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PNAS Papers on Mutation-Phenotype Machine Learning Method, Microviruses, More

Editor's Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted this week.

A University of Texas Southwestern Medical Center-led team presents a machine learning approach for matching chemically induced mutations with specific phenotypes in forward genetic studies using a combination of meiotic mapping and machine learning. The "Candidate Explorer" (CE) method brings genetic mapping features together into a score for assessing potential germline mutation-phenotype ties, the investigators say — an approach they used to find more than 2,300 mutations with flow cytometry-based circulating immune cell features in a screen of mutagenized mice. "In the future, the data from other screens will be released for public users of CE to interpret a wide range of phenotypic consequences that emanate from each mutation," the authors note, adding that "biomedically relevant phenotypic screens may ultimately enlighten the study of human phenotype and help to distinguish mechanisms of phenotypes caused by certain alleles."

University of Texas at Austin researchers characterize phage defense mechanisms and other features in small single-stranded viruses from the Microviridae family. Using Escherichia coli bacteria as a host, the team assessed microvirus models containing different genomic segment combinations, uncovering an apparent role for hypervariable pilot protein coding regions in defending against host infection by additional microviruses from other lineages. "Our results emphasize that competition between viruses is a considerable and often overlooked source of selective pressure," the authors report, "and by producing similar evolutionary outcomes in distinct lineages, it underlies the prevalence of hypervariable regions in the genomes of microviruses and perhaps beyond."

A team from France, Germany, and Spain tracks viral infection consequences in bacterial cells, focusing on alterations in Bacillus subtilis cells infected with the SPP1 bacteriophage. With imaging and other experiments done over time on B. subtilis cells infected with a fluorescently tagged version of the phage, the researchers saw signs that SPP1 quickly ramps up DNA content in infected cells, while taking over cell machinery and compartmentalizing viral processes into different parts of the cell's cytoplasm. "This spatial partition responds to the requirements for exponential replication of SPP1 genomes and for the assembly of hundreds of viral particles," they write. "Its similarities to remodeling of the cell nucleus by herpesviruses to invade the cell space were conserved to infect hosts of different domains of life."

The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.