Name: visualizing and analyzing intracellular transport of organelles and other cargos in astrocytes
Uploaded: 2019-08-28T15:00:00
Description: Watch this Scientific Journal Video about Visualizing and Analyzing Intracellular Transport of Organelles and Other Cargos in Astrocytes at JoVE.com

DNL was supported by the University of North Carolina at Chapel Hill (UNC) School of Medicine as a Simmons Scholar. TWR was supported by UNC PREP Grant R25 GM089569. Work using the UNC Neuroscience Center Microscopy Core Facility was supported, in part, by funding from the NIH-NINDS Neuroscience Center Support Grant P30 NS045892 and the NIH-NICHD Intellectual and Developmental Disabilities Research Center Support Grant U54 HD079124.

All animal procedures were performed with the approval of the University of North Carolina at Chapel Hill Animal Care and Use Committee (IACUC).
1. Brain dissection and culture of primary mouse astrocytes
NOTE: The following protocol was adapted from published methods, which follows the original procedure developed by McCarthy and deVellis13,14,15. Mixed cell cultures of McCa...

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Here, we describe an experimental approach to express, visualize, and track fluorescently tagged organelles and membrane proteins of interest using time-lapse video microscopy in high-purity primary mouse cortical MD astrocytes. We also outline a methodology for measuring particle dynamics. Direct visualization of protein and organelle dynamics in primary astrocytes provides a powerful tool to study the regulation of intracellular transport in these cells in vitro.
The methodology for establis...

Astrocytes are the most abundant cells in the adult central nervous system, where they perform unique developmental and homeostatic functions1. Astrocytes modulate synaptic development through direct contact with pre- and postsynaptic terminals as part of the tri-partite synapse, which contains neurotransmitter receptors, transporters, and cell adhesion molecules that facilitate synapse formation and neuron-astrocyte communication2. In addition, astrocytes actively control synaptic transmission and prevent neuronal excitotoxicity by rapidly removing excitatory neurotransmitters from the synaptic cleft, recycling neurotransmitters, and participating in synaptic pruning3,4,5,6. To enable these highly interactive functions, astrocytes communicate among themselves, with other glial cells, and with neurons through specialized membrane proteins, including cell adhesion molecules, aquaporins, ion channels, neurotransmitter transporters, and gap junction molecules. Astrocytes actively change the surface levels of these proteins in response to fluctuations in their intra- and extracellular environment7. Furthermore, changes in the levels and distribution of mitochondria, lipid droplets, and degradative and recycling organelles modulate energy supply, metabolite availability, and cellular clearing processes that are essential for astrocyte function and survival.
The dynamic changes in membrane protein and organelle trafficking and positioning in astrocytes are facilitated by the concerted function of motor proteins and adaptors that promote cargo motility8,9. Similarly, surface levels of membrane proteins are modulated through internalization and recycling events10. These cargos are transported via an intricate network of actin, microtubules, and possibly intermediate filaments tracks8. Studies based on immunofluorescence staining of end-binding protein 1 (EB1), which accumulates at the growing microtubule plus ends, suggest that in astrocytes bundles of microtubules radiate out from the perinucleus and extend their plus end towards the periphery11. However, a comprehensive examination of the organization and polarity of microtubules and other cytoskeletal elements using live-cell imaging is still lacking. While many of the mechanisms underlying the dynamics of organelles and membrane proteins have been extensively studied in neurons and other cell types, cargo motility in astrocytes is less well understood. Most of our current knowledge about changes in protein and organelle distribution in astrocytes is based on traditional antibody-based labeling of fixed preparation, which precludes precise spatial and temporal examination of cargo dynamics7,12.
Here, we describe a method to label membrane proteins and organelles for live imaging in high purity primary mouse astrocyte cultures. Using this protocol, we provide examples in which we track the dynamic localization of green fluorescent protein (GFP)-tagged membrane proteins in transfected astrocytes, including the gap junction protein connexin 43 (Cx43-GFP) and the excitatory amino acid transporter 1 (EAAT1-GFP). We also describe the use of a fluorescent acidotropic probe to visualize acidic organelles and follow their trafficking dynamics in live astrocytes. Finally, we demonstrate how to analyze the time-lapse data to extract and evaluate transport parameters for individual cargos.

<table>
	<tbody>
		<tr>
			<td>2.5% Trypsin (10x)</td>
			<td>Gibco</td>
			<td>15090-046</td>
			<td></td>
		</tr>
		<tr>
			<td>Benchtop Centrifuge</td>
			<td>Thermo Scientific</td>
			<td>75-203-637</td>
			<td>Sorvall ST8 Centrifuge</td>
		</tr>
		<tr>
			<td>Cell Culture Grade Water</td>
			<td>Gen Clone</td>
			<td>25-511</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell Culture Microscope</td>
			<td>Zeiss</td>
			<td>WSN-AXIOVERT A1</td>
			<td>Vert.A1 inverted scope, Inverted tissue culture microscope with fluorescent capabilities</td>
		</tr>
		<tr>
			<td>Cytosine Arabinoside</td>
			<td>Sigma</td>
			<td>C1768-100MG</td>
			<td>(AraC) Dissolve lyophilized powder in sterile cell culture grade water to make a 10mM stock, aliquot and freeze for long term storage</td>
		</tr>
		<tr>
			<td>DAPI</td>
			<td>Sigma</td>
			<td>D9542-5MG</td>
			<td>Dissolve lyophilized powder in deionized water to a maximum concentration of 20 mg/ml, heat or sonicate as necessary. Use at 300 nM for counterstaining.</td>
		</tr>
		<tr>
			<td>Dissecting Microscope</td>
			<td>Zeiss</td>
			<td></td>
			<td>Stemi 305</td>
		</tr>
		<tr>
			<td>Dissecting Scissors</td>
			<td>F.S.T</td>
			<td>14558-09</td>
			<td></td>
		</tr>
		<tr>
			<td>Dulbecco&#39;s Modified Eagle Medium</td>
			<td>Gen Clone</td>
			<td>25-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum</td>
			<td>Gemini</td>
			<td>100-106</td>
			<td>Heat-Inactivated</td>
		</tr>
		<tr>
			<td>FIJI (Fiji is Just Image J)</td>
			<td>NIH</td>
			<td>Version 1.52i</td>
			<td></td>
		</tr>
		<tr>
			<td>Fine Tip Tweezers</td>
			<td>F.S.T</td>
			<td>11254-20</td>
			<td>Style #5</td>
		</tr>
		<tr>
			<td>Fluorescence light source</td>
			<td>Excelitas</td>
			<td>012-63000</td>
			<td>X-Cite 120Q</td>
		</tr>
		<tr>
			<td>GFAP antibody</td>
			<td>Cell Signaling</td>
			<td>3670S</td>
			<td>GFAP (GA5) mouse monoclonal antibody</td>
		</tr>
		<tr>
			<td>Glass Bottom Dishes</td>
			<td>Mattek corporation</td>
			<td>P35G-1.5-14-C</td>
			<td>35 mm Dish | No. 1.5 Coverslip | 14 mm Glass Diameter | Uncoated</td>
		</tr>
		<tr>
			<td>Graefe Forceps</td>
			<td>F.S.T</td>
			<td>11054-10</td>
			<td>Graefe Iris Forceps with curved tips</td>
		</tr>
		<tr>
			<td>Green fluorescent dye that stains acidic compartments (late endosomes and lysosomes)</td>
			<td>Life Technologies</td>
			<td>L7526</td>
			<td>LysoTracker Green DND 26. Pre-dissolved in DMSOS to a 1mM stock solution. Dilute to the final working concentration in the growth medium or buffer of choice.</td>
		</tr>
		<tr>
			<td>Hank&#39;s Balanced Salt Solution (10x)</td>
			<td>Gibco</td>
			<td>14065-056</td>
			<td>Magnesium and calcium free</td>
		</tr>
		<tr>
			<td>Imaging Media</td>
			<td>Life Technologies</td>
			<td>A14291DJ</td>
			<td>Live Cell Imaging Solution</td>
		</tr>
		<tr>
			<td>Inverted Confocal Microscope</td>
			<td>Zeiss</td>
			<td></td>
			<td>LSM 780</td>
		</tr>
		<tr>
			<td>KymoToolBox</td>
			<td></td>
			<td></td>
			<td>https://github.com/fabricecordelieres/IJ_KymoToolBox</td>
		</tr>
		<tr>
			<td>Lipofection Enhancer Reagent</td>
			<td>Life Technologies</td>
			<td>11514015</td>
			<td>Plus Reagent</td>
		</tr>
		<tr>
			<td>Lipofection Reagent</td>
			<td>Life Technologies</td>
			<td>15338100</td>
			<td>Lipofectamine LTX reagent</td>
		</tr>
		<tr>
			<td>Orbital shaking incubator</td>
			<td>New Brunswick Scientific</td>
			<td>8261-30-1008</td>
			<td>Innova 4230 , orbital shaking incubator with temperature and speed control</td>
		</tr>
		<tr>
			<td>Penicillin/Strepomycin solution (100x)</td>
			<td>Gen Clone</td>
			<td>25-512</td>
			<td></td>
		</tr>
		<tr>
			<td>Phosphate Buffered Saline (10x)</td>
			<td>Gen Clone</td>
			<td>25-507x</td>
			<td></td>
		</tr>
		<tr>
			<td>Poly-D-Lysine Hydrobromide</td>
			<td>Sigma</td>
			<td>P7405</td>
			<td>Dissolve in Tris buffer, pH 8.5, at 1mg/mL. Freeze for long term storage. Avoid cycles of freezing and thawing</td>
		</tr>
		<tr>
			<td>Reduced serum medium</td>
			<td>Gibco</td>
			<td>31985-062</td>
			<td>OPTI-MEM</td>
		</tr>
		<tr>
			<td>Tissue Culture Flasks</td>
			<td>Olympus Plastics</td>
			<td>25-209</td>
			<td>75 cm^2. 100% angled neck access, 0.22um hydrophobic vented filter cap</td>
		</tr>
		<tr>
			<td>Tissue culture incubator</td>
			<td>Thermo Scientific</td>
			<td>51030285</td>
			<td>HERAcell VIOS 160i, tissue culture incubator with temperature, humidity, and CO2 control</td>
		</tr>
		<tr>
			<td>Tris-Base</td>
			<td>Sigma</td>
			<td>T1503</td>
			<td>8.402 g dissolved to one liter in water with 4.829 g Tris HCl to make 0.1 M Tris buffer, pH 8.5</td>
		</tr>
		<tr>
			<td>Tris-HCl</td>
			<td>Sigma</td>
			<td>T3253</td>
			<td>4.829 g dissolved to one liter in water with 8.402 g Tris Base to make 0.1 M Tris buffer, pH 8.5</td>
		</tr>
		<tr>
			<td>Trypsin-EDTA (0.25%), phenol red</td>
			<td>Gibco</td>
			<td>25200072</td>
			<td></td>
		</tr>
		<tr>
			<td>Vacuum-Driven Filter Systems</td>
			<td>Olympus Plastics</td>
			<td>25-227</td>
			<td>500 ml, PES membrane, 0.22 &#181;m</td>
		</tr>
		<tr>
			<td>Vannas scissors straight</td>
			<td>Roboz</td>
			<td>RS-5620</td>
			<td></td>
		</tr>
	</tbody>
</table>

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.

The protocol for establishing primary mouse MD astrocytes outlined above should yield reproducible, high quality cultures. Although cultures initially contain a mix of astrocytes, fibroblasts, and other glial cells, including microglia and oligodendrocytes (Figure 1Bi,Biv; red arrowheads), the addition of AraC to the mixed culture between DIV5-DIV7 minimizes the proliferation of these contaminant cells. The combined AraC treatment and shaking-based purification strategy enri...

Watch this Scientific Journal Video about Visualizing and Analyzing Intracellular Transport of Organelles and Other Cargos in Astrocytes at JoVE.com

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

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 ...

Our protocol can be used to investigate the motility and localization of astrocytic organelles or proteins under controlled extracellular environments and mild disease states. Unlike the MHA fixed preparations, which provide single snapshots of protein and organelle localization, our live imaging technique can be used to analyze particle dynamics in individual live astrocytes. The day before the transfection seed astrocytes at the appropriate density for imaging at 24 to 48 hours post transfection.Dilute the lipofection reagent in reduced serum medium to the appropriate experimental concentration. Dilute five micrograms of high purity DNA in 250 microliters of reduced serum medium and add five microliters of lipofection enhancer reagent to the tube. Mix the lipofection reagent with an equal volume of the DNA lipofection enhancer mix and incubate the solution for 15 minutes at room temperature.At the end of the incubation, remove the supernatant from the astrocyte culture and add 100 microliters of the transfection mix dropwise to the cells. After six hours at 37 degrees Celsius and 5%carbon dioxide, replace the transfection complex with an appropriate volume of astrocyte culture medium and return the cells to the cell culture incubator for an additional 24 to 72 hours. 30 minutes before the imaging, dilute a suitable lysosomal labeling probe in 200 microliters of astrocyte culture medium to a working concentration of one micromolar and label the astrocytes with a probe for 30 minutes at 37 degrees Celsius.Then wash the cells one time with warm astrocyte culture medium and replace the wash with imaging medium. Immediately after the probe labeling, place the astrocyte culture container into the appropriate adapter on the microscope stage and using EBI fluorescence light, locate the cells that express fluorescent proteins or probe. Use the digital camera to adjust the fluorescent sample illumination to visualize the selected cells and adjust the focus and zoom in to a single cell.Then use the Zoom and Definite Focus functions to acquire a single Z-stack time-lapse series at a frequency of one frame every two seconds for time intervals ranging between 300 and 500 seconds. Save and export the time-lapse images as AVI or TIFF stack files. To analyze the time-lapse images, open the time-lapse image sequence in ImageJ or Fiji and use the Split Channel tool to split the channels.In the eight bit green channel image, use the Segmented Line tool to trace a line along the trajectories of the particles using the same desired directional convention for all of the movies so that the polarity is consistent within and across all of the cells being studied. Double click the Line tool to adjust the line width to match the thickness of the track and run the Draw Kymo macro of the Kymo ToolBox plugin using a line width of 10. A prompt asking to calibrate the image in time and space will appear.Once calibrated, kymographs will be generated and can be saved as TIFF files. To assign particle trajectories, use the Segmented Line tool to manually track each particle in the kymograph for the full duration of the acquisition and use the ROI manager to record each particle trajectory as a region of interest. Save all of the regions of interest per each time-lapse video for further analysis and run the Analyze Kymo macro of the Kymo ToolBox plugin.A window will open asking to define the outward direction of particle motion from the nucleus of the cell of interest from the dropdown menu. The limit speed should be defined according to the sensitivity of the software for each cargo of interest and the line width should be adjusted to match the thickness of each particle trajectory. The Log All Data and Log Extrapolated Coordinates should be for calculation of the various cargo transport parameters.Click Okay. The data calculated for the individual tracks will then be pooled per kymograph and saved in text files specific to each image. Combining cytosine arabinoside treatment with the shaking based purification strategy enriches the purity of the astrocyte cultures over traditional protocols that include the purification step only.Lipofection based transfection allows the transient expression of proteins at levels that are optimal for live cell imaging without causing toxicity or affecting astrocyte viability. Similarly, the use of a fluorescent probe permits the rapid and efficient labeling of acidic endolysosomal organelles for the tracking of organelle dynamics and astrocytes. The time-lapse data from the imaging can be used to generate kymographs that track cargo motion in time and space.In these kymographs, anterograde movement of the indicated cargo is represented by trajectories with negative slopes, while retrograde movement is represented by trajectories with positive slopes. Stationary vesicles appear as vertical trajectories. In this analysis, quantification of the flux of a specific cargo through an area of the astrocyte revealed differences in the percentage of modal particles among cargoes that are likely representative of their normal base line motility in the region of the astrocyte within which the movies were acquired.The precise mapping of the change in the X, Y position along the full timescale for each particle obtained from the kymograph can also be used to evaluate other motion parameters, such as cargo velocity and run length. As this protocol requires high quality astrocyte cultures and efficient cargo labeling, the transfection reagent incubation time and acquisition timeline should be adjusted for each plasmid or cargo of interest. This protocol can be modified to characterize transport events in astrocytes in response to cell damage, toxicity, pathogenic mutations, synaptic activity, or changes in the intra or extracellular environment.

visualizing-analyzing-intracellular-transport-organelles-other-cargos

Research

JoVE Journal

Neuroscience

Fluorescence Recovery After Photobleaching (FRAP) of Fluorescence Tagged Proteins in Dendritic Spines of Cultured Hippocampal Neurons

FRAP has been used to quantify the mobility of GFP-tagged proteins. Using a strong excitation laser, the fluorescence of a GFP-tagged protein is bleached in the region of interest. The fluorescence of the region recovers when the unbleached GFP-tagged protein from outside of the region diffuses into the region of interest. The mobility of the protein is then analyzed by measuring the fluorescence recovery rate. This technique could be used to characterize protein mobility and turnover rate.
In this study, we express the (enhanced green fluorescent protein) EGFP vector in cultured hippocampal neurons. Using the Zeiss 710 confocal microscope, we photobleach the fluorescence signal of the GFP protein in a single spine, and then take time lapse images to record the fluorescence recovery after photobleaching. Finally, we estimate the percentage of mobile and immobile fractions of the GFP in spines, by analyzing the imaging data using ImageJ and Graphpad softwares.
This FRAP protocol shows how to perform a basic FRAP experiment as well as how to analyze the data.

Fluorescence Recovery After Photobleaching FRAP of Fluorescence Tagged Proteins in Dendritic Spines of Cultured Hippocampal Neurons

FRAP has been used to quantify the mobility of Green Fluorescence Protein (GFP)-tagged proteins in cultured cells. We examined the mobile/immobile fractions of the GFP by analyzing the fluorescence recovery percentage after photobleaching. In this study, FRAP was performed at spines of hippocampal neurons.

FRAP has been used to quantify the mobility of GFP-tagged proteins. Using a strong excitation laser, the fluorescence of a GFP-tagged protein is bleached ...

Isolation and Culture of Mouse Cortical Astrocytes

Astrocytes are an abundant cell type in the mammalian brain, yet much remains to be learned about their molecular and functional characteristics. In vitro astrocyte cell culture systems can be used to study the biological functions of these glial cells in detail. This video protocol shows how to obtain pure astrocytes by isolation and culture of mixed cortical cells of mouse pups. The method is based on the absence of viable neurons and the separation of astrocytes, oligodendrocytes and microglia, the three main glial cell populations of the central nervous system, in culture. Representative images during the first days of culture demonstrate the presence of a mixed cell population and indicate the timepoint, when astrocytes become confluent and should be separated from microglia and oligodendrocytes. Moreover, we demonstrate purity and astrocytic morphology of cultured astrocytes using immunocytochemical stainings for well established and newly described astrocyte markers. This culture system can be easily used to obtain pure mouse astrocytes and astrocyte-conditioned medium for studying various aspects of astrocyte biology.

Astrocytes have been recognized to be versatile cells participating in fundamental biological processes that are essential for normal brain development and function, and central nervous system repair. Here we present a rapid procedure to obtain pure mouse astrocyte cultures to study the biology of this major class of central nervous system cells.

Astrocytes  are an abundant cell type in the mammalian brain, yet much remains to be  learned about their molecular and functional characteristics. In ...

Imaging Intracellular Ca2+ Signals in Striatal Astrocytes from Adult Mice Using Genetically-encoded Calcium Indicators

Astrocytes display spontaneous intracellular Ca2+ concentration fluctuations ([Ca2+]i) and in several settings respond to neuronal excitation with enhanced [Ca2+]i signals. It has been proposed that astrocytes in turn regulate neurons and blood vessels through calcium-dependent mechanisms, such as the release of signaling molecules. However, [Ca2+]i imaging in entire astrocytes has only recently become feasible with genetically encoded calcium indicators (GECIs) such as the GCaMP series. The use of GECIs in astrocytes now provides opportunities to study astrocyte [Ca2+]i signals in detail within model microcircuits such as the striatum, which is the largest nucleus of the basal ganglia. In the present report, detailed surgical methods to express GECIs in astrocytes in vivo, and confocal imaging approaches to record [Ca2+]i signals in striatal astrocytes in situ, are described. We highlight precautions, necessary controls and tests to determine if GECI expression is selective for astrocytes and to evaluate signs of overt astrocyte reactivity. We also describe brain slice and imaging conditions in detail that permit reliable [Ca2+]i imaging in striatal astrocytes in situ. The use of these approaches revealed the entire territories of single striatal astrocytes and spontaneous [Ca2+]i signals within their somata, branches and branchlets. The further use and expansion of these approaches in the striatum will allow for the detailed study of astrocyte [Ca2+]i signals in the striatal microcircuitry.

Imaging Intracellular Ca2+ Signals in Striatal Astrocytes from Adult Mice Using Genetically-encoded Calcium Indicators

The properties and functions of astrocyte intracellular Ca2+ signals in the striatum remain incompletely explored. We describe methods to express genetically encoded calcium indicators in striatal astrocytes using adeno-associated viruses of serotype 2/5 (AAV2/5), as well as procedures to reliably image Ca2+ signals within striatal astrocytes in situ.

Astrocytes display spontaneous intracellular Ca2+ concentration fluctuations ([Ca2+]i) and in several settings respond to neuronal excitation with ...

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 ...

Analyzing Dendritic Morphology in Columns and Layers

In many regions of the central nervous systems, such as the fly optic lobes and the vertebrate cortex, synaptic circuits are organized in layers and columns to facilitate brain wiring during development and information processing in developed animals. Postsynaptic neurons elaborate dendrites in type-specific patterns in specific layers to synapse with appropriate presynaptic terminals. The fly medulla neuropil is composed of 10 layers and about 750 columns; each column is innervated by dendrites of over 38 types of medulla neurons, which match with the axonal terminals of some 7 types of afferents in a type-specific fashion. This report details the procedures to image and analyze dendrites of medulla neurons. The workflow includes three sections: (i) the dual-view imaging section combines two confocal image stacks collected at orthogonal orientations into a high-resolution 3D image of dendrites; (ii) the dendrite tracing and registration section traces dendritic arbors in 3D and registers dendritic traces to the reference column array; (iii) the dendritic analysis section analyzes dendritic patterns with respect to columns and layers, including layer-specific termination and planar projection direction of dendritic arbors, and derives estimates of dendritic branching and termination frequencies. The protocols utilize custom plugins built on the open-source MIPAV (Medical Imaging Processing, Analysis, and Visualization) platform and custom toolboxes in the matrix laboratory language. Together, these protocols provide a complete workflow to analyze the dendritic routing of Drosophila medulla neurons in layers and columns, to identify cell types, and to determine defects in mutants.

Here, we show how to analyze dendritic routing of Drosophila medulla neurons in columns and layers. The workflow includes a dual-view imaging technique to improve the image quality and computational tools for tracing, registering dendritic arbors to the reference column array and for analyzing the dendritic structures in 3D space.

In many regions of the central nervous systems, such as the fly optic lobes and the vertebrate cortex, synaptic circuits are organized in layers and ...

Visualization and Live Imaging of Oligodendrocyte Organelles in Organotypic Brain Slices Using Adeno-associated Virus and Confocal Microscopy

Neurons rely on the electric insulation and trophic support of myelinating oligodendrocytes. Despite the importance of oligodendrocytes, the advanced tools currently used to study neurons, have only partly been taken on by oligodendrocyte researchers. Cell type-specific staining by viral transduction is a useful approach to study live organelle dynamics. This paper describes a protocol for visualizing oligodendrocyte mitochondria in organotypic brain slices by transduction with adeno-associated virus (AAV) carrying genes for mitochondrial targeted fluorescent proteins under the transcriptional control of the myelin basic protein promoter. It includes the protocol for making organotypic coronal mouse brain slices. A procedure for time-lapse imaging of mitochondria then follows. These methods can be transferred to other organelles and may be particularly useful for studying organelles in the myelin sheath. Finally, we describe a readily available technique for visualization of unstained myelin in living slices by Confocal Reflectance microscopy (CoRe). CoRe requires no extra equipment and can be useful to identify the myelin sheath during live imaging.

Myelinating oligodendrocytes promote rapid action potential propagation and neuronal survival. Described here is a protocol for oligodendrocyte-specific expression of fluorescent proteins in organotypic brain slices with subsequent time-lapse imaging. Further, a simple procedure for visualizing unstained myelin is presented.

Neurons rely on the electric insulation and trophic support of myelinating oligodendrocytes. Despite the importance of oligodendrocytes, the advanced ...

Analyzing the Size, Shape, and Directionality of Networks of Coupled Astrocytes

It has become increasingly clear that astrocytes modulate neuronal function not only at the synaptic and single-cell levels, but also at the network level. Astrocytes are strongly connected to each other through gap junctions and coupling through these junctions is dynamic and highly regulated. An emerging concept is that astrocytic functions are specialized and adapted to the functions of the neuronal circuit with which they are associated. Therefore, methods to measure various parameters of astrocytic networks are needed to better describe the rules governing their communication and coupling and to further understand their functions.
Here, using the image analysis software (e.g., ImageJFIJI), we describe a method to analyze confocal images of astrocytic networks revealed by dye-coupling. These methods allow for 1) an automated and unbiased detection of labeled cells, 2) calculation of the size of the network, 3) computation of the preferential orientation of dye spread within the network, and 4) repositioning of the network within the area of interest.
This analysis can be used to characterize astrocytic networks of a particular area, compare networks of different areas associated to different functions, or compare networks obtained under different conditions that have different effects on coupling. These observations may lead to important functional considerations. For instance, we analyze the astrocytic networks of a trigeminal nucleus, where we have previously shown that astrocytic coupling is essential for the ability of neurons to switch their firing patterns from tonic to rhythmic bursting1. By measuring the size, confinement, and preferential orientation of astrocytic networks in this nucleus, we can build hypotheses about functional domains that they circumscribe. Several studies suggest that several other brain areas, including the barrel cortex, lateral superior olive, olfactory glomeruli, and sensory nuclei in the thalamus and visual cortex, to name a few, may benefit from a similar analysis.

Here we present a protocol to assess the organization of astrocytic networks. The described method minimizes bias to provide descriptive measures of these networks such as cell count, size, area, and position within a nucleus. Anisotropy is assessed with a vectorial analysis.

It has become increasingly clear that astrocytes modulate neuronal function not only at the synaptic and single-cell levels, but also at the network ...

Analyzing Mitochondrial Transport and Morphology in Human Induced Pluripotent Stem Cell-Derived Neurons in Hereditary Spastic Paraplegia

Neurons have intense demands for high energy in order to support their functions. Impaired mitochondrial transport along axons has been observed in human neurons, which may contribute to neurodegeneration in various disease states. Although it is challenging to examine mitochondrial dynamics in live human nerves, such paradigms are critical for studying the role of mitochondria in neurodegeneration. Described here is a protocol for analyzing mitochondrial transport and mitochondrial morphology in forebrain neuron axons derived from human induced pluripotent stem cells (iPSCs). The iPSCs are differentiated into telencephalic glutamatergic neurons using well-established methods. Mitochondria of the neurons are stained with MitoTracker CMXRos, and mitochondrial movement within the axons are captured using a live-cell imaging microscope equipped with an incubator for cell culture. Time-lapse images are analyzed using software with &#34;MultiKymograph&#34;, &#34;Bioformat importer&#34;, and &#34;Macros&#34; plugins. Kymographs of mitochondrial transport are generated, and average mitochondrial velocity in the anterograde and retrograde directions is read from the kymograph. Regarding mitochondrial morphology analysis, mitochondrial length, area, and aspect ratio are obtained using the ImageJ. In summary, this protocol allows characterization of mitochondrial trafficking along axons and analysis of their morphology to facilitate studies of neurodegenerative diseases.

Impaired mitochondrial transport and morphology are involved in various neurodegenerative diseases. The presented protocol uses induced pluripotent stem cell-derived forebrain neurons to assess mitochondrial transport and morphology in hereditary spastic paraplegia. This protocol allows characterization of mitochondrial trafficking along axons and analysis of their morphology, which will facilitate the study of neurodegenerative disease.

Neurons have intense demands for high energy in order to support their functions. Impaired mitochondrial transport along axons has been observed in human ...

Axonal Transport of Organelles in Motor Neuron Cultures using Microfluidic Chambers System

Motor neurons (MNs) are highly polarized cells with very long axons. Axonal transport is a crucial mechanism for MN health, contributing to neuronal growth, development, and survival. We describe a detailed method for the use of microfluidic chambers (MFCs) for tracking axonal transport of fluorescently labeled organelles in MN axons. This method is rapid, relatively inexpensive, and allows for the monitoring of intracellular cues in space and time. We describe a step by step protocol for: 1) Fabrication of polydimethylsiloxane (PDMS) MFCs; 2) Plating of ventral spinal cord explants and MN dissociated culture in MFCs; 3) Labeling of mitochondria and acidic compartments followed by live confocal imagining; 4) Manual and semiautomated axonal transport analysis. Lastly, we demonstrate a difference in the transport of mitochondria and acidic compartments of HB9::GFP ventral spinal cord explant axons as a proof of the system validity. Altogether, this protocol provides an efficient tool for studying the axonal transport of various axonal components, as well as a simplified manual for MFC usage to help discover spatial experimental possibilities.

Axonal transport is a crucial mechanism for motor neuron health. In this protocol we provide a detailed method for tracking the axonal transport of acidic compartments and mitochondria in motor neuron axons using microfluidic chambers.

Motor neurons (MNs) are highly polarized cells with very long axons. Axonal transport is a crucial mechanism for MN health, contributing to neuronal ...

In Vitro Wedge Slice Preparation for Mimicking In Vivo Neuronal Circuit Connectivity

In vitro slice electrophysiology techniques measure single-cell activity with precise electrical and temporal resolution. Brain slices must be relatively thin to properly visualize and access neurons for patch-clamping or imaging, and in vitro examination of brain circuitry is limited to only what is physically present in the acute slice. To maintain the benefits of in vitro slice experimentation while preserving a larger portion of presynaptic nuclei, we developed a novel slice preparation. This &#8220;wedge slice&#8221; was designed for patch-clamp electrophysiology recordings to characterize the diverse monaural, sound-driven inputs to medial olivocochlear (MOC) neurons in the brainstem. These neurons receive their primary afferent excitatory and inhibitory inputs from neurons activated by stimuli in the contralateral ear and corresponding cochlear nucleus (CN). An asymmetrical brain slice was designed which is thickest in the rostro-caudal domain at the lateral edge of one hemisphere and then thins towards the lateral edge of the opposite hemisphere. This slice contains, on the thick side, the auditory nerve root conveying information about auditory stimuli to the brain, the intrinsic CN circuitry, and both the disynaptic excitatory and trisynaptic inhibitory afferent pathways that converge on contralateral MOC neurons. Recording is performed from MOC neurons on the thin side of the slice, where they are visualized using DIC optics for typical patch-clamp experiments. Direct stimulation of the auditory nerve is performed as it enters the auditory brainstem, allowing for intrinsic CN circuit activity and synaptic plasticity to occur at synapses upstream of MOC neurons. With this technique, one can mimic in vivo circuit activation as closely as possible within the slice. This wedge slice preparation is applicable to other brain circuits where circuit analyses would benefit from preservation of upstream connectivity and long-range inputs, in combination with the technical advantages of in vitro slice physiology.

Integration of diverse synaptic inputs to neurons is best measured in a preparation that preserves all pre-synaptic nuclei for natural timing and circuit plasticity, but brain slices typically sever many connections. We developed a modified brain slice to mimic in vivo circuit activity while maintaining in vitro experimentation capability.

In vitro slice electrophysiology techniques measure single-cell activity with precise electrical and temporal resolution. Brain slices must be relatively ...