Molecular Signatures of Virome-host Interactions PDF Download

Author: Poornima Parameswaran
Publisher:
ISBN:
Category :
Languages : en
Pages :

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Book Description
Small RNAs that are 19-30 nucleotides in length use the genetic information encoded in their sequence to effect gene regulation in a sequence-directed manner. Infections with RNA viruses in plants, worms and flies generate short viral-derived RNAs ("vsRNAs") that map to the genome of the infecting virus. The regulated production of these vsRNAs and their engagement by the immune apparatus is essential for inhibiting viral growth, making vsRNAs important components of antiviral immunity in these organisms. RNA virus-derived vsRNA-mediated gene silencing is yet to be demonstrated in mammalian systems. We investigated diverse RNA virus-mammalian systems, and characterized changes in small RNA populations that occur during viral infection in animal cells using high-throughput sequencing. Due to the large number of samples to be analyzed, we designed DNA barcodes to 'tag' RNA samples from individual experiments, which facilitated sequencing in parallel from multiple samples. Our work demonstrated the generality of RNA virus-derived vsRNA production, and the ability of the cellular short RNA apparatus to engage these vsRNAs in worms during Flock House Virus replication, and in mammalian cells during infections with Hepatitis C, Polio, Dengue, Vesicular Stomatitis or West Nile virus. In addition to the appearance of vsRNAs during infection, we saw a number of specific changes in host-encoded small RNA (miRNA) profiles. For several infection models investigated in more detail, the RNAi and Interferon pathways modulated the abundance of vsRNAs. We found evidence for populations of vsRNAs that exist as duplexed small interfering RNAs ("siRNAs; " effectors of gene silencing) with zero to three nucleotide 3' overhangs. We also observed strand-selective loading of siRNAs onto Argonaute complexes, which are mediators of gene silencing. We quantitated the capacity of these HCVrep-derived vsRNAs to down-regulate target mRNAs in a sequence-specific manner in mammalian systems. We found that abundant HCVrep vsRNAs are not capable of mediating robust silencing (i.e. 2-fold or higher) of Luciferase reporters that have been engineered with vsRNA targets. Additionally, over-expression of siRNAs corresponding to five abundant vsRNAs failed to enhance silencing of Hepatitis C Virus mRNA. These results complement each other and suggest that in mammalian hosts, the virus may coexist with an abundant population of vsRNAs. Questions still remain as to whether robust gene silencing may be achieved by the cooperative action of abundant vsRNAs, or if abundant vsRNAs specifically inhibited from functioning in gene silencing, or alternatively, if they have novel roles in pathways distinct from gene silencing.

Author: R. Ahmed
Publisher: Wiley-Blackwell
ISBN:
Category : Medical
Languages : en
Pages : 754

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Book Description
Persistent Viral Infections Edited by Rafi Ahmed Emory Vaccine Center, Atlanta, USA and Irvin S. Y. Chen UCLA School of Medicine, Los Angeles, USA During the past decade much of our attention has focused on diseases associated with viral persistence. Major breakthroughs in immunology, and the advent of molecular approaches to study pathogenesis have increased our understanding of the complex virus-host interactions that occur during viral persistence. Persistent Viral Infections focuses on: * The pathogenesis and immunology of chronic infections * Animal models that provide, or have the potential to provide, major insights This volume will be essential reading for virologists, immunologists, oncologists and neurologists.

Author: Günther Witzany
Publisher: Springer Science & Business Media
ISBN: 940074899X
Category : Science
Languages : en
Pages : 432

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Book Description
A renaissance of virus research is taking centre stage in biology. Empirical data from the last decade indicate the important roles of viruses, both in the evolution of all life and as symbionts of host organisms. There is increasing evidence that all cellular life is colonized by exogenous and/or endogenous viruses in a non-lytic but persistent lifestyle. Viruses and viral parts form the most numerous genetic matter on this planet.

Author: D. Dhanasekaran
Publisher: CRC Press
ISBN: 1000353141
Category : Medical
Languages : en
Pages : 863

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Book Description
Microbiota are a promising and fascinating subject in biology because they integrate the microbial communities in humans, animals, plants, and the environment. In humans, microbiota are associated with the gut, skin, and genital, oral, and respiratory organs. The plant microbial community is referred to as "holobiont," and it is influential in the maintenance and health of plants, which themselves play a role in animal health and the environment. The contents of Microbiome-Host Interactions cover all areas as well as new research trends in the fields of plant, animal, human, and environmental microbiome interactions. The book covers microbiota in polar soil environments, in health and disease, in Caenorhabditis elegans, and in agroecosystems, as well as in rice root and actinorhizal root nodules, speleothems, and marine shallow-water hydrothermal vents. Moreover, this book provides comprehensive accounts of advanced next-generation DNA sequencing, metagenomic techniques, high-throughput 16S rRNA sequencing, and understanding nucleic acid sequence data from fungal, algal, viral, bacterial, cyanobacterial, actinobacterial, and archaeal communities using QIIME software (Quantitative Insights into Microbial Ecology). FEATURES Summarizes recent insight in microbiota and host interactions in distinct habitats, including Antarctic, hydrothermal vents, speleothems, oral, skin, gut, feces, reproductive tract, soil, root, root nodules, forests, and mangroves Illustrates the high-throughput amplicon sequencing, computational techniques involved in the microbiota analysis, downstream analysis and visualization, and multivariate analysis commonly used for microbiome analysis Describes probiotics and prebiotics in the composition of the gut microbiota, skin microbiome impact in dermatologic disease prevention, and microbial communities in the reproductive tract of humans and animals Presents information in a reachable way for students, teachers, researchers, microbiologists, computational biologists, and other professionals who are interested in strengthening or enlarging their knowledge about microbiome analysis with next-generation DNA sequencing in the different branches of the sciences

Author: Manja Marz
Publisher: MDPI
ISBN: 3039218824
Category : Science
Languages : en
Pages : 330

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Book Description
Virus bioinformatics is evolving and succeeding as an area of research in its own right, representing the interface of virology and computer science. Bioinformatic approaches to investigate viral infections and outbreaks have become central to virology research, and have been successfully used to detect, control, and treat infections of humans and animals. As part of the Third Annual Meeting of the European Virus Bioinformatics Center (EVBC), we have published this Special Issue on Virus Bioinformatics.

Author: Jacques Izard
Publisher: Academic Press
ISBN: 0124105084
Category : Science
Languages : en
Pages : 188

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Book Description
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.

Author: Erle S. Robertson
Publisher: Springer
ISBN: 3030041557
Category : Medical
Languages : en
Pages : 406

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Book Description
This book ventures into a new and exciting area of discovery that directly ties our current knowledge of cancer to the discovery of microorganisms associated with different types of cancers. Recent studies demonstrate that microorganisms are directly linked to the establishment of cancers and that they can also contribute to the initiation, as well as persistence of, the cancers. Microbiome and Cancer covers the current knowledge of microbiome and its association with human cancers. It provides important reading for novices, senior undergraduates in cancer and microbiology, graduate students, junior investigators, residents, fellows and established investigators in the fields of cancer and microbiology. We cover areas related to known, broad concepts in microbiology and how they can relate to the ongoing discoveries of the micro-environment and the changes in the metabolic and physiologic states in that micro-environment, which are important for the ongoing nurturing and survival of the poly-microbial content that dictates activities in that micro-environment. We cover the interactions of microorganisms associated with gastric carcinomas, which are important for driving this particular cancer. Additional areas include oral cancers, skin cancers, ovarian cancers, breast cancers, nasopharyngeal cancers, lung cancers, mesotheliomas, Hodgkin’s and non-Hodgkin’s lymphomas, glioblastoma multiforme, hepatocellular carcinomas, as well as the inflammatory response related to the infectious agents in cancers. This book covers the metabolic changes that occur because of infection and their support for development of cancers, chronic infection and development of therapeutic strategies for detection and control of the infection. The field of microbiome research has exploded over the last five years, and we are now understanding more and more about the context in which microorganisms can contribute to the onset of cancers in humans. The field of microbiome research has demonstrated that the human body has specific biomes for tissues and that changes in these biomes at the specific organ sites can result in disease. These changes can result in dramatic differences in metabolic shifts that, together with genetic mutations, will produce the perfect niche for establishment of the particular infection programmes in that organ site. We are just beginning to understand what those changes are and how they influence the disease state. Overall, we hope to bring together the varying degrees of fluctuations in the microbiome at the major organ sites and how these changes affect the normal cellular processes because of dysregulation, leading to proliferation of the associated tissues.

Author: Chuan Qin
Publisher: Frontiers Media SA
ISBN: 2889767361
Category : Science
Languages : en
Pages : 271

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Author: Ajit Varma
Publisher: Springer Science & Business Media
ISBN: 3642602681
Category : Science
Languages : en
Pages : 539

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Mycorrhiza - symbiotic associations between plant roots and fungi - play a major role in many fundamental plant functions such as mineral nutrition or stress resistance. As the link between plants and the soil, mycorrhiza are now of great interest for developing new strategies in sustainable agriculture. Since they allow a decreased use of fertilizer and pesticides, negative impacts on the environment can be minimized. With contributions from renowned international scientists, this manual offers a great variety of practical protocols for analyzing mycorrhiza, including the latest molecular, biochemical, genetical, and physiological techniques.

Author: Bas E. Dutilh
Publisher: Frontiers Media SA
ISBN: 2889453081
Category :
Languages : en
Pages : 218

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Book Description
Since the late 1800s, the discovery of new viruses was a gradual process. Viruses were described one by one using a suite of techniques such as (electron) microscopy and viral culture. Investigators were usually interested in a disease state within an organism, and expeditions in viral ecology were rare. The advent of metagenomics using high-throughput sequencing has revolutionized not only the rate of virus discovery, but also the nature of the discoveries. For example, the viral ecology and etiology of many human diseases are being characterized, non-pathogenic viral commensals are ubiquitous, and the description of environmental viromes is making progress. This Frontiers in Virology Research Topic showcases how metagenomic and bioinformatic approaches have been combined to discover, classify and characterize novel viruses.