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This Week in PNAS: Jan 6, 2010

In the early, online version PNAS this week, an American research team reports that they have identified five new viruses in Drosophila and mosquito cells by sifting through data from published small RNA libraries. Since invertebrates process replicating RNA virus genomes into small interfering RNAs to help clear them, the researchers were able to home in on viral sequences from fruit fly, mosquito, and nematode cells to find previously overlooked viruses in invertebrates in a culture-independent way.

Antonis Rokas and team tested the use of RNA-Seq to help decipher relationships in the tree of life. The researchers made phylogenetic inferences after generating reads from ten mosquito species' transcriptomes and assembling them into phylogenomic data matrices. "This approach is more efficient, data-rich, and economical than traditional PCR-based and EST-based methods and provides a scalable strategy for generating phylogenomic data matrices to infer the branches and twigs of the tree of life," they write.

An international research team reports on a way to examine protein-induced conformational changes in DNA. The real-time, in situ method relies on a combination of surface bound double-stranded DNA probes measuring electrical orientation and an optical technique assessing DNA conformational change kinetics. Those involved say the method is not only effective, but can also be scaled up for use in high-throughput assays.

Japanese researchers found duplicated mitochondrial genes in the rice nuclear genome that contribute to hybrid sterility in rice. Their functional analysis shows that genes coding for the mitochondrial ribosomal protein L27 are involved in pollen development — and reciprocal loss of these genes leads to reproductive isolation in cultivated and wild rice hybrid plants.

The Scan

Not Yet a Permanent One

NPR says the lack of a permanent Food and Drug Administration commissioner has "flummoxed" public health officials.

Unfair Targeting

Technology Review writes that a new report says the US has been unfairly targeting Chinese and Chinese-American individuals in economic espionage cases.

Limited Rapid Testing

The New York Times wonders why rapid tests for COVID-19 are not widely available in the US.

Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.