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A correct classification of fungi, including yeasts, is of prime importance to understand fungal biodiversity and to communicate about this diversity. Fungal genera are mainly defined based on phenotypic characteristics and the results of single or multigene-based phylogenetic analyses. However, because yeasts often have less phenotypic characters, their classification experienced a strong move towards DNA-based data, from short ribosomal sequences to multigene phylogenies and more recently to phylogenomics. Here, we explore the usefulness of various genomics-based parameters to circumscribe fungal genera more correctly taking the yeast domain as an example. Therefore, we compared the results of a phylogenomic analysis, average amino acid identity (AAI) values, the presence of conserved signature indels (CSIs), the percentage of conserved proteins (POCP) and the presence-absence patterns of orthologs (PAPO). These genome-based metrics were used to investigate their usefulness in demarcating 13 hitherto relatively well accepted genera in Saccharomycetaceae, namely Eremothecium, Grigorovia, Kazachstania, Kluyveromyces, Lachancea, Nakaseomyces, Naumovozyma, Saccharomyces, Tetrapisispora, Torulaspora, Vanderwaltozyma, Zygosaccharomyces and Zygotorulaspora. As a result, most of these genera are supported by the genomics-based metrics, but the genera Kazachstania, Nakaseomyces and Tetrapisispora were shown to be genetically highly diverse based on the above listed analyses. Considering the results obtained for the presently recognized genera, a range of 80-92 % POCP values and a range of 60-70 % AAI values might be valuable thresholds to discriminate genera in Saccharomycetaceae. Furthermore, the genus-specific genes identified in the PAPO analysis and the CSIs were found to be useful as synapomorphies to characterize and define genera in Saccharomycetaceae. Our results indicate that the combined monophyly-based phylogenomic analysis together with genomic relatedness indices and synapomorphies provide promising approaches to delineating yeast genera and likely those of filamentous fungi as well. The genera Kazachstania, Nakaseomyces and Tetrapisispora are revised and we propose eight new genera and 41 new combinations. Citation: Liu F, Hu Z-D, Yurkov A, et al. 2024. Saccharomycetaceae: delinaeation of fungal genera based on phylogenomic analyses, genomic relatedness indices and genomics-based synapomorphies. Persoonia 52: 1-21. https://doi.org/10.3767/persoonia.2024.52.01.

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Objective: To investigate the clinicopathological features of glomuvenous malformation (GVM). Methods: Thirty-one cases of GVM diagnosed at the Henan Provincial People's Hospital from January 2011 to December 2021 were collected. Their clinical and pathological features were analyzed. The expression of relevant markers was examined using immunohistochemistry. The patients were also followed up. Results: There were 16 males and 15 females in this study, with an average age of 11 years (range, 1-52 years). The locations of the disease included 13 cases in the limbs (8 cases in the upper limbs, 5 cases in the lower limbs), 9 cases in the trunks, and 9 cases in the foot (toes or subungual area). Twenty-seven of the cases were solitary and 4 were multifocal. The lesions were characterized by blue-purple papules or plaques on the skin surface, which grew slowly. The lumps became larger and appeared to be conspicuous. Microscopically, GVM mainly involved the dermis and subcutaneous tissue, with an overall ill-defined border. There were scattered or clustered irregular dilated vein-like lumens, with thin walls and various sizes. A single or multiple layers of relatively uniform cubic/glomus cells were present at the abnormal wall, with scattered small nests of the glomus cells. The endothelial cells in the wall of abnormal lumen were flat or absent. Immunohistochemistry showed that glomus cells strongly expressed SMA, h-caldesmon, and collagen IV. Malformed vascular endothelial cells expressed CD31, CD34 and ERG. No postoperative recurrence was found in the 12 cases. Conclusions: GVM is an uncommon type of simple venous malformation in the superficial soft tissue and different from the classical glomus tumor. Morphologically, one or more layers of glomus cells grow around the dilated venous malformation-like lumen, which can be combined with common venous malformations.

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We utilized in situ hybridization to detect expression and regulation of cytolysin mRNA in microglia, astrocytes and oligodendrocytes from newborn rat brains. Expression under natural culture conditions was undetectable or very low, even after 10 days of culture. Cytolysin mRNA expression in microglia, astrocytes and oligodendrocytes was up-regulated by IFN-gamma. This up-regulation in glial cells was slow, and characterized by a gradually increased expression until day 10 of culture. IFN-gamma-mediated up-regulation of cytolysin mRNA was markedly more prominent in oligodendrocytes than in microglia and astrocytes. Unexpectedly, a combination of LPS and IFN-gamma did not exhibit a synergistic effect in the induction of cytolysin mRNA expression in the three types of glial cells. On the contrary, LPS strongly inhibited IFN-gamma-mediated cytolysin mRNA expression in microglia, astrocytes and oligodendrocytes. These results reveal that there may exist a glial cell-dependent cytotoxic pathway within the CNS, and that inducible cytolysin may play an important role in destruction of oligodendrocytes or clearance of infiltrating cells within the CNS in inflammatory diseases such as multiple sclerosis or experimental allergic encephalomyelitis.

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Cellobiose:quinone oxidoreductase (CBQase) in the presence of cellobiose inhibits peroxidase-catalyzed oxidation of iodide to triiodide (I3). This inhibition is due to the two-electron reduction of I3- by CBQase. The apparent Km of I3- for this reaction is 120 microM and the specific activity is 57 mumol.min-1.mg-1. A proposed mechanism for I3- reduction by CBQase involves initial reduction of the flavin moiety by cellobiose to produce a dihydroflavin. This is followed by the substitution of one of the iodine atoms of I3- at the C(4a)-position of dihydroflavin to generate C(4a)-iododihydroflavin and two iodide ions. The C(4a)-iododihydroflavin eliminates HI to regenerate the oxidized CBQase.

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