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28 protocols using fk506

1

C2C12 and HEK293T Cell Culture and Differentiation

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C2C12 and HEK293T cells were purchased from ATCC (Manassas, VA) and were maintained at subconfluent densities in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin in a humidified incubator at 37°C in 5% CO2. For differentiation, C2C12 cells at >80% confluence were switched to DMEM supplemented with 2% horse serum and 2 μg/ml of bovine insulin (Sigma-Aldrich). FK506 (Cayman Chemical, Ann Arbor, MI) was added to the culture 24 h before initiation of differentiation, and FK506 was maintained in the differentiation medium at 2 μM. Medium containing FK506 was changed every day.
Mouse satellite cells were isolated from leg muscles of 3-to-6-week-old Brg1 conditional mice by the use of Percoll sedimentation followed by differential plating as described previously (20 (link)). Mice were housed in the animal care facility at the University of Massachusetts Medical School and used in accordance with a protocol approved by the Institutional Animal Care and Use Committee. Brg1-depleted primary myoblasts expressing wild-type Brg1 (WT-Brg1) or Brg1 mutated at sites of PKCβ1/Cn activity were generated as described previously (20 (link)). Primary myoblasts were grown and differentiated as described previously (20 (link)) on plates coated overnight in 0.02% collagen (Advanced BioMatrix, San Diego, CA).
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2

Neutrophil Nuclear Architecture Modulation

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In vitro differentiated neutrophils from ECOMG cells were used as a model system to study nuclear architecture in response to calcium influx in neutrophils. ECOMG cells were cultured and differentiated as previously described (Zhu et al. 2017 (link)). For inhibitors, neutrophils were treated with 10 µM Triptolide (Cayman), 100 µM 5,6-dichloro-1-β-D-ribofuranosyl-1H-benzimidazole (Cayman) or 10 µM flavopiridol (Cayman) for 30 min, or 2 µM FK506 for 2 h before activation. Primary B cells were treated with 2 µM FK506 (Cayman) for 2 h before activation. Inhibitors were kept in culture during activation time course. Acute degradation was induced by treating the cells with 0.5 µM dTAG-13 (Tocris) before activation. dTAG-13 was kept in culture during activation time course. The time series degradation experiments were performed by inducing protein degradation at the beginning of the time course and harvesting the samples at different time points. RPMI-1640 (Gibco) contains 0.42 mM calcium. Additional CaCl2 was supplied to the medium before activation to a final concentration of 1 mM. A23187 was purchased from Sigma and Cayman. Neutrophils were activated either using fast activation conditions (20 µM A23187 for 15 min), or using slow activation conditions (5 µM A23187 for 4 h). These two activation conditions were used throughout the manuscript unless otherwise mentioned.
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3

Cultivation and Characterization of Yeast Cells

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Cells were cultivated in EMM + E medium overnight and harvested by centrifugation (2,500 rpm, 3 min). Cells were washed by EMM-N medium three times and resuspended in the same medium. Cells (0.3 OD595) were cultivated for 24 h at 27°C. Then, cells were inoculated in EMM + E or EMM + S medium with or without nutrients or chemicals. The initial concentration of cells was 0.05 OD595 for assays in test tubes or 0.0033 OD595 for assays in 96 well plates. Cell growth in 96 well plates was assessed by measuring the turbidity at 595 nm using MULTISKAN FC (Thermo). SLF, FK506, and rapamycin were from Cayman, FUJIFILM, and AG Scientific, respectively. When cells were spotted on solid media, 5- or 10- fold serial dilution series were prepared in EMM-N medium, 5 μL of which were spotted. The highest concentration was 5 × 10ˆ5 cells/mL or 0.015 OD595.
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4

Pharmacological Regulation of Cell Migration

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MEF cells were treated with 1% DMSO, 20 µM BAPTA (Cayman Chemical), Y27632 5 µM (Cayman Chemical), 50 µM CK666 (Cayman Chemical), STO-609 acetate (Biotechne, #1551), A23187 (Cayman Chemical), 4 µM Blebbistatin (Cayman Chemical), 40 uM AIP (R&D Systems #5959/1), 50 µM CAS 1090893 (Millipore, #553511), 0.1 µg/ml RhoA inhibitor-I (Cytoskeleton, Inc, #CT-04), 2 µM FK-506 (Cayman Chemical, # 10007965), 300 nM FAK14 (Cayman Chemical, #14485), 10 µM BMS-5 (Cayman Chemical, #21072), or 2 µM ML-7 (Cayman Chemical, #11801) overnight during time-lapse imaging for random cell migration or followed by immunostaining.
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5

Modulating AMPAR Endocytosis in Neurons

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Anisomycin (62.5 µg/side dissolved in saline-containing 10% DMSO, the pH value was adjusted to 7.0) was obtained from Sigma-Aldrich. A Tat-conjugated peptide designed to block the regulated clathrin-coated endocytosis of AMPARs was used with a sequence of 869-YKEGYNVYG-877 (GluR23Y, 15 pmol/side). The scrambled control peptide in which the tyrosine residues were replaced by alanine had the AKEGANVAG sequence (GluR23A, 15 pmol/side). These peptides were purchased from Kelowna International Scientific Inc. (Sanchong Dist.) and were dissolved in saline. One microgram per side (1)-MK-801 maleate (Sigma-Aldrich) and 2.5 µg/side NVP-AAM077 (Sigma-Aldrich) were dissolved in 0.9% saline. One microgram per side ifenprodil (Abcam), 5 µg/side FK-506 (Cayman), 2.5 µg/side cyclosporine A (Sigma-Aldrich), 5 pmol/side calyculin A (Alomone Labs), and 10 ng/side okadaic acid (Sigma-Aldrich) were dissolved in 10% DMSO.
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6

Co-Transfection and Modulation of Protein Interactions

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HeLa and U2OS cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) and RPMI-1640 medium containing 10% fetal bovine serum (FBS; Hyclone and Gibco) supplemented with 1% penicillin and streptomycin. HeLa cells were grown on round coverslips (Marlenfeld GmbH & Co.) in a 24-well culture plate to 50–70% confluency. Transient co-transfection of plasmids expressing the desired protein pairs (FKBP12/FRB and p53N/MDM2N) was conducted using the XtremeGene Transfection Reagent (Roche) and Lipofectamine 3000 Reagent (ThermoFisher Scientific) according to the manufacturer’s instructions. Rapamycin (Calbiochem), FK-506 (Cayman), and Nutlin-3 (Sigma-Aldrich) were dissolved in dimethyl sulfoxide (DMSO) prior to treatment. Cmpd 7 was kindly provided by Dr. Peppi Prasit (USA).
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7

High-Pressure CO2 Extraction and Anti-Inflammatory Assay

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CO2 pure grade (99.95%, Air Liquide, Lisbon, Portugal) and EtOH (96%) were used for high pressure extraction experiments. Solvents used for conventional extractions purification steps and chromatographic analysis included ethyl acetate (99.98%, Fisher scientific U.K. Limited, Loughborough, UK), methanol (99.8%, Fisher scientific U.K. Limited, Loughborough, UK), dichloromethane (Honeywell Riedel-de Haën, Germany), distilled water, and ultrapure water purified with a Milli-Q water purification system (Merck Millipore, Billerica, MA, USA). For the inflammation assays, the inflammatory stimulus was carried out by the usage of MnCl2 (Merck, Darmstadt, Germany), and the anti-inflammatory positive control was carried by FK506 (Cayman Chemicals, Ann Arbor, MI, USA). Cellular lysis was preformed using Yeast Protein Extraction Reagent (Y-PER; ThermoFisher Scientific, Scientific, Rockford, IL, USA). To quantify the expression of reporter gene lacZ, we employed a solution buffer composed of Na2HPO4 (ROTH, Karlsruhe, Germany), NaH2PO4·H2O (Merck, Buchs, Switzerland), KCl (Panreac, Barcelona, Spain), and MgSO4·7H2O (Merck, Buchs, Switzerland), containing o-nitrophenyl β-D-galactopyranoside (ONPG; Sigma–Aldrich®–Poole, Dorset, UK). Nuclear staining was carried out using nuclear dye Hoechst 33342 (Sigma, Buchs, Switzerland).
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8

Subcutaneous FK506 Delivery in Mice

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Alzet osmotic pumps (Alzet, no. 2004) were used to administer FK506 (Cayman Chemical) to mice at a dose of 0.05mg per kg mouse body weight per day. Each pump was filled with 200ul of FK506, then implanted subcutaneously into the back of each mouse, slightly posterior to the scapulae, and the incision closed with wound clips.
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9

Regulation of MAP2B Protein Localization

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PCB 95 (2,2′,3,5′,6-pentachlorobiphenyl) was purchased from AccuStandard, (Lot #010610KS, New Haven, CT). All PCB 95 stock solutions were made in dry sterile dimethylsulfoxide (DMSO, Sigma-Aldrich, St. Louis, MO). Plasmid encoding microtubule-associated-protein-2B (MAP2B)-pCAG-fusion protein red (FusRed) or MAP2B fused to enhanced green fluorescent protein (MAP2B-pCAG-EGFP) were generously provided by Dr. Gary Wayman (University of Washington, Pullman, WA) and have been previously characterized (Wayman et al. 2006 (link)). Predesigned Ambion Silencer Select siRNAs targeting mTOR (s132719), raptor (s143003), rictor (s160195), or scrambled siRNA (#4390844) were purchased from Thermo Fisher Scientific (Waltham, MA). FK506 was purchased from Cayman Chemical (Ann Arbor, MI); 4EGI-1, from Tocris (Minneapolis, MN); and rapamycin, from Selleckchem (Houston, TX).
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10

Western Blot Analysis of Protein Expression

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Whole cell extracts were prepared by lysing cells in Laemmli buffer containing 1% SDS and 2% 2-mercaptoethanol. Lysates from equal numbers of cells were separated by 8 or 10% SDS PAGE, transferred to PVDF membranes (GE Healthcare), incubated with primary antibodies and detected with HRP-conjugated species-specific anti-immunoglobulin light chain antibodies (Jackson ImmunoResearch) and a Luminata HRP substrate (Millipore). Anti-HDAC1 (Abcam, ab7028) and anti-Tubulin beta (Developmental Studies Hybridoma Bank, University of Iowa) were used as loading controls. Anti-AP4 antibody was previously described24 (link). The following antibodies were purchased: anti-c-Myc (Cell Signaling, 9402S), anti-phospho STAT5 (PY694) (BD Biosciences, 611964), anti-Blimp-1 (Genscript, A01647-40), anti-T-bet (Santa Cruz, sc-21003). For translation inhibition and proteasome inhibition, 10 μM of cycloheximide (Sigma) or MG-132 (Sigma) was added to the cell culture. For inhibition of signaling pathways, 20 nM of U0126 (Cayman Chemical), 10 μM of SB203580 (Cayman Chemical), 50 nM of wortmannin (Cayman Chemical), 5 nM of FK506 (Cayman Chemical), or 2.5 nM of rapamycin (Cayman Chemical) was added to the cell culture.
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