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Science Papers Report on Splicing Enhancer, Point of Care Test for Sexual Transmitted Disease

The discovery of a previously unknown RNA structural element that acts as a splicing enhancer and plays a role in cancer progression is reported in Science this week. Aberrant alternative splicing is a hallmark of cancer, yet the underlying regulatory programs that control this process remain largely unknown, partly because the bioinformatic strategies for cis-regulatory element discovery fail to capture the contribution of RNA secondary structure to regulatory information. To overcome this, a group led by University of California, San Francisco, scientists adapted a previously developed computational framework that uses RNA structural and sequence information to identify cis-regulatory elements that are informative of transcriptomic changes to investigate the RNA sequence and structural code that governs a broader range of RNA-related processes such as splicing and RNA processing. Applying this tool to breast cancer sequencing and other data, the team uncovers a structural splicing enhancer that interacts with the RNA-binding protein SNRPA1 to promote cassette exon inclusion, driving breast cancer metastasis.

A low-cost point-of-care molecular test for the rapid detection of both sexually transmitted diseases and antimicrobial susceptibility is detailed in this week's Science Translational Medicine, offering a potential new tool to combat such infections in resource-poor settings. Current methods to detect STIs such as gonorrhea, cases of which have been ballooning worldwide, involve expensive and time-consuming nucleic acid amplification tests. To address this, a Johns Hopkins University-led team developed PROMPT, a portable and rapid cartridge-based PCR device that can simultaneously detect Neisseria gonorrhoeae, which causes gonorrhea, and genotype it for resistance to the antimicrobial drug ciprofloxacin in under 15 minutes. The test was evaluated using penile swab samples from sexual health clinics in Baltimore and Uganda, demonstrating overall sensitivity of 97.7 percent and specificity of 97.6 percent for pathogen detection and 100 percent concordance with culture results for ciprofloxacin resistance. "Compared to the leading industry [point-of-care] PCR diagnostic cartridges, our magnetofluidic cartridge design has potential to provide even faster results, contribute less plastic waste to the environment, and enable greater access to diagnostics in low-resource settings," the technology's developers write.

The Scan

NFTs for Genome Sharing

Nature News writes that non-fungible tokens could be a way for people to profit from sharing genomic data.

Wastewater Warning System

Time magazine writes that cities and college campuses are monitoring sewage for SARS-CoV-2, an approach officials hope lasts beyond COVID-19.

Networks to Boost Surveillance

Scientific American writes that new organizations and networks aim to improve the ability of developing countries to conduct SARS-CoV-2 genomic surveillance.

Genome Biology Papers on Gastric Cancer Epimutations, BUTTERFLY, GUNC Tool

In Genome Biology this week: recurrent epigenetic mutations in gastric cancer, correction tool for unique molecular identifier-based assays, and more.