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24 protocols using phenylacetic acid

1

Synthesis of Dyes from Diverse Substrates

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The substrates used for the synthesis of dyes [2-methylbenzothiazole, 4-pirydylcarbinol, diiodopropane, trimethylamine, phenylacetic acid chloride, N,N-dicycloheksacarbodiimide, diphenylacetic acid, p-(N,N-dimethylamino)benzaldehyde, p-pyrrolidinobenzaldehyde], 2-ethyl-2-(hydroxymethyl)-1,3-propanediol triacrylate [trimethylolpropane triacrylate (TMPTA)], and 1-methyl-2-pyrrolidinone (MP) were purchased from Aldrich (Poland) and were used without further purification. The purity of all chemical used was as required for spectroscopic studies (≥99 %).
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2

Production of Cellulose Nanocrystals from MCC

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Microcrystalline cellulose (MCC) AVICEL ® PH-101 was acquired from Sigma-Aldrich (France) and was used as the raw reference material for the production of cellulose nanocrystals (CNC). Phenylacetic acid (PhAA) and hydrocinnamic acid (BzAA) were obtained from Aldrich (France). Anisole and cyclohexane were purchased from Sigma-Aldrich (France). Sulphuric acid (> 95 wt%), chloroform, acetone, and ethanol were purchased from Chimie-Plus. PLA 4060D was purchased from Natureworks. The latter contains 12 mol% of D-lactic acid, which prevents crystallisation during film processing. All of the PLA samples were therefore amorphous.
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3

Histone Acetylation Analysis Protocol

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Recombinant p300 (1195–1662) was from Enzo and pCAF (503–668) was obtained from Caymen Chemical. (R)- and (S)-ibuprofen and celecoxib were purchased from Santa Cruz. Haloxyfop was purchased from Fluka. Salicylic acid, racemic ibuprofen, naproxen, ketoprofen, diclofenac, 5-fluoroSalicylic acid, phenylacetic acid, benzoic acid and sodium acetate were purchased from Sigma. All purchased chemicals were used without further purification unless otherwise noted. All synthesized CoA analogues were HPLC purified, with purity verified by LC-MS prior to use, and concentrations were measured by UV analysis on a Thermo-Fisher Nanodrop 2000 spectrophotometer in distilled and deionized water (ddH2O) using the molar extinction coefficient (ε) for Coenzyme A of 15,000 M−1cm−1 at λmax of 259 nm. Qubit Protein Assay kit (Life Technologies) was used to determine histone extract concentrations. Labchip EZ-Reader 12-sipper chip (#760404) and ProfilerPro Separation Buffer (#760367) were purchased from Perkin-Elmer. Antibodies11 used are as follows: H3K9Ac (9649P), H3K14Ac (7627P), H3K27Ac (8173) antibodies were purchased from Cell Signaling Technologies. The H2B K12/K15Ac (ab1759), total H2B (ab1790), and H3K56Ac (ab76307) antibodies were purchased from abcam. The pan-H4Ac (06–866) and pan-H3Ac (07–690) antibodies were purchased from Millipore Sigma.
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4

Quantification of Phenoxy Acid Herbicides

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Pestanal standards (purity greater than 99%) of the phenoxy acid herbicides 2-(4-chloro-2-methylphenoxy) propanoic acid (mecoprop), 2,4-dichlorophenoxyacetic acid (2,4-D), (4-chloro-2-methylphenoxy)acetic acid (MCPA), (2,4,5-trichlorophenoxy) acetic acid (2,4,5-T), 2-(2,4,5-trichlorophenoxy)propanoic acid (2,4,5-TP), 2,6-dichloro-pyridine-2-carboxylic acid (clopyralid), 2-(2,4-dichlorophenoxy)propanoic acid (dichloroprop) and [(3,5,6-trichloro-2-pyridinyl)oxy]acetic acid (triclopyr) were obtained from Labor Dr. Ehrenstorfer-Schäfers (Augsburg, Germany). Chemical standards of phenoxyacetic acid, benzoic acid and phenylacetic acid derivatives with purity greater than 95% were purchased from Sigma–Aldrich (St. Louis, MO, USA). Stock solutions (1.00 g L−1) of individual analytes were prepared by dissolving accurately weighed 10 mg of each solute in 10 mL of HPLC-grade acetonitrile (Carlo Erba Reagenti, Milano, Italy) and stored at 4 °C. HPLC-grade acetonitrile was acquired from Sigma-Aldrich (St. Louis, MO, USA). Double deionized water was obtained from a Milli-Q filtration/purification system (Millipore, Bedford, MA, USA).
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5

Synthesis of Carboxylic Acid Derivatives

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Pentylenetetrazole, phenylacetic acid and 2-Phenylbutyric acid were purchased from Sigmaaldrich (Germany). 3,4-Dimethoxyphenylacetic acid, 4-Phenylbutyric acid, 2-Thiophene ethanol, Fluorene-9-carboxylic acid, 1-Adamantanecarboxylic acid, 4-Biphenylacetic acid, 4-tert-Butylcyclohexane-carboxylic acid, and shikimic acid were obtained from Merck (Germany).
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6

HPLC Analysis of Ehrlich Metabolites

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Ehrlich metabolites (phenyl acetic acid, phenyl ethanol, p‐OH‐Phenylethanol and p‐OH‐phenylacetic acid) were identified via HPLC using an Agilent Zorbax Eclipse Plus C18 Column (4.6 × 100; 3.5 microns) operating at 40°C. The eluent was a gradient of acetonitrile and 20 mM KH2PO4 (pH 2) with 1% acetonitrile. The flow rate was 0.8 ml·min−1; it increased from 0 to 10% acetonitrile in 6 min and then climbed to 40% acetonitrile by 23 min. From 23 min to 27 min, the flow was 99% KH2PO4. Metabolites were measured at 214 nm using a diode array detector (DAD).
Phenylethanol, phenylacetic acid, p‐OH‐Phenylethanol and p‐OH‐phenylacetic acid standards were obtained from Sigma‐Aldrich (France). Solutions of 10 mM were created for each compound (in their specific solvents as per manufacturer’s instructions) and then diluted to final concentrations of 0.1, 0.2, 0.5, 1 and 2 mM for HPLC calibration.
Culture supernatants were treated with 1% (vol/vol) trifluoroacetic acid for at least one hour at 4 °C and were then centrifuged and filtered to 0.22 µm before HPLC analysis.
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7

Analytical Method for Phenolic Compounds

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The chemicals used as substrates or standards were catechol, propanoic acid, benzoic acid, phenyllactic acid, phenylacetic acid, 2-phenylpropanoic acid, 3-phenylpropanoic acid (3PPA), m-tolylacetic acid, p-tolylacetic acid, ibuprofen as sodium salt, diclofenac, ibufenac, naproxen, and ketoprofen, and were all obtained from Sigma-Aldrich (Steinheim, Germany). Other chemicals used were 3-fluorocatechol (Alfa Aesar, Karlsruhe, Germany), and cinnamic acid (Fluka, Buchs, Switzerland). HPLC-grade solvents were supplied by Scharlau (Barcelona, Spain); all other chemicals were of analytical purity.
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8

Spray-Dried Sour Whey Characterization

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Spray-dried sour whey was obtained from Laktopol (Suwałki, Poland). L-Phenylalanine, lactic acid, sodium sulfate, dichloromethane, diethyl ether, and Man Rogosa Sharpe (MRS) agar were purchased from Sigma-Aldrich (Poznań, Poland). Yeast extract and a medium with chloramphenicol were obtained from BTL (Łódź, Poland). Citric acid, Na2HPO4·2H2O, and MgCl2 were obtained from POCH (Gliwice, Poland). Inulin was purchased from Hortimex Plus (Konin, Poland). An EZ: Faast™ Kit for Free (Physiological) Amino Acids was obtained from Phenomenex (Aschaffenburg, Germany). The following reference aroma compounds were purchased from Sigma-Aldrich (Poznań, Poland): 2,3-butanedione, acetic acid, 3-methyl-1-butanol, methyl butanoate, 2,3-butanediol, butanoic acid, methyl hexanoate, dimethyl sulfone, ethyl hexanoate, hexanoic acid, phenylacetaldehyde, 2-phenylethanol, methyl octanoate, ethyl octanoate, phenylacetic acid, octanoic acid, methyl decanoate, vanillin, and lactic acid. The following stable isotopes were obtained from AromaLAB (Freising, Germany): [13C4] 2,3-butanedione, [13C1] acetic acid, [2H2] 3-methyl-1-butanol, [2H9] ethyl 3-methylbutanoate, [2H5] phenylacetaldehyde, [2H5] 2-phenylethanol, [2H3] vanillin, and [2H8] naphthalene.
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9

Enzymatic Assays and Growth Studies

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For growth studies and enzymatic assays high purity penicillin G sodium salt (Sigma, P3032), (+)-6-aminopenicillanic acid (Sigma, A70909), phenylacetic acid (Sigma, W287806), and other antibiotics, were purchased. Dextro-(−)-benzylpenicilloic acid hydrate (Sigma, S341967) was purchased from the Sigma-Aldrich collection of rare and unique chemicals. p-Nitroacetanilide (Sigma, 130648), p-nitroaniline (Sigma, 185310), 6-nitro-3-(phenylacetamido)benzoic acid (aka NIPAB, Pfaltz and Bauer, N10625), N-phenylacetyl-p-aminobenzoate (Sigma, P8529), L-glutamate 1-(p-nitroaniline) (Sigma, 49622), L-glutamate γ-(p-nitroaniline) (Sigma, G1135) and Nα-benzoyl-DL-arginine p-nitroaniline (Sigma, B4875) were purchased as enzyme substrates and standards. For the kinetics assays p-nitrophenol (MP Biomedicals, 102461) and m-nitrophenol (Acros organics, 172300100) were purchased as indicators for monitoring of enzyme reaction kinetics in pH-shift assays. All other compounds and buffers used were of standard molecular biology grade.
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10

Organic Synthesis Reagent Procurement

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Sucrose and diisopropyl azodicarboxylate (DIAD) were purchased from Fluorochem (Hadfield, UK). Triphenylphosphine (PPh3) and oxalyl chloride [(CO)2Cl2] were purchased from Alpha Aesar (Ward Hill, MA, USA). Lactose monohydrate, p-toluene sulfonic acid, 2,2-dimethoxypropane, tetrafluoro boric acid diethyl ether complex [HBF4.Et2O], phenylacetic acid, p-biphenyl acetic acid, p-phenyl benzoic acid, acetone [CH3C(O)CH3], dimethylformamide (DMF), dimethyl sulfoxide (DMSO), methanol (CH3OH), and methylene chloride (CH2Cl2) were purchased from Sigma-Aldrich (Milan, Italy).
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