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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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Expansion of Biological Pathways Based on Evolutionary Inference: Cell

Expansion of Biological Pathways Based on Evolutionary Inference: Cell | Virology and Bioinformatics from Virology.ca | Scoop.it

The availability of diverse genomes makes it possible to predict gene function based on shared evolutionary history. This approach can be challenging, however, for pathways whose components do not exhibit a shared history but rather consist of distinct “evolutionary modules.” We introduce a computational algorithm, clustering by inferred models of evolution (CLIME), which inputs a eukaryotic species tree, homology matrix, and pathway (gene set) of interest. CLIME partitions the gene set into disjoint evolutionary modules, simultaneously learning the number of modules and a tree-based evolutionary history that defines each module. CLIME then expands each module by scanning the genome for new components that likely arose under the inferred evolutionary model. Application of CLIME to ∼1,000 annotated human pathways and to the proteomes of yeast, red algae, and malaria reveals unanticipated evolutionary modularity and coevolving components. CLIME is freely available and should become increasingly powerful with the growing wealth of eukaryotic genomes.

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The deadliest Ebola outbreak in history

The deadliest Ebola outbreak in history | Virology and Bioinformatics from Virology.ca | Scoop.it
Follow this ongoing story here.
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Ebola treatments caught in limbo

Ebola treatments caught in limbo | Virology and Bioinformatics from Virology.ca | Scoop.it
Logistics and lack of funds keep experimental drugs and vaccines from being used in Africa outbreak.
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Ebola, Spreading in Africa, Could Land in US

Ebola, Spreading in Africa, Could Land in US | Virology and Bioinformatics from Virology.ca | Scoop.it
An Ebola outbreak that has killed at least 672 people in Guinea, Liberia and Sierra Leone could land in the U.S., health officials said.
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Analysis of Stop-Gain and Frameshift Variants in Human Innate Immunity Genes

Analysis of Stop-Gain and Frameshift Variants in Human Innate Immunity Genes | Virology and Bioinformatics from Virology.ca | Scoop.it
PLOS Computational Biology is an open-access (#PLOSCompBio: Analysis of Stop-Gain and Frameshift Variants in Human Innate Immunity Genes http://t.co/nw7bx47t8B)...

Via Gilbert Faure au nom de l'ASSIM
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Free eBook: Python for Biologists

Free eBook: Python for Biologists | Virology and Bioinformatics from Virology.ca | Scoop.it

Via burkesquires
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Phospholipase D facilitates efficient entry of influenza virus allowing escape from innate mmune inhibition

Role of phospholipase D in influenza from VICB members HA Brown, CW Lindsley, JS Daniels. #chemicalbiology http://t.co/u1xs7g7GxO

Via Mel Melendrez-Vallard
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Effects of two amino acid substitutions in the capsid proteins on the interaction of two cell-adapted PanAsia-1 strains of foot-and-mouth disease virus serotype O with...

Some cell-adapted strains of foot-and-mouth disease virus (FMDV) can utilize heparan sulfate (HS) as a receptor to facilitate viral infection in cultured cells. A number of independent sites on the capsid that might be involved in FMDV-HS interaction have been studied. However, the previously reported residues do not adequately explain HS-dependent infection of two cell-adapted PanAsia-1 strains (O/Tibet/CHA/6/99tc and O/Fujian/CHA/9/99tc) of FMDV serotype O.
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The Importance of Biological Safety

The Importance of Biological Safety | Virology and Bioinformatics from Virology.ca | Scoop.it
Biological safety is about ensuring that individuals, products and the environment as a whole are all kept as safe as possible from hazardous biological materials. Not only are more
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Avian Influenza Virus Transmissio... [Curr Top Microbiol Immunol. 2014] - PubMed - NCBI

Avian Influenza Virus Transmissio... [Curr Top Microbiol Immunol. 2014] - PubMed - NCBI | Virology and Bioinformatics from Virology.ca | Scoop.it

Influenza A viruses cause yearly epidemics and occasional pandemics. In addition, zoonotic influenza A viruses sporadically infect humans and may cause severe respiratory disease and fatalities. Fortunately, most of these viruses do not have the ability to be efficiently spread among humans via aerosols or respiratory droplets (airborne transmission) and to subsequently cause a pandemic. However, adaptation of these zoonotic viruses to humans by mutation or reassortment with human influenza A viruses may result in airborne transmissible viruses with pandemic potential. Although our knowledge of factors that affect mammalian adaptation and transmissibility of influenza viruses is still limited, we are beginning to understand some of the biological traits that drive airborne transmission of influenza viruses among mammals. Increased understanding of the determinants and mechanisms of airborne transmission may aid in assessing the risks posed by avian influenza viruses to human health, and preparedness for such risks. This chapter summarizes recent discoveries on the genetic and phenotypic traits required for avian influenza viruses to become airborne transmissible between mammals.

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The virus detective who discovered Ebola

The virus detective who discovered Ebola | Virology and Bioinformatics from Virology.ca | Scoop.it
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Why Has This Really Common Virus Only Just Been Discovered? – Phenomena: Not Exactly Rocket Science

Why Has This Really Common Virus Only Just Been Discovered? – Phenomena: Not Exactly Rocket Science | Virology and Bioinformatics from Virology.ca | Scoop.it
The most common viruses in your body don’t make you ill. Instead, they infect the legions of microbes that live in your gut. These bacteriophages, or phages for short, number in their trillions. An...
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Markov Chains

A visual explanation by Victor Powell/w text by Lewis Lehe
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Dr. Kent Brantly reported in ‘grave condition’ as he battles Ebola

Dr. Kent Brantly reported in ‘grave condition’ as he battles Ebola | Virology and Bioinformatics from Virology.ca | Scoop.it
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New method provides researchers with efficient tool for tagging proteins

New method provides researchers with efficient tool for tagging proteins | Virology and Bioinformatics from Virology.ca | Scoop.it

Aarhus University researchers have developed an easier method to create DNA–protein conjugates. The method can potentially strengthen the work involved in diagnosing diseases.


Via idtdna
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Potential 'universal' blood test for cancer discovered

Potential 'universal' blood test for cancer discovered | Virology and Bioinformatics from Virology.ca | Scoop.it
A simple blood test that can be used to diagnose whether people have cancer or not has been devised by researchers. The test will enable doctors to rule out cancer in patients presenting with certain symptoms, saving time and preventing costly and unnecessary invasive procedures such as colonoscopies and biopsies being carried out. Alternatively, it could be a useful aid for investigating patients who are suspected of having a cancer that is currently hard to diagnose.
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Lecture Slides | HRP214 | Stanford - Writing in the Sciences

Lecture Slides | HRP214 | Stanford - Writing in the Sciences | Virology and Bioinformatics from Virology.ca | Scoop.it
Chris Upton + helpers's insight:

Excellent!!!!!

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Genetic Dynamic Analysis of the Influenza A H5N1 NS1 Gene in China

Genetic Dynamic Analysis of the Influenza A H5N1 NS1 Gene in China | Virology and Bioinformatics from Virology.ca | Scoop.it
by Kaifa Wei, Yanhui Chen, Yina Lin, Yutian Pan
The direct precursors of the A/Goose/Guangdong/1/1996 (GS/GD) virus lineage and its reassortants have been established geographically and ecologically.

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#Chikungunya virus in the #US (@CDCgov, July 27 2014, edited)

#Chikungunya virus in the #US (@CDCgov, July 27 2014, edited) | Virology and Bioinformatics from Virology.ca | Scoop.it
[Source: US Centers for Disease Control and Prevention (CDC), full page: (LINK).]
Chikungunya virus in the United States [      ]
Updates of chikungunya case counts are publically released every Tuesday evening (MT).

Via Mel Melendrez-Vallard
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PLOS Genetics: Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution (2014)

PLOS Genetics: Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution (2014) | Virology and Bioinformatics from Virology.ca | Scoop.it

Mutualistic symbioses between eukaryotes and beneficial microorganisms of their microbiome play an essential role in nutrition, protection against disease, and development of the host. However, the impact of beneficial symbionts on the evolution of host genomes remains poorly characterized. Here we used the independent loss of the most widespread plant–microbe symbiosis, arbuscular mycorrhization (AM), as a model to address this question. Using a large phenotypic approach and phylogenetic analyses, we present evidence that loss of AM symbiosis correlates with the loss of many symbiotic genes in the Arabidopsis lineage (Brassicales). Then, by analyzing the genome and/or transcriptomes of nine other phylogenetically divergent non-host plants, we show that this correlation occurred in a convergent manner in four additional plant lineages, demonstrating the existence of an evolutionary pattern specific to symbiotic genes. Finally, we use a global comparative phylogenomic approach to track this evolutionary pattern among land plants. Based on this approach, we identify a set of 174 highly conserved genes and demonstrate enrichment in symbiosis-related genes. Our findings are consistent with the hypothesis that beneficial symbionts maintain purifying selection on host gene networks during the evolution of entire lineages.


Via Kamoun Lab @ TSL
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The CD8 Antiviral Factor (CAF) can suppress HIV-1 transcription from the Long Terminal Repeat (LTR) promoter in the absence of elements upstream of the CATATAA box

The CD8 Antiviral Factor (CAF) suppresses viral transcription from the HIV-1 Long Terminal Repeat (LTR) promoter in a non-cytolytic manner. However, the region on the LTR upon which CAF acts is unknown. Our objective was to determine the region on the LTR upon which CAF acts to suppress HIV-1 transcription.
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Viruses101 | Learn Science at Scitable

Viruses101 | Learn Science at Scitable | Virology and Bioinformatics from Virology.ca | Scoop.it
Viruses 101 will delve into the world of microscopic killers. Each post will explore a new virus ? its components, effects on victims, and its impact on the global community.
Julia Paoli's insight:

Two residents in Florida are the first in the U.S. to contract chikungunya locally.

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Astrology can aid healthcare - MP (UK)

Astrology can aid healthcare - MP (UK) | Virology and Bioinformatics from Virology.ca | Scoop.it

A Conservative MP has spoken of his belief in astrology and his desire to incorporate it into medicine.

David Tredinnick said he had spent 20 years studying astrology and healthcare and was convinced it could work.

The MP for Bosworth, a member of the health committee and the science and technology committee, said he was not afraid of ridicule or abuse.

"There is no logic in attacking something that has a proven track record," he told BBC News.

He said he had studied the Indian astrological system Iahiri and the way it was used by that country's government and recalled how Chris Patten, Britain's last governor of Hong Kong, had an official astrologer, whom Mr Tredinnick had consulted while on a parliamentary delegation there.

 
Chris Upton + helpers's insight:

WTF!  

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Sierra Leone's chief Ebola doctor contracts the virus | Top News | Reuters

Sierra Leone's chief Ebola doctor contracts the virus | Top News | Reuters | Virology and Bioinformatics from Virology.ca | Scoop.it
FREETOWN (Reuters) - The head doctor fighting the deadly tropical virus Ebola in Sierra Leone has himself caught the disease, the government said.
The 39-year-old Sheik Umar Khan, hailed as a national
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Mel Melendrez-Vallard's curator insight, July 25, 4:33 AM

Just a really sad reality of those on the front lines of defense against diseases like Ebola.

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Why an Ebola epidemic is spinning out of control

Why an Ebola epidemic is spinning out of control | Virology and Bioinformatics from Virology.ca | Scoop.it
Laurie Garrett says poor governance, ignorance and hysteria are worsening the Ebola epidemic in Sierra Leone, Guinea and Liberia.
Chris Upton + helpers's insight:

Where are those homeopathy "we can cure anything with our magic water" nuts when you need one?

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