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5 protocols using essentially fatty acid free bsa

1

Lipid Standards for Biophysical Analysis

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Essentially fatty acid-free BSA was obtained from Sigma-Aldrich (St. Louis, MO). 1,2-diheptadecanoyl-sn-glycero-3-phosphatidylcholine, 1,2-dinonadecanoyl-sn-glycero-3-phosphatidylcholine, and retinyl acetate were obtained from Larodan Fine Chemicals AB (Stockholm, Sweden) and Sigma-Aldrich and used as internal standards. Retinyl palmitate (RP) and cholesteryl oleate were purchased from Sigma-Aldrich. Lalistat 2 was a kind gift from Dr. Paul Helquist (Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN).
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2

TGFβ Signaling Pathway Inhibition Assay

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Subconfluent AG01523 or MRC5 fibroblasts were plated at 600000 cells/plate, starved for 24 hours in the presence of 0.05% essentially fatty acid free BSA (Sigma) and treated for 30 minutes in presence or absence of the following inhibitors: TGFβ receptor inhibitor (SB431542, 10 µM), MEK1/2 inhibitor (U0126, 10 µM), p38 inhibitors (SB203580 and SB202190, 10 µM), IKK inhibitor (BMS-345541, 10 µM), PI3K inhibitor (LY294002, 20 µM), HDAC inhibitor (TSA, 300 nM) or vehicle (DMSO). Cells were then incubated during 24 hours in the presence of TGFβ (4 ng/ml). Total RNA was extracted from cells using the Qiagen RNeasy extraction kit according to the manufacturer's instructions. Complementary DNA synthesis from total RNA was performed following the M-MLV reverse transcriptase (Invitrogen) protocol. Real time quantitative PCR (q-PCR) was performed using SYBR-green (ABgene kit) on an iCycler instrument (Bio-Rad) as described [30] (link). The expression of the RPLP0 and β-Actin genes was used to normalize q-PCR experiments. All q-PCR primer sequences used in this study are provided in Table S1.
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3

Investigating Synergistic Nutrient Effects

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Four SNC key nutritional ingredients that allowed in vitro testing were tested as single nutrients or as a mix of all four nutrients (SNCi). These nutrients were tested in a final concentration of 25 μM eicosapentaenoic acid (EPA) (Sigma-Aldrich), 12.5 μM docosahexaenoic acid (DHA) (Sigma-Aldrich), 1 mM L-leucine (Sigma-Aldrich) and 10 nM Vitamin D3 (Sigma-Aldrich or Cayman). Chosen concentrations of EPA and DHA were based on previous data showing significant increase in protein synthesis in C2C12 myotubes. L-leucine concentration of 1 mM was based on previous data showing increased protein synthesis in C2C12 myotubes. Vitamin D3 concentration of 10 nM was selected because of Salles et al. [42 (link)] showed significant increase in protein synthesis with 1 and 10 nM Vitamin D3 together with insulin and leucine as anabolic stimuli. For muscle cell assays, EPA and DHA were dissolved in 100% ethanol and further diluted in PBS + 2.5% essentially fatty acid free BSA (Sigma-Aldrich), Vitamin D3 was dissolved in 100% ethanol, L-leucine in differentiation medium. For tumor cell and organoid screening L-leucine was dissolved in PBS-Tween (0.1%); EPA, DHA and Vitamin D3 were dissolved in DMSO.
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4

TGFβ Regulation of PDGF Signaling

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Subconfluent MRC5 cells were plated at 200000 cells/well (six well plates), starved for 24 hours in the presence of 0.05% essentially fatty acid free BSA (Sigma) and treated with or without TGFβ (4 ng/ml) during 24 or 48 hours. Cells were washed with phosphate-buffered saline (PBS) and then lysed as described [30] (link). Equal amounts of total protein extracts were analyzed by SDS-PAGE, then transferred on a polyvinylidene difluoride membrane (PVDF) and subjected to antibodies against PDGF-D (1 µg/ml, Santa Cruz), PDGF-C (1 µg/ml, monoclonal antibody) or β-actin (0.5 µg/ml, Sigma).
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5

ELISA Peptide-Protein Binding Assay

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Recombinant proteins or peptides were diluted to 10 µg/mL in PBS, and 25 µL of the dilutions per well was used for coating at 4°C overnight in 384-well microtiter plates with high-binding surface (Corning, Tewksbury, MA, USA). The wells were then incubated with blocking solution (2% essentially fatty acid-free BSA (Sigma-Aldrich) in PBS at room temperature for 1.5 h, washed with PBS for 30 sec, and incubated at room temperature for 1.5 h with different concentrations of recombinant proteins in the presence of different concentrations of peptides. After washing 3 times with PBST (PBS with 0.05 % Tween 20) for 30 s, primary antibodies (diluted 1:300 in PBS) were applied for 1 h. The ELISA plate was washed 3 times for 5 min with PBST and incubated for 1 h with horseradish peroxidase-conjugated secondary antibody (diluted 1:1000 in PBS). The plate was rinsed again 3 times with PBST for 5 min. As horseradish peroxidase substrate, 25 µL ortho-phenylenediamine dihydrochloride (Thermo Fisher Scientific; 1 mg/mL) was added per well, and plates were incubated for 0.5–5 min. The color reaction was terminated with 2.4 M sulfuric acid, and the absorption was measured at 492 nm using the μQuantTM microplate spectrophotometer (Bio-Tek Instruments, Bad Friedrichshall, Germany).
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