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PLOS Computational Biology: The Roots of Bioinformatics in ISMB

PLOS Computational Biology: The Roots of Bioinformatics in ISMB | Virology and Bioinformatics from Virology.ca | Scoop.it
PLOS Computational Biology is an open-access
Nicolas Palopoli's insight:

Besides the interesting recall of the Intelligent Systems for Molecular Biology (ISMB) annual conferences on computational biology, it offers a nice insight into current state-of-the-art methodologies and upcoming trends in the discipline.

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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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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, Today, 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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Smallpox vaccine, ACAM2000: Sites and duration of viral shedding and effect of povidone iodine on scarification site shedding and immune response

The U.S. Department of Defense vaccinates personnel deployed to high-risk areas with the vaccinia virus (VACV)-based smallpox vaccine. Autoinoculations and secondary and tertiary transmissions due to VACV shedding from the vaccination site continue to occur despite education of vaccinees on the risks of such infections. The objectives of this study were to investigate, in naïve smallpox vaccinees, (a) whether the vaccination site can remain contagious after the scab separates and (b) whether the application of povidone iodine ointment (PIO) to the vaccination site inactivates VACV without affecting the immune response. When applied to the vaccination site starting on day 7, PIO reduced viral shedding without altering the immune response. The use of PIO in addition to a semipermeable dressing may reduce the rates of autoinoculation and contact transmission originating from the vaccination site in smallpox-vaccinated individuals.

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Biostars - Bioinformatics Explained

Biostars - Bioinformatics Explained | Virology and Bioinformatics from Virology.ca | Scoop.it

Tutorials and Q+A Forum for bioinformatic tools. 17 000 + users!

Kathleen McLeod's insight:

Could be an interesting resource!

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Gammaherpesvirus Co-infection with Malaria Suppresses Anti-parasitic Humoral Immunity

Gammaherpesvirus Co-infection with Malaria Suppresses Anti-parasitic Humoral Immunity | Virology and Bioinformatics from Virology.ca | Scoop.it
Author Summary Nearly 1 million deaths occur annually as a result of complications associated with P . falciparum infection, with children younger than 5 being the most susceptible age group. Earlier studies have demonstrated that children co-infected with P . falciparum and Epstein-Barr virus (EBV) have impaired immune responses to control EBV, and this can result in the development of a jaw tumor called endemic Burkitt’s lymphoma (eBL). It is not known if there is any impact of acute EBV infection on the generation of anti-malarial immunity. We have used mouse models of EBV [murine gammaherpesvirus 68 (MHV68)] and malaria ( P . yoelii XNL) to demonstrate that acute gammaherpesvirus infection can impair the generation of antibodies that control Plasmodium parasitemia, in turn causing a non-lethal P . yoelii XNL infection to become lethal. We identify a critical role for the MHV68 M2 protein in mediating the suppressive effect of acute MHV68 infection on the generation of humoral immunity to a secondary malaria infection. This work demonstrates that gammaherpesvirus infections can suppress the generation of an effective anti-malaria immune response and suggests that acute EBV infection should be investigated as a risk factor for the development of severe malaria in young children.
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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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Viral Interference: The Case of Influenza Viruses

It is well-known that infection of an organism, whether plant, animal or bacterium, with a virus can prevent or partially inhibit infection with another virus within the same host resulting in a “viral interference”. Although originally described for plant viruses in 1929, similar observations were made for bacteriophage and a plethora of animal viruses in the1940s and 1950s. In fact, Jenner reported that herpetic infections may prevent the development of vaccinia lesions in 1804, perhaps the first report of viral interference. These original reports have been well-supported through experimental studies in animals, as well as epidemiological and modeling studies, for a variety of viruses including influenza.

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Fighting HIV where no-one admits it's a problem - BBC News

Fighting HIV where no-one admits it's a problem - BBC News | Virology and Bioinformatics from Virology.ca | Scoop.it
HIV infection rates are soaring in Russia, but there is a reluctance to address the issue.
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Modification of promoter spacer length in vaccinia virus as a strategy to control the antigen expression

Vaccinia viruses (VACV) with distinct early promoters have been developed to enhance antigen expression and improve antigen-specific CD8 T cell responses. We generated several recombinant VACV based on the attenuated modified vaccinia Ankara (MVA) strain, which express GFP or the Leishmania LACK antigen under the control of an optimized promoter, using different spacer lengths. Longer spacer length increased GFP and LACK early expression, which correlated with an enhanced LACK-specific memory CD4 and CD8 T cell response. These results show the importance of promoter spacer length for early antigen expression by VACV and provide alternative strategies for the design of poxvirus-based vaccines.

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