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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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Pakistan: Over 450 parents held for refusing polio drops

Via The Express Tribune: At their peril: Over 450 parents held for refusing polio drops. Excerpt: The Khyber-Pakhtunkhwa government proved its determination to eradicate polio by arresting 471 parents who refused vaccine for their children, while authorities have also hired...
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Estimating the Life Course of Influenza A(H3N2) Antibody Responses ... - PubMed - NCBI

Abstract

The immunity of a host population against specific influenza A strains can influence a number of important biological processes, from the emergence of new virus strains to the effectiveness of vaccination programmes. However, the development of an individual's long-lived antibody response to influenza A over the course of a lifetime remains poorly understood. Accurately describing this immunological process requires a fundamental understanding of how the mechanisms of boosting and cross-reactivity respond to repeated infections. Establishing the contribution of such mechanisms to antibody titres remains challenging because the aggregate effect of immune responses over a lifetime are rarely observed directly. To uncover the aggregate effect of multiple influenza infections, we developed a mechanistic model capturing both past infections and subsequent antibody responses. We estimated parameters of the model using cross-sectional antibody titres to nine different strains spanning 40 years of circulation of influenza A(H3N2) in southern China. We found that "antigenic seniority" and quickly decaying cross-reactivity were important components of the immune response, suggesting that the order in which individuals were infected with influenza strains shaped observed neutralisation titres to a particular virus. We also obtained estimates of the frequency and age distribution of influenza infection, which indicate that although infections became less frequent as individuals progressed through childhood and young adulthood, they occurred at similar rates for individuals above age 30 y. By establishing what are likely to be important mechanisms driving epochal trends in population immunity, we also identified key directions for future studies. In particular, our results highlight the need for longitudinal samples that are tested against multiple historical strains. This could lead to a better understanding of how, over the course of a lifetime, fast, transient antibody dynamics combine with the longer-term immune responses considered here

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Phylogenomic analyses data of the avian phylogenomics project

Background:
Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology.

Via Mel Melendrez-Vallard
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Deadly bacteria, "Burkholderia pseudomallei" released from US high-security lab

Deadly bacteria, "Burkholderia pseudomallei" released from US high-security lab | Virology and Bioinformatics from Virology.ca | Scoop.it
Deadly bacteria, "Burkholderia pseudomallei" released from US high-security lab. Officials are investigating how a deadly type of bacteria was released from a high-security laboratory at the Tulane National Primate Center in Louisiana.
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Doctors curse up a storm to get parents to vaccinate

Doctors curse up a storm to get parents to vaccinate | Virology and Bioinformatics from Virology.ca | Scoop.it
Jimmy Kimmel delivered a takedown against anti-vaxxers on Thursday's show and topped it off with a PSA featuring real doctors who are so mad they made the spot into a bleep-fest. 
"I cannot f—king believe we have to make this PSA," said one doctor, while others complained they had to spend their day off making the video instead of binging Breaking Bad.

Via Ed Rybicki
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Ed Rybicki's curator insight, March 2, 7:45 AM

Fuckin' right!

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IVA: accurate de novo assembly of RNA virus genomes

Motivation: An accurate genome assembly from short read sequencing data is critical for downstream analysis, for example allowing investigation of variants within a sequenced population. However, assembling sequencing data from virus samples, especially RNA viruses, into a genome sequence is challenging due to the combination of viral population diversity and extremely uneven read depth caused by amplification bias in the inevitable reverse transcription and PCR amplification process of current methods.

Results: We developed IVA (Iterative Virus Assembler), a de novoassembler designed specifically for read pairs sequenced at highly variable depth from RNA virus samples. We tested IVA on datasets from 140 sequenced samples from HIV-1 or Influenza virus infected people and demonstrated that IVA outperforms all other virus de novo assemblers.

Availability: The software runs under Linux, has the GPLv3 licence and is freely available from http://sanger-pathogens.github.io/iva

Contact: iva@sanger.ac.uk

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Battling Infectious Diseases in the 20th Century: The Impact of Vaccines

Battling Infectious Diseases in the 20th Century: The Impact of Vaccines | Virology and Bioinformatics from Virology.ca | Scoop.it
The number of infected people, measured over 70-some years and across all 50 states and the District of Columbia, generally declined after vaccines were introduced.
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Vaccines work....

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Is Obesity Contagious? | Viruses101 | Learn Science at Scitable

Is Obesity Contagious? | Viruses101 | Learn Science at Scitable | Virology and Bioinformatics from Virology.ca | Scoop.it
Obesity is a growing problem in the United States. More than a third of all adults in the United States and seventeen percent of children from the ages of two to nineteen are obese according to the Center for Disease Control. A study published in the journal Pediatrics and conducted by two pediatric gastroenterologists from California, led by Dr.
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Phosphatidylserine Vesicles Enable Efficient En Bloc Transmission of Enteroviruses: Cell

Phosphatidylserine Vesicles Enable Efficient En Bloc Transmission of Enteroviruses: Cell | Virology and Bioinformatics from Virology.ca | Scoop.it
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Measles death in Germany prompts calls for mandatory vaccinations

Measles death in Germany prompts calls for mandatory vaccinations | Virology and Bioinformatics from Virology.ca | Scoop.it
Death of 18-month-old boy is the first fatality among 574 reported cases in the country’s worst measles outbreak in more than a decade
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Man's death leads to discovery of new virus in Kansas, CDC reports - CNN.com

The CDC has discovered a new virus, likely spread by tick bites, that may have contributed to a Kansas man's death, the agency said Friday.
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Evolution of Genome Size and Complexity in the Rhabdoviridae

Evolution of Genome Size and Complexity in the  Rhabdoviridae | Virology and Bioinformatics from Virology.ca | Scoop.it
Author Summary Understanding the patterns and mechanisms of genome evolution is one of the most important, yet least understood, aspects of RNA virus biology. The evolutionary challenge faced by RNA viruses is to maximize functional diversity within severe constraints on genome size. Here we show that rhabdoviruses, a family of RNA viruses that infect hosts as diverse as plants, insects and vertebrates, have an unusual capacity for genomic plasticity. By analysing the complete or near-complet
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BMC Genomics | Abstract | RNASeqBrowser: A genome browser for simultaneous visualization of raw strand specific RNAseq reads and UCSC genome browser custom tracks

Strand specific RNAseq data is now more common in RNAseq projects. Visualizing RNAseq data has become an important matter in Analysis of sequencing data. The most widely used visualization tool is the UCSC genome browser that introduced the custom track concept that enabled researchers to simultaneously visualize gene expression at a particular locus from multiple experiments. Our objective of the software tool is to provide friendly interface for visualization of RNAseq datasets.
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Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley

Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley | Virology and Bioinformatics from Virology.ca | Scoop.it

Summary

The microbial communities inhabiting the root interior of healthy plants, as well as the rhizosphere, which consists of soil particles firmly attached to roots, engage in symbiotic associations with their host. To investigate the structural and functional diversification among these communities, we employed a combination of 16S rRNA gene profiling and shotgun metagenome analysis of the microbiota associated with wild and domesticated accessions of barley (Hordeum vulgare). Bacterial families Comamonadaceae, Flavobacteriaceae, and Rhizobiaceae dominate the barley root-enriched microbiota. Host genotype has a small, but significant, effect on the diversity of root-associated bacterial communities, possibly representing a footprint of barley domestication. Traits related to pathogenesis, secretion, phage interactions, and nutrient mobilization are enriched in the barley root-associated microbiota. Strikingly, protein families assigned to these same traits showed evidence of positive selection. Our results indicate that the combined action of microbe-microbe and host-microbe interactions drives microbiota differentiation at the root-soil interface.

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▶ Jimmy Kimmel's Update on the Anti-Vaccination Discussion - YouTube

Last week on the show we got a group of real doctors together to do a public service announcement urging parents to vaccinate their kids. While a lot of peop...
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Strange medicine

Strange medicine | Virology and Bioinformatics from Virology.ca | Scoop.it
Set phages to “kill” SET a thief to catch a thief is an old proverb. In the 1920s, shortly after the discovery of viruses, it was put to good use by doctors....
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In 2013, measles killed more kids than car accidents or AIDS

In 2013, measles killed more kids than car accidents or AIDS | Virology and Bioinformatics from Virology.ca | Scoop.it
Measles was one of the top killers of children in 2013.

Measles killed 82,100 children under age 5 in 2013, ranking the disease at No. 7 on the list of the top causes of child death, according to recent statistics from the Global Burden of Disease study published in the Lancet. Lower respiratory infections like pneumonia were the number one killer, followed by malaria, diarrhea, nutritional deficiencies, congenital defects and meningitis. More small children died from measles in 2013 than died from drowning, road injuries or aids.

 


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100 years of phage: Phage Art by Anthony Weeks

100 years of phage: Phage Art by Anthony Weeks | Virology and Bioinformatics from Virology.ca | Scoop.it

Very pretty - and a good graphic history, too!


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EpiToolKit – A Web-based Workbench for Vaccine Design

Summary: EpiToolKit is a virtual workbench for immunological questions with a focus on vaccine design. It offers an array of immunoinformatics tools covering MHC genotyping, epitope and neo-epitope prediction, epitope selection for vaccine design, and epitope assembly. In its recently re-implemented version 2.0, EpiToolKit provides a range of new functionality and for the first time allows combining tools into complex workflows. For inexperienced users it offers simplified interfaces to guide the users through the analysis of complex immunological data sets.

Availability: http://www.epitoolkit.de

Contact: schubert@informatik.uni-tuebingen.de

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Context similarity scoring improves protein sequence alignments in the midnight zone

Context similarity scoring improves protein sequence alignments in the midnight zone | Virology and Bioinformatics from Virology.ca | Scoop.it
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Amid measles outbreaks, WHO calls for more vaccinations in Europe

Amid measles outbreaks, WHO calls for more vaccinations in Europe | Virology and Bioinformatics from Virology.ca | Scoop.it
UN agency has recorded 22,000 cases of the highly infectious disease since the start of 2014
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Man’s death leads to the discovery of a new virus

Man’s death leads to the discovery of a new virus | Virology and Bioinformatics from Virology.ca | Scoop.it
Scientists have described a previously unknown insect-borne virus, following the death of a man in the Kansas county of Bourbon in the US in mid-2014.

According to the US Centres for Disease Control and Prevention (CDC), the otherwise healthy, 50-year-old man was working outside on his property in mid-2014, when he sustained multiple tick bites, which led to an array of symptoms including fever, fatigue, rash, headaches, nausea and vomiting around two days after. After he was hospitalised, his white blood cell count dipped, his lungs and kidney started failing, and by day 11, suffered a heart attack, and died.

The culprit? Scientists were able to isolate a new virus from a blood sample collected from the patient nine days after he fell ill, and attributed it to the Thogotovirus genus in the virus family Orthomyxoviridae. This family contains six genera - Influenza virus A, Influenza virus B, Influenza virus C, Isavirus, Thogotovirus and Quaranjavirus.

The researchers say there’s a marked difference between the symptoms suffered by this man, and other known Thogotoviruses. As Liz Szabo reports at USA Today, Thogotoviruses usually cause diseases such as meningitis or encephalitis, where the lining of the brain becomes severely inflamed. But they've never seen these viruses destroy white blood cell counts like the Bourbon virus did to this man.

The team discusses this in the current edition of the CDC journal, Emerging Infectious Diseases: "Of the seven symptomatic human infections that have been associated with viruses in the genus Thogotovirus, most case-patients have had neurologic findings (e.g., meningitis, encephalitis) without any described abnormalities in blood counts. Although cerebrospinal fluid was not tested for the patient reported, his clinical signs and symptoms were not suggestive of neurologic infection. Furthermore, the patient did not have any respiratory symptoms that would be expected with other viruses that are known human pathogens in the large family of Orthomyxoviridae, such as influenza virus."

As of this month, this man is the only case of Bourbon virus disease that has been identified, but there are likely more cases that have yet to be diagnosed. “I think we have to assume this has been around for some time, and we haven’t been able to diagnose it,” Dana Hawkinson, an infectious disease specialist who treated the patient at the University of Kansas Medical Centre in Kansas City, told Denise Grady at The New York Times. “We suspect there have been milder cases and people have recovered from them, but we don’t have a lot of information.”

"It will be important to determine how widespread the Bourbon virus is in both ticks, insects, animals and humans and to grasp the spectrum of illness it is capable of causing," Amesh Adalja, senior associate at the Centre for Health Security at the University of Pittsburgh Medical Centre in the US, told USA Today. "The fact that a novel virus was discovered underscores the need for perpetual vigilance, in all locales, with respect to emerging infectious diseases. It is only by leaving no stone unturned when investigating unexplained illnesses that humans can best prepare for microbial threats."

The researchers report that right now, there is no treatment for the disease, no vaccine, and no lab tests to identify it. So those in the US at a high risk of tick bites are advised to wear insect repellents and long-sleeved shirts and pants when outdoors, and to avoid thickly wooded areas as much as possible.
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Virus-cutting enzyme helps bacteria remember a threat

Virus-cutting enzyme helps bacteria remember a threat | Virology and Bioinformatics from Virology.ca | Scoop.it

Bacteria may not have brains, but they do have memories, at least when it comes to viruses that attack them. Many bacteria have a molecular immune system which allows these microbes to capture and retain pieces of viral DNA that they have encountered in the past, in order to recognize and destroy it when it shows up again.


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Influenza Virus Reservoirs and Intermediate Hosts: Dogs, Horses, and New Possibilities for Influenza Virus Exposure of Humans

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Latest updates on today's emerging viruses of pandemic potential

The online version of Microbes and Infection at ScienceDirect.com, the world's leading platform for high quality peer-reviewed full-text journals.

Via Ed Rybicki
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Ed Rybicki's curator insight, February 20, 7:14 AM

Useful resource, and nice material on Ebola in particular.