Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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Viruses, Immunology & Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction

Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

A systematic quantitative analysis of temporal changes in host and viral proteins throughout the course of a productive infection could provide dynamic insights into virus-host interaction. We developed a proteomic technique called “quantitative temporal viromics” (QTV), which employs multiplexed tandem-mass-tag-based mass spectrometry. Human cytomegalovirus (HCMV) is not only an important pathogen but a paradigm of viral immune evasion. QTV detailed how HCMV orchestrates the expression of >8,000 cellular proteins, including 1,200 cell-surface proteins to manipulate signaling pathways and counterintrinsic, innate, and adaptive immune defenses. QTV predicted natural killer and T cell ligands, as well as 29 viral proteins present at the cell surface, potential therapeutic targets. Temporal profiles of >80% of HCMV canonical genes and 14 noncanonical HCMV open reading frames were defined. QTV is a powerful method that can yield important insights into viral infection and is applicable to any virus with a robust in vitro model.

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New Alignment Method to Speed Up De Novo Assembly of Whole Genomes

August 15, 2014 | This Thursday, a team of bioinformaticians from the National Biodefense Analysis and Countermeasures Center, the University of Maryland College Park, and sequencing company Pacific Biosciences posted information on their tool MHAP to the life sciences preprint server bioRxiv. MHAP, or MinHash Alignment Process, is a dramatically faster method for ordering DNA fragments sequenced on long-read technologies like the PacBio RS II Sequencer or the Oxford Nanopore MinION, making it easier to assemble whole genomes from scratch without the use of a reference genome.Bio-IT World previously covered MHAP following a presentation by senior author Adam Phillippy at the PacBio User Group Meeting this June; however, the newly released paper features much greater detail, including assemblies of the human genome and four important model organisms.

 


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Why HIV Virions Have Low Numbers of Envelope Spikes: Implications for Vaccine Development

Why HIV Virions Have Low Numbers of Envelope Spikes: Implications for Vaccine Development | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
From molecules to physiology
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Online collaboration: Scientists and the social network

Online collaboration: Scientists and the social network | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Why scholars use social media
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Picturing science: Royal Society launches scientific illustrations ‘print on demand’

Picturing science: Royal Society launches scientific illustrations ‘print on demand’ | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
GrrlScientist: The Royal Society has just launched a ‘print-on-demand’ service so the public can easily purchase high quality prints of nature and scientific illustrations from its library and archives.
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Bioinformatics at a Crossroad Again – Which Way Next? « Homolog.us – Bioinformatics

Bioinformatics at a Crossroad Again – Which Way Next? « Homolog.us – Bioinformatics | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

One of our readers asked – “If genome assembly becomes a solved problem, what’s next?”

We like to broaden the comment to argue that the entire field of bioinformatics is again at a turning point, because almost all difficult computational problems related to ‘next-generation sequencing’ have been solved satisfactorily. Readers are encouraged to express their differing opinions in the comment section.

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How A Computer Algorithm Predicted West Africa's Ebola Outbreak Before It Was Announced

How A Computer Algorithm Predicted West Africa's Ebola Outbreak Before It Was Announced | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The Ebola outbreak in West Africa is focusing a spotlight on a unique online tool run by experts in Boston that flagged a "mystery hemorrhagic fever" in forested areas of southeastern Guinea nine d...
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Samuel Viana's curator insight, August 15, 2014 2:53 PM

Um interessante algoritmo que combina fontes noticiosas, relativamente à frequência de notícias sobre surtos e à proveniência desses mesmos surtos, ajuda a prever a possibilidade de evolução de potenciais pandemias, antes de estas poderem escalar para níveis incontroláveis.

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A recombinant RNA bacteriophage system to identify functionally important nucleotides in a self-cleaving ribozyme

RNA bacteriophages like Qbeta and MS2 are well known for their high mutation rate, short infection cycle and strong selection against foreign inserts. The hammerhead ribozyme (HHRz) is a small self-cleaving RNA molecule whose active residues have previously been identified by mutational analysis of each individual base. Here the functionally important bases of HHRz were determined in a single screening experiment by inserting the HHRz into the genome of MS2.
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Can't imagine why I missed this!

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World Hepatitis Day Virtual Special Issue - Journal of Clinical Virology - Elsevier

World Hepatitis Day Virtual Special Issue - Journal of Clinical Virology - Elsevier | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Read the latest research for free

Viral hepatitis leads to liver disease and kills almost 1.4 million people every year. It is caused by...
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Science/AAAS | Special Collection: Ebola

Science/AAAS | Special Collection: Ebola | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Science/AAAS | Special Collection: Ebola #medicine #virology #onehealth http://t.co/vPrJoGhvfY
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Small RNAs: A New Paradigm in Plant-Microbe Interactions -

Small RNAs: A New Paradigm in Plant-Microbe Interactions - | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

A never-ending arms race drives coevolution between pathogens and hosts. In plants, pathogen attacks invoke multiple layers of host immune responses. Many pathogens deliver effector proteins into host cells to suppress host immunity, and many plants have evolved resistance proteins to recognize effectors and trigger robust resistance. Here, we discuss findings on noncoding small RNAs (sRNAs) from plants and pathogens, which regulate host immunity and pathogen virulence. Recent discoveries have unveiled the role of noncoding sRNAs from eukaryotic pathogens and bacteria in pathogenicity in both plant and animal hosts. The discovery of fungal sRNAs that are delivered into host cells to suppress plant immunity added sRNAs to the list of pathogen effectors. Similar to protein effector genes, many of these sRNAs are generated from transposable element (TE) regions, which are likely to contribute to rapidly evolving virulence and host adaptation. We also discuss RNA silencing that occurs between organisms.

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Coronavirus virulence genes with main focus on SARS-CoV envelope gene

Abstract

Coronavirus (CoV) infection is usually detected by cellular sensors, which trigger the activation of the innate immune system. Nevertheless, CoVs have evolved viral proteins that target different signaling pathways to counteract innate immune responses. Some CoV proteins act as antagonists of interferon (IFN) by inhibiting IFN production or signaling, aspects that are briefly addressed in this review. After CoV infection, potent cytokines relevant in controlling virus infections and priming adaptive immune responses are also generated. However, an uncontrolled induction of these proinflammatory cytokines can lead to pathogenesis and disease severity as described for SARS-CoV and MERS-CoV. The cellular pathways mediated by interferon regulatory factor (IRF)-3 and -7, activating transcription factor (ATF)-2/jun, activator protein (AP)-1, nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), and nuclear factor of activated T cells (NF-AT), are the main drivers of the inflammatory response triggered after viral infections, with NF-κB pathway the most frequently activated. Key CoV proteins involved in the regulation of these pathways and the proinflammatory immune response are revisited in this manuscript.

It has been shown that the envelope (E) protein plays a variable role in CoV morphogenesis, depending on the CoV genus, being absolutely essential in some cases (genus α CoVs such as TGEV, and genus β CoVs such as MERS-CoV), but not in others (genus β CoVs such as MHV or SARS-CoV). A comprehensive accumulation of data has shown that the relatively small E protein elicits a strong influence on the interaction of SARS-CoV with the host. In fact, after infection with viruses in which this protein has been deleted, increased cellular stress and unfolded protein responses, apoptosis, and augmented host immune responses were observed. In contrast, the presence of E protein activated a pathogenic inflammatory response that may cause death in animal models and in humans.

The modification or deletion of different motifs within E protein, including the transmembrane domain that harbors an ion channel activity, small sequences within the middle region of the carboxy-terminus of E protein, and its most carboxy-terminal end, which contains a PDZ domain-binding motif (PBM), is sufficient to attenuate the virus. Interestingly, a comprehensive collection of SARS-CoVs in which these motifs have been modified elicited full and long-term protection even in old mice, making those deletion mutants promising vaccine candidates. These data indicate that despite its small size, E protein drastically influences the replication of CoVs and their pathogenicity. Although E protein is not essential for CoV genome replication or subgenomic mRNA synthesis, it affects virus morphogenesis, budding, assembly, intracellular trafficking, and virulence. In fact, E protein is responsible in a significant proportion of the inflammasome activation and the associated inflammation elicited by SARS-CoV in the lung parenchyma. This exacerbated inflammation causes edema accumulation leading to acute respiratory distress syndrome (ARDS) and, frequently, to the death of infected animal models or human patients.

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Adaptive Evolution and Environmental Durability Jointly Structure Phylodynamic Patterns in Avian Influenza Viruses

Adaptive Evolution and Environmental Durability Jointly Structure Phylodynamic Patterns in Avian Influenza Viruses | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Avian influenza viruses (AIVs) have been pivotal to the origination of human pandemic strains. Despite their scientific and public health significance, however, there remains much to be understood about the ecology and evolution of AIVs in wild birds, where major pools of genetic diversity are generated and maintained. Here, we present comparative phylodynamic analyses of human and AIVs in North America, demonstrating (i) significantly higher standing genetic diversity and (ii) phylogenetic trees with a weaker signature of immune escape in AIVs than in human viruses. To explain these differences, we performed statistical analyses to quantify the relative contribution of several potential explanations. We found that HA genetic diversity in avian viruses is determined by a combination of factors, predominantly subtype-specific differences in host immune selective pressure and the ecology of transmission (in particular, the durability of subtypes in aquatic environments). Extending this analysis using a computational model demonstrated that virus durability may lead to long-term, indirect chains of transmission that, when coupled with a short host lifespan, can generate and maintain the observed high levels of genetic diversity. Further evidence in support of this novel finding was found by demonstrating an association between subtype-specific environmental durability and predicted phylogenetic signatures: genetic diversity, variation in phylogenetic tree branch lengths, and tree height. The conclusion that environmental transmission plays an important role in the evolutionary biology of avian influenza viruses—a manifestation of the “storage effect”—highlights the potentially unpredictable impact of wildlife reservoirs for future human pandemics and the need for improved understanding of the natural ecology of these viruses.

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virtualenv - running Python based software in isolation

virtualenv - running Python based software in isolation | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
#bioinformatics Tutorial: virtualenv - running Python based software in isolation http://t.co/9pbtuHSK8u

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Stop saying “Scientists discover…” instead say, “Prof. Doe’s team discovers…” | Simply Statistics

Stop saying “Scientists discover…” instead say, “Prof. Doe’s team discovers…” | Simply Statistics | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Chris Upton + helpers's insight:

Why should Prof. Doe get all the credit?

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Evolution and Genomics

Evolution and Genomics | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

immersive training opportunities | The European Workshop on Genomics is being planned for January 2015 and will be held in Cesky Krumlov, Czech Republic. Updates coming soon! Please sign-up for our email list to be notified!

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Margaret Thatcher's surprising relationship with Dorothy Hodgkin

Margaret Thatcher's surprising relationship with Dorothy Hodgkin | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
A new play explores one of the most intriguing friendships in the history of science and politics: Margaret Thatcher and Dorothy Hodgkin. Alice Bell spoke to playwright Adam Ganz
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Viruses101 | Learn Science at Scitable

Viruses101 | Learn Science at Scitable | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Viruses 101 will delve into the world of microscopic killers. Each post will explore a new virus ? its components, effects on victims, and its impact on the global community.
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Ebola Outbreak Declared an International Public Health Emergency

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Second experimental Ebola drug gains approval

Second experimental Ebola drug gains approval | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Following the use of the experimental Ebola treatment drug ZMapp on two U.S. aid workers in Liberia, the U.S. FDA has partially approved a second medication. The drug, TKM-Ebola, has been approved from the next phase of clinical trials.
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Ebolavirus vaccines and antivirals

Ebolavirus vaccines and antivirals | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
There has been substantial research into developing and testing active and passive vaccines and antiviral drugs, but none have yet been licensed for use in humans.
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Long non-coding RNAs in the regulation of the immune response: Trends in Immunology

Long non-coding RNAs in the regulation of the immune response: Trends in Immunology | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Highlights

 

•Widespread changes in lncRNA expresssion are associated with the immune response.•lncRNAs regulate the inflammatory response following activation of innate immunity.•lncRNAs regulate T cell differentiation and migration.•The action of long non-coding RNAs is mediated via diverse mechanisms. 

 

 

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A History of Bioinformatics (told from the Year 2039) - OpenHelix Blog

A History of Bioinformatics (told from the Year 2039). Leave a reply. A week or so back I was watching the chatter around the #ISMB / #BOSC2014 meeting, and saw a number of amusing and intriguing comments about Titus ...
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Exploring the potential of next-generation sequencing in diagnosis of respiratory viruses - J Clin Microbiol. 2014

Exploring the potential of next-generation sequencing in diagnosis of respiratory viruses - J Clin Microbiol. 2014 | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Efficient detection of human respiratory viral pathogens is crucial in the management of patients with acute respiratory tract infection. Sequence-independent amplification of nucleic acids combined with next-generation sequencing technology and bioinformatics analyses is a promising strategy for identification of pathogens in clinical and public health settings. It allows the characterization of hundreds of different known pathogens simultaneously and also novel pathogens that elude conventional testing. However, major hurdles for routine use exist, which include cost, turnaround time, and especially sensitivity of the assay as the detection limit is dependent on viral load, host genetic material, and sequencing depth. To obtain insight into these aspects, we analysed nasopharyngeal aspirates from a cohort of 81 children with respiratory disease from Thailand for the presence of respiratory viruses using both a sequence-independent next generation sequencing approach and routinely used real time diagnostic (RT)-PCR assays. With respect to rhino- and human metapneumovirus detection, the next generation sequencing approach was at least as sensitive as diagnostic real time (RT)-PCR in this small cohort, whereas for boca- and enterovirus, next generation-sequencing revealed to be less sensitive than real time (RT-)PCR. The advantage of the sequencing approach over real time (RT-)PCR was the immediate availability of virus typing information. Considering the development of platforms capable of generating more output data at declining costs, next generation sequencing remains of interest for future virus diagnosis in clinical and public health settings, certainly as an additional tool after screening with real time (RT-)PCR is negative.

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Mutations associated with severity of the pandemic influenza A(H1N1)pdm09 in humans: a systematic review and meta-analysis of epidemiological evidence - Arch Virol. 2014

Abstract

Mutations in the haemagglutinin (HA), non-structural protein 1 (NS1) and polymerase basic protein 2 (PB2) of influenza viruses have been associated with virulence. This study investigated the association between mutations in these genes in influenza A(H1N1)pdm09 virus and the risk of severe or fatal disease. Searches were conducted on the MEDLINE, EMBASE and Web of Science electronic databases and the reference lists of published studies. The PRISMA and STROBE guidelines were followed in assessing the quality of studies and writing-up. Eighteen (18) studies, from all continents, were included in the systematic review (recruiting patients 0 - 77 years old). The mutation D222G was associated with a significant increase in severe disease (pooled RD: 11 %, 95 % CI: 3.0 % - 18.0 %, p = 0.004) and the risk of fatality (RD: 23 %, 95 % CI: 14.0 %-31.0 %, p = < 0.0001). No association was observed between the mutations HA-D222N, D222E, PB2-E627K and NS1-T123V and severe/fatal disease. The results suggest that no virus quasispecies bearing virulence-conferring mutations in the HA, PB2 and NS1 predominated. However issues of sampling bias, and bias due to uncontrolled confounders such as comorbidities, and viral and bacterial coinfection, should be born in mind. Influenza A viruses should continue to be monitored for the occurrence of virulence-conferring mutations in HA, PB2 and NS1. There are suggestions that respiratory virus coinfections also affect virus virulence. Studies investigating the role of genetic mutations on disease outcome should make efforts to also investigate the role of respiratory virus coinfections.

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