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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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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.


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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.

 
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Networks of lexical borrowing and lateral gene transfer in language and genome evolution

Networks of lexical borrowing and lateral gene transfer in language and genome evolution | Virology and Bioinformatics from Virology.ca | Scoop.it

For a long time, both biologists and linguists have been using family trees to model how species and languages evolve. But in contrast to biology – where the tree model is generally accepted to be the most realistic way to model how eukaryotic species (species with nucleated cells, such as animals and plants) evolve – linguists have always treated language trees with a certain suspicion. They have emphasized that – given the important role that horizontal transmission plays in language history – such trees can only capture vertical aspects of language evolution, while horizontal aspects (which linguists traditionally model as “waves” that spread out in circles around a center in geographic space) are ignored.

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Implications of finding poliovirus in sewers of Brazil and Israel

Implications of finding poliovirus in sewers of Brazil and Israel | Virology and Bioinformatics from Virology.ca | Scoop.it
Why has wild poliovirus been detected in the sewers of Brazil and Israel, and what are the implications for the eradication effort?

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Ed Rybicki's curator insight, July 2, 5:12 AM

Not unexpectedly, a calm and thorough analysis of the potential problem from the "virology blog"!

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Two completely synthetic defective mastrevirus genomes recombine to produce viable virus

Two completely synthetic defective mastrevirus genomes recombine to produce viable virus | Virology and Bioinformatics from Virology.ca | Scoop.it

Although homologous recombination can potentially provide viruses with vastly more evolutionary options than are available through mutation alone, there are considerable limits on the adaptive potential of this important evolutionary process. Primary amongst these is the disruption of favourable co-evolved genetic interactions that can occur following the transfer of foreign genetic material into a genome. Although the fitness costs of such disruptions can be severe, in some cases they can be rapidly recouped either by compensatory mutations or secondary-recombination events. Here, we used a Maize streak virus (MSV) experimental model to explore both the extremes of recombination-induced genetic disruption, and the capacity of secondary-recombination to adaptively reverse almost lethal recombination events. Starting with two naturally occurring parental viruses, we synthesised two of the most extreme conceivable MSV chimaeras, each effectively carrying 182 recombination breakpoints and containing thorough reciprocal mixtures of parental polymorphisms. Although both chimaeras were severely defective and apparently non-infectious, neither had individual movement, encapsidation or replication associated genome regions that were on their own 'lethally recombinant'. Surprisingly, mixed inoculations of the chimaeras yielded symptomatic infections containing viruses with secondary-recombination events. These recombinants had only two to six breakpoints, had predominantly inherited the least defective of the chimeric parental genome fragments and were obviously far fitter than their synthetic parents. It is clearly evident therefore, that even when recombinationally disrupted virus genomes have extremely low fitness and there are no easily accessible routes to a full recovery, small numbers of secondary-recombination events can still yield tremendous fitness gains.

 

Ed Rybicki's insight:

Too ridiculously complicated for words, and I TOLD them just ONE synthetic genome would be worth publishing, but nooooo - they had to do it the difficult way.  A tour de force.  My function was just to try to make them to keep it simple(r).  Kudos Aderito et al.!

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Viruses: unlocking the greatest biodiversity on Earth.

There are about 10 times as many viruses in the oceans as there are bacteria and about 1000-fold less protists than bacteria. In fact, in a litre of coastal seawater there are more viruses than there are people on the planet. If one takes a drop of seawater and adds a nucleic-acid stain such as Yo-Pro, SYBR Green, or SYBR Gold and looks at it under a microscope, there are a myriad of tiny fluorescent dots that are reminiscent of a clear night sky (Fig. 1). Most of these dots are virus particles. If aliens randomly sampled Earth they would see a planet dominated by microbial life, most of which would be viruses. On average, there are about 10 million viruses and a mil- lion bacteria per litre of seawater or freshwater. If we compare the number of viruses in the oceans to the number of stars in the universe, there are about 1023 stars in the universe. In contrast, there are about 10 million-fold more viruses in the ocean than there are stars in the universe. If we took the 1030 viruses in the oceans and stretched them end-to-end, how far would they go? Assuming, the average length of a virus is about 100 nm, the viruses would stretch 1023 m, which is 1020 km. If converted to light years, by dividing by 1013 km, we end up with 10 million light years. The nearest star is Proxima Centauri, about 4.2 light years away; the Crab Supernova is 1000 light years away; our own gal- axy, the Milky Way, is about 150 000 light years across. In fact, all the viruses in the ocean end-to-end would stretch further than the nearest 60 galaxies. This may seem like a trivial calculation, but it is important on a number of levels. For one reason, these viruses are responsible for about Avogadro’s number, about 1024 infec- tions per second in the ocean. Each one of these events is an opportunity for lateral transfer of genes. Most of the genetic information on Earth probably resides within viruses. 

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Ed Rybicki's comment, July 2, 4:25 AM
Viva Suttle!!
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Life Cycle of the HIV virus

Life Cycle of the HIV virus | Virology and Bioinformatics from Virology.ca | Scoop.it
Produced
by Hybrid Medical Animation.

This 3D interactive scene explains the puzzle of the HIV virus, its life cycle, and how it reproduces itself in the host cell.
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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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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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Motifs tree: a new method for predicting post-translational modifications

Motifs tree: a new method for predicting post-translational modifications | Virology and Bioinformatics from Virology.ca | Scoop.it

Post-translational modifications (PTMs) are important steps in the maturation of proteins. Several models exist to predict specific PTMs, from manually detected patterns to machine learning methods. On one hand, the manual detection of patterns does not provide the most efficient classifiers and requires an important workload, and on the other hand, models built by machine learning methods are hard to interpret and do not increase biological knowledge.

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Associate Director Bioinformatic Solutions - QIAGEN

Position Description 

- Identify and evaluate new trends in development for clinical use of bioinformatics
- Define innovative bioinformatic software solutions and products for clinical use
- Develop new / enhance existing software products based on market/customer needs
- Establish long standing business relationships with academic institutes and KOLs

Position Requirements 

- MSc or PhD in bioinformatic, biology or other related sciences
- Minimum of 3 years relevant business experience including the lead of a bioinformatic team within the clinical or laboratory sector
- Know-how in requirement management and leading an assignment with dead-lines and restricted budget are an advantage
- Experience in handling regulatory processes (IVD, FDA) in medical engineering would be an advantage

Personal Requirements 

- Independent and efficient work approach 
- Ability to communicate and work interdisciplinary with internal and external customers as well as working with decentralized international teams
- Assertive demeanor with very good communication skills
- Fluent English skills
- Willingness to travel up to 30%

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Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction: Cell

Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction: Cell | Virology and Bioinformatics from Virology.ca | Scoop.it

A systematic quantitative analysis of temporal changes in host and viral proteins throughout the course of a productive infection could provide dynamic insights into virus-host interaction. We developed a proteomic technique called “quantitative temporal viromics” (QTV), which employs multiplexed tandem-mass-tag-based mass spectrometry. Human cytomegalovirus (HCMV) is not only an important pathogen but a paradigm of viral immune evasion. QTV detailed how HCMV orchestrates the expression of >8,000 cellular proteins, including 1,200 cell-surface proteins to manipulate signaling pathways and counterintrinsic, innate, and adaptive immune defenses. QTV predicted natural killer and T cell ligands, as well as 29 viral proteins present at the cell surface, potential therapeutic targets. Temporal profiles of >80% of HCMV canonical genes and 14 noncanonical HCMV open reading frames were defined. QTV is a powerful method that can yield important insights into viral infection and is applicable to any virus with a robust in vitro model.

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Rakesh Yashroy's curator insight, July 3, 4:38 PM

As such, host-pathogen signaling is fast becoming the field of immense interest @ https://en.wikipedia.org/wiki/Membrane_vesicle_trafficking

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Substitution Rates of the Internal Genes in the Novel Avian H7N9 Influenza Virus

Substitution Rates of the Internal Genes in the Novel Avian H7N9 Influenza Virus | Virology and Bioinformatics from Virology.ca | Scoop.it

TO THE EDITOR—As of 30 May 2013, the novel avian influenza A(H7N9) virus has caused 132 laboratory-confirmed infections, with 37 fatal cases [1]. As the temperature went up, the reported number of infections naturally declined, with only 3 cases reported in May 2013.

As of 4 June 2013, 36 genome sequences of the novel H7N9 viruses have been deposited in the GISAID database (Global Initiative on Sharing All Influenza Data; www.gisaid.org). Using all of the 36 genome sequences, we calculated the nucleotide substitution rates for each of the 8 gene segments with the single likelihood ancestral counting method [2]. Surprisingly, the substitution rates of the internal genes (except for PB2) were very high, with a similar magnitude to those of surface protein coding genes HA and NA (Figure 1A). In particular, the substitution rates of the M2 and NP genes were even higher than those of HA and NA.

 
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A field guide to whole-genome sequencing, assembly and annotation - Ekblom - 2014 - Evolutionary Applications - Wiley Online Library

Genome sequencing projects were long confined to biomedical model organisms and required the concerted effort of large consortia. Rapid progress in high-throughput sequencing technology and the simultaneous development of bioinformatic tools have democratized the field. It is now within reach for individual research groups in the eco-evolutionary and conservation community to generate de novo draft genome sequences for any organism of choice. Because of the cost and considerable effort involved in such an endeavour, the important first step is to thoroughly consider whether a genome sequence is necessary for addressing the biological question at hand. Once this decision is taken, a genome project requires careful planning with respect to the organism involved and the intended quality of the genome draft. Here, we briefly review the state of the art within this field and provide a step-by-step introduction to the workflow involved in genome sequencing, assembly and annotation with particular reference to large and complex genomes. This tutorial is targeted at scientists with a background in conservation genetics, but more generally, provides useful practical guidance for researchers engaging in whole-genome sequencing projects.

 
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BMC Microbiology | Abstract | Characterization of bacteriophage communities and CRISPR profiles from dental plaque

Dental plaque is home to a diverse and complex community of bacteria, but has generally been believed to be inhabited by relatively few viruses. We sampled the saliva and dental plaque from 4 healthy human subjects to determine whether plaque was populated by viral communities, and whether there were differences in viral communities specific to subject or sample type.
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