Viruses and Bioinformatics from Virology.uvic.ca
88.7K views | +7 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...
Bemol Sido's comment, October 10, 2015 5:28 AM
Thanks. Nice.
Bwana Moses's comment, May 25, 2016 6:13 AM
Great work. Keep it going.
Scooped by Chris Upton + helpers
Scoop.it!

Phylogenetic trees in R using ggtree

Phylogenetic trees in R using ggtree | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Recently, one R package which I like to use for visualizing phylogenetic trees got published. It’s called ggtree, and as you might guess from the name it is based on the popular ggplot2 packa…
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

The effective rate of influenza reassortment is limited during human infection

The effective rate of influenza reassortment is limited during human infection | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary The influenza virus is an important cause of disease in the human population. During the course of an infection the virus can evolve rapidly. An important mechanism of viral evolution is reassortment, whereby different segments of the influenza genome are shuffled with other segments, producing new viral combinations. Here we study natural selection and reassortment during the course of infections occurring in human hosts. Examining viral genome sequence data from these infections, we note that genetic variants that were acquired during the growth of viruses in culture are selected against in the human host. In addition, we find evidence that the effective rate of reassortment is low. We suggest that the spatial separation between viruses in different parts of the host airway may limit the extent to which genetically distinct segments reassort with one another. Within the global population of influenza viruses, reassortment remains an important factor. However, reassortment is not so rapid as to exclude the possibility of interactions between genome segments affecting the course of influenza evolution during a single infection.
more...
No comment yet.
Rescooped by Kenzibit from Immunology
Scoop.it!

Human immunity against EBV—lessons from the clinic

Human immunity against EBV—lessons from the clinic | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The mammalian immune system has evolved over many millennia to be best equipped to protect the host from pathogen infection. In many cases, host and pathogen have coevolved, each acquiring sophisticated ways of inducing or protecting from disease. Epstein-Barr virus (EBV) is a human herpes virus that infects >90% of individuals. Despite its ubiquity, infection by EBV is often subclinical; this invariably reflects the necessity of the virus to preserve its host, balanced with sophisticated host immune mechanisms that maintain viral latency. However, EBV infection can result in various, and often fatal, clinical sequelae, including fulminant infectious mononucleosis, hemophagocytic lymphohistiocytosis, lymphoproliferative disease, organomegaly, and/or malignancy. Such clinical outcomes are typically observed in immunosuppressed individuals, with the most extreme cases being Mendelian primary immunodeficiencies (PIDs). Although these conditions are rare, they have provided critical insight into the cellular, biochemical, and molecular requirements for robust and long-lasting immunity against EBV infection. Here, we review the virology of EBV, mechanisms underlying disease pathogenesis in PIDs, and developments in immune cell–mediated therapy to treat disorders associated with or induced by EBV infection.

Via Gilbert C FAURE
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

1 tip for effective data visualization in Python

1 tip for effective data visualization in Python | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Data visualization is a common way to represent tabular data in an easier to parse format. In this tutorial, you’ll learn how to make effective data visualizations in Python.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

ORCAN—a web-based meta-server for real-time detection and functional annotation of orthologs

Summary: ORCAN (ORtholog sCANner) is a web-based meta-server for one-click evolutionary and functional annotation of protein sequences. The server combines information from the most popular orthology-prediction resources, including four tools and four online databases. Functional annotation utilizes five additional comparisons between the query and identified homologs, including: sequence similarity, protein domain architectures, functional motifs, Gene Ontology term assignments and a list of associated articles. Furthermore, the server uses a plurality-based rating system to evaluate the orthology relationships and to rank the reference proteins by their evolutionary and functional relevance to the query. Using a dataset of ∼1 million true yeast orthologs as a sample reference set, we show that combining multiple orthology-prediction tools in ORCAN increases the sensitivity and precision by 1–2 percent points.
Availability and Implementation: The service is available for free at http://www.combio.pl/orcan/.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

phyx: Phylogenetic tools for Unix

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 data sets.
Availability and Implementation: phyx runs on POSIX-compliant operating systems. Source code, installation instructions, documentation, and example files are freely available under the GNU General Public License at https://github.com/FePhyFoFum/phyx
more...
No comment yet.
Rescooped by Chris Upton + helpers from Virology News
Scoop.it!

U.S. poultry industry threatened by new strain of bird flu

U.S. poultry industry threatened by new strain of bird flu | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Avian influenza is spreading rapidly across Europe and Asia, roiling the global poultry industry as farmers destroy millions of infected birds.

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

Peering below the diffraction limit: robust and specific sorting of viruses with flow cytometry

Peering below the diffraction limit: robust and specific sorting of viruses with flow cytometry | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Viruses are incredibly diverse organisms and impact all forms of life on Earth; however, individual virions are challenging to study due to their small size and mass, precluding almost all direct imaging or molecular analysis. Moreover, like microbes, the overwhelming majority of viruses cannot be cultured, impeding isolation, replication, and study of interesting new species. Here, we introduce PCR-activated virus sorting, a method to isolate specific viruses from a heterogeneous population. Specific sorting opens new avenues in the study of uncultivable viruses, including recovering the full genomes of viruses based on genetic fragments in metagenomes, or identifying the hosts of viruses. PAVS enables specific sorting of viruses with flow cytometry. A sample containing a virus population is processed through a microfluidic device to encapsulate it into droplets, such that the droplets contain different viruses from the sample. TaqMan PCR reagents are also included targeting specific virus species such that, upon thermal cycling, droplets containing the species become fluorescent. The target viruses are then recovered via droplet sorting. The recovered virus genomes can then be analyzed with qPCR and next generation sequencing. We describe the PAVS workflow and demonstrate its specificity for identifying target viruses in a heterogeneous population. In addition, we demonstrate recovery of the target viruses via droplet sorting and analysis of their nucleic acids with qPCR.
more...
No comment yet.
Rescooped by Ed Rybicki from Virology News
Scoop.it!

The evolution of sex-specific virulence in infectious diseases

The evolution of sex-specific virulence in infectious diseases | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Many infectious diseases are more likely to progress to serious illness or death in men than in women, which has been attributed to a stronger immune response in women.
more...
Ed Rybicki's curator insight, February 3, 2:22 AM
Sure, they can say that, but I can't say there's a sex-linked trait that allows people to access other dimensions for shopping, grumble grumble...
Rescooped by Chris Upton + helpers from Best
Scoop.it!

Skim over 1700 TED talks with this spreadsheet (updated - 2016)

Skim over 1700 TED talks with this spreadsheet (updated - 2016) | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
More than 400 hours' worth of inspiring videos listed in one spreadsheet

 

TED features some of the most inspiring presentations you can watch today from the comfort of your home--with prominent speakers covering all sorts of topics, from technology to business to design to entertainment (and beyond). With more than 1,700 TED talks to watch, it isn't easy to choose your next video. This spreadsheet lists them for you.

 

It's a crowdsourced Google Docs spreadsheet, so it's not the most attractive way to look at available talks. You could instead browse videos on TED to see thumbnails of talks and filter them by subject or other factors. 


Via Dr. Stefan Gruenwald
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

How to Record Video Notes With MoocNote

MoocNote is a free tool for taking notes while watching a YouTube or Vimeo video. All of your notes are timestamped and all of your note
more...
No comment yet.
Scooped by Vern Paetkau
Scoop.it!

Your travels are Written in your body - Common Science Space

Your travels are Written in your body - Common Science Space | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Our bones, teeth and hair carry in them an encrypted GPS log of where we’ve been. If you lived in Seattle through your childhood and moved to Chicago ten years ago, that is indelibly written there. There will also be a record of what you’ve eaten recently. Advances in the science and technology of reading... Continue Reading
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Picornavirus RNA is protected from cleavage by ribonuclease during virion uncoating and transfer across  membranes

Picornavirus RNA is protected from cleavage by ribonuclease during virion uncoating and transfer across  membranes | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Picornaviruses are a large family of important human and animal pathogens that include poliovirus, human rhinovirus and foot-and-mouth disease virus. Picornaviruses enter the host cell by hijacking one of the vesicle-mediated cellular entry routes. However, once the virus is internalized, the mechanism used to deliver the viral genome across the vesicle membrane and into the cytoplasm remains unclear and even controversial. Here we show that for poliovirus (a member of the enterovirus genus), viral RNA is translocated directly from the particle, across the vesicle membrane into the lumen of liposomes in a receptor-decorated liposome model, or cytoplasm during infection, without being exposed to external medium surrounding the liposomes or the lumen of the entry vesicle, respectively. Our results suggest that the interaction between the viral particle and the membrane results in a specific mechanism of viral genome delivery that not only directs but also protects the RNA so that it reaches the cytoplasm as an intact and functional molecule. Additionally, we show that this is also the case for equine rhinitis A virus, a member of the aphthovirus genus, whose genome delivery mechanism has previously been thought to differ significantly from the mechanism used by enteroviruses suggesting the possibility of a unified mechanism of RNA delivery for the entire picornavirus family.
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

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

Cocktail of bacteria-killing viruses prevents cholera infection in animal models

Cocktail of bacteria-killing viruses prevents cholera infection in animal models | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Oral administration of a cocktail of three viruses, all of which specifically kill cholera bacteria, prevents infection and cholera-like symptoms in animal model experiments, report scientists from Tufts University School of Medicine (TUSM) and the Sackler School of Graduate Biomedical Sciences at Tufts inNature Communications on Feb. 1. The findings are the first to demonstrate the potential efficacy of bacteria-killing viruses—known as bacteriophages, or phages—as an orally administered preventive therapy against an acute gastrointestinal bacterial disease.

 

“While phage therapy has existed for decades, our study is proof-of-principle that it can be used to protect against infection and intervene in the transmission of disease,” said senior study author Andrew Camilli, Ph.D., Howard Hughes Medical Institute Investigator and professor of molecular biology and microbiology at TUSM. “We are hopeful that phages can someday be a tool in the public health arsenal that helps decrease the global burden of cholera, which affects up to four million people around the world each year.”

 

In previous work, Camilli and colleagues searched for phages that are specific for Vibrio cholerae, the bacterium that causes cholera—a potentially lethal infectious disease marked by severe diarrhea and dehydration. While phages that kill V. cholerae are abundant in nature, the team identified three strains that uniquely retained the ability to kill V. cholerae within the small intestine, the site of infection in humans. These phages function by targeting bacterial surface receptors normally involved in infectiousness, making them ideal therapeutic candidates—to develop resistance, cholera bacteria must acquire mutations in these receptors, which cause the bacteria to become less infectious.


Via Dr. Stefan Gruenwald, Kenzibit
more...
Ed Rybicki's curator insight, February 13, 5:08 AM
While this great, it is a modern vindication of something no less a person that the co-discoverer of phages himself, Felix d'Herelle, advocated as a cure for dysentery - and put into practice in India in the 1920s, apparently (https://rybicki.wordpress.com/2015/02/17/happy-centenary-phages/). He was also the godfather of work done at the Eliava Institute in Georgia, which really laid the foundation of phage therapy.
Ed Rybicki's comment, February 13, 5:09 AM
Thanks! Great stuff.
Scooped by Ed Rybicki
Scoop.it!

Genome Sequence of the First Coleopteran Iflavirus Isolated from Western Corn Rootworm

Western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae), is the worst insect pest of maize in North America and is invasive in Europe (1). Management of WCR in the United States depends primarily on transgenic plants that express Bacillus thuringiensis (Bt) insecticidal toxins, but populations resistant to Bt toxins have been reported (2). Hence, novel control strategies for WCR management are needed. Small RNA viruses of insects, such as iflaviruses, have potential for insect pest management. Several iflaviruses have recently been discovered in the insect orders Hemiptera (3), Lepidoptera (4), and Hymenoptera (5–7). Here, we report the genome sequence of an iflavirus from WCR, the first identified from Coleoptera.

Ed Rybicki's insight:
Interesting because it could shed some light on evolutionary descent of these viruses - and push back the origin of picorna-like viruses by a good few million years.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

KNIME4NGS: a comprehensive toolbox for next generation sequencing analysis

Summary: Analysis of Next Generation Sequencing (NGS) data requires the processing of large datasets by chaining various tools with complex input and output formats. In order to automate data analysis, we propose to standardize NGS tasks into modular workflows. This simplifies reliable handling and processing of NGS data, and corresponding solutions become substantially more reproducible and easier to maintain. Here, we present a documented, linux-based, toolbox of 42 processing modules that are combined to construct workflows facilitating a variety of tasks such as DNAseq and RNAseq analysis. We also describe important technical extensions. The high throughput executor (HTE) helps to increase the reliability and to reduce manual interventions when processing complex datasets. We also provide a dedicated binary manager that assists users in obtaining the modules’ executables and keeping them up to date. As basis for this actively developed toolbox we use the workflow management software KNIME.
Availability and Implementation: See http://ibisngs.github.io/knime4ngs for nodes and user manual (GPLv3 license)
more...
No comment yet.
Rescooped by Chris Upton + helpers from Virology News
Scoop.it!

Proliferation of bird flu outbreaks raises risk of human pandemic

Proliferation of bird flu outbreaks raises risk of human pandemic | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The global spread of bird flu and the number of viral strains currently circulating and causing infections have reached unprecedented levels, raising the risk of a potential human outbreak, according to disease experts.

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

Self-assembly of hexahistidine-tagged tobacco etch virus capsid protein into microfilaments that induce IgG2-specific response against a soluble porcine reproductive and respiratory syndrome virus ...

Self-assembly of hexahistidine-tagged tobacco etch virus capsid protein into microfilaments that induce IgG2-specific response against a soluble porcine reproductive and respiratory syndrome virus ... | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Assembly of recombinant capsid proteins into virus-like particles (VLPs) still represents an interesting challenge in virus-based nanotechnologies. The structure of VLPs has gained importance for the development and design of new adjuvants and antigen carriers. The potential of Tobacco etch virus capsid protein (TEV CP) as adjuvant has not been evaluated to date. Two constructs for TEV CP expression in Escherichia coli were generated: a wild-type version (TEV-CP) and a C-terminal hexahistidine (His)-tagged version (His-TEV-CP). Although both versions were expressed in the soluble fraction of E. coli lysates, only His-TEV-CP self-assembled into micrometric flexuous filamentous VLPs. In addition, the His-tag enabled high yields and facilitated purification of TEV VLPs. These TEV VLPs elicited broader IgG2-specific antibody response against a novel porcine reproductive and respiratory syndrome virus (PRRSV) protein when compared to the potent IgG1 response induced by the protein alone. His-TEV CP was purified by immobilized metal affinity chromatography and assembled into VLPs, some of them reaching 2-μm length. TEV VLPs administered along with PRRSV chimeric protein changed the IgG2/IgG1 ratio against the chimeric protein, suggesting that TEV CP can modulate the immune response against a soluble antigen.
Ed Rybicki's insight:
Plant viruses: ultimate nanoparticles B-)
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Three novel bacteriophages isolated from the East African Rift Valley soda lakes

Soda lakes are unique environments in terms of their physical characteristics and the biology they harbour. Although well studied with respect to their microbial composition, their viral compositions have not, and consequently few bacteriophages that infect bacteria from haloalkaline environments have been described. Bacteria were isolated from sediment samples of lakes Magadi and Shala. Three phages were isolated on two different Bacillus species and one Paracoccus species using agar overlays. The growth characteristics of each phage in its host was investigated and the genome sequences determined and analysed by comparison with known phages. Phage Shbh1 belongs to the family Myoviridae while Mgbh1 and Shpa belong to the Siphoviridae family. Tetranucleotide usage frequencies and G + C content suggests that Shbh1 and Mgbh1 do not regularly infect, and have therefore not evolved with, the hosts they were isolated on here. Shbh1 was shown capable of infecting two different Bacillus species from the two different lakes demonstrating its potential broad-host range. Comparative analysis of their genome sequence with known phages revealed that, although novel, Shbh1 does share substantial amino acid similarity with previously described Bacillus infecting phages (Grass, phiNIT1 and phiAGATE) and belongs to the Bastille group, while Mgbh1 and Shpa are highly novel. The addition of these phages to current databases should help with metagenome/metavirome annotation efforts. We describe a highly novel Paracoccus infecting virus (Shpa) which together with NgoΦ6 and vB_PmaS_IMEP1 is one of only three phages known to infect Paracoccus species but does not show similarity to these phages.
Ed Rybicki's insight:
By my good friends and colleagues at UWC!  Nice one, guys B-)
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 reached 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, utility, and limitations of newly developed mouse and non-human primate models of ZIKV infection and pathogenesis.
more...
No comment yet.
Rescooped by Chris Upton + helpers from Best
Scoop.it!

Top 10 Data Mining Algorithms, Explained

Top 10 Data Mining Algorithms, Explained | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Top 10 data mining algorithms, selected by top researchers, are explained here, including what do they do, the intuition behind the algorithm, available implementations of the algorithms, why use them, and interesting applications.


Via Fernando Gil, Dr. Stefan Gruenwald
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Government scientists go rogue. What a great idea!

Government scientists go rogue. What a great idea! | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Government scientists are very worried, apparently with good reason, that their new boss wants to muzzle them. They've just come up wit
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Emergence of a Viral RNA Polymerase Variant during Gene Copy Number Amplification Promotes Rapid Evolution of Vaccinia Virus

IMPORTANCE Viruses can evolve quickly to defeat host immune functions. For poxviruses, little is known about how multiple adaptive mutations emerge in populations at the same time. In this study, we uncovered a means of vaccinia virus adaptation involving the accumulation of distinct genetic variants within a single population. We identified adaptive point mutations in the viral RNA polymerase gene A24R and, surprisingly, found that one of these mutations activates the nucleic acid sensing factor PKR. We also found that gene copy number variation (CNV) can provide dual benefits to evolving virus populations, including evidence that CNV facilitates the accumulation of a point mutation distant from the expanded locus. Our data suggest that transient CNV can accelerate the fixation of mutations conferring modest benefits, or even fitness trade-offs, and highlight how structural variation might aid poxvirus adaptation through both direct and indirect actions.
more...
No comment yet.