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36 protocols using lsm 510

1

Mesentery Wholemount Immunofluorescence Assay

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Normal or regenerating mesentery wholemounts were treated for 48 hrs with 2.0 mL of the primary antibody RN1 (1:1,000). Afterwards, the primary antibody was removed and the mesenteries were washed three times with 0.1M PBS. Then, the secondary antibody, GAM Cy3 (1:1,000), was applied overnight. The following day, the antibody was removed and the samples were washed three times with 0.1M PBS and mounted on a slide. For this, the mesentery was placed on a glass microscope slide, and using a pair of pins, it was completely extended, avoiding folds or wrinkles. 500–700μL of DAPI D9542 (10μg/mL) in 1:1 PBS:glycerol were carefully added to the tissue, so that the previous step of stretching was not disrupted. Then, a coverslip, was laid on the tissue and the slide was sealed using nail polish.
Slides with tissue sections or whole mounts were observed with a fluorescence microscope (Olympus BX51) and with a confocal laser scanning and difference interference-contrast (DIC) microscope (Carl Zeiss LSM510, Leica TCS SP2 or Olympus Fluoview FV300).
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2

Subcellular Localization of Fluorescent Proteins

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Subcellular localization using the pCambia1300 construct of the coding sequence with a GFP tag driven by a CaMV35S promoter, and the endoplasmic reticulum was labeled with CD3-959-mcherry. All of the fusion constructs were transformed into Agrobacterium tumefaciens strain GV3101, and the bacterial suspension of CD3-959-mCheey (OD600 = 1.0) was infiltrated into fully expanded leaves of 4-week-old N. benthamiana leaves with the equal proportion of Agrobacterium (OD600 = 1.0) using needleless ayringe. The fluorescence signals were examined after plants were grown under dark for 6 h and then grown under light for 48 h by a confocal laser scanning microscope (LSM510, LEICA, Wetzlar, Germany) after staining with DAPI in the dark for 10 min. The fluorescence of green (GFP), red (mCherry) and blue (DAPI) fluorescent proteins was excited at 488, 552 and 405 nm, respectively.
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3

Visualizing OsGLIP1 and OsGLIP2 Localization

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The full-length coding regions of OsGLIP1 and OsGLIP2 were amplified using primers GLIP1-GFP-F/R and GLIP2-GFP-F/R (S1 Table) and inserted into pUN1301 with in-frame fusion with GFP. The resulting constructs were transformed into TP309 to produce GFP fusion plants. GFP signals in roots were visualized using confocal laser scanning microscope (Zeiss LSM510 and Leica TCS SP8). For observation of protein localization in protoplasts, rice protoplasts were isolated from leaf sheaths of the OsGLIP1-GFP and OsGLIP2-GFP transgenic plants according to a previously reported method [64 (link)].
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4

Immunofluorescence Staining of 2D and 3D Cell Cultures

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Cells were fixed in 4% PBS (Fisher Scientific UK, 12579099)-paraformaldehyde for 15 min, incubated in 0.1% Triton-X-100 (Fisher Scientific UK, 11471632) for 5 min on ice, then in 0.2% fish skin gelatin (Sigma, G7041) in PBS for 1 h and stained for 1 h with an anti-E-cadherin (1:100, Santa Cruz sc-21791, mouse monoclonal 67A4) antibody. Protein expression was detected using Alexa Fluor 488 (1:400: Fisher Scientific UK) for 20 min. TO- PRO-3 (Invitrogen, T3605: 1:1000) was used to stain nucleic acids. For immunofluorescence staining of 3D cultures from MCF10A ER:HRAS V12 cells, acini were fixed with 4% paraformaldehyde for 40 min, permeabilized in 0.5% Triton X-100 for 10 min on ice and stained with Rhodamine-phalloidin (Molecular Probes, R415) for 1 h at room temperature. Acini were counterstained with DAPI. Samples were observed using a confocal microscope system (Carl Zeiss LSM 510 or LSM 710, or Leica SP8). Acquired images were analyzed using Photoshop (Adobe Systems, United States) according to the guidelines of the journal.
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5

Corneal Immunofluorescence Staining Protocol

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Corneal explants were fixed in 4% paraformaldehyde overnight, transferred to 30% sucrose/PBS solution overnight and embedded in OCT compound (Tissue-Tek, Sakura). Ten-micron-thick transversal frozen sections were cut with a cryo-microtome. Sections were stained with 1 μg/ml bis-benzimide Hoechst (Sigma-Aldrich) and mounted with Vectashield (DAKO). For the immunofluorescence CD34 staining, sections were thawed for 15 min at room temperature, washed in PBS for 15 min to remove OCT, permeabilized (0.1% Triton) for 15 min at room temperature and blocked in 2.5% horse serum/0.5% BSA/0.1% Triton for 30 min. Primary antibodies were incubated on sections overnight at 4 °C, and the secondary antibody incubated 90 min, at room temperature prior to Hoechst labeling and mounting. For the human corneas, the primary antibody used was 1:100 mouse anti-human CD34 (clone B1-3C5; AbCam, Cambridge, UK) and the secondary antibody 1:500 goat anti-mouse IgG-Alexa546 (Molecular probes, Invitrogen). For the dog corneas, the primary antibody used was 1:100 mouse anti-dog CD34-PE (clone 1H6, eBioscience) and the secondary antibody 1:500 goat anti-mouse IgG-Alexa Fluor 546 (Molecular probes, Invitrogen). Observations and acquisitions were performed with either a Zeiss LSM510 or a LEICA SP5 laser scanning confocal microscope. Image analyses were performed using MetaMorph software.
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6

Visualizing Plant Protein Localization

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The GFP- or mCherry-tagged AtBiP1, AtBiP2, AtBiP3, CMV MP, AtBiP1SP, AtBiP2AP, AtBiP3SP, AtBiP1ΔSP, AtBiP2ΔSP, AtERdj2A, and AtERdj3A were transiently expressed in N. benthamiana leaves using agroinfiltration, as described previously (Ham et al., 2012 (link)). Zeiss LSM510, Leica TCS SP5, and Leica Stellaris 5 were used for confocal imaging. GFP-tagged proteins were excited with 488 nm and emission was detected at 505–545 nm. The excitation and emission spectra of mCherry-tagged proteins were 561 nm and 587–624 nm, respectively.
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7

Confocal Microscopy Imaging of Larval Stages

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All specimens were examined as whole-mounts on laser scanning microscopes Zeiss LSM 510, Leica TCS SP5 and Leica TCS SPE with high aperture oil immersion objectives using appropriate wavelength-filter configuration settings. No fewer than 100 embryos were examined at each stage for each of the antibodies. For each larva, 40–150 0.5 μm thick optical sections were taken and processed with Zeiss LSM IB, Leica LAS AF, Bitplane Imaris and ImageJ. Three-dimensional (3D), rotatable reconstructions were produced using Imaris and converted into AVI files. A series of optical sections were also projected into single images and exported as TIFF images. These images were then adjusted for contrast and brightness and assembled into plates using Adobe Photoshop CS.
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8

Whole Mount Staining of Orb2, Bol, and Other Proteins

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Whole mount staining was performed as in [29] (link). Antibodies used were as follows: mouse anti-Orb2 2D11 and 4G8 IgG (undiluted, developed in the lab) [29] (link), rabbit anti-Bol (1∶1000, a gift from Steven Wasserman) [46] (link), monoclonal anti-β-Tubulin E7 1∶50 (Developmental Studies Hybridoma Bank), rabbit anti-aPKCζ (1∶1000, clone c-20, sc-216, Santa Cruz Biotechnology), rabbit anti-GFP (1∶1000, Cristea Lab, Princeton University). Rabbit polyclonal anti-Dlg-PDZ1 (1∶1000) and guinea pig anti-Bazooka (1∶500) were provided by Yu-Chiun Wang [47] (link). Actin was stained with Alexa488-phalloidin (Invitrogen, Carlsbad, CA). DNA was stained with Hoechst (1∶1000). Secondary antibodies used were goat anti-mouse IgG Alexa 488, 546 or 647, goat anti-rabbit Alexa 488, 546 or 647 (Molecular Probes, Inc.). Samples were mounted in Aqua-polymount on slides for an inverted Zeiss LSM510 or Leica SP5 confocal microscope.
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9

Confocal Imaging of Neuronal Dynamics

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Confocal stacks of fixed brains were made using Zeiss LSM 510 or Leica SP6 confocal microscopes. Neuronal cell culture imaging was conducted with an AxioCam camera mounted on an Olympus BX50WI microscope. DCN live imaging was conducted with a Leica SP6 resonance scanning confocal microsocope. In general, a confocal stack comprising the axonal projection of Dorsal Cluster Neurons (30–40 single projections) was recorded every 5 min. Resonance scanning allowed high scan speed with lower laser intensities and therefore ensures preservation of living tissue due to decreased photo-toxicity. Projection images were generated and further processed with ImageJ. For tracking of axon branches we have used the ‘simple neurite tracer’ a plugin for ImageJ from Mark Longair (Fiji, http://pacific.mpi-cbg.de).
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10

Visualizing Autophagy Activation in Cells

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Coverslips were placed into each well of a 12-well plate. Cells were plated on top of the cover slips and left to incubate with full media and 10 uL of anti-LC3 B GFP antibody (Molecular probes by Life Technologies, Waltham, MA, USA) for 1 h at room temperature and treated with EBSS over various time points. 4% paraformaldehyde (PFA) was added to each well at 4 °C and DAPI (4′,6-diamidino-2-phenylindole) was counterstained for 10 min. The cover slips were washed with PBS 3x and mounted onto microscope slides. The dry slides were visualized with a confocal microscope (Leica LSM 510, Wetzlar, Germany).
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