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What’s the Answer? (BioStar categories) | The OpenHelix Blog

What’s the Answer? (BioStar categories) | The OpenHelix Blog | Virology and Bioinformatics from Virology.ca | Scoop.it
This BioStar tidbit is a bit different.One thing that we haven't addressed since the site moved off the prior platform is that BioStar now has increased...
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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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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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Functional Genomics Approach for the Identification of Human Host Factors Supporting Dengue Viral Propagation - Springer

Functional Genomics Approach for the Identification of Human Host Factors Supporting Dengue Viral Propagation - Springer | Virology and Bioinformatics from Virology.ca | Scoop.it

Dengue virus (DENV) is endemic throughout tropical regions of the world and there are no approved treatments or anti-transmission agents currently available. Consequently, there exists an enormous unmet need to treat the human diseases caused by DENV and block viral transmission by the mosquito vector. RNAi screening represents an efficient method to expand the pool of known host factors that could become viable targets for treatments or provide rationale to consider available drugs as anti-DENV treatments. We developed a high-throughput siRNA-based screening protocol that can identify human DENV host factors. The protocol herein describes the materials and the procedures necessary to screen a human cell line in order to identify genes which are either necessary for or restrict DENV propagation at any stage in the viral life cycle.

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A virus that melts sea stars

A virus that melts sea stars | Virology and Bioinformatics from Virology.ca | Scoop.it
Sea star associated densovirus might be the cause of a lethal disease that melts these marine invertebrates into piles of slime and ossicles.
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The threat of zoonotic diseases

While zoonotic EIDs are a major concern globally, their impact in less developed countries is disproportionately high.
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Canada begins domestic trial of experimental Ebola vaccine

Canada begins domestic trial of experimental Ebola vaccine | Virology and Bioinformatics from Virology.ca | Scoop.it
TORONTO (Reuters) - Canada has launched a clinical trial of an experimental Ebola vaccine developed at its national microbiology laboratory and expects to have the results in early 2015, the government said on Friday.

Via Ed Rybicki
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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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Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza A virus infection - BMC Bioinformatics

Respiratory epithelial cells are the primary target of influenza virus infection in human. However, the molecular mechanisms of airway epithelial cell responses to viral infection are not fully understood. Revealing genome-wide transcriptional and post-transcriptional regulatory relationships can further advance our understanding of this problem, which motivates the development of novel and more efficient computational methods to simultaneously infer the transcriptional and post-transcriptional regulatory networks.
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BMC Research Notes | Abstract | DivA: detection of non-homologous and very divergent regions in protein sequence alignments

Sequence alignments are used to find evidence of homology but sometimes contain regions that are difficult to align which can interfere with the quality of the subsequent analyses. Although it is possible to remove problematic regions manually, this is non-practical in large genome scale studies, and the results suffer from irreproducibility arising from subjectivity. Some automated alignment trimming methods have been developed to remove problematic regions in alignments but these mostly act by removing complete columns or complete sequences from the MSA, discarding a lot of informative sites.
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Scripps Research Institute Scientists Reveal Weak Spots in Ebola’s Defenses

Scripps Research Institute Scientists Reveal Weak Spots in Ebola’s Defenses | Virology and Bioinformatics from Virology.ca | Scoop.it
News Release
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Camels are MERS Reservoirs | The Scientist Magazine®

Camels are MERS Reservoirs | The Scientist Magazine® | Virology and Bioinformatics from Virology.ca | Scoop.it
Researchers have concluded that these animals, known as the “ships of the desert,” can ferry the deadly coronavirus, perhaps infecting people.
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H5N8 Avian Flu Detected in the Netherlands and Britain

H5N8 Avian Flu Detected in the Netherlands and Britain | Virology and Bioinformatics from Virology.ca | Scoop.it
It was not clear if the outbreaks at poultry farms in the two countries were linked, but a British veterinary official said wild birds may have carried the disease.

The authorities ordered the slaughter of 150,000 chickens at the farm. News reports identified the strain as H5N8, which has never been detected in humans, according to the European Center for Disease Control and Prevention in Stockholm, but has been reported in birds in South Korea, China, Japan and, earlier this month, in Germany.

“This highly pathogenic variant of avian influenza is very dangerous for bird life,” the Dutch government said. “The disease can be transmitted from animals to humans.”


Via Ed Rybicki
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Dogs and wild animals can swap parvovirus

Dogs and wild animals can swap parvovirus | Virology and Bioinformatics from Virology.ca | Scoop.it
When canine parvovirus first emerged in 1978, it started a global pandemic that’s thought to have killed hundreds of thousands of dogs.

Via Ed Rybicki
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