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1

Quantifying MAPK Signaling in Fungal Hyphae

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Total proteins were isolated from 2-day-old vegetative hyphae grown in 5 x YEG culture (5g yeast extract, 10g glucose, 1L ddH2O) using TCA-acetone precipitation methods, and total protein concentrations were determined using the Enhanced BCA Protein Assay Kit (Beyotime, China). Protein extracts (50μg) were subjected to 12% SDS-PAGE (EpiZyme, China) and transferred to a PVDF membrane as described in previous research (Zhang et al., 2018 (link)). Primary antibodies, including anti-Phospho-p44/42 MAPK antibody #4370 (Cell Signaling Technology, Inc.), anti-ERK1/2 MAPK antibody (C-9): sc-514,302 (Santa Cruz Biotechnology, Inc.), and anti-GAPDH R1208-3 antibody (HUABIO, China), along with peroxidase (HRP)-conjugated goat anti-rabbit and goat anti-mouse secondary antibodies (Beyotime, China), were used in this study. An ECL chemiluminescent kit (Bio-Rad, United States) was used for Western blot detection.
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2

HUVEC Protein Extraction and Western Blot Analysis

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The samples of HUVECs were rinsed with phosphate-buffered saline (PBS) and then add 50 μl lysis buffer (Beijing Solarbio Science & Technology Co., Beijing, China) containing RIPA buffer, 1% PMSF and 0.1% protease inhibitor cocktail in 24-well plate at 4 °C for 20 min, and collected in the 1.5 ml tube. And subsequently, the tube was centrifuged for 15 min at 12000 rpm at 4 °C. The concentration of protein used BCA assay kit (Beijing Solarbio Science & Technology Co., Beijing, China). The sample proteins were separated by 12% SDS-PAGE (EpiZyme, Shanghai, China), and then transferred on the polyvinylidene fluoride (PVDF) membrane (Merck Millopore, USA). The membrane was blocked with 5% defatted milk at room temperature for one hour. After this, the membrane was incubated by Rabbit Anti-phospho-AKT1 (Thr34) polyclonal antibody (Bioss, Beijing, China) with a dilution of 1 : 1000 and incubated by GAPDH (Cell Signaling Technology, USA) with a dilution of 1 : 1000. In the next step, the membrane was rinsed three times using Tris–HCl buffered saline with Tween 20 (TBST), and it was incubated by each corresponding secondary antibody and washed three times. Subsequently, the membrane was visualized using a Fusion FX7 Multifunction imaging system (Vilber, France). And the p-AKT and the GAPDH band were analyzed using Image J (Java 1.8.0-172).
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3

Protein Expression Analysis by Western Blot

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Proteins were extracted, and the concentrations were determined using the Pierce™ BCA Protein Assay Kit (Thermo). Proteins were denatured at 100 °C for 10 min. After the proteins were separated by sodium dodecyl sulfate‒polyacrylamide gel electrophoresis (SDS‒PAGE, Epizyme, Shanghai, China), the gels were transferred onto polyvinylidene fluoride (PVDF) membranes (Millipore) and run at 250 mA for 90 min. Subsequently, the membranes were cut, blocked (5% skim milk powder), and incubated with diluted primary antibodies at 4 °C overnight. The primary antibodies were as follows: anti-GAPDH (ZEN-BIO 200306-7E4), anti-β-actin (ZEN-BIO 250132), anti-vinculin (ZEN-BIO R26085), anti-NR1D1 (ab174309), anti-NR1D2 (ab251948 and Protein Tech 13906-1-AP), anti-FOXM1 (CST20459), anti-LXRα (ab41902), anti-CCNB1 (CST12231), anti-CCNB2 (ab185622), anti-CENPA (CST2186), anti-CENPF (CST58982), anti-CDK1 (ZEN-BIO 200544), anti-survivin (CST2808), and anti-ARNTL (Protein Tech 14268-1-AP). The membranes were washed and incubated with secondary antibodies for 1 h according to the primary antibody sources. Immunoreactivity was visualized using enhanced chemiluminescent (ECL) chromogenic substrate (Millipore). The membranes were finally detected by using a ChemiDoc MP Imager System (Bio-Rad).
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4

Western Blotting of Lacrimal Gland Proteins

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Lacrimal gland tissue was extracted with Radioimmunoprecipitation Assay (RIPA) Lysis Buffer (Beyotime) mixed with phenylmethylsulfonyl fluoride (PMSF; Solarbio). Protein extracts were resolved via 10% sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS–PAGE; EPizyme, Shanghai, China) and then electrotransferred to a polyvinylidene difluoride membrane. After blocking, the membranes were probed with primary antibodies to AQP5 (1:2000, Abcam), α-SMA (1:2000, Abcam), GAPDH (1:3000, Kangchen, Shanghai, China), CHOP (1:500, Affinity Biosciences, Wuhan, China), Bax (1:1000, Affinity Biosciences), Bcl-2 (1:2000, Affinity Biosciences), Caspase12 (1:1000, Affinity Biosciences), and GRP78 (1:1000, Affinity Biosciences). Horseradish peroxidase–conjugated secondary antibodies were used, and the bands were developed using a Western Bright Electrochemiluminescence (ECL) substrate (Applygen, Beijing, China). GAPDH was used for normalization of expression [34 (link)].
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5

Protein Extraction and Western Blot

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Total proteins of cells were extracted by the RIPA lysis buffer (Beyotime, Shanghai, China) containing 1:1,000 protease/phosphates inhibitors (Apexbio, TX, USA). BCA Protein Quantification Kit (Vazyme, Jiangsu, China) was used to measure the concentration of proteins. 25–50 µg proteins mixing with loading buffer (Epizyme, Shanghai, China) were separated by 7.5%−12.5% SDS-PAGE (Epizyme, Shanghai, China) gel electrophoresis. The proteins were then transferred to PVDF membranes (Millipore, MA, USA), blocked with 5% nonfat milk (Cell signaling technology, MA, USA) for 2 h and incubated with primary antibodies at 4 °C overnight. The PVDF membranes were subsequently incubated with horseradish peroxidase-conjugated secondary antibodies for 2 h. The proteins were visualized using ultra-sensitive chemiluminescence (ECL) reagent (Uubio, Jiangsu, China) and detected by image analysis system Tanon 4800 (Tanon, Shanghai, China). Anti-GAPDH/β-actin antibody was used for normalization. The detailed antibody information was displayed in Supplementary Table S4.
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6

Rho GTPase Activation Assay Protocol

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At 12 h after appropriate treatments, RIPA buffer (Beyotime, Beijing, China) was used to lyse cells, and a BCA kit (Beyotime, China) was utilized to quantify protein concentrations therein. Samples were then boiled, and equal protein amounts from each sample (30 µg) were separated via SDS-PAGE (EpiZyme, China) prior to transfer onto PVDF membranes which were subsequently blocked with 5% BSA or 5% non-fat milk for 2 h at room temperature, and were then incubated overnight at 4 °C with appropriate primary antibodies (Additional file 3: Table S4). Blots were then probed for 1 h with secondary antibodies, and a high sensitivity electrochemiluminescence detection kit was used to detect protein bands with a chemiluminescence imaging system (Bio-Rad, USA). Densitometric analyses of protein bands were conducted with ImageJ.
A Rho Activation Assay Biochem Kit™ (Cat. #BK036) was purchased from Cytoskeleton, Inc. (Acoma St. CO, USA). The GTPase assay was performed according to the provided instructions.
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7

Photothermal Regulation of Protein Expression in SKOV-3 Cells

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SKOV-3 cells were incubated with mPt@PDA-RGD NPs (0, 50, 100, 200 µg/ml) for 6 hours, then irradiated with 808 nm (1.5 W/cm2) for 50 s. After washing with cold PBS, cell lysate (Servicebio, China) and protease inhibitor were used to lyse the cancer cells, followed by incubation for 30 min at 4°C. Then, proteins were extracted by centrifuging. The extracted proteins were separated by 10% sodium dodecyl sulfate - polyacrylamide gel electrophoresis (SDS-PAGE) (Epizyme, China). Then, the proteins were transferred to polyvinylidene fluoride (PVDF). The membranes were incubated with primary antibodies (actin 1:2,000, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) 1:1,000) at 4°C for 12 h. After washing three times, the membranes were incubated with secondary antibodies for 1 h, then washed with PBST, and the membranes were treated with chemiluminescence agents.
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8

Western Blot Analysis of UPR Markers

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Neutrophils were lysed by phenylmethylsulfonyl fluoride (PMSF, 1 mM) and radioimmunoprecipitation assay lysis (RIPA) buffer. After centrifugation, the total protein was obtained. Samples were then resolved on sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE, Epizyme; Shanghai, China) by standard procedure. Western blotting was performed as described previously [32 (link)]. Immunoblotting was performed with human primary antibodies to MCPIP-1 (Santa Cruz), inositol-requiring enzyme 1-α (IRE1-α, 1 : 100, Servicebio; Wuhan, China), protein kinase R-like endoplasmic reticulum kinase (PERK, 1 : 100, Servicebio), binding-immunoglobulin protein (BIP, 1 : 100, Servicebio), p65 (1 : 100, Servicebio), and β-actin (Abcam). For signal detection, the Odyssey Infrared Imaging System and Image Studio (LI-COR Biosciences; Lincoln, NE, USA) were used. ImageJ (National Institutes of Health; Bethesda, MD, USA) was used for quantification.
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9

Protein Extraction and Western Blotting

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Total protein was extracted using RIPA lysis buffer (Beyotime). Cytoplasmic and nuclear proteins were separated with the Nuclear and Cytoplasmic Protein Extraction Kit (Beyotime). BCA Protein Assay Kit (Beyotime) was utilised to detect the concentration of protein. The total protein (20 μg) was separated by 7.5% or 10% SDS–PAGE (Epizyme) and then transferred onto polyvinylidene fluoride (PVDF) membranes (Millipore). QuickBlock Blocking Buffer for Western Blot (Beyotime) was applied in blocking PVDF membranes. Table S1 lists specific information about antibodies used in the Western blotting assay.
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10

Western Blot Protein Quantification

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Proteins were extracted from tissues or cells with RIPA buffer (Epizyme, China). Total protein concentration was determined using a protein concentration detector. Proteins were separated by SDS-PAGE (Epizyme, China), transferred onto PVDF membranes (Millipore, Germany), and blocked with a solution of skim milk powder at a concentration of 5% for two hours. The target proteins were probed with corresponding primary antibodies at 4 °C overnight, and then washed with TBST followed by incubation with an HRP-conjugated secondary antibody at room temperature for one hour. Finally, the bands on membranes were visualized through chemiluminescence, and gray value analysis was performed using ImageJ software (v1.53, NIH, USA). Manufacturers and catalogs of antibodies used were listed in additional file 1: Table S1.
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