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105 protocols using iodomethane

1

Synthesis of JNJ-31020028 Compound

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JNJ-31020028 1 was commercially obtained from InvivoChem LLC (Libertyville, IL, USA). N,N-Dimethylformamide, 99.8%, Extra Dry was purchased from Fisher Scientific (Porto Salvo, Portugal). Sodium hydride, 57–63% oil dispersion, was purchased from Enzymatic (Santo Antão do Tojal, Portugal). Sodium hydroxide and iodomethane were purchased from Merck (Lisboa, Portugal). Air- and moisture-sensitive reagents or solutions were handled under nitrogen or argon atmosphere in a vacuum system using Schlenk techniques [31 ]. All the glassware was dried by heating. The solvents, such as dichloromethane and ethyl acetate, were purified by simple distillation.
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2

Synthesis of Chitosan-Based Nanoparticles

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Chloroauric acid (HAuCl4), sodium dodecyl sulfate (SDS), sodium azide, low molecular weight chitosan, MTT reagent, RPMI1640 cell culture medium, fetal bovine serum (FBS), and dialysis tubing with a molecular cutoff of 12000 Da were purchased from Sigma (UK). T47D human ductal breast epithelial tumor cell line was obtained from American Type Culture Collection (ATCC) (USA). FeCl3·6H2O (99.0%), FeCl2·4H2O (99.0%), NaOH, and acetic acid were purchased from Acros Organics (USA). Analytical HCl, NaCl, D-glucose, glutaraldehyde, N-methylpyrolidone (NMP), iodomethane, sodium hydroxide, sodium iodide, and acetone were purchased from Merck (Darmstadt, Germany). Deionized water was used in all experiments.
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3

Chitosan-Based Immunostimulant Nanoparticles

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CS (viscosity: 3.6 mPa·s [5 g/L]; degree of deacetylation: 93.8%) was purchased from Wako Pure Chemical Industries, Ltd. (Osaka, Japan). Dimethyl sulfoxide (DMSO), absolute ethanol, acetone, N-methylpyrrolidinone, iodomethane, sodium chloride, sodium iodide, and sodium hydroxide were purchased from Merck (Darmstadt, Germany). FUC (from Fucus vesiculosus), carbonate-bicarbonate buffer, 5% skim milk, methylcellulose, and fluorescein 5(6)-isothiocyanate (FITC) were obtained from Sigma–Aldrich (St. Louis, MO, USA). ODN 1826 (CpG ODN, 5-tccatgacgttcctgacgtt-3, molecular weight: 6364 g/mol, bases were phosphorothioate, ammonium salt) was purchased from InvivoGen (CA, USA). Dulbecco's modified Eagle medium (DMEM), SFM-900, Grace's insect medium, fetal bovine serum (FBS), l-glutamine, antibiotic solution (penicillin and streptomycin), and phosphate-buffered saline (PBS; pH 7.4) were supplied by Gibco BRL (Thermo Fisher Scientific, Inc., Waltham, MA, USA). The peroxidase-labeled secondary antibody, 3,3′,5,5′-tetramethylbenzidine (TMB) substrate, and TMB stop solution were obtained from KPL (Gaithersburg, MD, USA). Ultrapure water was obtained using a Milli-Q system (Millipore, Billerica, MA, USA).
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4

Synthesis and Characterization of Organic Compounds

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Reagents of analytical grade were used as received from their commercial sources. Benzyl chloride was obtained from ACROS Organics (Morris Plains, NJ, USA), potassium hydroxide from Riendemann Schmidt (Kajang, Malaysia), carbon disulfide from Fisher Scientific (Chino, CA, USA) and copper (II) acetate from R&M Chemicals (Essex, UK). Hydrazine hydrate, iodomethane, glyoxal, 2,3-hexanedione, 2,3-heptanedione, 2,3-pentanedione, 2,3-butanedione and copper (II) chloride were obtained from Merck (Darmstadt, Germany). Absolute ethanol, 95% ethanol, dimethyl sulfoxide, acetone and dimethylformamide were obtained from RCI Labscan (Bangkok, Thailand). Elemental analysis was conducted via a Vario MACRO CUBE CHNS analyser (Germany), while IR spectra were recorded using a PerkinElmer FTIR spectrophotometer (Waltham, MA, USA). Melting points were measured using an Electrothermal IA9100 melting point apparatus (Essex, UK).
1H NMR spectra were obtained via a Bruker FT-NMR 300 MHz (Germany). TLC was performed via 60F aluminium silica gel aluminium plates with a 254 nm fluorescent indicator from Merck (Darmstadt, Germany). UV-Vis spectroscopy was performed via a Biochrom UltroSpec 8000 spectrophotometer (Cambridge, UK).
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5

Chitosan-Based Antimicrobial and Antioxidant

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Chitosan (90% deacetylation, 150,000 Da), potassium iodide, sodium chloride, sodium triphosphate pentabasic (TPP), 1,1-diphenyl-2-picrylhydrazyl (DPPH), Mueller-Hinton agar (MHA), Mueller-Hinton Broth (MHB), Folin-Ciocalteu reagent, sodium carbonate, ciprofloxacin, tween 80 and chloramphenicol were purchased from Sigma-Aldrich, USA. Iodomethane, sodium hydroxide, N-methyl-2-pyrrolidone, acetone, acetic acid, ethanol, hydrochloric acid, methanol, Dulbecco’s modified eagle’s medium (DMEM) and phosphate-buffered saline (PBS) were purchased from Merck, Germany.
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6

Protein Sample Preparation Workflow

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Trifluoroacetic acid (TFA), ammonium bicarbonate (ABC), formic acid (FA), dithiothreitol (DTT), iodoacetamide (IAM), and Tween 20 were purchased from Sigma-Aldrich (St. Louis, MO, USA). Sodium hydroxide, DMSO, iodomethane and trichloromethane were purchased from Merck Millipore (Darmstadt, Germany). Trypsin was purchased from Promega (15,664 unit/mg, Sequence Grade, WI, USA). Acrylamide, SDS and TEMED were obtained from Bio-Rad (Hercules, CA, USA). Acetonitrile (ACN) was purchased from J.T. Baker (Phillipsburg, NJ, USA). Deionized water was generated with a Simplicity Ultrapure Water System (Millipore, Burlington, MA, USA) with a measured value of 18 MΩ.
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7

Synthesis and Characterization of Redox-Active Materials

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PPFSt was prepared as described in our earlier study [13 ]. F6-PBI was purchased from Yanjin Technology, Shenzhen, China. Sulfuric acid, methyl ethyl ketone, potassium hydroxide, 0.1 N standard hydrochloric acid and sodium chloride were purchased from Carl Roth GmbH, Karlsruhe, Germany. N-methyl-2-pyrrolidone (NMP) and diethyl ether were obtained from Sigma-Aldrich, Munich, Germany. N,N-dimethylacetamide was purchased from Acros Organics, Darmstadt, Germany. Sulfuric acid was purchased from VWR International, Bruchsal, Germany. 1-(2-dimethylaminoethyl)-5-mercaptotetrazole (DMAEMTZ) and triethylamine were purchased from TCI Chemicals, Eschborn, Germany. Iodomethane was purchased from Merck, Darmstadt, Germany. The vanadium electrolyte solution (1.6 M vanadium in 30% Sulfuric acid: 50% VO2+ and 50% V3+) was supplied by RIVA GmbH Batteries, Backnang, Germany. Nafion®212 (Nafion) was purchased from Ion Power GmbH, Munich, Germany.
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8

Glycoprotein Purification and Analysis

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Trypsin, sodium dihydrogen phosphate monohydrate, di-sodium hydrogen phosphate dihydrate, 1,4-dithioerythritol (DTE), 2-iodoacetamide (IAA), sodium borohydride, Dowex 50WX8 ion exchange resins, sodium hydroxide (NaOH), iodomethane, sDHB (9:1 mixture of 2,5-dihydroxybenzoic acid and 2-hydroxy-5-methoxy benzoic acid) and dextran were purchased from Merck (Taufkirchen, Germany). Acetonitrile (ACN) and anhydrous dimethyl sulfoxide (DMSO) were purchased from VWR International GmbH (Dresden, Germany). Trifluoroacetic acid (TFA) and acetic acid were purchased from Thermo Fisher Scientific (Schwerte, Germany). Peptide N-glycosidase F (PNGase F) was purchased from N-Zyme Scientifics (Doylestown, PA, USA). Methanol (MeOH) was purchased from Carl Roth GmbH + Co. KG (Karlsruhe, Germany). Milli-Q grade water was produced using a MilliQ Plus water purification system (Merck KGaA, Darmstadt, Germany). All the reagents were obtained in p.a. quality.
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9

Synthesis and Characterization of PIM-EA-TB Polymer

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The PIM-EA-TB polymer
(Sigma-Aldrich 918784; molecular weight approximately 70 KD; monomer
weight for C21H20N2 300 g mol–1; density approximately 1.1–1.3 g cm–3 or 3.7–4.3 mmol cm–3;21 (link) pore volume typically 30–26% (FFV),22 (link) therefore wet density approximately 1.4–1.7 g cm–3) was synthesized following a previously reported
method.23 (link) Iodomethane (99%), NaClO4 (≥98.0%), D2O (99.9% atom D, contains 0.05
wt % 3-(trimethylsilyl)propionic-2,2,3,3-d4 acid, sodium
salt as the internal standard), dimethyl sulfoxide, DMSO-d6 (99.9 atom % D), and chloroform were purchased from
Sigma-Aldrich. NaCl (99.5%) was purchased from Fisher Scientific Ltd.
Methanol (HPLC) was purchased from VWR Chemicals BDH. Agarose powder
was purchased from Melford Ltd. All reagents were applied and used
as received without further purification. All aqueous solutions were
prepared with ultrapure water with a resistivity not less than 18.2
MΩ·cm (20 °C), from a CE Instruments water purification
system.
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10

Glycoprotein Analysis by MALDI-TOF MS

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CNPs, GNs, ribonuclease B (RNase B) from bovine pancreas, fetuin from fetal bovine serum, 2,5-dihydroxybenzoic acid (DHB), iodomethane, and borane-ammonia complex were purchased from Sigma-Aldrich (St. Louis, MO). Human blood serum from disease-free subjects and patients with Barrett’s esophagus disease and esophageal adenocarcinoma were obtained from Dr. Zane Hammoud (Henry Ford Hospital, Detroit, MI) with all the needed institutional review board (IRB) approvals for sample collection. Microspin columns were purchased from Harvard Apparatus (Holliston, MA) and PNGase F with 10×G7 reaction buffer (0.5 M sodium phosphate) was obtained from New England Biolabs (Ipswich, MA). PGC and charcoal powders were HyperSep PGC cartridge (Thermo Scientific, Waltham, MA) and charcoal Macro SpinColumn (Harvard Apparatus, Holliston, MA), respectively. HPLC-grade water, ethanol, and acetonitrile (ACN) were used for the preparation of samples.
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