Viruses, Immunology & 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, Immunology & 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, Immunology & 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, 2017 12:46 PM
Thank You.
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Discovery of novel bat coronaviruses in south China that use the same receptor as MERS coronavirus

Previous studies suggested that the Middle East respiratory syndrome coronavirus (MERS-CoV) may have originated in bats. However, its evolutionary path from bats to humans remains unclear. In this study, we discovered 89 novel lineage C betacoronaviruses (BetaCoVs) in eight bat species. We provide the evidence of a MERS-related CoV derived from the great evening bat that uses the same host receptor as human MERS-CoV. This virus also provides evidence for a natural recombination event between the bat MERS-related CoV and another bat coronavirus HKU4. Our study expands the host ranges of MERS-related CoV and represents an important step toward establishing bats as the natural reservoir of MERS-CoV. These findings may lead to improved epidemiological surveillance of MERS-CoV and the prevention and control of the spread of MERS-CoV to humans.

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The STING behind dengue virus infection

Stabell et al. have revealed why human dengue viruses do not replicate to high titres in primate models. They found that the stimulator of interferon genes (STING) protein, which induces the production of type I interferon in infected cells to reduce viral titres, is cleaved by the dengue virus protease NS2B3 in humans but not in key primate models. STING cleavage occurred at an RG motif at amino acids 78 and 79, decreasing markers of an innate immune response and increasing viral replication in human cells. The analyses of STING sequences from all placental animals in Genbank, as well as from 16 non-human primate cell lines, revealed that only STING from three small apes and three small rodents encodes this RG motif. As introducing this RG motif into STING from rhesus macaque, marmoset and mouse rendered it susceptible to cleavage by dengue virus NS2B3, engineering model organisms so that their STING contains this motif could enhance the study of dengue viruses in animals.
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VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis | BMC Bioinformatics | Full Text

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis | BMC Bioinformatics | Full Text | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
RNA sequencing has become a ubiquitous technology used throughout life sciences as an effective method of measuring RNA abundance quantitatively in tissues and cells. The increase in use of RNA-seq technology has led to the continuous development of new tools for every step of analysis from alignment to downstream pathway analysis. However, effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts. Using the workflow management system Snakemake we have developed a user friendly, fast, efficient, and comprehensive pipeline for RNA-seq analysis. VIPER (Visualization Pipeline for RNA-seq analysis) is an analysis workflow that combines some of the most popular tools to take RNA-seq analysis from raw sequencing data, through alignment and quality control, into downstream differential expression and pathway analysis. VIPER has been created in a modular fashion to allow for the rapid incorporation of new tools to expand the capabilities. This capacity has already been exploited to include very recently developed tools that explore immune infiltrate and T-cell CDR (Complementarity-Determining Regions) reconstruction abilities. The pipeline has been conveniently packaged such that minimal computational skills are required to download and install the dozens of software packages that VIPER uses. VIPER is a comprehensive solution that performs most standard RNA-seq analyses quickly and effectively with a built-in capacity for customization and expansion.
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Ten simple rules for responsible referencing

Ten simple rules for responsible referencing | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
We researchers aim to read and write publications containing high-quality prose, exceptional data, arguments, and conclusions, embedded firmly in existing literature while making abundantly clear what we are adding to it. Through the inclusion of references, we demonstrate the foundation upon which our studies rest as well as how they are different from previous work. That difference can include literature we dispute or disprove, arguments or claims we expand, and new ideas, suggestions, and hypotheses we base upon published work. This leads to the question of how to decide which study or author to cite, and in what way.
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A stockpile of antiviral defences

A stockpile of antiviral defences | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The full list of weapons used by bacteria against viruses is not known. A computational approach has uncovered nine previously unidentified antiviral systems, encoded by genes near known defence genes in bacterial genomes.

Via Ed Rybicki
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The Last Days of Smallpox: Tragedy in Birmingham eBook: Mark Pallen: Amazon.ca: Kindle Store

The Last Days of Smallpox: Tragedy in Birmingham eBook: Mark Pallen: Amazon.ca: Kindle Store | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The Last Days of Smallpox: Tragedy in Birmingham eBook: Mark Pallen: Amazon.ca: Kindle Store
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Gifford Lab (CVR) - Footprints of ancient deltaretroviruses in bat genomes

Gifford Lab (CVR) - Footprints of ancient deltaretroviruses in bat genomes | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
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Understanding the drivers of MHC restriction of T cell receptors

Understanding the drivers of MHC restriction of T cell receptors | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Review Article

 

Jamie Rossjohn and colleagues review the structural and functional data that provide insight into the MHC restriction of T cell receptors. They discuss the non-mutually exclusive contributions of intrinsic germline-encoded motifs and developmental selection to MHC restriction.


Via Krishan Maggon , Gilbert C FAURE
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Influenza Infection in Humans Induces Broadly Cross-Reactive and Protective Neuraminidase-Reactive Antibodies

Influenza Infection in Humans Induces Broadly Cross-Reactive and Protective Neuraminidase-Reactive Antibodies | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Current influenza vaccines predominantly produce antibodies targeting the viral hemagglutinin
(HA). However, during natural infection, the body also produces antibodies targeting
the viral neuraminidase (NA). These NA antibodies can provide robust and broad protection
and could potentially be elicited prophylactically or via new vaccine strategies or
used therapeutically.

Via Ed Rybicki
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Boulders Beach penguins fall victim to bird flu outbreak

Boulders Beach penguins fall victim to bird flu outbreak | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The penguins of Boulders Beach have been placed under threat by the H5N8 strain of avian influenza.

Via Ed Rybicki
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Bats spread Ebola because they’ve evolved not to fight viruses

Bats spread Ebola because they’ve evolved not to fight viruses | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Bats can carry viruses like Ebola and Marburg that are lethal for humans. This may be because, in order to fly, their bodies have given up on fighting such viruses
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Scientists Finger Bats For Spreading Virus That Killed 24,000 Piglets In China : Goats and Soda : NPR

Scientists Finger Bats For Spreading Virus That Killed 24,000 Piglets In China : Goats and Soda : NPR | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
At first, tests were positive for porcine epidemic diarrhea virus. Then something strange happened. The pigs stopped testing positive for that virus — but kept getting sick.
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Viruses are falling from the skies

Viruses are falling from the skies | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

To determine how many viruses fall from the troposphere each day, automatic collectors were placed at two different locations in the Sierra Nevada Mountains of Spain at 1.75 km above sea level. Placing the collectors at this height allows sampling of air above the atmospheric boundary layer (pictured – image credit). Samples were retreived every 1-2 weeks over the course of two years and analyzed for the presence of viruses by flow cytometry after purification by centrifugation.

The results show that billions of viruses fall from the atmosphere each day: from 0.3 to 3.8 x 109 per square meter. Most (69%) of the viruses that descend from the atmosphere are attached to dust or organic aggregates. The rate of falling viruses was not substantially different over the course of the study nor between the two different sites.
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Concepts in Light Microscopy of Viruses

Concepts in Light Microscopy of Viruses | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Here, we provide an overview of recent technology for imaging cells and viruses by light microscopy, in particular fluorescence microscopy in static and live-cell modes. The review lays out guidelines for how novel fluorescent chemical probes and proteins can be used in light microscopy to illuminate cells, and how they can be used to study virus infections. We discuss advantages and opportunities of confocal and multi-photon microscopy, selective plane illumination microscopy, and super-resolution microscopy. We emphasize the prevalent concepts in image processing and data analyses, and provide an outlook into label-free digital holographic microscopy for virus research.
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PhyloProfile: Dynamic visualization and exploration of multi-layered phylogenetic profiles | Bioinformatics | Oxford Academic

PhyloProfile: Dynamic visualization and exploration of multi-layered phylogenetic profiles | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractSummary. Phylogenetic profiles form the basis for tracing proteins and their functions across species and through time. Novel genome sequences nowadays
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Entirely plasmid-based reverse genetics system for rotaviruses. - PubMed - NCBI

Rotaviruses (RVs) are highly important pathogens that cause severe diarrhea among infants and young children worldwide. The understanding of the molecular mechanisms underlying RV replication and pathogenesis has been hampered by the lack of an entirely plasmid-based reverse genetics system. In this study, we describe the recovery of recombinant RVs entirely from cloned cDNAs.

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A novel model for Crimean-Congo hemorrhagic fever virus

A novel model for Crimean-Congo hemorrhagic fever virus | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The article "A cynomolgus macaque model for Crimean–Congo haemorrhagic fever" in Nature Microbiology can be found here: https://rdcu.be/K2BD Crimean-Congo hemorrhagic fever virus: a serious, oftentimes deadly pathogen.

Via Ed Rybicki
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Gene Graphics: a genomic neighborhood data visualization web application | Bioinformatics | Oxford Academic

Gene Graphics: a genomic neighborhood data visualization web application | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractSummary. The examination of gene neighborhood is an integral part of comparative genomics but no tools to produce publication quality graphics of gene
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Complete genome direct RNA sequencing of influenza A virus

short highly conserved termi
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Vaccinia Virus C9 Ankyrin Repeat/F-Box Protein Is a Newly Identified Antagonist of the Type I Interferon-Induced Antiviral State

Poxviruses have another string to their anti-immunesystem bow.

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Images in The eyes have it: influenza virus infection beyond the respiratory tract

Images in The eyes have it: influenza virus infection beyond the respiratory tract | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Avian and human influenza A viruses alike have shown a capacity to use the eye as
a portal of entry and cause ocular disease in human beings. However, whereas influenza
viruses generally represent a respiratory pathogen and only occasionally cause ocular
complications, the H7 virus subtype stands alone in possessing an ocular tropism.
Clarifying what confers such non-respiratory tropism to a respiratory virus will permit
a greater ability to identify, treat, and prevent zoonotic human infection following
ocular exposure to influenza viruses; especially those within the H7 subtype, which
continue to cause avian epidemics on many continents.

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New computational approaches to understanding molecular protein function - file

Function is like beauty—its definition lies in the eye of the beholder or, in this case, the researcher. At the broadest level, we define organismal function—the function that the protein plays in the overall organism. This function can be observed by understanding the impact on the organism of deletion or mutation of the protein. Physiological function is the function the protein plays in pathways, such as metabolic or signaling pathways. Another level of function is the cellular level. Approaches to understanding cellular function attempt to identify a protein’s interaction partners and its location within the cell. Biochemical or molecular function is another level of function, one that identifies the molecular functional details of a functional site, including reaction mechanism, substrate binding, and molecular details of the binding of regulatory molecules. The International Union of Pure and Applied Chemistry (IUPAC) Enzyme Classification (EC) system was an early approach to identifying molecular function. The Gene Ontology (GO) system of classifying function recognizes ways of defining function, using distinct cellular components, molecular function, and biological process hierarchies [1]. The emphasis in the collection of research articles that comprise this Focus Feature is on understanding the different molecular functions that can exist within a protein superfamily and the features that define those differences.
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Denmark to build fence on German border to keep out African swine fever

Denmark to build fence on German border to keep out African swine fever | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The virus that causes African swine fever is harmless to humans, but fatal to pigs.
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Mutation 'gives bats edge over deadly viruses'

Mutation 'gives bats edge over deadly viruses' | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
A single mutation in an immunity gene may explain why bats can carry deadly viruses and not get sick.
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