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Computational Biology and Chemistry - A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses

Computational Biology and Chemistry - A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses | Virology and Bioinformatics from Virology.ca | Scoop.it

Mutual information (MI) is an approach commonly used to estimate the evolutionary correlation of 2 amino acid sites. Although several MI methods exist, prior to our contribution no systematic method had been developed to assess their performance, or to establish numerical thresholds to detect co-evolving amino acid sites. The current study performed a Markov chain Monte Carlo (MCMC) algorithm on influenza viral sequences to capture their evolutionary characteristics.

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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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Rebecca Schuman: The decline and fall of higher education

Rebecca Schuman: The decline and fall of higher education | Virology and Bioinformatics from Virology.ca | Scoop.it
When the helicopter generation entered university, suddenly everyone needed A’s, and everyone needed to know exactly what needed to be done to get one.
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BMC Bioinformatics | Abstract | jvenn: an interactive Venn diagram viewer

Venn diagrams are commonly used to display list comparison. In biology, they are widely used to show the differences between gene lists originating from different differential analyses, for instance. They thus allow the comparison between different experimental conditions or between different methods. However, when the number of input lists exceeds four, the diagram becomes difficult to read. Alternative layouts and dynamic display features can improve its use and its readability.
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HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers

HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers | Virology and Bioinformatics from Virology.ca | Scoop.it
First pass methods based on BLAST match are commonly used as an initial step to separate the different phylogenetic histories of genes in microbial genomes, and target putative horizontal gene transfer (HGT) events. This will continue to be necessary given the rapid growth of genomic data and the technical difficulties in conducting large-scale explicit phylogenetic analyses. However, these methods often produce misleading results due to their inability to resolve indirect phylogenetic links and their vulnerability to stochastic events.
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Influenza polymerase encoding mRNAs utilize atypical mRNA nuclear export

Influenza is a segmented negative strand RNA virus. Each RNA segment is encapsulated by influenza nucleoprotein and bound by the viral RNA dependent RNA polymerase (RdRP) to form viral ribonucleoproteins responsible for RNA synthesis in the nucleus of the host cell. Influenza transcription results in spliced mRNAs (M2 and NS2), intron-containing mRNAs (M1 and NS1), and intron-less mRNAs (HA, NA, NP, PB1, PB2, and PA), all of which undergo nuclear export into the cytoplasm for translation. Most cellular mRNA nuclear export is Nxf1-mediated, while select mRNAs utilize Crm1.
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Epitope-based approaches to a universal influenza vaccine - J Autoimmun. 2014

Epitope-based approaches to a universal influenza vaccine - J Autoimmun. 2014 | Virology and Bioinformatics from Virology.ca | Scoop.it

The development of vaccines has been one of the most important contributions of immunology to public health to date. Although several infectious diseases have all but vanished thanks to effective vaccines, the most common infectious disease, influenza, still represents a major threat to public health. This is more concerning than ever before in light of potentially virulent avian pandemic strains which have emerged in the last decade and infected human hosts, causing high morbidity and mortality. Despite considerable efforts to improve production of influenza vaccines and vaccinate large portions of the population annually, the currently available influenza vaccines are strain-specific and not effective enough. Considering the vulnerability of infants and elderly to seasonal influenza-related complications and the ever present public health threat of a deadly influenza pandemic, there is urgent need for a new kind of influenza vaccine. Ideally, such a vaccine should provide enhanced long term, multi-strain protection without compromising safety and in this way, dramatically improve global protection against seasonal and pandemic influenza viruses. This review highlights one approach to developing a universal influenza vaccine, which is based on highly conserved viral sequences, 'epitopes', that specifically activate humoral and/or cellular immune responses. This approach to vaccinology was pioneered by Prof Arnon, who initiated development of an epitope-based universal vaccine called Multimeric-001 (M-001), which has already been validated in clinical trials to induce broad immunity against A and B-Type, seasonal and pandemic strains.

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

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 ~2,000x 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 Middle African lineages ~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. Since 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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Scientists found the origins of the Ebola outbreak — by tracking its mutations

Scientists found the origins of the Ebola outbreak — by tracking its mutations | Virology and Bioinformatics from Virology.ca | Scoop.it
Genetic sequences of dozens of Ebola virus samples will provide much needed information for fighting the disease.
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Top 5 bash commands for handling data – Code, Think, Write

Top 5 bash commands for handling data – Code, Think, Write | Virology and Bioinformatics from Virology.ca | Scoop.it
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Scientific method: Statistical errors

Scientific method: Statistical errors | Virology and Bioinformatics from Virology.ca | Scoop.it
P values, the 'gold standard' of statistical validity, are not as reliable as many scientists assume.
Chris Upton + helpers's insight:

Worth repeating...

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Datavu: Useful Unix commands for exploring data

Datavu: Useful Unix commands for exploring data | Virology and Bioinformatics from Virology.ca | Scoop.it
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The EMPRES-i genetic module: a novel tool linking epidemiological outbreak information and genetic characteristics of influenza viruses

Combining epidemiological information, genetic characterization and geomapping in the analysis of influenza can contribute to a better understanding and description of influenza epidemiology and ecology, including possible virus reassortment events. Furthermore, integration of information such as agroecological farming system characteristics can provide new knowledge on risk factors of influenza emergence and spread. Integrating viral characteristics into an animal disease information system is therefore expected to provide a unique tool to trace-and-track particular virus strains; generate clade distributions and spatiotemporal clusters; screen for distribution of viruses with specific molecular markers; identify potential risk factors; and analyze or map viral characteristics related to vaccines used for control and/or prevention. For this purpose, a genetic module was developed within EMPRES-i (FAO’s global animal disease information system) linking epidemiological information from influenza events with virus characteristics and enabling combined analysis. An algorithm was developed to act as the interface between EMPRES-i disease event data and publicly available influenza virus sequences in OpenfluDB. This algorithm automatically computes potential links between outbreak event and sequences, which are subsequently manually validated by experts. Subsequently, other virus characteristics such as antiviral resistance can then be associated to outbreak data. To visualize such characteristics on a geographic map, shape files with virus characteristics to overlay on other EMPRES-i map layers (e.g. animal densities) can be generated. The genetic module allows export of associated epidemiological and sequence data for further analysis. FAO has made this tool available for scientists and policy makers. Contributions are expected from users to improve and validate the number of linked influenza events and isolate information as well as the quality of information. Possibilities to interconnect with other influenza sequence databases or to expand the genetic module to other viral diseases (e.g. foot and mouth disease) are being explored.

Database OpenfluDB URL: http://openflu.vital-it.ch

Database EMPRES-i URL: http://EMPRES-i.fao.org/

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Engineered plant virus resistance

Abstract

Virus diseases are among the key limiting factors that cause significant yield loss and continuously threaten crop production. Resistant cultivars coupled with pesticide application are commonly used to circumvent these threats. One of the limitations of the reliance on resistant cultivars is the inevitable breakdown of resistance due to the multitude of variable virus populations. Similarly, chemical applications to control virus transmitting insect vectors are costly to the farmers, cause adverse health and environmental consequences, and often result in the emergence of resistant vector strains. Thus, exploiting strategies that provide durable and broad-spectrum resistance over diverse environments are of paramount importance.

The development of plant gene transfer systems has allowed for the introgression of alien genes into plant genomes for novel disease control strategies, thus providing a mechanism for broadening the genetic resources available to plant breeders. Genetic engineering offers various options for introducing transgenic virus resistance into crop plants to provide a wide range of resistance to viral pathogens. This review examines the current strategies of developing virus resistant transgenic plants.

KeywordsBroad-spectrum resistance;Transgenic plants;Plant viruses;Gene silencing;Agrobacterium;Plant biotechnology


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Rabenstein, Frank's comment, August 28, 8:44 AM
Chris Upton and helpers, thank you rescooping
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Buying in to bioinformatics: an introduction to commercial sequence analysis software

Buying in to bioinformatics: an introduction to commercial sequence analysis software | Virology and Bioinformatics from Virology.ca | Scoop.it
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BMC Bioinformatics | Abstract | AliGROOVE -- visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support

Masking of multiple sequence alignment blocks has become a powerful method to enhance the
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New EBOV outbreak in DRC | epidemic

New EBOV outbreak in DRC | epidemic | Virology and Bioinformatics from Virology.ca | Scoop.it
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Genomic Characterization of a Circovirus Associated with Fatal Hemorrhagic Enteritis in Dog, Italy

Genomic Characterization of a Circovirus Associated with Fatal Hemorrhagic Enteritis in Dog, Italy | Virology and Bioinformatics from Virology.ca | Scoop.it

Dog circovirus (DogCV) was identified in an outbreak of enteritis in pups in Italy. The disease was observed in 6 young dachshunds pups of a litter from a breeding kennel and caused the death of 2 dogs. Upon full-genome analysis, the virus detected in one of the dead pups (strain Bari/411–13) was closely related to DogCVs that have been recently isolated in the USA. The present study, if corroborated by further reports, could represent a useful contribution to the knowledge of the pathogenic potential of DogCV and its association with enteritis in dogs.

 
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Improved reproducibility by assuring confidence in measurements in biomedical research : Nature Methods

'Irreproducibility' is symptomatic of a broader challenge in measurement in biomedical research. From the US National Institute of Standards and Technology (NIST) perspective of rigorous metrology, reproducibility is only one aspect of establishing confidence in measurements. Appropriate controls, reference materials, statistics and informatics are required for a robust measurement process. Research is required to establish these tools for biological measurements, which will lead to greater confidence in research results.
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Ebola Outbreak Strains Sequenced | The Scientist Magazine®

Ebola Outbreak Strains Sequenced | The Scientist Magazine® | Virology and Bioinformatics from Virology.ca | Scoop.it
Ninety-nine publicly available genomes could help researchers working to develop diagnostics, vaccines, and therapies. 
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Ed Rybicki's curator insight, August 31, 11:05 AM

99 Ebola genomes, out in cyberspace

99 Ebola genomes, out in cyberspace

And if one Ebola genome

Should accidentally mutate

There'd be...potentially one very frightening Ebola!

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Seals May Have Carried Tuberculosis To The New World – Phenomena: Not Exactly Rocket Science

Seals May Have Carried Tuberculosis To The New World – Phenomena: Not Exactly Rocket Science | Virology and Bioinformatics from Virology.ca | Scoop.it
Very few people suspected the seals. Kirsten Bos from the University of Tubingen certainly didn’t when she and her colleagues started studying three Peruvian skeletons. They were just trying to und...
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Genomes reveal start of Ebola outbreak

Jung Choi's insight:

An invaluable resource that cost the lives of 5 of the authors of the paper.

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Microbial impacts on insect evolutionary diversification: from patterns to mechanisms

Microbial impacts on insect evolutionary diversification: from patterns to mechanisms | Virology and Bioinformatics from Virology.ca | Scoop.it
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Immuno-PCR: molecular and Immunological techniques combined in DNA amplification

Immuno-PCR: molecular and Immunological techniques combined in DNA amplification | Virology and Bioinformatics from Virology.ca | Scoop.it
Introduction Since the first immunoassays were developed in the 1950's the variety of assay formats has increased dramatically.

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Alfredo Corell's curator insight, September 22, 2013 2:29 PM

This new method, termed immuno-polymerase chain reaction (immuno-PCR), benefits from the specificity of antibodies and the sensitivity of PCR. Several independent studies undertaken since the publication of this seminal paper have consistently demonstrated the advantages of this technique over traditional ELISA, some achieving more than a 50,000 fold increase in sensitivity over the equivalent immunoassay [2]. Furthermore, immuno-PCR can be used in a multiplex format and offers accurate quantitation.

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Tobacco-derived 'plantibodies' enter the fight against Ebola

Tobacco-derived 'plantibodies' enter the fight against Ebola | Virology and Bioinformatics from Virology.ca | Scoop.it
NEW YORK (Reuters) - Drugmakers' use of the tobacco plant as a fast and cheap way to produce novel biotechnology treatments is gaining global attention because of its role in an experimental Ebola therapy.The

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Ed Rybicki's curator insight, August 27, 2:20 AM

Nice account of ZMapp and some of the science behind it.

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Lecturer/Senior Lecturer (Level B/C) in Bioinformatics

Lecturer/Senior Lecturer (Level B/C) in Bioinformatics | Virology and Bioinformatics from Virology.ca | Scoop.it
Lecturer/Senior Lecturer (Level B/C) in Synthetic Biology, Research Fellow (Level B) in Synthetic Biology & Lecturer/Senior Lecturer (Level B/C) in Bioinformatics Apply now Job no: 494553 Work type: Continuing full time Vacancy type: External...

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[2013.12.02] Mads Albertsen: Extracting Genomes from Metagenomes

Invited lecture at University of Vienna on extracting genomes from metagenomes.

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