Viruses and Bioinformatics from Virology.uvic.ca
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Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History

"The history of click-speaking Khoe-San, and African populations in general, remains poorly understood. We genotyped ∼2.3 million SNPs in 220 southern Africans and found that the Khoe-San diverged from other populations ≥100,000 years ago, but structure within the Khoe-San dated back to about 35,000 years ago. Genetic variation in various sub-Saharan populations did not localize the origin of modern humans to a single geographic region within Africa; instead, it indicated a history of admixture and stratification. We found evidence of adaptation targeting muscle function and immune response, potential adaptive introgression of UV-light protection, and selection predating modern human diversification involving skeletal and neurological development. These new findings illustrate the importance of African genomic diversity in understanding human evolutionary history."

 

Ex Africa, semper aliquid novi...or old, in this case!

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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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Bwana Moses's comment, May 25, 2016 6:13 AM
Great work. Keep it going.
Bwana Moses's comment, March 7, 12:46 PM
Thank You.
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Sustained fecal-oral human-to-human transmission following a zoonotic event

Sustained fecal-oral human-to-human transmission following a zoonotic event | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Bacterial, viral and parasitic zoonotic pathogens that transmit via the fecal-oral route have a major impact on global health. However, the mechanisms underlying the emergence of such pathogens from the animal reservoir and their persistence in the human population are poorly understood. Here, we present a framework of human-to-human transmission of zoonotic pathogens that considers the factors relevant for fecal-oral human-to-human transmission route at the levels of host, pathogen, and environment. We discuss current data gaps and propose future research directions.


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Co-circulation of multiple genotypes of African swine fever viruses among domestic pigs in Zambia (2013-2015). - PubMed - NCBI

Co-circulation of multiple genotypes of African swine fever viruses among domestic pigs in Zambia (2013-2015). - PubMed - NCBI | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Transbound Emerg Dis. 2017 Mar 15. doi: 10.1111/tbed.12635. [Epub ahead of print]
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GMO - Common Science Space

GMO - Common Science Space | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
It’s a good idea to look critically at any powerful new technology, and the creation of genetically-modified organisms, GMOs, is no exception. Like any new technology, it might have unanticipated, deleterious consequences that outweigh any benefit. Many criticisms of GMO have of course been raised, as a brief interrogation of the internet will show. But unfortunately,... Continue Reading
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PISCES – alignment free RNA-seq quantiation and QC pipeline | RNA-Seq Blog

Matt Shirley -- PISCES: alignment free RNA-seq quantiation and QC pipeline
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Intraspecies transmission of viruses: Human-to-human transmission

Infection of humans by viruses from animal hosts — so-called zoonoses — occur relatively frequently around the world. Examples over the last few decades include human infections caused by avian influenza A viruses of hemagglutinin subtypes H5, H6, H7, H9, and H10, swine influenza A viruses of subtypes H1 and H3, Hendra virus and Nipah virus, Severe Acute Respiratory Syndrome (SARS)-coronavirus and Middle East Respiratory Syndrome (MERS)-coronavirus, West-Nile virus, and Ebola virus. Fortunately, most zoonotic infections occur as isolated cases or small clusters, posing little risk to the public at large. However, some zoonotic infections may trigger local or regional outbreaks, spread to humans in various parts of the world, or even result in widespread global outbreaks known as pandemics.


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How to think like a data scientist to become one

How to think like a data scientist to become one | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
We have all read the punchlines – data scientist is the sexiest job, there’s not enough of them and the salaries are very high. The role has been sold so well…
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Cross-species jumps may play unexpectedly big role in virus evolution: Comparing host and virus evolutionary trees reveals new insights into emergence of viral diseases

Cross-species jumps may play unexpectedly big role in virus evolution: Comparing host and virus evolutionary trees reveals new insights into emergence of viral diseases | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
On occasion, a virus may jump from one host species to another and adapt to the new host. Such cross-species transmission happens more often than expected, according to new research, and it may play a much bigger role in virus evolution than previously thought.

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All biology is computational biology

All biology is computational biology | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Here, I argue that computational thinking and techniques are so central to the quest of understanding life that today all biology is computational biology. Computational biology brings order into our understanding of life, it makes biological concepts rigorous and testable, and it provides a reference map that holds together individual insights. The next modern synthesis in biology will be driven by mathematical, statistical, and computational methods being absorbed into mainstream biological training, turning biology into a quantitative science.
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A Splash of River Water Now Reveals the DNA of All Its Creatures

A Splash of River Water Now Reveals the DNA of All Its Creatures | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Quick and inexpensive DNA sampling of a river, stream, or lake can now divulge what fish or other animals live there. This rapidly growing environmental DNA, or eDNA, technology is proving to be a game-changing conservation tool.
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Automated Glycan Assembly of Branched β-(1,3)-Glucans to Identify Antibody Epitopes - Chemical Communications (RSC Publishing)

Automated Glycan Assembly of Branched β-(1,3)-Glucans to Identify Antibody Epitopes - Chemical Communications (RSC Publishing) | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
β-(1,3)-Glucans exhibit immunomodulatory and anti-tumor effects. Since the isolation of pure β-(1,3)-glucan oligosaccharides from natural sources is complicated, especially when certain branching patterns are desired, chemical synthesis is frequently the only means of accessing these molecules. We report the
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There is no controversy - HPV vaccines are saving lives around the world

There is no controversy - HPV vaccines are saving lives around the world | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
HPV vaccine is now used in 84 countries, including the USA, Canada, Australia and most of Western Europe.

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Antigenic and immunosuppressive properties of a trimeric recombinant transmembrane envelope protein gp41 of HIV-1.

Antigenic and immunosuppressive properties of a trimeric recombinant transmembrane envelope protein gp41 of HIV-1. | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The transmembrane envelope (TM) protein gp41 of the human immunodeficiency virus-1 (HIV-1) plays an important role during virus infection inducing the fusio
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Mimivirus: leading the way in the discovery of giant viruses of amoebae : Nature Reviews Microbiology : Nature Research

Mimivirus: leading the way in the discovery of giant viruses of amoebae : Nature Reviews Microbiology : Nature Research | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The accidental discovery of the giant virus of amoeba — Acanthamoeba polyphaga mimivirus (APMV; more commonly known as mimivirus) — in 2003 changed the field of virology. Viruses were previously defined by their submicroscopic size, which probably prevented the search for giant viruses, which are visible by light microscopy. Extended studies of giant viruses of amoebae revealed that they have genetic, proteomic and structural complexities that were not thought to exist among viruses and that are comparable to those of bacteria, archaea and small eukaryotes. The giant virus particles contain mRNA and more than 100 proteins, they have gene repertoires that are broader than those of other viruses and, notably, some encode translation components. The infection cycles of giant viruses of amoebae involve virus entry by amoebal phagocytosis and replication in viral factories. In addition, mimiviruses are infected by virophages, defend against them through the mimivirus virophage resistance element (MIMIVIRE) system and have a unique mobilome. Overall, giant viruses of amoebae, including mimiviruses, marseilleviruses, pandoraviruses, pithoviruses, faustoviruses and molliviruses, challenge the definition and classification of viruses, and have increasingly been detected in humans.


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The blood DNA virome in 8,000 humans

The blood DNA virome in 8,000 humans | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Novel sequencing technologies offer insight into the virome in human samples. Here, we identify the viral DNA sequences in blood of over 8,000 individuals undergoing whole genome sequencing. This approach serves to identify 94 viruses; however, many are shown to reflect widespread DNA contamination of commercial reagents or of environmental origin. While this represents a significant limitation to reliably identify novel viruses infecting humans, we could confidently detect sequences and quantify abundance of 19 human viruses in 42% of individuals. Ancestry, sex, and age were important determinants of viral prevalence. This large study calls attention on the challenge of interpreting next generation sequencing data for the identification of novel viruses. However, it serves to categorize the abundance of human DNA viruses using an unbiased technique.
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Discovery of an HIV reservoir marker: A new avenue toward eliminating the virus

Discovery of an HIV reservoir marker: A new avenue toward eliminating the virus | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
French researchers have identified a marker that makes it possible to differentiate 'dormant' HIV-infected cells from healthy cells.
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Interleukin-18 Reduces Blood Glucose and Modulates Plasma Co... : Shock

Background: Dysregulation of glucose metabolism, including hyperglycemia with insulin resistance, is
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Study identifies rare strains of HIV, HTLV and HBV

Study identifies rare strains of HIV, HTLV and HBV | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Virology Highlights features highlighted articles published in Virology, with posts summarizing the research in the authors’ words.

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Ed Rybicki's curator insight, March 15, 11:09 AM
Valuable stuff: we need to do more of this in more of Africa.
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Protect this house: cytosolic sensing of viruses

Protect this house: cytosolic sensing of viruses | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The ability to recognize invading viral pathogens and to distinguish their components from those of the host cell is critical to initiate the innate immune response. The efficiency of this detection is an important factor in determining the susceptibility of the cell to viral infection. Innate sensing of viruses is, therefore, an indispensable step in the line of defense for cells and organisms. Recent discoveries have uncovered novel sensors of viral components and hallmarks of infection, as well as mechanisms by which cells discriminate between self and non-self. This review highlights the mechanisms used by cells to detect viral pathogens in the cytosol, and recent advances in the field of cytosolic sensing of viruses.


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Human Rhinovirus Diversity and Evolution: How Strange the Change from Major to Minor

Rhinoviruses are the most common causes of the common cold. Their many distinct lineages fall into “major” and “minor” groups that use different cell surface receptors to enter host cells. Minor-group rhinoviruses are more immunogenic in laboratory studies, although their patterns of transmission and their cold symptoms are broadly similar to those of the major group. Here we present evolutionary evidence that minor-group viruses are also more immunogenic in humans. A key finding is that rates of amino acid substitutions at exposed sites in the capsid proteins VP2, VP3, and VP1 tend to be elevated in minor-group relative to major-group viruses, while rates at buried sites show no consistent differences. A reanalysis of historical virus watch data also indicates a higher immunogenicity of minor-group viruses, consistent with our findings about evolutionary rates at amino acid positions most directly exposed to immune surveillance. The increased immunogenicity and speed of evolution in minor-group lineages may contribute to the very large numbers of rhinovirus serotypes that coexist while differing in virulence.
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Cross-species jumps may play unexpectedly big role in virus evolution: Comparing host and virus evolutionary trees reveals new insights into emergence of viral diseases

Cross-species jumps may play unexpectedly big role in virus evolution: Comparing host and virus evolutionary trees reveals new insights into emergence of viral diseases | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
On occasion, a virus may jump from one host species to another and adapt to the new host. Such cross-species transmission happens more often than expected, according to new research, and it may play a much bigger role in virus evolution than previously thought.
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Why CRISPR, other academia-produced technologies, should belong to everyone | Genetic Literacy Project

Why CRISPR, other academia-produced technologies, should belong to everyone | Genetic Literacy Project | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Why does anybody own CRISPR?  intellectual property in academia is a drain on the system. It’s a model that was ushered in decades ago with an aim to encou
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A Visual Language for Protein Design - ACS Synthetic Biology (ACS Publications)

A Visual Language for Protein Design - ACS Synthetic Biology (ACS Publications) | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
As protein engineering becomes more sophisticated, practitioners increasingly need to share diagrams for communicating protein designs. To this end, we present a draft visual language, Protein Language, that describes the high-level architecture of an engineered protein with easy-to-draw glyphs, intended to be compatible with other biological diagram languages such as SBOL Visual and SBGN. Protein Language consists of glyphs for representing important features (e.g., globular domains, recognition and localization sequences, sites of covalent modification, cleavage and catalysis), rules for composing these glyphs to represent complex architectures, and rules constraining the scaling and styling of diagrams. To support Protein Language we have implemented an extensible web-based software diagram tool, Protein Designer, that uses Protein Language in a “drag and drop” interface for visualization and computer-aided-design of engineered proteins, as well as conversion of annotated protein sequences to Protein Language diagrams and figure export. Protein Designer can be accessed at http://biocad.ncl.ac.uk/protein-designer/.
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Washington mumps outbreak continues to grow

Washington mumps outbreak continues to grow | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
On Thursday, Washington state reported 404 confirmed and probable cases of mumps since October.

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Ireland: Severe toll on elderly as flu death tally hits 75

Ireland: Severe toll on elderly as flu death tally hits 75 | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Severe toll on elderly as flu death tally hits 75 Eilish O'Regan February 24 2017 2:30 AM Flu has claimed the lives of 75 people so far this season and has taken

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