Download or read book Proteomic Studies of the Influenza Virus human Cell Interations written by Yimeng Wang and published by . This book was released on 2013 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt: Influenza A viruses (IAVs) continue to be a threat to human health. Despite extensive studies, the mechanisms underlying the IAVs-host interactions during IAV infection remain elusive. We employed quantitative proteomic methods to systematically explore the host cell protein expression responses to IAV infection and examine the function of a critical IAV protein called NS1 by identifying its host binding partners. Specifically, we used a 2-dimentional gel electrophoresis (2-DE) based proteomic method to screen host proteins whose expression was substantially altered by IAV. One critical protein named IkappaB kinase-gamma (IKKgamma) was found to be significantly down-regulated during IAV infection. Functional studies indicated that IKKgamma and IAVs were mutually inhibitory and IKKgamma might be the target for virus to inhibit IFN production. IAV protein NS1 is known to play critical roles in viral pathogenesis and host immune responses. Through 2-DE proteomic approach and mass spectrometry, we identified several novel host cellular proteins that were associated with NS1. First, we found that heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) interacted with NS1, affected replication, transcription, expression and nucleo-cytoplasmic translocation of NS1 mRNA, and the eventual whole virus replication. Second, two ATPase proteins, RUVBL1 and RUVBL2, were identified to associate with NS1 for regulation of cell apoptosis in the absence of IFNs. Third, based on previous finding of the interaction between a DEAD family protein designated as DDX100 and NS1 through a more sensitive proteomic approach called SILAC (stable isotope labeling with amino acids in cell culture), we found this interaction promoted virus replication through enhancing viral NS1 gene replication, transcription, and dsRNA unwinding. In summary, through quantitative proteomic, molecular and cell biology studies, we generated the global picture of host cell protein expression responses to IAV infection. For IAV NS1, several host cellular proteins were found to interact with NS1 to regulate the host cell action and virus proliferation.

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.

Download or read book Proteomics Method Development and Application for Interaction of Influenza Virus and Cells written by Hanzhi Wu and published by . This book was released on 2013 with total page 179 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Proteomic and Functional Studies of the Influenza A Virus PA X Protein written by Brittany Porter and published by . This book was released on 2019 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Viral RNA endonuclease activity is required for influenza A virus (IAV) replication. This activity resides in the polymerase acidic (PA) protein, which assembles into viral RNA-dependent RNA polymerase (RdRp) complexes and cleaves nascent host pre-mRNAs proximal to 5'-m7G caps, creating primers for viral mRNA synthesis. A rare (+1) ribosomal frameshifting event during translation of the PA open reading frame (ORF) creates the polymerase acidic-X (PA-X) protein. PA-X retains the amino-terminal PA RNA endonuclease domain, but contains a novel short carboxy-terminus, dubbed the X-ORF. Accumulating evidence indicates PA-X is a host shutoff protein functioning in the nucleus, selectively cleaving RNAs transcribed by host RNA polymerase II (pol II) while sparing RNA pol I, III, and viral transcripts. The molecular mechanism for this specificity remains to be elucidated. I hypothesize that PA-X gains access to target RNAs by X-ORF-mediated interaction with host proteins. In this study, I used a proximity labeling proteomic method known as BioID to identify host proteins that interact with the X-ORF. In BioID, fusion of the bait protein to a promiscuous biotin ligase allows efficient biotinylation of lysine residues on nearby proteins. X-ORF baits subjected to BioID included a 61-amino acid variant from A/Puerto Rico/8/1934 (H1N1) and a truncated 41-amino acid variant from A/California/7/2009 (H1N1), as well as a mutant X-ORF lacking basic residues required for nuclear localization. Affinity-purified proteins were trypsinized, subjected to reductive dimethylation with stable isotope tags, and identified by mass spectrometry. Using quantitative analysis, 29 high-confidence candidate X-ORF-interacting proteins were identified. X-ORF interacting proteins were validated using a luciferase-based functional assay in cells where each candidate host gene was silenced by short-hairpin RNAs. Through this study, the cleavage factor I (CFIm) complex proteins, cleavage and polyadenylation specificity factor subunit 5 (CPSF5) and CPSF6, were identified as required for PA-X function. The CFIm complex is poorly characterized but is known to influence site selection for mRNA 3'-end cleavage and polyadenylation. My observations are concordant with the emerging model for PA-X host shutoff activity, which has been shown to require canonical mRNA 3'-end processing mechanisms.

Download or read book Identification of Cellular Proteases Involved in Influenza A Virus Replication written by Mable Hagan and published by . This book was released on 2016 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Influenza viruses circulate worldwide and are a serious public health concern, causing annual epidemics of human respiratory tract infections. Reassortment of gene segments between different strains of influenza can generate new pandemic strains, like the 2009 H1N1 pandemic and the current H7N9 avian influenza virus. Vaccines are the most effective option to limit the impact of a pandemic, however preparation of a new vaccine takes months. Antiviral treatment is recommended until a vaccine is available, however the efficacy of current antivirals is highly susceptible to the development of resistance. These pitfalls prioritize the need to discover new compounds targeting essential functions of the virus. My thesis focuses on the identification of cellular proteases that are required for influenza virus replication to develop as potential antiviral targets. Proteolytic cleavage of influenza virus hemagglutinin (HA) is essential for infectivity. Although several cellular proteases have shown HA cleaving activity, these proteases demonstrate significant variation in the cleavage efficiency across the HA subtypes found in human and avian viruses, including some subtypes that are not cleaved by any of these proteases. This work aimed to identify novel cellular proteases that are involved in HA activation by using a human protease siRNA library to screen Caco2 cells infected with a seasonal GFP-expressing influenza virus. Potential proteases identified were validated using wild-type influenza viruses of different subtypes. The most promising protease candidate identified was MASP1, and a MASP1 stably-knocked down Caco2 (MASP1-KD) cell line was generated. MASP1 was shown to be essential for efficient replication of a broad range of influenza virus subtypes. Assessment of where MASP1 fits into the influenza virus life cycle revealed that MASP1 most likely is involved in later stages of viral replication. Comparison of the proteomic profiles between Caco2 and MASP1-KD cells further revealed possible cellular pathway interactions that MASP1 may be involved in. The discovery of a new role for MASP1 in the replication of influenza viruses, and possibly other viral families, provides a strong foundation for future studies to evaluate the effectiveness of MASP1 therapeutics and expands our knowledge of virus and host biology.

Download or read book Human Herpesviruses written by Ann Arvin and published by Cambridge University Press. This book was released on 2007-08-16 with total page 1325 pages. Available in PDF, EPUB and Kindle. Book excerpt: This comprehensive account of the human herpesviruses provides an encyclopedic overview of their basic virology and clinical manifestations. This group of viruses includes human simplex type 1 and 2, Epstein–Barr virus, Kaposi's Sarcoma-associated herpesvirus, cytomegalovirus, HHV6A, 6B and 7, and varicella-zoster virus. The viral diseases and cancers they cause are significant and often recurrent. Their prevalence in the developed world accounts for a major burden of disease, and as a result there is a great deal of research into the pathophysiology of infection and immunobiology. Another important area covered within this volume concerns antiviral therapy and the development of vaccines. All these aspects are covered in depth, both scientifically and in terms of clinical guidelines for patient care. The text is illustrated generously throughout and is fully referenced to the latest research and developments.

Download or read book RNA Tagging written by Manfred Heinlein and published by Humana. This book was released on 2021-08-08 with total page 490 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a compendium of state-of-the-art methods for the labeling, detection, and purification of RNA and RNA-protein complexes and thereby constitutes an important toolbox for researchers interested in understanding the complex roles of RNA molecules in development, signaling, and disease. Beginning with a section on in situ detection of RNA molecules using FISH techniques, the volume continues with parts exploring in vivo imaging of RNA transport and localization, imaging and analysis of RNA uptake and transport between cells, identification and analysis of RNA-binding proteins, guide RNAs in genome editing, as well as other specific analytical techniques. 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. Authoritative and practical, RNA Tagging: Methods and Protocols serves as a vital reference for researchers looking to further the increasingly important research in RNA biology.

Download or read book The Ribonucleic Acids written by P.R. Stewart and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 379 pages. Available in PDF, EPUB and Kindle. Book excerpt: The central role of the ribonucleic acids (RNA) in mediating the expression of information encoded in DNA in living cells is now well established. Research in this area of biology continues at a remarkable rate, and new and significant information appears almost daily in a wide range of journals, published symposia and specialist reviews. The diverse nature of this information makes it difficult for the newcomer to the field of RNA biochemistry to obtain a general view of established concepts, current activity, and new advances. Moreover, the reviews available are frequently concerned with insular aspects of these Ubiquitous molecules, or in the case of text books, the subject is treated as part of a general outline of proper ties of nucleic acids and thus may be superficial. The authors of the chapters in this collection attempt to provide a comprehensive, though not overly detailed, outline of the biologi cal roles of RNA. They have written for students with basic training in biochemistry, but otherwise with a wide variety of biological interests-plant physiology, virology, organelle bio chemistry, genetics, cell biology, differentiation and development. Viral RNA, which was dealt with as a separate chapter in the first edition, has been deleted from this edition because it is an unman ageably large single topic, and at the same time is addressed in a number of ways in many different places in the book.

Download or read book The Glycome written by Adeel Malik and published by CRC Press. This book was released on 2021-07-07 with total page 305 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides a comprehensive understanding of the enigmatic identity of the glycome, a complex but important area of research that has been largely ignored due to its complexity. The authors thoroughly deal with almost all aspects of the glycome, i.e., elucidation of the glycan identity enigma and its role in regulation of the cellular process, and in disease etiology. The book bridges the knowledge gap in understanding the glycome, from being a cell signature to its applications in disease etiology. In addition, it details many of the major insights regarding the possible role of the glycome in various diseases as a therapeutic marker. The book systematically covers the major aspects of the glycome, including the significance of substituting the diverse monosaccharide units to glycoproteins, the role of glycans in disease pathologies, and the challenges and advances in glycobiology. The authors stress the significance and huge encoding power of carbohydrates as well as provide helpful insights in framing the bigger picture. The Glycome: Understanding the Diversity and Complexity of Glycobiology details state-of-the-art developments and emerging challenges of glycome biology, which are going to be key areas of future research, not only in the glycobiology field but also in pharmaceutics.

Download or read book Virus Bioinformatics written by Manja Marz and published by MDPI. This book was released on 2020-02-21 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Influenza Virology written by Yoshihiro Kawaoka and published by Horizon Scientific Press. This book was released on 2006 with total page 367 pages. Available in PDF, EPUB and Kindle. Book excerpt: World renowned scientists critically review the most important issues in this rapidly expanding field.

Download or read book Human Influenza New Insights for the Healthcare Professional 2011 Edition written by and published by ScholarlyEditions. This book was released on 2012-01-09 with total page 35 pages. Available in PDF, EPUB and Kindle. Book excerpt: Human Influenza: New Insights for the Healthcare Professional: 2011 Edition is a ScholarlyPaper™ that delivers timely, authoritative, and intensively focused information about Human Influenza in a compact format. The editors have built Human Influenza: New Insights for the Healthcare Professional: 2011 Edition on the vast information databases of ScholarlyNews.™ You can expect the information about Human Influenza in this eBook to be deeper than what you can access anywhere else, as well as consistently reliable, authoritative, informed, and relevant. The content of Human Influenza: New Insights for the Healthcare Professional: 2011 Edition has been produced by the world’s leading scientists, engineers, analysts, research institutions, and companies. All of the content is from peer-reviewed sources, and all of it is written, assembled, and edited by the editors at ScholarlyEditions™ and available exclusively from us. You now have a source you can cite with authority, confidence, and credibility. More information is available at http://www.ScholarlyEditions.com/.

Download or read book Recoding Expansion of Decoding Rules Enriches Gene Expression written by John F. Atkins and published by Springer Science & Business Media. This book was released on 2010-03-10 with total page 473 pages. Available in PDF, EPUB and Kindle. Book excerpt: The literature on recoding is scattered, so this superb book ?lls a need by prov- ing up-to-date, comprehensive, authoritative reviews of the many kinds of recoding phenomena. Between 1961 and 1966 my colleagues and I deciphered the genetic code in Escherichia coli and showed that the genetic code is the same in E. coli, Xenopus laevis, and guinea pig tissues. These results showed that the code has been c- served during evolution and strongly suggested that the code appeared very early during biological evolution, that all forms of life on earth descended from a c- mon ancestor, and thus that all forms of life on this planet are related to one another. The problem of biological time was solved by encoding information in DNA and retrieving the information for each new generation, for it is easier to make a new organism than it is to repair an aging, malfunctioning one. Subsequently, small modi?cations of the standard genetic code were found in certain organisms and in mitochondria. Mitochondrial DNA only encodes about 10–13 proteins, so some modi?cations of the genetic code are tolerated that pr- ably would be lethal if applied to the thousands of kinds of proteins encoded by genomic DNA.

Download or read book Experimental Models of Multiple Sclerosis written by Ehud Lavi and published by Springer Science & Business Media. This book was released on 2008-01-03 with total page 892 pages. Available in PDF, EPUB and Kindle. Book excerpt: Multiple Sclerosis (MS) is an enigmatic immune mediated disease of the central nervous system that affects about 350,000 individuals in the US, and many more around the world. The mechanism of this disease is largely unknown and there is no cure for it. However, there are several well-characterized experimental animal models that help us understand and speculate about potential mechanisms of pathology in this disease. Many of the experimental therapies designed for this disease rely on testing the drugs in animal models before using it in clinical trials. This book combines for the first time the different experimental models for MS (including immune-mediated and viral) under one roof, and highlights aspects that are different or shared among these experimental models. It’s aim is to improve our understanding of this devastating disease and help us think about potential additional therapies for it.

Download or read book Influenza Virus written by Yohei Yamauchi and published by Humana. This book was released on 2019-09-11 with total page 663 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides researchers with widely used techniques for the study of virology, focusing on molecular biology and imaging to encourage mechanistic investigation of virus-host interactions. Chapters detail a broad range of methods from diagnosis, virus propagation, proteomics, haploid screening, lentiviral screening, virus entry, single molecule RNA imaging, correlative light and electron microscopy (CLEM), EM, light-sheet microscopy, biochemistry, viral transcription, physiological infection models, animal models, in vivo imaging, antigenic evolution, immunology to mathematical modelling. Reviews cover general influenza, clinical trials, both sides of the gain-of-function debate, and computational modelling. 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. Cutting-edge and thorough, Influenza Virus: Methods and Protocols aims to motivate experienced researchers and newcomers in the field and improve our overall understanding of influenza.

Download or read book Virology Methods Manual written by Hillar O. Kangro and published by Elsevier. This book was released on 1996-04-16 with total page 385 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Virology Methods Manual is a comprehensive source of methods for the study, manipulation, and detection of viruses. Edited by Brian Mahy and Hillar Kangro, this work describes the most up-to-date, definitive techniques, provided by experts in each area, and presented with easy-to-use, step-by-step protocols. This new manual will satisfy the needs of virologists and all those working with viruses who need a practical guide to methods that work! - Provides up-to-date techniques by experts worldwide - Presents common, step-by-step protocols in an attractive, easy-to-use fashion - Contains useful appendices including virus taxonomy, metabolic inhibitors, and Bio-safety in the virology laboratory

Download or read book Proteomics Approaches to Unravel Virus Vertebrate Host Interactions written by and published by Academic Press. This book was released on 2021-04-30 with total page 270 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteomics Approaches to Unravel Virus - Vertebrate Host Interactions, Volume 109 in the Advances in Virus Research series, highlights state-of-the art mass spectrometry techniques to elucidate the tight interplay of vertebrate viruses and their host cells. The volume includes chapters on Spatio-temporal resolution of host protein complexes during virus entry, Proteomic approaches to investigate gammaherpesvirus biology and associated tumorigenesis, Applications of Mass Spectrometry Imaging in Virus Research, Mapping surfaceome dynamics during viral infection, Characterization of proteolytic events in virus-host interactions, Dynamic protein network modulation upon viral infection, and much more. - Discusses the latest methodological breakthroughs in mass spectrometry-based proteomics - Reviews how technology has advanced our knowledge on virus-host interactions - Provides future perspectives on proteomics research in virology