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This Week in Nucleic Acids Research: Jan 9, 2013

In an effort to find new ways of inhibiting the reverse transcriptase enzyme in HIV-1, a University of Missouri at Columbia-led team turned to high-throughput sequencing in combination with a type of RNA enrichment known as "systematic evolution of ligands through exponential enrichment," or SELEX. As they write in the early, online edition of Nucleic Acids Research, the researchers' search uncovered shared motifs amongst the RNAs that bind to and inhibit HIV-1's reverse transcriptase, hinting at potential strategies for designing anti-HIV-1 aptamers that thwart the enzyme and, in turn, the replication of HIV-1.

The National University of Singapore's Richie Soong and his colleagues describe a program called Genome Bisulfite Sequencing Analyzer, or GBSA, in another Nucleic Acids Research study. The open-source software was designed as a means of assessing high-throughput, whole-genome bisulfite sequence information — data used to discern methylation patterns across the genome — in either gene-focused or gene-agnostic ways. "In essence," study authors say, "GBSA allows an investigator to explore not only known loci but also the genomic regions, for which methylation studies could lead to the discovery of new regulatory mechanisms."

Finally, Adam James Reid and Matthew Berriman, both with the Wellcome Trust Sanger Institute's parasite genomics group, outline a scheme for deciphering molecular interactions between a parasite and its host. Their method involves gauging gene expression profiles in each of the organisms and looking for profiles that shift in both organisms as they interact. From these correlated gene expression patterns, the pair notes, it's possible to narrow in on the genes at play when hosts and parasites — or any pair of organisms — interact with one another. "Our approach could be applied to study any interaction between species," they say, "for example, between a host and its parasites or pathogens, but also symbiotic and commensal pairings."