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6 protocols using benzamidine hcl

1

Yeast Protein Expression and Membrane Isolation

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Yeast transformants were inoculated in 4 ml of SD medium and grown at 28°C with shaking at 140 rev./min. After 24 h, cells were inoculated into 200 ml of SD medium and grown for 24 h under the same conditions. Cells were harvested and induced for protein expression in 1 litre of YPG medium at 24°C with shaking at 140 rev./min. After 18–19 h of induction, cells were collected by centrifugation at 3000 g for 5 min at 4°C and washed in 25 ml of ice-cold water. After centrifugation, cells were resuspended in 10 ml of lysis buffer [40 mM Hepes/NaOH, pH 7.5, 150 mM NaCl, 26% (v/v) glycerol, 0.1 mM PMSF, 1 μg/ml aprotinin, 1 μg/ml leupeptin, 1 μg/ml pepstatin A, 5 μg/ml antipain and 157 μg/ml benzamidine HCl (Sigma–Aldrich)] and vortex-mixed with glass beads (200 μm; Sigma–Aldrich). The cell lysate was clarified by two consecutive centrifugation steps at 1000 g for 10 min at 4°C and 10000 g for 15 min at 4°C. Membranes were subsequently collected by centrifugation at 125000 g for 1 h at 4°C. Pellets were homogenized in 1.5 ml of S-buffer (same as lysis buffer but containing 20% (v/v) glycerol) and the protein concentration was measured spectrophotometrically using a Nanodrop™ 1000 instrument (Thermo Fisher Scientific). Total yeast membranes were snap-frozen in liquid nitrogen and stored at −80°C.
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2

Quantification of Neutrophil Activation and Circulating APC in Thrombosis

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Blood was collected at least 6 months after the thrombotic event (median 1 year), i.e., in the stable phase of the disease. For the quantification of neutrophil activation markers, blood was collected in 4.5 mL Vacutainer tubes (BD Diagnostics, Franklin Lakes, NJ, USA) containing 0.5 mL of 0.109 M trisodium citrate. For the measurement of circulating APC, blood was collected two tubes containing 0.109 M trisodium citrate. Immediately after blood sampling (within 10 s), 46 μL of a mixture of 0.58 M benzamidine-HCl (Sigma Aldrich, Saint Louis, MO, USA) and 0.5 mM D-phenylalanyl-L-prolyl-L-arginine chloromethyl ketone·2HCl (PPACK, Calbiochem, Darmstadt Germany) was added to one citrate tube to inhibit circulating APC, and 46 μL of 1000 U/mL heparin (Rovi, Madrid, Spain) was added to the other citrate tube and the mixture was incubated at 37 °C for 30 min to force APC to complex to its major inhibitor, the protein C inhibitor (PCI) [14 (link)]. Plasma was obtained by centrifugation at 1.811× g for 30 min at 4 °C and stored in aliquots at −80 °C until further use. For DNA studies, blood was collected in tubes containing K3EDTA.
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3

Affinity-based Protein Purification Methods

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ThDP, NAD+, CoA, DTT, isopropyl 1-thio-β-D-galactopyranoside, imidazole, thiamin-HCl, glycerol, DNase I, and Micrococcal nuclease were from Affymetrix (Thermo Fisher Scientific, Waltham, MA, USA); 2-oxoglutaric acid, 2-oxoadipic acid, iodoacetamide, benzamidine HCl, disuccinimidyl dibutyric urea (DSBU or BuUrBu), 1.1′-carbonyl-diimidazole (CDI), and dimethyl sulfoxide were from Sigma-Aldrich (St. Louis, MO, USA). Formic acid solution was obtained from Fluka Analytical (Buchs, Switzerland); MS grade trypsin protease was from Pierce; Ni Sepharose® high-performance affinity media was from GE Healthcare (Chicago, IL, USA).
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4

Trypsin-induced Cartilage Alteration in Bovine Knee

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Bovine knee joints (n = 9) were obtained from the local abattoir (Atria Oyj, Kuopio, Finland) and specimens were harvested. In total, 18 samples (n = 9 + 9, osteochondral plugs, diameter = 7 mm) were prepared, two adjacent samples from lateroproximal parts of the patellae. One specimen from each pair was digested for 2.5 hours in 1 mg/mL trypsin (Sigma-Aldrich, St. Louis, MO, USA. trypsin treatment primarily affects cartilage proteoglycans, cleaving the molecules and altering the properties of the specimens; treatemen was specifically utilized to alter the relaxation times of the specimens.) at 37°C while the other sample remained in phosphate buffered saline (PBS) containing enzyme inhibitors (5 mM EDTA (VWR International LLC, West Chester, PA, USA) and 5 mM Benzamidine HCl (Sigma-Aldrich)). After the treatment, the samples were stored frozen at −20°C, acknowledging potential changes in the MRI characteristics of the specimens (29 (link),30 (link)). Prior to the measurements samples were thawed in a water bath at room temperature, and after the MRI measurement they were rinsed with fresh PBS and frozen again. A subset (n = 3 + 3) of the samples was subjected to another thaw-freeze cycle and an extra measurement; the subset was immersed in 1.0 mM gadopentetate solution for 24 hours and re-measured again using a subset of the same protocol.
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5

B Cell Lysis and Protein Extraction

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Lysates were prepared from B cell pellets stored at −80°C or from B cell cultures collected by centrifugation. Approximately 5 × 106 B cells were resuspended in 200 μL B cell lysis buffer (0.5% NP-40, 50 mM Tris pH 7.4, 200 mM NaCl, 1 mM EDTA, 1 mM Benzamidine HCl (B6506, Sigma), 1 mM PMSF (36978, Thermo Scientific), 5 μM β-mercaptoethanol, and 1 cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail tablet per 10 mL buffer (11836170001,Sigma)), and incubated on ice for 30 min. Lysates were sonicated using a Branson digital sonifier with a microtip until no longer viscous, and protein concentrations were measured by Bradford assay (5000001, Bio-Rad). 4x protein sample buffer (10% SDS, 50% glycerol, 0.05% Bromophenol blue, 200 mM Tris pH 6.8, 40 mM EDTA, 20% β-mercaptoethanol) was added to a final concentration of 1x, samples were boiled at 98°C 10 min and stored at −20°C.
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6

Bovine Osteochondral Plug Friction Tests

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Twenty-six mated, osteochondral plug pairs were cored from the femoral groove (12mm diameter) and patella (7mm) of seven freshly slaughtered, skeletally mature cows. All plugs were then frozen at −20 °C in 400 mOsm/kg saline containing GIBCO Anti-Anti stock solution (5x; Invitrogen, Grand Island, NY), ethylenediaminetetraacetic acid (5 mM; Sigma, St. Louis, MO), and benzamidine HCl (5 mM; Sigma B6506, St. Louis, MO). These same additives were included in all solutions that were exposed to the samples to prevent nonspecific cartilage degradation during the experiments as a result of the samples being left at room temperature or at 4 °C for extended periods. Prior to testing, all samples were thawed overnight at 4 °C. Twelve plug pairs were used to evaluate the frictional properties and wear prevention of saline, bovine synovial fluid (BSF), and 2.8M TEG during a long-duration torsional friction test (Study 1). In Study 2, three plug pairs were used to directly compare 2.8M TEG to BSF by testing the pairs in 2.8M TEG following testing in BSF. Finally, eleven plug pairs were used to evaluate the ability of BSF, Synvisc, and 2.8M TEG to improve the frictional properties of previously worn cartilage (Study 3). Group bias was controlled by using neighboring plug pairs from the same knees for each lubricant group.
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