cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26327050
title: Decoding host cell interaction– and fluconazole-induced metabolic alterations and drug resistance in <i>Candida auris</i>

description: <i>Candida auris</i> is an emerging drug-resistant pathogen associated with high mortality rates. This study aimed to explore the metabolic alterations and associated pathogenesis and drug resistance in fluconazole-treated <i>Candida auris</i>–host cell interaction. Compared with controls, secreted metabolites from fluconazole-treated <i>C. auris</i> and fluconazole-treated <i>C. auris</i>–host cell co-culture demonstrated notable anti-<i>Candida</i> activity. Fluconazole caused significant reductions in <i>C. auris</i> cell numbers and aggregated phenotype. Metabolites produced by <i>C. auris</i> with potential fungal colonization, invasion, and host immune evasion effects were identified. Metabolites known to enhance biofilm formation produced during <i>C. auris</i>–host cell interaction were inhibited by fluconazole. Fluconazole enhanced the production of metabolites with biofilm inhibition activity, including behenyl alcohol and decanoic acid. Metabolites with potential <i>Candida</i> growth inhibition activity such as 2-palmitoyl glycerol, 1-tetradecanol, and 1-nonadecene were activated by fluconazole. Different patterns of proinflammatory cytokine expression presented due to fluconazole concentration and host cell type (fibroblasts versus macrophages). This highlights the immune response’s complexity, emphasizing the necessity for additional research to comprehend cell-type-specific responses to antifungal therapies. Both host cell interaction and fluconazole treatment increased the expression of <i>CDR1</i> and <i>ERG11</i> genes, both associated with drug resistance. This study provides insights into pathogenesis in <i>C. auris</i> due to host cell interaction and fluconazole treatment. Understanding these interactions is crucial for enhancing fluconazole sensitivity and effectively combating <i>C. auris</i>.
DOI: 10.6084/m9.figshare.26327050.v1
title: Decoding host cell interaction– and fluconazole-induced metabolic alterations and drug resistance in <i>Candida auris</i>

description: <i>Candida auris</i> is an emerging drug-resistant pathogen associated with high mortality rates. This study aimed to explore the metabolic alterations and associated pathogenesis and drug resistance in fluconazole-treated <i>Candida auris</i>–host cell interaction. Compared with controls, secreted metabolites from fluconazole-treated <i>C. auris</i> and fluconazole-treated <i>C. auris</i>–host cell co-culture demonstrated notable anti-<i>Candida</i> activity. Fluconazole caused significant reductions in <i>C. auris</i> cell numbers and aggregated phenotype. Metabolites produced by <i>C. auris</i> with potential fungal colonization, invasion, and host immune evasion effects were identified. Metabolites known to enhance biofilm formation produced during <i>C. auris</i>–host cell interaction were inhibited by fluconazole. Fluconazole enhanced the production of metabolites with biofilm inhibition activity, including behenyl alcohol and decanoic acid. Metabolites with potential <i>Candida</i> growth inhibition activity such as 2-palmitoyl glycerol, 1-tetradecanol, and 1-nonadecene were activated by fluconazole. Different patterns of proinflammatory cytokine expression presented due to fluconazole concentration and host cell type (fibroblasts versus macrophages). This highlights the immune response’s complexity, emphasizing the necessity for additional research to comprehend cell-type-specific responses to antifungal therapies. Both host cell interaction and fluconazole treatment increased the expression of <i>CDR1</i> and <i>ERG11</i> genes, both associated with drug resistance. This study provides insights into pathogenesis in <i>C. auris</i> due to host cell interaction and fluconazole treatment. Understanding these interactions is crucial for enhancing fluconazole sensitivity and effectively combating <i>C. auris</i>.
DOI: 10.25549/kada-c126-18906
title: Brotherhood of Artists: correspondence

description: The original name of this organization, founded in 1970, was "Ethnic" (derived from the Ethnic Minorities Committee of the local Actors' Equity Association). It was changed to "Brotherhood of Artists at the second meeting.
DOI: 10.6084/m9.figshare.26514003
title: Genome-wide search and gene expression studies reveal candidate effectors with a role in pathogenicity and virulence in <i>Fusarium graminearum</i>

description: <i>Fusarium graminearum</i> causes Fusarium head blight (FHB) disease in wheat worldwide. Although <i>F. graminearum</i> is reported to secrete several effectors, their role in virulence and pathogenicity is unknown. The study aimed at identifying candidate genes with a role in pathogenicity and virulence using two different host systems, <i>Arabidopsis thaliana</i> and wheat, challenged with <i>F. graminearum</i> TN01. Detached leaf assay and histological studies revealed the virulent nature of TN01. A genome-wide in silico search revealed several candidate genes, of which 23 genes were selected based on reproducibility. Gene expression studies by reverse transcriptase–polymerase chain reaction (RT-PCR) in leaf tissues of Arabidopsis and the two wheat genotypes, the susceptible (Sonalika) and the resistant (Nobeoka Bozu/Nobeoka), compared with mock-treated controls in a time-course study using fungal- and plant-specific genes as internal controls revealed that these genes were differentially regulated. Further, expression of these candidates in <i>F. graminearum</i>–inoculated Sonalika and Nobeoka spikes compared with mock-treated controls revealed their role in pathogenicity and virulence. Gene ontology studies revealed that some of these secretory proteins possessed a role in apoptosis and ceratoplatanin and KP4 killer toxin syntheses. A three-dimensional protein configuration was performed by homology modeling using trRosetta. Further, real-time quantitative PCR (RT-qPCR) studies in <i>F. graminearum</i>–inoculated Arabidopsis and wheat at early time points of inoculation revealed an increased expression of the majority of these genes in Sonalika, suggesting their possible role in pathogenicity, whereas low mRNA abundance was observed for 11 of these genes in the resistant genotype, Nobeoka, compared with Sonalika, indicating their role in virulence of <i>F. graminearum</i>.
DOI: 10.6084/m9.figshare.26514003.v1
title: Genome-wide search and gene expression studies reveal candidate effectors with a role in pathogenicity and virulence in <i>Fusarium graminearum</i>

description: <i>Fusarium graminearum</i> causes Fusarium head blight (FHB) disease in wheat worldwide. Although <i>F. graminearum</i> is reported to secrete several effectors, their role in virulence and pathogenicity is unknown. The study aimed at identifying candidate genes with a role in pathogenicity and virulence using two different host systems, <i>Arabidopsis thaliana</i> and wheat, challenged with <i>F. graminearum</i> TN01. Detached leaf assay and histological studies revealed the virulent nature of TN01. A genome-wide in silico search revealed several candidate genes, of which 23 genes were selected based on reproducibility. Gene expression studies by reverse transcriptase–polymerase chain reaction (RT-PCR) in leaf tissues of Arabidopsis and the two wheat genotypes, the susceptible (Sonalika) and the resistant (Nobeoka Bozu/Nobeoka), compared with mock-treated controls in a time-course study using fungal- and plant-specific genes as internal controls revealed that these genes were differentially regulated. Further, expression of these candidates in <i>F. graminearum</i>–inoculated Sonalika and Nobeoka spikes compared with mock-treated controls revealed their role in pathogenicity and virulence. Gene ontology studies revealed that some of these secretory proteins possessed a role in apoptosis and ceratoplatanin and KP4 killer toxin syntheses. A three-dimensional protein configuration was performed by homology modeling using trRosetta. Further, real-time quantitative PCR (RT-qPCR) studies in <i>F. graminearum</i>–inoculated Arabidopsis and wheat at early time points of inoculation revealed an increased expression of the majority of these genes in Sonalika, suggesting their possible role in pathogenicity, whereas low mRNA abundance was observed for 11 of these genes in the resistant genotype, Nobeoka, compared with Sonalika, indicating their role in virulence of <i>F. graminearum</i>.
DOI: 10.6084/m9.figshare.26327052
title: Revision of <i>Alternaria</i> sections <i>Pseudoulocladium</i> and <i>Ulocladioides</i>: Assessment of species boundaries, determination of mating-type loci, and identification of Russian strains

description: <i>Alternaria</i> is a large genus within Pleosporaceae and consists of fungi that have up to recently been considered to be 15 separate genera, including <i>Ulocladium</i>. The majority of <i>Ulocladium</i> species after incorporation into <i>Alternaria</i> were placed in three sections: <i>Ulocladioides, Pseudoulocladium</i>, and <i>Ulocladium</i>. In this study, phylogeny of 26 reference strains of 22 species and 20 Russian <i>Ulocladium</i>-like isolates was recovered. The partial actin gene (<i>act</i>), <i>Alternaria</i> major allergen (<i>alta1</i>), calmodulin (<i>cal</i>), glyceraldehyde-3-phosphate dehydrogenase (<i>gapdh</i>), RNA polymerase II second largest subunit (<i>rpb2</i>), and translation elongation factor 1-α (<i>tef1</i>) were sequenced for Russian isolates. All these fungi were examined using multilocus phylogenetic analysis according to the genealogical concordance phylogenetic species recognition (GCPSR) principle and the coalescent-based model Poisson tree processes (PTP, mPTP) and evaluated for the presence of recombination. All strains were combined into two clades that corresponded to the <i>Pseudoulocladium</i> and <i>Ulocladioides</i> sections. The <i>Pseudoulocladium</i> clade included four reference strains and nine local isolates and considered to be a single species, whereas the <i>Ulocladioides</i> section comprises 11 species, instead of 17 names previously adopted. Nine species were abolished by joining four other species. Species <i>A. atra</i> and <i>A. multiformis</i> were combined into the single species <i>A. atra</i>. Five species, <i>A. brassicae-pekinensis, A. consortialis, A. cucurbitae, A. obovoidea</i>, and <i>A. terricola</i>, were united in the species <i>A. consortialis. Alternaria heterospora</i> and <i>A. subcucurbitae</i> were combined into one species, <i>A. subcucurbitae. Alternaria aspera, A. chartarum, A. concatenata</i>, and <i>A. septospora</i> were combined into a single species, <i>A. chartarum</i>. Also, amplification with two different primer sets was performed to define mating-type locus 1 (<i>MAT1</i>) idiomorph. All studied isolates were heterothallic, contradicting some prior studies. Twenty Russian <i>Ulocladium</i>-like isolates were assigned to five species of two sections, <i>A. atra, A. cantlous, A. chartarum, A. consortialis</i>, and <i>A. subcucurbitae</i>. Species <i>A. cantlous</i> and <i>A. subcucurbitae</i> were found in Russia for the first time.
DOI: 10.6084/m9.figshare.26327052.v1
title: Revision of <i>Alternaria</i> sections <i>Pseudoulocladium</i> and <i>Ulocladioides</i>: Assessment of species boundaries, determination of mating-type loci, and identification of Russian strains

description: <i>Alternaria</i> is a large genus within Pleosporaceae and consists of fungi that have up to recently been considered to be 15 separate genera, including <i>Ulocladium</i>. The majority of <i>Ulocladium</i> species after incorporation into <i>Alternaria</i> were placed in three sections: <i>Ulocladioides, Pseudoulocladium</i>, and <i>Ulocladium</i>. In this study, phylogeny of 26 reference strains of 22 species and 20 Russian <i>Ulocladium</i>-like isolates was recovered. The partial actin gene (<i>act</i>), <i>Alternaria</i> major allergen (<i>alta1</i>), calmodulin (<i>cal</i>), glyceraldehyde-3-phosphate dehydrogenase (<i>gapdh</i>), RNA polymerase II second largest subunit (<i>rpb2</i>), and translation elongation factor 1-α (<i>tef1</i>) were sequenced for Russian isolates. All these fungi were examined using multilocus phylogenetic analysis according to the genealogical concordance phylogenetic species recognition (GCPSR) principle and the coalescent-based model Poisson tree processes (PTP, mPTP) and evaluated for the presence of recombination. All strains were combined into two clades that corresponded to the <i>Pseudoulocladium</i> and <i>Ulocladioides</i> sections. The <i>Pseudoulocladium</i> clade included four reference strains and nine local isolates and considered to be a single species, whereas the <i>Ulocladioides</i> section comprises 11 species, instead of 17 names previously adopted. Nine species were abolished by joining four other species. Species <i>A. atra</i> and <i>A. multiformis</i> were combined into the single species <i>A. atra</i>. Five species, <i>A. brassicae-pekinensis, A. consortialis, A. cucurbitae, A. obovoidea</i>, and <i>A. terricola</i>, were united in the species <i>A. consortialis. Alternaria heterospora</i> and <i>A. subcucurbitae</i> were combined into one species, <i>A. subcucurbitae. Alternaria aspera, A. chartarum, A. concatenata</i>, and <i>A. septospora</i> were combined into a single species, <i>A. chartarum</i>. Also, amplification with two different primer sets was performed to define mating-type locus 1 (<i>MAT1</i>) idiomorph. All studied isolates were heterothallic, contradicting some prior studies. Twenty Russian <i>Ulocladium</i>-like isolates were assigned to five species of two sections, <i>A. atra, A. cantlous, A. chartarum, A. consortialis</i>, and <i>A. subcucurbitae</i>. Species <i>A. cantlous</i> and <i>A. subcucurbitae</i> were found in Russia for the first time.
DOI: 10.25549/kada-c126-21419
title: America and the World Economy: The New Era, lecture by Henry Chung
DOI: 10.6084/m9.figshare.26090967
title: Downfall of an empire: Unmasking the hidden diversity and distribution of the <i>Amanita rubescens</i> species complex

description: <i>Amanita</i> is one of the most salient mushroom genera due to its cultural, economic, and medical importance. Recently, many new <i>Amanita</i> species have been described worldwide, increasing the genus richness. However, several clades have cryptic diversity, and many species complexes have not yet been resolved. This is the case of the rubescent species in the <i>Validae</i> section, which have been widely cited under the name <i>Amanita rubescens</i> s.l. We used a four-locus matrix (nuc rDNA internal transcribed spacer [ITS] and 28S regions and genes for RNA polymerase II subunit 2 [<i>rpb2</i>], translation elongation factor 1-α [<i>tef1-α</i>], and β-tubulin [<i>tub2</i>]) to solve the phylogenetic relationships within the <i>Amanita</i> section <i>Validae</i>. To analyze the diversity and distribution patterns of species, we used an extensive ITS sequence sampling including environmental DNA databases. The phylogenetic analyses demonstrated that the <i>Validae</i> section is divided into three monophyletic and highly supported major clades: <i>Mappae, Validae</i>, and <i>Rubescentes</i>. At least 11 species-level clades within the <i>Rubescentes</i> clade were highly supported: <i>A. cruentilemurum</i> nom. prov. <i>A. brunneolocularis, A. rubescens</i> s.s. (European clade), <i>A. rubescens</i> s.s. (Asiatic clade), <i>A. orsonii</i> s.s. <i>A</i>. ‘<i>orsonii</i>,’ <i>A. aureosubucula</i> nom. prov., <i>A. novinupta, A. flavorubens</i>, and two undescribed North American species. We proved that <i>A. rubescens</i> s.s. has two segregated populations (European and Asiatic) and it is not naturally distributed in America. Furthermore, we found that America has more cryptic species within the <i>Rubescentes</i> clade than Eurasia.
DOI: 10.6084/m9.figshare.26167182.v1
title: Pinibarreniales, a new order of Sordariomycetes from pine barrens ecosystem

description: <i>Pinibarrenia chlamydospora</i>, sp. nov. isolated from the roots of highbush blueberry in the New Jersey Pine Barrens, is described and illustrated. Based on multigene phylogenetic analysis, as well as morphological and ecological characteristics, Pinibarreniales and Pinibarreniaceae are established to accommodate this novel lineage in Sordariomycetidae, Sordariomycetes. Pinibarreniales, Tracyllalales, and Vermiculariopsiellales are proposed to be included in the subclass Sordariomycetidae. Pinibarreniales likely have a wide distribution and forms association with Ericaceae plants that live in acidic and oligotrophic environments because its DNA barcode matches with environmental sequences from other independent ecological studies. The plant-fungal interaction experiment revealed negative impacts on <i>Arabidopsis</i>, indicating its pathogenicity. This uncovered new fungal lineage will contribute to a better understanding of the diversity and systematics of Sordariomycetes.
DOI: 10.6084/m9.figshare.26888578
title: aerobot

description: TODO
DOI: 10.6084/m9.figshare.26888578.v3
title: aerobot

description: TODO
DOI: 10.6084/m9.figshare.26090967.v2
title: Downfall of an empire: Unmasking the hidden diversity and distribution of the <i>Amanita rubescens</i> species complex

description: <i>Amanita</i> is one of the most salient mushroom genera due to its cultural, economic, and medical importance. Recently, many new <i>Amanita</i> species have been described worldwide, increasing the genus richness. However, several clades have cryptic diversity, and many species complexes have not yet been resolved. This is the case of the rubescent species in the <i>Validae</i> section, which have been widely cited under the name <i>Amanita rubescens</i> s.l. We used a four-locus matrix (nuc rDNA internal transcribed spacer [ITS] and 28S regions and genes for RNA polymerase II subunit 2 [<i>rpb2</i>], translation elongation factor 1-α [<i>tef1-α</i>], and β-tubulin [<i>tub2</i>]) to solve the phylogenetic relationships within the <i>Amanita</i> section <i>Validae</i>. To analyze the diversity and distribution patterns of species, we used an extensive ITS sequence sampling including environmental DNA databases. The phylogenetic analyses demonstrated that the <i>Validae</i> section is divided into three monophyletic and highly supported major clades: <i>Mappae, Validae</i>, and <i>Rubescentes</i>. At least 11 species-level clades within the <i>Rubescentes</i> clade were highly supported: <i>A. cruentilemurum</i> nom. prov. <i>A. brunneolocularis, A. rubescens</i> s.s. (European clade), <i>A. rubescens</i> s.s. (Asiatic clade), <i>A. orsonii</i> s.s. <i>A</i>. ‘<i>orsonii</i>,’ <i>A. aureosubucula</i> nom. prov., <i>A. novinupta, A. flavorubens</i>, and two undescribed North American species. We proved that <i>A. rubescens</i> s.s. has two segregated populations (European and Asiatic) and it is not naturally distributed in America. Furthermore, we found that America has more cryptic species within the <i>Rubescentes</i> clade than Eurasia.
DOI: 10.6084/m9.figshare.26167182
title: Pinibarreniales, a new order of Sordariomycetes from pine barrens ecosystem

description: <i>Pinibarrenia chlamydospora</i>, sp. nov. isolated from the roots of highbush blueberry in the New Jersey Pine Barrens, is described and illustrated. Based on multigene phylogenetic analysis, as well as morphological and ecological characteristics, Pinibarreniales and Pinibarreniaceae are established to accommodate this novel lineage in Sordariomycetidae, Sordariomycetes. Pinibarreniales, Tracyllalales, and Vermiculariopsiellales are proposed to be included in the subclass Sordariomycetidae. Pinibarreniales likely have a wide distribution and forms association with Ericaceae plants that live in acidic and oligotrophic environments because its DNA barcode matches with environmental sequences from other independent ecological studies. The plant-fungal interaction experiment revealed negative impacts on <i>Arabidopsis</i>, indicating its pathogenicity. This uncovered new fungal lineage will contribute to a better understanding of the diversity and systematics of Sordariomycetes.
DOI: 10.6084/m9.figshare.26210476
title: <i>Suillus hypogaeus</i>: First record of a truffle <i>Suillus</i>

description: <i>Suillus</i> (order Boletales) is a diverse genus of epigeous, mushroom-forming fungi native to temperate forests across the Northern Hemisphere; however, some species are also present in areas where Pinaceae has been introduced in the Southern Hemisphere. Unlike the closely related genus <i>Rhizopogon</i>, there are no described hypogeous, sequestrate species of <i>Suillus</i>. Here, we describe <i>Suillus hypogaeus</i>, the first known species of the genus with hypogeous, sequestrate sporocarps. Collections were made on Marys Peak in Benton County, Oregon, USA, at an elevation of 800 m in forests dominated by <i>Pseudotsuga menziesii</i> var. <i>menziesii</i>. The peridium is white, quickly staining pink to purple-reddish where bruised or cut. The gleba is pale yellow when young, becoming purple with maturity, and the basidiospores are obovoid, light yellow in KOH, and amyloid in Melzer’s reagent. Multilocus molecular phylogenetic analyses support the placement of <i>S. hypogaeus</i> among the <i>Larix</i> specialists in the spectabilis group of <i>Suillus</i>. Although <i>Larix</i> and <i>Pseudotsuga</i> are sister genera, <i>Larix</i> does not occur on Marys Peak or elsewhere in western Oregon. <i>Suillus hypogaeus</i>, therefore, represents both an independent origin of the hypogeous, sequestrate sporocarp within the Boletales and an independent host shift between <i>Larix</i> and <i>Pseudotsuga</i> within the genus <i>Suillus</i>.
DOI: 10.6084/m9.figshare.26210476.v1
title: <i>Suillus hypogaeus</i>: First record of a truffle <i>Suillus</i>

description: <i>Suillus</i> (order Boletales) is a diverse genus of epigeous, mushroom-forming fungi native to temperate forests across the Northern Hemisphere; however, some species are also present in areas where Pinaceae has been introduced in the Southern Hemisphere. Unlike the closely related genus <i>Rhizopogon</i>, there are no described hypogeous, sequestrate species of <i>Suillus</i>. Here, we describe <i>Suillus hypogaeus</i>, the first known species of the genus with hypogeous, sequestrate sporocarps. Collections were made on Marys Peak in Benton County, Oregon, USA, at an elevation of 800 m in forests dominated by <i>Pseudotsuga menziesii</i> var. <i>menziesii</i>. The peridium is white, quickly staining pink to purple-reddish where bruised or cut. The gleba is pale yellow when young, becoming purple with maturity, and the basidiospores are obovoid, light yellow in KOH, and amyloid in Melzer’s reagent. Multilocus molecular phylogenetic analyses support the placement of <i>S. hypogaeus</i> among the <i>Larix</i> specialists in the spectabilis group of <i>Suillus</i>. Although <i>Larix</i> and <i>Pseudotsuga</i> are sister genera, <i>Larix</i> does not occur on Marys Peak or elsewhere in western Oregon. <i>Suillus hypogaeus</i>, therefore, represents both an independent origin of the hypogeous, sequestrate sporocarp within the Boletales and an independent host shift between <i>Larix</i> and <i>Pseudotsuga</i> within the genus <i>Suillus</i>.