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This Week in Cell: May 1, 2019


An international team led by Ohio State University researchers presents findings from a DNA-based survey of marine virus genomes from nearly 200 samples from around the world for the Global Ocean Viromes 2.0 dataset or the Tara Oceans Polar Circle expedition. Using metagenomic sequencing, assembly, and viral detection methods, the researchers profiled samples collected at a range of depths in Arctic, Antarctic, Temperate, and Tropical regions, ultimately uncovering almost 196,000 viral populations. "Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions," they write, adding that viral diversity within and between populations "sometimes, but not always, paralleled those from macro-organisms."

German and Swiss researchers explore genetic and environmental contributors to the proteome output for a given genotype, or proteotype. After tallying proteotype variation based on protein co-variation and protein complex patterns in a meta-analysis of 11 publicly available mouse or human mass spec-based shotgun proteomic datasets, the team attempted to quantify to genetic sex and diet-related impacts on the abundance and composition of protein complexes. The results hint that almost 14 percent of protein complex variation was influenced by genetic sex, for example, while diet appeared to contribute to nearly 12 percent of protein complex variability, based on proteomic data for mice that received a specific diet type. "Leveraging the modular architecture of the proteome, we show that some complexes have a stable composition throughout different proteomic datasets, whereas other complexes are subject to considerable variation across cell types as well as individuals," the authors note.

Finally, researchers from the University of Zurich and elsewhere describe a single-cell atlas representing proteomic profiles in tumor and immune cells from 144 individuals with breast cancer, comparing them with breast tissue from 50 healthy individuals. With protein expression profiles for some 26 million cells assessed by mass-tag barcoding, tumor- or immune cell-specific antibody staining, and mass cytometry, the team documented heterogeneity in the tumor and immune cells, as well as the relationships between them. When they looked at the interactions between proteomic patterns in the tumor and immune cells in the context of the breast cancer patients' clinical outcomes, meanwhile, the authors saw "characteristics of ecosystems related to immunosuppression and poor prognosis."