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219 protocols using arabinose

1

Growth assay for cobalamin-deficient E. coli

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Growth assays were performed as previously described31 (link). Briefly, the cobalamin-deficient E. coli ΔFEC strain was transformed with various expression vectors to express BacAMt, ECF-CbrT or ECF-FolT2. Single colonies were then innoculated into M9 medium supplemented with 0.00001% (w/v) arabinose (Sigma-Aldrich) and 50 µg ml−1 methionine (Sigma-Aldrich). Cells were grown at 37 °C for 24 h and were then diluted with a ratio of 1:250 into 200 µl fresh M9 medium supplemented with 0.00001% (w/w) arabinose and either 1 nM cyano-cobalamin or 50 µg ml−1 methionine (Sigma-Aldrich) in 96-well plates (Greiner). Plates were sealed with sterile and gas-permeable foil (Breathe-Easy, Diversified Biotech) and incubated at 37 °C for 24 h. The OD600 was measured every 10 min on a SpectraMax ABS plus Microplate reader (Molecular Devices). The measurements were performed as biological triplicates each containing technical triplicates and collected using the instruments’ SoftMax Pro version 7.1.2 (Molecular Devices).
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2

Plasmid Copy Number Regulation in E. coli

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In this study, we used Escherichia coli K12 MG1655 bearing a ColE1-like (p15A) plasmid, pBGT, encoding for the β-lactamase resistance gene blaTEM-1 that confers resistance to ampicillin under a constitutive promoter, an GFPmut2 gene under an arabinose inducible promoter, and the araC repressor. Mean PCN = 19.12, s.d. = 1.5336 (link). As a control, a strain E. coli K12 MG1655 was used, carrying the construct araC − pBAD − gfp2 − blaTEM-1 inserted into the chromosome at the λ-phage integration site (attB). Strains bearing plasmid variants G54U and G55U contained a point mutation in the origin of replication: G to U changes at positions 54 and 55 of the RNAI placed in the loop of the central hairpin and affect the RNAI-RNAII kissing complex that controls plasmid replication and PCN. All experiments were conducted in Lysogeny Broth- Lenox (LB) (Sigma-L3022) supplemented with arabinose (0.5% w/v) and appropriate ampicillin concentrations were supplemented as indicated in each experiment. arabinose stocks solutions were prepared at 20% w/v by diluting 2 g of arabinose (Sigma-A91906) in 10 ml DD water sterilized by 0.22 μm filtration. AMP stock solutions (100 mg/ml) were prepared by diluting ampicillin (Sigma-A0166) directly in 0.5% w/v arabinose LB.
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3

Wolfberry Pollen Polysaccharide Extraction

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The wolfberry pollen was collected from the Ningxia Academy of Agriculture and Forestry Sciences (Yinchuan, Ningxia, China). Cellulose DEAE-52, Sephadex G-100 columns and monosaccharide standards (mannose, glucuronic acid, galacturonic acid, xylose, galactose, arabinose, and trehalose) were purchased from Sigma Chemical Co., Ltd. (St. Louis, MO, USA). HPLC-grade acetonitrile was purchased from TEDIA Co., Inc. (Fairfield, IA, USA). 1-phenyl-3-methyl-5-pyrazolone (PMP) high-glucose DMEM medium and fetal bovine serum were purchased from Gibco (Carlsbad, CA, USA). Penicillin-streptomycin double antibody and 0.25% trypsin were purchased from Solarbio Science & Technology Co., Ltd. (Beijing, China). 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) was purchased from KeyGEN BioTech Co., Ltd. Nanjing, China). In situ cell death detection kit and POD were purchased from Roche Diagnostics (Indianapolis, IN, USA) and DAPI was obtained from ZSGB-BIO Biological Co., Ltd. (Beijing, China). Annexin V-FITC cell apoptosis detection kit was purchased from Best Bio Biological Co., Ltd. (Shanghai, China).
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4

Chickpea Seed Polysaccharide Extraction and Bioactivity

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Chickpea seeds were obtained from the National Gene Bank (Beijing, China). DEAE Sepharose Fast Flow was obtained from GE Healthcare Bio-Sciences Co. (Piscataway, NJ, USA). Dextran with different molecular weight (5,000–670,000 Da), griess reagent, arabinose (Ara), rhamnose (Rha), mannose (Man), galactose (Gal), glucose (Glc), 1,1-diphenyl-2-picrylhydrazyl (DPPH), 2,2'-azinobis-(3-ethyl-benzothiazolin-6-sulfonic acid) diammonium salt (ABTS), and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) were purchased from Sigma-Aldrich (St. Louis, MS, USA). RPMI 1640 media, lipopolysaccharide (LPS), phosphate-buffered saline (PBS), and fetal bovine serum (FBS) were obtained from Gibco BRL Life Technologies (Thermo Fisher Scientific, NY, USA). Raw murine macrophage 264.7 (RAW 264.7) cells were purchased from the Cell Resources Center of the Chinese Academy of Sciences (Shanghai, China). OptEIA ELISA kits for tumor necrosis factor-α (TNF-α), MCP-1 and interleukin-6 (IL-6) were purchased from BD Biosciences (San Diego, CA, USA). A PathScan Antibody Array Kit was purchased from Cell Signaling Technology (Shanghai, China). All other chemicals and solvents used were analytical grade, unless otherwise specified.
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5

Extraction and Analysis of Himalayan Plant Polysaccharides

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Roots of Mirabilis himalaica (Edgew) heim were purchased from Qinghai Tibetan hospital in Qinghai (batch number: 20161023; Xining, Qinghai province, China). Dextran standards (5800, 11 800, 47 300, 100 000, 380 000, and 788 000 Da) were acquired from Pharmacia Biotech (Uppsala, Sweden). Standard monosaccharides (glucose, d-glucosamine hydrochloride, mannose, rhamnose, ribose, galactose, fucose, N-acetyl-d-glucosamine, d-galactosamine hydrochloride, xylose, fructose, arabinose, guluronic acid, mannuronic acid, galacturonic acid, glucuronic acid) were purchased from Sigma chemical. Dialysis membranes (size 36, MWCO = 8–14 kDa) were purchased from Wako. Acetic acid, acetic anhydride, sodium borohydride, chloroform, NaOH powder, DMSO, iodomethane, formic acid, methanol, trifluoroacetic acid were all analytical reagents.
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6

Characterization of Helvella leucopus

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The mature fruiting body samples were purchased in Bachu county, Xinjiang province, China and were identified by Guangdong Institute of Microbiology to be Helvella leucopus. Petroleum ether, anhydrous ethanol, and trichloromethane were procured from Sinopharm Chemical Reagent (Chemical Reagent Co., ltd., Beijing, China). The standards fucose, rhamnose, arabinose, galactose, glucose, xylose, mannose, fructose, and ribose were acquired from Sigma-Aldrich (St. Louis, MO, USA). In addition, RNA-easy Isolation Reagent, HiScript III-RT SuperMix, and ChamQ Universal SYBR qPCR Master Mix (Vazyme Biotech Co. ltd. Nanjing, Jiangsu, China) were used in this study.
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7

Analytical Reference Compounds for Chromatography

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Analytical and chromatographic grade reference compounds were used for this study: Xylose, arabinose, glucose, galactose, xylitol, mannitol, sorbitol, inositol, ribose, fructose, mannose, adonitol, sucrose, maltose, lactose, and maltitol were purchased from Sigma-Aldrich GmbH (Steinheim, Germany). HPLC grade acetonitrile was obtained from Sigma-Aldrich GmbH (Steinheim, Germany), and purified deionized water (18.2 mW/cm) was produced using the Millipore (Millipore, Bedford, MA, USA) water purification system.
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8

Constructing C-G-R Libraries for Screening

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C-G-R libraries were constructed by digesting pTorPE_C-G-R with SphI and XmaI. We amplified cpGFP with the appropriate linker library primers for each pool. PCR products were purified, digested with SphI and XmaI, and ligated into pTorPE_C-G-R that had been digested with the same enzymes. Bacteria were transformed with the contents of the ligation reaction and 5 plates were plated per library, resulting in ~30,000 individual clones per library. All three libraries were scraped, mixed together, and grown overnight at 37°C with 0.001% w/v Arabinose (Sigma) to induce expression. Cells were sorted for GFP expression on a FACS Aria flow cytometer. Eight bright fluorescent outliers were sorted into LB containing ampicillin and grown overnight at 37°C before undergoing DNA extraction.
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9

Salmonella Typhimurium Invasion Assay

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S. Typhimurium strains were grown under T3SS1-inducing conditions as previously described (14 (link)) (3.5-h subcultures in LB-Miller broth, with shaking at 220 rpm), and the invasion efficiency of bacterial strains was determined in gentamicin protection assays, following an established protocol (32 (link)). Invasion efficiency (the percentage of the inoculum internalized) for each strain is expressed as a percentage of the invasion efficiency for wild-type bacteria (set to 100%). For gene induction in broth, S. Typhimurium subcultures were treated with (i) 0.2% (wt/vol) arabinose (Sigma) for 1 h (2.5 h to 3.5 h of subculture growth) or (ii) 100 ng/ml ATc (Acros Organics) for 1.5 h (2 to 3.5 h of subculture growth) immediately prior to infection. HeLa cell infections were performed as previously described (32 (link)). For gene induction inside mammalian cells, (i) 1% (wt/vol) arabinose was added at t0 and maintained throughout infection, or (ii) 300 ng/ml ATc was added after the 10-min internalization step and maintained throughout infection.
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10

Antimicrobial and Antioxidant Evaluation

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Folin–Ciocalteu reagent (2 N), gallic acid, methanol, 2,2-Diphenyl-1-picrylhydrazyl (DPPH), sodium hydroxide (NaOH), glucose, and arabinose were purchased from Sigma-Aldrich (USA). Ethanol (98%), hydrogen peroxide (H2O2, 30%), sulphuric acid (H2SO4, 98%), and sodium carbonate (Na2CO3, 99.5%) were obtained from Panreac Quimica S.L.U (Castellar del Vallés, Barcelona, Spain). Phosphorous pentoxide (P2O5, 98.2%) was obtained from VWR Chemicals (Leuven, Belgium). D(+)-Xylose was supplied by Merck KGaA (Darmstadt, Germany). For microbiological analyses, tryptone soy broth (TSB), bacteriological agar, and peptone water were purchased from Scharlab (Barcelona, Spain). Strains of Escherichia coli (CECT 101) and Listeria innocua (CECT910) were obtained from the Spanish Type Collection (CECT, Universitat de València, València, Spain).
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