Viruses and Bioinformatics from Virology.uvic.ca
89.9K views | +38 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.
Scooped by Ed Rybicki
Scoop.it!

Innate Immune Responses of Bat and Human Cells to Filoviruses

Marburg (MARV) and Ebola (EBOV) viruses are zoonotic pathogens that cause severe hemorrhagic fever in humans. The natural reservoir of MARV is the Egyptian rousette bat (Rousettus aegyptiacus); that of EBOV is unknown but believed to be another bat species. The Egyptian rousette develops subclinical productive infection with MARV but is refractory to EBOV. Interaction of filoviruses with hosts is greatly affected by the viral interferon (IFN)-inhibiting domains (IID). Our study was aimed at characterization of innate immune responses to filoviruses and the role of filovirus IID in bat and human cells. The study demonstrated that EBOV and MARV replicate to similar levels in all tested cell lines, indicating that permissiveness for EBOV at cell and organism levels do not necessarily correlate. Filoviruses, particularly MARV, induced a potent innate immune response in rousette cells, which was generally stronger than that in human cells. Both EBOV VP35 and VP24 IID were found to suppress the innate immune response in rousette cells, but only VP35 IID appeared to promote virus replication. Along with IFN-α and IFN-β, IFN-γ was demonstrated to control filovirus infection in bat cells but not in human cells, suggesting host species specificity of the antiviral effect. The antiviral effects of bat IFNs appeared not to correlate with induction of IFN-stimulated genes 54 and 56, which were detected in human cells ectopically expressing bat IFN-α and IFN-β. As bat IFN-γ induced the type I IFN pathway, its antiviral effect is likely to be partially induced via cross talk.

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

Cas9-Mediated Viral Gene Targeting for Antiviral Therapy of Bombyx mori Nucleopolyhedrovirus

We developed a novel antiviral strategy by combining transposon-based transgenesis and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system for the direct cleavage of Bombyx mori nucleopolyhedrovirus (BmNPV) genome DNA to promote virus clearance in silkworms. We demonstrate that transgenic silkworms constitutively expressing Cas9 and guide RNAs targeting the BmNPV immediate early-1 (ie-1) and me53 genes effectively induce target-specific cleavage and subsequent mutagenesis, especially large (∼7-kbp) segment deletions in BmNPV genomes, and thus exhibit robust suppression of BmNPV proliferation. Transgenic animals exhibited higher and inheritable resistance to BmNPV infection than wild-type animals. Our approach will not only contribute to modern sericulture but also shed light on future antiviral therapy.

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

Nucleic and Amino Acid Sequences Support Structure-Based Viral Classification

Viral capsids protect nucleic acid genomes, which in turn encode capsid proteins. This tight coupling of protein shell and nucleic acids, together with strong functional constraints on capsid protein folding and architecture, leads to the hypothesis that capsid protein-coding nucleotide sequences may retain signatures of ancient viral evolution. We have been able to show that this is indeed the case, using the major capsid proteins of viruses forming icosahedral capsids. Importantly, we detected similarity at the nucleotide level between capsid protein-coding regions from viruses infecting cells belonging to all three domains of life, reproducing a previously established structure-based classification of icosahedral viral capsids.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

From crescent to mature virion: vaccinia virus assembly and maturation. - PubMed - NCBI


Abstract Vaccinia virus (VACV) has achieved unprecedented success as a live viral vaccine for smallpox which mitigated eradication of the disease. Vaccinia virus has a complex virion morphology and recent advances have been made to answer some of the key outstanding questions, in particular, the origin and biogenesis of the virion membrane, the transformation from immature virion (IV) to mature virus (MV), and the role of several novel genes, which were previously uncharacterized, but have now been shown to be essential for VACV virion formation. This new knowledge will undoubtedly contribute to the rational design of safe, immunogenic vaccine candidates, or effective antivirals in the future. This review endeavors to provide an update on our current knowledge of the VACV maturation processes with a specific focus on the initiation of VACV replication through to the formation of mature virions.

Viruses. 2014 Oct 7;6(10):3787-808. doi: 10.3390/v6103787. Research Support, Non-U.S. Gov't; Review

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

UniProt Protein Feature Viewer, a BioJS component

ProtVista is a comprehensive visualization tool for the graphical representation of protein sequence features in the UniProt Knowledgebase, experimental proteomics and variation public datasets. The complexity and relationships in this wealth of data pose a challenge in interpretation. Integrative visualization approaches such as provided by ProtVista are thus essential for researchers to understand the data and, for instance, discover patterns affecting function and disease associations.

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

node.dating: dating ancestors in phylogenetic trees in R | Bioinformatics | Oxford Academic

node.dating: dating ancestors in phylogenetic trees in R | Bioinformatics | Oxford Academic | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
more...
No comment yet.
Rescooped by Bwana Moses from Virology News
Scoop.it!

The sense behind retroviral anti-sense transcription

Retroviruses are known to rely extensively on the expression of viral proteins from the sense proviral genomic strand. Yet, the production of regulatory retroviral proteins from antisense-encoded viral genes is gaining research attention, due to their clinical significance. This report will discuss what is known about antisense transcription in Retroviridae, and provide new information about antisense transcriptional regulation through a comparison of Human Immunodeficiency Virus (HIV), Human T-cell Lymphotrophic Virus (HTLV-1) and endogenous retrovirus-K (ERVK) long terminal repeats (LTRs). We will attempt to demonstrate that the potential for antisense transcription is more widespread within retroviruses than has been previously appreciated, with this feature being the rule, rather than the exception.

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

Modelling Virus and Antibody Dynamics during Dengue Virus Infection Suggests a Role for Antibody in Virus Clearance

Modelling Virus and Antibody Dynamics during Dengue Virus Infection Suggests a Role for Antibody in Virus Clearance | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author Summary Dengue is a globally important viral disease. Despite this, there is still much unknown about the immunology, virology and epidemiology of dengue. As for all viral infections, the interaction between virus and immune response is a complex one. Using data collected from patients, we model how the virus replicates in an infected individual and how the human antibody response acts to control that replication. We show that the timing and magnitude of the growth and decline of virus and antibody levels in dengue-infected patients are consistent with antibody playing a key role in controlling infection. Our results are of use in the evaluation of potential antiviral drugs and vaccines.
more...
No comment yet.
Rescooped by Kenzibit from Next-generation sequencing (NGS)
Scoop.it!

Scientists assemble Zika virus mosquito genome from scratch

Scientists assemble Zika virus mosquito genome from scratch | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

A multi-institutional team has developed a new way to sequence genomes, which can assemble the genome of an organism, entirely from scratch, dramatically cheaper and faster.


Via Integrated DNA Technologies
more...
No comment yet.
Scooped by Bwana Moses
Scoop.it!

The Next Plague - Viruses: The Superstars Among Pathogenic Plague Microbes | American Council on Science and Health

The Next Plague - Viruses: The Superstars Among Pathogenic Plague Microbes | American Council on Science and Health | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The Next Plague - Viruses: The Superstars Among Pathogenic Plague Microbes https://t.co/WaSpyzyHuy
more...
No comment yet.
Rescooped by Chris Upton + helpers from Plagiarism
Scoop.it!

New report shares details about the anti-plagiarism software market 2016 global analysis and forecast to 2020 - WhaTech

Sandler Research, Global Anti-Plagiarism Software Market, Anti-Plagiarism Software Industry, Anti-Plagiarism Software Market Outlook, Anti-Plagiarism Software Market Research, Anti-Plagiarism Software Market Growth, Anti-Plagiarism Software Market...
Via Joel Bloch
more...
No comment yet.
Rescooped by Chris Upton + helpers from Virology News
Scoop.it!

Sustained fecal-oral human-to-human transmission following a zoonotic event

Sustained fecal-oral human-to-human transmission following a zoonotic event | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Bacterial, viral and parasitic zoonotic pathogens that transmit via the fecal-oral route have a major impact on global health. However, the mechanisms underlying the emergence of such pathogens from the animal reservoir and their persistence in the human population are poorly understood. Here, we present a framework of human-to-human transmission of zoonotic pathogens that considers the factors relevant for fecal-oral human-to-human transmission route at the levels of host, pathogen, and environment. We discuss current data gaps and propose future research directions.


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

Half Of All PhD Students Suffer From Psychological Distress

Half Of All PhD Students Suffer From Psychological Distress | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
PhD students are far more at risk from suffering from a mental health problem than the general population, according to a new study.
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Nucleic and Amino Acid Sequences Support Structure-Based Viral Classification

Viral capsids ensure viral genome integrity by protecting the enclosed nucleic acids. Interactions between the genome and capsid and between individual capsid proteins (i.e., capsid architecture) are intimate and are expected to be characterized by strong evolutionary conservation. For this reason, a capsid structure-based viral classification has been proposed as a way to bring order to the viral universe. The seeming lack of sufficient sequence similarity to reproduce this classification has made it difficult to reject structural convergence as the basis for the classification. We reinvestigate whether the structure-based classification for viral coat proteins making icosahedral virus capsids is in fact supported by previously undetected sequence similarity. Since codon choices can influence nascent protein folding cotranslationally, we searched for both amino acid and nucleotide sequence similarity. To demonstrate the sensitivity of the approach, we identify a candidate gene for the pandoravirus capsid protein. We show that the structure-based classification is strongly supported by amino acid and also nucleotide sequence similarities, suggesting that the similarities are due to common descent. The correspondence between structure-based and sequence-based analyses of the same proteins shown here allow them to be used in future analyses of the relationship between linear sequence information and macromolecular function, as well as between linear sequence and protein folds.

Ed Rybicki's insight:
Nice piece of work: using structure to infer ancient relationships has been done for a while, but getting backup from sequence data is really useful.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

What’s N50?

What’s N50? | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
This is the first 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…
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Animal Models of Zika Virus Infection, Pathogenesis, and Immunity

Zika virus (ZIKV) is an emerging mosquito-transmitted flavivirus that now causes epidemics affecting millions of people on multiple continents. The virus has received global attention because of some of its unusual epidemiological and clinical features, including persistent infection in the male reproductive tract and sexual transmission, an ability to cross the placenta during pregnancy and infect the developing fetus to cause congenital malformations, and its association with Guillain-Barré syndrome in adults. This past year has witnessed an intensive effort by the global scientific community to understand the biology of ZIKV and to develop pathogenesis models for the rapid testing of possible countermeasures. Here, we review the recent advances in and utility and limitations of newly developed mouse and nonhuman primate models of ZIKV infection and pathogenesis.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Prediction of virus-host protein-protein interactions mediated by short linear motifs

Prediction of virus-host protein-protein interactions mediated by short linear motifs | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Short linear motifs in host organisms proteins can be mimicked by viruses to create protein-protein interactions that disable or control metabolic pathways. Given that viral linear motif instances of host motif regular expressions can be found by chance, it is necessary to develop filtering methods of functional linear motifs. We conduct a systematic comparison of linear motifs filtering methods to develop a computational approach for predicting motif-mediated protein-protein interactions between human and the human immunodeficiency virus 1 (HIV-1). We implemented three filtering methods to obtain linear motif sets: 1) conserved in viral proteins (C), 2) located in disordered regions (D) and 3) rare or scarce in a set of randomized viral sequences (R). The sets C,D,R are united and intersected. The resulting sets are compared by the number of protein-protein interactions correctly inferred with them – with experimental validation. The comparison is done with HIV-1 sequences and interactions from the National Institute of Allergy and Infectious Diseases (NIAID). The number of correctly inferred interactions allows to rank the interactions by the sets used to deduce them: D∪R and C. The ordering of the sets is descending on the probability of capturing functional interactions. With respect to HIV-1, the sets C∪R, D∪R, C∪D∪R infer all known interactions between HIV1 and human proteins mediated by linear motifs. We found that the majority of conserved linear motifs in the virus are located in disordered regions. We have developed a method for predicting protein-protein interactions mediated by linear motifs between HIV-1 and human proteins. The method only use protein sequences as inputs. We can extend the software developed to any other eukaryotic virus and host in order to find and rank candidate interactions. In future works we will use it to explore possible viral attack mechanisms based on linear motif mimicry.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Hydrophobic proteins on virus surfaces can help purify vaccines

Hydrophobic proteins on virus surfaces can help purify vaccines | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Through experimental and computational tests, new research expands on the theory of virus surface hydrophobicity. By being slightly water-repellent, the outer layers of proteins in virus capsids affect how it interacts with cells and the environment. Understanding this more can improve vaccine production and virus detection.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

HiLive: real-time mapping of illumina reads while sequencing | Bioinformatics | Oxford Academic

HiLive: real-time mapping of illumina reads while sequencing | Bioinformatics | Oxford Academic | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
more...
No comment yet.
Scooped by burkesquires
Scoop.it!

Ross River Virus: Many Vectors and Unusual Hosts Make for an Unpredictable Pathogen

Ross River Virus: Many Vectors and Unusual Hosts Make for an Unpredictable Pathogen | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
@GertrudRey #ZIKA Ross River Virus, another MBV, can be transmitted from animals to humans.

https://t.co/1X2HmZO7PP
more...
No comment yet.
Rescooped by Kenzibit from Virology News
Scoop.it!

The sense behind retroviral anti-sense transcription

Retroviruses are known to rely extensively on the expression of viral proteins from the sense proviral genomic strand. Yet, the production of regulatory retroviral proteins from antisense-encoded viral genes is gaining research attention, due to their clinical significance. This report will discuss what is known about antisense transcription in Retroviridae, and provide new information about antisense transcriptional regulation through a comparison of Human Immunodeficiency Virus (HIV), Human T-cell Lymphotrophic Virus (HTLV-1) and endogenous retrovirus-K (ERVK) long terminal repeats (LTRs). We will attempt to demonstrate that the potential for antisense transcription is more widespread within retroviruses than has been previously appreciated, with this feature being the rule, rather than the exception.

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

The blood DNA virome in 8,000 humans

The blood DNA virome in 8,000 humans | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Novel sequencing technologies offer insight into the virome in human samples. Here, we identify the viral DNA sequences in blood of over 8,000 individuals undergoing whole genome sequencing. This approach serves to identify 94 viruses; however, many are shown to reflect widespread DNA contamination of commercial reagents or of environmental origin. While this represents a significant limitation to reliably identify novel viruses infecting humans, we could confidently detect sequences and quantify abundance of 19 human viruses in 42% of individuals. Ancestry, sex, and age were important determinants of viral prevalence. This large study calls attention on the challenge of interpreting next generation sequencing data for the identification of novel viruses. However, it serves to categorize the abundance of human DNA viruses using an unbiased technique.
more...
No comment yet.
Rescooped by Bwana Moses from DNA and RNA research
Scoop.it!

Dramatic evolution within human genome may have been caused by malaria parasite

Dramatic evolution within human genome may have been caused by malaria parasite | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

A genetic mutation that protects people from a common form of malaria spread like wildfire in sub-Saharan Africa about 42,000 years ago, according to a new study. Today, it’s nearly impossible to find somebody from this region who doesn’t have it. That makes the mutation one of the swiftest, strongest changes to the human genome yet seen—though it remains a mystery why this particular disease sparked such a dramatic evolutionary response.


Via Integrated DNA Technologies
more...
No comment yet.
Scooped by Bwana Moses
Scoop.it!

Antigenic and immunosuppressive properties of a trimeric recombinant transmembrane envelope protein gp41 of HIV-1.

Antigenic and immunosuppressive properties of a trimeric recombinant transmembrane envelope protein gp41 of HIV-1. | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The transmembrane envelope (TM) protein gp41 of the human immunodeficiency virus-1 (HIV-1) plays an important role during virus infection inducing the fusio
more...
No comment yet.
Rescooped by Chris Upton + helpers from Virology News
Scoop.it!

Mimivirus: leading the way in the discovery of giant viruses of amoebae : Nature Reviews Microbiology : Nature Research

Mimivirus: leading the way in the discovery of giant viruses of amoebae : Nature Reviews Microbiology : Nature Research | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The accidental discovery of the giant virus of amoeba — Acanthamoeba polyphaga mimivirus (APMV; more commonly known as mimivirus) — in 2003 changed the field of virology. Viruses were previously defined by their submicroscopic size, which probably prevented the search for giant viruses, which are visible by light microscopy. Extended studies of giant viruses of amoebae revealed that they have genetic, proteomic and structural complexities that were not thought to exist among viruses and that are comparable to those of bacteria, archaea and small eukaryotes. The giant virus particles contain mRNA and more than 100 proteins, they have gene repertoires that are broader than those of other viruses and, notably, some encode translation components. The infection cycles of giant viruses of amoebae involve virus entry by amoebal phagocytosis and replication in viral factories. In addition, mimiviruses are infected by virophages, defend against them through the mimivirus virophage resistance element (MIMIVIRE) system and have a unique mobilome. Overall, giant viruses of amoebae, including mimiviruses, marseilleviruses, pandoraviruses, pithoviruses, faustoviruses and molliviruses, challenge the definition and classification of viruses, and have increasingly been detected in humans.


Via Ed Rybicki
more...
No comment yet.