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The complete genome sequence of EC1-UPM, a novel N4-like bacteriophage that infects Escherichia coli O78:K80

The complete genome sequence of EC1-UPM, a novel N4-like bacteriophage that infects Escherichia coli O78:K80 | Virology and Bioinformatics from Virology.ca | Scoop.it
Bacteriophage EC1-UPM is an N4-like bacteriophage which specifically infects Escherichia coli O78:K80, an avian pathogenic strain that causes colibacillosis in poultry.
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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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It's a group effort - the curators:

It's a group effort - the curators: | Virology and Bioinformatics from Virology.ca | Scoop.it

get in touch if you want to help curate this topic

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'Indestructible' virus that can withstand boiling acid could help scientists ... - Daily Mail

'Indestructible' virus that can withstand boiling acid could help scientists ... - Daily Mail | Virology and Bioinformatics from Virology.ca | Scoop.it
Scientists at the University of Virginia hope that by unlocking the secrets of an 'indestructible' virus could herald a wave of new treatments for life-threatening diseases.
Kathleen McLeod's insight:

Learning more about A-DNA.

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Fecal virome analysis of three carnivores reveals a novel nodavirus and multiple gemycircularviruses

More knowledge about viral populations in wild animals is needed in order to better understand and assess the risk of zoonotic diseases. In this study we performed viral metagenomic analysis of fecal samples from three healthy carnivores: a badger (Meles meles), a mongoose (Herpestes ichneumon) and an otter (Lutra lutra) from Portugal. We detected the presence of novel highly divergent viruses in the fecal material of the carnivores analyzed, such as five gemycircularviruses. Four of these gemycircularviruses were found in the mongoose and one in the badger. In addition we also identified an RNA-dependent RNA polymerase gene from a putative novel member of the Nodaviridae family in the fecal material of the otter. Together these results underline that many novel viruses are yet to be discovered and that fecal associated viruses are not always related to disease. Our study expands the knowledge of viral species present in the gut, although the interpretation of the true host species of such novel viruses needs to be reviewed with great caution.

 
Ed Rybicki's insight:

The "faecovirome"!  And there is speculation that the gemycircularviruses (terrible name, really) are fungal viruses.

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Factors to Consider When Choosing a Lab for PhD Training

Factors to Consider When Choosing a Lab for PhD Training | Virology and Bioinformatics from Virology.ca | Scoop.it
A life-long career in scientific research depends alot on your PhD training as the primary “developmental” phase followed by the “pay-off” phase of postdoctoral training and beyond. Accruing the mu...
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Scanning for SIV's Sanctuaries in whole monkeys

Scanning for SIV's Sanctuaries in whole monkeys | Virology and Bioinformatics from Virology.ca | Scoop.it
Whole-body immunoPET scans of SIV-infected macaques reveal where the replicating virus hides.
 

Via Ed Rybicki
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Ed Rybicki's curator insight, May 29, 10:27 AM

Isn't technology wonderful?

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Pentagon accidentally sent live anthrax samples to labs via FedEx

The Pentagon this week said that it accidentally sent live anthrax samples to government and private laboratories in at least nine states, and to a US military base in South Korea. As the A...
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BMC Genomics | Full text | Global transcription of CRISPR loci in the human oral cavity

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) are active in acquired resistance against bacteriophage and plasmids in a number of environments. In the human mouth, CRISPR loci evolve to counteract oral phage, but the expression of these CRISPR loci has not previously been investigated. We sequenced cDNA from CRISPR loci found in numerous different oral bacteria and compared with oral phage communities to determine whether the transcription of CRISPR loci is specifically targeted towards highly abundant phage present in the oral environment.
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BMC Bioinformatics | Full text | InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

Set comparisons permeate a large number of data analysis workflows, in particular workflows in biological sciences. Venn diagrams are frequently employed for such analysis but current tools are limited.
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Human antibody specificities that confer protective immunity to poxvirus infections (VAC11P.1109)

Immunization with vaccinia virus (VACV) induces cross-protective immunity to variola, the causative agent of smallpox. However, the specificity and breadth of protective human Abs to poxviruses are largely unknown. We used a highly-optimized human hybridoma technology to generate a panel of 90 anti-VACV monoclonal Abs from vaccinia-immunized subjects or from subjects who had a history of naturally-acquired monkeypox infection. A large fraction of Abs from the panel (>40%) possessed neutralizing activity against VACV, cowpox and/or monkeypox viruses. Antibodies to a variety of envelope proteins in VACV extracellular virions (A33, B5) or mature virions (L1, A27, D8, H3) contributed substantially to neutralizing activity in vitro. For protective immunity in vivo, L1, A27, A33 and B5 antibodies conferred levels of protection that were comparable to those induced by live viral vaccination, especially when used in combination. Such antibody cocktails have promise for use in as immunotherapeutics in humans.

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Rational Design of Antibiotic Treatment Plans: A Treatment Strategy for Managing Evolution and Reversing Resistance

Rational Design of Antibiotic Treatment Plans: A Treatment Strategy for Managing Evolution and Reversing Resistance | Virology and Bioinformatics from Virology.ca | Scoop.it

The development of reliable methods for restoring susceptibility after antibiotic resistance arises has proven elusive. A greater understanding of the relationship between antibiotic administration and the evolution of resistance is key to overcoming this challenge. Here we present a data-driven mathematical approach for developing antibiotic treatment plans that can reverse the evolution of antibiotic resistance determinants.  Overall this study shows that there is promise for reversing the evolution of resistance through antibiotic treatment plans.

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Ocean's hidden world of plankton revealed in 'enormous database' - BBC News

Ocean's hidden world of plankton revealed in 'enormous database' - BBC News | Virology and Bioinformatics from Virology.ca | Scoop.it
Thousands of species of the ocean's tiniest organisms are revealed in a series of studies.
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Influenza A Virus on Oceanic Islands: Host and Viral Diversity in Seabirds in the Western Indian Ocean

by Camille Lebarbenchon, Audrey Jaeger, Chris Feare, Matthieu Bastien, Muriel Dietrich, Christine Larose, Erwan Lagadec, Gérard Rocamora, Nirmal Shah, Hervé Pascalis, Thierry Boulinier, Matthieu Le Corre, David E.
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Enhanced production of porcine circovirus type 2 virus-like particles in Sf9 cells by translational enhancers

OBJECTIVE:

To investigate the effect of three translational enhancers for enhancing transgene expression in baculovirus expression vector system using GFP as a reporter gene and selected translational enhancers to increase porcine circovirus type 2 (PCV2) VLPs production.

RESULTS:

P10UTR (the 3'-untranslated region from the baculovirus p10 gene), Syn21 (a synthetic AT-rich 21-bp sequence) and P10UTR/Syn21 increased the GFP yield by 1.4-, 4- and 4.8-fold, respectively. While IVS (intron from Drosophila myosin heavy chain gene) decreased the GFP yield by 65 %. Moreover, the synergy of P10UTR/Syn21 increased the yield of PCV2 VLPs by 4.1 fold (45 μg/106 cells) compared with standard baculovirus vector.

CONCLUSION:

The synergy of P10UTR/Syn21 is a potential strategy to improve the recombinant vaccine production besides PCV2 VLPs in BEVS.

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How the Herpes Virus Can Kill Cancer - US News

How the Herpes Virus Can Kill Cancer - US News | Virology and Bioinformatics from Virology.ca | Scoop.it
The genetically modified virus could stop the progression of melanoma.
Kathleen McLeod's insight:

A link to the associated paper so you can see what you think of the results ----> http://www.immunotherapyofcancer.org/content/2/S3/P91

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Please fund my grant, please fund my grant #ASM2015 pic.twitter.com/OLfi91A4ik

Please fund my grant, please fund my grant #ASM2015 pic.twitter.com/OLfi91A4ik | Virology and Bioinformatics from Virology.ca | Scoop.it
Chris Upton + helpers's insight:

Originally tweeted by: http://twitter.com/JoeBMcPhee

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Rescue of a duck circovirus from an infectious DNA clone in ducklings

Duck circovirus may predispose the host to immunosuppression and may serve as an immunological trigger for further complicated disease progression. Due to the lack of a cell culture system for propagating DuCV, little is known regarding the molecular biology and pathogenesis of DuCV. The aim of this study was to describe the construction and initial in vivo characterization of full-length DNA clones of DuCV (pIC-Mu2DuCV) and its infectivity under in vivo conditions.
Ed Rybicki's insight:

Using a technique derived straight out of plant virology - dimeric/partially dimeric tandem cloned copies of the genome, injected into the host.

They should have tried agroinfection B-)

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The most predictable disaster in the history of the human race. And it's not zombies.

...there's something out there that's as bad as war, something that kills as many people as war, and Gates doesn't think we're ready for it.

"Look at the death chart of the 20th century," he says, because he's the kind of guy that looks at death charts. "I think everybody would say there must be a spike for World War I. Sure enough, there it is, like 25 million. And there must be a big spike for World War II, and there it is, it's like 65 million. But then you'll see this other spike that is as large as World War II right after World War I, and most people, would say, 'What was that?'"

"Well, that was the Spanish flu."


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Ed Rybicki's curator insight, May 27, 9:56 AM

Yeah, yeah, yeah: there's a lot of people being saying similar things for a long time.  But now it's Bill Gates, so governments MAY pay attention!

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Chagas Disease vaccine works in mice

Chagas Disease vaccine works in mice | Virology and Bioinformatics from Virology.ca | Scoop.it
Chagas disease, caused by Trypanosoma cruzi and transmitted by insects in Latin America is among the most common tropical diseases, and so far without effective vaccine. A new study published in PL...
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Viral membrane fusion

Viral membrane fusion | Virology and Bioinformatics from Virology.ca | Scoop.it
A useful short review from Stephen Harrison which approaches viral memberane fusion from a structural biology standpoint.
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Video Tip of the Week: NCBI Tree Viewer | The OpenHelix Blog

Video Tip of the Week: NCBI Tree Viewer | The OpenHelix Blog | Virology and Bioinformatics from Virology.ca | Scoop.it
The helpful folks at NCBI have been ramping up their outreach. I've been watching a lot of their webinars, and they are trying different styles. The more
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IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data

IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data | Virology and Bioinformatics from Virology.ca | Scoop.it
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Distinct kinetics and pathways of apoptosis in influenza A and B virus infection

Distinct kinetics and pathways of apoptosis in influenza A and B virus infection | Virology and Bioinformatics from Virology.ca | Scoop.it

Highlights

 • Differences in apoptosis kinetics of Influenza A and B cell infection were observed.

• Both influenza A and B infection activate the PI3K/Akt survival pathway.• IκB/NF-κB survival pathway acts as major contributor for the differences observed.

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Experimental Evolution of an RNA Virus in Wild Birds: Evidence for Host-Dependent Impacts on Population Structure and Competitive Fitness

Experimental Evolution of an RNA Virus in Wild Birds: Evidence for Host-Dependent Impacts on Population Structure and Competitive Fitness | Virology and Bioinformatics from Virology.ca | Scoop.it
Author Summary Viruses are constantly emerging into new areas and pose significant challenges to public health. Chikungunya and West Nile viruses (WNV), both mosquito-borne RNA viruses, are quintessential examples of how increased globalization has facilitated the expansion of viruses into new territories. Rapid evolution of both of these agents has contributed to their rapid spread and health burden. Thus, characterizing how selection shapes zoonotic RNA viruses in their natural hosts is imp
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Flu virus, measles comparison inspires vaccine design

Flu virus, measles comparison inspires vaccine design | Virology and Bioinformatics from Virology.ca | Scoop.it
Researchers compared the flu and measles viruses to understand why the measles vaccine is so successful and the flu vaccine must be redesigned so often.
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Influenza A virus utilizes a suboptimal Kozak sequence to fine-tune virus replication and host response

The segment-specific non-coding regions (NCRs) of influenza A virus RNA genome play important roles in controlling viral RNA transcription, replication and genome packaging. In this report, we present, for the first time to our knowledge, a full view of the segment-specific NCRs of all influenza A viruses by bioinformatics analysis. Our systematic functional analysis revealed that the eight segment-specific NCRs identified could differentially regulate viral RNA synthesis and protein expression at both transcription and translation levels. Interestingly, a highly conserved suboptimal nucleotide at −3 position of the Kozak sequence, which downregulated protein expression at the translation level, was only present in the segment-specific NCR of PB1. By reverse genetics, we demonstrate that recombinant viruses with an optimized Kozak sequence at the −3 position in PB1 resulted in a significant multiple-cycle replication reduction that was independent of PB1-F2 expression. Our detailed dynamic analysis of virus infection revealed that the mutant virus displays slightly altered dynamics from the wild-type virus on both viral RNA synthesis and protein production. Furthermore, we demonstrated that the level of PB1 expression is involved in regulating type I IFN production. Together, these data reveal a novel strategy exploited by influenza A virus to fine-tune virus replication dynamics and host antiviral response through regulating PB1 protein expression.

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