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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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#Viral #metagenomic analysis of bushpigs (Potamochoerus larvatus) in Uganda identifies novel variants of Porcine parvovirus 4 and Torque teno sus virus 1 and 2

As a result of rapidly growing human populations, intensification of livestock production and increasing exploitation of wildlife habitats for animal agriculture, the interface between wildlife, livestock and humans is expanding, with potential...
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Accurate estimation of short read mapping qua... [Bioinformatics. 2012] - PubMed - NCBI

Several software tools specialize in the alignment of short next-generation sequencing reads to a reference sequence. Some of these tools report a mapping quality score for each alignment-in principle, this quality score tells researchers the likelihood that the alignment is correct.

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If the Mars rover finds water, it could be H2 ... uh oh!

If the Mars rover finds water, it could be H2 ... uh oh! | Virology and Bioinformatics from Virology.ca | Scoop.it

For all the hopes NASA has pinned on the rover it deposited on Mars last month, one wish has gone unspoken: Please don't find water. The rover's drill bits may be tainted with Earth microbes that could survive upon touching water.


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zoonotica: zoonotic infections

zoonotica:  zoonotic infections | Virology and Bioinformatics from Virology.ca | Scoop.it
A PhD student's blogging about zoonotic diseases and other cool science...
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How Not to Miss (Almost) Any Article on PubMed

How Not to Miss (Almost) Any Article on PubMed | Virology and Bioinformatics from Virology.ca | Scoop.it

Reading papers (still) remains the standard way to follow advances in our field(s), to track our collaborators/competitors, or to enjoy some digressive but scientifically entertaining moments.

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Uncovering the Genome’s Regulatory Code

Uncovering the Genome’s Regulatory Code | Virology and Bioinformatics from Virology.ca | Scoop.it

A new, automated method for mapping protein-DNA interactions may lead to advances in personalized medicine


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Early infection with respiratory syncytial virus impairs regulatory T cell function and increases susceptibility to allergic asthma : Nature Medicine : Nature Publishing Group

Early infection with respiratory syncytial virus impairs regulatory T cell function and increases susceptibility to allergic asthma : Nature Medicine : Nature Publishing Group | Virology and Bioinformatics from Virology.ca | Scoop.it
Recurrent infections with respiratory syncytial virus (RSV) early in life increase susceptibility to asthma. Nandini Krishnamoorthy et al. show that RSV infection of young mice impairs maternally transferred tolerance to allergens.
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Seasonal Flu Vaccine and Pandemic Flu Severity

Seasonal flu vaccines are targeted for strains of the influenza virus that public health officials believe will be most prevalent in the upcoming season. While the vaccine primes the immune system to protect against those specific strains, what does it mean for other future strains of the virus. Researchers present findings from a study showing ferrets who received the 2008-2009 seasonal vaccine experienced a more severe disease when exposed to the pandemic H1N1 influenza virus than ferrets who did not receive the vaccine.
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CDC - Seasonal Influenza (Flu) - H1N2 Variant Virus Detected in Minnesota

CDC Centers for Disease Control and Prevention Influenza Flu: H1N2 Variant Virus Detected in Minnesota.
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Have You Heard? Viral-Mediated Gene Therapy Restores Hearing

Have You Heard? Viral-Mediated Gene Therapy Restores Hearing | Virology and Bioinformatics from Virology.ca | Scoop.it

"Genetic loss of VGLUT3 in cochlear inner hair cells results in profound deafness. In this issue of Neuron, Akil et al. (2012) show that AAV-mediated introduction of wild-type VGLUT3 in the genetically deaf mouse cochlea results in significantly improved hearing."

 

Profoundly cool - using a defective virus to target specific cell types, to restore something as fundamental as hearing.  This could go a long way to restoring some of the potential that the gene therapy field was seen to have, before the disasters of death associated with recombinant adenovirus use, and leukaemia with recombinant retroviruses.


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What Caused the Yosemite Hantavirus Outbreak?: Scientific American

What Caused the Yosemite Hantavirus Outbreak?: Scientific American | Virology and Bioinformatics from Virology.ca | Scoop.it
With the Yosemite tourists having died from this normally high-altitude illness, we spoke with an infectious disease expert to see if hantavirus could spread to other areas of the country...
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Tracking Viruses from Animals to People

Tracking Viruses from Animals to People | Virology and Bioinformatics from Virology.ca | Scoop.it
Researchers discuss West Nile, hantavirus, and other diseases that cross from animals to people.
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PLoS Pathogens: OX40 Facilitates Control of a Persistent Virus Infection

PLoS Pathogens: OX40 Facilitates Control of a Persistent Virus Infection | Virology and Bioinformatics from Virology.ca | Scoop.it

A robust T cell response is the hallmark of an effective immune response to a variety of invading viruses. In many acute infections, the clearance of the viral pathogen is associated with a short and vigorous T cell response followed by development of pathogen-specific immune memory. However, some viruses can establish persistent infection in their respective host, during which an ongoing T cell response is required in order to prevent overwhelming viral replication. Little is known about the factors that sustain the T cell response in the persistent phase of a viral infection. In this report, we demonstrate that ligation of the OX40 molecule, which is expressed on T cells targeting the virus, is critically required in order to sustain the anti-viral immune response. We show that virus-specific, OX40-deficient T cells fail to accumulate sufficiently and consequently, mice lacking the OX40 receptor are incapable of controlling viral replication. Collectively our data establish OX40 as a crucial signaling molecule during a persistent viral infection.

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#BMC #Bioinformatics | Highly improved homopolymer aware nucleotide-protein alignments with 454 data

Roche 454 sequencing is the leading sequencing technology for producing long read high throughput sequence data. Unlike most methods where sequencing errors translate to base uncertainties, 454 sequencing inaccuracies create nucleotide gaps.
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Bacterial phylogenetic tree construction based on genomic translation stop signals

The efficiencies of the stop codons TAA, TAG, and TGA in protein synthesis termination are not the same. These variations could allow many genes to be regulated.
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allAfrica.com: 'HIV Vaccine Inevitable'

allAfrica.com: 'HIV Vaccine Inevitable' | Virology and Bioinformatics from Virology.ca | Scoop.it
allAfrica: African news and information for a global audience...

Scientists and scholars have singled out economical, biological, political and ethical challenges as some of the major factors slowing down the development of an HIV vaccine. Speaking to The Herald on the sidelines of the Aids Vaccine Conference in Boston, director of the Global HIV Vaccine Enterprise Mr Bill Snow said with sound and well-financed implementation, new HIV prevention strategies could produce important reductions in the 2,5 million HIV infections occurring each year.

He said scientists attending the conference would present more than 400 new research studies updating global progress in the search for a safe and effective HIV vaccine.

"HIV vaccine research is in its most promising era since the epidemic began," he said.

Mr Snow said the development of a safe and effective Aids vaccine remains central to efforts to bring the world significantly closer to the end of this epidemic.

He said the HIV vaccine is inevitable and there is need for political and economic will.

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Mrs Hill's curator insight, January 20, 8:49 AM

HIV Solutions

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Vaccine trial reveals chinks in HIV's armour

Vaccine trial reveals chinks in HIV's armour | Virology and Bioinformatics from Virology.ca | Scoop.it
Analysis identifies target for immune response that could improve AIDS vaccines.
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Trends in Microbiology - A cultured affair: HSV latency and reactivation in neurons

After replicating in surface epithelia, herpes simplex virus type-1 (HSV-1) enters the axonal terminals of peripheral neurons. The viral genome translocates to the nucleus, where it establishes a specialized infection known as latency, re-emerging periodically to seed new infections. Studies using cultured neuron models that faithfully recapitulate the molecular hallmarks of latency and reactivation defined in live animal models have provided fresh insight into the control of latency and connections to neuronal physiology. With this comes a growing appreciation for how the life cycles of HSV-1 and other herpesviruses are governed by key host pathways controlling metabolic homeostasis and cell identity.

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The Attenuated Genotype of Varicella-Zoster Virus Includes an ORF0 Transitional Stop Codon Mutation

Varicella-zoster virus (VZV) is the first of the human herpesviruses to be attenuated and subsequently approved as a live vaccine to prevent varicella and herpes zoster.

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Epidemiology of chicken an[a]emia virus in Central African Republic and Cameroon

Although chicken anemia virus (CAV) has been detected on all continents, little is known about this virus in sub-Saharan Africa. This study aimed to detect and characterize CAV for the first time in Central African Republic and in Cameroon.

 

Interesting stuff - coming out of places that are not much mentioned in the context of virology, except as sources of exotic viruses like Ebola.  While chicken infectious anAemia virus is not that charismatic a pathogen, it is an important virus of food animals - and, it seems, an under-appreciated disease agent in Africa.

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'There's Something Very Exciting Going On Here'

'There's Something Very Exciting Going On Here' | Virology and Bioinformatics from Virology.ca | Scoop.it
Stanford's new head of online learning explains his vision for how the Internet can remake college classrooms.

Via Ana Cristina Pratas
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Strudel - Comparative Map Viewer

Strudel - Comparative Map Viewer | Virology and Bioinformatics from Virology.ca | Scoop.it

Strudel - Comparative Map Viewer


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FastML: a web server for probabilistic reconstruction of ancestral sequences

Ancestral sequence reconstruction is essential to a variety of evolutionary studies. Here, we present the FastML web server, a user-friendly tool for the reconstruction of ancestral sequences. FastML implements various novel features that differentiate it from existing tools: (i) FastML uses an indel-coding method, in which each gap, possibly spanning multiples sites, is coded as binary data.

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10 Things Every Molecular Biologist Should Know

10 Things Every Molecular Biologist Should Know | Virology and Bioinformatics from Virology.ca | Scoop.it

There are so many things that molecular biologists need to know that are just not normally taught in formal settings like lectures and textbooks. Instead they are passed down by word of mouth, or learned through hard-won experience in the lab. But now Bitesize Bio offers a new way to pick up these vital nuggets of information through our blog articles, webinars and discussions.

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Ifitm3 Limits the Severity of Acute Influenza in Mice

Ifitm3 Limits the Severity of Acute Influenza in Mice | Virology and Bioinformatics from Virology.ca | Scoop.it

Interferon-induced transmembrane (IFITM) proteins are a family of viral restriction factors that inhibit the entry processes of several pathogenic viruses, including influenza A virus (IAV), in vitro. Here we report that IAV-infected knockout mice lacking the Ifitm locus on chromosome 7 exhibited accelerated disease progression, greater mortality, and higher pulmonary and systemic viral burdens as compared to wild type controls.

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