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29 protocols using element software

1

Quantifying Protein Distribution in Biofilms

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We used the in situ immunostaining image stacks for quantifying protein distribution using built-in functions of the Nikon Element software. First, background noise in the 561 nm channel was measured by taking images in locations without any biofilms and subtracted from the data. Next, a circular region of interest was manually defined that contains a single biofilm cluster. To be consistent, we only included biofilms of similar heights (25–30 µm) in the analysis. Subsequently, anti-FLAG-Cy3 signals at the glass surface ± 0.5 µm were added and the total signal over the entire biofilm height was integrated; the ratio between the two values was calculated to quantify the ability of the adhesin to preferentially localize at the biofilm-glass interface. The sizes of the puncta in the bap1ΔVelcro biofilms (Supplementary Fig. 2h) were manually measured using built-in tools in Nikon Element software.
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2

Live-cell Multicolor Confocal Imaging

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Cells plated on coverslips were mounted in Attofluor cell chambers (Life Technologies) and incubated with Hepes buffer containing 150 mM NaCl, 10 mM Hepes, 2.5 mM KCl and 0.2 mM CaCl2, 0.1% BSA, pH 7.4 were transferred on the Nikon Ti-E microscope (Nikon) equipped with a Z-driven piezo motor. Imaging were acquired using Nikon A1 confocal unit, through a 60X N.A=1.45 objective (Nikon). CFP, GFP or FITC, YFP, Tomato and mCherry were excited with 440, 488, 514 and 560 nm lasers (Melles Griot), respectively. Emission fluorescences were acquired using a Spectral Detection mode and collected by a 32-channels PMT. Typically, a Z-stack of 4 to 8 images (Z step = 500 nm) was acquired every 5 minutes during 45 to 60 minutes. Data acquisitions were done using Nikon Element Software (Nikon Corporation). After acquisition, raw data were spectrally deconvoluted using Nikon Element Software (Nikon). Every different analysis was done at the single cell level.
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3

Live-cell Multicolor Confocal Imaging

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Cells plated on coverslips were mounted in Attofluor cell chambers (Life Technologies) and incubated with Hepes buffer containing 150 mM NaCl, 10 mM Hepes, 2.5 mM KCl and 0.2 mM CaCl2, 0.1% BSA, pH 7.4 were transferred on the Nikon Ti-E microscope (Nikon) equipped with a Z-driven piezo motor. Imaging were acquired using Nikon A1 confocal unit, through a 60X N.A=1.45 objective (Nikon). CFP, GFP or FITC, YFP, Tomato and mCherry were excited with 440, 488, 514 and 560 nm lasers (Melles Griot), respectively. Emission fluorescences were acquired using a Spectral Detection mode and collected by a 32-channels PMT. Typically, a Z-stack of 4 to 8 images (Z step = 500 nm) was acquired every 5 minutes during 45 to 60 minutes. Data acquisitions were done using Nikon Element Software (Nikon Corporation). After acquisition, raw data were spectrally deconvoluted using Nikon Element Software (Nikon). Every different analysis was done at the single cell level.
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4

FRET-Based Assays for cAMP and Arrestin

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Cyclic AMP was assessed using FRET-based assays. Cells were transiently transfected with the FRET-based biosensors, Epac1-CFP/YFP54 (link) for measuring cAMP and PTHR-CFP with βarr2-YFP for measuring arrestin recruitment. Measurements were performed and analyzed as previously described41 (link). In brief, cells plated on poly-D-lysine coated glass coverslips were mounted in Attofluor cell chambers (Life Technologies), maintained in Hepes buffer containing 150 mM NaCl, 20 mM Hepes, 2.5 mM KCl and 0.1–10 mM CaCl2, 0.1% BSA, pH 7.4, and transferred on the Nikon Ti-E equipped with an oil immersion 40X N.A 1.30 Plan Apo objective and a moving stage (Nikon Corporation). CFP and YFP were excited using a mercury lamp. Fluorescence emissions were filtered using a 480 ± 20 nm (CFP) and 535 ± 15 nm (YFP) filter set and collected simultaneously with a LUCAS EMCCD camera (Andor Technology) using a DualView 2 (Photometrics) with a beam splitter dichroic long pass of 505 nm. Fluorescence data were extracted from single cell using Nikon Element Software (Nikon Corporation). The FRET ratio for single cells was calculated and corrected as previously described41 (link). Individual cells were perfused with buffer or with the ligand for the time indicated by the horizontal bar.
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5

FRET Analysis of cAMP Signaling

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Forster resonance energy transfer (FRET) analysis of cAMP production was performed in HEK293 cells transiently transfected with plasmids encoding PTH1R-WT or mutant, and the Epac1CFP/YFP FRET-based biosensor of intracellular cAMP68 (link). Cells plated on poly-D-lysine–coated glass coverslips were mounted in Attofluor cell chambers (Life Technologies); maintained in Hepes buffer containing 150 mM NaCl, 20 mM Hepes, 2.5 mM KCl, and 1 mM CaCl2, as well as 0.1% bovine serum albumin (BSA) (pH 7.4); and transferred on an in-verted Nikon Ti-E equipped with an oil immersion 40× numerical aperture (NA) 1.30 Plan Apo objective and a moving stage (Nikon Corporation). Recordings were performed at room temperature in single cells upon perfusion of agonist ligand or buffer for ~2 min (indicated by horizontal bar in graph) and during a subsequent washout period. The CFP and YFP fluorescent groups were excited with 440- and 514-nm lasers (Melles Griot), respectively. Fluorescence data were extracted using Nikon Element Software (Nikon Corpo- ration), and calculated as corrected CFP/YFP fluorescent ratios68 (link). Data were normalized to the FRET response induced by forskolin (10 μM) added at the end of test period.
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6

Live-cell imaging of mitotic response

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RPE1 cells stably expressing Histone H2B-RFP or MDA-MB-231 cells stably expressing Histone H2B-mCherry were plated on 4-chaamber 35 mm glass bottom dish at least one day prior to do imaging (#1.5 glass, Cellvis). Cells were treated with DMSO (control), PTX (10 nM), or ERI (10nM) 1 hour prior to imaging. High-temporal live-cell imaging was performed using a Nikon Ti2 inverted microscope equipped with a Hamamatsu Fusion camera, spectra-X LED light source (Lumencor), Shiraito PureBox (TokaiHit) and a Plan Apo 20x objective (NA = 0.75) controlled by Nikon Element software and Metamorph (Molecular Devices). Cells were recorded at 37°C with 5% CO2 in a stage-top incubator using the feedback control to maintain the growing media’s temperature (Tokai Hit, STX model). Image analysis was performed using Nikon Element software. Mitotic stages were determined by nuclear staining. The mitotic duration was measured from nuclear envelope breakdown (NEBD) to anaphase onset. Incidences of multi-nuclei, mitotic slippages and unaligned chromosome were analyzed. The experiments were independently repeated 2–3 times for mitotic duration measurements (total of n = 100), and P-values between variants were calculated by One-Way Anova and two-tailed t-test. P-values < 0.05 were considered significant.
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7

Adipocyte and Hepatic Lipid Analysis

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After euthanizing mice, adipose and liver tissue was collected and immediately put in 10% formalin. The tissue sections were embedded in paraffin and sectioned for hematoxylin and eosin (H&E) staining. To evaluate adipocyte morphology, H&E stained sections were analyzed under a light microscope (Nikon Element software, Nikon Inc., Melville, NY, USA). To evaluate lipid content in liver, Oil Red O staining was performed according to (Mehlem, Hagberg et al. 2013 (link)).
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8

Gastric Mucosal Lesion Analysis in Mice

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The mice were fasted for 24 h (with as libitum access to water) in metabolic cages and then were administered aspirin (200 mg/kg body weight), 6G + ASA (6G was given to mice in the same molar dose of aspirin), and GAS (GAS was given to mice in the same molar dose of aspirin) suspensions by oral gavage. At 4 h after the administration of test compounds, the mice were sacrificed by euthanization with isofluorane and then blood was collected from the heart. After sacrifice, mouse stomachs were removed and cut open along the greater curvature. The gastric contents were emptied, and the stomachs were then washed with PBS. Gastric mucosal lesions were observed under microscope at 10 × magnification and the size of the all lesions were measured and estimated manually. The inner surface was photographed by Nikon stereoscopic zoom microscope (SMZ1500) with DXM 1200 C digital camera system (0.7 × Relay lens) under Nikon Element Software (Nikon Corporation, Kanagawa, Japan). Next the gastric mucosal tissues were removed, frozen in liquid nitrogen and stored at −80 °C.
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9

Live-cell Confocal Imaging Protocol

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Cells plated on coverslips were mounted in Attofluor cell chambers (Life Technologies) and incubated with HEPES buffer containing 150 mM NaCl, 10 mM HEPES, 2.5 mM KCl and 0.2 mM CaCl2, 0.1% BSA, pH 7.4 were transferred on the Nikon Ti-E microscope (Nikon) equipped with a Z-driven piezo motor. Imaging was acquired using a Nikon A1 confocal unit, through a 60 × N.A. = 1.45 objective (Nikon). Fluorescent proteins or peptides containing CFP, GFP, YFP, Tomato or tetramethylrhodamine (TMR) were excited with 440-nm (CFP), 488-nm (GFP), 514-nm (YFP) or 560-nm (Tomato or TMR) lasers (Melles Griot). Data acquisitions were done using Nikon Element Software (Nikon Corporation). After acquisition, raw data were analyzed using ImageJ software. Each different analysis was done at the single-cell level.
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10

3D Fluorescence Microscopy Imaging

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Images were obtained sequentially at 200 nm steps along the z axis using Nikon Element software (Nikon), a Nikon Eclipse Ti microscope with image magnification yielding a 64 nm pixel size from a 100×/1.49NA (Apo TIRF) DIC oil immersion objective (Nikon) and an ANDOR Clara CCD camera (ANDOR). See details in [4 (link)].
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