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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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GEN | Insight & Intelligence™:Targeting Kinases Essential to Malaria Parasites

GEN | Insight & Intelligence™:Targeting Kinases Essential to Malaria Parasites | Virology and Bioinformatics from Virology.ca | Scoop.it
A large unmet medical need exists for effective new treatments for malaria in the developing world.
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What Are Quadratic Equations?

What Are Quadratic Equations? | Virology and Bioinformatics from Virology.ca | Scoop.it
Quadratic equations are basic to algebra and are the math behind parabolas, projectiles, satellite dishes and the golden ratio.
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Mysterious Childhood Paralysis Linked to a Common Cold Virus

Mysterious Childhood Paralysis Linked to a Common Cold Virus | Virology and Bioinformatics from Virology.ca | Scoop.it

Scientists have found evidence that a polio-like virus called EV-D68 is behind a mysterious outbreak of paralysis in children [in the USA] last year.

 

LAST YEAR, HUNDREDS of children across the country got sick with what looked like a common cold. Nothing to worry about: body aches, runny nose, coughing and sneezing. But then, mysteriously, a handful of those kids became paralyzed—first, just in an arm or a leg, and then spreading so far that some children needed a ventilator to breathe. The CDC reports that since August 2014, at least 115 children in 34 states have developed unexplained muscle weakness or paralysis, which they’re now calling acute flaccid myelitis. Doctors have urgently been hunting down the origin of this strange illness for over half a year, and now they think they’ve finally identified the culprit: enterovirus D68.

 


Via Ed Rybicki
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Ed Rybicki's curator insight, April 3, 7:46 AM

And it's going to spread...vaccine time, people!

Bio Restore 24's curator insight, April 19, 9:11 PM

Virus's and Bacteria keep changing their make up so that they can spread easier without being harmed by typical cleaning techniques.

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Virus Infects Winter Cereal Crops

Virus Infects Winter Cereal Crops | Virology and Bioinformatics from Virology.ca | Scoop.it
TWIN FALLS • A major disease threat to winter wheat and barley has appeared in fields across southern Idaho.

 

Barley yellow dwarf virus “is rampant from Parma to Ririe,” said Juliet Marshall, a University of Idaho Extension cereal pathologist in Idaho Falls. Some growers are killing infected fields and reseeding with other crops.

 


Via Ed Rybicki
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Ed Rybicki's curator insight, April 3, 7:42 AM

Ah, BYDV...back to my roots of 31 years ago, when I published a paper and a thesis on BYDV in SOuth African small grains.  It's never gone away.

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Video Tip of The Week: Jalview for multiple sequence alignment editing and visualization | The OpenHelix Blog

Video Tip of The Week: Jalview for multiple sequence alignment editing and visualization | The OpenHelix Blog | Virology and Bioinformatics from Virology.ca | Scoop.it
The multiple sequence alignment editing question recently on our What's the Answer? feature was popular. We have covered MSA editors in the past, and we include
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Plotting the elimination of dengue

Plotting the elimination of dengue | Virology and Bioinformatics from Virology.ca | Scoop.it
Dengue is a viral infection spread between humans by Aedes aegypti mosquitoes. Dengue causes flu-like symptoms, including intense headaches and joint pains.
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Efficiently Editing the Vaccinia Virus Genome by Using the CRISPR-Cas9 System

Vaccinia virus (VACV) continues to be used in immunotherapy for the prevention of infectious diseases and treatment of cancer since its use for the eradication of smallpox. However, the current method of editing the VACV genome is not efficient. Here, we demonstrate that the CRISPR-Cas9 system can be used to edit the VACV genome rapidly and efficiently. Additionally, a set of 8,964 computationally designed unique guide RNAs (gRNAs) targeting all VACV genes will be valuable for the study of VACV gene functions.

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Why Can't Mosquitos Transmit HIV? | Viruses101 | Learn Science at Scitable

Why Can't Mosquitos Transmit HIV? | Viruses101 | Learn Science at Scitable | Virology and Bioinformatics from Virology.ca | Scoop.it
Mosquitoes are carriers of various viruses from malaria to dengue. But mosquitoes can not transmit HIV. This article explores why mosquitoes are unable to transmit HIV, the virus that causes AIDS.
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Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing - BMC Genomics

Influenza viruses exist as a large group of closely related viral genomes, also called quasispecies. The composition of this influenza viral quasispecies can be determined by an accurate and sensitive sequencing technique and data analysis pipeline. We compared the suitability of two benchtop next-generation sequencers for whole genome influenza A quasispecies analysis: the Illumina MiSeq sequencing-by-synthesis and the Ion Torrent PGM semiconductor sequencing technique.
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Microbes scared to death by virus presence

Microbes scared to death by virus presence | Virology and Bioinformatics from Virology.ca | Scoop.it
The microbes could surrender to the harmless virus, but instead freeze in place, dormant, waiting for their potential predator to go away, according to a recent study in mBio.
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I love that: scared bacteria B-)

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N-glycosylation profiling of porcine reproductive and respiratory syndrome virus envelope glycoprotein 5 — ScienceDirect

N-glycosylation profiling of porcine reproductive and respiratory syndrome virus envelope glycoprotein 5 — ScienceDirect | Virology and Bioinformatics from Virology.ca | Scoop.it
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Nice free paper!

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An anonymous Canadian foundation grants $3 million to study naturopathic oncology

An anonymous Canadian foundation grants $3 million to study naturopathic oncology | Virology and Bioinformatics from Virology.ca | Scoop.it
It’s no secret that I don’t have a high opinion of naturopathy. Just enter the word “naturopathy” into the search box of this blog, and you’ll quickly see what I mean. Indeed, when last I mentioned the topic a couple of weeks ago, I was discussing the revelations of Britt Marie Hermes, a former naturopath…
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Teaching Evolution to Students Who Tell Me They’ll Pray for My Soul

Teaching Evolution to Students Who Tell Me They’ll Pray for My Soul | Virology and Bioinformatics from Virology.ca | Scoop.it

This essay is adapted from a piece originally printed in the March/April 2015 issue of Orion.  To teach evolution at the University of Kentucky is to teach at an institution steeped in the history of defending evolution education. The first effort to pass an anti-evolution law...

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Learning the Hard Way: My Journey from #AntiVaxx to Science

Learning the Hard Way: My Journey from #AntiVaxx to Science | Virology and Bioinformatics from Virology.ca | Scoop.it
Written by Tara Hills I’m writing this from quarantine, the irony of which isn’t lost on me. Emotionally I’m a bit raw. Mentally a bit taxed. Physically I’m fine.  All seven of my unvaccinated chil...
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Markov Chain Monte Carlo Without all the Bullshit

Markov Chain Monte Carlo Without all the Bullshit | Virology and Bioinformatics from Virology.ca | Scoop.it
I have a little secret: I don't like the terminology, notation, and style of writing in statistics. I find it unnecessarily complicated. This shows up when trying to read about Markov Chain Monte C...
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A Virus In Your Mouth Helps Fight The Flu

A Virus In Your Mouth Helps Fight The Flu | Virology and Bioinformatics from Virology.ca | Scoop.it
It's related to herpes. And it infects most of the world — about half of Americans, nearly all the developing world. But don't go out and get infected. The virus has a dark side, too.
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Replicating poxviruses for human cancer therapy. - PubMed - NCBI

Replicating poxviruses for human cancer therapy. - PubMed - NCBI | Virology and Bioinformatics from Virology.ca | Scoop.it

Naturally occurring oncolytic viruses are live, replication-proficient viruses that specifically infect human cancer cells while sparing normal cell counterparts. Since the eradication of smallpox in the 1970s with the aid of vaccinia viruses, the vaccinia viruses and other genera of poxviruses have shown various degrees of safety and efficacy in pre-clinical or clinical application for human anti-cancer therapeutics. Furthermore, we have recently discovered that cellular tumor suppressor genes are important in determining poxviral oncolytic tropism. Since carcinogenesis is a multi-step process involving accumulation of both oncogene and tumor suppressor gene abnormalities, it is interesting that poxvirus can exploit abnormal cellular tumor suppressor signaling for its oncolytic specificity and efficacy. Many tumor suppressor genes such as p53, ATM, and RB are known to play important roles in genomic fidelity/maintenance. Thus, tumor suppressor gene abnormality could affect host genomic integrity and likely disrupt intact antiviral networks due to accumulation of genetic defects, which would in turn result in oncolytic virus susceptibility. This review outlines the characteristics of oncolytic poxvirus strains, including vaccinia, myxoma, and squirrelpox virus, recent progress in elucidating the molecular connection between oncogene/tumor suppressor gene abnormalities and poxviral oncolytic tropism, and the associated preclinical/clinical implications. I would also like to propose future directions in the utility of poxviruses for oncolytic virotherapy.

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BMC Bioinformatics | Abstract | YOC, A new strategy for pairwise alignment of collinear genomes

Comparing and aligning genomes is a key step in analyzing closely related genomes. Despite the development of many genome aligners in the last 15 years, the problem is not yet fully resolved, even when aligning closely related bacterial genomes of the same species. In addition, no procedures are available to assess the quality of genome alignments or to compare genome aligners.
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The Evolution of Poxvirus Vaccines

The Evolution of Poxvirus Vaccines | Virology and Bioinformatics from Virology.ca | Scoop.it
After Edward Jenner established human vaccination over 200 years ago, attenuated poxviruses became key players to contain the deadliest virus of its own family: Variola virus (VARV), the causative agent of smallpox. Cowpox virus (CPXV) and horsepox virus (HSPV) were extensively used to this end, passaged in cattle and humans until the appearance of vaccinia virus (VACV), which was used in the final campaigns aimed to eradicate the disease, an endeavor that was accomplished by the World Health Or
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Awesome review

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Lack of Marburg Virus Transmission From Experimentally Infected to Susceptible In-Contact Egyptian Fruit Bats


Via Mel Melendrez-Vallard
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See How Diseases Spread in These Mesmerizing Graphics | WIRED

See How Diseases Spread in These Mesmerizing Graphics | WIRED | Virology and Bioinformatics from Virology.ca | Scoop.it
Scientists can visualize the spread of diseases in lots of ways. This viz treats swine flu like it's a commuter taking a train around the world.
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Rates of evolution in the 2014/2015 West African ebolavirus outbreak | epidemic

Rates of evolution in the 2014/2015 West African ebolavirus outbreak | epidemic | Virology and Bioinformatics from Virology.ca | Scoop.it
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Targeted diversity generation by intraterrestrial archaea and archaeal viruses

Targeted diversity generation by intraterrestrial archaea and archaeal viruses | Virology and Bioinformatics from Virology.ca | Scoop.it

In the evolutionary arms race between microbes, their parasites, and their neighbours, the capacity for rapid protein diversification is a potent weapon. Diversity-generating retroelements (DGRs) use mutagenic reverse transcription and retrohoming to generate myriad variants of a target gene. Originally discovered in pathogens, these retroelements have been identified in bacteria and their viruses, but never in archaea. Here we report the discovery of intact DGRs in two distinct intraterrestrial archaeal systems: a novel virus that appears to infect archaea in the marine subsurface, and, separately, two uncultivated nanoarchaea from the terrestrial subsurface. The viral DGR system targets putative tail fibre ligand-binding domains, potentially generating >1018 protein variants. The two single-cell nanoarchaeal genomes each possess ≥4 distinct DGRs. Against an expected background of low genome-wide mutation rates, these results demonstrate a previously unsuspected potential for rapid, targeted sequence diversification in intraterrestrial archaea and their viruses.

  
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Ebola: it hasn't gone away.

Ebola: it hasn't gone away. | Virology and Bioinformatics from Virology.ca | Scoop.it

We've just got blase about it.  And we shouldn't be - because even as the epidemic declines, there are more cases per day than in ANY previous outbreak.  

 

Ebola replication graphic from Russell Kightley Media


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101 questions with a bioinformatician #23: Todd Harris

101 questions with a bioinformatician #23: Todd Harris | Virology and Bioinformatics from Virology.ca | Scoop.it

Todd Harris is a Bioinformatics Consultant and Project Manager at WormBase.

 

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