Zhukova, N. | Search bioRxiv

bioRxiv2023

Pangenome- and genome-based taxonomic classification inference for the marine bacterial strain KMM 296 producing a highly active PhoA alkaline phosphatase and closely related Cobetia species

A strictly aerobic, Gram-stain-negative, rod-shaped and motile bacterium, designated strain KMM 296, isolated from the coelomic fluid of mussel Crenomytilus grayanus, was investigated in details due to its ability to produce a highly active alkaline phosphatase of the structural family PhoA. A previous taxonomic study placed the strain to the species Cobetia marina, a member of the family Halomonadaceae of the class Gammaproteobacteria. However, the comprehensive phylogenetic analysis based on 16S rRNA gene sequencing revealed that the strain KMM 296 is most closely related to Cobetia amphilecti NRIC 815T with the 16S rRNA gene sequence similarity of 100%. The mussel isolate grew with 0.5-19% NaCl and at 4 - 42{degrees}C and hydrolysed Tweens 20 and 40, and L-tyrosine. The DNA G+C content was 62.5 mol%. The prevalent fatty acids were C18:1 {omega}7c, C12:0 3-OH, C18:1 {omega}7c, C12:0 and C17:0 cyclo. The polar lipid profile was characterized by the presence of phosphatidylethanolamine, phosphatidylglycerol, phosphatidic acid, and unidentified aminolipid, phospholipid, and lipids. The major respiratory quinone was Q-8. According to phylogenetic evidence and similarity in the chemotaxonomic and genotypic properties of the mussel isolate and its nearest neighbors, the strain KMM 296 represents a member of the species C. amphilecti. A comparative analysis of the type strains genomes of the species C. amphilecti and C. litoralis showed that they belong to a single species. In addition, a high similarity of the genome sequences of C. pacifica NRIC 813T and C. marina LMG 2217T also allows suggesting the affiliation of these two species to one species. Based on the rules of priority, C. litoralis should be reclassified as a later heterotypic synonym of C. amphilecti, and C. pacifica is a later heterotypic synonym of C. marina. The emended descriptions of the species C. amphilecti and C. marina are also proposed.

microbiology↗

bioRxiv2022

A novel transcriptional signature identifies T-cell infiltration in high-risk paediatric cancer

Molecular profiling of the tumour immune microenvironment (TIME) has enabled the rational choice of immunotherapies in some adult cancers. In contrast, the TIME of paediatric cancers is relatively unexplored. We speculated that a more refined appreciation of the TIME in childhood cancers, rather than a reliance on commonly used biomarkers such as tumour mutation burden (TMB), neoantigen load and PD-L1 expression, is an essential prerequisite for improved immunotherapies in childhood solid cancers. We combined immunohistochemistry (IHC) and molecular profiling to develop an alternative, expression-based signature associated with CD8+ T-cell infiltration of the TIME in high-risk paediatric tumours. Using this novel 15-gene immune signature, Immune Paediatric Signature Score (IPASS), we estimate up to 31% of high-risk cancers harbour infiltrating T-cells. Our data provides new insights into the variable immune-suppressive mechanisms dampening responses in paediatric solid cancers. Effective immune-based interventions in high-risk paediatric cancer will require individualised analysis of the TIME.

cancer biology↗