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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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Bacterial Microbiome Move Over: the Gut Virome Makes Its Debut

Bacterial Microbiome Move Over: the Gut Virome Makes Its Debut | Virology and Bioinformatics from Virology.ca | Scoop.it
Just as commensal bacteria have been found to contribute to health, new data from mice have suggested that commensal viruses may help form and heal the gastrointestinal tract.
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H5N1: The strange tale of Canada’s Ebola vaccine

H5N1: The strange tale of Canada’s Ebola vaccine | Virology and Bioinformatics from Virology.ca | Scoop.it
Via The Star, a column by Thomas Walkom: The strange tale of Canada’s ebola vaccine. Excerpt: The strange case of Canada’s Ebola vaccine became even stranger Monday. That’s when the pharmaceutical multinational Merck announced it will pay $50 million for...
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#Wikipedia needs your $. Make your donation now

#Wikipedia needs your $. Make your donation now | Virology and Bioinformatics from Virology.ca | Scoop.it
Chris Upton + helpers's insight:

This is one cause, I don't complain about supporting.

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Visualization of protein sequence features using JavaScript and SVG with pViz.js

Visualization of protein sequence features using JavaScript and SVG with pViz.js | Virology and Bioinformatics from Virology.ca | Scoop.it
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Five ingredients to become a bioinformatician. - atcgeek

Five ingredients to become a bioinformatician. - atcgeek | Virology and Bioinformatics from Virology.ca | Scoop.it
How to become a bioinformatician? Many people, at different career stages, are trying to answer this question, looking for the best path to achieve the required knowledge to become a bioinformatician. Many academic institutions are provided with Bionformatics degrees at undergraduate and postgraduate level, and you can easily find free courses on the internet to get a […
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Mutation increases risk of infections

Mutation increases risk of infections | Virology and Bioinformatics from Virology.ca | Scoop.it
A pattern of genetic mutation has been found in avian flu that leads to a higher possibility of infections and diseases in humans....
Hannah Davis's insight:

Nature Communications paper can be found here:

http://www.nature.com/ncomms/2014/141120/ncomms6509/abs/ncomms6509.html

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Taking More Than One Vaccine at a Time Doesn't Hurt!

Taking More Than One Vaccine at a Time Doesn't Hurt! | Virology and Bioinformatics from Virology.ca | Scoop.it
The specific antigens given in vaccines represent only a small portion of the daily stimuli the immune system has to deal with.

Via Ed Rybicki
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Ed Rybicki's curator insight, November 21, 10:13 AM

ANYONE who has done some immunology could tell you that - but there are distressingly few of us...B-(

Erik Carter's comment, November 21, 10:52 AM
However, while it's not dangerous to give multiple vaccines at once, it can prove detrimental to the development of a good immune response. I used to work in a viral immunology lab that looked at heterologous immunity as well as simultaneous infections. If you're interested, look into Liisa Selin's research as UMass Medical School. It's very interesting, and a lot of fun to do.
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First complete view of flu virus' key machine revealed

First complete view of flu virus' key machine revealed | Virology and Bioinformatics from Virology.ca | Scoop.it
Washington, Nov 21 (ANI): A new research has come up with the first complete structure of one of the flu virus' key machines i.e. polymerase.
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Have Homeopaths Reached Peak Stupid?

Have Homeopaths Reached Peak Stupid? | Virology and Bioinformatics from Virology.ca | Scoop.it
Remove hot drinks and sharp objects from your immediate vicinity. Across the world, homeopaths today are trying to 'heal the oceans'. To do so, British homeopath, Grace DaSilva-Hill, has been writi...
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Giant viruses as you’ve never seen them before!

Giant viruses as you’ve never seen them before! | Virology and Bioinformatics from Virology.ca | Scoop.it

In this special issue of Virology, we highlight some of the stories that were presented during the 1st International Symposium on Giant Virus Biology.

The 25 presentations covered a wide range of topics, from biochemistry to genomics, from virus structure and assembly to ecological and evolutionary questions.

Here are just a few of the articles from the special issue:

Editorial introduction to “Giant Viruses” special issue of VirologyInfection cycles of large DNA viruses: Emerging themes and underlying questionsRevisiting the genome packaging in viruses with lessons from the “Giants”The expanding family MarseilleviridaeOrigin of giant viruses from smaller DNA viruses not from a fourth domain of cellular life

We are delighted to make these articles and all papers from the Virology Special Issue on Giant Virusesfreely available online.

Ed Rybicki's insight:

Excellent! And some day - soon, Flavia! - we will be contributing our own bricks to the emerging structure of Girology B-)

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Charting the life-course epidemiology of influenza

Interaction between the human immune system and influenza virus is predominantly driven by antigenic drift. In this process, ongoing mutation of the virus slowly changes its antigenic signature, eventually allowing the virus to infect people with immunity to earlier versions of the virus. Along with antigenic shifts, through which extreme changes in influenza A lead to pandemics (most often when genes from two or more different strains of influenza reassort to form a new subtype), antigenic drift is the dominant driver of influenza epidemiology. One of the most important results of antigenic drift is the need to periodically reformulate and annually administer influenza vaccine. On page 996 of this issue, Fonville et al. (1) use a technique called “antibody landscapes” to characterize antibody protection from the full spectrum of influenza strains, illuminating the interaction between new influenza exposures and past immunity
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Structural insight into cap-snatching and RNA synthesis by influenza polymerase : Nature

Structural insight into cap-snatching and RNA synthesis by influenza polymerase : Nature | Virology and Bioinformatics from Virology.ca | Scoop.it

Influenza virus polymerase uses a capped primer, derived by ‘cap-snatching’ from host pre-messenger RNA, to transcribe its RNA genome into mRNA and a stuttering mechanism to generate the poly(A) tail. By contrast, genome replication is unprimed and generates exact full-length copies of the template. Here we use crystal structures of bat influenza A and human influenza B polymerases (FluA and FluB), bound to the viral RNA promoter, to give mechanistic insight into these distinct processes. In the FluA structure, a loop analogous to the priming loop of flavivirus polymerases suggests that influenza could initiate unprimed template replication by a similar mechanism. Comparing the FluA and FluB structures suggests that cap-snatching involves in siturotation of the PB2 cap-binding domain to direct the capped primer first towards the endonuclease and then into the polymerase active site. The polymerase probably undergoes considerable conformational changes to convert the observed pre-initiation state into the active initiation and elongation states.

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Cows with human chromosomes enlisted to fight hantavirus

Cows with human chromosomes enlisted to fight hantavirus | Virology and Bioinformatics from Virology.ca | Scoop.it
Researchers have genetically engineered cows to produce human antibodies against the deadly hantavirus and possibly other diseases
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African Bats: Conservation in the Time of Ebola

African Bats: Conservation in the Time of Ebola | Virology and Bioinformatics from Virology.ca | Scoop.it
A guest post by Jen Guyton The last fragile wing finally came free from the threads of my mist net. I sank into the sand on the riverbank, took a deep breath, and tugged off my yellow deerskin glov...
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How ZMapp antibodies bind to Ebola virus

How ZMapp antibodies bind to Ebola virus | Virology and Bioinformatics from Virology.ca | Scoop.it
The structure of the antibodies in ZMapp bound to the Ebola virus glycoprotein reveal how they inhibit infection and how ZMapp might be improved.
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PyBamView: a browser-based application for viewing short read alignments

PyBamView: a browser-based application for viewing short read alignments | Virology and Bioinformatics from Virology.ca | Scoop.it
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Royal Jubilee lab takes big step forward with new microbiology technology - Saanich News

Royal Jubilee lab takes big step forward with new microbiology technology - Saanich News | Virology and Bioinformatics from Virology.ca | Scoop.it

The accuracy of the new robotic system is now 100 per cent for every single specimen

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Small Things Considered: Why CRISPR Doesn't Work in E. coli

Small Things Considered: Why CRISPR Doesn't Work in E. coli | Virology and Bioinformatics from Virology.ca | Scoop.it
by Elio | We received this query: »I enjoyed the article on your blog 'Six Questions About CRISPRs' by Merry Youle. I am an ex-lambdologist, having quit phage lambda in the early 70s and moved to GM-plants. There is one thing about CRISPR that I do not understand: Why did lambdologists not find CRISPR?
They found phage...
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101 questions with a bioinformatician #18: Richard Emes

101 questions with a bioinformatician #18: Richard Emes | Virology and Bioinformatics from Virology.ca | Scoop.it
Richard Emes is an Associate Professor and Reader in Bioinformatics at The
University of Nottingham. He is also the Director of the University's
Advanced Data Analysis Centre (ADAC).
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Teaching Bioinformatics in Concert

Teaching Bioinformatics in Concert | Virology and Bioinformatics from Virology.ca | Scoop.it

Can biology students without programming skills solve problems that require computational solutions? They can if they learn to cooperate effectively with computer science students. The goal of the in-concert teaching approach is to introduce biology students to computational thinking by engaging them in collaborative projects structured around the software development process. Our approach emphasizes development of interdisciplinary communication and collaboration skills for both life science and computer science students.

 
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PSU biologists discover HIV-like virus

PSU biologists discover HIV-like virus | Virology and Bioinformatics from Virology.ca | Scoop.it
It lives in volcanic hot springs, and studying it will give researchers a better understanding of how to treat the disease.

Via Ed Rybicki
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Ed Rybicki's curator insight, November 21, 10:06 AM

Yah, Sure. Sure it will...as my good wife, sitting here beside me says, "Why wouldn't you just study HIV? Or SIV? Or another lentivirus??"

Seriously: just like any breakthrough in crystallography of virus proteins "will lead to better vaccines!".

Maybe. If we're lucky.  Meanwhile, this is just another of Science By Hype.

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You catch what you eat: Viral metagenomics of US store bought beef, pork, and chicken

You catch what you eat: Viral metagenomics of US store bought beef, pork, and chicken | Virology and Bioinformatics from Virology.ca | Scoop.it
Wen Zhang, Linlin Li, Xutao Deng, Beatrix Kapusinszky, Eric Delwart

We describe here the metagenomics-derived viral sequences detected in beef, pork, and chicken purchased from stores in San Francisco. In beef we detected four previously reported viruses (two parvoviruses belonging to different genera, an anellovirus, and one circovirus-like virus) and one novel bovine polyomavirus species (BPyV2-SF) whose closest relatives infect primates. Detection of porcine hokovirus in beef indicated that this parvovirus can infect both ungulate species. In pork we detected four known parvoviruses from three genera, an anellovirus, and pig circovirus 2. Chicken meat contained numerous gyrovirus sequences including those of chicken anemia virus and of a novel gyrovirus species (GyV7-SF). Our results provide an initial characterization of some of the viruses commonly found in US store-bought meats which included a diverse group of parvoviruses and viral families with small circular DNA genomes. Whether any of these viruses can infect humans will require testing human sera for specific antibodies.

 

Ed Rybicki's insight:

Being a vegetarian suddenly seems attractive B-)

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Antibody landscapes after influenza virus infection or vaccination

We introduce the antibody landscape, a method for the quantitative analysis of antibody-mediated immunity to antigenically variable pathogens, achieved by accounting for antigenic variation among pathogen strains. We generated antibody landscapes to study immune profiles covering 43 years of influenza A/H3N2 virus evolution for 69 individuals monitored for infection over 6 years and for 225 individuals pre- and postvaccination. Upon infection and vaccination, titers increased broadly, including previously encountered viruses far beyond the extent of cross-reactivity observed after a primary infection. We explored implications for vaccination and found that the use of an antigenically advanced virus had the dual benefit of inducing antibodies against both advanced and previous antigenic clusters. These results indicate that preemptive vaccine updates may improve influenza vaccine efficacy in previously exposed individuals.

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Structure of influenza A polymerase bound to the viral RNA promoter : Nature

The influenza virus polymerase transcribes or replicates the segmented RNA genome (viral RNA) into viral messenger RNA or full-length copies. To initiate RNA synthesis, the polymerase binds to the conserved 3′ and 5′ extremities of the viral RNA. Here we present the crystal structure of the heterotrimeric bat influenza A polymerase, comprising subunits PA, PB1 and PB2, bound to its viral RNA promoter. PB1 contains a canonical RNA polymerase fold that is stabilized by large interfaces with PA and PB2. The PA endonuclease and the PB2 cap-binding domain, involved in transcription by cap-snatching, form protrusions facing each other across a solvent channel. The 5′ extremity of the promoter folds into a compact hook that is bound in a pocket formed by PB1 and PA close to the polymerase active site. This structure lays the basis for an atomic-level mechanistic understanding of the many functions of influenza polymerase, and opens new opportunities for anti-influenza drug design.

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