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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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BMC Bioinformatics | Abstract | Seq2Ref: a web server to facilitate functional interpretation

The size of the protein sequence database has been exponentially increasing due to advances in genome sequencing.
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Can you predict how a disease will spread in a population?

Can you predict how a disease will spread in a population? | Virology and Bioinformatics from Virology.ca | Scoop.it
How, when and where a pathogen is transmitted between two individuals in a population is crucial in understanding and predicting how a disease will spread.
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JENNIFER LOPEZ FIGHTING PERTUSSIS. GET THE VACCINE FOR YOU AND YOUR BABY. Important, see the video - click HERE.

Chris Upton + helpers's insight:

Powerful ad for vaccines.

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Twitter / drflanders : Deaths from vaccine-preventable ...

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Nucleic Acid-Sensing Toll-like Receptors Are Essential for the Control of Endogenous Retrovirus Viremia and ERV-Induced Tumors

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Kenzibit's curator insight, February 4, 2013 4:13 AM

The genome of vertebrates contains endogenous retroviruses (ERVs) that are largely nonfunctional relicts of ancestral germline infection by exogenous retroviruses. However, in some mouse strains ERVs are actively involved in disease. Here we report that nucleic acid-recognizing Toll-like receptors 3, 7, and 9 (TLR 3, TLR7, and TLR9) are essential for the control of ERVs. Loss of TLR7 function caused spontaneous retroviral viremia that coincided with the absence of ERV-specific antibodies. Importantly, additional TLR3 and TLR9 deficiency led to acute T cell lymphoblastic leukemia, underscoring a prominent role for TLR3 and TLR9 in surveillance of ERV-induced tumors. Experimental ERV infection induced a TLR3-, TLR7-, and TLR9-dependent group of “acute-phase” genes previously described in HIV and SIV infections. Our study suggests that in addition to their role in innate immunity against exogenous pathogens, nucleic acid-recognizing TLRs contribute to the immune control of activated ERVs and ERV-induced tumors.

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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.
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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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BMC Bioinformatics | Abstract | HTQC: a fast quality control toolkit for Illumina sequencing data

Illumina sequencing platform is widely used in genome research. Sequence reads quality assessment and control are needed for downstream analysis.
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Natural Killer Cell Dependent Within-Host Competition Arises during Multiple MCMV Infection: Consequences for Viral Transmission and Evolution

Natural Killer Cell Dependent Within-Host Competition Arises during Multiple MCMV Infection: Consequences for Viral Transmission and Evolution | Virology and Bioinformatics from Virology.ca | Scoop.it
From molecules to physiology
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Women have stronger immune systems than men -- and it's all down to X-chromosome related microRNA

Women have stronger immune systems than men -- and it's all down to X-chromosome related microRNA | Virology and Bioinformatics from Virology.ca | Scoop.it
As anyone familiar with the phrase "man-flu" will know women consider themselves to be the more robust side of the species when it comes to health and illness. Now new research seems to support the idea.
Ed Rybicki's insight:

No, that's just sexist...except when it's true.  Like HSV2 vaccines not being as effective in men.

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A 10-step guide to party conversation for bioinformaticians | Genome Biology

{no abstract}
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On the lighter side...

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Ed Rybicki's comment, February 5, 2013 2:53 AM
Subscription required...! B-(
"All research articles in Genome Biology are open access. The journal also publishes a range of other articles that are available to subscribers."
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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)
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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.