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7 protocols using ultrasonic water bath

1

Cryogenic Cheese Powder Extraction

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Approximately 20 g Turkish white cheese sample was blended with liquid nitrogen and ground cryogenically using a Waring Lextra 2 speed blender (East Windsor, NJ, USA) to produce a fine cheese powder.
Water-soluble extracts followed the procedure described by Subramanian et al. (18 (link)) and were prepared by mixing 0.1 g of the cheese powder with 0.5 mL of distilled water. The mixture was sonicated by an ultrasonic water bath (Fisher Scientific, Pittsburgh, PA) for 10 s to extract water-soluble components, and then 0.5 mL chloroform was added to remove the complex fats, vortexed for 30 s, and the mixture was centrifuged at 15,700 × g for 3 min at 25°C (Megafuge 8, Thermo Fisher Scientific, Waltham, MA, USA). Supernatants (200 μL) were mixed with 200 μL absolute ethanol to precipitate the complex proteins in the mixture and centrifuged at 15,700 × g for 3 min at 25°C. The supernatant was employed for further spectroscopic analysis.
Methanol and ethanol extracts were prepared by mixing 0.1 g of the cheese powder with either 1.0 mL of 100% methanol or 100% ethanol solutions. The mixtures were sonicated by using an ultrasonic water bath (Fisher Scientific, Pittsburgh, PA) for 10 s to break down the cheese clumps and improve the extraction of components and centrifuged at 15,700 × g for 3 min at 25°C. The supernatant was employed for further spectroscopic analysis.
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2

Adipogenic Differentiation and Secretion Assay

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Human ASCs were plated at 5 × 103/cm2 and differentiated in chemically defined medium for 28 days. Culture medium and lysed cell supernatant were individually collected on 14 and 28 days. Cells were lysed using 1% Triton-X solution (Sigma-Aldrich, St. Louis, MO). Cell culture lysate was collected by scrapping with a cell scraper (Fisher-Scientific) and briefly sonicated for 10 s using an ultrasonic water bath (Fisher-Scientific) on ice. Total secreted human adiponectin and leptin were measured using ELISA (R&D, Minneapolis, MN) per our prior methods2 (link)10 (link)11 (link)16 (link)17 (link). Absorbance was read using a microplate reader (Biorad, Hercules, CA). DNA content was measured using Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies) per our prior methods. A high-range standard curve of 1 μg/mL was used for measuring the DNA concentration of the samples per our prior methods. The samples were prepared in a 96 well black bottom plate (Fisher-Scientific) with absorbance read using microplate reader and standard fluorescein wavelengths (excitation ~480 nm, emission ~520 nm; Molecular Devices, Sunnyvale, CA). Total triglycerides and glycerol contents were measured by processing the sample lysate with Free Glycerol Determination kit (Sigma-Aldrich) per our prior methods2 (link)10 (link)11 (link)16 (link)17 (link).
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3

Sulfated Lactosyl Archaeol Lipid Formulation

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Sulfated lactosyl archaeol (SLA; 6′-sulfate-β-D-Galp-(1,4)-β-D-Glcp-(1,1)-archaeol) was synthesized, as described previously [20 ]. Cy5.5-OVA conjugate was purchased from Nanocs (New York, NY, USA), while CellVueTM NIR815 was purchased from Thermofisher Scientific (Waltham, MA, USA).
Thin-film hydration archaeosomes were prepared, as previously described [10 (link)]. In brief, SLA lipid that was dissolved in chloroform/methanol underwent solvent removal under N2 gas with mild heating to form a thin lipid film. Dried lipids were then hydrated in Milli-Q water for more than 12 h to form a uniform lipid suspension. Next, sonication was applied at 40 °C in an ultrasonic water bath (Fisher Scientific, Ottawa, ON, Canada) for up to an hour until the desired particle size (~100 nm) was obtained. After that, 10 × PBS (Millipore Sigma Canada, Oakville, Ontario) was added and archaeosomes stored at 2–8 °C until used. Note that we have previously demonstrated that archaeosomes stored under similar conditions were stable up to 6 months of testing, which was well beyond the storage time of ~1 month in the current study [21 (link)]. On the day of immunization, antigen solution (ovalbumin; OVA; type VI, Sigma-Aldrich, St. Louis, MO, USA) was added to the pre-formed archaeosomes to reach a desired final concentration.
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4

Quantification of Candida and Enterococcus

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Thermanox™ coverslips were first washed with PBS and sonicated in 1 mL of PBS at 35 kHz in an ultrasonic water-bath (Fisher Scientific, Paisley, UK) for 10 min to dislodge cells. DNA was extracted from sonicated samples using the QIAamp DNA mini kit, as per manufacturer’s instructions (Qiagen, Crawley, UK). PCR was carried out as previously prescribed [38 (link)], using the Step-One plus real time PCR machine and StepOne software V2.3 (Life Technologies, Paisley, UK). Briefly, C. albicans/E. faecalis DNA was added to a PCR mastermix containing Fast SYBR® Green (Thermo Fisher Scientific, Paisley, UK) and specific forward and reverse primers (Table 3) within irradiated RNase-free water. Serial dilutions of bacterial/fungal DNA extracted from 1 × 108 cells/mL were also included to create a standard curve for each species. The applied thermal cycles were as follow: 50 °C for 2 min, 95 °C for 2 min, 40 cycles of 95 °C for 3 s and 60 °C for 30 s. Finally, colony forming equivalents (CFE) was calculated in relation to each species standard curve.
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5

Comparative Evaluation of Bovine, Porcine, and Fish Gelatin

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Three different gelatin samples of bovine (Sigma-Aldrich, St. Louis, MO, USA), porcine (Sigma-Aldrich, St. Louis, MO, USA) and fish (Sigma-Aldrich, St. Louis, MO, USA) sources were used in this study (see Table 1). The bloom value for fish gelatin in Table 1 is not given by Sigma-Aldrich since Thies20 reported that cold-water fish gelatin typically does not gel at 10 °C, hence its bloom strength is not apparent. The samples at different concentrations were dissolved in distilled water using an ultrasonic water bath (Fisher Scientific, Germany) at 45 °C for 20 min until clear solution was acquired for each sample. A total of 81 standard gelatin solutions which consists of 27 samples for each bovine, porcine and fish gelatins of nine concentrations between 4% (w/v) to 20% (w/v) were prepared for this study.

General descriptions of gelatin samples used in this study.

GelatinCompany nameBatch noGelatin typeBloom value
bovineSigma-AldrichSLBN8199VB ~ 225
porcineSigma-AldrichSLBQ9498VA ~ 300
Cold water fishSigma-AldrichSLBQ3114VSolidNot stated
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6

Physicochemical Characterization of ENMs

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The hydrodynamic diameter (D H ) and zeta potential (ζ) of the comparator ENMs were determined by dynamic light scattering (DLS) analysis using a Zetasizer Nano ZS (Malvern, UK). The ENMs were sonicated in an ultrasonic water bath (Fisherbrand, 150 W, 50-60 Hz) for 30 min to form a stable aqueous suspension. To better characterize the physiochemical properties of the NPs in the biological milieu, the D H and ζ of the nanoparticles in the complete cell culture medium dispersant were also analyzed. In this case, the suspension was prepared by adding the NPs into the cell culture medium followed by incubation in an incubator for 30 min at 37 °C and 5% CO 2 . Subsequently, the NPs were collected by ultracentrifugation at 12 000 rpm for 10 min and allowed to resuspend in DI water for further analysis.
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7

Candida Persistence on Dry Surfaces

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To assess the persistence of Candida species on dry, non-porous substrates methods were adapted from Welsh et al (2017) with slight modifications [7] . To simulate microbial spillages within the nosocomial environment, various growth conditions were used: PBS, artificial saliva (AS) and 10% fetal calf serum (FCS; Sigma-Aldrich, Dorset, UK). Cells were grown and standardised as described above to 1x10 8 cells/mL in selected media. Standardised cell suspensions were added to Thermanox TM cover slips (Fisher Scientific, Loughborough, UK) and allowed to adhere for 90 minutes before removing media and washing to remove non-adherent cells. Following washing, biomass was subsequently removed from the cover slips via sonication in 1mL PBS in an ultrasonic water bath (Fisher Scientific, Loughborough, UK) at 35kHz for 10 minutes, defined as Day 0. In addition, cells were also maintained at ambient temperature for a period of 14 days after initial adherence. Following growth and sonication, biomass was serially diluted for viable cell quantification using the miles and misra colony counting technique.
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