Viruses and Bioinformatics from Virology.uvic.ca
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A DNA virus with the capsid of an RNA virus

A DNA virus with the capsid of an RNA virus | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A new virus has been discovered that appears to have sequences from both an RNA and a DNA virus.
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Ed Rybicki's comment, July 23, 2012 5:01 AM
Ken: this is a rescoop of a paper from April or earlier...?
Kenzibit's comment, July 23, 2012 5:14 AM
Yes Ed, but I initially thought you could rescoop interesting articles after some time to make sure those who missed it back then see's it this time. Actually my bad and will prevent that next time. Thanks for the alert.
Viruses and Bioinformatics from Virology.uvic.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: | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

get in touch if you want to help curate this topic

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Bemol Sido's comment, October 10, 2015 5:28 AM
Thanks. Nice.
Bwana Moses's comment, May 25, 6:13 AM
Great work. Keep it going.
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Structure of human astrovirus could lead to antiviral therapies, vaccines

Structure of human astrovirus could lead to antiviral therapies, vaccines | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Human astroviruses infect nearly everyone during childhood, causing diarrhea, vomiting, and fever.
Via Bwana Moses
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Donate | Bad Science Watch

Donate | Bad Science Watch | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Help combat homeopathy etc. Help set standards!  Your monthly gift: $5.00 $10.00 $25.00 $50.00 $75.00 $100.00 Show your support for our work by becoming a monthly donor! With a monthly donation via PayPal, 

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How Epstein-Barr Virus Hijacks B Cells To Cause Blood Cancer | The Scientist Magazine®

How Epstein-Barr Virus Hijacks B Cells To Cause Blood Cancer | The Scientist Magazine® | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Scientists describe a mechanism by which EBV controls the expression of two genes, leading B cells to replicate out of control and avoid apoptosis.

Via Gilbert C FAURE
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Gilbert C FAURE's curator insight, November 19, 2:45 AM
C. Wood et al., "MYC activation and BCL2L11 silencing by a tumour virus through the large-scale reconfiguration of enhancer-promoter hubs," Science, 354:857-61, 2016.
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Interferon lambda 4 expression is suppressed by the host during viral infection

Interferon lambda 4 expression is suppressed by the host during viral infection | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Interferon (IFN) lambdas are critical antiviral effectors in hepatic and mucosal infections. Although IFNλ1, IFNλ2, and IFNλ3 act antiviral, genetic association studies have shown that expression of the recently discovered IFNL4 is detrimental to hepatitis C virus (HCV) infection through a yet unknown mechanism. Intriguingly, human IFNL4 harbors a genetic variant that introduces a premature stop codon. We performed a molecular and biochemical characterization of IFNλ4 to determine its role and regulation of expression. We found that IFNλ4 exhibits similar antiviral activity to IFNλ3 without negatively affecting antiviral IFN activity or cell survival. We show that humans deploy several mechanisms to limit expression of functional IFNλ4 through noncoding splice variants and nonfunctional protein isoforms. Furthermore, protein-coding IFNL4 mRNA are not loaded onto polyribosomes and lack a strong polyadenylation signal, resulting in poor translation efficiency. This study provides mechanistic evidence that humans suppress IFNλ4 expression, suggesting that immune function is dependent on other IFNL family members.
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libFLASM: a software library for fixed-length approximate string matching

libFLASM: a software library for fixed-length approximate string matching | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Approximate string matching is the problem of finding all factors of a given text that are at a distance at most k from a given pattern. Fixed-length approximate string matching is the problem of finding all factors of a text of length n that are at a distance at most k from any factor of length ℓ of a pattern of length m. There exist bit-vector techniques to solve the fixed-length approximate string matching problem in time under the edit and Hamming distance models, where w is the size of the computer word; as such these techniques are independent of the distance threshold k or the alphabet size. Fixed-length approximate string matching is a generalisation of approximate string matching and, hence, has numerous direct applications in computational molecular biology and elsewhere. We present and make available libFLASM, a free open-source C++ software library for solving fixed-length approximate string matching under both the edit and the Hamming distance models. Moreover we describe how fixed-length approximate string matching is applied to solve real problems by incorporating libFLASM into established applications for multiple circular sequence alignment as well as single and structured motif extraction. Specifically, we describe how it can be used to improve the accuracy of multiple circular sequence alignment in terms of the inferred likelihood-based phylogenies; and we also describe how it is used to efficiently find motifs in molecular sequences representing regulatory or functional regions. The comparison of the performance of the library to other algorithms show how it is competitive, especially with increasing distance thresholds. Fixed-length approximate string matching is a generalisation of the classic approximate string matching problem. We present libFLASM, a free open-source C++ software library for solving fixed-length approximate string matching. The extensive experimental results presented here suggest that other applications could benefit from using libFLASM, and thus further maintenance and development of libFLASM is desirable.

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WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning

WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author Summary Identifying functionally equivalent proteins between species is a fundamental problem in comparative genetics. While orthology does not guarantee functional equivalence, the identification of orthologs—genes in different organisms that diverged by speciation—is often the first step in approaching this problem. Many methods are available for predicting orthologs. Recent approaches combine methods and filter candidate predictions by “voting”—assigning confidence to ortholog pairs based on the number of predictions by independent methods. Although voting is a heuristic, it maintains precision while increasing recall. Here we employ machine learning to optimize voting by learning which methods make better predictions and, in essence, giving those methods more votes. We present a new tool called WORMHOLE that predicts a strict subclass of orthologs called least diverged orthologs (LDOs) with a high level of functional specificity by learning features of orthology that are encoded in the patterns of predictions made by 17 constituent methods. We validate WORMHOLE using multiple measures of evolutionary divergence and functional relatedness, including community standards provided by the Quest for Orthologs consortium. WORMHOLE’s particular strength lies in predicting LDOs between distantly related species, where orthology is difficult to identify and is of critical importance for comparative biology.
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Can the year you were born affect your risk of getting serious flu?

Can the year you were born affect your risk of getting serious flu? | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The headline sounds like something your clueless relative would forward off social media, but it may be true: Birth year affects flu susceptibility.

Via Ian M Mackay, PhD
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MEvoLib v1.0: the first molecular evolution library for Python

MEvoLib v1.0: the first molecular evolution library for Python | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Molecular evolution studies involve many different hard computational problems solved, in most cases, with heuristic algorithms that provide a nearly optimal solution. Hence, diverse software tools exist for the different stages involved in a molecular evolution workflow. We present MEvoLib, the first molecular evolution library for Python, providing a framework to work with different tools and methods involved in the common tasks of molecular evolution workflows. In contrast with already existing bioinformatics libraries, MEvoLib is focused on the stages involved in molecular evolution studies, enclosing the set of tools with a common purpose in a single high-level interface with fast access to their frequent parameterizations. The gene clustering from partial or complete sequences has been improved with a new method that integrates accessible external information (e.g. GenBank’s features data). Moreover, MEvoLib adjusts the fetching process from NCBI databases to optimize the download bandwidth usage. In addition, it has been implemented using parallelization techniques to cope with even large-case scenarios. MEvoLib is the first library for Python designed to facilitate molecular evolution researches both for expert and novel users. Its unique interface for each common task comprises several tools with their most used parameterizations. It has also included a method to take advantage of biological knowledge to improve the gene partition of sequence datasets. Additionally, its implementation incorporates parallelization techniques to enhance computational costs when handling very large input datasets.
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CDC approves the two-dose HPV vaccine, instead of three

CDC approves the two-dose HPV vaccine, instead of three | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
In a move that could boost HPV vaccination rates, the U.S. Centers for Disease Control and Prevention on Wednesday said younger adolescents need only two doses of the vaccine, rather than three as previously recommended.
Via Ed Rybicki
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The Human Virome 

The Human Virome  | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Some of our resident viruses may be beneficial.

Via Ed Rybicki, Kenzibit
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Ed Rybicki's curator insight, November 1, 11:23 AM
EXCELLENT article.
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Repurposed Transcriptomic Data Reveal Small Viral RNA Produced by Influenza Virus during Infection in Mice. - PubMed - NCBI

PLoS One. 2016 Oct 27;11(10):e0165729. doi: 10.1371/journal.pone.0165729. eCollection 2016.
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Vaccinia Virus Uses Retromer-Independent Cellular Retrograde Transport Pathways To Facilitate the Wrapping of Intracellular Mature Virions during Virus Morphogenesis

Vaccinia Virus Uses Retromer-Independent Cellular Retrograde Transport Pathways To Facilitate the Wrapping of Intracellular Mature Virions during Virus Morphogenesis | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
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Dampened antiviral immunity to intravaginal exposure to RNA viral pathogens allows enhanced viral replication

Dampened antiviral immunity to intravaginal exposure to RNA viral pathogens allows enhanced viral replication | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Understanding the host immune response to vaginal exposure to RNA viruses is required to combat sexual transmission of this class of pathogens. In this study, using lymphocytic choriomeningitis virus (LCMV) and Zika virus (ZIKV) in wild-type mice, we show that these viruses replicate in the vaginal mucosa with minimal induction of antiviral interferon and inflammatory response, causing dampened innate-mediated control of viral replication and a failure to mature local antigen-presenting cells (APCs). Enhancement of innate-mediated inflammation in the vaginal mucosa rescues this phenotype and completely inhibits ZIKV replication. To gain a better understanding of how this dampened innate immune activation in the lower female reproductive tract may also affect adaptive immunity, we modeled CD8 T cell responses using vaginal LCMV infection. We show that the lack of APC maturation in the vaginal mucosa leads to a delay in CD8 T cell activation in the draining lymph node and hinders the timely appearance of effector CD8 T cells in vaginal mucosa, thus further delaying viral control in this tissue. Our study demonstrates that vaginal tissue is exceptionally vulnerable to infection by RNA viruses and provides a conceptual framework for the male to female sexual transmission observed during ZIKV infection.
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The Strange Lifestyle of Multipartite Viruses

The Strange Lifestyle of Multipartite Viruses | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Multipartite viruses have one of the most puzzling genetic organizations found in living organisms.
Via Bwana Moses
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‘Antisense’ compounds offer new weapon against influenza A 

‘Antisense’ compounds offer new weapon against influenza A  | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Challenging a long-held convention, University researchers have shown they can inhibit the influenza A virus by targeting its genomic RNA with “antisense” compounds.


Via Integrated DNA Technologies
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In a mouse model of infection, vaccine-induced CD4 T cells have adverse effect

In a mouse model of infection, vaccine-induced CD4 T cells have adverse effect | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A study led by investigators at Beth Israel Deaconess Medical Center (BIDMC) has found that a vaccine that elicits only CD4 T cells against a mouse model of a chronic viral infection results in an overwhelming -- and lethal -- inflammatory response.
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Structure of Aichi Virus 1 and Its Empty Particle: Clues to Kobuvirus Genome Release Mechanism

IMPORTANCE Aichi virus 1 (AiV-1) is a human pathogen that can cause diarrhea, abdominal pain, nausea, vomiting, and fever. AiV-1 is identified in environmental screening studies with higher frequency and greater abundance than other human enteric viruses. Accordingly, 80 to 95% of adults worldwide have suffered from AiV-1 infections. We determined the structure of the AiV-1 virion. Based on the structure, we show that antiviral compounds that were developed against related enteroviruses are unlikely to be effective against AiV-1. The surface of the AiV-1 virion has a unique topology distinct from other related viruses from the Picornaviridae family. We also determined that AiV-1 capsids form compact shells even after genome release. Therefore, AiV-1 genome release requires large localized and probably reversible reorganization of the capsid.

Ed Rybicki's insight:
Smart little nanomachines, viruses!
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A novel type of cosavirus from children with nonpolio acute flaccid paralysis

Human cosavirus (HCoSV) is a genus recently identified in the family Picornaviridae, which contains important pathogens to human health. Here, a novel type of HCoSV strain, cosavirus-zj-1 (GenBank no. KX545380), was identified in the fecal sample of a child with nonpolio acute flaccid paralysis (AFP) in China. Phylogenetic and sequence analyses suggested that this virus strain belonged to a new genotype in HCoSV B species. Our data show that surveillance of HCoSV is necessary for detecting viral agents in children with AFP, despite being the low detection rate.

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Marek’s disease herpesvirus vaccines integrate into chicken host chromosomes 

Marek’s disease (MD) is a lymphotropic and oncogenic disease of chickens that can lead to death in susceptible and unvaccinated host birds. The causative pathogen, MD virus (MDV), a highly oncogenic alphaherpesvirus, integrates into host genome near the telomeres. MD occurrence is controlled across the globe by biosecurity, selective breeding for enhanced MD genetic resistance, and widespread vaccination of flocks using attenuated serotype 1 MDV or other serotypes. Despite over 40 years of usage, the specific mechanism(s) of MD vaccine-related immunity and anti-tumor effects are not known. Here we investigated the cytogenetic interactions of commonly used MD vaccine strains of all three serotypes (HVT, SB-1, and Rispens) with the host to determine if all were equally capable of host genome integration. We also studied the dynamic profiles of chromosomal association and integration of the three vaccine strains, a first for MD vaccine research. Our cytogenetic data provide evidence that all three MD vaccine strains tested integrate in the chicken host genome as early as 1 day after vaccination similar to oncogenic strains. However, a specific, transformation-associated virus-host phenotype observed for oncogenic viruses is not established. Our results collectively provide an updated model of MD vaccine-host genome interaction and an improved understanding of the possible mechanisms of vaccinal immunity. Physical integration of the oncogenic MDV genome into host chromosomes along with cessation of viral replication appears to have joint signification in MDV’s ability to induce oncogenic transformation. Whereas for MD vaccine serotypes, a sustained viral replication stage and lack of the chromosome-integrated only stage were shared traits during early infection.

Ed Rybicki's insight:
...but don't cause cancers, apparently? Bit sinister for OTHER herpesvirus vaccines though?!
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Has a new mutation in the Ebola virus made it deadlier?

Has a new mutation in the Ebola virus made it deadlier? | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
But the researchers were analyzing viral sequences to address different questions—such as the viral mutation rate—or only looked at samples isolated in the early days of the outbreak. “You have to do wet experiments sometimes,” Luban says. “All of the algorithm crunching suggested Ebola is Ebola is Ebola. These two experiments say it doesn’t matter what the computers say. The virus is more infectious.”

Via Ian M Mackay, PhD
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Collaboration Is Beautiful | Bioinformatics meets graphic design

Collaboration Is Beautiful | Bioinformatics meets graphic design | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
EMBL-EBI bioinformatics collaborate with the London-based design company Science Practice to discover new scientific perspectives
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How to knock out herpesvirus RNA transport — with applications from cold sores to cancer

How to knock out herpesvirus RNA transport — with applications from cold sores to cancer | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A new approach has been developed to combat diseases caused by herpesvirus infections, including everything from cold sores to cancer.

 

Researchers at the University of Leeds have discovered a way to prevent herpesviruses hijacking important pathways in cells which are required for the virus to replicate and cause disease.

Professor Adrian Whitehouse from the School of Molecular Biology and Astbury Centre for Structural Molecular Biology at the University led the five year study, the results of which are published today in the journal Nature Microbiology.

 

Prof Whitehouse said: "We've spent several years demonstrating that a protein found in all herpesviruses, recruits a protein complex in the host cell, called human TREX, to help stabilise and transport herpesvirus RNAs out of a cell's nucleus so they are turned into viral proteins. "Now we have identified a compound which can disrupt this essential virus-host cell interaction which in turn prevents herpesviruses replicating and producing infectious particles."

 

The approach the researchers used was unique as it targeted the enzyme activity of a key component of the cellular human TREX complex, known as UAP56.  Inhibiting t his activity prevented the remodelling of the human TREX complex which stopped the interaction with the viral protein.

 

The project is a collaboration between virologists led by Professor Whitehouse and a team of chemists led by Dr Richard Foster also from the University of Leeds. Dr Foster's team performed a virtual screen of thousands of compounds to identify potential inhibitors. These were then tested for their ability to stop herpesvirus replication without damaging the host cell.


Via Dr. Stefan Gruenwald
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Emily's comment, November 21, 12:57 AM
Look great
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A Single Amino Acid Dictates Protein Kinase R Susceptibility to Unrelated Viral Antagonists. - PubMed - NCBI

Abstract During millions of years of coevolution with their hosts, cytomegaloviruses (CMVs) have succeeded in adapting to overcome host-specific immune defenses, including the protein kinase R (PKR) pathway. Consequently, these adaptations may also contribute to the inability of CMVs to cross species barriers.

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Nanoparticle vaccines against dengue fever?

Nanoparticle vaccines against dengue fever? | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Every year more than 350 million people in over 120 countries contact dengue fever, which can cause symptoms ranging from aching muscles and a skin rash to life-threatening haemorrhagic fever. Researchers have struggled to create effective vaccines against dengue virus, in part because four distinct serotypes of the virus cause dengue fever and a vaccine…
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