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20 protocols using phosphate buffered saline (pbs)

1

Rucola Seedlings Inoculation with Rhodococcus Strains

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Rucola (Eruca sativa L.) seeds were washed in Tween 80 1% (Sigma, United States) for 2 min, surface sterilized with sodium hypochlorite 12% (NaOCl, Roth, Germany) for 8 min and washed three times in sterile deionized water for 2 min. Sterilized seeds were placed on Hoagland’s solution (Sigma, United States) with 0.8% agar to germinate 4 days. Rhodococcus strains were pre-grown in TSB. Overnight grown cultures were washed two times in 1x PBS (AppliChem, Germany) and diluted to a concentration of 107 CFUs. Seedlings were inoculated in the prepared bacterial solution of RL1, BG43, and djl6 for 1 h under shaking at 160 rpm at 28°C. Seedlings inoculated in 1x PBS served as negative control. Inoculated seedlings were transferred to an axenic system with 80 ml sterile quartz sand and 20 ml Hoagland’s solution in a sterile Phytatray II (Sigma, United States). Seedlings inoculated with RL1 were additionally transferred on plates with 0.5x Murashige and Skoog Medium (0.5x MS) including vitamins (Duchefa Biochemie, Netherlands); pH was adjusted to 5.7 with 2N KOH. No additional sucrose was added to 0.5x MS. The axenic system was placed in a Phytochamber (Weiss Technik, Modell SGC120PG2, Germany) with 23°C, 55% humidity, day-night-cycle 12 h : 12 h. After seven and 14 days freshly harvested roots were washed in 1x PBS, fixed in 55% EtOH and 1x PBS mix and stored at –20°C until further use.
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2

MTT Assay for Cell Viability Assessment

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Cell viability was assessed using a 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltertazolium Bromide (MTT) (Invitrogen, Carlsbad, CA, USA) assay, and 15,000 cells were seeded into 96-well plates (NUNC, Langenselbold, Germany). After 24 h, cells were treated with increasing doses of AP (5–50 µM) for 24 h. To assess cell viability, 50 μL of MTT lysis solution with a final concentration of 0.5 mg/mL in 1X PBS (AppliChem, Darmstadt, Germany) was first added to each well followed by 30 min incubation at 37 °C. The MTT solution was discarded and 50 μL of DMSO (Sigma-Aldrich, Taufkirchen, Germany) was added to each well. For the readout, a multi-scanner micro-plate reader (VersaMax Microplate Reader, Molecular Diagnostics, CA, USA) was used to measure the absorbance at 570 nm with a background absorbance of 670 nm.
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3

Preparation of Antibiotic Broth Medium

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Antibiotic broth medium No. 3 (complex medium) was purchased from Oxoid LTD (Hampshire, Great Britain). Pyruvic acid, sucrose, KH2PO4, KOH, and (NH4)2SO4 were purchased from Roth (Karlsruhe, Germany). D-glucose, MgSO4·7 H2O, and FeSO4·7 H2O were obtained from Merck (Darmstadt, Germany). Trehalose and NaCl were purchased from Fluka (Buchs, Schwitzerland). Ectoine (≥99%) for lactate deydrogenase stress experiments was purchased from bitop AG (Witten, Germany). HydroxyEctoine (≥99%) for lactate dehydrogenase (LDH) stress experiments was isolated from H. elongata strain DSM 2581T in our laboratories. Freeze-dried LDH (rabbit muscle) and nicotinamide adenine dinucleotide were purchased from Sigma (Steinheim, Germany). Phosphate buffered saline (PBS) was purchased from AppliChem (Darmstadt, Germany). Ectoine (≥99.0%) and hydroxyEctoine (≥98%) for spin lable and Fourier transform infrared (FTIR) experiments were purchased from Sigma (USA). Perdeuterated spin probe Tempone-d16 (4-Oxo-2,2,6,6-tetramethylpiperidine-d16-1-oxyl; Figure 7 inset) was a kind gift of Prof. I. Grigoriev (Institute of Organic Chemistry of the Russian Academy of Sciences, Novosibirsk, Russia).
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4

Comprehensive Reagent Acquisition for Molecular Assays

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Tris HCl, GuSCN, MgCl2, HCl, NaOH, CH3COOH, NaHCO3, NaOAc, 2-mercaptoethanol, octanoic acid, isopropanol, and ethanol were acquired from Sigma-Aldrich (St. Louis, MO, USA). NaCl, phosphate-buffered saline (PBS), and Dextran blue 2000 kDa (DEXB) were obtained from Applichem (Darmstadt, Germany), and Merck KGaA (Darmstadt, Germany), respectively. Na2EDTA was obtained from Fluka (Geneva, Switzerland), and PEG20000 was obtained from Loba Chemie (Mumbai, India). EDTA spray-coated vacutainers were obtained from Fisher Scientific (Waltham, MA, USA). Glycogen, the RiboLockRNAse inhibitor, the MMLV reaction buffer, and MMLV reverse transcriptase were acquired from Fermentas (Vilnius, Lithuania). Primers and probes for reverse transcription and TaqMan qPCR (Table 1) and dNTPs were synthesized at the organic synthesis Laboratory of ICBFM SB RAS (Novosibirsk, Russia), and the 10× PCR buffer and Taq DNA polymerase were obtained from BiolabMix (Novosibirsk, Russia). Cel-miR-39-3p was synthesized in the Laboratory of Medicinal Chemistry (ICBFM SB RAS, Novosibirsk, Russia).
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5

Cytotoxicity of Zearalenone Analogs

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The reagents used were Eagle’s Minimum Essential Medium (EMEN) (Quality Biological, Gaithersburg, MD, USA); Fetal Bovine Serum (FBS) (Biowest, South America Origin); Keratinocyte Medium (KM) (ScienCell Research Laboratories, Carlsbad, CA, USA); dimethyl sulfoxide (DMSO), hydrogen peroxide 30% v/v, and phosphate-buffered saline (PBS) were supplied by Panreac (Applichem, Barcelona, Spain); α-ZEL and β-ZEL (MW: 320.38 g/mol) standards, penicillin, streptomycin, Trypsin–EDTA, and 2.7-dichlorofluorescein diacetate (DCFH-DA) were purchased from Sigma-Aldrich (St. Louis, MO, USA).
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6

Cytotoxicity Assay of Test Compounds

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The intrinsic cytotoxicity of test compounds was determined by a MTT assay as previously described [42 (link),49 (link)]. AsPC1, MDA-MB-231, FaDu, HT-29, and U87-MG cells were seeded at a density of 5000 cells/well, and MV3 and PC-3 cells were seeded at a density of 3000 cells/well in 96-well plates (Starlab GmbH, Hamburg, Germany or Greiner Bio-One, Frickenhausen, Germany); all were allowed to attach overnight. Subsequently, cells were exposed to increasing concentrations of the test compounds. After 72 h, MTT solution (5 mg/mL 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, in phosphate-buffered saline, Applichem, Darmstadt, Germany or Sigma Aldrich, Steinheim, Germany) was added to determine cell survival. The formazan dye was dissolved in DMSO after 1 h and absorbance was measured at 570 nm and 690, respectively, nm in a Multiskan microplate photometer (Thermo Fisher Scientific, Waltham, MA, USA) and a Cytation 5 Imaging Reader (BioTEK, Santa Clara, CA, USA). Concentration effect curves were generated using nonlinear regression with GraphPad Prism and mean IC50 values were calculated based on at least three independent experiments in duplicates.
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7

Mouse Liver Decellularization Protocol

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Mice were anesthetized by intaperitoneal injection of diazepam and hypnorm (1:1, 200 μl). Hepatic portal vein was cannulated and liver perfusion was carried out at 37 °C and at the speed of 5 ml/min. Mouse liver was perfused sequentially with heparinized phosphate buffered saline (PBS) (12.5 U heparin/ml, AppliChem, Darmstadt, Germany) for 10 min, 1% SDS and 1% Triton X-100 for 2 h each followed by perfusion with water for 30 min and PBS for 2 h. To evaluate the decellularization efficiency fresh mouse liver and decellularized liver samples were minced. DNA content was quantified after proteinase K digestion using a NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE). All decellularized liver samples contained less than 200 ng/mg DNA.
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8

Expression and Purification of Truncated Tau Protein

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Human truncated tau151-391 (numbering according to the longest human tau isoform Tau40) was expressed in Escherichia coli strain BL21(DE3) (Sigma-Aldrich, St. Louise, Missouri, United States) from a pET-17 expression vector and purified from bacterial lysates as described previously [39 (link)], except that the phosphocellulose step was omitted and size-exclusion chromatography was performed in PBS (137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4, pH 7.4) (AppliChem GmbH, Darmstadt, Germany). Purified tau protein was stored in PBS in working aliquots at −70°C. The purity of tau protein was subsequently verified by gradient SDS gel electrophoresis (5 to 20% gel), Coomassie blue staining and Western blot analysis with DC25 antibody (AXON Neuroscience SE (Bratislava, Slovakia), recognizes residues 347–354 of the longest human tau isoform Tau40). The fluorescently tagged tau protein was prepared by labelling with Alexa Fluor 546 (Invitrogen, Carlsbad, California, United States) according to the manufacturer’s recommendations.
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9

PLGA Nanoparticles for Rifampicin Delivery

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PLGA (Resomer RG 502 H; molecular weight [MW] = 7.000–17.000) was purchased from Evonik Industries AG (Essen, Germany), and polyvinyl alcohol (PVA; Mowiol® 18–88; MW ~130.000), ethyl acetate (American Chemical Society grade), Brij® 30, sodium chloride (NaCl), and rifampicin were purchased from Sigma Aldrich (St Louis, MO, USA). Dimethyl sulfoxide (DMSO) was purchased from Merck KGaA (Darmstadt, Germany). MTT was purchased from AppliChem (Darmstadt, Germany), and PBS, Dulbecco’s Modified Eagle’s Medium (DMEM) high glucose (with 10% fetal bovine serum, 4,5 mmol L-glutamine, 30 mmol [4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid], and 5% penicillin–streptomycin), and Roswell Park Memorial Institute (RPMI) without phenol red media were purchased from Gibco (Darmstadt, Germany). Schaedler Broth was purchased from BD (Franklin Lakes, NJ, USA). The light-weight PP monofilament mesh implant was provided by aimecs® GmbH (Pfarrkirchen, Germany).
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10

Quantifying Lipid Accumulation in DENV-Infected Cells

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ORO staining was undertaken essentially as previously described [70 (link)]. BHK-21 or Huh-7 cells were seeded at a density that allowed 80–90% confluence to be reached within 24 h, after which cells were mock infected or infected with DENV 2 for 2 h before being cultured for 24 h under standard conditions in complete media containing 10 or 25 µM of BBR or an equivalent volume of DMEM or milli-Q water. After incubation, cells were fixed with 10% formalin in PBS (Applichem, Munich, Germany) for 1 h. After fixing, cells were washed with 60% isopropanol prior to staining with filtered Oil Red O (Sigma-Aldrich, St. Louis, MO, USA) for 10 min, followed by washing with distilled water twice. ORO was eluted with 100% isopropanol and supernatant was transferred to a new tube and the absorbance was and measured at 490 nm (EZ Read 2000, Biochrom Ltd., Cambridge, UK).
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