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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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Bats May Be Carrying the Next SARS Pandemic

Bats May Be Carrying the Next SARS Pandemic | Virology and Bioinformatics from Virology.ca | Scoop.it

In November 2002, a deadly new virus emerged suddenly in the south of China. In less than a year, the disease it caused, known as SARS, spread to 33 countries, sickening more than 8000 people and killing more than 700. Then it disappeared. Now, researchers say, they have for the first time isolated a closely related virus from bats in China that can infect human cells. "This shows, that right now in China, there are bats carrying a virus that can directly infect people, and cause another SARS pandemic," says Peter Daszak, one of the authors and president of EcoHealth Alliance in New York City.

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Large-Scale Multiple Sequence Alignment and Tree Estimation Using SATé

SATé is a method for estimating multiple sequence alignments and trees that has been shown to produce highly accurate results for datasets with large numbers of sequences. Running SATé using its default settings is very simple, but improved accuracy can be obtained by modifying its algorithmic parameters. We provide a detailed introduction to the algorithmic approach used by SATé, and instructions for running a SATé analysis using the GUI under default settings. We also provide a discussion of how to modify these settings to obtain improved results, and how to use SATé in a phylogenetic analysis pipeline.

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Live Vaccines

Live vaccines are one of the more advanced applications of engineered bacteria.In this study, Splitter and coworkers engineer laboratory strains of E. coli a...
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Rapid molecular haemagglutinin subtyping of Avian Influenza isolates by specific real-time RT-PCR tests

Sixteen haemagglutinin (HA) subtypes of avian influenza viruses (AIV) have been described to date. Rapid subtype identification of any AIV is of major interest because of the possible serious consequences for the poultry industry and even public health. Molecular techniques currently allow immediate accurate subtype characterisation prior to virus isolation. In this study, a set of fourteen specific real-time RT-PCR methods were developed and evaluated for AIV HA subtyping (H1-H4, H6-H8, H10-H16), H5 and H9 being excluded on the basis of the current validity of the European Union (EU) recommended specific assays. Specific primers and probes sets for each HA-subtype were designed to hybridise the largest isolates range within each single subtype, considering the Eurasian lineage as a major target. The robustness and general application of the 14 HA-subtype methods were verified by the analysis of 110 AIV isolates belonging to all 16 HA-subtypes, performed in different laboratories. The developed real-time RT-PCR assays proved to be highly specific and revealed suitable sensitivity, allowing direct HA-subtyping of clinical material. In summary, this study provides for the first time a panel of molecular tests using specific hydrolysis probes for rapid and complete AIV HA-subtype identification.

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Hemagglutinin receptor specificity and structural analyses of respiratory droplet transmissible H5N1 viruses

Two ferret-adapted H5N1 viruses capable of respiratory droplet transmission have been reported with mutations in the hemagglutinin receptor-binding site and stalk domains. Glycan microarray analysis reveals that both viruses exhibit a strong shift towards binding to ‘human-type' α2-6 sialosides, but with notable differences in fine specificity. Crystal structure analysis further shows that the stalk mutation causes no obvious perturbation of the receptor-binding pocket, consistent with its impact on hemagglutinin stability without effecting receptor specificity.

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Scientists Reveal Structure of HIV Protein Key to Cell Entry

Scientists Reveal Structure of HIV Protein Key to Cell Entry | Virology and Bioinformatics from Virology.ca | Scoop.it
Bethesda, MD (Scicasts) – Using protein engineering and two different cutting-edge structural biology imaging techniques, researchers have developed a detailed picture of the protein largely responsible for enabling HIV to enter human immune cells...
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NBA Superstar Chris Bosh: Here's Why You Should Learn to Code | Wired Opinion | Wired.com

NBA Superstar Chris Bosh: Here's Why You Should Learn to Code | Wired Opinion | Wired.com | Virology and Bioinformatics from Virology.ca | Scoop.it
Miami Heat's Chris Bosh: "I began to notice that the world around me was spinning on an axis powered by varying patterns of 1s and 0s.
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Setting the Record Straight: Debunking All the Flu Vaccine Myths

Setting the Record Straight: Debunking All the Flu Vaccine Myths | Virology and Bioinformatics from Virology.ca | Scoop.it
It’s that time again — that time when dozens of spurious articles pop up all over the web touting all the dangers of the flu vaccine.
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Model virus structure shows why there's no cure for common cold

Model virus structure shows why there's no cure for common cold | Virology and Bioinformatics from Virology.ca | Scoop.it

In a pair of landmark studies that exploit the genetic sequencing of the "missing link" cold virus, rhinovirus C, scientists at the University of Wisconsin-Madison have constructed a three-dimensional model of the pathogen that shows why there is no cure yet for the common cold.

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Trouble at the lab

Trouble at the lab | Virology and Bioinformatics from Virology.ca | Scoop.it
“I SEE a train wreck looming,” warned Daniel Kahneman, an eminent psychologist, in an open letter last year. The premonition concerned research on a phenomenon...
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Chinese bats likely source of SARS virus, researchers report - Fogarty International Center @ NIH

Chinese bats likely source of SARS virus, researchers report - Fogarty International Center @ NIH | Virology and Bioinformatics from Virology.ca | Scoop.it

Scientists say they've produced "the clearest evidence yet" the SARS virus originated in Chinese horseshoe bats and that direct bat-to-human transmission is "plausible." The 2002 severe acute respiratory syndrome coronavirus (SARS-CoV) pandemic was one of the most significant public health events in recent history and researchers have been studying the virus to better understand how it is transmitted to prepare for future outbreaks.

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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 | Virology and Bioinformatics from Virology.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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GenomeTools

GenomeTools | Virology and Bioinformatics from Virology.ca | Scoop.it
The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary.
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Explain Bioinformatics to Your Grandmother!

Explain Bioinformatics to Your Grandmother! | Virology and Bioinformatics from Virology.ca | Scoop.it

What are you working on? You have certainly been asked that question many times, whether it be at a Saturday night party, during a discussion with your neighbors, or at a family gathering. Communicating with a lay audience about scientific subjects and making them attractive is a difficult task. But difficult or not, you will have to do it for many years, not only with your family and friends, but also with your colleagues and collaborators. So, better learn now! Although not usually taught, the ability to explain your work to others is an essential skill in science, where communication plays a key role. Using some examples of the French Regional Student Group activities, we discuss here (i) why it is important to have such communication skills, (ii) how you can get involved in these activities by using existing resources or working with people who have previous experience, and (iii) what you get out of this amazing experience. We aim to motivate you and provide you with tips and ideas to get involved in promoting scientific activities while getting all the benefits.

 

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Samuel Viana's curator insight, November 1, 2013 9:14 PM

Se um dia tiverem de explicar o que andam a fazer para ganhar a vida, para não terem de usar o termo chavão "Bioinformática",  sempre podem usar umas quantas estratégias (em inglês)...

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Genome Scale Evolution of Myxoma Virus Reveals Host-Pathogen Adaptation and Rapid Geographic Spread

The evolutionary interplay between myxoma virus (MYXV) and the European rabbit (Oryctolagus cuniculus) following release of the virus in Australia in 1950 as a biological control is a classic example of host-pathogen coevolution. We present a detailed genomic and phylogeographic analysis of 30 strains of MYXV, including the Australian progenitor strain Standard Laboratory Strain (SLS), 24 Australian viruses isolated from 1951 to 1999, and three isolates from the early radiation in Britain from 1954 and 1955. We show that in Australia MYXV has spread rapidly on a spatial scale, with multiple lineages cocirculating within individual localities, and that both highly virulent and attenuated viruses were still present in the field through the 1990s. In addition, the detection of closely related virus lineages at sites 1,000 km apart suggests that MYXV moves freely in geographic space, with mosquitoes, fleas, and rabbit migration all providing means of transport. Strikingly, despite multiple introductions, all modern viruses appear to be ultimately derived from the original introductions of SLS. The rapidity of MYXV evolution was also apparent at the genomic scale, with gene duplications documented in a number of viruses. Duplication of potential virulence genes may be important in increasing the expression of virulence proteins and provides the basis for the evolution of novel functions. Mutations leading to loss of open reading frames were surprisingly frequent and in some cases may explain attenuation, but no common mutations that correlated with virulence or attenuation were identified.

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Structure-Based Design of a Fusion Glycoprotein Vaccine for Respiratory Syncytial Virus

Respiratory syncytial virus (RSV) is the leading cause of hospitalization for children under 5 years of age. We sought to engineer a viral antigen that provides greater protection than currently available vaccines and focused on antigenic site Ø, a metastable site specific to the prefusion state of the RSV fusion (F) glycoprotein, as this site is targeted by extremely potent RSV-neutralizing antibodies. Structure-based design yielded stabilized versions of RSV F that maintained antigenic site Ø when exposed to extremes of pH, osmolality, and temperature. Six RSV F crystal structures provided atomic-level data on how introduced cysteine residues and filled hydrophobic cavities improved stability. Immunization with site Ø–stabilized variants of RSV F in mice and macaques elicited levels of RSV-specific neutralizing activity many times the protective threshold.

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The emergence of H7N9 viruses: a chance to redefine correlates of protection for influenza virus vaccines

The emergence of H7N9 and development of candidate vaccines against these viruses provides a timely opportunity for the influenza community to re-evaluate the mechanisms of protection and develop novel surrogate markers for pandemic as well as seasonal influenza virus vaccines. We urgently need to conduct detailed kinetic studies of the humoral and cellular immune responses induced after vaccination bearing in mind that correlates of protection may vary with vaccine formulation. The limited number of clinical studies with H7 vaccines has shown evidence of poor immunogenicity and we must seize this opportunity to improve our understanding of immunological mechanisms and correlates of protection.

 
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Topology of viral evolution

Evolution is mediated not only by random mutations over a number of generations (vertical evolution), but also through the mixture of genomic material between individuals of different lineages (horizontal evolution). The standard evolutionary representation, the phylogenetic tree, faithfully represents the former but not the latter scenario. Although many elaborations have been developed to address this issue, there is still no agreed-upon method of incorporating both vertical and horizontal evolution. Here, we present an alternative strategy based on algebraic topology to study evolution. This method extends beyond the limits of a tree to capture directly even complex horizontal exchanges between multiple parental strains, as well as uncover broader reticulate patterns, including the segregation of segments during reassortment.

 
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New HPV vaccine promises to prevent 85% of invasive cervical cancer : OBGYN News

New HPV vaccine promises to prevent 85% of invasive cervical cancer : OBGYN News | Virology and Bioinformatics from Virology.ca | Scoop.it
An investigational 9-valent human papillomavirus vaccine could prevent up to 85% of invasive cervical cancer, according to a spokesman for Merck, the company developing the product.
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Ed Rybicki's curator insight, November 1, 2013 2:42 AM

They added types 31, 33, 45, 52 and 58 - interesting!

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Infection Inception: DNA in virus in virus in amoeba in eye

Infection Inception: DNA in virus in virus in amoeba in eye | Virology and Bioinformatics from Virology.ca | Scoop.it

Earlier this year, a 17-year-old French woman arrived at her ophthalmologist with pain and redness in her left eye. She had been using tap water to dilute the cleaning solution for her contact lenses, and even though they were meant to be replaced every month, she would wear them for three. As a result, the fluid in her contact lens case had become contaminated with three species of bacteria, an amoeba calledAcanthamoeba polyphaga that can caused inflamed eyes.

The mystery of the woman’s inflamed eyes was solved, but Bernard La Scolaand Christelle Desnues looked inside the amoeba, they found more surprises.

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Virus-induced fever might change bacteria from commensal to pathogen

Virus-induced fever might change bacteria from commensal to pathogen | Virology and Bioinformatics from Virology.ca | Scoop.it
How Neisseria changes from a commensal to a pathogen is by avoiding destruction by the immune response, possibly triggered by fever caused by a viral infection.
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Entire human genome gets sequenced for the first time in SA

CAPE TOWN - In a first for Africa, the entire human genome has been broken down and analysed on South African soil.

It comes 10 years after the International Genome Project was completed.

Shareefa Dalvie, a PhD student from the University of Cape Town recently won a competition to work on state-of-the-art sequencing equipment for her research proposal, which could help unlock the answers behind understanding the genetic factors of this disorder.

Ed Rybicki's insight:

Go Stellenbosch...B-)

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United States to approve potent oral drugs for hepatitis C

United States to approve potent oral drugs for hepatitis C | Virology and Bioinformatics from Virology.ca | Scoop.it
Improved treatments offer hope for eradication of viral liver infection.
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Evolution may favor flu mutations that increase mammalian transmissibility

Evolution may favor flu mutations that increase mammalian transmissibility | Virology and Bioinformatics from Virology.ca | Scoop.it
TweetEvolution in avian flu viruses may favor mutations that make the disease more transmissible in mammals, according to a study recently published in Nature Communications.

Via Mel Melendrez-Vallard
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Sandwalk: ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution

Sandwalk: ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution | Virology and Bioinformatics from Virology.ca | Scoop.it
Chris Upton + helpers's insight:

What should be taught about evolution....

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