Phylogenomic analysis of the Candida auris-Candida haemuli clade and related taxa in the Metschnikowiaceae, and proposal of thirteen new genera, fifty-five new combinations and nine new species.

Candida is a polyphyletic genus of asexually reproducing yeasts in the Saccharomycotina with more than 400 species that occur in almost all families of the subclass and its name is strongly connected with the infectious disease candidiasis. During the last two decades, approximately half of the Candida species have been reassigned into more than 36 already existing genera and 14 newly proposed genera, but the polyphyletic feature of the genus largely remained. Candida auris is an important, globally emerging opportunistic pathogen that has caused life-threatening outbreaks in healthcare facilities worldwide. This species belongs to the Candida auris-Candida haemuli (CAH) clade in the Metschnikowiaceae, a clade that contains multidrug-resistant clinically relevant species, but also species isolated from natural environments. The clade is phylogenetically positioned remotely from the type species of the genus Candida that is Candida vulgaris (currently interpreted as a synonym of Candida tropicalis) and belongs to the family Debaryomycetaceae. Although previous phylogenetic and phylogenomic studies confirmed the position of C. auris in the Metschnikowiaceae, these analyses failed to resolve the position of the CAH clade within the family and its delimitation from the genera Clavispora and Metschnikowia. To resolve the position of the CAH clade, phylogenomic and comparative genomics analyses were carried out to address the phylogenetic position of C. auris and related species in the Metschnikowiaceae using several metrics, such as the average amino acid identity (AAI) values, the percentage of conserved proteins (POCP) and the presence-absence patterns of orthologs (PAPO). Based on those approaches, 13 new genera are proposed for various Candida and Hyphopichia species, including members of the CAH clade in the Metschnikowiaceae. As a result, C. auris and related species are reassigned to the genus Candidozyma. Fifty-five new combinations and nine new species are introduced and this will reduce the polyphyly of the genus Candida. Citation: Liu F, Hu Z-D, Zhao X-M, et al. 2024. Phylogenomic analysis of the Candida auris-Candida haemuli clade and related taxa in the Metschnikowiaceae, and proposal of thirteen new genera, fifty-five new combinations and nine new species. Persoonia 52: 22-43. https://doi.org/10.3767/persoonia.2024.52.02 .

Saccharomycetaceae: delineation of fungal genera based on phylogenomic analyses, genomic relatedness indices and genomics-based synapomorphies.

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.

[Development of a Ranking Tool for Scientificity, Transparency and Applicability of Clinical Practice Guidelines].

Objective: To address the limitations of existing methods and tools for evaluating clinical practice guidelines, we aimed to develop a comprehensive instrument focusing on the three main dimensions of guideline development: scientificity, transparency, applicability. We will use it to rank the guidelines according to the scores. We abbreviated it as STAR, and its reliability, validity and usability were also tested. Methods: A multidisciplinary expert working group was set up, including methodologists, statisticians, journal editors, medical professionals, and others. Scoping review, Delphi methods and hierarchical analysis were used to determine the final checklist of STAR. Results: The new instrument contained 11 domains and 39 items. Intrinsic reliability of each domain was indicated by Cronbach's α coefficient, with a average value of 0.646. The Cohen's kappa coefficients for methodological evaluators and clinical evaluators were 0.783 and 0.618. The overall content validity index was 0.905. The R2 for the criterion validity analysis was 0.76. The average score for usability of the items was 4.6, and the mean time spent to evaluate each guideline was 20 minutes. Conclusion: The instrument has good reliability, validity and evaluating efficiency, and can be used for evaluating and ranking guidelines more comprehensively.

[Arf6 regulates endometriotic epithelial-mesenchymal transition and mitochondrial distribution].

Objective: To investigate the role of adenosine diphosphate ribosylation factor 6 (Arf6) in the pathogenesis of endometriosis. Methods: Endometrial tissues were sampled from women who were hospitalized in the Affiliated Hospital of Medical School of Ningbo University and Ningbo Women and Children's Hospital from November 2020 to May 2021 with endometriosis (n=44, endometriosis group) and without endometriosis (n=17, control group). The expression of Arf6 protein in the endometrial tissues was detected by western blot. Endometrial epithelial cells from both groups were primary cultured and the distribution of intracellular mitochondria was detected by immunofluorescence. The expression of Arf6 protein was down-regulated by small interference RNA (siRNA), the distribution of mitochondria in cells with decreased Arf6 protein expression was observed, and the expression of mitochondria-related proteins development and differentiation enhancing factor 1 (DDEF1, also called AMAP1), reactive oxygen species 1 (ROS1) and epithelial-mesenchymal transition (EMT)-related proteins E-cadherin, vimentin were detected. Transwell assay was used to detect the changes in the migration ability of the cells. Results: Compared with the control group, ectopic endometrial tissue of endometriosis group showed high expression of Arf6 protein (0.174±0.019 vs 0.423±0.033; t=29.630, P<0.01); and in ectopic endometrial epithelial cells, mitochondria were distributed near the edge of the cell membrane. While Arf6 expression was down-regulated by siRNA, the distribution of mitochondria in ectopic cells returned to natural, close to the control level. In addition, the expression levels of AMAP1 and ROS1 in ectopic cells after Arf6 protein knockdown were significantly decreased. Transwell assay results indicated that knockdown of Arf6 could reduce the migration ability of ectopic epithelial cells [migration cell count: (34.3±7.5) cells]; and immunofluorescence verified low expression of E-cadherin but high expression of vimentin in ectopic epithelial cells, whereas knockdown of Arf6 protein E-cadherin expression increased but vimentin expression decreased. Conclusions: High expression of Arf6 protein in ectopic endometrial epithelial cells leads to the distribution of mitochondria tending to membrane marginalization, while inducing EMT, which are involved in the mechanism of endoheterosis pathogenesis.

Notch signaling is involved in regulation of LPS-induced macrophage apoptosis through JNK/NF-kB signaling pathway.

Notch signaling plays a critical role in the development and function of macrophages. The aim of the present study was to investigate the relationship between Notch signaling pathway and macrophage apoptosis after LPS stimulation. In RAW 264.7 cells, the mRNA expression of Jagged1, Hes1, Hes 5 and GM-CSF, and protein expression of NICD1 and GM-CSF were increased after LPS stimulation. Inhibition of Notch signaling by γ-secretase inhibitor DAPT and the suppression of Notch1 expression using siRNA both significantly prevented LPS induced activation of JNK and NF-kB, and simultaneously the expression of GM-CSF was also down regulated significantly. JNK inhibitor SP600125 was used to block the phosphorylation of JNK signaling, Western blot results showed that the activation of NF-kB was blocked and expression of GM-CSF was down-regulated. Finally, flow cytometry analyses showed that the Notch signaling was involved in the regulation of macrophage apoptosis after LPS stimulation. Our study showed that the Notch signaling pathway was activated and involved in the regulation of macrophage apoptosis after LPS stimulation through JNK/ NF-kB signaling regulated GM-CSF expression.

Diversity and phylogeny of basidiomycetous yeasts from plant leaves and soil: Proposal of two new orders, three new families, eight new genera and one hundred and seven new species.

Nearly 500 basidiomycetous yeast species were accepted in the latest edition of The Yeasts: A Taxonomic Study published in 2011. However, this number presents only the tip of the iceberg of yeast species diversity in nature. Possibly more than 99 % of yeast species, as is true for many groups of fungi, are yet unknown and await discovery. Over the past two decades nearly 200 unidentified isolates were obtained during a series of environmental surveys of yeasts in phyllosphere and soils, mainly from China. Among these isolates, 107 new species were identified based on the phylogenetic analyses of nuclear ribosomal DNA (rDNA) [D1/D2 domains of the large subunit (LSU), the small subunit (SSU), and the internal transcribed spacer region including the 5.8S rDNA (ITS)] and protein-coding genes [both subunits of DNA polymerase II (RPB1 and RPB2), the translation elongation factor 1-α (TEF1) and the mitochondrial gene cytochrome b (CYTB)], and physiological comparisons. Forty-six of these belong to 16 genera in the Tremellomycetes (Agaricomycotina). The other 61 are distributed in 26 genera in the Pucciniomycotina. Here we circumscribe eight new genera, three new families and two new orders based on the multi-locus phylogenetic analyses combined with the clustering optimisation analysis and the predicted similarity thresholds for yeasts and filamentous fungal delimitation at genus and higher ranks. Additionally, as a result of these analyses, three new combinations are proposed and 66 taxa are validated.

[Anemia status of Chinese rural women of reproductive age in 2012].

Objective: To study the hemoglobin concentration, anemia status and its determinant factors among Chinese rural women of reproductive age in 2012. Methods: This was a cross-sectional study. The data was obtained from the National Free Preconception Health Examination Project (NFPHEP). A total of 712 101 Chinese rural reproductive age women aged 21-49 years old who came from 193 counties of 30 provinces were included. The demographic characteristics were obtained from questionnaires. Hemoglobin concentration was measured using the cyanomethemoglobin method. The definition of anemia we used was recommended by World Health Organization, and was adjusted according to altitude level. The hemoglobin concentration level, the prevalence of anemia and its 95% CI was calculated. Determinant factors of anemia such as demographic characteristics and histories of pregnancy and miscarriage were analyzed using logistic regression. Results: In 2012, the level of hemoglobin concentration in Chinese rural women of reproductive age was (127.77±13.47) g/L, with the lowest in 21-24 years group, which was (127.54±13.54) g/L, and highest in 35-39 years group, which was (128.39±14.12) g/L. In terms of region, the hemoglobin concentration level was lowest in central south, which was (125.79±12.00) g/L, and highest in southwest, which was (129.91±14.37) g/L. The prevalence of anemia in Chinese rural women of reproductive age was 24.80%, with the highest seen in 21-24 years, which was 25.92% (95% CI: 25.74%-26.11%), and lowest in 30-34 years, which was 23.61% (95% CI: 23.37%-23.85%). The prevalence in northwest (28.31%, 95% CI: 28.01%-28.61%) was the highest among all regions, and the prevalence in east (20.88%, 95% CI: 20.68%-21.09%) was the lowest. Conclusions: The prevalence of anemia in Chinese rural reproductive age women was 24.80% in 2012. The anemia prevalence was higher among women who were young, had low educational level, and lived in northwest region.

[Significance of hydroxymethylglutaryl-CoA synthase 2 on prognosis of esophageal squamous cell carcinoma].

Objective: To explore the roll and function of hydroxymethylglutaryl-CoA synthase 2 (HMGCS2) in the development and progression of human esophageal squamous cell carcimoma(ESCC). Method: Using immunohistochemistry, the expression of HMGCS2 was determined in 150 primary ESCC patients from July 2002 to December 2005 in the People's Hospital of Linzhou City, Henan Province. And HMGCS2 over-expression ESCC cell lines were established to verify HMGCS2 gene function. Result: In 150 cases of ESCCs, the expression rate of HMGCS2 was 58% (87/150), which was lower than 72% (108/150) in paired normal tissues, the difference was statistically significant (P=0.013). HMGCS2 down-regulated expression was associated with tumor cell differentiation (P=0.022), pT status (P=0.036), pN status (P=0.017) and TNM stage(P=0.012). The 5-years disease-specific survival (DSS) in down HMGCS2 expression group (14 months) was poorer than those in normal expression group (20 months; P=0.002). In addition, multivariate Cox regression analysis showed that HMGCS2 expression (Wald=7.136, P=0.008) was an independent risk factor for DSS. Furthermore, functional studies demonstrated that HMGCS2 gene could suppress the tumorigenic ability of ESCC cells (OD: 0.79±0.04 vs 1.25±0.68; P=0.01), the formation of colone (number of colones: 30±10 vs 189±15, P=0.002), and cell motility (number of cells: 27±14 vs 222±40, P=0.009). Conclusion: HMGCS2 can inhibit the proliferation and migration of ESCC cells, and could be an important candidate tumor suppressor gene for ESCC.

Efficacy and safety of fosaprepitant in the prevention of nausea and vomiting following highly emetogenic chemotherapy in Chinese people: A randomized, double-blind, phase III study.

The prevention of chemotherapy-induced nausea and vomiting was one of the most challenging supportive care issues in oncology, especially to highly emetogenic chemotherapy (HEC). A total of 645 patients were randomized into fosaprepitant group (fosaprepitant/placebo 150 mg d1 in combination with granisetron and dexamethasone) or aprepitant group (aprepitant/placebo 125 mg d1; 80 mg d2-d3 plus granisetron and dexamethasone).The primary endpoint was the percentage of patients who had a complete response (CR) over the entire treatment course (0-120 hr, overall phase [OP]). It was assessed by using a non-inferiority model, with a non-inferiority margin of 10%. The difference of the CR rate was compared between two groups with chi-square analysis. Six hundred and twenty-six patients were included in the per protocol analysis. The percentage of patients with a CR in the fosaprepitant group was not inferior to that in the aprepitant group (90.85% versus 94.17%, p = .1302) during OP. Whether the cisplatin-based chemotherapy or not, the CR rate of the fosaprepitant group was not inferior to that of the aprepitant group. Both regimens were well tolerated. The most common adverse event was constipation. Fosaprepitant provided effective and well-tolerated control of nausea and vomiting associated with HEC in Chinese patients.

[Advances on epidemiological research of human infections with novel avian influenza A (H7N9) virus].

Human infections with novel avian influenza A(H7N9)virus was an emerging infectious disease discovered in March, 2013. As of June30, 2016, 770 cases of H7N9 were reported in worldwide including 315 deaths with 40.9% of high case fatality rate. Yangtze River Delta and Pearl River Delta were the high-prevalence area. Formerly, the cases of H7N9 were concentrated on the municipalities. However, most of the case-patients were from smaller cities or rural areas nowadays. The H7N9 human infections mainly occurred in winter and spring every waves as similar as seasonal and H5N1 human infections. Middle aged and old (the median age was 61 years) male patients were occupied the large proportion among the cases of H7N9. In addition, the phenomenon of the limited and unsustained human-to-human transmission were existed. At present, the 4 major epidemic waves had happened and human infections with novel avian influenza A (H7N9) virus could be outbreak regularly in China. In this paper, the pathogenic characteristics and disease distribution of H7N9 influenza A viruses were elaborated, with both transmission factors and control measures, which were helpful to provide the scientific evidence for prevention and control in H7N9avian influenza epidemic.

[Investigation on folic acid supplementation status among Chinese women in the first trimester of pregnancy].

OBJECTIVE: To investigate folic acid (FA) supplementation status among Chinese rural reproductive women in their early pregnancy, and to provide evidence for the evaluation of FA supplementation project from national basic public health services. METHODS: The data on intake status of FA supplementation from "National Free Preconception Health Examination Project (NFPHEP)" database between January 1, 2010 and December 31, 2012 was used and analyzed.A total of 902 270 women who achieved follow-up during early pregnancy from 220 pilot counties of 31 provinces were recruited. RESULTS: From 2010 to 2012, the rate of FA intake among women recuited were 73.58% (134 131/182 289), 75.88% (329 288/433 970) and 76.53% (218 896/286 011), respectively, which increased year by year (χtrend(2)=13 371.8, P<0.001). Among 682 315 women who took FA, 350 738(51.40%) women began to take FA 3 months before amenorrhea; 130 683 (19.15%) women began to take FA 1-2 months before amenorrhea, and 200 894 (29.44%) began to take FA after amenorrhea.Among 682 315 women who took FA, 645 310 (94.58%) women took it regularly, and 342 418 (50.18%) women took FA in a standardized way. CONCLUSIONS: The status of FA intake among Chinese rural women in the first trimester of pregnancy was good, and 75.62% (682 315/902 270) of them took FA.It is also important for basic public health services to improve the rate of FA intake and increase the rate of taking FA in a standardized way in Chinese rural pregnant women.

[Clinical results of transepithelial corneal collagen cross-linking in the treatment of keratoconus].

OBJECTIVE: To evaluate the effect of transepithelial corneal collagen cross-linking (CXL) in the treatment of keratoconus. METHODS: Prospective study. Sixteen eyes of 16 patients with keratoconus underwent transepithelial CXL, and the fellow eyes were considered as the controls. The mean age was (22.4±6.5) years old. In the CXL group, topical anesthesia (0.1% tetracaine) was given for 15 minutes, and 0.5% riboflavin was applied until saturated in the anterior chamber. Then an ultraviolet A irradiance of 3 mW/cm(2) on the cornea was performed for 30 minutes. Postoperative corneal reepithelization time was recorded. Preoperative and postoperative examinations included uncorrected distance visual acuity (UDVA), corrected distance visual acuity (CDVA), refractive error, topography, corneal biomechanical parameters, thinnest corneal thickness, and endothelial cell density. RESULTS: The mean corneal reepithelization time was 1.0(1.0 to 2.0) days. In the transepithelial CXL group, at the end of the 12-month follow-up, CDVA and refractive outcomes were significantly improved (P<0.05). Maximum K-value, anterior and posterior elevations were significantly decreased by (-2.23 ± 2.82)D (t=-3.153, P=0.007), (-4.69 ± 4.99) µm (t=-3.758, P=0.002), and (-13.94 ± 25.81) µm (t=-2.160, P=0.047), respectively. Corneal hysteresis, corneal resistance factor, thinnest corneal thickness, and endothelial cell density showed no significant difference (P>0.05). The differences in the changes of UDVA, CDVA, spherical equivalent refraction, and maximum K-value between the CXL and control groups were significant at 12 months (P<0.05). CONCLUSION: Transepithelial CXL is effective in optimizing the irregular corneal surface of keratoconus, and might halt its progression. (Chin J Ophthalmol, 2016, 52: 525-530).

[Finite element analysis of astigmatic keratotomy based on corneal biomechanical properties].

OBJECTIVE: To establish a finite-element biomechanical model of astigmatic keratotomy, and to investigate the impact of surgical parameters on corneal deformation, stress distribution and astigmatism correction. METHODS: With Rhinoceros modeling and Abaqus finite element analysis software, a three-dimensional finite-element model of astigmatic cornea was developed, and surgical parameters such as incision optical zone, incision depth and length were varied. Postoperative corneal stress, apical deformation and astigmatism correction were assessed. RESULTS: A significant increase of stress was noticed near corneal incisions, and maximum corneal stress decreased with the increase of incision depth. Both anterior and posterior corneal surface moved slightly forward postoperatively. Maximum corneal stress was 340 392, 361 022 and 214 187 Pa, and anterior and posterior apical deformation was 49.80, 51.64, 55.53 µm and 54.15, 55.91, 59.67 µm, with 45°, 60° and 90° in arc length of the incision, respectively. The refractive power decreased in steep meridian and increased in flat meridian, resulting in a total decrease of corneal astigmatism. The magnitude of astigmatism correction was 0.85, 1.59, 2.23 and 3.06 D with 30°, 45°, 60° and 90° in arc length of the incision, respectively. CONCLUSIONS: The finite-element biomechanical model of astigmatic keratotomy could be used to predict the optical outcomes after surgery. The magnitude of astigmatism correction is positively correlated with the surgical incision arc length. (Chin J Ophthalmol, 2016, 52: 674-680).

Phylogeny of tremellomycetous yeasts and related dimorphic and filamentous basidiomycetes reconstructed from multiple gene sequence analyses.

The Tremellomycetes (Basidiomycota) contains a large number of unicellular and dimorphic fungi with stable free-living unicellular states in their life cycles. These fungi have been conventionally classified as basidiomycetous yeasts based on physiological and biochemical characteristics. Many currently recognised genera of these yeasts are mainly defined based on phenotypical characters and are highly polyphyletic. Here we reconstructed the phylogeny of the majority of described anamorphic and teleomorphic tremellomycetous yeasts using Bayesian inference, maximum likelihood, and neighbour-joining analyses based on the sequences of seven genes, including three rRNA genes, namely the small subunit of the ribosomal DNA (rDNA), D1/D2 domains of the large subunit rDNA, and the internal transcribed spacer regions (ITS 1 and 2) of rDNA including 5.8S rDNA; and four protein-coding genes, namely the two subunits of the RNA polymerase II (RPB1 and RPB2), the translation elongation factor 1-α (TEF1) and the mitochondrial gene cytochrome b (CYTB). With the consideration of morphological, physiological and chemotaxonomic characters and the congruence of phylogenies inferred from analyses using different algorithms based on different data sets consisting of the combined seven genes, the three rRNA genes, and the individual protein-coding genes, five major lineages corresponding to the orders Cystofilobasidiales, Filobasidiales, Holtermanniales, Tremellales, and Trichosporonales were resolved. A total of 45 strongly supported monophyletic clades with multiple species and 23 single species clades were recognised. This phylogenetic framework will be the basis for the proposal of an updated taxonomic system of tremellomycetous yeasts that will be compatible with the current taxonomic system of filamentous basidiomycetes accommodating the 'one fungus, one name' principle.

Multigene phylogeny and taxonomic revision of yeasts and related fungi in the Ustilaginomycotina.

The subphylum Ustilaginomycotina (Basidiomycota, Fungi) comprises mainly plant pathogenic fungi (smuts). Some of the lineages possess cultivable unicellular stages that are usually classified as yeast or yeast-like species in a largely artificial taxonomic system which is independent from and largely incompatible with that of the smut fungi. Here we performed phylogenetic analyses based on seven genes including three nuclear ribosomal RNA genes and four protein coding genes to address the molecular phylogeny of the ustilaginomycetous yeast species and their filamentous counterparts. Taxonomic revisions were proposed to reflect this phylogeny and to implement the 'One Fungus = One Name' principle. The results confirmed that the yeast-containing classes Malasseziomycetes, Moniliellomycetes and Ustilaginomycetes are monophyletic, whereas Exobasidiomycetes in the current sense remains paraphyletic. Four new genera, namely Dirkmeia gen. nov., Kalmanozyma gen. nov., Golubevia gen. nov. and Robbauera gen. nov. are proposed to accommodate Pseudozyma and Tilletiopsis species that are distinct from the other smut taxa and belong to clades that are separate from those containing type species of the hitherto described genera. Accordingly, new orders Golubeviales ord. nov. with Golubeviaceae fam. nov. and Robbauerales ord. nov. with Robbaueraceae fam. nov. are proposed to accommodate the sisterhood of Golubevia gen. nov. and Robbauera gen. nov. with other orders of Exobasidiomycetes. The majority of the remaining anamorphic yeast species are transferred to corresponding teleomorphic genera based on strongly supported phylogenetic affinities, resulting in the proposal of 28 new combinations. The taxonomic status of a few Pseudozyma species remains to be determined because of their uncertain phylogenetic positions. We propose to use the term pro tempore or pro tem. in abbreviation to indicate the single-species lineages that are temporarily maintained.

Phylogenetic classification of yeasts and related taxa within Pucciniomycotina.

Most small genera containing yeast species in the Pucciniomycotina (Basidiomycota, Fungi) are monophyletic, whereas larger genera including Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces are polyphyletic. With the implementation of the "One Fungus = One Name" nomenclatural principle these polyphyletic genera were revised. Nine genera, namely Bannoa, Cystobasidiopsis, Colacogloea, Kondoa, Erythrobasidium, Rhodotorula, Sporobolomyces, Sakaguchia and Sterigmatomyces, were emended to include anamorphic and teleomorphic species based on the results obtained by a multi-gene phylogenetic analysis, phylogenetic network analyses, branch length-based methods, as well as morphological, physiological and biochemical comparisons. A new class Spiculogloeomycetes is proposed to accommodate the order Spiculogloeales. The new families Buckleyzymaceae with Buckleyzyma gen. nov., Chrysozymaceae with Chrysozyma gen. nov., Microsporomycetaceae with Microsporomyces gen. nov., Ruineniaceae with Ruinenia gen. nov., Symmetrosporaceae with Symmetrospora gen. nov., Colacogloeaceae and Sakaguchiaceae are proposed. The new genera Bannozyma, Buckleyzyma, Fellozyma, Hamamotoa, Hasegawazyma, Jianyunia, Rhodosporidiobolus, Oberwinklerozyma, Phenoliferia, Pseudobensingtonia, Pseudohyphozyma, Sampaiozyma, Slooffia, Spencerozyma, Trigonosporomyces, Udeniozyma, Vonarxula, Yamadamyces and Yunzhangia are proposed to accommodate species segregated from the genera Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces. Ballistosporomyces is emended and reintroduced to include three Sporobolomyces species of the sasicola clade. A total of 111 new combinations are proposed in this study.

Phylogeny of yeasts and related filamentous fungi within Pucciniomycotina determined from multigene sequence analyses.

In addition to rusts, the subphylum Pucciniomycotina (Basidiomycota) includes a large number of unicellular or dimorphic fungi which are usually studied as yeasts. Ribosomal DNA sequence analyses have shown that the current taxonomic system of the pucciniomycetous yeasts which is based on phenotypic criteria is not concordant with the molecular phylogeny and many genera are polyphyletic. Here we inferred the molecular phylogeny of 184 pucciniomycetous yeast species and related filamentous fungi using maximum likelihood, maximum parsimony and Bayesian inference analyses based on the sequences of seven genes, including the small subunit ribosomal DNA (rDNA), the large subunit rDNA D1/D2 domains, the internal transcribed spacer regions (ITS 1 and 2) of rDNA including the 5.8S rDNA gene; the nuclear protein-coding genes of the two subunits of DNA polymerase II (RPB1 and RPB2) and the translation elongation factor 1-α (TEF1); and the mitochondrial gene cytochrome b (CYTB). A total of 33 monophyletic clades and 18 single species lineages were recognised among the pucciniomycetous yeasts employed, which belonged to four major lineages corresponding to Agaricostilbomycetes, Cystobasidiomycetes, Microbotryomycetes and Mixiomycetes. These lineages remained independent from the classes Atractiellomycetes, Classiculomycetes, Pucciniomycetes and Tritirachiomycetes formed by filamentous taxa in Pucciniomycotina. An updated taxonomic system of pucciniomycetous yeasts implementing the 'One fungus = One name' principle will be proposed based on the phylogenetic framework presented here.

Towards an integrated phylogenetic classification of the Tremellomycetes.

Families and genera assigned to Tremellomycetes have been mainly circumscribed by morphology and for the yeasts also by biochemical and physiological characteristics. This phenotype-based classification is largely in conflict with molecular phylogenetic analyses. Here a phylogenetic classification framework for the Tremellomycetes is proposed based on the results of phylogenetic analyses from a seven-genes dataset covering the majority of tremellomycetous yeasts and closely related filamentous taxa. Circumscriptions of the taxonomic units at the order, family and genus levels recognised were quantitatively assessed using the phylogenetic rank boundary optimisation (PRBO) and modified general mixed Yule coalescent (GMYC) tests. In addition, a comprehensive phylogenetic analysis on an expanded LSU rRNA (D1/D2 domains) gene sequence dataset covering as many as available teleomorphic and filamentous taxa within Tremellomycetes was performed to investigate the relationships between yeasts and filamentous taxa and to examine the stability of undersampled clades. Based on the results inferred from molecular data and morphological and physiochemical features, we propose an updated classification for the Tremellomycetes. We accept five orders, 17 families and 54 genera, including seven new families and 18 new genera. In addition, seven families and 17 genera are emended and one new species name and 185 new combinations are proposed. We propose to use the term pro tempore or pro tem. in abbreviation to indicate the species names that are temporarily maintained.

Sevoflurane induces neurotoxicity in young mice through FAS/FASL signaling.

Sevoflurane, the most widely used anesthetic in clinical practice, has been shown to induce apoptosis, inhibit neurogenesis, and cause learning and memory impairment in young mice. However, the underlying mechanism is still unknown. In this study, wild-type and the FAS- or FAS ligand (FASL)-knockout mice (age 7 days) were exposed to sevoflurane or pure oxygen. Western blotting was used to examine the expression of FAS protein. Terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) and bromodeoxyuridine (BrdU) staining were employed to quantify the apoptotic cells and newborn cells in the hippocampus and Morris water maze (MWM) in order to evaluate learning and memory status. Sevoflurane significantly increased the expression of FAS protein in wild-type mice. Compared to FAS- and FASL-knockout mice treated with sevoflurane, sevoflurane-treated wild-type mice exhibited more TUNEL-positive hippocampal cells and less BrdU-positive hippocampal cells. The MWM showed that compared with FAS- and FASL-knockout mice treated with sevoflurane, sevoflurane treatment of wild-type mice significantly prolonged the escape latency and reduced platform crossing times. These data suggest that sevoflurane induces neurotoxicity in young mice through FAS-FASL signaling.