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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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WHO can't fully deal with Ebola outbreak, health official warns

WHO can't fully deal with Ebola outbreak, health official warns | Virology and Bioinformatics from Virology.ca | Scoop.it
International health officials warned Thursday that recent budget cuts have impeded the ability of the World Health Organization to respond to the Ebola outbreak that has killed at least 603 people in Guinea, Liberia and Sierra Leone.
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The Forgotten Woman Who Made Microbiology Possible

The Forgotten Woman Who Made Microbiology Possible | Virology and Bioinformatics from Virology.ca | Scoop.it
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Ed Rybicki's comment, Today, 3:38 AM
From her kitchen, we will note. Where she "...cooked both the family's meals and the beef stock that the bacteria ate in her kitchen". Maybe it's past time that technicians were formally acknowledged, and not just at the end of the papers??
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Great moments in science (if Twitter had existed)

Great moments in science (if Twitter had existed) | Virology and Bioinformatics from Virology.ca | Scoop.it
Dean Burnett: What if Twitter had been around at the time of famous scientists and scientific breakthroughs?
Chris Upton + helpers's insight:

Be sure to read the comments too.

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CREATE Cornerstone: Introduction to Scientific Thinking, a New Course for STEM-Interested Freshmen, Demystifies Scientific Thinking through Analysis of Scientific Literature

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Novel Drosophila Viruses Encode Host-Specific Suppressors of RNAi

Novel Drosophila Viruses Encode Host-Specific Suppressors of RNAi | Virology and Bioinformatics from Virology.ca | Scoop.it
From molecules to physiology
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Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design

Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design | Virology and Bioinformatics from Virology.ca | Scoop.it

Summary: Codon optimization has been widely used for designing synthetic genes to improve their expression in heterologous host organisms. However, most of the existing codon optimization tools consider a single design criterion and/or implement a rather rigid user interface to yield only one optimal sequence, which may not be the best solution. Hence, we have developed Codon Optimization OnLine (COOL), which is the first web tool that provides the multi-objective codon optimization functionality to aid systematic synthetic gene design. COOL supports a simple and flexible interface for customizing various codon optimization parameters such as codon adaptation index, individual codon usage and codon pairing. In addition, users can visualize and compare the optimal synthetic sequences with respect to various fitness measures. User-defined DNA sequences can also be compared against the COOL optimized sequences to show the extent by which the user’s sequences can be further improved.

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Novel Drosophila Viruses Encode Host-Specific Suppressors of RNAi

Novel Drosophila Viruses Encode Host-Specific Suppressors of RNAi | Virology and Bioinformatics from Virology.ca | Scoop.it

The ongoing conflict between viruses and their hosts can drive the co-evolution between host immune genes and viral suppressors of immunity. It has been suggested that an evolutionary ‘arms race’ may occur between rapidly evolving components of the antiviral RNAi pathway ofDrosophila and viral genes that antagonize it. We have recently shown that viral protein 1 (VP1) of Drosophila melanogaster Nora virus (DmelNV) suppresses Argonaute-2 (AGO2)-mediated target RNA cleavage (slicer activity) to antagonize antiviral RNAi. Here we show that viral AGO2 antagonists of divergent Nora-like viruses can have host specific activities. We have identified novel Nora-like viruses in wild-caught populations of D. immigrans (DimmNV) and D. subobscura (DsubNV) that are 36% and 26% divergent from DmelNV at the amino acid level. 

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What Would It Take to Stop AIDS by 2030?

What Would It Take to Stop AIDS by 2030? | Virology and Bioinformatics from Virology.ca | Scoop.it
The United Nations announced today that the global HIV/AIDS epidemic could be slowed to a trickle within the next two decades. Can it be done?
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T cell mediated immunity to influenza: mechanisms of viral control: Trends in Immunology

T cell mediated immunity to influenza: mechanisms of viral control: Trends in Immunology | Virology and Bioinformatics from Virology.ca | Scoop.it

Infection with influenza A virus (IAV) is a major cause of worldwide morbidity and mortality. Recent findings indicate that T cell immunity is key to limiting severity of disease arising from IAV infection, particularly in instances where antibody immunity is ineffective. As such, there is a need to understand better the mechanisms that mediate effective IAV-specific cellular immunity, especially given that T cell immunity must form an integral part of any vaccine designed to elicit crossreactive immunity against existing and new strains of influenza virus. Here, we review the current understanding of cellular immunity to IAV, highlighting recent findings that demonstrate important roles for both CD4+ and CD8+ T cell immunity in protection from IAV-mediated disease.

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A dedicated database system for handling multi-level data in systems biology - Source Code for Biology and Medicine

Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic, incomplete and distributed among public databases. This leads to difficulties in data accessibility and often results in errors when data are merged and integrated from varied resources. Therefore, integration and management of systems biological data remain very challenging.
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Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery. - J Virol Methods. 2014

The discovery of new or divergent viruses using metagenomics and high-throughput sequencing has become more commonplace. The preparation of a sample is known to have an effect on the representation of virus sequences within the metagenomic dataset yet comparatively little attention has been given to this. Physical enrichment techniques are often applied to samples to increase the number of viral sequences and therefore enhance the probability of detection. With the exception of virus ecology studies, there is a paucity of information available to researchers on the type of sample preparation required for a viral metagenomic study that seeks to identify an aetiological virus in an animal or human diagnostic sample. A review of published virus discovery studies revealed the most commonly used enrichment methods, that were usually quick and simple to implement, namely low-speed centrifugation, filtration, nuclease-treatment (or combinations of these) which have been routinely used but often without justification. These were applied to a simple and well-characterised artificial sample composed of bacterial and human cells, as well as DNA (adenovirus) and RNA viruses (influenza A and human enterovirus), being either non-enveloped capsid or enveloped viruses. The effect of the enrichment method was assessed by both quantitative real-time PCR and metagenomic analysis that incorporated an amplification step. Reductions in the absolute quantities of bacteria and human cells were observed for each method as determined by qPCR, but the relative abundance of viral sequences in the metagenomic dataset remained largely unchanged. A 3-step method of centrifugation, filtration and nuclease-treatment showed the greatest increase in the proportion of viral sequences. This study provides a starting point for the selection of a purification method in future virus discovery studies, and highlights the need for more data to validate the effect of enrichment methods on different sample types, amplification, bioinformatics approaches and sequencing platforms. This study also highlights the potential risks that may attend selection of a virus enrichment method without any consideration for the sample type being investigated.

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RNA Viruses: A Case Study of the Biology of Emerging Infectious Diseases

There are 180 currently recognized species of RNA virus that can infect humans, and on average, 2 new species are added every year. RNA viruses are routinely exchanged between humans and other hosts (particularly other mammals and sometimes birds) over both epidemiological and evolutionary time: 89% of human-infective species are considered zoonotic and many of the remainder have zoonotic origins. Some viruses that have crossed the species barrier into humans have persisted and become human-adapted viruses, as exemplified by the emergence of HIV-1. Most, however, have remained as zoonoses, and a substantial number have apparently disappeared again. We still know relatively little about what determines whether a virus is able to infect, transmit from, and cause disease in humans, but there is evidence that factors such as host range, cell receptor usage, tissue tropisms, and transmission route all play a role. Although systematic surveillance for potential new human viruses in nonhuman hosts would be enormously challenging, we can reasonably aspire to much better knowledge of the diversity of mammalian and avian RNA viruses than exists at present.

Via Ed Rybicki
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New Research Finds a Way to Predict Which HIV Patients Will Respond Better to Future Therapeutic Vaccine - Vaccine Nation : Vaccine Nation

New Research Finds a Way to Predict Which HIV Patients Will Respond Better to Future Therapeutic Vaccine - Vaccine Nation : Vaccine Nation | Virology and Bioinformatics from Virology.ca | Scoop.it
A new study suggests that HIV patients with a higher level of a particular biomarker may respond more favourably to an experimental HIV therapeutic vaccine
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You're not allowed bioinformatics anymore

You're not allowed bioinformatics anymore | Virology and Bioinformatics from Virology.ca | Scoop.it
"Ah welcome! Come in, come in!” said the institute director as Professor Smith appeared for their scheduled 2pm meeting. “I want to talk to you about your latest proposal”, the director continued. ...
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Persistence and Availability of Web Services in Computational Biology

Persistence and Availability of Web Services in Computational Biology | Virology and Bioinformatics from Virology.ca | Scoop.it

We found that 72% of Web sites are still available at the published addresses, only 9% of services are completely unavailable. Older addresses often redirect to new pages. We checked the functionality of all available services: for 33%, we could not test functionality because there was no example data or a related problem; 13% were truly no longer working as expected; we could positively confirm functionality only for 45% of all services.

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Robert Kennedy's Dangerous Anti-Vaccine Activism

Robert Kennedy's Dangerous Anti-Vaccine Activism | Virology and Bioinformatics from Virology.ca | Scoop.it
Robert F. Kennedy Jr. is coming out with a new book that claims thimerosal in vaccines causes autism. This claim has been thoroughly discredited, but RFK Jr. believes that it's all a big conspiracy and that he's right. His crazy anti-vaccine views coupled with his fame make for an especially dangerous combination.
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PRADA: pipeline for RNA sequencing data analysis


Via Mel Melendrez-Vallard
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Practical data management takes its show on the road

Practical data management takes its show on the road | Virology and Bioinformatics from Virology.ca | Scoop.it

This title should really read “Practical data management takes its show ACROSS the road” because that’s what I’m actually doing. Next week, I’ll be a co-instructor for the second Data Carpentry bootcamp at MSU’s BEACON Center, which is right across the street from me. Who said agricultural ecologists don’t get to travel?

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Larger Mammalian Body Size Leads to Lower Retroviral Activity

Larger Mammalian Body Size Leads to Lower Retroviral Activity | Virology and Bioinformatics from Virology.ca | Scoop.it
From molecules to physiology
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Journaled String Tree - A scalable data structure for analyzing thousands of similar genomes on your laptop

Journaled String Tree - A scalable data structure for analyzing thousands of similar genomes on your laptop | Virology and Bioinformatics from Virology.ca | Scoop.it

Next generation sequencing (NGS) has revolutionized biomedical research in the last decade and led to a continues stream of developments in bioinformatics addressing the need for fast and space efficient solutions for analyzing NGS data. Often researchers need to analyze a set of genomic sequences which stem from closely related species or are indeed individuals of the same species. Hence the analyzed sequences are very similar. For analyses where local changes in the examined sequence induce only local changes in the results it is obviously desirable to examine identical or similar regions not repeatedly.

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Manipulation of DNA repair pathways for herpesvirus replication

Manipulation of DNA repair pathways for herpesvirus replication | Virology and Bioinformatics from Virology.ca | Scoop.it

Herpes simplex virus 1 (HSV-1) replicates in the nucleus and induces chromosomal DNA damage, including DNA double-strand breaks (DSBs). Host cells repair DSBs by non-homologous end joining (NHEJ) or homologous recombination, but how the cell chooses between these pathways and the impact of this decision on viral replication has been unclear. Karttunen et al. now show that HSV-1 inhibits NHEJ by triggering the Fanconi anaemia pathway. HSV-1 infection induced mono-ubiquitination of the two Fanconi anaemia pathway effectors, FANCI and FANCI-D2, which resulted in their redistribution from sites of DNA damage to viral replication compartments. Furthermore, HSV-1 replication was severely reduced in cells lacking components of the Fanconi anaemia pathway, and inhibition of NHEJ in these cells was sufficient to restore viral growth. These data suggest that HSV-1 manipulates the Fanconi anaemia pathway to suppress NHEJ and promote viral replication.

  Herpesvirus graphic from Russell Kightley Media
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An Introduction To Applied Bioinformatics by gregcaporaso

An Introduction To Applied Bioinformatics by gregcaporaso | Virology and Bioinformatics from Virology.ca | Scoop.it

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Comprehensive human virus screening using high-throughput sequencing with a user-friendly representation of bioinformatics analysis: a pilot study.

High-throughput sequencing (HTS) provides the means to analyze clinical specimens at unprecedented molecular detail. While this technology has been successfully applied to virus discovery and other related areas of research, HTS methodology has yet to be exploited for use in a clinical setting for routine diagnostics. Here, a bioinformatics pipeline (ezVIR) was designed to process HTS data from any of the standard platforms and to evaluate the entire spectrum of known human viruses at once, providing results that are easy to interpret and customizable. The pipeline works by identifying the most likely viruses present in the specimen given the sequencing data. Additionally, ezVIR can generate optional reports for strain typing, genome coverage histograms, and can perform cross-contamination analysis for specimens prepared in series. In this pilot study, the pipeline was challenged using HTS data from 20 clinical specimens representative of those most often collected and analyzed in daily practice. The specimens (5 cerebrospinal fluids, 7 bronchoalveolar lavages, 5 plasma, 2 serums and 1 nasopharyngeal aspirate) were originally found to be positive for a diverse range of DNA or RNA viruses by routine molecular diagnostics. The ezVIR pipeline correctly identified 14/14 specimens containing viruses with genomes < 40,000 bp, and 4/6 specimens positive for large genome viruses. Although further validation is needed to evaluate sensitivity and to define detection cut-offs, results obtained in this pilot study indicate that the overall detection success rate, coupled to the ease of interpreting the analysis reports, makes it worth considering using HTS for clinical diagnostics.

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Useful Review on Rotavirus

Rotaviruses (RV) are ubiquitous, highly infectious, segmented double-stranded RNA genome viruses of importance in public health because of the severe acute gastroenteritis they cause in young children and many animal species. They are very well adapted to their host, with symptomatic and asymptomatic reinfections being virtually universal during the first 3 years of life. Antibodies are the major arm of the immune system responsible for protecting infants from RV reinfection. The relationship between the virus and the B cells (Bc) that produce these antibodies is complex and incompletely understood: most blood-circulating Bc that express RV-specific immunoglobulin (Ig) on their surface (RV-Ig) are naive Bc and recognize the intermediate capsid viral protein VP6 with low affinity. When compared to non-antigen-specific Bc, RV-Bc are enriched in CD27+ memory Bc (mBc) that express IgM. The Ig genes used by naive RV-Bc are different than those expressed by RV-mBc, suggesting that the latter do not primarily develop from the former. Although RV predominantly infects mature villus enterocytes, an acute systemic viremia also occurs and RV-Bc can be thought of as belonging to either the intestinal or systemic immune compartments. Serotype-specific or heterotypic RV antibodies appear to mediate protection by multiple mechanisms, including intracellular and extracellular homotypic and heterotypic neutralization. Passive administration of RV-Ig can be used either prophylactically or therapeutically. A better understanding of the Bc response generated against RV will improve our capacity to identify improved correlates of protection for RV vaccines.

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Genetics of Phage Lysis

We have been witnessing an increased interest in bacteriophage studies focused on their use as antibacterial agents to fight pathogenic bacteria. This interest is a consequence of the phages' ability to lyse a bacterial host. Until recently, little was known about the mechanisms used by mycobacteriophages to induce lysis of their complex hosts. However, studies on Ms6-induced lysis have changed this scenario and provided new insights into the mechanisms of bacteriophage-induced lysis. Specific lysis protein genes have been identified in mycobacteriophage genomes, reflecting the particular mycobacterial cell envelope composition. These include enzymes that target mycolic acid–containing lipids and proteins that participate in the secretion of the phage endolysin, functioning as chaperone-like proteins. This chapter focuses on the current knowledge of mycobacteriophage-induced lysis, starting with an overview of phage lysis and basic features of the lysis players.
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