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CoRAL: Classification of RNAs by Analysis of Length

CoRAL: Classification of RNAs by Analysis of Length | Virology and Bioinformatics from Virology.ca | Scoop.it
Recent advances in high-throughput sequencing allow researchers to examine the transcriptome in more detail than ever before.

Via Mel Melendrez-Vallard
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Virology and Bioinformatics from Virology.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: | Virology and Bioinformatics from Virology.ca | Scoop.it

get in touch if you want to help curate this topic

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GTPB: IB14S Introductory Bioinformatics, Second course - Home

GTPB: IB14S Introductory Bioinformatics, Second course - Home | Virology and Bioinformatics from Virology.ca | Scoop.it

Via Pedro Fernandes
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Pedro Fernandes's curator insight, December 4, 4:47 AM

This is a 4 day course with minimal pre-requisites that aims at equipping the participants with means to deal with biological sequence data at various levels. In the last day we will focus on NGS data analysis at a basic level.

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Antibodies discovery could lead to universal dengue vaccine

Antibodies discovery could lead to universal dengue vaccine | Virology and Bioinformatics from Virology.ca | Scoop.it
A group of international researchers has identified a new class of antibodies that can neutralise all four types of the dengue virus. The discovery could lead to the development of better vaccines and tests that could eventually lead to reductions in the incidence of the virus, which affects over 100 million people each year.
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FDA approves Gardasil 9 for prevention of cancers caused by five additional types of HPV

FDA approves Gardasil 9 for prevention of cancers caused by five additional types of HPV | Virology and Bioinformatics from Virology.ca | Scoop.it
The U.S. Food and Drug Administration today approved Gardasil 9 (Human Papillomavirus 9-valent Vaccine, Recombinant) for the prevention of certain diseases caused by nine types of Human Papillomavirus (HPV). Covering nine HPV types, five more HPV types than Gardasil (previously approved by the FDA), Gardasil 9 has the potential to prevent approximately 90 percent of cervical, vulvar, vaginal and anal cancers.

 

Thanks to Russell Kightley Media for the cervical cancer graphic


Via Ed Rybicki
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The Problem Of The Parotid Paramyxovirus (aka Mumps)

The Problem Of The Parotid Paramyxovirus (aka Mumps) | Virology and Bioinformatics from Virology.ca | Scoop.it
The recent outbreak of mumps in the NHL reveals how a vaccine-preventable disease can make a comeback.
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Can you spell   V-A-C-C-I-N-E  ?

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Alpharetroviral Vectors: From a Cancer-Causing Agent to a Useful Tool for Human Gene Therapy

Alpharetroviral Vectors: From a Cancer-Causing Agent to a Useful Tool for Human Gene Therapy | Virology and Bioinformatics from Virology.ca | Scoop.it

Gene therapy using integrating retroviral vectors has proven its effectiveness in several clinical trials for the treatment of inherited diseases and cancer. However, vector-mediated adverse events related to insertional mutagenesis were also observed, emphasizing the need for safer therapeutic vectors. Paradoxically, alpharetroviruses, originally discovered as cancer-causing agents, have a more random and potentially safer integration pattern compared to gammaretro- and lentiviruses. In this review, we provide a short overview of the history of alpharetroviruses and explain how they can be converted into state-of-the-art gene delivery tools with improved safety features. We discuss development of alpharetroviral vectors in compliance with regulatory requirements for clinical translation, and provide an outlook on possible future gene therapy applications. Taken together, this review is a broad overview of alpharetroviral vectors spanning the bridge from their parental virus discovery to their potential applicability in clinical settings

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Influenza Virus-Host Interactome Screen as a Platform for Antiviral Drug Development

Influenza Virus-Host Interactome Screen as a Platform for Antiviral Drug Development | Virology and Bioinformatics from Virology.ca | Scoop.it
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Ebola vaccine trial 'interrupted'

Ebola vaccine trial 'interrupted' | Virology and Bioinformatics from Virology.ca | Scoop.it

The clinical trial of an Ebola vaccine in Switzerland has been interrupted after some patients complained of joint pains in their hands and feet.

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The HIV Mutation Browser: A Resource for Human Immunodeficiency Virus Mutagenesis and Polymorphism Data

The HIV Mutation Browser: A Resource for Human Immunodeficiency Virus Mutagenesis and Polymorphism Data | Virology and Bioinformatics from Virology.ca | Scoop.it
PLOS Computational Biology is an open-access
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Not Just a Theory—The Utility of Mathematical Models in Evolutionary Biology

Not Just a Theory—The Utility of Mathematical Models in Evolutionary Biology | Virology and Bioinformatics from Virology.ca | Scoop.it
PLOS Biology is an open-access, peer-reviewed journal that features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines.
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Mega2: validated data-reformatting for linkage and association analyses - Source Code for Biology and Medicine

In a typical study of the genetics of a complex human disease, many different analysis programs are used, to test for linkage and association. This requires extensive and careful data reformatting, as many of these analysis programs use differing input formats. Writing scripts to facilitate this can be tedious, time-consuming, and error-prone. To address these issues, the open source Mega2 data reformatting program provides validated and tested data conversions from several commonly-used input formats to many output formats.
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pH-Dependent entry of chikungunya virus fusion into mosquito cells

Millions of human infections caused by arthropod-borne pathogens are initiated by the feeding of an infected mosquito on a vertebrate. However, interactions between the viruses and the mosquito vector, which facilitates successful infection and transmission of virus to a subsequent vertebrate host, are still not fully understood.
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E5564 inhibits immunosuppressive cytokine IL-10 induction promoted by HIV-1 Tat protein

In HIV-1 infected patients, production of interleukin-10 (IL-10), a highly immunosuppressive cytokine, is associated with progression of infection toward AIDS. HIV-1 Tat protein, by interacting with TLR4-MD2 at the membrane level, induces IL-10 production by primary human monocytes and macrophages. In the present study we evaluated the effect of the TLR4 antagonist Eritoran tetrasodium (E5564) on HIV-1 Tat-induced IL-10 production.
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Scientists tallied up all the advice on Dr. Oz's show. Here's what they found.

We now have science to quantify the quackery on TV.
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KmerStream: streaming algorithms for k-mer abundance estimation

KmerStream: streaming algorithms for k-mer abundance estimation | Virology and Bioinformatics from Virology.ca | Scoop.it
RT @assemblathon: KmerStream: streaming algorithms for k-mer abundance estimation: http://t.co/VnfkQGMJPv

Via Mel Melendrez-Vallard, Pedro Fernandes
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Virology Journal | Full text | Plant-based vaccines against viruses

Plant-made or “biofarmed” viral vaccines are some of the earliest products of the technology of plant molecular farming, and remain some of the brightest prospects for the success of this field. Proofs of principle and of efficacy exist for many candidate viral veterinary vaccines; the use of plant-made viral antigens and of monoclonal antibodies for therapy of animal and even human viral disease is also well established. This review explores some of the more prominent recent advances in the biofarming of viral vaccines and therapies, including the recent use of ZMapp for Ebolavirus infection, and explores some possible future applications of the technology.
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Dengue fever vaccine on the cards after novel antibody discovery

Dengue fever vaccine on the cards after novel antibody discovery | Virology and Bioinformatics from Virology.ca | Scoop.it
The antibodies could be used to treat dengue fever or develop a vaccine that works against all four strains of virus
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Genevisible: new Google-like search engine for genes

Genevisible identifies the most significant tissues, cell lines, diseases or perturbations regulating a gene of interest
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An Evolutionary Battle Against Bacteria

An Evolutionary Battle Against Bacteria | Virology and Bioinformatics from Virology.ca | Scoop.it
A recent study illustrates how our ancestors evolved new defenses to starve meningitis-causing bacteria of the iron they need to grow.
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ENHANCING INFECTIOUS DISEASE MAPPING WITH OPEN ACCESS RESOURCES - Eurosurveillance

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ECOD: An Evolutionary Classification of Protein Domains

ECOD: An Evolutionary Classification of Protein Domains | Virology and Bioinformatics from Virology.ca | Scoop.it
PLOS Computational Biology is an open-access
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Viral suppressors of the RIG-I-mediated interferon response are pre-packaged in influenza virions : Nature Communications : Nature Publishing Group

Viral suppressors of the RIG-I-mediated interferon response are pre-packaged in influenza virions : Nature Communications : Nature Publishing Group | Virology and Bioinformatics from Virology.ca | Scoop.it

The type I interferon (IFN) response represents the first line of defence to invading pathogens. Internalized viral ribonucleoproteins (vRNPs) of negative-strand RNA viruses induce an early IFN response by interacting with retinoic acid inducible gene I (RIG-I) and its recruitment to mitochondria. Here we employ three-dimensional stochastic optical reconstruction microscopy (STORM) to visualize incoming influenza A virus (IAV) vRNPs as helical-like structures associated with mitochondria. Unexpectedly, an early IFN induction in response to vRNPs is not detected. A distinct amino-acid motif in the viral polymerases, PB1/PA, suppresses early IFN induction. Mutation of this motif leads to reduced pathogenicity in vivo, whereas restoration increases it. Evolutionary dynamics in these sequences suggest that completion of the motif, combined with viral reassortment can contribute to pandemic risks. In summary, inhibition of the immediate anti-viral response is ‘pre-packaged’ in IAV in the sequences of vRNP-associated polymerase proteins.

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Human Viruses and Cancer

Human Viruses and Cancer | Virology and Bioinformatics from Virology.ca | Scoop.it
To date, seven viruses have been consistently linked to different types of human cancer, and infections are estimated to account for up to 20% of all cancer cases worldwide.
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Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch

Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch | Virology and Bioinformatics from Virology.ca | Scoop.it

Knowledge of ancient viruses is limited due to their low concentration and poor preservation in ancient specimens. Using a viral particle-associated nucleic acid enrichment approach, we genetically characterized one complete DNA and one partial RNA viral genome from a 700-y-old fecal sample preserved in ice. Using reverse genetics, we reconstituted the DNA virus, which replicated and systemically spread in a model plant species. Under constant freezing conditions, encapsidated viral nucleic acids may therefore be preserved for centuries. Our finding indicates that cryogenically preserved materials can be repositories of ancient viral nucleic acids, which in turn allow molecular genetics to regenerate viruses to study their biology.

 
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MicroRNA miR-320a and miR-140 inhibit mink enteritis virus infection by repression of its receptor, feline transferrin receptor

Mink enteritis virus (MEV) is one of the most important pathogens in the mink industry. Recent studies have shed light into the role of microRNAs (miRNAs), small noncoding RNAs of length ranging from 18¿23 nucleotides (nt), as critical modulators in the host-pathogen interaction networks. We previously showed that miRNA miR-181b can inhibit MEV replication by repression of viral non-structural protein 1 expression. Here, we report that two other miRNAs (miR-320a and miR-140) inhibit MEV entry into feline kidney (F81) cells by downregulating its receptor, transferrin receptor (TfR), by targeting the 3¿ untranslated region (UTR) of TfR mRNA, while being themselves upregulated.
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Molecular mechanism of the enhanced viral fitness contributed by secondary mutations in the hemagglutinin protein of oseltamivir resistant H1N1 influenza viruses: modeling studies of antibody and r...

The envelope protein hemagglutinin (HA) of influenza viruses is primarily associated with host antibody and receptor interactions. The HA protein is known to maintain a functional balance with neuraminidase (NA), the other major envelope protein. Prior to 2007-2008, human seasonal H1N1 viruses possessing the NA H274Y mutation, which confers oseltamivir resistance, generally had low growth capability. Subsequently, secondary mutations that compensate for the deleterious effect of the NA H274Y mutation have been identified. The molecular mechanism of how the defect could be counteracted by these secondary mutations is not fully understood. We studied here the effect of three such mutations (T86K, K144E and R192K) in the HA protein, which are located at either the HA receptor binding site or in the H1N1 antigenic sites. Molecular docking and dynamics studies showed that, of the three mutations, the R192K mutation could have mediated neutralizing antibody escape and decreased receptor binding affinity, either or both of which may have contributed to increased viral fitness. The study suggests the molecular basis of enhanced viral fitness induced by secondary mutations in the evolution of oseltamivir-resistant influenza strains.

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