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22 protocols using microcystin lr

1

Synthesis and Characterization of MLi-2 Inhibitor

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MLi-2 inhibitor was synthesized by Natalia Shpiro (University of Dundee) as described previously (Fell et al., 2015 (link)). Calyculin A (ab141784) and Okadaic Acid (ab120375) were purchased from Abcam. Microcystin-LR was obtained from Enzo Life Sciences (ALX-350-012).
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2

Synthesis and Characterization of LRRK2 Modulators

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GSK3357679A [25 (link)]was synthesized at GlaxoSmithKline. MLi-2 was synthesized by Natalia Shpiro (University of Dundee) as described previously [16 (link)]. GZD-824 (#21508) and Rebastinib (#21465) were purchased from Cambridge Bioscience and Ponatinib (#4274) from Tocris. Microcystin-LR was purchased from Enzo Life Sciences (#ALX-350-012-M001). Human recombinant full length wild-type Flag-LRRK2 (#A15198) and Flag-LRRK2[G2019S] (#A15201) were from ThermoFisher Scientific. Diisopropylfluorophosphate was from Sigma (#D0879).
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3

Protein Extraction and Immunoblotting Protocol

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For protein extracts, cells were washed with ice-cold PBS, prior to lysis with Triton lysis buffer (1 % Triton X-100, 40 mM HEPES, pH 7.4, 120 mM NaCl, 10 mM sodium pyrophosphate, 10 mM glycerol 2-phosphate, 50 mM NaF, 1 μM EDTA, 1 mM Microcystin-LR (Enzo life sciences, ALX-350–012-C500) and protease inhibitor cocktail (Sigma, P8340)). Lysates were clarified by centrifugation at 20,000 g for 15 min at 4°C, and protein concentrations were determined with a Bradford assay (Biorad, 500–0006). 20–30 μg protein lysates were subjected to SDS-PAGE followed by immunoblotting using the following primary antibodies: NADK2 (Abcam, ab181028; 1:1000), FLAG (CS, 14793; 11:1000), β-actin (Sigma, A5316; 1:5000), and HRP-conjugated anti-mouse (CST, 7076; 1:5000) and anti-rabbit (CST, 7074; 1:5000) secondary antibodies were used.
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4

Protein Extraction from Frozen Mouse Tissues

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Frozen mouse tissues were weighed and added to a 10-fold volume excess of ice-cold lysis buffer containing 50 mM Tris–HCl, pH 7.5, 1% (v/v) Triton X-100, 1 mM EGTA, 1 mM sodium orthovanadate, 50 mM NaF, 0.1% (v/v) 2-mercaptoethanol, 10 mM 2-glycerophosphate, 5 mM sodium pyrophosphate, 0.1 µg/ml microcystin-LR (Enzo Life Sciences), 270 mM sucrose and complete EDTA-free protease inhibitor cocktail (Sigma–Aldrich Cat # 11836170001), and homogenised using a POLYTRON homogenizer (KINEMATICA) on ice (5 s homogenisation, 10 s interval and 5 s homogenisation). Lysates were centrifuged at 20 800 g for 30 min at 4°C and supernatants were used for Bradford assay and immunoblot analysis. Protein lysate (10–40 mg) was obtained from each tissue sample.
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5

Mitotic Protein Immunopurification Protocol

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Stable HeLa FRT TRex cell lines were induced with doxycycline and pre-synchronized with a thymidine block before a final arrest overnight in mitosis with taxol. Mitotic cells were harvested by shake-off and lysed in lysis buffer (50 mM Tris pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% NP-40) supplemented with 2 ng/ml Microcystin-LR (Enzo Life Sciences), 1 mM DTT, 20 mM NEM, and EDTA-free protease inhibitor cocktail (Roche). The cleared lysate was added to GFP-trap (ChromoTek) beads and the mixture was incubated at 4°C for 1 hour. The beads were washed twice in lysis buffer and resuspended in 2×LDS sample buffer and boiled for 10 min at 95°C for elution of proteins captured by the GFP-trap. Samples were analyzed by western blotting the same day as the immunopurification to avoid de-SUMOylation of targets.
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6

Immunoprecipitation and Kinase Assay of Flag-PKN1 and Flag-PKN2

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Flag-PKN1 and Flag-PKN2 were transiently transfected into 293T cells, with torin or rapamycin added 4 h before cell harvest at where indicated. Cells were lysed in a buffer containing 20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 0.5% Triton X-100, 1 mM PMSF, 2 mM DTT, 5 mM EDTA, 5 μg/mL each of aprotinin/leupeptin/pepstatin, and 1:100 dilution of phosphatase inhibitor cocktail #1 and #2 (Roche). The cell extracts were incubated with M2-agarose (Sigma A2220) at 4°C for 4 h, and the beads were washed five times with the wash buffer carrying 20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 0.1% Triton X-100, 1 mM DTT, 0.1 mM EDTA, 1 μg/mL each of aprotinin/leupeptin/pepstatin, 2 mM sodium vanadate, and 0.4 μM Microcystin-LR (Enzo Life Sciences, Farmingdale, NY, Inc. #350-012-C100). The beads were either used directly in the kinase assays, or further eluted at room temperature with 20 μg/mL of Flag peptide in the wash buffer. The kinase assays were typically carried out at 30°C for 15–30 min in a 25 μL volume reaction of 50 mM Hepes, pH 7.0, 2 mM MgCl2, 1 mg/mL BSA, 1 mM EGTA, 1 mM DTT, 0.1 mM ATP, 20 mM β-glycerophosphate, 0.15 mM sodium vanadate, 5 μg/mL each of aprotinin/leupeptin/pepstatin, 0.004% SDS, 2–5 μg substrate, the kinase, and 0.1 μL of γ-32P-ATP. The reactions were stopped by the addition of SDS-PAGE loading buffer (1× final concentration).
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7

Glycogen Synthase Regulation Analysis

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Rabbit liver glycogen and pancreatic α-amylase were from Sigma. Microcystin-LR was from Enzo Life Sciences. NADH was from Apollo Scientific. Antibodies against pS8 GYS1 and pS8/S11 GYS1 were kindly donated by D. Grahame Hardie (University of Dundee). pS641 GYS1 (#3891) and total GYS1 (#3893) antibodies were from Cell Signaling Technologies. Total GYS1 (sc-81173) and PP1c (sc-7182) antibodies were from Santa Cruz Biotechnology. pS641/645 GYS1 (S486A, 3rd bleed) and GN1 (S197C, 1st bleed) antibodies were generated by the Division of Signal Transduction Therapy (DSTT) at the University of Dundee as previously described [4] (link). Peroxidase conjugated secondary antibodies were from Jackson Immunoresearch. Glutathione Sepharose 4B, NHS-Sepharose FF, Superdex 200 3.2/300, Q-Sepharose HP and Enhanced Chemiluminescent (ECL) reagent were from GE Healthcare. Gel filtration standards were from Bio-Rad (151-1901). All other reagents, unless otherwise indicated, were from Sigma.
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8

Extraction and Analysis of Proteins from Human Brain Tissue

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Human brain samples were provided by the Queen Square Brain Bank for Neurological Disorders (UCL, London). Frozen human cingulate cortex samples were weighed and added to a 10-fold volume excess of ice-cold lysis buffer containing 50 mM Tris–HCl pH 7.5, 1% (v/v) Triton X-100, 1 mM EGTA, 1 mM sodium orthovanadate, 50 mM sodium fluoride, 10 mM β-glycerophosphate, 5 mM sodium pyrophosphate, 0.1 µg/ml Microcystin-LR (Enzo Life Sciences), 270 mM sucrose and complete EDTA-free protease inhibitor cocktail ((Sigma–Aldrich Cat # 11836170001), and homogenised using POLYTRON homogenizer (KINEMATICA) on ice (5 s homogenisation, 10 s interval and 5 s homogenisation). Lysates were centrifuged at 20 800 g for 10 min at 4°C. Supernatants were collected, quantified by the Bradford assay (Thermo Scientific) and subjected to immunoblot analysis.
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9

Rapid Tissue Lysis and Protein Extraction

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Frozen mouse tissues were rapidly defrosted in the ice-cold lysis buffer [50 mM Tris–HCl, pH 7.5, 1% (v/v) Triton X-100, 1 mM EGTA, 1 mM sodium orthovanadate, 50 mM NaF, 10 mM 2-glycerophosphate, 5 mM sodium pyrophosphate, 0.1 µg/ml microcystin-LR (Enzo Life Sciences), 270 mM sucrose, and complete EDTA-free protease inhibitor cocktail (Sigma–Aldrich Cat # 11836170001)] and homogenised using a POLYTRON homogeniser (KINEMATICA) on ice (5 s homogenisation, 10 s interval, and 5 s homogenisation). Lysates were clarified by centrifugation at 20 800 g for 30 min at 4°C and supernatants were quantified by Bradford assay and used for subsequent immunoblot analysis.
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10

Isolation and Solubilization of HeLa Nuclear Pellet

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HeLa nuclear extract was prepared from isolated nuclei from approximately 1 billion HeLa S3 cells, as described (Dignam et al.)78 (link). The insoluble pellet from the nuclear extract (i.e. the nuclear pellet) was solubilized with 100 mM HEPES pH 7.9, 2 mM MgCl2, 100 mM KCl, 20% (v/v) glycerol, protease inhibitors (0.25 mM PMSF, 1 mM Sodium metabisulfite, 1 mM Benzamidine, 1 mM DTT), phosphatase inhibitors (1 µM Microcystin LR (Enzo Lifesciences, Farmingdale, NY), 0.1 mM Sodium orthovanadate, 10 mM beta-glycerophosphate, 5 mM sodium fluoride, 1 mM sodium pyrophosphate (all Sigma)), and nucleases Benzonase (200 U/mL) and DNAse I (50 U/mL). The pellet was chopped, dounce homogenized 20 times and mixed overnight with a stir bar at 4 °C. The extract was cleared by centrifugation at 14,000 x g and aliquoted for storage at −80 °C.
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