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The only hitherto known species of the monotypic genus Tromeropsis, the rarely reported T. microtheca, is redescribed from recent collections on mostly little decayed, grayed, xeric, sun-exposed wood of decorticated trunks and branches of different gymnosperms, exceptionally angiosperms, from different humid regions of central Europe and a dry area in Macaronesia. Two further, very similar species are here newly described from decayed xeric wood of different angiosperm trees and shrubs from dry to arid regions of North America, Australia, and Macaronesia. Characteristics of the genus are: black sessile apothecia, dark olivaceous exudate, fissitunicate multi-spored asci, minute, cylindrical to ellipsoid, hyaline ascospores, a yeast-like asexual morph, and, in some species, a synanamorph with allantoid conidia formed on integrated conidiogenous cells reminiscent of the genus Lecythophora but with holoblastic conidiogenesis. A lectotype is designated for the type species of the likewise sexually typified, monotypic, illegitimate genus Microspora, M. dura, which was re-examined from the original material and found to be a later synonym of T. microtheca. Nuclear rDNA data were obtained from two collections of T. microtheca and four collections of the two new species. DNA sequences of T. microtheca match those from asexual morph isolates or environmental samples in public databases. Different misapplied names attributed to sequences from asexual morph isolates gained from coniferous wood from northern Europe, North America, and eastern Asia were re-identified as T. microtheca. A very close relationship between Tromeropsis and the type species of the asexually typified genus Symbiotaphrina, S. buchneri, was observed. Independent molecular phylogenetic analyses of three rDNA regions (partial SSU, ITS, partial LSU) each place Tromeropsis and the type species of Symbiotaphrina in a single supported clade without showing clear limits between the two genera. Based on multigene analysis, Symbiotaphrina was recently placed together with the small order Xylonales in the new class Xylonomycetes. We here validate the order Symbiotaphrinales previously published as nom. nud. and describe the family Symbiotaphrinaceae. Since the name Symbiotaphrina was validated one year before Tromeropsis was published, and is more widely used, it is adopted here and T. microtheca combined into Symbiotaphrina. rDNA data further suggest that two members of the asexually typified genus Hyphozyma, H. lignicola and H. sanguinea, belong to Symbiotaphrina, whereas the type species of Hyphozyma, H. variabilis, clusters in the Thelebolales (Leotiomycetes), where it is a later synonym of Cleistothelebolus nipigonensis, the type species of Cleistothelebolus. The new combinations S. lignicola and S. sanguinea are proposed, to which the newly described species S. desertorum and S. larreae are added. Based on their close relationship and a similar yeast-like asexual morph in pure culture, we hypothesize that the life cycles of all these wood-inhabiting taxa include a symbiotic phase in the gut of arthropods and, conversely, we suppose that the life cycles of S. buchneri and S. kochii include unknown sexual morphs growing on plant substrate. [ABSTRACT FROM AUTHOR]

Saccharina latissima is a brown seaweed used as a food ingredient. The aim of this work was to study possible differences between S. latissima chemical composition, color, mode of cultivation, harvesting period and site and its environmental conditions. Water temperature, salinity, radiation, and fluorescence were monitored in each harvesting site. Chemical composition of S. latissima varied greatly with period and site, with a high content of carbohydrates and ash. Crude protein content varied from 3.7 % to 12.8 %, with a higher concentration observed in wild samples harvested in Bas-St. Laurent (11.1-12.8 %). Cultivated seaweed also presented a high crude protein (12.2 %) and ash (52 % against 27 % in wild samples) concentrations, but crude fiber and carbohydrates concentrations were lower, reaching up to 2.7 and 1.9-fold, respectively, than those in wild seaweeds. S. latissima presented a more intense yellow color in June. A trend of darker and more green-colored seaweeds when cultivated in the end of summer was confirmed. Our results suggest that variations in chemical components and chromaticity of this species are probably affected by complex interactions of environmental conditions., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors. Published by Elsevier Ltd.)

Air pollution has been linked to an increased risk of several respiratory diseases in children, especially respiratory tract infections. The present study aims to evaluate the association between pediatric emergency department (PED) presentations for bronchiolitis and air pollution. PED presentations due to bronchiolitis in children aged less than 1 year were retrospectively collected from 2007 to 2018 in Padova, Italy, together with daily environmental data. A conditional logistic regression based on a time-stratified case-crossover design was performed to evaluate the association between PED presentations and exposure to NO 2 , PM2.5, and PM10. Models were adjusted for temperature, relative humidity, atmospheric pressure, and public holidays. Delayed effects in time were evaluated using distributed lag non-linear models. Odds ratio for lagged exposure from 0 to 14 days were obtained. Overall, 2251 children presented to the PED for bronchiolitis. Infants' exposure to higher concentrations of PM10 and PM2.5 in the 5 days before the presentation to the PED increased the risk of accessing the PED by more than 10%, whereas high concentrations of NO 2 between 2 and 12 days before the PED presentation were associated with an increased risk of up to 30%. The association between pollutants and infants who required hospitalization was even greater. A cumulative effect of NO 2 among the 2 weeks preceding the presentation was also observed. In summary, PM and NO 2 concentrations are associated with PED presentations and hospitalizations for bronchiolitis. Exposure of infants to air pollution could damage the respiratory tract mucosa, facilitating viral infections and exacerbating symptoms., (© 2022 The Authors. Risk Analysis published by Wiley Periodicals LLC on behalf of Society for Risk Analysis.)

ddPCR is becoming one of the most widely used tool in the field of eDNA-based aquatic monitoring. Although emulsion PCR used in ddPCR confers a partial mitigation to inhibition due to the high number of reactions for a single sample (between 10K and 20K), it is not impervious to it. Our results showed that inhibition impacts the amplitude of fluorescence in positive droplets with a different intensity among rivers. This signal fluctuation could jeopardize the use of a shared threshold among samples from different origin, and thus the accurate assignment of the positive droplets which is particularly important for low concentration samples such as eDNA ones: amplification events are scarce, thus their objective discrimination as positive is crucial. Another issue, related to target low concentration, is the artifactual generation of high fluorescence droplets ('stars'). Indeed, these could be counted as positive with a single threshold solution, which in turn could produce false positive and incorrect target concentration assessments. Approximating the positive and negative droplets distribution as normal, we proposed here a double threshold method accounting for both high fluorescence droplets ('stars') and PCR inhibition impact in delineating positive droplets clouds. In the context of low concentration template recovered from environmental samples, the application of this method of double threshold establishment could allow for a consistent sorting of the positive and negative droplets throughout ddPCR data generated from samples with varying levels of inhibitor contents. Due to low concentrations template and inhibition effects, Quantasoft software produced an important number of false negatives and positive comparatively to the double threshold method developed here. This case study allowed the detection of the invasive crayfish P. leniusculus in 32 out of 34 sampled sites from two main rivers (Alzette and Sûre) and five of their tributaries (Eisch, Attert, Mamer, Wiltz and Clerve)., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2022 Porco et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

LAMP assays are becoming increasingly popular in the field of invasive species detection but are still underused in eDNA-based monitoring. Here, we propose a LAMP assay designed to detect the North American crayfish species Pacifastacus leniusculus in water samples from streams. The presence of P. leniusculus was detected through this new LAMP assay in all but one of the nine sites sampled. No correlation was found between ddPCR absolute concentration measurements and the number of LAMP-positive technical replicates. However, we showed that using dependent technical replicates could significantly enhance the detection sensitivity of the LAMP assay. Applied to other assays, it could improve sensitivity and thus allow for a more efficient use of eDNA-based LAMP assays for invasive species detection in aquatic ecosystems., (© 2022. The Author(s).)

Rationale: Outdoor air pollution contributes to asthma development and exacerbations, yet its effects on airway pathology have not been defined in children. Objectives: To explore the possible link between air pollution and airway pathology, we retrospectively examined the relationship between environmental pollutants and pathological changes in bronchial biopsy specimens from children undergoing a clinically indicated bronchoscopy. Methods: Structural and inflammatory changes (basement membrane [BM] thickness, epithelial loss, eosinophils, neutrophils, macrophages, mast cells, and lymphocytes) were quantified in biopsy specimens by using immunohistochemistry. The association between exposure to particulate matter less than 10 μm in aerodynamic diameter (PM 10 ), SO 2 and NO 2 and biopsy findings was evaluated by using a generalized additive model with Gamma family to allow for overdispersion, adjusted for atmospheric pressure, temperature, humidity, and wheezing. Results: Overall, 98 children were included (age 5.3 ± 2.9 yr; 53 with wheezing/45 without wheezing). BM thickness increased with prolonged exposure to PM 10 (rate ratio [RR], 1.29; 95% confidence interval [CI], 1.09-1.52), particularly in children with wheezing. Prolonged exposure to PM 10 was also associated with eosinophilic inflammation in children with wheezing (RR, 3.16; 95% CI, 1.35-7.39). Conversely, in children without wheezing, increased PM 10 exposure was associated with a reduction of eosinophilic inflammation (RR, 0.12; 95% CI, 0.02-0.6) and neutrophilic inflammation (RR, 0.36; 95% CI, 0.14-0.89). Moreover, NO 2 exposure was also linked to reductions in neutrophil infiltration (RR, 0.57; 95% CI, 0.34-0.93) and eosinophil infiltration (RR, 0.33; 95% CI, 0.14-0.77). Conclusions: Different patterns of association were observed in children with wheezing and in children without wheezing. In children without wheezing, exposure to PM 10 and NO 2 was linked to reduced eosinophilic and neutrophilic inflammation. Conversely, in children with wheezing, prolonged exposure to PM 10 was associated with increased BM thickness and eosinophilic inflammation, suggesting that it might contribute to asthma development by promoting airway remodeling and inflammation.

Spent brewer's yeast ( Saccharomyces sp.), the second most generated by-product from the brewing industry, contains bioactive and nutritional compounds with high added value such as proteins (40-50%), polysaccharides, fibers and vitamins. Molecules of interest from agro-industrial by-products need to be extracted, separated, concentrated, and/or purified so that a minimum purity level is achieved, allowing its application. Enzymatic hydrolysis has been successfully used in the production of peptides and protein hydrolysates. The obtained hydrolysates require efficient downstream processes such as membrane technology, which is an important tool for the recovery of thermolabile and sensitive compounds from complex mixtures, with low energy consumption and high specificity. The integration of membrane techniques that promote the separation through sieving and charge-based mechanisms is of great interest to improve the purity of the recovered fractions. This review is specifically addressed to the application of membrane technologies for the recovery of peptides from yeast protein hydrolysates. Fundamental concepts and practical aspects relative to the ultrafiltration of agro-industrial protein hydrolysates will be described. Challenges and perspectives involving the recovery of peptides from yeast protein hydrolysates will be presented and thoroughly discussed.

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11 th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.

Large-scale oil production from oil sands deposits in Alberta, Canada has raised concerns about environmental impacts, such as the magnitude of air pollution emissions. This paper reports compound emission rates ( E ) for 69-89 nonbiogenic volatile organic compounds (VOCs) for each of four surface mining facilities, determined with a top-down approach using aircraft measurements in the summer of 2013. The aggregate emission rate ( aE ) of the nonbiogenic VOCs ranged from 50 ± 14 to 70 ± 22 t/d depending on the facility. In comparison, equivalent VOC emission rates reported to the Canadian National Pollutant Release Inventory (NPRI) using accepted estimation methods were lower than the aE values by factors of 2.0 ± 0.6, 3.1 ± 1.1, 4.5 ± 1.5, and 4.1 ± 1.6 for the four facilities, indicating underestimation in the reported VOC emissions. For 11 of the combined 93 VOC species reported by all four facilities, the reported emission rate and E were similar; but for the other 82 species, the reported emission rate was lower than E The median ratio of E to that reported for all species by a facility ranged from 4.5 to 375 depending on the facility. Moreover, between 9 and 53 VOCs, for which there are existing reporting requirements to the NPRI, were not included in the facility emission reports. The comparisons between the emission reports and measurement-based emission rates indicate that improvements to VOC emission estimation methods would enhance the accuracy and completeness of emission estimates and their applicability to environmental impact assessments of oil sands developments., Competing Interests: The authors declare no conflict of interest.

Glyphium encompasses species with erect, carbonaceous ligulate to dolabrate ascomata that are strongly laterally compressed and dehisce along a longitudinal slit. The five currently recognized members of the genus are separated primarily by whether the ascospores disassociate into part-spores within the ascus. Glyphium has traditionally been placed in Mytilinidiaceae (Mytilinidiales, Pleosporomycetidae, Dothideomycetes). The present study, based on freshly collected material of G. elatum and G. grisonense, was initiated to determine the phylogenetic placement of Glyphium. Phylogenies inferred from the analysis of sequences of six gene regions (nuLSU, nuSSU, mtSSU, TEF1, RPB1, RPB2) derived from six accessions indicate that Glyphium belongs to Patellariales (Pleosporomycetidae, Dothideomycetes). Our phylogenies also support the phylogenetic relationship of Patellaria and Hysteropatella within this order. The nomenclatural history of Glyphium is summarized and a key to species is provided., (© 2015 by The Mycological Society of America.)

RNA-directed DNA methylation in Arabidopsis thaliana depends on the upstream synthesis of 24-nucleotide small interfering RNAs (siRNAs) by RNA POLYMERASE IV (Pol IV) and downstream synthesis of non-coding transcripts by Pol V. Pol V transcripts are thought to interact with siRNAs which then recruit DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) to methylate DNA. The SU(VAR)3-9 homologues SUVH2 and SUVH9 act in this downstream step but the mechanism of their action is unknown. Here we show that genome-wide Pol V association with chromatin redundantly requires SUVH2 and SUVH9. Although SUVH2 and SUVH9 resemble histone methyltransferases, a crystal structure reveals that SUVH9 lacks a peptide-substrate binding cleft and lacks a properly formed S-adenosyl methionine (SAM)-binding pocket necessary for normal catalysis, consistent with a lack of methyltransferase activity for these proteins. SUVH2 and SUVH9 both contain SRA (SET- and RING-ASSOCIATED) domains capable of binding methylated DNA, suggesting that they function to recruit Pol V through DNA methylation. Consistent with this model, mutation of DNA METHYLTRANSFERASE 1 (MET1) causes loss of DNA methylation, a nearly complete loss of Pol V at its normal locations, and redistribution of Pol V to sites that become hypermethylated. Furthermore, tethering SUVH9 [corrected] with a zinc finger to an unmethylated site is sufficient to recruit Pol V and establish DNA methylation and gene silencing. These results indicate that Pol V is recruited to DNA methylation through the methyl-DNA binding SUVH2 and SUVH9 proteins, and our mechanistic findings suggest a means for selectively targeting regions of plant genomes for epigenetic silencing.

Pyrimidopyrimidine derivatives 1 were prepared as rigid thioanalogues of merbarone (a catalytic topoisomerase II inhibitor) and screened as antiproliferative agents against different tumor cell lines. A number of the synthesized compounds emerged as cytotoxic in cell-based assays (MT-4, HeLa and MCF-7 cells) at low micromolar concentrations. In a National Cancer Institute screening, selected member of the series showed a broad spectrum of antiproliferative activity against various tumours (melanoma, renal, CNS, colon and breast cancers). The acid-base and steric properties of the substituent at position 7 of the pyrimidopyrimidine scaffold deeply affected potency. Enzymatic assays evidenced that a subset of tested derivatives efficiently inhibit topoisomerase IIα accordingly to merbarone mechanism of action. However this property does not fully rationalize the cytotoxicity data of the full ligand panel, suggesting that different target(s) should be additionally involved., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

The use of nucleic acids as drugs represents a consistently growing approach. Different therapeutical strategies take advantage of the biological and biophysical properties of DNA and RNA to properly modulate activity of selected targets. A peculiar characteristic of these molecules is their structural flexibility which allows them to assume distinct foldings depending upon their sequence and/or environment. During the last twenty years this has led to the theoretical and experimental development of oligonucleotide aptamers, short sequences which can recognize a target with specificity and affinity comparable to antibodies. A leading example is represented by the Thrombin aptamer (15fTBA), a 15-mer DNA selected by its high affinity for the exosite I (fibrinogen binding site) of the coagulation factor. The very stable protein-DNA complex formation is the result of complementarities between the two macromolecules promoted by the aptamer sequence and folding as well as of electrostatic interactions generated by the charge balance at the binding site/s. Here, we investigated the relative role of these contributions and their involvement in defining the biological properties of the resulting complex. Thus we compared the Thrombin binding and inhibition properties of TBA to those of unrelated single stranded oligonucleotides. Additionally, the differences between the two protein exosites were assessed by using 29hTBA, a longer (29-mer) aptamer known to bind exosite II (heparin binding site). A subtle balance of aptamer folding and sequence is shown to cooperate with charge density for effective and selective recognition of exosite I or exosite II by TBAs.