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13 protocols using 5 bromo 4 chloro 3 indolyl β d galactopyranoside

1

Senescence-Associated β-Galactosidase Assay

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Cell fixation was performed in 0.5% glutaraldehyde/PBS for 15 min at RT. After washes in 1 mM MgCl2/PBS, pH 6, the cells were incubated in staining solution [2 mg/ml 5‐bromo‐4‐chloro‐3‐indolyl‐β‐D‐galactopyranoside (Sigma, B4252), 1.64 mg/ml K3Fe(CN)6, 2.1 mg/ml K4Fe(CN)6.3H2O in 1 mM MgCl2 1, pH 6] at 37°C, for 24 hr. The production of a blue precipitate within the cytoplasm, as observed under an inverted microscope, determined the lysosomal SA‐β‐gal activity (Dimri et al., 1995).
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2

Senescence and Telomerase Activity Assays

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Senescence was quantified by the activity of senescence-associated β-galactosidase (SA β-gal) at pH 6, as described (Itahana et al. 2013 (link); Martín-Pardillos et al. 2013 (link)), using 5-bromo-4-chloro-3-indolyl-β-d-galactopyranoside (Sigma), after fixing the cells with paraformaldehyde.
Telomerase activity was determined by a fluorescence-based telomeric repeat amplification protocol (TRAP) using a TRAPEZE XL Telomerase Detection Kit (Millipore International, Inc., Darmstadt, Germany). Fluorescence was quantified using a DTX 880 Multimode plate reader (Beckman Coulter, Fullerton, CA).
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3

Adenovirus-Mediated Gene Transduction Assay

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The cell line indicated in each experiment was seeded at 5×105 cells per 35-mm dish and infected the following day using a multiplicity of infection (MOI) of 1 of Ad-LacZ virus preparation diluted in culture medium to a final volume of 500 μL. The transduction was carried out at 37°C for 4 h before adding 1.5 mL of fresh medium. The cells were then cultured at 37°C for 12 to 72 h before harvesting for assays where HT1080 cells were transduced with equal volumes of adenovirus-containing cell lysate and later stained with X-gal (5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside, Sigma Aldrich) or cell lysate was incubated with O-nitrophenyl-beta-D-galactopyranoside (ONPG, Sigma Aldrich), both protocols as described previously (25 (link)).
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4

EGFR-Targeted Enzyme Reporter Assay

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Biotinylated EGF for the EGFR was linked to biotinylated β-gal using fluorophore-conjugated SA. Ligand, linker, and reporter fragment were mixed in a molar ratio 1:1:3 at room temperature for 1 h. Excess d-biotin was added to block any remaining unbound SA sites. In the case of control assays, untargeted reporter complex was prepared with d-biotin, in place of the ligand, mixed with linker and reporter fragment in a molar ration 1:1:3. The ligand-complex was then diluted to 500 mL with cell feeding media (DMEM, 10% fetal bovine serum, 1% penicillin–streptomycin) and added directly to coverslips seeded with cells overexpressing human EGFR. Cells were incubated with EGF ligand-complex for 1 h at 37 °C. The cells were then fixed with 4% paraformaldehyde, rinsed with X-gal wash buffer, and stained overnight at 37 °C with 1 mg mL−1 X-gal (5-bromo-4-chloro-3-indolyl-β-d-galactopyranoside; Sigma; St Louis, MO, USA) in 5 mM K3Fe(CN)6, 5 mM K4Fe(CN)6, and 2 mM MgCl2 in PBS. Cells were rinsed twice with PBS for 5 min. Images were captured by a Retiga EXi camera connected to a Leica DM4000 B upright microscope (Leica Microsystems; Wetzlar, Germany).
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5

Antimicrobial Susceptibility Testing using Novel Agents

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Four antimicrobial agents: cefepime (Bristol-Myers Squibb), ceftazidime (Polpharma), cefotaxime (Sigma), ceftriaxone (the Institute of Biotechnology and Antibiotics, Warsaw) and ofloxacin (Sigma), as well as EPI Phe-Arg-β-naphthylamide (PAβN; Sigma), were used in the study to determine the MIC values of antimicrobial agents ± EPI. Detection of ESβL production by Gram-negative rods was determined using antibiotic discs from Becton Dickinson. For the selection of transformants and transconjugants during construction of the P. aeruginosa PAO1161 ΔampC mutant, ampicillin (Sigma), carbenicillin (Sigma), rifampicin (Sigma), isopropyl-β-D-thiogalactopyranoside (Sigma) and 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (Sigma) were used.
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6

Embryonic β-Galactosidase Staining

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After fixation of mutant and control E13.5 embryos in 0.2% glutaraldehyde in PBS for 30 min at room temperature, embryos were washed three times in rinse solution (0.005% Nonidet P-40 and 0.01% sodium deoxycholate in PBS) and then stained in 5 mM potassium ferricyanide, 2 mM MgCl2, 0.4%β-gal (5-Bromo-4-chloro-3-indolyl β-D-galactopyranoside, B4252 Sigma Aldrich) in PBS for 2–3 h at room temperature followed by 2 times rinse in PBS and post-fixation in 3.7% formaldehyde. Frozen 20 µm sections were mounted on slides and fixed in 0.2% glutaraldehyde in PBS for 10 min on ice. Slides were incubated in detergent rinse solution for 10 min, then stained in β-gal staining solution at 37 °C for 2–3 h and post-fixed in 3.7% PFA for 2 h. Slides were counterstained with Nuclear Fast Red and Eosin solution.
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7

Senescence-Associated β-Galactosidase Assay

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Senescence was determined by measuring the senescence-associated β-galactosidase (SA-β-Gal) activity. Briefly, cells were fixed for 3–5 min at room temperature in 3% formaldehyde and incubated with fresh SA-β-Gal staining at 37°C for 3 h. The staining solution included 1 mg/mL of 5-bromo-4-chloro-3-indolyl β-d-galactopyranoside (B4252, Sigma-Aldrich), 40 mM citric acid/sodium phosphate (pH 6.0), 5 mM potassium ferrocyanide (P3289, Sigma), 5 mM potassium ferricyanide (P4066, Sigma), 150 mM NaCl (S9888, Sigma), and 2 mM MgCl2 (M9272, Sigma). The percentage of senescent cells was calculated by the number of β-galactosidase positive cells (blue) out of a total number of cells per field. Images were acquired with an IX51 Olympus inverted fluorescent microscope.
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8

Senescence Induction and Detection

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z-VAD-fmk (ApexBio) was dissolved in DMSO and used at a final concentration of 20 μM. Staurosporine (Sigma Aldrich) was dissolved in DMSO and used at a final concentration of 1μM. MCC950 (Sigma Aldrich) was dissolved in DMSO and used at a final concentration of 10μM. Sytox Green (Life Technologies) was used at a final concentration of 500nM. Hoechst 33342 was dissolved in DMSO and used at a final concentration of 0.33μg/ml. Bleomycin sulfate (ApexBio) was dissolved in DMSO and used at a final concentration of 75μg/ml. 5-Bromo-4-chloro-3-indolyl β-D-galactopyranoside (Sigma) was used at a final concentration of 1mg/ml. Senescence associated β-Galactosidase staining solution (SA-Gal) was made as previously described (67 (link)). Puromycin (Invivogen) was used at a final concentration of 1μg/ml.
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9

Embryonic β-Galactosidase Staining

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After fixation of mutant and control E13.5 embryos in 0.2% glutaraldehyde in PBS for 30 min at room temperature, embryos were washed three times in rinse solution (0.005% Nonidet P-40 and 0.01% sodium deoxycholate in PBS) and then stained in 5 mM potassium ferricyanide, 2 mM MgCl2, 0.4%β-gal (5-Bromo-4-chloro-3-indolyl β-D-galactopyranoside, B4252 Sigma Aldrich) in PBS for 2–3 h at room temperature followed by 2 times rinse in PBS and post-fixation in 3.7% formaldehyde. Frozen 20 µm sections were mounted on slides and fixed in 0.2% glutaraldehyde in PBS for 10 min on ice. Slides were incubated in detergent rinse solution for 10 min, then stained in β-gal staining solution at 37 °C for 2–3 h and post-fixed in 3.7% PFA for 2 h. Slides were counterstained with Nuclear Fast Red and Eosin solution.
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10

Measuring Protein-Protein Interactions Using Yeast Two-Hybrid

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The Interaction Trap two-hybrid system was used (Gyuris et al., 1993 (link)). Plasmids pEG202, pJG4-5, and pSH18-34 and the strain EGY48 were kindly provided by Dr. R. Brent (Fred Hutchinson Cancer Research Center, Seattle, WA). To measure β-galactosidase activity, EGY48 cells bearing the lexAop-lacZ reporter plasmid pSH18-34 were cotransformed with the appropriate pEG202- and pJG4-5–derived plasmids and streaked out on 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside containing Synthetic Dextrose/Gal/Raf-His-Trp-Ura plates (0.67% yeast nitrogen base [Difco], 7 g/liter Na2HPO4, 3 g/liter NaH2PO4, 2% galactose, 1% raffinose, 40 mg/ml leucine, 80 mg/liter 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside [Sigma Chemicals], and 2% agar, pH 7). Pictures were taken after 2 d of growth at 24°C.
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