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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Threatwatch: Mother virus of China's deadly bird flu - health - 31 January 2014 - New Scientist

Threatwatch: Mother virus of China's deadly bird flu - health - 31 January 2014 - New Scientist | Virology and Bioinformatics from Virology.ca | Scoop.it
Ten years after H5N1, more deadly bird flu has emerged from China, most recently a strain called H10N8. Is it time to target the virus spawning them all?
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A Broadly Implementable Research Course in Phage Discovery and Genomics for First-Year Undergraduate Students

A Broadly Implementable Research Course in Phage Discovery and Genomics for First-Year Undergraduate Students | Virology and Bioinformatics from Virology.ca | Scoop.it
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Robust estimation of microbial diversity in theory and in practice

Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao’s estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics (‘Hill diversities’), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao’s estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity.

 
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Plant pest destruction goes viral

Plant pest destruction goes viral | Virology and Bioinformatics from Virology.ca | Scoop.it
Fusion of a viral coat protein to an insect-specific neurotoxin delivers the molecule into aphids where it is insecticidal.

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Virology Journal | Abstract | Adeno-associated virus type 2 preferentially integrates single genome copies with defined breakpoints

Adeno-associated virus (AAV) serotype 2 prevalently infects humans and is the only described eukaryotic virus that integrates site-preferentially. In a recent high throughput study, the genome wide distribution of AAV-2 integrants was determined using Integrant Capture Sequencing (IC-Seq). Additional insight regarding the integration of AAV-2 into human genomic DNA could be gleaned by low-throughput sequencing of complete viral-chromosomal junctions.

Findings: In this study, 140 clones derived from Integrant-Capture Sequencing were sequenced. 100 met sequence inclusion criteria, and of these 39 contained validated junction sequences. These unique sequences were analyzed to investigate the structure and location of viral-chromosomal junctions.

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Biologists make first mouse model for MERS

Biologists make first mouse model for MERS | Virology and Bioinformatics from Virology.ca | Scoop.it

A remedy for Middle East respiratory syndrome (MERS), the coronavirus outbreak from Saudi Arabia that has killed 77 of the 180 people who have contracted it, has so far eluded researchers. But they have now created the first mouse model of the disease, which could enable faster testing of drugs and vaccines. The method used to make mice susceptible to MERS might also provide a quick way to study future pandemic viruses in mice.Mice with human receptor for coronavirus provide a faster way to test vaccines.

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BMC Bioinformatics | Abstract | Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline

Massively parallel DNA sequencing generates staggering amounts of data. Decreasing cost, increasing throughput, and improved annotation have expanded the diversity of genomics applications in research and clinical practice. This expanding scale creates analytical challenges: accommodating peak compute demand, coordinating secure access for multiple analysts, and sharing validated tools and results.
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siRNA Screen of Early Poxvirus Genes Ident... [Cell Host Microbe. 2014] - PubMed - NCBI

Poxvirus genome uncoating is a two-step process. First, cytoplasmic viral cores are activated and early viral genes are expressed. Next, cores are disassembled and the genomes released. This second step depends on an early viral factor(s) that has eluded identification for over 40 years. We used a large-scale, high-throughput RNAi screen directed against vaccinia virus (VACV) to identify the VACV AAA+ ATPase D5 as the poxvirus uncoating factor. We show that the ATPase activity of D5 is required for uncoating. Superresolution microscopy suggests that D5 acts directly at viral cores for genome release. Thus, the putative helicase D5 is a multifunctional protein required for genome uncoating and replication. Additionally, in vivo delivery of anti-D5 siRNAs reduced virus production in a mouse model of VACV infection. These results demonstrate the use of virus-targeting RNAi libraries to investigate viral gene function and suggest therapeutic avenues.

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Science in Seconds | Know Everything

Science in Seconds | Know Everything | Virology and Bioinformatics from Virology.ca | Scoop.it
With videos, current news and dazzling images, Science in Seconds brings you the most engaging science content available on the web.

 

The Nobel prize in Chemistry in 2008 was awarded to 3 scientists that development green fluorescent protein (GFP) as a technique that makes organisms glow.  This is more than just some fun body paint and a rave or two, the researchers were able to splice together genes from jellyfish and a normal gene that would allow scientists to watch the behaviour of proteins in living cells.

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Great explanation of GFP uses

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PLOS Pathogens: Variation in RNA Virus Mutation Rates across Host Cells

PLOS Pathogens: Variation in RNA Virus Mutation Rates across Host Cells | Virology and Bioinformatics from Virology.ca | Scoop.it
Abstract

"It is well established that RNA viruses exhibit higher rates of spontaneous mutation than DNA viruses and microorganisms. However, their mutation rates vary amply, from 10−6 to 10−4 substitutions per nucleotide per round of copying (s/n/r) and the causes of this variability remain poorly understood. In addition to differences in intrinsic fidelity or error correction capability, viral mutation rates may be dependent on host factors. Here, we assessed the effect of the cellular environment on the rate of spontaneous mutation of the vesicular stomatitis virus (VSV), which has a broad host range and cell tropism. Luria-Delbrück fluctuation tests and sequencing showed that VSV mutated similarly in baby hamster kidney, murine embryonic fibroblasts, colon cancer, and neuroblastoma cells (approx. 10−5 s/n/r). Cell immortalization through p53 inactivation and oxygen levels (1–21%) did not have a significant impact on viral replication fidelity. This shows that previously published mutation rates can be considered reliable despite being based on a narrow and artificial set of laboratory conditions. Interestingly, we also found that VSV mutated approximately four times more slowly in various insect cells compared with mammalian cells. This may contribute to explaining the relatively slow evolution of VSV and other arthropod-borne viruses in nature."

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Avian influenza H7N9 outbreak now at 246 cases in China, HK culls 20,000 birds

Avian influenza H7N9 outbreak now at 246 cases in China, HK culls 20,000 birds | Virology and Bioinformatics from Virology.ca | Scoop.it
Chinese health authorities reported on six additional confirmed human avian influenza A(H7N9) cases in various China provinces yesterday, according to a Hong Ko
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Nuclear IFI16 induction of IRF-3 si... [Proc Natl Acad Sci U S A. 2012] - PubMed - NCBI

PubMed comprises more than 23 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
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White Plague is the New Black Plague | Viruses101 | Learn Science at Scitable

White Plague is the New Black Plague | Viruses101 | Learn Science at Scitable | Virology and Bioinformatics from Virology.ca | Scoop.it
A new plague, known as the white plague, has killed 70 -80% of the coral in the Caribbean and is on the loose. Single stranded DNA viruses may be the cause of the destruction.
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Plant-produced virus-like particle vaccines

Virus-like particles (VLPs) are possibly the best candidates for safe, immunogenic, efficacious and inexpensive vaccines, for both animals and humans. Well-characterized human and animal viruses such as hepatitis B and C, HIV and papillomaviruses, rotaviruses, norovirus, foot-and-mouth disease viruses and even influenza A virus proteins have all been successfully investigated for VLP formation. Proteins have been produced in transgenic plants and via transient expression techniques; simple structures and structures depending on more than one protein, naked and enveloped particles, and peptides displayed on other viruses have all been made. There have been multiple proofs of concept, and more than a few proofs of efficacy. This chapter covers the history of VLP production in plants, and explores a few examples in detail to illustrate the potential of such a mode of production for human and animal medicine.


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Ed Rybicki's curator insight, February 4, 2014 5:12 AM

For those of you with brass in pocket...B-)

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H1N-What? Wading Through the Alphabet Soup of Flu Virus Names

H1N-What? Wading Through the Alphabet Soup of Flu Virus Names | Virology and Bioinformatics from Virology.ca | Scoop.it
Muddled about all the new flu viruses?

It’s hard to keep up with the changing names in the news. H1Nwhat? Bird flu. Pig flu. MERS. SARS. Here ...

Via Ed Rybicki
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Bloody bats just would have to be different!!!

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Ed Rybicki's curator insight, February 4, 2014 10:22 AM

Great post on flu.

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Genome-wide Consequences of Deleting Any Single Gene

Genome-wide Consequences of Deleting Any Single Gene | Virology and Bioinformatics from Virology.ca | Scoop.it

Mutation of any single gene may cause a genomic imbalance, with consequences sufficient to drive adaptive genetic changes. This complicates genetic analyses but is a logical consequence of losing a functional unit originally acquired under pressure during evolution.

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Suspicious Virus Makes Rare Cross-Kingdom Leap From Plants to Honeybees | The Artful Amoeba, Scientific American Blog Network

Suspicious Virus Makes Rare Cross-Kingdom Leap From Plants to Honeybees | The Artful Amoeba, Scientific American Blog Network | Virology and Bioinformatics from Virology.ca | Scoop.it
When HIV jumped from chimpanzees to humans sometime in the early 1900s, it crossed a gulf spanning several million years of evolution. But tobacco ringspot virus, ...
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Ed Rybicki's curator insight, February 3, 2014 5:22 AM

OK, a bit flawed, but a nice blog post.  To be followed by mine, soon!

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Beijing smog contains witches' brew of microbes

Beijing smog contains witches' brew of microbes | Virology and Bioinformatics from Virology.ca | Scoop.it

For people racked by the dreaded ‘Beijing cough’, it is all too clear that particles in the city’s thick smogs pose a public-health problem. But much less clear is the impact — or even the identity — of the microbes that also drift through the brown haze.

 

Chinese researchers have now used genome sequencing to identify about 1,300 different microbial species in an exceptionally soupy smog that hit Beijing in January 2013 (ref. 1). Reassuringly, most of the microbes they found are benign — but a few are responsible for allergies and respiratory disease in humans. And on days with heavier pollution, the proportion of DNA from these allergens and pathogens increased, suggesting that they might present an additional health threat to vulnerable groups, such as older people or those with weakened immune systems.

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Christopher Irons's curator insight, January 31, 2014 6:48 PM

Normally we think of microbes on surfaces, but air laced with bacteria and more requires a new way of thinking!

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Comparison of host cell gene expression in cowpox, m... [Virol J. 2013] - PubMed - NCBI

Comparison of host cell gene expression in cowpox, m... [Virol J. 2013] - PubMed - NCBI | Virology and Bioinformatics from Virology.ca | Scoop.it

Despite their close genetic relationship, the expression profiles induced by infection with different orthopoxviruses vary significantly. It may be speculated that these differences at the cellular level contribute to the individual characteristics of cowpox, monkeypox and vaccinia virus infections in certain host species.

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How to flip the switch on HIV-related cancer

How to flip the switch on HIV-related cancer | Virology and Bioinformatics from Virology.ca | Scoop.it
Researchers have identified a critical component in the virus that causes Kaposi's sarcoma, the most common cancer among people infected with HIV.

In this study, which appears in the peer-reviewed journal PLOS Pathogens, the team identified a cluster of viral microRNA molecules that are necessary to transform healthy cells into cancerous ones. When this microRNA cluster was suppressed, the cells died after they were infected with KSHV.

Flipping the switch and turning the cluster back “on,” however, allowed the cells to stay alive and become malignant when infected with the virus.

Using advanced genomic methods, the researchers also found that the microRNAs target the IκBα protein and the NF-κB cellular pathway, both of which are associated with cancer development.


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Structure-based discovery of Middle East respiratory syndrome coronavirus fusion inhibitor

Structure-based discovery of Middle East respiratory syndrome coronavirus fusion inhibitor | Virology and Bioinformatics from Virology.ca | Scoop.it

Abstract-

A novel human coronavirus, Middle East respiratory syndrome coronavirus (MERS-CoV), has caused outbreaks of a SARS-like illness with high case fatality rate. The reports of its person-to-person transmission through close contacts have raised a global concern about its pandemic potential. Here we characterize the six-helix bundle fusion core structure of MERS-CoV spike protein S2 subunit by X-ray crystallography and biophysical analysis. We find that two peptides, HR1P and HR2P, spanning residues 998–1039 in HR1 and 1251–1286 in HR2 domains, respectively, can form a stable six-helix bundle fusion core structure, suggesting that MERS-CoV enters into the host cell mainly through membrane fusion mechanism. HR2P can effectively inhibit MERS-CoV replication and its spike protein-mediated cell–cell fusion. Introduction of hydrophilic residues into HR2P results in significant improvement of its stability, solubility and antiviral activity. Therefore, the HR2P analogues have good potential to be further developed into effective viral fusion inhibitors for treating MERS-CoV infection.
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$1000 Genomes for $2000

$1000 Genomes for $2000 | Virology and Bioinformatics from Virology.ca | Scoop.it
Getting an accurate genome sequence requires that you collect the data at least twice argue Robasky, Lewis, and Church in their recent opinion piece in Nat. Rev. Genetics [1]. The DNA sequencing world kicked off 2014 with an audacious start.
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The Canadian War on Science: A long, unexaggerated, devastating chronological indictment

The Canadian War on Science: A long, unexaggerated, devastating chronological indictment | Virology and Bioinformatics from Virology.ca | Scoop.it
This is a brief chronology of the current Conservative Canadian government’s long campaign to undermine evidence-based scientific, environmental and technical decision-making.
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'Helix': One virologist's take ... - The Global Dispatch

'Helix': One virologist's take ... - The Global Dispatch | Virology and Bioinformatics from Virology.ca | Scoop.it
'Helix': One virologist's take ...
The Global Dispatch
The “virology” is a major fail and really pulls me out of any willing-suspension-of-disbelief I'm trying (hard) to get going.
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Ed Rybicki's curator insight, January 27, 2014 2:34 AM

Really good deconstruction of what sounds like a badly-premised series: pity people can't get the damn science right!