Virology and Bioinformatics from Virology.ca
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Viruses buoy life at hydrothermal vents | Science News

Viruses buoy life at hydrothermal vents | Science News | Virology and Bioinformatics from Virology.ca | Scoop.it
Using hijacked genes, deep-sea viruses help sulfur-eating bacteria generate power in the plumes of hydrothermal vents.
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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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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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The Evolutionary Histories of Antiretroviral Proteins SERINC3 and SERINC5 Do Not Support an Evolutionary Arms Race in Primates

Importance Restriction factors are host proteins that block viral infection and replication. Many viruses, like HIV-1 and related retroviruses, evolved accessory proteins to counteract these restriction factors. The importance of these interactions is evidenced by the intense adaptive selection pressures that dominates the evolutionary histories of both the host and viral genes involved in this so-called arms race. The dynamics of these arms races can point to mechanisms by which these viral infections can be prevented. Two human genes were recently identified as targets of an HIV-1 accessory protein important for viral infectivity: SERINC3 and SERINC5. Unexpectedly, we found that these SERINC genes, unlike other host restriction factors, show no evidence of a recent evolutionary arms race with viral pathogens.
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Daily tip twitter accounts

Daily tip twitter accounts | Virology and Bioinformatics from Virology.ca | Scoop.it
List of Twitter accounts that give daily tips in various areas of math, science, and software development
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Most Popular Coding Languages of 2016

Most Popular Coding Languages of 2016 | Virology and Bioinformatics from Virology.ca | Scoop.it

Every year, we publish data on the "Most Popular Coding Languages" based on
hundreds of thousands of data points we've collected by processing over
1,200,000+ challenge submissions in (now) 26 different programming
languages. This gives us a pretty valuable insight on what the trends are
in hiring demand amongst tech companies for the upcoming year. It's data we
hope will be especially helpful for new computer science graduates or
coders looking to stay ahead of the curve. (CodeEval is now being used as a
classroom tool in a number of schools, from university programs to boot
camps.)

OK. On to the results.

For the fifth year in a row, Python retains it's #1 dominance followed by
Java, C++, and Javascript.

This year's most noticeable changes were a 27% increase in C# submissions,
a 15% surge in Java, as well as a 21% increase in C submissions. While
still reigning champ we saw a 14% drop in Python submissions as well as a
17% decline in Ruby usage. 

 


Via Pablo Vicente Munuera
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Multiplexed Sequencing for Novel Viral Pathogens | Insight & Intelligence™ | GEN

Multiplexed Sequencing for Novel Viral Pathogens | Insight & Intelligence™ | GEN | Virology and Bioinformatics from Virology.ca | Scoop.it
As frequent travelers go, viruses are among the least welcome arrivals. They easily elude TSA agents, but they will have a harder time getting past the newer microarray platforms.
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Tight spaces cause spreading cancer cells to divide improperly

Tight spaces cause spreading cancer cells to divide improperly | Virology and Bioinformatics from Virology.ca | Scoop.it
Researchers are using rolled-up transparent nanomembranes to mimic tiny blood vessels and study how cancer cells divide in these tight spaces.
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Reverse Transcriptase with Proofreading Capabilities Created | The Scientist Magazine®

Reverse Transcriptase with Proofreading Capabilities Created | The Scientist Magazine® | Virology and Bioinformatics from Virology.ca | Scoop.it
Using directed evolution, researchers selected a DNA polymerase to copy RNA into DNA.
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Computational clustering for viral reference proteomes

Motivation: The enormous number of redundant sequenced genomes has hindered efforts to analyze and functionally annotate proteins. As the taxonomy of viruses is not uniformly defined, viral proteomes pose special challenges in this regard. Grouping viruses based on the similarity of their proteins at proteome scale can normalize against potential taxonomic nomenclature anomalies.

Results: We present Viral Reference Proteomes (Viral RPs), which are computed from complete virus proteomes within UniProtKB. Viral RPs based on 95, 75, 55, 35 and 15% co-membership in proteome similarity based clusters are provided. Comparison of our computational Viral RPs with UniProt’s curator-selected Reference Proteomes indicates that the two sets are consistent and complementary. Furthermore, each Viral RP represents a cluster of virus proteomes that was consistent with virus or host taxonomy. We provide BLASTP search and FTP download of Viral RP protein sequences, and a browser to facilitate the visualization of Viral RPs.

Availability and implementation: http://proteininformationresource.org/rps/viruses/
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Contagious cancers more common in nature than thought, can spread between species

Contagious cancers more common in nature than thought, can spread between species | Virology and Bioinformatics from Virology.ca | Scoop.it
Contagious cancers are a scary idea to begin with, but scientists have made some startling new discoveries about them – they are likely more common in nature than originally thought, and some can even spread between species.
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Nextstrain: Real-time tracking of Zika virus evolution

"Nextstrain allows to view real-time tracking of Zika virus evolution and segment it according to sample time and location"
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Virus Hacks Host Genome, Steals CRISPR to Protect Itself

Virus Hacks Host Genome, Steals CRISPR to Protect Itself | Virology and Bioinformatics from Virology.ca | Scoop.it
Viruses have often been described as the ultimate parasite, shedding all of their nonessential parts and leaving behind an extremely efficient genetic transfer apparatus. Phage viruses have evolved to infect various bacteria proficiently and hijack their replication machinery to make more viruses. Yet, this often doesn’t preclude a different virus from concomitantly infecting the same bacterium and competing with or overtaking the original phage invader.


Via Ed Rybicki, Kenzibit
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Ed Rybicki's curator insight, June 17, 6:24 AM
HATE the word "hack" in the context of infection: so lazy!
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Vineyard virus denialism compromises proactive estates’ efforts

Vineyard virus denialism compromises proactive estates’ efforts | Virology and Bioinformatics from Virology.ca | Scoop.it
THE problem of vineyard virus has been a recurring theme among serious wine writers in SA — one that the critics and commentators have taken more seriously than many of the players more directly affected by the problem. This is partly because growers would like to wish it away, and probably believe that if they hear no evil and speak no evil, there will be no evil.

Those who care about wine quality refuse to be silent about it because the fruit from virus-infected vines is palpably impaired.

The virus most prevalent in SA is leaf-roll. Once it has infected a vine, it is there for life. If it is not in the original plant material; it is spread by mealy bugs or by pruning secateurs. Once it is in a vineyard, if it is not isolated and the plant removed, everything will finally be infected. Clearly, doing nothing about it is not a great strategy: it is a bit like ignoring your HIV and hoping it will not become AIDS.

Ed Rybicki's insight:
Now for a SERIOUS virus....
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Nobel Laureates Condemn GMO Opposition, Urge Governments to Support “Genetic Modification”

Nobel Laureates Condemn GMO Opposition, Urge Governments to Support “Genetic Modification” | Virology and Bioinformatics from Virology.ca | Scoop.it
Today, 107 Nobel Laureates have come together to call upon governments around the world to support and advance “genetic modification” technologies in agriculture and reject the fear-based campaigns opposing genetically modified organisms (GMOs) that are built upon falsehoods and denial. The Laureates released  a strongly worded statement addressed “To the Leaders of Greenpeace, the United Nations and Governments around the world.” In their words, “We urge Greenpeace and its supporters to re-examine the experience of farmers and consumers worldwide with crops and foods improved through biotechnology, recognize the findings of authoritative scientific bodies and regulatory agencies, and abandon their campaign…
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The Feat of Packaging Eight Unique Genome Segments

The Feat of Packaging Eight Unique Genome Segments | Virology and Bioinformatics from Virology.ca | Scoop.it
Influenza A viruses harbor a segmented RNA genome that is organized into eight distinct viral ribonucleoprotein (vRNP) complexes. Although a segmented genome may be a major advantage to adapt to new host environments, it comes at the cost of a highly sophisticated genome packaging mechanism. Newly synthesized vRNPs conquer the cellular endosomal recycling machinery to…
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Butter doesn't increase risk of heart disease after all

Butter doesn't increase risk of heart disease after all | Virology and Bioinformatics from Virology.ca | Scoop.it
Butter has been welcomed back into Americans’ diets, and a new study finds that it isn't as bad for our arteries as once believed.
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Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody

Author Summary IAV causes seasonal epidemics and periodic pandemics that result in significant morbidity and mortality worldwide. The effectiveness of influenza vaccines is highly variable because the virus evolves rapidly and causes antibody mismatch. The use of neuraminidase inhibitors, the current standard of treatment for IAV infection, is limited by their lack of efficacy beyond 48 hours of symptom onset and by the emergence of drug resistant viruses. Recently, broadly neutralizing antibodies targeting the conserved stalk region of IAV HA have been discovered. These antibodies are able to block the infection of many or even all IAV strains, and hold great promise as the next generation of anti-flu treatment. Nonetheless, virus resistance to these antibodies has not been thoroughly studied despite the common view that broadly neutralizing stalk-binding antibodies are less permissive for mutational escape due to the functional importance of their highly conserved epitopes. In this study, we isolated three resistant viruses to a stalk-binding antibody that was previously shown to neutralize all IAV tested. Interestingly, they use two distinct mechanisms to escape the antibody, abolishing antibody binding or enhancing membrane fusion. Our study emphasizes the need to consider novel escape mechanisms when studying virus resistance to broadly neutralizing stalk-binding antibodies.
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Origins of the 2009 H1N1 influenza pandemic in swine in Mexico

Origins of the 2009 H1N1 influenza pandemic in swine in Mexico | Asia is considered an important source of influenza A virus (IAV) pandemics, owing to large, diverse viral reservoirs in poultry and swine. However, the zoonotic origins of the 2009 A/H1N1 influenza pandemic virus (pdmH1N1) remain unclear, due to conflicting evidence from swine and humans. There is strong evidence that the first human outbreak of pdmH1N1 occurred in Mexico in early 2009. However, no related swine viruses have been detected in Mexico or any part of the Americas, and to date the most closely related ancestor viruses were identified in Asian swine. Here, we use 58 new whole-genome sequences from IAVs collected in Mexican swine to establish that the swine virus responsible for the 2009 pandemic evolved in central Mexico. This finding highlights how the 2009 pandemic arose from a region not considered a pandemic risk, owing to an expansion of IAV diversity in swine resulting from long-distance live swine trade.
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UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB

Results: We propose a method for the automatic annotation of protein sequences in the UniProt Knowledgebase (UniProtKB) by comparing their domain architectures, classifying proteins based on the similarities and propagating functional annotation. The performance of this method was measured through a cross-validation analysis using the Gene Ontology (GO) annotation of a sub-set of UniProtKB/Swiss-Prot. The results demonstrate the effectiveness of this approach in detecting functional similarity with an average F-score: 0.85. We applied the method on nearly 55.3 million uncharacterized proteins in UniProtKB/TrEMBL resulted in 44 818 178 GO term predictions for 12 172 114 proteins. 22% of these predictions were for 2 812 016 previously non-annotated protein entries indicating the significance of the value added by this approach.

Availability and implementation: The results of the method are available at: ftp://ftp.ebi.ac.uk/pub/contrib/martin/DAAC/.

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ORFanFinder: automated identification of taxonomically restricted orphan genes

Motivation: Orphan genes, also known as ORFans, are newly evolved genes in a genome that enable the organism to adapt to specific living environment. The gene content of every sequenced genome can be classified into different age groups, based on how widely/narrowly a gene’s homologs are distributed in the context of species taxonomy. Those having homologs restricted to organisms of particular taxonomic ranks are classified as taxonomically restricted ORFans.

Results: Implementing this idea, we have developed an open source program named ORFanFinder and a free web server to allow automated classification of a genome’s gene content and identification of ORFans at different taxonomic ranks. ORFanFinder and its web server will contribute to the comparative genomics field by facilitating the study of the origin of new genes and the emergence of lineage-specific traits in both prokaryotes and eukaryotes.

Availability and implementation: http://cys.bios.niu.edu/orfanfinder

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GenVisR: Genomic Visualizations in R

Summary: Visualizing and summarizing data from genomic studies continues to be a challenge. Here, we introduce the GenVisR package to addresses this challenge by providing highly customizable, publication-quality graphics focused on cohort level genome analyses. GenVisR provides a rapid and easy-to-use suite of genomic visualization tools, while maintaining a high degree of flexibility by leveraging the abilities of ggplot2 and Bioconductor.

Availability and Implementation: GenVisR is an R package available via Bioconductor (https://bioconductor.org/packages/GenVisR) under GPLv3. Support is available via GitHub (https://github.com/griffithlab/GenVisR/issues) and the Bioconductor support website.
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Identification of Zika Virus and Dengue Virus Dependency Factors using Functional Genomics: Cell Reports

Identification of Zika Virus and Dengue Virus Dependency Factors using Functional Genomics: Cell Reports | Virology and Bioinformatics from Virology.ca | Scoop.it
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Assemblytics: a web analytics tool for the detection of variants from an assembly. - PubMed - NCBI

Assemblytics is a web app for detecting and analyzing variants from a de novo genome assembly aligned to a reference genome. It incorporates a unique anchor filtering approach to increase robustness to repetitive elements, and identifies six classes of variants based on their distinct alignment signatures. Assemblytics can be applied both to comparing aberrant genomes, such as human cancers, to a reference, or to identify differences between related species. Multiple interactive visualizations enable in-depth explorations of the genomic distributions of variants.
AVAILABILITY AND IMPLEMENTATION:
http://assemblytics.com, https://github.com/marianattestad/assemblytics ;

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Sandia researchers discover mechanism for Rift Valley fever virus infection - Scienmag

Sandia researchers discover mechanism for Rift Valley fever virus infection - Scienmag | Virology and Bioinformatics from Virology.ca | Scoop.it
LIVERMORE, Calif. -- Viruses can't live without us -- literally. As obligate parasites, viruses need a host cell to survive and grow. Scientists are exploiting this characteristic by developing t..
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fqtools: an efficient software suite for modern FASTQ file manipulation

Many Next Generation Sequencing analyses involve the basic manipulation of input sequence data before downstream processing (e.g. searching for specific sequences, format conversion or basic file statistics). The rapidly increasing data volumes involved in NGS make any dataset manipulation a time-consuming and error-prone process. I have developed fqtools; a fast and reliable FASTQ file manipulation suite that can process the full set of valid FASTQ files, including those with multi-line sequences, whilst identifying invalid files. Fqtools is faster than similar tools, and is designed for use in automatic processing pipelines.

Availability and implementation: fqtools is open source and is available at: https://github.com/alastair-droop/fqtools.
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