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12 protocols using xl 90

1

Isolation and Characterization of MSC-Derived Exosomes

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Human MSCs were obtained from ATCC (PCS-500–012). Authentication and validation were performed to confirm the identity of the cells by flow cytometry characterization of common MSC surface markers75 . Exosomes were collected as previously described12 (link). In brief, MSCs were cultured until 80% confluence and washed by serum-free medium three times. Then, the cells were incubated with serum-free medium for another three days to allow exosome secretion. The conditioned media were then collected and filtered through 0.22 μm to remove residual cells and debris. We then performed ultracentrifugation at 100,000 g for 2 hours to collect MSC-XOs (Beckman Coulter XL90 ultracentrifuge). In several experiments, fluorescently labeled exosomes were used. Purified MSC-XOs were mixed with 1 μM DiD or DiR (Invitrogen, Life Technologies) and incubated for 30 min at 4°C, then free dye was removed through centrifugal filters (10 KDa). MSC-XOs were washed three times with PBS.
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2

APOE Epigenetic Modulation via Lentiviral Delivery

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Lentivirus containing dCas9-TET1 (#84475, Addgene) or dCas9-dTET1 (#84479, Addgene) coding plasmids, as well as one out of three gRNAs (gRNA_1, 2, and 3) coding plasmids designed for the APOE last exon, were produced in HEK293T cells co-transfected with the Δ8.9 and VSV-g plasmids using Lipofectamine 3000 Transfection Reagent (L3000015, Invitrogen). After 48 hr, cell culture supernatant was collected and filtered through a 0.45 μm filter. Lentivirus were collected through ultracentrifugation (25,000 rpm, 3 hr, 4°C) using an SW-41Ti rotor in a Beckman XL-90 ultracentrifuge. Virus were resuspended in PBS 1× and stored at –80°C. For infection, a pool of lentivirus containing dCas9-TET1 or dCas9-dTET1, as well as gRNA_1, 2, or 3 coding plasmids, was used to infect seeded U-2 OS cells. After 24 hr, antibiotic selection was performed with 1.5 μg/mL puromycin, and infection proceeded for more 48 hr. 3 days post-infection, cells were harvested and genomic DNA was extracted for subsequent protocols.
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3

Isolation and Purification of Outer Membrane Vesicles

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100 ml cultures were grown in LB at 37°C, with agitation at 200 rpm. Once the OD600 reached 0.5–0.6, expression of ClyA-Bla was induced with 0.2% L-arabinose and grown for a further 16 h. Cells were then pelleted at 6000xg, and the supernatants were removed and filtered with a 0.45um syringe filter. Aliquots of filtered supernatants were spread on LB agar and grown overnight at 37°C to check that all viable cells had been removed by filtration. 25 ml of filtered supernatants were centrifuged in a Beckman XL90 ultracentrifuge using a 70Ti rotor at 100,000xg (30,000 rpm) for 2 h at 4°C. After centrifugation, supernatants were removed, and the OMV pellets were resuspended in 1 ml colorless DMEM or sterile water (for TEM) and stored at -20°C.
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4

Lentiviral Transduction of Induced Pluripotent Stem Cells

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HEK 293T cells were used for lentiviral production, followed by concentration by ultra-centrifugation. Briefly, a second generation packaging system composed of three plasmids (transfer vector with expression construct LV-GFP, the packaging plasmid psPAX2, and the envelope protein expression plasmid pMD2.G – pMD2.G, a gift from Didier Trono (Addgene plasmid # 122591; RRID: Addgene_12259), was mixed in a ratio of 2:1:1 in DMEM (Thermofisher Scientific) and Fugene6 transfection reagent (Roche) and 293T cells were transfected during 4 h to overnight. The supernatant from the transfected plate was collected every 24 h in serum-free conditions and concentrated by ultracentrifugation (Beckman XL-90) at 90.000 rpm for 2 h at 4°C. The concentrated viral solution was passed through a 0.45 μm low-protein binding filter and aliquots were used to transfect the hiPSCs lines. The cell lines F002.1A.13, Gibco® iPSC6.2 and EMC24i/R2 (C6) were successfully transfected, by first incubating the cells in a 24-well plate during 30 min at 37°C with E8 medium, 10 μM ROCKi and 5 μg/mL of Polybreme (Sigma). Then, LV-GFP previously dissolved in E8 was added dropwise and the cells were incubated during 1 h30 min. Culture medium was then changed daily. After cell growth and expansion, FACS sorting of GFP+ cells was performed using BD FACSAriaTM III (BD Biosciences-US) in order to obtain pure populations.
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5

Bacteriophage Isolation and Purification

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Bacteriophages were isolated by using P. tolaasii strains as the host strains. Various sewage samples obtained from a rural area of Cheongju, Korea, were mixed with the host bacterial culture for primary isolation of the phages. The mixture was added to a 0.75% semisolid agar medium at a 1:2 ratio (v/v) and poured onto a 1.5% solid agar plate. The double-layered plate was incubated for 15 h at 25°C. One of the phage plaques in the incubated plate was chosen and added to the overnight culture of the corresponding P. tolaasii host strain.
Following the method described by Chibani-Chennoufi et al. (2004) (link), phage lysate was a supernatant obtained by centrifuging the culture medium inoculated with the phage and host strain. NaCl was added to the phage lysate at a concentration of 10%, incubated for 1 h at 0°C, and centrifuged at 6,000 ×g for 10 min. Polyethylene glycol (PEG-6000) was added to the supernatant at a concentration of 10% and incubated for 1 h at 0°C. Phages were collected by centrifugation at 19,000 ×g for 10 min (XL-90; Beckman Coulter, Pasadena, CA, USA). The precipitated phages were resuspended in a phage buffer (50 mM tris(hydroxymethyl)aminomethane-HCl, 150 mM NaCl, 20 mM NH4Cl, 10 mM MgCl2, 1 mM CaCl2, 0.2% gelatin, pH 7.4). The resuspended phages were filtered using a 0.2 μm microfilter and stored at −70°C.
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6

Isolation and Analysis of Membrane-Associated Proteins

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Samples were homogenized in hypotonic homogenization buffer (20 mM Tris-HCl, pH 7.8, 3 mM MgCl2, 10 mM NaCl, 0.0005 mg/ml, 2 mM sodium vanadate, 20 mM sodium fluoride, 0.5 mM DTT, and 1 mM PMSF) on ice and centrifuged at 15,000 g for 30 min at 4°C to separate cytosolic proteins from intracellular and plasma membranes. The pellet was resuspended in 0.5 M Na2CO3, transferred to a 5%/35%/45% sucrose (in Na2CO3) flotation gradient and spun at 36,000 rpm for 18 h using a preparative ultracentrifuge model XL-90 (NVT90 rotor; Beckman Coulter Life Sciences). Fractions obtained from the sucrose gradient were diluted in hypotonic buffer and spun at 15,000 g for 30 min at 4°C. Pellets (25 μl) were resuspended in RIPA buffer and 2× Laemmli buffer. About 30 μl of each sample was loaded in 10% SDS-PAGE and transferred to PVDF membranes for 1 h at 220 mA. Nonspecific binding was blocked with 5% nonfat milk and 2% BSA. The samples were incubated overnight at 4°C with TRPV4 (1:500; Alomone Labs), flotillin (1:200; Santa Cruz Biotechnology), Cav-1 (1:1,000; Cell Signaling), and α-SMA (1:500; Sigma-Aldrich) antibodies, followed by anti-mouse (1:5,000; BioRad) or anti-rabbit (1:5,000; Cell Signaling) HRP-conjugated secondary antibodies. The blotted proteins were developed with an enhanced chemiluminescence kit (Thermo Fisher Scientific).
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7

Polymeric Nanoparticles for 9-NC Delivery

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PLGA and PLGA-PEG polymeric nanoparticles incorporating 9-NC were prepared by nanoprecipitation technique. Briefly, the exact quantity of polymer and drug were dissolved in acetone and dispersed in the aqueous phase (pH, 3) containing polyvinyl alcohol as stabilizer.
The prepared nanoparticle suspension was stirred for 3 h at room temperature to evaporate the organic solvent. Subsequently, the nanoparticles were separated by ultracentrifugation (Beckman, XL-90, USA) at 30,000 rpm and 4° C for 20 min and lyophilized using a lyophilizer (ZibrusVaco 10-II-E; Germany) to obtain a fine powder of 9-NC-loaded nanoparticles (10 ).
The mean size and zeta potential of nanoparticles were measured by dynamic light scattering (DLS) (Zeta nanosizer, Malvern, France) at 25° C and at a scattering angle of 90°. Encapsulation efficiency was determined by dissolving 20 mg of nanoparticles in 4 ml acetone by ultrasonicator (Tecna 3, USA). Concentrations of 9-NC in replicated samples were determined at 370 nm using a UV-Vis spectrophotometer (UVmini-1240, Japan). The encapsulation efficiency was calculated by the following equation:
Encapsulation efficiency (%)=(Drug quantity in nanoparticles / Drug quantity originally used) × 100      (1)
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8

Liposome-Mediated MxiN and Spa47 Interaction Assay

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Asolectin, a natural soybean phospholipid mixture, was made to 8.7 mg/mL in the buffer corresponding to the protein(s) tested and was briefly sonicated using a probe sonicator. The lipid mixture was extruded at 50 °C using a 100 nm pore-sized membrane and an Avanti polar lipids extruder. Two micromolar MxiN was incubated with 4.4 mg/mL liposomes for 30 min at room temperature in 20 mM Tris, 100 mM NaCl, 5 mM DTT, pH 7.9. The mixture was brought up to 30% sucrose and 600 μL was transferred to an 11 x 60 mm ultracentrifugation tube and overlaid with 3 mL of 22.5% sucrose followed by 150 μL of buffer containing no sucrose. The samples were centrifuged in a Beckman SW-60 rotor using a Beckman XL-90 ultracentrifuge at 4 °C and 250,000 x g for 1 h 45 min. 100 μL aliquots were taken from the top, middle, and bottom regions of the sucrose gradient and analyzed for protein content by SDS-PAGE. This assay also monitored in vitro MxiN/Spa47 interactions by testing the ability of each Spa47 construct to “float” with liposomes in the presence and absence of MxiN. One micromolar Spa47 was prepared in the presence and absence of 2 μM MxiN, incubated with 4.4 mg/mL asolectin liposomes, and analyzed as described above for MxiN alone.
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9

Microglia-Derived EV Isolation and Characterization

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The EVs were isolated from 4 mL of SFM medium from 4 × 106 PBS‐ or LPS‐stimulated ex vivo microglia (24 hours). The methodology used is a slight modification of method used by Gabrielli and collegues.29 The medium was pre‐cleared by 2 centrifugations at 300 × g for 10 minutes. EVs containing microvesicles and exosomes together were pelleted from the supernatant by a centrifugation step at 100,000 × g for 1 hour with an ultracentifuge (Beckman XL‐90). Tunable Resistive Pulse Sensing (TRPS) technique, by Izon qNano instrument (Izon, New Zealand), was used to measure the size distribution and concentration of EVs. Izon EV reagent kit was used for both pretreating the pore and suspending EVs in order to prevent EV binding to the pore or spontaneous EV aggregation. EV pellets were re‐suspended in a volume of 100 μL. NP200 nanopore (100–400 nm diameter range; Izon) was used for sample analysis and the same nanopore was used throughout the experiment. The values for applied voltage, pressure and pore stretch were kept constant for all EV samples and relative calibration particle recordings. CPC200 calibration particles (carboxylated polystyrene particles diluted following the manufacturer's instruction; Izon) were used as standards. Data acquisition and analysis were performed using Izon Control Suite software (version V3.2).
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10

Liposome-binding Assay for IpaC

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IpaC was incubated with asolectin liposomes for 30 min at room temperature in PBS at 3 μM and 4.4 mg/mL, respectively. Following incubation, the mixture was brought up to 30% sucrose with the addition of a concentrated sucrose stock solution. 500 μL of this solution was transferred to an 11 × 60 mm ultracentrifugation tube and overlaid with 3 mL of 22.5% sucrose in PBS followed by 150 μL of PBS to form a discontinuous sucrose gradient with protein and liposomes at the bottom of the gradient. The samples were centrifuged in a Beckman SW-60 rotor using a Beckman XL-90 ultra-centrifuge for 1 hr 45 min at 310,000 x g and 4°C. 100 μL aliquots were taken from the top, middle and bottom regions of the centrifuged solution and were analyzed for protein content using SDS-PAGE followed by protein detection with Oriole UV-fluorescent stain and a BioRad ChemiDoc MP imager. Biorad Image Lab software was used to perform densitometry analysis and quantitatively compare the protein levels detected in each fraction of the gradient to determine the extent of interaction between liposomes and IpaC.
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