Name: characterizing multiscale mechanical properties of brain tissue using atomic force microscopy, impact indentation, and rheometry
Uploaded: 2016-09-06T12:30:00
Description: Watch this Scientific Journal Video about Characterizing Multiscale Mechanical Properties of Brain Tissue Using Atomic Force Microscopy, Impact Indentation, and Rheometry at JoVE.com

We acknowledge support of this work by the National Multiple Sclerosis Society and Simons Center for the Social Brain. BQ acknowledges support from the U.S. National Defense Science &amp; Engineering Graduate Fellowship program.

Ethics Statement: All experimental protocols were approved by the Animal Research Committee of Boston Children&#39;s Hospital and comply with the National Institutes of Health Guide for the Care and Use of Laboratory Animals.
1. Mouse Brain Tissue Acquisition Procedures (for AFM-enabled indentation and impact indentation)
<ol>
	<li>Prepare a ketamine/xylazine mixture to anesthetize the mice. Combine 5 ml ketamine (500 mg/ml), 1 ml xylazine (20 mg/ml) and 7 ml of 0.9% saline solution.</li>
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<ol>
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Each technique presented in this paper measures different facets of brain tissue&#39;s mechanical properties. Creep compliance and stress relaxation moduli are a measure of time-dependent mechanical properties. The storage and loss moduli represent rate-dependent mechanical properties. Impact indentation also measures rate-dependent mechanical properties, but in the context of energy dissipation. When characterizing tissue mechanical properties, both AFM-enabled indentation and rheology are commonly used methods. AFM-ena...

Most soft-tissues comprising biological organs are mechanically and structurally complex, of low stiffness compared to mineralized bone or engineered materials, and exhibit non-linear and time-dependent deformation. Compared to other tissues in the body, brain tissue is remarkably compliant, with elastic moduli E on the order of 100s of Pa 1. Brain tissue exhibits structural heterogeneity with distinct and interdigitated gray and white matter regions that also differ functionally. Understanding brain tissue mechanics will aid in the design of materials and computational models to mimic the response of the brain during injury, facilitate prediction of mechanical damage, and enable engineering of protective strategies. Additionally, such information can be used to consider design targets for tissue regeneration, and to better understand structural changes in brain tissue that are associated with diseases such as multiple sclerosis and autism. Here, we describe and demonstrate several experimental approaches that are available to characterize the viscoelastic properties of mechanically compliant tissues including brain tissue, at the micro-, meso-, and macro-scales.
At the microscale, we conducted creep-compliance and force relaxation experiments using atomic force microscope (AFM)-enabled indentation. Typically, AFM-enabled indentation is used to estimate the elastic modulus (or instantaneous stiffness) of a sample 2-4. However, the same instrument can also be used to measure microscale viscoelastic (time- or rate-dependent) properties 5-10. The principle of these experiments, shown in Figure 1, is to indent an AFM cantilevered probe into the brain tissue, maintain a specified magnitude of force or indentation depth, and measure the corresponding changes in indentation depth and force, respectively, over time. Using these data, we can calculate the creep compliance JC and relaxation modulus GR, respectively.
At the mesoscale, we conducted impact indentation experiments in fluid-immersed conditions that maintain the tissue structure and hydration levels, using a pendulum-based instrumented nanoindenter. The experimental setup is illustrated in Figure 2. As the pendulum swings into contact with the tissue, probe displacement is recorded as a function of time until the oscillating pendulum comes to rest within the tissue. From the resulting damped harmonic oscillatory motion of the probe, we can calculate the maximum penetration depth xmax, energy dissipation capacity K, and dissipation quality factor Q (which relates to the rate of energy dissipation) of the tissue 11,12.
At the macroscale, we used a parallel plate rheometer to quantify the frequency dependent shear elastic moduli, termed the storage modulus G&#39; and loss modulus G&#34;, of the tissue. In this type of rheometry, we apply a harmonic angular strain (and corresponding shear strain) at known amplitudes and frequencies and measure the reactional torque (and corresponding shear stress), as shown in Figure 3. From the resulting amplitude and phase lag of the measured torque and geometric variables of the system, we can calculate G&#39; and G&#34; at applied frequencies of interest 13,14.

<table border="0" cellpadding="0" cellspacing="0" width="1078">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:381px;">Xylaxine</td>
			<td style="width:161px;">Lloyd Laboratoried</td>
			<td style="width:135px;"></td>
			<td style="width:401px;">perscription drug</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Ketamine</td>
			<td>AnaSed Injections</td>
			<td></td>
			<td>perscription drug</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Vibratome (Vibrating blade microtome)</td>
			<td>Leica</td>
			<td>VT1200</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Hibernate-A Medium</td>
			<td>Gibco</td>
			<td>A1247501</td>
			<td>CO2-independent neural medium for adult tissue</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Atomic Force Microscope, MFP-3D-BIO</td>
			<td>Asylum Research</td>
			<td>-</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Petri Dish Heater</td>
			<td>Asylum Research</td>
			<td>-</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">AFM Probe, 0.03 N/m, 10 um radius borosilicate sphere</td>
			<td>Novascan</td>
			<td>PT.GS</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Cell-Tak</td>
			<td>Corning</td>
			<td>354240</td>
			<td>mussel-derived bioadhesive</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Sodium Bicarbonate</td>
			<td>Sigma-Aldrich</td>
			<td>S5761</td>
			<td>alternate suppliers can be used</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Sodium Hydroxide, 1N</td>
			<td>Sigma-Aldrich</td>
			<td>59223C</td>
			<td>alternate suppliers can be used</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Instrumented Indenter, NanoTest Vantage</td>
			<td>Micro Materials Ltd.</td>
			<td>-</td>
			<td>probe tip needs to be machined (steel flat punch, 1mm diameter, 4-5 mm length)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">NanoTest Liquid Cell</td>
			<td>Micro Materials Ltd.</td>
			<td>-</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Parallel Plate Rheometer MCR501</td>
			<td>Anton-Parr</td>
			<td>-</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">PP25&#160;</td>
			<td>Anton-Parr</td>
			<td>-</td>
			<td>25 mm diameter flat measurement plate</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Adhesive Sandpaper</td>
			<td>McMaster-Carr</td>
			<td>4184A48</td>
			<td>alternate suppliers can be used</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Loctite 4013 Instant Adhesive</td>
			<td>Henkel</td>
			<td>20268</td>
			<td>alternate suppliers can be used</td>
		</tr>
	</tbody>
</table>

characterizing multiscale mechanical properties of brain tissue using atomic force microscopy, impact indentation, and rheometry

To design and engineer materials inspired by the properties of the brain, whether for mechanical simulants or for tissue regeneration studies, the brain tissue itself must be well characterized at various length and time scales. Like many biological tissues, brain tissue exhibits a complex, hierarchical structure. However, in contrast to most other tissues, brain is of very low mechanical stiffness, with Young&#39;s elastic moduli E on the order of 100s of Pa. This low stiffness can present challenges to experimental characterization of key mechanical properties. Here, we demonstrate several mechanical characterization techniques that have been adapted to measure the elastic and viscoelastic properties of hydrated, compliant biological materials such as brain tissue, at different length scales and loading rates. At the microscale, we conduct creep-compliance and force relaxation experiments using atomic force microscope-enabled indentation. At the mesoscale, we perform impact indentation experiments using a pendulum-based instrumented indenter. At the macroscale, we conduct parallel plate rheometry to quantify the frequency dependent shear elastic moduli. We also discuss the challenges and limitations associated with each method. Together these techniques enable an in-depth mechanical characterization of brain tissue that can be used to better understand the structure of brain and to engineer bio-inspired materials.

Figure 4 shows representative indentation and force vs. time responses (Figure 4B,E) for creep compliance and force relaxation experiments, given an applied force or indentation depth (Figure 4A,D), respectively. Using these data and the geometry of the system, the creep compliance Jc(t) and force relaxation moduli GR(t) can be calculated for different regions of the brain (Figure 4C,F</stro...

Watch this Scientific Journal Video about Characterizing Multiscale Mechanical Properties of Brain Tissue Using Atomic Force Microscopy, Impact Indentation, and Rheometry at JoVE.com

Characterizing Multiscale Mechanical Properties of Brain Tissue Using Atomic Force Microscopy, Impact Indentation, and Rheometry

We present a set of techniques to characterize the viscoelastic mechanical properties of brain at the micro-, meso-, and macro-scales.

To design and engineer materials inspired by the properties of the brain, whether for mechanical simulants or for tissue regeneration studies, the brain ...

The overall goal of these mechanical characterization techniques is to measure the viscoelastic properties of biological tissue at different length scales and loading rates. These methods can be used to answer key questions in biological engineering. For example, how does the brain deform under very high rates of loading, or how do diseases like multiple sclerosis or autism affect the mechanical properties of the brain tissue.The main advantage of these techniques is for materials of very low stiffness and very high hydration, like a biological tissue, you can test over a wide range of loading conditions, and you can also test over a wide range of material volumes, down to the level of a single cell, and up to the level of an entire brain. The implications of these techniques, extends towards modeling of the response of brain during injury, which is important for engineering protective strategies. Though this method can provide insight into brain mechanical properties, it can also be applied to other compliant biological tissues, such as heart and liver.During the mechanical characterization of compliant tissues, establishing appropriate contact between the measurement probe and the tissue is crucial. Carefully load an AFM probe with a nominal spring constant of 0.03 newtons per meter and a 20 micrometer diameter borosilicate bead into the probe holder. Place a brain slice mounted in a petri dish onto an AFM stage-mounted heater that has been pre-warmed to 37 degrees celsius.Then add about two milliliters of pre-warmed medium. Next, carefully add a drop of medium onto the AFM probe to protect it from breaking due to surface tension when it is lowered into the medium surrounding the brain slice. Then reposition the AFM head onto the stage, and begin lowering the head until it is submerged in the medium.Using the optical microscope, move the stage so that the region of interest is below the calibrated AFM probe, then lower the AFM probe to make contact with the surface of the tissue. In order to conduct the creep compliance experiments, construct an applied force function in the software's function editor. The function consists of a 0.1 second ramp to a set point of 5 nanonewton which is held for 20 seconds followed by a one second ramp down to zero nanonewton.The software will record data on the AFM probe's indentation into the tissue during the applied force function. After running the creep compliance experiment, conduct force relaxation experiments by creating an applied indentation function in the software. Run this function while the software collects data on the force experienced by the AFM probe as it indents into the tissue.To begin impact indentation tests, match a spherical probe by sliding it onto the pendulum using tweezers. Then attach the fused quartz sample post onto the plate and screw the plate into the translational stage. To enable dynamic impact experiments on hydrated brain tissues, first perform the liquid cell calibration.Go to the Calibration menu in the software, select Liquid Cell and follow the software prompts to make contact with the fused quartz sample. Next, select Normal for the Indenter Type, and use the default value of 0.05 millinewtons for the Indenter Load. Then click on continue to perform the calibration for the normal indenter configuration.Now move the sample stage back by at least five millimeters and mount the lever arm. Repeat the liquid cell calibration in the new configuration by selecting Liquid Cell for the indenter type. Click Continue to obtain the liquid cell calibration factor.Next, increase the capacitor plate spacing. Increasing the capacitor plate spacing will increase the maximum measurable depth which is necessary when testing highly compliant materials. With a wrench, turn the three nuts that control the capacitor plate spacing clockwise in small increments.After each complete clockwise turn, select Bridge Box Adjustment under the Maintenance menu and obtain a good pendulum test. Continue to slowly adjust the nuts until the Approx. Depth Calibration reads a value of 70, 000 nanometers per volt or higher.Then position a new limit stop at the bottom of the pendulum that can be switched on and off via a power supply. Retract the original limit stop sitting behind the pendulum to remove a potential obstruction of the pendulum motion and allow for higher impact velocities as well as higher penetration depths into compliant samples. Turn on the power supply for the solenoid and set it to 10 volts.Next, go to the Experiment menu and select Impact and Adjust Impulse Displacement. Follow the software instructions to calibrate the swing distance of the pendulum. When the impact indentation setup is fully complete, aspirate the medium and dry the brain slice.Then use a thin layer of cyanoacrylate adhesive to secure the sliced brain to the aluminum sample post. Then slide the liquid cell over the second O-ring on the sample post, and fill the liquid cell with five milliliters of carbon-dioxide-independent medium to fully immerse the tissue. Move the bath in the negative X direction until the tip on the lever arm is properly located above the bath.Next, move in the positive Z direction until the tip is fully submerged in the bath and is in front of the sample. Using the Sample Stage Control window, carefully make contact, and then back the stage away from the sample surface by about 30 micrometers. Under the Experiment menu, click Impact and setup an impact experiment.Choose a specific impulse load that will relate directly to the resulting impact velocity based on the swing distance calibration. And then run the scheduled experiment. When the pendulum swings back and the sample surface continues to move to the measurement plane, turn the bottom limit switch off.The displacement of the probe as a function of time will be recorded by the software. Attach sand paper to the 25 millimeter diameter measurement probe. Next, attach the thermal system and mount the probe.Finally, attach another piece of sand paper to the bottom plate aligned with the top plate. Calibrate the rheometer as per the manufacturers instructions. First, zero the force on the probe.Second, establish contact between the probe and the bottom plate. Then measure the inertia of the probe. Finally, perform a motor adjustment.Then slowly lower the measurement plate. When the plate is within a millimeter of the tissue, lower it in 0.1 millimeter increments until the plate is fully in contact with the top surface of the tissue and the measured normal force is of the desired value. Pipe out a small volume of medium on the edges of the sample to maintain hydration during the procedure.Lower the thermal hood. Next, click File, New, and under the Gel tab select Frequency Sweep. Then click on window measurement one frequency sweep and double click on the oscillation box.Enter the frequency range, the strain, and the number of points. Finally, select OK and click Start to initiate the frequency sweep. Here are representative indentation and force versus time responses for both creep compliance and force relaxation experiments.Using these data and the geometry of the system, the creep compliance and force relaxation moduli can be calculated for different regions of the brain. Impact indentation measures the mechanical properties of the tissue at high rates of spatially and temporally concentrated loading. The resulting impact response parameters can be quantified at different impact velocities which provides a means to study the rate-dependent properties of the tissue.Rheology measures the frequency-dependent viscoelastic properties of bulk tissue in terms of the storage and loss moduli. The storage modulus is nearly an order of magnitude larger than the loss modulus at low frequencies, indicating that elastic properties dominate the behavior of brain tissue. While attempting this procedure, it is important to keep the tissue adequately hydrated or immersed in a fluid that helps the tissue maintain its proper structure.The development of these demonstrated techniques has paved the way for materials researchers to design an optimize synthetic gels that can mimic the mechanical response of the brain. After watching this video, you should have a good understanding of how atomic force microscope enabled indentation, impact indentation, and rheology are used to characterize the viscoelastic mechanical properties of tissue. When interpreting the collected data, remember the underlying assumption that the deformed volume of the tissue is structurally homogeneous and elastically isotropic.This is not necessarily true for all biological tissues. As your questions about mechanics of biological tissues become better defined, you can choose one or more of these mechanical experiments to answer the question at the appropriate length scale or time scale of interest.

characterizing-multiscale-mechanical-properties-brain-tissue-using

Research

JoVE Journal

Neuroscience

Preparation of Mouse Brain Tissue for Immunoelectron Microscopy

Transmission electron microscopy (TEM) is extremely useful for visualizing microglial, oligodendrocytic, astrocytic, and neuronal subcellular compartments (dendrite, dendritic spine, axon, axon terminal, perikaryon), as well as their intracellular organelles and cytoskeleton, in the central nervous system at high spatial resolution. Combined with TEM, pre-embedding immunocytochemistry allows the discrimination of cellular elements with few distinctive features and identification criteria (e.g., microglial perikarya and processes, when using an antibody against the microglia-specific marker Iba1 (ionized calcium binding adaptor molecule 1; as presented here)), identifying the neurotransmitter contents of cellular elements (e.g., serotonergic) and their ultrastructural localization of soluble or membrane-bound proteins (e.g., 5 HT1A and EphA4 receptors). Here, we describe a protocol for transcardiac perfusion of mice with acrolein fixative, removal and sectioning of the brain, as well as immunoperoxidase-diaminobenzidine (DAB) staining, resin embedding, and ultrathin sectioning of the brain sections. Upon completion of these procedures, the immunostained material is ready for examination with TEM. When rigorously performed, this technique provides an excellent compromise between optimal ultrastructural preservation and immunocytochemical detection.

We describe a protocol for transcardiac perfusion of mice, removal and sectioning of the brain, as well as immunoperoxidase staining, resin embedding, and ultrathin sectioning of the brain sections. Upon completion of these procedures, the immunostained material is ready for examination with transmission electron microscopy.

Transmission electron microscopy (TEM) is extremely useful for visualizing microglial, oligodendrocytic, astrocytic, and neuronal subcellular compartments ...

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 ...

The Olfactory System as a Model to Study Axonal Growth Patterns and Morphology In Vivo

The olfactory system has the unusual capacity to generate new neurons throughout the lifetime of an organism. Olfactory stem cells in the basal portion of the olfactory epithelium continuously give rise to new sensory neurons that extend their axons into the olfactory bulb, where they face the challenge to integrate into existing circuitry. Because of this particular feature, the olfactory system represents a unique opportunity to monitor axonal wiring and guidance, and to investigate synapse formation. Here we describe a procedure for in vivo labeling of sensory neurons and subsequent visualization of axons in the olfactory system of larvae of the amphibian Xenopus laevis. To stain sensory neurons in the olfactory organ we adopt the electroporation technique. In vivo electroporation is an established technique for delivering fluorophore-coupled dextrans or other macromolecules into living cells. Stained sensory neurons and their axonal processes can then be monitored in the living animal either using confocal laser-scanning or multiphoton microscopy. By reducing the number of labeled cells to few or single cells per animal, single axons can be tracked into the olfactory bulb and their morphological changes can be monitored over weeks by conducting series of in vivo time lapse imaging experiments. While the described protocol exemplifies the labeling and monitoring of olfactory sensory neurons, it can also be adopted to other cell types within the olfactory and other systems.

The Olfactory System as a Model to Study Axonal Growth Patterns and Morphology In Vivo

We describe a protocol for in vivo labeling of olfactory sensory neurons by electroporation and subsequent confocal laser-scanning or multiphoton microscopy to visualize neuronal morphology and its development over time.

The olfactory system has the unusual capacity to generate new neurons throughout the lifetime of an organism. Olfactory stem cells in the basal portion of ...

Closed-loop Neuro-robotic Experiments to Test Computational Properties of Neuronal Networks

Information coding in the Central Nervous System (CNS) remains unexplored. There is mounting evidence that, even at a very low level, the representation of a given stimulus might be dependent on context and history. If this is actually the case, bi-directional interactions between the brain (or if need be a reduced model of it) and sensory-motor system can shed a light on how encoding and decoding of information is performed. Here an experimental system is introduced and described in which the activity of a neuronal element (i.e., a network of neurons extracted from embryonic mammalian hippocampi) is given context and used to control the movement of an artificial agent, while environmental information is fed back to the culture as a sequence of electrical stimuli. This architecture allows a quick selection of diverse encoding, decoding, and learning algorithms to test different hypotheses on the computational properties of neuronal networks.

In this paper, an experimental framework to perform closed-loop experiments is presented, in which information processing (i.e., coding and decoding) and learning of neuronal assemblies are studied during the continuous interaction with a robotic body.

Information coding in the Central Nervous System (CNS) remains unexplored. There is mounting evidence that, even at a very low level, the representation ...

Using Fluorescence Activated Cell Sorting to Examine Cell-Type-Specific Gene Expression in Rat Brain Tissue

The brain is comprised of four primary cell types including neurons, astrocytes, microglia and oligodendrocytes. Though they are not the most abundant cell type in the brain, neurons are the most widely studied of these cell types given their direct role in impacting behaviors. Other cell types in the brain also impact neuronal function and behavior via the signaling molecules they produce. Neuroscientists must understand the interactions between the cell types in the brain to better understand how these interactions impact neural function and disease. To date, the most common method of analyzing protein or gene expression utilizes the homogenization of whole tissue samples, usually with blood, and without regard for cell type. This approach is an informative approach for examining general changes in gene or protein expression that may influence neural function and behavior; however, this method of analysis does not lend itself to a greater understanding of cell-type-specific gene expression and the effect of cell-to-cell communication on neural function. Analysis of behavioral epigenetics has been an area of growing focus which examines how modifications of the deoxyribonucleic acid (DNA) structure impact long-term gene expression and behavior; however, this information may only be relevant if analyzed in a cell-type-specific manner given the differential lineage and thus epigenetic markers that may be present on certain genes of individual neural cell types. The Fluorescence Activated Cell Sorting (FACS) technique described below provides a simple and effective way to isolate individual neural cells for the subsequent analysis of gene expression, protein expression, or epigenetic modifications of DNA. This technique can also be modified to isolate more specific neural cell types in the brain for subsequent cell-type-specific analysis.

The goal of this protocol is to use the fluorescence activated cell sorting (FACS) technique to sort specific types of neural cells for subsequent analysis of cell-type-specific gene expression, epigenetic markers, and or protein expression.

The brain is comprised of four primary cell types including neurons, astrocytes, microglia and oligodendrocytes. Though they are not the most abundant ...

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, ...

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.

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, ...

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 ...