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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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Global migration of influenza A viruses in swine : Nature

Global migration of influenza A viruses in swine : Nature | Virology and Bioinformatics from Virology.ca | Scoop.it

The complex and unresolved evolutionary origins of the 2009 H1N1 influenza pandemic exposed major gaps in our knowledge of the global spatial ecology and evolution of influenza A viruses in swine (swIAVs). Here we undertake an expansive phylogenetic analysis of swIAV sequence data and demonstrate that the global live swine trade strongly predicts the spatial dissemination of swIAVs, with Europe and North America acting as sources of viruses in Asian countries. In contrast, China has the world’s largest swine population but is not a major exporter of live swine, and is not an important source of swIAVs in neighbouring Asian countries or globally. A meta-population simulation model incorporating trade data predicts that the global ecology of swIAVs is more complex than previously thought, and the United States and China’s large swine populations are unlikely to be representative of swIAV diversity in their respective geographic regions, requiring independent surveillance efforts throughout Latin America and Asia.

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Emerging Viral Diseases: The One Health Connection: Workshop Summary

Emerging Viral Diseases: The One Health Connection: Workshop Summary | Virology and Bioinformatics from Virology.ca | Scoop.it
In the past half century, deadly disease outbreaks caused by novel viruses of animal origin - Nipah virus in Malaysia, Hendra virus in Australia, Hantavirus in the United States, Ebola virus in Africa, along with HIV (human immunodeficiency virus), several influenza subtypes, and the SARS (sudden acute respiratory syndrome) and MERS (Middle East respiratory syndrome) coronaviruses - have underscored the urgency of understanding factors influencing viral disease emergence and spread. Emerging Viral Diseases is the summary of a public workshop hosted in March 2014 to examine factors driving the appearance, establishment, and spread of emerging, re-emerging and novel viral diseases; the global health and economic impacts of recently emerging and novel viral diseases in humans; and the scientific and policy approaches to improving domestic and international capacity to detect and respond to global outbreaks of infectious disease. This report is a record of the presentations and discussion of the event.
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Download a FREE PDF of the book!

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bionode

Bionode provides pipeable UNIX command line tools and JavaScript APIs for bioinformatic analysis workflows.

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Coronavirus Website - Ministry of Health

Coronavirus Website - Ministry of Health | Virology and Bioinformatics from Virology.ca | Scoop.it
Middle East Respiratory Syndrome - Coronavirus Website

Via Ian M Mackay, PhD
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It's time to reboot bioinformatics education

It's time to reboot bioinformatics education | Virology and Bioinformatics from Virology.ca | Scoop.it
Nearly 15 years after completion of the human genome, undergraduate and graduate programs still aren't adequately training future scientists with the basic bioinformatics skills needed to be succes...
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Proteome-Wide Lysine Acetylation in Cortical Astrocytes and Alterations That Occur during Infection with Brain Parasite Toxoplasma gondii

Proteome-Wide Lysine Acetylation in Cortical Astrocytes and Alterations That Occur during Infection with Brain Parasite  Toxoplasma gondii | Virology and Bioinformatics from Virology.ca | Scoop.it
Lysine acetylation is a reversible post-translational modification (PTM) that has been detected on thousands of proteins in nearly all cellular compartments. The role of this widespread PTM has yet to be fully elucidated, but can impact protein localization, interactions, activity, and stability. Here we present the first proteome-wide survey of lysine acetylation in cortical astrocytes, a subtype of glia that is a component of the blood-brain barrier and a key regulator of neuronal function and plasticity. We identified 529 lysine acetylation sites across 304 proteins found in multiple cellular compartments that largely function in RNA processing/transcription, metabolism, chromatin biology, and translation. Two hundred and seventy-seven of the acetylated lysines we identified on 186 proteins have not been reported previously in any other cell type. We also mapped an acetylome of astrocytes infected with the brain parasite, Toxoplasma gondii . It has been shown that infection with T . gondii modulates host cell gene expression, including several lysine acetyltransferase (KAT) and deacetylase (KDAC) genes, suggesting that the host acetylome may also be altered during infection. In the T . gondii -infected astrocytes, we identified 34 proteins exhibiting a level of acetylation >2-fold and 24 with a level of acetylation <2-fold relative to uninfected astrocytes. Our study documents the first acetylome map for cortical astrocytes, uncovers novel lysine acetylation sites, and demonstrates that T . gondii infection produces an altered acetylome.
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MiniPoll: Reaction to a Scientifically Inaccurate Statement

MiniPoll: Reaction to a Scientifically Inaccurate Statement | Virology and Bioinformatics from Virology.ca | Scoop.it
When someone says something scientifically inaccurate at a dinner party, how do you react? We asked the scientific community how they handle this situation. Here is what we found:
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Oseltamivir Expands Quasispecies of Influenza Virus through Cell-to-cell Transmission : Nature

Oseltamivir Expands Quasispecies of Influenza Virus through Cell-to-cell Transmission : Nature | Virology and Bioinformatics from Virology.ca | Scoop.it
The population of influenza virus consists of a huge variety of variants, called quasispecies, due to error-prone replication. Previously, we reported that progeny virions of influenza virus become infected to adjacent cells via cell-to-cell transmission pathway in the presence of oseltamivir. During cell-to-cell transmission, viruses become infected to adjacent cells at high multiplicity since progeny virions are enriched on plasma membrane between infected cells and their adjacent cells. Co-infection with viral variants may rescue recessive mutations with each other. Thus, it is assumed that the cell-to-cell transmission causes expansion of virus quasispecies. Here, we have demonstrated that temperature-sensitive mutations remain in progeny viruses even at non-permissive temperature by co-infection in the presence of oseltamivir. This is possibly due to a multiplex infection through the cell-to-cell transmission by the addition of oseltamivir. Further, by the addition of oseltamivir, the number of missense mutation introduced by error-prone replication in segment 8 encoding NS1 was increased in a passage-dependent manner. The number of missense mutation in segment 5 encoding NP was not changed significantly, whereas silent mutation was increased. Taken together, we propose that oseltamivir expands influenza virus quasispecies via cell-to-cell transmission, and may facilitate the viral evolution and adaptation
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Viral Virtuosos | The Scientist Magazine®

Viral Virtuosos | The Scientist Magazine® | Virology and Bioinformatics from Virology.ca | Scoop.it
New understanding of noncoding RNAs may solve a long-standing puzzle about how viruses orchestrate lifelong infections.
 

Via Centre for Biomedical Research
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Measles cases haven’t swayed Canadian anti-vaxxers, survey finds

Measles cases haven’t swayed Canadian anti-vaxxers, survey finds | Virology and Bioinformatics from Virology.ca | Scoop.it
Sixty-five per cent of respondents cited health concerns as the reason their child hadn’t been vaccinated, while 19 per cent said it was because of their religious beliefs
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Which religions say you can't vaccinate your kids?

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The final verdict on homeopathy: it’s a placebo

The final verdict on homeopathy: it’s a placebo | Virology and Bioinformatics from Virology.ca | Scoop.it
I reported previously on this blog that the Australian National Health and Medical Research Council (NH&MRC) has made the most thorough and independent assessment of homeopathy in the history of this form of alternative therapy. The report published at the time was preliminary, and further evidence from parties that were critical of it needed to be taken into account. Today (11/3/2015), the NH&MRC has released its final report on homeopathy. In essence, it concluded that there is no scientific b
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Tardigrades are so tough, they can survive outer space

Tardigrades are so tough, they can survive outer space | Virology and Bioinformatics from Virology.ca | Scoop.it
Boil them, deep-freeze them, crush them, dry them out or blast them into space: tardigrades will survive it all and come back for more
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This 17-Year-Old Has Discovered DNA Mutations That Could Combat HIV And Meningitis

This 17-Year-Old Has Discovered DNA Mutations That Could Combat HIV And Meningitis | Virology and Bioinformatics from Virology.ca | Scoop.it
High schooler Andrew Jin is answering previously unasked questions in biology.
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PLOS Pathogens: Catch Me If You Can: The Link between Autophagy and Viruses

PLOS Pathogens: Catch Me If You Can: The Link between Autophagy and Viruses | Virology and Bioinformatics from Virology.ca | Scoop.it
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Ebola’s fast evolution questioned

Ebola’s fast evolution questioned | Virology and Bioinformatics from Virology.ca | Scoop.it
Genome-sequencing study finds the virus evolving more slowly than thought, but others say the focus should be on monitoring the effects of new mutations.
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A Novel Host-Proteome Signature for Distinguishing between Acute Bacterial and Viral Infections

A Novel Host-Proteome Signature for Distinguishing between Acute Bacterial and Viral Infections | Virology and Bioinformatics from Virology.ca | Scoop.it
Bacterial and viral infections are often clinically indistinguishable, leading to inappropriate patient management and antibiotic misuse. Bacterial-induced host proteins such as procalcitonin, C-reactive protein (CRP), and Interleukin-6, are routinely used to support diagnosis of infection. However, their performance is negatively affected by inter-patient variability, including time from symptom onset, clinical syndrome, and pathogens. Our aim was to identify novel viral-induced host proteins that can complement bacterial-induced proteins to increase diagnostic accuracy. Initially, we conducted a bioinformatic screen to identify putative circulating host immune response proteins. The resulting 600 candidates were then quantitatively screened for diagnostic potential using blood samples from 1002 prospectively recruited patients with suspected acute infectious disease and controls with no apparent infection. For each patient, three independent physicians assigned a diagnosis based on comprehensive clinical and laboratory investigation including PCR for 21 pathogens yielding 319 bacterial, 334 viral, 112 control and 98 indeterminate diagnoses; 139 patients were excluded based on predetermined criteria. The best performing host-protein was TNF-related apoptosis-inducing ligand (TRAIL) (area under the curve [AUC] of 0.89; 95% confidence interval [CI], 0.86 to 0.91), which was consistently up-regulated in viral infected patients. We further developed a multi-protein signature using logistic-regression on half of the patients and validated it on the remaining half. The signature with the highest precision included both viral- and bacterial-induced proteins: TRAIL, Interferon gamma-induced protein-10, and CRP (AUC of 0.94; 95% CI, 0.92 to 0.96). The signature was superior to any of the individual proteins (P<0.001), as well as routinely used clinical parameters and their combinations (P<0.001). It remained robust across different physiological systems, times from symptom onset, and pathogens (AUCs 0.87-1.0). The accurate differential diagnosis provided by this novel combination of viral- and bacterial-induced proteins has the potential to improve management of patients with acute infections and reduce antibiotic misuse.
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Origins and evolution of viruses of eukaryotes: The ultimate modularity

Origins and evolution of viruses of eukaryotes: The ultimate modularity | Virology and Bioinformatics from Virology.ca | Scoop.it

Viruses and other selfish genetic elements are dominant entities in the biosphere, with respect to both physical abundance and genetic diversity. Various selfish elements parasitize on all cellular life forms. The relative abundances of different classes of viruses are dramatically different between prokaryotes and eukaryotes. In prokaryotes, the great majority of viruses possess double-stranded (ds) DNA genomes, with a substantial minority of single-stranded (ss) DNA viruses and only limited presence of RNA viruses. In contrast, in eukaryotes, RNA viruses account for the majority of the virome diversity although ssDNA and dsDNA viruses are common as well. Phylogenomic analysis yields tangible clues for the origins of major classes of eukaryotic viruses and in particular their likely roots in prokaryotes. Specifically, the ancestral genome of positive-strand RNA viruses of eukaryotes might have been assembled de novo from genes derived from prokaryotic retroelements and bacteria although a primordial origin of this class of viruses cannot be ruled out. Different groups of double-stranded RNA viruses derive either from dsRNA bacteriophages or from positive-strand RNA viruses. The eukaryotic ssDNA viruses apparently evolved via a fusion of genes from prokaryotic rolling circle-replicating plasmids and positive-strand RNA viruses. Different families of eukaryotic dsDNA viruses appear to have originated from specific groups of bacteriophages on at least two independent occasions. Polintons, the largest known eukaryotic transposons, predicted to also form virus particles, most likely, were the evolutionary intermediates between bacterial tectiviruses and several groups of eukaryotic dsDNA viruses including the proposed order “Megavirales” that unites diverse families of large and giant viruses. Strikingly, evolution of all classes of eukaryotic viruses appears to have involved fusion between structural and replicative gene modules derived from different sources along with additional acquisitions of diverse genes.

 

Graphic by Ed Rybicki

  


Via Ed Rybicki
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Ed Rybicki's curator insight, March 19, 6:35 AM

Wow...!  A tour de force.  Quite simply, says it all.  REALLY nice piece of work!!  And of course, they back me up in my view of how ss(-)RNA viruses evolved. Again B-)

Rabenstein, Frank's curator insight, March 23, 10:59 AM

Thank you Ed for this.

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United Kingdom: Huge increase in chikungunya due to Caribbean and South America travel | Outbreak News Today

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Health Canada licensing of natural remedies 'a joke,' doctor says

Health Canada licensing of natural remedies 'a joke,' doctor says | Virology and Bioinformatics from Virology.ca | Scoop.it
Natural and homeopathic products, which are often sold alongside over-the-counter pharmaceutical drugs on store shelves, may be backed by little to no scientific evidence, and there’s no way for consumers to tell.
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Not laughing!

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Origins and evolution of viruses of eukaryotes: The ultimate modularity.

Viruses and other selfish genetic elements are dominant entities in the biosphere, with respect to both physical abundance and genetic diversity. Various selfish elements parasitize on all cellular life forms. The relative abundances of different classes of viruses are dramatically different between prokaryotes and eukaryotes. In prokaryotes, the great majority of viruses possess double-stranded (ds) DNA genomes, with a substantial minority of single-stranded (ss) DNA viruses and only limited presence of RNA viruses. In contrast, in eukaryotes, RNA viruses account for the majority of the virome diversity although ssDNA and dsDNA viruses are common as well. Phylogenomic analysis yields tangible clues for the origins of major classes of eukaryotic viruses and in particular their likely roots in prokaryotes. Specifically, the ancestral genome of positive-strand RNA viruses of eukaryotes might have been assembled de novo from genes derived from prokaryotic retroelements and bacteria although a primordial origin of this class of viruses cannot be ruled out. Different groups of double-stranded RNA viruses derive either from dsRNA bacteriophages or from positive-strand RNA viruses. The eukaryotic ssDNA viruses apparently evolved via a fusion of genes from prokaryotic rolling circle-replicating plasmids and positive-strand RNA viruses. Different families of eukaryotic dsDNA viruses appear to have originated from specific groups of bacteriophages on at least two independent occasions. Polintons, the largest known eukaryotic transposons, predicted to also form virus particles, most likely, were the evolutionary intermediates between bacterial tectiviruses and several groups of eukaryotic dsDNA viruses including the proposed order "Megavirales" that unites diverse families of large and giant viruses. Strikingly, evolution of all classes of eukaryotic viruses appears to have involved fusion between structural and replicative gene modules derived from different sources along with additional acquisitions of diverse genes.

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The Causes and Consequences of Changes in Virulence following Pathogen Host Shifts

The Causes and Consequences of Changes in Virulence following Pathogen Host Shifts | Virology and Bioinformatics from Virology.ca | Scoop.it

Emerging infectious diseases are often the result of a host shift, where the pathogen originates from a different host species. Virulence—the harm a pathogen does to its host—can be extremely high following a host shift (for example Ebola, HIV, and SARs), while other host shifts may go undetected as they cause few symptoms in the new host. Here we examine how virulence varies across host species by carrying out a large cross infection experiment using 48 species of Drosophilidae and an RNA virus. Host shifts resulted in dramatic variation in virulence, with benign infections in some species and rapid death in others. The change in virulence was highly predictable from the host phylogeny, with hosts clustering together in distinct clades displaying high or low virulence. High levels of virulence are associated with high viral loads, and this may determine the transmission rate of the virus.

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MERS kills 10 in Saudi after surge in virus deaths

MERS kills 10 in Saudi after surge in virus deaths | Virology and Bioinformatics from Virology.ca | Scoop.it
Ten more people have died in Saudi Arabia from the MERS virus since last week, health ministry data showed on Friday, adding to a surge in cases over the past month.

Via Ed Rybicki
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Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

Conservation of transcription factor binding specificities across 600 million years of bilateria evolution | Virology and Bioinformatics from Virology.ca | Scoop.it
Drosophila has almost all transcription factor binding specificities available to humans; and human transcription factors with divergent specificities operate in cell types that are not found in fruit flies.
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FDA Gives HIV 'Functional Cure' Go-Ahead For Human Trials

FDA Gives HIV 'Functional Cure' Go-Ahead For Human Trials | Virology and Bioinformatics from Virology.ca | Scoop.it
The FDA has approved the continuation of human trials on a possible functional cure for HIV and AIDs patients.
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Rakesh Yashroy's curator insight, March 17, 9:55 AM

Good research with immense future for treating HIV infection.

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Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution

Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution | Virology and Bioinformatics from Virology.ca | Scoop.it
Ed Rybicki's insight:

There is no "may" about it: plant genomes, like our own, have lots of bits from elsewhere.  And they're ORGANIC!

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