Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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Reduction in Human Papillomavirus (HPV) Prevalence Among Young Women Following HPV Vaccine Introduction in the United States, National Health and Nutrition Examination Surveys, 2003–2010

Reduction in Human Papillomavirus (HPV) Prevalence Among Young Women Following HPV Vaccine Introduction in the United States, National Health and Nutrition Examination Surveys, 2003–2010 | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Conclusions. Within 4 years of vaccine introduction, the vaccine-type HPV prevalence decreased among females aged 14–19 years despite low vaccine uptake. The estimated vaccine effectiveness was high.

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Viruses, Immunology & Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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It's a group effort - the curators:

It's a group effort - the curators: | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

get in touch if you want to help curate this topic

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Bwana Moses's comment, May 25, 2016 6:13 AM
Great work. Keep it going.
Bwana Moses's comment, March 7, 12:46 PM
Thank You.
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Viruses and mobile elements as drivers of evolutionary transitions

Viruses and mobile elements as drivers of evolutionary transitions | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The history of life is punctuated by evolutionary transitions which engender emergence of new levels of biological organization that involves selection acting at increasingly complex ensembles of biological entities. Major evolutionary transitions includ
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Suppression of Poxvirus Replication by Resveratrol. - PubMed - NCBI

Front Microbiol. 2017 Nov 17;8:2196. doi: 10.3389/fmicb.2017.02196. eCollection 2017.
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Flu epidemic claims the lives of more than 200 Victorians this year

Flu epidemic claims the lives of more than 200 Victorians this year | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Australia's flu epidemic is expected to claim the lives of more than 200 people in Victoria this year, with more than 40,000 cases confirmed in the state and one in ten people sent to intensive care.

Via Ian M Mackay, PhD
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Algorithms for Phylogenetics | FifteenEightyFour | Cambridge University Press

Algorithms for Phylogenetics | FifteenEightyFour | Cambridge University Press | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Tandy Warnow explores difficulties in phylogeny estimation and how training the next-generation of algorithm developers will enable breakthroughs.
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 The curious “science” of integrative medicine (a lot of quackery) - a good explanation!

 The curious “science” of integrative medicine (a lot of quackery) - a good explanation! | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
I recently attended (and live-tweeted) an integrative medicine conference called “Get Your Life Back NOW!” held in Orlando, FL on November 3-4, 2017. There were actually three separate but related …
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Rapid re-identification of human samples using portable DNA sequencing

Rapid re-identification of human samples using portable DNA sequencing | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
DNA fingerprinting by portable nanopore sequencing is a novel re-identification method with applications in (clinical) laboratories and biobanks.
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Gene Therapy Hits a Peculiar Roadblock: A Virus Shortage

Gene Therapy Hits a Peculiar Roadblock: A Virus Shortage | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Revolutionary new treatments depend on tailor-made viruses, but laboratories cannot make them fast enough.
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The full transcription map of mouse papillomavirus type 1 (MmuPV1) in mouse wart tissues

The full transcription map of mouse papillomavirus type 1 (MmuPV1) in mouse wart tissues | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Papillomavirus (PV) infections lead to development of both benign warts and cancers. Because PVs are epitheliotropic and species specific, it has been extremely challenging to study PV infection in the context of a naturally occurring infection in a tractable laboratory animal. The recent discovery of the papillomavirus, MmuPV1, that infects laboratory mice, provides an important new animal model system for understanding the pathogenesis of papillomavirus-associated diseases. By using state of the art RNA-seq to provide deep sequencing analysis of what regions of the viral genome are transcribed and PacBio Iso-seq that produces longer reads to define the complete sequences of individual transcripts in combination with several conventional technologies to confirm transcription starts sites, splice sites, and polyadenylation sites, we provide the first detailed description of the MmuPV1 transcript map using RNA from MmuPV1-induced mouse warts. This study reveals the presence of mRNA transcripts capable of coding for ten protein products in the MmuPV1 genome and leads to correctly re-assigning the E1^E4, L2 and L1 coding regions. We were able to detect individual transcripts from the infected wart tissues by RT-PCR, Northern blot and RNA ISH, to define the temporal onset of productive viral infection and to ectopically express a predicted viral protein for functional studies. The constructed MmuPV1 transcript map provides a foundation to advance our understanding of papillomavirus biology and pathogenesis.
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PipelineDog: a simple and flexible graphic pipeline construction and maintenance tool | Bioinformatics | Oxford Academic

PipelineDog: a simple and flexible graphic pipeline construction and maintenance tool | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractSummary. Analysis pipelines are an essential part of bioinformatics research, and ad hoc pipelines are frequently created by researchers for prototypin
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Synima: a Synteny imaging tool for annotated genome assemblies - BMC Bioinformatics

Synima: a Synteny imaging tool for annotated genome assemblies - BMC Bioinformatics | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Background
Ortholog prediction and synteny visualization across whole genomes are valuable methods for detecting and representing a range of evolutionary processes such as genome expansion, chromosomal rearrangement, and chromosomal translocation. Few standalone methods are currently available to visualize synteny across any number of annotated genomes.

Results
Here, I present a Synteny Imaging tool (Synima) written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for their use. Synima has a range of graphical parameters including size, colours, order, and labels, which are specified in a config file generated by the first run of Synima – and can be subsequently edited. Synima runs quickly on a command line to generate informative and publication quality figures. Synima is open source and freely available from https://github.com/rhysf/Synima under the MIT License.

Conclusions
Synima should be a valuable tool for visualizing synteny between two or more annotated genome assemblies.


Via Ronny Kellner, Matt Agler, Jessie Uehling
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Hazard Characterization of Modified Vaccinia Virus Ankara Vector: What Are the Knowledge Gaps?

Hazard Characterization of Modified Vaccinia Virus Ankara Vector: What Are the Knowledge Gaps? | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Modified vaccinia virus Ankara (MVA) is the vector of choice for human and veterinary applications due to its strong safety profile and immunogenicity in vivo. The use of MVA and MVA-vectored vaccines against human and animal diseases must comply with regulatory requirements as they pertain to environmental risk assessment, particularly the characterization of potential adverse effects to humans, animals and the environment. MVA and recombinant MVA are widely believed to pose low or negligible risk to ecosystem health. However, key aspects of MVA biology require further research in order to provide data needed to evaluate the potential risks that may occur due to the use of MVA and MVA-vectored vaccines. The purpose of this paper is to identify knowledge gaps in the biology of MVA and recombinant MVA that are of relevance to its hazard characterization and discuss ongoing and future experiments aimed at providing data necessary to fill in the knowledge gaps. In addition, we presented arguments for the inclusion of uncertainty analysis and experimental investigation of verifiable worst-case scenarios in the environmental risk assessment of MVA and recombinant MVA. These will contribute to improved risk assessment of MVA and recombinant MVA vaccines.
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Begomoviral Movement Protein Effects in Human and Plant Cells: Towards New Potential Interaction Partners

Begomoviral Movement Protein Effects in Human and Plant Cells: Towards New Potential Interaction Partners | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Geminiviral single-stranded circular DNA genomes replicate in nuclei so that the progeny DNA has to cross both the nuclear envelope and the plasmodesmata for systemic spread within plant tissues. For intra- and intercellular transport, two proteins are required: a nuclear shuttle protein (NSP) and a movement protein (MP). New characteristics of ectopically produced Abutilon mosaic virus (AbMV) MP (MPAbMV), either authentically expressed or fused to a yellow fluorescent protein or epitope tags, respectively, were determined by localization studies in mammalian cell lines in comparison to plant cells. Wild-type MPAbMV and the distinct MPAbMV: reporter protein fusions appeared as curled threads throughout mammalian cells. Co-staining with cytoskeleton markers for actin, intermediate filaments, or microtubules identified these threads as re-organized microtubules. These were, however, not stabilized by the viral MP, as demonstrated by nocodazole treatment. The MP of a related bipartite New World begomovirus, Cleome leaf crumple virus (ClLCrV), resulted in the same intensified microtubule bundling, whereas that of a nanovirus did not. The C-terminal section of MPAbMV, i.e., the protein’s oligomerization domain, was dispensable for the effect. However, MP expression in plant cells did not affect the microtubules network. Since plant epidermal cells are quiescent whilst mammalian cells are proliferating, the replication-associated protein RepAbMV protein was then co-expressed with MPAbMV to induce cell progression into S-phase, thereby inducing distinct microtubule bundling without MP recruitment to the newly formed threads. Co-immunoprecipitation of MPAbMV in the presence of RepAbMV, followed by mass spectrometry identified potential novel MPAbMV-host interaction partners: the peptidyl-prolyl cis-trans isomerase NIMA-interacting 4 (Pin4) and stomatal cytokinesis defective 2 (SCD2) proteins. Possible roles of these putative interaction partners in the begomoviral life cycle and cytoskeletal association modes are discussed.
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An Early American Smallpox Vaccine Based on Horsepox — NEJM

An Early American Smallpox Vaccine Based on Horsepox — NEJM | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Correspondence from The New England Journal of Medicine — An Early American Smallpox Vaccine Based on Horsepox
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Frontiers | HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts | Microbiology

Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimised and validated workflow for taxonomic and functional characterisation of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Broad functional classification of the predicted genes is provided by assignment of COG microbial functional category classifications using EggNOG and higher resolution functional analysis is achieved by searching for enrichment of specific Swiss-Prot keywords within the viral metagenome. Application of HoloVir to viral metagenomes from the coral Pocillopora damicornis and the sponge Rhopaloeides odorabile demonstrated that HoloVir provides a valuable tool to characterise holobiont viral communities across species, environments, or experiments.
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Viruses hijack a long non-coding RNA

Viruses hijack a long non-coding RNA | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
​​​​​​​Manipulation of host-cell metabolism is an essential aspect of viral replication cycles. Viral co-option of a cellular long non-protein-coding RNA has now been found to be a key step in this process.
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Vaginal lactic acid elicits an anti-inflammatory response from human cervicovaginal epithelial cells and inhibits production of pro-inflammatory mediators associated with HIV acquisition

Vaginal lactic acid elicits an anti-inflammatory response from human cervicovaginal epithelial cells and inhibits production of pro-inflammatory mediators associated with HIV acquisition | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Article Report

Via Gilbert C FAURE
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Computational biologists: moving to the driver's seat

Computational biologists: moving to the driver's seat | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The recent shift of computational biologists from bioinformatics service providers to leaders of cutting-edge programs highlights the accompanying cultural and conceptual changes that should be implemented by funding bodies and academic institutions.
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We asked 272 bioinformaticians…name something that makes you angry: more reflections on the poor state of software documentation.

We asked 272 bioinformaticians…name something that makes you angry: more reflections on the poor state of software documentation. | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Image from flickr user wonderlane I'd like to share the details of a recent survey conducted by Nick Loman and Thomas Connor that tried to understand current issues with bioinformatics practice and training. The survey was announced on twitter and attracted almost 300 responses. Nick and Tom have ki
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"Mind Who you Kiss; HPV Virus That Kills Faster Than HIV/AIDS can be Gotten Through Kissing." NOT!!

"Mind Who you Kiss; HPV Virus That Kills Faster Than HIV/AIDS can be Gotten Through Kissing." NOT!! | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Students from Kisii University, Kenya and the general public at large have been warned against kissing carelessly due to an outbreak of Human papilloma virus, which has seen several people admitted at Kisii level 5 hospital after testing positive to the disease. HPV is an infectious viral disease which cause mouth cancer and is transmitted…

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Ed Rybicki's curator insight, November 29, 4:09 AM
I don't know what this is, but it ain't HPV: herpes type 1, maybe; from the look of those tonsils, something NASTY and bacterial as well - but this type of hype has to get stamped on for being the rubbish that it is. Kenyan newspapers obviously don't have decent fact checkers.
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Viral unmasking of cellular 5S rRNA pseudogene transcripts induces RIG-I-mediated immunity

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Zika virus kills brain cancer stem cells - Scienmag: Latest Science and Health News

Zika virus kills brain cancer stem cells - Scienmag: Latest Science and Health News | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
While Zika virus causes devastating damage to the brains of developing fetuses, it one day may be an effective treatment for glioblastoma, a deadly form of brain cancer. New research from Washington University School of Medicine in..
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Vaccinia Virus Natural Infections in Brazil: The Good, the Bad, and the Ugly

Vaccinia Virus Natural Infections in Brazil: The Good, the Bad, and the Ugly | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The orthopoxviruses (OPV) comprise several emerging viruses with great importance to human and veterinary medicine, including vaccinia virus (VACV), which causes outbreaks of bovine vaccinia (BV) in South America. Historically, VACV is the most comprehensively studied virus, however, its origin and natural hosts remain unknown. VACV was the primary component of the smallpox vaccine, largely used during the smallpox eradication campaign. After smallpox was declared eradicated, the vaccination that conferred immunity to OPV was discontinued, favoring a new contingent of susceptible individuals to OPV. VACV infections occur naturally after direct contact with infected dairy cattle, in recently vaccinated individuals, or through alternative routes of exposure. In Brazil, VACV outbreaks are frequently reported in rural areas, affecting mainly farm animals and humans. Recent studies have shown the role of wildlife in the VACV transmission chain, exploring the role of wild rodents as reservoirs that facilitate VACV spread throughout rural areas. Furthermore, VACV circulation in urban environments and the significance of this with respect to public health, have also been explored. In this review, we discuss the history, epidemiological, ecological and clinical aspects of natural VACV infections in Brazil, also highlighting alternative routes of VACV transmission, the factors involved in susceptibility to infection, and the natural history of the disease in humans and animals, and the potential for dissemination to urban environments.
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Structures and Functions of the Envelope Glycoprotein in Flavivirus Infections

Structures and Functions of the Envelope Glycoprotein in Flavivirus Infections | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Flaviviruses are enveloped, single-stranded RNA viruses that widely infect many animal species. The envelope protein, a structural protein of flavivirus, plays an important role in host cell viral infections. It is composed of three separate structural envelope domains I, II, and III (EDI, EDII, and EDIII). EDI is a structurally central domain of the envelope protein which stabilizes the overall orientation of the protein, and the glycosylation sites in EDI are related to virus production, pH sensitivity, and neuroinvasiveness. EDII plays an important role in membrane fusion because of the immunodominance of the fusion loop epitope and the envelope dimer epitope. Additionally, EDIII is the major target of neutralization antibodies. The envelope protein is an important target for research to develop vaccine candidates and antiviral therapeutics. This review summarizes the structures and functions of ED I/II/III, and provides practical applications for the three domains, with the ultimate goal of implementing strategies to utilize the envelope protein against flavivirus infections, thus achieving better diagnostics and developing potential flavivirus therapeutics and vaccines.
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Antibody Competition Reveals Surface Location of HPV L2 Minor Capsid Protein Residues 17–36

Antibody Competition Reveals Surface Location of HPV L2 Minor Capsid Protein Residues 17–36 | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The currently available nonavalent human papillomavirus (HPV) vaccine exploits the highly antigenic L1 major capsid protein to promote high-titer neutralizing antibodies, but is limited to the HPV types included in the vaccine since the responses are highly type-specific. The limited cross-protection offered by the L1 virus-like particle (VLP) vaccine warrants further investigation into cross-protective L2 epitopes. The L2 proteins are yet to be fully characterized as to their precise placement in the virion. Adding to the difficulties in localizing L2, studies have suggested that L2 epitopes are not well exposed on the surface of the mature capsid prior to cellular engagement. Using a series of competition assays between previously mapped anti-L1 monoclonal antibodies (mAbs) (H16.V5, H16.U4 and H16.7E) and novel anti-L2 mAbs, we probed the capsid surface for the location of an L2 epitope (aa17–36). The previously characterized L1 epitopes together with our competition data is consistent with a proposed L2 epitope within the canyons of pentavalent capsomers.
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Metagenomic Analysis of Therapeutic PYO Phage Cocktails from 1997 to 2014

Metagenomic Analysis of Therapeutic PYO Phage Cocktails from 1997 to 2014 | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Phage therapy has regained interest in recent years due to the alarming spread of antibiotic resistance. Whilst phage cocktails are commonly sold in pharmacies in countries such as Georgia and Russia, this is not the case in western countries due to western regulatory agencies requiring a thorough characterization of the drug. Here, DNA sequencing of constituent biological entities constitutes a first step. The pyophage (PYO) cocktail is one of the main commercial products of the Georgian Eliava Institute of Bacteriophage, Microbiology and Virology and is used to cure skin infections. Since its first production in the 1930s, the composition of the cocktail has been periodically modified to add phages effective against emerging pathogenic strains. In this paper, we compared the composition of three PYO cocktails from 1997 (PYO97), 2000 (PYO2000) and 2014 (PYO2014). Based on next generation sequencing, de novo assembly and binning of contigs into draft genomes based on tetranucleotide distance, thirty and twenty-nine phage draft genomes were predicted in PYO97 and PYO2014, respectively. Of these, thirteen and fifteen shared high similarity to known phages. Eleven draft genomes were found to be common in the two cocktails. One of these showed no similarity to publicly available phage genomes. Representatives of phages targeting E. faecalis, E. faecium, E. coli, Proteus, P. aeruginosa and S. aureus were found in both cocktails. Finally, we estimated larger overlap of the PYO2000 cocktail to PYO97 compared to PYO2014. Using next generation sequencing and metagenomics analysis, we were able to characterize and compare the content of PYO cocktails separated by 17 years in time. Even though the cocktail composition is upgraded every six months, we found it to remain relatively stable over the years.
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