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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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Computational analysis of four human adenovirus type 4 genomes reveals molecular evolution through two interspecies recombination events

Computational analysis of four human adenovirus type 4 genomes reveals molecular evolution through two interspecies recombination events | Virology and Bioinformatics from Virology.ca | Scoop.it

Computational analysis of human adenovirus type 4 (HAdV-E4), a pathogen that is the only HAdV member of species E, provides insights into its zoonotic origin and molecular adaptation. Its genome encodes a domain of the major capsid protein, hexon, from HAdV-B16 recombined into the genome chassis of a simian adenovirus.

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Viral Bioinformatics Resource Center | Viral Bioinformatics Resource Center

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Using Social Media for Scientists Who Swear They Never Would

Using Social Media for Scientists Who Swear They Never Would | Virology and Bioinformatics from Virology.ca | Scoop.it
Dear lab rat,If you found this article on Facebook (or Twitter or Reddit or Google Plus or whatever social media site you prowl), you can stop reading...
Kenzibit's insight:

Worth reading :)

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Ed Rybicki's comment, August 6, 2013 7:20 AM
...sparked a whole lecture (http://www.slideshare.net/edrybicki/why-to-use-social-media) and a series of tweets - thanks, Ken! I wondered how I got to the paper, and it must have been via this post.
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miRandola: The Extracellular / Circulating microRNA Database

miRandola: The Extracellular / Circulating microRNA Database | Virology and Bioinformatics from Virology.ca | Scoop.it

MicroRNAs (miRNAs) are small (approximately 22 nt) noncoding RNAs that play an important role in the regulation of various biological processes through their interaction with cellular messenger RNAs. They are frequently dysregulated in cancer and have shown promise as tissue-based markers for cancer classification and prognostication. Extracellular miRNAs in serum, plasma, saliva, urine and other body fluids have recently been shown to be associated with various pathological conditions including cancer. miRNAs circulate in the bloodstream in a highly stable, extracellular form, thus they may be used as blood-based biomarkers for cancer and other diseases.

 

Circulating miRNAs are protected by encapsulation in membrane-bound vesicles such as exosomes, but the majority of circulating miRNAs in human plasma and serum cofractionate with Argonaute2 (Ago2) protein, rather than with vesicles. In the present work, we performed a comprehensive classification of different extracellular circulating miRNA types. A direct link to the knowledge base miRò together with the inclusion of datamining facilities allow users to infer possible biological functions of the circulating miRNAs and their connection with the phenotype. To our knowledge miRandola is the first database that provides information about all kind of extracellular miRNAs and we believe that it will constitute a very important resource for researchers.


Via Dr. Stefan Gruenwald
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Predicting Network Activity from High Throughput Metabolomics

Predicting Network Activity from High Throughput Metabolomics | Virology and Bioinformatics from Virology.ca | Scoop.it
PLOS Computational Biology is an open-access

Via Biswapriya Biswavas Misra
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Biswapriya Biswavas Misra's curator insight, July 26, 2013 11:25 PM
Abstract

The functional interpretation of high throughput metabolomics by mass spectrometry is hindered by the identification of metabolites, a tedious and challenging task. We present a set of computational algorithms which, by leveraging the collective power of metabolic pathways and networks, predict functional activity directly from spectral feature tables without a priori identification of metabolites. The algorithms were experimentally validated on the activation of innate immune cells.

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Cross-reactive human B cell and T cell epitopes between influenza A and B viruses

Influenza A and B viruses form different genera, which were originally distinguished by antigenic differences in their nucleoproteins and matrix 1 proteins.
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svapls: an R package to correct for hidden factors of variability in gene expression studies

Hidden variability is a fundamentally important issue in the context of gene expression studies. Collected tissue samples may have a wide variety of hidden effects that may alter their transcriptional landscape significantly.
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PLOS ONE: Selective Light-Triggered Release of DNA from Gold Nanorods Switches Blood Clotting On and Off

PLOS ONE: Selective Light-Triggered Release of DNA from Gold Nanorods Switches Blood Clotting On and Off | Virology and Bioinformatics from Virology.ca | Scoop.it

Blood clotting is a precise cascade engineered to form a clot with temporal and spatial control. Current control of blood clotting is achieved predominantly by anticoagulants and thus inherently one-sided. Here we use a pair of nanorods (NRs) to provide a two-way switch for the blood clotting cascade by utilizing their ability to selectively release species on their surface under two different laser excitations. We selectively trigger release of a thrombin binding aptamer from one nanorod, inhibiting blood clotting and resulting in increased clotting time. We then release the complementary DNA as an antidote from the other NR, reversing the effect of the aptamer and restoring blood clotting. Thus, the nanorod pair acts as an on/off switch. One challenge for nanobiotechnology is the bio-nano interface, where coronas of weakly adsorbed proteins can obscure biomolecular function. We exploit these adsorbed proteins to increase aptamer and antidote loading on the nanorods.

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Microbial Informatics and Experimentation: Beginner's guide to comparative bacterial genome analysis using next-generation sequence data

High throughput sequencing is now fast and cheap enough to be considered part of the toolbox for investigating bacteria, and there are thousands of bacterial genome sequences available for comparison in the public domain.
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Rice gall dwarf virus exploits tubules to facilitate viral spread among cultured insect vector cells

Rice gall dwarf virus exploits tubules to facilitate viral spread among cultured insect vector cells | Virology and Bioinformatics from Virology.ca | Scoop.it

Rice gall dwarf virus exploits tubules to facilitate viral spread among cultured insect vector cells derived from leafhopper Recilia dorsalis 

 

REOVIRUS GRAPHIC COURTESY OF RUSSELL KIGHTLEY MEDIA

Ed Rybicki's insight:

I always wondered what those tubules were for...because they've been seen in plant cells for a LONG time by EM sectioning; geminiviruses also make them - and they are also (non-propagatively) transmitted by insects.  COuld be a more common way of getting around than we knew.

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Cytomegalovirus load in whole blood is more reliable for predicting and assessing CMV disease than pp65 antigenaemia

Cytomegalovirus load in whole blood is more reliable for predicting and assessing CMV disease than pp65 antigenaemia | Virology and Bioinformatics from Virology.ca | Scoop.it

CMV is a common cause of disease in immunocompromised patients. Because sampling of the diseased organ can be invasive, markers of systemic CMV reactivation such as pp65 and CMV viral load are commonly used to monitor patients at risk of CMV disease. In this retrospective analysis, the performance of these markers was compared in solid organ transplant recipients, patients with haematological malignancies and HIV infection. Both assays were sensitive markers of reactivation, however, the predictive value for disease of a positive result for both was low. Compared to viral load, the pp65 assay was a less sensitive marker of CMV reactivation. It was only positive when the viral load was greater than 3 log (10) copies/ml whole blood and was negative in 10 instances when the viral load was between 3 and 5 logs. In concordantly positive samples, the number of pp65 positive cells varied widely relative to the viral load and the number of positive cells counted could not be used to predict disease likelihood with any certainty. To conclude, CMV viral load provides a more consistent guide to determine likelihood of disease than pp65 count and is a more sensitive marker of CMV reactivation.

 Herpesvirus graphic by Russell Kightley Media

Ed Rybicki's insight:

It gives me great peasure to tout this paper by my Medical School colleagues - for a nice piece of work which should improve C[yto]MV detection.  Because CMV is cucmber mosaic virus, obviously, and no-one cares about that.  Except cucmbers.

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Herpes Virus Genome, The Pressure Is On

Abstract

 

Herpes simplex virus type 1 (HSV-1) packages its micrometers-long double-stranded DNA genome into a nanometer-scale protein shell, termed the capsid. Upon confinement within the capsid, neighboring DNA strands experience repulsive electrostatic and hydration forces as well as bending stress associated with the tight curvature required of packaged DNA. By osmotically suppressing DNA release from HSV-1 capsids, we provide the first experimental evidence of a high internal pressure of tens of atmospheres within a eukaryotic human virus, resulting from the confined genome. Furthermore, the ejection is progressively suppressed by increasing external osmotic pressures, which reveals that internal pressure is capable of powering ejection of the entire genome from the viral capsid. Despite billions of years of evolution separating eukaryotic viruses and bacteriophages, pressure-driven DNA ejection has been conserved. This suggests it is a key mechanism for viral infection and thus presents a new target for antiviral therapies.

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Oyster deaths linked to hot weather

Oyster deaths linked to hot weather | Virology and Bioinformatics from Virology.ca | Scoop.it
A number of oysters have been killed following the outbreak of a virus in Carlingford Lough in County Down, linked to recent hot weather.
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Genome editing: Improved technique makes it easier to add or delete genes in living cells

Genome editing: Improved technique makes it easier to add or delete genes in living cells | Virology and Bioinformatics from Virology.ca | Scoop.it

Earlier this year, MIT researchers developed a way to easily and efficiently edit the genomes of living cells. Now, the researchers have discovered key factors that influence the accuracy of the system, an important step toward making it safer for potential use in humans, says Feng Zhang, leader of the research team. 

With this technology, scientists can deliver or disrupt multiple genes at once, raising the possibility of treating human disease by targeting malfunctioning genes. To help with that process, Zhang’s team, led by graduate students Patrick Hsu and David Scott, has now created a computer model that can identify the best genetic sequences to target a given gene.

“Using this, you will be able to identify ways to target almost every gene. Within every gene, there are hundreds of locations that can be edited, and this will help researchers narrow down which ones are better than others,” says Zhang, the W.M. Keck Assistant Professor in Biomedical Engineering at MIT and senior author of a paper describing the new model, appearing in the July 21 online edition of Nature Biotechnology.

The genome-editing system, known as CRISPR, exploits a protein-RNA complex that bacteria use to defend themselves from infection. The complex includes short RNA sequences bound to an enzyme called Cas9, which slices DNA. These RNA sequences are designed to target specific locations in the genome; when they encounter a match, Cas9 cuts the DNA. 



Via Dr. Stefan Gruenwald
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Going Viral—Fluorescent Probes to Image Viruses and Their Host Cell Interactions | Life Technologies

Going Viral—Fluorescent Probes to Image Viruses and Their Host Cell Interactions | Life Technologies | Virology and Bioinformatics from Virology.ca | Scoop.it
The overarching goal of viral research is to understand the interactions between virus and host cell in the context of infection.
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A Subway Map Of The Metabolism [Infographic] | Popular Science

A Subway Map Of The Metabolism [Infographic] | Popular Science | Virology and Bioinformatics from Virology.ca | Scoop.it

Via Isabel Etayo, sonia ramos
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PLOS Pathogens: Genomic Analysis of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Provides Insight into the Origins of an Emergent Plant Disease (2013)

PLOS Pathogens: Genomic Analysis of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Provides Insight into the Origins of an Emergent Plant Disease (2013) | Virology and Bioinformatics from Virology.ca | Scoop.it

The origins of crop diseases are linked to domestication of plants. Most crops were domesticated centuries – even millennia – ago, thus limiting opportunity to understand the concomitant emergence of disease. Kiwifruit (Actinidia spp.) is an exception: domestication began in the 1930s with outbreaks of canker disease caused by P. syringae pv. actinidiae(Psa) first recorded in the 1980s. Based on SNP analyses of two circularized and 34 draft genomes, we show that Psa is comprised of distinct clades exhibiting negligible within-clade diversity, consistent with disease arising by independent samplings from a source population. Three clades correspond to their geographical source of isolation; a fourth, encompassing thePsa-V lineage responsible for the 2008 outbreak, is now globally distributed. Psa has an overall clonal population structure, however, genomes carry a marked signature of within-pathovar recombination. SNP analysis of Psa-V reveals hundreds of polymorphisms; however, most reside within PPHGI-1-like conjugative elements whose evolution is unlinked to the core genome. Removal of SNPs due to recombination yields an uninformative (star-like) phylogeny consistent with diversification of Psa-V from a single clone within the last ten years. Growth assays provide evidence of cultivar specificity, with rapid systemic movement of Psa-V inActinidia chinensis. Genomic comparisons show a dynamic genome with evidence of positive selection on type III effectors and other candidate virulence genes. Each clade has highly varied complements of accessory genes encoding effectors and toxins with evidence of gain and loss via multiple genetic routes. Genes with orthologs in vascular pathogens were found exclusively within Psa-V. Our analyses capture a pathogen in the early stages of emergence from a predicted source population associated with wild Actinidia species. In addition to candidate genes as targets for resistance breeding programs, our findings highlight the importance of the source population as a reservoir of new disease.


Via Kamoun Lab @ TSL
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World Hepatitis Day Virtual Special Issue - Virology - Elsevier

World Hepatitis Day Virtual Special Issue - Virology - Elsevier | Virology and Bioinformatics from Virology.ca | Scoop.it
World Hepatitis Day, 28 July 2013
This is hepatitis. Know it. Confront it

Every year on 28 July, the World Health Organization and partners...
Ed Rybicki's insight:

Can we have a Papillomavirus day, too?

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Cross-reactive human B cell and T cell epitopes between influenza A and B viruses

Influenza A and B viruses form different genera, which were originally distinguished by antigenic differences in their nucleoproteins and matrix 1 proteins.
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Virology Journal | Abstract | West Nile virus methyltransferase domain interacts with protein kinase G

The flaviviral nonstructural protein 5 (NS5) is a phosphoprotein, though the precise identities and roles of many specific phosphorylations remain unknown.
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Biophysicist obtains first experimental evidence of pressure inside the herpes virus

Biophysicist obtains first experimental evidence of pressure inside the herpes virus | Virology and Bioinformatics from Virology.ca | Scoop.it

Herpes viruses are like tiny powder kegs waiting to explode.  For more than 20 years scientists suspected that herpes viruses were packaged so full of genetic material that they built up an internal pressure so strong it could shoot viral DNA into a host cell during infection. No one had been able to prove that theory until now.

Ed Rybicki's insight:

The virus as jack-in-the-box - nice piece of proof!

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H5N1: Adenoviruses: Another cross-species threat

H5N1: Adenoviruses: Another cross-species threat | Virology and Bioinformatics from Virology.ca | Scoop.it
Thanks to Jeffery Norris for sending the link to this report in PLOS ONE: Experimental Cross-Species Infection of Common Marmosets by Titi Monkey Adenovirus.
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Heartland virus: One more reason to avoid ticks

Heartland virus: One more reason to avoid ticks | Virology and Bioinformatics from Virology.ca | Scoop.it
Ticks also transmit Lyme disease, a malaria-like disease, and a virus that seems to trigger meat allergies.
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