The authors thank Giorgio Carlini for the technical support in developing the confinement structure and dott. Ornella LoBrutto for the thorough revision of the manuscript. The research leading to these results has received funding from the European Union&#39;s 7th Framework Programme (ICT-FET FP7/2007-2013, FET Young Explorers scheme) under grant agreement 284772 BRAIN BOW (www.brainbowproject.eu).

The experimental protocol was approved by the European Animal Care Legislation (2010/63/EU), by the Italian Ministry of Health in accordance with the D.L. 116/1992 and by the guidelines of the University of Genova (Prot. N. 13130, May 2011). All efforts were made to reduce the number of animals for the project and to minimize their suffering.
1. Preparation of Materials and Supports
<ol>
	<li>Construct the mold to build the PDMS (Poly-Dimethyl-Siloxane) constraint by means of a CNC (Computer Numerical Control) milling machine. Such a mold is realized in polycarbonate with the central cylinder in polytetrafluoroethylene (PTFE). This material allows an easier extraction of the mask once the PDMS has hardened. 
	NOTE: The design of the mold has been performed by Computer-Aided-Design (CAD) and then delivered to the CNC milling machine.</li>
	<li>Prepare the PDMS elastomer. PDMS is an organic polymer. It is composed of two elements, a curing agent and a polymer. Mix them by a volume ratio of 1:10, one part of curing agent and nine parts of polymer. Put the two components in a Petri dish, shake and insert the mix in the vacuum chamber for 10 min&#160;to eliminate air bubbles. 3 g&#160;of PDMS are sufficient for one constraint.</li>
	<li>Construct the PDMS constraint. Insert the PDMS material into the molder and put it into the oven for 30 min&#160;at 120 &#176;C. The PDMS constraint has the shape of an ideal cylinder with an external and internal diameter of 22.0 and 3.0 mm, respectively and a height of 650 &#181;m.</li>
	<li>The day before the plating, couple the mask to the active area of the Micro-Electrode Arrays (MEAs) by means of a tweezer under a stereomicroscope and sterilize the PDMS mask in the oven at 120 &#176;C.</li>
	<li>Sterilize the glass microbeads (nominal diameter of 40&#177;2 &#181;m; certified mean diameter of 42.3&#177;1.1 &#181;m) in 70% ethanol for 2 hr&#160;in a conical vial and rotate every 30 min&#160;to expose all microbeads.&#160;</li>
	<li>Remove the ethanol solution from the vial and rinse the microbeads two times with sterilized water.</li>
	<li>Condition the central part of the MEA area delimited by the PDMS mask (diameter equals to 3.0 mm) with 24 &#181;l of mixed solution of Poly-D-Lysine and Laminin at 0.05 &#956;g/ml.</li>
	<li>Coat the microbeads with adhesion proteins, Laminin and Poly-D-Lysine at 0.05 &#181;g/ml and leave them overnight in the incubator at 37 &#176;C, to obtain a stable and long-lasting neuronal network.</li>
	<li>Remove the adhesion factors both from the glass surface of the MEA and from the glass microbeads. Aspirate approximately 95% of the coating solution with a pipette and apply a small volume- 24&#181;l- of sterile water on the MEA surface. Aspirate again more than 95% of the water and let the MEA dry under the laminar hood for 1 hr&#160;before plating the cells. 
	NOTE: In the case of microbeads instead, aspirate the coating solution and make a first wash with sterilized water and a second one with the basal medium and its supplement such as B27, in order to condition the glass surface where neurons will be plated. Do not let the microbeads dry. Leave them in suspension in the culture medium inside the vial.</li>
	<li>Distribute, by means of a pipette -200 &#181;l-, the suspension of treated microbeads (about 32,000) onto a multiwell plate with membrane insert (pore diameter 0.4 &#181;m) where they will self-assemble forming a uniform layer.</li>
	<li>Fill each well of the membrane with 0.5 ml of medium and put it in the incubator (T = 37.0 oC, CO2 = 5%) until the neurons are ready to be plated (3.2).</li>
</ol>
2. Dissection of Embryos and Dissociation of Tissue
<ol>
	<li>House adult female rats (200-250 g) at a constant temperature (22 &#177; 1 &#176;C) and relative humidity (50%) under a regular light&#8211;dark schedule (light-on 7 AM&#8211;7 PM) in the animal facility. Ensure that food and water are freely available.</li>
	<li>Anesthetize a pregnant female rat after 18 days of development (E18) using 3% isoflurane. Then, sacrifice the animal by cervical dislocation.</li>
	<li>Remove hippocampi from each rat embryo and place them into ice cold Hank&#8217;s balanced salt solution without Ca2+ and Mg2+. At day 18 of development hippocampus and cortex tissues are very soft and do not need to be cut into small pieces. Further details can be found18,19.</li>
	<li>Dissociate the tissue in 0.125% of Trypsin/Hank&#8217;s solution containing 0.05% of DNAse for 18-20 min at 37 &#176;C.</li>
	<li>Remove the supernatant solution with a Pasteur pipette and stop the enzymatic digestion by adding medium with 10% fetal bovine serum (FBS) for 5 min.</li>
	<li>Remove the medium with FBS and wash once with the medium with its supplement, 1% L-glutamine, gentamicin 10 &#181;g/ml. Remove again the medium with a Pasteur pipette and refill it again with a small amount (500 &#181;l) of growth medium with its supplement, 1% L-glutamine, gentamicin 10 &#181;g/ml.</li>
	<li>Dissociate the tissue pellet mechanically with a narrow Pasteur pipette until a milky suspension of cells is apparent. It is not necessary to centrifuge the cell suspension.</li>
	<li>Dilute the small volume of cell suspension with the growth medium to obtain a final volume of 2.0 ml. Count the obtained cellular concentration with a hemocytometer chamber. Dilute this concentration at 1:5 in order to obtain the desired cell concentration of 600-700 cells/&#181;l.</li>
</ol>
3. Cell Plating
<ol>
	<li>Plate cells at a density of about 2,000 cells/mm2 onto the active area of the MEA, defined by the PDMS constraint to create a 2D neuronal network. 
	NOTE: Each hippocampus contains about 5 x 105 cells, (1 x 106 for a single embryo). Dissect 6 embryos to get a total amount of 6 x 10 6 cells in 2 ml, and an estimated concentration of 3,000 cells/&#181;l. Dilute this concentration at 1:5 in order to obtain the desired cell concentration and plate about 600-700 cells/&#181;l. If the MEA area delimited by the PDMS constraint is about 7.065 mm2, and the total number of plated cells 600 cells/&#181;l x 24 &#181;l = 14,400 cells, the final density of 2,038 cells/mm2.</li>
	<li>Place the MEA devices into the incubator with humidified CO2 atmosphere (5%) at 37 &#176;C.</li>
	<li>Distribute 160 &#181;l of the suspension with a cell concentration of 600-700 cells/&#181;l (about 100,000 cells) onto the surface of the microbeads monolayer positioned inside the multiwell plates to complete the preliminary step for the construction of three-dimensional culture. Put the multiwell plates in the incubator with humidified CO2 atmosphere (5%) at 37 &#176;C.</li>
</ol>
4. 3D Neuronal Network Construction
<ol>
	<li>6-8 hr&#160;after the plating, transfer the suspension (microbeads with neurons) from the multiwell plates very carefully inside the area delimited by the PDMS constraint by using a pipette set for a volume of about 30-40 &#181;l. After each transfer, wait for about half a minute, to allow the microbeads to self-assemble in a hexagonal compact structure.</li>
	<li>Once all the layers are deposited and spontaneously assembled, refill with a large drop of about 300 &#181;l of medium the top of the area delimited by the PDMS constraint.</li>
	<li>Put the 3D structure coupled to the MEA in incubator (T = 37.0 oC, CO2 = 5%) for 48 hr&#160;before adding a final volume (about 1 ml) of growth medium culture with its supplement. 
	NOTE: Consider the total number of beads on the multiwell plates with membrane insert (30,000) and the number of beads on a single layer onto the MEA device (6,000). The resulting 3D structure is composed of 5 layers of microbeads and cells. Taking into account that the 3D neuronal network is not geometrically perfect, the resulting 3D structure could be composed of 5-8 layers.</li>
	<li>The day after plating, carefully add the final volume of the medium (about 900 &#181;l) inside the MEA ring. Maintain the 3D cultures in a humidified CO2 atmosphere (5%) at 37 &#176;C for 4-5 weeks. Replace half of the medium once a week.</li>
</ol>
5. Confocal Microscopy Acquisition
<ol>
	<li>Fix the biological samples to the stage of the microscope in a holder. Set the laser (Argon, 496-555 nm), the scan speed (400 Hz) at which to acquire the image, the gain and offset (-0.3%) of PMT for each image to capture the correct bandwidth emission filter and in order to avoid saturation and to increase the signal to noise ratio. The Results Section reports the values used to acquire the images of Figure 4.</li>
	<li>For the acquisition of the z-stack sequence, first select, the value of z position of the top and the bottom layer of the sample, and then select the step size to make the acquisition.</li>
</ol>

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D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bioengineered+functional+brain-like+cortical+tissue.">Bioengineered functional brain-like cortical tissue.</a> Proc Natl Acad Sci U S. 111, 13811-13816 (2014).</li><li>Banker, G., Goslin, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Culturing Nerve Cell. , (1998).</li><li>Hales, C. M., Rolston, J. D., Potter, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=How+to+culture,+record+and+stimulate+neuronal+networks+on+Micro-electrode+arrays+(MEAs).">How to culture, record and stimulate neuronal networks on Micro-electrode arrays (MEAs).</a> J. Vis. Exp. (39), (2010).</li><li>Jayakumar, R., Prabaharan, M., Nair, S. V., Tamura, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Novel+chitin+and+chitosan+nanofibers+in+biomedical+applications.">Novel chitin and chitosan nanofibers in biomedical applications.</a> Biotech. Adv. 28, 142-150 (2010).</li><li>Crompton, K. 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The authors declare that they have no competing financial interests.

In this work, a novel experimental in vitro platform made up of 3D engineered neuronal cultures coupled to MEAs for network electrophysiology has been presented. The use of microbeads as scaffold to allow the neuritic outgrowth along the z-axis has been tailored to be integrated with the planar MEA. In this way, the obtained micro-system results in a valid and reliable in vitro 3D model to study the emergent electrophysiological dynamics16.
MEA recording s...

In vitro two-dimensional (2D) neural networks coupled to Micro-Electrode Arrays (MEAs)arethe gold-standard experimental model adopted to study the interplay between neuronal dynamics and the underlying connectivity. During the development, neurons recreate complex networks which display well definedspatio-temporalpatternsof activity1,2 (i.e., bursts, network bursts, random spiking activity). MEAs record the electrophysiological activity from many sites (from tens to thousands of microelectrodes), allowing a detailed investigation of the expressed dynamics at the network level. In addition, the use of dissociated cultures makes possibile to design engineered-networks. It is easier to understand in this way the functional relationships between the recorded electrophysiological activity and the parameters of the network organization like cell density3, degree of modularity4,5, presence of heterogeneous neuronal populations6, etc. However, all in vitro studies on dissociated cultured cells are based on 2D neuronal networks. This approach leads to oversimplifications with respect to the in vivo (intrinsically 3-dimensional, 3D) system: (i) in a 2D model, somata and growth cones are flattened and the axons-dendrites outgrowth cannot spread in all directions7. (ii) 2D in vitro networks exhibit stereotyped electrophysiological dynamics dominated by bursting activity involving most of the neurons of the network8.
Recently, different solutions have been developed to allow the construction of in vitro 3D dissociated neuronal networks. The common idea consists in creating a scaffold where neurons can grow in a 3D fashion. Such a scaffold can be realized with polymer gels and solid porous matrices9-13. By exploiting the mechanical properties of the polymers, it is possible to embed cells inside these structures by defining a uniform block of 3D cultures of neurospheres11. The main feature of this approach is the rigid mechanical property of the neurospheres9,12. However, these materials have limited porosity, and they do not guarantee cell migration inside the matrix. To overcome this drawback, a possible solution consists in slicing the matrix into &#8216;unit&#8217; modules. Unfortunately, the size and shape diversity of the particles could hamper the packing into regular layered structures. In7, Cullen and coworkers designed a 3D neuronal construct made up of neurons and/or astrocytes within a bioactive extracellular matrix-based scaffold. Such an engineered neural tissue allowed in vitro investigations to study and manipulate neurobiological responses within 3D micro-environments. This model consisted of neurons and glia distributed throughout the extracellular matrix (ECM) and/or hydrogel scaffolds (500-600 &#181;m thick). In this condition, an optimum cell viability (greater than 90%) was found by plating cells at a final density of about 3,750 - 5,000 cells/mm3. It must be noted that such a density value is far lower than the one in the in vivo condition, where the cell density of the mouse brain cortex is about 90,000 cells/mm314. To overcome this limitation Pautot and coworkers15 realized a 3D in vitro system where cell density and network connectivity are controlled to resemble in vivo conditions while enabling real-time imaging of the network. Practically, this method is based on the concept that dissociated cultured neurons are able to grow on silica microbeads. These beads provide a growth surface large enough for neuronal cell bodies to adhere and for their arborizations to grow, mature, extend, and define synaptic contacts to other neurons. This method exploits the spontaneous assembly properties of mono-dispersed beads to form 3D layered hexagonal arrays containing distinct subsets of neurons on different layers with constrained connectivity among neurons on different beads. The achieved cell density with this method was about 75,000 cells/mm3.
Recently, we have adapted Pautot&#8217;s method to MEAs16: the obtained results show that the 3D electrophysiological activity presents a wider repertoire of activities than the one expressed by 2D networks.&#160;3D mature cultures exhibit an enhanced dynamic in which both network burst and random spike activity coexist. Similarly, Tang-Schomer and coworkers17 realized a silk protein-based porous scaffold which maintains a primary cortical culture in vitro for some months, and recorded the electrophysiological activity by means of a tungsten electrode.
In this work, the experimental procedures to build 3D neuronal networks coupled to MEAs will be described.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>Laminin</td>
			<td>Sigma-Aldrich</td>
			<td>L2020</td>
			<td>0.05 &#181;g/ml</td>
		</tr>
		<tr>
			<td>Poly-D-lysine</td>
			<td>Sigma-Aldrich</td>
			<td>P6407</td>
			<td>0.05 &#181;g/ml</td>
		</tr>
		<tr>
			<td>Trypsin</td>
			<td>Gibco</td>
			<td>25050-014</td>
			<td align="left">0.125% diluted 1:2 in HBSS w\o CA++, MG++</td>
		</tr>
		<tr>
			<td>DNAase</td>
			<td>Sigma-Aldrich</td>
			<td>D5025</td>
			<td>0.05% diluted&#160; in Hanks solution</td>
		</tr>
		<tr>
			<td>Neurobasal</td>
			<td>Gibco Invitrogen</td>
			<td>21103049</td>
			<td>culture medium</td>
		</tr>
		<tr>
			<td>B27</td>
			<td>Gibco Invitrogen</td>
			<td>17504044</td>
			<td>2% medium supplent</td>
		</tr>
		<tr>
			<td>Fetal bovine serum (FBS)</td>
			<td>Sigma-Aldrich</td>
			<td>F-2442</td>
			<td>10%</td>
		</tr>
		<tr>
			<td>Glutamax-I&#160;</td>
			<td>Gibco</td>
			<td>35050038</td>
			<td>0.5 mM</td>
		</tr>
		<tr>
			<td>gentamicin</td>
			<td>Sigma-Aldrich</td>
			<td>G.1272</td>
			<td>5mg/liter</td>
		</tr>
		<tr>
			<td>Poly-Dimethyl-Siloxane (PDMS)</td>
			<td>Corning Sigma</td>
			<td>481939</td>
			<td>curing agent and the polymer</td>
		</tr>
		<tr>
			<td>Micro-Electrode Arrays</td>
			<td>Multi Channel Systems (MCS)</td>
			<td>60MEA200/30-Ti-pr</td>
			<td>MEA with: Electrode grid 8x8; Electrode spacing and diameter 200 and 30 &#181;m, respectively; plastic ring without thread</td>
		</tr>
		<tr>
			<td>Microbead</td>
			<td>Distrilab-Duke Scientific</td>
			<td>9040</td>
			<td>&#160;1gr Glass Part.Size Stds 40 &#181;m</td>
		</tr>
		<tr>
			<td>Transwell</td>
			<td>Costar Sigma</td>
			<td>CLS 3413</td>
			<td>multiwell plates with membrane insert (6.5 mm diameter porous 0.4 &#181;m)</td>
		</tr>
		<tr>
			<td>HBSS w\o Ca++ ,Mg++&#160;</td>
			<td>Gibco Invitrogen</td>
			<td>14175-052</td>
			<td></td>
		</tr>
		<tr>
			<td>Hanks Buffer Solution&#160;</td>
			<td>Sigma&#160;</td>
			<td>H8264</td>
			<td></td>
		</tr>
		<tr>
			<td>Teflon</td>
			<td>Sigma</td>
			<td>430935-5G</td>
			<td>polytetrafluoroethylene</td>
		</tr>
		<tr>
			<td>Rat</td>
			<td>Sprague Dawley</td>
			<td>Wistar Rat</td>
			<td></td>
		</tr>
		<tr>
			<td>Confocal Microscopy Upright</td>
			<td>Leica</td>
			<td>TCS SP5 AOBS</td>
			<td></td>
		</tr>
		<tr>
			<td>20.0x0.50 WATER objective</td>
			<td>Leica</td>
			<td>Leica HCX APO L U-V-I&#160;</td>
			<td></td>
		</tr>
		<tr>
			<td>40.0x0.80 WATER objective</td>
			<td>Leica</td>
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			<td>25.0x0.95 WATER objective</td>
			<td>Leica</td>
			<td>HCX IRAPO L</td>
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interfacing 3d engineered neuronal cultures to micro-electrode arrays: an innovative in vitro experimental model

Currently, large-scale networks derived from dissociated neurons growing and developing in vitro on extracellular micro-transducer devices are the gold-standard experimental model to study basic neurophysiological mechanisms involved in the formation and maintenance of neuronal cell assemblies. However, in vitro studies have been limited to the recording of the electrophysiological activity generated by bi-dimensional (2D) neural networks. Nonetheless, given the intricate relationship between structure and dynamics, a significant improvement is necessary to investigate the formation and the developing dynamics of three-dimensional (3D) networks. In this work, a novel experimental platform in which 3D hippocampal or cortical networks are coupled to planar Micro-Electrode Arrays (MEAs) is presented. 3D networks are realized by seeding neurons in a scaffold constituted of glass microbeads (30-40 &#181;m in diameter) on which neurons are able to grow and form complex interconnected 3D assemblies. In this way, it is possible to design engineered 3D networks made up of 5-8 layers with an expected final cell density. The increasing complexity in the morphological organization of the 3D assembly induces an enhancement of the electrophysiological patterns displayed by this type of networks. Compared with the standard 2D networks, where highly stereotyped bursting activity emerges, the 3D structure alters the bursting activity in terms of duration and frequency, as well as it allows observation of more random spiking activity. In this sense, the developed 3D model more closely resembles in vivo neural networks.

In this experimental procedure, a relevant role is played by the microbeads that define the mechanical scaffold for the growth of the 3D neuronal network. Figures 1A and B display the arrangement of the microbeads (nominal diameter of 40&#177;2 &#181;m; certified mean diameter of 42.3&#177; 1.1 &#181;m) in the plane. The peculiarity of such structures is that microbeads spontaneously self-assemble defining a compact hexagonal geometry (Figure 1B and C). The so generated scaffold guarante...

Watch this Scientific Journal Video about Interfacing 3D Engineered Neuronal Cultures to Micro-Electrode Arrays: An Innovative In Vitro Experimental Model at JoVE.com

Interfacing 3D Engineered Neuronal Cultures to Micro-Electrode Arrays: An Innovative In Vitro Experimental Model

In this work, a novel experimental model in which 3D neuronal cultures are coupled to planar Micro-Electrode Arrays (MEAs) is presented. 3D networks are built by seeding neurons in a scaffold made up of glass microbeads on which neurons grow and form interconnected 3D structures.

Interfacing 3D Engineered Neuronal Cultures to Micro-Electrode Arrays: An Innovative In Vitro Experimental Model

Currently, large-scale networks derived from dissociated neurons growing and developing in vitro on extracellular micro-transducer devices are the ...

interfacing-3d-engineered-neuronal-cultures-to-micro-electrode-arrays

Research

JoVE Journal

Neuroscience

10.0K Views.  University of Genova. In this work, a novel experimental model in which 3D neuronal cultures are coupled to planar Micro-Electrode Arrays (MEAs) is presented. 3D networks are built by seeding neurons in a scaffold made up of glass microbeads on which neurons grow and form interconnected 3D structures.

Video: Interfacing 3D Engineered Neuronal Cultures to Micro-Electrode Arrays: An Innovative In Vitro Experimental Model

Multi-electrode Array Recordings of Neuronal Avalanches in Organotypic Cultures

The cortex is spontaneously active, even in the absence of any particular input or motor output. During development, this activity is important for the migration and differentiation of cortex cell types and the formation of neuronal connections1. In the mature animal, ongoing activity reflects the past and the present state of an animal into which sensory stimuli are seamlessly integrated to compute future actions. Thus, a clear understanding of the organization of ongoing i.e. spontaneous activity is a prerequisite to understand cortex function. 
Numerous recording techniques revealed that ongoing activity in cortex is comprised of many neurons whose individual activities transiently sum to larger events that can be detected in the local field potential (LFP) with extracellular microelectrodes, or in the electroencephalogram (EEG), the magnetoencephalogram (MEG), and the BOLD signal from functional magnetic resonance imaging (fMRI). The LFP is currently the method of choice when studying neuronal population activity with high temporal and spatial resolution at the mesoscopic scale (several thousands of neurons). At the extracellular microelectrode, locally synchronized activities of spatially neighbored neurons result in rapid deflections in the LFP up to several hundreds of microvolts. When using an array of microelectrodes, the organizations of such deflections can be conveniently monitored in space and time. 
Neuronal avalanches describe the scale-invariant spatiotemporal organization of ongoing neuronal activity in the brain2,3. They are specific to the superficial layers of cortex as established in vitro4,5, in vivo in the anesthetized rat 6, and in the awake monkey7. Importantly, both theoretical and empirical studies2,8-10 suggest that neuronal avalanches indicate an exquisitely balanced critical state dynamics of cortex that optimizes information transfer and information processing.
In order to study the mechanisms of neuronal avalanche development, maintenance, and regulation, in vitro preparations are highly beneficial, as they allow for stable recordings of avalanche activity under precisely controlled conditions. The current protocol describes how to study neuronal avalanches in vitro by taking advantage of superficial layer development in organotypic cortex cultures, i.e. slice cultures, grown on planar, integrated microelectrode arrays (MEA; see also 11-14).

A robust way to study neuronal avalanches, i.e. scale-invariant spatio-temporal activity bursts, indicative of critical state dynamics in cortex. Avalanches emerge spontaneously in developing superficial layers of cultured cortex which allows for long-term measurements of the activity with planar integrated multi-electrode arrays (MEA) under precisely controlled conditions.

The cortex is spontaneously active, even in the absence of any particular input or motor output.  During development, this activity is important for the ...

Organotypic Slice Cultures of Embryonic Ventral Midbrain: A System to Study Dopaminergic Neuronal Development in vitro

The mouse is an excellent model organism to study mammalian brain development due to the abundance of molecular and genetic data. However, the developing mouse brain is not suitable for easy manipulation and imaging in vivo since the mouse embryo is inaccessible and opaque. Organotypic slice cultures of embryonic brains are therefore widely used to study murine brain development in vitro. Ex-vivo manipulation or the use of transgenic mice allows the modification of gene expression so that subpopulations of neuronal or glial cells can be labeled with fluorescent proteins. The behavior of labeled cells can then be observed using time-lapse imaging. Time-lapse imaging has been particularly successful for studying cell behaviors that underlie the development of the cerebral cortex at late embryonic stages 1-2. Embryonic organotypic slice culture systems in brain regions outside of the forebrain are less well established. Therefore, the wealth of time-lapse imaging data describing neuronal cell migration is restricted to the forebrain 3,4. It is still not known, whether the principles discovered for the dorsal brain hold true for ventral brain areas. In the ventral brain, neurons are organized in neuronal clusters rather than layers and they often have to undergo complicated migratory trajectories to reach their final position. The ventral midbrain is not only a good model system for ventral brain development, but also contains neuronal populations such as dopaminergic neurons that are relevant in disease processes. While the function and degeneration of dopaminergic neurons has been investigated in great detail in the adult and ageing brain, little is known about the behavior of these neurons during their differentiation and migration phase 5. We describe here the generation of slice cultures from the embryonic day (E) 12.5 mouse ventral midbrain. These slice cultures are potentially suitable for monitoring dopaminergic neuron development over several days in vitro. We highlight the critical steps in generating brain slices at these early stages of embryonic development and discuss the conditions necessary for maintaining normal development of dopaminergic neurons in vitro. We also present results from time lapse imaging experiments. In these experiments, ventral midbrain precursors (including dopaminergic precursors) and their descendants were labeled in a mosaic manner using a Cre/loxP based inducible fate mapping system 6.

Organotypic Slice Cultures of Embryonic Ventral Midbrain: A System to Study Dopaminergic Neuronal Development in vitro

A method to generate organotypic slices from the E12.5 murine embryonic midbrain is described. The organotypic slice cultures can be used to observe the behavior of dopaminergic neurons or other ventral midbrain neurons.

The  mouse is an excellent model organism to study mammalian brain development due  to the abundance of molecular and genetic data. However, the ...

VisioTracker, an Innovative Automated Approach to Oculomotor Analysis

Investigations into the visual system development and function necessitate quantifiable behavioral models of visual performance that are easy to elicit, robust, and simple to manipulate. A suitable model has been found in the optokinetic response (OKR), a reflexive behavior present in all vertebrates due to its high selection value. The OKR involves slow stimulus-following movements of eyes alternated with rapid resetting saccades. The measurement of this behavior is easily carried out in zebrafish larvae, due to its early and stable onset (fully developed after 96 hours post fertilization (hpf)), and benefitting from the thorough knowledge about zebrafish genetics, for decades one of the favored model organisms in this field. Meanwhile the analysis of similar mechanisms in adult fish has gained importance, particularly for pharmacological and toxicological applications.
Here we describe VisioTracker, a fully automated, high-throughput system for quantitative analysis of visual performance. The system is based on research carried out in the group of Prof. Stephan Neuhauss and was re-designed by TSE Systems. It consists of an immobilizing device for small fish monitored by a high-quality video camera equipped with a high-resolution zoom lens. The fish container is surrounded by a drum screen, upon which computer-generated stimulus patterns can be projected. Eye movements are recorded and automatically analyzed by the VisioTracker software package in real time.
Data analysis enables immediate recognition of parameters such as slow and fast phase duration, movement cycle frequency, slow-phase gain, visual acuity, and contrast sensitivity.
Typical results allow for example the rapid identification of visual system mutants that show no apparent alteration in wild type morphology, or the determination of quantitative effects of pharmacological or toxic and mutagenic agents on visual system performance.

The VisioTracker is an automated system for the quantitative analysis of visual performance of larval and small adult fish based on the recording of eye movements. It features full control over visual stimulus properties and real-time analysis, enabling high-throughput research in fields such as visual system development and function, pharmacology, neural circuit studies and sensorimotor integration.

Investigations into the visual system development and function necessitate quantifiable behavioral models of visual performance that are easy to elicit, ...

Fast Micro-iontophoresis of Glutamate and GABA: A Useful Tool to Investigate Synaptic Integration

One of the fundamental interests in neuroscience is to understand the integration of excitatory and inhibitory inputs along the very complex structure of the dendritic tree, which eventually leads to neuronal output of action potentials at the axon. The influence of diverse spatial and temporal parameters of specific synaptic input on neuronal output is currently under investigation, e.g. the distance-dependent attenuation of dendritic inputs, the location-dependent interaction of spatially segregated inputs, the influence of GABAergig inhibition on excitatory integration, linear and non-linear integration modes, and many more.
With fast micro-iontophoresis of glutamate and GABA it is possible to precisely investigate the spatial and temporal integration of glutamatergic excitation and GABAergic inhibition. Critical technical requirements are either a triggered fluorescent lamp, light-emitting diode (LED), or a two-photon scanning microscope to visualize dendritic branches without introducing significant photo-damage of the tissue. Furthermore, it is very important to have a micro-iontophoresis amplifier that allows for fast capacitance compensation of high resistance pipettes. Another crucial point is that no transmitter is involuntarily released by the pipette during the experiment.
Once established, this technique will give reliable and reproducible signals with a high neurotransmitter and location specificity. Compared to glutamate and GABA uncaging, fast iontophoresis allows using both transmitters at the same time but at very distant locations without limitation to the field of view. There are also advantages compared to focal electrical stimulation of axons: with micro-iontophoresis the location of the input site is definitely known and it is sure that only the neurotransmitter of interest is released. However it has to be considered that with micro-iontophoresis only the postsynapse is activated and presynaptic aspects of neurotransmitter release are not resolved. In this article we demonstrate how to set up micro-iontophoresis in brain slice experiments.

In this article we introduce fast micro-iontophoresis of neurotransmitters as a technique to investigate integration of postsynaptic signals with high spatial and temporal precision.

One of the fundamental interests in neuroscience is to understand the integration of excitatory and inhibitory inputs along the very complex structure of ...

Sex Stratified Neuronal Cultures to Study Ischemic Cell Death Pathways

Sex differences in neuronal susceptibility to ischemic injury and neurodegenerative disease have long been observed, but the signaling mechanisms responsible for those differences remain unclear. Primary disassociated embryonic neuronal culture provides a simplified experimental model with which to investigate the neuronal cell signaling involved in cell death as a result of ischemia or disease; however, most neuronal cultures used in research today are mixed sex. Researchers can and do test the effects of sex steroid treatment in mixed sex neuronal cultures in models of neuronal injury and disease, but accumulating evidence suggests that the female brain responds to androgens, estrogens, and progesterone differently than the male brain. Furthermore, neonate male and female rodents respond differently to ischemic injury, with males experiencing greater injury following cerebral ischemia than females. Thus, mixed sex neuronal cultures might obscure and confound the experimental results; important information might be missed. For this reason, the Herson Lab at the University of Colorado School of Medicine routinely prepares sex-stratified primary disassociated embryonic neuronal cultures from both hippocampus and cortex. Embryos are sexed before harvesting of brain tissue and male and female tissue are disassociated separately, plated separately, and maintained separately. Using this method, the Herson Lab has demonstrated a male-specific role for the ion channel TRPM2 in ischemic cell death. In this manuscript, we share and discuss our protocol for sexing embryonic mice and preparing sex-stratified hippocampal primary disassociated neuron cultures. This method can be adapted to prepare sex-stratified cortical cultures and the method for embryo sexing can be used in conjunction with other protocols for any study in which sex is thought to be an important determinant of outcome.

Primary disassociated embryonic hippocampal neuronal cultures are useful for investigating the signaling mechanisms involved in neuron death. Sexing the embryos before the isolation and dissociation of the hippocampus allows the preparation of separate male and female cultures, which enables the researcher to identify and investigate sex-specific cell signaling.

Sex differences in neuronal susceptibility to ischemic injury and neurodegenerative disease have long been observed, but the signaling mechanisms ...

A Procedure for Implanting Organized Arrays of Microwires for Single-unit Recordings in Awake, Behaving Animals

In vivo electrophysiological recordings in the awake, behaving animal provide a powerful method for understanding neural signaling at the single-cell level. The technique allows experimenters to examine temporally and regionally specific firing patterns in order to correlate recorded action potentials with ongoing behavior. Moreover, single-unit recordings can be combined with a plethora of other techniques in order to produce comprehensive explanations of neural function. In this article, we describe the anesthesia and preparation for microwire implantation. Subsequently, we enumerate the necessary equipment and surgical steps to accurately insert a microwire array into a target structure. Lastly, we briefly describe the equipment used to record from each individual electrode in the array. The fixed microwire arrays described are well-suited for chronic implantation and allow for longitudinal recordings of neural data in almost any behavioral preparation. We discuss tracing electrode tracks to triangulate microwire positions as well as ways to combine microwire implantation with immunohistochemical techniques in order to increase the anatomical specificity of recorded results.

Implanting organized arrays of microwires for use in single-unit electrophysiological recordings presents a number of technical challenges.&#160;Methods for performing this technique and the equipment necessary are described.&#160;Also, the beneficial use of organized microwire arrays to record from distinct neural subregions with high spatial selectivity is discussed.

In vivo electrophysiological recordings in the awake, behaving animal provide a powerful method for understanding neural signaling at the single-cell ...

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 ...

Neural Activity Propagation in an Unfolded Hippocampal Preparation with a Penetrating Micro-electrode Array

This protocol describes a method for preparing a new in vitro flat hippocampus preparation combined with a micro-machined array to map neural activity in the hippocampus. The transverse hippocampal slice preparation is the most common tissue preparation to study hippocampus electrophysiology. A longitudinal hippocampal slice was also developed in order to investigate longitudinal connections in the hippocampus. The intact mouse hippocampus can also be maintained in vitro because its thickness allows adequate oxygen diffusion. However, these three preparations do not provide direct access to neural propagation since some of the tissue is either missing or folded. The unfolded intact hippocampus provides both transverse and longitudinal connections in a flat configuration for direct access to the tissue to analyze the full extent of signal propagation in the hippocampus in vitro. In order to effectively monitor the neural activity from the cell layer, a custom made penetrating micro-electrode array (PMEA) was fabricated and applied to the unfolded hippocampus. The PMEA with 64 electrodes of 200 &#181;m in height could record neural activity deep inside the mouse hippocampus. The unique combination of an unfolded hippocampal preparation and the PMEA provides a new in-vitro tool to study the speed and direction of propagation of neural activity in the two-dimensional CA1-CA3 regions of the hippocampus with a high signal to noise ratio.

We have developed an in vitro unfolded hippocampus which preserves CA1-CA3 array of neurons. Combined with the penetrating micro-electrode array, neural activity can be monitored in both the longitudinal and transverse orientations. This method provides advantages over hippocampal slice preparations as the propagation in the entire hippocampus can be recorded simultaneously.

This protocol describes a method for preparing a new in vitro flat hippocampus preparation combined with a micro-machined array to map neural activity in ...

Time-dependent Increase in the Network Response to the Stimulation of Neuronal Cell Cultures on Micro-electrode Arrays

Micro-electrode arrays (MEAs) can be used to investigate drug toxicity, design paradigms for next-generation personalized medicine, and study network dynamics in neuronal cultures. In contrast with more traditional methods, such as patch-clamping, which can only record activity from a single cell, MEAs can record simultaneously from multiple sites in a network, without requiring the arduous task of placing each electrode individually. Moreover, numerous control and stimulation configurations can be easily applied within the same experimental setup, allowing for a broad range of dynamics to be explored. One of the key dynamics of interest in these in vitro studies has been the extent to which cultured networks display properties indicative of learning. Mouse neuronal cells cultured on MEAs display an increase in response following training induced by electrical stimulation. This protocol demonstrates how to culture neuronal cells on MEAs; successfully record from over 95% of the plated dishes; establish a protocol to train the networks to respond to patterns of stimulation; and sort, plot, and interpret the results from such experiments. The use of a proprietary system for stimulating and recording neuronal cultures is demonstrated. Software packages are also used to sort neuronal units. A custom-designed graphical user interface is used to visualize post-stimulus time histograms, inter-burst intervals, and burst duration, as well as to compare the cellular response to stimulation before and after a training protocol. Finally, representative results and future directions of this research effort are discussed.

Mouse neuronal cells cultured on multi-electrode arrays display an increase in response following electrical stimulation. This protocol demonstrates how to culture neurons, how to record activity, and how to establish a protocol to train the networks to respond to patterns of stimulation.

Micro-electrode arrays (MEAs) can be used to investigate drug toxicity, design paradigms for next-generation personalized medicine, and study network ...

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 ...