Extensive remodeling of sugar metabolism through gene loss and horizontal gene transfer in a eukaryotic lineage.

BACKGROUND: In yeasts belonging to the subphylum Saccharomycotina, genes encoding components of the main metabolic pathways, like alcoholic fermentation, are usually conserved. However, in fructophilic species belonging to the floral Wickerhamiella and Starmerella genera (W/S clade), alcoholic fermentation was uniquely shaped by events of gene loss and horizontal gene transfer (HGT). RESULTS: Because HGT and gene losses were first identified when only eight W/S-clade genomes were available, we collected publicly available genome data and sequenced the genomes of 36 additional species. A total of 63 genomes, representing most of the species described in the clade, were included in the analyses. Firstly, we inferred the phylogenomic tree of the clade and inspected the genomes for the presence of HGT-derived genes involved in fructophily and alcoholic fermentation. We predicted nine independent HGT events and several instances of secondary loss pertaining to both pathways. To investigate the possible links between gene loss and acquisition events and evolution of sugar metabolism, we conducted phenotypic characterization of 42 W/S-clade species including estimates of sugar consumption rates and fermentation byproduct formation. In some instances, the reconciliation of genotypes and phenotypes yielded unexpected results, such as the discovery of fructophily in the absence of the cornerstone gene (FFZ1) and robust alcoholic fermentation in the absence of the respective canonical pathway. CONCLUSIONS: These observations suggest that reinstatement of alcoholic fermentation in the W/S clade triggered a surge of innovation that goes beyond the utilization of xenologous enzymes, with fructose metabolism playing a key role.

The role of glycated hemoglobin in the diagnosis of prediabetes and diabetes mellitus in young women with polycystic ovary syndrome.

OBJECTIVE: To compare glycated hemoglobin (HbA1c) and the oral glucose tolerance test (OGTT) for the diagnosis of prediabetes and diabetes in young women with polycystic ovary syndrome (PCOS). PATIENTS AND DESIGN: This cross-sectional study included 154 women aged 20-40 years with a diagnosis of PCOS, who were screened for prediabetes and diabetes by the OGTT and HbA1c. Women with diabetes, hyperprolactinemia, thyroid or adrenal diseases, and anemia and users of hormonal contraception or corticosteroids were excluded. MEASUREMENTS: Clinical, biochemical and ultrasound data were collected from the electronic medical records. The women were classified as having normal glucose metabolism, prediabetes, or diabetes based on the diagnostic tests. Sensitivity and specificity were calculated and the Kappa method was used to assess agreement between the two methods. RESULTS: According to the OGTT and HbA1c values, 79.2% and 76% of the women were within the normal range, respectively, 16.8% and 19.5% had prediabetes, and 4% and 4.5% had diabetes (p > .05). The Kappa coefficient of 0.41 (95% confidence interval: 0.24-0.58) indicated medium agreement between methods. Considering the OGTT as the gold standard, the specificity of HbA1c was 89.5% and sensitivity was 85.7% in the diagnosis of prediabetes and 100% and 66.7%, respectively, in the diagnosis of diabetes. CONCLUSION: The HbA1c, when compared to the OGTT, showed high sensitivity and specificity in the diagnosis of prediabetes in young women with PCOS.

Phylogenomic delineation of two new species of ascomycetous yeasts, Wickerhamiella koratensis sp. nov. and Wickerhamiella limtongiae sp. nov., and proposal of two synonyms, Wickerhamiella infanticola and Wickerhamiella tropicalis.

Two novel ascomycetous yeast species of the genus Wickerhamiella are proposed based on isolates obtained in Thailand from food waste and the fruiting body of a polypore fungus, and on a combination of conventional DNA-barcode sequence analyses and whole-genome phylogenies. We focus on a particular subclade of the genus Wickerhamiella that contains species found in anthropic environments and describe Wickerhamiella limtongiae sp. nov. (DMKU-FW31-5T=PYCC 9022T=TBRC 15055T), found on food waste samples. In an adjacent clade, we describe Wickerhamiella koratensis sp. nov. (DMKU-KO16T=PYCC 8908T=TBRC 14869T), which represents the closest relative of Wickerhamiella slavikovae and was isolated from the fruiting body of Bjerkandera sp. In the subclade of W. limtongiae sp. nov., we propose that Wickerhamiella infanticola should be regarded as a synonym of Wickerhamiella sorbophila and that Wickerhamiella tropicalis should be regarded as a synonym of Wickerhamiella verensis.

Taxogenomic analyses of Starmerella gilliamiae f.a, sp. nov. and Starmerella monicapupoae f.a., sp. nov., two novel species isolated from plant substrates and insects.

Four yeast isolates collected from flowers from different ecosystems in Brazil, one from fruit of Nothofagus alpina in Argentina, three from flowers of Neltuma chilensis in Chile and one obtained from the proventriculus of a female bumblebee in Canada were demonstred, by analysis of the sequences of the internal transcribed spacer (ITS) region and D1/D2 domains of the large subunit rRNA gene, to represent two novel species of the genus Starmerella. These species are described here as Starmerella gilliamiae f.a, sp. nov. (CBS 16166T; Mycobank MB 851206) and Starmerella monicapupoae f.a., sp. nov. (PYCC 8997T; Mycobank MB 851207). The results of a phylogenomic analysis using 1037 single-copy orthogroups indicated that S. gilliamiae is a member of a subclade that contains Starmerella opuntiae, Starmerella aceti and Starmerella apicola. The results also indicated that S. monicapupoae is phylogenetically related to Starmerella riodocensis. The two isolates of S. monicapupoae were obtained from flowers in Brazil and were probably vectored by insects that visit these substrates. Starmerella gilliamiae has a wide geographical distribution having been isolated in flowers from Brazil and Chile, fruit from Argentina and a bumblebee from Canada.

A glimpse at an early stage of microbe domestication revealed in the variable genome of Torulaspora delbrueckii, an emergent industrial yeast.

Microbe domestication has a major applied relevance but is still poorly understood from an evolutionary perspective. The yeast Torulaspora delbrueckii is gaining importance for biotechnology but little is known about its population structure, variation in gene content or possible domestication routes. Here, we show that T. delbrueckii is composed of five major clades. Among the three European clades, a lineage associated with the wild arboreal niche is sister to the two other lineages that are linked to anthropic environments, one to wine fermentations and the other to diverse sources including dairy products and bread dough (Mix-Anthropic clade). Using 64 genomes we assembled the pangenome and the variable genome of T. delbrueckii. A comparison with Saccharomyces cerevisiae indicated that the weight of the variable genome in the pangenome of T. delbrueckii is considerably smaller. An association of gene content and ecology supported the hypothesis that the Mix-Anthropic clade has the most specialized genome and indicated that some of the exclusive genes were implicated in galactose and maltose utilization. More detailed analyses traced the acquisition of a cluster of GAL genes in strains associated with dairy products and the expansion and functional diversification of MAL genes in strains isolated from bread dough. In contrast to S. cerevisiae, domestication in T. delbrueckii is not primarily driven by alcoholic fermentation but rather by adaptation to dairy and bread-production niches. This study expands our views on the processes of microbe domestication and on the trajectories leading to adaptation to anthropic niches.

Association between sickle cell disease and periodontal disease: A systematic review.

Previous studies have evaluated the association between sickle cell disease (SCD) and periodontal disease; however, their effect on the periodontal parameters remains unclear. This systematic review aimed to investigate whether individuals with sickle cell disease (SCD) increase the risks of periodontal disease more than those without. For the selection of eligible studies, an electronic search was conducted in the MEDLINE/PubMed, Web of Science, Cochrane Library, and Scopus databases. The meta-analysis was based on the inversion of variance using the mean difference (MD) of the continuous outcomes. The quality assessment of included studies was performed using the JBI Critical Appraisal Tools. In total, 13 studies and 2381 participants were included in the qualitative analysis, while 9 studies were considered for the meta-analysis. The meta-analysis indicated that patients with SCD present similar Plaque Index, Clinical Attachment Level, Bleeding on Probing, and Probing Depth when compared to healthy patients (p > .05). However, the Gingival Index was higher for patients with SCD (p = .0002; MD: 0.20). Compared to healthy patients, patients with SCD did not have an increase in periodontal parameters, except for the gingival index. However, further well-designed studies are recommended to reassess the association between SCD and periodontal diseases.

Do microbes evade domestication? - Evaluating potential ferality among diastatic Saccharomyces cerevisiae.

Certain lineages of the wine, beer and bread yeast Saccharomyces cerevisiae have diastatic activity. They contain the chimeric gene STA1 that codes for an extracellular glucoamylase which enables the strains to degrade starch and dextrins. Beer contaminations by diastatic yeasts can be dangerous because they can cause super-attenuation due to the consumption of otherwise non-fermentable oligosaccharides, gushing and off-flavours. Given that diastatic yeasts can be used for beer fermentation it is important to understand the relationship between production and contaminant strains, their natural reservoirs and entry routes into the brewery. Here, we analyze real cases of contamination in a Portuguese craft brewery over a period of 18 months. By analyzing with whole genome sequencing several contaminants, we show that recurrent contaminations by diastatic yeasts are caused by environmental strains. Moreover, some beer contaminants were closely related to diastatic environmental strains isolated in Botswana. We observed the widespread presence of domestication signatures in diastatic strains. Moreover, the combined phylogeny of STA1 and its ancestor, SGA1, suggested a single STA1 origin, as ancient as the entire lineage of diastatic yeasts. Together, our results suggest that diastatic yeasts isolated in natural settings could be escaping from domestication settings and becoming feral.

Assessment of fetal heart aortic and pulmonary valve annulus area by three-dimensional ultrasonography: reference curves and applicability in congenital heart diseases.

OBJECTIVES: To determine reference curves for fetal aortic and pulmonary valve annulus area by three-dimensional ultrasonography using the spatio-temporal image correlation (STIC) in the rendering mode, and to ascertain its applicability in congenital heart disease (CHD). METHODS: We performed a retrospective cross-sectional study of 328 normal fetuses and 42 fetuses with CHD between 20 and 33 weeks 6 days of gestation. The outflow plane view of the great vessels was used to measure the areas of the valvar annuli, and the measurements were performed in systole. A linear regression model adjusted according to the determination coefficient (R2) was utilized to construct the reference intervals. The concordance correlation coefficient (CCC) was used to calculate the reproducibility of the mitral and tricuspid valve areas. RESULTS: The mean ± standard deviation (SD) of the aortic and pulmonary valve annulus areas ranged from 6.6 ± 1.2 to 32.9 ± 1.1 mm2 and 10.7 ± 1.3 to 40.3 ± 1.2 mm2, respectively. We observed a linear relationship and strong positive correlation between the area of the aortic and pulmonary valve annuli with r=0.97 and 0.96, respectively. Good intra (CCC=0.99) and interobserver agreement (CCC=0.98) was observed for the measurement of the aortic valve annulus area. A good intra (CCC=0.99) and interobserver (CCC=0.97) agreement was also observed for the measurement of the pulmonary valve annulus area. The mean ± SD of the difference of the areas of the aortic and pulmonary valve annuli between the normal fetuses and those with CHD were -1.801 ± 1.429 mm2 (p=0.208) and -1.033 ± 1.467 mm2 (p<0.0001), respectively. CONCLUSIONS: The reference curves for the areas of the aortic and pulmonary valve annuli of fetal hearts were determined, and showed good inter and intraobserver reproducibility. The constructed reference curves showed applicability in different types of CHD.

Global distribution of IRC7 alleles in Saccharomyces cerevisiae populations: a genomic and phenotypic survey within the wine clade.

The adaptation to the different biotic and abiotic factors of wine fermentation has led to the accumulation of numerous genomic hallmarks in Saccharomyces cerevisiae wine strains. IRC7, a gene encoding a cysteine-S-ß-lyase enzyme related volatile thiols production in wines, has two alleles: a full-length allele (IRC7F ) and a mutated one (IRC7S ), harbouring a 38 bp-deletion. Interestingly, IRC7S -encoding a less active enzyme - appears widespread amongst wine populations. Studying the global distribution of the IRC7S allele in different yeast lineages, we confirmed its high prevalence in the Wine clade and demonstrated a minority presence in other domesticated clades (Wine-PDM, Beer and Bread) while it is completely missing in wild clades. Here, we show that IRC7S -homozygous (HS) strains exhibited both fitness and competitive advantages compared with IRC7F -homozygous (HF) strains. There are some pieces of evidence of the direct contribution of the IRC7S allele to the outstanding behaviour of HS strains (i.e., improved response to oxidative stress conditions and higher tolerance to high copper levels); however, we also identified a set of sequence variants with significant co-occurrence patterns with the IRC7S allele, which can be co-contributing to the fitness and competitive advantages of HS strains in wine fermentations.

Phaffia brasiliana sp. nov., a yeast species isolated from soil in a Cerrado-Atlantic Rain Forest ecotone site in Brazil.

During studies of yeasts associated with soil in a Cerrado-Atlantic Rain Forest ecotone site in Brazil, three orange-pigmented yeast strains were isolated from samples collected in Minas Gerais state, Brazil. Molecular analyses combining the 26S rRNA gene (D1/D2 domains) and the internal transcribed spacer (ITS) sequences as well as whole-genome sequence data showed that these strains could not be ascribed to any known species in the basidiomycetous genus Phaffia, and thus they are considered to represent a novel species for which the name Phaffia brasiliana sp. nov. is proposed. The holotype is CBS 16121T and the MycoBank number is MB 839315. The occurrence of P. brasiliana in a tropical region is unique for the genus, since all other species occur in temperate regions. Two factors appear to contribute to the distribution of the novel taxon: first, the region where it was found has relatively moderate temperature ranges and, second, an adaptation to grow or withstand temperatures higher than those of the other species in the genus seems to be in place.

Cryolevonia gen. nov. and Cryolevonia schafbergensis sp. nov., a cryophilic yeast from ancient permafrost and melted sea ice.

A cryophilic basidiomycetous yeast unable to grow at 18 °C or higher temperatures was isolated from a subsurface permafrost layer collected in the Eastern Swiss Alps and from melted sea ice collected in the Artic at Frobisher Bay, Nunavut, Canada. Phylogenetic analyses employing combined sequences of the D1/D2 domain and ITS region indicated that the two new isolates belong to the family Camptobasidiaceae of the class Microbotryomycetes but are distantly related to any of the currently recognized species and genera. Consequently, the novel genus Cryolevonia, and the novel species Cryolevonia schafbergensis (type strain PYCC 8347T=CBS 16055T) are proposed to accommodate this cryophilic yeast. Although sparse hyphae and teliospore-like stuctures were observed upon prolonged incubation, a sexual cycle was not observed and therefore C. schafbergensis is documented solely from its asexual stage.

Occlusal device with extraoral retention: An occlusal technique for patients with Down syndrome.

Temporomandibular disorders associated with bruxism have a high prevalence rate in the overall population, including individuals with Down syndrome (DS). Occlusal devices have been prescribed for the treatment of temporomandibular disorders and prevention of tooth wear due to bruxism. Patients with DS have restrictions concerning treatment with occlusal devices, with an increased risk of swallowing and asphyxia, because of limitations with cognitive ability and motor deficiency. Therefore, an occlusal device with extraoral retention was developed to improve the safety for a patient with DS. An extraoral transverse rod was connected to the occlusal device to prevent it from being swallowed. The patient used the device safely for 4 weeks.

Papiliotrema plantarum sp. nov., a novel tremellaceous sexual yeast species.

During a survey of the yeast community associated with the phylloplane of corn in Thailand, a basidiomycetous yeast strain belonging to the genus Papiliotrema was isolated. Analyses of the D1/D2 domains of the 26S (LSU) rRNA gene and complete ITS region supported the recognition of a novel species, for which the name Papiliotrema plantarum sp. nov. is proposed (type strain DMKU-CP801T=CBS 15220T=PYCC 7257T). Another strain of P. plantarum sp. nov., isolated in French Guiana, was found to be sexually compatible with the Thai isolate and mycelium with clamp connections, basidia and basidiospores were observed in culture. The basidial morphology of P. plantarum combined features previously observed for Papiliotrema bandonii and Papiliotrema fuscus, which represent the only sexual species hitherto known in the genus, i.e. transversely septate basidia, with sexual structures of the Tremella type.

Occultifur mephitis f.a., sp. nov. and other yeast species from hypoxic and elevated CO2 mofette environments.

An inventory of culturable yeasts from the soil and water of natural CO2 springs (mofettes) in northeast Slovenia is presented. In mofettes, CO2 of geological origin reaches the soil surface causing temporarily and spatially stable hypoxic environments in soil and water. In total, 142 yeast strains were isolated and identified from high CO2 and control meadow soil, meadow ground-water, forest pond and stream water. All water locations showed below-ground CO2 release. They were assigned to six basidiomycetous yeast genera (six species) and 11 ascomycetous genera (18 species). All ascomycetous yeasts, with the exception of Debaryomyces hansenii, were able to grow under elevated CO2 and fermented glucose. Candida sophiae-reginae, Pichia fermentans and Candida vartiovaarae were the dominating species in meadow and forest high CO2 exposed water. Meyerozyma guilliermondii and Wickerhamomyces anomalus predominated in high CO2 exposed soils. Using high dilution plating of a mofette soil sample, four strains of an unknown basidiomycetous species were isolated and are here newly described as Occultifur mephitis based on molecular phylogenetic and phenotypic criteria. The type strain of Occultifur mephitis is EXF-6436T[CBS 14611=PYCC 7049, LT594852 (D1/D2), KX929055 (ITS)]. An additional three isolated strains are EXF-6437 (LT594853, KX929056), EXF-6473 (LT594863, KX929057) and EXF-6482 (LT594867, KX929054), as well as a strain reported from previous studies isolated from a leaf of Cistus albidus in Portugal (CBS 10223=PYCC 6067), EU002842 (D1/D2), KY308183 (ITS).

Libkindia masarykiana gen. et sp. nov., Yurkovia mendeliana gen. et sp. nov. and Leucosporidium krtinense f.a. sp. nov., isolated from temperate forest soils.

One hundred and ninety-eight isolates of soil yeasts were isolated from mixed temperate forests in the Czech Republic, and their abundance and distribution in the litter and soil were evaluated using amplicon sequencing of soil fungal communities. Abundant taxa with no close identified hits were selected for further characterization as potential novel species of yeasts. Phylogenetic analyses using sequences of the D1/D2 domain, the ITS region and RPB1 and TEF1 genes support the recognition of the following three novel species belonging to the subphylum Pucciniomycotina, class Microbotryomycetes: Leucosporidium krtinense f.a. sp. nov. (type strain PYCC 6879T=KT96T=CBS 14304T=DSM 101892T), Yurkovia mendeliana sp. nov. (type strain PYCC 6884T=KT152T=CBS 14273T=DSM 101889T) and Libkindia masarykiana sp. nov. (type strain PYCC 6886T=KT310T=CBS 14275T=DSM 101891T). Since the latter two novel taxa cannot be assigned to existing genera, two new genera, Libkindia gen. nov. and Yurkovia gen. nov., are also described.

Cryptotrichosporon argae sp. nov., Cryptotrichosporon brontae sp. nov. and Cryptotrichosporon steropae sp. nov., isolated from forest soils.

Yeast strains belonging to the basidiomycetous genus Cryptotrichosporon were isolated from forest soils in Serra da Arrábida Natural Park in Portugal. Similar to the already-known representatives of this genus, the new isolates formed pigmented colonies of a distinctive pale orange colour. Phylogenetic analyses employing concatenated sequences of the D1/D2 domains of the 26S (large subunit) rRNA gene and the internal transcribed spacer (ITS) region supported the recognition of three novel species: Cryptotrichosporon argae sp. nov. (type strain CM 19T=CBS 14376T=PYCC 7010T=DSM 104550T; MycoBank accession number MB 817168), Cryptotrichosporon brontae sp. nov. (type strain CM 1562T=CBS 14303T=PYCC 7011T=DSM 104551T; MycoBank accession number MB 817077) and Cryptotrichosporon steropae sp. nov. (type strain OR 395T=CBS 14302T=PYCC 7012T=DSM 104552T; MycoBank accession number MB 817078).

Local climatic conditions constrain soil yeast diversity patterns in Mediterranean forests, woodlands and scrub biome.

Soil yeasts represent a poorly known fraction of the soil microbiome due to limited ecological surveys. Here, we provide the first comprehensive inventory of cultivable soil yeasts in a Mediterranean ecosystem, which is the leading biodiversity hotspot for vascular plants and vertebrates in Europe. We isolated and identified soil yeasts from forested sites of Serra da Arrábida Natural Park (Portugal), representing the Mediterranean forests, woodlands and scrub biome. Both cultivation experiments and the subsequent species richness estimations suggest the highest species richness values reported to date, resulting in a total of 57 and 80 yeast taxa, respectively. These values far exceed those reported for other forest soils in Europe. Furthermore, we assessed the response of yeast diversity to microclimatic environmental factors in biotopes composed of the same plant species but showing a gradual change from humid broadleaf forests to dry maquis. We observed that forest properties constrained by precipitation level had strong impact on yeast diversity and on community structure and lower precipitation resulted in an increased number of rare species and decreased evenness values. In conclusion, the structure of soil yeast communities mirrors the environmental factors that affect aboveground phytocenoses, aboveground biomass and plant projective cover.

Cystofilobasidium intermedium sp. nov. and Cystofilobasidium alribaticum f.a. sp. nov., isolated from Mediterranean forest soils.

Multiple isolates belonging to the basidiomycetous genus Cystofilobasidium were obtained from forest soils in Serra da Arrábida Natural Park in Portugal. Phylogenetic analyses employing concatenated sequences of the D1/D2 domain and ITS region support the recognition of two novel species: Cystofilobasidium alribaticum f.a., sp. nov. (type strain CBS 14164T = PYCC 6956T = DSM 101473T) and Cystofilobasidium intermedium sp. nov. (type strain CBS 14089T = PYCC 6856T = DSM 101474T). Whereas C. alribaticum f. a. sp. nov. does not form hyphae, even when different strains are crossed, C. intermedium sp. nov. is self-fertile and forms mycelium with teliospores that upon germination give rise to slender basidia. The most remarkable physiological trait of the two novel species is their ability to grow at 35 °C, a property not observed for remaining species of the genus.

Connective tissue graft as a biological barrier for guided tissue regeneration in intrabony defects: a histological study in dogs.

BACKGROUND: The use of the autogenous periosteal graft as biological barrier has been proposed for periodontal regeneration. The aim of this study was to evaluate the histometric findings of the subepithelial connective tissue graft as barrier in intrabony defects compared to a bioabsorbable membrane. METHODS: Three-walled intrabony defects were created surgically in the mesial aspect of the right and left maxillary canines in five healthy mongrel dogs. The defects were chronified, and two types of barriers were randomly carried out for guided tissue regeneration in a split-mouth design: the test group with a subepithelial connective tissue graft and the control group with a bioabsorbable membrane. The specimens were processed for histometric analyses of the epithelium (E), connective tissue (CT), newly formed cementum (NC), new bone (NB), and total newly formed tissues (NFT). RESULTS: The test side showed smaller mean of NC (3.6 ± 1.2), NB (2.1 ± 0.7), and NFT (7.7 ± 0.8) than the control group (NC 7.3 ± 0.5; NB 5.3 ± 1.3; NFT 10.1 ± 2.2; P < 0.05). No statistically significant differences were verified for E (test 3.1 ± 2.0; control 2.8 ± 2.1; P > 0.05) and CT (test 2.5 ± 1.1; control 2.0 ± 0.5; P > 0.05) between groups. CONCLUSION: The bioabsorbable membrane was more effective in maintaining the space for periodontal regeneration than periosteal connective graft when used as barrier. CLINICAL RELEVANCE: The bioabsorbable membrane showed more favorable regenerative results in intrabony defects in dogs than the subepithelial connective tissue graft as biological barrier.

Torque Analysis of a Triple Acid-Etched Titanium Implant Surface.

The present study aimed to evaluate the removal torque of titanium implants treated with triple acid etching. Twenty-one rats were used in this study. For all animals, the tibia was prepared with a 2 mm drill, and a titanium implant (2 × 4 mm) was inserted after treatment using the subtraction method of triple acid etching. The flaps were sutured. Seven animals were killed 14, 28, and 63 days after implant installation, and the load necessary for removing the implant from the bone was evaluated by using a torque meter. The torque values were as follows: 3.3 ± 1.7 Ncm (14 days), 2.2 ± 1.3 Ncm (28 days), and 6.7 ± 1.4 Ncm (63 days). The torque value at the final healing period (63 days) was statistically significantly different from that at other time points tested (ANOVA, p = 0.0002). This preliminary study revealed that treatment with triple acid etching can create a promising and efficient surface for the process of osseointegration.