Viruses and Bioinformatics from Virology.uvic.ca
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[VIDEO] Amateur Scientists Discover Galactic Bubbles

Amateur scientists have made a effervescent discovery: The Milky Way Galaxy is bubbling like a glass of champagne. Visit http://science.nasa.gov/ for more.

 

Articles about ASTRONOMY: http://www.scoop.it/t/science-news?tag=astronomy

 


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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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Ebola vaccine developed in Canada shows promising results

Ebola vaccine developed in Canada shows promising results | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A phase 1 randomized controlled trial has found an Ebola virus disease (EVD) vaccine, developed in Canada, was well-tolerated with no safety concerns, and high antibodies were presen
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 Hepatitis B Virus Immunopathology, Model Systems, and Current Therapies

Most people develop acute HBV-related hepatitis that is controlled by both humoral and cellular immune responses following acute infection. However, a number of individuals in HBV-endemic areas fail to resolve the infection and consequently become chronic carriers. While a vaccine is available and new antiviral drugs are being developed, elimination of persistently infected cells is still a major issue. Standard treatment in HBV infection includes IFN-α, nucleoside, or nucleotide analogues, which has direct antiviral activity and immune modulatory capacities. However, immunological control of the virus is often not durable. A robust T-cell response is associated with control of HBV infection and liver damage; however, HBV-specific T cells are deleted, dysfunctional or become exhausted in chronic hepatitis patients. As a result, efforts to restore virus-specific T-cell immunity in chronic HBV patients using antiviral therapy, immunomodulatory cytokines, or therapeutic vaccination have had little success. Adoptive cell transfer of T cells with specificity for HBV antigen+ cells represents an approach aiming to ultimately eliminate residual hepatocytes carrying HBV covalently closed circular DNA (cccDNA). Here, we discuss recent findings describing HBV immunopathology, model systems and current therapies.
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Viral vectors travel longer distances than previously thought

Viral vectors travel longer distances than previously thought | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Gene transfer is seen as a hopeful therapy for Alzheimer's and Parkinson's patients. The approach involves using harmless laboratory-produced viruses to introduce important genes into the brain cells. In a study on mice

Via Gilbert C FAURE
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Phyx: phylogenetic tools for unix | Bioinformatics | Oxford Academic

Abstract Summary: The ease with which phylogenomic data can be generated has drastically escalated the computational burden for even routine phylogenetic investigations. To address this, we present phyx : a collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects (alignments, trees and MCMC logs). Modelled after Unix/GNU/Linux command line tools, individual programs perform a single task and operate on standard I/O streams that can be piped to quickly and easily form complex analytical pipelines. Because of the stream-centric paradigm, memory requirements are minimized (often only a single tree or sequence in memory at any instance), and hence phyx is capable of efficiently processing very large datasets.
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A systemic macrophage response is required to contain a peripheral poxvirus infection

A systemic macrophage response is required to contain a peripheral poxvirus infection | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Prior to the eradication of variola virus, the orthopoxvirus that causes smallpox, one-third of infected people succumbed to the disease. Despite many complications, smallpox vaccination using vaccinia virus enabled a successful eradication of the disease. Following smallpox eradication, vaccinia (the smallpox vaccine) remains a widely used vaccine vector, so any information about the immune response to the vector can help engineer safer vaccines, or treatment, following complications of immunization. During natural infection, orthopoxviruses spread from a peripheral site of infection to become systemic. This study elucidates the early requirement of innate immune cells to control spread of the smallpox vaccine vector after a peripheral infection. We report that systemic populations of cells, rather than those recruited to the site of infection, are responsible for preventing virus dissemination. The viral control mediated by these cell subsets presents a potential target for therapies and rational vaccine design.
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The effect of intrauterine devices on acquisition and clearance of human papillomavirus

The effect of intrauterine devices on acquisition and clearance of human papillomavirus | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Previous studies have shown a decrease in cervical cancer associated with intrauterine
device use. It has been hypothesized that intrauterine device use may alter the natural
history of human papillomavirus infections, preempting development of precancerous
lesions of the cervix and cervical cancer, but the effect of intrauterine devices
on the natural history of human papillomavirus infection and subsequent development
of cervical cancer is poorly understood.
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In Vivo Imaging of Influenza Virus Infection in Immunized Mice

Immunization is the cornerstone of seasonal influenza control and represents an important component of pandemic preparedness strategies. Using a bioluminescent reporter virus, we demonstrate the application of noninvasive in vivo imaging system (IVIS) technology to evaluate the preclinical efficacy of candidate vaccines and immunotherapy in a mouse model of influenza. Sequential imaging revealed distinct spatiotemporal kinetics of bioluminescence in groups of mice passively or actively immunized by various strategies that accelerated the clearance of the challenge virus at different rates and by distinct mechanisms. Imaging findings were consistent with conclusions derived from virus titers in the lungs and, notably, were more informative than conventional efficacy endpoints in some cases. Our findings demonstrate the reliability of IVIS as a qualitative approach to support preclinical evaluation of candidate medical countermeasures for influenza in mice.

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In Vivo Imaging of Influenza Virus Infection in Immunized Mice

Immunization is the cornerstone of seasonal influenza control and represents an important component of pandemic preparedness strategies. Using a bioluminescent reporter virus, we demonstrate the application of noninvasive in vivo imaging system (IVIS) technology to evaluate the preclinical efficacy of candidate vaccines and immunotherapy in a mouse model of influenza. Sequential imaging revealed distinct spatiotemporal kinetics of bioluminescence in groups of mice passively or actively immunized by various strategies that accelerated the clearance of the challenge virus at different rates and by distinct mechanisms. Imaging findings were consistent with conclusions derived from virus titers in the lungs and, notably, were more informative than conventional efficacy endpoints in some cases. Our findings demonstrate the reliability of IVIS as a qualitative approach to support preclinical evaluation of candidate medical countermeasures for influenza in mice.
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Research shows new Zika virus vaccine that offers 100% protection in mice

Research shows new Zika virus vaccine that offers 100% protection in mice | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Research presented by Farshad Guirakhoo, Ph.D., Chief Scientific Officer, GeoVax, Inc., at the ASM Microbe 2017 meeting showed a new Zika virus vaccine that gives 100% protection in mice.
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The hidden order in DNA diffusion

The hidden order in DNA diffusion | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The movement of DNA molecules seemingly explained by random motion conceals a more orderly march.
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Brisbane researchers discover native Australian plant can kill Zika virus

Brisbane researchers discover native Australian plant can kill Zika virus | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
QUT News article
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Modified viruses deliver death to antibiotic-resistant bacteria

Modified viruses deliver death to antibiotic-resistant bacteria | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Engineered microbes turn a bacterium's immune response against itself using CRISPR.
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Impaired downregulation of NKG2D ligands by Nef protein from elite controllers sensitizes HIV-1-infected cells to ADCC.

J Virol. 2017 Jun 14. pii: JVI.00109-17. doi: 10.1128/JVI.00109-17. [Epub ahead of print]
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Simulome: a genome sequence and variant simulator | Bioinformatics | Oxford Academic

Summary: Simulome provides a powerful and easy to use tool for creating prokaryotic pseudo-genomes. It provides options that can be used in combination to create mutated variants of the simulated genome, which allows for controlled testing of specific genomic conditions. Simulome can be used in combination with real reads generated from next-generation sequencing platforms, or with simulated reads.
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Viruses

Viruses | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it


Special Issue "Viruses of Protozoa"  

Viruses, an international, peer-reviewed Open Access journal.

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The Types Of Cancer You Can Get From HPV

The Types Of Cancer You Can Get From HPV | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
New study suggests HPV-related genital infection can cause cervical, anal, vulvar, and vaginal cancers.
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Influenza: A viral world war

Influenza: A viral world war | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The 1918 influenza pandemic probably infected one-third of the world's population at the time — 500 million people. It killed between 50 million and 100 million; by contrast, Second World War deaths numbered around 60 million. Why is this catastrophe

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A greedy alignment-free distance estimator for phylogenetic inference

A greedy alignment-free distance estimator for phylogenetic inference | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Alignment-free sequence comparison approaches have been garnering increasing interest in various data- and compute-intensive applications such as phylogenetic inference for large-scale sequences. While k-mer based methods are predominantly used in real applications, the average common substring (ACS) approach is emerging as one of the prominent alignment-free approaches. This ACS approach has been further generalized by some recent work, either greedily or exactly, by allowing a bounded number of mismatches in the common substrings. We present ALFRED-G, a greedy alignment-free distance estimator for phylogenetic tree reconstruction based on the concept of the generalized ACS approach. In this algorithm, we have investigated a new heuristic to efficiently compute the lengths of common strings with mismatches allowed, and have further applied this heuristic to phylogeny reconstruction. Performance evaluation using real sequence datasets shows that our heuristic is able to reconstruct comparable, or even more accurate, phylogenetic tree topologies than the kmacs heuristic algorithm at highly competitive speed. ALFRED-G is an alignment-free heuristic for evolutionary distance estimation between two biological sequences. This algorithm is implemented in C++ and has been incorporated into our open-source ALFRED software package (
http://alurulab.cc.gatech.edu/phylo

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Novel vaccine therapy can generate immune responses in patients with HPV-related head and neck cancer

A novel vaccine therapy can generate immune responses in patients with head and neck squamous cell carcinoma (HNSCCa), according to researchers at the Abramson Cancer Center of the University of Pennsylvania.
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A lightning-fast flu virus detector

A lightning-fast flu virus detector | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Scientists have built a novel biosensor for the rapid detection of human influenza A virus using a modified poly (3,4-ethylenedioxythiophene) conducting polymer. The voltage-sensing detector was almost 100 times more sensitive than conventional tests, and distinguished between human and avian flu strains. The use of this biosensor may provide point-of-care testing and help prevent the outbreak of flu pandemics.
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A Primer for Computational Biology — A Primer for Computational Biology 1.0 documentation

Free online book
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10 ways to use social media to get your research noticed

10 ways to use social media to get your research noticed | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Four experts offer their advice on getting the most out of social media as an academic
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Iron availability affects West Nile virus infection in its mosquito vector

Iron availability affects West Nile virus infection in its mosquito vector | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Mosquitoes are responsible for transmission of viruses, including dengue, West Nile and chikungunya viruses. Female mosquitoes are infected when they blood-feed on vertebrates, a required step for oogenesis. During this process, mosquitoes encounter high iron loads. Since iron is an essential nutrient for most organisms, including pathogens, one of the defense mechanisms for the host includes sequestration of iron away from the invading pathogen. Here, we determine whether iron availability affects viral replication in mosquitoes. To elucidate effect of iron availability on mosquito cells during infection, Culex cells were treated with either ferric ammonium citrate (FAC) or the iron chelator, deferoxamine (DFX). Real time RT-PCR was performed using ferritin (heavy chain) and NRAMP as a measure of iron homeostasis in cells. To determine iron requirement for viral replication, Culex cells were knocked down for NRAMP using dsRNA. Finally, the results were validated in Culex mosquito-infection model, by treating infected mosquitoes with DFX to reduce iron levels. Our results show that infection of Culex cells led to induction in levels of ferritin (heavy chain) and NRAMP mRNAs in time-dependent manner. Results also showed that treatment of cells with FAC, reduced expression of NRAMP (iron transporter) and increase levels of ferritin (heavy chain). Interestingly, increasing iron levels increased viral titers; while reducing intracellular iron levels, either by NRAMP knock-down or using DFX, reduced viral titers. The results from Culex mosquito infection showed that mosquitoes treated with DFX had reduced viral titers compared with untreated controls in midgut as well as carcass 8 days pi. Saliva from mosquitoes treated with DFX also showed reduced viral titers compared with untreated controls, indicating low viral transmission capacity. Our results indicate that iron is required for viral replication in mosquito cells. Mosquitoes respond to viral infection, by inducing expression of heavy chain ferritin, which sequesters available iron, reducing its availability to virus infected cells. The data indicates that heavy chain ferritin may be part of an immune mechanism of mosquitoes in response to viral infections.
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