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23 protocols using sterile 96 well plate

1

Preparation of Sterile Adhesive Specimens

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The cover of a sterile 96-well plate (Corning/Costar, New York, NY, USA) was used for specimen preparation [42 (link)]. A total volume of 30 μL of the adhesives was added to the round indentions on the cover with a micropipette (Eppendorf, Hamburg, Germany). All visible air bubbles were carefully removed using a hypodermic needle (Weigao Group Medical Polymer Co., Ltd., Weihai, China). The adhesive was photopolymerized for 10 seconds (s) by a light-emitting diode (LED) curing light (Elipar S10; 3M ESPE) with a polyester strip covering to obtain a specimen disk of 8 mm in diameter and 0.5 mm thick. The power density of the light was maintained at 1200 mW/cm2. All specimens were immersed in distilled water at 37 °C and agitated constantly with a magnetic stirrer (CJJ 78-1; Shuai Deng Instrument Co., Ltd., Shanghai, China) for 1 hour (h) to remove unpolymerized monomers [43 (link)]. The obtained disks were dried at room temperature and then were sterilized using ultraviolet light for 1 h [34 (link)].
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2

Determining Garlic and Ginger Oil's Sub-Inhibitory Concentration

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The sub-inhibitory concentration (SIC) of garlic and ginger oil was determined according to a previously published protocol [10 (link)]. Two-fold dilutions of garlic and ginger oil (0, 2.5, 1.25, 0.625, 0.312, 0.156, 0.078, 0.039%) were prepared in a sterile 96-well plate (Costar, Corning, NY, USA) containing 100 μL of TSB broth. Ethanol was also included at the concentrations found in the corresponding garlic and ginger samples. Wells were subsequently inoculated with 100 μL of S. infantis, S. typhimurium, or S. enteritidis (~106 CFU/mL). Plates were placed in a Cytation 5 multimode microplate reader (Agilent, Santa Clara, CA, USA) and incubated at 37 °C for 24 h with OD600 readings taken every 30 min. Following incubation, samples were diluted, plated onto XLD plates, and incubated for 24 h at 37 °C for Salmonella enumeration. All concentrations were run in duplicate, and experiments were repeated three times for each Salmonella strain. The highest concentration of phytochemicals that did not inhibit Salmonella growth was selected as the SIC and used in subsequent experiments.
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3

Neutralizing Antibody Assay for EBOV and SUDV

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Dilutions of the antibody of interest were made in a sterile 96 well plate (Costar/Corning Incorporated, Corning, NY) in Eagle Minimum Essential Media (EMEM) (Sigma Aldrich, St. Louis, MO) supplemented with 5% FBS. In sterile 6 well plate (Costar/Corning Incorporated, Corning, NY), 125 μL of authentic EBOV or SUDV diluted to 1200 pfu/mL were added to each well and the plates were incubated at 37 °C for 1 hour. Virus was added to a well containing media alone (no antibody) as a control for 100% infection. Vero-E6 cells were exposed to 100 μL of the virus/antibody mixture and incubated at 37 °C for an additional hour. During this time, the plates were gently rocked every 15 minutes to ensure homogeneity and prevent drying. After 1 hour of incubation, 2 mLs of primary overlay (EMEM with 10% FBS and 1% Gentamicin (Sigma Aldrich, St. Louis, MO) with 1% SeaKem ME agarose (Lonza, Cohasset, MN)) was added to each well and the plates were incubated at 37 °C for 6 days. On Day 7 post-exposure to virus, neutral red solution (EMEM with 10% FBS and 1% Gentamicin with 5% neutral red (Gibco/Invitrogen, Grand Island, NY)) was added to all cell-containing wells and cells were incubated at 37 °C overnight. Infection was scored by counting the number of plaques per well, using the number of plaques on the control well (no antibody) as 100% infection.
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4

Enzyme-Linked Immunosorbent Assay for CRP Detection

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The general procedures for ELISA were as follows: All ELISA analysis was carried out on a sterile, 96-well plate (Costar). 50 μl of each sample was added to each well. Plates were blocked with 3% bovine serum albumin (BSA) and washed with phosphate buffered saline (PBS)-Tween (Sigma). The primary antibody used was a monoclonal anti-C-reactive protein antibody (CRP-8, Sigma) produced in a mouse; the secondary antibody was an anti-mouse IgG (whole molecule)–peroxidase antibody produced in rabbit (Sigma). Both were used at 1:40,000 dilution. Positive and negative controls were included in analysis and all samples were tested in triplicate. The developing substrate used was 3, 3′, 5, 5′, tetramethylbenzidine (TMB) liquid substrate (Sigma). ELISA plates were left to develop for 10 min prior to addition of 2 M sulfuric acid. Plates were read at 450 nm on a BioTek EL800 plate reader using Gen5 software.
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5

Minimum Inhibitory Concentration Assay for Antimicrobial Compounds

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The minimum inhibitory concentration of the compounds against all strains using stand REMA assay protocols [14 (link)]. Briefly, 100 μL of relevant growth media was added to all wells of a sterile 96-well plate (Corning Incorporated, Corning, NY, USA). The wells in rows A to H in columns 1 received 94.88 μL of growth medium (7H9 media was supplemented with 0.2% casamino acids, 24 μg/mL pantothenate and 10% OADC, Beckton Dickinson, Sparks, MD, USA). Compounds were added to rows A1-H1 (quadruplet per compound) followed by 1:2 serial dilutions across the plate to column 11 were 100 μL of excess medium was discarded from the wells in column 11. The bacterial cultures at 0.5 McFarland standard diluted 1:25 was added to the wells in rows A to H in columns 1 to 11 (100 μL), where the wells in column 12 served as drug-free controls (positive and negative). The plates were sealed with parafilmTM and incubated at 37 °C, unless 30 °C was stated as the optimum for the organism. Freshly prepared filter sterilised resazurin (0.2% w/v, Sigma Aldrich, Dorset, UK) was filter sterilised and 10 μL added to all wells and re-incubated at 37 °C or 30 °C for 24 h or until the positive and negative controls showed a clear result.
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6

Bacterial Growth Rate Determination

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Three biological replicates from TB28 and JM136 were grown from single colonies in M9+Glucose (M9) [1× M9 salts (Sigma-Aldrich M9956), 1× Amino Acids (Sigma-Aldrich M5550), 0.4% glucose, 1× Vitamins (Sigma-Aldrich M6895), 2 mM MgSO4, 100 µM CaCl2] as overnights at 30 °C. The following day, the overnights’ OD600 were measured with a nanodrop and diluted to an OD600 of 0.1 in 200 μl M9 using a Corning Costar sterile 96-well plate. The 96-well plate was incubated in a Tecan Infinite M200 Pro set at 30 °C, where it would measure the OD600 of designated wells once every 30 min for 23.5 h, shaking the plate for 3 min at 220 rpm before measuring. To obtain the growth rate, the linear phase of the log-transformed growth curve data was fitted to a straight line. The slope of that line was used to calculate the doubling time through the equation below. Doublingtime=log10(2)slope
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7

Bacterial Growth on Sialic Acid and Mucins

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Overnight bacterial cultures grown (shaking) in LB broth at 37 °C were pelleted by centrifugation, washed three times with M9 media, and resuspended in M9 media. Resuspended cultures were then diluted 1:100 in 200 μL M9 media supplemented with 0.2% N-acetylneuraminic acid (sialic acid, Carbosynth) or purified porcine stomach mucins (Sigma) into a sterile 96-well plate (Corning) and incubated at 37 °C with shaking for 24 h. The optical density at 600 nm (OD600) was taken every 20 min using a Varioskan LUX microplate reader (Thermo Fisher). Each experiment was performed with at least three biological replicates. The results were confirmed by measuring bacterial densities in CFU per ml of culture in parallel experiments run in test tubes.
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8

Microbial Susceptibility Testing Protocol

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For the MIC determination, the standard CLSI broth microdilution method (Clinical and Laboratory Standards Institute, 2015 ) was used with modifications. Two–fold serially–diluted AMRP in TSB was prepared and 50 µl aliquots of these preparations were dispensed into the wells of a sterile 96–well plate (Corning, Tewksbury, MA, United States). Overnight cultures of the test organisms (Table 3) were used and their 10−3 dilutions in TSB were prepared. Aliquots (50 µl) of diluted cultures were added to the wells of the sterile 96–well plate. The MIC was determined as the lowest concentration of the AMRP which inhibited the visible growth of bacterial or fungal culture after incubation at 37°C for 24 h (for bacteria) or at 22–25°C for 3–6 days (for fungi).
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9

Evaluating Vau-1, Vau-2, and Arbutin on BM-derived Neutrophils

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BM-derived neutrophils were resuspended at the concentration 2.4 × 106/mL in 10% FCS/RPMI medium, and seeded in a volume of 100 µl on a sterile 96 well-plate (Corning, Wiesbaden, Germany). Cells were cultured in the presence of the methanolic extract Vau-1 or Vau-2 or arbutin at concentration 50 µg/mL, all dissolved in DMSO. The pure compound arbutin was isolated previously from the methanolic extract of V. turrilliana [18 (link)] (Figure 2A, chemical structure). In some experiments, the cells were cultured in the presence of increasing concentrations of Vau-1/Vau-2, ranging from (0.025 to 1000 μg/mL) or of arbutin at concentrations ranging from 0.025 to 490 μg/mL (0.09–1800 μM). After 36 h the cells were fixed, stained with Janus Green dye (Abcam, Cambridge, UK) and washed 3 times with dH2O. The dye was eluted by washing with elution buffer (Abcam, Cambridge, UK). The OD 630 nm was measured in samples in triplicate. Janus Green is a basic vital stain that determines cell density and specifically stains the mitochondria in living cells. The vitality was calculated as a percentage of control and according to the formula below:
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10

Quantifying Yeast Biofilm Formation

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The crystal violet assay was used to evaluate the ability of S. cerevisiae to form biofilm [29 (link), 30 (link)]. Briefly, yeast cells were harvested and resuspended in YPD medium with an OD600 = 1.0 after 20 h of cultivation at 30 °C. A volume of 20 μL of yeast cells and 180 μL of YPD medium were placed into a sterile 96-well plate (Corning, NY, USA), which was cultured for 72 h at 30 ℃, each strain was performed in quadruplicate and the mean value (± SD) was calculated. Following incubation, removed the medium from biofilm-containing wells and gently washed the wells twice with 200 μL of phosphate-buffered saline (PBS) to remove free cells. The biofilms were then stained for 10 min with 200 μL of crystal violet solution (0.1%) at room temperature, repeatedly washed with PBS and allowed to air dry. Finally, 200 μL of acetic acid (33%) was added to every well and incubated at 150 rpm for 30 min at room temperature. The absorbance of 570 nm was measured by a microplate reader (Thermo Scientific™ Multiskan™ FC).
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