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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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Researchers identify new behavior for the human macrophage

Researchers at the Institute of Human Virology of the University of Maryland School of Medicine have identified a new behavior for the human macrophage that provides new explanations for several features of HIV biology, including how the virus...
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5000 views for Virology and Bioinformatics Scoop.it

5000 views for Virology and Bioinformatics Scoop.it | Virology and Bioinformatics from Virology.ca | Scoop.it

Thanks to all the co-curators!!

Keep it up!

Chris

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Ed Rybicki's comment, July 20, 2012 3:53 AM
We work hard for the money...B-)
Chris Upton + helpers's comment, July 20, 2012 4:41 PM
I thought I just promised fame, not money!
Ed Rybicki's comment, July 23, 2012 4:57 AM
Exactly - no money, no work...B-) Seriously, this is for fun!
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New drug could cure nearly any viral infection - MIT News Office

New drug could cure nearly any viral infection - MIT News Office | Virology and Bioinformatics from Virology.ca | Scoop.it
Researchers at MIT’s Lincoln Lab have developed technology that may someday cure the common cold, influenza and other ailments.
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The proof that Aids can be cured?

The proof that Aids can be cured? | Virology and Bioinformatics from Virology.ca | Scoop.it
Aids researchers believe the time may have come to think the unthinkable: a growing body of expert opinion believes a cure for HIV infection is no longer a scientific impossibility but a realistic goal that scientists could reach in the very near...
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Did Silencing Suppression Counter-Defensive Strategy Contribute to Origin and Evolution of the Triple Gene Block Coding for Plant Virus Movement Proteins? | Frontiers in Plant Physiology

Did Silencing Suppression Counter-Defensive Strategy Contribute to Origin and Evolution of the Triple Gene Block Coding for Plant Virus Movement Proteins? | Frontiers in Plant Physiology | Virology and Bioinformatics from Virology.ca | Scoop.it

Comparison of gene silencing in tissues and whole organisms shows intriguing similarities between plants and animals  despite that they are very different from each other in many aspects related to the cell-to-cell communications. Interestingly, one of the shared mechanisms is the reprogramming of intracellular silencing pathways and intercellular communications during development of virus infections. As a part of their counter-defensive strategy, viruses encode silencing suppressors to inhibit various stages of the silencing process.

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Ed Rybicki's comment, July 23, 2012 5:00 AM
What is more interesting is that plant viruses have co-opted DIFFERENT machinery from hosts to move - and use very different genes to suppress silencing, meaning there are a plethora of different ways to achieve the same thing.
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Mapping Zoonoses | The Scientist

Mapping Zoonoses | The Scientist | Virology and Bioinformatics from Virology.ca | Scoop.it

Mapping Zoonoses |...Emerging Zoonotic Disease Events, 1940-2012
This maps locates zoonotic events over the past 72 years, with recent events in blue. Like earlier analyses, the study shows western Europe and western USA are hotspots. Recent events, however, show an increasingly higher representation of developing countries.

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Brain Mosaic | The Scientist

Brain Mosaic | The Scientist | Virology and Bioinformatics from Virology.ca | Scoop.it
The paper
J.K. Baillie et al., “Somatic retrotransposition alters the genetic landscape of the human brain,” Nature, 479:534-37, 2011.

The finding
Mobile genetic elements may be a source of DNA sequence variation in normal human brain tissue. Geoff Faulkner, now at the University of Queensland, and colleagues showed that retrotransposons, which can copy themselves and integrate into new sites in a cell’s genome, move much more frequently in brain cells compared to germline cells.

The moving target
Although previous research had shown that there was variation among different people’s brains in the frequency of retrotransposon insertions, none had been mapped to specific locations in the genome. Faulkner’s group mapped retrotransposon insertions in donors’ brain cells, compared them to those found in their blood cells (used as a proxy for germline cells), and identified tens of thousands of unique insertions in brain tissue.

The open slot
Retrotransposons didn’t insert randomly—they preferred to slip into genes being actively transcribed, suggesting their mobility may be under more control than previously recognized, says Isaac Kohane of Harvard Medical School.

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H1N1 vaccine may be linked to rare nerve disorder

H1N1 vaccine may be linked to rare nerve disorder | Virology and Bioinformatics from Virology.ca | Scoop.it

"The H1N1 (swine) flu vaccine was associated with a small but significant risk for developing a rare nervous disorder called Guillain–Barré syndrome (GBS), say doctors in a report detailed in the July 11 issue of the Journal of the American Medical Association (JAMA).
The study, conducted in Quebec, rekindles the still-controversial connection between Guillain–Barré syndrome (GBS) and the 1976 swine flu outbreak, which halted that year's flu vaccination program in the United States. It also raises questions about vaccines for flu strains originating in swine.
This latest analysis, led by Philippe De Wals of Laval University, Quebec City, Canada, followed 4.4 million residents vaccinated against the H1N1 "swine flu" in late 2009. Over the next six months, 25 people who received the vaccine developed GBS. Across the Quebec province, however, another 58 people who were not vaccinated also developed GBS.
De Wals said that, regarding the entire population, the number of GBS cases attributed to the swine flu vaccine was about 2 per 1 million doses, but that the benefits of immunization outweigh the risks."

 

And later in the article, they say that another much larger study from 2011 showed NO such risk - which in this study in any case, was VERY low (2 per million).  Nice little review on GB syndrome, in any case.


Via Ed Rybicki
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Influenza: Five questions on H5N1

Influenza: Five questions on H5N1 | Virology and Bioinformatics from Virology.ca | Scoop.it

Great piece on H5N1 by Ed Yong, including the following 5 questions (and some answers).

Q1: Why is it so successful"

Q2: Where is it now?

Q3: How does it kill?

Q4: Will it become transmissible in humans?

Q5: What else could cause a pandemic?

 

Apropos the latter, he says:

"H9N2 may be an equally plausible pandemic candidate.... It generally goes unnoticed, but has hunkered down among Asia's poultry, caused occasional outbreaks in humans and can reassort with seasonal flu. Some strains already have mutations that are associated with greater transmissibility in mammals. H7N7 is similarly widespread and under-reported. In 2003, it flared up in the Netherlands, infecting 89 people and killing a veterinarian. Virologists hope that by understanding the secrets that allow H5N1 to spread and kill, they are in a better position to assess the risk posed by other subtypes."


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Viroporins: structure and biological functions : Abstract : Nature Reviews Microbiology

Viroporins are small, hydrophobic proteins that are encoded by a wide range of clinically relevant animal viruses. When these proteins oligomerize in host cell membranes, they form hydrophilic pores that disrupt a number of physiological properties of the cell. Viroporins are crucial for viral pathogenicity owing to their involvement in several diverse steps of the viral life cycle. Thus, these viral proteins, which include influenza A virus matrix protein 2 (M2), HIV-1 viral protein U (Vpu) and hepatitis C virus p7, represent ideal targets for therapeutic intervention, and several compounds that block their pore-forming activity have been identified. Here, we review recent studies in the field that have advanced our knowledge of the structure and function of this expanding family of viral proteins.

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PLoS Pathogens: Identifying Host Factors That Regulate Viral Infection

One goal of virology research is to identify viral and host factors involved in infection, in order to develop antiviral therapies. Drugs targeting viral proteins have certain key disadvantages. They often affect only a specific viral species or subtype. Also, the low-fidelity polymerases of many medically important viruses, including HIV and influenza, make them prone to rapid mutations, leading to development of drug resistance. In addition, viruses encode few proteins, limiting the number of available targets.
Targeting host proteins is a practical alternative. Viruses use host proteins at multiple stages of their life cycles. Identifying host functions subverted by viruses will further our understanding of viral life cycles and may provide a catalog of novel drug targets that are unlikely to mutate following therapy. Furthermore, targeting the host may result in therapies with a broader range than traditional antivirals. Exciting progress has been made in recent years in this field; the development of new genomic and proteomic tools enables identification of interacting host factors at an unprecedented scale and level of detail. Together with the use of bioinformatics, these approaches hold promise for accelerating our understanding of virus–host interactions.
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UW scientists discover why human body cannot fight HIV infection

University of Washington researchers have made a discovery that sheds light on why the human body is unable to adequately fight off HIV infection. The researchers discovered that the viral protein vpu, which is created by HIV during infection, directly interferes with the immune response protein IRF3 to dampen the ability of the immune system to protect against virus infection.

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A RIBOSOME-BINDING, 3’ TRANSLATIONAL ENHANCER HAS A T-SHAPED STRUCTURE AND ENGAGES IN A LONG DISTANCE RNA:RNA INTERACTION

A RIBOSOME-BINDING, 3’ TRANSLATIONAL ENHANCER HAS A T-SHAPED STRUCTURE AND ENGAGES IN A LONG DISTANCE RNA:RNA INTERACTION | Virology and Bioinformatics from Virology.ca | Scoop.it

Many plant RNA viruses contain elements in their 3’ UTRs that enhance translation. The PTE (Panicum mosaic virus-like translational enhancer) of Pea enation mosaic virus (PEMV) binds to eIF4E, but how this affects translation from the 5’ end is unknown. We have discovered a three-way branched element just upstream of the PEMV PTE that engages in a long-distance kissing-loop interaction with a coding sequence hairpin that is critical for translation of a reporter construct and accumulation of the viral genome in vivo.

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MicrobeWorld - TWiM #37: Microbial Jekyll and Hyde

MicrobeWorld - TWiM #37: Microbial Jekyll and Hyde | Virology and Bioinformatics from Virology.ca | Scoop.it
MicrobeWorld explores the world of microbes with vivid images and descriptions. Learn about microbiology, what microbiologists do, how they do it, and current topics in the news.
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PLoS ONE: Broad-Spectrum Antiviral Therapeutics

PLoS ONE: Broad-Spectrum Antiviral Therapeutics | Virology and Bioinformatics from Virology.ca | Scoop.it

Currently there are relatively few antiviral therapeutics, and most which do exist are highly pathogen-specific or have other disadvantages. We have developed a new broad-spectrum antiviral approach, dubbed Double-stranded RNA (dsRNA) Activated Caspase Oligomerizer (DRACO) that selectively induces apoptosis in cells containing viral dsRNA, rapidly killing infected cells without harming uninfected cells. We have created DRACOs and shown that they are nontoxic in 11 mammalian cell types and effective against 15 different viruses, including dengue flavivirus, Amapari and Tacaribe arenaviruses, Guama bunyavirus, and H1N1 influenza. We have also demonstrated that DRACOs can rescue mice challenged with H1N1 influenza. DRACOs have the potential to be effective therapeutics or prophylactics for numerous clinical and priority viruses, due to the broad-spectrum sensitivity of the dsRNA detection domain, the potent activity of the apoptosis induction domain, and the novel direct linkage between the two which viruses have never encountered.

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Nanoparticle Completely Eradicates Hepatitis C Virus - IEEE Spectrum

Nanoparticle Completely Eradicates Hepatitis C Virus - IEEE Spectrum | Virology and Bioinformatics from Virology.ca | Scoop.it
A nanoparticle consists of an enzyme that destroys disease-related proteins and DNA that tells the enzyme where the proteins are located...
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An Introduction to Interactive Programming in Python

An Introduction to Interactive Programming in Python | Virology and Bioinformatics from Virology.ca | Scoop.it

Joe Warren, Scott Rixner, John Greiner, Stephen Wong

Rice University

 

This course is designed to be a fun introduction to the basics of programming in Python. Our main focus will be on building simple interactive games such as Pong, Blackjack and Asteroids.

 

This course is designed to help students with very little or no computing background learn the basics of building simple interactive applications. Our language of choice, Python, is an easy-to learn, high-level computer language that is used in many of the computational courses offered on Coursera. To make learning Python easy, we have developed a new browser-based programming environment that makes developing interactive applications in Python simple. These applications will involve windows whose contents are graphical and respond to buttons, the keyboard and the mouse.

 

Part of:  University-Lectures-Online


Via Dr. Stefan Gruenwald
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Futurity.org – Engineered bacteria kill malaria parasite

Futurity.org – Engineered bacteria kill malaria parasite | Virology and Bioinformatics from Virology.ca | Scoop.it
Research news from leading universities...
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Virus-like particles speed bacterial evolution : Nature News

Virus-like particles speed bacterial evolution : Nature News | Virology and Bioinformatics from Virology.ca | Scoop.it

"In the ocean, genes can hop between bacteria with unexpected ease, thanks to strange virus-like particles that shuttle genes from one species to another. These particles, called gene-transfer agents (GTAs), insert DNA into bacterial genomes so frequently that gene transfer in the ocean may occur 1,000 to 100 million times more often than previously thought. This suggests that GTAs have had a powerful role in evolution."

 

Yes, I know it's old, but I missed it, and I have a project on oceanic viromics, so...

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Closer to a cure? Chemists synthesize compound that flushes out latent HIV

Closer to a cure? Chemists synthesize compound that flushes out latent HIV | Virology and Bioinformatics from Virology.ca | Scoop.it
A new collection of compounds, called "bryologs" -- derived from a tiny marine organism -- activate hidden reservoirs of the virus that currently make the disease nearly impossible to eradicate.
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Articles of Significant Interest: J Virol August 2012

The First Metagenomic Analysis of the Air Virome

Airborne viruses are expected to be ubiquitous in the atmosphere and are regarded as major environmental risk factors in the pathogenesis of complex diseases. Whon et al. (p. 8221–8231) demonstrate that viral abundances in the near-surface atmosphere are inversely correlated with temperature and absolute humidity, which increased from autumn to winter and decreased toward spring. The first metagenomic analysis of air viromes revealed dominance of plant-associated single-stranded DNA (ssDNA) geminivirus-related viruses followed by animal-infecting circovirus-related viruses showing evolutionary relationships to previously known ssDNA viruses. These findings suggest that the near-surface atmosphere is a largely unexplored reservoir of novel plant- and animal-associated viruses with high diversity.


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Free access to British scientific research within two years

Free access to British scientific research within two years | Virology and Bioinformatics from Virology.ca | Scoop.it

Radical shakeup of academic publishing will allow papers to be put online and be accessed by universities, firms and individuals.


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PLoS Pathogens: Polydnaviruses as Symbionts and Gene Delivery Systems

PLoS Pathogens: Polydnaviruses as Symbionts and Gene Delivery Systems | Virology and Bioinformatics from Virology.ca | Scoop.it

"The Polydnaviridae was recognized as a family of viruses in 1995, and is currently divided into two genera named the Bracovirus and Ichnovirus [3]. Polydnavirus (PDV) virions consist of enveloped nucleocapsids and package multiple circular, double-stranded (ds) DNAs with aggregate sizes that range from 190 to more than 500 kbp [4]. PDVs are also strictly associated with insects called parasitoid wasps (Hymenoptera), which are free living nectar feeders as adults but which develop during their immature stages by feeding inside the body of another insect (the host) [3], [4]. Recent studies, however, indicate that PDVs differ from all other known viruses in ways that challenge traditional views of what viruses are and how they function."

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Vaccines backfire: Veterinary vaccines found to combine into new infectious viruses

Vaccines backfire: Veterinary vaccines found to combine into new infectious viruses | Virology and Bioinformatics from Virology.ca | Scoop.it

Two different vaccine viruses -- used simultaneously to control the same condition [infectious laryngotracheitis virus] in chickens -- have combined to produce new infectious viruses.

"Comparisons of the vaccine strains and the new recombinant strains have shown that both the recombinant strains cause more severe disease, or replicate to a higher level than the parent vaccine strains that gave rise to them".

 

Sad, but a logical consequence of using live viruses...now, if they'd used virus-like particle vaccines, or even subunit surface proteins, the problem would not have arisen - but that's expensive for a poultry vaccine.  Unless you make them in plants??  Go green, guys!!


Via Ed Rybicki
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Accuracy of RNA-Seq and its dependence on sequencing depth | RNA-Seq Blog

Accuracy of RNA-Seq and its dependence on sequencing depth | RNA-Seq Blog | Virology and Bioinformatics from Virology.ca | Scoop.it

Paper via RNA-Seq Blog - that's right a whole blog about RNA-Seq

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