Analysis of Brain Mitochondria Using Serial Block-Face Scanning Electron Microscopy

The overall goal of the serial block-face scanning electron microscopy technique is to analyze mitochondrial morphology, structure, distribution, volume, and number in a defined region of the mouse brain. This method can help answer many key questions in neurobiology, such as whether changes in brain mitochondria structure, number, and distribution contribute substantially to neurodegenerative and neurodevelopmental disorders. The main advantage of this technique is that it automates the process of imaging serial sections by incorporating a custom ultramicrotome built into the low vacuum scanning electron microscope chamber.

To begin the experiment, wash the previously prepared glutaraldehyde-fixed tissues three times for five minutes each in 0.1 molar cacodylate buffer. Post-fix the tissues with 1 milliliter of cacodylate buffered 0.1%tannic acid for 30 minutes at room temperature. After post-fixing, wash the tissues in cacodylate buffer.

Dissolve 0.3 grams of potassium ferrocyanide and 0.86 grams of sodium cacodylate in 10 milliliters of distilled water. Just before use, add 10 milliliters of 4%osmium tetroxide and stain the tissues with 2%osmium ferrocyanide solution for 90 minutes on ice. After staining, wash the tissue in distilled water.

Treat the samples with freshly prepared 1%thiocarbohydrazide or TCH solution for 20 minutes at room temperature. Then wash the samples. Next, stain the tissues with 2%aqueous osmium tetroxide for one hour.

After staining, wash the tissues with distilled water. Incubate the samples overnight in 1%uranyl acetate in distilled water at 4 degrees Celsius. The next day, rinse the tissues in distilled water and incubate them with Welton's lead aspartate stain in an oven.

Obtaining the best possible stainings of tissues is critical to imaging, as poor staining results in a charging phenomenon on the sample that makes imaging difficult or impossible. Wash the tissue in distilled water. Dehydrate the samples through a graded series of alcohol using chilled solutions of ethanol for five minutes each, followed by a 100%ethanol dehydration three times for 10 minutes each.

Wash the samples two times for 15 minutes each in propylene oxide. Place the tissues in a 1:1 mix of embedding resin and propylene oxide, cap the vial, and incubate the tissues overnight. Uncap the vial after two hours so that the propylene oxide evaporates over the nine-hour period.

Transfer the tissues to 100%fresh embedding resin in clean vials for two hours. Embed the samples in fresh embedding resin in flat molds containing printed paper labels and cure them in an oven. After one hour, check the tissue placement and alignment and adjust if necessary.

Trim the samples to the area of interest and mount them onto an aluminum pin using gelling cyanoacrylate super glue. Then coat the sample with colloidal silver paste around the sides of the block to provide a conductive path to the aluminum pin. Examine the tissue specimens using a scanning electron microscope system equipped with an in-chamber ultramicrotome stage and a low kilovolt backscattered electron detector.

Image the samples with these settings. Begin analysis by selecting Image, Type, then 8-bit to convert the images to 8-bit TIFF format from the original proprietary 16-bit. If automatic contrast and/or brightness conversion during this step is not ideal for images, reopen the 16-bit images and press Image, Adjust, Brightness/Contrast.

Select a range that works for all images and press Apply. Then perform the conversion. If there was unacceptable image movement between slices, align the image stacks by selecting Plugins, Registration, and Linear Stack Alignment with SIFT and set the alignment for translation-only mode rather than rigid body.

Enlarge the canvas size prior to registration by selecting Image, Adjust, Canvas Size. Alternatively, reduce the image to an area of interest by selecting the desired region and then cropping it. If necessary, scale images to a smaller, more manageable size using ImageJ, then selecting Image and Scale.

Confocal microscopy on low-density neuronal cultures showed that mitochondria residing in neuronal soma form a reticular network, whereas those residing in distal neurites exhibit a discrete elongated morphology. Using the serial block-face scanning electron microscopy, or SBFSEM technique, the mitochondria, dendrites, and axonal varicosities were clearly observed in the mouse brain. Three-day reconstructions of mitochondria in the neurites of mouse brain tissue displayed a difference in size between dendritic and axonal mitochondria.

Data extracted from a representative 2-D SBFSEM image revealed that the volume or size of mitochondria residing within the neuronal presynapses was significantly smaller than those residing in the extrasynaptic region. The images acquired by SBFSEM analysis provide increased resolution to visual the ultrastructural characteristics of individual mitochondria. It is possible to classify the cellular compartment of mitochondria by determining its proximity to readily identifiable structures like non-synaptic somatic mitochondria and presynaptic mitochondria.

This technique can be done in about seven days, which includes three days of staining, two days for resin curing, one day of imaging to produce a stack suitable for this analysis, and about two to four hours for image post-processing in preparation for the analysis. This procedure can also be used in conjunction with other methods for imaging mitochondria such as live imaging with genetically labeled mitochondria to answer questions about mitochondrial trafficking and the dynamics of their fission and fusion.