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28 protocols using α d glucose

1

Yeast Nitrogen Starvation Assay

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Strains were grown in synthetic complete medium containing 0.7% (wt/vol) yeast nitrogen base (BD Difco) and 2% (wt/vol) α-d-glucose (Sigma) at 30°C. Cells were washed three to five times and starved in nitrogen starvation medium with 0.17% (wt/vol) yeast nitrogen base without amino acids and ammonium sulfate (BD Difco) and 2% (wt/vol) α-d-glucose buffered at pH 6.2 using 50 mM MES-KOH as described in Suzuki et al. (2011) (link), supplemented with the nucleobases adenine, guanine, cytosine, and thymidine at a final concentration of 0.4 mM each or NAC (Sigma) at a final concentration of 10 mM when indicated.
To analyze respiratory competence, cells were plated onto YPD plates containing 1% (wt/vol) yeast extract (Serva), 2% (wt/vol) bacto-peptone (Merck), and 2% (wt/vol) α-d-glucose, and colony color was assessed and quantified. Because all strains contained the ade2 mutation, on YPD, white and sectored colonies were classified as respiratory deficient and red colonies were classified as respiratory competent.
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2

Spectral Characterization of Saccharide Solutions

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d-(+)-Glucose (or d-glucose, anhydrous, ≥99% purity), d-(−)-fructose (or d-fructose, anhydrous, ≥99% purity), and d-(+)-sucrose (or d-sucrose, anhydrous, ≥99% purity) from the Lach-Ner Group, and α-d-(+)-glucose (or α-d-glucose, anhydrous, 96%) from Sigma-Aldrich were used in this study without further purification. Saccharide powders were dissolved and thoroughly mixed in an appropriate amount of distilled water in volumetric flasks to yield concentrations C of 0.25 mol dm−3 ≡ 0.25 M, 0.50 M, and 3.00 M.
Before measuring the spectral responses of d-glucose and d-fructose, their solutions were first left at rest for 24 hours to reach the state of their anomeric equilibrium at a given temperature. Solutions of d-sucrose, which is a non-reducing and therefore mutarotation inactive saccharide, were measured just after 4 hours, only to ensure perfect dissolution. Mutarotation ellipsometric experiments on α-d-glucose were performed right away with freshly prepared solution.
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3

Gardnerella Isolate Cultivation Protocol

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Gardnerella isolates of different species (52 (link)) were obtained from the Laboratory of Bacteriology, University of Ghent, Belgium. These isolates include strains purchased from culture collections and fresh isolates from BV patients obtained from the University Clinic Bruges. Gardnerella isolates were grown on chocolate (Choc) agar plates (Becton, Dickinson) under anaerobic conditions in an anaerobic chamber equipped with anaerobic atmosphere generation bags (Sigma-Aldrich) for 48 h. All isolates were cultured in New York City broth III (NYCB), consisting of 10 mM HEPES (Sigma-Aldrich), 15 g/L proteose peptone (Sigma-Aldrich), 3.8 g/L yeast extract (Thermo Fisher Scientific), 86 mM sodium chloride (Carl Roth), and 28 mM α-d-glucose (Sigma-Aldrich), supplemented with 10% horse serum (HS) (Thermo Fisher Scientific). Table S1 lists all Gardnerella and Lactobacillus isolates studied.
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4

Spectrophotometric Quantification of Olive Leaf Compounds

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TPC was determined spectrophotometrically at 760 nm with the Folin–Ciocalteu reagent (Sigma Aldrich), using gallic acid as standard (Sigma Aldrich) [14 (link)]. The phenolic content is expressed as gallic acid equivalents (GAE). Dissolved sugars were also determined spectrophotometrically with a reagent containing l-tryptophan and boric acid (both from Sigma Aldrich) dissolved in concentrated sulfuric acid (Sigma Aldrich) [15 (link)]. This method can quantify sugars that can act as reducing agents and since most monosaccharides and oligosaccharides can be mild reductants, it was chosen as a suitable method for this analysis. The calibration standard for this method was α-d-glucose (Sigma Aldrich) and detection was performed at 525 nm. Both spectrophotometric methods gave concentrations of extracted compounds expressed as grams per liter of solvent (g/L). The data presented in this work are expressed as grams of extracted compounds per kilograms of olive leaf powder (g/kg) simply by dividing their concentration in the liquid phase by the solid–liquid ratio. This gives us an overestimate of the extracted material because there is a considerable amount of retention in the solid phase (approximately 30%) but is presented in this way to express the whole amount of extractable material. Error bars correspond to the standard deviation of measurements carried out in triplicate.
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5

Electrochemical Sensor Development Protocol

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Polyvinyl chloride (PVC, selectophore, high molecular weight), agarose (low EEO), potassium tetrakis(4-chlorophenyl)borate (selectophore, ≥ 98%), sodium ionophore X (selectophore, function tested), α-d-glucose (anhydrous, 96%), pyruvic acid (98%), and AuNPs(20 nm diameter, stabilized suspension in citrate buffer) were supplied by Sigma-Aldrich Co., LLC (Japan). Phosphate-buffered saline (PBS(-), pH 7.1), 0.05 M Tris–HCl buffer solution (pH 7.6), tetrahydrofuran (THF, 99.5%, with stabilizer), potassium chloride (KCl, 99.5%), sodium chloride (NaCl, 99.5%) and ammonium chloride (NH4Cl, 99.5%), bis(2-Ethylhexyl) sebacate (DOS), magnesium chloride (MnCl2, 97%), urea (99%), and UA (98%) were purchased from FUJIFILM Waco Pure Chemical Corporation (Japan). Carbon grease (CG, particle size < 40 nm) was provided by KITACO Co., Ltd (Japan). Ag/AgCl ink for reference electrode was obtained from ALS Co., Ltd. PC plates were supplied by HAKUDO Corporation. CPE (MS-550) was purchased from Ecologa Japan Co., Ltd.
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6

Potassium chloride and glucose protocol

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Potassium chloride, α-(d)-glucose and l-glutamine were purchased from Sigma-Aldrich; osmolyte solutions were prepared using deionised water and were stored overnight at 4 °C before use. The solution pH was measured by means of a pH meter (Eutech Instruments, WP 600 series meter, model PC 650) in order to detect potential variations with respect to the neutral value due to the presence of glutamine (because of its ionisation in water, as amino acid).
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7

Lipid Preparation for Cellular Studies

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LPC 18:1 (Avanti Polar Lipids) in chloroform was aliquoted under argon, evaporated under nitrogen until dry and stored at −20°C under argon until use. LPC aliquots were dissolved in PBS to yield a stock solution (3 mM) and used fresh for every experiment. NaCl, KCl and CaCl2 were from Roth, KH2PO4 and NaHCO3 from Merck (Darmstadt, Germany), MgSO4 was from Fluka and α-D-Glucose was from Sigma-Aldrich.
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8

Cultivation of Gardnerella species

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G. vaginalis ATCC 14018T, G. leopoldii UGent 06.41T, G. piotii UGent 18.01T and G. swidsinskii GS 10234T were grown on chocolate (Choc) agar plates (Becton Dickinson, Franklin Lakes, NJ, USA) at 37 °C under anaerobic conditions (10% CO2, 10% H2, 80%N2, Concept 400, Anaerobic Workstation). Liquid cultures were prepared in New York City Broth III (10 mM HEPES (Sigma Aldrich, Burlington, MA, USA), 15 g/L Proteose Peptone No. 3 (Becton Dickinson), 3.8 g/L yeast extract (Thermo Fisher Scientific, Waltham, MA, USA), 86 mM sodium chloride (Carl Roth, Karlsruhe, Germany), 28 mM α-D-glucose (Sigma–Aldrich)), at pH 5 (NYB5), supplemented with 10% horse serum (HS, Thermo Fisher Scientific) (NYB5 + HS).
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9

Trehalose Synthesis Protocol

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α-d-Glucose, α,α′-trehalose, allyl bromide, Amberlite IR-120H resin, hydrochloric acid, ethanol, methanol, vinyl acetate, D2O, CD3OD and CDCl3 were purchased from Sigma Aldrich. Potassium hydroxide was purchased from Carlo Erba. Azobisisobutyronitrile (AIBN) was purchased from Fluka. Acetone was purchased from VWR International. All the chemicals were reagent grade and were used without further purification.
Amberlite IR-120H resin (250 mg) was activated by washing with methanol (3 × 10 min, 1.25 ml each time) and standing overnight in methanol (1.25 ml).
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10

Glucose Utilization Profiling of Campylobacter spp.

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Campylobacter jejuni strain 81116 (NCTC11828), C. coli NCTC 11366 and three C. hepaticus isolates, C. hepticus HV10, C. hepaticus 19L and C. hepaticus 44L were used in glucose utilization studies. After cultures were grown in HBA for 3 days, cells were collected and resuspended in physiological saline (0.9% NaCl) to an OD600 of 1.0. The medium used to test the ability of C. hepaticus to utilize glucose consisted of inorganic salts (IS) as described previously (Alazzam et al., 2011 (link)). L-cysteine (0.2 mM) was used as a nitrogen source, and α-D-glucose (10 mM) (Sigma) was used as the sole carbon source. The experiment was carried out in 24-well plates. Each well-contained 100 μl of culture (OD600 = 1). Controls included culture in IS plus L-cysteine only and IS plus α-D-glucose only. 2,3,5 tetrazolium chloride (TTC) (Sigma) (0.0665 g/L) was used as an indicator in all wells (Menolasino, 1959 (link)). A color change is observed in growing cultures, indicating utilization. The color change results were read after 36 h of incubation at 37°C. C. hepaticus, C. jejuni, and C. coli were also grown in Brucella broth to confirm their viability. The experiment was repeated twice, each time in biological triplicate.
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