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30 protocols using sodium citrate tribasic dehydrate

1

Biomimetic Extracellular Matrix Synthesis

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HEP sodium salt from porcine intestinal mucosa (≥180 USP units/mg, BioReagent, suitable for cell culture), PSS (Mw ~ 70,000 g/mol), sodium citrate tribasic dehydrate (ACS reagent), citric acid monohydrate (ACS reagent), 4-Nitrophenyl phosphate disodium salt hexahydrate (pNPP), sodium acetate anhydrous, and Trizma® base were purchased from Sigma-Aldrich, St. Louis, MO, USA. Eagle’s Minimum Essential Medium (EMEM, ATCC® 30-2003™) and BJ fibroblast cell (ATCC® CRL-2522™) were purchased from ATCC, Manassas, VA, USA. Dulbecco’s phosphate-buffered saline (PBS, L0615) and Trypsin-EDTA 1X in PBS (L0940) were purchased from Dominique Dutscher, Bernolsheim, France. TA was obtained from Alfa Aesar, Haverhill, MA, USA. Purified type 1 COL was purchased from Symatese, Chaponost, France. Sodium dodecyl sulfate (SDS) was obtained from Prolabo, Warszawa, Poland. Sodium chloride was obtained from VWR, Radnor, PA, USA. Triton® X-100 was purchased from Fisher Scientific, Waltham, MA, USA. Milli-Q water (18.2 MΩ·cm at 25 °C) supplied by Advantage A10 (MERCK) was used in the entire study. All the materials were used as received.
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2

Synthesis and Characterization of Silver Nanoparticles

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Silver nitrate (AgNO3, 99.9999%),
tannic acid (purissimum grade), sodium citrate tribasic dehydrate
(citrate, ≥99%), sodium hydrosulfide (NaHS), poly(vinylpyrrolidone)
(PVP, average MW = 29,000 Da and 55,000 Da), sodium borohydride (NaBH4, ≥99%), hydrogen peroxide (H2O2, 30 wt %), ethylene glycol (EG), nitric acid (HNO3, >99.999%,
trace metal basis), and a silver standard for ICP (Fluka, TraceCERT
1001 ± 2 mg/L Ag in HNO3) were purchased from Sigma-Aldrich
(St. Louis, MO). Hydrochloric acid (HCl, >99.999%, trace metal
basis),
sodium chloride (NaCl, 99.6%), Luria-Bertani broth (LB, Miller), BD
Bacto dehydrated agar, and glycerol were purchased from Fisher Scientific
(Waltham, MA). All reagents were used as received unless otherwise
indicated. All chemicals were dissolved in deionized (DI) water obtained
from a Milli-Q ultrapure water purification system. NANOpure water
(Thermo Scientific, ≥18.2 MΩ cm) was used in the preparation
of all solutions associated with AgNP synthesis. Before use, all glassware
and Teflon-coated stir bars were washed with aqua regia (3:1 ratio
of concentrated HCl and HNO3 by volume) and rinsed thoroughly
with water. Caution: aqua regia is highly toxic and corrosive and
requires proper personal protective equipment. Aqua regia should be
handled in a fume hood only.
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3

Cultivation of Strain E264 in M20 Medium

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Seed cultures were prepared by inoculating 5 mL LB with 20 μL of a cryo stock of strain E264 and incubated at 37 °C, 180 rpm, 24 hours. Note that we start the seed culture directly from frozen stocks rather than from single colonies for reproducibility purposes. Also note that this cultivation procedure follows inoculation method 3 recently described by Kragh et al.32 Aliquots of the seed culture were used to inoculate 50 mL of M20 medium21 (link) [l-glutamic acid (Sigma Aldrich) 20 g/L, l-alanine (Sigma Aldrich) 0.2 g/L, sodium citrate tribasic dehydrate (Sigma Aldrich) 1.0 g/L, disodium hydrogen phosphate (Sigma Aldrich) 20 g/L, potassium chloride (Sigma Aldrich) 0.5 g/L, sodium sulfate anhydrous (Fisher Scientific) 0.5 g/L, magnesium chloride (Sigma Aldrich) 0.2 g/L, calcium chloride (Sigma Aldrich) 0.0076 g/L, iron (II) sulfate heptahydrate (MP Biomedicals) 0.01 g/L, manganese sulfate heptahydrate (Macron Chemicals) 0.0076 g/L, pH 7.0] until an OD600 of ~0.01 was reached (~200-400 μL seed). Cultivations were performed in 250-mL Erlenmeyer flasks. Production cultures were incubated at 42 °C, 180 rpm, for one to three days.
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4

Synthesis of Multifunctional Gold Nanoparticles

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Hydrogen tetrachloroaurate (III) (≥99.9%) (Catalogue no. 50790), sodium citrate tribasic dehydrate (≥99.0%) (Catalogue no. 54641), hyaluronic acid (Molecular weight- 1.5 to 1.8 × 106 Da; catalogue no. 53747), polyethylene glycol (average Mn 400; catalogue no. 202398), 1-ethyl-3-(-3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) (catalogue no. E7750), and N-hydroxysuccinimide (NHS) (catalogue no. 130672) were purchased from Sigma-Aldrich and used without further purification. Dulbecco’s Modified Eagle’s medium (DMEM; catalogue no.11995065), Fetal Bovine Serum (South American origin FBS; catalogue no.10270106), Penicillin-Streptomycin (catalogue no. 15140122), Phosphate buffered saline (PBS; catalogue no: 10010023) and Trypsin-EDTA (catalogue no. 25200056) were procured from GIBCO, Invitrogen, USA. ACK lysing buffer (catalogue no. A1049201) was purchased from Thermo Fisher Scientific, USA.
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5

Functionalized Gold Nanoparticle Synthesis

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Tetrachloroauric (III) trihydrate (HAuCl4·3H2O: 99.9%), sodium citrate tribasic dehydrate (≥99%) and hydroquinone (≥99%) were purchased from Sigma-Aldrich. Heterobifunctional polyethylene glycol OPSS-PEG-SVA (3.4 kDa, OPSS-PEG-SVA-3400) were purchased from Laysan Bio Inc. Poly(ethylene glycol) 2-mercaptoethyl ether acetic acid (Thiol-PEG-Carboxyl, 600 Da, PG2-CATH-600) were purchased from Nanocs Inc. Fluorescein isothiocyanate–dextran (FITC-dextran) and WST-1 cell proliferation reagent (05015944001) was purchased from Sigma-Aldrich. Propidium iodide (PI) is purchased from Cayman chemical (14289). Mouse IgG isotype control (Ctrl Ab, 31901) was purchased from Invitrogen. Anti-PAR2 antibody (MAB3949) was purchased from R&D systems. Anti-JAM-A antibody BV16 was kindly provided by Dr. Elisabetta Dejana’s lab.32 (link) Human cerebral microvessel endothelial cells (hCMEC/D3) were purchased from EMD Millipore. HEK293 cell with Ca2+ indicator TN-XXL was kindly provided by Dr. Paul Slesinger’s lab.44 (link) PAR2 agonist 2-aminothiazol-4-yl-LIGRL-NH2 (2AT) was provided by Dr. Theodore Price’s lab.40 (link) Somatostatin (SST) was purchased from Sigma-Aldrich (S9129). Pierce modified lowery protein assay kit was obtained from ThermoFisher Scientific (23240).
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6

Synthesis and Characterization of Nanoparticles

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Gold(III) chloride trihydrate (HAuCl4·3H2O), sodium citrate tribasic dehydrate
(Na3Cit·2H2O), silver nitrate (AgNO3), 4-chloroaniline (4-CA, 98%), 3-chloroaniline (3-CA, 99%),
2-chloroaniline (2-CA, 98%), 2,4-dichloroaniline (99%), 3-bromoaniline
(3-BA), 3-nitroaniline (3-NA), melamine, and 4-mercaptobenzoic acid
(4-MBA) were purchased from Sigma-Aldrich. Sodium borohydride (NaBH4), hydrochloride acid (HCl), and ethanol were purchased from
Fisher Scientific. Malachite green isothiocyanate (MGITC) was acquired
from Invitrogen Corp. (Grand Island, NY). Thiolated poly(ethylene
glycol) (HS-PEG; 5 kDa) was purchased from Nanocs.
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7

Sugar Beet Leaves Phytochemical Characterization

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The SBLs were of a sugar beet plant (Beta Vulgaris L., var. SMART DJERBA-KWS) aged 10 months (March–January 2021), cultivated at a local farm in Padova, Italy. The area and weight of the SBLs were about 20–30 cm2 and 2–3.5 g, respectively. They were transported to the laboratory in thermal boxes.
All the chemicals and solvents used in this work were of analytical grade. Sodium hydroxide, citric acid, sodium citrate tribasic dehydrate, sulfuric acid, hydrochloric acid, EtOH, MeOH, polyvinylpolypyrrolidone, triton X-100, 3,3′-dithiodipropionic acid, barium hydroxide, sodium acetate, potassium carbonate, sodium methoxide, acetonitrile, sodium carbonate, Folin–Ciocalteu reagent, gallic acid, Trolox, iron(III) chloride, 2,4,6-Tri(2-pyridyl)-s-triazine (TPTZ), and 2,2-diphenyil-1- picrylhydrazyl (DPPH) were bought from Sigma (St. Louis, MO, USA). AccQTag Ultra Derivatization Kit, and 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC) were purchased from Waters (Milford, CT, USA). The water utilized in all the analyzes was deionized and distilled.
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8

Proteomic Sample Preparation Protocol

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Acrylamide/bis-acrylamide 30% solution (37.5:1), β-mercaptoethanol (molecular biology grade), Coomassie Brilliant Blue R250 (CBB), DL-dithiothreitol (HSCH2CH(OH)CH(OH)CH2SH, 99%) (DTT), glycerol (HOCH2CH(OH)CH2OH, 86–88%), iodoacetamide (IAA, ICH2CONH2, 99%), sodium citrate tribasic dehydrate (HOC(COONa)(CH2COONa)2·2H2O, 99%), sodium carbonate (Na2CO3, 99%), tris-base (NH2C(CH2OH)3), trifluoroacetic acid (CF3COOH, 99%), trypsin from bovine pancreas and the Sigma Marker wide range 6.5–200 kDa were purchased from Sigma-Aldrich. Formaldehyde for molecular biology (36.5–38% in H2O) and sodium dodecyl sulfate (SDS, CH3(CH2)11SO4Na) were purchased from Panreac. Bromophenol-blue was purchased from Riedel-de Haen. Hydrogen tetrachloroaurate (III) hydrate (HAuCl4·xH2O) (99.9%-Au) (49% Au) at 10% w/v was purchased from Strem Chemicals. Ammoniumbicarbonate (AMBIC, NH4HCO3, 99.5%) and formic acid (HCOOH, 95%) were purchased from Fluka.
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9

Polymer Nanoparticle Synthesis and Characterization

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The following chemicals were obtained from commercial suppliers and used as received: the polymer poly(d,l-lactic-co-glycolic acid) 50 : 50 (PLGA; MW 38 000–54 000 Da, Tg 46–50 °C), under the commercial name of Resomer® RG 504 was purchased from Boehringer Ingelheim (Ingelheim, Germany) and Evonik Industries (Evonik Röhm GmbH, Germany). Sodium cholate, chloroauric acid (HAuCl4·3H2O), sodium citrate tribasic dehydrate ≥99.0% (Na3C6H5O7·2H2O), PVA (polyvinyl alcohol) MW 85 000–124 000 Da, 97–99% hydrolyzed, taurocholic acid sodium salt hydrate ≥95% (TLC), ethyl acetate ACS reagent, dodecanethiol, phosphotungstic acid hydrate as a contrast agent for microscopy and fluorescent molecule pyrene ≥99.0% were purchased from Sigma Aldrich (St Louis, MO, USA).
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10

Neutrophil Activation and Oxidative Stress

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Phenylephrine hydrochloride, glycogen, N-formyl-L-methionyl-L-leucyl-L-phenylalanine, Nω-nitroL-arginine methyl ester (L-NAME), sodium nitroprusside (SNP), percoll, sodium citrate tribasic dehydrate, 5-amino-2,3-dihydro-1,4-phthalazinedione (luminol), trypan blue and NaOCl for preparation of HOCl were all from Sigma-Aldrich Chemie (Steinheim, Germany), ONOO from Calbiochem (La Jolla, CA) and the other chemicals were of p.a. purity purchased from Lachema (Brno, Czech Republic).
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