Viruses and Bioinformatics from Virology.uvic.ca
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New technology shows promise in taking the guesswork out of vaccine development

New technology shows promise in taking the guesswork out of vaccine development | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Scientists from the Center for Innovations in Medicine in the Biodesign Institute at Arizona State University have developed a comprehensive, microchip-based technology, called immunosignature diagnosis, which can rapidly and comprehensively...
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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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Virus purification by CsCl density gradient using non-ultracentrifugation

Virus purification by cesium chloride (CsCl) density gradient, which generally requires an expensive ultracentrifuge, is an essential technique in virology. Here, we optimized virus purification by CsCl density gradient using general centrifugation (40,000 × g, 2 h, 4 °C), which showed almost the same purification ability as conventional CsCl density gradient ultracentrifugation (100,000 × g, 1 h, 4 °C) using phages S13′ and φEF24C. Moreover, adenovirus strain JM1/1 was also successfully purified by this method. We suggest that general centrifugation can become a less costly alternative to ultracentrifugation for virus purification by CsCl densiy gradient and will thus encourage research in virology.

Ed Rybicki's insight:
This is actually quite a big deal - and strange that it should have taken so long for someone to figure out, when density gradient centrifugation in CsCl has been known for 60-odd years, that one can do it in a high-speed as opposed to an ultracentrifuge! I'll bet you the same thing will work with Optiprep/iodixanol, too.
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PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies | Bioinformatics | Oxford Academic

PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies | Bioinformatics | Oxford Academic | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractMotivation. Genome sequencing projects sometimes uncover more organisms than expected, especially for complex and/or non-model organisms. It is therefo
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Zika DNA Vaccine Proven Safe 

Zika DNA Vaccine Proven Safe  | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Results are in from the first phase 1 clinical trial for a Zika vaccine, and they are very promising. A new generation DNA-based Zika vaccine, developed by Wistar scientists in collaboration with Inovio Pharmaceuticals and GeneOne Life Science, was found to be safe and well tolerated by all study participants and was able to elicit an immune response against Zika, opening the door to further and larger trials to move this vaccine forward.

 

“The Wistar Institute has been a leading developer of vaccines for the protection of children and families for decades,” said David B. Weiner, Ph.D., executive vice president of The Wistar Institute and director of Wistar’s Vaccine & Immunotherapy Center, who spearheaded the research team that developed the vaccine. “In light of Wistar’s history of vaccine creation and the work taking place in my lab and with collaborators, we hope to create a vaccine that will benefit humankind.”

 

Zika virus is a mosquito-borne infection associated with birth defects and neurological complications in adults, for which no approved vaccine or treatment is currently available. In the fall of 2015, after news of global Zika outbreaks was reported in Africa, Southeast Asia, the Pacific Islands, and many South American countries, Dr. Weiner and his collaborators got to work and put in place a plan to develop reagents, animal models, assays and potential vaccine candidates for initial testing.

 

The team had developed a new synthetic DNA-based vaccine technology that can be applied to a variety of infectious diseases and they set to implement this resource for the development of a Zika vaccine. The results of their combined efforts was GLS-5700, a DNA vaccine that contains the DNA instructions for the host to learn how to mount an immune response against a specific Zika virus antigen.

 

DNA-based vaccines brought about a revolution in vaccine research because they are much faster to develop and implement than traditional vaccines, which take several years from the start to the first tests. Weiner and his team were able create the Zika vaccine candidate in just about six months.

 

After it proved safe and effective in pre-clinical trials, the vaccine received FDA approval for clinical testing in June 2016, and participants were enrolled in the phase 1 trial between August and September.


Via Integrated DNA Technologies, Dr. Stefan Gruenwald
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ComplexInsight's curator insight, October 12, 3:01 AM
Very welcome news regarding initial ZIka virus trials.
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The world is running out of antibiotics

The world is running out of antibiotics | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Bacteria resistant to antibiotic treatments and increased costs are causing depleting effective remedies to cure certain illnesses.
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This 'breakthrough' protein glue could save lives in emergencies

This 'breakthrough' protein glue could save lives in emergencies | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Australian and American biomedical engineers have developed a stretchy surgical glue that rapidly heals wounds, a "breakthrough" that has the potential to save lives in emergencies, its designers say.

 

The injectable glue, MeTro, is based on a naturally occurring protein called tropaelastin. It is applied directly to the wound and is then activated with UV light to form a complete seal, eliminating the need for staples or stitches. Its elasticity means it's designed to work well on shape-changing internal organs like the lungs and heart.

 

A study published in journal Science Translational Medicine showed the glue quickly and successfully sealed incisions in the arteries and lungs of rodents and the lungs of pigs.


Via Dr. Stefan Gruenwald
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Dorothy Retha Cook's curator insight, October 6, 3:19 PM

An emergency fix that really stick to yah!/What's gluing in health tody? 

Victor Jimenez's curator insight, October 7, 4:37 PM
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Monkeypox hits Bayelsa, medical doctor, 10 others quarantined

Monkeypox hits Bayelsa, medical doctor, 10 others quarantined | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Simon Utebor, Yenagoa

Fear has gripped the residents of Bayelsa State as a deadly viral epidemic known as "monkeypox" has broken out in th
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The Man Behind Next-Generation Sequencing and the $1,000 Genome

The Man Behind Next-Generation Sequencing and the $1,000 Genome | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The European Biotech News Website
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In vivo virulence of MHC-adapted AIDS virus serially-passaged through MHC-mismatched hosts

In vivo virulence of MHC-adapted AIDS virus serially-passaged through MHC-mismatched hosts | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary CD8+ T-cell responses exert considerable control over replication of HIV and select for viral escape mutations. Recent studies have suggested that these major histocompatibility complex class I (MHC-I)-associated mutations accumulate in populations and make viruses less pathogenic in vitro. Other studies have shown that some of these escape mutations can revert after passage to MHC-I-disparate hosts. In an attempt to reconcile these apparently conflicting results, we serially passaged a virus isolate through MHC-I-mismatched hosts in the macaque AIDS model of simian immunodeficiency virus (SIV) infection. Here we show an increase in the in vivo virulence of an MHC-I-adapted virus despite a reduction in in vitro viral replication capacity. Only a few of the selected escape mutations reverted after transmission to MHC-I-disparate recipients. Results clearly showed that MHC-I-adapted SIVs that have been serially-transmitted through MHC-I-mismatched hosts can have higher in vivo virulence in MHC-I-matched hosts despite their lower in vitro viral fitness. This study suggests that HIVs may become less sensitive to CD8+ T cell responses and could have increased in vivo virulence by adaptation to MHC-I in human populations.
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Human infection with avian influenza A(H7N9) virus – China

Human infection with avian influenza A(H7N9) virus – China | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
On 18, 25 August and 4 September 2017, the National Health and Family Planning Commission of China (NHFPC) notified WHO of four additional laboratory-confirmed cases of human infection with avian influenza A(H7N9) virus in China.Details of the case-p

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Digoxin reveals a functional connection between HIV-1 integration preference and T-cell activation

Digoxin reveals a functional connection between HIV-1 integration preference and T-cell activation | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary HIV-1 integrates more frequently within transcribed host genes, however we do not understand the biological significance of this. We found that a drug called digoxin inhibits wild type HIV-1 more potently than an HIV-1 bearing a single point mutation in the capsid protein. Here we show that digoxin represses HIV-1 gene expression and in parallel inhibits CD4+ T-cell activation and metabolism. When we analysed the integration sites of wild type and mutant HIV-1, we discovered that wild type virus integrates within or near genes involved in CD4+ T-cell activation and metabolism more often than the mutant virus. Because these are the very same genes repressed by digoxin, the integration bias of wild type virus makes it more susceptible than mutant virus to silencing by the drug. Digoxin unmasked a functional link between HIV-1 integration and T-cell activation, which may affect HIV-1 latency and reactivation.
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Discovery of two small circular ssDNA viruses associated with the whitefly Bemisia tabaci

The complete genome sequences of two novel small circular DNA viruses isolated from sweet-potato whiteflies collected in Central-West (AdDF) and Southeast (AdO) regions of Brazil were determined by Next Generation Sequencing (NGS), and confirmed by cloning and Sanger sequencing. The genomes are 2,199 and 2,211 nt-long, respectively, encoding a putative coat protein (CP) and a replication-associated protein (Rep) and showing a genomic organization typical of viruses from the family Genomoviridae. Phylogenetic analysis with deduced amino acid sequences of Rep indicates that the virus from AdO is closely related to other members of the genus Gemycircularvirus, while the virus from AdDF is related to those of the genus Gemyduguivirus. These new genomoviruses are tentatively named bemisia-associated genomovirus AdO and bemisia-associated genomovirus AdDF.


Via Ed Rybicki
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Ed Rybicki's curator insight, October 18, 5:07 AM
I would be willing to bet some serious money that this is why my good friend Hanokh Czosnek and colelagues have persistently claimed that TYLCV replicates in whiteflies: the promiscuity of Rep-DNA interactions among ssDNA viruses could allow low-level replication of the geminiviral genome by the genomovirus Rep??
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Microbial genome analysis: the COG approach. - PubMed - NCBI

Microbial genome analysis: the COG approach. - PubMed - NCBI | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Brief Bioinform. 2017 Sep 14. doi: 10.1093/bib/bbx117. [Epub ahead of print]
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BioQueue: a novel pipeline framework to accelerate bioinformatics analysis | Bioinformatics | Oxford Academic

BioQueue: a novel pipeline framework to accelerate bioinformatics analysis | Bioinformatics | Oxford Academic | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractMotivation. With the rapid development of Next-Generation Sequencing, a large amount of data is now available for bioinformatics research. Meanwhile, t
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HeLa Nucleic Acid Contamination in The Cancer Genome Atlas Leads to the Misidentification of Human Papillomavirus 18

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Researchers make breakthrough in search for African Swine Fever vaccine

Researchers make breakthrough in search for African Swine Fever vaccine | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Researchers in Australia and the US have uncovered genetic data they believe may contain the key to developing a vaccine for African Swine Fever

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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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Researchers create molecule that could 'kick and kill' HIV - Scienmag: Latest Science and Health News

Researchers create molecule that could 'kick and kill' HIV - Scienmag: Latest Science and Health News | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Credit: CDC/A. Harrison and Dr. P. Feorino
In lab animals, a particle developed by UCLA, Stanford, NIH scientists awakens dormant virus cells and then knocks them out
Current anti-AIDS drugs are highly effective at making HIV undetectable and allo..
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Ancient Viruses Are Buried in Your DNA

Ancient Viruses Are Buried in Your DNA | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Endogenous retroviruses wormed into the human genome eons ago. Today viral genes continue to produce a variety of mysterious proteins in the body.


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A novel mechanism of antibody-mediated enhancement of flavivirus infection

A novel mechanism of antibody-mediated enhancement of flavivirus infection | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Antibodies are an important component of antiviral host responses and their binding to the surface of virus particles usually leads to neutralization of viral infectivity. In some instances, however, antibodies at sub-neutralizing concentrations can enhance infection of certain cells, because they facilitate the uptake of infectious virus-antibody complexes through interactions with antibody-specific cellular receptors (Fcγ receptors). This mechanism is designated antibody-dependent enhancement of infection and implicated in the pathogenesis of dengue and possibly Zika virus infections, both mosquito-transmitted flaviviruses. Here we describe a novel mechanism of infection enhancement by antibodies that is independent of interactions with Fcγ receptors, using another important human-pathogenic flavivirus, tick-borne encephalitis virus. We demonstrate that binding of a specific antibody to the envelope protein E at the viral surface promotes the exposure of a structural element that interacts with the lipids of the cellular plasma membrane, thus increasing infection. Our study provides new insights into mechanisms that potentially modulate the antiviral effects of antibody populations present in post-infection sera.

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Avian influenza H9N2 virus isolated from air samples in LPMs in Jiangxi, China

Avian influenza H9N2 virus isolated from air samples in LPMs in Jiangxi, China | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Recently, avian influenza virus has caused repeated worldwide outbreaks in humans. Live Poultry Markets (LPMs) play an important role in the circulation and reassortment of novel Avian Influenza Virus (AIVs). Aerosol transmission is one of the most important pathways for influenza virus to spread among poultry, from poultry to mammals, and among mammals. In this study, air samples were collected from LPMs in Nanchang city between April 2014 and March 2015 to investigate possible aerosol transmission of AIVs. Air samples were detected for Flu A by Real-Time Reverse Transcription-Polymerase Chain Reaction (RRT-PCR). If samples were positive for Flu A, they were inoculated into 9- to 10-day-old specific-pathogen-free embryonated eggs. If the result was positive, the whole genome of the virus was sequenced by MiSeq. Phylogenetic trees of all 8 segments were constructed using MEGA 6.05 software. To investigate the possible aerosol transmission of AIVs, 807 air samples were collected from LPMs in Nanchang city between April 2014 and March 2015. Based on RRT-PCR results, 275 samples (34.1%) were Flu A positive, and one virus was successfully isolated with embryonated eggs. The virus shared high nucleotide homology with H9N2 AIVs from South China. Our study provides further evidence that the air in LPMs can be contaminated by influenza viruses and their nucleic acids, and this should be considered when choosing and evaluating disinfection strategies in LPMs, such as regular air disinfection. Aerosolized viruses such as the H9N2 virus detected in this study can increase the risk of human infection when people are exposed in LPMs.
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HCV-induced autophagosomes are generated via homotypic fusion of phagophores that mediate HCV RNA replication

HCV-induced autophagosomes are generated via homotypic fusion of phagophores that mediate HCV RNA replication | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Autophagy is a catabolic process that is important for maintaining cellular homeostasis. During autophagy, crescent membrane structures known as phagophores first appear in the cytoplasm, which then expand to form enclosed double-membrane vesicles known as autophagosomes. It has been shown that hepatitis C virus (HCV) induces autophagy and uses autophagosomal membranes for its RNA replication. In this report, we studied the biogenesis pathway of HCV-induced autophagosomes and demonstrated that phagophores induced by HCV originated from the endoplasmic reticulum and undergo homotypic fusion to generate autophagosomes, and that the HCV RNA replication complex is assembled on phagophores prior to the formation of autophagosomes. These findings provided important information for understanding how an RNA virus controls this important cellular pathway for its replication.
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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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