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opencc-by-4.0Jun 2023View details →

Figs 1, 2. Aspergillus flavus. 1 in Symptomatology of termite Coptotermes curvignathus Holmgren (Rhinotermitidae) after fungi infection of Aspergillus flavus

Figs 1, 2. Aspergillus flavus. 1 – colony on Potato Dextrose Agar (PDA); 2 – morphology of conidia: (1) vesicles; (2) metula; (3) fialid; (4) conidiospores; (5) conidiophore.

opencc-by-4.0Jun 2023View details →

Figs 3–6 in Symptomatology of termite Coptotermes curvignathus Holmgren (Rhinotermitidae) after fungi infection of Aspergillus flavus

Figs 3–6. Body surface morphology of Coptotermes curvignathus infected with Aspergillus flavus. 3 – negative control; 4 – 1st day after application; 5 – 3rd day; 6 – 7th day.

opencc-by-4.0Jan 2023View details →

Figure 1 in Amazonian soil fungi are efficient degraders of glyphosate herbicide; novel isolates of Penicillium, Aspergillus, and Trichoderma

Figure 1. Mass spectrum resulting from the HPLC-MS of the isolated Penicillium 4A21 filtered. The filtrate presents possible peaks of glyphosate (170.07), AMPA (112.13) and sarcosine (89).

opencc-by-4.0Sep 2022View details →

Deciphering interactions between the marine dinoflagellate Prorocentrum lima and the fungus Aspergillus pseudoglaucus

The comprehension of microbial interactions is one of the key challenges in marine microbial ecology. This study focused on exploring chemical interactions between the toxic dinoflagellate Prorocentrum lima and a filamentous fungal species, Aspergillus pseudoglaucus, which has been isolated from the microalgal culture. Such interspecies interactions are expected to occur even though they were rarely studied. Here, a co-culture system was designed in a dedicated microscale marine-like condition. This system allowed to explore microalgal-fungal physical and metabolic interactions in presence and absence of the bacterial consortium. Microscopic observation showed an unusual physical contact between the fungal mycelium and dinoflagellate cells. To delineate specialized metabolome alterations during microalgal-fungal co-culture metabolomes were monitored by high-performance liquid chromatography coupled to high-resolution mass spectrometry. In-depth multivariate statistical analysis using dedicated approaches highlighted (1) the metabolic alterations associated with microalgal-fungal co-culture, and (2) the impact of associated bacteria in microalgal metabolome response to fungal interaction. Unfortunately, only a very low number of highlighted features were fully characterised. However, an up-regulation of the dinoflagellate toxins okadaic acid and dinophysistoxin 1 was observed during co-culture in supernatants. Such results highlight the importance to consider microalgal-fungal interactions in the study of parameters regulating toxin production.

opencc-bySep 2023View details →

Advancements in QSAR modelling: Decision trees and rotation forest for prediction of Aspergillus anti-inflammatory metabolites

This study presents applications of advancements in QSAR modelling for predicting nitric oxide (NO) inhibitors and anti-inflammatory metabolites from the Aspergillus genus. Inflammation-related diseases remain a pressing concern, necessitating the identification of effective anti-inflammatory compounds. Using decision trees, the Ranker method, and CorrelationAtrributeEval as a base classifier for attribute selection together with Rotation Forest and Adaboost as enhancers, we explored their potential with different classifiers including Artificial Neural Networks and J48 Trees. The proposed QSAR models employed an ensemble approach with Rotation Forest and Adaboost.M1, applying an automated KNIME workflow. Seven molecular descriptors were selected and trained on a comprehensive dataset of diverse anti-inflammatory Aspergillus specialised metabolites. Results showed that the Rotation Forest-enhanced version outperformed other models, capturing complex structure-activity relationships and improving predictive performance. Chemical characteristics of electrotopological state, topological distances, and functional groups including secondary amides and alcohols contribute to important anti-inflammatory effects. The developed QSAR model showed good predictive performance for anti-inflammatory Aspergillus metabolites, focusing on their NO inhibitory activity. These results can contribute to the discovery of novel anti-inflammatory drugs based on computational techniques.

opencc-zeroApr 2024View details →

Azole resistance mechanisms and population structure of Aspergillus fumigatus on retail plant products

Aspergillus fumigatus is a ubiquitous saprotroph and human-pathogenic fungus that is life-threatening to the immunocompromised. Triazole-resistant A. fumigatus was found in patients without prior treatment with azoles, leading researchers to conclude that resistance had developed in agricultural environments where azoles are used against plant pathogens. Previous studies have documented azole-resistant A. fumigatus across agricultural environments, but few have looked at retail plant products. Our objectives were to determine if azole-resistant A. fumigatus is prevalent in retail plant products produced in the United States (U.S.), as well as to identify the resistance mechanism(s) and population genetic structure of these isolates. Five hundred twenty-five isolates were collected from retail plant products and screened for azole resistance. Twenty-four isolates collected from compost, soil, flower bulbs, and raw peanuts were pan-azole resistant. Resistant isolates had the TR34/L98H, TR46/Y121F/T289A, G448S, and H147Y cyp51A alleles, all known to underly pan-azole resistance, as well as WT alleles, suggesting that non-cyp51A-mechanisms contribute to pan-azole resistance in some isolates. Minimum spanning networks showed two lineages containing isolates with TR alleles or the F46Y/M172V/E427K allele, and discriminant analysis of principle components (DAPC) identified three primary clusters. This is consistent with previous studies detecting three clades of A. fumigatus and identifying pan-azole-resistant isolates with TR alleles in a single clade. We found pan-azole resistance in U.S. retail plant products, particularly compost and flower bulbs, which indicates the risk of exposure to these products for susceptible populations and that highly resistant isolates are likely distributed worldwide on these products.

opencc-zeroJun 2022View details →

A monograph of Aspergillus section Candidi

Aspergillus section Candidi encompasses white- or yellow-sporulating species mostly isolated from indoor and cave environments, food, feed, clinical material, soil and dung. Their identification is non-trivial due to largely uniform morphology. This study aims to re-evaluate the species boundaries in the section Candidi and present an overview of all existing species along with information on their ecology. For the analyses, we assembled a set of 113 strains with diverse origin. For the molecular analyses, we used DNA sequences of three house-keeping genes (benA, CaM and RPB2) and employed species delimitation methods based on a multispecies coalescent model. Classical phylogenetic methods and genealogical concordance species recognition approaches were used for comparison. Phenotypic studies involved comparisons of macromorphology on four cultivation media, seven micromorphological characters and growth at temperatures ranging from 10 to 45 °C. Based on our results, all currently accepted species gained further support, while two new species are proposed (A. magnus and A. tenebricus). In addition, we proposed the new name A. neotritici to replace an invalidly described A. tritici. The revised section Candidi now comprises nine species, some of which manifest a high level of intraspecific genetic and/or phenotypic variability (e.g. A. subalbidus and A. campestris) while others are more uniform (e.g. A. candidus or A. pragensis). The growth rates on different media and at different temperatures, colony colours, production of soluble pigments, stipe dimensions and vesicle diameters contributed the most to species differentiation.

opencc-by-4.0May 2024View details →

Data and code AEM article: Catching some air: A method to spatially quantify aerial triazole resistance in Aspergillus fumigatus

<h2>Name</h2> Catching_some_air <h2><a href="#description"></a>Description</h2> This script project was written to visualise and analyse the data used in the manuscript: Catching some air: A method to spatially quantify aerial triazole resistance in Aspergillus fumigatus. In the R script we load and clean the data from the international air sampling pilot, analyse it, generate figures of the sampled regions, the CFU totals and resistance fractions. The genotyping and phenotyping data of isolated resistant strains. The following files are required to run this R script: <ul> <li>RF_air_IP_cleaned.csv This fine contains total and resistance counts as well as metadata on samples from international air sampling pilot and includes the following variables:</li> </ul> Sample ID: an arbitrary number given to the packages prior to them being handed out   Country: Country in which sample was taken Region: Circular area with a 50 km radius within which the samples were clustered for analysis City/Town: City/Town in which the sample was taken Start date: date on which the trap was deployed and the stickers exposed to the air End date: date on which the trap was taken down and the stickers were re-covered and no longer exposed to the air Total.ITR: A. fumigatus CFU count in the permissive layer of the itraconazole-treated plate Res.ITR: CFU count of colonies that had breached the surface of the itraconazole-treated layer after incubation and were visually (with the unaided eye) sporulating. RF.ITR: The itraconazole (~4 mg/L) resistance fraction = Res.ITR/Total.ITR Total.VOR: A. fumigatus CFU count in the permissive layer of the voriconazole-treated plate Res.VOR: CFU count of colonies that had breached the surface of the voriconazole-treated layer after incubation and were visually (with the unaided eye) sporulating. RF.VOR: The voriconazole (~2 mg/L) resistance fraction = Res.VOR/Total.VOR Total control: CFU count on the untreated growth control plate Date.Batch: The date on which proccessing of the sample was started. To be more specific, the date at which Flamingo medium was poured over the seals of the sample and incubation was started. Note: note on the sample based on either information given the participant or observations in the lab. Exclude: Binary to quickly filter out samples that were considered unsuitable for further analysis either because low or high CFU counts. See manuscript for rationale. Lat: Latitude at the centre of the sampled region, does not relate to sample-specific location. Long: Longitude at the centre of the sampled region, does not relate to sample specific location. <ul> <li>Weather_data_IP_study_nov_dec_jan22_23.csv : contains raw weather data of the sampled regions during the sampling interval of the pilot downloaded from: <a href="https://cds.climate.copernicus.eu/cdsapp#!/dataset/reanalysis-era5-single-levels-monthly-means?tab=overview" target="_blank" rel="nofollow noreferrer noopener">https://cds.climate.copernicus.eu/cdsapp#!/dataset/reanalysis-era5-single-levels-monthly-means?tab=overview</a> (see link for full description of the data and the units). Contains the following variables:</li> </ul> Region: Circular area with a 50 km radius within which the samples were clustered for analysis Wind Nov : 10 m Wind speed (m/S) for the month november 2022 This parameter is the horizontal speed of the wind, or movement of air, at a height of ten metres above the surface of the Earth. Wind Dec : 10 m Wind speed (m/S) for the month december 2022 This parameter is the horizontal speed of the wind, or movement of air, at a height of ten metres above the surface of the Earth. Wind Jan : 10 m Wind speed (m/S) for the month januari 2023 This parameter is the horizontal speed of the wind, or movement of air, at a height of ten metres above the surface of the Earth. UV Nov: UV radiation at the surface (J/m^2) for the month november 2022. This parameter is the amount of ultraviolet (UV) radiation reaching the surface. It is the amount of radiation passing through a horizontal plane. UV Dec: UV radiation at the surface (J/m^2) for the month december 2022. This parameter is the amount of ultraviolet (UV) radiation reaching the surface. It is the amount of radiation passing through a horizontal plane. UV Jan: UV radiation at the surface (J/m^2) for the month januari 2023. This parameter is the amount of ultraviolet (UV) radiation reaching the surface. It is the amount of radiation passing through a horizontal plane. Temp Nov: Temperature (K) for the month november 2022. This parameter is the temperature of air at 2m above the surface of land, sea or inland waters. 2m temperature is calculated by interpolating between the lowest model level and the Earth's surface, taking account of the atmospheric conditions. Temp Dec: Temperature (K) for the month december 2022. This parameter is the temperature of air at 2m above the surface of land, sea or inland waters. 2m temperature is calculated by interpolating between the lowest model level and the Earth's surface, taking account of the atmospheric conditions. Temp Jan: Temperature (K) for the month januari 2023. This parameter is the temperature of air at 2m above the surface of land, sea or inland waters. 2m temperature is calculated by interpolating between the lowest model level and the Earth's surface, taking account of the atmospheric conditions. Precipitation Nov: Total precipitation (m) for the month november 2022. This parameter is the accumulated liquid and frozen water, comprising rain and snow, that falls to the Earth's surface. It is the sum of large-scale precipitation and convective precipitation. Precipitation Dec: Total precipitation (m) for the month december 2022. This parameter is the accumulated liquid and frozen water, comprising rain and snow, that falls to the Earth's surface. It is the sum of large-scale precipitation and convective precipitation. Precipitation Jan: Total precipitation (m) for the month januari 2023. This parameter is the accumulated liquid and frozen water, comprising rain and snow, that falls to the Earth's surface. It is the sum of large-scale precipitation and convective precipitation. lat_rep: Latitude at the centre of the sampled region, does not relate to sample specific location. lon_rep: Longitude at the centre of the sampled region, does not relate to sample specific location. <ul> <li>Genotyping_IP_cleaned.csv : contains the TR-type genotypes of the isolated resistant strains Contains the following variable:</li> </ul> Order: Ordering variable included in the file to readily be able to order the isolates by the order in which they were isolated. Contains the following variables: Strain: Strain code with "I" for strains isolated from itraconazole and V for strains isolated from voriconazole followed by a number indicating the order in which they were isolated from the air sample plate. Air sample: The plate/air sample from which the isolate originates Triazole: The triazole treatment the resistant strain grew on can be ITRA (itraconazole) or VORI (voriconazole) Country: Country in which sample was taken Region: Circular area with a 50 km radius within which the samples were clustered for analysis <h2><a href="#project-status"></a>Project status</h2> The manuscript has been published in AEM under the DOI: https://doi.org/10.1128/aem.00271-24

opencc-by-4.0Jul 2024View details →

Adaptative Survival of Aspergillus fumigatus to Echinocandins Arises from Cell Wall Remodeling Beyond β-1,3-glucan Synthesis Inhibition

Unprocessed Solid-state NMR and Molecular Dynamics data sets for the manuscript titled "Adaptative Survival of Aspergillus fumigatus to Echinocandins Arises from Cell Wall Remodeling Beyond β-1,3-glucan Synthesis Inhibition"

opencc-by-4.0Jun 2024View details →

100 años de investigación en Aspergillus niger

Open the record for dataset details and reuse information.

opencc-by-4.0Jul 2024View details →

Molecular biology techniques for fungal identification: focus on Aspergillus spp.

This tutorial summarises the main steps to identify through a molecular approach Aspergillus species isolated from food samples. It starts with introducing the Aspergillus genus, its economic and medical importance, and latest updates in taxonomy. The polyphasic approach for Aspergillus identification was introduced based on Samson et al., 2014. An overview on each of the stage to conduct molecular identification is provided, including examples of different DNA extraction protocols, PCR analysis with Aspergillus species recommended primers, Sanger’s sequencing, and interpretation of BLAST results.

opencc-by-4.0Oct 2024View details →

Genomic localization bias of secondary metabolite gene clusters and association with histone modifications in Aspergillus

Table S4 (Distribution of Orthologous groups) associated with the publication 'Genomic localization bias of secondary metabolite gene clusters and association with histone modifications in Aspergillus' is deposited at Zenodo.

opencc-zeroDec 2022View details →

Reducing the number of accepted species in Aspergillus series Nigri

The Aspergillus series Nigri contains biotechnologically and medically important species. They can produce hazardous mycotoxins, which is relevant due to the frequent occurrence of these species on foodstuffs and in the indoor environment. The taxonomy of the series has undergone numerous rearrangements, and currently, there are 14 species accepted in the series, most of which are considered cryptic. Species-level identifications are, however, problematic or impossible for many isolates even when using DNA sequencing or MALDI-TOF mass spectrometry, indicating a possible problem in the definition of species limits or the presence of undescribed species diversity. To re-examine the species boundaries, we collected DNA sequences from three phylogenetic markers (benA, CaM and RPB2) for 276 strains from series Nigri and generated 18 new whole-genome sequences. With the three-gene dataset, we employed phylogenetic methods based on the multispecies coalescence model, including four single-locus methods (GMYC, bGMYC, PTP and bPTP) and one multilocus method (STACEY). From a total of 15 methods and their various settings, 11 supported the recognition of only three species corresponding to the three main phylogenetic lineages: A. niger, A. tubingensis and A. brasiliensis. Similarly, recognition of these three species was supported by the GCPSR approach (Genealogical Concordance Phylogenetic Species Recognition) and analysis in DELINEATE software. We also showed that the phylogeny based on benA, CaM and RPB2 is suboptimal and displays significant differences from a phylogeny constructed using 5 752 single-copy orthologous proteins; therefore, the results of the delimitation methods may be subject to a higher than usual level of uncertainty. To overcome this, we randomly selected 200 genes from these genomes and performed ten independent STACEY analyses, each with 20 genes. All analyses supported the recognition of only one species in the A. niger and A. brasiliensis lineages, while one to four species were inconsistently delimited in the A. tubingensis lineage. After considering all of these results and their practical implications, we propose that the revised series Nigri includes six species: A. brasiliensis, A. eucalypticola, A. luchuensis (syn. A. piperis), A. niger (syn. A. vinaceus and A. welwitschiae), A. tubingensis (syn. A. chiangmaiensis, A. costaricensis, A. neoniger and A. pseudopiperis) and A. vadensis. We also showed that the intraspecific genetic variability in the redefined A. niger and A. tubingensis does not deviate from that commonly found in other aspergilli. We supplemented the study with a list of accepted species, synonyms and unresolved names, some of which may threaten the stability of the current taxonomy.

opencc-zeroDec 2022View details →

Taxonomy of Aspergillus series Versicolores: Species reduction and lessons learned about intraspecific variability

Aspergillus series Versicolores members occur in a wide range of environments and substrates such as indoor environments, food, clinical materials, soil, caves, marine or hypersaline ecosystems. The taxonomy of the series has undergone numerous re-arrangements including a drastic reduction in the number of species and subsequent recovery to 17 species in the last decade. The identification to species level is however problematic or impossible in some isolates even using DNA sequencing or MALDI-TOF mass spectrometry indicating a problem in the definition of species boundaries. To revise the species limits, we assembled a large dataset of 518 strains. From these, a total of 213 strains were selected for the final analysis according to their calmodulin (CaM) genotype, substrate and geography. This set was used for phylogenetic analysis based on five loci (benA, CaM, RPB2, Mcm7, Tsr1). Apart from the classical phylogenetic methods, we used multispecies coalescence (MSC) model-based methods, including one multilocus method (STACEY) and five single-locus methods (GMYC, bGMYC, PTP, bPTP, ABGD). Almost all species delimitation methods suggested a broad species concept with only four species consistently supported. We also demonstrated that the currently applied concept of species is not sustainable as there are incongruences between single-gene phylogenies resulting in different species identifications when using different gene regions. Morphological and physiological data showed overall lack of good, taxonomically informative characters, which could be used for identification of such a large number of existing species. The characters expressed either low variability across species or significant intraspecific variability exceeding interspecific variability. Based on the above-mentioned results, we reduce series Versicolores to four species, namely A. versicolor, A. creber, A. sydowii and A. subversicolor, and the remaining species are synonymized with either A. versicolor or A. creber. The revised descriptions of the four accepted species are provided. They can all be identified by any of the five genes used in this study. Despite the large reduction in species number, identification based on phenotypic characters remains challenging, because the variation in phenotypic characters is high and overlapping among species, especially between A. versicolor and A. creber. Similar to the 17 narrowly defined species, the four broadly defined species do not have a specific ecology and are distributed worldwide. We expect that the application of comparable methodology with extensive sampling could lead to a similar reduction in the number of cryptic species in other extensively studied Aspergillus species complexes and other fungal genera.

opencc-by-4.0Feb 2023View details →

Raw Data for the article: Growth Performance and Recovery of Nosocomial Aspergillus spp. in Blood Culture Bottles

Theoretically, Aspergillus spp. grow in culture media, but frequently, blood cultures of patients with invasive Aspergillosis are negative, even if until now, the reasons are not clear. This aspect underlines the lack of a good strategy for the cultivation and isolation of Aspergillus spp. In order to develop a complete analytical method to detect Aspergillus in clinical and pharmaceutical samples, we investigated the growth performance of two blood culture systems versus the pharmacopeia standard method. At &lt;72 h, all test systems showed comparable sensitivity, about 1-2 conidia. However, the subculture analysis showed a suboptimal recovery for the methods, despite the positive growth and the visualization of the "Aspergillus balls" in the culture media. To investigate this issue, we studied three different subculture approaches: (i) the use of a sterile subculture unit, (ii) the use of a sterile subculture unit and the collection of a larger aliquot (100 µL), following vigorous agitation of the vials, and (iii) to decapsulate the bottle, withdrawing and centrifuging the sample, and aliquot the pellet onto SDA plates. Our results showed that only the third procedure recovered Aspergillus from all positive culture bottles. This work confirmed that our strategy is a valid and faster method to culture and isolate Aspergillus spp. from blood culture bottles.

opencc-by-4.0Mar 2023View details →

Figure 7 in Supported ionic liquid phase facilitated catalysis with lipase from Aspergillus oryzae for enhance enantiomeric resolution of racemic ibuprofen - NCN project OPUS, grant no. 2020/37/B/ST8/00693.

Figure 7. presents the scheme of ionic liquid immobilization on the silica surface. The file relates to the composite material manufactured for the NCN project OPUS, grant no. 2020/37/B/ST8/00693.

opencc-zeroMay 2023View details →

Virulence of three Aspergillus species to the model insect Galleria mellonella and the contribution of ergot alkaloids to the pathogenic potential of Aspergillus leporis

Opportunistically pathogenic fungi have varying potential to cause disease in animals. Factors contributing to their virulence include specialized metabolites, which is some cases evolved in contexts unrelated to pathogenesis. Specialized metabolites that increase fungal virulence in the model insect Galleria mellonella include the ergot alkaloids fumigaclavine C in Aspergillus fumigatus (syn. Neosartorya fumigata) and lysergic acid α-hydroxyethylamide (LAH) in the entomopathogen Metarhizium brunneum. Three species of Aspergillus recently found to accumulate high concentrations of LAH were investigated for their pathogenic potential in G. mellonella. Aspergillus leporis was most virulent, A. hancockii was intermediate, and A. homomorphus had very little pathogenic potential. Aspergillus leporis and A. hancockii emerged from and sporulated on dead insects, thus completing their asexual life cycles. Inoculation by injection resulted in more lethal infections than did topical inoculation, indicating A. leporis and A. hancockii were pre-adapted for insect pathogenesis but lacked an effective means to breach the insect's cuticle. All three species accumulated LAH in infected insects, with A. leporis accumulating the most. Concentrations of LAH in A. leporis were similar to those observed in the entomopathogen M. brunneum. LAH was eliminated from A. leporis through a CRISPR/Cas9-based gene knockout, and the resulting strain had reduced virulence to G. mellonella. The data indicate A. leporis and A. hancockii have considerable pathogenic potential and that LAH increases the virulence of A. leporis.

opencc-zeroJun 2023View details →

Analyses of ergot alkaloid production in Aspergillus leporis and an easD knockout and sequences for phylogenetic analyses of rugulovasine-associated genes

Ergot alkaloids are fungal specialized metabolites that are important in agriculture and serve as sources of several pharmaceuticals. Aspergillus leporis is a soil saprotroph that possesses two ergot alkaloid biosynthetic gene clusters encoding lysergic acid amide production. We identified two additional, partial biosynthetic gene clusters within the A. leporis genome containing some of the ergot alkaloid synthesis (eas) genes required to make two groups of clavine ergot alkaloids, fumigaclavines and rugulovasines. Clavines possess unique biological properties compared to lysergic acid derivatives. Bioinformatic analyses indicated the fumigaclavine cluster contained functional copies of easA, easG, easD, easM, and easN. Genes resembling easQ and easH, which are required for rugulovasine production, were identified in a separate gene cluster. The pathways encoded by these partial, or satellite, clusters would require intermediates from the previously described lysergic acid amide pathway to synthesize a product. Chemical analyses of A. leporis cultures revealed the presence of fumigaclavine A. Rugulovasine was only detected in a single sample, however, prompting a heterologous expression approach to confirm functionality of easQ and easH. An easA knockout strain of Metarhizium brunneum, which accumulates the rugulovasine precursor chanoclavine-I aldehyde, was chosen as expression host. Strains of M. brunneum expressing easQ and easH from A. leporis accumulated rugulovasine as demonstrated through mass spectrometry analysis. These data indicate that A. leporis is exceptional among fungi in having the capacity to synthesize products from three branches of the ergot alkaloid pathway and for utilizing an unusual satellite cluster approach to achieve that outcome.