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Viral Particles Drive Rapid Differentiation of Memory B Cells into Secondary Plasma Cells Producing Increased Levels of Antibodies [ANTIGEN RECOGNITION AND RESPONSES]

Extensive studies have been undertaken to describe naive B cells differentiating into memory B cells at a cellular and molecular level. However, relatively little is known about the fate of memory B cells upon Ag re-encounter.

Via Gilbert Faure au nom de l'ASSIM
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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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Buying in to bioinformatics: an introduction to commercial sequence analysis software Brief Bioinform. 2014

Advancements in high-throughput nucleotide sequencing techniques have brought with them state-of-the-art bioinformatics programs and software packages. Given the importance of molecular sequence data in contemporary life science research, these software suites are becoming an essential component of many labs and classrooms, and as such are frequently designed for non-computer specialists and marketed as one-stop bioinformatics toolkits. Although beautifully designed and powerful, user-friendly bioinformatics packages can be expensive and, as more arrive on the market each year, it can be difficult for researchers, teachers and students to choose the right software for their needs, especially if they do not have a bioinformatics background. This review highlights some of the currently available and most popular commercial bioinformatics packages, discussing their prices, usability, features and suitability for teaching. Although several commercial bioinformatics programs are arguably overpriced and overhyped, many are well designed, sophisticated and, in my opinion, worth the investment. If you are just beginning your foray into molecular sequence analysis or an experienced genomicist, I encourage you to explore proprietary software bundles. They have the potential to streamline your research, increase your productivity, energize your classroom and, if anything, add a bit of zest to the often dry detached world of bioinformatics.

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SDT: A Virus Classification Tool Based on Pairwise ... [PLoS One. 2014] - PubMed - NCBI

SDT: A Virus Classification Tool Based on Pairwise ... [PLoS One. 2014] - PubMed - NCBI | Virology and Bioinformatics from Virology.ca | Scoop.it

The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome sequences. Taxonomic classification approaches that are based on pairwise genetic identity measures are potentially highly automatable and are progressively gaining favour with the International Committee on Taxonomy of Viruses (ICTV). There are, however, various issues with the calculation of such measures that could potentially undermine the accuracy and consistency with which they can be applied to virus classification.  

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Codifying Collegiality: Recent Developments in Data Sharing Policy in the Life Sciences

Codifying Collegiality: Recent Developments in Data Sharing Policy in the Life Sciences | Virology and Bioinformatics from Virology.ca | Scoop.it
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HIV’s unkind cut

HIV’s unkind cut | Virology and Bioinformatics from Virology.ca | Scoop.it

Sainski et al. reveal how an inactive caspase fragment spawned by HIV infection can still kill T cells.

HIV triggers a precipitous decline in the number of CD4 T cells. One way that the virus slays these cells is by provoking apoptosis. But one aspect of the apoptotic mechanism remains puzzling. The HIV protease trims the apoptosis-promoting cellular enzyme caspase 8. The resulting fragment, known as Casp8p41, is enzymatically inert but nonetheless induces cell death.

Sainski et al. discovered that Casp8p41 binds to a proapoptotic protein called Bak. The researchers determined that caspase 8 carries a domain that fits into a groove on Bak and switches the protein on. However, the C terminus of caspase 8 normally overhangs this domain and prevents it from interacting with Bak. When HIV infects a CD4 T cell, the protease cuts away caspase 8’s C terminus, exposing the Bak-activating domain. Bak molecules can then oligomerize and trigger cell death by spurring mitochondria to become leaky. Mutating two amino acids in the Bak-binding domain made cells less susceptible to viral infection.

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Here’s Where We Stand With Ebola

Here’s Where We Stand With Ebola | Virology and Bioinformatics from Virology.ca | Scoop.it
It’s nine months into the biggest Ebola outbreak in history, and the situation is only going from bad to worse. The outbreak simmered slowly in West Africa from December 2013, when the first case was retrospectively documented, through March, when it was first recognized by international authorities. It began gaining...
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Influenza: Cellular proteins go viral | Nature Communications | Nature Publishing Group

Influenza: Cellular proteins go viral | Nature Communications | Nature Publishing Group | Virology and Bioinformatics from Virology.ca | Scoop.it

Viral particles produced in different species are composed of different proteins despite the viruses being genetically identical, reports a study published online in Nature Communications. The study identifies a set of cellular proteins that are consistently incorporated from the host into influenza viral particles and highlights the ability of flu viruses to possess distinct, host-dependent properties.

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Virology Journal | Abstract | Novel norovirus recombinants detected in South Africa

Noroviruses (NoV) are the leading cause of viral gastroenteritis worldwide. Recombination frequently occurs within and between NoV genotypes and recombinants have been implicated in sporadic cases, outbreaks and pandemics of NoV. There is a lack of data on NoV recombinants in Africa and therefore their presence and diversity was investigated in South Africa (SA).
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Op-Ed: Ebola is everybody’s business

Op-Ed: Ebola is everybody’s business | Virology and Bioinformatics from Virology.ca | Scoop.it

The images are beamed around the world. Emaciated bodies, lying solo at hospital gates, in one-bedroom corrugated iron shantytown shacks, in bare makeshift hospital rooms or on potholed, muddy streets.  Poor people are dying in mostly undignified settings, often alone, often shunned by fearful family and friends or an absent health system. The lucky few who reach humanitarian centres have a chance to survive, but it is mostly against great and often insurmountable odds. And sadly, even if many people do make it to some form of help, they are failed because there simply is no health system able to offer the basic level of healthcare, to which every single human being in the world should be entitled to access as a human right.

As was the case for many years with HIV, those who have the means and money to buy a hospital bed where they can access clean water, some medication, caring and trained healthcare workers or a basic intravenous drip, have a chance of survival or at the very least a dignified and pain-free end. However for thousands of west Africans contracting Ebola has been a painful, debilitating and undignified death sentence.

In many ways the ever-growing Ebola epidemic is showing up the fault lines, not only in buckling or collapsed health systems, but in society’s failure to show solidarity with the “them”, with the poor and voiceless.

The 2014 Ebola outbreak needs to become a moment where those who follow will mark it as a turning point where the world rallied; where donors, rich countries and health agencies acted decisively to invest in health systems on which billions of vulnerable people rely, but are failed daily.

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PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme

High-throughput transcriptome sequencing (RNA-seq) technology promises to discover novel protein-coding and non-coding transcripts, particularly the identification of long non-coding RNAs (lncRNAs) from de novo sequencing data. This requires tools that are not restricted by prior gene annotations, genomic sequences and high-quality sequencing.
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Myxoma virus oncolytic efficiency can be enhanced

Myxoma virus oncolytic efficiency can be enhanced | Virology and Bioinformatics from Virology.ca | Scoop.it

Myxoma virus (MYXV) is one of many animal viruses that exhibit oncolytic properties in transformed human cells. Compared to orthopoxviruses like vaccinia (VACV), MYXV spreads inefficiently, which could compromise its use in treating tumors and their associated metastases. 

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The Scale of the Universe - An Interactive Visual Understanding of How Small Viruses and Microorganisms Really Are

Zoom from the edge of the universe to the quantum foam of spacetime and learn about everything in between.
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CorMut: an R/Bioconductor package for computing correlated mutations based on selection pressure

Summary: Correlated mutations constitute a fundamental idea in evolutionary biology, and understanding correlated mutations will, in turn, facilitate an understanding of the genetic mechanisms governing evolution. CorMut is an R package designed to compute correlated mutations in the unit of codon or amino acid mutation. Three classical methods were incorporated, and the computation results can be represented as correlation mutation networks. CorMut also enables the comparison of correlated mutations between two different evolutionary conditions.

Availability and implementation: CorMut is released under the GNU General Public License within bioconductor project, and freely available athttp://bioconductor.org/packages/release/bioc/html/CorMut.html.

Contact: mal@chinaaids.cn or yshao08@gmail.com

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Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science Aug. 2014

In its largest outbreak, Ebola virus disease is spreading through Guinea, Liberia, Sierra Leone, and Nigeria. We sequenced 99 Ebola virus genomes from 78 patients in Sierra Leone to ~2000× coverage. We observed a rapid accumulation of interhost and intrahost genetic variation, allowing us to characterize patterns of viral transmission over the initial weeks of the epidemic. This West African variant likely diverged from central African lineages around 2004, crossed from Guinea to Sierra Leone in May 2014, and has exhibited sustained human-to-human transmission subsequently, with no evidence of additional zoonotic sources. Because many of the mutations alter protein sequences and other biologically meaningful targets, they should be monitored for impact on diagnostics, vaccines, and therapies critical to outbreak response.

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Investigating the Genomic Origins of the 2014 Ebola Outbreak

Investigating the Genomic Origins of the 2014 Ebola Outbreak | Virology and Bioinformatics from Virology.ca | Scoop.it

Since March of this year, the Ebola virus in West Africa has infected and killed thousands of people in the region and gripped the world's attention. Despite treatment and containment efforts, the epidemic persists with a fatality rate of a staggering 52 percent, according to the World Health Organization.


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Rabies Rapid Transit System

Rabies Rapid Transit System | Virology and Bioinformatics from Virology.ca | Scoop.it
Rabies virus hijacks the transport systems of neurons, manipulating axonal transport machinery to get to the central nervous system at maximum speed.
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Ebola Doctor Shortage Eases as Volunteers Step Forward

Ebola Doctor Shortage Eases as Volunteers Step Forward | Virology and Bioinformatics from Virology.ca | Scoop.it
Even with the volunteers, experts say, there will be a long gap before hospitals can be fully staffed to care for the growing numbers of Ebola patients.
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Mapping the zoonotic niche of Ebola virus disease in Africa

Mapping the zoonotic niche of Ebola virus disease in Africa | Virology and Bioinformatics from Virology.ca | Scoop.it

Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. - See more at: http://elifesciences.org/content/3/e04395#sthash.QDp91BHi.dpuf

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The influence of taxon sampling on Bayesian divergence time inference under scenarios of rate heterogeneity among lineages

The influence of taxon sampling on Bayesian divergence time inference under scenarios of rate heterogeneity among lineages | Virology and Bioinformatics from Virology.ca | Scoop.it

Although taxon sampling is commonly considered an important issue in phylogenetic inference, it is rarely considered in the Bayesian estimation of divergence times. In fact, the studies conducted to date have presented ambiguous results, and the relevance of taxon sampling for molecular dating remains unclear. In this study, we developed a series of simulations that, after six hundred Bayesian molecular dating analyses, allowed us to evaluate the impact of taxon sampling on chronological estimates under three scenarios of among-lineage rate heterogeneity. The first scenario allowed us to examine the influence of the number of terminals on the age estimates based on a strict molecular clock. The second scenario imposed an extreme example of lineage specific rate variation, and the third scenario permitted extensive rate variation distributed along the branches. We also analyzed empirical data on selected mitochondrial genomes of mammals. Our results showed that in the strict molecular-clock scenario (Case I), taxon sampling had a minor impact on the accuracy of the time estimates, although the precision of the estimates was greater with an increased number of terminals. The effect was similar in the scenario (Case III) based on rate variation distributed among the branches. Only under intensive rate variation among lineages (Case II) taxon sampling did result in biased estimates. The results of an empirical analysis corroborated the simulation findings. We demonstrate that taxonomic sampling affected divergence time inference but that its impact was significant if the rates deviated from those derived for the strict molecular clock. Increased taxon sampling improved the precision and accuracy of the divergence time estimates, but the impact on precision is more relevant. On average, biased estimates were obtained only if lineage rate variation was pronounced.

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Virology tidbits

Virology tidbits | Virology and Bioinformatics from Virology.ca | Scoop.it

This blog is about trivia, current research and general topics concerning animal and human #viruses.

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“History of Microbiology” | Microbiology with Educator.com

History of Microbiology” | Microbiology with Educator.com ▻Watch more at http://educator.com/biology/microbiology/carpenter/ Understand your Microbiology homework and ace the test...
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Effect of Formaldehyde Inactivation on Poliovirus

Inactivated polio vaccines, which have been used in many countries for more than 50 years, are produced by treating live poliovirus (PV) with formaldehyde. However, the molecular mechanisms underlying virus inactivation are not well understood. Infection by PV is initiated by virus binding to specific cell receptors, which results in viral particles undergoing sequential conformational changes that generate altered structural forms (135S and 80S particles) and leads to virus cell entry. We have analyzed the ability of inactivated PV to bind to the human poliovirus receptor (hPVR) using various techniques such as ultracentrifugation, fluorescence-activated cell sorting flow cytometry and real-time reverse transcription-PCR (RT-PCR). The results showed that although retaining the ability to bind to hPVR, inactivated PV bound less efficiently in comparison to live PV. We also found that inactivated PV showed resistance to structural conversion in vitro, as judged by measuring changes in antigenicity, the ability to bind to hPVR, and viral RNA release at high temperature. Furthermore, viral RNA from inactivated PV was shown to be modified, since cDNA yields obtained by RT-PCR amplification were severely reduced and no infectious virus was recovered after RNA transfection into susceptible cells.

 

Ed Rybicki's insight:

People have been treating poliovirus with formaldehyde for over 60 years - and it's only NOW that someone thought to study in detail what happens!

 

I love this stuff: analytical centrifugation could have been done any time in the last fifty years (and has been, in determining structural transitions) but the newer techniques such as flow cytometry and RT-PCR could not. Analytically determining now what was empirically observed to work when polio vaccines were first made, is a historically important vindication of pioneering work that has almost made the viruses go away.

 

Simple and obvious findings, essentially - it is obvious that methylene bridging between amino acids would affect structural transitions; so too that HCHO treatment would kill viral ssRNA - but it hadn't been DONE properly previously.  Great stuff!

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The evolution of pandemic influenza: evidence from India, 1918-19

The 1918-19 'Spanish' Influenza was the most devastating pandemic in recent history, with estimates of global mortality ranging from 20 to 50 million. The focal point of the pandemic was India, with an estimated death toll of between 10 and 20 million. We will characterize the pattern of spread, mortality, and evolution of the 1918 influenza across India using spatial or temporal data.
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Will the Ebola virus go airborne? (And is that even the right question?)

Will the Ebola virus go airborne? (And is that even the right question?) | Virology and Bioinformatics from Virology.ca | Scoop.it
The virus spreads through contact with bodily fluids. What if that changes?
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Virus Variation Resource pages for Ebolavirus, MERS coronoavirus give quick and easy access to related sequences and other data

Virus Variation Resource pages for Ebolavirus, MERS coronoavirus give quick and easy access to related sequences and other data | Virology and Bioinformatics from Virology.ca | Scoop.it
NCBI has created resource pages for Ebolavirus and MERS coronavirus, giving users an easy way to find all sequences related to these pathogens. These pages aggregate links to virus data at NCBI and also provide important links out to other information at the CDC, WHO, and HealthMap.
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Conserved and host-specific features of influenza virion architecture

Conserved and host-specific features of influenza virion architecture | Virology and Bioinformatics from Virology.ca | Scoop.it

Viruses use virions to spread between hosts, and virion composition is therefore the primary determinant of viral transmissibility and immunogenicity. However, the virions of many viruses are complex and pleomorphic, making them difficult to analyse in detail. Here we address this by identifying and quantifying virion proteins with mass spectrometry, producing a complete and quantified model of the hundreds of host-encoded and viral proteins that make up the pleomorphic virions of influenza viruses. We show that a conserved influenza virion architecture is maintained across diverse combinations of virus and host. This ‘core’ architecture, which includes substantial quantities of host proteins as well as the viral protein NS1, is elaborated with abundant host-dependent features. As a result, influenza virions produced by mammalian and avian hosts have distinct protein compositions. Finally, we note that influenza virions share an underlying protein composition with exosomes, suggesting that influenza virions form by subverting microvesicle production.

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