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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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Used contact lens solution hosts giant virus, ecosystem of parasites

Used contact lens solution hosts giant virus, ecosystem of parasites | Virology and Bioinformatics from Virology.ca | Scoop.it

In July of last year, researchers in France described a rather disturbing example of what could happen if you're not careful about cleaning your contact lenses. A 17-year-old patient had been wearing monthly lenses well past their expiration date, and rinsing them with a cleaning solution she'd diluted with tap water. The end result was an eye infection...

 

Via @carlzimmer

 

Research article:

"Provirophages and transpovirons as the diverse mobilome of giant viruses"

http://dx.doi.org/10.1073/pnas.1208835109


Via Cesar Sanchez
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Ron Fouchier has named the new coronavirus HCoV-EMC (for Erasmus Medical Center)

Ron Fouchier has named the new coronavirus HCoV-EMC (for Erasmus Medical Center) | Virology and Bioinformatics from Virology.ca | Scoop.it
Original Article from The New England Journal of Medicine — Isolation of a Novel Coronavirus from a Man with Pneumonia in Saudi Arabia...
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MicrobeWorld - Viral DNA in Birds: Viruses Taste Like Chicken

MicrobeWorld - Viral DNA in Birds: Viruses Taste Like Chicken | Virology and Bioinformatics from Virology.ca | Scoop.it

Like other organisms, the genomes of birds are riddled with DNA sequences from retroviruses. A study mBio this week examined the genomes of three species of birds for these proviruses and followed the expression of genes during development. What role these viral proteins might play in bird biology is not yet known, but in chickens, a surprising 20% of proviruses are translated during embryo development.

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Major breakthrough in HIV prevention

Major breakthrough in HIV prevention | Virology and Bioinformatics from Virology.ca | Scoop.it
MELBOURNE researchers have developed cows' milk that can defend human cells against HIV.

Lead researcher, University of Melbourne's Marit Kramski said they vaccinated pregnant cows - which cannot contract human immunodeficiency virus - with an HIV protein [Env?] and studied the first milk produced by the cow after birth.

HIV cases in Australia on the rise

Dr Kramski said this first milk, called colostrum, produced milk high in antibodies to protect its newborn against disease.

The researchers were able to inhibit the virus from infecting cells when "combing the virus cells with milk" [sic - I think they mean combining the virus with milk containing antibodies].

 

I think this is very interesting, and has potential for trial in monkeys - not humans, because there is the little problem of the antibodies that would go into a virucidal cream being from cows - meaning they would elicit an immune response, unlike the humanised anti-HIV monoclonals being made in plants by the Fraunhofer Institute.

 

Still, using cow's milk is an inventive thing to do - and sounds like a very cheap source of antibodies.  Except that colostrum is ONLY produced immediately after birth of a calf, so it will nothing like as cheap as milk.


Via Ed Rybicki
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Virology Journal | Identification of different lineages of #measles virus strains circulating in Uttar Pradesh, North India

Genetic analysis of measles viruses associated with recent cases and outbreaks has proven to bridge information gaps in routine outbreak investigations and has made a substantial contribution to measles control efforts by helping to identify the...
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Evolution 101: Synthetic Biology

Evolution 101: Synthetic Biology | Virology and Bioinformatics from Virology.ca | Scoop.it

Synthetic biology is a new frontier in biological research where scientists and engineers are creating living systems out of molecular chemistry. In the last half century, the fundamental biochemical pieces and processes that comprise the phenomena of life have been isolated and studied by scientists in the laboratory. This reductionist approach to molecular biology has yielded enormous insight into the basic molecular units that govern life, such as genes encoded on DNA.


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Poxvirus Cell Entry: How Many Proteins Does it Take?

For many viruses, one or two proteins enable cell binding, membrane fusion and entry. The large number of proteins employed by poxviruses is unprecedented and may be related to their ability to infect a wide range of cells.
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HPV shots don't make girls promiscuous, study says - San Jose Mercury News

HPV shots don't make girls promiscuous, study says - San Jose Mercury News | Virology and Bioinformatics from Virology.ca | Scoop.it

CHICAGO -- Shots that protect against cervical cancer do not make girls promiscuous, according to the first study to compare medical records for vaccinated and unvaccinated girls.

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Current Topics in Genome Analysis 2012

Current Topics in Genome Analysis 2012 | Virology and Bioinformatics from Virology.ca | Scoop.it

Current Topics in Genome Analysis 2012

A lecture series covering contemporary areas in genomics and bioinformatics

January 11 - April 25, 2012


Via Pedro Fernandes, Chris Upton + helpers
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DNA Viruses: The Really Big Ones (Giruses)

DNA Viruses: The Really Big Ones (Giruses) | Virology and Bioinformatics from Virology.ca | Scoop.it

Viruses with genomes greater than 300 kb and up to 1200 kb are being discovered with increasing frequency. These large viruses (often called giruses) can encode up to 900 proteins and also many tRNAs. Consequently, these viruses have more protein-encoding genes than many bacteria, and the concept of small particle/small genome that once defined viruses is no longer valid. Giruses infect bacteria and animals although most of the recently discovered ones infect protists. Thus, genome gigantism is not restricted to a specific host or phylogenetic clade.

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Homeopathy; what's the harm? by Simon Singh | The 10:23 Campaign | #ten23

Homeopathy; what's the harm? by Simon Singh | The 10:23 Campaign | #ten23 | Virology and Bioinformatics from Virology.ca | Scoop.it
Homeopathy doesn't work; it's just sugar and water. But it doesn't do any harm, right? Wrong! Simon Singh tells us why.
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Vast differences in polar ocean microbial communities

Vast differences in polar ocean microbial communities | Virology and Bioinformatics from Virology.ca | Scoop.it
An international team of scientists has found that a clear difference exists between the marine microbial communities in the Southern and Arctic oceans.

 

Via @drosophilas

 

Image: RIA Novosti archive, image #186141 / Nikolai Zaytsev / CC-BY-SA 3.0

 

Research article:

Pole-to-pole biogeography of surface and deep marine bacterial communities

http://dx.doi.org/10.1073/pnas.1208160109


Via Cesar Sanchez
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HTS mappers

HTS mappers | Virology and Bioinformatics from Virology.ca | Scoop.it

This page attempts to provide an up-to-date compendium of HTS mappers initially provided in the review article "Tools for mapping high-throughput sequencing data", submitted.

If you are a developer and your mapper is not listed or you want to update the data for your mapper then please let us know by filling this form. We will be happy to add them to the list. Any suggestions are welcome.

Mappers Timeline

Mappers time line (since 2001). DNA mappers are plotted in blue, RNA mappers in red, miRNA mappers in green, and bisulfite mappers in purple. Gray dotted lines connect related mappers (extensions or new major versions). The time line only includes mappers with peer-reviewed publications and the date corresponds to the earliest date of publication.


Via Pedro Fernandes
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RNA teams up to beat selfish rivals

RNA teams up to beat selfish rivals | Virology and Bioinformatics from Virology.ca | Scoop.it

RNA molecules can team up to dominate more selfish rivals, in a way that might have allowed genetic information to survive in an early ‘RNA world’.


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PLOS ONE: Metagenomic Exploration of Viruses throughout the Indian Ocean

PLOS ONE: Metagenomic Exploration of Viruses throughout the Indian Ocean | Virology and Bioinformatics from Virology.ca | Scoop.it

19 water samples were collected aboard the Sorcerer II sailing vessel from the southern Indian Ocean in an effort to more thoroughly understand the lifestyle strategies of the microbial inhabitants of this ultra-oligotrophic region

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iPhylo: OneZoom

iPhylo: OneZoom | Virology and Bioinformatics from Virology.ca | Scoop.it

James Rosindell's OneZoom tree viewer is out and the paper describing the viewer has been published in PLoS One

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Cold #viruses point the way to new #cancer therapies

Cold #viruses point the way to new #cancer therapies | Virology and Bioinformatics from Virology.ca | Scoop.it
Cold viruses generally get a bad rap -- which they've certainly earned -- but new findings by a team of scientists suggest that these viruses might also be a valuable ally in the fight against cancer.
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#Bioinformatics: Analysis Scripts — Biolinux

#Bioinformatics: Analysis Scripts — Biolinux | Virology and Bioinformatics from Virology.ca | Scoop.it

Scripts are a way of linking tasks together to process large numbers of data items or to automate a series of tasks. Common utility tasks in bioinformatics include things like sequence formatting or blast report parsing.


Via Mohamed Nadhir Djekidel
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#Virology #podcast TWiV 203: Mark Challberg, a cold room kind of guy

#Virology #podcast TWiV 203: Mark Challberg, a cold room kind of guy | Virology and Bioinformatics from Virology.ca | Scoop.it
Vincent and Rich meet up with Mark Challberg to talk about his scientific career studying viral DNA replication, and his transition to an NIH Program Officer.
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Jumping DNA rides aboard a virus, which infects a giant virus, which infects an amoeba, which infected a woman’s eye | Not Exactly Rocket Science | Discover Magazine

Jumping DNA rides aboard a virus, which infects a giant virus, which infects an amoeba, which infected a woman’s eye | Not Exactly Rocket Science | Discover Magazine | Virology and Bioinformatics from Virology.ca | Scoop.it
Medicine & health | Earlier this year, a 17-year-old French woman arrived at her ophthalmologist with pain and redness in her left eye.
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Subversion of cytokine networks by virally encoded decoy receptors.

PubMed comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
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Pyrosequencing-Based Transcriptome Analysis of the Asian Rice Gall Midge Reveals Differential Response during Compatible and Incompatible Interaction

Pyrosequencing-Based Transcriptome Analysis of the Asian Rice Gall Midge Reveals Differential Response during Compatible and Incompatible Interaction | Virology and Bioinformatics from Virology.ca | Scoop.it

Abstract: The Asian rice gall midge (Orseolia oryzae) is a major pest responsible for immense loss in rice productivity. Currently, very little knowledge exists with regard to this insect at the molecular level. The present study was initiated with the aim of developing molecular resources as well as identifying alterations at the transcriptome level in the gall midge maggots that are in a compatible (SH) or in an incompatible interaction (RH) with their rice host. Roche 454 pyrosequencing strategy was used to develop both transcriptomics and genomics resources that led to the identification of 79,028 and 85,395 EST sequences from gall midge biotype 4 (GMB4) maggots feeding on a susceptible and resistant rice variety, TN1 (SH) and Suraksha (RH), respectively. Comparative transcriptome analysis of the maggots in SH and RH revealed over-representation of transcripts from proteolysis and protein phosphorylation in maggots from RH. In contrast, over-representation of transcripts for translation, regulation of transcription and transcripts involved in electron transport chain were observed in maggots from SH. This investigation, besides unveiling various mechanisms underlying insect-plant interactions, will also lead to a better understanding of strategies adopted by insects in general, and the Asian rice gall midge in particular, to overcome host defense.


Via Biswapriya Biswavas Misra
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Virology Serological evidence of ebolavirus infection in bats, China

The genus Ebolavirus of the family Filoviridae currently consists of five species. All species, with the exception of Reston ebolavirus, have been found in Africa and caused severe human diseases.
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McMaster researchers fighting cancer with viruses - Hamilton

McMaster researchers fighting cancer with viruses - Hamilton | Virology and Bioinformatics from Virology.ca | Scoop.it
New research funded by the Terry Fox Foundation indicate that viruses can help stop tumor growth.
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Lab Apps for Scientists

Lab Apps for Scientists | Virology and Bioinformatics from Virology.ca | Scoop.it

Oligo melting temperatures—there’s an app for that? Yes, there really is. Smartphones and tablets have quickly entered the lab environment, and for most routine lab tasks, there probably really is an app for that.


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