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5 protocols using protein marker 6

1

Proteomic Profiling of Brucella ovis

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Protein profiles of whole-cell bacterial lysates were obtained by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), followed by Coomassie blue staining (23 (link)). Proteins were separated in 14% acrylamide/bisacrylamide gels using a Protean II xi cell (Bio-Rad, Hercules, CA, United States) and pre-stained protein marker VI (Applichem-Panreac, Barcelona, Spain) as a protein standard.
The proteomic analysis of SDS-PAGE protein bands was performed in the proteomics facility of Centro de Investigación del Cáncer, Salamanca, Spain, following its standardized procedures. In brief, selected protein bands were excised from the gels and trypsin-digested proteins were submitted to reversed-phase LC–MS/MS using a nano-UHPLC system (NanoElute, Bruker Daltonics, Germany) coupled to a hybrid trapped ion mobility-quadrupole time-of-flight mass spectrometer Tims TOF Pro (Bruker Daltonics, Germany) via a modified nano-electrospray ion source (Captive Spray, Bruker Daltonics, Germany). Protein identification was done by searching the MS/MS spectra against the Brucella ovis Uniprot proteome database with the Andromeda algorithm (24 (link)) and the MAXQUANT (25 (link)). Protein relative abundance was compared using the iBAQ score (26 (link)).
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2

Immunoblotting Protocol for Protein Analysis

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Proteins were separated on precast Mini-PROTEAN TGX gradient gels (4–15% or 4–20%, Bio-Rad) or self-made Tris-glycine gels and transferred (200 mA for 90 min, or 55 V for 75 min) onto 0.45-μm Immobilon-IP polyvinylidene fluoride membranes (Millipore) or 0.45-μm nitrocellulose membranes (Millipore) using the Mini Trans-Blot Cell System (Bio-Rad). Protein Marker VI (10–245 kDa) prestained (AppliChem) was used. Membranes were blocked with 2.5% BSA in TBST (50 mM Tris HCl (pH 7.6), 150 mM NaCl, 0.05% Tween-20). Blots were incubated overnight at 4 °C with primary antibodies. Blots were washed three times (each 5 min) with TBST and incubated for 1 h at RT with secondary antibodies (HRP-conjugated for chemiluminescence). Subsequently, blots were washed twice with TBST and once with TBS (50 mM Tris HCl (pH 7.6) and 150 mM NaCl). For chemiluminescence visualization, blots were incubated with the ECL Prime Western blotting detection reagent (GE Healthcare) and detected with ChemiDoc Imaging System (Bio-Rad).
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3

Gel-based separation and imaging of ABPs

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A total of 12 µL (i.e., 4 µg protein) of each sample were used per run. Four batches of 22 samples each were run in parallel at 120 V for 120 min in the dark on 12 or 18% Criterion TGX Stain-Free Precast Gel (Bio-Rad) in running buffer (25 mM Tris base, 190 mM glycin, 0.1% w/v SDS, pH 8.3) together with Protein Marker VI (AppliChem, Darmstadt, Germany) and three “dummy samples” to stabilize the gel run and prevent edge effects. Directly after the run, gels were scanned using the Typhoon TRIO Variable Mode Imager (GE, Munich, Germany). Images were taken at 450 PTM and 50 μm pixel resolution with fluorescence Cy3/TAMRA for ABPs MV151 and MVB127 while the Cy2 fluorescence channel was used for LW124. After the scan, the UV-inducible protein stain in the gels was activated for 5 min on the Gel Doc EZ Imager (Bio-Rad) and total protein stain was imaged.
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4

SDS-PAGE Protein Separation Protocol

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Electrophoresis was performed using the general principle [38 ] and Omni Page electroblotter (Cleaver Scientific). OTf PC2 of the test samples was diluted to a final concentration of 2 mg/mL protein, using 2-mercaptoethanol Laemmli buffer (Sigma Aldrich) and bromophenol blue (Sigma Aldrich). After incubating the samples for 10 minutes at 96°C, 5 μL of each sample was loaded on a polyacrylamide migration gel of 10% and a concentration gel of 4%. A molecular marker, Protein Marker VI (AppliChem), containing a mixture of 12 proteins with molecular weight ranging from 10 to 245 kDa, was also run on the gel. Electrophoresis was performed at 90 mV and 185 mA, for 90 minutes, and staining was performed with Coommassie Brilliant Blue R250 (Sigma Aldrich).
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5

Western Blot Analysis of SLC9C1 in Sea Urchin

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Sperm flagella and heads from S. purpuratus, CHO K1 cells stably expressing HA-tagged SpSLC9C1 (SpSLC9C1-HA), and CHO K1 control cells (mock) were lysed by sonification in a hypotonic buffer containing 10 mM Hepes/NaOH, pH 7.4, 2 mM EDTA, and protease inhibitor mixture mPIC (Sigma Aldrich, St. Louis, USA). The suspension was centrifuged for 10 min at 500 × g. The supernatant was used for Western blotting. Twenty µg protein per lane were separated by SDS-PAGE using a precast NuPage Novex 7% Tris-Acetat Protein Gel (Thermo Fisher Scientific, Waltham, USA). The samples were heated for 5 min at 95 °C prior to separation. Protein Marker VI (AppliChem, Darmstadt, Germany) and HiMark Pre-Stained Protein Standard (Thermo Fisher Scientific) were used as molecular weight markers. Proteins were transferred onto an Immobilon FL PVDF membrane (Merck Millipore, Darmstadt, Germany), probed with antibodies, and analyzed using the Odyssey Imaging System (LI-COR, Bad Homburg, Germany). All figure panels were taken from the same western blot. Figures were prepared using CorelDrawX6 and Photo-PaintX6 software (both from Corel Corporation). Primary antibodies were: SpSLC9C1-SU2 (1:3000), rat-anti-HA (1:3000; Roche Applied Science catalog no. 11867431001, Penzberg, Germany). Secondary antibodies were as follows: IRDye680 and IR800 antibodies (LI-COR, 1:25,000).
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