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Characterizing New Viruses in Rice

Novel mastreviruses identified in Australian wild rice

Simona Kraberger, Andrew D.W. Geering, Matthew Walters, Darren P. Martin, Arvind Varsani

Virus Research, vol 238, pg 193-197, 15 June 2017. Link to article.

The deep sequencing techniques made possible by next-generation sequencing technologies enable research into, among other things, viral diversity. Considering the vast majority of viruses in the world do not affect human existence at all, this might appear to be a rather esoteric pursuit. However, increased understanding of viral populations leads to increased understanding of the characteristics that make certain viruses more or less destructive, or that restrict their targeted host species, or that create vulnerabilities and weaknesses in the virus’s defense.

In this case, the researchers sampled wild rice plants around Australia for viruses, specifically searching for a type of virus called mastrevirus that infects grasses and economically important crops such as chickpeas and maize. Because the genome of this particular type of virus is circular single-stranded DNA. a specific extraction kit could be used that selected for viral DNA to the exclusion of any plant or bacterial contaminant. The resulting DNA was sequenced on an Illumina machine to determine whether any mastrevirus-specific sequence was present, and primers were designed based off of those identified sequence to enable the circular viral genome from each rice sample to be sequenced individually using Sanger sequencing. Based on this, two complete and previously unknown mastrevirus genomes were discovered – the first two mastreviruses shown to infect any variety of rice.

As the authors conclude, the “discovery of novel mastreviruses within both cultivated grasses and their uncultivated relatives [… is] an essential first step in identifying instances where these viruses are in the process of emerging as pathogens of economic significance.”

Posted in Literature

RNA-sequencing for Transposon Identification

Identifying transposon insertions and their effects from RNA sequencing data.

Julian R. de Ruiter, Sjors M. Kas, Eva Schut, David J. Adams, Marco J. Koudijs, Lodewyk F.A. Wessels, Jos Jonkers.

Nucleic Acids Research gkx461. DOI Link to Article

Continue reading “RNA-sequencing for Transposon Identification”

Posted in Literature

Early Diagnostic Biomarkers for Lung Cancer: Exosomal miRNAs

Evaluation of tumor-derived exosomal miRNA as potential diagnostic biomarkers for early stage non-small-cell lung cancer using next-generation sequencing.

Xiance Jin, Yanfan Chen, Hanbin Chen, Shaoran Fei, Didi Chen, Xiaona Cai, Linger Liu, Baochai Lin, Huafang Su, Lihao Zhao, Meng Su, Huanle Pan, Lanxiao Shen, Deyao Xie, Congying Xie.

Clinical Cancer Research, June 12 2017. DOI: 10.1158/1078-0432.CCR-17-0577 Link to Article

Continue reading “Early Diagnostic Biomarkers for Lung Cancer: Exosomal miRNAs”