Viruses, Immunology & 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, Immunology & 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, Immunology & 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, 2017 12:46 PM
Thank You.
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Teaching Bioinformatics

Teaching Bioinformatics | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
We teach a lot of bioinformatics. Here are some public resources we rely on. These are pulled from twitter, the web, and all over the place, and the text ended up being used elsewhere. Please feel …
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Ectromelia Virus Affects Mitochondrial Network Morphology, Distribution, and Physiology in Murine Fibroblasts and Macrophage Cell Line

Ectromelia Virus Affects Mitochondrial Network Morphology, Distribution, and Physiology in Murine Fibroblasts and Macrophage Cell Line | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Mitochondria are multifunctional organelles that participate in numerous processes in response to viral infection, but they are also a target for viruses. The aim of this study was to define subcellular events leading to alterations in mitochondrial morphology and function during infection with ectromelia virus (ECTV). Early in infection of L929 fibroblasts and RAW 264.7 macrophages, mitochondria gathered around viral factories. Later, the mitochondrial network became fragmented, forming punctate mitochondria that co-localized with the progeny virions. ECTV-co-localized mitochondria associated with the cytoskeleton components. Mitochondrial membrane potential, mitochondrial fission–fusion, mitochondrial mass, and generation of reactive oxygen species (ROS) were severely altered later in ECTV infection leading to damage of mitochondria. These results suggest an important role of mitochondria in supplying energy for virus replication and morphogenesis. Presumably, mitochondria participate in transport of viral particles inside and outside of the cell and/or they are a source of membranes for viral envelope formation. We speculate that the observed changes in the mitochondrial network organization and physiology in ECTV-infected cells provide suitable conditions for viral replication and morphogenesis.

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Bioinformatics Meets Virology: The European Virus Bioinformatics Center’s Second Annual Meeting

Bioinformatics Meets Virology: The European Virus Bioinformatics Center’s Second Annual Meeting | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The Second Annual Meeting of the European Virus Bioinformatics Center (EVBC), held in Utrecht, Netherlands, focused on computational approaches in virology, with topics including (but not limited to) virus discovery, diagnostics, (meta-)genomics, modeling, epidemiology, molecular structure, evolution, and viral ecology. The goals of the Second Annual Meeting were threefold: (i) to bring together virologists and bioinformaticians from across the academic, industrial, professional, and training sectors to share best practice; (ii) to provide a meaningful and interactive scientific environment to promote discussion and collaboration between students, postdoctoral fellows, and both new and established investigators; (iii) to inspire and suggest new research directions and questions. Approximately 120 researchers from around the world attended the Second Annual Meeting of the EVBC this year, including 15 renowned international speakers. This report presents an overview of new developments and novel research findings that emerged during the meeting.
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Early Antiretroviral Therapy Preserves Functional Follicular Helper T and HIV-Specific B Cells in the Gut Mucosa of HIV-1–Infected Individuals

Early Antiretroviral Therapy Preserves Functional Follicular Helper T and HIV-Specific B Cells in the Gut Mucosa of HIV-1–Infected Individuals | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
HIV-1 infection is associated with B cell dysregulation and dysfunction. In HIV-1–infected patients, we previously reported preservation of intestinal lymphoid structures and dendritic cell maturation pathways after early combination antiretroviral therapy (e-ART), started during the acute phase...

Via Krishan Maggon
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Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny | Bioinformatics | Oxford Academic

Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractSummary. The Genome Context Viewer is a visual data-mining tool that allows users to search across multiple providers of genome data for regions with s
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RNA-seq alignment – where methodological progress can still occur

RNA-seq alignment – where methodological progress can still occur | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Many tools are available for RNA-seq alignment and expression quantification, with comparative value being hard to establish. Benchmarking assessments often highlight methods’ good performance, but are focused on either model data or fail to explain variation in performance. This leaves us to ask, what is the most meaningful way to assess different alignment choices? And importantly, where is there room for progress? Researchers from the Cold Spring Harbor Laboratory explore the answers to these two questions by performing an exhaustive assessment of the STAR aligner. They assess STAR’s performance across a range of alignment parameters using common metrics, and then on biologically focused tasks. They find technical metrics such as fraction mapping or expression profile correlation to be uninformative, capturing properties unlikely to have any role in biological discovery. Surprisingly, the researchers find that changes in alignment parameters within a wide range have little impact on both technical and biological performance. Yet, when performance finally does break, it happens in difficult regions, such as X-Y paralogs and MHC genes. They believe improved reporting by developers will help establish where results are likely to be robust or fragile, providing a better baseline to establish where methodological progress can still occur.
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The complexities of viral mutation rates

Many viruses evolve rapidly. This is due, in part, to their high mutation rates. Mutation rate estimates for over 25 viruses are currently available. Here, we review the population genetics of virus mutation rates. We specifically cover the topics of mutation rate estimation, the forces that drive the evolution of mutation rates, and how the optimal mutation rate can be context-dependent.
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Universal evolutionary selection for high dimensional silent patterns of information hidden in the redundancy of viral genetic code

Our model suggests that long substrings of nucleotides in the coding regions of viruses from all classes, often also repeat in the corresponding viral hosts from all domains of life. Selection for these substrings cannot be explained only by such phenomena as codon usage bias, horizontal gene transfer, and the encoded proteins. Genes encoding structural proteins responsible for building the core of the viral particles were found to include more host-repeating substrings, and these substrings tend to appear in the middle parts of the viral coding regions. In addition, in human viruses these substrings tend to be enriched with motives related to transcription factors and RNA binding proteins. The host-repeating substrings are possibly related to the evolutionary pressure on the viruses to effectively interact with host's intracellular factors and to efficiently escape from the host's immune system.
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Virulent Poxviruses Inhibit DNA Sensing by Preventing STING Activation

Poxviruses are double-stranded DNA viruses replicating in the cytosol and hence likely to trigger cytosolic DNA sensing. Here, we investigated the activation of innate immune signaling by 4 different strains of the prototypic poxvirus vaccinia virus (VACV) in a cell line proficient in DNA sensing. Infection with the attenuated VACV strain MVA activated IRF-3 via cGAS and STING, and accordingly STING dimerized and was phosphorylated during MVA infection. Conversely, VACV strains Copenhagen and Western Reserve inhibited STING dimerization and phosphorylation during infection and in response to transfected DNA and cyclic GMP-AMP, thus efficiently suppressing DNA sensing and IRF-3 activation.

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515 Free Online Programming & Computer Science Courses You Can Start in April

"Five years ago, universities like MIT and Stanford first opened up free online courses to the public. Today, more than 700 schools around the world have created thousands of free online courses."

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Expanding the toolbox for 3D genomics

The ability to visualize and study the 3D folding of chromosomes in cells has been propelled forward by several major technological advances in the past two decades. Two new studies now further expand the scientific toolbox for studying chromosome conformation by providing novel methodologies for accurate mapping of genome topology and predicting the topological effects of genomic structural variation.
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Antiviral T-Cells for Adenovirus in the Pre-Transplant Period: a Bridge Therapy for Severe Combined Immunodeficiency

Antiviral T-Cells for Adenovirus in the Pre-Transplant Period: a Bridge Therapy for Severe Combined Immunodeficiency | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
• Virus specific T-cell therapy was safely utilized in a patient with severe combined immunodeficiency in the pre-transplant period without graft versus host disease.• VST infusion followed by transplant was associated with clearance of disseminated adenovirus.• VST infusion may be an effective...

Via Krishan Maggon
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Gifford Lab (CVR) - GLUE: a flexible software system for virus sequence analysis

Gifford Lab (CVR) - GLUE: a flexible software system for virus sequence analysis | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Rob Gifford's insight:
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CSBB – Computational Suite for Bioinformaticians and Biologists

*RNA-Seq processing for human, mouse, frog and zebrafish

*ChIP-Seq processing for human, mouse and frog

*ATAC-Seq processing for human, mouse and frog
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UA Biologists Find Answer to 100-Year-Old Question

UA Biologists Find Answer to 100-Year-Old Question | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
University of Arizona biology researchers have made a discovery that helps resolve a conundrum that has puzzled scientists for more than a century. The UA team, headed by Michael S. Barker, assistant professor and director of bioinformatics in the UA Department of Ecology and Evolutionary Biology, has found that polyploidy, the duplication of whole genomes, has occurred many times during the evolution of insects, the most diverse group of animals. 
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Virus Variation Resource – improved response to emergent viral outbreaks | Nucleic Acids Research | Oxford Academic

Virus Variation Resource – improved response to emergent viral outbreaks | Nucleic Acids Research | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Abstract. The Virus Variation Resource is a value-added viral sequence data resource hosted by the National Center for Biotechnology Information. The resource
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CRISPR genetic screens to discover host–virus interactions

CRISPR genetic screens to discover host–virus interactions | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Viruses impose an immense burden on human health. With the goal of treating and preventing viral infections, researchers have carried out genetic screens to improve our understanding of viral dependencies and identify potential anti-viral strategies. The emergence of CRISPR genetic screening tools has facilitated this effort by enabling host–virus screens to be undertaken in a more versatile and fidelitous manner than previously possible. Here we review the growing number of CRISPR screens which continue to increase our understanding of host–virus interactions.
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Mustguseal: a server for multiple structure-guided sequence alignment of protein families | Bioinformatics | Oxford Academic

Mustguseal: a server for multiple structure-guided sequence alignment of protein families | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractMotivation. Comparative analysis of homologous proteins in a functionally diverse superfamily is a valuable tool at studying structure-function relatio
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How to create your own auto direct message Twitter bot for free 

Creating a welcome message for your new followers in Twitter is the first step to getting more people to engage with your tweets and links. As you might know, there are many online services that help you send auto direct messages (DMs) to your new followers. But I think it’s crazy how online services charge between $5 to $15 for a simple tool that creates bots, when you can build your own for free.
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If you use twitter for science communication, this might be helpful to you!
 
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Basic data analysis on Twitter with Python

a simple data analysis program that takes a given number of tweets, analyzes them, and displays the data in a scatter plot
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Hepatitis A vaccine immune response 22 years after vaccination

In the United States, the incidence of hepatitis A virus (HAV) infection has been reduced through universal childhood vaccination. However, the duration of immunogenicity for the hepatitis A vaccine is not known. We report on the 22 year follow‐up time point of a cohort of Alaska children who were randomized to three different vaccine schedules: A) 0, 1, and 2 months; B) 0, 1, and 6 months; and C) 0, 1, and 12 months. Among 46 participant available for follow‐up, 40 (87%) maintained protective levels of anti‐hepatitis A antibody. These results indicate that a supplemental booster dose is not yet necessary at or before the 22‐year time point.
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If you want to learn Data Science, start with one of these programming classes

A year ago, I was a numbers geek with no coding background. After trying an online programming course, I was so inspired that I enrolled in one of the best computer science programs in Canada.

Two weeks later, I realized that I could learn everything I needed through edX, Coursera, and Udacity instead. So I dropped out.
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Virulent Poxviruses Inhibit DNA Sensing by Preventing STING Activation

Poxviruses are double-stranded DNA viruses replicating in the cytosol and hence likely to trigger cytosolic DNA sensing. Here, we investigated the activation of innate immune signaling by 4 different strains of the prototypic poxvirus vaccinia virus (VACV) in a cell line proficient in DNA sensing. Infection with the attenuated VACV strain MVA activated IRF-3 via cGAS and STING, and accordingly STING dimerized and was phosphorylated during MVA infection. Conversely, VACV strains Copenhagen and Western Reserve inhibited STING dimerization and phosphorylation during infection and in response to transfected DNA and cyclic GMP-AMP, thus efficiently suppressing DNA sensing and IRF-3 activation.
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Mitochondria’s Bacterial Origins Upended | The Scientist Magazine®

Contrary to some hypotheses, the organelle did not descend from any known lineage of Alphaproteobacteria, researchers find.
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