Download or read book JGI Fungal Genomics Program written by and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here.

Download or read book Fungal Genomics Program written by and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

Download or read book Fungal Genomics for Energy and Environment written by and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Sequencing Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 200 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

Download or read book Fueling the Future with Fungal Genomes written by and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Genomes of fungi relevant to energy and environment are in focus of the JGI Fungal Genomic Program. One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts and pathogens) and biorefinery processes (cellulose degradation and sugar fermentation) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Science Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 400 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics will lead to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here.

Download or read book Genomic Encyclopedia of Fungi written by and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

Download or read book MycoCosm an Integrated Fungal Genomics Resource written by and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: MycoCosm is a web-based interactive fungal genomics resource, which was first released in March 2010, in response to an urgent call from the fungal community for integration of all fungal genomes and analytical tools in one place (Pan-fungal data resources meeting, Feb 21-22, 2010, Alexandria, VA). MycoCosm integrates genomics data and analysis tools to navigate through over 100 fungal genomes sequenced at JGI and elsewhere. This resource allows users to explore fungal genomes in the context of both genome-centric analysis and comparative genomics, and promotes user community participation in data submission, annotation and analysis. MycoCosm has over 4500 unique visitors/month or 35000+ visitors/year as well as hundreds of registered users contributing their data and expertise to this resource. Its scalable architecture allows significant expansion of the data expected from JGI Fungal Genomics Program, its users, and integration with external resources used by fungal community.

Download or read book Fungal Genomics written by Minou Nowrousian and published by Springer Science & Business Media. This book was released on 2014-03-24 with total page 398 pages. Available in PDF, EPUB and Kindle. Book excerpt: The volume is divided into four sections, the first of which, Genome Sequences and Beyond, illustrates the impact of genome-based information and techniques on research ranging from model organisms like yeast to less-studied basal fungal lineages. Furthermore, it highlights novel types of analysis made possible by multi-genome comparisons as well as the impact of genomics on culture collections and vice versa. The second section, Cell and Developmental Biology, addresses questions that are important for fungal biology, e.g. the development of fungal fruiting bodies, and biology in general, e.g. chromatin organization and circadian rhythms. The third section, Genomics for Biotechnology, covers the search for plant biomass-converting enzymes in fungal genomes and work with industrially important fungi. The fourth section, focusing on Pathogenicity, offers chapters on the genomic analysis of plant and animal/human pathogens. It illustrates how genomics at all levels, from genome to metabolome, is used to study mechanisms of the interactions of fungi with other organisms.

Download or read book MycoCosm Portal written by and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: MycoCosm is a fungal genomics portal (http://jgi.doe.gov/fungi), developed by the US Department of Energy Joint Genome Institute to support integration, analysis and dissemination of fungal genome sequences and other omics data by providing interactive web-based tools. MycoCosm also promotes and facilitates user community participation through the nomination of new species of fungi for sequencing, and the annotation and analysis of resulting data. By efficiently filling gaps in the Fungal Tree of Life, MycoCosm will help address important problems associated with energy and the environment, taking advantage of growing fungal genomics resources.

Download or read book Fungal Genomics written by Ronald P. de Vries and published by Humana. This book was released on 2019-06-21 with total page 291 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume details protocols covering nearly all aspects of fungal genomics. New and updated chapters guide the reader through experimental genomics, biotechnologies, and the analysis and processing of data. Written in the highly 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Fungal Genomics : Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

Download or read book Harnessing the Flow of Data from Fungi at JGI written by and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) managed by Lawrence Berkeley National Laboratory, is the only user facility in the world devoted to problems of energy and environment. With over one million species, fungi--which include mushrooms--represent one of the largest under-explored branches of the Tree of Life. Together with its community of more than 1,000 scientific collaborators, JGI helping to unlock the secrets encoded in the genomes of fungi to advance a better understanding of the global carbon cycle and to develop new biotechnology products, next-generation biofuels, and medicines.

Download or read book Fungal Phylogenetics and Phylogenomics written by and published by Academic Press. This book was released on 2017-11-17 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fungal Phylogenetics and Phylogenomics, Volume 100, the latest release in the Advances in Genetics series, presents users with new chapters that delve into such topics as the Advances of fungal phylogenomics and the impact on fungal systematics, Data crunching for fungal phylogenomics: insights into data collection and phylogenetic inference based on genome data for fungi, Genomic and epigenomic traits of emerging fungal pathogens, Advances in fungal gene cluster diversity and evolution, Phylogenomics of Fusarium oxysporum species complex, Phylogenomic analyses of pathogenic yeasts, and the Phylogenetics and phylogenomics of rust fungi. The series continually publishes important reviews of the broadest interest to geneticists and their colleagues in affiliated disciplines, critically analyzing future directions. Critically analyzes future directions for the study of clinical genetics Written and edited by recognized leaders in the field Presents new medical breakthroughs that are occurring as a result of advances in our knowledge of genetics

Download or read book Mycoses in AIDS Patients written by Geert Cauwenbergh and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 329 pages. Available in PDF, EPUB and Kindle. Book excerpt: The World Health Organization estimates that at least five million people worldwide are infected with human immunodeficiency virus (HIV) Of these about 100,000 are in Asia and Oceania, 500,000 in Europe, 2 million in the Americas and 2.5 million in Africa (Mann, 1989). The acquired immunodeficiency syndrome is characterized by a derangement in cell-mediated immunity leading to opportunistic infections with for example Mycobacterium spp., Candida spp., Cryptococcus neoformans, Pneumocystis carinii, Toxoplasma gondii and Cryptosporidium. The third symposium on "Topics in Mycology" brought together 265 experts from 32 countries to discuss the epidemiology, immmunological and pathogenetic aspects of AIDS and its opportunistic infections in general and fungal infections in particular. Pneumocystis carinii pneumonia is by far the commonest opportunistic infection in AIDS patients. The nature and classification of P. carinii is still controversial. In search for its true taxonomic affinities an introductory paper formulates a number of key questions. Candidosis is another frequent opportunistic infection. A number of papers discuss the possibility that selective pressures may operate on Candida albicans within the AIDS population and influence its nature: this might have an impact on prophylaxis and curative and/or suppressive therapy.

Download or read book Plant Microbe Symbiosis Fundamentals and Advances written by Naveen Kumar Arora and published by Springer Science & Business Media. This book was released on 2013-08-15 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plant microbe interaction is a complex relationship that can have various beneficial impacts on both the communities. An urgent need of today’s world is to get high crop yields in an ecofriendly manner. Utilization of beneficial and multifaceted plant growth promoting (PGP) microorganisms can solve the problem of getting enhanced yields without disturbing the ecosystem thus leading to sustainability. For this to achieve understanding of the intricate details of how the beneficial microbes form associations with the host plant and sustain that for millions of years must be known. A holistic approach is required wherein the diversity of microbes associated with plant and the network of mechanisms by which they benefit the host must be studied and utilized. ‘Plant Microbe Symbiosis – Fundamentals and Advances’ provides a comprehensive understanding of positive interactions that occur between plant and microorganisms and their utilization in the fields. The book reviews the enormous diversity of plant associated microbes, the dialog between plant-microbes-microbes and mechanisms of action of PGP microbes. Utilization of PGPRs as nutrient providers, in combating phytopathogens and ameliorating the stressed and polluted soils is also explained. Importantly, the book also throws light on the unanswered questions and future direction of research in the field. It illustrates how the basic knowledge can be amalgamated with advanced technology to design the future bioformulations.

Download or read book Review of the Department of Energy s Genomics GTL Program written by National Research Council and published by National Academies Press. This book was released on 2006-04-19 with total page 102 pages. Available in PDF, EPUB and Kindle. Book excerpt: The U.S. Department of Energy (DOE) promotes scientific and technological innovation to advance the national, economic, and energy security of the United States. Recognizing the potential of microorganisms to offer new energy alternatives and remediate environmental contamination, DOE initiated the Genomes to Life program, now called Genomics: GTL, in 2000. The program aims to develop a predictive understanding of microbial systems that can be used to engineer systems for bioenergy production and environmental remediation, and to understand carbon cycling and sequestration. This report provides an evaluation of the program and its infrastructure plan. Overall, the report finds that GTL's research has resulted in and promises to deliver many more scientific advancements that contribute to the achievement of DOE's goals. However, the DOE's current plan for building four independent facilities for protein production, molecular imaging, proteome analysis, and systems biology sequentially may not be the most cost-effective, efficient, and scientifically optimal way to provide this infrastructure. As an alternative, the report suggests constructing up to four institute-like facilities, each of which integrates the capabilities of all four of the originally planned facility types and focuses on one or two of DOE's mission goals. The alternative infrastructure plan could have an especially high ratio of scientific benefit to cost because the need for technology will be directly tied to the biology goals of the program.

Download or read book 21st Century Guidebook to Fungi written by David Moore and published by Cambridge University Press. This book was released on 2020-05-08 with total page 611 pages. Available in PDF, EPUB and Kindle. Book excerpt: The mysterious world of fungi is once again unearthed in this expansive second edition. This textbook provides readers with an all-embracing view of the kingdom fungi, ranging in scope from ecology and evolution, diversity and taxonomy, cell biology and biochemistry, to genetics and genomics, biotechnology and bioinformatics. Adopting a unique systems biology approach - and using explanatory figures and colour illustrations - the authors emphasise the diverse interactions between fungi and other organisms. They outline how recent advances in molecular techniques and computational biology have fundamentally changed our understanding of fungal biology, and have updated chapters and references throughout the book in light of this. This is a fascinating and accessible guide, which will appeal to a broad readership - from aspiring mycologists at undergraduate and graduate level to those studying related disciplines. Online resources are hosted on a complementary website.

Download or read book 2012 U S Department of Energy written by and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The mission of the U.S. Department of Energy Joint Genome Institute (DOE JGI) is to serve the diverse scientific community as a user facility, enabling the application of large-scale genomics and analysis of plants, microbes, and communities of microbes to address the DOE mission goals in bioenergy and the environment. The DOE JGI's sequencing efforts fall under the Eukaryote Super Program, which includes the Plant and Fungal Genomics Programs; and the Prokaryote Super Program, which includes the Microbial Genomics and Metagenomics Programs. In 2012, several projects made news for their contributions to energy and environment research.

Download or read book Genomics of Soil and Plant Associated Fungi written by Benjamin A. Horwitz and published by Springer Science & Business Media. This book was released on 2013-08-30 with total page 394 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume addresses the similarities and also the differences in the genomes of soil saprophytes, symbionts, and plant pathogens by using examples of fungal species to illustrate particular principles. It analyzes how the specific interactions with the hosts and the influence of the environment may have shaped genome evolution. The relevance of fungal genetic research and biotechnological applications is shown for areas such as plant pathogenesis, biomass degradation, litter decomposition, nitrogen assimilation, antibiotic production, mycoparasitism, energy, ecology, and also for soil fungi turning to human pathogens. In addition to the model organisms Neurospora and Aspergillus, the following species are covered providing a view of pathogens and mutualists: Trichoderma, Fusarium oxysporum, Cochliobolus heterostrophus, Penicillium chrysogenum, Rhizopus oryzae, Podospora anserina, and species belonging to Agaricomycetes, Archaeorhizomycetes and Magnaporthaceae. Ecology and potential applications have guided the choice of fungal genes to be studied and it will be fascinating to follow the trends of future sequencing projects.