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14 protocols using nis elements d v 4

1

Fungal Culture Characterization Protocol

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Cultures were incubated on oatmeal agar (OA, which favours synnema development), malt extract agar (MEA) and dichloran 18 % glycerol agar (DG18) plates (recipes from Samson et al. 2010 ) at 25 °C in the dark. After 14 d, growth rates were measured and colony characters noted. Colony colours were rated following the charts of Rayner (1970) . Dried herbarium material was rehydrated in sterile water, which was then replaced by Shear's mounting media for photomicroscopy (Crous et al. 2009 ). Measurements and descriptions of microscopic structures were made from cultures grown on synthetic nutrient agar (SNA, Samson et al. 2010 ) at 25 °C in the dark for 14 d, mounted in 85 % lactic acid. Macroscopic photographs were made with a Nikon SMZ25 stereo microscope equipped with a Nikon DS-Ri2 high-definition colour camera head. Photomicrographs of diagnostic structures were made with a Zeiss Axio Imager A2 microscope equipped with a Nikon DS-Ri2 high-definition colour camera head, using differential interference contrast (DIC) optics and the Nikon software NIS-elements D v. 4.50.
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2

Characterization of Fungal Isolates

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All isolates were characterised following the protocols described by Leslie & Summerell (2006) and Lombard et al. (2019) (link) using PDA, oatmeal agar (OA, recipe in Crous et al. 2019 ), synthetic nutrient-poor agar (SNA; Nirenberg 1976 ) and carnation leaf agar (CLA; Fisher et al. 1982 ). Colony morphology, pigmentation, odour and growth rates were evaluated on PDA after 7 d at 24 °C using a 12/12 h light/dark cycle with near UV and white fluorescent light. Colour notations were done using the colour charts of Rayner (1970) . Micromorphological characters were examined using water as mounting medium on a Zeiss Axioskop 2 plus with Differential Interference Contrast (DIC) optics and a Nikon AZ100 dissecting microscope both fitted with Nikon DS-Ri2 high definition colour digital cameras to photo-document fungal structures. Measurements were taken using the Nikon software NIS-elements D v. 4.50 and the 95 % confidence levels were determined for the conidial measurements with extremes given in parentheses. For all other fungal structures examined, only the extremes are presented. To facilitate the comparison of relevant micro- and macroconidial features, composite photo plates were assembled from separate photographs using PhotoShop CSS.
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3

Fungal Characterization through Standardized Protocols

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Cultures were incubated on oatmeal agar (OA), malt extract agar (MEA) and dichloran 18 % glycerol agar (DG18) plates (recipes Samson et al. 2010 ) at 25 °C in the dark. After 14 d the colony diameters were measured and the colony characters noted. Colony colours were rated according to Rayner (1970) . Measurements and descriptions of microscopic structures were made from cultures grown on synthetic nutrient agar (SNA, Samson et al. 2010 ) at 25 °C in the dark for 14 d or longer to ensure ascomata development. Slide preparations of the asexual morph structures were made with the sellotape technique (Schubert et al. 2007 (link)) or mounted in 85 % lactic acid, like the sexual morph structures. Photographs of characteristic structures were made with a Zeiss Axio Imager A2 microscope equipped with a Nikon DS-Ri2 high-definition colour camera head using differential interference contrast (DIC) optics and the Nikon software NIS-elements D v. 4.50. Furthermore, growth at 36 °C and 40 °C in the dark on OA was tested.
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4

Comprehensive Fungal Characterization Protocol

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All isolates were characterised following the protocols described by Leslie & Summerell (2006) using potato dextrose agar (PDA; recipe in Crous et al. 2009 ), synthetic nutrient-poor agar (SNA; Nirenberg 1976 ) and carnation leaf agar (CLA; Fisher et al. 1982 ). Colony morphology, pigmentation, odour and growth rates were evaluated on PDA after 3 and 7 d at 24 °C with a 12/12 h cool fluorescent light/dark cycle as described by Sandoval-Denis et al. (2018) (link) and using the colour charts of Rayner (1970) . Micromorphological characters were examined using water as mounting medium on a Zeiss Axioskop 2 plus with Differential Interference Contrast (DIC) optics and a Nikon AZ100 stereomicroscope both fitted with Nikon DS-Ri2 high definition colour digital cameras to photo-document fungal structures. Measurements were taken using the Nikon software NIS-elements D v. 4.50 and the 95 % confidence levels were determined for the conidial measurements with extremes given in parentheses. For all other fungal structures examined, only the extremes are presented. To facilitate the comparison of relevant micro- and macroconidial features, composite photo plates were assembled from separate photographs using PhotoShop CSS.
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5

Fungal Isolate Characterization Protocols

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All isolates were characterised following the protocols described by Leslie & Summerell (2006) and Lombard et al. (2019) using PDA, oatmeal agar (OA, recipe in Crous et al. 2019 ), synthetic nutrient-poor agar (SNA; Nirenberg 1976 ) and carnation leaf agar (CLA; Fisher et al. 1982 ). Colony morphology, pigmentation, odour and growth rates were evaluated on PDA after 7 d at 24 °C in the dark. Colour notations was done using the colour charts of Rayner (1970) . Micromorphological characters were examined using water as mounting medium on a Nikon Eclipse 80i and/or Zeiss Axioskop 2 plus with Differential Interference Contrast (DIC) optics and a Nikon AZ100 stereomicroscope, all fitted with Nikon DS-Ri2 high definition colour digital cameras to photo-document fungal structures. Measurements were taken using the Nikon software NIS-elements D v. 4.50 of at least 30 fungal structures and the 95 % confidence levels were determined for the conidial measurements with extremes given in parentheses. For all other fungal structures examined, only the extremes are presented. To facilitate the comparison of relevant micro- and macroconidial features, composite photo plates were assembled from separate photographs using PhotoShop CSS.
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6

Morphological Characterization of Fungal Isolates

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Isolates were grown on potato carrot agar (PCA, Crous et al., 2009 ) and synthetic nutrient-poor agar (SNA, Nirenberg, 1976 ) at moderate temperatures under CoolWhite fluorescent light with an 8 h photoperiod. After 7 and 14 d the growth rates were measured and the colony characters noted. Colony colours were rated according to Rayner (1970) . Morphological descriptions of asexual structures were made for isolates grown on SNA for 7 d. Slides were prepared with the cellotape technique (Schubert et al. 2007 (link)) using Titan Ultra Clear Tape (Conglom Inc., Toronto, Canada) and Shear's medium as mounting fluid. Morphological descriptions of sexual structures were made for isolates grown on PCA for 14 d, with 85 % lactic acid as mounting fluid. The mean plus/minus standard deviation values were derived from measurements of 30 structures, with extremes given in parentheses. Photographs of characteristic structures were made with a Zeiss Axio Imager A2 microscope equipped with a Nikon DS-Ri2 high-definition colour camera using differential interference contrast (DIC) optics and the Nikon software NIS-elements D v. 4.50. Adobe Bridge CS5.1 and Adobe Photoshop CS5 Extended, v. 12.1, were used for the final editing and photographic preparation. Nomenclatural data were deposited in MycoBank (Crous et al. 2004 ).
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7

Phenotypic characterization of Aspergillus acidohumus

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Macroscopic characters were studied on Czapek Yeast Autolysate agar (CYA), CYA supplemented with 5 % NaCl (CYAS), Yeast Extract Sucrose agar (YES), Creatine Sucrose agar (CREA), Dichloran 18 % Glycerol agar (DG 18), Oatmeal agar (OA) and Malt Extract agar (MEA, Oxoid malt) (Samson et al. 2010 ). To enhance the growth, the ex-type culture of A. acidohumus CBS 141577, isolated from acid soil from China, was additionally inoculated on Cherry Decoction agar (CHA) (Crous et al. 2009 ). The isolates were inoculated at three points on 90 mm Petri dishes and incubated for 7 d at 25 °C in darkness. In addition, CYA and MEA plates were incubated at 30 °C and 37 °C. After 7 d of incubation, colony diameters were recorded. The colony texture, degree of sporulation, obverse and reverse colony colours, the production of soluble pigments and exudates were determined. Light microscope preparations were made from 1 wk old colonies grown on MEA. Lactic acid (60 %) was used as mounting fluid. Ethanol (96 %) was used to remove excess conidia and prevent air bubbles. A Zeiss Stereo Discovery V20 dissecting microscope and Zeiss AX10 Imager A2 light microscope equipped with Nikon DS-Ri2 cameras and software NIS-Elements D v4.50 were used to capture digital images.
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8

Immunofluorescence Staining Protocol for Cell Analysis

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Immunofluorescence stainings were performed using protocol reported previously (Vinaiphat and Thongboonkerd, 2018 (link), Yoodee et al., 2021 (link)). Briefly, the cells were fixed with 4 % paraformaldehyde/PBS at 25 °C for 15 min, permeabilized with 0.1 % Triton X-100/PBS at 25 °C for 15 min, and then washed with membrane preserving buffer (PBS containing 0.1 mM CaCl2 and 1 mM MgCl2). The cells were incubated with 5 % bovine serum albumin (BSA)/PBS at 25 °C for 30 min to block non-specific binders and then with mouse monoclonal anti-LMNA (Santa Cruz Biotechnology) or mouse monoclonal anti-ZO-1 (Invitrogen) antibody (both at 1:50 in 1 % BSA/PBS) at 37 °C for 1 h. After three washes with PBS, the cells were incubated with goat anti-mouse IgG conjugated with Alexa Fluor 488 (green) (Invitrogen) (1:5,000) mixed with Hoechst dye (Invitrogen) (1:1,000) in 1 % BSA/PBS at 37 °C for 1 h. After extensive washes with PBS and mounting on a glass slide, the cells were examined and imaged under Eclipse 80i fluorescence microscope (Nikon). Quantitative intensity data were measured from at least 100 cells in ≥ 10 random high-power fields (HPFs) per each biological sample using NIS-Elements D V.4.11 (Nikon). Using this software, distribution of the immunofluorescence signal was analyzed in its spectral format to localize protein expression.
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9

Quantifying Vimentin Expression in Macrophages

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After COM treatment, the si-Control-transfected and si-Vimentin-transfected macrophages were adhered on a coverslip, fixed by 4% (v/v) paraformaldehyde/PBS at 25°C for 15 min, and then permeabilized with 0.2% Triton X-100/PBS at 25°C for 15 min. After washing, the cells were incubated at 4°C overnight with mouse monoclonal anti-vimentin antibody (Santa Cruz Biotechnology) (diluted 1:50 in 1% BSA/PBS). After washing, the cells were incubated with corresponding secondary antibody conjugated with Alexa Fluor 488 (Invitrogen) (diluted 1:2,000 in 1% BSA/PBS) at 25°C for 1 h. Finally, the cells were extensively washed with PBS and mounted onto a glass slide using 50% glycerol in PBS. The cells were imaged by using Nikon Eclipse 80i fluorescence microscope (Nikon). Expression level of vimentin was quantitated by measuring mean fluorescence intensity from at least 50 cells in 10 random HPF of each sample using NIS-Elements D V.4.11 software (Nikon).
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10

Immunofluorescence Analysis of ARID1A Expression

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The cells were grown on a coverslip and treated as described above. After rinsing with PBS, the cells were fixed with 4% (v/v) paraformaldehyde/PBS at 25 °C for 15 min and then permeabilized with 0.1% Triton X-100/PBS at 25°C for 15 min. After washing, non-specific bindings were blocked with 1% BSA in PBS at 25 °C for 30 min and the cells were incubated at 4 °C overnight with mouse monoclonal anti-ARID1A (Santa Cruz Biotechnology) (1:50 in 1% BSA/PBS). After another washing step, the cells were incubated with corresponding secondary antibody conjugated with Alexa Fluor 488 (Invitrogen) (1:2,000 in 1% BSA/PBS) at 25 °C for 1 h. Nuclei were counterstained by Hoechst dye (Sigma-Aldrich) (1:2,000 in 1% BSA/PBS). Finally, the cells were extensively washed with PBS and mounted onto a glass slide using 50% glycerol in PBS. Cellular imaging was done by using Nikon Eclipse 80i fluorescence microscope (Nikon; Tokyo, Japan) and expression level of ARID1A was analyzed by measuring mean fluorescence intensity from at least 100 cells in ≥10 random high-power fields (HPFs) of each sample using NIS-Elements D V.4.11 (Nikon).
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