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Introduction: Recurrent aphthous stomatitis (RAS) is a prevalent ulcerative condition affecting oral mucosa., Objectives: A systematic review and meta-analysis was performed to compare the level of neutrophil to lymphocyte ratio (NLR) between individuals with RAS and those who are healthy., Methods: A systematic search for relevant publications before June 21, 2022, was conducted using Web of Science, PubMed, and Scopus. The results were presented as the standardized mean difference (SMD) with a 95% confidence interval (CI), and a random-effects model was used to calculate pooled effects due to the presence of significant heterogeneity. Quality assessment was performed using the Newcastle-Ottawa scale., Results: Overall, 13 article with were included in the analysis. NLR was higher among patients with RAS compared to healthy controls (SMD = 0.50, 95% CI = -0.20 to 0.79, P = 0.001, I 2 = 91.5%). In the subgroup analysis based on the study design, it was found that retrospective studies showed higher levels of NLR in patients with RAS compared to healthy controls (SMD = 0.62, 95% CI= 0.16 to 1.08, P < 0.01), but these results were not applied to prospective studies (SMD = 0.35, 95% CI = -0.03 to 0.74, P < 0.07)., Conclusion: Elevated neutrophil to lymphocyte ratio revealed crosstalk between systematic inflammation and RAS.

ATP2B1 encodes plasma membrane calcium-transporting-ATPase1 and plays an essential role in maintaining intracellular calcium homeostasis that regulates diverse signaling pathways. Heterozygous de novo missense and truncating ATP2B1 variants are associated with a neurodevelopmental phenotype of variable expressivity. We describe a proband with distinctive craniofacial gestalt, Pierre-Robin sequence, neurodevelopmental and growth deficit, periventricular heterotopia, brachymesophalangy, cutaneous syndactyly, and persistent hypocalcemia from primary hypoparathyroidism. Proband-parent trio exome sequencing identified compound heterozygous ATP2B1 variants: a maternally inherited splice-site (c.3060+2 T > G) and paternally inherited missense c.2938 G > T; p.(Val980Leu). Reverse-transcription-PCR on the proband's fibroblast-derived mRNA showed aberrantly spliced ATP2B1 transcripts targeted for nonsense-mediated decay. All correctly-spliced ATP2B1 mRNA encoding p.(Val980Leu) functionally causes decreased cellular Ca 2+ extrusion. Immunoblotting showed reduced fibroblast ATP2B1. We conclude that biallelic ATP2B1 variants are the likely cause of the proband's phenotype, strengthening the association of ATP2B1 as a neurodevelopmental gene and expanding the phenotypic characterization of a biallelic loss-of-function genotype., (© 2023. The Author(s).)

Calcium (Ca 2+ ) is a universal second messenger involved in synaptogenesis and cell survival; consequently, its regulation is important for neurons. ATPase plasma membrane Ca 2+ transporting 1 (ATP2B1) belongs to the family of ATP-driven calmodulin-dependent Ca 2+ pumps that participate in the regulation of intracellular free Ca 2+ . Here, we clinically describe a cohort of 12 unrelated individuals with variants in ATP2B1 and an overlapping phenotype of mild to moderate global development delay. Additional common symptoms include autism, seizures, and distal limb abnormalities. Nine probands harbor missense variants, seven of which were in specific functional domains, and three individuals have nonsense variants. 3D structural protein modeling suggested that the variants have a destabilizing effect on the protein. We performed Ca 2+ imaging after introducing all nine missense variants in transfected HEK293 cells and showed that all variants lead to a significant decrease in Ca 2+ export capacity compared with the wild-type construct, thus proving their pathogenicity. Furthermore, we observed for the same variant set an incorrect intracellular localization of ATP2B1. The genetic findings and the overlapping phenotype of the probands as well as the functional analyses imply that de novo variants in ATP2B1 lead to a monogenic form of neurodevelopmental disorder., Competing Interests: Declaration of interests R.P. is an employee of GeneDx, Inc. All other authors declare no competing interests., (Copyright © 2022 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)

Biological waste degradation is the main driving factor for landfill emissions. In a 2-year laboratory experiment simulating different landfill in-situ aeration scenarios, the microbial degradation of solid waste under different oxygen conditions (treatments) was investigated. Nine landfill simulation reactors were operated in triplicates under three distinct treatments. Three were kept anaerobic, three were aerated for 706 days after an initial anaerobic phase and three were aerated for 244 days in between two anaerobic phases. In total, 36 solid and 36 leachate samples were taken. Biolog® EcoPlates™ were used to assess the functional diversity of the microbial community. It was possible to directly relate the functional diversity to the biodegradability of MSW (municipal solid waste), measured as RI 4 (respiration index after 4 days). The differences between the treatments in RI 4 as well as in carbon and polymer degradation potential were small. Initially, a RI 4 of about 6.5 to 8 mg O 2 kg -1 DW was reduced to less than 1 mg O 2 kg -1 DW within 114 days of treatment. After the termination of aeration, an increase 3 mg O 2 kg -1 DW was observed. By calculating the integral of the Gompertz equation based on spline interpolation of the Biolog® EcoPlates™ results after 96 h two substrate groups mainly contributing to the biodegradability were identified: carbohydrates and polymers. The microbial activity of the respective microbial consortium could thus be related to the biodegradability with a multilinear regression model., (© 2021. The Author(s).)

In this review, we argue that there is much to be learned by transferring knowledge from research on lignocellulose degradation to that on plastic. Plastic waste accumulates in the environment to hazardous levels, because it is inherently recalcitrant to biological degradation. Plants evolved lignocellulose to be resistant to degradation, but with time, fungi became capable of utilising it for their nutrition. Examples of how fungal strategies to degrade lignocellulose could be insightful for plastic degradation include how fungi overcome the hydrophobicity of lignin (e.g. production of hydrophobins) and crystallinity of cellulose (e.g. oxidative approaches). In parallel, knowledge of the methods for understanding lignocellulose degradation could be insightful such as advanced microscopy, genomic and post-genomic approaches (e.g. gene expression analysis). The known limitations of biological lignocellulose degradation, such as the necessity for physiochemical pretreatments for biofuel production, can be predictive of potential restrictions of biological plastic degradation. Taking lessons from lignocellulose degradation for plastic degradation is also important for biosafety as engineered plastic-degrading fungi could also have increased plant biomass degrading capabilities. Even though plastics are significantly different from lignocellulose because they lack hydrolysable C-C or C-O bonds and therefore have higher recalcitrance, there are apparent similarities, e.g. both types of compounds are mixtures of hydrophobic polymers with amorphous and crystalline regions, and both require hydrolases and oxidoreductases for their degradation. Thus, many lessons could be learned from fungal lignocellulose degradation., (Copyright © 2021. Published by Elsevier Inc.)

Fungi comprise one of the most diverse groups of eukaryotes with many cryptic species that are difficult to identify. In this chapter, we detail a protocol for the molecular identification of the most industrially relevant species of Trichoderma-T. reesei. We first describe how a single spore culture should be isolated and used for the sequencing of the diagnostic fragment of the tef1 gene. Then, we provide two alternative methods that can be used for molecular identification and offer the diagnostic oligonucleotide hallmark of the tef1 sequence that is present in sequences of all T. reesei strains known to date and that is therefore suitable for reliable and straightforward identification.

The filamentous fungus Trichoderma reesei (Hypocreales, Ascomycota) is an efficient industrial cell factory for the production of cellulolytic enzymes used for biofuel and other applications. Therefore, researches addressing T. reesei are relatively advanced compared to other Trichoderma spp. because of the significant bulk of available knowledge, multiple genomic data, and gene manipulation techniques. However, the established role of T. reesei in industry has resulted in a frequently biased understanding of the biology of this fungus. Thus, the recent studies unexpectedly show that the superior cellulolytic activity of T. reesei and other Trichoderma species evolved due to multiple lateral gene transfer events, while the innate ability to parasitize other fungi (mycoparasitism) was maintained in the genus, including T. reesei. In this chapter, we will follow the concept of ecological genomics and describe the ecology, distribution, and evolution of T. reesei, as well as critically discuss several common misconceptions that originate from the success of this species in applied sciences and industry.

Aims: Sustainable agriculture requires effective and safe biofertilizers and biofungicides with low environmental impact. Natural ecosystems that closely resemble the conditions of biosaline agriculture may present a reservoir for fungal strains that can be used as novel bioeffectors., Methods and Results: We isolated a library of fungi from the rhizosphere of three natural halotolerant plants grown in the emerging tidal salt marshes on the south-east coast of China. DNA barcoding of 116 isolates based on the rRNA ITS1 and 2 and other markers (tef1 or rpb2) revealed 38 fungal species, including plant pathogenic (41%), saprotrophic (24%) and mycoparasitic (28%) taxa. The mycoparasitic fungi were mainly species from the hypocrealean genus Trichoderma, including at least four novel phylotypes. Two of them, representing the taxa Trichoderma arenarium sp. nov. (described here) and T. asperelloides, showed antagonistic activity against five phytopathogenic fungi, and significant growth promotion on tomato seedlings under the conditions of saline agriculture., Conclusions: Trichoderma spp. of salt marshes play the role of natural biological control in young soil ecosystems with a putatively premature microbiome., Significance and Impact of the Study: The saline soil microbiome is a rich source of halotolerant bioeffectors that can be used in biosaline agriculture., (© 2020 The Authors. Journal of Applied Microbiology published by John Wiley & Sons Ltd on behalf of Society for Applied Microbiology.)

When resources are limited, the hypocrealean fungus Trichoderma guizhouense can overgrow another hypocrealean fungus Fusarium oxysporum, cause sporadic cell death and arrest growth. A transcriptomic analysis of this interaction shows that T. guizhouense undergoes a succession of metabolic stresses while F. oxysporum responded relatively neutrally but used the constitutive expression of several toxin-encoding genes as a protective strategy. Because of these toxins, T. guizhouense cannot approach it is potential host on the substrate surface and attacks F. oxysporum from above. The success of T. guizhouense is secured by the excessive production of hydrogen peroxide (H 2 O 2 ), which is stored in microscopic bag-like guttation droplets hanging on the contacting hyphae. The deletion of NADPH oxidase nox1 and its regulator, nor1 in T. guizhouense led to a substantial decrease in H 2 O 2 formation with concomitant loss of antagonistic activity. We envision the role of NOX proteins in the antagonism of T. guizhouense as an example of metabolic exaptation evolved in this fungus because the primary function of these ancient proteins was probably not linked to interfungal relationships. In support of this, F. oxysporum showed almost no transcriptional response to T. guizhouense Δnox1 strain indicating the role of NOX/H 2 O 2 in signalling and fungal communication., (© 2019 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.)

A taxonomic description of all castes of Colobopsis explodens Laciny & Zettel, sp. n. from Borneo, Thailand, and Malaysia is provided, which serves as a model species for biological studies on "exploding ants" in Southeast Asia. The new species is a member of the Colobopsis cylindrica (COCY) group and falls into a species complex that has been repeatedly summarized under the name Colobopsis saundersi (Emery, 1889) (formerly Camponotus saundersi ). The COCY species group is known under its vernacular name "exploding ants" for a unique behaviour: during territorial combat, workers of some species sacrifice themselves by rupturing their gaster and releasing sticky and irritant contents of their hypertrophied mandibular gland reservoirs to kill or repel rivals. This study includes first illustrations and morphometric characterizations of males of the COCY group: Colobopsis explodens Laciny & Zettel, sp. n. and Colobopsis badia (Smith, 1857). Characters of male genitalia and external morphology are compared with other selected taxa of Camponotini. Preliminary notes on the biology of C. explodens Laciny & Zettel, sp. n. are provided. To fix the species identity of the closely related C. badia , a lectotype from Singapore is designated. The following taxonomic changes within the C. saundersi complex are proposed: Colobopsis solenobia (Menozzi, 1926), syn. n. and Colobopsis trieterica (Menozzi, 1926), syn. n. are synonymized with Colobopsis corallina Roger, 1863, a common endemic species of the Philippines. Colobopsis saginata Stitz, 1925, stat. n ., hitherto a subspecies of C. badia , is raised to species level.

Unlike most other fungi, molds of the genus Trichoderma (Hypocreales, Ascomycota) are aggressive parasites of other fungi and efficient decomposers of plant biomass. Although nutritional shifts are common among hypocrealean fungi, there are no examples of such broad substrate versatility as that observed in Trichoderma. A phylogenomic analysis of 23 hypocrealean fungi (including nine Trichoderma spp. and the related Escovopsis weberi) revealed that the genus Trichoderma has evolved from an ancestor with limited cellulolytic capability that fed on either fungi or arthropods. The evolutionary analysis of Trichoderma genes encoding plant cell wall-degrading carbohydrate-active enzymes and auxiliary proteins (pcwdCAZome, 122 gene families) based on a gene tree / species tree reconciliation demonstrated that the formation of the genus was accompanied by an unprecedented extent of lateral gene transfer (LGT). Nearly one-half of the genes in Trichoderma pcwdCAZome (41%) were obtained via LGT from plant-associated filamentous fungi belonging to different classes of Ascomycota, while no LGT was observed from other potential donors. In addition to the ability to feed on unrelated fungi (such as Basidiomycota), we also showed that Trichoderma is capable of endoparasitism on a broad range of Ascomycota, including extant LGT donors. This phenomenon was not observed in E. weberi and rarely in other mycoparasitic hypocrealean fungi. Thus, our study suggests that LGT is linked to the ability of Trichoderma to parasitize taxonomically related fungi (up to adelphoparasitism in strict sense). This may have allowed primarily mycotrophic Trichoderma fungi to evolve into decomposers of plant biomass.

Trichoderma guizhouense NJAU 4742 (Harzianum clade) can suppress the causative agent of banana wild disease Fusarium oxysporum f. sp. cubense 4 (Foc4). To identify genes involved in this trait, we used T-DNA insertional mutagenesis and isolated one mutant that was unable to overgrow Foc4 and had reduced antifungal ability. Using the high-efficiency thermal asymmetric interlaced-PCR, the T-DNA was located in the terminator of a neutral metalloprotease gene (encoding a MEROPS family M35 protease), which was named nmp1. The antifungal activity of the mutant was recovered by retransformation with wild-type nmp1 gene. The purified NMP1 (overexpressed in Pichia pastoris) did not inhibit the growth and germination of other fungi in vitro. Its addition, however, partly recovered the antifungal activity of the mutant strain against some fungi. The expression of nmp1 is induced by the presence of fungi and by dead fungal biomass, but the time-course of transcript accumulation following the physical contact depends on mode of interaction: it increases in cases of long-lasting parasitism and decreases if the prey fungus is dead shortly after or even before the contact (predation). We thus conclude that NMP1 protein of T. guizhouense has major importance for mycotrophic interactions and defence against other fungi., (© 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Currently, researchers turn to natural processes such as using biological microorganisms in order to develop reliable and ecofriendly methods for the synthesis of metallic nanoparticles. In this study, we have investigated extracellular biosynthesis of silver nanoparticles using four Aspergillus species including A. fumigatus, A. clavatus, A. niger, and A. flavus. We have also analyzed nitrate reductase activity in the studied species in order to determine the probable role of this enzyme in the biosynthesis of silver nanoparticles. The formation of silver nanoparticles in the cell filtrates was confirmed by the passage of laser light, change in the color of cell filtrates, absorption peak at 430 nm in UV-Vis spectra, and atomic force microscopy (AFM). There was a logical relationship between the efficiencies of studied Aspergillus species in the production of silver nanoparticles and their nitrate reductase activity. A. fumigatus as the most efficient species showed the highest nitrate reductase activity among the studied species while A. flavus exhibited the lowest capacity in the biosynthesis of silver nanoparticles which was in accord with its low nitrate reductase activity. The present study showed that Aspergillus species had potential for the biosynthesis of silver nanoparticles depending on their nitrate reductase activity.

Background: Essential Oils (EOs) possess antibacterial properties and represent a natural source to treat infections and prevent food spoilage. Their chemical composition might be affected by the environmental condition and the developmental growth stages of the plant., Objectives: The current study aimed to determine the variations in chemical compositions and antimicrobial activities of the EOs of Ocimum sanctum L. at different stages of harvesting., Materials and Methods: The oils constituents were analyzed by gas chromatography/mass spectrometry (GC/MS). The effects of three different harvest stages of O. sanctum EOs against most common causes of food-borne were evaluated by broth micro-dilution method as recommended by the Clinical and Laboratory Standards Institute (CLSI)., Results: The analysis of the EOs indicated that eugenol was the major compound of the EOs at all developmental stages which reached its maximum level at the second stage. The results showed that the tested EOs exhibited antimicrobial activities against all of the examined pathogens at concentrations of 0.125-32 µL/mL, except Pseudomonas aeruginosa which was only inhibited by high concentrations of the floral budding and full flowering EOs. EO distilled from the second developmental growth stage (floral budding) of O. sanctum exhibited the strongest antibacterial activities against the food borne bacteria., Conclusions: Considering the wide range of antimicrobial activities of the examined EOs, they might have the potential to be used to manage infectious diseases or extend the shelf life of food products.

Background: Anabolic-androgenic steroids (AAS) abuse by the athletes has dramatically increased during the recent decades. These substances might increase the skin lipids and enhance the cutaneous microbial proliferation., Objectives: The current study aimed to investigate the potential side effects of AAS on the bacterial microflora colonization of the bodybuilders` skin., Patients and Methods: The skin samples of 94 male bodybuilders (71 AAS users, 23 non-AAS users) and 46 subjects of the control group, with similar gender and age, were cultured and incubated in both aerobic condition to isolate Staphylococcus aureus and anaerobic condition for Propionibacterium acnes. The isolated bacteria were identified by standard microbiological techniques., Results: The skin lesions were more frequent in the body builders than the controls. Moreover, statistically significant differences were also observed in skin lesions among the AAS users and the non-AAS user athletes. The prevalence of S. aureus and P. acnes in the athletes was higher than that of the control group. In addition, there was a significant difference in distribution of P. acnes between the bodybuilders who used AAS and those who did not., Conclusions: A higher number of bacterial flora was found in the bodybuilders particularly those using AAS in comparison to the controls, which might be due to the influence of these AAS on the skin microflora and transmission of the bacteria through the direct contact of the naked skin with the exercise instruments.

Objectives: Over the past two decades, there has been a growing trend in using oral hygienic products from natural resources such as essential oils and plant extracts. Nepeta cataria L. is a member of the mint family (Labiatae) with several medicinal properties. The objective of this study was to determine the chemical composition and antimicrobial activities of essential oils (EOs) from N. cataria leaves against pathogens causing oral infections., Materials and Methods: The chemical composition of EOs from N. cataria was analyzed by gas chromatography/mass spectrometry (GC/MS). The antimicrobial activity of the essential oil was evaluated by broth micro-dilution in 96 well plates as recommended by the Clinical and Laboratory Standards Institute (CLSI) methods. The plates were incubated at 30°C for 24-48 h (fungi) or at 37°C for 24 h (bacteria)., Results: The analysis of the EOs indicated that 4a-α, 7-α, 7a-β-nepetalactone (55-58%), and 4a-α, 7-β, 7a-α-nepetalactone (30-31.2%) were the major compounds of the EOs at all developmental stages. The tested EOs exhibited antimicrobial activities against the tested bacteria at concentrations of 0.125-4 μL/mL. Moreover, the oils entirely inhibited the growth of Candida species at a concentration less than 1 μL/mL., Conclusion: Based on these results, the EO of N. cataria can possibly be used as an antimicrobial agent in the treatment and control of oral pathogens.

Nepeta cataria L. is traditionally consumed as a food additive. The effects of three different harvest stages of N. cataria essential oils (EOs) against most common causes of food-borne infections were evaluated by broth microdilution method as recommended by the Clinical and Laboratory Standards Institute (CLSI). The chemical composition of the EOs from N. cataria has been analyzed by gas chromatography/mass spectrometry (GC/MS). The analysis of the EOs indicated that 4a-α,7-α,7a-β-nepetalactone (55-58%) and 4a-α,7-β,7a-α-nepetalactone (30-31.2%) were the major compounds of the EOs at all developmental stages. The results showed that the tested EOs exhibited antimicrobial activities against the food-borne pathogens at concentrations of 0.125-2 μL/mL. Based on these results, the EO of N. cataria can possibly be used in food products as a natural preservative agent.

Context: Candida species are opportunistic yeasts that cause infections ranging from simple dermatosis to potentially life-threatening fungemia. The emergence of resistance to antifungal drugs has been increased in the past two decades., Aim: the present study we determined to find out the susceptibility profiles of clinical isolates of Candida species against four antifungal drugs, including amphotericin B, ketoconazole, fluconazole and itraconazole., Materials and Methods: Antifungal susceptibility testing of the yeasts was done in accordance with the proposed guidelines for antifungal disk diffusion susceptibility testing of yeasts based on the CLSI document M44-A., Results: A total of 206 yeast isolates were assessed. Among the evaluated Candida species, the highest rates of resistance to ketoconazole were seen in Candida glabrata (16.6%) and Candida albicans (3.2%). Susceptibility and intermediate response to fluconazole were seen in 96.6% and 3.4% of the Candida isolates, respectively. A total of 19 (9.2%) yeast isolates showed petite phenomenon including 11 C. glabrata, 3 C. albicans, 2 Candida dubliniensis and one isolate of each Candida krusei and Candida parapsilosis., Conclusion: The high number of petite mutation in the isolated yeasts should be seriously considered since it may be one of the reasons of antifungal treatment failure.

The variations in quantity and quality of essential oils (EOs) from the aerial parts of cultivated Satureja hortensis were determined at different stages of harvesting. The EOs of air-dried samples were obtained by hydrodistillation and analyzed by gas chromatography/mass spectrometry (GC/MS). The antimicrobial activity of the EOs was investigated by broth microdilution methods. The amount of EOs (w/w, %) were 2.3, 2.5, 2.0, and 1.8% at floral budding, full flowering, immature fruit, and ripened fruit stages, respectively. gamma-Terpinene was the major compound of the EO at all developmental stages, except the ripened fruit stage when it was replaced by carvacrol (46.4%). The EOs exhibited strong antibacterial activities against the tested bacteria. Moreover, the EOs either inhibited or killed the examined yeasts at concentrations ranging from 0.03-8.0 microL/mL. Considering the wide range of antimicrobial activities of the examined EOs, they might have potential to be used in the management of infective agents.

The aim of the study was to assess the reliability of human blood agar media (HuBA) in identifying Streptococcus pyogenes by hemolysis analysis. We analyze several factors that might affect the accuracy of HuBA media for microbial analysis, including incubation time, blood group, Rh factor and presence of antistreptolysin-o., (Copyright © 2011 Elsevier B.V. All rights reserved.)

Background: Zataria multiflora Boiss. is a traditional and popular spice in Iran. The effects of 3 ecotypes (ECTPs) of Z. multiflora essential oils (EOs) against most common causes of food-borne and nosocomial infections were evaluated., Materials and Methods: The antimicrobial activities of the EOs were examined by broth microdilution method as recommended by the Clinical and Laboratory Standards Institute (CLSI). The chemical compositions of the EOs from 3 ECTPs of Z. multiflora have been analyzed by gas chromatography-mass spectrometry., Results: Analysis of the EOs indicated that 3 chemotypes were present in Z. multiflora, including carvacrol, thymol-carvacrol, and linalool, whereas previous studies have only found carvacrol and thymol. Inhibition studies showed that the tested EOs entirely inhibited the growth of yeasts at concentrations of less than 1 μL/mL. Moreover, the oils exhibited significant bacteriostatic and bactericidal activities against Gram-positive and Gram-negative bacteria at concentrations ranging from 0.12 to 8 μL/mL., Conclusion: These results suggest that the EOs from Z. multiflora should be investigated further for possible use in antimicrobial products and food preservatives.