Viruses and Bioinformatics from Virology.uvic.ca
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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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Determining the subcellular location of new proteins from microscope images using local features

Determining the subcellular location of new proteins from microscope images using local features | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
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Google Drive - Quick reference guide for teachers and students

Google Drive - Quick reference guide for teachers and students | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Having trouble getting your head around Google Drive and / or Google Docs?
Well stress no more with this great printable guide to using Google Drive.

Via John Evans, Franc Viktor Nekrep
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Pippa Davies @PippaDavies 's comment, August 26, 2013 9:51 PM
Thanks Maria!:)
Ann Sciabarrasi's curator insight, December 22, 2013 7:01 PM

looks helpful

Mary Mourton's curator insight, March 17, 2016 11:55 AM

Google Drive provides many great options for easy access to administrative tasks on a mobile device. Edgalaxy provides a basic printable guide to using Google Drive on your computer (not the app) as a great starting point with its use.

Carol

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Signatures of mutational processes in human cancer

Signatures of mutational processes in human cancer | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Via Gerd Moe-Behrens, Pedro Fernandes
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Gerd Moe-Behrens's curator insight, August 15, 2013 5:01 PM

An important cancer research paper:

*Signatures of mutational processes in human cancer*

by
Ludmil B. Alexandrov,Serena Nik-Zainal,David C. Wedge,Samuel A. J. R. Aparicio,Sam Behjati,Andrew V. Biankin,Graham R. Bignell,Niccolò Bolli,Ake Borg,Anne-Lise Børresen-Dale,Sandrine Boyault,Birgit Burkhardt,Adam P. Butler,Carlos Caldas,Helen R. Davies, Christine Desmedt,Roland Eils,Jórunn Erla Eyfjörd,John A. Foekens, Mel Greaves,Fumie Hosoda,Barbara Hutter,Tomislav Ilicic,Sandrine Imbeaud,Marcin Imielinsket al.

"All cancers are caused by somatic mutations; however, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single cancer class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, ‘kataegis’, is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer, with potential implications for understanding of cancer aetiology, prevention and therapy."

 


http://bit.ly/142ZgNG

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Experimental Ebola treatment protects some primates even after disease symptoms appear

Experimental Ebola treatment protects some primates even after disease symptoms appear | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Scientists have successfully treated the deadly Ebola virus in infected animals following onset of disease symptoms, according to a new article.
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PLOS Computational Biology: Software for Computing and Annotating Genomic Ranges

PLOS Computational Biology: Software for Computing and Annotating Genomic Ranges | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.

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Pathogen blocks host death receptor signalling by arginine GlcNAcylation of death domains

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BioINFO Project

BioINFO Project | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
We are currently developing a large number of very useful tools for Biotechnology. These tools are meant to provide the academic community with free and reliable web applications for Bioinformatics and Genome research.
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Texas won’t mess with facts on evolution

Texas won’t mess with facts on evolution | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The Texas Board of Education, whose members oversee the content of textbooks, has long been stacked with people who question evolution.
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Cross-neutralization of four paramyxoviruses by a human monoclonal antibody

Abstract

Broadly neutralizing antibodies reactive against most and even all variants of the same viral species have been described for influenza and HIV-1 (ref. 1). However, whether a neutralizing antibody could have the breadth of range to target different viral species was unknown. Human respiratory syncytial virus (HRSV) and human metapneumovirus (HMPV) are common pathogens that cause severe disease in premature newborns, hospitalized children2, 3 and immune-compromised patients2, 4, 5, and play a role in asthma exacerbations6. Although antisera generated against either HRSV or HMPV are not cross-neutralizing7, we speculated that, because of the repeated exposure to these viruses, cross-neutralizing antibodies may be selected in some individuals. Here we describe a human monoclonal antibody (MPE8) that potently cross-neutralizes HRSV and HMPV as well as two animal paramyxoviruses: bovine RSV (BRSV) and pneumonia virus of mice (PVM). In its germline configuration, MPE8 is HRSV-specific and its breadth is achieved by somatic mutations in the light chain variable region. MPE8 did not result in the selection of viral escape mutants that evaded antibody targeting and showed potent prophylactic efficacy in animal models of HRSV and HMPV infection, as well as prophylactic and therapeutic efficacy in the more relevant model of lethal PVM infection. The core epitope of MPE8 was mapped on two highly conserved anti-parallel β-strands on the pre-fusion viral F protein, which are rearranged in the post-fusion F protein conformation. Twenty-six out of the thirty HRSV-specific neutralizing antibodies isolated were also found to be specific for the pre-fusion F protein. Taken together, these results indicate that MPE8 might be used for the prophylaxis and therapy of severe HRSV and HMPV infections and identify the pre-fusion F protein as a candidate HRSV vaccine.

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New Explanation for Key Step in Anthrax Infection Proposed

New Explanation for Key Step in Anthrax Infection Proposed | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Boulder, CO (Scicasts) – A new hypothesis concerning a crucial step in the anthrax infection process has been advanced by scientists at the National Institute of Standards and Technology (NIST) and the U.S.
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Pandoravirus, bigger and unlike anything seen before

Pandoravirus, bigger and unlike anything seen before | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Pandoraviruses, which are physically and genetically unlike any previously known viruses, are now the biggest known viruses.

Via Ed Rybicki
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Ed Rybicki's curator insight, August 2, 2013 6:35 AM

Nice commentary from Vincent Racaniello.

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Influenza virus hemagglutinin stalk-based antibodies and vaccines

Influenza virus hemagglutinin stalk-based antibodies and vaccines | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Antibodies against the conserved stalk domain of the hemagglutinin are currently being discussed as promising therapeutic tools against influenza virus infections. Because of the conservation of the stalk domain these antibodies are able to broadly neutralize a wide spectrum of influenza virus strains and subtypes. Broadly protective vaccine candidates based on the epitopes of these antibodies, for example, chimeric and headless hemagglutinin structures, are currently under development and show promising results in animals models. These candidates could be developed into universal influenza virus vaccines that protect from infection with drifted seasonal as well as novel pandemic influenza virus strains therefore obviating the need for annual vaccination, and enhancing our pandemic preparedness.

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Measles Outbreak Traces To Vaccine-Refusing Megachurch

Measles Outbreak Traces To Vaccine-Refusing Megachurch | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Texas measles outbreak tracing to vaccine-refusing megachurch endangers residents of two counties and has health officials in neighboring Oklahoma on guard.
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Twitter for Sci-Ed Part 1: Teaching in 140 characters or less | Sci-Ed

Several other authors have discussed reasons why scientists should be using Twitter, including this excellent post on Deep Sea News and this post through theAmerican Geophysical Union. For a more personal opinion, Dr Jeremy Segrottgave his thoughts after he used Twitter for a three months. Scientists are realizing that social media is an important way to translate knowledge to the public when done well, and Twitter provides another avenue by which this can be accomplished.

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Is Rabies Really 100% Fatal?

Is Rabies Really 100% Fatal? | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Eight years ago, Jeanna Giese stunned the scientific community by becoming the first known person to survive Rabies without vaccination. Now, research and a new rabies treatment plan have called into question Rabies's supposed 100% fatality rate.

Via Ed Rybicki
Chris Upton + helpers's insight:

In biology, 100% is.....

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Ed Rybicki's curator insight, August 23, 2013 6:18 AM

Fascinating post from a young blogger!

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Evolution on the inside track: How viruses in gut bacteria change over time

Evolution on the inside track: How viruses in gut bacteria change over time | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The digestive tract is home to a vast colony of bacteria, as well as the myriad viruses that prey upon them. Because the bacteria species vary from person to person, so does this viral population, the virome.
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Gretel Posadas's curator insight, August 23, 2013 7:39 AM

Evolution On the Inside Track: How #Viruses in Gut #Bacteria Change Over Time...by Samuel Minot, Alexandra Bryson, Christel Chehoud, Gary D. Wu, James D. Lewis, all from Penn, are co-authors.

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Bat Out of Hell? Egyptian Tomb Bat May Harbor MERS Virus | Science/AAAS | News

Bat Out of Hell? Egyptian Tomb Bat May Harbor MERS Virus | Science/AAAS | News | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Scientists say they are one step closer to understanding the origins of Middle East respiratory syndrome (MERS), the deadly viral disease that has been spreading in the Middle East for more than a year. They have found a small fragment of the virus's genome in an Egyptian tomb bat from Saudi Arabia, suggesting that these bats are a source of the virus—although another animal species may act as the bridge to humans.

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Middle East Respiratory Syndrome Coronavirus in Bats, Saudi Arabia

Middle East Respiratory Syndrome Coronavirus in Bats, Saudi Arabia | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

The source of human infection with Middle East respiratory syndrome coronavirus remains unknown. Molecular investigation indicated that bats in Saudi Arabia are infected with several alphacoronaviruses and betacoronaviruses.  Virus from 1 bat showed 100% nucleotide identity to virus from the human index case-patient. Bats might play a role in human infection.

Ed Rybicki's insight:

"Although neither detection of MERS CoV in bats nor contact of human MERS patients with bats have been reported, a role for bats in human infection cannot be excluded because contact can be indirect (mediated through another animal vector or fomites)."

Yup: avoid bat crap.  And preferably bats, too.

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A Minor Thing of Major Importance: Penn Study Finds A New Gene Expression Mechanism

A Minor Thing of Major Importance: Penn Study Finds A New Gene Expression Mechanism | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A rare, small RNA turns a gene-splicing machine into a switch that controls the expression of hundreds of human genes.
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The genesis and source of the H7N9 influenza viruses causing human infections in China

Abstract

A novel H7N9 influenza A virus first detected in March 2013 has since caused more than 130 human infections in China, resulting in 40 deaths1, 2. Preliminary analyses suggest that the virus is a reassortant of H7, N9 and H9N2 avian influenza viruses, and carries some amino acids associated with mammalian receptor binding, raising concerns of a new pandemic1, 3, 4. However, neither the source populations of the H7N9 outbreak lineage nor the conditions for its genesis are fully known5. Using a combination of active surveillance, screening of virus archives, and evolutionary analyses, here we show that H7 viruses probably transferred from domestic duck to chicken populations in China on at least two independent occasions. We show that the H7 viruses subsequently reassorted with enzootic H9N2 viruses to generate the H7N9 outbreak lineage, and a related previously unrecognized H7N7 lineage. The H7N9 outbreak lineage has spread over a large geographic region and is prevalent in chickens at live poultry markets, which are thought to be the immediate source of human infections. Whether the H7N9 outbreak lineage has, or will, become enzootic in China and neighbouring regions requires further investigation. The discovery here of a related H7N7 influenza virus in chickens that has the ability to infect mammals experimentally, suggests that H7 viruses may pose threats beyond the current outbreak. The continuing prevalence of H7 viruses in poultry could lead to the generation of highly pathogenic variants and further sporadic human infections, with a continued risk of the virus acquiring human-to-human transmissibility.

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Searching for virus phylotypes

Motivation: Large phylogenies are being built today to study virus evolution, trace the origin of epidemics, establish the mode of transmission and survey the appearance of drug resistance. However, no tool is available to quickly inspect these phylogenies and combine them with extrinsic traits (e.g. geographic location, risk group, presence of a given resistance mutation), seeking to extract strain groups of specific interest or requiring surveillance.

Results: We propose a new method for obtaining such groups, which we call phylotypes, from a phylogeny having taxa (strains) annotated with extrinsic traits. Phylotypes are subsets of taxa with close phylogenetic relationships and common trait values. The method combines ancestral trait reconstruction using parsimony, with combinatorial and numerical criteria measuring tree shape characteristics and the diversity and separation of the potential phylotypes. A shuffling procedure is used to assess the statistical significance of phylotypes. All algorithms have linear time complexity. This results in low computing times, typically a few minutes for the larger data sets with a number of shuffling steps. Two HIV-1 data sets are analyzed, one of which is large, containing >3000 strains of HIV-1 subtype C collected worldwide, where the method shows its ability to recover known clusters and transmission routes, and to detect new ones.

Availability: This method and companion tools are implemented in an interactive Web interface (www.phylotype.org), which provides a wide choice of graphical views and output formats, and allows for exploratory analyses of large data sets.

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Newly Discovered Marine Viruses Offer Glimpse Into Untapped Biodiversity - Science Daily (press release)

Newly Discovered Marine Viruses Offer Glimpse Into Untapped Biodiversity - Science Daily (press release) | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Newly Discovered Marine Viruses Offer Glimpse Into Untapped Biodiversity Science Daily (press release) Researchers of the University of Arizona's Tucson Marine Phage Lab have discovered a dozen new types of unknown viruses that infect different...

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