Virology and Bioinformatics from Virology.ca
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PLOS Computational Biology: The Roots of Bioinformatics in ISMB

PLOS Computational Biology: The Roots of Bioinformatics in ISMB | Virology and Bioinformatics from Virology.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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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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Bemol Sido's comment, October 10, 2015 5:28 AM
Thanks. Nice.
Bwana Moses's comment, May 25, 6:13 AM
Great work. Keep it going.
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Newly discovered multicomponent virus is the first of its kind to infect animals

Newly discovered multicomponent virus is the first of its kind to infect animals | Virology and Bioinformatics from Virology.ca | Scoop.it
A story about Science from Phys.org, as featured in Newsfusion's Science News app.
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Tips for effective use of BLAST and other NCBI tools

The National Center for Biotechnology Information (NCBI) provides one of the most extensive sets of web-based tools for biological research. The tools are indispensable when planning genomics experiments, including for qPCR, NGS, and CRISPR. In this presentation, Dr Matt McNeill takes a practical look at getting started with the wealth of NCBI tools, and shares some relevant tips to help you sift through the tools and options that we regularly use. In particular, he focuses on commonly adjusted parameters that will allow you to more effectively use the powerful Basic Local Alignment Algorithm Tool (BLAST) to identify off-target hybridization/annealing events. Dr McNeill also covers practical examples using NCBI tools to design assays.


Via Integrated DNA Technologies
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CRISPR inspires new tricks to edit genes

CRISPR inspires new tricks to edit genes | Virology and Bioinformatics from Virology.ca | Scoop.it
CRISPR/Cas9 has been a rockstar gene-editing tool for just four years and it’s already being tweaked to do more things better.
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The Ins and Outs of Multipartite Plant Viruses

The Ins and Outs of Multipartite Plant Viruses | Virology and Bioinformatics from Virology.ca | Scoop.it
Viruses possessing a non-segmented genome require a specific recognition of their nucleic acid to ensure its protection in a capsid. A similar feature exists for viruses having a segmented genome, usually consisting of viral genomic segments joined together into one viral entity. While this appears as a rule for animal viruses, the majority of segmented…
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Smallpox eradication 'giant' Donald Henderson dies at 87 - BBC News

Smallpox eradication 'giant' Donald Henderson dies at 87 - BBC News | Virology and Bioinformatics from Virology.ca | Scoop.it

US doctor Donald Henderson, who led a successful campaign to wipe out #smallpox worldwide, has died at the age of 87.

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ZBP1/DAI is an innate sensor of influenza virus triggering the NLRP3 inflammasome and programmed cell death pathways

ZBP1/DAI is an innate sensor of influenza virus triggering the NLRP3 inflammasome and programmed cell death pathways | Virology and Bioinformatics from Virology.ca | Scoop.it
People infected with influenza get sick not only because of the presence of virus but also because of the inflammatory immune response. Now, Kuriakose et al . report that the protein ZBP1/DAI (Z-DNA binding protein 1/DNA-dependent activator of IFN regulatory factors) senses influenza A virus (IAV) and may contribute to this inflammatory pathogenesis. They found that ZBP1/DAI triggered cell death and inflammatory responses after IAV infection, and that ZBP1/DAI deficiency protected mice from IAV-related mortality. These mice had decreased inflammation and less epithelial damage than control animals. If these findings hold true in humans, ZBP1/DAI may be a host-directed target to decrease the severity of IAV pathogenesis.
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Chimeric RSV virus-like particles confer protection against respiratory syncytial virus infection

Chimeric RSV virus-like particles confer protection against respiratory syncytial virus infection | Virology and Bioinformatics from Virology.ca | Scoop.it
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Statistical relevance—relevant statistics, part II: presenting experimental data

Statistical relevance—relevant statistics, part II: presenting experimental data | Virology and Bioinformatics from Virology.ca | Scoop.it
In the first part of this article series, I discussed general guidelines for analyzing the results of scientific experiments (Klaus, 2015). The next step is the graphical representation of the results. The importance of data presentation should not be underestimated as figures are a key component of both data analysis and publications. Graphics are an important analytical tool as they can help to reveal patterns and illustrate differences. The appropriate plotting of data can also strengthen or even replace more formal statistical procedures, such as hypothesis tests. In the context of scientific publications, figures should guide the reader through the article and provide a clear and precise representation of the experimental results.

In this article, I will focus primarily on key principles and good practices for presenting small‐to‐medium datasets with the aim of comparing results from different experimental groups. As a general rule, authors should show as much of the actual data as possible instead of summarizing datasets via means or variances. Even larger datasets can be displayed efficiently using an appropriate plot; bars and boxes to visualize summary statistics can serve as additional visual guides. To adapt the methods described in this article, readers can download a supplementary “notebook” (see Code EV1) with code to generate the plots in the R language (R Core Team, 2015). Additionally, this web tool (http://embojserver.embl.de) generates the bee swarm plots and dot plots discussed later in the article. Apart from the topics discussed in this article, there are many more aspects that require attention. The “Scientific Figure Design Course” material by the Bioinformatics unit of the Babraham Institute (Babraham Bioinformatics, 2015) and the book by Tufte (1983) are valuable references.

I start with a discussion of displaying small‐scale experimental datasets. Let us assume that we have a fluorescent marker for detecting a recombination event in …
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Viruses 'more dangerous in the morning' - BBC News

Viruses 'more dangerous in the morning' - BBC News | Virology and Bioinformatics from Virology.ca | Scoop.it
Viruses are more dangerous when they infect their victims in the morning, a University of Cambridge study suggests.
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Structure and Genome Release Mechanism of the Human Cardiovirus Saffold Virus 3

Structure and Genome Release Mechanism of the Human Cardiovirus Saffold Virus 3 | Virology and Bioinformatics from Virology.ca | Scoop.it
In order to initiate an infection, viruses need to deliver their genomes into cells. This involves uncoating the genome and transporting it to the cytoplasm. The process of genome delivery is not well understood for nonenveloped viruses. We address this gap in our current knowledge by studying the uncoating of the nonenveloped human cardiovirus Saffold virus 3 (SAFV-3) of the family Picornaviridae. SAFVs cause diseases ranging from gastrointestinal disorders to meningitis. We present a structure of a native SAFV-3 virion determined to 2.5 Å by X-ray crystallography and an 11-Å-resolution cryo-electron microscopy reconstruction of an “altered” particle that is primed for genome release. The altered particles are expanded relative to the native virus and contain pores in the capsid that might serve as channels for the release of VP4 subunits, N termini of VP1, and the RNA genome. Unlike in the related enteroviruses, pores in SAFV-3 are located roughly between the icosahedral 3- and 5-fold axes at an interface formed by two VP1 and one VP3 subunit. Furthermore, in native conditions many cardioviruses contain a disulfide bond formed by cysteines that are separated by just one residue. The disulfide bond is located in a surface loop of VP3. We determined the structure of the SAFV-3 virion in which the disulfide bonds are reduced. Disruption of the bond had minimal effect on the structure of the loop, but it increased the stability and decreased the infectivity of the virus. Therefore, compounds specifically disrupting or binding to the disulfide bond might limit SAFV infection.

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Gene Drives: Biological Shield or Ecological Menace?

The biomedical applications of CRISPR/Cas9 and related genome editing tools have generally focused on the development of research tools, animal models, and molecular therapies for human diseases. A bold new application of this technology to environmental biology has recently been developed. This application, known as a gene drive, is based on a concept earlier described by Austin Burk in the context of using homing endonuclease technology to rapidly alter the genome of an outbred population.1

In the gene drive design, sequences for the Cas enzyme and the short guide RNAs (sgRNAs) are flanked by the genomic sequences targeted for editing, between which is also inserted a functional gene of interest (GOI) (Fig. 1). These constructs are known as gene drives because when they are introduced into a population by breeding, they spread exponentially through an inheritance pattern known as the “mutagenic chain reaction” (MCR).2,3 The design of these constructs enables an initial event in which the familiar homology-dependent repair (HDR) occurs. Because the Cas gene, sgRNA coding, and GOI sequences “ride along” with the transposition of the target sequences, the gene drive allele becomes homozygous shortly after the “carrier” mates with a wild-type organism. Instead of being diluted in the general population, the gene drive alleles rapidly increase in frequency, effectively taking over in the matter of a few generations.
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Beyond CRISPR: A guide to the many other ways to edit a genome

Beyond CRISPR: A guide to the many other ways to edit a genome | Virology and Bioinformatics from Virology.ca | Scoop.it

The CRISPR–Cas9 tool enables scientists to alter genomes practically at will. Hailed as dramatically easier, cheaper and more versatile than previous technologies, it has blazed through labs around the world, finding new applications in medicine and basic research.

 

But for all the devotion, CRISPR–Cas9 has its limitations. It is excellent at going to a particular location on the genome and cutting there, says bioengineer Prashant Mali at the University of California, San Diego. “But sometimes your application of interest demands a bit more.”

 

The zeal with which researchers jumped on a possible new gene-editing system called NgAgo earlier in 2016 reveals an undercurrent of frustration with CRISPR–Cas9 — and a drive to find alternatives. “It’s a reminder of how fragile every new technology is,” says George Church, a geneticist at Harvard Medical School in Boston, Massachusetts.

 

NgAgo is just one of a growing library of gene-editing tools. Some are variations on the CRISPR theme; others offer new ways to edit genomes.

 

CRISPR–Cas9 may one day be used to rewrite the genes responsible for genetic diseases. But the components of the system — an enzyme called Cas9 and a strand of RNA to direct the enzyme to the desired sequence — are too large to stuff into the genome of the virus most commonly used in gene therapy to shuttle foreign genetic material into human cells.

 

A solution comes in the form of a mini-Cas9, which was plucked from the bacterium Staphylococcus aureus1. It’s small enough to squeeze into the virus used in one of the gene therapies currently on the market. Last December, two groups used the mini-me Cas9 in mice to correct the gene responsible for Duchenne muscular dystrophy.

 

Cas9 will not cut everywhere it’s directed to — a certain DNA sequence must be nearby for that to happen. This demand is easily met in many genomes, but can be a painful limitation for some experiments. Researchers are looking to microbes to supply enzymes that have different sequence requirements so that they can expand the number of sequences they can modify.

One such enzyme, called Cpf1, may become an attractive alternative. Smaller than Cas9, it has different sequence requirements and is highly specific4, 5.

 

Another enzyme, called C2c2, targets RNA rather than DNA — a feature that holds potential for studying RNA and combating viruses with RNA genomes6.

 


Via Dr. Stefan Gruenwald
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Virus hunters search for the next deadly outbreak

Virus hunters search for the next deadly outbreak | Virology and Bioinformatics from Virology.ca | Scoop.it
Meet the researchers who enter the depths of the earth in search of deadly pathogens with the potential to cause outbreaks.

Via Ian M Mackay, PhD, Ed Rybicki
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Ed Rybicki's curator insight, August 25, 10:41 AM
And here in South Africa, what's more!! Although as a former explorer of bat-infested caves, I think rats may be a better target?
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Non-selective Packaging of Rift Valley Fever Virus Genome Segments

Author Summary The bunyavirus family is one of the largest virus families on Earth, of which several members cause severe disease in humans, animals or plants. Little is known about the mechanisms that facilitate the production of infectious bunyavirus virions, which should contain at least one copy of the small (S), medium (M) and large (L) genome segment. In this study, we investigated the genome packaging process of the Rift Valley fever virus (RVFV) by visualizing individual genome segments inside infected cells and virions. Experiments performed with wild-type virus, two- and four-segmented variants, and a variant with a codon-shuffled M segment showed that the production of infectious virions is a non-selective process and is unlikely to involve the formation of a supramolecular viral RNA complex. These observations have broad implications for understanding the bunyavirus replication cycle and may facilitate the development of new vaccines and the identification of novel antiviral targets.
Ed Rybicki's insight:
So: pretty much random, then? Interesting!
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Exploring the virome of diseased horses

Exploring the virome of diseased horses | Virology and Bioinformatics from Virology.ca | Scoop.it
Metagenomics was used to characterize viral genomes in clinical specimens of horses with various organ-specific diseases of unknown aetiology. A novel parvovirus as well as a previously described hepacivirus closely related to human hepatitis C viru

Via Bradford Condon
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Zika Virus: Two or Three Lineages?

Zika Virus: Two or Three Lineages? | Virology and Bioinformatics from Virology.ca | Scoop.it

Via Ed Rybicki
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Ed Rybicki's curator insight, August 23, 9:54 AM
This is interesting for a number of reasons: one, because it nails down slightly more convincingly where Zika came from; two, because it introduces the concept of a wider range of genotypes than we knew about; three, because vaccines that might be expected to protect against Asian and African 1 types, might conceivably not protect against African II. And given the lesson of dengue types and vaccines and the potential for ADE, that might not be a good thing....
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Fc receptors in antibody-dependent enhancement of viral infections - Taylor - 2015 - Immunological Reviews - Wiley Online Library

Fc receptors in antibody-dependent enhancement of viral infections - Taylor - 2015 - Immunological Reviews - Wiley Online Library | Virology and Bioinformatics from Virology.ca | Scoop.it

Via Gilbert C FAURE, Kenzibit
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Analysis of cis and trans Requirements for DNA Replication at the Right-End Hairpin of the Human Bocavirus 1 Genome

Analysis of cis and trans Requirements for DNA Replication at the Right-End Hairpin of the Human Bocavirus 1 Genome | Virology and Bioinformatics from Virology.ca | Scoop.it
IMPORTANCE Human bocavirus 1 (HBoV1) causes acute respiratory tract infections in young children. The duplex HBoV1 genome replicates in HEK293 cells and produces progeny virions that are infectious in well-differentiated airway epithelial cells. A recombinant AAV2 vector pseudotyped with an HBoV1 capsid has been developed to efficiently deliver the cystic fibrosis transmembrane conductance regulator gene to human airway epithelia. Here, we identified both cis-acting elements and trans-acting proteins that are required for HBoV1 DNA replication at the right-end hairpin in HEK293 cells. We localized the minimal replication origin, which contains both NS1 nicking and binding sites, to a 46-nucleotide sequence in the right-end hairpin. The identification of these essential elements of HBoV1 DNA replication acting both in cis and in trans will provide guidance to develop antiviral strategies targeting viral DNA replication at the right-end hairpin and to design next-generation recombinant HBoV1 vectors, a promising tool for gene therapy of lung diseases.

Ed Rybicki's insight:
Interesting because it throws a little doubt into long-established models of parvovirus replication - because it's an autonomously-replicating virus
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Could SMALLPOX return from the grave?

Could SMALLPOX return from the grave? | Virology and Bioinformatics from Virology.ca | Scoop.it
Scientists are worried that the deadly disease smallpox could return because permafrost is melting close to where hundreds of infected bodies were buried in Siberia, Russia.

Via Ian M Mackay, PhD
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Ed Rybicki's curator insight, August 17, 4:08 AM
Ya. No. I am willing to bet the possibility of there being any viable virus there is so small as to be no chance at all.  But they should test it.
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Distinct Viral Lineages from Fish and Amphibians Reveal the Complex Evolutionary History of Hepadnaviruses

Distinct Viral Lineages from Fish and Amphibians Reveal the Complex Evolutionary History of Hepadnaviruses | Virology and Bioinformatics from Virology.ca | Scoop.it
IMPORTANCE Hepadnaviruses are responsible for significant disease in humans (hepatitis B virus) and have been reported from a diverse range of vertebrates as both exogenous and endogenous viruses. We report the full-length genome of a novel hepadnavirus from a fish and the first hepadnavirus genome from an amphibian. The novel fish hepadnavirus, sampled from bluegills, was more closely related to mammalian hepadnaviruses than to other fish viruses. This phylogenetic pattern reveals that, although hepadnaviruses have likely been associated with vertebrates for hundreds of millions of years, they have also been characterized by species jumping across wide phylogenetic distances.

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Two stationary kinds of bacteria can move when mixed

Two stationary kinds of bacteria can move when mixed | Virology and Bioinformatics from Virology.ca | Scoop.it
Bacteria stuck when alone on a dry surface get moving — and get faster — when they evolve together.
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Highly Efficient Delivery of Adeno-Associated Viral Vectors to the Primate Retina

Adeno-associated virus (AAV) has emerged as the preferred vector for targeting gene expression to the retina. Subretinally injected AAV can efficiently transduce retinal pigment epithelium and photoreceptors in primate retina. Inner and middle primate retina can be transduced by intravitreally delivered AAV, but with low efficiency. This is due to dilution of vector, potential neutralization of capsid because it is not confined to the immune-privileged retinal compartment, and the presence of the inner limiting membrane (ILM), a barrier separating the vitreous from the neural retina. We here describe a novel “subILM” injection method that addresses all three issues. Specifically, vector is placed in a surgically induced, hydrodissected space between the ILM and neural retina. In an initial experiment, we injected viscoelastic (Healon®), a substance we confirmed was biocompatible with AAV, to create a subILM bleb and subsequently injected AAV2-GFP into the bleb after irrigation with basic salt solution. For later experiments, we used a Healon–AAV mixture to place single, subILM injections. In all cases, subILM delivery of AAV was well tolerated—no inflammation or gross structural changes were observed by ophthalmological examination or optical coherence tomography. In-life fluorescence imaging revealed profound transgene expression within the area of the subILM injection bleb that persisted for the study duration. Uniform and extensive transduction of retinal ganglion cells (RGCs) was achieved in the areas beneath the subILM bleb. Transduction of Müller glia, ON bipolar cells, and photoreceptors was also observed. Robust central labeling from green fluorescent protein-expressing RGCs confirmed their continued survival, and was observed in the lateral geniculate nucleus, the superior colliculus, and the pretectum. Our results confirm that the ILM is a major barrier to transduction by AAV in primate retina and that, when it is circumvented, the efficiency and depth to which AAV2 promotes transduction of multiple retinal cell classes are greatly enhanced.

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Moderna Therapeutics Deal with Merck: Are personalized vaccines here?

Moderna Therapeutics Deal with Merck: Are personalized vaccines here? | Virology and Bioinformatics from Virology.ca | Scoop.it
Moderna Therapeutics Deal with Merck: Are personalized vaccines here? Reporter: Stephen J. Williams, Ph.D. Take aways: RNA based vaccines are a cost-effective method of developing and manufacturing a personalized cancer vaccine strategy; traditional vaccine methodology has not met with much success as a cancer therapeutic Most of the older RNA vaccine technology depended on isolated…

Via Gilbert C FAURE
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