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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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How Viruses Hijack the ERAD Tuning Machinery

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An essential step during the intracellular life cycle of many positive-strand RNA viruses is the rearrangement of host cell membranes to generate membrane-bound replication platforms. For example, Nidovirales and Flaviviridae subvert the membrane of the endoplasmic reticulum (ER) for their replication. However, the absence of conventional ER and secretory pathway markers in virus-induced ER-derived membranes has for a long time hampered a thorough understanding of their biogenesis.

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Molecular Flipbook: easy way to make videos with structures

Molecular Flipbook: easy way to make videos with structures | Virology and Bioinformatics from Virology.ca | Scoop.it
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A pathogenicity determinant maps to the N-terminal coat protein region of the Pepino mosaic virus genome

A pathogenicity determinant maps to the N-terminal coat protein region of the Pepino mosaic virus genome | Virology and Bioinformatics from Virology.ca | Scoop.it

Pepino mosaic virus poses a worldwide threat to the tomato industry. Considerable differences at the genetic level allow for distinction of four main genotypic clusters, however the basis for phenotypic outcome is difficult to elucidate. This work reports the generation of wild-type PepMV infectious clones of both EU (mild) and CH2 (aggressive) genotypes, from which chimeric infectious clones were created. Phenotypic analysis in three solanaceous hosts; N. benthamiana, D. stramonium and S. lycopersicum, indicated a PepMV pathogenicity determinant to map to the 3’-terminal region of the genome. Increased aggression was only observed in N. benthamiana, showing this factor to be host specific. The determinant was localised to amino acids 11-26 of the N-terminal CP region, this is the first report of this region functioning as virulence factor in PepMV. 

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We're nothing if not current here - even if we DID have to go to the PDF version and copy the abstract, because it's too hot off the press to have an online one yet B-)

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Tailoring Your Proteome View

Tailoring Your Proteome View | Virology and Bioinformatics from Virology.ca | Scoop.it
Computational tools can streamline the development of targeted proteomics experiments.
 
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Nitazoxanide: A first-in-class broad-spectrum antiviral agent

Originally developed and commercialized as an antiprotozoal agent, nitazoxanide was later identified as a first-in-class broad-spectrum antiviral drug and has been repurposed for the treatment of influenza. A Phase 2b/3 clinical trial recently published in The Lancet Infectious Diseases found that oral administration of nitazoxanide 600 mg twice daily for five days reduced the duration of clinical symptoms and reduced viral shedding compared to placebo in persons with laboratory-confirmed influenza. The same study also suggested a potential benefit for subjects with influenza-like illness who did not have influenza or other documented respiratory viral infection. From a chemical perspective, nitazoxanide is the scaffold for a new class of drugs called thiazolides. These small-molecule drugs target host-regulated processes involved in viral replication. Nitazoxanide is orally bioavailable and safe with extensive post-marketing experience involving more than 75 million adults and children. A new dosage formulation of nitazoxanide is presently undergoing global Phase 3 clinical development for the treatment of influenza. Nitazoxanide inhibits a broad range of influenza A and B viruses including influenza A(pH1N1) and the avian A(H7N9) as well as viruses that are resistant to neuraminidase inhibitors. It is synergistic with neuraminidase inhibitors, and combination therapy with oseltamivir is being studied in humans as part of ongoing Phase 3 clinical development. Nitazoxanide also inhibits the replication of a broad range of other RNA and DNA viruses including respiratory syncytial virus, parainfluenza, coronavirus, rotavirus, norovirus, hepatitis B, hepatitis C, dengue, yellow fever, Japanese encephalitis virus and human immunodeficiency virus in cell culture assays. Clinical trials have indicated a potential role for thiazolides in treating rotavirus and norovirus gastroenteritis and chronic hepatitis B and chronic hepatitis C. Ongoing and future clinical development is focused on viral respiratory infections, viral gastroenteritis and emerging infections such as dengue fever.

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Adaptive Evolution and Environmental Durability Jointly Structure Phylodynamic Patterns in Avian Influenza Viruses

Adaptive Evolution and Environmental Durability Jointly Structure Phylodynamic Patterns in Avian Influenza Viruses | Virology and Bioinformatics from Virology.ca | Scoop.it

Avian influenza viruses (AIVs) have been pivotal to the origination of human pandemic strains. Despite their scientific and public health significance, however, there remains much to be understood about the ecology and evolution of AIVs in wild birds, where major pools of genetic diversity are generated and maintained. Here, we present comparative phylodynamic analyses of human and AIVs in North America, demonstrating (i) significantly higher standing genetic diversity and (ii) phylogenetic trees with a weaker signature of immune escape in AIVs than in human viruses. To explain these differences, we performed statistical analyses to quantify the relative contribution of several potential explanations. We found that HA genetic diversity in avian viruses is determined by a combination of factors, predominantly subtype-specific differences in host immune selective pressure and the ecology of transmission (in particular, the durability of subtypes in aquatic environments). Extending this analysis using a computational model demonstrated that virus durability may lead to long-term, indirect chains of transmission that, when coupled with a short host lifespan, can generate and maintain the observed high levels of genetic diversity. Further evidence in support of this novel finding was found by demonstrating an association between subtype-specific environmental durability and predicted phylogenetic signatures: genetic diversity, variation in phylogenetic tree branch lengths, and tree height. The conclusion that environmental transmission plays an important role in the evolutionary biology of avian influenza viruses—a manifestation of the “storage effect”—highlights the potentially unpredictable impact of wildlife reservoirs for future human pandemics and the need for improved understanding of the natural ecology of these viruses.

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virtualenv - running Python based software in isolation

virtualenv - running Python based software in isolation | Virology and Bioinformatics from Virology.ca | Scoop.it
#bioinformatics Tutorial: virtualenv - running Python based software in isolation http://t.co/9pbtuHSK8u

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Stop saying “Scientists discover…” instead say, “Prof. Doe’s team discovers…” | Simply Statistics

Stop saying “Scientists discover…” instead say, “Prof. Doe’s team discovers…” | Simply Statistics | Virology and Bioinformatics from Virology.ca | Scoop.it
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Why should Prof. Doe get all the credit?

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Evolution and Genomics

Evolution and Genomics | Virology and Bioinformatics from Virology.ca | Scoop.it

immersive training opportunities | The European Workshop on Genomics is being planned for January 2015 and will be held in Cesky Krumlov, Czech Republic. Updates coming soon! Please sign-up for our email list to be notified!

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Margaret Thatcher's surprising relationship with Dorothy Hodgkin

Margaret Thatcher's surprising relationship with Dorothy Hodgkin | Virology and Bioinformatics from Virology.ca | Scoop.it
A new play explores one of the most intriguing friendships in the history of science and politics: Margaret Thatcher and Dorothy Hodgkin. Alice Bell spoke to playwright Adam Ganz
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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.
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Ebola Outbreak Declared an International Public Health Emergency

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Second experimental Ebola drug gains approval

Second experimental Ebola drug gains approval | Virology and Bioinformatics from Virology.ca | Scoop.it
Following the use of the experimental Ebola treatment drug ZMapp on two U.S. aid workers in Liberia, the U.S. FDA has partially approved a second medication. The drug, TKM-Ebola, has been approved from the next phase of clinical trials.
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Influenza A Virus Attenuation by Codon Deoptimization of the NS Gene for Vaccine Development

Influenza viral infection represents a serious public health problem that causes contagious respiratory disease, which is most effectively prevented through vaccination to reduce transmission and future infection. The nonstructural (NS) gene of influenza A virus encodes an mRNA transcript that is alternatively spliced to express two viral proteins, the nonstructural protein 1 (NS1) and the nuclear export protein (NEP). The importance of the NS gene of influenza A virus for viral replication and virulence has been well described and represents an attractive target to generate live attenuated influenza viruses with vaccine potential.

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The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing | Virology and Bioinformatics from Virology.ca | Scoop.it
PLOS Biology is an open-access, peer-reviewed journal that features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines.
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A Sensitive Tool for Detecting Indels

A Sensitive Tool for Detecting Indels | Virology and Bioinformatics from Virology.ca | Scoop.it

A team from Cold Spring Harbor Laboratory has released an algorithm, called Scalpel, for finding insertions and deletions in next generation sequencing data sets. Scalpel, which is open source and available for download on SourceForge, outperformed the popular tools GATK HaplotypeCaller and SOAPindel in test runs on both simulated and real whole human exomes.

Like other indel callers, Scalpel works by performing de novo assembly of regions of interest, so that misalignment to the reference genome cannot obscure the presence of an insertion or deletion. Scalpel's innovation is to repeatedly check its assembly before comparing to the reference genome, to account for simple sequence repeats that are a regular source of error in indel calling. When Scalpel assembles an exon, it collects reads that map to that exon (including partial matches), splits them into k-mers, and creates a de Bruijn graph to span the exon; however, if it detects repeats in the map, it iteratively increases the size of the k-mers by one base until the repeats are eliminated. This ensures that the final assembly of the exon is highly accurate while minimizing compute time.

 
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AliView: a fast and lightweight alignment viewer and editor for large data sets.

Summary: AliView is an alignment viewer and editor designed to meet the requirements of next generation sequencing era phylogenetic datasets. AliView handles alignments of unlimited size in the formats most commonly used, i.e. Fasta, Phylip, Nexus, Clustal and MSF. The intuitive graphical interface makes it easy to inspect, sort, delete, merge and realign sequences as part of the manual filtering process of large data sets. AliView also works as an easy to use alignment editor for small as well as large data sets.

Availability: AliView is released as open-source software under the GNU General Public License, version 3.0 (GPLv3), and is available at GitHub (www.github.com/AliView). The program is cross-platform and extensively tested on Linux, Mac OS X and Windows systems. Downloads and help are available at http://ormbunkar.se/aliview

Contact: anders.larsson@ebc.uu.se

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Using Clinician's Search Query Data to Monitor Influenza Epidemics

Search query information from a clinician's database, UpToDate, is shown to timely predict influenza epidemics in the United States. Our results show that digital disease surveillance tools based on experts' databases may be able to provide an alternative, reliable and stable signal for accurate predictions of flu outbreaks.

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

Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction | 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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New Alignment Method to Speed Up De Novo Assembly of Whole Genomes

August 15, 2014 | This Thursday, a team of bioinformaticians from the National Biodefense Analysis and Countermeasures Center, the University of Maryland College Park, and sequencing company Pacific Biosciences posted information on their tool MHAP to the life sciences preprint server bioRxiv. MHAP, or MinHash Alignment Process, is a dramatically faster method for ordering DNA fragments sequenced on long-read technologies like the PacBio RS II Sequencer or the Oxford Nanopore MinION, making it easier to assemble whole genomes from scratch without the use of a reference genome.Bio-IT World previously covered MHAP following a presentation by senior author Adam Phillippy at the PacBio User Group Meeting this June; however, the newly released paper features much greater detail, including assemblies of the human genome and four important model organisms.

 


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Why HIV Virions Have Low Numbers of Envelope Spikes: Implications for Vaccine Development

Why HIV Virions Have Low Numbers of Envelope Spikes: Implications for Vaccine Development | Virology and Bioinformatics from Virology.ca | Scoop.it
From molecules to physiology
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Online collaboration: Scientists and the social network

Online collaboration: Scientists and the social network | Virology and Bioinformatics from Virology.ca | Scoop.it
Why scholars use social media
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Picturing science: Royal Society launches scientific illustrations ‘print on demand’

Picturing science: Royal Society launches scientific illustrations ‘print on demand’ | Virology and Bioinformatics from Virology.ca | Scoop.it
GrrlScientist: The Royal Society has just launched a ‘print-on-demand’ service so the public can easily purchase high quality prints of nature and scientific illustrations from its library and archives.
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Bioinformatics at a Crossroad Again – Which Way Next? « Homolog.us – Bioinformatics

Bioinformatics at a Crossroad Again – Which Way Next? « Homolog.us – Bioinformatics | Virology and Bioinformatics from Virology.ca | Scoop.it

One of our readers asked – “If genome assembly becomes a solved problem, what’s next?”

We like to broaden the comment to argue that the entire field of bioinformatics is again at a turning point, because almost all difficult computational problems related to ‘next-generation sequencing’ have been solved satisfactorily. Readers are encouraged to express their differing opinions in the comment section.

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How A Computer Algorithm Predicted West Africa's Ebola Outbreak Before It Was Announced

How A Computer Algorithm Predicted West Africa's Ebola Outbreak Before It Was Announced | Virology and Bioinformatics from Virology.ca | Scoop.it
The Ebola outbreak in West Africa is focusing a spotlight on a unique online tool run by experts in Boston that flagged a "mystery hemorrhagic fever" in forested areas of southeastern Guinea nine d...
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Samuel Viana's curator insight, August 15, 11:53 AM

Um interessante algoritmo que combina fontes noticiosas, relativamente à frequência de notícias sobre surtos e à proveniência desses mesmos surtos, ajuda a prever a possibilidade de evolução de potenciais pandemias, antes de estas poderem escalar para níveis incontroláveis.

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Case Fatality Rate for ebolavirus | epidemic

Case Fatality Rate for ebolavirus | epidemic | Virology and Bioinformatics from Virology.ca | Scoop.it
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