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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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MicroMicrobe • Microbial image of the month This is a fabulous...

MicroMicrobe • Microbial image of the month This is a fabulous... | Virology and Bioinformatics from Virology.ca | Scoop.it
Microbial image of the month


This is a fabulous photograph of a bacteriophage (or phage), a virus that infects bacteria.
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Roy Cutler's curator insight, February 6, 2013 10:36 AM

What my students should bear in mind is how small this thing is and good the photograph given that size.

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Top Stories : Stanford’s Gene Therapy Helps Block HIV’s Ability to Bind to CD4s

Top Stories : Stanford’s Gene Therapy Helps Block HIV’s Ability to Bind to CD4s | Virology and Bioinformatics from Virology.ca | Scoop.it
Scientists at Stanford University School of Medicine have created an advanced method of engineering CD4 cells to resist HIV infection.
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Pyteomics-a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics.

Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics. It provides modules for reading LC-MS/MS data, search engine output, protein sequence databases, theoretical prediction of retention times, electrochemical properties of polypeptides, mass and m/z calculations, and sequence parsing. Pyteomics is available under Apache license; release versions are available at the Python Package Index http://pypi.python.org/pyteomics , the source code repository at http://hg.theorchromo.ru/pyteomics , documentation at http://packages.python.org/pyteomics . Pyteomics.biolccc documentation is available at http://packages.python.org/pyteomics.biolccc/ . Questions on installation and usage can be addressed to pyteomics mailing list: pyteomics@googlegroups.com.

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The CDC Tells More of the Truth than Usual about Flu Vaccine Effectiveness (Peter Sandman article)

The CDC Tells More of the Truth than Usual about Flu Vaccine Effectiveness (Peter Sandman article)
Chris Upton + helpers's insight:

Very good read...

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MSF Responds To Increase In Measles in Southwestern Pakistan | Doctors Without Borders

MSF Responds To Increase In Measles in Southwestern Pakistan | Doctors Without Borders | Virology and Bioinformatics from Virology.ca | Scoop.it
Cases of measles are on the increase in the eastern region of Pakistan’s Balochistan Province.
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Coronaviruses in bats from Mexico. [J Gen Virol. 2013] - PubMed - NCBI

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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Dual Short Upstream Open Reading Frames Control Translation of a Herpesviral Polycistronic mRNA

Dual Short Upstream Open Reading Frames Control Translation of a Herpesviral Polycistronic mRNA | Virology and Bioinformatics from Virology.ca | Scoop.it

Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiologic agent of multicentric Castleman's disease, primary effusion lymphoma and Kaposi's sarcoma. KSHV expresses a number of transcripts with the potential to generate multiple proteins, yet relies on the cellular translation machinery that is primed to synthesize only one protein per mRNA. Here we report that the viral transcript encompassing ORF35–37 is able to direct synthesis of two proteins and that the translational switch is regulated by two short upstream open reading frames (uORFs) in the native 5′ untranslated region. uORFs are elements commonly found upstream of mammalian genes that function to interfere with unrestrained ribosomal scanning and thus repress translation of the major ORF. The sequence of the viral uORF appears unimportant, and instead functions to position the translation machinery in a location that favors translation of the downstream major ORF, via a reinitiation mechanism. Thus, KSHV uses a host strategy generally reserved to repress translation to instead allow for the expression of an internal gene.

 

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The Battle between Rotavirus and Its Host for Control of the Interferon Signaling Pathway

The Battle between Rotavirus and Its Host for Control of the Interferon Signaling Pathway | Virology and Bioinformatics from Virology.ca | Scoop.it
From molecules to physiology
Kenzibit's insight:

Viral pathogens must overcome innate antiviral responses to replicate successfully in the host organism. Some of the mechanisms viruses use to interfere with antiviral responses in the infected cell include preventing detection of viral components, perturbing the function of transcription factors that initiate antiviral responses, and inhibiting downstream signal transduction. RNA viruses with small genomes and limited coding space often express multifunctional proteins that modulate several aspects of the normal host response to infection. One such virus, rotavirus, is an important pediatric pathogen that causes severe gastroenteritis, leading to ~450,000 deaths globally each year. In this review, we discuss the nature of the innate antiviral responses triggered by rotavirus infection and the viral mechanisms for inhibiting these responses.

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Kenzibit's curator insight, January 31, 2013 1:17 PM

Viral pathogens must overcome innate antiviral responses to replicate successfully in the host organism. Some of the mechanisms viruses use to interfere with antiviral responses in the infected cell include preventing detection of viral components, perturbing the function of transcription factors that initiate antiviral responses, and inhibiting downstream signal transduction. RNA viruses with small genomes and limited coding space often express multifunctional proteins that modulate several aspects of the normal host response to infection. One such virus, rotavirus, is an important pediatric pathogen that causes severe gastroenteritis, leading to ~450,000 deaths globally each year. In this review, we discuss the nature of the innate antiviral responses triggered by rotavirus infection and the viral mechanisms for inhibiting these responses.

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Differential unfolded protein response during Chikungunya and Sindbis virus infection: CHIKV nsP4 suppresses eIF2alpha phosphorylation

Chikungunya (CHIKV) and Sindbis (SINV) are arboviruses belonging to the alphavirus genus within the Togaviridae family. They cause frequent epidemics of febrile illness and long-term arthralgic sequelae that affect millions of people each year.
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Pharmaceutical Microbiology Online: Drinking water is rich in microbial life

Pharmaceutical Microbiology Online: Drinking water is rich in microbial life | Virology and Bioinformatics from Virology.ca | Scoop.it
Flow cytometry (FCM) studies have been used for the quantification of microbial cells in drinking water. A recent study has shown that drinking water contains100 to 10,000 times more living cells than the conventional plate count method would suggest. 
Chris Upton + helpers's insight:

I'm not surprised.

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PNAS | Molecular and microscopic evidence of viruses in marine copepods

PNAS | Molecular and microscopic evidence of viruses in marine copepods | Virology and Bioinformatics from Virology.ca | Scoop.it
Abstract

As dominant members of marine mesozooplankton communities, copepods play critical roles in oceanic food webs and biogeochemical cycling. Despite the ecological significance of copepods, little is known regarding the causes of copepod mortality, and up to 35% of total copepod mortality cannot be accounted for by predation alone. Viruses have been established as ecologically important infectious agents in the oceans; however, viral infection has not been investigated in mesozooplankton communities. Here we used molecular and microscopic techniques to document viral infection in natural populations of the calanoid copepods Acartia tonsa (Dana) and Labidocera aestiva(Wheeler) in Tampa Bay, FL. Viral metagenomics revealed previously undocumented viruses in each species, named Acartia tonsa copepod circo-like virus (AtCopCV) andLabidocera aestiva copepod circo-like virus (LaCopCV). LaCopCV was found to be extremely prevalent and abundant in L. aestiva populations, with up to 100% prevalence in some samples and average viral loads of 1.13 × 105 copies per individual. 

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Ed Rybicki's curator insight, January 31, 2013 4:03 AM

Well, of course there would be: viruses are everywhere and in everything.

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Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web

Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web | Virology and Bioinformatics from Virology.ca | Scoop.it
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The PB2, PA, HA, NP, and NS genes of a highly pathogenic avian influenza virus A/whooper swan/Mongolia/3/2005 (H5N1) are responsible for pathogenicity in ducks

Wild ducks are the natural hosts of influenza A viruses. Duck influenza, therefore, has been believed inapparent infection with influenza A viruses, including highly pathogenic avian influenza viruses (HPAIVs) in chickens.
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Researchers turn to Twitter to track the flu

Researchers turn to Twitter to track the flu | Virology and Bioinformatics from Virology.ca | Scoop.it
(Relaxnews) - As flu season takes its toll across North American and Europe, Johns Hopkins University in the US is using Twitter to build a tool to track the epidemic.
Ed Rybicki's insight:

A use for Twitter!!  Excellent!  Finally!!

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Engineered oncolytic herpes virus inhibits ovarian and breast cancer metastases - Medical Xpress

Engineered oncolytic herpes virus inhibits ovarian and breast cancer metastases - Medical Xpress | Virology and Bioinformatics from Virology.ca | Scoop.it
Engineered oncolytic herpes virus inhibits ovarian and breast cancer metastases Medical Xpress "Numerous laboratories worldwide are using viruses as more specific weapons against cancer cells, called oncolytic viruses", says Campadelli-Fiume,...
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Bioinformatics Knowledge Vital to Careers | The Scientist Magazine®

Bioinformatics is growing up. Science's hottest information tool is coming into adolescence and has transformed the way research is conducted.

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Reassortment Complements Spontaneous Mutation in Influenza A Virus NP and M1 genes to Accelerate Adaptation to a New Host

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Detection of novel viruses in porcine fecal samples from China

Pigs are well known source of human infectious disease. To better understand the spectrum of viruses present in pigs, we utilized the 454 Life Sciences GS-FLX high-throughput sequencing platform to sequence stool samples from healthy pigs.
Ed Rybicki's insight:

The rise and rise of deep sequencing as a means of detecting viruses - some day, all virus detection may be done this way!

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A novel DNA vaccine expressing the Ag85A-HA2 fusion protein provides protection against influenza A virus and Staphylococcus aureus

Secondary pneumonia due to Staphylococcus aureus (S. aureus) causes significant morbidity and mortality.
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Researchers unveil first artificial enzyme created by evolution in a test tube

Researchers unveil first artificial enzyme created by evolution in a test tube | Virology and Bioinformatics from Virology.ca | Scoop.it
There's a wobbly new biochemical structure in Burckhard Seelig's lab at the University of Minnesota that may resemble what enzymes looked like billions of years ago, when life on earth began to evolve – long before they became ingredients for new...
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Why hypothesis and significance tests ask the wrong questions

Why hypothesis and significance tests ask the wrong questions | Virology and Bioinformatics from Virology.ca | Scoop.it
Empirical science needs data. But all data are subject to random variation, and random variation obscures patterns in data.
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Ed Rybicki's comment, February 2, 2013 9:50 AM
I have a saying up on my wall: "F** the hypotheses, let's just discover something"!
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123 Against HPV - info

This website provides information for the general
public on HPV (Human Papillomavirus), its links
with cervical cancer and genital warts, and the
HPV vaccination.

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Blue-sky HIV test chip will upload results to the cloud : Spoonful of Medicine

Blue-sky HIV test chip will upload results to the cloud : Spoonful of Medicine | Virology and Bioinformatics from Virology.ca | Scoop.it
In Rwanda, the most densely populated country in Africa, there are approximately 190,000 people living with HIV, with electronic records facilitating care for over 90,000 of them.
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ChromoZoom: a flexible, fluid, web-based genome browser

ChromoZoom: a flexible, fluid, web-based genome browser | Virology and Bioinformatics from Virology.ca | Scoop.it

ummary: Current web-based genome browsers require repetitious user input to scroll over long distances, alter the drawing density of elements or zoom through multiple orders of magnitude. Generally, either the server or the client is responsible for the majority of data processing, resulting in either servers having to receive and handle data relevant only to one user, or clients redundantly processing widely viewed data. ChromoZoom pre-renders and caches general-use tracks into tiled images on the server and serves them in an interactive web interface with inertial scrolling and precise, fluent zooming via the mouse wheel or trackpad. Custom tracks in several formats can be rendered by client-side code alongside the pre-rendered tracks, minimizing server load because of user-specific rendering and eliminating the need to transmit private data. ChromoZoom thereby enables rapid and simultaneous exploration of curated, experimental and personal genomic datasets.

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