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12 protocols using advanced protein assay reagent

1

Bicinchoninic Acid Protein Assay

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Protein was determined by bicinchoninic acid protein assay (Life Technologies) using BSA as standard; for the cholesterol uptake experiments, protein was determined using Advanced Protein Assay reagent (Cytoskeleton, Denver, CO).
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2

Labeling of Nanoparticles with Fluorescent Dyes

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NLPs were labeled with either AF647 (stability experiments) or AF750 (biodistribution experiments) by incubating the NLPs with the respective reactive dye for at least 2 hrs (5∶1 dye∶NLP molar ratio). The reaction was performed in PBS buffer containing 5 mM sodium bicarbonate, pH 8.2. After completion of the reaction, 10 mM Tris pH 8.0 was added to quench any unreacted dye and incubated for 30 minutes. The samples were then run on SEC (Superdex 200 PC 3.2/30 column, GE Healthcare, Piscataway, NJ) to purify out the labeled NLP from unreacted dye (0.15 mL/min flow rate). The SEC fractions corresponding to the NLP were then pooled and concentrated using 50 kDa MWCO spin concentrators. The apoE422k concentration was determined using the Advanced Protein Assay Reagent (Cytoskeleton Inc., Denver, CO), where BSA was used as the standard. The concentrated NLP samples were then stored at 4°C until further use.
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3

Quantifying Insulin-Stimulated Glucose Uptake

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For the glucose uptake studies, the 24-hour corticosterone- and/or insulin-treated cells were washed with PBS and stimulated with 0, 20, or 100 nM insulin in 0.1% FF-BSA (03117057001, Roche Diagnostics) in PBS for 15 minutes. Next, 0.05 µCi of 2-[1-14C]-deoxy-d-glucose (PerkinElmer, Waltham, MA) in 0.1% FF-BSA was added to the medium. After an additional 5-minute incubation, the cells were washed twice with cold PBS, lysed with 0.2% SDS solution (Merck, Hohenbrunn, Germany), and protein content in cell lysates was quantified using Advanced protein assay reagent (Cytoskeleton, Denver, CO). Cell lysates were transferred to a scintillation glass vial and homogenized in a scintillation cocktail (Optiphase HiSafe 3, PerkinElmer Health Sciences, Groningen, Netherlands). Radioactivity was detected with a liquid scintillation analyzer (Tri-Carb 2910TR, Packard, PerkinElmer) and reported in counts per minute normalized to protein content.
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4

Protein Assay and Tropomyosin ELISA

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Advanced Protein Assay Reagent was obtained from Cytoskeleton (ADV01, Denver, CO, USA). Tropomyosin ELISA kit (EL-TPM) was obtained from InBio (Charlottesville, VA, USA).
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5

Actin Polymerization and Depolymerization Kinetics

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Before polymerization, actin (20%, pyrene-labeled) in G-buffer was supplemented with 1 mM EGTA and 50 μM MgCl2 to convert Ca—actin to Mg—actin and then incubated on ice for 10 min [34 (link)]. Polymerization was induced by adding 100 mM KCl, 2 mM MgCl2, and 0.5 mM ATP. After polymerization for 12 min or overnight at 22°C, 30 μM latrunculin A (Sigma, Tokyo, Japan) was added to induce depolymerization. Rates of polymerization and depolymerization were monitored by measuring the fluorescence intensity of pyrene.
The critical concentrations of WT and G146V actins were measured by sedimentation assays. Different concentrations of actin (0.5 μM~3.0 μM) were polymerized in F-buffer (10 mM HEPES pH 7.4, 2 mM MgCl2, 100 mM KCl, 0.5 mM ATP, 0.5 mM DTT) for 3 hr at 21°C, and were ultracentrifuged. Amounts of protein in pellets were determined by Advanced Protein Assay Reagent (Cytoskeleton, Denver, CO).
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6

Overexpression and Assay of Alcohol Dehydrogenase

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The strains were grown to OD600 of ~0.4 in 5 mL Luria Broth (LB) medium at 37 °C, followed by addition of 1 mM isopropyl-β-D-thio-galactoside (IPTG). Protein overexpression was performed at 30 °C for 2 h. Then 1.8 mL of cells were centrifuged at 17,000g for 10 min, resuspended in 300 μL BugBuster Protein Extraction Reagent (Novagen, San Diego, CA, USA), and incubated at room temperature for 20 min for cell lysis. The samples were centrifuged 16,000g for 20 min at 4 °C. Supernatants were taken for enzyme assays. ADH activities were measured by following the reduction of aldehyde with NADH or NADPH at 340 nm at 37 °C using a Synergy H1 Hybrid Plate Reader (BioTek Instruments, Inc., Winooski, VT). The enzyme assay was performed in a 96-well format as a 200 μL reaction. The reaction mixture was made up of 86 μL of H2O, 10 μL of 1 M MOPS (pH 7.0), 4 μL of 10 mM NAD(P)H in 10 mM Tris–HCl (pH 7.0), 50 μL of 100 mM aldehyde, and 50 μL diluted enzyme (10 μL cell lysate in 40 μL phosphate buffer (pH 7.5)). One unit of activity is defined as the oxidation of 1 μmol of NAD(P)H per minute per mg protein. Protein concentrations were measured using Advanced Protein Assay Reagent (Cytoskeleton Inc., Denver, CO). Bovine Serum Albumin (NEB) was used to prepare a standard curve.
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7

Isolation and Characterization of Syncytiotrophoblast-Derived Microparticles

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This study was approved by the local ethical committee (Cantonal Institutional Review Board of Basel, Switzerland). In all cases, written informed consent was received. Human term placentas from uncomplicated pregnancies and placentas from cases with preeclampsia were collected in the Department of Obstetrics and Gynecology, University Hospital of Basel, within 1 h following elective or secondary cesarean section. Explants from villous tissue were set in culture in a controlled atmosphere (37°C, 20% oxygen/5% carbon dioxide) as described previously (19 (link)). STBM were isolated from the culture supernatants by a three-step centrifugation procedure at 4°C, namely 1000 × g for 10 min, 10,000 × g for 10 min, and 60,000 × g for 90 min. The microparticle-containing pellet was washed with PBS, re-suspended in PBS/5% sucrose and stored at −20°C until use. The protein content of the STBM was quantified with the Advanced Protein Assay Reagent (Cytoskeleton Inc., Denver, CO, USA) and STBM were standardized for protein concentrations as indicated in the figure legends.
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8

Liposome-based Protein Conjugation Protocol

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Preparation of the liposomes and protein conjugation were performed as previously described (Ingale et al., 2016 (link)). In brief, liposomes were prepared using a mixture of DSPC (1,2-distearoyl-sn-glycero-3-phosphocholine), cholesterol, and DGS-NTA(Ni2+) ((1,2-dioleoyl-sn-glycero-3-[(N-(5-amino-1-carboxypentyl) iminodiacetic acid)succinyl] (nitrilotriacetic acid nickel salt)) in a molar ratio of 60:36:4, respectively. The components were dissolved in chloroform, mixed and desicated overnight under vacuum. The formed lipid film was hydrated in PBS for 2 hr at 37°C, with constant shaking followed by sonication. The liposomes were extruded by sequentially passing through 1.0, 0.8, 0.2, and 0.1 μm membrane filters (Whatman Nuclepore Track-Etch membranes). To conjugate the His-tagged trimers, 900 μg total protein was incubated with 300 μl liposomes. The trimer-liposomes were separated from excess free protein using a Superdex 200 size-exclusion column. Trimer-liposome fractions were pooled and quantitated using a standard curve generated by soluble trimer using the Advanced Protein Assay Reagent (Cytoskeleton). Samples were stored at 4°C and checked by EM negative stain analysis and BLI for antigenicity prior to each immunization as previously described (Bale et al., 2017 (link)).
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9

Chitin Extraction and Protein Quantification

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Chitin extracts were prepared by adding chitin samples to PBS-T (100 mg/mL) and vortexing for 30 s. Extraction continued with gentle agitation on a rocking platform for 2 h at room temperature. Samples were centrifuged at 2000× g to allow separation of the protein extract from chitin solids.
APA Buffer was prepared by mixing 4 mL of deionized water and 1 mL of Advanced Protein Assay Reagent (Cytoskeleton Inc., Cat. No. ADV01). For protein quantification, ready APA Buffer (1 mL) was mixed with 10 µL of the chitin extract in an Eppendorf tube and thoroughly mixed by gentle inversion. Similarly, a ‘blank’ was prepared by mixing APA buffer (1 mL) with 10 µL of PBS-T in an Eppendorf tube and mixed by gentle inversion. The samples and ‘blank’ were transferred to a cuvette with 1 cm pathlength. A spectrophotometer (Implen NanoPhotometer™ P-Class, Munich, Germany) was used to measure the OD at 590 nm of the blank sample, which was subtracted from the OD values measured for chitin samples. Protein concentration was determined using the formula OD590 = 30 µg protein/mL reagent/cm light pathlength.
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10

Preparation of recombinant dGAE (tau 297–391)

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The preparation of recombinant dGAE (tau 297–391) has been described previously [30 (link)]. Briefly, dGAE was expressed in bacteria and, following heat treatment, purified by P11 phosphocellulose chromatography. 2-(N-morpholino)ethanesulfonic acid (MES), pH 6.25, was used instead of piperazine-N,N′-bis(ethanesulfonic acid) (PIPES) in some cases. The protein fractions were eluted with 50 mM PIPES (pH 6.8) or 50 mM MES (pH 6.25), each supplemented with 1 mM EGTA, 5 mM ethylenediaminetetraacetic acid (EDTA), 0.2 mM MgCl2 and 5 mM 2-mercaptoethanol containing 0.1–1 M KCl. The peak for elution of tau, at 0.3–0.5 M KCl, was dialyzed against 80 mM PIPES buffer (pH 6.8), 1 mM EGTA, 5 mM EDTA, 0.2 mM MgCl2, 5 mM 2-mercaptoethanol, or phosphate buffer (PB) (10 mM; pH 7.4). The dGAE protein concentration. was measured using Advanced Protein Assay Reagent (Cytoskeleton, Inc. Denver, CO, USA.) using bovine serum albumin as a standard. The protein was diluted with 10 mM phosphate buffer (pH 7.4) and, for all experiments, the dGAE was used at a concentration of 100 μM (Table 1).
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