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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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Virology and Bioinformatics from Virology.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: | Virology and Bioinformatics from Virology.ca | Scoop.it

get in touch if you want to help curate this topic

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A Bioinformatics Pipeline for the Analyses of Viral Escape Dynamics and Host Immune Responses during an Infection. - Biomed Res Int. 2014

A Bioinformatics Pipeline for the Analyses of Viral Escape Dynamics and Host Immune Responses during an Infection. - Biomed Res Int. 2014 | Virology and Bioinformatics from Virology.ca | Scoop.it

Rapidly mutating viruses, such as hepatitis C virus (HCV) and HIV, have adopted evolutionary strategies that allow escape from the host immune response via genomic mutations. Recent advances in high-throughput sequencing are reshaping the field of immuno-virology of viral infections, as these allow fast and cheap generation of genomic data. However, due to the large volumes of data generated, a thorough understanding of the biological and immunological significance of such information is often difficult. This paper proposes a pipeline that allows visualization and statistical analysis of viral mutations that are associated with immune escape. Taking next generation sequencing data from longitudinal analysis of HCV viral genomes during a single HCV infection, along with antigen specific T-cell responses detected from the same subject, we demonstrate the applicability of these tools in the context of primary HCV infection. We provide a statistical and visual explanation of the relationship between cooccurring mutations on the viral genome and the parallel adaptive immune response against HCV.

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Constructing Vaccines [HD Animation] - YouTube

See an organised list of all the animations: http://doctorprodigious.wordpress.com/hd-animations/
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Ewan's Blog: bioinformatician at large: Scaling up bioinformatics training online

Ewan's Blog: bioinformatician at large: Scaling up bioinformatics training online | Virology and Bioinformatics from Virology.ca | Scoop.it
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CDC Media Statement on Newly Discovered Smallpox Samples

On July 1, 2014, the National Institutes of Health (NIH) notified the appropriate regulatory agency, the Division of Select Agents and Toxins (DSAT) of the Centers for Disease Control and Prevention (CDC), that employees discovered vials labeled ”variola,” commonly known as smallpox, in an unused portion of a storage room in a Food and Drug Administration (FDA) laboratory located on the NIH Bethesda campus.

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Evolution and Ecology of Influenza A Viruses.

Wild aquatic bird populations have long been considered the natural reservoir for influenza A viruses with virus transmission from these birds seeding other avian and mammalian hosts. While most evidence still supports this dogma, recent studies in bats have suggested other reservoir species may also exist. Extensive surveillance studies coupled with an enhanced awareness in response to H5N1 and pandemic 2009 H1N1 outbreaks is also revealing a growing list of animals susceptible to infection with influenza A viruses. Although in a relatively stable host-pathogen interaction in aquatic birds, antigenic, and genetic evolution of influenza A viruses often accompanies interspecies transmission as the virus adapts to a new host. The evolutionary changes in the new hosts result from a number of processes including mutation, reassortment, and recombination. Depending on host and virus these changes can be accompanied by disease outbreaks impacting wildlife, veterinary, and public health.

 

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Bushmeat in the Time of Ebola | VICE News

Bushmeat in the Time of Ebola | VICE News | Virology and Bioinformatics from Virology.ca | Scoop.it
VICE News went to the bushmeat markets in Liberia, where the most recent outbreak of the deadly Ebola virus is said to have originated.
Ken Yaw Agyeman-Badu's insight:

I love this documentary - Bushmeat in the Time of Ebola.

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Ed Rybicki's curator insight, July 10, 11:14 AM
Thanks, Ken!
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Detection of viral protein-protein interaction by microplate-format luminescence-based mammalian interactome mapping (LUMIER)

Detection of viral protein-protein interaction by microplate-format luminescence-based mammalian interactome mapping (LUMIER) | Virology and Bioinformatics from Virology.ca | Scoop.it

In 2005, Barrios-Rodiles and colleagues developed a luminescence-based mammalian interactome mapping(LUMIER)method for detecting dynamic PPI networks in mammalian cells(Barrios-Rodiles M, et al., 2005). This methodology has been successfully used to map some signaling pathways(Braun P, et al., 2009; Miller B W, et al., 2009). LUMIER is similar in principle to the traditional coimmunoprecipitation(Co-IP)method, which allows detection of binary PPIs in a native condition. It involves the generation of two fusion constructs: one is an epitope-tagged protein(the bait protein)expression plasmid, while the other consists of a cDNA-expressing fused protein of the Renillaluciferase(RL)enzyme and a protein of interest(the prey protein). When coexpressed in mammalian cells(Figure 1A), their potential interactions are determined by performing an RL enzyme assay on the precipitated complexes that are precipitated by an antibody against the epitope tag.

 
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Agroinfection of sweet potato by vacuum infi ltration of an infectious sweepovirus

Agroinfection of sweet potato by vacuum infi ltration of an infectious sweepovirus | Virology and Bioinformatics from Virology.ca | Scoop.it
Abstract: Sweepovirus is an important monopartite begomovirus that infects plants of the genusIpomoea worldwide. Development of artifi cial infection methods for sweepovirus using agroinoculation is a highly efficient means of studying infectivity in sweet potato. Unlike other begomoviruses, it has proven difficult to infect sweet potato plants with sweepoviruses using infectious clones. A novel sweepovirus, called Sweet potato leaf curl virus-Jiangsu (SPLCV-JS), was recently identifi ed in China. In addition, the infectivity of the SPLCV-JS clone has been demonstrated in Nicotiana benthamiana. Here we describe the agroinfection of the sweet potato cultivar Xushu 22 with the SPLCV-JS infectious clone using vacuum infi ltration. Yellowing symptoms were observed in newly emerged leaves. Molecular analysis confirmed successful inoculation by the detection of viral DNA. A synergistic effect of SPLCV-JS and the heterologous betasatellite DNA-β of Tomato yellow leaf curl China virus isolate Y10 (TYLCCNV-Y10) on enhanced symptom severity and viral DNA accumulation was confi rmed. The development of a routine agroinoculation system in sweet potato with SPLCV-JS using vacuum infi ltration should facilitate the molecular study of sweepovirus in this host and permit the evaluation of virus resistance of sweet potato plants in breeding programs. 
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A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors - Proc Natl Acad Sci U S A. 2014

Although segmented and unsegmented RNA viruses are commonplace, the evolutionary links between these two very different forms of genome organization are unclear. We report the discovery and characterization of a tick-borne virus--Jingmen tick virus (JMTV)--that reveals an unexpected connection between segmented and unsegmented RNA viruses. The JMTV genome comprises four segments, two of which are related to the nonstructural protein genes of the genus Flavivirus (family Flaviviridae), whereas the remaining segments are unique to this virus, have no known homologs, and contain a number of features indicative of structural protein genes. Remarkably, homology searching revealed that sequences related to JMTV were present in the cDNA library from Toxocara canis (dog roundworm; Nematoda), and that shared strong sequence and structural resemblances. Epidemiological studies showed that JMTV is distributed in tick populations across China, especially Rhipicephalus and Haemaphysalis spp., and experiences frequent host-switching and genomic reassortment. To our knowledge, JMTV is the first example of a segmented RNA virus with a genome derived in part from unsegmented viral ancestors.

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Scientists Have Developed a Flu Strain Capable of Evading Your Immune System - VICE News

Scientists Have Developed a Flu Strain Capable of Evading Your Immune System - VICE News | Virology and Bioinformatics from Virology.ca | Scoop.it
RT
Scientists Have Developed a Flu Strain Capable of Evading Your Immune System
VICE News
Such "antigenic escape" studies have been performed routinely in virology labs for 30 years.
Clara MacDonald's insight:

Good example of how an article can induce panic in the general public, while the goal of the research is understandable. 

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Scientist who discovered Ebola: ‘This is unprecedented’

Scientist who discovered Ebola: ‘This is unprecedented’ | Virology and Bioinformatics from Virology.ca | Scoop.it
By Mick Krever, CNN

The scientist who discovered the Ebola virus said that a current outbreak of the deadly bug in West Africa, in which 467 people have died, is “unprecedented.”

“One, [this is] the first time in West Africa that we have such an outbreak,” Dr.
Ken Yaw Agyeman-Badu's insight:

Dr. Peter Piot discovered Ebola 40 years ago. His 3 reasons why this outbreak is different

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Identity and Access Management's Role in Secure Cloud Collaboration - eSecurity Planet

Identity and Access Management's Role in Secure Cloud Collaboration - eSecurity Planet | Virology and Bioinformatics from Virology.ca | Scoop.it
As enterprises demand more secure cloud-based externalization, companies like Exostar are answering the call with IAM solutions.
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Dengue Vaccine Candidate demonstrates promising results in Phase III efficacy study | Outbreak News Today

Dengue Vaccine Candidate demonstrates promising results in Phase III efficacy study | Outbreak News Today | Virology and Bioinformatics from Virology.ca | Scoop.it
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Influenza A Virus Host Shutoff Disables Antiviral Stress-Induced Translation Arrest

Influenza A Virus Host Shutoff Disables Antiviral Stress-Induced Translation Arrest | Virology and Bioinformatics from Virology.ca | Scoop.it
by Denys A. Khaperskyy, Mohamed M. Emara, Benjamin P. Johnston, Paul Anderson, Todd F.
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Python bumps off Java as top learning language

Python bumps off Java as top learning language | Virology and Bioinformatics from Virology.ca | Scoop.it
Python's simpler syntax and ability to scale up for enterprise development have made it the preferred language choice for learning to code.
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SimFlu: A simulation tool for predicting the variation pattern of influenza A virus.

SimFlu: A simulation tool for predicting the variation pattern of influenza A virus. | Virology and Bioinformatics from Virology.ca | Scoop.it

Since the first pandemic outbreak of avian influenza A virus (H5N1 subtype) in 1997, the National Center for Biotechnology Information (NCBI) has provided a large number of influenza virus sequences with well-organized annotations. Using the time-series sequences of influenza A viruses, we developed a simulation tool for influenza virus, named SimFlu, to predict possible future variants of influenza viruses. SimFlu can create variants from a seed nucleotide sequence of influenza A virus using the codon variation parameters included in the SimFlu package. The SimFlu library provides pre-calculated codon variation parameters for the H1N1, H3N2, and H5N1 subtypes of influenza A virus isolated from 2000 to 2011, allowing the users to simulate their own nucleotide sequences by selecting their preferred parameter options. SimFlu supports three operating systems - Windows, Linux, and Mac OS X. SimFlu is publicly available at http://lcbb.snu.ac.kr/simflu.

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Google Genomics — Google Developers

Google Genomics — Google Developers | Virology and Bioinformatics from Virology.ca | Scoop.it
Gives access to Google Genomics.

Explore genetic variation interactively.Compare entire cohorts in seconds with SQL-like queries. Compute transition/transversion ratios, genome-wide association, allelic frequency and more.

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Chris Upton + helpers's curator insight, July 4, 12:42 PM

Generally...   I hate Google...

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Simple chained guide trees give high-quality protein multiple sequence alignments Boyce K, Sievers F, Higgins DG

Guide trees are used to decide the order of sequence alignment in the progressive multiple sequence alignment heuristic. These guide trees are often the limiting factor in making large alignments, and considerable effort has been expended over the years in making these quickly or accurately. In this article we show that, at least for protein families with large numbers of sequences that can be benchmarked with known structures, simple chained guide trees give the most accurate alignments. These also happen to be the fastest and simplest guide trees to construct, computationally. Such guide trees have a striking effect on the accuracy of alignments produced by some of the most widely used alignment packages. There is a marked increase in accuracy and a marked decrease in computational time, once the number of sequences goes much above a few hundred. This is true, even if the order of sequences in the guide tree is random.

 

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Forgotten vials of smallpox found in Bethesda, Md.

Forgotten vials of smallpox found in Bethesda, Md. | Virology and Bioinformatics from Virology.ca | Scoop.it
Forgotten vials of smallpox found in storage room
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Analysis of molecular variation in porcine reproductive and respiratory syndrome virus in China between 2007 and 2012

Analysis of molecular variation in porcine reproductive and respiratory syndrome virus in China between 2007 and 2012 | Virology and Bioinformatics from Virology.ca | Scoop.it
Abstract: In the present study, 89 porcine reproductive and respiratory syndrome virus (PRRSV) isolates in China during 2007 to 2012 were randomly selected from the GenBank genetic sequence database. Evolutionary characteristics of these isolates were analyzed based on the sequences of non-structural protein 2 (Nsp2) and glycoprotein 5 (GP5). The genetic variations of the isolates were also compared with six representative strains. The results showed that a high degree of genetic diversity exists among the PRRSV population in China. Highly pathogenic PRRSV isolates, with a discontinuous deletion of a 30 amino acid residue in the Nsp2 region, remained the most dominant virus throughout 2007-2012 in China. Owing to the extensive use of representative vaccine strains, natural recombination events occurred between strains. Three isolates-HH08, DY, and YN-2011-were more closely related to vaccine strains than the other isolates. Both YN-2011 and DY were the evolutionary products of recombination events between strains SP and CH-1R. The results of the present study provide useful information for the epidemiology of PRRSV as well as for vaccine development. 
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Viral exploitation of actin:force-generation and scaffolding functions in viral infection

Viral exploitation of actin:force-generation and scaffolding functions in viral infection | Virology and Bioinformatics from Virology.ca | Scoop.it
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Acanthamoeba polyphaga mimivirus and other giant viruses: an open field to outstanding discoveries

In 2003, Acanthamoeba polyphaga mimivirus (APMV) was first described and began to impact researchers around the world, due to its structural and genetic complexity. This virus founded the family Mimiviridae. In recent years, several new giant viruses have been isolated from different environments and specimens. Giant virus research is in its initial phase and information that may arise in the coming years may change current conceptions of life, diversity and evolution. Thus, this review aims to condense the studies conducted so far about the features and peculiarities of APMV, from its discovery to its clinical relevance.
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▶ Ebola virus explained in 60 seconds (video)

Here's our 60 look at why Ebola is so deadly. The World Health Organization (WHO) has called for "drastic action" to contain an Ebola outbreak in West Africa that has killed nearly 500 people. 
It is the world's largest outbreak in terms of cases, deaths and geographical spread.


Via Ed Rybicki
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A more intuitive approach to computerized clustering

A more intuitive approach to computerized clustering | Virology and Bioinformatics from Virology.ca | Scoop.it

Clustering algorithms help parse large amounts of data, find correlations within subsets of the data, and assess similarity among elements within these subsets. They have become a hot field in recent years, as they have applications in astronomy, bioinformatics, and pattern recognition. Now there's a new entrant in the arena, which clusters by fast search and then finds density peaks. It clusters data based on distance to a cluster center (as in K-means), but also detects non-spherical clusters (DBSCAN).

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High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments

High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments | Virology and Bioinformatics from Virology.ca | Scoop.it

Marine sediments cover two-thirds of our planet and harbor huge numbers of living prokaryotes. Long-term survival of indigenous microorganisms within the deep subsurface is still enigmatic, as sources of organic carbon are vanishingly small. To better understand controlling factors of microbial life, we have analyzed viral abundance within a comprehensive set of globally distributed subsurface sediments. Phages were detected by electron microscopy in deep (320 m below seafloor), ancient (~14 Ma old) and the most oligotrophic subsurface sediments of the world’s oceans (South Pacific Gyre (SPG)). The numbers of viruses (104–109 cm−3, counted by epifluorescence microscopy) generally decreased with sediment depth, but always exceeded the total cell counts. The enormous numbers of viruses indicate their impact as a controlling factor for prokaryotic mortality in the marine deep biosphere. The virus-to-cell ratios increased in deeper and more oligotrophic layers, exhibiting values of up to 225 in the deep subsurface of the SPG. High numbers of phages might be due to absorption onto the sediment matrix and a diminished degradation by exoenzymes. However, even in the oldest sediments, microbial communities are capable of maintaining viral populations, indicating an ongoing viral production and thus, viruses provide an independent indicator for microbial life in the marine deep biosphere.

 
Via Mya Breitbart
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