Virology and Bioinformatics from Virology.ca
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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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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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Bacteriocins – a viable alternative to antibiotics?

Bacteriocins – a viable alternative to antibiotics? | Virology and Bioinformatics from Virology.ca | Scoop.it
Bacteriocins, antimicrobial peptides produced by certain bacteria, might warrant serious consideration as alternatives to traditional antibiotics.
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Deans write to Obama about CIA vaccine scheme in Pakistan

Deans write to Obama about CIA vaccine scheme in Pakistan | Virology and Bioinformatics from Virology.ca | Scoop.it
Deans of public health schools sent a letter to President Obama, criticizing the use of a vaccination campaign by the CIA to hunt for Osama bin Laden.
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Virus-Encoded microRNAs: An Overview and a Look to the Future

Virus-Encoded microRNAs: An Overview and a Look to the Future | Virology and Bioinformatics from Virology.ca | Scoop.it
From molecules to physiology
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ZMap - Wellcome Trust Sanger Institute

ZMap - Wellcome Trust Sanger Institute | Virology and Bioinformatics from Virology.ca | Scoop.it

ZMap is a genome browser written in C with the aim of providing fast access to high volume data. Data may be requested from a variety of disparate sources in parallel and cached locally allowing new tracks to be loaded or the view of current data adjusted without delay. Multiple views of the data may be presented and tracks configured for different levels of detail. ZMap interfaces seamlessly to the Seqtools package and forms part of the Otterlace genome annotation system used by the HAVANA group at the Wellcome Trust Sanger Institute.

ZMap may also be used as a standalone browser taking data either from external soruces or from simple GFF files held locally.

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On Constructing Suffix Arrays and LCP Arrays in External Memory « Homologus

On Constructing Suffix Arrays and LCP Arrays in External Memory « Homologus | Virology and Bioinformatics from Virology.ca | Scoop.it
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Biochemistry Free and Easy | Department of Biochemistry and Biophysics

Biochemistry Free and Easy | Department of Biochemistry and Biophysics | Virology and Bioinformatics from Virology.ca | Scoop.it

Kevin Ahern and Indira Rajagopal have published an electronic book aimed at helping students learn the basics of biochemistry in a fun and engaging format.  The book incorporates original songs, recordings, verses and links to over 100 video lectures.  

As its name implies, THE BOOK IS FREE.

Chris Upton + helpers's insight:

I looked at the iPad version.  It's very nicely laid out and content is super clear.

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Cartilage in joints secretes antimicrobial factor

Cartilage in joints secretes antimicrobial factor | Virology and Bioinformatics from Virology.ca | Scoop.it
‘’It is clear that we might not ever see global warming, the apocalyptic scenario is that when I need a new hip in 20 years I’ll die from a routine infection because we’ve run out of antibiotics.’’ This statement was given by Dame Sally Davies...
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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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MicroMicrobe • Winter Viruses and How to Beat Them BBC2 aired...

Winter Viruses and How to Beat Them


BBC2 aired another informative program on viruses last night; if you missed it due to a clash with Miranda, you can still catch up on ‘Winter Viruses and How to Beat Them’.
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A large-scale evaluation of computational protein function prediction : Nature Methods : Nature Publishing Group

A large-scale evaluation of computational protein function prediction : Nature Methods : Nature Publishing Group | Virology and Bioinformatics from Virology.ca | Scoop.it
A report on the results of the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment.

Via Loiret David
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J Biomol NMR: Solution structure of the Magnaporthe oryzae avirulence protein AvrPiz-t (2013)

J Biomol NMR: Solution structure of the Magnaporthe oryzae avirulence protein AvrPiz-t (2013) | Virology and Bioinformatics from Virology.ca | Scoop.it

The AvrPiz-t gene encodes a small protein predicted to be secreted that shows no homology to known proteins and is 108 amino acids in length. AvrPiz-t can suppress programmed cell death (PCD) induced by BAX in tobacco, suggesting that it might contribute to the pathogenicity of M. oryzae. These data suggested that AvrPiz-t functions primarily as a virulence effector contributing to the pathogenicity of M. oryzae. To further understand the mechanism of the pathogenicity-associated function of AvrPiz-t, we determined its solution structure.


Via Kamoun Lab @ TSL
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One Of My Favorite Charts On The Power Of Vaccines

One Of My Favorite Charts On The Power Of Vaccines | Virology and Bioinformatics from Virology.ca | Scoop.it
I'm posting this because I found the graphic in a file folder on my computer and didn't want to lose it. It's originally from my profile of Bill Gates from last year's Forbes Power List issue.

Via Ed Rybicki
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Virus Musings

Lessons from Schmallenberg (virus)

Whilst I haven't spoken to one, being a UK sheep farmer at the moment can't be much fun. Schmallenberg virus (SBV) is robbing farmers of lambs as well as being an altogether disturbing and unpleasant experience. How long it remains an issue will only become apparent with time. It's worth looking at whether this outbreak of SBV represents a sign of what's to come.

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Why the Flu Is So Relentless, and How Technology Might Help

Why the Flu Is So Relentless, and How Technology Might Help | Virology and Bioinformatics from Virology.ca | Scoop.it
Researchers are developing quick-brew vaccines and ones that catch multiple strains of flu.
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Translational Bioinformatics: PLOS Computational Biology presents an educational resource for an emerging field | PLOS Biologue

Translational Bioinformatics: PLOS Computational Biology presents an educational resource for an emerging field | PLOS Biologue | Virology and Bioinformatics from Virology.ca | Scoop.it

PLOS Computational Biology is pleased to announce the launch of a new collection of Education articles:  “Translational Bioinformatics”. This collection is presented as an online “book” which could serve as a reference tool for a graduate level introductory course, marking a step in an exciting new direction for the Education section of the journal.

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