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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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Deeper than ancestry.com, 'EvoCor' identifies gene relationships | Virginia Tech News | Virginia Tech

Deeper than ancestry.com, 'EvoCor' identifies gene relationships | Virginia Tech News | Virginia Tech | Virology and Bioinformatics from Virology.ca | Scoop.it
A team led by Gregorio Valdez of the Virginia Tech Carilion Research Institute has designed a search engine that identifies genes that are functionally linked.
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Virus Detected in Human Cell Line | The Scientist Magazine®

Virus Detected in Human Cell Line | The Scientist Magazine® | Virology and Bioinformatics from Virology.ca | Scoop.it
A line of human fetal glial cells is infected with a human polyomavirus, researchers report.
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Mystery over origins of pig virus contributes to spread and anxiety

Mystery over origins of pig virus contributes to spread and anxiety | Virology and Bioinformatics from Virology.ca | Scoop.it
Swine veterinarian Bill Minton thought the baby pigs dying at a farm in western Ohio had a bad case of gastro-enteritis and was stumped when lab results came back with no indication of what had killed them.
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Past issues of Microbiology Today | Society for General Microbiology

Past issues of Microbiology Today | Society for General Microbiology | Virology and Bioinformatics from Virology.ca | Scoop.it
Past issues of the Society for General Microbiology's magazine, Microbiology Today are available online.
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Nigeria: Ebonyi - Re-Occurrence of Lassa Fever, Cause for Concern - CMD

Nigeria: Ebonyi - Re-Occurrence of Lassa Fever, Cause for Concern - CMD | Virology and Bioinformatics from Virology.ca | Scoop.it
The Chief Medical Director (CMD) of Federal Teaching Hospital Abakaliki (FETHA), Ebonyi State, Dr. Paul Ezeonu, has warned that last month's outbreak of Lassa fever in the hospital which affected 22 medical and health workers as well as the re-occurrence of cases of Lassa fever in the state calls for serious concern.
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When microbes kill us, it‘s often by accident – Ed Yong – Aeon

When microbes kill us, it‘s often by accident – Ed Yong – Aeon | Virology and Bioinformatics from Virology.ca | Scoop.it
We assume that microbes evolved to attack humans when actually we are just civilian casualties in a much older war
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"Its virulence – its ability to cause disease – is not an adaptation against its host. It is a side effect, a fluke. It kills through coincidence."

 

Thank you for that!!!!!

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Bioinformatics for Beginners!

Documenting my Experience Learning Bioinformatics from the Almost Begining
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Difference in cytokine production and cell cycle progression induced by Epstein-Barr virus Lmp1 deletion variants in Kmh2, a Hodgkin lymphoma cell line

Epstein-Barr virus (EBV) is associated with 20-40% of Hodgkin’s Lymphoma (HL) cases. EBV-encoded latent membrane protein 1 (LMP1) is a well-known oncogenic protein and two C-terminal deletion variants, del30-LMP1 and del69-LMP1, have been described in animal models to be more tumorigenic than the wild-type form. This work aims to detail the implication of LMP1 in the development of HL and to characterize the particular effects of these variants.
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Anger over 'invisible' rabies toll

Anger over 'invisible' rabies toll | Virology and Bioinformatics from Virology.ca | Scoop.it

"A shortage of funds for vaccinating dogs is costing the lives of tens of thousands of children every year."

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Evolution of Pathogen Specialisation in a Host Metapopulation: Joint Effects of Host and Pathogen Dispersal

Evolution of Pathogen Specialisation in a Host Metapopulation: Joint Effects of Host and Pathogen Dispersal | Virology and Bioinformatics from Virology.ca | Scoop.it

Metapopulation processes are important determinants of epidemiological and evolutionary dynamics in host-pathogen systems, and are therefore central to explaining observed patterns of disease or genetic diversity. In particular, the spatial scale of interactions between pathogens and their hosts is of primary importance because migration rates of one species can affect both spatial and temporal heterogeneity of selection on the other. In this study we developed a stochastic and discrete time simulation model to specifically examine the joint effects of host and pathogen dispersal on the evolution of pathogen specialisation in a spatially explicit metapopulation. We consider a plant-pathogen system in which the host metapopulation is composed of two plant genotypes. The pathogen is dispersed by air-borne spores on the host metapopulation. The pathogen population is characterised by a single life-history trait under selection, the infection efficacy. We found that restricted host dispersal can lead to high amount of pathogen diversity and that the extent of pathogen specialisation varied according to the spatial scale of host-pathogen dispersal. We also discuss the role of population asynchrony in determining pathogen evolutionary outcomes.

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A global compendium of human dengue virus occurrence

A global compendium of human dengue virus occurrence | Virology and Bioinformatics from Virology.ca | Scoop.it
Scientific Data, Published online: 27 May 2014; | doi:10.1038/sdata.2014.4

Via Mel Melendrez-Vallard
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4 Revolutionary Ways to Predict Pandemics

4 Revolutionary Ways to Predict Pandemics | Virology and Bioinformatics from Virology.ca | Scoop.it

Increasingly we are looking towards big data and analytics to help us with everything from how best to utilise your manufacturing capacity, to analysing potential candidates for emerging infectious diseases. But big data has been around for a number of years in the field of pandemic prediction. Here we have 4 of revolutionary methods that have been developed over the last five or so years to predict the emergence and spread of an pandemic, as well as offering advice on how best to deal with them.

 

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Out Today: The First Catalog Of All The Proteins In The Human Body

Out Today: The First Catalog Of All The Proteins In The Human Body | Virology and Bioinformatics from Virology.ca | Scoop.it

Two teams of scientists are publishing today first drafts of the human proteome. The proteome is a catalog of all of the different proteins the human body makes. This is a big accomplishment.

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Unmasking a viral invader

Unmasking a viral invader | Virology and Bioinformatics from Virology.ca | Scoop.it
A study from Harvard Medical School provides the first comprehensive description of how cytomegalovirus, or CMV, hijacks human cells and suggests entirely new ways to combat the infection.
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Potentially fatal parechovirus afflicting babies prompts urgent Queensland probe

A little-known virus that can be fatal in young babies has prompted Queensland scientists to undertake urgent medical research.

Parechovirus was first reported in Australia in December last year and there have now been dozens of cases across the country.

There have been 11 confirmed cases of babies in Queensland with the infection..

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TB in China: a New Epidemic of an Old Disease

TB in China: a New Epidemic of an Old Disease | Virology and Bioinformatics from Virology.ca | Scoop.it

How China handles drug-resistant tuberculosis will have a big effect on the problem globally, by Cesar Chelala


Via Cesar Sanchez, Mel Melendrez-Vallard
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Royal Jubilee Hospital, Victoria, Vancouver Island, to Be the First Canadian Hospital to Install the BD Kiestra™ TLA Fully Automated Microbiology Lab System

MISSISSAUGA, Ontario, May 20, 2014 /PRNewswire/ -- BD (Becton, Dickinson and Company), a leading global medical technology company, today announced an agreement with Island Health to install the BD Kiestra™ Total Lab Automation (TLA) system. This fully-automated microbiology system will be installed at the Island Health's Royal Jubilee Hospital site by the 4th quarter of calendar year 2014 making Island Health the first Regional Health Authority in Canada to implement the system. The BD Kiestra TLA system is designed to streamline the entire microbiology testing process and shorten the time to results, enabling clinicians faster access to diagnostic information.
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Scientists discover how deadly ebola virus 'punches' its way into human cells

Scientists discover how deadly ebola virus 'punches' its way into human cells | Virology and Bioinformatics from Virology.ca | Scoop.it
At first, cells contain the ebola virus in a vesicle awaiting disposal, but the pH level of the vesicle triggers the virus to make a molecular fist and it punches its way out.
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Tackling soil diversity with the assembly of large, complex metagenomes

Tackling soil diversity with the assembly of large, complex metagenomes | Virology and Bioinformatics from Virology.ca | Scoop.it

Abstract

The large volumes of sequencing data required to sample deeply the microbial communities of complex environments pose new challenges to sequence analysis. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires substantial computational resources. We combine two preassembly filtering approaches—digital normalization and partitioning—to generate previously intractable large metagenome assemblies. Using a human-gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes totaling 398 billion bp (equivalent to 88,000 Escherichia coligenomes) from matched Iowa corn and native prairie soils. The resulting assembled contigs could be used to identify molecular interactions and reaction networks of known metabolic pathways using the Kyoto Encyclopedia of Genes and Genomes Orthology database. Nonetheless, more than 60% of predicted proteins in assemblies could not be annotated against known databases. Many of these unknown proteins were abundant in both corn and prairie soils, highlighting the benefits of assembly for the discovery and characterization of novelty in soil biodiversity. Moreover, 80% of the sequencing data could not be assembled because of low coverage, suggesting that considerably more sequencing data are needed to characterize the functional content of soil.

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Targeting Membrane-Bound Viral RNA Synthesis Reveals Potent Inhibition of Diverse Coronaviruses Including the Middle East Respiratory Syndrome Virus

"Coronaviruses raise serious concerns as emerging zoonotic viruses without specific antiviral drugs available. Here we screened a collection of 16671 diverse compounds for anti-human coronavirus 229E activity and identified an inhibitor, designated K22, that specifically targets membrane-bound coronaviral RNA synthesis. K22 exerts most potent antiviral activity after virus entry during an early step of the viral life cycle. Specifically, the formation of double membrane vesicles (DMVs), a hallmark of coronavirus replication, was greatly impaired upon K22 treatment accompanied by near-complete inhibition of viral RNA synthesis. K22-resistant viruses contained substitutions in non-structural protein 6 (nsp6), a membrane-spanning integral component of the viral replication complex implicated in DMV formation, corroborating that K22 targets membrane bound viral RNA synthesis. Besides K22 resistance, the nsp6 mutants induced a reduced number of DMVs, displayed decreased specific infectivity, while RNA synthesis was not affected. Importantly, K22 inhibits a broad range of coronaviruses, including Middle East respiratory syndrome coronavirus (MERS–CoV), and efficient inhibition was achieved in primary human epithelia cultures representing the entry port of human coronavirus infection. Collectively, this study proposes an evolutionary conserved step in the life cycle of positive-stranded RNA viruses, the recruitment of cellular membranes for viral replication, as vulnerable and, most importantly, druggable target for antiviral intervention. We expect this mode of action to serve as a paradigm for the development of potent antiviral drugs to combat many animal and human virus infections."

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The interferon-inducible antiviral protein daxx is not essential for interferon-mediated protection against avian sarcoma virus

The antiviral protein Daxx acts as a restriction factor of avian sarcoma virus (ASV; Retroviridae) in mammalian cells by promoting epigenetic silencing of integrated proviral DNA. Although Daxx is encoded by a type I (alpha/beta) interferon-stimulated gene, the requirement for Daxx in the interferon anti-retroviral response has not been elucidated. In this report, we describe the results of experiments designed to investigate the role of Daxx in the type I interferon-induced anti-ASV response.
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Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology

Giant DNA viruses are visible under a light microscope and their genomes encode more proteins than some bacteria or intracellular parasitic eukaryotes. There are two very distinct types and infect unicellular protists such as Acanthamoeba. On one hand, Megaviridae possess large pseudoicosahedral capsids enclosing a megabase-sized adenine–thymine-rich genome, and on the other, the recently discovered Pandoraviruses exhibit micron-sized amphora-shaped particles and guanine–cytosine-rich genomes of up to 2.8 Mb. While initiating a survey of the Siberian permafrost, we isolated a third type of giant virus combining the Pandoravirus morphology with a gene content more similar to that of icosahedral DNA viruses. This suggests that pandoravirus-like particles may correspond to an unexplored diversity of unconventional DNA virus families.

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Inferring Host Gene Subnetworks Involved in Viral Replication

Inferring Host Gene Subnetworks Involved in Viral Replication | Virology and Bioinformatics from Virology.ca | Scoop.it

Systematic, genome-wide loss-of-function experiments can be used to identify host factors that directly or indirectly facilitate or inhibit the replication of a virus in a host cell. We present an approach that combines an integer linear program and a diffusion kernel method to infer the pathways through which those host factors modulate viral replication. The inputs to the method are a set of viral phenotypes observed in single-host-gene mutants and a background network consisting of a variety of host intracellular interactions. The output is an ensemble of subnetworks that provides a consistent explanation for the measured phenotypes, predicts which unassayed host factors modulate the virus, and predicts which host factors are the most direct interfaces with the virus. We infer host-virus interaction subnetworks using data from experiments screening the yeast genome for genes modulating the replication of two RNA viruses. Because a gold-standard network is unavailable, we assess the predicted subnetworks using both computational and qualitative analyses. We conduct a cross-validation experiment in which we predict whether held-aside test genes have an effect on viral replication. Our approach is able to make high-confidence predictions more accurately than several baselines, and about as well as the best baseline, which does not infer mechanistic pathways. We also examine two kinds of predictions made by our method: which host factors are nearest to a direct interaction with a viral component, and which unassayed host genes are likely to be involved in viral replication. Multiple predictions are supported by recent independent experimental data, or are components or functional partners of confirmed relevant complexes or pathways. Integer program code, background network data, and inferred host-virus subnetworks are available at http://www.biostat.wisc.edu/~craven/chasman_host_virus/.

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Chikungunya virus adaptation to a mosquito vector correlates with only few point mutations in the viral envelope glycoprotein

Like most arthropod-borne viruses (arboviruses), chikungunya virus (CHIKV) is a RNA virus maintained in nature in an alternating cycle of replication between invertebrate and vertebrate hosts. It has been assumed that host alternation restricts arbovirus genome evolution and imposes fitness trade-offs. Despite their slower rates of evolution, arboviruses still have the capacity to produce variants capable to exploit new environments.

To test whether the evolution of the newly emerged epidemic variant of CHIKV (E1-226V) is constrained by host alternation, the virus was alternately-passaged in hamster-derived BHK-21 cells and Aedes aegypti-derived Aag-2 cells. It was also serially-passaged in BHK-21 or Aag-2 cells to promote adaptation to one cell type and presumably, fitness cost in the bypassed cell type. After 30 passages, obtained CHIKV strains were genetically and phenotypically characterized using in vitro and in vivo systems.

Serially- and alternately-passaged strains can be distinguished by amino-acid substitutions in the E2 glycoprotein, responsible for receptor binding. Two substitutions at positions E2-64 and E2-208 only lower the dissemination of the variant E1-226V in Ae. aegypti. These amino-acid changes in the E2 glycoprotein might affect viral infectivity by altering the interaction between CHIKV E1-226V and the cellular receptor on the midgut epithelial cells in Ae. aegypti but not in Aedesalbopictus.

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New coronavirus inhibitor exhibits antiviral activity by blocking viral hijacking of host

New coronavirus inhibitor exhibits antiviral activity by blocking viral hijacking of host | Virology and Bioinformatics from Virology.ca | Scoop.it
Since the SARS epidemic in 2003, coronaviruses have been on the watch list for emerging pathogens, and the ongoing outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) confirmed that they represent a serious threat. No specific drugs exist against coronaviruses so far, but an article ...
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