Viruses and Bioinformatics from Virology.uvic.ca
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Viruses and Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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The arable ecosystem as battleground for emergence of new human pathogens

The arable ecosystem as battleground for emergence of new human pathogens | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Disease incidences related to Escherichia coli and Salmonella enterica infections by consumption of (fresh) vegetables, sprouts, and occasionally fruits made clear that these pathogens are not only transmitted to humans via the "classical" routes of meat, eggs, and dairy products, but also can be transmitted to humans via plants or products derived from plants. Nowadays, it is of major concern that these human pathogens, especially the ones belonging to the taxonomical family of Enterobacteriaceae, become adapted to environmental habitats without losing their virulence to humans. Adaptation to the plant environment would lead to longer persistence in plants, increasing their chances on transmission to humans via consumption of plant-derived food. One of the mechanisms of adaptation to the plant environment in human pathogens, proposed in this paper, is horizontal transfer of genes from different microbial communities present in the arable ecosystem, like the ones originating from soil, animal digestive track systems (manure), water and plants themselves. Genes that would confer better adaptation to the phytosphere might be genes involved in plant colonization, stress resistance and nutrient acquisition and utilization. Because human pathogenic enterics often were prone to genetic exchanges via phages and conjugative plasmids, it was postulated that these genetic elements may be hold key responsible for horizontal gene transfers between human pathogens and indigenous microbes in agroproduction systems. In analogy to zoonosis, we coin the term phytonosis for a human pathogen that is transmitted via plants and not exclusively via animals.

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Evidence for subclinical H5N1 avian influenza infections among Nigerian poultry workers.

In recent years Nigeria has experienced sporadic incursions of highly pathogenic H5N1 avian influenza among poultry. In 2008, 316 poultry-exposed agricultural workers, and 54 age-group matched non-poultry exposed adults living in the Enugu or Ebonyi States of Nigeria were enrolled and then contacted monthly for 24 months to identify acute influenza-like-illnesses. Annual follow-up sera and questionnaire data were collected at 12 and 24 months. Participants reporting influenza-like illness completed additional questionnaires, and provided nasal and pharyngeal swabs and acute and convalescent sera. Swab and sera specimens were studied for evidence of influenza A virus infection. Sera were examined for elevated antibodies against 12 avian influenza viruses by microneutralization and 3 human viruses by hemagglutination inhibition.

Chris Upton + helpers's insight:

Could be worrisome...

 

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Tamiflu-resistant influenza: parsing the genome for the culprits

Tamiflu-resistant influenza: parsing the genome for the culprits | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Abstract

"Tamiflu is one of the few available treatments for those who come down with the flu. But the virus quickly develops resistance; multiplying at a rate of several generations a day, these tiny pathogens rapidly accumulate genetic mutations. Because of this, they have a good chance of developing counterattacks to the antiviral. How can these infinitesimal variations be identified within the immensity of the virus’ genetic code? EPFL researchers have created a computer tool that can shed light on the flu virus’ formidable adaptability. They were able to find mutations that conferred resistance that had up to this point not yet been identified. Their software has been made freely available to researchers everywhere, and is the subject of an article published in the journal PLOS Genetics. "

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Slime mold microfluidic logical gates

Abstract

"We demonstrate how logical operations can be implemented in ensembles of protoplasmic tubes of acellular slime mold Physarum polycephalum. The tactile response of the protoplasmic tubes is used to actuate analogs of two- and four-input logical gates and memory devices. The slime mold tube logical gates display results of logical operations by blocking flow in mechanically stimulated tube fragments and redirecting the flow to output tube fragments. We demonstrate how XOR and NOR gates are constructed. We also exemplify circuits of hybrid gates and a memory device. The slime mold based gates are non-electronic, simple and inexpensive, and several gates can be realized simultaneously at sites where protoplasmic tubes merge."

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Ebola outbreak unprecedented - MSF

Ebola outbreak unprecedented - MSF | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

The Ebola outbreak that has killed 78 people in Guinea is "unprecedented", a medical charity has said.

An official with Medecins Sans Frontieres (MSF) said the spread of the disease across the country made it very difficult to control.

The West African state is facing a battle to contain the outbreak after cases were reported in areas that are hundreds of kilometres apart.

Ebola is spread by close contact and kills between 25% and 90% of victims.

"We are facing an epidemic of a magnitude never before seen in terms of the distribution of cases," Mariano Lugli, a co-ordinator in Guinea for the aid group said.

"This geographical spread is worrisome because it will greatly complicate the tasks of the organisations working to control the epidemic," Mr Lugli added.

Ed Rybicki's insight:

"Liberia's Health Minister Walter Gwenigale on Monday warned people to stop having sex because the virus was spread via bodily fluids.

This was in addition to existing advice to stop shaking hands and kissing."  So: sexual AND social intercourse are out??

But seriously: in the 1976 Sudan outbreak, one man spread Ebola to quite a few woman, through sex - so it can and does happen.

 
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New Phytologist: Cospeciation vs host-shift speciation: methods for testing, evidence from natural associations and relation to coevolution (2013)

New Phytologist: Cospeciation vs host-shift speciation: methods for testing, evidence from natural associations and relation to coevolution (2013) | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Hosts and their symbionts are involved in intimate physiological and ecological interactions. The impact of these interactions on the evolution of each partner depends on the time-scale considered. Short-term dynamics – ‘coevolution’ in the narrow sense – has been reviewed elsewhere. We focus here on the long-term evolutionary dynamics of cospeciation and speciation following host shifts. Whether hosts and their symbionts speciate in parallel, by cospeciation, or through host shifts, is a key issue in host–symbiont evolution. In this review, we first outline approaches to compare divergence between pairwise associated groups of species, their advantages and pitfalls. We then consider recent insights into the long-term evolution of host–parasite and host–mutualist associations by critically reviewing the literature. We show that convincing cases of cospeciation are rare (7%) and that cophylogenetic methods overestimate the occurrence of such events. Finally, we examine the relationships between short-term coevolutionary dynamics and long-term patterns of diversification in host–symbiont associations. We review theoretical and experimental studies showing that short-term dynamics can foster parasite specialization, but that these events can occur following host shifts and do not necessarily involve cospeciation. Overall, there is now substantial evidence to suggest that coevolutionary dynamics of hosts and parasites do not favor long-term cospeciation.


Via Kamoun Lab @ TSL, Adam Taranto
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Scrambled Egg Virus: mutations explain ineffectiveness of 2012 flu vaccine

Scrambled Egg Virus: mutations explain ineffectiveness of 2012 flu vaccine | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

A report published in PLoS ONE last week has shed light on why the effectiveness of the 2012 flu vaccine proved to be well below expectations.

Despite assurances by the US Centres for Disease Control and Prevention (CDC) in November 2012 that “most (90%) of influenza viruses…are well matched to the 2012-2013 influenza vaccine,” post season analysis found that the 2012 vaccine was just 46% effective in 18-49 year olds against the dominant strain that year (H3N2), 50% in 50-64 year olds, and a mere 9% in those over the age of 65.

So why was the vaccine (and perhaps even subsequent vaccines) so poorly matched to the virus strain?

The authors, led by Danuta M. Skowronski, report that three mutations, resulting from the process through which viruses are prepared for mass production, were to blame for the vaccines lack of effectiveness.

- See more at: http://www.vaccinenation.org/2014/03/28/scrambled-egg-virus-mutations-explain-ineffectiveness-2012-flu-vaccine/#sthash%2EL11GDjAF%2Edpuf

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MRFalign: Protein Homology Detection through Alignment of Markov Random Fields

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
PLOS Computational Biology is an open-access
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Building the Ultimate Yeast Genome

When geneticist Ronald Davis first suggested a decade ago that his colleagues try to create artificial yeast chromosomes and install them in a living cell, Jef Boeke didn't think much of the idea. Davis, who is at the Stanford University School of Medicine in California, was known as a visionary. He proposed that a lab-made yeast would be the next step in the then-emerging field of synthetic biology. But Boeke couldn't see the point of replicating what nature had already made, especially because designing and synthesizing a 12.5-million-base genome seemed onerous, or even impossible. As Boeke listened to Davis's talk at a major yeast genetics meeting in 2004 in Seattle, he says, "I remember thinking 'Why on Earth would you want to do that?' "

How times have changed. Boeke, a geneticist who recently moved to New York University Langone Medical Center in New York City, and his colleagues have just finished the first complete synthetic yeast chromosome and are well on their way to putting together several more, thanks to technological advances in manufacturing DNA and a global army of collaborators, mainly undergraduate students.

Other researchers have synthesized a bacterium's full genome, but the yeast job is orders of magnitude more complex. For starters, Saccharomyces cerevisiae has 16 chromosomes compared with the one in bacteria. Yet if the effort by Boeke and his army succeeds, it should offer broad benefits. "It gives us the ability to fully explore the yeast genome," Davis says. "If you really want to understand an organism, you should be able to design or redesign one."

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A promoter-level mammalian expression atlas : Nature : Nature Publishing Group

A promoter-level mammalian expression atlas : Nature : Nature Publishing Group | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
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First comprehensive atlas of human gene activity released | HSPH News | Harvard School of Public Health

First comprehensive atlas of human gene activity released | HSPH News | Harvard School of Public Health | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Boston, MA — A large international consortium of researchers has produced the first comprehensive, detailed map of the way genes work across the major cells and tissues of the human body. The findings describe the complex networks that govern gene activity, and the new information could play a crucial role in identifying the genes involved with disease.

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Exploiting bacteriophages for human health

Exploiting bacteriophages for human health | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
This short review is worth reading because it takes a thoughtful and holistic approach to the idea of phage therapy.
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Chris Upton + helpers's curator insight, March 27, 2014 11:51 AM

Via Alan Cann's excellent MicrobiologyBytes site

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Health News - Researchers solve paradox of virus construction

Health News - Researchers solve paradox of virus construction | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Abstract "A new study has solved a long-standing puzzle of how common viruses reproduce themselves during an infection, opening up new possibilities for treating a range of diseases from HIV to the common cold. "

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The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes

The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Background. As whole genome sequence data from bacterial isolates becomes cheaper to generate, computational methods are needed to correlate sequence data with biological observations. Here we present the large-scale BLAST score ratio (LS-BSR) pipeline, which rapidly compares the genetic content of hundreds to thousands of bacterial genomes, and returns a matrix that describes the relatedness of all coding sequences (CDSs) in all genomes surveyed. This matrix can be easily parsed in order to identify genetic relationships between bacterial genomes. Although pipelines have been published that group peptides by sequence similarity, no other software performs the rapid, large-scale, full-genome comparative analyses carried out by LS-BSR.Results. To demonstrate the utility of the method, the LS-BSR pipeline was tested on 96 Escherichia coli and Shigella genomes; the pipeline ran in 163 min using 16 processors, which is a greater than 7-fold speedup compared to using a single processor. The BSR values for each CDS, which indicate a relative level of relatedness, were then mapped to each genome on an independent core genome single nucleotide polymorphism (SNP) based phylogeny. Comparisons were then used to identify clade specific CDS markers and validate the LS-BSR pipeline based on molecular markers that delineate between classical E. coli pathogenic variant (pathovar) designations. Scalability tests demonstrated that the LS-BSR pipeline can process 1,000 E. coli genomes in 27–57 h, depending upon the alignment method, using 16 processors.Conclusions. LS-BSR is an open-source, parallel implementation of the BSR algorithm, enabling rapid comparison of the genetic content of large numbers of genomes. The results of the pipeline can be used to identify specific markers between user-defined phylogenetic groups, and to identify the loss and/or acquisition of genetic information between bacterial isolates. Taxa-specific genetic markers can then be translated into clinical diagnostics, or can be used to identify broadly conserved putative therapeutic candidates.
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Bioafrica.net - News: PhD and/or MSc Scholarship available - Computer Science

Bioafrica.net - News: PhD and/or MSc Scholarship available - Computer Science | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The causes and consequences of HIV transmission and drug resistance - Computer Science PhD and MSc studentships available at UKZN/CSIR Meraka Centre for Artificial Intelligence Research (CAIR) for the MRC Flagship research project.
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Nano-paper filter removes viruses - Uppsala University, Sweden

Nano-paper filter removes viruses - Uppsala University, Sweden | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Researchers at the Division of Nanotechnology and Functional Materials, Uppsala University have developed a paper filter, which can remove virus particles with the efficiency matching that of the best industrial virus filters. The paper filter consists of 100 percent high purity cellulose nanofibers, directly derived from nature.
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Biologists: this is why bioinformaticians hate you...

Biologists: this is why bioinformaticians hate you... | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

The Wellcome Trust have released a data set showing article processing charges paid in 2012-2013, and you can download the results here.  I’d like to join with everyone else in congratulating the Wellcome Trust on collecting and releasing these figures, and I think MRC, BBSRC, NERC and other funding bodies should follow.

Having said that, this dataset represents everything that’s bad about science – just not in the way you might think.  Biologists: this is why bioinformaticians hate you:

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Clinical bioinformatics for microbiology

Clinical bioinformatics for microbiology | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A week or two ago I went to an interesting meeting about the clinical bioinformatics training scheme. This is a clinical scientist training programme, akin to those that train clinical geneticists ...
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WHO South-East Asia Region certified polio-free

New Delhi, 27 March: WHO South-East Asia Region, home to a quarter of the world’s population, was certified polio-free today by an independent commission under the WHO certification process. This is the fourth of six WHO Regions to be certified, marking an important step towards global polio eradication. With this step, 80% of the world’s population now lives in certified polio-free regions.

An independent panel of 11 experts in public health, epidemiology, virology, clinical medicine and related specialties constituting the South-East Asia Regional Certification Commission for Polio Eradication (SEA-RCCPE) met for two days to review evidence from countries before reaching the decision that all 11 countries of the Region are now polio-free and have met the requirements for certification.

Before a Region can be certified polio-free, several conditions must be satisfied such as: at least three years of zero confirmed cases due to indigenous wild poliovirus; excellent laboratory-based surveillance for poliovirus; demonstrated capacity to detect, report, and respond to imported cases of poliomyelitis; and assurance of safe containment of polioviruses in laboratories (introduced since 2000).

Ed Rybicki's insight:

This is, seriously, a VERY big deal: the beginning of the end for a virus!!

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The Tripartite Virions of the Brome Mosaic Virus Have Distinct Physical Properties that Affect the Timing of the Infection Process

IMPORTANCE Viruses with genomes packaged in distinct virions could theoretically release the genomes at different times to regulate the timing of gene expression. Using an RNA virus composed of three particles, we demonstrate that the RNA in one of the virions is released more easily than the other two in vitro. The differential RNA release is due to distinct interactions between the viral capsid protein and the RNAs. The ease of RNA release is also correlated with the more rapid accumulation of that RNA in infected plants. Our study identified a novel role for capsid-RNA interactions in the regulation of a viral infection.

Ed Rybicki's insight:

Yet again, new insights from an old virus - using a mix of old (centrifugation) and new (atomic force microscopy) techniques.  And showing that it is also the sequence that is important. Thanks to Frank Rabenstein for alerting me to this!

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Ten Simple Rules for Effective Computational Research

Ten Simple Rules for Effective Computational Research | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
PLOS Computational Biology is an open-access
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The Camel Connection

On 21 March 2012, a 25-year-old student in Jordan started coughing. A few days later, he developed fever and shortness of breath. He was admitted to a hospital, where he ended up in intensive care. By the time he died on 25 April, several nurses and doctors had developed similar symptoms. One of them died, too. Then the mystery disease disappeared again.

 

Two years later, it's clear that the outbreak was the prelude to a protracted struggle against what is now known as the Middle East respiratory syndrome (MERS) virus. And although scientists still have lots of unanswered questions, evidence is mounting that camels play a key role in spreading the new pathogen. The camel-borne threat may extend far beyond the Middle East. Last month, a team led by Malik Peiris, an infectious disease researcher at the University of Hong Kong, showed that almost all camels in four Egyptian abattoirs had MERS antibodies in their blood; most had been imported from Ethiopia and Sudan, suggesting the virus may reside in large parts of Africa.

 

As a result, scientists are shifting their focus from human cases to camels. "It is becoming ever clearer that MERS is a classic zoonosis," says virologist Christian Drosten of the University of Bonn in Germany. "We need to concentrate more on the animals." One idea gaining traction is to vaccinate camels. "Protecting camels right now may be the single most important thing we can do to protect humans," says Michael Osterholm, director of the Center for Infectious Disease Research and Policy at the University of Minnesota, Twin Cities.

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GEN | News Highlights:GSK Joins Partners in Marrying Genomics with Big Data

GEN | News Highlights:GSK Joins Partners in Marrying Genomics with Big Data | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

GlaxoSmithKline (GSK) is joining the European Bioinformatics Institute (EMBL-EBI) and the Wellcome Trust Sanger Institute in launching a research collaboration intended to speed up drug discovery by integrating genomics with big data.

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