Antibiotics, most carbon sources, CCCP, NaN3, malonate, furfural, DMSO, K2CO3, and N,N-dimethylformamide were purchased from Sigma-Aldrich. Arabinose and gluconic acid potassium were purchased from Acros Organics. D-Glucose, disodium citrate, mannitol, LB (Miller formulation), and PBS were purchased from Fisher Scientific. M9 minimal medium (parts A and B, containing 7 g/L K2HPO4, 3 g/L KH2HPO4, 1 g/L (NH4)2SO4, 0.1 g/L MgSO4, 0.588 g/L sodium citrate) was purchased from MP Biomedicals. DiBAC4(3) and Texas red sulfonyl chloride were purchased from Life Technologies.
Arabinose
Manufactured by Thermo Fisher Scientific
Sourced in United States
Arabinose is a monosaccharide sugar commonly found in plant cell walls. It serves as a component in various biochemical processes and is used in research and industrial applications.
Automatically generated - may contain errors
Lab products found in correlation
Tetracycline, by Merck Group (2 mentions)
Xylose, by Thermo Fisher Scientific (2 mentions)
Isopropyl β d 1 thiogalactopyranoside iptg, by GoldBio (2 mentions)
Phosphate buffered saline (pbs), by Thermo Fisher Scientific (1 mentions)
Dimethyl sulfoxide (dmso), by Merck Group (1 mentions)
N n dimethylformamide (dmf), by Merck Group (1 mentions)
D glucose, by Thermo Fisher Scientific (1 mentions)
Mannitol, by Thermo Fisher Scientific (1 mentions)
Furfural, by Merck Group (1 mentions)
Dibac4 3, by Thermo Fisher Scientific (1 mentions)
K2co3, by Merck Group (1 mentions)
Texas red sulfonyl chloride, by Thermo Fisher Scientific (1 mentions)
Malonate, by Merck Group (1 mentions)
M9 minimal medium, by MP Biomedicals (1 mentions)
Ethidium bromide, by Thermo Fisher Scientific (1 mentions)
Ciprofloxacin, by Thermo Fisher Scientific (1 mentions)
Ampicillin, by Merck Group (1 mentions)
Rifampicin, by Thermo Fisher Scientific (1 mentions)
Chloramphenicol, by Merck Group (1 mentions)
Clindamycin hydrochloride, by Tokyo Chemical Industry (1 mentions)
14 protocols using arabinose
1
Microbial Metabolism Evaluation Protocol
2
Antibiotic Susceptibility Testing Protocol
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The minimum inhibitory concentration was measured using a broth micro-dilution method according to CLSI guidance with 1 % arabinose (Acros Organics) [64, 65 ]. Compounds were chosen because they are exported by different Ade systems: ampicillin (Sigma), chloramphenicol (Sigma), ciprofloxacin (Acros Organics), clindamycin hydrochloride (TCI Chemicals), ethidium bromide (Acros Organics), rifampicin (Fisher) and tetracycline (Sigma).
3
Detailed Cultivation of E. coli K-12 MG1655
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Throughout this study, E. coli K-12 strain MG1655 and its derivatives (see Table S1 in the supplemental material) were used. Cultures were typically grown aerobically overnight (ca. 16 h) to stationary phase in lysogeny broth (LB) (59 ) on an orbital shaker (200 rpm) at 37°C or at 30°C when required during strain construction. Late-exponential-phase cultures were obtained by diluting stationary-phase cultures 1/100 or 1/1,000 in fresh LB or AB medium (60 (link)) (supplemented with 10 μg/mL thiamine, 5 μg/mL uracil, and 0.5% Casamino Acids) and allowing growth for 3 to 4 h. When appropriate, the medium was supplemented with a final concentration of 100 μg/mL ampicillin (Fisher Scientific), 30 μg/mL chloramphenicol (Acros Organics), 50 μg/mL kanamycin (Applichem), or 0.2% arabinose (Acros Organics).
4
Establishing a Multicomponent Biosynthesis System
5
Characterization of Zip-Lignin Hybrid Poplar
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Zip‐lignin hybrid poplar from line 7 (L7) and wild‐type hybrid poplar from line P39 (WT) trees were greenhouse grown from clonally propagated trees. Plant stems were harvested from eight‐month‐old trees, hand‐debarked, air‐dried, and stored at room temperature prior to processing. Sodium hydroxide (NaOH, certified ACS pellets) was purchased from Fisher Scientific (Fair Lawn, NJ, USA). Sodium sulfide (Na2S), sodium thiosulfate solution (Na2S2O3, 1 m ), [D6]DMSO and [D5]pyridine were purchased from Sigma–Aldrich (St. Louis, MO, USA). Sulfuric acid (72 % w/w), potassium permanganate (KMnO4, 0.100 N), cupriethylenediamine solution (CED, 1 m ), and chlorine dioxide (ClO2) were purchased from Ricca Chemical Company (Arlington, TX, USA). Potassium iodide (KI, 99 %) was purchased from Alfa Aesar (Ward Hill, MA, USA). Starch (soluble potato, powder) was purchased from J. T. Baker (Phillipsburg, NJ, US). Sugars (arabinose, galactose, glucose, mannose, xylose, all 99+%) were purchased from Acros Organics (Geel, Belgium).
6
Culturing Escherichia coli with Selective Antibiotics
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Escherichia coli strains were grown in Luria-Bertani broth (LB; Difco) at 24 C and 240 rpm with the following selective antibiotics and inducing reagents used at the indicated concentrations: carbenicillin, 50 μg/ml; chloramphenicol, 20 μg/ml; isopropyl β-d -1-thiogalactopyranoside (IPTG; Gold Biotechnology), 1.0 mM or 0.1 mM; arabinose (Alfa Aesar), 0.2% (wt/vol).
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7
E. coli Recombinant Protein Expression
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E. coli DH10B (Invitrogen, Waltham, MA) was used for plasmid cloning and recombinant protein expression. LB media (BD-Difco, Franklin Lakes, NJ) was utilized as the culture media. The working antibiotic concentrations were as follows: 50 μg/mL chloramphenicol (Daejung Chemicals, Siheung, Republic of Korea) and 50 μg/mL gentamicin (KisanBio, Seoul, Republic of Korea). Primers used in this study were synthesized and purchased from Macrogen (Seoul, Republic of Korea). AzF (Chem-Impex, Wood Dale, IL), a non-canonical amino acid, was included as a substrate for aaRS. Arabinose (Alfa Aesar, Haverhill, MA) and isopropyl β-d -1-thiogalactopyranoside (IPTG, Bioneer, Daejeon, Republic of Korea) were applied as inducers.
8
Overproduction and Purification of EspF-CPG2
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1 mL of an overnight culture of C. rodentium-EspF-CPG2 was added to 1 L LB media containing 30 μg/mL chloramphenicol and 1% arabinose (purchased from Alfa Aesar at 99% purity, resuspended in DI water and sterile filtered with a Gelman Laboratory Acrodisc® (Andwin Scientific, Schaumburg, IL, USA) syringe filter, 0.2 μm) and grown overnight at 37 °C with shaking. Cells were pelleted by centrifugation at 4000 rpm for 20 min at 4 °C. Pellets were resuspended with 25 mL CPG2 buffer. Cells were lysed by sonication with a Fisherbrand™ Model 120 Sonic Dismembrator with the 1/8-inch probe. Lysate was centrifuged again to remove cellular debris before aspirating off the liquid layer.
9
Characterization of Coffee Parchment Biopolymer Composites
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The coffee parchment was provided by local farmers in San Gil, Santander, Colombia. Partially hydrolyzed polyvinyl alcohol (PVA) was purchased from SUQUIN (Bucaramanga, Colombia). Bentonite was purchased from Biocombustibles Sostenibles del Caribe S.A (Santa Marta, Colombia). Alginate was purchased from Jinan Boss Chemical Industry Co. (Jinan, China). Ethanol (99% purity) was purchased from JT Baker (Fisher Scientific, Thermo Fisher Scientific, Waltham, MA, USA). Ammonium chloride (NH4Cl, purity 99.9% for analysis) was purchased from Merck (Merck KGaA, Darmstadt, Germany). Acetonitrile was purchased from Merck (Merck KGaA, Darmstadt, Germany). Glucose, xylose, arabinose, and dextran standards (6, 20 and 40 kDa) were purchased from Alfa Aesar (Haverhill, MA, USA). Distilled water was used for all the experiments. Ultrapure water was used for chromatography analysis.
10
E. coli Growth and Induction
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