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8 protocols using vivaspin 500 centrifugal concentrator

1

Quantifying Skeletal Muscle ATP in Mice

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The level of ATP in the skeletal muscle tissue of mice was determined using a commercially available microplate assay kit (ATP Colorimetric/Fluorometric Assay Kit, cat.N. MAK190-1KT, Sigma-Aldrich, St. Louis, MO, USA). After decapitation of animals, the muscle tissue (quadriceps) was rapidly excised, immediately frozen in liquid nitrogen, and stored at −80 °C. A lysate for the assay was obtained from 10 mg of frozen homogenized tissue, which was blended with 100 µl of ATP assay buffer and then deproteinized using a 10kDa MWCO spin filter (Vivaspin 500 centrifugal concentrator, Sartorius AG, Goettingen, Germany) in accordance with the manufacturer’s recommendations. A 5 µL volume of lysate was used in the assay. The samples were processed as suggested by the manufacturer of the kit, using the appropriate standard concentrations of ATP to obtain a calibration curve. The fluorescence (λex = 535/ λem = 587 nm) was measured on Tecan Spark 10M plate reader (Tecan, Männedorf, Switzerland). The concentration of ATP was expressed in pmol/µL of tissue extract.
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2

Protein Extraction and Enzymatic Assays

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One g of the frozen powder (see above) was resuspended at 4°C in 3 mL of 100 mM HEPES (pH 7.5), 2 mM EDTA and 2 mM dithiothreitol, 1 mM PMSF and 10 mL/L protease inhibitor cocktail (Sigma P9599), and centrifuged at 14,000 x g for 20 min. The supernatant was desalted by ultrafiltration on Vivaspin 500 centrifugal concentrator (Sartorius) and the protein extract thus obtained was assayed for enzymatic activities. AGP activity was measured following the two-step assay method described in [57 (link)]. SS activity was measured according to [32 (link)]. One unit (U) is defined as the amount of enzyme that catalyzes the production of 1 μmol of product per min.
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3

Exosome Isolation and Quantification Protocol

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Culture supernatants were centrifuged at 2,000 x g for 10 min at room temperature (RT) and at 10,000 x g for 30 min at 4°C followed by filtration on 0.22 µm syringe-filters (Millipore, SLGP033RB). Pre-conditioned supernatants were concentrated from 50 ml to 1 ml on Vivacell 100 filter units (Sartorius, VC1042). Aliquots (1 mL) of concentrated supernatants were loaded on mini-SEC columns,40 and exosomes were eluted with PBS. Exosomes were collected in the void volume fraction #4 (1 mL). For some experiments, particularly Western blots, #4 fractions were concentrated using 100,000 MWCO Vivaspin 500 Centrifugal Concentrators (Sartorius, VS0142) by centrifugation at 2,000 x g for 10–15 min. To determine protein concentration in the isolated exosome fraction #4, Pierce BCA protein assay kit (Thermo Scientific, 23227) was used according to the manufacturer’s instructions.
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4

Isolation and Characterization of Exosomes

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Exosomes were isolated by size exclusion chromatography (SEC) as previously described.26 (link) Exosomes were collected in fraction #4 (1 mL). For some experiments, #4 mini-SEC fractions were concentrated to 1 µg/µL using 100 000 MWCO Vivaspin 500 Centrifugal Concentrators (Sartorius Corp, #7321011) at 5000 × g for 5–10 min. Protein contents were measured using the BCA protein assay kit (Thermo Scientific, REF 23225). Transmission electron microscopy (TEM), tunable resistive pulse sensing measurements, and western blots were used to determine morphology, size, particle concentration, and protein cargo of exosomes as previously described by us.27 (link)
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5

Extraction and Purification of Exosomes from Mouse Blood

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To extract autologous exosomes, mouse blood was rapidly collected with a 28-gauge syringe by cardiac puncture under isoflurane. Approximately 800 μL of whole blood was drawn from a single mouse and added into an EDTA-coated tube. The plasma sample was centrifuged at 2000 × g for 20 min at 4 °C to remove cells and debris. After samples were re-centrifuged to remove debris, exosome precipitation reagent (Invitrogen) with a volume equivalent to the 1/5 of the total sample volume was added to the samples. The samples were thoroughly mixed by vortexing and incubated for 10 min at room temperature, followed by centrifugation at 10 000 × g for 5 min at 4 °C. After removing supernatant, 100 μL PBS was added in order to resuspend the exosome. Exosomes were loaded into 50 kDa cut-off centrifugal filter (Sartorius Vivaspin 500 Centrifugal Concentrators) and centrifuged at 15 000 × g for 15 min to remove small peptides.
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6

Purification of Recombinant Protein from Yeast

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Cell pellets corresponding to 200 mL culture were resuspended in 4 mL of breaking buffer (50 mM sodium phosphate buffer, pH 7.5, 1 mM EDTA, 5% (v/v) glycerol, 10 mM imidazole, 1 mM PMSF) to obtain an OD600 of 50. Lysis of cells was achieved by addition of glass beads and repeated vortexing for 30 s followed by 30 s incubation on ice. After 20 min of treatment cell debris was removed by centrifugation (14.800g, 4 °C, 10 min). Protein crude extract was loaded on a gravity column with 1 mL Profinity™ IMAC Ni-charged Resin (Bio-Rad Laboratories, München, Germany) and incubated for 2 h with orbital shaking at 4 °C. After washing with 10 mL of 50 mM sodium phosphate buffer (pH 7.5) containing 300 mM NaCl and 30 mM imidazole, elution was performed with 600 µL of 50 mM sodium phosphate buffer (pH 7.5) containing 300 mM NaCl and 500 mM imidazole. The elution was repeated three more times. Fractions with LOX activity were pooled, dialyzed overnight against 50 mM sodium phosphate buffer (pH 7.0) and concentrated by ultrafiltration using Vivaspin 500 centrifugal concentrators (Sartorius Stedim Biotech, Göttingen, Germany) with a molecular weight cutoff of 50 000. Samples were analyzed via SDS–PAGE and protein concentration was determined by the Bradford method using bovine serum albumin as standard.33 (link) Protein was stored in small aliquots at −80 °C until required.
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7

Fluorescent Antibody Labeling Protocol

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All chemicals were of the highest purity grade available and were purchased from Sigma-Aldrich (St. Louis, MO, USA) unless stated differently. DyLight fluorescent dyes D550 and D633 complete kits for antibody labeling and maleimide-based thiol-coupling, as well as Pierce Dye Removal columns, were purchased from ThermoFisher (ThermoFisher Scientific Inc., Waltham, MA, USA). Endo Hf was obtained from New England Biolabs (Ipswich, MA, USA). Mini-PROTEAN TGX Stain-Free precast gels, Precision Plus Protein WesternC standard marker, and trans blot turbo pack 0.2 µm nitrocellulose membrane were obtained from Bio-Rad Laboratories (Hercules, CA, USA). Vivaspin 500 centrifugal concentrators were obtained from Sartorius (Göttingen, DE, USA), α-cellulose with a particle size of 125 µm was obtained from a commercially available preparation from Sigma (C8002). Microscope slides of 1 mm thickness were obtained from DWK Life Sciences (Wertheim, DE, USA) and coverslips #1 (0.13–0.16 mm) were purchased from Epredia-Fisher Scientific (Waltham, MA, USA).
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8

ApoE Dialysis and Buffer Exchange

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ApoE was either extensively dialysed overnight in 20 mM PB (16 mM Na2HPO4, 4 mM NaH2PO4) at pH 7.4 using Slide-A-Lyzer™ Dialysis Cassettes with a molecular weight cutoff (MWCO) of at 3.5 kDa (Thermo Fisher) or buffer exchanged using disposable Vivaspin® 500 centrifugal concentrators with an MWCO of 3 kDa or Vivaspin® 20 centrifugal concentrators with an MWCO of 3 or 10 kDa (Sartorius).
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