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This Week in Nature: Nov 8, 2012

In Nature, researchers from the Massachusetts Institute of Technology and the University of California, San Francisco, describe the creation of genetic programs from layered logic gates in single cells. To do so, they developed a set of transcriptional AND gates in Escherichia coli, which integrate two promoter inputs and control one promoter output. As a result, the AND gate can be layered by having the output promoter of an upstream circuit serve as the input promoter for a downstream circuit. The work, the researchers say, demonstrates successful layering of orthogonal logic gates, “a design strategy that could enable the construction of large, integrated circuits in single cells.”

In Nature Genetics, a team from the National Institutes of Health reports on the discovery of recurrent somatic mutations that cause endometrial cancer. The researchers sequenced the exome of 13 primary serous endometrial tumors. They then sequenced 18 genes showing recurrence in an additional 40 tumors, as well as three of these genes in 23 cell-cell, 67 endometrioid, and 18 mixed-histology endometrial tumors. They identified a high frequency of somatic mutations in genes associated with chromatin remodeling or the ubiquitin ligase complex, “implicating frequent mutational disruption of these processes in the molecular pathogenesis” of this form of cancer.

Also in Nature Genetics, investigators from DeCode Genetics publish the results of a whole-genome sequencing study that identified a rare genetic variant associated with prostate cancer. This variant is weakly correlated with previously reported risk variants at the same loci, and “its association remains significant after adjustment for all known risk-associated variants.”

The Scan

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.

SpliceVault Portal Provides Look at RNA Splicing Changes Linked to Genetic Variants

The portal, described in Nature Genetics, houses variant-related messenger RNA splicing insights drawn from RNA sequencing data in nearly 335,700 samples — a set known as the 300K-RNA resource.

Automated Sequencing Pipeline Appears to Allow Rapid SARS-CoV-2 Lineage Detection in Nevada Study

Researchers in the Journal of Molecular Diagnostics describe and assess a Clear Labs Dx automated workflow, sequencing, and bioinformatic analysis method for quickly identifying SARS-CoV-2 lineages.

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.