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76 protocols using lsm 410

1

3D-TrIm Instrument Design Protocol

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The 3D-TrIm instrument design is shown in Extended Data Fig. 1 and consists of 3D-SMART tracking excitation optics and 3D-FASTR imaging excitation optics coupled through a commercial confocal microscope (Zeiss LSM 410, modified by LSM Tech), piezoelectric stage, and microscope objective to join both setups together. The microscope is controlled by custom code LabVIEW code.
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2

Localization of BrHMA3 in Tobacco Protoplasts

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The full-length coding sequence of BrHMA3 (cv. Chiifu) was amplified without the stop codon. The sequence was cloned into the vector pSAT6A-eGFP-N1 (BamHI and KpnI) under the control of the Cauliflower mosaic virus 35S promoter. The 35S:BrHMA3-eGFP fragment was introduced into the expression vector pRCS2-ocs-nptII (PI-PspI). pCAMBIA-1302 vector with a 35S-eGFP (enhanced green fluorescent protein) fragment was used as a control. The constructs were transferred into Agrobacterium tumefaciens strain GV3101 and transiently expressed in tobacco (Nicotiana benthamiana) leaves (Xu et al., 2017 (link)). The protoplasts of the tobacco mesophyll cells were isolated after the removal of the cell wall by cellulase. A vector containing the AtTIP2.3 gene (At5g47450) and mCherry was co-transferred as a tonoplast-localized marker. Fluorescence of the protoplasts was observed under a confocal laser scanning microscope (LSM410; Carl Zeiss) with the excitation and emission wavelengths of 488 nm and 509 nm for GFP, and 580 nm and 610 nm for mCherry, respectively. Primers used are listed in Supplementary Table S3.
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Osteoclast Resorption Pit Analysis

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Osteoclasts were replated on dentine slices for 10 h–12 h in the presence of TNF-α. Resorbed areas were scanned using Bio-Rad confocal microscopy essentially as previously described.47 (link) The dentine slices mounted on No. 1 coverslips were viewed with a 40 × 0.6 NA air objective. Images were recorded in the epi-reflection mode using the 488-nm line of the argon laser in a 512 × 512-pixel format. Data collection and processing were accomplished with the Zeiss LSM 410 software package. Photomicrographs were stored in a TIFF image format. The area of the pit was determined from the free-hand traced perimeter using the LSM software Area Measurement function. Images were stored in TIF format and processed by Adobe Photoshop (Adobe Systems Inc.).47 (link)
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4

Exosome Labeling and Uptake in hFOB1.19 Cells

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Exosomes were labeled using the PKH67 Green Fluorescent Cell Linker Kit according to the manufacturer’s instructions. In brief, 100 µl exosomes isolated from PC3 cells with different treatments were diluted in 1 ml diluent C from the kit and 6 µl PKH26 dye was diluted in 1 ml diluent C. The dilutions were mixed continuously for 30 s and kept at room temperature for 5 min. Then 2 ml 10% BSA(Seyotin, Guangzhou, China) in PBS was added to quench the staining. Labeled exosomes were washed in 10 ml PBS and collected by centrifugation at 100,000 g for 70 min. hFOB1.19 cells were then incubated with exosomes for 24 h. After washing with PBS, cells were fixed with 4% paraformaldehyde for 10 minutes. Nuclei were stained with DAPI solution. Images were captured by a confocal laser scanning microscope LSM410 (Carl Zeiss, Germany)
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5

Immunofluorescence Analysis of Actinin 4 and L-type Calcium Channel β3 Subunit

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Ros 17/2.8 cells and MG63 cells were plated on chamber slides (NalgeNunc International, Naperville, IL, USA). When the cells were extended thoroughly, they were washed three times with PBS and fixed with 4% paraformaldehyde in PBS for 25 min. Following three washes with PBS, the cells were permeabilized with 0.1% Triton X-100 for 5 min at room temperature. Then they were blocked with 1% BSA for 1 h at room temperature followed by three washes with PBS. The cells were incubated with anti-actinin 4 antibody (Abcam, Cambridge, MA, USA) and anti-β3 subunit antibody (Alomone, Jerusalem, Israel) at 4°C over night and 30 min at room temperature the next day with gently rocking. After washing with PBS for 10 min for three times, the cells were incubated with the secondary antibodies with labeled with Rhodamine or FITC (Jackson Lab., Barharbor, Maine, USA) at room temperature for 2.5 h shield from light. After three washes with PBS likewise, cells were counterstained with DAPI nuclear stain for 5 min and washed once with PBS, and mounted with Vectashield and reserved at 4°C shield from light. The fluorescent signals were visualized by confocal microscopy (LSM 410; Carl Zeiss, Oberkochen, Germany).The co-localization of actinin 4 and L-type calcium channel β3 subunit was determined by evaluating at least five samples.
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Visualization of Spheroid Viability

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Two weeks after 5-FC, PDT or 5-FC+ PDT treatment, 2–3 spheroids from the various experimental and control groups were transferred to glass bottomed imaging dishes, stained using a combination of Hoechst 33342 and Ethidium Homodimer 1 (Invitrogen H1399, Carlsbad, CA) for 1 h, washed and visualized using a two photon inverted Zeiss laser-scanning fluorescent microscope (LSM 410, Carl Zeiss, Jena, Germany). Fluorescent images were pseudo-colored blue (live) and red (dead).
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7

Enriched Islet Cell Aggregation Assay

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Sorted α- or β-cells were counted and cultured in 500 μL of CMRL-1066 with 10% FBS and 5.6 mM glucose for a period of 3 days in Corning Ultra-Low Attachment plates (Corning/Costar, Ithaca, NY). Each well contained either 20k sorted α-cells, mixed α- (20k) and β-cells (20k), or approximately 50k dispersed but non-sorted cells containing approximately 20k α-cells, calculated based on the α-cell percentage determined by flow cytometry. The cells were given 72 h to aggregate in culture. Intact human islets were included as controls.
Samples of the sorted cells were concentrated on glass slides by cytocentrifugation, fixed in 2.5% paraformaldehyde for 10 min, and then immunofluorescence stained for human glucagon (Sigma, Cat. #G2654), insulin (Dako, Cat. #A0564), Somatostatin (SST, ZYMED, Cat. #18-0078) and ghrelin (Abcam, Cat. #ab209790) to confirm purity. Secondary antibodies conjugated with Dylight-dyes (Jackson ImmunoResearch) were used for fluorescence detection. Digital images of fluorescence-labeled cells were acquired using a Zeiss fluorescence axial microscope attached with a digital camera or with a Zeiss LSM410 confocal laser-scanning microscope.
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8

Transient Expression of pBI121-BplMYBs-GFP in Onion Cells

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The pBI121-BplMYBs-GFP fusion gene and pBI121-GFP (control) were transiently expressed in onion epidermal cells using the particle bombardment (Bio-Rad) method. The transformed cells were then cultured on MS medium for 24–48 h and analyzed using a confocal laser-scanning microscope at 488 nm (LSM410, Zeiss, Jena, Germany).
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9

Examining E-cadherin Distribution in IL-6-stimulated Cells

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HCT116 cells seeded on glass cover slips were stimulated with IL-6/sIL-6R for 72 h. After being washed twice with PBS, cells were fixed for 15 min at room temperature in paraformaldehyde (4% in PBS). Cells were then incubated with 0.1% Triton X-100 in PBS for 1 min for permeabilization. After being washed twice, cells were treated with 1% BSA in PBS for another 1 h. Cells were reacted with rabbit anti-E-cadherin antibody (Cell Signaling Technology, Danvers, MA, USA) (1:100 dilution in PBS) for 2 h at room temperature. Slides were washed twice and incubated with FITC-conjugated goat anti-rabbit IgG for another 1 h. DAPI containing mounting solution (SlowFad Gold, Thermo Fisher Scientific, Waltham, MA, USA) was used to mount the slides. E-cadherin distribution was then observed under a confocal microscope (Zeiss, LSM 410). Blue fluorescence (derived from DAPI) represented nuclei and green fluorescence indicated E-cadherin.
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10

Biofilm Dynamics Imaged by Confocal Microscopy

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For direct observation of the effect of the drug on the dynamics of biofilm formation, Confocal Laser Scanning Microscopy was performed on bacterial biofilms of select organisms namely, S. aureus (ATCC 29213), S. epidermidis (ATCC 35984), and E. coli (ATCC 25922) with and without adding CurQDs as per need, on poly-L-lysine coated 8-well cell chambered slides (Nunc, Denmark) as described earlier with minor modifications (Pitts et al., 2003 (link); Schlafer and Meyer, 2016 (link)). Briefly, biofilms were formed in the presence of serially double-diluted concentrations of CurQDs at 37°C for 48 h. BHI-broth without the drug served as negative control. The biofilms were incubated with 6.6 μM concentration of DAPI (Invitrogen, United States) for 30 min in dark and were analyzed by Carl Zeiss Confocal systems.
The effect of drug CurQDs over 72 h bacterial biofilms was assessed as above. The chambers were visualized with the Zeiss LSM 410 with 63X 1.4 NA oil objective lens. All images were obtained and analyzed using ZenBlue imaging software. Co-localization maps were also constructed to study and interpret the interaction of autoflourescent Curcumin and DAPI.
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