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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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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New database of DNA viruses and retroviruses debuts

New database of DNA viruses and retroviruses debuts | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
There are more microbes in, on, and around the planet than there are stars in the Milky Way. Microbes affect food production; air quality; natural breakdown of plants, trees and biomass; soil quality for agriculture; and much more. To work with these microbes, scientists need to learn more about how microbes and viruses interact. Viruses influence microbes' abilities to work. Scientists at the U.S. Department of Energy (DOE) Joint Genome Institute built the largest publicly available database fo
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Academic Writing (#AcWri) – Raul Pacheco-Vega, PhD

This page is dedicated to suggestions I provide to improve scholars, professors and students’ writing. These tips have worked for me, and I hope they will work for you! My Top 10 Tips to Improve Your Academic Writing
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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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Genome Mining of Natural Products Could Lead to Novel Therapeutics | GEN Genetic Engineering & Biotechnology News - Biotech from Bench to Business | GEN

Genome Mining of Natural Products Could Lead to Novel Therapeutics | GEN Genetic Engineering & Biotechnology News - Biotech from Bench to Business | GEN | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
RODEO program identifies gene clusters that indicate an organism's ability to synthesize therapeutically promising molecules
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KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies

KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Motivation: De novo assembly of whole genome shotgun (WGS) next-generation sequencing (NGS) data benefits from high-quality input with high coverage. However, in practice, determining the quality and quantity of useful reads quickly and in a reference-free manner is not trivial. Gaining a better understanding of the WGS data, and how that data is utilized by assemblers, provides useful insights that can inform the assembly process and result in better assemblies.
Results: We present the K-mer Analysis Toolkit (KAT): a multi-purpose software toolkit for reference-free quality control (QC) of WGS reads and de novo genome assemblies, primarily via their k-mer frequencies and GC composition. KAT enables users to assess levels of errors, bias and contamination at various stages of the assembly process. In this paper we highlight KAT’s ability to provide valuable insights into assembly composition and quality of genome assemblies through pairwise comparison of k-mers present in both input reads and the assemblies.
Availability and Implementation: KAT is available under the GPLv3 license at: https://github.com/TGAC/KAT.
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Points of Significance : Statistics for Biologists

Points of Significance : Statistics for Biologists | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A collection of articles from the publisher of Nature that discusses statistical issues biologists should be aware of and provides practical advice to improve the statistical rigor and reproducibility of their work.
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