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Virology and Bioinformatics from Virology.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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Cytosolic DNA sensors regulating type I interferon induction 10.1016/j.it.2011.08.004 : Trends in Immunology | ScienceDirect.com

Cytosolic DNA sensors regulating type I interferon induction 10.1016/j.it.2011.08.004 : Trends in Immunology | ScienceDirect.com | Virology and Bioinformatics from Virology.ca | Scoop.it

Type I interferon (IFN) induction is a crucial anti-pathogen response mediated by innate immune stimulation.

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Toward Genetics-Based Virus Taxonomy: Comparative Analysis of a Genetics-Based Classification and the Taxonomy of Picornaviruses

"In this study, we compare the GENETIC classification with the expert-based picornavirus taxonomy and outline differences in the underlying frameworks regarding the relation of virus groups and genetic diversity that represent, respectively, the structure and content of a classification."

 

And they make the rather breathtaking statement that:

"Virus taxonomy has received little attention from the research community despite its broad relevance".

Really, guys?  As a longtime member of various ICTV committees, I have to say the bovine excreta content is high in this assertion...  But otherwise, a welcome addition to the taxonomic debates.

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PLoS Pathogens: Human Cytomegalovirus Clinical Strain-Specific microRNA miR-UL148D Targets the Human Chemokine RANTES during Infection

PLoS Pathogens: Human Cytomegalovirus Clinical Strain-Specific microRNA miR-UL148D Targets the Human Chemokine RANTES during Infection | Virology and Bioinformatics from Virology.ca | Scoop.it

The human cytomegalovirus (HCMV) clinical strain Toledo and the attenuated strain AD169 exhibit a striking difference in pathogenic potential and cell tropism.

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Three-dimensional analysis of ribonucleoprotein complexes in influenza A virus : Nature Communications : Nature Publishing Group

Although genome segmentation provides advantages such as genetic reassortment, which contributes to the emergence of novel strains with pandemic potential, it complicates the genome packaging of progeny virions.

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Research Associate/Scientist- Cell Biology And Molecular Virology

Have cell,research and/or biology skills? About Novartis Institute for Biomedical Research: At Novartis Institutes for BioMedical Research (NIBR), the global research organization of Novartis, we...
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A world within a tumour – new study shows just how complex cancer can be

A world within a tumour – new study shows just how complex cancer can be | Virology and Bioinformatics from Virology.ca | Scoop.it

Cancer is a puzzle of staggering complexity. Every move towards a solution seems to reveal yet another layer of mystery. For a start, cancer isn’t a single disease, so we can dispense with the idea of a single “cure”. There are over 200 different types, each with their own individual quirks. Even for a single type – say, breast cancer – there can be many different sub-types that demand different treatments. Even within a single subtype, one patient’s tumour can be very different from another’s. They could both have very different sets of mutated genes, which can affect their prognosis and which drugs they should take.


Via Dr. Stefan Gruenwald
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How world's smallest DNA virus evolved in rare parakeets

How world's smallest DNA virus evolved in rare parakeets | Virology and Bioinformatics from Virology.ca | Scoop.it

New insight into a rare virus that is threatening to wipe out the Mauritius parakeet - one of the world's most endangered species of parrot.


Via AJCann
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Full-length sequences of eleven HCV genotype 2 isolates representing 5 subtypes and 6 unclassified lineages with unique geographic distributions and genetic variation patterns

Full-length sequences of eleven HCV genotype 2 isolates representing 5 subtypes and 6 unclassified lineages with unique geographic distributions and genetic variation patterns | Virology and Bioinformatics from Virology.ca | Scoop.it

In this study, we characterized full-length HCV genome sequences for 11 genotype 2 isolates. They were isolated in the sera of 11 patients residing in Canada of whom 4 had an African origin. Full-length genomes were obtained by PCR amplification each with 18-25 overlapping fragments. Five isolates represent the first complete genomes of subtypes 2d, 2e, 2j, 2m, and 2r, while the other 6 correspond to variants that do not group within any assigned subtypes. These sequences had lengths of 9508-9825 nucleotides and each contained a single ORF encoding 3012-3106 amino acids. Predicted amino acids were carefully inspected and unique variation patterns were recognized, especially for a 2e isolate QC64. Phylogenetic analysis of complete genome sequences provides the evidence that there are a total of 16 subtypes, of which 11 have been here described. Co-analysis with 68 partial NS5B sequences also differentiated 18 assigned subtypes, 2a-2r, and 8 additional lineages within genotype 2, which is consistent with the analysis of complete genome sequences. The data from this study now allows for 10 assigned subtypes and for 6 additional lineages of HCV genotype 2 to have their full-length genomes defined.

 

Image courtesy of Russell Kightely Media

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MicrobialEvolution.org | A forum for exchange and discussion amongst educators and students in microbial evolution

This website is primarily designed to be a resource for educators in microbial evolution. These will largely be college professors, but we also aim to include ideas useful for high school courses, etc.

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Novel Gene linked to herpes-related cold sores

Novel Gene linked to herpes-related cold sores | Virology and Bioinformatics from Virology.ca | Scoop.it

Researchers have identified a human chromosome containing a specific gene associated with susceptibility to herpes simplex labialis (HSL), the common cold sore. The gene C21ORF91 encodes a cytoplasmic protein with currently unknown function. Cold sores occur when the herpes virus reactivates from its quiescent state within the nerve, infecting the lip, nose, or face.


Via Dr. Stefan Gruenwald
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HealthMap | Flu Near You

HealthMap | Flu Near You | Virology and Bioinformatics from Virology.ca | Scoop.it
Do you have it in you? Join the Flu Near You project to help track flu activity in the United States.

 

Citizen bioinformatics...B-)

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Into the Eye of the Cytokine Storm

The cytokine storm has captured the attention of the public and the scientific community alike, and while the general notion of an excessive or uncontrolled release of proinflammatory cytokines is well known, the concept of a cytokine storm and the biological consequences of cytokine overproduction are not clearly defined.

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PhiSiGns

PhiSiGns | Virology and Bioinformatics from Virology.ca | Scoop.it

PhiSiGns is a web-based and standalone application that provides a simple and convenient tool to identify signature genes and design primers for PCR amplification of related genes from environmental samples.

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Amazon.com: Quasispecies: Concept and Implications for Virology (Current Topics in Microbiology and Immunology) eBook: Esteban Domingo: Kindle Store

Amazon.com: Quasispecies: Concept and Implications for Virology (Current Topics in Microbiology and Immunology) eBook: Esteban Domingo: Kindle Store...

 

But US$145 for a KINDLE edition??  As opposed to $179 for a hardback and LESS than $140 for a softcover???  Get your pricing model right, guys!!!

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PLoS Pathogens: Influenza A Virus Infection of Human Primary Dendritic Cells Impairs Their Ability to Cross-Present Antigen to CD8 T Cells

PLoS Pathogens: Influenza A Virus Infection of Human Primary Dendritic Cells Impairs Their Ability to Cross-Present Antigen to CD8 T Cells | Virology and Bioinformatics from Virology.ca | Scoop.it

Influenza A virus (IAV) infection is normally controlled by adaptive immune responses initiated by dendritic cells (DCs).

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PLoS Pathogens: Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection

PLoS Pathogens: Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection | Virology and Bioinformatics from Virology.ca | Scoop.it
Deep sequencing technologies have the potential to transform the study of highly variable viral pathogens by providing a rapid and cost-effective approach to sensitively characterize rapidly evolving viral quasispecies.
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Internally deleted WNV genomes isolated from exotic birds in New Mexico: Function in cells, mosquitoes, and mice 10.1016/j.virol.2012.01.028 : Virology | ScienceDirect.com

Internally deleted WNV genomes isolated from exotic birds in New Mexico: Function in cells, mosquitoes, and mice 10.1016/j.virol.2012.01.028 : Virology | ScienceDirect.com | Virology and Bioinformatics from Virology.ca | Scoop.it

West Nile virus, (WNV), (Flaviviridae: Flavivirus) is a mosquito borne virus now endemic to the United States.

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Genetic changes in bacteria tracked

Genetic changes in bacteria tracked | Virology and Bioinformatics from Virology.ca | Scoop.it

Eight mutations occurred in the common bacteria Staphylococcus aureus as it turned from an innocuous resident inside one person's nose into a fatal blood infection, an Oxford University study has found.

 

Via @DailyScan

 

Research article: http://www.pnas.org/content/early/2012/02/27/1113219109.abstract


Via Cesar Sanchez
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H5N1 Pandemic Information News: Map: Worldwide Confirmed ...

H5N1 Pandemic Information News: Map: Worldwide Confirmed ... | Virology and Bioinformatics from Virology.ca | Scoop.it
Map: Worldwide Confirmed Human Cases Updated. Click on image to enlarge. Click on title for postmark descriptions. Located on the right side-bar for future reference. Posted by Commonground at 6:44 AM ...

Via Elsevier Microbiol*
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Microbial Metagenomics Summer Course 2012 - MSU Metagenomics

Microbial Metagenomics Summer Course 2012 - MSU Metagenomics | Virology and Bioinformatics from Virology.ca | Scoop.it

Microbial metagenomics course, June 3 - June 16th, Michigan State University: http://t.co/IXBu9RHO...


Via Elsevier Microbiol*
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Genetic variation and recombination in Aichi virus

Aichi virus (AiV), a member of the genus Kobuvirus in the family Picornaviridae, causes gastroenteritis in humans. It was noted that AiV differs from other picornaviruses in its unusually high C content and a very high degree of genome-ordered RNA secondary structures. However, the genetic variability and mutational restrictions on a full-genome scale have not been studied. In addition to the available five complete AiV genomes, we determined here another five complete coding sequences of AiV sampled in Germany, 2004. Distinctive AiV genetic features included a low incidence of recombination along the genome without obvious hotspots or spared regions and very low rates of synonymous and non-synonymous variation supporting an absence of AiV serotypes. In addition, the absence of recombination between AiV genotypes A and B suggested the existence of reproductively isolated taxonomic units below the species level.

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Indonesia: 50 dead in rabies outbreak

Via The Jakarta Globe: Rabies Outbreak Kills 50 in Indonesia's Maluku Province. Excerpt: Ambon, Maluku.
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Influenza virus budding requires F1Fo-ATPase

Influenza virus budding requires F1Fo-ATPase | Virology and Bioinformatics from Virology.ca | Scoop.it

The identification of host factors involved in virus replication is important to understand virus life cycles better. Accordingly, we sought host factors that interact with the influenza viral nonstructural protein 2 by using coimmunoprecipitation followed by mass spectrometry. Among proteins associating with nonstructural protein 2, we focused on the β subunit of the F1Fo-ATPase.


Via AJCann
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Ed Rybicki's comment, March 7, 2012 2:59 AM
You know an interesting thing: that is almost certainly NOT true in a heterologous system, flu HA protein will bud out virus-like particles from plant (but not insect) cells, when expressed alone. Insect cells appear to need the M protein as well - but not NS2.
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How Your Cat Is Making You Crazy

How Your Cat Is Making You Crazy | Virology and Bioinformatics from Virology.ca | Scoop.it
Jaroslav Flegr is no kook. And yet, for years, he suspected his mind had been taken over by parasites that had invaded his brain. So the prolific biologist took his science-fiction hunch into the lab.
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An inhibitory function of WW domain-containing host proteins in RNA virus replication 10.1016/j.virol.2012.01.020 : Virology | ScienceDirect.com

An inhibitory function of WW domain-containing host proteins in RNA virus replication 10.1016/j.virol.2012.01.020 : Virology | ScienceDirect.com | Virology and Bioinformatics from Virology.ca | Scoop.it

To identify new genes affecting Tomato bushy stunt virus (TBSV) replication in yeast model host, we are studying protein families, whose members have been identified during previous high throughput screening.

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