In PLOS Genetics, a Comenius University in Bratislava-led team presents findings from a genomic, transcriptomic, and proteomic analysis of Candida parapsilosis, a yeast species capable of metabolizing benzene- or benzoic acid-derived compounds. With short- and long-read sequence data, the team put together a 13 megabase, chromosome-level genome assembly for a C. parapsilosis strain called CLIB214, which was originally isolated from a patient treated for diarrhea in Puerto Rico. Along with their genome annotation efforts and phylogenetic analyses, the authors used RNA sequencing, proteomic profiling, and gene knockout-based transcription factor analyses to delve into the gentisate and 3-oxoadipate pathways that C. parapsilosis uses to deal with hydroxyderivative compounds. "We show that the genes coding for the substrate transporters and enzymes involved in both pathways are co-expressed and regulated by the transcriptional activators Otf1p and Gtf1p, respectively," they report, adding that the findings "reveal the connections of both pathways to central metabolism and organelle biogenesis and provide an insight into [the] evolution of metabolism of hydroxyaromatic compounds."
For a paper in PLOS One, researchers at the University of Michigan and Duke University search for genetic contributors to sepsis with an eye to developing a polygenic risk score. Starting with a genome-wide association study involving 2,261 sepsis patients and almost 13,100 unaffected controls profiled at some 14 million SNPs, the team came up with distinct polygenic risk scores for forms of sepsis known as Sepsis-2 and Sepsis-3, based on 772 Sepsis-2-associated variants and 442 variants associated with Sepsis-3. Through multivariate adjustment, the authors narrowed in on variants in dozens of genes apiece that were independently linked to either Sepsis-2 or Sepsis-3, along with 25 variants with overlapping associations in both sepsis types. "Sepsis-2 and Sepsis-3 have both separate and shared genetic variants," they write, noting that "[m]ost genetic variants have small effects sizes, but cumulatively, the polygenic risk scores have good discrimination."
Using single-cell RNA sequencing, investigators in the UK track Trypanosoma brucei transcriptomics across the trypanosomiasis-causing parasite's developmental stages. As it reports in PLOS Pathogens, the team performed single-cell RNA-seq on 388 trypanosome individuals isolated from the salivary glands, midgut, and other parts of infected tsetse fly vectors, identifying distinct cell types, transcriptional, and morphological features in the trypanosomes. "[W]e applied single-cell RNA sequencing to explore the heterogeneous trypanosome populations in the tsetse fly," the authors write, noting that their data is being made available to other members of the parasitology community through an online single-cell atlas resource.