This project has received funding from the European Research Council (ERC) under the European Union&#39;s Horizon 2020 research and innovation programme (grant agreement No 803589), the Israel Science Foundation (ISF grant No. 1815/18), and the Canada-Israel grants (CIHR-ISF, grant No. 2591/18). We thank Nechama Novick for commenting on the whole manuscript.

Experimental protocols were approved by the Hebrew University Animal Care and Use Committee and met the guidelines of the National Institute of Health Guide for the Care and Use of Laboratory Animals.
1. Viral vector transduction
NOTE: Viral vector transduction is used to express fluorophores in the brain.
<ol>
	<li>Use an atlas (e.g., Allen Brain Atlas) to locate the relevant coordination of the target area. 
	NOTE: 3D atlases can be found online (e.g.,&#160;http://connectivity.brain-map.org/3d-viewer).</li>
	<li>Using stereotactic surgery, inject the viral vectors into the relevant brain structure. See9 for a detailed protocol.</li>
	<li>Wait for 3-6 weeks for fluorophore expression. 
	NOTE: A short period of time is enough if only cell bodies need to be marked. A long period of time will be needed if the axonal projections are relevant to the question, as it takes longer for the fluorophores to express in axons, which can be several millimeters long.</li>
	<li>Validate the specificity and penetrance of fluorophore expression (both of viral expression and TG animals) beforehand (Figure 1A). Before proceeding with the CLARITY procedure, designate at least one brain for thin slices and make sure the fluorophore expression is both strong and specific to the target cell feature.</li>
</ol>
2. CLARITY
NOTE: This method renders the brain transparent within 2-6 weeks.
<ol>
	<li>Perform transcranial perfusion on animals using cold Phosphate-buffered Saline (PBS) followed by 4% Paraformaldehyde (PFA) in PBS. Remove the brain and keep it in PFA overnight at 4 &#176;C in a 50 mL tube or a similar container. 
	NOTE: Before transcranial perfusion is performed, the animal must be deeply anesthetized. In the examples presented in this protocol, all animals were anesthetized using Ketamine and Xylazine (90% and 10%, respectively).</li>
	<li>Replace PFA with Hydrogel Solution (HS; see Table 1) for 48 h at 4 &#176;C. 
	NOTE: Do not allow the materials to become warmer than the refrigeration temperature (4-8 &#176;C) at this stage, or the Hydrogel will polymerize. The HS used in this protocol contains 2% acrylamide, unlike previous protocols suggesting 4%22 or 1%17. The benefit of 2% is detailed in the discussion section. When preparing the HS, work on an ice-cold surface. Store it at -20 &#176;C.</li>
	<li>Degassing 
	NOTE: The purpose of this stage is to remove all free oxygen from the tissue as O2 interferes with the polymerization process. Any nonO2 gas can be used (e.g., N2, CO2); N2 is recommended.
	<ol>
		<li>Transfer the N2 from the tank via a 5 mm (internal) flexible tubing, connected to a 19 G needle at its end (Figure 1B).</li>
		<li>Make two small holes (needle-wide) in the cap of the tube: one to introduce the gas and the other to allow the air to leave the tube (Figure 1C).</li>
		<li>Attach the pipe from the N2 gas to the tube and replace the gases for approximately 30 min at room temperature (RT).</li>
		<li>Remove the pipe and immediately seal the holes with modeling clay on every tube (Figure 1D).</li>
	</ol>
	</li>
	<li>Transfer the degassed sealed tubes to a 37 &#176;C bath for 3.5 h to polymerize the HS, which will become a gel. Be careful not to shake the tubes (Figure 1E).</li>
	<li>Extract the brain from the tube and gently remove the polymerized gel from around it using laboratory wipes. Make sure no residual gel remains attached to the surface of the tissue, as it might react with the solution in the following steps, inhibiting the tissue clearing process (Figure 1F). 
	NOTE: Because the gel contained PFA, the extraction should be done under a fume hood.</li>
	<li>Slice the brain if the question at hand requires only a part of it. Divide it in half or into very thick slices that contain all areas of interest (Figure 1G).</li>
	<li>Place the slices in the First Clearing Solution (CS1, see Table 2) in a new container and shake at 70 rpm for 24 h at 37 &#176;C.</li>
	<li>Follow the steps described below to transfer the brain from CS1 to the second Clearing Solution (CS2, see Table 2).
	<ol>
		<li>Prepare a perforated tube for the brain in advance (Figure 1H).</li>
		<li>Preheat CS2 to 40-45 &#176;C in a beaker large enough to contain the tube. Do this on a hotplate with a stirrer. Ensure the temperature does not reach 55 &#176;C to prevent the bleaching of the expressed proteins.</li>
		<li>Place the beaker filled with CS2 and the perforated tube on a stirring device (a 2 L beaker in Figure 1I). Set a moderate stirring rate that will cause the liquid to flow without distorting the tissue. 
		NOTE: Within 2-6 weeks, the tissue will become transparent (the process starts at the periphery and moves inward toward the central brain structures). The decision as to when the tissue is &#34;clear enough&#34; is up to personal judgment. The brain should be sufficiently transparent for imaging under the microscope without interference (Figure 1J not clear enough; Figure 1K clear enough). Surpassing the point at which the tissue is clear enough may cause loss of tissue rigidity.</li>
	</ol>
	</li>
	<li>Transfer from CS2 into PBST (0.5% Triton X-100 in PBS, see Table 2) in a new container at 37 &#176;C with mild shaking (70 rpm) for 24 h. 
	NOTE: In the PBST, the tissue will become whitish (Figure 1L). The clarity will return (and improve) when embedded in the Refractive Index Matching Solution (RIMS, see step 2.14).</li>
	<li>Replace the PBST with new PBST. Keep under the same conditions (37 &#176;C with mild shaking) for another 24 h.</li>
	<li>Replace PBST again with new PBST and keep at RT for 24 h.</li>
	<li>Transfer to PBS at RT for 24 h.</li>
	<li>Replace the PBS and leave at RT for an additional 24 h.</li>
	<li>Remove the brain from PBS and transfer it to RIMS at 37 &#176;C overnight. 
	NOTE: Initially, ripples in the RIMS may surround the brain. This protocol was designed and validated using two specific commercial RIMS (see Table 3). However, the protocol should not differ when using other RIMS (commercial or self-made).</li>
	<li>Keep the tissue at RT for another 24 h or until the solution reaches full equilibrium, i.e., when the tissue becomes transparent, and the solution no longer contains any visible ripples (Figure 1M).</li>
	<li>If the tissue is transparent, proceed to the chamber preparation. If at this point, the tissue becomes white instead of transparent (due to aggregates of residual SDS molecules), clean the sample again by repeating steps 2.9 and 2.10, and transfer the tissue to CS2 (step 2.8) for a few days, followed by all the steps until step 2.15.</li>
</ol>
3. Chamber preparation
NOTE: Each sample requires a slide with an imaging chamber in which the sample will be placed.
<ol>
	<li>Place the sample in the middle of the slide.</li>
	<li>Using a hot glue gun, create walls at the edges of the slide, almost as high as the tissue. Make sure to leave a small gap (approximately 5 mm) at one of the corners (Figure 2A,B).</li>
	<li>Apply 1-2 drops of the RIMS on the sample to keep the upper surface moist and prevent bubbles forming between the coverslip and the tissue.</li>
	<li>Immediately after applying the RIMS drops, add the last layer of hot glue to the walls (so that they reach the height of the brain/slice) and progress immediately (while the hot glue is still liquid) to step 3.5.</li>
	<li>Seal the top with a coverslip, placing it as evenly as possible on the top of the still-warm hot glue layer (Figure 2C).</li>
	<li>Fill the chamber with the RIMS through the gap left in the hot glue walls (Figure 2D,E).</li>
	<li>Close the gap with hot glue. Leave no air inside (Figure 2F).</li>
	<li>If the hot glue walls extend beyond the borders of the slide, cut the extending edges (Figure 2G).</li>
	<li>If the objective used for imaging is immersed, add another 2-3 mm of glue to the walls above the coverslip so that the immersion solution will last for a longer period (Figure 2H).</li>
</ol>
4. Imaging (confocal or two-photon)
<ol>
	<li>Check whether the stage can hold the chamber, as the thickness of the chamber can reach several millimeters. 
	NOTE: For example, the confocal microscope (see the Table of Materials) used in this protocol is equipped with several stages (e.g., circular, rectangular). Whichever stage is chosen to hold the chamber is irrelevant as long as its parameters fit the chamber sizes.</li>
	<li>Work with an objective with a sufficient working distance, i.e., a minimal working distance &#8805;3 mm, as the brain region of interest may be a few millimeters in depth, and the coverslip may not be completely straight as it was placed manually. 
	NOTE: As a demonstration, the results presented in Figure 1, Video 1, and Video 2 were obtained under a two-photon microscope using a water immersion 16x objective with a 3 mm working distance and magnification of 2.4 to obtain a 652 x 483 &#181;m field of view and a z-stack with 0.937 &#181;m intervals between the planes.</li>
	<li>Perform multiple-area imaging, which may take a few hours or even days. Make sure there is ample free storage in the computer as the size of each image can reach up to tens of gigabits. 
	NOTE: CLARITY imaging may result in significantly more image sections in depth. Therefore, the intensities used to capture the expression should be relatively low to prevent overexpression during the image summation.</li>
	<li>For immersion objectives, check the liquid routinely while imaging and supplement with additional liquid if needed. 
	NOTE: During the imaging of the data presented in Video 3, water was added to the surface of the chamber every 6-8 h to combat evaporation.</li>
	<li>After the image has been acquired, view and analyze it using several different software packages. 
	NOTE: Recommended software includes Imaris and SyGlass for both visualization and analysis. The precise pipeline for optimized reconstruction of astrocytes using Imaris software has been described previously9. In short, the Imaris features used in this study were Filaments to fully reconstruct cell structures and Spots to extract the position in the space of all the somata.</li>
</ol>

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The authors have no conflicts of interest to disclose.

Tissue clearing methods present a revolutionary tool in brain research, inviting questions that could not previously have been asked. From targeting the properties of a small group of cells, a single cell, or even a single synapse, CLARITY now enables the targeting of total cell populations or long-range connectivity features by using relevant fluorophores.
The outcome of the fluorophore expression and CLARITY procedure combination is not binary; many factors may interfere with the procedure l...

In recent years, the knowledge of astrocyte function and how they interact with neuronal circuits has increased dramatically. Astrocytes can influence plasticity1,2, assist in neuronal postinjury recovery3,4, and even induce de novo neuronal potentiation, with recent studies exhibiting the importance of astrocytes in memory acquisition and reward, previously regarded as purely neuronal functions5,6,7. A feature of particular interest in astrocyte research is the spatial arrangement of the cells, which maintain unique spatial organizations in the hippocampus and other brain structures8,9,10. Unlike the neuronal dendrites that intertwine between cell somata, hippocampal astrocytes inhabit visually distinguishable territories with slight overlap between their processes, creating distinct domains8,11,12,13. The evidence supporting the participation of astrocytes in neuronal circuits does not support the lack of detailed anatomical description of such populations and the neurons in their domains14.
Viral vector transduction procedures, along with transgenic animals (TG), have been popularized as a toolset to investigate brain structures, functions, and cell interactions15,16. The utilization of different promoters allows the targeting of specific cells according to their genetic properties, activation levels17,18, or projection targets. Different viruses can express different colored fluorophores in different populations. A virus can be combined with the endogenous expression of fluorophores in TG, or TG animals can be used without the need for viruses. These techniques are widely used for neuronal marking, and some labs have started using them with modifications specialized for targeting other cell types, such as astrocytes5,9,19.
The CLARITY technique, first described in 201320,21, enables the study of thick brain slices by making the entire brain transparent while leaving the microscopic structures intact. By combining the two methods-viral vector transduction and tissue clearing-the option of examining the spatial interactions between different cell type populations is now available. Most astrocyte-neuron interaction studies were performed on thin brain slices, resulting in images of incomplete astrocytes due to their large domains, thus radically restricting the number of analyzed cells. The use of the CLARITY technique allows single-cell resolution characterization of cell populations in large-scale volumes simultaneously. Imaging fluorescently tagged cell populations in clear brains does not deliver synaptic resolution but permits thorough characterization of the spatial interactions between astrocytes and a variety of neuronal cell types.
For that reason, we harnessed these state-of-the-art techniques to investigate the properties of astrocytes throughout the dorsal CA1, imaging all lamina (Stratum Radiatum, pyramidal layer, and Stratum Oriens). We measured tens of thousands of astrocytes (with viral penetrance of &#62;96%5), thereby analyzing the information of the entire astrocytic population around CA1. With efficient penetrance of the neuronal markers, we could record the interactions between the entire population of CA1 astrocytes and the four types of neuronal cells-parvalbumin (PV), somatostatin (SST), VIP inhibitory neurons, and excitatory pyramidal cells9.
Several experiments were performed using a combination of fluorescence from TG animals and differently colored viral vectors (all inhibitory cells), while others (excitatory) utilized two viral vectors expressing different fluorophores under different promoters9. This paper presents a detailed protocol, including the tagging of the desired cells in the brain, making the brain transparent using a modified CLARITY procedure, as well as imaging and analyzing complete brain structures, using various procedures and software.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>AAV1-GFAP::TdTomato</td>
			<td>ELSC Vector Core Facility (EVCF)</td>
			<td></td>
			<td>viral vector used to detect astrocytes</td>
		</tr>
		<tr>
			<td>AAV5-CaMKII::eGFP</td>
			<td>ELSC Vector Core Facility (EVCF)</td>
			<td></td>
			<td>viral vector used to detect neurons</td>
		</tr>
		<tr>
			<td>AAV5-CaMKII::H2B-eGFP</td>
			<td>ELSC Vector Core Facility (EVCF)</td>
			<td></td>
			<td>viral vector used to detect neuronal nuclei</td>
		</tr>
		<tr>
			<td>AAV5-CaMKII::TdTomato</td>
			<td>ELSC Vector Core Facility (EVCF)</td>
			<td></td>
			<td>viral vector used to detect neurons</td>
		</tr>
		<tr>
			<td>Acrylamide (40%)</td>
			<td>Bio-rad</td>
			<td>#161-0140</td>
			<td></td>
		</tr>
		<tr>
			<td>Bisacrylamide (2%)</td>
			<td>Bio-rad</td>
			<td>#161-0142</td>
			<td></td>
		</tr>
		<tr>
			<td>Boric acid</td>
			<td>Sigma</td>
			<td>#B7901</td>
			<td>Molecular weight - 61.83 g/mol</td>
		</tr>
		<tr>
			<td>Confocal microscope, scanning, FV1000</td>
			<td>Olympus</td>
			<td></td>
			<td>4x objective (UPlanSApo, 0.16 NA)</td>
		</tr>
		<tr>
			<td>Imaris software</td>
			<td>Bitplane, UK</td>
			<td></td>
			<td>A software that allows 3D analysis of images</td>
		</tr>
		<tr>
			<td>NaOH</td>
			<td>Sigma</td>
			<td>#S5881</td>
			<td></td>
		</tr>
		<tr>
			<td>PBS</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>PFA 4%</td>
			<td>EMS</td>
			<td>#15710</td>
			<td></td>
		</tr>
		<tr>
			<td>RapiClear</td>
			<td>SunJin lab</td>
			<td>#RC147002</td>
			<td></td>
		</tr>
		<tr>
			<td>RapiClear CS</td>
			<td>SunJin lab</td>
			<td>#RCCS002</td>
			<td></td>
		</tr>
		<tr>
			<td>SDS</td>
			<td>Sigma</td>
			<td>#L3771</td>
			<td></td>
		</tr>
		<tr>
			<td>SyGlass software</td>
			<td></td>
			<td></td>
			<td>A software that allows 3D analysis of images using virtual reality</td>
		</tr>
		<tr>
			<td>Tris base 1 M</td>
			<td>Bio-rad</td>
			<td>#002009239100</td>
			<td>Molecular weight - 121.14 g/mol</td>
		</tr>
		<tr>
			<td>Triton X-100</td>
			<td>ChemCruz</td>
			<td>#sc-29112A</td>
			<td></td>
		</tr>
		<tr>
			<td>Two photon microscope</td>
			<td>Neurolabware</td>
			<td></td>
			<td>Ti:sapphire laser (Chameleon Discovery TPC, Coherent), GaAsP photo-multiplier tubes (Hamamatsu, H10770-40) , bandpass filter (Semrock), water immersion 16x objective (Nikon, 0.8 NA)&#160;</td>
		</tr>
		<tr>
			<td>VA-044 Initiator</td>
			<td>Wako</td>
			<td>#011-19365</td>
			<td></td>
		</tr>
	</tbody>
</table>

investigation of spatial interaction between astrocytes and neurons in cleared brains

Combining viral vector transduction and tissue clearing using the CLARITY method makes it possible to simultaneously investigate several types of brain cells and their interactions. Viral vector transduction enables the marking of diverse cell types in different fluorescence colors within the same tissue. Cells can be identified genetically by activity or projection. Using a modified CLARITY protocol, the potential sample size of astrocytes and neurons has grown by 2-3 orders of magnitude. The use of CLARITY allows the imaging of complete astrocytes, which are too large to fit in their entirety in slices, and the examination of the somata with all their processes. In addition, it provides the opportunity to investigate the spatial interaction between astrocytes and different neuronal cell types, namely, the number of pyramidal neurons in each astrocytic domain or the proximity between astrocytes and specific inhibitory neuron populations. This paper describes, in detail, how these methods are to be applied.

Successful clearing of thick brain tissue slices results in a new range of questions that can be asked regarding the properties of large cell populations as opposed to the properties of single cells or neighboring groups of cells. To achieve successful results, one should strictly adhere to the CLARITY protocol, as there is a wide range of parameters that need to be considered to reduce the variance between samples (e.g., percentage of clarity, fluorescence information, swollenness parameters).
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Investigation of Spatial Interaction Between Astrocytes and Neurons in Cleared Brains

Combining viral vector transduction and brain clearing using the CLARITY method allows the investigation of a large number of neurons and astrocytes simultaneously.

Combining viral vector transduction and tissue clearing using the CLARITY method makes it possible to simultaneously investigate several types of brain ...

investigation-spatial-interaction-between-astrocytes-neurons-cleared

Research

JoVE Journal

Neuroscience

2.4K Views.  The Hebrew University of Jerusalem. Combining viral vector transduction and brain clearing using the CLARITY method allows the investigation of a large number of neurons and astrocytes simultaneously.

Video: Investigation of Spatial Interaction Between Astrocytes and Neurons in Cleared Brains

Dissection and Culture of Commissural Neurons from Embryonic Spinal Cord

Commissural neurons have been widely used to investigate the mechanisms underlying axon guidance during embryonic spinal cord development. The cell bodies of these neurons are located in the dorsal spinal cord and their axons follow stereotyped trajectories during embryonic development. Commissural axons initially project ventrally towards the floorplate. After crossing the midline, these axons turn anteriorly and project towards the brain. Each of these steps is regulated by the action of several guidance cues. Cultures highly enriched in commissural neurons are ideally suited for many experiments addressing the mechanisms of axon pathfinding, including turning assays, immunochemistry and biochemistry. Here, we describe a method to dissect and culture commissural neurons from E13 rat dorsal spinal cord. First, the spinal cord is isolated and dorsal strips are dissected out. The dorsal tissue is then dissociated into a cell suspension by trypsinization and mechanical disruption. Neurons are plated onto poly-L-lysine-coated glass coverslips or tissue-culture dishes. After 30 hours in vitro, most neurons have extended an axon. The purity of the culture (Yam et al. 2009), typically over 90%, can be assessed by immunolabeling with the commissural neuron markers DCC, LH2 and TAG1 (Helms and Johnson, 1998). This neuronal preparation is a useful tool for in vitro studies of the cellular and molecular mechanisms of commissural axon growth and guidance during spinal cord development.

This video demonstrates a method to dissect and culture commissural neurons from E13 rat dorsal spinal cord. Dissociated commissural neurons are useful to study the cellular and molecular mechanisms of axon growth and guidance.

Commissural neurons have been widely used to investigate the mechanisms underlying axon guidance during embryonic spinal cord development. The cell bodies ...

Tactile Conditioning And Movement Analysis Of Antennal Sampling Strategies In Honey Bees (Apis mellifera L.)

Honey bees (Apis mellifera L.) are eusocial insects and well known for their complex division of labor and associative learning capability1, 2. The worker bees spend the first half of their life inside the dark hive, where they are nursing the larvae or building the regular hexagonal combs for food (e.g. pollen or nectar) and brood3. The antennae are extraordinary multisensory feelers and play a pivotal role in various tactile mediated tasks4, including hive building5 and pattern recognition6. Later in life, each single bee leaves the hive to forage for food. Then a bee has to learn to discriminate profitable food sources, memorize their location, and communicate it to its nest mates7. Bees use different floral signals like colors or odors7, 8, but also tactile cues from the petal surface9 to form multisensory memories of the food source. Under laboratory conditions, bees can be trained in an appetitive learning paradigm to discriminate tactile object features, such as edges or grooves with their antennae10, 11, 12, 13. This learning paradigm is closely related to the classical olfactory conditioning of the proboscis extension response (PER) in harnessed bees14. The advantage of the tactile learning paradigm in the laboratory is the possibility of combining behavioral experiments on learning with various physiological measurements, including the analysis of the antennal movement pattern.

Tactile Conditioning And Movement Analysis Of Antennal Sampling Strategies In Honey Bees Apis mellifera L.

In this protocol we show how to condition harnessed honey bees to tactile stimuli and introduce a 2D motion capture technique for analyzing the kinematics of fine-scale antennal sampling pattern.

Honey bees (Apis mellifera L.) are eusocial insects and well known for their complex division of labor and associative learning capability1, 2. The worker ...

An Engulfment Assay: A Protocol to Assess Interactions Between CNS Phagocytes and Neurons

Phagocytosis is a process in which a cell engulfs material (entire cell, parts of a cell, debris, etc.) in its surrounding extracellular environment and subsequently digests this material, commonly through lysosomal degradation. Microglia are the resident immune cells of the central nervous system (CNS) whose phagocytic function has been described in a broad range of conditions from neurodegenerative disease (e.g., beta-amyloid clearance in Alzheimer&#8217;s disease) to development of the healthy brain (e.g., synaptic pruning)1-6. The following protocol is an engulfment assay developed to visualize and quantify microglia-mediated engulfment of presynaptic inputs in the developing mouse retinogeniculate system7. While this assay was used to assess microglia function in this particular context, a similar approach may be used to assess other phagocytes throughout the brain (e.g., astrocytes) and the rest of the body (e.g., peripheral macrophages) as well as other contexts in which synaptic remodeling occurs (e.g. ,brain injury/disease).

Microglia are the resident immune cells of the central nervous system (CNS) with a high capacity to phagocytose or engulf material in their extracellular environment. Here, a broadly applicable, reliable, and highly quantitative assay for visualizing and measuring microglia-mediated engulfment of synaptic components is described.

Phagocytosis is a process in which a cell engulfs material (entire cell, parts of a cell, debris, etc.) in its surrounding extracellular environment and ...

Isolation, Culture and Long-Term Maintenance of Primary Mesencephalic Dopaminergic Neurons From Embryonic Rodent Brains

Degeneration of mesencephalic dopaminergic (mesDA) neurons is the pathological hallmark of Parkinson&#8217;s diseae. Study of the biological processes involved in physiological functions and vulnerability and death of these neurons is imparative to understanding the underlying causes and unraveling the cure for this common neurodegenerative disorder. Primary cultures of mesDA neurons provide a tool for investigation of the molecular, biochemical and electrophysiological properties, in order to understand the development, long-term survival and degeneration of these neurons during the course of disease. Here we present a detailed method for the isolation, culturing and maintenance of midbrain dopaminergic neurons from E12.5 mouse (or E14.5 rat) embryos. Optimized cell culture conditions in this protocol result in presence of axonal and dendritic projections, synaptic connections and other neuronal morphological properties, which make the cultures suitable for study of the physiological, cell biological and molecular characteristics of this neuronal population.

The causes of degeneration of midbrain dopaminergic neurons during Parkinson&#8217;s disease are not fully understood. Cellular culture systems provide an essential tool for study of the neurophysiological properties of these neurons. Here we present an optimized protocol, which can be utilized for in vitro modeling of neurodegeneration.

Degeneration of mesencephalic dopaminergic (mesDA) neurons is the pathological hallmark of Parkinson&#8217;s diseae. Study of the biological processes ...

Protocol for Three-dimensional Confocal Morphometric Analysis of Astrocytes

As glial cells in the brain, astrocytes have diverse functional roles in the central nervous system. In the presence of harmful stimuli, astrocytes modify their functional and structural properties, a condition called reactive astrogliosis. Here, a protocol for assessment of the morphological properties of astrocytes is presented. This protocol includes quantification of 12 different parameters i.e. the surface area and volume of the tissue covered by an astrocyte (astrocyte territory), the entire astrocyte including branches, cell body, and nucleus, as well as total length and number of branches, the intensity of fluorescence immunoreactivity of antibodies used for astrocyte detection, and astrocyte density (number/1,000 &#181;m2). For this purpose three-dimensional (3D) confocal microscopic images were created, and 3D image analysis software such as Volocity 6.3 was used for measurements. Rat brain tissue exposed to amyloid beta1-40 (A&#946;1-40) with or without a therapeutic&#160;intervention was used to present the method. This protocol can also be used for 3D morphometric analysis of other cells from either in vivo or in vitro conditions.

Astrocytes in the CNS change their functional and structural properties in response to harmful stimuli. This report presents a protocol for assessment of three-dimensional astrocyte morphology in diseased conditions or after therapeutic interventions.

As glial cells in the brain, astrocytes have diverse functional roles in the central nervous system. In the presence of harmful stimuli, astrocytes modify ...

Assessing Spatial Learning and Memory in Small Squamate Reptiles

Clinical research has leveraged a variety of paradigms to assess cognitive decline, commonly targeting spatial learning and memory abilities. However, interest in the cognitive processes of nonmodel species, typically within an ecological context, has also become an emerging field of study. In particular, interest in the cognitive processes in reptiles is growing although experimental studies on reptilian cognition are sparse. The few reptilian studies that have experimentally tested for spatial learning and memory have used rodent paradigms modified for use in reptiles. However, ecologically important aspects of the physiology and behavior of this taxonomic group must be taken into account when testing for spatially based cognition. Here, we describe modifications of the dry land Barnes maze and associated testing protocol that can improve performance when probing for spatial learning and memory ability in small squamate reptiles. The described paradigm and procedures were successfully used with male side-blotched lizards (Uta stansburiana), demonstrating that spatial learning and memory can be assessed in this taxonomic group with an ecologically relevant apparatus and protocol.

This paper describes a modification of the Barnes maze, a standard rodent paradigm used to assess spatial memory and learning, for use in small squamate reptiles.

Clinical research has leveraged a variety of paradigms to assess cognitive decline, commonly targeting spatial learning and memory abilities. However, ...

A Simple One-step Dissection Protocol for Whole-mount Preparation of Adult Drosophila Brains

There is an increasing interest in using Drosophila to model human brain degenerative diseases, map neuronal circuitries in adult brains, and study the molecular and cellular basis of higher brain functions. A whole-mount preparation of adult brains with well-preserved morphology is critical for such whole brain-based studies, but can be technically challenging and time-consuming. This protocol describes an easy-to-learn, one-step dissection approach of an adult fly head in less than 10 s, while keeping the intact brain attached to the rest of the body to facilitate subsequent processing steps. The procedure helps remove most of the eye and tracheal tissues normally associated with the brain that can interfere with the later imaging step, and also places less demand on the quality of the dissecting forceps. Additionally, we describe a simple method that allows convenient flipping of the mounted brain samples on a coverslip, which is important for imaging both sides of the brains with similar signal intensity and quality. As an example of the protocol, we present an analysis of dopaminergic (DA) neurons in adult brains of WT (w1118) flies. The high efficacy of the dissection method makes it particularly useful for large-scale adult brain-based studies in Drosophila.

A Simple One-step Dissection Protocol for Whole-mount Preparation of Adult Drosophila Brains

The adult Drosophila brain is a valuable system for studying neuronal circuitry, higher brain functions, and complex disorders. An efficient method to dissect whole brain tissue from the small fly head will facilitate brain-based studies. Here we describe a simple, one-step dissection protocol of adult brains with well-preserved morphology.

There is an increasing interest in using Drosophila to model human brain degenerative diseases, map neuronal circuitries in adult brains, and study the ...

Isolation and RNA Extraction of Neurons, Macrophages and Microglia from Larval Zebrafish Brains

To gain a detailed understanding of the role of different CNS cells during development or the establishment and progression of brain pathologies, it is important to isolate these cells without changing their gene expression profile. The zebrafish model provides a large number of transgenic fish lines in which specific cell types are labelled; for example neurons in the NBT:DsRed line or macrophages/microglia in the mpeg1:eGFP line. Furthermore, antibodies have been developed to stain specific cells, such as microglia with the 4C4 antibody.
Here, we describe the isolation of neurons, macrophages and microglia from larval zebrafish brains. Central to this protocol is the avoidance of an enzymatic tissue digestion at 37 &#176;C, which could modify cellular profiles. Instead a mechanical system of tissue homogenization at 4 &#176;C is used. This protocol entails homogenization of brains into cell suspension, their immuno-staining and the isolation of neurons, macrophages and microglia by FACS. Afterwards, we extracted RNA from those cells and evaluated their quality/quantity. We managed to obtain RNA of high quality (RNA Integrity Number (RIN) &#62; 7) to perform qPCR on macrophages/microglia and neurons, and transcriptomic analysis on microglia. This approach enables a better characterization of these cells, as well as a clearer understanding about their role in development and pathologies.

We present a protocol to isolate neurons, macrophages and microglia from larval zebrafish brains under physiological and pathological conditions. Upon isolation, RNA is extracted from these cells to analyze their gene expression profile. This protocol allows for the collection of high-quality RNA for performing downstream analysis like qPCR and transcriptomics.

To gain a detailed understanding of the role of different CNS cells during development or the establishment and progression of brain pathologies, it is ...

High-Resolution 3D Imaging of Rabies Virus Infection in Solvent-Cleared Brain Tissue

The visualization of infection processes in tissues and organs by immunolabeling is a key method in modern infection biology. The ability to observe and study the distribution, tropism, and abundance of pathogens inside of organ tissues provides pivotal data on disease development and progression. Using conventional microscopy methods, immunolabeling is mostly restricted to thin sections obtained from paraffin-embedded or frozen samples. However, the limited 2D image plane of these thin sections may lead to the loss of crucial information on the complex structure of an infected organ and the cellular context of the infection. Modern multicolor, immunostaining-compatible tissue clearing techniques now provide a relatively fast and inexpensive way to study high-volume 3D image stacks of virus-infected organ tissue. By exposing the tissue to organic solvents, it becomes optically transparent. This matches the sample&#8217;s refractive indices and eventually leads to a significant reduction of light scattering. Thus, in combination with long free working distance objectives, large tissue sections up to 1 mm in size can be imaged by conventional confocal laser scanning microscopy (CLSM) at high resolution. Here, we describe a protocol to apply deep-tissue imaging after tissue clearing to visualize rabies virus distribution in infected brains in order to study topics like virus pathogenesis, spread, tropism, and neuroinvasion.

Novel, immunostaining-compatible tissue clearing techniques like the ultimate 3D imaging of solvent-cleared organs allow the 3D visualization of rabies virus brain infection and its complex cellular environment. Thick, antibody-labeled brain tissue slices are made optically transparent to increase imaging depth and to enable 3D analysis by confocal laser scanning microscopy.

The visualization of infection processes in tissues and organs by immunolabeling is a key method in modern infection biology. The ability to observe and ...

Visualizing and Analyzing Intracellular Transport of Organelles and Other Cargos in Astrocytes

Astrocytes are among the most abundant cell types in the adult brain, where they play key roles in a multiplicity of functions. As a central player in brain homeostasis, astrocytes supply neurons with vital metabolites and buffer extracellular water, ions, and glutamate. An integral component of the &#8220;tri-partite&#8221; synapse, astrocytes are also critical in the formation, pruning, maintenance, and modulation of synapses. To enable these highly interactive functions, astrocytes communicate among themselves and with other glial cells, neurons, the brain vasculature, and the extracellular environment through a multitude of specialized membrane proteins that include cell adhesion molecules, aquaporins, ion channels, neurotransmitter transporters, and gap junction molecules. To support this dynamic flux, astrocytes, like neurons, rely on tightly coordinated and efficient intracellular transport. Unlike neurons,&#160;where intracellular trafficking has been extensively delineated, microtubule-based transport in astrocytes has been less studied. Nonetheless, exo- and endocytic trafficking of cell membrane proteins and intracellular organelle transport orchestrates astrocytes&#8217; normal biology, and these processes are often affected in disease or in response to injury. Here we present a straightforward protocol to culture high quality murine astrocytes, to fluorescently label astrocytic proteins and organelles of interest, and to record their intracellular transport dynamics using time-lapse confocal microscopy. We also demonstrate how to extract and quantify relevant transport parameters from the acquired movies using available image analysis software (i.e., ImageJ/FIJI) plugins.

Here we describe an in vitro live-imaging method to visualize intracellular transport of organelles and trafficking of plasma membrane proteins in murine astrocytes. This protocol also presents an image analysis methodology to determine cargo transport itineraries and kinetics.

Astrocytes are among the most abundant cell types in the adult brain, where they play key roles in a multiplicity of functions. As a central player in ...

Investigation of Spatial Interaction Between Astrocytes and Neurons in Cleared Brains

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Chapters in this video

Dissection and Culture of Commissural Neurons from Embryonic Spinal Cord

Tactile Conditioning And Movement Analysis Of Antennal Sampling Strategies In Honey Bees (Apis mellifera L.)

An Engulfment Assay: A Protocol to Assess Interactions Between CNS Phagocytes and Neurons

Isolation, Culture and Long-Term Maintenance of Primary Mesencephalic Dopaminergic Neurons From Embryonic Rodent Brains

Protocol for Three-dimensional Confocal Morphometric Analysis of Astrocytes

Assessing Spatial Learning and Memory in Small Squamate Reptiles

A Simple One-step Dissection Protocol for Whole-mount Preparation of Adult Drosophila Brains

Isolation and RNA Extraction of Neurons, Macrophages and Microglia from Larval Zebrafish Brains

High-Resolution 3D Imaging of Rabies Virus Infection in Solvent-Cleared Brain Tissue

Visualizing and Analyzing Intracellular Transport of Organelles and Other Cargos in Astrocytes