Viruses and Bioinformatics from Virology.uvic.ca
92.5K views | +1 today
Follow
 
Scooped by Ed Rybicki
onto Viruses and Bioinformatics from Virology.uvic.ca
Scoop.it!

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!

more...
No comment yet.
Viruses and Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
Your new post is loading...
Your new post is loading...
Scooped by Chris Upton + helpers
Scoop.it!

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

more...
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.
Rescooped by Kenzibit from Virology News
Scoop.it!

Health Ministry to provide free HPV vaccine to Thai children

Health Ministry to provide free HPV vaccine to Thai children | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
BANGKOK – The Permanent Secretary of the Public Health Ministry disclosed that free HPV vaccine will be distributed to Thai children this July to maximize the prevention of rectal cancer in Thailand next year. Public Health Ministry Permanent Secretary Sophon Mekthon said the Ministry of Public Health’s objective is to make sure Thai people are …

Via Ed Rybicki
more...
No comment yet.
Scooped by Bwana Moses
Scoop.it!

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.
more...
No comment yet.
Scooped by Bwana Moses
Scoop.it!

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]
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

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.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Viruses

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


Special Issue "Viruses of Protozoa"  

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

more...
No comment yet.
Scooped by Kenzibit
Scoop.it!

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.
more...
No comment yet.
Rescooped by Chris Upton + helpers from Virology News
Scoop.it!

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

Via Ed Rybicki
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

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

).
more...
No comment yet.
Scooped by Bwana Moses
Scoop.it!

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.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

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.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

A Primer for Computational Biology — A Primer for Computational Biology 1.0 documentation

Free online book
more...
No comment yet.
Rescooped by Kenzibit from Virology News
Scoop.it!

Host and viral traits predict zoonotic spillover from mammals

The majority of human emerging infectious diseases are zoonotic, with viruses that originate in wild mammals of particular concern (for example, HIV, Ebola and SARS). Understanding patterns of viral diversity in wildlife and determinants of successful cross-species transmission, or spillover, are therefore key goals for pandemic surveillance programs. However, few analytical tools exist to identify which host species are likely to harbour the next human virus, or which viruses can cross species boundaries. Here we conduct a comprehensive analysis of mammalian host–virus relationships and show that both the total number of viruses that infect a given species and the proportion likely to be zoonotic are predictable. After controlling for research effort, the proportion of zoonotic viruses per species is predicted by phylogenetic relatedness to humans, host taxonomy and human population within a species range—which may reflect human–wildlife contact. We demonstrate that bats harbour a significantly higher proportion of zoonotic viruses than all other mammalian orders. We also identify the taxa and geographic regions with the largest estimated number of ‘missing viruses’ and ‘missing zoonoses’ and therefore of highest value for future surveillance. We then show that phylogenetic host breadth and other viral traits are significant predictors of zoonotic potential, providing a novel framework to assess if a newly discovered mammalian virus could infect people.

Via Ed Rybicki
more...
No comment yet.
Rescooped by Kenzibit from Host Cell & Pathogen Interactions
Scoop.it!

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.
more...
No comment yet.
Scooped by Bwana Moses
Scoop.it!

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
more...
No comment yet.
Scooped by Bwana Moses
Scoop.it!

 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.
more...
No comment yet.
Rescooped by Kenzibit from Immunology and Biotherapies
Scoop.it!

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
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

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.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

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.
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

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.
more...
No comment yet.
Rescooped by Bwana Moses from Viral Modeling and Simulation
Scoop.it!

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.

Via burkesquires
more...
No comment yet.
Rescooped by burkesquires from Viral Modeling and Simulation
Scoop.it!

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.
more...
No comment yet.
Scooped by Bwana Moses
Scoop.it!

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.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

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.
more...
No comment yet.