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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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GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis

Motivation: Gene clusters are arrangements of functionally related genes on a chromosome. In bacteria, it is expected that evolutionary pressures would conserve these arrangements due to the functional advantages they provide.

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Rewritable memory encoded into DNA

Rewritable memory encoded into DNA | Virology and Bioinformatics from Virology.ca | Scoop.it
Difficulty of the task is indicative of the need for new tools in synthetic biology, researchers say.
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PLoS Pathogens: Influence of Microbiota on Viral Infections

PLoS Pathogens: Influence of Microbiota on Viral Infections | Virology and Bioinformatics from Virology.ca | Scoop.it
Most pathogens gain access to the host through surfaces of the body that are exposed to the surrounding environment and rife with resident microorganisms, termed microbiota. Microbiota play an integral role in modulating host health. One significant benefit of the microbiota is that they provide protection against incoming bacterial pathogens
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Largest virus discovered in ocean water off Chile - visible under light microscope

Largest virus discovered in ocean water off Chile - visible under light microscope | Virology and Bioinformatics from Virology.ca | Scoop.it

The largest virus yet discovered - bigger than some bacteria - is isolated from sea water pulled up off the coast of Chile. Called Megavirus chilensis, it is 10 to 20 times wider than the average virus. It just beats the previous record holder, Mimivirus, which was found in a water cooling tower in the UK in 1992. The particle measures about 0.7 micrometres (thousandths of a millimetre) in diameter and you don't need an electron microscope to see it; you can see it with an ordinary light microscope.


Via Dr. Stefan Gruenwald
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Oncolytic Viruses: The Power of Directed Evolution

Oncolytic Viruses: The Power of Directed Evolution | Virology and Bioinformatics from Virology.ca | Scoop.it
Attempts at developing oncolytic viruses have been primarily based on rational design. However, this approach has been met with limited success.
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www.virology.ca

www.virology.ca | Virology and Bioinformatics from Virology.ca | Scoop.it

 

 

 

 

 

Whats here:  - Resources for analysis of large DNA viruses.

  Databases of viral genomic information (genes, gene families, and genomes).

  Software to perform comparative genomics analyses.

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Measles — United States, 2011 MMWR

Measles — United States, 2011 MMWR | Virology and Bioinformatics from Virology.ca | Scoop.it

"In 2000, the United States achieved measles elimination (defined as interruption of year-round endemic measles transmission) (1). However, importations of measles into the United States continue to occur, posing risks for measles outbreaks and sustained measles transmission. During 2011, a total of 222 measles cases (incidence rate: 0.7 per 1 million population) and 17 measles outbreaks (defined as three or more cases linked in time or place) were reported to CDC, compared with a median of 60 (range: 37–140) cases and four (range: 2–10) outbreaks reported annually during 2001–2010. This report updates an earlier report on measles in the United States during the first 5 months of 2011 (2). Of the 222 cases, 112 (50%) were associated with 17 outbreaks, and 200 (90%) were associated with importations from other countries, including 52 (26%) cases in U.S. residents returning from abroad and 20 (10%) cases in foreign visitors. Other cases associated with importations included 67 (34%) linked epidemiologically to importations, 39 (20%) with virologic evidence suggesting recent importation, and 22 (11%) linked to cases with virologic evidence of recent importation. Most patients (86%) were unvaccinated or had unknown vaccination status.

 

The increased numbers of outbreaks and measles importations into the United States underscore the ongoing risk for measles among unvaccinated persons and the importance of vaccination against measles (3)."

 

Amen!!  It is VERY revealing that so many cases were associated with imported virus infections - 90%!!  And almost HALF of those came from Europe, rather than from some developing country.

 

I thank Linda Stannard for the paramyxovirus EM

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Berkeley Lab Scientists Generate Electricity From Viruses « Berkeley Lab News Center

Berkeley Lab Scientists Generate Electricity From Viruses « Berkeley Lab News Center | Virology and Bioinformatics from Virology.ca | Scoop.it
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Detection of hepatitis C virus RNA in dried blood spots

Detection of hepatitis C virus RNA in dried blood spots | Virology and Bioinformatics from Virology.ca | Scoop.it
Journal of Clinical Virology, An estimated 130–170 million people worldwide are chronically infected with HCV
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New microscope able to 'see' atoms for first time: Atomic structure of tiny virus imaged

New microscope able to 'see' atoms for first time: Atomic structure of tiny virus imaged | Virology and Bioinformatics from Virology.ca | Scoop.it

UCLA researchers report in the April 30 edition of the journal Cell that they have imaged a virus structure at a resolution high enough to effectively "see" atoms, the first published instance of imaging biological complexes at such a resolution. The research team, led by Hong Zhou, UCLA professor of microbiology, immunology and molecular genetics, used cryo-electron microscopy to image the structure at 3.3 angstroms. An angstrom is the smallest recognized division of a chemical element and is about the distance between the two hydrogen atoms in a water molecule.


Via Dr. Stefan Gruenwald
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Single cell genomics center launched at Broad Institute

Single cell genomics center launched at Broad Institute | Virology and Bioinformatics from Virology.ca | Scoop.it

Analyzing cell-to-cell differences is crucial to answering important biological questions, such as how cancer spreads or how best to coax pluripotent stem cells to become specialized cells like neurons. However, understanding how cells differ from each other means conducting experiments on individual cells, a very difficult feat.

Now, a new center at the Broad Institute in Cambridge, Massachusetts, suggests that single-cell genomics is moving from the proof-of-concept phase to reality.


Via Dr. Stefan Gruenwald
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New drug TKM-PLK1 uses stealth to stop cancer cell reproduction

New drug TKM-PLK1 uses stealth to stop cancer cell reproduction | Virology and Bioinformatics from Virology.ca | Scoop.it

A new investigational drug designed to stop cancer cells from reproducing may offer hope for patients with advanced solid tumor cancers. TKM-PLK-1 targets a protein called polo-like kinase 1 (PLK1) that promotes tumor cell reproduction. It prevents the tumor from completing cell division, resulting in death of the cancer cell. TCRS, a partnership of the Translational Genomics Research Institute (TGen) and Scottsdale Healthcare, will be among the first in the world to study the treatment in humans. The new drug is being developed as a treatment for patients with advanced solid tumor cancers who are not well served by current therapy. The Phase 1 clinical trial will evaluate the safety, tolerability and how the body metabolizes TKM-PLK1.

 

Clinical trials of TKM-PLK1 for qualified patients are now open at TGen Clinical Research Services (TCRS) at Scottsdale Healthcare, part of the Virginia G. Piper Cancer Center. Researchers hope to enroll up to 52 patients in clinical trials of the drug in three centers across the U.S. Tekmira Pharmaceuticals Corp. of Vancouver, Canada, (http://www.tekmirapharm.com) developed the drug.


Via Dr. Stefan Gruenwald
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Ranking Vaccines: A Prioritization Framework - Phase I: Demonstration of Concept and a Software Blueprint - Institute of Medicine

Ranking Vaccines: A Prioritization Framework - Phase I: Demonstration of Concept and a Software Blueprint - Institute of Medicine | Virology and Bioinformatics from Virology.ca | Scoop.it
Ranking Vaccines: A Prioritization Framework describes a decision-support model and the blueprint of a software called Strategic Multi-Attribute Ranking Tool for Vaccines, or SMART Vaccines, that should help decision makers prioritize new vaccines...

In this first phase report, the IOM offers a framework and proof of concept to account for various factors influencing vaccine prioritization—demographic, economic, health, scientific, business, programmatic, social, policy factors and public concerns. Ranking Vaccines: A Prioritization Framework describes a decision-support model and the blueprint of software—called Strategic Multi-Attribute Ranking Tool for Vaccines or SMART Vaccines. SMART Vaccines should be of help to decision makers. SMART Vaccines Beta is not available for public use, but SMART Vaccines 1.0 is expected to be released at the end of the second phase of this study, when it will be fully operational and capable of guiding discussions about prioritizing the development and introduction of new vaccines.

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GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies

Motivation: The increasing availability of second-generation high-throughput sequencing (HTS) technologies has sparked a growing interest in de novo genome sequencing. This in turn has fueled the need for reliable means of obtaining high-quality draft genomes from short-read sequencing data.

 

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Virus-based piezoelectric energy generation : Nature Nanotechnology : Nature Publishing Group

Virus-based piezoelectric energy generation : Nature Nanotechnology : Nature Publishing Group | Virology and Bioinformatics from Virology.ca | Scoop.it
A thin film of M13 bacteriophage generates piezoelectric energy that is used to power a liquid-crystal display.

 

"Piezoelectric materials can convert mechanical energy into electrical energy1, 2, and piezoelectric devices made of a variety of inorganic materials3, 4, 5 and organic polymers6 have been demonstrated. However, synthesizing such materials often requires toxic starting compounds, harsh conditions and/or complex procedures7. Previously, it was shown that hierarchically organized natural materials such as bones8, collagen fibrils9, 10 and peptide nanotubes11, 12 can display piezoelectric properties. Here, we demonstrate that the piezoelectric and liquid-crystalline properties of M13 bacteriophage (phage) can be used to generate electrical energy. Using piezoresponse force microscopy, we characterize the structure-dependent piezoelectric properties of the phage at the molecular level. We then show that self-assembled thin films of phage can exhibit piezoelectric strengths of up to 7.8 pm V−1. We also demonstrate that it is possible to modulate the dipole strength of the phage, hence tuning the piezoelectric response, by genetically engineering the major coat proteins of the phage. Finally, we develop a phage-based piezoelectric generator that produces up to 6 nA of current and 400 mV of potential and use it to operate a liquid-crystal display. Because biotechnology techniques enable large-scale production of genetically modified phages, phage-based piezoelectric materials potentially offer a simple and environmentally friendly approach to piezoelectric energy generation."

 

Vironanobiotechnology: coming soon to a cell phone near you.

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The Last Measle Fundraiser Video

The Last Measle - a short , animated video explaining the measles from a child's perspective

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How did AIDS/HIV begin? From chimps to man - a history lesson

How did AIDS/HIV begin? From chimps to man - a history lesson | Virology and Bioinformatics from Virology.ca | Scoop.it

The story begins sometime close to 1921, somewhere between the Sanaga River in Cameroon and the Congo River in the former Belgian Congo. It involves chimps and monkeys, hunters and butchers, “free women” and prostitutes, syringes and plasma-sellers, evil colonial lawmakers and decent colonial doctors with the best of intentions. And a virus that, against all odds, appears to have made it from one ape in the central African jungle to one Haitian bureaucrat leaving Zaire for home and then to a few dozen men in California gay bars before it was even noticed — about 60 years after its journey began.

 

New York Times version.


Via Dr. Stefan Gruenwald
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Shingles Vaccine Deemed Safe in Large Study

Shingles Vaccine Deemed Safe in Large Study | Virology and Bioinformatics from Virology.ca | Scoop.it
The shingles vaccine is “generally safe and well tolerated,” according to a study of nearly 200,000 patients.

Shingles, or herpes zoster, is a painful rash caused by reactivation of chickenpox virus that has remained dormant in the body. Up to 1 million Americans, more than half of whom are 60 or older, are diagnosed with shingles every year, the researchers write.

Researchers analyzed data of 193,083 vaccinated patients aged 50 or older for certain side effects that could be related to the shingles vaccine.

The researchers found no increased risk in the first six weeks after vaccination for stroke, heart disease, infections of the brain or spinal cord or other brain diseases, Bell's palsy, or Ramsay-Hunt syndrome, which can occur when the virus that causes shingles affects the facial nerve near an ear.

An increased risk of allergic reaction was found in the first week after receiving the shingles vaccine.

A majority of these reactions involved an inflammatory response at the injection site, involving symptoms such as redness, swelling, and mild pain.


Via Ed Rybicki
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BGI debuts 'EasyGenomics' cloud-based bioinformatics solution for omics ... - Phys.Org (press release)

BGI debuts 'EasyGenomics' cloud-based bioinformatics solution for omics ... - Phys.Org (press release) | Virology and Bioinformatics from Virology.ca | Scoop.it
BGI debuts 'EasyGenomics' cloud-based bioinformatics solution for omics ...Phys.Org (press release)EasyGenomics integrates various popular next generation sequencing (NGS) analysis workflows including whole genome resequencing, exome resequencing,...

Via Pedro Fernandes, Mohamed Nadhir Djekidel
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Journal Virol Methods - A simple, rapid and efficient way to obtain infectious clones of potyviruses

Journal Virol Methods - A simple, rapid and efficient way to obtain infectious clones of potyviruses | Virology and Bioinformatics from Virology.ca | Scoop.it

"The availability of an infectious cDNA clone is a prerequisite for genetic studies on RNA viruses. However, despite important improvement in molecular biology techniques during the last decades, obtaining such clones often remains tedious, time-consuming and rather unpredictable. In the case of potyviruses, cDNA clones are frequently unstable due to the toxicity of some viral proteins for bacteria. The problem can be overcome by inserting introns into the viral sequence but this requires additional steps in the cloning process and depends on the availability of suitable restriction sites in the viral sequence or adjunction of such sites by mutagenesis. Homologous recombination in yeast rather than in vitro restriction and ligation can be used to build infectious clones or other viral constructs. This paper describes how, by using recombination in yeast and fusion PCR, infectious intron-containing clones were obtained within a few weeks for two strains of watermelon mosaic virus (WMV, Potyvirus), whereas previous attempts using “classical” cloning techniques had failed repeatedly. Using the same approach, intronless infectious clones of two other potyviruses, zucchini yellow mosaic virus (ZYMV) and papaya ringspot virus (PRSV), were obtained in less than two weeks."

 

I am a sucker for good techniques like this one: long ago I helped invent a technique for idiot-proof cDNA cloning of the 3' of the genome (Pappu et al., J Virol Methods. 1993 Jan;41(1):9-20), and have kept a watchful eye on potyvirus genome cloning ever since - and it is a challenge, because they are >10kb in length.  This is an elegant solution to an old problem.

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The impact of endogenous retroviruses on antiviral immunity

The impact of endogenous retroviruses on antiviral immunity | Virology and Bioinformatics from Virology.ca | Scoop.it

NIMR virologists and immunologists have shown that endogenous retroviruses can enhance antiviral immunity. The research is published in PLoS Pathogens.

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A quantitative proteomic analysis of lung epithelial (A549) cells infected with 2009 pandemic influenza A virus using stable isotope labelling with amino acids in cell culture - Dove - 2012 - PROTE...

A quantitative proteomic analysis of lung epithelial (A549) cells infected with 2009 pandemic influenza A virus using stable isotope labelling with amino acids in cell culture - Dove - 2012 - PROTE... | Virology and Bioinformatics from Virology.ca | Scoop.it

Influenza A virus is one of the world's major uncontrolled pathogens, causing seasonal epidemics as well as global pandemics. This was evidenced by the recent emergence and now prevalence of the 2009 swine origin pandemic H1N1 influenza A virus. In this study, quantitative proteomics using stable isotope labelling with amino acids in cell culture was used to investigate the changes in the host cell proteome in cells infected with pandemic H1N1 influenza A virus. The study was conducted in A549 cells that retain properties similar to alveolar cells. Several global pathways were affected, including cell cycle regulation and lipid metabolism, and these could be correlated with recent microarray analyses of cells infected with influenza A virus. Taken together, both quantitative proteomics and transcriptomic approaches can be used to identify potential cellular proteins whose functions in the virus life cycle could be targeted for chemotherapeutic intervention

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The Wisdom of the Slime Mold

The Wisdom of the Slime Mold | Virology and Bioinformatics from Virology.ca | Scoop.it
There is a slime mold known as Physarum polycephalum that lives in forests around the world. It feeds on various kinds of microscopic particles. As it forages for food, protoplasmic tubes of slime extend out and bifurcate like tree branches; whenever it happens upon a source of nutrients, it gathers into a bloblike formation. The whole thing — blobs connected by tubes — is a single organism, and the network serves to transport nutrients throughout its “body.”

 

An interesting fact about this slime mold is that it is highly intelligent — or at least it behaves as if it is. In locating food in its environment, it builds networks that have been shown to be optimally efficient in transporting the nutrients over the area in question. If placed in a maze, for instance, with a source of food outside the maze, the slime mold will discover the shortest path out.

Via Dr. Stefan Gruenwald
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New monomeric site-specific nucleases for genome editing

New monomeric site-specific nucleases for genome editing | Virology and Bioinformatics from Virology.ca | Scoop.it

Targeted manipulation of complex genomes often requires the introduction of a double-strand break at defined locations by site-specific DNA endonucleases. Here, we describe a monomeric nuclease domain derived from GIY-YIG homing endonucleases for genome-editing applications. Fusion of the GIY-YIG nuclease domain to three-member zinc-finger DNA binding domains generated chimeric GIY-zinc finger endonucleases (GIY-ZFEs). Significantly, the I-TevI-derived fusions (Tev-ZFEs) function in vitro as monomers to introduce a double-strand break, and discriminate in vitro and in bacterial and yeast assays against substrates lacking a preferred 5'-CNNNG-3' cleavage motif. The Tev-ZFEs function to induce recombination in a yeast-based assay with activity on par with a homodimeric Zif268 zinc-finger nuclease. We also fused the I-TevI nuclease domain to a catalytically inactive LADGLIDADG homing endonuclease (LHE) scaffold. The monomeric Tev-LHEs are active in vivo and similarly discriminate against substrates lacking the 5'-CNNNG-3' motif. The monomeric Tev-ZFEs and Tev-LHEs are distinct from the FokI-derived zinc-finger nuclease and TAL effector nuclease platforms as the GIY-YIG domain alleviates the requirement to design two nuclease fusions to target a given sequence, highlighting the diversity of nuclease domains with distinctive biochemical properties suitable for genome-editing applications.


Via dromius, Dr. Stefan Gruenwald
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Virus Power: Scientists Wring Electricity From Microscopic Batteries | Txchnologist

Harmless viruses can assemble into novel energy-harvesting materials in a way far more environmentally friendly than such substances are normally manufactu...
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