Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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Deeper than ancestry.com, 'EvoCor' identifies gene relationships | Virginia Tech News | Virginia Tech

Deeper than ancestry.com, 'EvoCor' identifies gene relationships | Virginia Tech News | Virginia Tech | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
A team led by Gregorio Valdez of the Virginia Tech Carilion Research Institute has designed a search engine that identifies genes that are functionally linked.
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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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Cancer immunotherapy and the value of cure

Cancer immunotherapy and the value of cure | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Patients value anticancer therapies that provide durable clinical responses; immune-checkpoint inhibitors can provide such benefit for patients with some advanced-stage malignancies, albeit only for a minority of those treated. Modern oncology value frameworks have set efficacy thresholds in an attempt to assess the clinical benefit of anticancer therapeutics. But, is the benefit of durable cancer control reflected in these thresholds?

Via Krishan Maggon
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Free Technology for Teachers: Three Tools for Combining Maps With Timelines

Free Technology for Teachers: Three Tools for Combining Maps With Timelines | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Creating timelines whose events are directly connected to a map display is a good way for students to see correlations between location
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WHO warns over measles immunisation rates as cases rise 300% across Europe | Society | The Guardian

WHO warns over measles immunisation rates as cases rise 300% across Europe | Society | The Guardian | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
2017 saw more than 21,000 cases and 35 deaths, with large outbreaks in one in four countries, says World Health Organisation
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Celebrate Failing - Matt Harris, Ed.D. - International EdTech Specialist

Celebrate Failing - Matt Harris, Ed.D. - International EdTech Specialist | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Though there were a host of professional learning takeaways for me, one stood out as a real actionable item. Funny, this same theme came up at every conference I attended: Celebrating Failing.

Via John Evans
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Airway T cells protect against RSV infection in the absence of antibody

Airway T cells protect against RSV infection in the absence of antibody | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Article

Via Gilbert C FAURE
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Viruses - lots of them - are falling from the sky

Viruses - lots of them - are falling from the sky | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

An astonishing number of viruses are circulating around the Earth's atmosphere -- and falling from it -- according to new research from scientists in Canada, Spain and the U.S.

 

The study marks the first time scientists have quantified the viruses being swept up from the Earth's surface into the free troposphere, that layer of atmosphere beyond Earth's weather systems but below the stratosphere where jet airplanes fly. The viruses can be carried thousands of kilometers there before being deposited back onto the Earth's surface.

 

"Every day, more than 800 million viruses are deposited per square metre above the planetary boundary layer -- that's 25 viruses for each person in Canada," said University of British Columbia virologist Curtis Suttle, one of the senior authors of a paper in the International Society for Microbial Ecology Journal that outlines the findings.

 

"Roughly 20 years ago we began finding genetically similar viruses occurring in very different environments around the globe," says Suttle. "This preponderance of long-residence viruses traveling the atmosphere likely explains why -- it's quite conceivable to have a virus swept up into the atmosphere on one continent and deposited on another."

 

Bacteria and viruses are swept up in the atmosphere in small particles from soil-dust and sea spray. Suttle and colleagues at the University of Granada and San Diego State University wanted to know how much of that material is carried up above the atmospheric boundary layer above 2,500 to 3,000 meters. At that altitude, particles are subject to long-range transport unlike particles lower in the atmosphere.

 

Using platform sites high in Spain's Sierra Nevada Mountains, the researchers found billions of viruses and tens of millions of bacteria are being deposited per square meter per day. The deposition rates for viruses were nine to 461 times greater than the rates for bacteria.


Via Dr. Stefan Gruenwald
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Newcastle scientists reveal hidden secrets of Sir Alexander Fleming’s medical breakthroughs - Chronicle Live

Newcastle scientists reveal hidden secrets of Sir Alexander Fleming’s medical breakthroughs - Chronicle Live | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
How Sir Alexander Fleming's medical breakthroughs may contribute to recurrent patient infections
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Fast Sequence Inspection with ORFfinder + SmartBLAST

Fast Sequence Inspection with ORFfinder + SmartBLAST | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
This blog post is intended for all BLAST users. ORFfinder is a graphical analysis tool for finding open reading frames (ORFs). We've been working on a few updates, and we'd like to find out what you think about them. Read on to find out what you can do with the new ORFfinder. Start with the…
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G2S: A web-service for annotating genomic variants on 3D protein structures | Bioinformatics | Oxford Academic

G2S: A web-service for annotating genomic variants on 3D protein structures | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractMotivation. Accurately mapping and annotating genomic locations on 3D protein structures is a key step in structure-based analysis of genomic variants
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Discovery of a proteinaceous cellular receptor for a norovirus

Discovery of a proteinaceous cellular receptor for a norovirus | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
There's no escaping norovirus when you have it—the symptoms from this gastroenteritis-causing virus, though brief, are often debilitating. Preventing infections will rely on improving our understanding of how norovirus enters host cells. Orchard et al. show that the entry of murine norovirus (MNoV) into host cells requires a protein called CD300lf. In cell culture, mouse cells needed to express CD300lf in order for MNoV binding, entry, and replication to occur. Deleting the gene encoding CD300lf in mice protected them against MNoV infection. Human cells expressing CD300lf allowed MNoV to break the species barrier, a finding that may lead to new insights into the infectivity of this virus.

Science , this issue p. [933][1]

[1]: /lookup/doi/10.1126/science.aaf1220
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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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We finally know how vampire bats are able to drink blood and survive

We finally know how vampire bats are able to drink blood and survive | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Vampire bats are probably not the cuddliest of critters, considering nearly their entire food source consists of blood.

 

There are three types of bats who solely drink blood, the common vampire bat (Desmodus rotundus), the hairy-legged vampire bat (Diphylla ecaudata), and the white-winged vampire bat (Diaemus youngi). All three of these animals evolved from bats who eat fruit, but we still aren't sure how they managed to make the huge leap to the minimally nutritious, and relatively dangerous activity of drinking blood.

 

This is because subsisting on just blood, called hematophagy, is very uncommon. The amount of liquid can overwhelm the kidneys, too much can cause iron poisoning, and excessive protein isn't good for the body either. And blood is super high in protein (93 percent), but extremely low in carbohydrates (1 percent) and vitamins. Plus there are a bunch of blood-borne diseases.

 

The international group of researchers took samples of the bats' droppings to look at something called the 'hologenome' – the entire set of genes of an organism, including all the bacteria and other microbes that make that creature their home. They analyzed the common vampire bat's hologenome against a number of insect-, fruit-, or meat-eating bats to try and determine what makes the vampire bat so weird.

 

What they found is that the gut microbes in the bat were an especially unique combination, which most other bats (or other mammals) wouldn't be able to stomach. In fact, more than 280 of the bacterial species found in the droppings are known to cause disease in other mammals.

 

"The data suggests that there is a close evolutionary relationship between the gut microbiome and the genome of the vampire bat for adaptation to sanguivory (feeding exclusively on blood)," biologist Marie Zepeda Mendoza of the University of Copenhagen in Denmark explains.

 

The researchers also found that the vampire bat's genome had more transposons, also known as 'jumping genes' - genes in the DNA that are able to multiply and move around the genome. There was as much as a 2.2 fold increase in the amount of one particular transposon, called MULE-MuDR in the vampire bat, compared to other types of bats the researchers looked at. The extra MULE-MuDR copies were mostly found in areas involved in immune response, viral defence and metabolism. The researchers think this helps the bat better process the huge amount of blood it can ingest per day, without getting sick. "It is clear from our results that the common vampire bat has adapted to sanguivory through a close relationship between its genome and gut microbiome," the researchers write in the paper.

 
 

Via Dr. Stefan Gruenwald
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Impact and Effectiveness of the Quadrivalent Human Papillomavirus Vaccine: A Systematic Review of 10 Years of Real-world Experience | Clinical Infectious Diseases | Oxford Academic

Impact and Effectiveness of the Quadrivalent Human Papillomavirus Vaccine: A Systematic Review of 10 Years of Real-world Experience | Clinical Infectious Diseases | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
This systematic review assessed the global impact and effectiveness of quadrivalent human
papillomavirus (HPV) vaccination on HPV infection and diseas
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The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification | Microbiome | Full Text

The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification | Microbiome | Full Text | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The International Committee on Taxonomy of Viruses (ICTV) classifies viruses into families, genera and species and provides a regulated system for their nomenclature that is universally used in virus descriptions. Virus taxonomic assignments have traditionally been based upon virus phenotypic properties such as host range, virion morphology and replication mechanisms, particularly at family level. However, gene sequence comparisons provide a clearer guide to their evolutionary relationships and provide the only information that may guide the incorporation of viruses detected in environmental (metagenomic) studies that lack any phenotypic data. The current study sought to determine whether the existing virus taxonomy could be reproduced by examination of genetic relationships through the extraction of protein-coding gene signatures and genome organisational features. We found large-scale consistency between genetic relationships and taxonomic assignments for viruses of all genome configurations and genome sizes. The analysis pipeline that we have called ‘Genome Relationships Applied to Virus Taxonomy’ (GRAViTy) was highly effective at reproducing the current assignments of viruses at family level as well as inter-family groupings into orders. Its ability to correctly differentiate assigned viruses from unassigned viruses, and classify them into the correct taxonomic group, was evaluated by threefold cross-validation technique. This predicted family membership of eukaryotic viruses with close to 100% accuracy and specificity potentially enabling the algorithm to predict assignments for the vast corpus of metagenomic sequences consistently with ICTV taxonomy rules. In an evaluation run of GRAViTy, over one half (460/921) of (near)-complete genome sequences from several large published metagenomic eukaryotic virus datasets were assigned to 127 novel family-level groupings. If corroborated by other analysis methods, these would potentially more than double the number of eukaryotic virus families in the ICTV taxonomy. A rapid and objective means to explore metagenomic viral diversity and make informed recommendations for their assignments at each taxonomic layer is essential. GRAViTy provides one means to make rule-based assignments at family and order levels in a manner that preserves the integrity and underlying organisational principles of the current ICTV taxonomy framework. Such methods are increasingly required as the vast virosphere is explored.
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Defective RNA sensing by RIG-I in severe influenza virus infection

Clin Exp Immunol. 2018 Feb 17. doi: 10.1111/cei.13120. [Epub ahead of print]
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CRISPR-based Technology Can Detect Viral DNA

DETECTR relies on Cas12a, an enzyme described in 2015. Like its molecular cousin Cas9, ..., Cas12a snips DNA. But instead of snipping only the DNA strand it binds, Cas12a chops other DNA, too.

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Tricked or trapped—Two decoy mechanisms in host–pathogen interactions

Tricked or trapped—Two decoy mechanisms in host–pathogen interactions | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
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Ravaged by a poorly studied viral disease, cacao trees are dying

Ravaged by a poorly studied viral disease, cacao trees are dying | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Picture this: It's Valentine's Day, and you head out to buy some pralines. Except you can't find any. No matter which store you visit, gummy bears and hard candy have taken the place on the shelves where the chocolate heart
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SmartBLAST: Faster BLASTp search results in a graphical view

SmartBLAST: Faster BLASTp search results in a graphical view | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
BLAST (Basic Local Alignment Search Tool) is a popular tool for finding sequences in a given database that are similar to a query sequence. Traditionally, BLAST displays these results as a sorted list of matches between the query and each database sequence. While this display is useful for examining how each subject sequence matches the…
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Inferring synteny between genome assemblies: a systematic evaluation | BMC Bioinformatics | Full Text

Inferring synteny between genome assemblies: a systematic evaluation | BMC Bioinformatics | Full Text | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Genome assemblies across all domains of life are being produced routinely. Initial analysis of a new genome usually includes annotation and comparative genomics. Synteny provides a framework in which conservation of homologous genes and gene order is identified between genomes of different species. The availability of human and mouse genomes paved the way for algorithm development in large-scale synteny mapping, which eventually became an integral part of comparative genomics. Synteny analysis is regularly performed on assembled sequences that are fragmented, neglecting the fact that most methods were developed using complete genomes. It is unknown to what extent draft assemblies lead to errors in such analysis. We fragmented genome assemblies of model nematodes to various extents and conducted synteny identification and downstream analysis. We first show that synteny between species can be underestimated up to 40% and find disagreements between popular tools that infer synteny blocks. This inconsistency and further demonstration of erroneous gene ontology enrichment tests raise questions about the robustness of previous synteny analysis when gold standard genome sequences remain limited. In addition, assembly scaffolding using a reference guided approach with a closely related species may result in chimeric scaffolds with inflated assembly metrics if a true evolutionary relationship was overlooked. Annotation quality, however, has minimal effect on synteny if the assembled genome is highly contiguous. Our results show that a minimum N50 of 1 Mb is required for robust downstream synteny analysis, which emphasizes the importance of gold standard genomes to the science community, and should be achieved given the current progress in sequencing technology.
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When are pathogen genome sequences informative of transmission events?

When are pathogen genome sequences informative of transmission events? | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
informational limitations of genetic sequence data in certain outbreak scenarios, and demonstrate the need to expand the toolkit of outbreak reconstruction tools to integrate other types of epidemiological data
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