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18 protocols using le 80k

1

Polysome Fractionation of BMDM

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Polysome fractionation protocol was adapted from Stastna et al (Stastna et al, 2018 ). Briefly, Fmr1+/+ and Fmr1−/− BMDM were treated with PA (500 µM) for 6 h followed by cycloheximide (100 µg/ml) for 10 min prior to lysis with buffer (100 mM KCl, 20 mM Tris pH 7.5, 5 mM MgCl2, 0.4% NP‐40, 100 µg/ml cycloheximide, 0.1 U RNase inhibitor and protease inhibitor cocktail). Clear lysates were loaded to 10–50% sucrose gradient (in Beckman Coulter Thinwall, Ultra‐Clear tubes, 344059) and centrifuged (in Beckman LE‐80K) for 120 min at 28,4061 g at 4°C in a swinging bucket rotor (Beckman SW41) with no‐brake. Each gradient was collected as 17 fractions in microcentrifuge tubes with continuous monitoring of absorbance at 254 nm (Biologic LP (pump), Biorad 731‐8300; BioFrac, Biorad 741‐0002) and frozen immediately at −80°C for further analysis.
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2

Comprehensive Cell and Animal Studies

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The photos from the colony formation assays and animal study were collected by Nikon D3200 (pixel dimension: 3020*1728, 8 bit) from October, 2011 to December, 2014 in Tianjin Life Science Research Center. EGFP and RFP intensity was tested using an F-4500 fluorescence spectrophotometer (HITACHI, Tokyo, Japan). EGFP intensity is normalized to RFP intensity. qRT-PCR was performed using the Bio-RAD™ iQ5 fluorescence quantitative PCR instrument. Lab Works™ Image Acquisition and Analysis Software (UVP) were used for the quantification of the western blot bands in the form of gray intensities (pixel dimension: 3020*1728, 8 bit, UVP, U.S.A.) from October, 2011 to January, 2015 in Tianjin Life Science Research Center. The Sucrose gradient sedimentation assay were performed with the Beckman ultracentrifugation LE-80 K with SW28ti rotor at 25,000 rpm for 4 hrs at 4 °C.
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3

Isolation of Plasma Membrane Nanoparticles

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To acquire the cell membranes for nanoparticle coating, T cells and CAR-T cells were washed by PBS twice and then harvested. The cells were suspended in hypotonic lysing buffer consisting of 20 mM Tris-HCl, 10 mM KCl, 2 mM MgCl2, and 1 EDTA-free mini protease inhibitor tablet per 10 mL of solution and disrupted using a dounce homogenizer with a tightfitting pestle. The entire solution was subjected to 20 passes before spinning down at 3,200 g for 5 min. The supernatant was saved, while the pellet was resuspended in hypotonic lysing buffer and subjected to another 20 passes and spun down again. The supernatants were pooled and centrifuged at 20,000 g for 30 min, after which the pellet was discarded and the supernatant was centrifuged again at 80,000 g for 1.5 h using an ultra-speed centrifuge (LE-80K, Beckman Coulter, USA). The pellet containing the plasma membrane material was then washed once with 10 mM Tris-HCl and 1 mM EDTA and collected. Then, CAR-T vesicles (CVs) and T cell vesicles (TVs) were obtained by physically extruding the pellet for 11 passes through a 400-nm polycarbonate porous membrane on a mini extruder (Avanti Polar Lipids, USA).
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4

TCUEAP1 Phage Purification Protocol

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Lysates for TCUEAP1 phage purification were prepared by infecting 200 ml of E. anophelis ANO15 in early log-phase with TCUEAP1 at a multiplicity of infection (MOI) of about 1.0, and incubating with aeration for 4 h. Crude lysates were centrifuged and the supernatants were passed through a membrane filter with a pore size of 0.45 μm. The phage particles were concentrated by centrifugation for 2 h at 39,000 × g in a Beckman Avanti J-25I. The pellets were re-suspended in 1.0 ml of TE buffer and purified by banding on the block gradient of CsCl representing 1.2, 1.3, and 1.4 g/cm3 (2 ml for each block) in ultracentrifugation. The ultracentrifugation conditions were 107,200 × g for 3 h at 4°C with the SW41Ti rotor in a Beckman LE-80K. The phage band collected was dialyzed against the TE buffer and then stored at 4°C until further use.
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5

Purification and Membrane Coating of MDSCs

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Membrane coating was prepared as our previous literature [26 ,28 ]. Briefly, MDSCs were disrupted using a Dounce homogenizer. The entire solution was subjected to 20 passes before spinning down at 3200g for 5 min. The supernatants were saved and centrifuged at 20000g for 30 min, after which the pellet was discarded and the supernatant was centrifuged again at 80000g for 2 h using an ultra-speed centrifuge (LE-80 K, Beckman Coulter, USA). The pellets containing the cell membranes were washed once in 1 mM EDTA and 10 mM Tris-HCl, and then collected as purified MDSCs membranes. Then MDSCs membrane-vesicles were obtained by physically extruding the pellets for several passes through 400 nm and 200 nm microporous membranes with an Avanti mini-extruder (Avanti Polar Lipids, USA). Subsequently, the MDSCs membrane-vesicles and GSM were mixed and extruded 11 times through a 200 nm microporous membranes and excess MDSCs membrane-vesicles were removed by centrifugation to obtain GSMM.
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6

Measuring Serum Lipid Profiles

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Blood samples were obtained after 8–12 h fast. Cholesterol, triglycerides, HDL cholesterol and apolipoprotein B were measured in serum using colorimetric assays (Unicel DxC 600 Synchron Clinical System Beckman Coulter). VLDL lipoproteins were isolated using sequential ultracentrifugation (Optimal Beckman LE80-K) of 40,000 RPM at 4 °C for 18 h. Serum aliquots (3.5 mL) were centrifuged at background density of 1.006 Kg/L, VLDL-C and VLDL-triglycerides levels in the ultracentrifugal bottom fraction were analyzed by calorimetric assays (Unicel DxC 600 Synchron Clinical System Beckman Coulter). LDL and VLDL cholesterol were calculated using the Friedewald’s equation (VLDL-F, LDL-F), Sampson’s method (VLDL-S, LDL-S) and the calculation proposed by Martin et al. (VLDL-M, LDL-M). LDL-C was also calculated using VLDL-C measures by ultracentrifugation to approximate a gold-standard for comparative assessments.
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7

Lentivirus Production in HEK293T Cells

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HEK293T cells (1 × 107 cells in a 15-cm dish) were co-transfected with lentiviral vector plasmid pFG12 or pFG12-VGTE (25 μg) and helper plasmids (6.25 μg pRSV-rev, 12.5 μg pHCMV-G, and 7.5 μg pMDLg/pRRE-M). The plasmids and PEI (Polyscience, 23966) were mixed for 10 min in serum-free DMEM at a ratio of 1:4. The medium was refreshed at 8 h post-transfection. The culture supernatant was harvested 48 h after transfection, filtered through a 0.45-μm filter, and concentrated via ultracentrifugation (Beckman, LE-80K) at 82,000 × g for 1.5 h at 4°C. The supernatant was discarded gently after ultracentrifugation, and 200 μL serum-free DMEM was added to the tube. The pellet was suspended overnight at 4°C. On the next day, the medium containing the lentiviral particles was dispensed into a 25-μL per tube and stored at -80°C for further study. The lentiviral particle titer was determined by infecting TZM-bl cells with serial dilutions of the stock solution. The lentiviral particle titer was generally approximately 108 transducing units (TU)/mL.
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8

Mucin Purification by Density-Gradient Centrifugation

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Mucins were solubilized in 4 M guanidine chloride solution containing 10 mM dithiothreitol, 5 mM ethylenediaminetetraacetic acid, 10 mM benzamidine, 5 mM N-ethylmaleimide, 0.1 mg/mL soy bean trypsin inhibitor, and 1 mM phenylmethanesulfonyl fluoride.
Cesium chloride was added to an initial density of 1.4 g/mL and mucins were purified by isopycnic density-gradient centrifugation (Beckman Coulter LE80K ultracentrifuge; 70.1 Ti rotor, 417 600 g at 15°C for 72 h). Fractions of 1 mL were collected from the bottom of the tube and analyzed for periodic acid-Schiff (PAS) reactivity and density. The mucin-containing fractions were pooled, dialyzed against water, and lyophilized.
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9

Measuring SERCA2 ATPase Activity

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Microsomes containing ER membrane vesicles were isolated from murine cardiomyocytes using a Beckman ultracentrifuge LE-80K (Brea, CA, USA). ATPase activity of sarco(endo)plasmic reticulum Ca2+-ATPase 2 (SERCA2) was determined through measurement of Ca2+ uptake assisted by a Fura-2-based method. Microsomes were incubated in an assay buffer (100 mM KCl, 10 mM HEPES (pH 7.4), 10 mM oxalate, 5 mM MgCl2, 10 μM ruthenium red, and 2 μM Fura-2). The uptake reaction was initiated by addition of 5 mM ATP and 2 μM Ca2+. The fluorescence ratio (excitation at 340 and 380 nm) was recorded at 510 nm emission using a fluorescence microplate reader (BioTek). Rate of Ca2+ uptake was derived from the linear slope following addition of Ca2+ [46 (link)].
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10

Hypoxia-induced Exosome Isolation

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Exosomes were isolated from conditioned medium by differential ultracentrifugation as described previously 8, 18. Exosome‐free medium (prepared using FCS centrifuged for at least 1 hr at 200,000 × g, followed by 0.2 μm filter‐sterilization) was added to cells grown to ~75% confluence for 24 hrs. During the 24‐hr culturing period cells were exposed to hypoxia (2% O2), or ambient oxygen level (20% O2). The conditioned medium was centrifuged for 15 min. at 1500 × g to remove cellular debris, after which larger microvesicles were removed by centrifugation for 30 min. at 10,000 × g. Exosomes were isolated by centrifugation for 60 min. at 100,000 × g, and subsequently washed twice by resuspending in PBS and centrifugation for 60 min. at 100,000 × g. Centrifugation was performed using a Beckman LE‐80K centrifuge with SW32‐Ti and SW60‐Ti rotors (Beckman Instruments, Indianapolis, IN, USA).
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