Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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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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Biological templating: Using a virus to speed up modern computers

Biological templating: Using a virus to speed up modern computers | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The traditional process of making tiny wires can reach a temperature of around 720 K, a heat that causes a binary-type material to separate. For the first time in history, the researchers showed that by using the M13 bacteriophage -- a kind of virus -- a low-temperature construction of tiny germanium-tin-oxide wires and memory can be achieved.
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Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence | Virus Evolution | Oxford Academic

Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence | Virus Evolution | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Abstract. Molecular phylogenetics is often used to estimate the time since the divergence of modern gene sequences. For highly diverged sequences, such phyloge
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A new approach to studying the flu

It has been difficult to study the exact number and location of these proteins on any individual virus, however. The go-to method in cell biology would involve attaching a fluorescent protein to the area of interest; the light makes the area easier to image and study.

But trying to attach fluorescent proteins to the molecules that make up a flu virus is like trying to get a third person on a tandem bike: There just isn't room. The fluorescent proteins are about the same size as the flu proteins; introducing such a relatively large element throws the virus out of whack.

In order to move past the labeling difficulties, Vahey adapted a method that is typically used to label a specific area on a protein called, appropriately, "site-specific labeling." Instead of using a fluorescent protein, he inserted sequences five- to 10-amino-acids-long into the proteins that make up Influenza A virus. This is the most common flu virus, and also the most dangerous to humans. After inserting these short sequences, he introduced enzymes and small amounts of fluorescent dyes. These enzymes take different dye molecules and connect them to the engineered viral proteins, giving researchers the ability to see individual proteins without disrupting how they - or the virus they make up - functions.

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PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP | Bioinformatics | Oxford Academic

PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractSummary. The Phylogenetic Analysis with Space/Time models (PHAST) package is a widely used software package for comparative genomics that has been free
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Host and viral determinants of influenza A virus species specificity

Host and viral determinants of influenza A virus species specificity | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
In this Review, we examine the host barriers that influenza A viruses of animals, especially birds, must overcome to initiate a pandemic in humans and describe how, on crossing the species barrier, the virus mutates to establish new interactions with the human host. This knowledge is used to inform risk assessments for future pandemics and to identify virus–host interactions that could be targeted by novel intervention strategies.
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Charting the diversity of Uncultured Viruses of Archaea and Bacteria

Viruses of Archaea and Bacteria are among the most abundant and diverse biological entities on Earth. Unraveling their biodiversity has been challenging due to methodological limitations. Recent advances in culture-independent techniques, such as metagenomics, shed light on viral dark matter, revealing thousands of new viral genomes at an unprecedented scale. However, these novel genomes have not been properly classified and the evolutionary associations between them were not resolved. Here, we performed phylogenomic analysis of nearly 200,000 viral genomic sequences to establish GL-UVAB: Genomic Lineages of Uncultured Viruses of Archaea and Bacteria. GL-UVAB yielded a 44-fold increase in the amount of classified genomes. The pan-genome content of the identified lineages revealed their infection strategies, potential to modulate host physiology and mechanisms to escape resistance systems. Furthermore, using GL-UVAB for annotating metagenomes from multiple ecosystems revealed elusive habitat distribution patterns of viral communities. These findings expand the understanding of the diversity, evolution and ecology of viruses of prokaryotes.
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A statistical method to identify recombination in bacterial genomes based on SNP incompatibility | BMC Bioinformatics | Full Text

A statistical method to identify recombination in bacterial genomes based on SNP incompatibility | BMC Bioinformatics | Full Text | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Phylogeny estimation for bacteria is likely to reflect their true evolutionary histories only if they are highly clonal. However, recombination events could occur during evolution for some species. The reconstruction of phylogenetic trees from an alignment without considering recombination could be misleading, since the relationships among strains in some parts of the genome might be different than in others. Using a single, global tree can create the appearance of homoplasy in recombined regions. Hence, the identification of recombination breakpoints is essential to better understand the evolutionary relationships of isolates among a bacterial population. Previously, we have developed a method (called ACR) to detect potential breakpoints in an alignment by evaluating compatibility of polymorphic sites in a sliding window. To assess the statistical significance of candidate breakpoints, we propose an extension of the algorithm (ptACR) that applies a permutation test to generate a null distribution for comparing the average local compatibility. The performance of ptACR is evaluated on both simulated and empirical datasets. ptACR is shown to have similar sensitivity (true positive rate) but a lower false positive rate and higher F1 score compared to basic ACR. When used to analyze a collection of clinical isolates of Staphylococcus aureus, ptACR finds clear evidence of recombination events in this bacterial pathogen, and is able to identify statistically significant boundaries of chromosomal regions with distinct phylogenies. ptACR is an accurate and efficient method for identifying genomic regions affected by recombination in bacterial genomes.
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What The World's First Marine Genomics Institute Aims To Do

What The World's First Marine Genomics Institute Aims To Do | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The world's first marine genomics research institute opened in Gloucester, Massachusettes.
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Ten simple rules for collaboratively writing a multi-authored paper

Ten simple rules for collaboratively writing a multi-authored paper | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
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Viruses | Free Full-Text | Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes

Viruses | Free Full-Text | Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Base-By-Base is a comprehensive tool for the creation and editing of multiple sequence alignments that is coded in Java and runs on multiple platforms. It can be used with gene and protein sequences as well as with large viral genomes, which themselves can contain gene annotations. This report describes new features added to Base-By-Base over the last 7 years. The two most significant additions are: (1) The recoding and inclusion of “consensus-degenerate hybrid oligonucleotide primers” (CODEHOP), a popular tool for the design of degenerate primers from a multiple sequence alignment of proteins; and (2) the ability to perform fuzzy searches within the columns of sequence data in multiple sequence alignments to determine the distribution of sequence variants among the sequences. The intuitive interface focuses on the presentation of results in easily understood visualizations and providing the ability to annotate the sequences in a multiple alignment with analytic and user data.
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Thanatin from the spined soldier bug is a new type of antibiotic against gram-negative bacteria

Thanatin from the spined soldier bug is a new type of antibiotic against gram-negative bacteria | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

With the increasing resistance of many Gram-negative bacteria to existing classes of antibiotics, identifying new paradigms in antimicrobial discovery is an important research priority. Of special interest are the proteins required for the biogenesis of the asymmetric Gram-negative bacterial outer membrane (OM)

 

Seven Lpt proteins (LptA to LptG) associate in most Gram-negative bacteria to form a macromolecular complex spanning the entire envelope, which transports lipopolysaccharide (LPS) molecules from their site of assembly at the inner membrane to the cell surface, powered by adenosine 5′-triphosphate hydrolysis in the cytoplasm. The periplasmic protein LptA comprises the protein bridge across the periplasm, which connects LptB2FGC at the inner membrane to LptD/E anchored in the OM.

 

Scientists now show that the naturally occurring, insect-derived antimicrobial peptide thanatin targets LptA and LptD in the network of periplasmic protein-protein interactions required to assemble the Lpt complex, leading to the inhibition of LPS transport and OM biogenesis in Escherichia coli.


Via Dr. Stefan Gruenwald
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Carlos Garcia Pando's comment, November 19, 5:31 AM
Nature comes to our rescue again, 100 years later. I hope this does not get mainstream medication until more restrictive laws and regulations for antibiotics are in place, so we do not lose this advantage in a few years
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12 Tips On How To Negotiate A Job Offer To Increase Your Starting Salary In Industry | Cheeky Scientist | Negotiation Strategies

12 Tips On How To Negotiate A Job Offer To Increase Your Starting Salary In Industry | Cheeky Scientist | Negotiation Strategies | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Whether or not you understand how negotiating works, it's being used against you. Here are 12 tips on how to negotiate a job offer for a higher salary.
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Computer logic meets cell biology: how cell science is getting an upgrade

Computer logic meets cell biology: how cell science is getting an upgrade | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
When manipulating the functions of cells, researchers need to take a multidisciplinary approach.
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Prisoners of war — host adaptation and its constraints on virus evolution | Nature Reviews Microbiology

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Sequencing in the time of Ebola

Sequencing in the time of Ebola | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
These studies collectively highlight the impact that real-time sequencing of the viral genome as part of a concerted outbreak response can have on public health, and call for genomic surveillance toolkits that can be deployed rapidly in low-resource settings, which are at higher risk of epidemic diseases. The fast-moving field of NGS technologies and accompanying bioinformatics is quickly responding to this need with new systems more adept to field work, with less dependence on infrastructure, such as electricity and internet connection.
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iHam & pyHam: visualizing and processing hierarchical orthologous groups | Bioinformatics | Oxford Academic

iHam & pyHam: visualizing and processing hierarchical orthologous groups | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractSummary. The evolutionary history of gene families can be complex due to duplications and losses. This complexity is compounded by the large number of
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– How to Read a Scientific Paper

– How to Read a Scientific Paper | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
  It’s one of the first, and likely most intimidating, assignments for a fledgling science reporter. “Here,” your editor says. “Write up this paper that’s coming out in Science this week.” And…
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Bio-Linux: A stable, portable scientific research Linux distribution

Bio-Linux: A stable, portable scientific research Linux distribution | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Linux distro's integrated software approach offers powerful bioinformatic data analysis with a familiar look and feel.
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Choice of assembly software has a critical impact on virome characterisation

Choice of assembly software has a critical impact on virome characterisation
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Scientists discover a new route to antibiotics using gene editing

Scientists discover a new route to antibiotics using gene editing | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Scientists have discovered a new chemical process – also known as a biosynthetic pathway – in bacteria which could lead to a new generation of antibiotics being produced and manufactured.

Researchers at The University of Manchester’s School of Chemistry say their new pathway includes an enzyme, called a carboxylase, which adds CO2 to
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10 Sites for Checking Plagiarism via @ dkapuler

10 Sites for Checking Plagiarism via @ dkapuler | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
"Plagiarism  is the "wrongful appropriation" and "stealing and publication" of another  author 's "language, thoughts, ideas, o

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Anti-vaccination stronghold in N.C. hit with state’s worst chickenpox outbreak in 2 decades - The

Anti-vaccination stronghold in N.C. hit with state’s worst chickenpox outbreak in 2 decades - The | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
As of Friday, there were 36 cases of chickenpox at the Asheville Waldorf School, which serves children from nursery school to sixth grade in Asheville, N.C.
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Ten simple rules for delivering live distance training in bioinformatics across the globe using webinars

Ten simple rules for delivering live distance training in bioinformatics across the globe using webinars | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
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A systems biology approach to unravelling the complexities of immune system development and function

A systems biology approach to unravelling the complexities of immune system development and function | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
05 December 2018 12:00 p.m. ET Register now! Speakers Petter Brodin, M.D., Ph.D. Karolinska Institute  Stockholm, Sweden Yueh-hsiu Chien, Ph.D. Stanford University  Stanford, CA Moderated by Sean Sanders, Ph.D. Science/AAAS Washington, DC Sponsored by Olink Proteomics Immune systems are found in most living organisms. They reflect the common challenges of existing in a potentially hostile external environment, and often exhibit a complex, ever-changing interplay between specialized cell types, potent effector molecules, and exogenously acquired molecules and organisms. In our own immune systems, changes in the delicate homeostatic balance can lead to major problems, such as allergic responses or autoimmune diseases. Understanding how our immune system functions is difficult because of the plethora of different cell types and biomolecules involved, and because of its extremely dynamic nature. It is in constant coevolution with pathogens and must respond rapidly and specifically in each individual to a vast array of potential threats. Two major limitations of human immune system studies are their reliance on relatively few targeted assays and their potentially limited diversity within the samples examined. Studies that can provide genuine answers for immunological questions may require a systems biology approach that examines large numbers of different cell types and their interplay with real-time effector biomolecules, preferably using diverse sample cohorts. This webinar will focus on two such breakthrough studies (published in the journals Cell and Nature, respectively), which employ a broad, systems biology approach to better understand early postnatal immune system development, and the immunological control of latent infections. During the webinar, the speakers will: Describe how combining approaches such as mass cytometry, protein biomarker discovery, and transcriptomics provides valuable insights into complex immunological systems Reveal how the immune system develops in newborn children, and the external factors that influence this process Offer new insights into the complex pathophysiology of latent infections with Mycobacterium tuberculosis, using a multi-omic, multicohort approach Answer your questions during the live broadcast! This webinar will last for approximately 60 minutes. Speaker bios Petter Brodin, M.D., Ph.D. Karolinska Institute  Stockholm, Sweden Dr. Brodin is a pediatrician at the Karolinska University Hospital and an associate professor of immunology at the Karolinska Institute, both located in Stockholm, Sweden. He is also director of the National Mass Cytometry Facility at Sweden’s Science for Life Laboratory. He performed postdoctoral training with Mark Davis at the Stanford University School of Medicine (2012–2013) and developed an interest in the use of systems-level analyses as a means to advance human immunology. The Brodin lab now investigates human immune system variation, the factors that underlie this variation, and particularly how the external environment shapes our immune system in early life. The lab is also developing methods for systems-level profiling of immune function in various patient groups in order to improve clinical decision-making and outcomes. Yueh-hsiu Chien, Ph.D. Stanford University  Stanford, CA Dr. Chien is a professor in the Department of Microbiology and Immunology and in the immunology program at Stanford University. The question of how gamma-delta (γδ) T cells contribute to host immune defense has been the focus of her research group since soon after these cells were discovered. They have made several landmark discoveries, including isolating the T-cell receptor δ gene and showing that γδ T cells and αβ T cells are distinct in their antigen recognition and activation requirements, and also in their antigen-specific repertoire and effector-function development. These aspects allow γδ T cells to occupy unique temporal and functional niches to initiate and regulate the inflammatory response. More recently, Chien’s group also started to analyze the human immune system using systems biology approaches, such as exploring the effects of tuberculosis on the immune system. Dr. Chien holds a B.S. in chemistry from National Taiwan University and a Ph.D. in chemistry from the University of Illinois at Urbana-Champaign. She did her postdoctoral training at the California Institute of Technology.   Sean Sanders, Ph.D. Science/AAAS Washington, DC Dr. Sanders did his undergraduate training at the University of Cape Town, South Africa, and his Ph.D. at the University of Cambridge, UK, supported by the Wellcome Trust. Following postdoctoral training at the National Institutes of Health and Georgetown University, Dr. Sanders joined TranXenoGen, a startup biotechnology company in Massachusetts working on avian transgenics. Pursuing his parallel passion for writing and editing, Dr. Sanders joined BioTechniques as an editor, before joining Science/AAAS in 2006. Currently Dr. Sanders is the Senior Editor for Custom Publishing for the journal Science and Program Director for Outreach. Sponsored by

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