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Open Forum Infectious Diseases Jan 2023Fungal species have undergone and continue to undergo significant nomenclatural change, primarily due to the abandonment of dual species nomenclature in 2013 and the... (Review)
Review
Fungal species have undergone and continue to undergo significant nomenclatural change, primarily due to the abandonment of dual species nomenclature in 2013 and the widespread application of molecular technologies in taxonomy allowing correction of past classification errors. These have effected numerous name changes concerning medically important species, but by far the group causing most concern are the yeasts. Among common species, , , , , and have been changed to , , , , and , respectively. There are currently no guidelines for microbiology laboratories on implementing changes, and there is ongoing concern that clinicians will dismiss or misinterpret laboratory reports using unfamiliar species names. Here, we have outlined the rationale for name changes across the major groups of clinically important fungi and have provided practical recommendations for managing change.
PubMed: 36632423
DOI: 10.1093/ofid/ofac559 -
Poultry Science Dec 2019Probiotics are considered the preferred alternatives to antibiotics for growth promotion and disease prevention. Previous studies have confirmed that Diutina rugosa...
Probiotics are considered the preferred alternatives to antibiotics for growth promotion and disease prevention. Previous studies have confirmed that Diutina rugosa SD-17 has the potential as a probiotic. We evaluated the probiotic effect of D. rugosa SD-17 on 360 one-day-old Hy-line brown chickens that were divided into 2 groups, and each group contained 6 replicate pens with 30 birds per pen. The chickens were fed with basal diet supplemented with or without D. rugosa SD-17, and the effects of D. rugosa SD-17 on growth performance, intestine morphology, and immune status were assessed. Body weight was significantly improved from week 3 to 6 (P < 0.05), and the feed conversion ratio was significantly improved in weeks 1 and 2 (P < 0.001). The length of the duodenum was lengthened significantly in week 3 (P < 0.05), and supplementation of D. rugosa SD-17 significantly increased villus height and villus height to crypt depth ratio in the ileum in week 3 (P < 0.05). Expressions of tight-junction-related genes of zonula occludens-2 and occludin in the ileum were significantly increased (P < 0.05). The proliferation capacity of blood lymphocytes stimulated by concanavalin A was significantly enhanced (P < 0.05), and the proportion of helper T (Th) cells increased significantly (P < 0.05). Expressions of Th1 cell markers IL-2 and interferon (IFN)-γ and immune-related genes of IL-1β, transforming growth factor-β, and IFN-γ in ileum were significantly increased (P < 0.05). These results indicated that D. rugosa SD-17 improved the growth and regulated immunity of chickens, and could be optimized for use as a feed additive for livestock and poultry.
Topics: Animal Feed; Animals; Chickens; Diet; Intestines; Probiotics; Random Allocation; Saccharomycetales
PubMed: 31350991
DOI: 10.3382/ps/pez428 -
G3 (Bethesda, Md.) Dec 2019Infections caused by opportunistic yeast pathogens have increased over the last years. These infections can be originated by a large number of diverse yeast species of...
Infections caused by opportunistic yeast pathogens have increased over the last years. These infections can be originated by a large number of diverse yeast species of varying incidence, and with distinct clinically relevant phenotypic traits, such as different susceptibility profiles to antifungal drugs, which challenge diagnosis and treatment. (syn. ) and (syn. ) are two opportunistic rare yeast pathogens, which low incidence (< 1%) limits available clinical experience. Furthermore, these yeasts have elevated Minimum Inhibitory Concentration (MIC) levels to at least one class of antifungal agents. This makes it more difficult to manage their infections, and thus they are associated with high rates of mortality and clinical failure. With the aim of improving our knowledge on these opportunistic pathogens, we assembled and annotated their genomes. A phylogenomics approach revealed that genes specifically duplicated in each of the two species are often involved in transmembrane transport activities. These genomes and the reconstructed complete catalog of gene phylogenies and homology relationships constitute useful resources for future studies on these pathogens.
Topics: Candida; Genome Size; Genome, Fungal; Genome, Mitochondrial; Phylogeny; Sequence Analysis, DNA
PubMed: 31575637
DOI: 10.1534/g3.119.400762 -
Brazilian Journal of Microbiology :... Dec 2021Yeast isolates from flowers and fruits from a Brazilian forest were studied. The yeasts were identified at species and strain level by PCR-RFLP and PCR-RAPD,...
Yeast isolates from flowers and fruits from a Brazilian forest were studied. The yeasts were identified at species and strain level by PCR-RFLP and PCR-RAPD, respectively. The 46 isolated yeasts were classified into 11 different species belonging to the genera Candida, Diutina, Hanseniaspora, Meyerozyma, Pichia, Rhodotorula, and Torulaspora. A total of 20 different strains were found. In order to ascertain the probiotic potential, the resistance to gastrointestinal conditions, autoaggregation, and hydrophobicity assays were studied, along with the capacity to form biofilm. The results indicate that, although most of the strains presented better results than Saccharomyces boulardii (the only strain recognized as a probiotic yeast), four strains were the most promising, namely, Rhodotorula mucilaginosa 32, Meyerozyma caribbica 35, and Diutina rugosa 12 and 45, according to the Duncan test. Several biotechnological properties were evaluated. D. rugosa inhibited Dekkera bruxellensis. The assimilation or fermentation of seven sugars was tested, and only five of the yeasts did not show a capacity to assimilate any of the sugars under aerobic conditions. However, all strains were able to ferment at least one of the sugars under anaerobic conditions. As far as enzyme production is concerned, positive results were only found for the enzymes' amylase, pectinase, and protease. D. rugosa 42 and Hanseniaspora opuntiae 18, followed of Pichia kluyveri 26, showed high values for the production of melatonin. In conclusion, the results of this study show that several non-Saccharomyces present probiotic characteristics, and these have good potential for industrial applications in the food or biotechnology industries.
Topics: Biotechnology; Ecosystem; Fermentation; Fruit; Probiotics; Random Amplified Polymorphic DNA Technique; Sugars; Yeasts
PubMed: 34595728
DOI: 10.1007/s42770-021-00541-z -
Bioorganic Chemistry Apr 2021Candida rugosa lipase (CRL) is an enzyme commonly used in medicinal and biotechnological applications. Allosteric modulators of CRL could aid in modifying lipase-related...
Candida rugosa lipase (CRL) is an enzyme commonly used in medicinal and biotechnological applications. Allosteric modulators of CRL could aid in modifying lipase-related diseases as well as improving biotechnological processes. Thus, a combinatorial approach of computational in-silico and high-throughput in-vitro screening was used to identify allosteric modulators of CRL. The screening of natural product libraries resulted in 132 compounds of which 53 were tested in-vitro. Subsequently, four inhibitors and three enhancers were identified of which rutin and cynaroside represented the strongest inhibitors of CRL activity (IC50: 227 ± 26 µM and 446 ± 15 µM, respectively) and NP-008496 the strongest enhancer (EC50: 425 ± 18 µM). All three compounds were predicted to bind the same allosteric site suggesting a common mechanism. Therefore, the present study demonstrated a reliable work-flow, identified an allosteric site of CRL and determined inhibitors and enhancers with numerous potential medical and biotechnological applications.
Topics: Allosteric Site; Biological Products; Dose-Response Relationship, Drug; Enzyme Inhibitors; Kinetics; Lipase; Molecular Docking Simulation; Molecular Structure; Saccharomycetales; Structure-Activity Relationship
PubMed: 33639364
DOI: 10.1016/j.bioorg.2021.104732 -
International Journal of Molecular... Jul 2023Clopidogrel is a chiral compound widely used as an antiplatelet medication that lowers the risk of blood clots, strokes, and heart attacks. The main aim of the study...
Clopidogrel is a chiral compound widely used as an antiplatelet medication that lowers the risk of blood clots, strokes, and heart attacks. The main aim of the study presented herein was to obtain ()-clopidogrel, which is commercially available in treatments, via the kinetic resolution of racemic clopidogrel carboxylic acid with the use of lipase from and a two-phase reaction medium containing an ionic liquid. For this purpose, the enantioselective biotransformation of clopidogrel carboxylic acid and chiral chromatographic separation with the use of a UPLC-MS/MS system were optimized. The best kinetic resolution parameters were obtained by using a catalytic system containing lipase from OF as a biocatalyst, cyclohexane and [EMIM][BF4] as a two-phase reaction medium, and methanol as an acyl acceptor. The enantiomeric excess of the product was ee = 94.21% ± 1.07 and the conversion was c = 49.60% ± 0.57%, whereas the enantioselectivity was E = 113.40 ± 1.29. The performed study proved the possibility of obtaining ()-clopidogrel with the use of lipase as a biocatalyst and a two-phase reaction medium containing an ionic liquid, which is in parallel with green chemistry methodology and does not require environmentally harmful conditions.
Topics: Ionic Liquids; Clopidogrel; Chromatography, Liquid; Tandem Mass Spectrometry; Lipase; Stereoisomerism
PubMed: 37446300
DOI: 10.3390/ijms241311124 -
Scientific Reports Jul 2020Microbial detoxification has been proposed as a new alternative for removing toxins and pollutants. In this study, the biodetoxification activities of yeasts against...
Microbial detoxification has been proposed as a new alternative for removing toxins and pollutants. In this study, the biodetoxification activities of yeasts against aflatoxin B and zinc were evaluated by HPLC and voltammetric techniques. The strains with the best activity were also subjected to complementary assays, namely biocontrol capability and heavy-metal resistance. The results indicate that the detoxification capability is toxin- and strain-dependent and is not directly related to cell growth. Therefore, we can assume that there are some other mechanisms involved in the process, which must be studied in the future. Only 33 of the 213 strains studied were capable of removing over 50% of aflatoxin B, Rhodotrorula mucilaginosa being the best-performing species detected. As for zinc, there were 39 strains that eliminated over 50% of the heavy metal, with Diutina rugosa showing the best results. Complementary experiments were carried out on the strains with the best detoxification activity. Biocontrol tests against mycotoxigenic moulds showed that almost 50% of strains had an inhibitory effect on growth. Additionally, 53% of the strains grew in the presence of 100 mg/L of zinc. It has been proven that yeasts can be useful tools for biodetoxification, although further experiments must be carried out in order to ascertain the mechanisms involved.
Topics: Aflatoxin B1; Biodegradation, Environmental; Chromatography, High Pressure Liquid; Environmental Pollutants; Food Safety; Metals, Heavy; Pichia; Rhodotorula; Saccharomyces cerevisiae; Saccharomycetales; Wastewater; Yeasts; Zinc
PubMed: 32647290
DOI: 10.1038/s41598-020-68154-4 -
Journal of Chemical Information and... Feb 2021Lipases are enzymes able to catalyze the hydrolysis or synthesis of triglycerides, depending on the reaction conditions, whereas sterol esterases show the same ability...
Lipases are enzymes able to catalyze the hydrolysis or synthesis of triglycerides, depending on the reaction conditions, whereas sterol esterases show the same ability on sterol esters. Structurally, both kinds of enzymes display an α/β-hydrolase fold, with a substrate-binding pocket formed by a hydrophobic cavity covered by a mobile lid. However, it has been reported that some lipases from the -like family display wide substrate specificity on both triglycerides and sterol esters. Among them, enzymes with different biotechnological applications, such as the lipase isoenzymes produced by and the sterol esterase from , have been exhaustively characterized and their crystal structures are available. Differences in substrate affinity among these proteins have been attributed to changes in their hydrophobicity. In this work, we analyzed the full catalytic mechanisms of these proteins using molecular dynamics tools, gaining insight into their mechanistic properties. In addition, we developed an protocol to predict the substrate specificity using and lipases as model enzymes and triglycerides and cholesterol esters with different fatty acid chain lengths as model substrates. The protocol was validated by comparing the results with those described in the literature. These results would be useful to perform virtual screening of substrates for enzymes of the -like family with unknown catalytic properties.
Topics: Candida; Lipase; Ophiostoma; Saccharomycetales; Sterol Esterase; Substrate Specificity
PubMed: 33555857
DOI: 10.1021/acs.jcim.0c01151 -
Bioengineering (Basel, Switzerland) Aug 2023This work demonstrated the feasibility of an industrial-scale aerated static pile composting system for treating one of the common biowastes-soybean curd residue. The...
This work demonstrated the feasibility of an industrial-scale aerated static pile composting system for treating one of the common biowastes-soybean curd residue. The mixing ratios of the feedstock were optimized to achieve a carbon-nitrogen ratio and a moisture level in the ranges of 25-35 and 60-70%, respectively. This open-air composting system required 6-7 months to obtain a mature compost. Solvita and seed germination tests further confirmed the maturity of the compost, with 25% compost extract concentration yielding the best germination index in the absence of phytotoxicity. The bacterial and fungal compositions of the compost piles were further examined with metagenomic analysis. spp., spp., and spp. were among the unique bacteria found, and , , and were among the unique fungi found in the compost piles, suggesting the presence of good microorganisms for degrading the organic biowastes.
PubMed: 37627823
DOI: 10.3390/bioengineering10080938 -
Biomolecules Jun 2021Water content is an important factor in lipase-catalyzed reactions in organic media but is frequently ignored in the study of lipases by molecular dynamics (MD)...
Water content is an important factor in lipase-catalyzed reactions in organic media but is frequently ignored in the study of lipases by molecular dynamics (MD) simulation. In this study, lipase B, lipase and lipase were used as research models to explore the mechanisms of lipase in micro-aqueous organic solvent (MAOS) media. MD simulations indicated that lipases in MAOS systems showed unique conformations distinguished from those seen in non-aqueous organic solvent systems. The position of water molecules aggregated on the protein surface in MAOS media is the major determinant of the unique conformations of lipases and particularly impacts the distribution of hydrophilic and hydrophobic amino acids on the lipase surface. Additionally, two maxima were observed in the water-lipase radial distribution function in MAOS systems, implying the formation of two water shells around lipase in these systems. The energy landscapes of lipases along solvent accessible areas of catalytic residues and the minimum energy path indicated the dynamic open states of lipases in MAOS systems differ from those in other solvent environments. This study confirmed the necessity of considering the influence of the microenvironment on MD simulations of lipase-catalyzed reactions in organic media.
Topics: Basidiomycota; Cellular Microenvironment; Computational Biology; Fungal Proteins; Hydrophobic and Hydrophilic Interactions; Lipase; Molecular Dynamics Simulation; Protein Structure, Secondary; Protein Structure, Tertiary; Saccharomycetales; Water
PubMed: 34200257
DOI: 10.3390/biom11060848