Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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PLOS Computational Biology: The Roots of Bioinformatics in ISMB

PLOS Computational Biology: The Roots of Bioinformatics in ISMB | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
PLOS Computational Biology is an open-access
Nicolas Palopoli's insight:

Besides the interesting recall of the Intelligent Systems for Molecular Biology (ISMB) annual conferences on computational biology, it offers a nice insight into current state-of-the-art methodologies and upcoming trends in the discipline.

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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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Clustergrammer Web App — Clustergrammer 1.1.0 documentation

Clustergrammer Web App — Clustergrammer 1.1.0 documentation | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
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Discovery explains how the chickenpox and shingles virus remains dormant

Discovery explains how the chickenpox and shingles virus remains dormant | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
A research team led by UCL and Erasmus University has found a missing piece to the puzzle of why the virus that causes chickenpox and shingles can remain dormant for decades in human cells. Described in a recent paper in Nature Communications, researchers discovered there is an RNA transcript in the varicella zoster virus (VZV), that continues to remain active after a person has recovered from chickenpox. Most adults worldwide are infected with VZV, which stays dormant after chickenpox has cleared, but can reactivate later in life – in about 30% of people – as shingles, which causes both a painful rash and the potential for more serious complications including debilitating pain, blindness or a stroke. “It’s been more than 30 years since VZV latency in human nerve cells was first described, and ever since then, researchers have been trying to identify the factor that causes the virus to remain latent. Our discovery provides an important step forward towards control of this virus,” said the study’s lead author, Professor Judith Breuer (UCL Infection & Immunity). Previous studies were unable to identify how VZV latency works, partly because, unlike the herpes simplex viruses, which are also alphaherpesviruses that remains dormant after initial infection, there are no animal models of VZV latency. To overcome this challenge, the researchers developed a new technique using human neurons that were obtained very quickly after the patients had died (6 hours on average), when previous studies had shown that fewer post mortem changes had occurred in the tissues. Of the 18 donors, the neurons of 13 of them were infected with both herpes simplex and VZV, enabling the researchers to compare their findings against the better-understood model of herpes simplex. The researchers extracted nucleic acid from the neurons and sequenced the RNA, comparing it with models of the VZV genome. They found that only one VZV RNA transcript was detectable in all the neurons, which they called the latency-associated transcript. The researchers also confirmed that only one herpes simplex transcript is detectable when dormant, something that has been queried in the past. They supported their findings by infecting cells in the lab with VZV and found that the latency-associated transcript inhibits the expression of a gene that is critical to viral replication, suggesting that the transcript may play a key role in determining whether the virus is actively replicating or remaining dormant. “Our findings are now helping us understand how VZV can remain dormant for so long. Further research will tell us more about how exactly this RNA transcript works, and what happens differently when VZV reactivates later in life to cause shingles.  “We hope our discovery can help the eventual development of a new, improved vaccine that instead of causing dormancy, entirely prevents VZV infection,” said the study’s first author, Dr Daniel Depledge, who conducted the research at UCL before moving to New York University. The researchers say their discovery was made possible by a combination of high quality human clinical specimens from the Netherlands Brain Bank and specialised highly sensitive molecular detection technologies developed at UCL. The study was conducted by researchers at UCL, Erasmus University, Kobe University, the University of Colorado and the University of Veterinary Medicine Hanover. The research was supported by the Medical Research Foundation, the Medical Research Council, the Ministry of Education, Culture, Science, Sports and Technology of Japan, the National Institute for Health Research University College London Hospitals Biomedical Research Centre, and the National Institutes of Health. Links Image Electron micrograph of a varicella zoster virus (Credit: Centre for Disease Control/Dr. Erskine Palmer/B.G. Partin, Source: Public Health Image Library) Media contact Chris Lane Tel: +44 (0)20 7679 9222 Email: chris.lane [at] ucl.ac.uk
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Molecular Epidemiology and the Transformation of HIV Prevention | HIV | JAMA | JAMA Network

Molecular Epidemiology and the Transformation of HIV Prevention | HIV | JAMA | JAMA Network | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
This Viewpoint describes the addition of HIV nucleotide sequence data collected through molecular surveillance to traditional epidemiologic investigation as an...
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Flu virus finally sequenced in its native form

Flu virus finally sequenced in its native form | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Direct sequencing of RNA molecules such as virus genomes should help to unpick role of mysterious chemical modifications.

Via Ed Rybicki
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FPA - Two Confirmed Cases of Monkey Pox in Liberia since 1970 (Not Four As Reported)

FPA - Two Confirmed Cases of Monkey Pox in Liberia since 1970 (Not Four As Reported) | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Monkey pox infections in Liberia


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Critics see only risks, no benefits in horsepox paper

Critics see only risks, no benefits in horsepox paper | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
A highly controversial study in which researchers synthesized the horsepox virus from scratch was finally published in PLOS ONE on 19 January. The study stirred alarm when Science first reported about it in July 2017 because it might give would-be terrorists a recipe to construct smallpox virus, a major human scourge vanquished in 1980. And now that the paper is out, many scientists say it doesn't answer the most pressing question: Why did they do it? The team claims its work, funded by Tonix, a pharmaceutical company headquartered in New York City, could lead to a safer, more effective vaccine against smallpox. But safe smallpox vaccines already exist, and critics say there is no market for a horsepox-based replacement.
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What is hepatitis A and how can you get it from eating frozen fruit?

What is hepatitis A and how can you get it from eating frozen fruit? | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Hepatitis A is a virus that infects the liver. Symptoms usually take 15-50 days to develop after initial infection and typically last for several weeks or sometimes longer.
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Potential use of rapamycin in HIV infection

Potential use of rapamycin in HIV infection | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The strong need for the development of alternative anti-HIV agents is primarily due to the emergence of strain-resistant viruses, the need for sustained adherence to complex treatment regimens and the toxicity of currently used antiviral drugs.

Via Krishan Maggon
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Discovery of novel bat coronaviruses in south China that use the same receptor as MERS coronavirus

Previous studies suggested that the Middle East respiratory syndrome coronavirus (MERS-CoV) may have originated in bats. However, its evolutionary path from bats to humans remains unclear. In this study, we discovered 89 novel lineage C betacoronaviruses (BetaCoVs) in eight bat species. We provide the evidence of a MERS-related CoV derived from the great evening bat that uses the same host receptor as human MERS-CoV. This virus also provides evidence for a natural recombination event between the bat MERS-related CoV and another bat coronavirus HKU4. Our study expands the host ranges of MERS-related CoV and represents an important step toward establishing bats as the natural reservoir of MERS-CoV. These findings may lead to improved epidemiological surveillance of MERS-CoV and the prevention and control of the spread of MERS-CoV to humans.

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The STING behind dengue virus infection

Stabell et al. have revealed why human dengue viruses do not replicate to high titres in primate models. They found that the stimulator of interferon genes (STING) protein, which induces the production of type I interferon in infected cells to reduce viral titres, is cleaved by the dengue virus protease NS2B3 in humans but not in key primate models. STING cleavage occurred at an RG motif at amino acids 78 and 79, decreasing markers of an innate immune response and increasing viral replication in human cells. The analyses of STING sequences from all placental animals in Genbank, as well as from 16 non-human primate cell lines, revealed that only STING from three small apes and three small rodents encodes this RG motif. As introducing this RG motif into STING from rhesus macaque, marmoset and mouse rendered it susceptible to cleavage by dengue virus NS2B3, engineering model organisms so that their STING contains this motif could enhance the study of dengue viruses in animals.
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VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis | BMC Bioinformatics | Full Text

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis | BMC Bioinformatics | Full Text | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
RNA sequencing has become a ubiquitous technology used throughout life sciences as an effective method of measuring RNA abundance quantitatively in tissues and cells. The increase in use of RNA-seq technology has led to the continuous development of new tools for every step of analysis from alignment to downstream pathway analysis. However, effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts. Using the workflow management system Snakemake we have developed a user friendly, fast, efficient, and comprehensive pipeline for RNA-seq analysis. VIPER (Visualization Pipeline for RNA-seq analysis) is an analysis workflow that combines some of the most popular tools to take RNA-seq analysis from raw sequencing data, through alignment and quality control, into downstream differential expression and pathway analysis. VIPER has been created in a modular fashion to allow for the rapid incorporation of new tools to expand the capabilities. This capacity has already been exploited to include very recently developed tools that explore immune infiltrate and T-cell CDR (Complementarity-Determining Regions) reconstruction abilities. The pipeline has been conveniently packaged such that minimal computational skills are required to download and install the dozens of software packages that VIPER uses. VIPER is a comprehensive solution that performs most standard RNA-seq analyses quickly and effectively with a built-in capacity for customization and expansion.
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Ten simple rules for responsible referencing

Ten simple rules for responsible referencing | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
We researchers aim to read and write publications containing high-quality prose, exceptional data, arguments, and conclusions, embedded firmly in existing literature while making abundantly clear what we are adding to it. Through the inclusion of references, we demonstrate the foundation upon which our studies rest as well as how they are different from previous work. That difference can include literature we dispute or disprove, arguments or claims we expand, and new ideas, suggestions, and hypotheses we base upon published work. This leads to the question of how to decide which study or author to cite, and in what way.
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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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Viruses can evolve in parallel in related species

Viruses can evolve in parallel in related species | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Viruses are more likely to evolve in similar ways in related species—raising the risk that they will "jump" from one species to another, new research shows. Scientists from the universities of Exeter and Cambridge compared viruses that evolved in different species and found "parallel genetic changes" were more likely if two host species were closely related. The findings suggest that when a new virus appears in a species such as chimpanzees, closely related species like humans may become vulnerable too. Such jumps, also known as host shifts, are a major source of infectious disease, with viruses such as HIV, Ebola and SARS coronavirus all thought to have jumped into humans from other species. The researchers used deep sequencing of genomes to track the evolution of viruses in 19 species of flies. "Our findings show that when a virus adapts to one host, it might also become better adapted to closely related host species," said Dr Ben Longdon, of the University of Exeter. "This may explain in part why host shifts tend to occur between related species. However, we sometimes see the same mutations occurring in distantly related host species, and this may help explain why viruses may sometimes jump between distantly related host species. "At present we know very little about how viruses shift from one host species to another, so research like this is important if we want to understand and ultimately predict emerging viral diseases." The fruit flies used in the study were 19 species from the Drosophilidae family, which shared a common ancestor 40 million years ago. The paper, published in the journal PLOS Pathogens, is entitled: "Host shifts result in parallel genetic changes when viruses evolve in closely related species." Explore further: Cross-species jumps may play unexpectedly big role in virus evolution More information: Ben Longdon et al, Host shifts result in parallel genetic changes when viruses evolve in closely related species, PLOS Pathogens (2017). DOI: 10.1101/226175
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Study produces clearest images to date of HSV-1, the virus that causes cold sores

Study produces clearest images to date of HSV-1, the virus that causes cold sores | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
UCLA researchers have produced the clearest 3-D images to date of the virus that causes cold sores, herpes simplex virus type 1, or HSV-1. The images enabled them to map the virus' structure and offered new insights into ...
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Found: A new form of DNA in our cells: Scientists have tracked down an elusive 'tangled knot' of DNA

Found: A new form of DNA in our cells: Scientists have tracked down an elusive 'tangled knot' of DNA | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
In a world first, researchers have identified a new DNA structure -- called the i-motif -- inside cells. A twisted 'knot' of DNA, the i-motif has never before been directly seen inside living cells.
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Effects of pre-existing orthopoxvirus-specific immunity on the performance of Modified Vaccinia virus Ankara-based influenza vaccines

Effects of pre-existing orthopoxvirus-specific immunity on the performance of Modified Vaccinia virus Ankara-based influenza vaccines | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The replication-deficient orthopoxvirus modified vaccinia virus Ankara (MVA) is a promising vaccine vector against various pathogens and has an excellent safety record. However, pre-existing vector-specific immunity is frequently suggested to be a drawback of MVA-based vaccines. To address this issue, mice were vaccinated with MVA-based influenza vaccines in the presence or absence of orthopoxvirus-specific immunity. Importantly, protective efficacy of an MVA-based influenza vaccine against a homologous challenge was not impaired in the presence of orthopoxvirus-specific pre-existing immunity. Nonetheless, orthopoxvirus-specific pre-existing immunity reduced the induction of antigen-specific antibodies under specific conditions and completely prevented induction of antigen-specific T cell responses by rMVA-based vaccination. Notably, antibodies induced by vaccinia virus vaccination, both in mice and humans, were not capable of neutralizing MVA. Thus, when using rMVA-based vaccines it is important to consider the main correlate of protection induced by the vaccine, the vaccine dose and the orthopoxvirus immune status of vaccine recipients.
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Extensive conservation of prokaryotic ribosomal binding sites in known and novel picobirnaviruses - ScienceDirect

Extensive conservation of prokaryotic ribosomal binding sites in known and novel picobirnaviruses - ScienceDirect | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Currently, the Leviviridae and Cystoviridae are the only two recognized families of prokaryotic RNA viruses. Picobirnaviruses, which are bisegmented d…
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Homemade microscope reveals how a cancer-causing virus clings to our DNA

Homemade microscope reveals how a cancer-causing virus clings to our DNA | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Using a homemade, high-tech microscope, scientists at the University of Virginia School of Medicine have revealed how a cancer-causing virus anchors itself to our DNA. That discovery could pave the way for doctors to cure ...
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Viruses are falling from the skies

Viruses are falling from the skies | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

To determine how many viruses fall from the troposphere each day, automatic collectors were placed at two different locations in the Sierra Nevada Mountains of Spain at 1.75 km above sea level. Placing the collectors at this height allows sampling of air above the atmospheric boundary layer (pictured – image credit). Samples were retreived every 1-2 weeks over the course of two years and analyzed for the presence of viruses by flow cytometry after purification by centrifugation.

The results show that billions of viruses fall from the atmosphere each day: from 0.3 to 3.8 x 109 per square meter. Most (69%) of the viruses that descend from the atmosphere are attached to dust or organic aggregates. The rate of falling viruses was not substantially different over the course of the study nor between the two different sites.
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Concepts in Light Microscopy of Viruses

Concepts in Light Microscopy of Viruses | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Here, we provide an overview of recent technology for imaging cells and viruses by light microscopy, in particular fluorescence microscopy in static and live-cell modes. The review lays out guidelines for how novel fluorescent chemical probes and proteins can be used in light microscopy to illuminate cells, and how they can be used to study virus infections. We discuss advantages and opportunities of confocal and multi-photon microscopy, selective plane illumination microscopy, and super-resolution microscopy. We emphasize the prevalent concepts in image processing and data analyses, and provide an outlook into label-free digital holographic microscopy for virus research.
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PhyloProfile: Dynamic visualization and exploration of multi-layered phylogenetic profiles | Bioinformatics | Oxford Academic

PhyloProfile: Dynamic visualization and exploration of multi-layered phylogenetic profiles | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractSummary. Phylogenetic profiles form the basis for tracing proteins and their functions across species and through time. Novel genome sequences nowadays
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Entirely plasmid-based reverse genetics system for rotaviruses. - PubMed - NCBI

Rotaviruses (RVs) are highly important pathogens that cause severe diarrhea among infants and young children worldwide. The understanding of the molecular mechanisms underlying RV replication and pathogenesis has been hampered by the lack of an entirely plasmid-based reverse genetics system. In this study, we describe the recovery of recombinant RVs entirely from cloned cDNAs.

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A novel model for Crimean-Congo hemorrhagic fever virus

A novel model for Crimean-Congo hemorrhagic fever virus | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The article "A cynomolgus macaque model for Crimean–Congo haemorrhagic fever" in Nature Microbiology can be found here: https://rdcu.be/K2BD Crimean-Congo hemorrhagic fever virus: a serious, oftentimes deadly pathogen.

Via Ed Rybicki
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