Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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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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A Novel Activation Mechanism of Avian Influenza Virus H9N2 by Furin

Avian influenza H9N2 is prevalent in waterfowl and has become endemic in poultry in Asia and the Middle East. H9N2 influenza viruses have served as a reservoir of internal genes for other influenza viruses that infect humans, and several cases of human infection by H9N2 influenza viruses have indicated its pandemic potential. Fortunately, an extensive surveillance program enables close monitoring of H9N2 influenza viruses worldwide and has generated a large repository of virus sequences and phylogenetic information. Despite the large quantity of sequences in different databases, very little is known about specific virus isolates and their pathogenesis. Here, we characterize a low pathogenicity avian influenza virus (LPAI), A/chicken/Israel/810/2001 (H9N2), which is representative of influenza virus strains that have caused severe morbidity and mortality in poultry farms. We show that under certain circumstances the Israel810 HA can be activated by furin, a hallmark of highly pathogenic avian influenza virus (HPAI). We demonstrate that Israel810 HA can be cleaved in cells with high levels of furin expression, and that a mutation that eliminates a glycosylation site in HA1 allows the Israel810 HA to gain universal cleavage in cell culture. Pseudoparticles generated from Israel810 HA, or the glycosylation mutant, transduce cells efficiently. In contrast, introduction of a polybasic cleavage site into Israel810 HA leads to pseudoviruses that are compromised for transduction. Our data indicate a mechanism for an H9N2 evolutionary pathway that may allows it to gain virulence in a distinct manner from H5 and H7 influenza viruses.

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HIV virus spread, evolution studied through computer modeling

HIV virus spread, evolution studied through computer modeling | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Researchers at Los Alamos National Laboratory are investigating the complex relationships between the spread of the HIV virus in a population (epidemiology) and the actual, rapid evolution of the virus (phylogenetics) within each patient’s body.
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Is the 'Other' Malaria Getting More Dangerous? | Science/AAAS | News

Is the 'Other' Malaria Getting More Dangerous? | Science/AAAS | News | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

"Abstract- Two new genetic studies of a parasite that causes malaria suggest that it may be evolving new ways to invade human blood cells. The development could make certain strains of the parasite more dangerous for populations who have some natural immunity. Now roughly 95% of people in sub-Saharan Africa—where the malaria burden is the highest—are thought to be resistant to the parasite in question, Plasmodium vivax. If the parasite were to overcome their genetic defense against the disease, it would potentially threaten hundreds of millions more people than it does today."

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Fruit bat population covering central Africa carries two deadly viruses

Fruit bat population covering central Africa carries two deadly viruses | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
A population of fruit bats which is found across much of continental Africa is widely infected with two deadly viruses that could spread to humans, new research reveals.

Via Ed Rybicki
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Ed Rybicki's curator insight, November 20, 2013 1:57 AM

Lagos bat virus (similar to rabies) and a henipavirus - which is interesting, because there have been no reports of human infection with one of those in Africa.  Furry cockroaches, is what I say....

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Fred Sanger (1918 – 2013) | MRC Laboratory of Molecular Biology

Fred Sanger (1918 – 2013) | MRC Laboratory of Molecular Biology | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Fred Sanger has the distinction of being the only scientist to have been awarded the Nobel Prize for Chemistry twice: in 1958 and 1980.

 
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Learning how to run a lab: interviews with principal investigators - PLoS Comput Biol. 2013

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From deep sequencing to viral tagging: recent advances in viral metagenomics Bioessays. 2013

Culture-independent high-throughput sequencing has provided unprecedented insights into microbial ecology, particularly for Earth's most ubiquitous and diverse inhabitants - the viruses. A plethora of methods now exist for amplifying the vanishingly small amounts of nucleic acids in natural viral communities in order to sequence them, and sequencing depth is now so great that viral genomes can be detected and assembled even amid large concentrations of non-viral DNA. Complementing these advances in amplification and sequencing is the ability to physically link fluorescently labeled viruses to their host cells via high-throughput flow sorting. Sequencing of such isolated virus-host pairs facilitates cultivation-independent exploration of the natural host range of viruses. Within the next decade, as these technologies become widespread, we can expect to see a systematic expansion of our knowledge of viruses and their hosts.

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Investigative Genetics | Full text | The man behind the fingerprints: an interview with Professor Sir Alec Jeffreys

In this interview we talk with Professor Sir Alec Jeffreys about DNA fingerprinting, his wider scientific career, and the past, present and future of forensic DNA applications.
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Frontiers for Young Minds

Frontiers for Young Minds | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Frontiers for Young Minds is a scientific open access journal edited by and for kids.
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Could the Black Death Actually Have Been an Ebola-like Virus? | Viruses101 | Learn Science at Scitable

Could the Black Death Actually Have Been an Ebola-like Virus? | Viruses101 | Learn Science at Scitable | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Bubonic Plague has long been thought to be the cause of the Black Death. But new findings now point to an ebola-like virus as the real culprit. Find out the reasons for and against this radical theory.
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PLOS Pathogens: Identification of the Adenovirus E4orf4 Protein Binding Site on the B55α and Cdc55 Regulatory Subunits of PP2A: Implications for PP2A Function, Tumor Cell Killing and Viral Replication

PLOS Pathogens: Identification of the Adenovirus E4orf4 Protein Binding Site on the B55α and Cdc55 Regulatory Subunits of PP2A: Implications for PP2A Function, Tumor Cell Killing and Viral Replication | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

The adenovirus E4orf4 protein when expressed alone at high levels induces the death of human cancer cells but not normal primary cells. It also is toxic in the yeast Saccharomyces cerevisiae, which we have used as a model system in some studies. Toxicity induced by the E4orf4 protein is largely dependent on its ability to associate with the highly conserved B/B55/Cdc55 class of regulatory subunits of protein phosphatase 2A (PP2A), of which the mammalian B55α species is best characterized structurally. We showed previously that binding to B55α appears to inhibit PP2A activity against at least some substrates. In the present study, we mapped the E4orf4 binding site on both yeast Cdc55 and mammalian B55α and propose how such binding may inhibit PP2A activity. The implications of E4orf4 binding on PP2A activity are of significant scientific interest in terms of the process by which PP2A recognizes and dephosphorylates its substrates. We also propose that E4orf4 binding in the context of viral replication serves the quite different function of introducing novel substrates for dephosphorylation by the PP2A holoenzyme.

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Bird Flu Strain Jumps From Animals To People For The First Time

Bird Flu Strain Jumps From Animals To People For The First Time | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
H6N1 bird flu has been identified in a woman in Taiwan.  (RT @PopSci: A strain of bird flu that had previously only infected poultry has now spread to a human http://t.co/WYIfjcyjcv)...
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Characterization of the non-coding regions of the 1918 influenza A H1N1 virus

The terminal non-coding region (NCR) sequences of the eight gene segments of the influenza A/Brevig Mission/1/1918 (H1N1) virus were determined by rapid amplification of cDNA ends (RACE). Chimeric viruses encoding the open reading frames of the 1918 virus but flanked by either the wild-type 1918 NCR sequences, or the NCR sequences of two other H1N1 virus strains, A/WSN/1933 and A/New York/312/2001 were produced. No growth differences between the NCR variant 1918 influenza viruses were noted.

 
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HPV: Sex, cancer and a virus

HPV: Sex, cancer and a virus | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Human papillomavirus is causing a new form of head and neck cancer— leaving researchers scrambling to understand risk factors, tests and treatments.
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Protein evolution along phylogenetic histories under structurally constrained substitution models

Protein evolution along phylogenetic histories under structurally constrained substitution models | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Motivation: Models of molecular evolution aim at describing the evolutionary processes at the molecular level. However, current models rarely incorporate information from protein structure. Conversely, structure-based models of protein evolution have not been commonly applied to simulate sequence evolution in a phylogenetic framework, and they often ignore relevant evolutionary processes such as recombination. A simulation evolutionary framework that integrates substitution models that account for protein structure stability should be able to generate more realistic in silico evolved proteins for a variety of purposes.

 
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Video Tip of the Week: IGB, Integrated Genome Browser | The OpenHelix Blog

Recently in a paper we are working on we were asked to cover a bit more about various styles or types of genome browsers that are available. And the timing was

Via Mel Melendrez-Vallard
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Dengue fever found in Key West, but not Tucson

Dengue fever found in Key West, but not Tucson | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Tweet  At the annual meeting of the American Society of Tropical Medicine and Hygiene on Thursday, scientists discussed research about the comparison of dengue fever found in Key West, Fla., and not in Tucson, Ariz.

Via Mel Melendrez-Vallard
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Current Biology - Neanderthal and Denisovan retroviruses in modern humans

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SummaryIn the June 5th 2012 issue of Current Biology, Agoni et al.[1] reported finding 14 endogenous retrovirus (ERV) loci in the genome sequences of Neanderthal and/or Denisovan fossils (both ∼40,000 years old) that are not found in the human reference genome sequence. The authors [1] concluded that these retroviruses were infecting the germline of these archaic hominins at or subsequent to their divergence from modern humans (∼400,000 years ago). However, in our search for unfixed ERVs in the modern human population, we have found most of these loci. We explain this apparent contradiction using population genetic theory and suggest that it illustrates an important phenomenon for the study of transposable elements such as ERVs."
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Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition - PLoS Comput Biol. 2013

Key steps in a viral life-cycle, such as self-assembly of a protective protein container or in some cases also subsequent maturation events, are governed by the interplay of physico-chemical mechanisms involving various spatial and temporal scales. These salient aspects of a viral life cycle are hence well described and rationalised from a mesoscopic perspective. Accordingly, various experimental and computational efforts have been directed towards identifying the fundamental building blocks that are instrumental for the mechanical response, or constitute the assembly units, of a few specific viral shells. Motivated by these earlier studies we introduce and apply a general and efficient computational scheme for identifying the stable domains of a given viral capsid. The method is based on elastic network models and quasi-rigid domain decomposition. It is first applied to a heterogeneous set of well-characterized viruses (CCMV, MS2, STNV, STMV) for which the known mechanical or assembly domains are correctly identified. The validated method is next applied to other viral particles such as L-A, Pariacoto and polyoma viruses, whose fundamental functional domains are still unknown or debated and for which we formulate verifiable predictions. The numerical code implementing the domain decomposition strategy is made freely available

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MERS Coronavirus Could Be A Slowly Growing Epidemic

MERS Coronavirus Could Be A Slowly Growing Epidemic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The WHO has been informed of four new cases of MERS-CoV and a new study has made the case for the coronavirus becoming a
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Second isirv antiviral group conference: overview - Hurt - 2013 - Influenza and Other Respiratory Viruses - Wiley Online Library

Second isirv antiviral group conference: overview - Hurt - 2013 - Influenza and Other Respiratory Viruses - Wiley Online Library | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
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Compound Found in Sharks Has Anti-Viral Potential | Viruses101 | Learn Science at Scitable

Compound Found in Sharks Has Anti-Viral Potential | Viruses101 | Learn Science at Scitable | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
A compound found in sharks, known as Squalamine, is beleived to have potential as an antiviral medicine for humans. How will this affect sharks?
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PLOS Pathogens: Global Rescue of Defects in HIV-1 Envelope Glycoprotein Incorporation: Implications for Matrix Structure

PLOS Pathogens: Global Rescue of Defects in HIV-1 Envelope Glycoprotein Incorporation: Implications for Matrix Structure | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

One of the enduring problems in HIV-1 research is the mechanism of incorporation of the viral envelope (Env) glycoprotein into viral particles. Several models have been proposed ranging from an entirely passive process to a requirement for binding of Env by the matrix (MA) domain of the Gag precursor polyprotein. It is clear that specific regions within MA and Env play important roles, as mutations in these domains can prevent Env incorporation. We have identified a point mutation in MA that rescues a broad range of Env-incorporation defective mutations, located both in MA and in Env. Our investigations into the mechanism of rescue have revealed the importance of interactions between MA monomers at a trimeric interface. Our results are consistent with previously published crystallographic models and now provide functional support for the existence of MA trimers in the immature Gag lattice. Furthermore, as the modification of trimer interactions plays a role in the rescue of Env incorporation, we propose that MA trimerization and the organization of the MA lattice may be critical factors in Env incorporation.

 

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Free Visual Dictionary & Thesaurus | Online Dictionary | Associated Words | Synonyms Dictionary at SnappyWords.com

Free Visual Dictionary & Thesaurus | Online Dictionary | Associated Words | Synonyms Dictionary at SnappyWords.com | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Chris Upton + helpers's insight:

this is fun; I'm not in the dictionary

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Links to Recombinant Software Detection/Analysis Software

Welcome to the comprehensive list of recombination analysis software maintained by the Robertson Lab.

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