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 Microbial Comparative Genomics and Pangenomics New Tools Approaches And Insights Into Gene and Genome Evolution written by Paulo Jorge Dias and published by Frontiers Media SA. This book was released on 2024-11-11 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: Comparative Genomics is the field of knowledge dedicated to the analysis and comparison of genes and genomes. The scientific areas comprised in this field include subjects as diverse as (just naming a few): 1) the development of algorithms for the alignment of genes, whole genomes, short- and long sequencing reads, 2) the search for remote sequence similarity, 3) the discovery of motifs and sequence patterns, 4) the identification of gene families, 5) the detection of ortholog/paralog groups, 6) the reconstruction of evolutionary history of the genes, 7) the detection of signs of selective forces exerted over genes and genomes, 8) the reconstruction of ancestral DNA and genome sequences, 9) the detection and analysis of genome synteny, 10) the inference of ancestral gene order, among others. In addition, an important new sub-field of Comparative Genomics has emerged in the last decade, referred to as Pangenomics, making available improved tools to analyze the exponential genomic data accumulating since the development of Second- and Third-Generation Sequencing Technologies.

Download or read book Pan genomics Applications Challenges and Future Prospects written by Debmalya Barh and published by Academic Press. This book was released on 2020-03-06 with total page 476 pages. Available in PDF, EPUB and Kindle. Book excerpt: Pan-genomics: Applications, Challenges, and Future Prospects covers current approaches, challenges and future prospects of pan-genomics. The book discusses bioinformatics tools and their applications and focuses on bacterial comparative genomics in order to leverage the development of precise drugs and treatments for specific organisms. The book is divided into three sections: the first, an "overview of pan-genomics and common approaches, brings the main concepts and current approaches on pan-genomics research; the second, "case studies in pan-genomics, thoroughly discusses twelve case, and the last, "current approaches and future prospects in pan-multiomics, encompasses the developments on omics studies to be applied on bacteria related studies. This book is a valuable source for bioinformaticians, genomics researchers and several members of biomedical field interested in understanding further bacterial organisms and their relationship to human health. - Covers the entire spectrum of pangenomics, highlighting the use of specific approaches, case studies and future perspectives - Discusses current bioinformatics tools and strategies for exploiting pangenomics data - Presents twelve case studies with different organisms in order to provide the audience with real examples of pangenomics applicability

Download or read book The Pangenome written by Hervé Tettelin and published by . This book was released on 2020-10-09 with total page 310 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. This work was published by Saint Philip Street Press pursuant to a Creative Commons license permitting commercial use. All rights not granted by the work's license are retained by the author or authors.

Download or read book Evolutionary Genomics written by Maria Anisimova and published by Humana Press. This book was released on 2012-03-08 with total page 556 pages. Available in PDF, EPUB and Kindle. Book excerpt: Together with early theoretical work in population genetics, the debate on sources of genetic makeup initiated by proponents of the neutral theory made a solid contribution to the spectacular growth in statistical methodologies for molecular evolution. Evolutionary Genomics: Statistical and Computational Methods is intended to bring together the more recent developments in the statistical methodology and the challenges that followed as a result of rapidly improving sequencing technologies. Presented by top scientists from a variety of disciplines, the collection includes a wide spectrum of articles encompassing theoretical works and hands-on tutorials, as well as many reviews with key biological insight. Volume 2 begins with phylogenomics and continues with in-depth coverage of natural selection, recombination, and genomic innovation. The remaining chapters treat topics of more recent interest, including population genomics, -omics studies, and computational issues related to the handling of large-scale genomic data. Written in the highly successful Methods in Molecular BiologyTM series format, this work provides the kind of advice on methodology and implementation that is crucial for getting ahead in genomic data analyses. Comprehensive and cutting-edge, Evolutionary Genomics: Statistical and Computational Methods is a treasure chest of state-of the-art methods to study genomic and omics data, certain to inspire both young and experienced readers to join the interdisciplinary field of evolutionary genomics.

Download or read book Microbial Pathogenomics written by Hilde de Reuse and published by Karger Medical and Scientific Publishers. This book was released on 2009-01-01 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: 'Microbial Pathogenomics' contains a unique collection of reviews demonstrating how genomics has revolutionized our understanding of virulence, host-adaptation strategies and the evolution of bacterial pathogens. Current technologies - computational tools and functional approaches to genome analysis - are carefully documented and clearly illustrated. These include visualization tools for genome comparison, databases, in silico metabolic reconstructions and function prediction as well as interactomics for the study of protein-protein interactions. The concepts of pan-genomics and reverse vaccinology are introduced as strategies when addressing the challenge presented by bacterial diversity in the prevention and treatment of infectious diseases. The authors explore individual bacterial pathogens and discuss the mechanisms that have contributed to their evolutionary success. Special cases of host adaptation, for example, are illustrated by Helicobacter pylori and 'Mycobacterium tuberculosis' which are human-specific and highly persistent; further bacteria discussed include 'Escherichia coli, Campylobacter, Pseudomonas, Legionella, Bartonella, Burkholderia' and 'Staphylococcus'.'Microbial Pathogenomics' provides the reader with a global view of key aspects and future trends in bacterial pathogenomics and evaluates their impact on the understanding and treatment of infectious diseases. Well illustrated and accessible to both specialists and nonspecialists, it is recommended not only for researchers in microbiology, genomics and biotechnology, but also for lecturers and teachers.

Download or read book The Barley Genome written by Nils Stein and published by Springer. This book was released on 2018-08-18 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an overview of the state-of-the-art in barley genome analysis, covering all aspects of sequencing the genome and translating this important information into new knowledge in basic and applied crop plant biology and new tools for research and crop improvement. Unlimited access to a high-quality reference sequence is removing one of the major constraints in basic and applied research. This book summarizes the advanced knowledge of the composition of the barley genome, its genes and the much larger non-coding part of the genome, and how this information facilitates studying the specific characteristics of barley. One of the oldest domesticated crops, barley is the small grain cereal species that is best adapted to the highest altitudes and latitudes, and it exhibits the greatest tolerance to most abiotic stresses. With comprehensive access to the genome sequence, barley’s importance as a genetic model in comparative studies on crop species like wheat, rye, oats and even rice is likely to increase.

Download or read book The Maize Genome written by Jeffrey Bennetzen and published by Springer. This book was released on 2018-11-24 with total page 390 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses advances in our understanding of the structure and function of the maize genome since publication of the original B73 reference genome in 2009, and the progress in translating this knowledge into basic biology and trait improvement. Maize is an extremely important crop, providing a large proportion of the world’s human caloric intake and animal feed, and serving as a model species for basic and applied research. The exceptionally high level of genetic diversity within maize presents opportunities and challenges in all aspects of maize genetics, from sequencing and genotyping to linking genotypes to phenotypes. Topics covered in this timely book range from (i) genome sequencing and genotyping techniques, (ii) genome features such as centromeres and epigenetic regulation, (iii) tools and resources available for trait genomics, to (iv) applications of allele mining and genomics-assisted breeding. This book is a valuable resource for researchers and students interested in maize genetics and genomics.

Download or read book Bacterial Pangenomics written by Alessio Mengoni and published by . This book was released on 2015 with total page 298 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Game Changer Next Generation Sequencing and Its Impact on Food Microbiology written by Jennifer Ronholm and published by Frontiers Media SA. This book was released on 2018-04-26 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in next-generation sequencing technologies (NGS) are revolutionizing the field of food microbiology. Microbial whole genome sequencing (WGS) can provide identification, characterization, and subtyping of pathogens for epidemiological investigations at a level of precision previously not possible. This allows for connections and source attribution to be inferred between related isolates that may be overlooked by traditional techniques. The archiving and global sharing of genome sequences allow for retrospective analysis of virulence genes, antimicrobial resistance markers, mobile genetic elements and other novel genes. The advent of high-throughput 16S rRNA amplicon sequencing, in combination with the advantages offered by massively parallel second-generation sequencing for metagenomics, enable intensive studies on the microbiomes of food products and the impact of foods on the human microbiome. These studies may one day lead to the development of reliable culture-independent methods for food monitoring and surveillance. Similarly, RNA-seq has provided insights into the transcriptomes and hence the behaviour of bacterial pathogens in food, food processing environments, and in interaction with the host at a resolution previously not achieved through the use of microarrays and/or RT-PCR. The vast un-tapped potential applications of NGS along with its rapidly declining costs, give this technology the ability to contribute significantly to consumer protection, global trade facilitation, and increased food safety and security. Despite the rapid advances, challenges remain. How will NGS data be incorporated into our existing global food safety infrastructure? How will massive NGS data be stored and shared globally? What bioinformatics solutions will be used to analyse and optimise these large data sets? This Research Topic discusses recent advances in the field of food microbiology made possible through the use of NGS.

Download or read book Psychrophiles From Biodiversity to Biotechnology written by Rosa Margesin and published by Springer. This book was released on 2017-06-22 with total page 685 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cold adaptation includes a complex range of structural and functional adaptations at the level of all cellular constituents, and these adaptations render cold-adapted organisms particularly useful for biotechnological applications. This book presents the most recent knowledge of (i) boundary conditions for microbial life in the cold, (ii) microbial diversity in various cold ecosystems, (iii) molecular cold adaptation mechanisms and (iv) the resulting biotechnological perspectives.

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 Omics Technologies and Bio engineering written by Debmalya Barh and published by Academic Press. This book was released on 2017-12-01 with total page 645 pages. Available in PDF, EPUB and Kindle. Book excerpt: Omics Technologies and Bio-Engineering: Towards Improving Quality of Life, Volume 1 is a unique reference that brings together multiple perspectives on omics research, providing in-depth analysis and insights from an international team of authors. The book delivers pivotal information that will inform and improve medical and biological research by helping readers gain more direct access to analytic data, an increased understanding on data evaluation, and a comprehensive picture on how to use omics data in molecular biology, biotechnology and human health care. - Covers various aspects of biotechnology and bio-engineering using omics technologies - Focuses on the latest developments in the field, including biofuel technologies - Provides key insights into omics approaches in personalized and precision medicine - Provides a complete picture on how one can utilize omics data in molecular biology, biotechnology and human health care

Download or read book The Chickpea Genome written by Rajeev K. Varshney and published by Springer. This book was released on 2018-01-02 with total page 152 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book sheds new light on the chickpea genome sequencing and resequencing of chickpea germplasm lines and provides insights into classical genetics, cytogenetics, and trait mapping. It also offers an overview of the latest advances in genome sequencing and analysis. The growing human population, rapid climate changes and limited amounts of arable land are creating substantial challenges in connection with the availability and affordability of nutritious food for smallholder farmers in developing countries. In this context, climate smart crops are essential to alleviating the hunger of the millions of poor and undernourished people living in developing countries. In addition to cereals, grain legumes are an integral part of the human diet and provide sustainable income for smallholder farmers in the arid and semi-arid regions of the world. Among grain legumes, the chickpea (Cicer arietinum) is the second most important in terms of production and productivity. Besides being a rich source of proteins, it can fix atmospheric nitrogen through symbiosis with rhizobia and increase the input of combined nitrogen. Several abiotic stresses like drought, heat, salinity, together with biotic stresses like Fusarium wilt, Ascochyta blight, and Botrytis grey mould have led to production losses, as the chickpeas is typically grown in the harsh climates of our planet’s semi-arid regions.

Download or read book Microbial Megaplasmids written by Edward Schwartz and published by Springer Science & Business Media. This book was released on 2009-01-29 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: Megaplasmids are extrachromosomal genetic elements in the size range of 100 kb and larger. They are found in physiologically and phylogenetically diverse groups of bacteria and archaea. By definition, megaplasmids are not essential for the viability of their hosts under all growth conditions, but paradoxically many megaplasmids carry the genetic information for the defining and characteristic traits of the organism in which they reside. Microbial Megaplasmids reviews our knowledge of the extensively studied representatives, such as the catabolic plasmids of the pseudomonads, the rhizobial Sym plasmids, the Ti plasmids of the genus Agrobacterium and the giant enterobacterial virulence plasmids. It also presents snapshots of more recently discovered megaplasmids. The contribution of megaplasmids to the biology of their hosts is described, highlighting the interactions between megaplasmid and chromosomal genes.

Download or read book Forest and Nature Governance written by Bas Arts and published by Springer Science & Business Media. This book was released on 2012-09-22 with total page 261 pages. Available in PDF, EPUB and Kindle. Book excerpt: Today, problems such as deforestation, biodiversity loss and illegal logging have provoked various policy responses that are often referred to as forest and nature governance. In its broadest interpretation, governance is about the many ways in which public and private actors from the state, market and/or civil society govern public issues at multiple scales. This book takes a fresh perspective on the study of forest and nature governance. Departing from ‘practice theory’, and building upon scholars like Giddens, Bourdieu, Reckwitz, Schatzki and Callon, it seeks to move beyond established understandings of institutions, actors, and knowledge. In so doing, it not only presents an innovative conceptual and methodological framework for a practice based approach, but also rich case studies and ethnographies. Finally, this book is about how actors involved in governance talk about and work with trees, forests, biodiversity, wildlife, and so on, while acting upon forest policies, environmental discourses, codes of conduct, or scientific insights.

Download or read book Metagenomics for Microbiology written by Jacques Izard and published by Academic Press. This book was released on 2014-11-07 with total page 188 pages. Available in PDF, EPUB and Kindle. Book excerpt: Concisely discussing the application of high throughput analysis to move forward our understanding of microbial principles, Metagenomics for Microbiology provides a solid base for the design and analysis of omics studies for the characterization of microbial consortia. The intended audience includes clinical and environmental microbiologists, molecular biologists, infectious disease experts, statisticians, biostatisticians, and public health scientists. This book focuses on the technological underpinnings of metagenomic approaches and their conceptual and practical applications. With the next-generation genomic sequencing revolution increasingly permitting researchers to decipher the coding information of the microbes living with us, we now have a unique capacity to compare multiple sites within individuals and at higher resolution and greater throughput than hitherto possible. The recent articulation of this paradigm points to unique possibilities for investigation of our dynamic relationship with these cellular communities, and excitingly the probing of their therapeutic potential in disease prevention or treatment of the future. - Expertly describes the latest metagenomic methodologies and best-practices, from sample collection to data analysis for taxonomic, whole shotgun metagenomic, and metatranscriptomic studies - Includes clear-headed pointers and quick starts to direct research efforts and increase study efficacy, eschewing ponderous prose - Presented topics include sample collection and preparation, data generation and quality control, third generation sequencing, advances in computational analyses of shotgun metagenomic sequence data, taxonomic profiling of shotgun data, hypothesis testing, and mathematical and computational analysis of longitudinal data and time series. Past-examples and prospects are provided to contextualize the applications.