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4 protocols using metamorph basic software

1

Quantifying Fluorescence in Brain Sections

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Fixed cerebral tissues were sectioned on a vibratome (VT1000P, Leica) at 100 μm thickness. Every sixth coronal section, for a total of six sections representative of the cranio-caudal axis between +1.10 AP to −2.46 AP, were mounted (Superfrost Plus Microscope Slides, Fisher Scientific) with ProLong Gold Antifade with 4’,6-diamidino-2-phenylindole (DAPI) (Invitrogen) and cover slipped (22×40 mm, Fisherfinest Premium Cover Glass, Fisher Scientific). A stereomacroscope (MVX10, Olympus) with a 0.63x objective (MV PLAPO, 0.15NA) and a 2x zoom was used to perform epifluorescence microscopy. Image acquisition was controlled with MetaMorph Basic software (Molecular Devices). A wavelength of 525 nm and a 607/40 nm BP emission filter were used for excitation and detection of OA-555, respectively. Exposure times were kept constant across all experimental groups and time points. ImageJ was used for image quantification. Regions of interest (ROI) were drawn around the ipsilateral and contralateral total hemisphere, cortex, white matter (corpus callosum and external capsule), hippocampus, and subcortex. The percent area above a pre-determined threshold level (50 AU, 8-bit depth) was measured in each ROI.
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2

Cardiomyocyte Proliferation and Sarcomere Analysis

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To study proliferation and sarcomere development in the native healthy and CDH+ hearts, sections were stained for nuclei (Hoechst 33258), Ki67 (Abcam, rabbit polyclonal), and sarcomeric α-actinin (Sigma, mouse monoclonal). Briefly, the samples were washed with PBS, then blocked with 5% donkey serum and 1% bovine serum albumin (BSA) for 1 h at room temperature. Incubation with primary antibodies was for 1 h, followed by 3 PBS washes, then incubation with secondary antibodies (AlexaFluor 488 donkey anti-rabbit IgG, AlexaFluor 555 donkey anti-mouse IgG; Invitrogen) for 1 h. After washing with PBS, the samples were imaged on an Olympus IX8I microscope with Metamorph Basic software (version 7.7.4.0, Molecular Devices). Image analysis to determine cardiomyocyte proliferation and sarcomere length was carried out as described below in sections Cell proliferation measurements and Cardiac cell culture with exogenous nitrofen.
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3

Membrane Potential Measurement Protocol

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To verify that both treatments led to alterations in resting cell membrane potential, the voltage sensitive dye Bis-(1,3-dibutylbarbituric acid)-trimethine oxonol (DiBAC4(3)) was used [28 (link)-30 (link)]. Briefly, a stock solution was prepared at a concentration of 2 mM and diluted 1:4000 [28 (link)] in the media described above. Fluorescent images were obtained for each of the groups described above using an Olympus IX81 microscope (Olympus America, Chelmsford, Massachusetts) equipped with Metamorph Basic software (version 7.7.4.0, Molecular Devices, Sunnyvale, CA) and subsequently analyzed in ImageJ (v1.45s, NIH, Bethesda, MD). Fluorescence intensity ratio was measured as the cell membrane fluorescence intensity divided by the background intensity. A minimum of 149 cells per condition was measured. The ratio reflects the relative membrane potential with a larger ratio corresponding to a more depolarized membrane.
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4

Visualizing Cell Morphology in ECM-Fibrin Gels

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Immunostaining was used to assess cell morphology and make measurements over
time within the ECM-fibrin gels. Briefly, samples were fixed at 1, 7, and 21 days in 4%
paraformaldehyde (PFA) for 2 hr at 4°C. Cells were permeabilized with 0.1%
TritonX-100 in PBS for approximately 30 min at room temperature and then blocked with 5%
donkey serum and 1% bovine serum albumin (BSA) in PBS for 2 hr at 37°C. Actin
fibers and nuclei were stained using TRITC-labeled Phalloidin (Sigma) and Hoechst 33342
(Invitrogen), respectively, for 2 hr at 37°C. Samples were washed several times
with PBST and then imaged using an Olympus IX81 microscope equipped with spinning disk
confocal and Metamorph Basic software (version 7.7.4.0, Molecular Devices).
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