Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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The Hallmarks of Cancer 8: Tumor-Promoting Inflammation | Guest Blog, Scientific American Blog Network

The Hallmarks of Cancer 8: Tumor-Promoting Inflammation | Guest Blog, Scientific American Blog Network | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The Hallmarks of Cancer are ten underlying principles shared by all cancers. You can read the first seven Hallmarks of Cancer articles here. The eighth Hallmark ...
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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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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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Microbial Bioinformatics starter kit

Microbial Bioinformatics starter kit | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
by Lauren Cowley
Hello
You’re new to Bioinformatics and have no idea where to start. Let me suggest you give these tutorials/helpages a go:

https://c2-d2.github.io/hanage-lab/Bioinformatics-for-bacterial-population-genomics/
https://learnpythonthehardway.org
http://epidemic.bio.ed.ac.uk/how_to_read_a_phylogeny
https://angus.readthedocs.io/en/2017/
https://norwegianveterinaryinstitute.github.io/BioinfTraining/
https://bitsandbugs.org/2017/06/26/salmonella-genomic-epidemiology-exercise/
https://bitsandbugs.org/2016/09/22/guideline-to-bioinformatics-tools/


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The Myth of the Milkmaid | NEJM

The Myth of the Milkmaid | NEJM | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Perspective from The New England Journal of Medicine — The Myth of the Milkmaid
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Data for free: viral metagenomics in human RNASeq data

Data for free: viral metagenomics in human RNASeq data | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
tl;dr Even with a polydT bead RNASeq extraction, you can find interesting metagenomic data, as many single stranded RNA viruses hav
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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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Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
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Re-Assembly and Analysis of an Ancient Variola Virus Genome

Re-Assembly and Analysis of an Ancient Variola Virus Genome | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
We report a major improvement to the assembly of published short read sequencing data from an ancient variola virus (VARV) genome by the removal of contig-capping sequencing tags and manual searches for gap-spanning reads. The new assembly, together with camelpox and taterapox genomes, permitted new dates to be calculated for the last common ancestor of all VARV genomes. The analysis of recently sequenced VARV-like cowpox virus genomes showed that single nucleotide polymorphisms (SNPs) and amino acid changes in the vaccinia virus (VACV)-Cop-O1L ortholog, predicted to be associated with VARV host specificity and virulence, were introduced into the lineage before the divergence of these viruses. A comparison of the ancient and modern VARV genome sequences also revealed a measurable drift towards adenine + thymine (A + T) richness.
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Researchers Learn from Plant Viruses to Protect Crops

Researchers Learn from Plant Viruses to Protect Crops | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Plants are locked in an ancient arms race with hostile viruses, but genome editing is giving crops the upper hand.


Via Integrated DNA Technologies
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About  kallisto

kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. On benchmarks with standard RNA-Seq data, kallisto can quantify 30 million human reads in less than 3 minutes on a Mac desktop computer using only the read sequences and a transcriptome index that itself takes less than 10 minutes to build. Pseudoalignment of reads preserves the key information needed for quantification, and kallisto is therefore not only fast, but also as accurate as existing quantification tools. In fact, because the pseudoalignment procedure is robust to errors in the reads, in many benchmarks kallisto significantly outperforms existing tools. kallisto is described in detail in: Nicolas L Bray, Harold Pimentel, Páll Melsted and Lior Pachter, Near-optimal probabilistic RNA-seq quantification, Nature Biotechnology 34, 525–527 (2016), doi:10.1038/nbt.3519 To use kallisto download the software and visit the Getting started page for a quick tutorial. More information about kallisto, including a demonstration of its use, is available in the materials from the first kallisto-sleuth workshop.
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