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Confocal Fluorescence Microscopy: A Technique to Determine the Localization of Proteins in Mouse Fibroblasts

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Confocal fluorescence microscopy is a specialized imaging technique for localization of a protein or antigen of interest in a cell or tissue sample by labeling the antigen with an antibody-conjugated fluorescent dye and detecting the fluorescent signal. It offers higher spatial resolution than wide-field fluorescence microscopy, with the help of two pinholes placed at the focal planes of the objective lens, giving it the name confocal. It enables users to visualize the staining at a subcellular level, such as the differentiation between surface membrane staining from intracellular staining.

A confocal microscope follows a similar basic principle as a classic fluorescence microscope. The beam from a light source, usually a laser for confocal, is reflected by a dichroic mirror and focused by an objective lens on the sample. This light excites the fluorophores to emit a different wavelength, which travels back through the objective lens and dichroic mirror to a camera or eyepiece.

The enhanced resolution of a confocal microscope is mainly due to the presence of two pinholes, which are very small holes for light to pass through on the excitation and emission light paths. The pinholes are strategically placed at the focal plane of the objective lens. Now, let's switch to a side view schematic of the microscope arrangement to review the light path. After passing through the excitation pinhole, the excitation light beam has the effect of originating from a focal point, which enables the objective lens to then focus the light to a point on the sample as well. The emission beam from this focal point converges at the emission pinhole, which allows it to pass through. Now during excitation, fluorophores within the light path, above and below the focal point, are also slightly excited. While the emission light originating from the focal point passes through the pinhole, the emissions from the out-of-focus points converge before or after the emission pinhole, and are hence blocked, resulting in reduced background fluorescence.

The excitation-emission-detection cycle needs to be repeated for each imaging point in the region of interest, which can be done in a few different ways. For example, laser scanning confocal uses galvanometer scanning mirrors, which deflect the excitation light at different angles. Hence, sweeping the light beam across the specimen in the XY plane. Spinning disc confocal uses a disc with an array of pinholes, which rotates to shift the arrangement of the pinholes. This enables users to illuminate multiple small imaging points in the sample each time, gradually covering the whole area as the disc rotates. As a result of the pinholes, the XY image at the detector represents a narrow Z plane. Therefore, images can be collected from a series of consecutive Z planes, often referred to as a Z stack. From these images, an appropriate software can generate a 3D depiction of the fluorescence signal pattern in the sample.

In this protocol, you will observe immunostaining of mouse fibroblasts, followed by imaging on a confocal microscope to differentially visualize a cell surface protein and a lysosomal protein.

To begin, using sterile techniques, resuspend the cells of interest in 500 microliters of growth media per well, and then seed them into the wells of a four-well chamber slide. Here, we are using mouse fibroblasts that were transfected to express the antigen-presenting molecule, CD1d. To allow cells to adhere to the glass, place the chamber slide in a 5% carbon dioxide incubator at 37 degrees Celsius, and incubate overnight. In the morning, aspirate the media from each well, and then wash the cells once with 500 microliters of PBS for a few seconds.

To fix the cells, add 500 microliters of 1% paraformaldehyde solution into each well, and incubate for 15 minutes at room temperature. After the incubation, collect the paraformaldehyde into an appropriate hazardous liquid waste container, and then remove any remnants of the fixative by washing the cells three times with PBS for a few seconds.

To allow antibody penetration into the cells, add 500 microliters of permeabilization buffer to each well, and incubate on the bench for 15 minutes at room temperature. After permeabilization, wash the cells briefly three times with 500 microliters of PBS. Next, add 500 microliters of blocking buffer to each well, and incubate for one hour at four degrees Celsius to prevent nonspecific antibody binding.

Prepare the primary antibodies, anti-CD1d and anti-LAMP-1, at appropriate working concentrations. Then, aspirate the buffer from the wells and cover the cells in each well with 500 microliters of diluted primary antibody solution and then incubate the slide on a flat surface overnight at four degrees Celsius. The next morning, dilute the secondary antibodies, in this case an anti-mouse and anti-rat antibody with distinct fluorescent tags, in blocking buffer to appropriate working concentrations. Next, aspirate the primary antibody solution from the wells and then wash the cells four times with 500 microliters of PBS. Then, add 500 microliters of the diluted secondary antibody solution to each well, and incubate at room temperature for one hour in the dark. After the incubation, aspirate the secondary antibody solution and wash the wells four times with 500 microliters of PBS to remove any unbound secondary antibody.

To mount the samples after the final wash, carefully detach and remove the chambers from the slide. To remove the residual PBS, hold the slide at an angle over a delicate task wipe, and remove the fluid from the edges without touching the cells. Once the excess PBS is removed, add one drop of antifade mounting medium, containing the nuclear stain DAPI, onto each section of cells. Next, take a 20-by-60-millimeter coverslip, and using just fingertips start lowering the coverslip slowly on either edge, taking care to avoid bubble formation over the cells. Wipe off any extra mounting medium on the slides with a delicate task wipe and store the slides in the dark at room temperature for up to a week.

To begin imaging the cells, first click on the NIS software icon on the desktop. Once in the control window, click on the TiPad tab at the top, and choose the desired objective for imaging. Then, load the slide with cells onto the stage, and center it beneath the lens. Next, on the A1plus Compact GUI tab next to the TiPad tab, set up the lasers appropriate for the fluorophores used. Click on the gear symbol to open the dye and spectral settings menu. Once the dye and spectral settings menu is open, select the channels needed and set the laser for each channel. Then, select the appropriate emissions in the drop down menu under the first dichroic mirror. Next, under A1plus Compact GUI window, click on Ch.Series to set up the line channel series, which sets up whether the lasers used will fire on the sample simultaneously or sequentially.

After that, start scanning by clicking the arrow-tip icon on the top. At this point, while the imaging is live, under A1plus Compact GUI window, click on the sliding scale, and modify the pinhole size to assure limiting out-of-focus light. Next, adjust the high voltage and offset settings under each laser to appropriate levels by using the sliding scales to enable detection of the specific staining while limiting any potential background staining. If a positive staining sample is available, start by imaging this sample for each channel to make sure the laser settings yield optimal signal-to-noise ratios. After setting the optimal HV and offset values for each laser, click on the ND Acquisition tab, and then select the Z icon to set up the parameters for the z series.

Next, while acquiring a live image of the sample, first set the bottom by finding the bottom of the image and clicking the bottom button. Then, find the top position of the sample and click the top button. Set the step size either by specifically typing the preferred step size in microns for each step or by specifying how many total steps are needed. To select the desired size/ pixel resolution of the image, click the Aiplus Compact GUI window, and under the size icon, select the desired resolution.

To decrease the noise of the image, you can select the drop-down menu next to the theta symbol to average the selected number of images. After this, click the Run Now tab on the ND Acquisition menu in order to start imaging the sample. After imaging is complete, save the image by clicking file, then save as, which will export the image file with the extension dot-nd2. Finally, repeat the process for each of the other samples.

In this experiment, mouse fibroblasts expressing the surface glycoprotein gene CD1d were fixed, immunostained, and imaged on a confocal microscope. This image shows a single section of a Z stack at 40X magnification, where CD1d is stained in red. The sample was costained with LAMP-1, a lysosomal marker, in green. Nuclear stain DAPI was used to show the nuclei of the cells.

In a composite image where the three different channels are merged, the appearance of yellow results from overlap of the red and green channels, and indicates an area where CD1d and LAMP-1 are co-localized in the lysosomes. Areas where only one color is present indicate the presence of CD1d or LAMP-1 without co-localization. This image shows a 3D rendering of the cells constructed from images captured in the z-stack and this method enabled the construction of a side view of this group of cells. This following image shows a slice out of the z-stack at 100X magnification, demonstrating the expression patterns of these two proteins in greater detail. The pink outlined box on the right side of the image displays the cross-section of the x-coordinate designated by the pink line in the image, which represents the side view at the pink line. Similarly, the blue outlined box on the bottom of the image shows the cross-section of the y-coordinate designated by the blue line in the image, which represents the front view at the blue line. The 3D rendering of the z-stack image enables users to view the image in 3D, visualizing all of the x, y, and z planes. This can be used to study co-localization of the different stains at different regions within the cell.

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