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Cell Studies on Digital Embryo Approach, Oxygen Response Screens, Genomic View of SARS-CoV-2

A research team from Germany and Italy presents a MorphoSeq computational approach for coming up with a "canonical digital embryo" based on single-cell RNA sequencing (scRNA-seq) and light sheet imaging data on individual cells. The researchers applied this approach to Phallusia mammillata chordate model embryos followed up to the gastrulation stage, reconstructing the expression and spatial orientation for cells from several lineages in the early stages of P. mammillata sea squirt development. "Our results demonstrate that the unbiased mapping of scRNA-seq data by the MorphoSeq framework yields a spatiotemporally resolved atlas of gene expression at the single-cell level in a developing embryo and links it to morphological features," they report.

Researchers from the Massachusetts General Hospital and the Broad Institute share findings from a CRISPR gene editing-based screen for genes contributing to cell growth in high- or low oxygen conditions. Based on results from gene knockout screens done under conditions of 21 percent, 5 percent, or 1 percent oxygen, the team highlighted 213 genes that appear to mediate cell responses to high oxygen conditions, including components of mitochondrial pathways. On the other hand, the authors note that genes involved in lipid metabolism and peroxisome activity were among the more than 100 candidate genes for low oxygen response in the knockout screens. "Our resource nominates genetic diseases whose severity may be modulated by oxygen," they note, "and links hundreds of genes to oxygen homeostasis."

Finally, in a Cell commentary article, a pair of investigators from Fudan University and the University of Sydney look at what is known about the emergence of SARS-COV-2, and what may still be learned using genomic sequence data — from its relationship to other characterized betacoronaviruses and potential zoonotic origins to its mutation rate and future surveillance strategies. "[T]rying to determine the exact pattern and genomic ancestry of recombination events is difficult, particularly as many of the recombinant regions may be small and are likely to change as we sample more viruses related to SARS-CoV-2," the authors note. "To resolve these issues, it will again be necessary to perform a far wider sampling of viral diversity in animal populations."