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12 protocols using mncl2

1

Cell Migration Dynamics on Guidance Cues

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Cells were plated at 40,000-50,000 cells ml-1 in 2 ml of media in 35 mm dishes. MDA-MB-231 cells were incubated for 2 hrs supplemented with blebbistatin (Sigma Aldrich), ML-7 (Sigma Aldrich), Y-27632 (Calbiochem, Billerica, MA, USA), P5D2 β1 integrin blocking antibody (mouse mAb, ascites, from Mark Ginsberg, University of California, San Diego) [41 (link)], calyculin A (Santa Cruz Biotechnology, Dallas, TX, USA) and MnCl2 (Fisher) and MTLn3 cells were incubated for 12 hrs with supplemented with calyculin A, MnCl2, Y-27632, and P5D2 on contact guidance cues in imaging media. Substrates with attached cells were inverted onto two strips of double sided tape attached to a microscope slide to generate a flow chamber. The chamber was filled with imaging media and sealed with a 1:1:1 mixture of vasoline, lanolin and paraffin wax. Chambers were imaged by phase contrast microscopy on a heated stage at 37°C every 2 min for 12 hrs. Images were captured at 10× (NA 0.50, Nikon) as described above.
Cell centroids were identified and tracked manually using the MTrackJ plugins of ImageJ (National Institutes of Health, Bethesda, MD, USA). Cell speed and directionality were calculated over a time lag of 2 min averaged over 12 hrs as described in a previous paper [15 ].
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2

Growth Curve Assay in Bacteria

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All growth curves were carried out in the rich growth medium described for each strain above. For each growth curve, bacterial strains were streaked from −80°C stocks 2 days prior to the assay. Overnight cultures were treated at stationary phase or grown for 12 to 15 h in 5 ml of medium in 15-ml conical tubes, and 1 μl of overnight culture was added to 100 μl of medium in a round-bottom 96-well plate (Corning, Corning, NY). MnCl2 (Thermo Fisher, Waltham, MA, or Sigma Millipore, St. Louis, MO) was prepared as a 100 mM stock in deionized water, sterile filtered, and stored at room temperature. Individual components of the growth assay were added to the 96-well plate in the following order: growth medium, growth medium containing additional Mn, and growth medium containing compound. Immediately after adding compound, cultures were added and optical density absorbance at 600 nm (OD600) at the zero-time point was established. Ninety-six-well plates were grown at 37°C in a shaking incubator and removed periodically for OD600 measurements with a plate reader (BioTek, Winooski, VT). Alternatively, kinetic reads were carried out in the plate reader at 37°C with linear shaking.
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3

Antibody Characterization and Experimental Conditions

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Monoclonal antibodies were against GPP130 (Linstedt et al., 1997 (link)), myc (Evan et al., 1985 (link); Jesch et al., 2001 (link)), HA (H3663, Clone HA-7; Sigma), giantin (Linstedt and Hauri, 1993 (link)), GFP (SAB2702197, clone GT859; Sigma), sortilin (Cat# 612100, clone 48/Neurotensin; BD Biosciences), and tubulin (T6557, clone GTU-88; Sigma). Polyclonal antibodies were against GPP130 (Puri et al., 2002 (link)), TMEM165 (NBP1-90651; Novus Biologicals), GAPDH (14C10; Cell Signaling Technology), and sortilin (a kind gift from Claus M. Petersen, Aarhus University [ Petersen et al., 1997 (link)]). Secondary antibodies were Alexa 488 anti-mouse (Cat#A28175; Thermo Fisher Scientific), Alexa 488 anti-rabbit (Cat#A27034; Thermo Fisher Scientific), Alexa 555 anti-rabbit (Cat#A27039; Thermo Fisher Scientific), Alexa 555 anti-mouse (Cat#A28180; Thermo Fisher Scientific), and horseradish peroxidase–conjugated goat anti-mouse (Cat#170-6516; Sigma) and goat anti-rabbit antibodies (Cat#170-6515; Sigma). AP12998 was from Clontech (called D/D solubilizer, Cat#635054). Cycloheximide (Cat#C7698) and monensin (Cat#M5273) were from Sigma. ECL blotting substrate (Cat#32209) and MnCl2 (Cat#M87-500) were from Thermo Fisher Scientific.
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4

Polyadenylation Assay for RNA Analysis

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PAT assay was performed and adapted from the previous report67 (link). Total RNAs were isolated from the MDA-MB-231 cells transduced with Ad-LacZ/Ad-TIS21 for 48 h. To abolish the higher ordered secondary structure at the 3′-end, RNA samples were heated at 65 °C for 5 min and immediately placed on ice. The samples were incubated for 2 h at 37 °C with 10× PAP buffer, 1 μl of PAP (1 U/μL), 1 mM MnCl2, and 1 mM GTP (Thermo Fisher Scientific, Waltham, MA) in a 20 µL reaction mixture. PAP buffer, PAP, and MnCl2 (BioVision, Milpitas, CA). Ten microliters of Guanylated RNA was used for cDNA reaction (20 μL). The first-strand cDNA synthesis was primed by oligo(dCT). As specificity control, oligo(dT) was used. The RT reaction was stopped by denaturation at 95 °C (3 min) and the cDNA product was applied to PCR amplification using Gene-specific forward and reverse primers (38 cycles) and examined by agarose gel electrophoresis.
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5

Metal-Dependent Nuclease Activity Assay

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Inorganic salts including MgCl2, MnCl2, CaCl2, CoCl2, CuCl2, NiCl2, ZnCl2, FeCl2, FeCl3, and Mg(NO3)2 were from Thermo Fisher Scientific with a minimum purity of 99.99%. Mn(NO3)2 with 98% purity was from Sigma-Aldrich. Stock solutions (100 mM) were prepared by dissolving inorganic salts in nuclease-free water. Unless otherwise stated, metal-dependent nuclease activity was measured in the presence of 10 mM divalent metal ion or 10 mM EDTA. For metal ion concentration-dependent assay, increasing concentrations of metal ions (from 0.2 to 10 mM) were incubated with either 2 nM circular M13mp18 ssDNA or 4 nM circular pUC19 dsDNA in the presence of Mg2+ or Mn2+ for 30 min at 37°C. Reactions were terminated by adding 1 μL of Proteinase K. For kinetic study, reactions were quenched at different time points and were run on 1% agarose gel. Error bars are presented as mean ± SEM.
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6

Purification of Metal-Binding Proteins

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All chemicals and materials used in this study are of the highest purity grade. CuCl2, GdCl3, and MnCl2 were purchased from Fisher Scientific and Sigma. N-(2-acetamido)-2-aminoethanesulfonic acid (ACES), isopropyl-β-D-thiogalactoside (IPTG), Tris base, Tris hydrochloride, and sodium chloride were purchased from Fisher Scientific. Imidazole was purchased from Acros.
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7

Bacillus subtilis Biofilm Cultivation Protocol

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Bacillus subtilis NCIB 3610 amyE::PtapA-Ypet strain (ES2107) was used for all experiments. The strain was cultured on lysogeny broth (LB)-agar plates prepared from Miller LB (Acros Organics, Fair Lawn, NJ) and 1.5% agar powder (Molecular Genetics, Fisher Scientific, Waltham, MA). LB agar plates were streaked with B. subtilis ES2107 from frozen stocks and incubated at 30°C for 15 h.
B. subtilis biofilms were grown on MSgg, a B. subtilis biofilm-promoting medium (5 mM potassium phosphate [pH 7]) (Fisher Scientific, Waltham, MA), 100 mM MOPS (morpholinepropanesulfonic acid [pH 7]) (Sigma-Aldrich, St. Louis, MO), 2 mM MgCl2 (Fisher Scientific, Waltham, MA), 700 μM CaCl2 (Alfa Aesar, Haverhill, MA), 50 μM MnCl2 (Fisher Scientific, Waltham, MA), 50 μM FeCl3 (Sigma-Aldrich, St. Louis, MO), 1 μM ZnCl2 (Sigma-Aldrich, St. Louis, MO), 2 μM thiamine hydrochloride (Fisher Scientific, Waltham, MA), 0.5% glycerol (Fisher Scientific, Waltham, MA), and 0.5% glutamate (Sigma-Aldrich, St. Louis, MO). For MSgg agar plates, 1.5% agar (BD) was added to the medium, and approximately 5-ml plates were poured.
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8

Hydrogel-based Cell Attachment Assay

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Hydrogel discs were placed in ultralow binding polystyrene well plates (Corning) to ensure cells attach to hydrogels and not the plate surface. Hydrogels were washed with Hank’s buffered salt solution (HBSS, Thermo) for at least 3 days before seeding cells. Cells were seeded at a low density (25 cells/mm2). After seeding, hydrogels were washed thoroughly to remove unattached cells. Drug treatments of 3 μM MnCl2 (Fisher Scientific), 200 nM cilengitide (Cayman) and 5 μM CK869 (Cayman) were applied during and after cell adhesion to substrates. To evaluate the number of live cells seeded on the substrate, cells were detached by incubating with Accutase Cell Detachment Solution (Innovative Cell Technologies, Inc.) for 10 min at 37 °C. Cells were then washed by centrifugation and directly added to HBSS containing calcein AM (1:2000; Biotium), ethidium bromide (1:2000; Thermo Fisher Scientific), and a predefined number of allophycocyanin (APC) beads (BD). After incubation at room temperature for 10 min, the samples were analyzed for live and dead cell number by flow cytometry.
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9

Enzymatic Synthesis and Radiolabeling of Glycosides

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Reagents used were analytical grade and were obtained from the following sources: quercetin, FeSO4, CuSO4, and ZnCl2 were from MilliporeSigma (St. Louis, MO, USA); kaempferol was from Indofine (Hillsborough, NJ, USA), UDP-glucose was from Calbiochem (Gibbstown, NJ, USA), UDP- [U-14C] glucose was from PerkinElmer (Boston, MA, USA); Midiprep plasmid extraction kit was obtained from Promega (Madison, WI, USA). Miniprep plasmid extraction kit, MgCl2, MnCl2, KCl, and NaCl were purchased from Fisher Scientific (Waltham, MA, USA); CaCl2 was from Acros Organics (Morris Plains, Morris, NJ, USA); Na2SO4 was from Merk (Kenilworth, NJ, USA). Bovine thrombin was obtained from MP Biomedicals (Solon, OH, USA).
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10

Metal-Affinity Chromatography Protocol

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Cell fractionations were performed with Cell Fractionation Kit (CST9038). Kinase inhibitors Wortmannin (Selleck S2758), and LY294002 (Selleck S1105) were used at the indicated doses. Etoposide (Sigma, E1383) and doxorubicin (Selleck, S1208), insulin (Invitrogen 41400‐045), EGF (Sigma E9644), PDGF (Sigma SRP3123) and IGF (Sigma SRP3069) were used at the indicated doses. MG132 (Enzo Life Science, BML‐PI102) was used at the indicated doses. TTM and penicillamine were purchased from Sigma. Metals including CuSO4, ZnCl2, Fe(NO3)3, Ni(NO3)2, AgNO3, LiCl, MnCl2, CaCl2, and MgCl2 were purchased from Fisher Scientific. Copper‐PDC beads were purchased from Affiland. Metal resin was generated with the metal ions with Glutathione‐Sepharose slurry (Pierce) or NTA Agarose (Qiagen 30310) for 1 h in room temperature and washed twice with phosphate buffered saline (PBS) buffer.
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