both theoretical and practical relevance in genome biology and medicine. From a theoretical perspective it provides insights in the understanding of the minimal requirements for cellular life and plays a key role in the emerging field of synthetic biology; from a practical perspective, it facilitates efficient identification of potential drug targets (e.g., antibiotics) in novel pathogens. However, characterizing essential genes of an organism requires sophisticated experimental studies that are expensive and time consuming. The goal of this research study was to investigate machine learning methods to accurately classify/predict "essential genes" in newly sequenced microbial genomes based solely on their genomic sequence data. This study formulates the predication of essential genes problem as a binary classification problem and systematically investigates applicability of three different supervised classification methods for this task. In particular, Decision Tree (DT), Support Vector Machine (SVM), and Artificial Neural Network (ANN) based classifier models were constructed and trained on genomic features derived solely from gene sequence data of 14 experimentally validated microbial genomes whose essential genes are known. A set of 52 relevant genomic sequence derived features (including gene and protein sequence features, protein physio-chemical features and protein sub-cellular features) was used as input for the learners to learn the classifier models. The training and test datasets used in this study reflected between-class imbalance (i.e. skewed majority class vs. minority class) that is intrinsic to this data domain and essential genes prediction problem. Two imbalance reduction techniques (homology reduction and random under sampling of 50% of the majority class) were devised without artificially balancing the datasets and compromising classifier generalizability. The classifier models were trained and evaluated using 10-fold stratified cross validation strategy on both the full multi-genome datasets and its class imbalance reduced variants to assess their predictive ability of discriminating essential genes from non-essential genes. In addition, the classifiers were also evaluated using a novel blind testing strategy, called LOGO (Leave-One-Genome-Out) and LOTO (Leave-One-Taxon group-Out) tests on carefully constructed held-out datasets (both genome-wise (LOGO) and taxonomic group-wise (LOTO)) that were not used in training of the classifier models. Prediction performance metrics, accuracy, sensitivity, specificity, precision and area under the Receiver Operating Characteristics (AU-ROC) were assessed for DT, SVM and ANN derived models. Empirical results from 10 X 10-fold stratified cross validation, Leave-One-Genome-Out (LOGO) and Leave-One-Taxon group-Out (LOTO) blind testing experiments indicate SVM and ANN based models perform better than Decision Tree based models. On 10 X 10-fold cross validations, the SVM based models achieved an AU-ROC score of 0.80, while ANN and DT achieved 0.79 and 0.68 respectively. Both LOGO (genome-wise) and LOTO (taxon-wise) blind tests revealed the generalization extent of these classifiers across different genomes and taxonomic orders.
Download or read book Size Limits of Very Small Microorganisms written by National Research Council and published by National Academies Press. This book was released on 1999-10-13 with total page 171 pages. Available in PDF, EPUB and Kindle. Book excerpt: How small can a free-living organism be? On the surface, this question is straightforward-in principle, the smallest cells can be identified and measured. But understanding what factors determine this lower limit, and addressing the host of other questions that follow on from this knowledge, require a fundamental understanding of the chemistry and ecology of cellular life. The recent report of evidence for life in a martian meteorite and the prospect of searching for biological signatures in intelligently chosen samples from Mars and elsewhere bring a new immediacy to such questions. How do we recognize the morphological or chemical remnants of life in rocks deposited 4 billion years ago on another planet? Are the empirical limits on cell size identified by observation on Earth applicable to life wherever it may occur, or is minimum size a function of the particular chemistry of an individual planetary surface? These questions formed the focus of a workshop on the size limits of very small organisms, organized by the Steering .Group for the Workshop on Size Limits of Very Small Microorganisms and held on October 22 and 23, 1998. Eighteen invited panelists, representing fields ranging from cell biology and molecular genetics to paleontology and mineralogy, joined with an almost equal number of other participants in a wide-ranging exploration of minimum cell size and the challenge of interpreting micro- and nano-scale features of sedimentary rocks found on Earth or elsewhere in the solar system. This document contains the proceedings of that workshop. It includes position papers presented by the individual panelists, arranged by panel, along with a summary, for each of the four sessions, of extensive roundtable discussions that involved the panelists as well as other workshop participants.
Download or read book Essential Genes and Genomes written by Ren Zhang and published by Humana. This book was released on 2022-11-12 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides state-of-the-art information on gene essentiality screenings in a wide variety of organisms, i.e. screening for protein-coding genes and other genomic elements that are required by an organism to survive under specific conditions. With a focus on the two techniques that have revolutionized the field, the collection begins with chapters employing CRISPR/Cas9-based approaches followed by Tn-seq-based approaches, but later chapters also delve into other techniques for exploring essential genes, such as bioinformatics methods. Written for the highly successful Methods in Molecular Biology series, chapters include 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. Comprehensive and authoritative, Essential Genes and Genomes: Methods and Protocols is an ideal guide for researchers attempting to strip genetics down to its fundamentals.
Download or read book The Pangenome written by Hervé Tettelin and published by Springer Nature. This book was released on 2020-04-30 with total page 311 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Escherichia Coli and Salmonella written by Frederick C. Neidhardt and published by . This book was released on 1996 with total page 2822 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the long–awaited second edition of an invaluable classic! Escherichia coli occupies a central role in contemporary molecular biology. It is the unicellular organism about which most is known – all molecular and cellular biologists will want a copy of this book. In 154 chapters, 250 expert authors and editors present the state of the art. Completely rewritten and restructured, the second edition offers a whole new approach to the subject.
Download or read book The Chemistry of Microbiomes written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2017-07-19 with total page 133 pages. Available in PDF, EPUB and Kindle. Book excerpt: The 21st century has witnessed a complete revolution in the understanding and description of bacteria in eco- systems and microbial assemblages, and how they are regulated by complex interactions among microbes, hosts, and environments. The human organism is no longer considered a monolithic assembly of tissues, but is instead a true ecosystem composed of human cells, bacteria, fungi, algae, and viruses. As such, humans are not unlike other complex ecosystems containing microbial assemblages observed in the marine and earth environments. They all share a basic functional principle: Chemical communication is the universal language that allows such groups to properly function together. These chemical networks regulate interactions like metabolic exchange, antibiosis and symbiosis, and communication. The National Academies of Sciences, Engineering, and Medicine's Chemical Sciences Roundtable organized a series of four seminars in the autumn of 2016 to explore the current advances, opportunities, and challenges toward unveiling this "chemical dark matter" and its role in the regulation and function of different ecosystems. The first three focused on specific ecosystemsâ€"earth, marine, and humanâ€"and the last on all microbiome systems. This publication summarizes the presentations and discussions from the seminars.
Download or read book A Systems Biology Approach to Bacterial Gene Essentiality written by Afonso Martins Bravo and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Thèse. Biologie. Médecine. 2023
Download or read book Structural Approaches to Sequence Evolution written by Ugo Bastolla and published by Springer Science & Business Media. This book was released on 2007-05-26 with total page 375 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent advances in understanding the thermodynamics of macromolecules, the topological properties of gene networks, the organization and mutation capabilities of genomes, and the structure of populations make it possible to incorporate these key elements into a broader and deeply interdisciplinary view of molecular evolution. This book gives an account of such a new approach, through clear tutorial contributions by leading scientists.
Download or read book Vulnerability and Robustness in the Essential Gene Complement of Two Bacterial Species Profiled with CRISPRi written by Melanie Silvis and published by . This book was released on 2020 with total page 153 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bacterial essential genes contribute to the most fundamental processes of cellular life. The study of their functions in vivo has long been intractable to systematic genetic approaches, which are fundamental to understanding pathway level connections that govern cellular life and are a requirement for dissecting the complex cellular processes to which essential genes contribute. In Chapter 1 of this work I review recent advances in mapping gene-phenotype relationships in bacteria using the CRISPR-based technology, CRISPR interference (CRISPRi) for titratable gene knockdowns, focusing on their applications to the studies of essential genes, the exploration of chemical-genetic interactions, and the prospects for disentangling complex phenotypes in diverse bacterial species. In Chapter 2 I describe my analysis of the essential gene functions in the model Gram-negative bacterium Escherichia coli and the model Gram-positive Bacillus subtilis using datasets from paired chemical-genetic screens. In this work I identify both shared and Gram-negative specific mechanisms of collateral sensitization to antibiotic action. In Chapter 3 I investigate a fundamental property of essential genes, which is the relationship between their expression level and the cellular growth rate. Here, further developing CRISPRi tools in bacteria to predictably titrate knockdown efficacy, I interpret the knockdown-fitness relationships of each essential gene in E. coli and B. subtilis, discovering broad conservation of constraints setting and maintaining expression levels across these diverged species.
Download or read book Genome scale Prediction of Conditional Gene Essentiality Across the Bacterial Kingdom written by Dilfuza Djamalova and published by . This book was released on 2024 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Essential Bioinformatics written by Jin Xiong and published by Cambridge University Press. This book was released on 2006-03-13 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Essential Bioinformatics is a concise yet comprehensive textbook of bioinformatics, which provides a broad introduction to the entire field. Written specifically for a life science audience, the basics of bioinformatics are explained, followed by discussions of the state-of-the-art computational tools available to solve biological research problems. All key areas of bioinformatics are covered including biological databases, sequence alignment, genes and promoter prediction, molecular phylogenetics, structural bioinformatics, genomics and proteomics. The book emphasizes how computational methods work and compares the strengths and weaknesses of different methods. This balanced yet easily accessible text will be invaluable to students who do not have sophisticated computational backgrounds. Technical details of computational algorithms are explained with a minimum use of mathematical formulae; graphical illustrations are used in their place to aid understanding. The effective synthesis of existing literature as well as in-depth and up-to-date coverage of all key topics in bioinformatics make this an ideal textbook for all bioinformatics courses taken by life science students and for researchers wishing to develop their knowledge of bioinformatics to facilitate their own research.
