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15 protocols using 35 mm dish

1

Droplet-based Protein Phase Separation Assay

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After droplet formation, an aliquot of the reaction mixture (200 μM 25QP-GFP in 10% dextran, 150 mM NaCl, 50 mM Na2HPO4/NaH2PO4, pH 7.4) was added to a glass-bottomed dish (35mm dish, 14mm glass diameter; MatTek) that had been treated with 30 mg/mL BSA (Sigma) for 30 mins. The dish was sealed to prevent evaporation and the droplets were imaged by time-lapse fluorescence microscopy using the custom-built TIRF microscope described above (Total Internal Reflection Fluorescence (TIRF) Microscopy), set up in a configuration with the fast steering mirror angled to improve signal-to-noise ratio. Images were collected every 10 s for 1 – 2 hr until the droplets had converted. The laser was operated at 0.1% power (∼0.1mW) and was further reduced in power by placing a half-wave plate and polarizing beam splitter (Thorlabs) in the beam path. Experiments were carried out at room temperature (21°C).
The circularity of the droplets over time was measured by applying automatic local thresholding to each frame using the Otsu method (Otsu, 1979 ) in Fiji to create a binary image of the droplets, then measuring the areas and perimeters. CRs were calculated as described (Intensity and circularity ratios) in R and the mean CR in the field of view was plotted over time.
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2

Transient Transfection and Imaging of Toxoplasma Parasites

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For each condition 1 × 107 parasites were transiently transfected with 30 µg of pTub SAG1ΔGPI-mCherry plasmid (Heaslip et al., 2016 (link)) and immediately added to a confluent HFF monolayer in a Mattek 35 mm dish, coverslip 1.5. 12–15 hr after infection the monolayers were washed three times with pre-warmed Gibco Fluorobrite DMEM supplemented with 4% Fetal Bovine Serum. The coverslips were immediately used for imaging. The acquisitions were made with an Olympus IX71 coupled to a DELTAVISION Elite imaging system in a 37°C environmental chamber. The acquisition for each condition were made sequentially from the washing step to the acquisition with a random order to avoid any artifactual data. The acquisition analysis was made with Fiji and the MTrackJ plugin. The data represent three independent experiments. At least 42 parasites and 273 direct runs were counted per strain. The results were statistically tested with a one-way ANOVA test plus a multiple comparison Dunnett’s test comparing all means to the ΔCAPCAP mean in GraphPad Prism 7. The data presented are as mean ± s.d.
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3

Quantifying Pseudomonas aeruginosa Biofilms

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At the desired concentrations of L-methionine and ivacaftor, PAO-1 was cultured for 24 hours on 14mm glass coverslips within a 35mm dish (MatTek, Ashland, MA). PAO-1 biofilms were stained with SYTO9 and propidium iodide (PI) staining (BacLight™ Live/Dead Bacterial Viability Kit; Molecular Probes, Eugene, OR). The viability was measured with confocal laser scanning microscopy (A1R, Nikon, Tokyo, Japan) and image analyses were performed with ImageJ national institute of health (NIH) image processing software.23 The quantitative structural parameters of the biofilms such as volume and thickness, were extracted from confocal stack images and analyzed. The average z-stacks of 1 μm were acquired from each biofilm horizontal plane with a maximum of five stacks at different fields of view. The quantification of biomass, representing overall volume of cells in the biofilm was carried out using free bioImage_L (www.bioimagel.com. Malmö, Sweden).24 (link)
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4

Fibrin Gel Encapsulation of Actin-GFP 3T3 Cells

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Actin-GFP 3T3 fibroblast cells (8 × 103 cells) were mixed with 10 µl of a 20 U/ml thrombin solution (Omrix Biopharmaceuticals). Then, 10 µl of a 10 mg/ml fluorescently labeled fibrinogen (Omrix Biopharmaceuticals) suspension was placed on a no. 1.5 coverslip in a 35-mm dish (MatTek Corporation) and mixed gently with cell-thrombin suspension. The resulting fibrin gel was placed in the incubator for 20 min to polymerize, after which, warm medium was added to cover the gel. The fibrin gels had an approximate shape of half a sphere, attached to the bottom surface of a coverslip, with a gel height of approximately 2–3 mm.
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5

Quantifying Antibiotic Effects on PAO-1 Biofilms

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To create pre-formed PAO-1 biofilms, PAO-1 was cultured for 24 hours on 14mm glass coverslips within a 35mm dish (MatTek, Ashland, MA). In the pre-formed PAO-1 biofilms, stents containing loaded drugs (ciprofloxacin and azithromycin) were placed in a 24-well tissue culture plate and cultured for an additional 3 days. Stents without loaded drugs (bare stents) were also introduced to serve as a negative control. To visualize both viable and dead bacterial populations, biofilms were stained with SYTO9 and propidium iodide (PI) (BacLight™ Live/Dead Bacterial Viability Kit; Molecular Probes, Eugene, OR). The biofilm was three-dimensionally reconstructed using NIS Elements microscopy imaging software and quantified. The proportions of live and dead bacteria were also quantified using BioFilmAnalyzer v.1.0 (https://bitbucket.org/rogex/biofilmanalyzer/downloads/)22 by counting fluorescence specific pixels in digital fluorescent images. Four different images per condition were selected for analysis.
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6

Fibrin Gel Formation with Actin-GFP Cells

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Actin-GFP 3T3 fibroblast cells (5 × 103 cells) were mixed with 10 μl of a 20 U/ml Thrombin solution (Omrix Biopharmaceuticals). Then, 10 μl of a 10 mg/ml fluorescently labeled fibrinogen (Omrix Biopharmaceuticals) suspension—labeled with Alexa Fluor 546 as we described previously [54 (link)]—was placed on a #1.5 coverslip in a 35-mm dish (MatTek Life Sciences) and mixed with the cells+Thrombin suspension. The resulting fibrin gel was placed in the incubator for 20 min to polymerize, after which, warm medium was added to cover the gel.
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7

COX-2 Fluorescence Imaging Protocol

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SMMC7721, BEL7402, and LO2 cells were at the exponential phase for the fluorescence experiments. The cells were collected and seeded into a glass-bottomed dish (Mat Tek, 35 mm dish with 20 mm wells) and cultured for 24 hours. Then, the medium was changed and replaced with medium containing COX-2 FP (5.0 μM), and the dishes were incubated for 30 minutes in a 37 °C, 5% CO2 environment. A fluorescence microscope was used to continuously observe the cells (λex = 488 nm, λem 550 ± 20 nm).
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8

Immortal Mouse Melanocyte Cell Line Imaging

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The immortal mouse melanocyte cell line melan-a, derived from a black mouse (generous gift of Dorothy C. Bennett, St. George's Hospital Medical School, London, UK), was cultured on glass-bottom dishes (35 mm dish; MatTek, Ashland, MA) as described previously50 (link)51 (link). Plasmids were transfected into melan-a cells by using FuGENE 6 (Promega, Madison, WI) or Lipofectamine 2000 reagents (Invitrogen Corp., Carlsbad, CA), each according to its manufacturer's instructions. Two or three days after transfection, the cells were fixed in 4% paraformaldehyde, permeabilized with 0.05% saponin (Sigma-Aldrich) and 0.5% BSA in PBS, and stained with anti-Lamp-1 antibody (1/1000 dilution) and/or anti-GFP antibody (1/1000 dilution). The antibodies were visualized with anti-rat Alexa Fluor 488/633-conjugated IgG and/or anti-rabbit Alexa Fluor 488-conjugated IgG (Invitrogen Corp.), and the cells were examined for fluorescence with a confocal fluorescence microscope (FV500; Olympus, Tokyo, Japan). The images were processed with Adobe Photoshop software (CS4).
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9

Fibrin Gel Formation for 2D Cell Division Studies

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To prepare flat gels for studies of cell division on 2D fibrin substrates, 10 µl of 5 mg/ml fibrinogen was mixed with 10 µl of 20 U/ml thrombin, placed on a No. 1.5 coverslip in a 35-mm dish (MatTek Corporation), and incubated for 15 min. A sterile coverslip was placed on top of the gel to flatten it. After addition of phosphate-buffered saline to fill the well, the coverslip was removed and the cells were cultured on the gels. The thickness of the gel was measured by confocal imaging of gel-embedded fluorescent beads to be ∼200 µm.
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10

3T3 Fibroblasts and HUVEC Co-Culture in Fibrin Gel

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3T3 fibroblasts-GFP-actin (∼3,000 cells) and HUVEC-RFP (∼3,000 cells) were mixed with 20 µl of 5 mg/ml fibrinogen (Omrix Biopharmaceuticals). In a separate vial, red 0.5 µm carboxylated fluorescent particles (Ex 580/Em 605; Invitrogen) were mixed with 20 µl of a 20 U/ml thrombin solution (Omrix Biopharmaceuticals) and vortexed for 1 min to a final particle concentration of 0.05%. The thrombin suspension was placed on a No. 1.5 coverslip in a 35-mm dish (MatTek Corporation), and mixed gently with the fibrinogen suspension. The resulting fibrin gel was placed in the incubator for 15 min to fully polymerize, after which warm medium (50% fibroblast, 50% HUVEC medium) was added to cover the gel. For imaging of cell division without measurement of matrix displacements, fibrin gels were made in a similar way but without including fluorescent particles.
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