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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Solution to Vaccine Mystery Starts to Crystallize

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More than 80 years ago, manufacturers started spiking vaccines with alum, an additive, termed an adjuvant, that spurs a stronger reaction from the immune system. Yet scientists have struggled to explain exactly how alum, a catch-all term for several types of aluminum-containing adjuvants, does this. Recently, researchers have floated at least three possible mechanisms, including one that involves DNA spilled from dying cells. The reason alum works so well, several studies suggest, is that it trips an alarm that alerts the immune system when cells are in trouble. Insights into how alum works might allow researchers to design replacements that retain alum's advantages but lose some of its shortcomings.

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MERS Virus Not Yet a Global Emergency, WHO Panel Says - ScienceInsider

MERS Virus Not Yet a Global Emergency, WHO Panel Says - ScienceInsider | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

A special panel established by the World Health Organization (WHO) decided today that the novel coronavirus that has been infecting people in the Middle East is "very concerning," but does not yet constitute a "public health emergency of international concern." The new pathogen, known as Middle East respiratory syndrome (MERS) virus, has sickened 82 people and killed 45 of them so far.

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Dual virus-receptor duel

Dual virus-receptor duel | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A study of two viruses that bind to the same cell surface receptor protein reveals how a cellular protein can change to prevent infection without affecting its role in the cell.
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PLOS Pathogens: Mutated and Bacteriophage T4 Nanoparticle Arrayed F1-V Immunogens from Yersinia pestis as Next Generation Plague Vaccines

PLOS Pathogens: Mutated and Bacteriophage T4 Nanoparticle Arrayed F1-V Immunogens from Yersinia pestis as Next Generation Plague Vaccines | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Abstract

Pneumonic plague is a highly virulent infectious disease with 100% mortality rate, and its causative organism Yersinia pestis poses a serious threat for deliberate use as a bioterror agent. Currently, there is no FDA approved vaccine against plague. The polymeric bacterial capsular protein F1, a key component of the currently tested bivalent subunit vaccine consisting, in addition, of low calcium response V antigen, has high propensity to aggregate, thus affecting its purification and vaccine efficacy. We used two basic approaches, structure-based immunogen design and phage T4 nanoparticle delivery, to construct new plague vaccines that provided complete protection against pneumonic plague...

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Genetic test fingers viral, bacterial infections

Genetic test fingers viral, bacterial infections | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

By differentiating between bacterial and viral fevers, a new test may help doctors decide whether to prescribe antibiotics.

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An Ocean of Viruses | The Scientist Magazine®

An Ocean of Viruses | The Scientist Magazine® | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Viruses abound in the world’s oceans, yet researchers are only beginning to understand how they affect life and chemistry from the water’s surface to the sea floor.
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Pseudomonas DING proteins as human transcriptional regulators and HIV-1 antagonists

Pseudomonas DING proteins as human transcriptional regulators and HIV-1 antagonists | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
.Background: Anti-HIV-1 therapy depends upon multiple agents that target different phases of the viral replication cycle.
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Solving DNA puzzles is overwhelming computer systems, researchers warn

Solving DNA puzzles is overwhelming computer systems, researchers warn | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Solving DNA puzzles is overwhelming computer systems, researchers warn
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Bioinformatics for Beginners – File Formats Part 3. – Alignments ...

Bioinformatics for Beginners – File Formats Part 3. – Alignments ... | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The generally used file formats for sequence based alignments are the SAM and BAM formats. These files can contain information about mapped and unmapped reads, the contigs of the reference sequence that was used ...
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Gene therapy treats children with rare diseases

Gene therapy treats children with rare diseases | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

A virus derived from HIV can safely fix broken immune systems and correct genetic diseases, suggest two new studies involving children with rare conditions.

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Jonathan Kay: Canadian doctors explain why so many of us die badly

Jonathan Kay: Canadian doctors explain why so many of us die badly | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Often, it's not doctors who are pushing dying patients into aggressive, futile end-of-life medical treatments, but guilt-ridden relatives who can't bear the idea of 'pulling the plug'
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Characterization of H7N9 influenza A viruses isolated from humans

Characterization of H7N9 influenza A viruses isolated from humans | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Avian influenza A viruses rarely infect humans; however, when human infection and subsequent human-to-human transmission occurs, worldwide outbreaks (pandemics) can result. The recent sporadic infections of humans in China with a previously unrecognized avian influenza A virus of the H7N9 subtype (A(H7N9)) have caused concern owing to the appreciable case fatality rate associated with these infections (more than 25%), potential instances of human-to-human transmission1, and the lack of pre-existing immunity among humans to viruses of this subtype. Here we characterize two early human A(H7N9) isolates, A/Anhui/1/2013 (H7N9) and A/Shanghai/1/2013 (H7N9); hereafter referred to as Anhui/1 and Shanghai/1, respectively. In mice, Anhui/1 and Shanghai/1 were more pathogenic than a control avian H7N9 virus (A/duck/Gunma/466/2011 (H7N9); Dk/GM466) and a representative pandemic 2009 H1N1 virus (A/California/4/2009 (H1N1pdm09); CA04). Anhui/1, Shanghai/1 and Dk/GM466 replicated well in the nasal turbinates of ferrets. In nonhuman primates, Anhui/1 and Dk/GM466 replicated efficiently in the upper and lower respiratory tracts, whereas the replicative ability of conventional human influenza viruses is typically restricted to the upper respiratory tract of infected primates. By contrast, Anhui/1 did not replicate well in miniature pigs after intranasal inoculation. Critically, Anhui/1 transmitted through respiratory droplets in one of three pairs of ferrets. Glycan arrays showed that Anhui/1, Shanghai/1 and A/Hangzhou/1/2013 (H7N9) (a third human A(H7N9) virus tested in this assay) bind to human virus-type receptors, a property that may be critical for virus transmissibility in ferrets. Anhui/1 was found to be less sensitive in mice to neuraminidase inhibitors than a pandemic H1N1 2009 virus, although both viruses were equally susceptible to an experimental antiviral polymerase inhibitor. The robust replicative ability in mice, ferrets and nonhuman primates and the limited transmissibility in ferrets of Anhui/1 suggest that A(H7N9) viruses have pandemic potential.

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Largest cancer database launched

Largest cancer database launched | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The world's largest database of cancer patients is being set up in England in an attempt to revolutionise care, Public Health England has announced.

Via Sandrine Palcy
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Sandrine Palcy's curator insight, June 14, 2013 8:08 AM

UK at forefront of personalised medicine.

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Giant Pandoravirus is 1,000 times larger than influenca virus and contains 2556 genes

Giant Pandoravirus is 1,000 times larger than influenca virus and contains 2556 genes | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Giant viruses turn out to be everywhere. It was the very giant-ness of giant viruses that allowed them to be overlooked for so long. Scientists first discovered viruses in the late 1800s when they were puzzled by a disease that beset tobacco plants. They mashed up wilted tobacco leaves with water and passed the mixture through fine porcelain filters that trapped bacteria and fungi. The clear liquid could still make healthy tobacco leaves sick. The Dutch botanist Martinus Beijerinck dubbed it “a contagious living fluid.”

 

In the 1930s, the invention of powerful microscopes finally allowed scientists to see viruses. They found that viruses were unlike ordinary cells: they didn’t generate their own fuel; they didn’t grow or divide. Instead, viruses invaded cells, hijacking their biochemistry to make new copies of themselves. Being small and simple seemed like part of the viral way of life, allowing them to replicate fast.

 

It wasn’t until 2003 that a team of French researchers discovered the first giant virus. They had been puzzling over sphere-shaped objects that were the size of bacteria but contained no bacterial DNA. Eventually they realized that they were looking at a monstrously oversized virus, containing 979 genes, much less than the newly discovered Pandoravirus.

 

Those first giant viruses were isolated from amoebae living in water from a cooling tower. Once scientists realized that viruses could be so large, they changed their search parameters and started finding other species in all manner of places, from swamps to rivers to contact lens fluid.

 

And along the way the biggest viruses got bigger. In 2011, Dr. Claverie and his colleagues set a new record with megaviruses, a type of giant virus with 1,120 genes they discovered in sea water off the coast of Chile. They then dug into the sediment below that sea water and discovered pandoravirsues, with more than twice as many genes.

 

Dr. Claverie speculates that pandoraviruses and other giant viruses evolved from free-living microbes that branched off from other life several billion years ago. “The type of cells they may have evolved from may have disappeared,” he said.

 

The idea that giant viruses represent separate branches on the tree of life is a controversial one that many other experts aren’t ready to embrace. “They provide no evidence for that notion, so it seems a distraction to me,” said T. Martin Embley, a professor of evolutionary molecular biology at Newcastle University.

 

Despite those reservations, Dr. Embley and other researchers hail pandoraviruses as an important discovery. “I think it’s wonderful that such crazy and divergent lifeforms continue to be discovered,” said Tom Williams, Dr. Embley’s colleague at Newcastle University.

 

The new study also drives home the fact that giant viruses are far from rare. Shortly after discovering pandoraviruses in sea floor sediment, Dr. Claverie and his colleagues found them in water from a lake in Australia, 10,000 miles away. “It definitely indicates that they must not be rare at all,” said Dr. Claverie.

 

Giant viruses may be so common, in fact, that they may be hiding inside of us, too. In a paper published online on July 2 in The Journal of Infectious Diseases, French researchers offered evidence that giant viruses dwell in healthy people. They isolated a new giant virus from blood donated by a healthy volunteer, and then found antibodies and other signs of the virus in four other donors.

 

Giant viruses may lurk harmlessly in our bodies, invading the amoebae we harbor. Whether they can make us sick is an open question. “I don’t believe we have the proof at the moment that these viruses could infect humans,” said Dr. Claverie.


Via Dr. Stefan Gruenwald
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Tomas Moravec's comment, July 23, 2013 4:14 AM
It is surprising how these large gyus avoided discovery for such a long time.
Ed Rybicki's comment, July 23, 2013 4:17 AM
Well, if they look like bacteria, and we are still finding new exemplars of those...
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Influenza: Pathways to human adaptation

Influenza: Pathways to human adaptation | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

An outbreak of avian H7N9 influenza in humans was reported in early 2013. Structural and infection studies are helping to reveal how these viruses can adapt to infect, and potentially transmit in, new species.

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Empty decoys divert antibodies from neutralizing gene therapy in cell, animal studies

Gene therapy researchers have produced a bioengineered decoy that fools the immune system and prevents it from mistakenly defeating the benefits delivered by a corrective gene.
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The wheat powdery mildew genome shows the unique evolution of an obligate biotroph

The wheat powdery mildew genome shows the unique evolution of an obligate biotroph | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Thomas Wicker and colleagues report the whole-genome sequencing of four wheat powdery mildew (Blumeria graminis forma specialis tritici) isolates from different geographic regions.
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PLOS Neglected Tropical Diseases: Sequential Waves of Gene Expression in Patients with Clinically Defined Dengue Illnesses Reveal Subtle Disease Phases and Predict Disease Severity

PLOS Neglected Tropical Diseases: Sequential Waves of Gene Expression in Patients with Clinically Defined Dengue Illnesses Reveal Subtle Disease Phases and Predict Disease Severity | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Background

Dengue virus (DENV) infection can range in severity from mild dengue fever (DF) to severe dengue hemorrhagic fever (DHF) or dengue shock syndrome (DSS). Changes in host gene expression, temporally through the progression of DENV infection, especially during the early days, remains poorly characterized. Early diagnostic markers for DHF are also lacking.

Methodology/Principal Findings

In this study, we investigated host gene expression in a cohort of DENV-infected subjects clinically diagnosed as DF (n = 51) and DHF (n = 13) from Maracay, Venezuela. Blood specimens were collected daily from these subjects from enrollment to early defervescence and at one convalescent time-point. Using convalescent expression levels as baseline, two distinct groups of genes were identified: the “early” group, which included genes associated with innate immunity, type I interferon, cytokine-mediated signaling, chemotaxis, and complement activity peaked at day 0–1 and declined on day 3–4; the second “late” group, comprised of genes associated with cell cycle, emerged from day 4 and peaked at day 5–6. The up-regulation of innate immune response genes coincided with the down-regulation of genes associated with viral replication during day 0–3. Furthermore, DHF patients had lower expression of genes associated with antigen processing and presentation, MHC class II receptor, NK and T cell activities, compared to that of DF patients. These results suggested that the innate and adaptive immunity during the early days of the disease are vital in suppressing DENV replication and in affecting outcome of disease severity. Gene signatures of DHF were identified as early as day 1.

Conclusions/Significance

Our study reveals a broad and dynamic picture of host responses in DENV infected subjects. Host response to DENV infection can now be understood as two distinct phases with unique transcriptional markers. The DHF signatures identified during day 1–3 may have applications in developing early molecular diagnostics for DHF.

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Resistance to Neuraminidase Inhibitors Conferred by an R292K Mutation in a Human Influenza Virus H7N9 Isolate Can Be Masked by a Mixed R/K Viral Population

We characterized the A/Shanghai/1/2013 virus isolated from the first confirmed human case of A/H7N9 disease in China. The A/Shanghai/1/2013 isolate contained a mixed population of R (65%; 15/23 clones) and K (35%; 8/23 clones) at neuraminidase (NA) residue 292, as determined by clonal sequencing. A/Shanghai/1/2013 with mixed R/K at residue 292 exhibited a phenotype that is sensitive to zanamivir and oseltamivir carboxylate by the enzyme-based NA inhibition assay. The plaque-purified A/Shanghai/1/2013 with dominant K292 (94%; 15/16 clones) showed sensitivity to zanamivir that had decreased by >30-fold and to oseltamivir carboxylate that had decreased by >100-fold compared to its plaque-purified wild-type counterpart possessing dominant R292 (93%, 14/15 clones). In Madin-Darby canine kidney (MDCK) cells, the plaque-purified A/Shanghai/1/2013-NAK292 virus exhibited no reduction in viral titer under conditions of increasing concentrations of oseltamivir carboxylate (range, 0 to 1,000 µM) whereas the replication of the plaque-purified A/Shanghai/1/2013-NAR292 and the A/Shanghai/2/2013 viruses was completely inhibited at 250 µM and 31.25 µM of oseltamivir carboxylate, respectively. Although the plaque-purified A/Shanghai/1/2013-NAK292 virus exhibited lower NA enzyme activity and a higher Km for 2′-(4-methylumbelliferryl)-α-D-N-acetylneuraminic acid than the wild-type A/Shanghai/1/2013-NAR292 virus, the A/Shanghai/1/2013-NAK292 virus formed large plaques and replicated efficiently in vitro. Our results confirmed that the NA R292K mutation confers resistance to oseltamivir, peramivir, and zanamivir in the novel human H7N9 viruses. Importantly, detection of the resistance phenotype may be masked in the clinical samples containing a mixed population of R/K at NA residue 292 in the enzyme-based NA inhibition assay.

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Viruses Don’t Care About Your View: Why ABC Shouldn’t Have Hired Jenny McCarthy | TIME.com

Viruses Don’t Care About Your View: Why ABC Shouldn’t Have Hired Jenny McCarthy | TIME.com | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Giving a job on The View to a anti-vaccine celebrity sends a dangerous message about public health and science in general
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How Many Microbes Are Hiding Among Us?

How Many Microbes Are Hiding Among Us? | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Microbes are everywhere—even inside us. But because so many of these bugs won't grow in the lab, scientists have had a tough time figuring out just who they are and how they live. That may soon change. By sequencing the DNA in individual cells, researchers have gotten to know 200 new microbes—and they may be able to characterize many more.

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UberCloud Experiment now open to bioinformatics and ...

Now the UberCloud Experiment is open also to organizations focusing on bioinformatics and computational biology. The UberCloud Experiment started in mid-2012 with the aim of exploring the end-to-end process employed ...
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10 truths a supervisor will never tell you

10 truths a supervisor will never tell you | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
There are some important dos and don’ts to bear in mind when choosing someone to oversee your doctoral thesis, advises Tara Brabazon
Chris Upton + helpers's insight:

Title is a bit misleading, but it's useful advice.

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Mel Melendrez-Vallard's curator insight, July 12, 2013 7:20 AM

Per Chris Upton--title a bit misleading but actually has some nice insight that I never considered when looking at PhD programs.

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Bacteriology: Toxins in tandem

Bacteriology: Toxins in tandem | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

During the complex process of infection, nothing is more fascinating than the interplay between host immunity and pathogen virulence — particularly in asymptomatic carriers, who seem to be in perfect health while normally life-threatening organisms replicate within them. The most infamous such carrier was 'Typhoid Mary', a cook in the United States who infected more than 50 people with typhoid fever by passing on the causative bacterium Salmonella Typhi (Fig. 1). Another perplexing feature of these bacteria is the existence of the closely related Salmonella Typhimurium, which does not cause life-threatening infections despite having apparently similar virulence properties to S. Typhi. A paper by Song et al.1, published on Nature's website today, places several key pieces in this puzzle.

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ABC's The View: Just Say No to adding Jenny McCarthy to The View. Petition that supports vaccination.

ABC's The View: Just Say No to adding Jenny McCarthy to The View

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