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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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Long non-coding RNAs in the regulation of the immune response: Trends in Immunology

Long non-coding RNAs in the regulation of the immune response: Trends in Immunology | Virology and Bioinformatics from Virology.ca | Scoop.it

Highlights

 

•Widespread changes in lncRNA expresssion are associated with the immune response.•lncRNAs regulate the inflammatory response following activation of innate immunity.•lncRNAs regulate T cell differentiation and migration.•The action of long non-coding RNAs is mediated via diverse mechanisms. 

 

 

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Stanford biologists watch RNA fold in real time

Stanford biologists watch RNA fold in real time | Virology and Bioinformatics from Virology.ca | Scoop.it

Stanford biologists watch RNA fold in real time - The researchers kept the growing RNA strand taut in a "dumbbell" setup. Two beads were held in place by optical traps.


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New Videogame Lets Amateur Researchers Mess with RNA

New Videogame Lets Amateur Researchers Mess with RNA | Virology and Bioinformatics from Virology.ca | Scoop.it
Jessica Fournier has a job that makes poor use of her talents. She spends her days stocking sneakers at a warehouse outside Grand Rapids, Mi...

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CSH: #Evolution of Protein Synthesis from an RNA World

CSH: #Evolution of Protein Synthesis from an RNA World | Virology and Bioinformatics from Virology.ca | Scoop.it

Because of the molecular complexity of the ribosome and protein synthesis, it is a challenge to imagine how translation could have evolved from a primitive RNA World.

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Three-dimensional analysis of ribonucleoprotein complexes in influenza A virus : Nature Communications : Nature Publishing Group

Although genome segmentation provides advantages such as genetic reassortment, which contributes to the emergence of novel strains with pandemic potential, it complicates the genome packaging of progeny virions.

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Delivering Silence | The Scientist

Delivering Silence | The Scientist | Virology and Bioinformatics from Virology.ca | Scoop.it
Since the discovery of RNA interference almost 15 years ago, researchers have tried to devise effective ways to get these short gene-silencing transcripts inside cells. But techniques for in vivo delivery have fallen short. For therapies that require long-term gene knockdown, DNA viruses that insert the microRNA (miRNA) genes into the target cell’s genome were the best bet. But that approach produced large numbers of miRNAs, which overloaded the miRNA-processing proteins in the nucleus and resulted in cellular toxicity. For short-term therapies, mature miRNAs encapsulated in liposomes or conjugated to cholesterol were used, but they have been difficult to target to a specific cell type.

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Global Organization of a Positive-strand RNA Virus Genome

Global Organization of a Positive-strand RNA Virus Genome | Virology and Bioinformatics from Virology.ca | Scoop.it

The genomes of many important pathogenic viruses are made of RNA. These genomes encode viral proteins and contain regulatory sequences and structures. In some viruses, distant regions of the RNA genome can interact with each other via base pairing, which suggests that certain genomes may take on well-defined conformations. This concept was investigated using a tombusvirus RNA genome that contains several long-range RNA interactions. The results of microscopic and biochemical analyses indicated a compact genome conformation with structured regions radiating from a central core. The structural model was compatible with some, but not all, long-range interactions, suggesting that the genome is a dynamic molecule that assumes different conformations. The analysis also revealed new structural features of the genome, some of which were shown to be functionally relevant. This study advances our understanding of the role played by global structure in virus genome function and provides a model to further investigate its in role virus reproduction. We anticipate that organizational principles revealed by this investigation will be applicable to other viruses.

  
Ed Rybicki's insight:

Plant viruses rule OK...!  Or biophysical investigations of their genomes do.  Seriously, this is an impressive piece of work, that points up the fact that information content of a genome definitely does not stop with the sequence.

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Expanding networks of RNA virus evolution

In a recent BMC Evolutionary Biology article, Huiquan Liu and colleagues report two new genomes of double-stranded RNA (dsRNA) viruses from fungi and use these as a springboard to perform an extensive phylogenomic analysis of dsRNA viruses.

The results support the old scenario of polyphyletic origin of dsRNA viruses from different groups of positive-strand RNA viruses and additionally reveal extensive horizontal gene transfer between diverse viruses consistent with the network-like rather than tree-like mode of viral evolution. Together with the unexpected discoveries of the first putative archaeal RNA virus and a RNA-DNA virus hybrid, this work shows that RNA viral genomics has major surprises to deliver.

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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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RNA sequencing - just my prediction

After the nanopore sequencing gets sorted out, the next thing will be the sequencing of RNA by a similar method. 

Reoviruses already kind of do it:

http://www.ncbi.nlm.nih.gov/pubmed/19914820

 

 

http://news.sciencemag.org/sciencenow/2012/03/dna-sequencing-without-the-fuss.html?ref=hp

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An inhibitory function of WW domain-containing host proteins in RNA virus replication 10.1016/j.virol.2012.01.020 : Virology | ScienceDirect.com

An inhibitory function of WW domain-containing host proteins in RNA virus replication 10.1016/j.virol.2012.01.020 : Virology | ScienceDirect.com | Virology and Bioinformatics from Virology.ca | Scoop.it

To identify new genes affecting Tomato bushy stunt virus (TBSV) replication in yeast model host, we are studying protein families, whose members have been identified during previous high throughput screening.

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RNomics' Posterous site

RNomics' Posterous site | Virology and Bioinformatics from Virology.ca | Scoop.it

blogging about RNA, evolution, origin of life, genomics, drug discovery, etc

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