Viruses and Bioinformatics from Virology.uvic.ca
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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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Viruses and Bioinformatics from Virology.uvic.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: | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

get in touch if you want to help curate this topic

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Bwana Moses's comment, May 25, 2016 6:13 AM
Great work. Keep it going.
Bwana Moses's comment, March 7, 12:46 PM
Thank You.
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Pandemics, Politics and the Spanish Flu | The Tyee

One of the worst plagues in human history is largely forgotten now. For our own sakes, it’s time to remember what happened.
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A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome

A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Advancements in Next Generation Sequencing (NGS) technologies regarding throughput, read length and accuracy had a major impact on microbiome research by significantly improving 16S rRNA amplicon sequencing. As rapid improvements in sequencing platforms and new data analysis pipelines are introduced, it is essential to evaluate their capabilities in specific applications. The aim of this study was to assess whether the same project-specific biological conclusions regarding microbiome composition could be reached using different sequencing platforms and bioinformatics pipelines. Chicken cecum microbiome was analyzed by 16S rRNA amplicon sequencing using Illumina MiSeq, Ion Torrent PGM, and Roche 454 GS FLX Titanium platforms, with standard and modified protocols for library preparation. We labeled the bioinformatics pipelines included in our analysis QIIME1 and QIIME2 (de novo OTU picking [not to be confused with QIIME version 2 commonly referred to as QIIME2]), QIIME3 and QIIME4 (open reference OTU picking), UPARSE1 and UPARSE2 (each pair differs only in the use of chimera depletion methods), and DADA2 (for Illumina data only). GS FLX+ yielded the longest reads and highest quality scores, while MiSeq generated the largest number of reads after quality filtering. Declines in quality scores were observed starting at bases 150–199 for GS FLX+ and bases 90–99 for MiSeq. Scores were stable for PGM-generated data. Overall microbiome compositional profiles were comparable between platforms; however, average relative abundance of specific taxa varied depending on sequencing platform, library preparation method, and bioinformatics analysis. Specifically, QIIME with de novo OTU picking yielded the highest number of unique species and alpha diversity was reduced with UPARSE and DADA2 compared to QIIME. The three platforms compared in this study were capable of discriminating samples by treatment, despite differences in diversity and abundance, leading to similar biological conclusions. Our results demonstrate that while there were differences in depth of coverage and phylogenetic diversity, all workflows revealed comparable treatment effects on microbial diversity. To increase reproducibility and reliability and to retain consistency between similar studies, it is important to consider the impact on data quality and relative abundance of taxa when selecting NGS platforms and analysis tools for microbiome studies.
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Python Plotting for Exploratory Analysis

Python Plotting for Exploratory Analysis | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Interactive comparison of Python plotting libraries for exploratory data analysis. Examples of using Pandas plotting, plotnine, Seaborn, and Matplotlib. Includes comparison with ggplot2 for R.
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Vaccinia virus encodes a novel inhibitor of apoptosis that associates with the apoptosome.

Apoptosis selectively eliminates dangerous cells such as virus-infected cells. Poxviruses express apoptosis antagonists to neutralize this anti-viral host defense. The vaccinia virus (VACV) M1 ankyrin (ANK) protein, a protein with no previously ascribed function, inhibits apoptosis. M1 interacts with the apoptosome and prevents procaspase-9 processing as well as downstream procaspase-3 cleavage in several cell types and under multiple conditions. M1 is the first poxviral protein reported to associate with and prevent the function of the apoptosome, giving a more detailed picture of the threats VACV encounters during infection. Dysregulation of apoptosis is associated with several human diseases. One potential treatment of apoptosis-related diseases is through the use of designed ANK repeat proteins (DARPins), similar to M1, as caspase inhibitors. Thus, the study of the novel anti-apoptosis effects of M1 via apoptosome association will be helpful for understanding how to control apoptosis using either natural or synthetic molecules.
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Archaeal biology: Plasmid propagation by virus-like particles

A defining feature that differentiates plasmids from viruses is their mechanism of propagation from cell to cell. Plasmids are transferred from donor to recipient as naked DNA, through cell–cell contact or in unstructured extracellular vesicles. A new study describes a novel mechanism of plasmid dissemination in archaea that uses specialized membrane vesicles similar to a virus. Electron microscopy of Halorubrum lacusprofundi R1S1 revealed virus-like particles (VLPs) budding from the surface of cells. Isolated VLPs were able to infect a plasmid-free H. lacusprofundi strain, resulting in the biogenesis of VLPs. The VLPs contained a ~50 kb plasmid that encodes proteins that were found to specifically incorporate into the VLPs. The authors hypothesize that these proteins carry out roles similar to vesicle coatamers that drive the assembly of transport vesicles and that this mechanism of DNA transfer may represent an evolutionary link between viruses and plasmids.
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Extrinsically derived TNF is primarily responsible for limiting antiviral CD8+ T cell response magnitude

Extrinsically derived TNF is primarily responsible for limiting antiviral CD8+ T cell response magnitude | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
TNF is a pro-inflammatory cytokine produced by both lymphoid and non-lymphoid cells. As a consequence of the widespread expression of its receptors (TNFR1 and 2), TNF plays a role in many important biological processes. In the context of influenza A virus (IAV) infection, TNF has variably been implicated in mediating immunopathology as well as suppression of the immune response. Although a number of cell types are able to produce TNF, the ability of CD8+ T cells to produce TNF following viral infection is a hallmark of their effector function. As such, the regulation and role of CD8+ T cell-derived TNF following viral infection is of great interest. Here, we show that the biphasic production of TNF by CD8+ T cells following in vitro stimulation corresponds to distinct patterns of epigenetic modifications. Further, we show that a global loss of TNF during IAV infection results in an augmentation of the peripheral virus-specific CD8+ T cell response. Subsequent adoptive transfer experiments demonstrated that this attenuation of the CD8+ T cell response was largely, but not exclusively, conferred by extrinsic TNF, with intrinsically-derived TNF making only modest contributions. In conclusion, TNF exerts an immunoregulatory role on CD8+ T cell responses following IAV infection, an effect that is largely mediated by extrinsically-derived TNF.

Via Gilbert C FAURE
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PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization | Bioinformatics | Oxford Academic

PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization | Bioinformatics | Oxford Academic | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Abstract. Motivation: Comparative and evolutionary studies utilize phylogenetic trees to analyze and visualize biological data. Recently, several web-based too
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Natural killer cells attenuate cytomegalovirus-induced hearing loss in mice

Natural killer cells attenuate cytomegalovirus-induced hearing loss in mice | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Cytomegalovirus (CMV) transmission from an infected mother to her fetus is a leading cause of permanent hearing loss in children, but the contributing processes are not clear. In this report, we utilized a mouse model, which recapitulates many features of congenital CMV mediated childhood hearing loss, to demonstrate that natural killer cells (NK), a component of early host immune response to infection, play a critical protective role in CMV-induced hearing loss. Specifically, we determined that NK cells interact with CMV infected cells through binding of the NK cell receptor, Ly49H, with a virally-encoded protein, m157, expressed on the cell surface of CMV infected inner ear cells, to mediate the protective effect. Findings from this study provide insight into the host immune response during CMV-induced hearing loss in mice.
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Zika genomics urgently need standardized and curated reference sequences

Zika genomics urgently need standardized and curated reference sequences | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Emerging viral epidemics pose a threat to public health globally. The recent spread of the Zika virus (ZIKV) across the Pacific region and the Americas is particularly disturbing, given its association with severe birth malformations.
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Die Another Day: Inhibition of Cell Death Pathways by Cytomegalovirus

Die Another Day: Inhibition of Cell Death Pathways by Cytomegalovirus | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Multicellular organisms have evolved multiple genetically programmed cell death pathways that are essential for homeostasis. The finding that many viruses encode cell death inhibitors suggested that cellular suicide also functions as a first line of defence against invading pathogens. This theory was confirmed by studying viral mutants that lack certain cell death inhibitors. Cytomegaloviruses, a family of species-specific viruses, have proved particularly useful in this respect. Cytomegaloviruses are known to encode multiple death inhibitors that are required for efficient viral replication. Here, we outline the mechanisms used by the host cell to detect cytomegalovirus infection and discuss the methods employed by the cytomegalovirus family to prevent death of the host cell. In addition to enhancing our understanding of cytomegalovirus pathogenesis we detail how this research has provided significant insights into the cross-talk that exists between the various cell death pathways.
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A new single-nucleotide polymorphism linked to severe influenza disease

Clear links between human genes and susceptibility to influenza disease are scarce. A recent study uncovers a gene variant coupled to severe influenza, and shows how it hampers the expression of an antiviral gene that is key to immune cell survival.

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Course: Introduction to Synthetic Biology - New York

Course: Introduction to Synthetic Biology - New York | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Eventbrite - SynBioBeta presents Course: Introduction to Synthetic Biology - New York - Friday, September 15, 2017 at 7 West 34th Street, New York, NY. Find event and ticket information.

Via Gerd Moe-Behrens
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What web browsers and proteins have in common: Researchers discover molecular 'add-ons' that customize protein interfaces

What web browsers and proteins have in common: Researchers discover molecular 'add-ons' that customize protein interfaces | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

The researchers discovered tiny bits of molecular material -- which they named "add-ons" -- on the outer edges of the protein interface that customize what a protein can do. They chose the name because the add-ons customize the interface between proteins the way software add-ons customize a web interface with a user.

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Adaptation of influenza A (H7N9) virus in primary human airway epithelial cells

Adaptation of influenza A (H7N9) virus in primary human airway epithelial cells | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
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The David J. Sencer CDC Museum, a Smithsonian Affiliate

The David J. Sencer CDC Museum, a Smithsonian Affiliate | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Ebola:  CDC Centers for Disease Control and Prevention David J. Sencer CDC Museum Homepage

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The eBioKit, a stand-alone educational platform for bioinformatics

The eBioKit, a stand-alone educational platform for bioinformatics | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Bioinformatics skills have become essential for many research areas; however, the availability of qualified researchers is usually lower than the demand and training to increase the number of able bioinformaticians is an important task for the bioinformatics community. When conducting training or hands-on tutorials, the lack of control over the analysis tools and repositories often results in undesirable situations during training, as unavailable online tools or version conflicts may delay, complicate, or even prevent the successful completion of a training event. The eBioKit is a stand-alone educational platform that hosts numerous tools and databases for bioinformatics research and allows training to take place in a controlled environment. A key advantage of the eBioKit over other existing teaching solutions is that all the required software and databases are locally installed on the system, significantly reducing the dependence on the internet. Furthermore, the architecture of the eBioKit has demonstrated itself to be an excellent balance between portability and performance, not only making the eBioKit an exceptional educational tool but also providing small research groups with a platform to incorporate bioinformatics analysis in their research. As a result, the eBioKit has formed an integral part of training and research performed by a wide variety of universities and organizations such as the Pan African Bioinformatics Network (H3ABioNet) as part of the initiative Human Heredity and Health in Africa (H3Africa), the Southern Africa Network for Biosciences (SAnBio) initiative, the Biosciences eastern and central Africa (BecA) hub, and the International Glossina Genome Initiative.

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Authorship for sale: Some journals willing to add authors to papers they didn’t write - Retraction Watch

Authorship for sale: Some journals willing to add authors to papers they didn’t write - Retraction Watch | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Got $300? Then you can be added as an author to a paper — even if you had no role in the research. That’s right — some journals are willing to add authors to papers they didn’t write, often for a fee. This realization comes from one of the many sting experiments we’ve witnessed over …
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PrePost SEO

PrePost SEO | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Free Online SEO Tools: plagiarism checker, grammar checker, image compressor, website seo checker, article rewriter, back link checker
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Re-Assembly and Analysis of an Ancient Variola Virus Genome

Re-Assembly and Analysis of an Ancient Variola Virus Genome | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
We report a major improvement to the assembly of published short read sequencing data from an ancient variola virus (VARV) genome by the removal of contig-capping sequencing tags and manual searches for gap-spanning reads. The new assembly, together with camelpox and taterapox genomes, permitted new dates to be calculated for the last common ancestor of all VARV genomes. The analysis of recently sequenced VARV-like cowpox virus genomes showed that single nucleotide polymorphisms (SNPs) and amino acid changes in the vaccinia virus (VACV)-Cop-O1L ortholog, predicted to be associated with VARV host specificity and virulence, were introduced into the lineage before the divergence of these viruses. A comparison of the ancient and modern VARV genome sequences also revealed a measurable drift towards adenine + thymine (A + T) richness.
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Reversible unfolding of infectious prion assemblies reveals the existence of an oligomeric elementary brick

Reversible unfolding of infectious prion assemblies reveals the existence of an oligomeric elementary brick | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Prions are self-propagating assemblies with all necessary and sufficient replicative information stored in the 3D structure of the misfolded form of PrP called PrPSc. Since the emergence of the prion theory in the 80s, many attempts have been done to identify prion replicative information at molecular scale. Different models have been constructed based on a broad panel of experimental observations and some of them predict the existence of periodic elements constituting prion assemblies. Here, by using partial unfolding approaches, we trapped an oligomeric conformer that we called suPrP, which could constitute the elementary brick of prion assemblies. Once isolated, this elementary brick is devoid of infectivity. However, it becomes infectious once condensated into larger assemblies. The identification of the elementary PrP building block provides a new structural basis for understanding prion replicative information storage and spreading.
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Vaccine advocacy 101

Vaccine advocacy 101 | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
I recently finished a 2-year stint as an American Society for Microbiology Distinguished Lecturer. It’s an excellent program–ASM pays all travel expenses for lecturers, who speak at ASM…
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AUSTRALIA in the grip of the worst flu outbreak ever [maybe]

AUSTRALIA in the grip of the worst flu outbreak ever [maybe] | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Photo sunshinecoastdaily.com.au AUSTRALIA is in the grip of the worst flu outbreak on record and experts are urging people to have

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HBV RNA pre-genome encodes specific motifs that mediate interactions with the viral core protein that promote nucleocapsid assembly

HBV RNA pre-genome encodes specific motifs that mediate interactions with the viral core protein that promote nucleocapsid assembly | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Formation of the hepatitis B virus nucleocapsid is an essential step in the viral lifecycle, but its assembly is not fully understood. We report the discovery of sequence-specific interactions between the viral pre-genome and the hepatitis B core protein that play roles in defining the nucleocapsid assembly pathway. Using RNA SELEX and bioinformatics, we identified multiple regions in the pre-genomic RNA with high affinity for core protein dimers. These RNAs form stem-loops with a conserved loop motif that trigger sequence-specific assembly of virus-like particles (VLPs) at much higher fidelity and yield than in the absence of RNA. The RNA oligos do not interact with preformed RNA-free VLPs, so their effects must occur during particle assembly. Asymmetric cryo-electron microscopy reconstruction of the T = 4 VLPs assembled in the presence of one of the RNAs reveals a unique internal feature connected to the main core protein shell via lobes of density. Biophysical assays suggest that this is a complex involving several RNA oligos interacting with the C-terminal arginine-rich domains of core protein. These core protein–RNA contacts may play one or more roles in regulating the organization of the pre-genome during nucleocapsid assembly, facilitating subsequent reverse transcription and acting as a nucleation complex for nucleocapsid assembly.

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