Download or read book Identification of Novel Positive strand RNA Viruses by Metagenomic Analysis of Archaea dominated Yellowstone Hot Springs written by Benjamin Bolduc and published by . This book was released on 2012 with total page 12 pages. Available in PDF, EPUB and Kindle. Book excerpt: There are no known RNA viruses that infect Archaea. Filling this gap in our knowledge of viruses will enhance our understanding of the relationships between RNA viruses from the three domains of cellular life and, in particular, could shed light on the origin of the enormous diversity of RNA viruses infecting eukaryotes. We describe here the identification of novel RNA viral genome segments from high-temperature acidic hot springs in Yellowstone National Park in the United States. These hot springs harbor low-complexity cellular communities dominated by several species of hyperthermophilic Archaea. A viral metagenomics approach was taken to assemble segments of these RNA virus genomes from viral populations isolated directly from hot spring samples. Analysis of these RNA metagenomes demonstrated unique gene content that is not generally related to known RNA viruses of Bacteria and Eukarya. However, genes for RNA-dependent RNA polymerase (RdRp), a hallmark of positive-strand RNA viruses, were identified in two contigs. One of these contigs is approximately 5,600 nucleotides in length and encodes a polyprotein that also contains a region homologous to the capsid protein of nodaviruses, tetraviruses, and birnaviruses. Phylogenetic analyses of the RdRps encoded in these contigs indicate that the putative archaeal viruses form a unique group that is distinct from the RdRps of RNA viruses of Eukarya and Bacteria. Collectively, our findings suggest the existence of novel positive-strand RNA viruses that probably replicate in hyperthermophilic archaeal hosts and are highly divergent from RNA viruses that infect eukaryotes and even more distant from known bacterial RNA viruses. These positive-strand RNA viruses might be direct ancestors of RNA viruses of eukaryotes.

Download or read book Analysis of Archaeal Viruses and Characterization of Their Communities in Yellowstone National Park written by Benjamin Ian Bolduc and published by . This book was released on 2014 with total page 244 pages. Available in PDF, EPUB and Kindle. Book excerpt: Viruses infecting the Archaea - the third domain of life - are the least understood of all viruses. Despite only 100 archaeal viruses being described, work on these viruses revealed a remarkable level of morphological and genetic diversity unmatched by their bacterial and eukaryotic counterparts, whose numbers range over 6000. Study of these archaeal viruses could gain insight into fundamental aspects of biology and reveal underlying evolutionary connections spanning the three domains of life, including the origin of life. In addition, we understand very little about their community structures in natural environments. To address these daunting tasks, a viral metagenomics approach was undertaken using next generation sequencing technologies. Despite this, only a fragmented view of the viral communities is possible in natural ecosystems. Therefore, this dissertation sought to apply a network-based approach in combination with viral metagenomics to not only describe natural viral communities, but to find and characterize the first RNA viruses out of acidic, high-temperature hot springs in Yellowstone National Park, USA. These hot springs harbor low complexity cellular communities dominated by several species of hyperthermophilic Archaea. The results of this dissertation show that this approach can identify distinct viral populations and provide insights into the viral community. Furthermore, the viral communities of these hot springs are relatively stable over the course of the sampling time period. In addition, a number of viral clusters - each representing a viral family at the taxonomic level - are likely previously uncharacterized DNA viruses infecting archaeal hosts. This approach demonstrates the utility of combining viral community sequencing with a network analysis to understand viral community structures in natural ecosystems. Additional analysis of these viral metagenomes led to the identification of novel RNA viral genome segments. Since no RNA virus infecting Archaea is known to exist, this dissertation also sought to more fully characterize these sequences. Genes for RNA-dependent RNA polymerases, a hallmark of positive-strand RNA viruses were identified, suggesting the existence of novel positive-strand RNA viruses likely replicating in hyperthermophilic archaeal hosts and are highly divergent from RNA viruses infecting eukaryotes and are even more distant from known bacterial RNA viruses.

Download or read book Biocommunication of Archaea written by Guenther Witzany and published by Springer. This book was released on 2017-09-27 with total page 335 pages. Available in PDF, EPUB and Kindle. Book excerpt: Archaea represent a third domain of life with unique properties not found in the other domains. Archaea actively compete for environmental resources. They perceive themselves and can distinguish between ‘self’ and ‘non-self’. They process and evaluate available information and then modify their behaviour accordingly. They assess their surroundings, estimate how much energy they need for particular goals, and then realize the optimum variant. These highly diverse competences show us that this is possible owing to sign(aling)- mediated communication processes within archaeal cells (intra-organismic), between the same, related and different archaeal species (interorganismic), and between archaea and nonarchaeal organisms (transorganismic). This is crucial in coordinating growth and development, shape and dynamics. Such communication must function both on the local level and between widely separated colony parts. This allows archaea to coordinate appropriate response behaviors in a differentiated manner to their current developmental status and physiological influences. This book will orientate further investigations on how archaeal ecosphere inhabitants communicate with each other to coordinate their behavioral patterns and whats the role of viruses in this highly dynamic interactional networks.

Download or read book Microbial Ecology of Extreme Environments written by Caroline Chénard and published by Springer. This book was released on 2017-03-15 with total page 254 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book explores microbial lifestyles, biochemical adaptations, and trophic interactions occurring in extreme environments. By summarizing the latest findings in the field it provides a valuable reference for future studies. Spark ideas for biotechnological and commercial exploitation of microbiomes at the extremes of life are presented. Chapters on viruses complement this highly informative book. In a vertical journey through the microbial biosphere it covers aspects of cold environments, hot environments, extreme saline environments, and extreme pressure environments, and more. From the deep sea, through polar deserts, up to the clouds in the air - the diversity of microbial life in all habitats is described, explored, and comprehensively reviewed. Possible biotechnical applications are discussed. This book aims to provide a useful reference for those who want to start a research program in extreme microbiology and, hopefully, inspire new research directions.

Download or read book Fields Virology Emerging Viruses written by Peter M. Howley and published by Lippincott Williams & Wilkins. This book was released on 2020-02-11 with total page 2597 pages. Available in PDF, EPUB and Kindle. Book excerpt: Now in four convenient volumes, Field’s Virology remains the most authoritative reference in this fast-changing field, providing definitive coverage of virology, including virus biology as well as replication and medical aspects of specific virus families. This volume of Field’s Virology: Emerging Viruses, 7th Edition covers recent changes in emerging viruses, providing new or extensively revised chapters that reflect these advances in this dynamic field.

Download or read book Thermophilic Microbes in Environmental and Industrial Biotechnology written by Tulasi Satyanarayana and published by Springer Science & Business Media. This book was released on 2013-03-25 with total page 951 pages. Available in PDF, EPUB and Kindle. Book excerpt: The existence of life at high temperatures is quiet fascinating. At elevated temperatures, only microorganisms are capable of growth and survival. Many thermophilic microbial genera have been isolated from man-made (washing machines, factory effluents, waste streams and acid mine effluents) and natural (volcanic areas, geothermal areas, terrestrial hot springs, submarine hydrothermal vents, geothermally heated oil reserves and oil wells, sun-heated litter and soils/sediments) thermal habitats throughout the world. Both culture-dependent and culture-independent approaches have been employed for understanding the diversity of microbes in hot environments. Interest in their diversity, ecology, and physiology has increased enormously during the past few decades as indicated by the deliberations in international conferences on extremophiles and thermophiles held every alternate year and papers published in journals such as Extremophiles. Thermophilic moulds and bacteria have been extensively studied in plant biomass bioconversion processes as sources of industrial enzymes and as gene donors. In the development of third generation biofuels such as bioethanol, thermophilic fungal and bacterial enzymes are of particular interest. The book is aimed at bringing together scattered up-to-date information on various aspects of thermophiles such as the diversity of thermophiles and viruses of thermophiles, their potential roles in pollution control and bioremediation, and composting.

Download or read book Bacteriophages written by David R. Harper and published by Springer Nature. This book was released on 2021-01-30 with total page 1376 pages. Available in PDF, EPUB and Kindle. Book excerpt: This first major reference work dedicated to the mannifold industrial and medical applications of bacteriophages provides both theoretical and practical insights into the emerging field of bacteriophage biotechnology. The book introduces to bacteriophage biology, ecology and history and reviews the latest technologies and tools in bacteriophage detection, strain optimization and nanotechnology. Usage of bacteriophages in food safety, agriculture, and different therapeutic areas is discussed in detail. This book serves as essential guide for researchers in applied microbiology, biotechnology and medicine coming from both academia and industry.

Download or read book Advanced Techniques for Studying Microorganisms in Extreme Environments written by Étienne Yergeau and published by Walter de Gruyter GmbH & Co KG. This book was released on 2019-10-21 with total page 218 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book will highlight advanced techniques that were recently used for studying microorganisms in extreme environments. Recent technological leaps in the study of microorganisms in the environment now make it possible to comprehensively study microbes in the environment. Extreme environments could benefit from the application of these techniques, but many challenges such as low biomass, low activity and slow growth has prevented their wide adoption. This book will review recent application of state-of-the-art techniques in extreme environments, helping researcher and graduate students get a better knowledge of the tools available.

Download or read book Biocommunication of Phages written by Guenther Witzany and published by Springer Nature. This book was released on 2020-06-29 with total page 499 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the first book to systemize all levels of communicative behavior of phages. Phages represent the most diverse inhabitants on this planet. Until today they are completely underestimated in their number, skills and competences and still remain the dark matter of biology. Phages have serious effects on global energy and nutrient cycles. Phages actively compete for host. They can distinguish between ‘self’ and ‘non-self’ (complement same, preclude others). They process and evaluate available information and then modify their behaviour accordingly. These diverse competences show us that this capacity to evaluate information is possible owing to communication processes within phages (intra-organismic), between the same, related and different phage species (interorganismic), and between phages and non-phage organisms (transorganismic). This is crucial in coordinating infection strategies (lytic vs. lysogenic) and recombination in phage genomes. In 22 chapters, expert contributors review current research into the varying forms of phage biocommunication and Phagetherapy. Biocommunication of Phages aims to assess the current state of research, to orient further investigations on how phages communicate with each other to coordinate their behavioral patterns, and to inspire further investigation of the role of non-phage viruses (non-lytic, non-prokaryotic) in these highly dynamic interactional networks.

Download or read book Plant Virus Host Interaction written by R.K. Gaur and published by Academic Press. This book was released on 2021-01-12 with total page 584 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plant Virus-Host Interaction: Molecular Approaches and Viral Evolution, Second Edition, provides comprehensive coverage of molecular approaches for virus-host interaction. The book contains cutting-edge research in plant molecular virology, including pathogenic viroids and transport by insect vectors, interference with transmission to control viruses, synergism with pivotal coverage of RNA silencing, and the counter-defensive strategies used by viruses to overcome the silencing response in plants. This new edition introduces new, emerging proteins involved in host-virus interactions and provides in-depth coverage of plant virus genes’ interactions with host, localization and expression. With contributions from leading experts, this is a comprehensive reference for plant virologists, molecular biologists and others interested in characterization of plant viruses and disease management. Introduces new, emerging proteins involved during the host-virus interaction and new virus strains that invade new crops through recombination, resorting and mutation Provides molecular approaches for virus-host interaction Highlights RNA silencing and counter-defensive strategies for disease management Discusses the socioeconomic implications of viral spread and mitigation techniques

Download or read book Trends in Quorum Sensing and Quorum Quenching written by V. Ravishankar Rai and published by CRC Press. This book was released on 2020-05-04 with total page 628 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book on Trends in Quorum Sensing and Quorum Quenching: New Perspectives and Applications focuses on the recent advances in the field of quorum sensing in bacteria and the novel strategies developed for quorum sensing inhibition. The topics covered are multidisciplinary and wide-ranging,and includes quorum sensing phenomenon in pathogenic bacteria, food spoilers, and agriculturally relevant bacteria. The applications of quorum sensing inhibitors such as small molecules, bioactives, natural compounds, and quorum quenching enzymes in controlling bacterial infections in clinical settings, agriculture and aquaculture are discussed. The potential use of quorum quenching enzymes for mitigating biofouling is also covered. Special focus is given to exploring quorum sensing inhibitors from microbes and flora inhabiting biodiversity rich regions including tropical rain forests and marine environments. Key features: Covers the fundamental aspects, the progress and challenges in the field of quorum sensing and quorum quenching Reviews quorum sensing in Gram-positive and Gram-negative bacteria of clinical, agricultural, and industrial relevance Discusses the application and future trends of quorum sensing inhibitors from lab to clinical and environmental settings Provides comprehensive coverage on molecular mechanisms in bacterial signaling

Download or read book Diversity of Putative Archaeal RNA Viruses in Metagenomic Datasets of a Yellowstone Acidic Hot Spring written by Hongming Wang and published by . This book was released on 2015 with total page 6 pages. Available in PDF, EPUB and Kindle. Book excerpt: Two genomic fragments (5,662 and 1,269 nt in size, GenBank accession no. JQ756122 and JQ756123, respectively) of novel, positive-strand RNA viruses that infect archaea were first discovered in an acidic hot spring in Yellowstone National Park (Bolduc et al., 2012). To investigate the diversity of these newly identified putative archaeal RNA viruses, global metagenomic datasets were searched for sequences that were significantly similar to those of the viruses. A total of 3,757 associated reads were retrieved solely from the Yellowstone datasets and were used to assemble the genomes of the putative archaeal RNA viruses. Nine contigs with lengths ranging from 417 to 5,866 nt were obtained, 4 of which were longer than 2,200 nt; one contig was 204 nt longer than JQ756122, representing the longest genomic sequence of the putative archaeal RNA viruses. These contigs revealed more than 50% sequence similarity to JQ756122 or JQ756123 and may be partial or nearly complete genomes of novel genogroups or genotypes of the putative archaeal RNA viruses. Sequence and phylogenetic analyses indicated that the archaeal RNA viruses are genetically diverse, with at least 3 related viral lineages in the Yellowstone acidic hot spring environment.

Download or read book Microbes from Hell written by Patrick Forterre and published by University of Chicago Press. This book was released on 2016-10-07 with total page 282 pages. Available in PDF, EPUB and Kindle. Book excerpt: Patrick Forterre is a leading expert on archaea and thermophiles, and in Microbes from Hell (originally published as Microbes de l enfer by Belin, 2007) he offers an engaging, colorful overview of Archaea: single-celled microorganisms that were initially found in extreme habitats such as Yellowstone s volcanic hot springs. He starts with a history of Archaea s discovery and the conceptual revolution it sparked in our understanding of life s evolution; then, in the second chapter, he provides a personal account of his own search for thermophiles. In chapter three, Mr. Forterre discusses the challenges of living in high-temperature environments along with the ways in which thermophiles have adapted to them. In chapters four and five, he examines their relationships to other organisms as well as their role in the early evolution of life. Last, he presents the latest discoveries in thermophile research."

Download or read book Population Genomics Microorganisms written by Martin F. Polz and published by Springer. This book was released on 2019-01-07 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt: Population genomics is a rapidly emerging field that has the potential to transform our understanding of how evolutionary forces shape genomic diversity among microbes. There have already been considerable advances in understanding gene flow and spread of adaptive traits, and in linking epidemiology with evolutionary biology. The current challenge is to find unifying evolutionary principles for organisms that display a wide range of reproductive biology – from highly clonal to promiscuous – and for which the vast majority have eluded cultivation. This requires interdisciplinary approaches that incorporate novel computational tools, testing of existing and novel population genetic models, and creative new ways of linking genetic diversity to ecological factors. This pioneering book will discuss the advances made and promises of population genomics in microorganisms, outlining some of the key theoretical and practical challenges for microbial population genomics, including defining and identifying populations, genomics-based reverse ecology and building appropriate tools to understand microbes in a variety of complex environments.

Download or read book Structure and Physics of Viruses written by Mauricio G. Mateu and published by Springer Science & Business Media. This book was released on 2013-06-04 with total page 734 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book contemplates the structure, dynamics and physics of virus particles: From the moment they come into existence by self-assembly from viral components produced in the infected cell, through their extracellular stage, until they recognise and infect a new host cell and cease to exist by losing their physical integrity to start a new infectious cycle. (Bio)physical techniques used to study the structure of virus particles and components, and some applications of structure-based studies of viruses are also contemplated. This book is aimed first at M.Sc. students, Ph.D. students and postdoctoral researchers with a university degree in biology, chemistry, physics or related scientific disciplines who share an interest or are actually working on viruses. We have aimed also at providing an updated account of many important concepts, techniques, studies and applications in structural and physical virology for established scientists working on viruses, irrespective of their physical, chemical or biological background and their field of expertise. We have not attempted to provide a collection of for-experts-only reviews focused mainly on the latest research in specific topics; we have not generally assumed that the reader knows all of the jargon and all but the most recent and advanced results in each topic dealt with in this book. In short, we have attempted to write a book basic enough to be useful to M.Sc and Ph.D. students, as well as advanced and current enough to be useful to senior scientists with an interest in Structural and/or Physical Virology.

Download or read book Recent Discoveries in Evolutionary and Genomic Microbiology written by Anton G. Kutikhin and published by Frontiers Media SA. This book was released on 2015-08-04 with total page 101 pages. Available in PDF, EPUB and Kindle. Book excerpt: This collection represents certain discoveries that were made in evolutionary and genomic microbiology during the recent ten years. We attempted to shed light on topical issues of microbial evolution and microbiome biology. In our eyes, these articles are of an excellent quality and may be helpful both for casual readers and for specialists in the field.

Download or read book Global host proteomic responses to virus infection written by Kevin Coombs and published by Frontiers E-books. This book was released on with total page 121 pages. Available in PDF, EPUB and Kindle. Book excerpt: The field of virology has seen explosive growth in the past few decades. A large amount of effort has gone into successfully delineating virus evolution, genetic diversity, immunology, pathogenesis, structure, vaccine development, viral gene expression and genomic replication strategies. In addition, considerable recent work has been focusing on cellular responses to infection as well as how viruses may induce transformation and oncogenesis. Viruses are obligate intracellular parasites and thus absolutely dependent upon host cells. Not surprisingly, they often cause profound changes in cells, including apoptosis, death and signalling, to name a few perturbations. Thus, the molecular signals for how viruses induce pathophysiological alterations in their hosts have been of growing recent interest. Cellular and organismal responses, such as those induced by virus infection, are invariably mediated by changes in gene and protein expression and modification. Thus, there has been keen interest in understanding how gene and protein expressions and modifications are quantitatively and qualitatively affected by such challenges. From a historical perspective, most early work that examined host protein responses to virus infection employed “biased” approaches, in which investigators targeted a limited number, or only one cellular molecule of interest. Completion of many organisms’ genome sequences has allowed the global “non-biased” simultaneous analysis of the entire repertoire of cellular mRNA species, the transcriptome, by gene micro-arrays. This has provided significant information about how cellular gene expressions are altered by virus-induced perturbations, but has not provided as much information about the encoded proteins. This results for several reasons, including, but not limited to the fact that gene expression levels cannot accurately predict protein expression levels, nor the types and extent of post-translational modifications, many genes encode multiple proteins through splice variants, and protein activity may be affected by a large number of conditions, including phosphorylation. Recent technological and bioinformatic approaches make it now possible to begin to extend similar global analyses to probe the cellular proteome, the repertoire of the actual effector molecules. One general strategy has been to take advantage of improved separations technologies, as well as greatly improved mass spectrometry resolution, to quantitatively or comparatively measure hundreds or thousands of proteins. Proteins from multiple conditions (i.e., mock-infected and infected) may be differentially labelled by various techniques, such as 2D-DIGE, ICAT, iTRAQ, SILAC, with 18O during peptide preparation, and/or by various other methods, and then compared to measure comparative alterations in the levels of proteins induced by the virus infection. Such analyses have also been extended by using “label-free” methods for more efficient multiplexing applications, and/or by examining specific protein modifications. In addition, concerted efforts to raise antibodies against all cellular proteins have resulted in the development of “antibody arrays,” which are also generally used for quantitative or comparative assays. Finally, while assays, such as the above, are generally limited to delineating the absolute amount of specific proteins, newer technologies have been developed that allow the simultaneous probing of hundreds of proteins’ functions. Assays, such as “Activity Based Protein Profiling”, are designed to probe enzymatic activity, with current focus on broad-spectrum proteases and other enzymatic classes. This Research Topic will provide an overview of many of these methods, as well as numerous specific examples of each approach, and how they are used to better delineate the ways viruses affect cellular responses during infection.