Viruses and Bioinformatics from Virology.uvic.ca
94.1K views | +15 today
Follow
 
Scooped by Chris Upton + helpers
onto Viruses and Bioinformatics from Virology.uvic.ca
Scoop.it!

Are we missing half of the viruses in the ocean?

Are we missing half of the viruses in the ocean? | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
There are lots of viruses in seawater - but maybe we're not seeing the whole picture?
Chris Upton + helpers's insight:

From MicrobiologyBytes

more...
No comment yet.
Viruses and Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
Your new post is loading...
Your new post is loading...
Scooped by Cindy
Scoop.it!

Next step in the ongoing arms race between myxoma virus and wild rabbits in Australia is a novel disease phenotype

In host–pathogen arms races, increases in host resistance prompt counteradaptation by pathogens, but the nature of that counteradaptation is seldom directly observed outside of laboratory models. The best-documented field example is the coevolution of myxoma virus (MYXV) in European rabbits. To understand how MYXV in Australia has continued to evolve in wild rabbits under intense selection for genetic resistance to myxomatosis, we compared the phenotypes of the progenitor MYXV and viral isolates from the 1950s and the 1990s in laboratory rabbits with no resistance. Strikingly, and unlike their 1950s counterparts, most virus isolates from the 1990s induced a highly lethal immune collapse syndrome similar to septic shock. Thus, the next step in this canonical case of coevolution after a species jump has been further escalation by the virus in the face of widespread host resistance.
more...
No comment yet.
Rescooped by Kenzibit from Virology News
Scoop.it!

Scientists develop improved, potentially safer plant-made Zika vaccine

Scientists develop improved, potentially safer plant-made Zika vaccine | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
ASU Biodesign Institute scientist Qiang 'Shawn' Chen has led his research team to develop the world's first plant-based Zika vaccine that could be more potent, safer and cheaper to produce than any other efforts to date.

Via Ed Rybicki
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Disentangling the origins of virophages and polintons

Virophages and polintons are part of a complex system that also involves eukaryotes, giant viruses, as well as other viruses and transposable elements. Virophages are cosmopolitan, being found in environments ranging from the Amazon River to Antarctic hypersaline lakes, while polintons are found in many single celled and multicellular eukaryotes. Virophages and polintons have a shared ancestry, but their exact origins are unknown and obscured by antiquity and extensive horizontal gene transfer (HGT). Paleovirology can help disentangle the complicated gene flow between these two, as well as their giant viral and eukaryotic hosts. We outline the evidence and theoretical support for polintons being descended from viruses and not vice versa. In order to disentangle the natural history of polintons and virophages, we suggest that there is much to be gained by embracing rigorous metagenomics and evolutionary analyses. Methods from paleovirology will play a pivotal role in unravelling ancient relationships, HGT and patterns of cross-species transmission.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Can bioinformatics be more accessible? | RNA-Seq Blog

Can bioinformatics be more accessible? | RNA-Seq Blog | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Our courses contain projects crafted using open source data contain detailed biological information, broken down into digestible, easy-to-manipulate visualizations, offering scientists and students alike a new means of working with ‘omics data—without expensive the technology and coursework.
Introducing…. (drumroll) T-BioInfo in Education 
As we get ready to launch, we need you to help millions of non-bioinformaticians get their hands on the wonderful public domain data that has been collecting dust at the NIH servers. For now, users are invited to test our two courses, “Introduction to the Power of Big Data and Bioinformatics” and “Transcriptomics”.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

EzMap: a simple pipeline for reproducible analysis of the human virome | Bioinformatics | Oxford Academic

EzMap: a simple pipeline for reproducible analysis of the human virome | Bioinformatics | Oxford Academic | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
SummaryIn solid-organ transplant recipients, a delicate balance between immunosuppression and immunocompetence must be achieved, which can be difficult to monitor in real-time. Shotgun sequencing of cell-free DNA (cfDNA) has been recently proposed as a new way to indirectly assess immune function in transplant recipients through analysis of the status of the human virome. To facilitate exploration of the utility of the human virome as an indicator of immune status, and to enable rapid, straightforward analyses by clinicians, we developed a fully automated computational pipeline, EzMap, for performing metagenomic analysis of the human virome. EzMap combines a number of tools to clean, filter, and subtract WGS reads by mapping to a reference human assembly. The relative abundance of each virus present is estimated using a maximum likelihood approach that accounts for genome size, and results are presented with interactive visualizations and taxonomy-based summaries that enable rapid insights. The pipeline is automated to run on both workstations and computing clusters for all steps. EzMap automates an otherwise tedious and time-consuming protocol and aims to facilitate rapid and reproducible insights from cfDNA.Availability and ImplementationEzMap is freely available at https://github.com/dekoning-lab/ezmap.Contactjason.dekoning@ucalgary.caSupplementary informationSupplementary data are available at Bioinformatics online.
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Tomato leaf curl New Delhi virus: a widespread bipartite begomovirus 

Tomato leaf curl New Delhi virus: a widespread bipartite begomovirus  | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Tomato leaf curl New Delhi virus (ToLCNDV) is an exceptional Old World bipartite begomovirus. On the Indian subcontinent, a region in which monopartite DNA satellite‐associated begomoviruses wit
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Addition of αGal HyperAcute™ technology to recombinant avian influenza vaccines induces strong low-dose antibody responses

Addition of αGal HyperAcute™ technology to recombinant avian influenza vaccines induces strong low-dose antibody responses | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Highly pathogenic avian influenza represents a severe public health threat. Over the last decade, the demand for highly efficacious vaccines against avian influenza viruses has grown, especially after the 2013 H7N9 outbreak in China that resulted in over 600 human cases with over 200 deaths. Currently, there are several H5N1 and H7N9 influenza vaccines in clinical trials, all of which employ traditional oil-in-water adjuvants due to the poor immunogenicity of avian influenza virus antigens. In this study, we developed potent recombinant avian influenza vaccine candidates using HyperAcute™ Technology, which takes advantage of naturally-acquired anti-αGal immunity in humans. We successfully generated αGal-positive recombinant protein and virus-like particle vaccine candidates of H5N1 and H7N9 influenza strains using either biological or our novel CarboLink chemical αGal modification techniques. Strikingly, two doses of 100 ng αGal-modified vaccine, with no traditional adjuvant, was able to induce a much stronger humoral response in αGT BALB/c knockout mice (the only experimental system readily available for testing αGal in vivo) than unmodified vaccines even at 10-fold higher dose (1000 ng/dose). Our data strongly suggest that αGal modification significantly enhances the humoral immunogenicity of the recombinant influenza vaccine candidates. Use of αGal HyperAcute™ technology allows significant dose-sparing while retaining desired immunogenicity. Our success in the development of highly potent H5N1 and H7N9 vaccine candidates demonstrated the potential of αGal HyperAcute™ technology for the development of vaccines against other infectious diseases.
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Tissue-specific control of latent CMV reactivation by regulatory T cells

Tissue-specific control of latent CMV reactivation by regulatory T cells | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Cytomegalovirus (CMV) infection in both mice and humans is normally initially contained by a vigorous adaptive immune response that drives the virus into latency in multiple tissues. However, the immunologic mechanisms that control latency are not well understood. In this report, we have examined the role of regulatory T cells (Treg) in a mouse model of CMV infection. Interestingly, depletion of regulatory T cells had profound consequences on MCMV latent infection, depending upon the tissue. In the spleen, Treg depletion enhanced CD8+ T cell responses and reduced reactivatable latent infection from the spleen. In striking contrast, in the salivary gland, Treg depletion enhanced the production of IL-10 from CD4+ T cells as well as viral reactivation. Thus, Treg play divergent and tissue specific roles in controlling MCMV reactivation from latency.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Poxviruses Utilize Multiple Strategies to Inhibit Apoptosis

Poxviruses Utilize Multiple Strategies to Inhibit Apoptosis | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Cells have multiple means to induce apoptosis in response to viral infection. Poxviruses must prevent activation of cellular apoptosis to ensure successful replication. These viruses devote a substantial portion of their genome to immune evasion. Many of these immune evasion products expressed during infection antagonize cellular apoptotic pathways. Poxvirus products target multiple points in both the extrinsic and intrinsic apoptotic pathways, thereby mitigating apoptosis during infection. Interestingly, recent evidence indicates that poxviruses also hijack cellular means of eliminating apoptotic bodies as a means to spread cell to cell through a process called apoptotic mimicry. Poxviruses are the causative agent of many human and veterinary diseases. Further, there is substantial interest in developing these viruses as vectors for a variety of uses including vaccine delivery and as oncolytic viruses to treat certain human cancers. Therefore, an understanding of the molecular mechanisms through which poxviruses regulate the cellular apoptotic pathways remains a top research priority. In this review, we consider anti-apoptotic strategies of poxviruses focusing on three relevant poxvirus genera: Orthopoxvirus, Molluscipoxvirus, and Leporipoxvirus. All three genera express multiple products to inhibit both extrinsic and intrinsic apoptotic pathways with many of these products required for virulence
more...
No comment yet.
Scooped by Bwana Moses
Scoop.it!

Novartis Using HIV Virus as Part of Gene Therapy | The Sleuth Journal

Novartis Using HIV Virus as Part of Gene Therapy | The Sleuth Journal | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Like the viruses most commonly used so far, HIV is a retrovirus. Scientists have taken copies of its genome and integrated them into the human genome. It is
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Preventive effect of human papillomavirus vaccination on the development of uterine cervical lesions in young Japanese women. - PubMed - NCBI

Preventive effect of human papillomavirus vaccination on the development of uterine cervical lesions in young Japanese women. - PubMed - NCBI | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
J Obstet Gynaecol Res. 2017 Jul 14. doi: 10.1111/jog.13419. [Epub ahead of print]
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Cross-species jumps may play unexpectedly big role in virus evolution

Cross-species jumps may play unexpectedly big role in virus evolution | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
On occasion, a virus may jump from one host species to another and adapt to the new host. Such cross-species transmission happens more often than expected, according to new research published in PLOS Pathogens, and it ma
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Seeing a virus in action

Seeing a virus in action | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
"In the past, scientists have tried to infer what's happening in a molecular-scale biological process by looking at a still photo at the start and a still photo at the end of a process," said Abbas Ourmazd, UWM distinguished professor. "But you then don't know what happens in between. With this method, we are in a position to watch biological machines perform their functions." By combining concepts from machine learning, differential geometry, graph theory and diffraction physics, the researchers created an algorithm able to reconstruct sequential images.

The work, done in collaboration with Professor Brenda Hogue, a virologist at Arizona State University, and Andrew Aquila and his colleagues at the Linac Coherent Light Source at SLAC, is published today in the journal Nature Methods.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

(20) Is bioinformatics a lucrative career option for biologists? - YouTube

Bioinformatics discussions and training videos. Hosted by Maria Nattestad.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Humanized mouse models to study human cell-mediated and humoral responses to dengue virus

Several candidate dengue virus vaccines are in clinical trials and show promise as an effective measure to control dengue. However, it is becoming clear that additional vaccine candidates may be needed as there is concern about the durability of the immune response to all four serotypes of vaccine components and efficacy varies dependent on the immune status of the individual. The lack of an appropriate animal model to mimic human dengue has deterred the development of vaccines and anti-viral therapies to dengue virus. The focus of this review is to discuss advances in the development of humanized animal models and to highlight how they could be used for antiviral and dengue vaccine testing if limitations with cell-mediated immunity and seroconversion to IgG are overcome.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Scientists use gene editing to eliminate viruses in live pigs

Scientists use gene editing to eliminate viruses in live pigs | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Scientists have edited the pig genome to deactivate a family of retroviruses. The results hold important implications for transplant medicine in humans. The shortage of human organs and tissues for transplantation represents one of the most significant unmet medical needs.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

SubCons: a new ensemble method for improved human subcellular localization predictions | Bioinformatics | Oxford Academic

SubCons: a new ensemble method for improved human subcellular localization predictions | Bioinformatics | Oxford Academic | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
MotivationKnowledge of the correct protein subcellular localization is necessary for understanding the function of a protein. Unfortunately large-scale experimental studies are limited in their accuracy. Therefore, the development of prediction methods has been limited by the amount of accurate experimental data. However, recently large-scale experimental studies have provided new data that can be used to evaluate the accuracy of subcellular predictions in human cells. Using this data we examined the performance of state of the art methods and developed SubCons, an ensemble method that combines four predictors using a Random Forest classifier.ResultsSubCons outperforms earlier methods in a dataset of proteins where two independent methods confirm the subcellular localization. Given nine subcellular localizations, SubCons achieves an F1-Score of 0.79 compared to 0.70 of the second best method. Furthermore, at a FPR of 1% the true positive rate (TPR) is over 58% for SubCons compared to less than 50% for the best individual predictor.Availability and ImplementationSubCons is freely available as a webserver (http://subcons.bioinfo.se) and source code from https://bitbucket.org/salvatore_marco/subcons-web-server. The golden dataset as well is available from http://subcons.bioinfo.se/pred/download.Contactarne@bioinfo.seSupplementary informationSupplementary data are available at Bioinformatics online.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Use of AAScatterPlot tool for monitoring the evolution of the hemagglutinin cleavage site in H9 avian influenza viruses | Bioinformatics | Oxford Academic

Use of AAScatterPlot tool for monitoring the evolution of the hemagglutinin cleavage site in H9 avian influenza viruses | Bioinformatics | Oxford Academic | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
MotivationViruses rapidly evolve due to their error-prone genome replication, and identifying which mutations are selected for during evolution is critical for virus surveillance efforts. Here we introduce a scatter plot tool (AAScatterPlot) that easily shows the selection and avoidance of certain protein mutations based on biochemical properties. We demonstrate its utility for monitoring the evolution of H9 avian influenza viruses from China between 2005 and 2015, particularly at the hemagglutinin (HA) proteolytic cleavage site (PCS) that can affect virus activation and pathogenicity.ResultsGiven genome sequences, the AAScatterPlot tool compacts into a single plot, information about the hydropathy index, Van der Waals volume, chemical property and occurrence frequency of amino acid residues. The tool also shows the range of residues that could arise from a single point mutation in the genome, which can then be compared against the observed residues to identify mutation constraints. Through this approach, we found that the 2nd position towards the N-terminus side of the HA PCS (P2 position) avoided hydrophobic residues, whereas the P3 position avoided hydrophilic residues.Availability and ImplementationAAScatterPlot is available at https://github.com/WhittakerLab/AAScatterPlot.Contactgary.whittaker@cornell.eduSupplementary informationSupplementary data are available at Bioinformatics online.
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Exogenously applied dsRNA molecules from ZYMV genome move systemically and protect cucurbits

Exogenously applied dsRNA molecules from ZYMV genome move systemically and protect cucurbits | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Zucchini yellow mosaic virus (ZYMV) causes serious damage in a large number of cucurbits, and control measures are necessary. Transgenic cucurbits expressing parts of the ZYMV genome have been show
Ed Rybicki's insight:
SUCH a cool finding! And it's stable enough that you could probably spray it?  Thanks to my old friend Richard Lee for finding this B-)
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Cross-seeding of prions by aggregated α-synuclein leads to transmissible spongiform encephalopathy

Cross-seeding of prions by aggregated α-synuclein leads to transmissible spongiform encephalopathy | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Aggregation of misfolded proteins or peptides is a common feature of neurodegenerative diseases. Recent years have witnessed a growing number of reports of overlap in neuropathological features specific to two or more neurodegenerative diseases in individual patients. However, the origin for the overlap remains unclear. One possibility is that disease that have mixed brain pathologies might arise from cross-seeding of one amyloidogenic protein by fibrillar states of unrelated proteins. The current study examined whether prion replication can be induced by cross-seeding by α-synuclein or Aβ peptide in their aggregated states. We found that α-synuclein aggregates display cross-seeding activity and trigger misfolding of the prion protein (PrPC) in vitro, producing self-replicating PrP states. Non-fibrillar α-synuclein or fibrillar Aβ failed to cross-seed misfolding of PrPC. Remarkably, misfolded PrP triggered by fibrillar α-synuclein in vitro propagated in animals and, upon serial transmission, produced clinical prion diseases. In summary, the current work documents direct cross-seeding between unrelated amyloidogenic proteins associated with different neurodegenerative diseases. This study suggests that early interaction between unrelated amyloidogenic proteins might underlie the etiology of mixed neurodegenerative proteinopathies.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

MHCflurry: open-source class I MHC binding affinity prediction

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
more...
Won Gi Yoo's curator insight, August 10, 10:19 PM
Share your insight
Scooped by Bwana Moses
Scoop.it!

Epigenetic Control of Human Endogenous Retrovirus Expression: Focus on Regulation of Long-Terminal Repeats (LTRs)

Epigenetic Control of Human Endogenous Retrovirus Expression: Focus on Regulation of Long-Terminal Repeats (LTRs) | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Transposable elements, including endogenous retroviruses (ERVs), comprise almost 45% of the human genome. This could represent a significant pathogenic burden but it is becoming more evident that many of these elements have a positive contribution to make to normal human physiology. In particular, the contributions of human ERVs (HERVs) to gene regulation and the expression of noncoding RNAs has been revealed with the help of new and emerging genomic technologies. HERVs have the common provirus structure of coding open reading frames (ORFs) flanked by two long-terminal repeats (LTRs). However, over the course of evolution and as a consequence of host defence mechanisms, most of the sequences contain INDELs, mutations or have been reduced to single LTRs by recombination. These INDELs and mutations reduce HERV activity. However, there is a trade-off for the host cells in that HERVs can provide beneficial sources of genetic variation but with this benefit comes the risk of pathogenic activity and spread within the genome. For example, the LTRs are of critical importance as they contain promoter sequences and can regulate not only HERV expression but that of human genes. This is true even when the LTRs are located in intergenic regions or are in antisense orientation to the rest of the gene. Uncontrolled, this promoter activity could disrupt normal gene expression or transcript processing (e.g., splicing). Thus, control of HERVs and particularly their LTRs is essential for the cell to manage these elements and this control is achieved at multiple levels, including epigenetic regulations that permit HERV expression in the germline but silence it in most somatic tissues. We will discuss some of the common epigenetic mechanisms and how they affect HERV expression, providing detailed discussions of HERVs in stem cell, placenta and cancer biology.
more...
No comment yet.
Rescooped by burkesquires from Viral Modeling and Simulation
Scoop.it!

Genome-wide analysis of influenza viral RNA and nucleoprotein association | Nucleic Acids Research | Oxford Academic

Genome-wide analysis of influenza viral RNA and nucleoprotein association | Nucleic Acids Research | Oxford Academic | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Influenza A virus (IAV) genomes are composed of eight single-stranded RNA segments that are coated by viral nucleoprotein (NP) molecules. Classically, the interaction between NP and viral RNA (vRNA) is depicted as a uniform pattern of ‘beads on a string’. Using high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP), we identified the vRNA binding profiles of NP for two H1N1 IAV strains in virions. Contrary to the prevailing model for vRNA packaging, NP does not bind vRNA uniformly in the A/WSN/1933 and A/California/07/2009 strains, but instead each vRNA segment exhibits a unique binding profile, containing sites that are enriched or poor in NP association. Intriguingly, both H1N1 strains have similar yet distinct NP binding profiles despite extensive sequence conservation. Peaks identified by HITS-CLIP were verified as true NP binding sites based on insensitivity to DNA antisense oligonucleotide-mediated RNase H digestion. Moreover, nucleotide content analysis of NP peaks revealed that these sites are relatively G-rich and U-poor compared to the genome-wide nucleotide content, indicating an as-yet unidentified sequence bias for NP association in vivo. Taken together, our genome-wide study of NP–vRNA interaction has implications for the understanding of influenza vRNA architecture and genome packaging.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

The Institute for the Study of Non–Model Organisms and other fantasies


While there are many reasons for our collective reluctance to pursue these orphaned genetic elements, lack of funding probably ranks at the top of the list.

Thus there is a great need for an institute devoted entirely to the study of uncharacterized genes. SWAT-like teams of investigators at the institute would be tasked with rapidly characterizing these genes. A battery of reagents, including antibodies, green fluorescent protein constructs, mutants, RNAi and CRISPR constructs, and purified proteins, would be developed for this work. Once every year, the results of their efforts would be published in PLoS Neglected Genes.

In the entrance hall of this well-funded institute would be a Rube Goldberg exhibit, the kind you see at airports, consisting of ramps, tubes, levels, pulleys, paddles, and springs that transport ping-pong balls. Once a year, on April 14th (the declared date of completion of sequencing the human genome), all 365 researchers would gather around the exhibit for the “Selection Ceremony.” Each would grab a ball as it bounces off a small trampoline. These balls would have the gene identification numbers of 365 randomly selected, uncharacterized genes. The researchers’ task is clear: they have a year to characterize their assigned genes.

Cindy's insight:
A fun and exciting read!
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

DNA sequencing and big data open a new frontier in the hunt for new viruses

DNA sequencing and big data open a new frontier in the hunt for new viruses | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Cross-species jumps may play unexpectedly big role in virus evolution
more...
No comment yet.