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19 protocols using skim milk powder

1

Bacterial Growth in Milk with EEP and Ethanol

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Bacterial growth was tested in sterilized skim milk (Skim Milk Powder, Oxoid) and in cow’s milk, pasteurized at 63°C for 30 minutes. Total bacterial counts were determined in Plate Count Agar (Oxoid) at 30°C for 72 hours before and after milk pasteurization. An overnight culture of each microorganism (the Gram+ ones and P. fluorescens) was inoculated at 1% in each type of milk with 2% EEP (P2), 5% EEP (P5), 2% ethanol (E2), 5% ethanol (E5) and in milk alone (control). After 24 hours at 37°C (25°C for P. fluorescens), bacterial counts were determined on the following media (Oxoid): Listeria Selective Agar Base with Oxford Supplement for L. monocytogenes (Heo et al., 2014 (link)), Baird Parker Agar with Egg Yolk-Tellurite for coagulase-positive staphylococci (UNI, 2004 ), Mannitol Egg Yolk Polymixin Agar for B. cereus (FDA BAM, 2017), Pseudomonas Agar Base with CFC Supplement for P. fluorescens (Chiesa et al., 2014 ).
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2

Nrf2-Mediated Antioxidant Pathway Study

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All the chemicals used in the current study were of analytical grade. Primary antibodies (Nrf-2, HO-1, PSD95, Phosphorylated c-Jun N- Kinase, SYP, β-actin) Sodium dodecyl sulfate (SDS), Scopolamine (Santa Cruz, CA, USA), Tetra methylene diamine (Temed), Ammonium per sulfate (APS) (Daejung Chemicals and Metals Co. Ltd, Korea), Tissue protein extraction reagent (T-PER), Methanol (Sigma Aldrich, Burlington, MA, United States), Skim Milk Powder (Oxoid Ltd, Basingstoke, UK), RNA wait (Beijing Solar bio Science and Technology Co. Ltd), Enhanced Chemiluminescence (ECL) solution A (Luminol) and solution B (Peroxide solution) and secondary antibody (anti-mouse) (Bio-Rad, United States) were bought while folicitin was gifted by Dr. Umar Farooq.
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3

Protein Extraction and Western Blot Analysis

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Total protein was extracted with RIPA and PMSF buffer and quantified using a bicinchoninic acid (BCA) protein assay kit (Beyotime, China). A total of 40 μg of protein was subjected to 12% SDS-PAGE electrophoresis. After SDS-PAGE, proteins were transferred to a polyvinylidene difluoride (PVDF) membrane. The membrane was blocked with 5% skim milk powder (OXOID, UK) for 2 h and then incubated with primary antibody at 4°C overnight. After three washes with 1 × TBST, the membrane was incubated with secondary antibodies (HRP-conjugated 1 : 1000) at room temperature for 2 h. The intensity of the specific immunoreactive bands was detected by enhanced chemiluminescence (ECL) after washing with 1 × TBST three times again. Antibodies for Akt1 (ab32505; 1 : 500), phospho-Akt1 (pS473, ab81283; 1 : 500), p53 (ab32389; 1 : 500), Bax (ab32505; 1 : 1,000), Bcl-2 (ab32124; 1 : 250), procaspase-9 (ab32539; 1 : 500), cleaved-caspase-9 (ab133520; 1 : 500), caspase-3 (ab32351; 1 : 500), caspase-3 active (ab32042; 1 : 500), p21 (ab109520; 1 : 500), CDC2 (ab133327; 1 : 1000), phospho-CDC2 (Py15, ab133463, 1 : 1000), cyclin B1 (ab32053; 1 : 1000), and beta-tubulin (ab108342; 1 : 1000) were from Abcam.
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4

Antimicrobial Evaluation of Vancomycin, Auranofin, and Linezolid

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Auranofin, linezolid (Chem-Impex International, Wood Dale, IL, USA) and vancomycin hydrochloride (Gold Biotechnology, St. Louis, MO, USA) were purchased from commercial vendors. Skim milk powder was purchased from Oxoid (Basingstoke, Hants, UK). Brain heart infusion (BHI), tryptic soy broth (TSB), Tryptic soy agar (TSA) and enterococcosel agar were purchased from Becton, Dickinson and Company (Cockeysville, MD, USA) and phosphate-buffered saline (PBS) was purchased from Corning (Manassas, VA, USA). Egg yolk emulsion was purchased from HIMEDIA Laboratories (Thane, MH, India). Defibrinated horse blood was obtained from Hemostat Laboratories (Dixon, CA, USA). Clinical isolates of VRE (Table S1) were obtained from the Biodefense and Emerging Infections Research Resources Repository (BEI Resources) and the American Type Culture Collection (ATCC).
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5

Western Blot Analysis of Cellular Proteins

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After treatment, cells were collected and resuspended in PBS, and mixed with isometric RIPA buffer containing 1% protease inhibitor at 4 °C for 30 min. After centrifuge at 10000 g for 5 min, the supernatant was mixed with equal volume of 2 × loading buffer and heated to 95 °C for 5 min. Proteins were loaded on polyacrylamide gel and run at stock gel (5%) for 15 min (90 V) and at separated gel (8%) for 70 min (130 V). Proteins were resolved on an 8% SDS/PAGE gel and subsequently transferred to a PVDF membrane (Millipore). After blocked with TBS buffer containing 5% skim milk powder (Oxoid) for 30 min, the membrane was incubated in TBS buffer containing 5% milk and primary antibodies against P-gp (1:2500, abcam), PARP-1 (1:1000, abcam), PAR (1:2000, abcam), β-tubulin (1:5000, abcam) for 2 h, respectively, and washed with TBS buffer (5 min × 5). The membrane was further incubated in TBS buffer containing 5% milk and secondary antibodies (1:5000, goat anti-rabbit, Pierce) for 1 h, and washed with TBS buffer (5 min × 5). Bands were visualized by WesternBright ECL (Advansta) and pictures were taken by an imaging system (GE Healthcare Bio-sciences AB). Multi-exposure images were obtained. The expression level of β-tubulin was used as a standard to normalize the expression of other proteins.
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6

Western Blot Analysis of Signaling Proteins

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Isolated CECs were lysed with RIPA buffer (150 mM sodium chloride, 1% Triton X-100, 0.1% SDS, 50 mM Tris, pH 8.0) containing protease inhibitor cocktail (Sigma). The proteins were separated by 10%–15% SDS–PAGE and blotted onto a PVDF membrane (Bio-Rad). Membranes were blocked in TBS containing 0.1% Tween® 20 (Fisher BioReagents) and 5% skim milk powder (Oxoid) for 1 h at room temperature. Membranes were incubated with total β-catenin (H-102) (Santa Cruz Biotechnology), non-phospho (active) β-catenin (Ser33/37/Thr41), p-53 (Ser15) and EphB2 (D2X2I) obtained from Cell Signaling, or p-GSK-3α/β (Tyr279/216), p21 (F-5), and DKK-1 (B-7) from Santa Cruz Biotechnology. β-actin (Cell Signaling), GAPDH (Sigma), or β-tubulin (Thermo Fisher Scientific) was used as loading control. Typically, the primary antibodies were used at 1:1000 at 4°C overnight incubation. After washing three times with TBST, the membranes were incubated with goat anti-rabbit IgG-AP (Santa Cruz Biotechnology) or goat anti-mouse IgG-AP (Cell Signaling) at 1:20000 for 1 h at room temperature. Protein–antibody complexes were visualized using a chemiluminescent substrate Tropix® CDP-Star® (Applied Biosystems) and detected on CL-X Posure™ Film (Thermo Scientific). Each western blot was repeated at least three times, and the protein expression levels were determined by densitometry analysis and ImageJ.
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7

Enzymatic Activities and EPS Production

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Proteolytic and lipolytic activities were evaluated according to Meng et al. [1 (link)] using Plate Count Agar supplemented with 1% (w/v) skim milk powder (Oxoid, Milan, Italy) and Tributyrin Agar (Merck, France) media, respectively. Exopolysaccharides (EPS) production was tested on both MRS and mMRS, in which glucose was replaced by 10% of sucrose, following the method described by Meng and co-workers [1 (link)]. The NSLAB strains’ ability to produce diacetyl was evaluated according to Ribeiro et al. [23 (link)]. Diacetyl production was indicated by the formation of a red ring at the top of the tubes. Based on the presence and intensity of the red colour, the strains were scored as no (−), moderate (+), high (++), or strong (+++) diacetyl producers.
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8

Western Blot Protein Detection

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Samples were separated by SDS-PAGE (10% or 12% acrylamide gel) and transferred to a PVDF membrane (Immobilon-P, 0.45 μm, Millipore) at 300mA for 3h. The membranes were blocked in PBS/5% Milk (Skim milk powder, Oxoid) and incubated with a primary antibody for 1h diluted in PBS/0.1% Tween/5% Milk, washed thrice for 10min in PBS/0.1% Tween and incubated with the secondary antibody for 45min diluted in PBS/0.1% Tween/5% Milk and washed thrice again in PBS/0.1% Tween. The filter was incubated with ECL reagent (SuperSignal West Dura Extended Duration Substrate, Thermo Fisher Scientific) and the signal was detected using the Chemidoc XRS+ imager (Bio-Rad) or Amersham Imager 600.
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9

Impedance Profiling of Starter Bacteria

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Eighty strains representing four starter lactic acid bacteria species, Lactobacillus helveticus, Lactobacillus delbrueckii subsp. bulgaricus, Lactococcus lactis, and Streptococcus thermophilus (Table 1), were analyzed by impedance measurements. The strains, belonging to the collection of the Laboratory of Food Microbiology of the Department of Food Science of University of Parma, have been previously isolated from dairy matrixes and identified by16S rRNA sequencing.
Strains, maintained as frozen stocks cultures in MRS (Oxoid, Ltd., Basingstoke, United Kingdom) (Lactobacillus), or M17 (Oxoid Ltd.) (Lactococcus and Streptococcus) broth containing 20% (v/v) glycerol at −80°C, were recovered in MRS or M17 broth by two overnight sub-culturing (5% v/v) at 42°C for Lactobacillus and Streptococcus, and 30°C for Lc. lactis. Then, other 28 h sub-culturing (5% v/v) of each strain in skim milk powder (Oxoid Ltd.), reconstituted to 10% (w/v) and sterilized at 110°C for 30 min (SSM), were performed before use.
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10

Molecular Mechanisms of Oxidative Stress

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All chemicals used in our experiments were sterile and stored according to their respective protocols. Purchased chemicals were dextrose, chloroform, tween, ammonium persulfate, and tetramethylethylenediamine (Daejung Chemicals and Metals Co. Ltd, Gyeonggi-do, Shiheung, South Korea); RNA wait (Beijing Solarbio Science & Technology Co., Ltd., Beijing, China); phosphate-buffered saline, sodium dodecyl sulfate, scopolamine (Santa Cruz, CA, USA); enhanced chemiluminescence solution A and B (Bio-Rad Laboratories, Inc., Biotechnology Company Philadelphia, PA, USA); tissue protein extraction reagent and methanol (Thermo Scientific, Meridian Rd., Rockford, IL 61101 USA); Trizma base (Sigma Aldrich, Burlington, MA, USA); skim milk powder (Oxoid Ltd, Wade Road, Basingstoke, Hants, UK), Ranuncoside (provided by Umar Farooq). The primary antibodies were purchased from Santa Cruz, CA, USA, while the secondary antibody, i.e., anti-mouse IgG, was purchased from Promega, Madison, WI, USA (Table 1).

List of primary and secondary antibodies with catalog number.

S.#Antibodies NameCatalog #
1Anti-HO-1sc-136960
2Anti-Nrf-2sc-365949
3Anti- NF–ĸbsc- 8008
4Anti-COX-2sc-376661
5Anti-TNF-αsc- 52,746
6Anti-β actinsc-47778
7Goat anti-mouse (IgG-HRPs) secondary antibodiesW4028
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