Name: analysis of brain mitochondria using serial block-face scanning electron microscopy
Uploaded: 2016-07-09T15:00:00
Description: Watch this Scientific Journal Video about Analysis of Brain Mitochondria Using Serial Block-Face Scanning Electron Microscopy at JoVE.com

We thank Sidney Walker for providing technical help. This work was supported in part by a grant from the National Institute of Health (1R01EY024712-01A1).

Ethics Statement: Procedures involving animal subjects have been approved by the Institutional Animal Care and Use Committee (IACUC) at Virginia Tech.
Caution: Extreme precautions must be taken when handling and disposing several components used in this protocol. Before use, the local institutional guidelines and health and safety practices must be established and followed, particularly for osmium tetroxide, which is volatile and extremely poisonous, uranyl acetate, which is both a heavy metal and source of radioactivity, and lead nit...

The complexity of the nervous system poses a significant challenge in reconstructing large tissue volumes and analyzing the morphology and distribution of organelles such as mitochondria with adequate resolution. Multiple cells including neurons, oligodendrocytes and astrocytes with numerous processes extended in three dimensions interact within the brain tissue 43. Since mitochondria resides both in the soma of cells and distant processes, mitochondrial morphology is extremely pleomorphic in the nervous syste...

Mitochondria are dynamic organelles which change their shape and location depending on the cellular cues and needs, in tight interaction with cell cytoskeleton, and in response to cellular events such as calcium currents in neurons 1. Mitochondria also interact with other cellular organelles e.g. endoplasmic reticulum, which in turn regulates their dynamics and metabolism2. Mitochondrial morphology shows heterogeneity in different cell types i.e. the shape of the organelle varies from tubular to that consisting of sheets, sacks and ovals 3. It has been shown that mitochondrial fusion and fission cycle proteins can regulate the location, size, shape and distribution of mitochondria 4. Moreover, changes in mitochondrial shape are associated with neurodegeneration, neuronal plasticity, muscle atrophy, calcium signaling, reactive oxygen species generation as well as lifespan and cell death implicating that cell-specific mitochondrial morphology is critical for the maintenance of normal cellular function 5-11.
A major bioenergetic function of mitochondria is to generate adenosine triphosphate (ATP) by executing a series of metabolic reactions that involve complete breakdown of nutrients (i.e. glucose, fatty-acids or amino-acids) via the TCA cycle and OXPHOS pathways 12. The human brain constitutes only 2% of body weight however it consumes ~20% of total energy produced making it an extremely energy demanding organ 13. It is therefore not surprising that mitochondrial dysfunction in humans leads to a large number of neurological manifestations 14-17. Genetic mutations in OXPHOS components that impair ATP generation leads to mitochondrial disorders 17,18, which are clinically heterogeneous group of disorders with a prevalence of ~1 : 5,000 individuals, and one of the most common cause of metabolic disorders in children and adults. Deficit of mitochondria-derived ATP affects multiple organ systems with high energy demanding organs such as brain, heart and skeletal muscles being predominantly affected in these patients 14,17,18. In recent years, multiple studies have provided evidence for mitochondrial dysfunction in both neurodevelopmental and neurodegenerative disorders 15-17,19,20. Since mitochondria are essential and critical for brain development and function, it is imperative to develop protocols that can analyze changes in brain mitochondrial morphology, structure, size, number and distribution under both healthy and diseased states. Mouse models with mitochondrially-targeted green fluorescent protein (GFP) have been produced to visualize mitochondrial movements and localization in the brain 21,22. While this is an extremely useful tool to examine mitochondrial motility and general distribution, there are some drawbacks which include limited resolution and sensitivity of fluorescence microscopy. These attributes make it difficult to track the relatively small sized mitochondria. Similarly, serial transmission electron microscopy has been successfully used to view synaptic mitochondria 23, but this method is very time consuming. Mitochondrial morphology is known to be highly dynamic as they undergo continuous fission and fusion cycles, and in most cells mitochondria maintain a highly connected network 24-26. Neurons are highly polarized cells with multiple dendrites and extended axons, and mitochondria that form a connected reticular network in the cell body may have to separate as they make their way through these neurites (Figure 1). This makes brain mitochondria extremely varied in size and shape. For example, using serial block-face scanning electron microscopy (SBFSEM) technique, we previously observed that the difference in the volume or size of extrasynaptic mitochondria to mitochondria present in the nerve terminals may be as much as sixteen fold 27.
There are several approaches for performing volume analyses 28, which includes serial section TEM 29, automated tape collecting ultramicrotome SEM 30, focused ion beam SEM 31, and SBFSEM 32. The SBFSEM analysis has advantages in that it has the resolution to provide quantitative data on the morphological shape, size, distribution and number of organelles such as mitochondria in areas up to 1 mm of the brain. The technical operation is also the least demanding, with data acquisition and analysis within capabilities of many biological labs that lack previous EM experience. The advent of commercial instruments for generating serial section-like images has made 3D ultrastructural analysis of tissues a routine technique, which further permits an unbiased volumetric analysis in a rapid and repeatable manner28. The SBFSEM was first described and used in the field of neurobiology in 2004 32, based on an idea introduced by Leighton in 1981 33. Multiple studies since then have established this technique as a major tool in reconstruction analysis of neuronal circuitry 34. Furthermore, for many smaller scale projects, it provides reconstruction analysis to identify cellular organelles 27,35-39. Since, the acquired images are derived from low voltage back scatter electrons, new staining protocols which combine different known heavy metal staining techniques were developed to increase the resolution 40.
In this paper, we provide a protocol for utilizing 3D electron microscopy imaging and volumetric analysis of brain mitochondria based on methods that have previously been used by us and others 38,39,41. The tissue post-processing methods used were as previously described by Deerinck et al40.

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			<td>C57BL/6J mice</td>
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			<td>664</td>
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			<td>Isoflurane</td>
			<td>VETone, tradename Fluriso</td>
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			<td>Dissection tray</td>
			<td>Fisher scientific&#160;</td>
			<td>S65105&#160;</td>
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			<td>Dissection scissors</td>
			<td>Ted Pella Inc.</td>
			<td>1316</td>
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			<td>Butterfly canula</td>
			<td>Exel International</td>
			<td>26704</td>
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			<td>Phosphate buffer saline</td>
			<td>Sigma-Aldrich</td>
			<td>P4417-100TAB</td>
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			<td>Filter (0.45 micron)</td>
			<td>EMD Millipore</td>
			<td>NC0813356</td>
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			<td>Vibratome sectioning system</td>
			<td>Ted Pella Inc.</td>
			<td>Vibratome 3000</td>
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			<td>Sodium Cacodylate</td>
			<td>EMS</td>
			<td>12300</td>
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			<td>Potassium Ferrocyanide</td>
			<td>J.T. Baker</td>
			<td>14459-95-1</td>
			<td></td>
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			<td>Osmium Tetroxide 4% Solution</td>
			<td>EMS</td>
			<td>19150</td>
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			<td>Thiocarbohydrazide</td>
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			<td>21900</td>
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			<td>L-Aspartic Acid</td>
			<td>Sigma-Aldrich</td>
			<td>A93100</td>
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			<td>Potassium Hydroxide</td>
			<td>Acros Organics</td>
			<td>43731000</td>
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			<td>Lead Nitrate</td>
			<td>EMS</td>
			<td>17900</td>
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			<td>EMbed-812 EMBEDDING KIT</td>
			<td>EMS</td>
			<td>14120</td>
			<td>Contains Embed 812&#160; resin, DDSA, NMA, and DMP-30.</td>
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			<td>Glutaraldehyde 25% EM Grade</td>
			<td>Polysciences Inc.</td>
			<td>1909</td>
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			<td>Paraformaldehyde</td>
			<td>EMS</td>
			<td>19202</td>
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			<td>Uranyl Acetate</td>
			<td>EMS</td>
			<td>22400</td>
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			<td>Ethanol</td>
			<td>EMS</td>
			<td>15055</td>
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			<td>Propylene Oxide</td>
			<td>EMS</td>
			<td>20400</td>
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			<td>Embedding Mold</td>
			<td>EMS</td>
			<td>70907</td>
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			<td>Aluminum specimen pin</td>
			<td>EMS</td>
			<td>70446</td>
			<td></td>
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			<td>Colloidal Silver Liquid</td>
			<td>EMS</td>
			<td>12630</td>
			<td></td>
		</tr>
		<tr>
			<td>Razor</td>
			<td>EMS</td>
			<td>72000</td>
			<td></td>
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		<tr>
			<td>Super Glue (Loctite Gel Control)</td>
			<td>Loctite</td>
			<td>234790</td>
			<td>Hardware/craft stores carry this item</td>
		</tr>
		<tr>
			<td>Conductive epoxy</td>
			<td>Ted Pella Inc.</td>
			<td>16043</td>
			<td></td>
		</tr>
		<tr>
			<td>Scanning electron microscope</td>
			<td>Zeiss</td>
			<td>Sigma VP</td>
			<td></td>
		</tr>
		<tr>
			<td>In chamber ultramicrotome for SEM</td>
			<td>Gatan Inc.</td>
			<td>3View2</td>
			<td>Can be designed for other SEMs</td>
		</tr>
		<tr>
			<td>Trimming microscope for pin preparation</td>
			<td>Gatan Inc.</td>
			<td colspan="2">supplied as part of 3View system</td>
		</tr>
		<tr>
			<td>Low kV backscattered electron detector</td>
			<td>Gatan Inc.</td>
			<td>3V-BSED</td>
			<td></td>
		</tr>
		<tr>
			<td>ImageJ/ Fiji processing package&#160;</td>
			<td colspan="2">ImageJ ver 1.50b, FIJI download Oct 1, 2015</td>
			<td><a href="http://zoi.utia.cas.cz/files/imagej_api.pdf">http://zoi.utia.cas.cz/files/imagej_api.pdf</a></td>
		</tr>
		<tr>
			<td></td>
			<td></td>
			<td></td>
			<td>http://rsb.info.nih.gov/ij/</td>
		</tr>
		<tr>
			<td></td>
			<td></td>
			<td></td>
			<td><a href="http://www.icmr.ucsb.edu/programs/3DWorkshop/Uchic-2015_FIJI_Tutorial.pdf">http://www.icmr.ucsb.edu/programs/3DWorkshop/Uchic-2015_FIJI_Tutorial.pdf</a></td>
		</tr>
		<tr>
			<td></td>
			<td></td>
			<td></td>
			<td><a href="http://fiji.sc/TrakEM2">http://fiji.sc/TrakEM2</a></td>
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analysis of brain mitochondria using serial block-face scanning electron microscopy

Human brain is a high energy consuming organ that mainly relies on glucose as a fuel source. Glucose is catabolized by brain mitochondria via glycolysis, tri-carboxylic acid (TCA) cycle and oxidative phosphorylation (OXPHOS) pathways to produce cellular energy in the form of adenosine triphosphate (ATP). Impairment of mitochondrial ATP production causes mitochondrial disorders, which present clinically with prominent neurological and myopathic symptoms. Mitochondrial defects are also present in neurodevelopmental disorders (e.g. autism spectrum disorder) and neurodegenerative disorders (e.g. amyotrophic lateral sclerosis, Alzheimer&#39;s and Parkinson&#39;s diseases). Thus, there is an increased interest in the field for performing 3D analysis of mitochondrial morphology, structure and distribution under both healthy and disease states. The brain mitochondrial morphology is extremely diverse, with some mitochondria especially those in the synaptic region being in the range of &#60;200 nm diameter, which is below the resolution limit of traditional light microscopy. Expressing a mitochondrially-targeted green fluorescent protein (GFP) in the brain significantly enhances the organellar detection by confocal microscopy. However, it does not overcome the constraints on the sensitivity of detection of relatively small sized mitochondria without oversaturating the images of large sized mitochondria. While serial transmission electron microscopy has been successfully used to characterize mitochondria at the neuronal synapse, this technique is extremely time-consuming especially when comparing multiple samples. The serial block-face scanning electron microscopy (SBFSEM) technique involves an automated process of sectioning, imaging blocks of tissue and data acquisition. Here, we provide a protocol to perform SBFSEM of a defined region from rodent brain to rapidly reconstruct and visualize mitochondrial morphology. This technique could also be used to provide accurate information on mitochondrial number, volume, size and distribution in a defined brain region. Since the obtained image resolution is high (typically under 10 nm) any gross mitochondrial morphological defects may also be detected.

We demonstrate that the brain mitochondrial morphology and size is heterogeneous in different neuronal sub-compartments. Confocal microscopy on low density neuronal cultures transduced with lentivirus expressing mitochondrially-targeted green fluorescent protein showed that mitochondria residing in neuronal soma form a reticular network, whereas those residing in distal neurites exhibit a discrete elongated morphology (Figure 1 A-B). Using the SBFSEM technique, the mitoch...

Watch this Scientific Journal Video about Analysis of Brain Mitochondria Using Serial Block-Face Scanning Electron Microscopy at JoVE.com

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

Mitochondrial visualization and analysis from mammalian brain tissue is a challenging task. Here, we describe how three dimensional (3D) reconstruction analysis from the serial block-face scanning electron microscopy (SBFSEM) can be used to gain insights on the morphological and volumetric analysis of this critical energy generating organelle.

Human brain is a high energy consuming organ that mainly relies on glucose as a fuel source. Glucose is catabolized by brain mitochondria via glycolysis, ...

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.

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Research

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Neuroscience

Studying Synaptic Vesicle Pools using Photoconversion of Styryl Dyes

The fusion of synaptic vesicles with the plasma membrane (exocytosis) is a required step in neurotransmitter release and neuronal communication. The vesicles are then retrieved from the plasma membrane (endocytosis) and grouped together with the general pool of vesicles within the nerve terminal, until they undergo a new exo- and endocytosis cycle (vesicle recycling). These processes have been studied using a variety of techniques such as electron microscopy, electrophysiology recordings, amperometry and capacitance measurements. Importantly, during the last two decades a number of fluorescently labeled markers emerged, allowing optical techniques to track vesicles in their recycling dynamics. One of the most commonly used markers is the styryl or FM dye 1; structurally, all FM dyes contain a hydrophilic head and a lipophilic tail connected through an aromatic ring and one or more double bonds (Fig. 1B). A classical FM dye experiment to label a pool of vesicles consists in bathing the preparation (Fig. 1Ai) with the dye during the stimulation of the nerve (electrically or with high K+). This induces vesicle recycling and the subsequent loading of the dye into recently endocytosed vesicles (Fig. 1Ai-iii). After loading the vesicles with dye, a second round of stimulation in a dye-free bath would trigger the FM release through exocytosis (Fig. 1Aiv-v), process that can be followed by monitoring the fluorescence intensity decrease (destaining).

Although FM dyes have contributed greatly to the field of vesicle recycling, it is not possible to determine the exact localization or morphology of individual vesicles by using conventional fluorescence microscopy. For that reason, we explain here how FM dyes can also be used as endocytic markers using electron microscopy, through photoconversion. The photoconversion technique exploits the property of fluorescent dyes to generate reactive oxygen species under intense illumination. Fluorescently labeled preparations are submerged in a solution containing diaminobenzidine (DAB) and illuminated. Reactive species generated by the dye molecules oxidize the DAB, which forms a stable, insoluble precipitate that has a dark appearance and can be easily distinguished in electron microscopy 2,3. As DAB is only oxidized in the immediate vicinity of fluorescent molecules (as the reactive oxygen species are short-lived), the technique ensures that only fluorescently labeled structures are going to contain the electron-dense precipitate. The technique thus allows the study of the exact location and morphology of actively recycling organelles.

FM dyes have been of invaluable help in the understanding of synaptic dynamics. FMs are normally followed under the fluorescent microscope during different stimulation conditions. However, photoconversion of FM dyes combined with electron microscopy allows the visualization of distinct synaptic vesicle pools, among other ultrastructure components, in synaptic boutons.

The fusion of synaptic vesicles with the plasma membrane (exocytosis) is a required step in neurotransmitter release and neuronal communication. The ...

Focussed Ion Beam Milling and Scanning Electron Microscopy of Brain Tissue

This protocol describes how biological samples, like brain tissue, can be imaged in three dimensions using the focussed ion beam/scanning electron microscope (FIB/SEM). The samples are fixed with aldehydes, heavy metal stained using osmium tetroxide and uranyl acetate. They are then dehydrated with alcohol and infiltrated with resin, which is then hardened. Using a light microscope and ultramicrotome with glass knives, a small block containing the region interest close to the surface is made. The block is then placed inside the FIB/SEM, and the ion beam used to roughly mill a vertical face along one side of the block, close to this region. Using backscattered electrons to image the underlying structures, a smaller face is then milled with a finer ion beam and the surface scrutinised more closely to determine the exact area of the face to be imaged and milled. The parameters of the microscope are then set so that the face is repeatedly milled and imaged so that serial images are collected through a volume of the block. The image stack will typically contain isotropic voxels with dimenions as small a 4 nm in each direction. This image quality in any imaging plane enables the user to analyse cell ultrastructure at any viewing angle within the image stack.

This protocol describes how resin embedded brain tissue can be prepared and imaged in the three dimensions in the focussed ion beam, scanning electron microscope.

This protocol describes how biological samples, like brain tissue, can be imaged in three dimensions using the focussed ion beam/scanning electron ...

Functional Neuroimaging Using Ultrasonic Blood-brain Barrier Disruption and Manganese-enhanced MRI

Although mice are the dominant model system for studying the genetic and molecular underpinnings of neuroscience, functional neuroimaging in mice remains technically challenging. One approach, Activation-Induced Manganese-enhanced MRI (AIM MRI), has been used successfully to map neuronal activity in rodents 1-5. In AIM MRI, Mn2+ acts a calcium analog and accumulates in depolarized neurons 6,7. Because Mn2+ shortens the T1 tissue property, regions of elevated neuronal activity will enhance in MRI. Furthermore, Mn2+ clears slowly from the activated regions; therefore, stimulation can be performed outside the magnet prior to imaging, enabling greater experimental flexibility. However, because Mn2+ does not readily cross the blood-brain barrier (BBB), the need to open the BBB has limited the use of AIM MRI, especially in mice.
One tool for opening the BBB is ultrasound. Though potentially damaging, if ultrasound is administered in combination with gas-filled microbubbles (i.e., ultrasound contrast agents), the acoustic pressure required for BBB opening is considerably lower. This combination of ultrasound and microbubbles can be used to reliably open the BBB without causing tissue damage 8-11.
Here, a method is presented for performing AIM MRI by using microbubbles and ultrasound to open the BBB. After an intravenous injection of perflutren microbubbles, an unfocused pulsed ultrasound beam is applied to the shaved mouse head for 3 minutes. For simplicity, we refer to this technique of BBB Opening with Microbubbles and UltraSound as BOMUS 12. Using BOMUS to open the BBB throughout both cerebral hemispheres, manganese is administered to the whole mouse brain. After experimental stimulation of the lightly sedated mice, AIM MRI is used to map the neuronal response.
To demonstrate this approach, herein BOMUS and AIM MRI are used to map unilateral mechanical stimulation of the vibrissae in lightly sedated mice 13. Because BOMUS can open the BBB throughout both hemispheres, the unstimulated side of the brain is used to control for nonspecific background stimulation. The resultant 3D activation map agrees well with published representations of the vibrissae regions of the barrel field cortex 14. The ultrasonic opening of the BBB is fast, noninvasive, and reversible; and thus this approach is suitable for high-throughput and/or longitudinal studies in awake mice.

A technique is described for broadly opening the blood-brain barrier in the mouse using microbubbles and ultrasound. Using this technique, manganese can be administered to the mouse brain. Because manganese is an MRI contrast agent that accumulates in depolarized neurons, this approach enables imaging of neuronal activity.

Although mice are the dominant model system for studying the genetic and molecular underpinnings of neuroscience, functional neuroimaging in mice remains ...

Genetic Manipulation of Cerebellar Granule Neurons In Vitro and In Vivo to Study Neuronal Morphology and Migration

Developmental events in the brain including neuronal morphogenesis and migration are highly orchestrated processes. In vitro and in vivo analyses allow for an in-depth characterization to identify pathways involved in these events. Cerebellar granule neurons (CGNs) that are derived from the developing cerebellum are an ideal model system that allows for morphological analyses. Here, we describe a method of how to genetically manipulate CGNs and how to study axono- and dendritogenesis of individual neurons. With this method the effects of RNA interference, overexpression or small molecules can be compared to control neurons. In addition, the rodent cerebellar cortex is an easily accessible in vivo system owing to its predominant postnatal development. We also present an in vivo electroporation technique to genetically manipulate the developing cerebella and describe subsequent cerebellar analyses to assess neuronal morphology and migration.

Genetic Manipulation of Cerebellar Granule Neurons In Vitro and In Vivo to Study Neuronal Morphology and Migration

Neuronal morphogenesis and migration are crucial events underlying proper brain development. Here, we describe methods to genetically manipulate cultured cerebellar granule neurons and the developing cerebellum for the assessment of morphology and migratory characteristics of neurons.

Developmental events in the brain including neuronal morphogenesis and migration are highly orchestrated processes. In vitro and in vivo analyses allow ...

Peering at Brain Polysomes with Atomic Force Microscopy

The translational machinery, i.e., the polysome or polyribosome, is one of the biggest and most complex cytoplasmic machineries in cells. Polysomes, formed by ribosomes, mRNAs, several proteins and non-coding RNAs, represent integrated platforms where translational controls take place. However, while the ribosome has been widely studied, the organization of polysomes is still lacking comprehensive understanding. Thus much effort is required in order to elucidate polysome organization and any novel mechanism of translational control that may be embedded. Atomic force microscopy (AFM) is a type of scanning probe microscopy that allows the acquisition of 3D images at nanoscale resolution. Compared to electron microscopy (EM) techniques, one of the main advantages of AFM is that it can acquire thousands of images both in air and in solution, enabling the sample to be maintained under near physiological conditions without any need for staining and fixing procedures. Here, a detailed protocol for the accurate purification of polysomes from mouse brain and their deposition on mica substrates is described. This protocol enables polysome imaging in air and liquid with AFM and their reconstruction as three-dimensional objects. Complementary to cryo-electron microscopy (cryo-EM), the proposed method can be conveniently used for systematically analyzing polysomes and studying their organization.

While ribosome structure has been extensively characterized, the organization of polysomes is still understudied. To overcome this lack of knowledge, we present here a detailed preparation protocol for accurate imaging of mammalian polysomes by atomic force microscopy (AFM) in air and liquid.

The translational machinery, i.e., the polysome or polyribosome, is one of the biggest and most complex cytoplasmic machineries in cells. Polysomes, ...

Preparation of Non-human Primate Brain Tissue for Pre-embedding Immunohistochemistry and Electron Microscopy

Despite all the technological advances at the light microscopy&#160;level, electron microscopy remains the only tool in neuroscience to examine and characterize ultrastructural and morphological details of neurons, such as synaptic contacts. Good preservation of brain tissue for electron microscopy can be obtained by rigorous cryo-fixation methods, but these techniques are rather costly and limit the use of immunolabeling, which is crucial to understand the connectivity of identified neuronal systems. Freeze-substitution methods have been developed to allow the combination of cryo-fixation with immunolabeling. However, the reproducibility of these methodological approaches usually relies on costly freezing devices. Moreover, achieving reliable results with this technique is very time-consuming and skill-challenging. Hence, the traditional chemically fixed brain, particularly with acrolein fixative, remains a time-efficient and low-cost method to combine electron microscopy with immunohistochemistry. Here, we provide a reliable experimental protocol using chemical acrolein fixation that leads to the preservation of primate brain tissue and is compatible with pre-embedding immunohistochemistry and transmission electron microscopic examination.

Here, we provide an easy, low-cost, and time-efficient protocol to chemically fix primate brain tissue with acrolein fixative, allowing for long-term preservation that is compatible with pre-embedding immunohistochemistry for transmission electron microscopy.

Despite all the technological advances at the light microscopy&#160;level, electron microscopy remains the only tool in neuroscience to examine and ...

Chronic Implantation of Whole-cortical Electrocorticographic Array in the Common Marmoset

Electrocorticography (ECoG) allows the monitoring of electrical field potentials from the cerebral cortex with high spatiotemporal resolution. Recent development of thin, flexible ECoG electrodes has enabled conduction of stable recordings of large-scale cortical activity. We have developed a whole-cortical ECoG array for the common marmoset. The array continuously covers almost the entire lateral surface of cortical hemisphere, from the occipital pole to the temporal and frontal poles, and it captures whole-cortical neural activity in one shot. This protocol describes a chronic implantation procedure of the array in the epidural space of the marmoset brain. Marmosets have two advantages regarding ECoG recordings, one being the homologous organization of anatomical structures in humans and macaques, including frontal, parietal, and temporal complexes. The other advantage is that the marmoset brain is lissencephalic and contains a large number of complexes, which are more difficult to access in macaques with ECoG, that are exposed to the brain surface.These features allow direct access to most cortical areas beneath the surface of the brain. This system provides an opportunity to investigate global cortical information processing with high resolutions at a sub-millisecond order in time and millimeter order in space.

We have developed a whole-cortical electrocorticographic array for the common marmoset that continuously covers almost the entire lateral surface of cortex, from the occipital pole to the temporal and frontal poles. This protocol describes a chronic implantation procedure of the array in the epidural space of the marmoset brain.

Electrocorticography (ECoG) allows the monitoring of electrical field potentials from the cerebral cortex with high spatiotemporal resolution. Recent ...

Using Near-infrared Fluorescence and High-resolution Scanning to Measure Protein Expression in the Rodent Brain

Neuroscience is the study of how cells in the brain mediate various functions. Measuring protein expression in neurons and glia is critical for the study of neuroscience as cellular function is determined by the composition and activity of cellular proteins. In this article, we describe how immunocytochemistry can be combined with near-infrared high-resolution scanning to provide a semi-quantitative measure of protein expression in distinct brain regions. This technique can be used for single or double protein expression in the same brain region. Measuring proteins in this fashion can be used to obtain a relative change in protein expression with an experimental manipulation, molecular signature of learning and memory, activity in molecular pathways, and neural activity in multiple brain regions. Using the correct proteins and statistical analysis, functional connectivity among brain regions can be determined as well. Given the ease of implementing immunocytochemistry in a laboratory, using immunocytochemistry with near-infrared high-resolution scanning can expand the ability of the neuroscientist to examine neurobiological processes at a systems level.

Here, we present a protocol that uses near-infrared dyes in conjunction with immunohistochemistry and high-resolution scanning to assay proteins in brain regions.

Neuroscience is the study of how cells in the brain mediate various functions. Measuring protein expression in neurons and glia is critical for the study ...

Delivery of Antibodies into the Brain Using Focused Scanning Ultrasound

Only a small fraction of therapeutic antibodies targeting brain diseases are taken up by the brain. Focused ultrasound offers a possibility to increase uptake of antibodies and engagement through transient opening of the blood-brain barrier (BBB). In our laboratory, we are developing therapeutic approaches for neurodegenerative diseases in which an antibody in various formats is delivered across the BBB using microbubbles, concomitant with focused ultrasound application through the skull targeting multiple spots, an approach we refer to as scanning ultrasound (SUS). The mechanical effects of microbubbles and ultrasound on blood vessels increases paracellular transport across the BBB by transiently separating tight junctions and enhances vesicle- mediated transcytosis, allowing antibodies and therapeutic agents to effectively cross. Moreover, ultrasound also facilitates the uptake of antibodies from the interstitial brain into brain cells such as neurons where the antibody distributes throughout the cell body and even into neuritic processes. In our studies, fluorescently labeled antibodies are prepared, mixed with in-house prepared lipid-based microbubbles and injected into mice immediately before SUS is applied to the brain. The increased antibody concentration in the brain is then quantified. To account for alterations in normal brain homeostasis, microglial phagocytosis can be used as a cellular marker. The generated data suggest that ultrasound delivery of antibodies is an attractive approach to treat neurodegenerative diseases.

Presented here is a protocol to transiently open the blood-brain barrier (BBB) either focally or throughout a mouse brain to deliver fluorescently-labeled antibodies and activate microglia. Also presented is a method to detect the delivery of antibodies and microglia activation by histology.

Only a small fraction of therapeutic antibodies targeting brain diseases are taken up by the brain. Focused ultrasound offers a possibility to increase ...

Serial Block-Face Scanning Electron Microscopy (SBEM) for the Study of Dendritic Spines

Three-dimensional electron microscopy (3D EM) gives a possibility to analyze morphological parameters of dendritic spines with nanoscale resolution. In addition, some features of dendritic spines, such as volume of the spine and post-synaptic density (PSD) (representing post-synaptic part of the synapse), presence of presynaptic terminal, and smooth endoplasmic reticulum or atypical form of PSD (e.g., multi-innervated spines), can be observed only with 3D EM. By employing serial block-face scanning electron microscopy (SBEM) it is possible to obtain 3D EM data easier and in a more reproducible manner than when performing traditional serial sectioning. Here we show how to prepare mouse hippocampal samples for SBEM analysis and how this protocol can be combined with immunofluorescence study of dendritic spines. Mild fixation perfusion allows us to perform immunofluorescence studies with light microscopy on one half of the brain, while the other half was prepared for SBEM. This approach reduces the number of animals to be used for the study.

Serial Block-Face Scanning Electron Microscopy SBEM for the Study of Dendritic Spines

Serial Block-Face Scanning Electron Microscopy (SBEM) is applied to image and analyze dendritic spines in the murine hippocampus.

Three-dimensional electron microscopy (3D EM) gives a possibility to analyze morphological parameters of dendritic spines with nanoscale resolution. In ...