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10 protocols using trifluoroacetic acid

1

Mycelial Hydrolysis and Analysis

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Samples (5 mg) of a deproteinized mycelial mattress from wild type (WT) and mutants, and different culture conditions were hydrolyzed in 3 ml of trifluoroacetic acid (Riedel-deHaen, Seelze, Germany) in sealed ampoules at 110°C for 16 h. Samples were then evaporated to dryness in a desiccator using NaOH pellets and silica gel as the adsorbent under reduced pressure. The dried hydrolysates were dissolved in 5 ml of distilled water for further analysis.
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2

Comprehensive Metabolic Analysis Protocol

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Lead nitrate (Pb(NO3)2), sodium lauryl sulfate, creatinine anhydrous, propionic acid, lithium d-, and l-lactate, acetylacetone, 37% formaldehyde, cimetidine, indoleacetic acid, methylumbelliferone, and methylumbelliferyl N-acetyl-β-d-glucosaminide were purchased from Sigma-Aldrich Fine Chemicals Inc. (MO, USA). Formic acid, HPLC grade acetonitrile (ACN), ethanol and methanol (MeOH) were purchased from Merck (Darmstadt, Germany). Hippuric acid, 2,2′-dipyridyl disulfate (DPDS), triphenylphosphine (TPP) and 4-nitro-7-piperazino-2,1,3-benzoxadiazole (NBD-PZ) were purchased from Tokyo Chemical Industry Co., Ltd. (Tokyo, Japan). 5-Aminolevulinic acid hydrochloride and guanidinoacetic acid were purchased from Alfa Aesar (MA, USA). Sulbactam was purchased from Cayman Chemical (Michigan, USA). Acetic acid was purchased from Hayashi Pure Chemical Ind.,Ltd. (Osaka, Japan). Trifluoroacetic acid (TFA) was purchased from Riedel-de Haën (Seelze, Germany). 3-(Trimethylsilyl)propionic-2,2,3,3-d4 acid sodium salt (TSP) was purchased from Cambridge Isotope Laboratories (MA, USA). 1,1-Dimethylbiguanide hydrochloride (metformin) was purchased from Santa Cruz Biotechnology, Inc. (Texas, USA). Protein Assay Dye Reagent was purchased from Bio-Rad Laboratories (California, USA).
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3

Chromatographic Purification of Proteins

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Molecular exclusion column Superdex-200 (10 × 300 mm) was purchased from GE Healthcare (USA). Reverse phase chromatography column C18 Vydac (250 × 4.6 mm) from Alltech Grade Division (USA). Chromogenic substrates (S-2251, S-2222, S-2238 and S-2288) and plasmin from Chromogenix AB (Italy). Human fibrinogen, factor Xa and double chain tPA (tcu-PA) from American Diagnostic (Greenwich, USA). ADP from Chrono-log (USA). Molecular mass markers for SDS-PAGE from Invitrogen Corporation (USA). Trifluoroacetic acid from Riedel-de Haën (Germany). Spectra Multicolor Broad Range Protein Ladder (Thermo Scientific, USA). Ammonium acetate, hydrochloric acid and acetic acid from Merck (Germany). Ethylenediaminetetraacetic acid (EDTA), ε-aminocaproic acid (EACA), bovine thrombin, dithiothreitol (DTT), rabbit anti plasmin, goat anti-rabbit IgG peroxidase-conjugated and other reagents were purchased from Sigma (Sigma Chemical Co., USA).
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4

Peptide Synthesis Reagents and Materials

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Preloaded Wang resins, amino acids and coupling reagents purchased from NovaBiochem (Nottingham, England). The other chemicals for peptide synthesis were purchased from Sigma Aldrich (Carlsbad, CA, USA). Acrylic acid (Aldrich, Seelze, Germany), N-vinyl-2-pyrrolidone, ethyl acetate, benzoyl peroxide and cobalt naphthenate (Fluka, Seelze, Germany), Tetrahydrofuran (THF), trifluoroacetic acid (TFA), Thioanisole (Riedel-de Haen, Hannover, Germany), 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (Sigma, Carlsbad, CA, USA) were of analytical grade. NaH2PO4, Na2H-PO4.7H2O, NaCl were obtained from Fluka (Seelze, Germany) and NaN3 was from Applichem (Darmstadt, Germany).
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5

Caffeic Acid Quantification and Stability

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Caffeic acid (3,4-Dihydroxycinnamic acid) was acquired from Sigma-Aldrich, St. Louis, MO, and used as received without further purification. The molecular structure of caffeic acid in non-hydrolyzed form is illustrated in Table 1. Iron (II) sulfate heptahydrate (FeSO4•7H2O) was acquired from Panreac, Barcelona, Spain, and hydrogen peroxide (H2O2 30% w/w) and titanium (IV) oxysulfate solution 1.9–2.1%, for determination of hydrogen peroxide, were acquired from Sigma-Aldrich, St. Louis, MO, USA. Sodium sulfite anhydrous (Na2SO3) was acquired from Merk, Darmstadt, Germany. Trifluoroacetic acid (HPLC grade, ≥99.0%) was acquired from Riedel-de Haën, Seelze, Germany, and acetonitrile (HPLC grade, ≥99.9%) was acquired from Chem-Lab, Zedelgem, Belgium. For pH adjustment, sodium hydroxide (NaOH) from Labkem, Barcelona, Spain, it was used, along with sulfuric acid (H2SO4, 95%) from Scharlau, Barcelona, Spain. Deionized water was used to prepare the respective solutions.
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6

Extraction and Analysis of L. aegyptiaca Fiber

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Dried fruit fibers of L. aegyptiaca were purchased from a local market in Taipei, Taiwan. N-acetylglucosamine, glucosamine, and ketamine were supplied by Sigma (St. Louis, MO, USA). Glucose and galactose were obtained from Nihon Shiyaku Industrial (Taipei, Taiwan). Trifluoroacetic acid and pyridine were provided by Riedel-de Haën (Seelze, Germany). n-Butanol was from Hayashi Pure Chemical (Osaka, Japan). Thin-layer chromatography (TLC) plates (Kieselgel 5554) and the solvents for high-performance liquid chromatography (HPLC) and analytical-grade reagents were obtained from Merck (Hohenbrunn, Germany). Pentobarbital was supplied by Siegfried AG (Zofingen, Switzerland).
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7

Peptide Synthesis and Protein Modification

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Heparin sodium salt from porcine intestinal mucosa and VEGF was purchased from Sigma-Aldrich (St Louis, MO, USA). Rink amide resin (0.75 mM/g) and fluorenylmethoxycarbonyl (Fmoc) amino acids were purchased from BeadTech (Ansan, South Korea). 2-(1H-benzotriazol-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate was purchased from AAPPTec (Louisville, KY, USA). Piperidine, diisopropylethylamine, triisopropylsilane, phenol, and thioanisole were obtained from Sigma-Aldrich. Tetrahydrofuran acetonitrile and trifluoroacetic acid were purchased from Honeywell (Morris Plains, NJ, USA). 1,2-Ethanedithiol was purchased from Sigma-Aldrich. Diethyl ether, N,N-dimethylformamide, N-methylpyrrolidone, and other chemicals were of analytical grade. Selective antibodies for FAK (3283), p-FAK (3283S), ERK (9101), p-ERK (9101S), Akt (9271), p-Akt (9271S), MMP2 (4022S), and MMP9 (3862S) were purchased from Cell Signaling Technology (Danvers, MA, USA). All other reagents and products were purchased from Sigma-Aldrich unless noted otherwise.
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8

Analytical Characterization of Cyclosporin A

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Samples of CycA and isoA were provided by
TEVA Czech Industries (Opava-Komárov, Czech Republic). HPLC
grade methanol, trifluoroacetic acid (TFA), formic acid (FA), acetonitrile
(ACN), and LC-MS grade water were purchased from Honeywell (Prague,
Czech Republic). Deuterated solvents CD2Cl2 (99.80%D),
CD3OD (99.80%D), and D2O (99.96%D) were purchased
from VWR (Prague, Czech Republic), sodium trifluoroacetate (NaTFA),
and α-cyano-4-hydroxycinnamic acid (CHCA) were from Sigma-Aldrich
(Prague, Czech Republic), sodium iodide (NaI) was from Waters Corporation
(Wilmslow, U.K.) and peptide calibration standard II was from Bruker
Daltonics (Bremen, Germany).
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9

Comprehensive Profiling of Phytochemicals and Antibacterial Activity

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Acetic acid, methanol, sodium chloride, and sucrose were purchased from Chembur (Piekary Śląskie, Poland), trifluoroacetic acid purchased from Honeywell Riedel-de Haen (Seelz, Germany). HPLC-grade methanol and acetonitrile were purchased in Merck (Darmstadt, Germany). Plant culture media components, plant growth regulators NAA (naphthalene-1-acetic acid), BAP (6-benzylaminopurine) and IBA (indole-3-butyric acid) and agar were purchased in Duchefa Biochemie (Haarlem, Netherlands). The following commercially available standards for HPLC analyses were used: verbascoside, isoverbascoside, verbenaline and hastatoside (ChromaDex®, Los Angeles, California, USA) and caffeic acid, chlorogenic acid, ferulic acid, protocatechuic acid, rosmarinic acid, vanillic acid (Sigma-Aldrich Co., Munich, Germany). Scutellarin, scutellarein and apigenin 7-glucuronide obtained from ChemFaces (Wuhan, Hubei, China). Bacterial culture media: nutrient agar (NA), Müller-Hinton Broth (MHB) and Müller-Hinton agar (MHA) were purchased in BTL (Łódź, Poland). Resazurin sodium was purchased from Sigma-Aldrich Co. (St. Louis, USA). Ferrous chloride (FeCl2) was obtained from Carlo Erba (Milan, Italy). Unless indicated otherwise all chemicals were purchased from Sigma-Aldrich (Milan, Italy).
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10

HPLC-UV Analysis of Quinolones and Sulfonamides

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The quinolones (Fig. S1) and sulfonamides (Fig. S2) under investigation were supplied by different pharmaceutical companies. Pure HPLC-grade acetonitrile, methanol, and dimethylsulfoxide were supplied by Scarlau (Barcelona, Spain). The other chemicals used in this study, including ortho-phosphoric acid, trifluoroacetic acid, sodium dihydrogen orthophosphate, and sodium hydroxide were supplied by Honeywell Riedel-de Haën (Seelze, Germany).
The instruments used in this study included a Jenway 3510, Essex-UK, England pH meter equipped with a glass electrode, and Agilent 1260 HPLC-UV series.
Each drug’s stock solution (2 mg mL− 1) was prepared with a suitable solvent either (methanol, dimethylsulfoxide, water, or acetonitrile). These solutions were stored at 4 °C and then diluted with the mobile phase to achieve sample concentrations ranging (0.05–1 mg mL− 1) before analysis.
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