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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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BlaSTorage: a fast package to parse, manage and store BLAST results

BlaSTorage: a fast package to parse, manage and store BLAST results | Virology and Bioinformatics from Virology.ca | Scoop.it
Background

Large-scale sequence studies requiring BLAST-based analysis produce huge amounts of data to be parsed. BLAST parsers are available, but they are often missing some important features, such as keeping all information from the raw BLAST output, allowing direct access to single results, and performing logical operations over them.

Findings

We implemented BlaSTorage, a Python package that parses multi BLAST results and returns them in a purpose-built object-database format. Unlike other BLAST parsers, BlaSTorage retains and stores all parts of BLAST results, including alignments, without loss of information; a complete API allows access to all the data components.

Conclusions

BlaSTorage shows comparable speed of more basic parser written in compiled languages as C++ and can be easily integrated into web applications or software pipelines.

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Rice-based oral antibody fragment prophylaxis and therapy against rotavirus infection

Rice-based oral antibody fragment prophylaxis and therapy against rotavirus infection | Virology and Bioinformatics from Virology.ca | Scoop.it

Rotavirus-induced diarrhea is a life-threatening disease in immunocompromised individuals and in children in developing countries. We have developed a system for prophylaxis and therapy against rotavirus disease using transgenic rice expressing the neutralizing variable domain of a rotavirus-specific llama heavy-chain antibody fragment (MucoRice-ARP1). MucoRice-ARP1 was produced at high levels in rice seeds using an overexpression system and RNAi technology to suppress the production of major rice endogenous storage proteins. Orally administered MucoRice-ARP1 markedly decreased the viral load in immunocompetent and immunodeficient mice. The antibody retained in vitro neutralizing activity after long-term storage (>1 yr) and boiling and conferred protection in mice even after heat treatment at 94°C for 30 minutes. High-yield, water-soluble, and purification-free MucoRice-ARP1 thus forms the basis for orally administered prophylaxis and therapy against rotavirus infections.

 Rotavirus graphic courtesy of Russell Kightley Media

Ed Rybicki's insight:

Going Green - increasingly, the sensible thing to do.

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Parasitic worm genome uncovers potential drug targets

Parasitic worm genome uncovers potential drug targets | Virology and Bioinformatics from Virology.ca | Scoop.it
Researchers have identified five enzymes that are essential to the survival of a parasitic worm that infects livestock worldwide and is a great threat to global food security.
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World Environment News - Measles-like virus may be cause of dolphin deaths on U.S. coast - Planet Ark

World Environment News - Measles-like virus may be cause of dolphin deaths on U.S. coast - Planet Ark | Virology and Bioinformatics from Virology.ca | Scoop.it
A measles-like virus that suppresses the immune system could be the reason an extraordinary number of bottlenose dolphins have died after becoming stranded along the U.S. East Coast, a panel of dolphin experts said on Tuesday.

Via Gaye Rosier
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Synergistic effects of sequential infection with highly pathogenic porcine reproductive and respiratory syndrome virus and porcine circovirus type 2

Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of porcine reproductive and respiratory syndrome (PRRS) and porcine circovirus type 2 (PCV2) is associated with postweaning multisystemic wasting syndrome (PMWS) in pigs. Coinfection with highly pathogenic PRRSV (HP-PRRSV) and PCV2 in the field has recently become extensive in some Asian countries. A synergistic pathogenicity between PRRSV and PCV2 infections has previously been reported. However, the consequences of the sequential infection of pigs with these two viruses are unknown.

HP-PRRSV infection followed by PCV2 infection enhanced the replication of both viruses in the experimental piglets and led to more-severe clinical signs and lesions, indicating greater synergistic effects during the sequential infection of piglets with HP-PRRSV and then PCV2.

 


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Digital Conference | BioBricks Foundation SB6.0: The Sixth International Meeting on Synthetic Biology

Digital Conference | BioBricks Foundation SB6.0: The Sixth International Meeting on Synthetic Biology | Virology and Bioinformatics from Virology.ca | Scoop.it
The preeminent meeting in Synthetic Biology, covering biotechnologies, biosafety, biosecurity & bioethics, July 9-11, 2013 at Imperial College in London UK.
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MaGnET: Malaria Genome Exploration Tool

MaGnET: Malaria Genome Exploration Tool | Virology and Bioinformatics from Virology.ca | Scoop.it

Summary: The Malaria Genome Exploration Tool (MaGnET) is a software tool enabling intuitive ‘exploration-style’ visualization of functional genomics data relating to the malaria parasite, Plasmodium falciparum. MaGnET provides innovative integrated graphic displays for different datasets, including genomic location of genes, mRNA expression data, protein–protein interactions and more. Any selection of genes to explore made by the user is easily carried over between the different viewers for different datasets, and can be changed interactively at any point (without returning to a search).

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Influenza virus hemagglutinin stalk-based antibodies and vaccines

Influenza virus hemagglutinin stalk-based antibodies and vaccines | Virology and Bioinformatics from Virology.ca | Scoop.it

Antibodies against the conserved stalk domain of the hemagglutinin are currently being discussed as promising therapeutic tools against influenza virus infections. Because of the conservation of the stalk domain these antibodies are able to broadly neutralize a wide spectrum of influenza virus strains and subtypes. Broadly protective vaccine candidates based on the epitopes of these antibodies, for example, chimeric and headless hemagglutinin structures, are currently under development and show promising results in animals models. These candidates could be developed into universal influenza virus vaccines that protect from infection with drifted seasonal as well as novel pandemic influenza virus strains therefore obviating the need for annual vaccination, and enhancing our pandemic preparedness.

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Measles Outbreak Traces To Vaccine-Refusing Megachurch

Measles Outbreak Traces To Vaccine-Refusing Megachurch | Virology and Bioinformatics from Virology.ca | Scoop.it
Texas measles outbreak tracing to vaccine-refusing megachurch endangers residents of two counties and has health officials in neighboring Oklahoma on guard.
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Twitter for Sci-Ed Part 1: Teaching in 140 characters or less | Sci-Ed

Several other authors have discussed reasons why scientists should be using Twitter, including this excellent post on Deep Sea News and this post through theAmerican Geophysical Union. For a more personal opinion, Dr Jeremy Segrottgave his thoughts after he used Twitter for a three months. Scientists are realizing that social media is an important way to translate knowledge to the public when done well, and Twitter provides another avenue by which this can be accomplished.

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Is Rabies Really 100% Fatal?

Is Rabies Really 100% Fatal? | Virology and Bioinformatics from Virology.ca | Scoop.it
Eight years ago, Jeanna Giese stunned the scientific community by becoming the first known person to survive Rabies without vaccination. Now, research and a new rabies treatment plan have called into question Rabies's supposed 100% fatality rate.

Via Ed Rybicki
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In biology, 100% is.....

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Ed Rybicki's curator insight, August 23, 2013 6:18 AM

Fascinating post from a young blogger!

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Evolution on the inside track: How viruses in gut bacteria change over time

Evolution on the inside track: How viruses in gut bacteria change over time | Virology and Bioinformatics from Virology.ca | Scoop.it
The digestive tract is home to a vast colony of bacteria, as well as the myriad viruses that prey upon them. Because the bacteria species vary from person to person, so does this viral population, the virome.
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Gretel Posadas's curator insight, August 23, 2013 7:39 AM

Evolution On the Inside Track: How #Viruses in Gut #Bacteria Change Over Time...by Samuel Minot, Alexandra Bryson, Christel Chehoud, Gary D. Wu, James D. Lewis, all from Penn, are co-authors.

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Genome compression: A novel approach for large collections

Genome compression: A novel approach for large collections | Virology and Bioinformatics from Virology.ca | Scoop.it

We show how to obtain several times higher compression ratio than of the best reported results, on two large genome collections (1092 human and 775 plant genomes). Our input are VCF files restricted to their essential fields. More precisely, our novel LZ-style compression algorithm squeezes a single human genome to about 400KB. The key to high compression is to look for similarities across the whole collection, not just against one reference sequence, what is typical for existing solutions.

Availability: http://sun.aei.polsl.pl/tgc (also as Supplementary material) under a free license.

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Why are vaccine-preventable diseases coming back?

Why are vaccine-preventable diseases coming back? | Virology and Bioinformatics from Virology.ca | Scoop.it
In recent years, there have been more vaccine-preventable disease outbreaks. Why are they happening?

Via Ed Rybicki
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Ed Rybicki's curator insight, August 28, 2013 4:49 PM

Because people have stopped frakin' vaccinations...!

Paul Britton's comment, August 29, 2013 5:56 AM
Hi Ed, absolutely correct. It could also be the fact that as vaccinating has been so sucessful people no longer see the diseases and assume they have gone and no longeer need vaccinations!!!
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Transmission of REV viruses from mammals to birds was probably an unexpected consequence of medical research

Transmission of REV viruses from mammals to birds was probably an unexpected consequence of medical research | Virology and Bioinformatics from Virology.ca | Scoop.it

A report published today (August 27) in PLOS Biology tells the surprising story of reticuloendotheliosis virus (REV) evolution and how, in the 1930s, unwitting malaria researchers were most likely responsible for transmitting REV from mammals to birds. The report highlights the importance of modern-day virus monitoring to limit potentially adverse transmission effects.

 

“It’s a very interesting story. That malarial research could have led to zoonosis from mammal to bird is pretty surprising,” said Eric Delwart, a professor of laboratory medicine at the University of California, San Francisco, who was not involved in the research. “It’s basically an example of a contamination that went rogue . . . and extraordinary bad luck.”

 

Retroviruses integrate into genomic DNA of host cells to borrow the cells’ transcription machinery and replicate. On occasion, such integration events happen in germline cells—such as sperm and eggs—and can thus be passed on to offspring, forever changing the host genome. Scientists like Robert Gifford, a professor at the Aaron Diamond AIDS Research Center in New York City, examine these integrated viral sequences—or viral fossils—in animals’ genomes to investigate the evolutionary history of viruses.

 

While studying the viral fossils of Madagascan mammals, Gifford made a surprising discovery. “We turned up this sequence in the ring-tailed mongoose genome that was very closely related to REV,” he said.

 

REV is a retrovirus that infects poultry and wild game birds, causing an array of disease symptoms, including anemia, immunosuppression, and the production of runts. Evidence from genome sequencing studies had suggested that it originated in mammals, but most sequence similarities mapped only to fragments of REV. Because of these fragmented similarities, “I had always assumed, as had probably other virologists, that these viruses had been circulating in birds for a long time,” said John Coffin, a professor of molecular biology and microbiology at Tufts University in Boston, who also was not involved in the work.

 

The copies of REV fossils Gifford found in two species of mongoose, however, showed full length similarity to bird REVs. “It made us curious because it is very unusual to have an avian retrovirus be so closely related to a mammalian retrovirus,” he said. “It suggested that there had been a transmission quite recently.” Indeed, the exchange turned out to have occurred less than a century ago.

 

After finding the REV sequences in mongoose, and a paper desribing a full-length REV in the egg-laying mammal echidna, Gifford analyzed the genomes of another 42 mammalian species, again finding nothing but REV fragments. He then analyzed the sequences of all known REVs isolated from birds to determine which were most similar to the mongoose and echidna REVs, and therefore, which species was likely to have been infected first.

 

The most similar bird REVs were two that had been isolated separately from ducks—one in 1959, the other in 1972.  Importantly, the source of REV infection in these animals was deemed to be contaminated stocks of Plasmodium lophurae—a malarial parasite. In fact, evidence of a then-unknown infectious agent contaminating stocks of P. Iophurae had surfaced as early as 1941.

 

Continuing the historical detective work, Gifford discovered that P. lophurae had been isolated just once, in 1937, from a Bornean Crested Firebacked pheasant at the New York Zoological Park (now the Bronx Zoo). Researchers planned to use this bird parasite as a model for studying human malaria, and after isolating it from pheasant, they had passaged the parasite in chickens for mass production.


Via Dr. Stefan Gruenwald
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Bernhard H. Schmitz's comment, September 2, 2013 5:15 AM
Right!
Juan Carlos Cañadilla's comment, September 2, 2013 7:55 AM
Yes!
Mel Melendrez-Vallard's comment, September 2, 2013 9:06 AM
I liked the article and I agree it did get people thinking...one of many possible thoughts on the subject.
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The Case for Suing Parents Who Don’t Vaccinate Their Kids

The Case for Suing Parents Who Don’t Vaccinate Their Kids | Virology and Bioinformatics from Virology.ca | Scoop.it

What if a mother decided not to vaccinate her daughter for measles, based on rumors that the vaccine causes autism, and her daughter gets the disease at the age of 4 and passes it to a 1-year-old, who is too young for the vaccine, at her day care center. And what if that baby dies? 


Via Ed Rybicki
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Human APOBEC3A Isoforms Translocate to the Nucleus and Induce DNA Double Strand Breaks Leading to Cell Stress and Death

Human APOBEC3A Isoforms Translocate to the Nucleus and Induce DNA Double Strand Breaks Leading to Cell Stress and Death | Virology and Bioinformatics from Virology.ca | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
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Mesozoic Mondays at Jurassic Forest: Cladistics - How we understand relationships of animals

Mesozoic Mondays at Jurassic Forest: Cladistics - How we understand relationships of animals | Virology and Bioinformatics from Virology.ca | Scoop.it
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Determining the subcellular location of new proteins from microscope images using local features

Determining the subcellular location of new proteins from microscope images using local features | Virology and Bioinformatics from Virology.ca | Scoop.it
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Google Drive - Quick reference guide for teachers and students

Google Drive - Quick reference guide for teachers and students | Virology and Bioinformatics from Virology.ca | Scoop.it
Having trouble getting your head around Google Drive and / or Google Docs?
Well stress no more with this great printable guide to using Google Drive.

Via John Evans, Franc Viktor Nekrep
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Chris Upton + helpers's comment, August 26, 2013 3:48 PM
got it...
Pippa Davies @PippaDavies 's comment, August 26, 2013 9:51 PM
Thanks Maria!:)
Ann Sciabarrasi's curator insight, December 22, 2013 7:01 PM

looks helpful

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Signatures of mutational processes in human cancer

Signatures of mutational processes in human cancer | Virology and Bioinformatics from Virology.ca | Scoop.it

Via Gerd Moe-Behrens, Pedro Fernandes
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Gerd Moe-Behrens's curator insight, August 15, 2013 5:01 PM

An important cancer research paper:

*Signatures of mutational processes in human cancer*

by
Ludmil B. Alexandrov,Serena Nik-Zainal,David C. Wedge,Samuel A. J. R. Aparicio,Sam Behjati,Andrew V. Biankin,Graham R. Bignell,Niccolò Bolli,Ake Borg,Anne-Lise Børresen-Dale,Sandrine Boyault,Birgit Burkhardt,Adam P. Butler,Carlos Caldas,Helen R. Davies, Christine Desmedt,Roland Eils,Jórunn Erla Eyfjörd,John A. Foekens, Mel Greaves,Fumie Hosoda,Barbara Hutter,Tomislav Ilicic,Sandrine Imbeaud,Marcin Imielinsket al.

"All cancers are caused by somatic mutations; however, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single cancer class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, ‘kataegis’, is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer, with potential implications for understanding of cancer aetiology, prevention and therapy."

 


http://bit.ly/142ZgNG

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Experimental Ebola treatment protects some primates even after disease symptoms appear

Experimental Ebola treatment protects some primates even after disease symptoms appear | Virology and Bioinformatics from Virology.ca | Scoop.it
Scientists have successfully treated the deadly Ebola virus in infected animals following onset of disease symptoms, according to a new article.
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