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114 protocols using a0545

1

Western Blot Analysis of Lipolytic Enzymes

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Frozen specimens of mesenteric fat were homogenized in 20 mM of Tris–HCl buffer (pH 7.8) containing 0.2 % of Triton X-100 and protease inhibitor cocktail (Sigma, USA), and centrifuged. Aliquots of supernatant (10 μg of protein) were separated by 10 % of SDS-PAGE and electroblotted onto Immuno-Blot™ PVDF Membrane (Bio-Rad Laboratories, Hercules, CA, USA). The membrane was blocked by incubation with a blocking buffer and then incubated with rabbit polyclonal anti-HSL antibody (SCB45041763, Sigma-Aldrich USA), polyclonal anti-phospho-HSL antibody (pSer522 in human/Ser563 in rat; SAB4501763, Sigma-Aldrich USA), anti-ABHD5 antibody (AV42055, Sigma-Aldrich USA), anti-ATGL antibody (sc-67355, Santa Cruz Biotechnology USA), anti-G0S2 antibody (sc-133424, Santa Cruz Biotechnology USA), and anti-actin antibody (A0545, Sigma-Aldrich USA). The secondary HRP-conjugated antibodies were obtained from Sigma Aldrich (A0545). The reactions were visualized with SuperSignal West Pico chemiluminescent substrate (Thermo Fisher Scientific, Inc., Rockford, IL, USA). The bands visualized on the film following chemiluminescent detection were compared with the molecular mass protein markers visible on the membrane after electroblotting (SM26634, Fermentas). The film was adjusted to the membrane in such way that the membrane edges were visible on the film.
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2

Phosphorylation Analysis of S6K in Plants

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To detect the phosphorylation status of S6K, 50 mg plant aerial tissue was used for protein extraction using 1.5 mL extraction buffer of 1 × PBS, pH 7.4, containing 250 mM sucrose, Protease Inhibitor Cocktail (Sigma-Aldrich, P9599) and PhosSTOP phosphatase inhibitor (Roche, 4906845001). Three times of centrifugation, 1 k × g for 5 min, 14 k × g for 5 min and 135 k × g for 30 min, were conducted to separate the soluble proteins. The supernatant from the last centrifugation was separated, concentrated to 200 μL using an Amicon Ultra centrifugal unit (Millipore, UFC501024), and then mixed with 40 μL 6 × Laemmli buffer. Proteins were denatured by incubation at 95°C for 10 min. Protein samples were separated on 15% SDS-PAGE with 8M urea and blotted to PVDF membranes (Bio-Rad, 1620177). Blots were blocked with 5% milk for 1 hr at room temperature. Blots were incubated with primary antibodies of either anti-S6K (Agrisera, AS12 1855) or anti-S6K-phosphorylated (Abcam, ab207399) overnight at 4°C and subsequently with secondary HRP conjugated goat anti-rabbit antibody (Sigma-Aldrich, A0545) for 1 hr at room temperature.
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3

Protein Expression Analysis in gmNZ9000

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All experimental procedures in this section were performed according to previously described methods [48 (link), 49 (link)]. Briefly, gene expression in gmNZ9000 was induced with 1.25 ng/mL nisin (MoBiTec) for 3–4 h in 2-mL cultures. Bacterial cells and supernatants were separated by centrifugation, and protein samples were prepared. These samples were subjected to sodium dodecyl sulfate–polyacrylamide gel electrophoresis (10 % (v/v) polyacrylamide). Electrophoresed proteins were visualized by gel staining with Coomassie Brilliant Blue or transferred from the gel onto a polyvinylidene difluoride membrane for western blotting. Western blotting was performed with mouse anti-His-tag Ab (1/1000) (652501; BioLegend, San Diego, CA, USA) or rabbit anti-HO-1 Ab (1/1000) (SAB2101053; Sigma-Aldrich, St. Louis, MO, USA), followed by incubation with horseradish peroxidase (HRP)-conjugated goat anti-mouse IgG Ab (1/5000) (A4416; Sigma-Aldrich) or HRP-conjugated goat anti-rabbit IgG Ab (1/5000) (A0545; Sigma-Aldrich). The experiments were repeated three times.
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4

Immunoblotting Analysis of Sigma-1 Receptor in Tumor Samples

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Tumor samples were processed as described earlier [54 (link)]. Preparation of cell lysates, SDS-PAGE and immunoblotting were performed as described elsewhere [55 (link)]. In brief, 40–80 µg protein per lane was transferred to PVDF membranes using a semi-dry transfer system (Bio-Rad Laboratories, Hercules, CA, USA). Membranes were blocked for 60–90 min with non-fat dry milk powder (5%, w/v) in Tris-buffered saline containing 0.05% (v/v) Tween 20 (TBS-T). For detection of Sig1R, membranes were incubated with primary antibodies in bovine serum albumin (BSA, 2% w/v) in TBS-T (PA5-30372, 1:500, Thermo Fisher Scientific (Waltham, MA, USA), (tumor samples), respectively, ab53852, 1:200, Abcam (Cambridge, UK) (cell lysates)), followed by incubation with peroxidase-conjugated secondary antibody (anti-rabbit IgG, A0545, 1:5000, Sigma-Aldrich, Steinheim, Germany). Proteins were visualized using Super Signal West Pico/Femto Chemiluminescent Substrate (Thermo Fisher Scientific) and a CELVIN®S Chemiluminescence Imaging system (Biostep, Burkhardtsdorf, Germany). For detection of loading control, membranes were stripped and further processed using mouse anti-β-actin antibody (A5316, 1:1000, Sigma-Aldrich) and anti-mouse IgG (A9044, 1:10,000, Sigma-Aldrich) as described elsewhere [54 (link)].
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5

Western Blot Analysis of LAMP3, E-cadherin, and β-actin

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The protein expression levels of LAMP3, E-cadherin, and β-actin were analyzed by western blot assay. Following treatments, cells were harvested in radioimmunoprecipitation assay lysis buffer (Beyotime Institute of Biotechnology, Shanghai, China) supplemented with protease inhibitor cocktail (Sigma-Aldrich; Merck KGaA). Equal amount of protein (~20 µg) was resolved in 12% SDS-PAGE and transferred onto polyvinylidene fluoride membranes. Following blocking with 5% non-fat dry milk in TBS/0.1% Tween-20 (TBST) buffer, membranes were incubated with primary antibodies at 4°C overnight. Following three washes with TBST, the membranes were incubated with horseradish peroxidase (HRP)-conjugated secondary antibodies for 1 h at room temperature. Following washing, the membranes were developed using chemiluminescence substrate (RPN2232; GE Healthcare Life Sciences, Little Chalfont, UK) and imaged. The antibodies used were: Mouse anti-β-actin (ab8227; 1:5,000; Abcam), anti-mouse HRP-conjugated IgG (A9044; 1:5,000; Sigma-Aldrich; Merck KGaA), anti-rabbit HRP-conjugated IgG (A0545; 1:5,000; Sigma-Aldrich; Merck KGaA), anti-E-Cadherin (3195; 1:1,000; Cell Signaling Technology, Inc., Danvers, MA, USA), anti-LAMP3 (ab83659; 1:1,000; Abcam).
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6

Immunoblotting of mCherry and GFP Proteins

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Protein extraction and immunoblotting were performed as described in Zhang et al. (2018) (link). Primary antibodies were used at the following dilutions: anti-mCherry (ab183628; Abcam), 1:3,000; anti-GFP from mouse IgG1κ (clones 7.1 and 13.1; Roche), 1:1,000. The secondary antibodies used were anti-rabbit horseradish peroxidase conjugate (A0545; Sigma) diluted 1:50,000 for mCherry or m-IgGκ BP-HRP (sc-516102; Santa Cruz Biotechnology) diluted 1:5,000 for GFP. Blots were then washed and developed with enhanced chemiluminescence reagent SuperSignal West Pico Chemiluminescent Substrate or SuperSignal West Femto Maximum Sensitivity Substrate (Thermo Fisher Scientific), as required.
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7

Western Blot for Protein Quantification

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Western blot was performed as described (3 (link),37 (link)). Briefly, 0.1 OD600 bacterial culture was collected by centrifugation for 2 min at 8000 rpm at 4°C, and resuspended in 100 μl 1× protein loading buffer. After heating for 5 min at 95°C, 0.02 OD600 of cell lysate was separated on a 10% SDS-PAGE gel. Proteins were transferred onto a NC membrane (#10600002, GE Healthcare) for 60 min at 100 V in transfer buffer (25 mM Tris, 190 mM glycine, 20% methanol, pH 8.3). Membranes were blocked for 1 h at room temperature in 1× TBST (20 mM Tris, 150 mM NaCl, 0.1% Tween20, pH 7.6) buffer with 5% (w/v) Difco™ skim milk (#6307915, BD). After blocking, membranes were incubated at room temperature for 1 h with monoclonal α-FLAG (Sigma-Aldrich #F1804; 1:1000) or polyclonal α-GroEL (Sigma-Aldrich #G6532; 1:5000) antibodies diluted in 1× TBST buffer containing 3% BSA. Following three washes for 30 min in 1× TBST buffer, membranes were incubated with secondary α-mouse or α-rabbit HRP-linked antibodies (Sigma-Aldrich #A0168 or #A0545; 1:5000) diluted in 1× TBST buffer containing 3% BSA. After another three washes for 30 min in 1× TBST buffer, chemiluminescence was developed using the Novex™ ECL Chemiluminescent Substrate Reagent Kit (#WP20005, Thermo Fisher Scientific), visualized on ChemiDocTM XRS+, and quantified using ImageLabTM Software (both Biorad).
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8

Western Blot for Protein Analysis

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Cells were incubated in RIPA buffer (0.5% deoxycholate, 1% NP-40, 50 mM Tris at pH 8, 150 mM NaCl, 0.1% SDS) for 20 min on ice and centrifuged at 13,000 rpm for 10 min before SDS loading buffer addition to the supernatant. In the case of H3 and H3K9me3 immunoblots, cells were sonicated three times for 10 sec in lysis buffer (1% SDS, 1% Triton, 10 mM Tris at pH 7.5, 450 mM NaCl) before the addition of SDS loading buffer. Protein extracts were resolved on 3%–8% NuPAGE Tris-acetate gels or 4%–12% Bis-Tris (Invitrogen) according to the manufacturer's instructions and transferred onto PVDF membranes (Invitrogen). The latter were blocked in TBS containing 0.1% Tween 20 (Sigma) and 3% nonfat dry milk for 1 h followed by an overnight incubation at 4°C with primary antibodies (Supplemental Table S2). The appropriate horseradish peroxidase-coupled secondary antibodies were used to reveal the proteins (antimouse at 1:10,000 [Sigma, A2554] and antirabbit at 1:10,000 [Sigma, A0545]) using a luminol-based enhanced chemiluminescence HRP substrate (Super Signal West Dura Extended Duration Substrate, Thermo Scientific).
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9

Western Blot Analysis of Bacterial Proteins

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Proteins were resolved on 10% (for DnaA) or 12.5% (for HdaA, M2-HdaB, CcrM or GFP-HdaA) SDS-PAGE gels. Proteins were electro-transferred to PVDF membranes (Merck Millipore, MA, USA). Immuno-detection was performed with polyclonal antibodies. Anti-DnaA (24 (link)), anti-HdaA (12 (link)), anti-CcrM (25 (link)) (all three produced by immunizing rabbits at Josman LLC) and anti-rabbit conjugated to horse-radish peroxidase (HRP) (A0545 from Sigma, USA) sera were diluted 1:10 000. Anti-GFP (MA5–15256-HRP from Thermo Fischer Scientific, USA) and anti-FLAG (F3165 from Sigma, USA) sera were diluted 1:10 000. Anti-mouse conjugated to HRP (W4021 from Promega, USA) was diluted 1:5000. Immobilon Western Blotting Chemo-luminescence HRP substrate (Merck Millipore, MA, USA) was used and membranes were scanned with a Fusion FX (Vilber Lourmat, FR) instrument to detect the chemiluminescent signal. Relative band intensities on images were quantified using the ImageJ software.
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10

Colon Tissue Immunohistochemistry Protocol

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Paraffin-embedded colon tissue were sectioned at 5 μm, deparaffinized and permeabilized with Triton X-100 (Sigma-Aldrich) and heat antigen retrieved with Bull’s Eye Decloaker (Biocare Medical). Slides were then blocked for endogenous peroxidase with Bloxall blocking solution (Vector Lab) followed by blocking with either 3% bovine serum albumin, or mouse on mouse blocking reagent (Vector Lab). Anti-IL11 (ab10558; PA5-36544, Invitrogen), anti-CD45 (1:100; ab10558, Abcam), anti-LGALS3 (1 μg/ml; CL8942AP, Cedarlane) amd anti-LAMP2 (1 μg/ml; 550292, BD Bioscience) were added and incubated overnight at 4°C. Anti-rabbit (1:100; ab27478, Abcam) and anti-rat IgG (1 μg/ml; sc-2026, Santa Cruz) isotype controls were added as respective negative controls. Slides were incubated with anti-rabbit IgG peroxidase (1:500, A0545, Sigma-Aldrich) and anti-rat IgG peroxidase (MP-7404, Vector Lab) followed by chromogen development with ImmPACT® DAB peroxidase substrate kit (SK-4105, Vector Lab) according to manufacturer’s instructions. Lastly, Gill’s haematoxylin (H-3401, Vector Lab) was added for nuclear counterstain. To control for unspecific binding, primary antibody isotype controls were included and images are presented in S3 Fig.
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