Skip to main content
Premium Trial:

Request an Annual Quote

This Week in PNAS: Aug 28, 2012

In PNAS this week, a pair of researchers from the University of Washington presents a way to tune gene networks in Escherichia coli. The method combines "the straightforward tunability of
translation initiation rates via the [ribosome binding site] spacer region with the high mutation rate and strong bias for insertion/deletion mutations inherent to simple sequence repeats (SSR)," the duo says. SSRs are then placed between the Shine-Dalgarno sequence and the start codon of the target gene, sequences the pair dubs rbSSR sequences. "We believe the same approach we have used to engineer highly tunable elements with simple sequence repeats can be extended to other network parameters in bacteria and to higher organisms by tuning the spacing between known regulatory motifs such as those responsible for transcription initiation or intron splicing efficiency," the duo adds.

Also in PNAS, California Institute of Technology researchers examine whether gene regulatory networks control developmental gene expression patterns. To do so, they developed a Boolean computational model of endomesoderm specification in the sea urchin embryo. "The Boolean computational model we present here provides a direct test of whether the observed dynamic sequence of spatial and temporal gene expression can be computed by using the information included in the GRN model," they write. "Indeed we find that, with a few exceptions, the Boolean computation suffices to reconstruct the observed spatial and temporal gene expression patterns, and this supports the idea that GRN models may contain the necessary information to operate large-scale developmental spatial specification systems."

Finally, researchers led by Shu-Bing Qian at Cornell University introduce their global translational initiation sequencing, or GTI-seq, method that allows for the global mapping of translation initiation sites. The method uses both lactimidomycin and cycloheximide, ribosome E-site translation inhibitors, to detect initiation and elongation events. "A systematic, high-throughput method like GTI-seq offers a top-down approach, in which one can identify a set of candidate genes for intensive study," the authors write. "GTI-seq is readily applicable to broad fields of fundamental biology."

The Scan

Study Links Evolution of Longevity, Social Organization in Mammals

With the help of comparative phylogenetics and transcriptomics, researchers in Nature Communications see ties between lifespan and social organization in mammals.

Tumor Microenvironment Immune Score Provides Immunotherapy Response, Prognostic Insights

Using multiple in situ analyses and RNA sequence data, researchers in eBioMedicine have developed a score associated with immunotherapy response or survival.

CRISPR-Based Method for Finding Cancer-Associated Exosomal MicroRNAs in Blood

A team from China presents in ACS Sensors a liposome-mediated membrane fusion strategy for detecting miRNAs carried in exosomes in the blood with a CRISPR-mediated reporter system.

Drug Response Variants May Be Distinct in Somatic, Germline Samples

Based on variants from across 21 drug response genes, researchers in The Pharmacogenomics Journal suspect that tumor-only DNA sequences may miss drug response clues found in the germline.