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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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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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Involvement of host regulatory pathways during geminivirus infection: a novel platform for generating durable resistance

Geminiviruses are widely distributed throughout the world and cause devastating yield losses in almost all the economically important crops. In this review, the newly identified roles of various novel plant factors and pathways participating in plant–virus interaction are summarized with a particular focus on the exploitation of various pathways involving ubiquitin/26S proteasome pathway, small RNA pathways, cell division cycle components, and the epigenetic mechanism as defense responses during plant–pathogen interactions. Capturing the information on these pathways for the development of strategies against geminivirus infection is argued to provide the basis for new genetic approaches to resistance.

  

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Poxvirus Countermeasures During an Emergency in the United States

Poxvirus Countermeasures During an Emergency in the United States | Virology and Bioinformatics from Virology.ca | Scoop.it

Although smallpox was eradicated worldwide by 1980, national security experts remain concerned that it could be used in a deliberate attack. The United States and other governments have given priority to developing and stockpiling vaccines and antivirals to protect their populations from the potential reintroduction of this deadly disease. Public health officials are also concerned about the spread of related zoonotic orthopoxviruses such as monkeypox and cowpox, against which smallpox vaccine provides protection. This report analyzes how medical countermeasures available in the US Strategic National Stockpile will be given priority and used in the event of an intentional or accidental release of smallpox in the United States.

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Rift Valley fever virus' proteins imitate human DNA repair factors

Rift Valley fever virus' proteins imitate human DNA repair factors | Virology and Bioinformatics from Virology.ca | Scoop.it
A potential mechanism to combat diseases caused by haemorrhagic fever viruses has been discovered by researchers at the University of Montreal's Department of Biochemistry and Molecular Medicine. These diseases present a dramatic risk to human health as they often spread quickly and kill a high percentage ...
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Identification and molecular characterization of a novel monopartite geminivirus associated with mulberry mosaic dwarf disease

Identification and molecular characterization of a novel monopartite geminivirus associated with mulberry mosaic dwarf disease | Virology and Bioinformatics from Virology.ca | Scoop.it

High-throughput sequencing of small sRNAs allowed the identification of a novel DNA virus in a Chinese mulberry tree affected by a disease showing mosaic and dwarfing symptoms. Rolling circle amplification and polymerase chain reaction with specific primers, followed by sequencing of eight independent full-length clones, showed that this virus has a monopartite circular DNA genome (~2.95 kb) containing ORFs in both polarity strands, as previously reported for geminiviruses. A field survey showed the close association of the virus with diseased mulberries, so we tentatively named the virus as mulberry mosaic dwarf-associated virus (MMDaV). MMDaV genome codes for five and two putative proteins in the virion-sense and in the complementary-sense strands, respectively. Although three MMDaV virion-sense putative proteins did not share sequence homology with any protein in databases, functional domains [coiled-coil and transmembrane (TM) domain] were identified in two of them. In addition, the protein containing a TM domain was encoded by an ORF located in a similar genomic position in MMDaV and in several other geminiviruses. As reported for members of the genera Mastrevirus and Becurtovirus, MMDaV replication-associated proteins are expressed through the alternative splicing of an intron, which was shown to be functional in vivo. A similar intron was found in the genome of citrus chlorotic dwarf-associated virus (CCDaV), a divergent geminivirus recently found in citrus. Based on pairwise comparisons and phylogenetic analyses, CCDaV and MMDaV appear to be closely related to each other, thus supporting their inclusion in a putative novel genus in the family Geminiviridae.

 

Geminivirus graphic by Russell Kightley Media

  
Ed Rybicki's insight:

Keep on looking, and we'll keep finding 'em...

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After Nearly Claiming His Life, Ebola Lurked in a Doctor’s Eye

After Nearly Claiming His Life, Ebola Lurked in a Doctor’s Eye | Virology and Bioinformatics from Virology.ca | Scoop.it
Dr. Ian Crozier, who survived an Ebola infection last fall, calls himself a poster child for “post-Ebola syndrome,” which is also being reported in West Africa.
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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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Transmission of influenza A viruses

Transmission of influenza A viruses | Virology and Bioinformatics from Virology.ca | Scoop.it

Influenza A viruses cause respiratory infections that range from asymptomatic to deadly in humans. Widespread outbreaks (pandemics) are attributable to ‘novel’ viruses that possess a viral hemagglutinin (HA) gene to which humans lack immunity. After a pandemic, these novel viruses form stable virus lineages in humans and circulate until they are replaced by other novel viruses. The factors and mechanisms that facilitate virus transmission among hosts and the establishment of novel lineages are not completely understood, but the HA and basic polymerase 2 (PB2) proteins are thought to play essential roles in these processes by enabling avian influenza viruses to infect mammals and replicate efficiently in their new host. Here, we summarize our current knowledge of the contributions of HA, PB2, and other viral components to virus transmission and the formation of new virus lineages.

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Continual Reintroduction of Human Pandemic H1N1 Influenza A Viruses into Swine in the United States, 2009 to 2014

Continual Reintroduction of Human Pandemic #H1N1 #Influenza A Viruses into ... - Journal of Virology : http://t.co/mwHwHFtKur
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Knockdown of different influenza A virus subtypes in cell culture by a single antisense oligodeoxyribonucleotide

Knockdown of different influenza A virus subtypes in cell culture by a single antisense oligodeoxyribonucleotide | Virology and Bioinformatics from Virology.ca | Scoop.it

Influenza is a heavy socially significant viral infection that affects humans, birds, and wild and domestic animals. The threat of existing and new highly pathogenic subtypes of influenza A virus (IAV) makes it necessary to develop an effective drug that may affect different IAV strains. For this purpose, oligodeoxynucleotides (DNA fragments) attached to titanium dioxide (TiO2) nanoparticles through a polylysine linker, forming TiO2·PL-DNA nanocomposites, that penetrated into cells without transfection agents were used. For the first time, efficient (≥99.9%) suppression of the reproduction of different subtypes of IAV, including highly pathogenic H5N1 and H1N1, was achieved. These results were obtained using the TiO2·PL-DNA nanocomposite bearing a single antisense oligodeoxynucleotide (0.1μM) targeted to the conserved 3'-noncoding region of RNA segment 5, which is common to all tested strains. Very efficient suppression of the reproduction of different subtypes of IAV was probably achieved due to the use of the proposed delivery system for oligonucleotides in the form of the TiO2·PL-DNA nanocomposites. These results indicate the possibility of creating an efficient drug to affect existing and newly emerging pathogenic IAV strains.

 

Influenza virus graphic by Russell Kightley Media

 

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Biologist advances cancer research with new data analysis techniques

Biologist advances cancer research with new data analysis techniques | Virology and Bioinformatics from Virology.ca | Scoop.it
Patience and persistence are beginning to pay off for University of Montana Professor Mark Grimes, whose research about the behavior of cell proteins in childhood cancer recently was published by the Public Library of Science Computational Biology.
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Complete Regression of Metastatic Cervical Cancer After Treatment With Human Papillomavirus–Targeted Tumor-Infiltrating T Cells

Complete Regression of Metastatic Cervical Cancer After Treatment With Human Papillomavirus–Targeted Tumor-Infiltrating T Cells | Virology and Bioinformatics from Virology.ca | Scoop.it

Purpose Metastatic cervical cancer is a prototypical chemotherapy-refractory epithelial malignancy for which better treatments are needed. Adoptive T-cell therapy (ACT) is emerging as a promising cancer treatment, but its study in epithelial malignancies has been limited. This study was conducted to determine if ACT could mediate regression of metastatic cervical cancer.

Patients and Methods Patients enrolled onto this protocol were diagnosed with metastatic cervical cancer and had previously received platinum-based chemotherapy or chemoradiotherapy. Patients were treated with a single infusion of tumor-infiltrating T cells selected when possible for human papillomavirus (HPV) E6 and E7 reactivity (HPV-TILs). Cell infusion was preceded by lymphocyte-depleting chemotherapy and was followed by administration of aldesleukin.

Results Three of nine patients experienced objective tumor responses (two complete responses and one partial response). The two complete responses were ongoing 22 and 15 months after treatment, respectively. One partial response was 3 months in duration. The HPV reactivity of T cells in the infusion product (as measured by interferon gamma production, enzyme-linked immunospot, and CD137 upregulation assays) correlated positively with clinical response (P = .0238 for all three assays). In addition, the frequency of HPV-reactive T cells in peripheral blood 1 month after treatment was positively associated with clinical response (P = .0238).

Conclusion Durable, complete regression of metastatic cervical cancer can occur after a single infusion of HPV-TILs. Exploratory studies suggest a correlation between HPV reactivity of the infusion product and clinical response. Continued investigation of this therapy is warranted.

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MapMyFlu: visualizing spatio-temporal relationships between related influenza sequences

MapMyFlu: visualizing spatio-temporal relationships between related influenza sequences | Virology and Bioinformatics from Virology.ca | Scoop.it

Understanding the molecular dynamics of viral spreading is crucial for anticipating the epidemiological implications of disease outbreaks. In the case of influenza, reassortments or point mutations affect the adaption to new hosts or resistance to anti-viral drugs and can determine whether a new strain will result in a pandemic infection or a less severe progression. To this end, tools integrating molecular information with epidemiological parameters are important to understand how molecular characteristics reflect in the infection dynamics. We present a new web tool, MapMyFlu, which allows to spatially and temporally display influenza viruses related to a query sequence on a Google Map based on BLAST results against the NCBI Influenza Database. Temporal and geographical trends appear clearly and may help in reconstructing the evolutionary history of a particular sequence. The tool is accessible through a web server, hence without the need for local installation. The website has an intuitive design and provides an easy-to-use service, and is available at http://mapmyflu.ipmb.uni-heidelberg.de

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