Viruses and Bioinformatics from Virology.uvic.ca
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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!

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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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Targeting TNF and TNF Receptor Pathway in HIV-1 Infection: from Immune Activation to Viral Reservoirs

Targeting TNF and TNF Receptor Pathway in HIV-1 Infection: from Immune Activation to Viral Reservoirs | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Several cellular functions such as apoptosis, cellular proliferation, inflammation, and immune regulation involve the tumor necrosis factor-α (TNF)/TNF receptor (TNFR) pathway. Human immunodeficiency virus 1 (HIV-1) interacts with the TNF/TNFR pathway. The activation of the TNF/TNFR pathway impacts HIV-1 replication, and the TNF/TNFR pathway is the target of HIV-1 proteins. A hallmark of HIV-1 infection is immune activation and inflammation with increased levels of TNF in the plasma and the tissues. Therefore, the control of the TNF/TNFR pathway by new therapeutic approaches could participate in the control of immune activation and impact both viral replication and viral persistence. In this review, we will describe the intricate interplay between HIV-1 proteins and TNF/TNFR signaling and how TNF/TNFR activation modulates HIV-1 replication and discuss new therapeutic approaches, especially anti-TNF therapy, that could control this pathway and ultimately favor the clearance of infected cells to cure HIV-infected patients.
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T Cell-Mediated Immunity towards Yellow Fever Virus and Useful Animal Models

T Cell-Mediated Immunity towards Yellow Fever Virus and Useful Animal Models | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The 17D line of yellow fever virus vaccines is among the most effective vaccines ever created. The humoral and cellular immunity elicited by 17D has been well characterized in humans. Neutralizing antibodies have long been known to provide protection against challenge with a wild-type virus. However, a well characterized T cell immune response that is robust, long-lived and polyfunctional is also elicited by 17D. It remains unclear whether this arm of immunity is protective following challenge with a wild-type virus. Here we introduce the 17D line of yellow fever virus vaccines, describe the current state of knowledge regarding the immunity directed towards the vaccines in humans and conclude with a discussion of animal models that are useful for evaluating T cell-mediated immune protection to yellow fever virus.
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The frenemies within: Viruses, retrotransposons, and plasmids that naturally infect Saccharomyces yeasts.

The frenemies within: Viruses, retrotransposons, and plasmids that naturally infect Saccharomyces yeasts. | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Viruses are a major focus of current research efforts because of their detrimental impact on humanity and their ubiquity within the environment. Bacteriophages have long been used to study host‐viru
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Peptide in frog slime can kill flu - Futurity

Peptide in frog slime can kill flu - Futurity | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A component of a South Indian frog's skin mucus kills H1 influenza viruses. "I was almost knocked off my chair," says Joshy Jacob.

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How CRISPR can fight antibiotic-resistant infections

How CRISPR can fight antibiotic-resistant infections | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Researchers are developing a probiotic to make disease-causing bacteria self-destruct.
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Scientists engineer human-germ hybrid molecules to attack drug-resistant bacteria

Scientists engineer human-germ hybrid molecules to attack drug-resistant bacteria | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Inspired by viruses that attack and kill bacteria, researchers at The Rockefeller University have created an entirely new weapon against disease-causing bacteria that shows great promis
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Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families

Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Emerging infectious diseases are often characterized by host switching events, in which a pathogen jumps from its original host to infect a novel species. However, given the ecological and genetic barriers a virus must overcome to jump species and adapt to new hosts, it might be reasonable to assume that successful cross-species transmission is a relatively rare occurrence and that viruses are instead more likely to co-diverge with their hosts. Using a comparative co-phylogenetic analysis performed at the scale of virus family we have revealed that co-divergence is relatively infrequent among 19 diverse families of RNA and DNA viruses, such that cross-species transmission plays a central role in virus evolution. Host jumping was especially common in viruses with RNA genomes, and by drawing broad-scale comparisons our analysis reveals which virus families have a greater propensity to jump species barriers and hence successfully emerge in new hosts. Finally, our data suggest that sampling more viruses increases the likelihood of detecting host jumping events.
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GeoVax Awarded $658,000 NIH Grant for its HIV Vaccine Program

ATLANTA, GA - (NewMediaWire) - April 03, 2017 - GeoVax Labs, Inc. (OTCQB: GOVX), a biotechnology company developing human vaccines, announced today it ha

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The N50 filtering problem

The N50 filtering problem | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
This is the second in a series of posts where we explain the N50 (Nx) metric, discuss the problems surrounding it, give solutions to those problems, and suggest an alternative N50 metric for transc…
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Zika virus

Zika virus | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Created using more than 10,000 images captured by a high-resolution technique, called cryo-electron microscopy, this illustration of the Zika virus reveals something like a topographic map of the infecting agent. This zoomed-in illustration shows not just the envelope that encircles the virus, but also the RNA (in yellow) that lives inside it and allows the virus to replicate.

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Identification of HIV-1 Tat-Associated Proteins Contributing to HIV-1 Transcription and Latency

Identification of HIV-1 Tat-Associated Proteins Contributing to HIV-1 Transcription and Latency | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Human immunodeficiency virus type 1 (HIV-1) Tat is a virus-encoded trans-activator that plays a central role in viral transcription. We used our recently developed parallel analysis of in vitro translated open reading frames (ORFs) (PLATO) approach to identify host proteins that associate with HIV-1 Tat. From this proteomic assay, we identify 89 Tat-associated proteins (TAPs). We combine our results with other datasets of Tat or long terminal repeat (LTR)-associated proteins. For some of these proteins (NAT10, TINP1, XRCC5, SIN3A), we confirm their strong association with Tat. These TAPs also suppress Tat-mediated HIV-1 transcription. Removing suppression of HIV-1 transcription benefits the reversal of post-integrated, latent HIV-1 proviruses. We demonstrate that these transcriptionally suppressing TAPs contribute to HIV-1 latency in Jurkat latency (J-LAT) cells. Therefore, our proteomic analysis highlights the previously unappreciated TAPs that play a role in maintaining HIV-1 latency and can be further studied as potential pharmacological targets for the “shock and kill” HIV-1 cure strategy.
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Replication and Oncolytic Activity of an Avian Orthoreovirus in Human Hepatocellular Carcinoma Cells

Replication and Oncolytic Activity of an Avian Orthoreovirus in Human Hepatocellular Carcinoma Cells | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Oncolytic viruses are cancer therapeutics with promising outcomes in pre-clinical and clinical settings. Animal viruses have the possibility to avoid pre-existing immunity in humans, while being safe and immunostimulatory. We isolated an avian orthoreovirus (ARV-PB1), and tested it against a panel of hepatocellular carcinoma cells. We found that ARV-PB1 replicated well and induced strong cytopathic effects. It was determined that one mechanism of cell death was through syncytia formation, resulting in apoptosis and induction of interferon stimulated genes (ISGs). As hepatitis C virus (HCV) is a major cause of hepatocellular carcinoma worldwide, we investigated the effect of ARV-PB1 against cells already infected with this virus. Both HCV replicon-containing and infected cells supported ARV-PB1 replication and underwent cytolysis. Finally, we generated in silico models to compare the structures of human reovirus- and ARV-PB1-derived S1 proteins, which are the primary targets of neutralizing antibodies. Tertiary alignments confirmed that ARV-PB1 differs from its human homolog, suggesting that immunity to human reoviruses would not be a barrier to its use. Therefore, ARV-PB1 can potentially expand the repertoire of oncolytic viruses for treatment of human hepatocellular carcinoma and other malignancies.
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Phage Therapy Saves Patient from Drug-Resistant Microbes | GEN Genetic Engineering & Biotechnology News - Biotech from Bench to Business | GEN

Phage Therapy Saves Patient from Drug-Resistant Microbes | GEN Genetic Engineering & Biotechnology News - Biotech from Bench to Business | GEN | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Intravenous viruses used to target deadly bacterium; dramatic case suggests potential alternative to failing antibiotics
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Epidemiology and genotype distribution of human papillomavirus (HPV) in Southwest China: a cross-sectional five years study in non-vaccinated women

Large-size data on type-specific HPV prevalence in Southwest China are required to estimate the cervical cancer burden in the country and to prepare for HPV-based cervical screening program and further HPV vaccination of China. This HPV study is a pooled analysis of data from five years in Chongqing of China, which is cross-sectional in design using data collecting. 


The type-specific prevalence rate of HPV 16 and HPV 18 were a little lower than the mean of international meta-analyses. Single HPV genotype infection was predominantly detected in different groups of cervical lesions in Chongqing, and HPV16, 52, 58 were the priority HPV types. The HPV genotyping study was found to be valuable for planning further preventive program for cervical cancer.

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Towards a structural understanding of RNA synthesis by negative strand RNA viral polymerases

Towards a structural understanding of RNA synthesis by negative strand RNA viral polymerases | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Highlights
• Crystal and cryo-EM structures of NSV polymerases influenza, La Crosse and VSV.
• Segmented and non-segmented NSV polymerases have a similar extended core architecture.
• Influenza and LACV structures show how the vRNA promoter is bound.
• The cap-snatching mechanism of influenza polymerase (sNSV) is explained.
• VSV (nsNSV) capping domains block product exit and thus need to rearrange.
• Separate exit channels for template and product allow replication within the RNP context.

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Fast and accurate phylogeny reconstruction using filtered spaced-word matches | Bioinformatics | Oxford Academic

Fast and accurate phylogeny reconstruction using filtered spaced-word matches | Bioinformatics | Oxford Academic | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
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Chikungunya Virus (CHIKV) in the Americas

Chikungunya Virus (CHIKV) in the Americas | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

22532 suspected cases (22532 in Central and South America, 0 in the Caribbean, 0 in North America), 7358 confirmed cases (14 North America, 5 Caribbean, 7336 Central and South America) (7350 autochthonous transmission and 8 travel related imported cases)


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New antibody test can detect person’s risk for developing HPV-related cancer of the oropharynx

New antibody test can detect person’s risk for developing HPV-related cancer of the oropharynx | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Cancer of the oropharynx has become increasingly common: In the United States alone, the number of newly diagnosed cases has tripled over the past three decades. About 70 percent of these tumors are caused by infection with human papillomavirus (HPV) type 16.

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An aspirin a day keeps the grim reaper away

An aspirin a day keeps the grim reaper away | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Low-dose aspirin is good for you. Any brand of aspirin  will do, Bayer or otherwise. Should you take an aspirin every day t
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The N50 misassembly problem

The N50 misassembly problem | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
This is the third in a series of posts where we explain the N50 (Nx) metric, discuss the problems surrounding it, give solutions to those problems, and suggest an alternative N50 metric for transcr…
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Needle free vaccine delivery on the horizon

Researchers are developing a new type of drug delivery system that could allow people to self administer vaccines without the use of needles. Ben Gruber ha

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New antibody test can detect person’s risk for developing HPV-related cancer of the oropharynx

New antibody test can detect person’s risk for developing HPV-related cancer of the oropharynx | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Cancer of the oropharynx has become increasingly common: In the United States alone, the number of newly diagnosed cases has tripled over the past three decades. About 70 percent of these tumors are caused by infection with human papillomavirus (HPV) type 16.

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