We would like to thank Maria Eugenia Bernis for photographing the procedures. We also thank Emily Burnside, Emily Handley, Thorben Pietralla, Max Schelski, and Sina Stern for reading and discussing the manuscript. We are grateful to our outstanding technical assistants, Jessica Gonyer, Blanca Randel, and Anh-Tuan Pham. We acknowledge the valuable support of the DZNE&#39;s light microscope facility and animal facility. This work was supported by Deutsche Forschungsgesellschaft (DFG), the International Foundation for Research in Paraplegia (IRP), and Wings for Life (to F.B). F.B. is a member of the excellence cluster ImmunoSensation2, the SFBs 1089 and 1158, and is a recipient of the Roger De Spoelberch Prize.

<ol>
	<li>Schelski, M., Bradke, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neuronal+polarization:+From+spatiotemporal+signaling+to+cytoskeletal+dynamics.">Neuronal polarization: From spatiotemporal signaling to cytoskeletal dynamics.</a> Molecular and Cellular Neurosciences. 84, 11-28 (2017).</li><li>Lowery, L. A., Van Vactor, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+trip+of+the+tip:+understanding+the+growth+cone+machinery.">The trip of the tip: understanding the growth cone machinery.</a> Nature Reviews: Molecular Cell Biology. 10 (5), 332-343 (2009).</li><li>Stoeckli, E. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Understanding+axon+guidance:+are+we+nearly+there+yet.">Understanding axon guidance: are we nearly there yet.</a> Development. 145 (10), (2018).</li><li>Bradke, F., Dotti, C. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+role+of+local+actin+instability+in+axon+formation.">The role of local actin instability in axon formation.</a> Science. 283 (5409), 1931-1934 (1999).</li><li>Neukirchen, D., Bradke, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cytoplasmic+linker+proteins+regulate+neuronal+polarization+through+microtubule+and+growth+cone+dynamics.">Cytoplasmic linker proteins regulate neuronal polarization through microtubule and growth cone dynamics.</a> Journal of Neuroscience. 31 (4), 1528-1538 (2011).</li><li>Witte, H., Bradke, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+role+of+the+cytoskeleton+during+neuronal+polarization.">The role of the cytoskeleton during neuronal polarization.</a> Current Opinion in Neurobiology. 18 (5), 479-487 (2008).</li><li>Witte, H., Neukirchen, D., Bradke, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microtubule+stabilization+specifies+initial+neuronal+polarization.">Microtubule stabilization specifies initial neuronal polarization.</a> Journal of Cell Biology. 180 (3), 619-632 (2008).</li><li>Nichol, R. H., Catlett, T. S., Onesto, M. M., Hollender, D., Gomez, T. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Environmental+elasticity+regulates+cell-type+specific+RHOA+signaling+and+neuritogenesis+of+human+neurons.">Environmental elasticity regulates cell-type specific RHOA signaling and neuritogenesis of human neurons.</a> Stem Cell Reports. 13 (6), 1006-1021 (2019).</li><li>Santos, T. E., 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=Axon+growth+of+CNS+neurons+in+three+dimensions+is+amoeboid+and+independent+of+adhesions.">Axon growth of CNS neurons in three dimensions is amoeboid and independent of adhesions.</a> Cell Reports. 32 (3), 107907 (2020).</li><li>Mitchison, T., Kirschner, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cytoskeletal+dynamics+and+nerve+growth.">Cytoskeletal dynamics and nerve growth.</a> Neuron. 1 (9), 761-772 (1988).</li><li>Lin, C. H., Thompson, C. A., Forscher, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cytoskeletal+reorganization+underlying+growth+cone+motility.">Cytoskeletal reorganization underlying growth cone motility.</a> Current Opinion in Neurobiology. 4 (5), 640-647 (1994).</li><li>Myers, J. P., Gomez, T. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Focal+adhesion+kinase+promotes+integrin+adhesion+dynamics+necessary+for+chemotropic+turning+of+nerve+growth+cones.">Focal adhesion kinase promotes integrin adhesion dynamics necessary for chemotropic turning of nerve growth cones.</a> Journal of Neuroscience. 31 (38), 13585-13595 (2011).</li><li>Turney, S. G., 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=Nerve+growth+factor+stimulates+axon+outgrowth+through+negative+regulation+of+growth+cone+actomyosin+restraint+of+microtubule+advance.">Nerve growth factor stimulates axon outgrowth through negative regulation of growth cone actomyosin restraint of microtubule advance.</a> Molecular Biology of the Cell. 27 (3), 500-517 (2016).</li><li>Schindelin, J., 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=Fiji:+an+open-source+platform+for+biological-image+analysis.">Fiji: an open-source platform for biological-image analysis.</a> Nature Methods. 9 (7), 676-682 (2012).</li><li>Noctor, S. C., Flint, A. C., Weissman, T. A., Dammerman, R. S., Kriegstein, A. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neurons+derived+from+radial+glial+cells+establish+radial+units+in+neocortex.">Neurons derived from radial glial cells establish radial units in neocortex.</a> Nature. 409 (6821), 714-720 (2001).</li><li>Noctor, S. C., Martinez-Cerdeno, V., Ivic, L., Kriegstein, A. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cortical+neurons+arise+in+symmetric+and+asymmetric+division+zones+and+migrate+through+specific+phases.">Cortical neurons arise in symmetric and asymmetric division zones and migrate through specific phases.</a> Nature Neuroscience. 7 (2), 136-144 (2004).</li><li>Ferent, J., Zaidi, D., Francis, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Extracellular+control+of+radial+glia+proliferation+and+scaffolding+during+cortical+development+and+pathology.">Extracellular control of radial glia proliferation and scaffolding during cortical development and pathology.</a> Frontiers in Cell and Developmental Biology. 8, 578341 (2020).</li><li>Dent, E. W., Gupton, S. L., Gertler, F. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+growth+cone+cytoskeleton+in+axon+outgrowth+and+guidance.">The growth cone cytoskeleton in axon outgrowth and guidance.</a> Cold Spring Harbor Perspectives in Biology. 3 (3), (2011).</li><li>Dupraz, S., 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=RhoA+controls+axon+extension+independent+of+specification+in+the+developing+brain.">RhoA controls axon extension independent of specification in the developing brain.</a> Current Biology. 29 (22), 3874-3886 (2019).</li><li>Azzarelli, R., Oleari, R., Lettieri, A., Andre, V., Cariboni, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vitro,+ex+vivo+and+in+vivo+techniques+to+study+neuronal+migration+in+the+developing+cerebral+cortex.">In vitro, ex vivo and in vivo techniques to study neuronal migration in the developing cerebral cortex.</a> Brain Sciences. 7 (5), (2017).</li><li>Humpel, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Organotypic+brain+slice+cultures:+A+review.">Organotypic brain slice cultures: A review.</a> Neuroscience. 305, 86-98 (2015).</li><li>Namba, T., 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=Pioneering+axons+regulate+neuronal+polarization+in+the+developing+cerebral+cortex.">Pioneering axons regulate neuronal polarization in the developing cerebral cortex.</a> Neuron. 81 (4), 814-829 (2014).</li><li>Shah, B., 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=Rap1+GTPases+are+master+regulators+of+neural+cell+polarity+in+the+developing+neocortex.">Rap1 GTPases are master regulators of neural cell polarity in the developing neocortex.</a> Cerebral Cortex. 27 (2), 1253-1269 (2017).</li><li>Wiegreffe, C., Feldmann, S., Gaessler, S., Britsch, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Time-lapse+confocal+imaging+of+migrating+neurons+in+organotypic+slice+culture+of+embryonic+mouse+brain+using+in+utero+electroporation.">Time-lapse confocal imaging of migrating neurons in organotypic slice culture of embryonic mouse brain using in utero electroporation.</a> Journal of Visualized Experiments: JoVE. (125), (2017).</li><li>de Anda, F. C., Meletis, K., Ge, X., Rei, D., Tsai, L. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Centrosome+motility+is+essential+for+initial+axon+formation+in+the+neocortex.">Centrosome motility is essential for initial axon formation in the neocortex.</a> Journal of Neuroscience. 30 (31), 10391-10406 (2010).</li><li>Sakakibara, A., 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=Dynamics+of+centrosome+translocation+and+microtubule+organization+in+neocortical+neurons+during+distinct+modes+of+polarization.">Dynamics of centrosome translocation and microtubule organization in neocortical neurons during distinct modes of polarization.</a> Cerebral Cortex. 24 (5), 1301-1310 (2014).</li><li>Schatzle, P., Kapitein, L. C., Hoogenraad, C. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Live+imaging+of+microtubule+dynamics+in+organotypic+hippocampal+slice+cultures.">Live imaging of microtubule dynamics in organotypic hippocampal slice cultures.</a> Methods in Cell Biology. 131, 107-126 (2016).</li><li>Qu, X., Kumar, A., Bartolini, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Live+imaging+of+microtubule+dynamics+at+excitatory+presynaptic+boutons+in+primary+hippocampal+neurons+and+acute+hippocampal+slices.">Live imaging of microtubule dynamics at excitatory presynaptic boutons in primary hippocampal neurons and acute hippocampal slices.</a> STAR Protocols. 2 (1), 100342 (2021).</li><li>Tonnesen, J., Katona, G., Rozsa, B., Nagerl, U. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spine+neck+plasticity+regulates+compartmentalization+of+synapses.">Spine neck plasticity regulates compartmentalization of synapses.</a> Nature Neuroscience. 17 (5), 678-685 (2014).</li><li>Buchsbaum, I. Y., Cappello, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neuronal+migration+in+the+CNS+during+development+and+disease:+insights+from+in+vivo+and+in+vitro+models.">Neuronal migration in the CNS during development and disease: insights from in vivo and in vitro models.</a> Development. 146 (1), (2019).</li><li>Rigby, M. J., Gomez, T. M., Puglielli, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Glial+cell-axonal+growth+cone+interactions+in+neurodevelopment+and+regeneration.">Glial cell-axonal growth cone interactions in neurodevelopment and regeneration.</a> Frontiers in Neuroscience. 14, 203 (2020).</li><li>Barnes, A. P., Polleux, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Establishment+of+axon-dendrite+polarity+in+developing+neurons.">Establishment of axon-dendrite polarity in developing neurons.</a> Annual Review of Neuroscience. 32, 347-381 (2009).</li></ol>

The authors have nothing to disclose.

How the growth cones sense and react to their surrounding environment to coordinate simultaneous axon extension and guidance is still a matter of debate3,18. Pioneering studies in 2D substrates provided a glimpse into the fundamental molecular mechanisms generating the forces that drive growth cone dynamics during axon formation, outgrowth, and navigation2,10,11,12,19. More recently, studies in 3D matrices revealed how much influence a third dimension has in the behavior of the growth cone and consequently in axon growth8,9. Nevertheless, the intricate mechanisms instructing growth cone dynamics in vivo remain to be thoroughly examined.
Preparation of organotypic slice cultures from IUE or EUE brains is widely utilized and well-documented. It has become a golden standard allowing scientists to gain insights into the development and behavior of neurons in the living brain tissue20,21. Indeed, this technique has been successfully utilized in combination with various high-resolution imaging techniques to visualize specific molecular processes and morphological events in situ. Such studies include, but are not limited to axon formation and extension19,22, cortical neuronal migration19,22,23,24, centrosome dynamics25,26, microtubule dynamics27, as well as the functional dynamics of pre-and postsynaptic compartments28,29.
This protocol addresses a gap in experimental neurobiology, visualizing the growth cone dynamics of developing cortical neurons in situ, in ex vivo acute brain slice cultures, and the tools to analyze the data obtained.
Acute brain slice cultures were utilized to establish this protocol because they (1) with some practice, are easy to generate; (2) present an accessible system to study growth cones embedded in a quasi-fully-physiological environment, yet transparent enough to allow high-resolution live-cell imaging; (3) can be expanded for its use with a myriad of transgenic mouse lines; (4) combined with either IUE or EUE, provide virtually unlimited potential to deliver molecular tools to evaluate the performance of growth cones and axons in vivo under loss/gain of function regimes, along with fluorescent reporters and cytoskeleton probes.
This methodology was described in the context of both EUE and IUE. Although still a highly reliable method, EUE resulted in an increased incidence of brain slices showing a disorganized RG network compared to those obtained with IUE as a delivery method (Figure 4C). Disturbances in the RG array strongly affect neuronal migration and the pattern of axon elongation30,31. These are key parameters that predict where to find axons for analysis at a given time and the type of environment they are navigating. Brain slices with a significantly disrupted RG network typically have impaired cortical neuron stratification. This, in turn, produces axons with chaotic trajectories. Therefore, it is strongly recommended to control for the structural integrity of the RG network. Interestingly, poor structural integrity correlates with increased age of the embryonic brain. Indeed, such effects in younger E12.5-E13.5 embryos were typically not observed19.
The present protocol is thorough and straightforward. Nevertheless, there are a few critical steps where special care and attention must be taken to obtain optimal results. These have been expressly noted in the protocol and include (1) tuning the amount of DNA used in the electroporation to get sparse labeling; (2) avoiding damage during the extraction of brains; (3) controlling the temperature of the agarose during brain casing; (4) troubleshooting the ideal percentage of agarose for brains of a given age; and (5) selection of fluorophores, the experience of which follows. During protocol optimization, the performance of several fluorophores in live-cell in situ imaging was tested. Monomeric GFP variants EGFP and NeonGreen for the preparation of the LifeAct- and Lyn-tagged plasmids were chosen for this protocol (Figure 5A,B). Additionally, the RFP variant mScarlet was tested and found highly suitable for this set-up (data not shown). Multimeric tRFP (dimer) and ZsGreen (tetramer) (Figure 5C and Supplementary Video 1, right) were also tested. These fast-folding super-bright fluorophores are recommended when the method requires rapid fluorescent signal generation after DNA delivery.
A common practice in using slice cultures is to utilize slices from different brains to test control and experimental conditions. This represents an inherent source of unwanted variability. Here, an expression system that enables independent modification of neighboring neurons and reporters&#39; expression for identification was used. Note that in this demonstration (Figure 5C), there were no differences between neurons expressing either of the fluorophores. However, as an example, such a plasmid mix combined with a transgenic mouse line harboring a Cre-sensitive gene will label with tRFP (Dre-sensitive) neurons that remained as wild type. In contrast, the ZsGreen (also Cre-sensitive) will label the recombined neurons. Hence, growth cones of the two different genotypes, and likely also phenotypes, could be studied side-by-side simultaneously in the same brain slice.
Localization of axons and growth cones for analysis is an important consideration. Cortical neurons polarize while radially migrating from the ventricular zone (VZ) toward the cortical plate (CP). During this process, neurons form a leading process (a future dendrite) and a trailing process that will become the axon, eventually joining pioneering axons in the intermediate zone (IZ), establishing axon tracts32. Therefore, to capture axonal growth cones, imaging was done on axonal fibers in the IZ, including axons exiting the CP and early-generated axons already associated with axonal bundles; or eventually, in fibers that transverse the IZ and extend below it (Figure 7).
This protocol makes it feasible to perform super-resolution imaging of neurons within organotypic slices. Historically, light scattering was a significant problem faced when imaging thick specimens. Over the last two decades, extensive advances in optical technologies made imaging of thick specimens possible. Here, a long working distance objective was used to visualize smaller structures better, such as growth cones. Unavoidably, this protocol does not capture more detailed events such as retrograde actin flow or microtubule dynamics. The long-working distance objective, which necessitates a lower Numerical Aperture (NA), preserves information from thick slices. However, it was also possible to adapt this protocol to use with objectives of shorter working distance. This required a smooth transfer of slices to a glass-bottomed dish to preserve structural integrity. However, using this method resulted in shorter survival-~15 h-due to loss of gas exchange (data not shown). Unlike 2D cultures, growth cones in 3D occupy a larger volume and require movement-artifact compensation in the z-axis. To increase the ability to image detailed events, modern confocal technology must be utilized. Therefore, it is recommended to use a fast-scanning z-stack motor, such as the z-Galvo available on highly sensitive confocal microscopes33.
Of note, this protocol presents three main limitations. First, it is often challenging to control levels of expression/number of expressing cells of any given plasmid in vivo. This introduces variability between all slices even when maintaining the same plasmid concentration. Therefore, the selection of the regulatory elements in the expression vectors used must be predetermined with care. Second, imaging detailed events using membrane inserts is currently not feasible. This second limitation may be overcome with the methodological updates proposed in the previous paragraph. Lastly, growth cones are highly photosensitive and can quickly become photobleached. Therefore, frequent imaging of the growth cones, for as little as 5 min using laser scanning microscopes can often collapse the growth cones. In this regard, new advancement in light-sheet microscopy generated devices can be adapted for long-term imaging of the brain slices34.
Protocols of this like are envisioned to open new research avenues, allowing a better understanding of what it takes for a growth cone to read and react toward a complex in vivo environment, and more importantly, to unravel the mechanics of this sophisticated interplay.

Neurons are highly polarized cells that represent the basic computational unit in the nervous system. They receive and emit information that relies upon compartmentalization of input and output sites: dendrites and axons, respectively1. During development, axons extend while navigating an incredible complex environment to reach their destination. Axon navigation is guided by the growth cone, a sensory structure located at the tip of the developing axon. The growth cone is responsible for detecting environmental cues and translating them into the dynamical spatial reorganization of its cytoskeleton2,3. The resulting morpho-mechanical reactions instruct the growth cone to extend or retract from the triggering cue, leading to specific axon maneuvers.
The current understanding of axon extension and growth cone dynamics stems from studies evaluating axon growth over two-dimensional (2D) substrates2,4,5,6,7. These pioneering studies identified sophisticated interplay between growth cones and growth substrates and revealed striking differences dependent on substrate characteristics such as adhesiveness and stiffness8,9. Led by these insights, extracellular environmental cues were hypothesized to dictate axon growth, with the growth cone cytoskeleton executing this growth2,10,11,12. Notably, neurons can extend axons in non-adhesive substrates (e.g., poly-lysine, poly-ornithine)13. Moreover, substrate rigidity can influence axon growth rate independent of cell adhesive complexes8. Hence, studying growth cone dynamics in 2D substrates alone cannot accurately model the balance of forces that arise from the interaction of axonal growth cones with physiologically relevant three-dimensional (3D) environments, such as those found in vivo.
To overcome the limitations of the 2D assays, axon growth and growth cone dynamics have been studied in 3D matrices8,9. These matrices pose more physiological context yet allow studying cell-intrinsic mechanisms of axon growth. It enables growth cone examination in a single-cell fashion in a variety of conditions and pharmacological treatments9. In such 3D environments, axons displayed distinct cytoskeletal dynamics and grew faster than those observed in 2D cultured neurons9. These elegant studies demonstrated the influence of an extra dimension on the reorganization of the growth cone cytoskeleton and, consequently, on its behavior.
Despite apparent advantages presented by 3D matrices over 2D surfaces in supporting native-like neuronal development and axon growth, they remain a simplified synthetic scaffold that cannot reflect the complexity of dynamics observed in central nervous system (CNS) tissue. Here, delivery of reporter plasmids by ex utero and in utero electroporation was combined with brain organotypic slice culture and in situ live super-resolution imaging to analyze growth cone dynamics within a physiological context. This methodology allows visualization of developing axons while experiencing the 3-dimensionality of in vivo environments and the complexity of its physicochemical composition. Lastly, user-friendly procedures to measure axon growth and growth cone dynamics using commonly licensed and publicly available software are described.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Adson Forceps</td>
			<td>Fine Science Tools</td>
			<td>11006-12</td>
			<td></td>
		</tr>
		<tr>
			<td>Alexa Fluor 488</td>
			<td>Invitrogen</td>
			<td>A21202</td>
			<td>Goat Anti-Mouse</td>
		</tr>
		<tr>
			<td>Alexa Fluor 647</td>
			<td>Invitrogen</td>
			<td>A21236</td>
			<td>Goat Anti-Mouse</td>
		</tr>
		<tr>
			<td>Anti-Vimentin antibody</td>
			<td>sigma-Aldrich</td>
			<td>V2258-.2ML</td>
			<td>Monoclonal mouse, clone LN-6, ascites fluid</td>
		</tr>
		<tr>
			<td>B27 supplement</td>
			<td>ThermoFisher Scientific</td>
			<td>17504044</td>
			<td></td>
		</tr>
		<tr>
			<td>Betadine</td>
			<td>B. Braun</td>
			<td>3864154</td>
			<td></td>
		</tr>
		<tr>
			<td>Biozym Sieve GP Agarose</td>
			<td>Biozyme</td>
			<td>850080</td>
			<td></td>
		</tr>
		<tr>
			<td>Braunol, Spr&#252;hflasche</td>
			<td>B. Braun</td>
			<td>3864073</td>
			<td></td>
		</tr>
		<tr>
			<td>Buprenorphine (Temgesic)</td>
			<td>GEHE Pharma</td>
			<td>345928</td>
			<td></td>
		</tr>
		<tr>
			<td>DAPI</td>
			<td>sigma-Aldrich</td>
			<td>D9542</td>
			<td></td>
		</tr>
		<tr>
			<td>DMZ unevirsal electrode puller</td>
			<td>Zeitz</td>
			<td>NA</td>
			<td></td>
		</tr>
		<tr>
			<td>Electric razor</td>
			<td>Andes</td>
			<td>NA</td>
			<td>ProClip UltraEdge Super 2-Speed model</td>
		</tr>
		<tr>
			<td>Enrofloxacin (Baytril)</td>
			<td>Bayer</td>
			<td>3543238</td>
			<td>2,5% (wt/vol)</td>
		</tr>
		<tr>
			<td>Eppendorf microloader pipette tips</td>
			<td>FischerScientific</td>
			<td>10289651</td>
			<td></td>
		</tr>
		<tr>
			<td>Fast Green FCF</td>
			<td>Sigma-Aldrich</td>
			<td>F7252-5G</td>
			<td>Dye content &#8805; 85 %</td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum</td>
			<td>ThermoFisher Scientific</td>
			<td>10500064</td>
			<td></td>
		</tr>
		<tr>
			<td>Fiji 2.1.0</td>
			<td>NIH</td>
			<td>NA</td>
			<td>https://imagej.net/software/fiji/downloads</td>
		</tr>
		<tr>
			<td>Fine Scissors</td>
			<td>Fine Science Tools</td>
			<td>14058-09</td>
			<td>ToughCut/Straight/9cm</td>
		</tr>
		<tr>
			<td>FluoroDish Cell Culture Dish</td>
			<td>World Precision Instruments</td>
			<td>FD5040-100</td>
			<td></td>
		</tr>
		<tr>
			<td>Fluoromount Aqueous Mounting Medium</td>
			<td>sigma-Aldrich</td>
			<td>F4680-25ML</td>
			<td></td>
		</tr>
		<tr>
			<td>Glucose</td>
			<td>MedPex</td>
			<td>3705391</td>
			<td>5%</td>
		</tr>
		<tr>
			<td>GlutaMAX Supplement</td>
			<td>ThermoFisher Scientific</td>
			<td>35050061</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycine</td>
			<td>Sigma-Aldrich</td>
			<td>G8898</td>
			<td></td>
		</tr>
		<tr>
			<td>HBSS</td>
			<td>Life Technologies</td>
			<td>14025092</td>
			<td>calcium, magnesium, no phenol red</td>
		</tr>
		<tr>
			<td>Horse serum</td>
			<td>Pan-Biotech</td>
			<td>P30-0711</td>
			<td></td>
		</tr>
		<tr>
			<td>Imaris 9.7.2</td>
			<td>Bitplane</td>
			<td>NA</td>
			<td>https://imaris.oxinst.com/products/imaris-for-neuroscientists</td>
		</tr>
		<tr>
			<td>Isoflurane</td>
			<td>Virbac</td>
			<td>NA</td>
			<td></td>
		</tr>
		<tr>
			<td>Isotonic saline solution</td>
			<td>B. Braun</td>
			<td>8609261</td>
			<td>0.90%</td>
		</tr>
		<tr>
			<td>Leica VT1200 S vibratome</td>
			<td>Leica</td>
			<td>14048142066</td>
			<td></td>
		</tr>
		<tr>
			<td>LSM 880 with Airyscan</td>
			<td>Zeiss</td>
			<td>NA</td>
			<td></td>
		</tr>
		<tr>
			<td>Metacam</td>
			<td>Venusberg Apotheke</td>
			<td>8890217</td>
			<td>5 mg/ml</td>
		</tr>
		<tr>
			<td>Mice</td>
			<td>Janvier Labs</td>
			<td>NA</td>
			<td>C57BL/6JRj</td>
		</tr>
		<tr>
			<td>Micro-Adson Forceps</td>
			<td>Fine Science Tools</td>
			<td>11018-12</td>
			<td></td>
		</tr>
		<tr>
			<td>Micropipette Storage Jar</td>
			<td>World Precision Instruments</td>
			<td>E210</td>
			<td>&#160;16.16.27</td>
		</tr>
		<tr>
			<td>Microsoft Excel</td>
			<td>Microsoft</td>
			<td>NA</td>
			<td>https://www.microsoft.com/en-us/microsoft-365/p/excel/cfq7ttc0k7dx?activetab=pivot:overviewtab</td>
		</tr>
		<tr>
			<td>Millicell Cell Culture Insert</td>
			<td>EMD Millipore</td>
			<td>PICM0RG50</td>
			<td>30&#160;mm, hydrophilic PTFE, 0.4&#160;&#181;m</td>
		</tr>
		<tr>
			<td>Moria Perforated Spoons</td>
			<td>Fine Science Tools</td>
			<td>10370-18</td>
			<td></td>
		</tr>
		<tr>
			<td>Moria Spoon</td>
			<td>Fine Science Tools</td>
			<td>10321-08</td>
			<td></td>
		</tr>
		<tr>
			<td>Neurobasal Medium, minus phenol red</td>
			<td>ThermoFisher Scientific</td>
			<td>12348017</td>
			<td></td>
		</tr>
		<tr>
			<td>Neuropan-2 supplement</td>
			<td>Pan-Biotech</td>
			<td>P07-11010</td>
			<td></td>
		</tr>
		<tr>
			<td>Normal goat serum</td>
			<td>Abcam</td>
			<td>ab138478</td>
			<td></td>
		</tr>
		<tr>
			<td>Olsen-Hegar Needle Holder with Scissors</td>
			<td>Fine Science Tools</td>
			<td>12002-12</td>
			<td></td>
		</tr>
		<tr>
			<td>p-Tub-alpha-1-Dre</td>
			<td>Addgene</td>
			<td>133925</td>
			<td></td>
		</tr>
		<tr>
			<td>p-Tub-alpha-1-iCre</td>
			<td>Addgene</td>
			<td>133924</td>
			<td></td>
		</tr>
		<tr>
			<td>p-Tub-alpha-1-LifeAct-GFP</td>
			<td>Addgene</td>
			<td>175437</td>
			<td></td>
		</tr>
		<tr>
			<td>Parafilm</td>
			<td>VWR</td>
			<td>52858-000</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraformaldehyde</td>
			<td>sigma-Aldrich</td>
			<td>P6148</td>
			<td></td>
		</tr>
		<tr>
			<td>PBS</td>
			<td>Sigma-Aldrich</td>
			<td>P3813-10PAK</td>
			<td></td>
		</tr>
		<tr>
			<td>pCAG-lox-rox-STOP-rox-tRFP-lox-Lyn-ZsGreen</td>
			<td>Addgene</td>
			<td>175438</td>
			<td></td>
		</tr>
		<tr>
			<td>pCAG-lox-STOP-lox-Lyn-mNeonGreen</td>
			<td>Addgene</td>
			<td>175257</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin</td>
			<td>ThermoFisher Scientific</td>
			<td>15140122</td>
			<td></td>
		</tr>
		<tr>
			<td>PicoNozzle Kit v2</td>
			<td>World Precision Instruments</td>
			<td>5430-ALL</td>
			<td></td>
		</tr>
		<tr>
			<td>Platinum Tweezertrodes</td>
			<td>Harvard Apparatus</td>
			<td>45-0487</td>
			<td>1 mm / 3 mm</td>
		</tr>
		<tr>
			<td>QIAGEN Maxi kit</td>
			<td>QIAGEN</td>
			<td>12162</td>
			<td></td>
		</tr>
		<tr>
			<td>Reflex wound closure Clip</td>
			<td>World Precision Instruments</td>
			<td>500344-10</td>
			<td>7 mm</td>
		</tr>
		<tr>
			<td>Sekundenkleber Pattex Mini Trio</td>
			<td>Lyreco</td>
			<td>4722659</td>
			<td></td>
		</tr>
		<tr>
			<td>Square wave electroporation system ECM830</td>
			<td>Harvard Apparatus</td>
			<td>W3 45-0052</td>
			<td></td>
		</tr>
		<tr>
			<td>Sterile gauze</td>
			<td>Braun Askina</td>
			<td>9031216</td>
			<td></td>
		</tr>
		<tr>
			<td>Sterile lubricant eye ointment</td>
			<td>Bayer Vital</td>
			<td>PZN1578675</td>
			<td></td>
		</tr>
		<tr>
			<td>Sterile surgical gloves</td>
			<td>Sempermed</td>
			<td>14C0451</td>
			<td></td>
		</tr>
		<tr>
			<td>Sucrose</td>
			<td>Roth</td>
			<td>4621.2</td>
			<td></td>
		</tr>
		<tr>
			<td>Supramid 5-0 surgical silk sutures</td>
			<td>B. Braun</td>
			<td>NA</td>
			<td></td>
		</tr>
		<tr>
			<td>Thin-wall glass capillaries</td>
			<td>World Precision Instruments</td>
			<td>TW100-4</td>
			<td></td>
		</tr>
		<tr>
			<td>Triton X-100</td>
			<td>Sigma-Aldrich</td>
			<td>X100</td>
			<td></td>
		</tr>
		<tr>
			<td>Vannas spring scissors</td>
			<td>Fine Science Tools</td>
			<td>15000-03</td>
			<td></td>
		</tr>
		<tr>
			<td>&#181;-Slide 8 Well Glass Bottom</td>
			<td>Ibidi</td>
			<td>80827</td>
			<td></td>
		</tr>
	</tbody>
</table>

in situ visualization of axon growth and growth cone dynamics in acute ex vivo embryonic brain slice cultures

During neuronal development, axons navigate the cortical environment to reach their final destinations and establish synaptic connections. Growth cones -the sensory structures located at the distal tips of developing axons- execute this process. Studying the structure and dynamics of the growth cone is crucial to understanding axonal development and the interactions with the surrounding central nervous system (CNS) that enable it to form neural circuits. This is essential when devising methods to reintegrate axons into neural circuits following injury in fundamental research and pre-clinical contexts. Thus far, the general understanding of growth cone dynamics is primarily founded on studies of neurons cultured in two dimensions (2D). Although undoubtedly fundamental to the current knowledge of growth cone structural dynamics and response to stimuli, 2D studies misrepresent the physiological three-dimensional (3D) environment encountered by neuronal growth cones in intact CNS tissue. More recently, collagen gels were employed to overcome some of these limitations, enabling the investigation of neuronal development in 3D. However, both synthetic 2D and 3D environments lack signaling cues within CNS tissue, which direct the extension and pathfinding of developing axons. This protocol provides a method for studying axons and growth cones using organotypic brain slices, where developing axons encounter physiologically relevant physical and chemical cues. By combining fine-tuned in utero and ex utero electroporation to sparsely deliver fluorescent reporters along with super-resolution microscopy, this protocol presents a methodological pipeline for the visualization of axon and growth cone dynamics in situ. Furthermore, a detailed toolkit description of the analysis of long-term and live-cell imaging data is included.

Representative results obtained with the described method workflow are shown. E15.5 mice were used in the present demonstration, though this protocol is easily adaptable&#160;to virtually all embryonic ages ranging from E11 to late E17. In this protocol, either ex utero electroporation (EUE; Figure 2A, 2C-I) or in utero electroporation (IUE; Figure 2B,C, and 2J-Q) were used to deliver plasmids into the progenitor neurons lining the lateral ventricles. These progenitors are the source of future cortical projecting neurons (CPN)15,16. Plasmid mixes were prepared to drive sparse neuron-specific expression of either membrane-targeted (Lyn)-mNeonGreen (Figure 1A) or LifeAct-enhanced (E)GFP (Figure 1B) to evaluate the overall behavior and actin dynamics in growth cones, respectively. Furthermore, a plasmid mix aimed to label individual neurons with either turbo(t)-RFP or zoanthus sp. (Zs) green fluorescent protein (ZsGreen) (Figure 1C) was included. This facilitates the monitoring of growth cone behavior from independent neighboring neurons.
Brain dissection from electroporated embryos is a crucial step that needs to be carefully performed to obtain high-quality slices, preserving the native brain structure. Dissection instruments and vibratome were prepared beforehand and carefully ethanol-sterilized (Figure 3A,B). Next, the heads of electroporated embryos were carefully dissected and the brains were extracted. Here, representative dissection of brains from the embryos subjected to EUE at E15 (Figure 3C-F) and E12.5 (Figure 3G-J) are shown. Brains are immediately encased in an agarose matrix, sliced, and placed on PTFE membrane inserts within a bottom-glass dish for incubation (Figure 3K-M).
The health status of brain slices is a significant point for control to ensure reliable results. A visual inspection for any contamination was performed daily. Additionally, once the culture was finalized, the brain slices are fixed and subjected to immunohistochemistry. Here,4&#8242;,6-diamidino-2-phenylindole (DAPI) was used to control the overall cellular organization and vimentin staining to reveal glial organization; particularly, radial glia (RG) scaffold. Typically, successfully cultured brain slices derived from either IUE or EUE show normal cellular distribution as revealed by DAPI and a somewhat organized array of RG with apically oriented pial-contacting processes17 (Figure 4A,B respectively). Occasionally, marked disturbances in the RG scaffolding in cultured brain slices are observed, especially in those derived from EUE electroporation (Figure 4C). Brain slices with extremely disorganized RG scaffold show impaired neuronal migration and defective axon growth (not shown). Hence, controlling the RG scaffold is an easy post-culture method to sort the data obtained from reliable brain slices.
Brain slices derived from either IUE or EUE with Lyn-mNeonGreen-expressing plasmid mix result in similar sparse neuron labeling. A representative pyramidal CPN expressing Lyn-mNeonGreen and the dynamic behavior of its growth cone is shown as an example (Figure 5A and Supplementary Video 1, top left). In addition, neurons were labeled using a plasmid expressing an actin probe to analyze actin dynamics of axonal growth cones in situ (Figure 5B and Supplementary Video 1, bottom left). In situ experiments were also performed with a dual-Cre/Dre fluorophore-expressing plasmid design (Figure 1C and Supplementary Video 1, right). tRFP or ZsGreen fluorophores in this plasmid could be specifically and individually activated by either Dre or Cre recombinases, respectively, in neighboring neurons (Figure 5C). This experimental line-up allows side-by-side analysis of growth cones from control neurons with neighboring modified neurons (any given loss or gain of function). This circumvents variability arising from the use of different slices to test control and experimental conditions.
Kymographs generated from the recorded movie were analyzed, from which dynamic growth parameters such as protrusive activity over time and growth length can be easily obtained (Figure 6A). Note that a simple adjustment in the temporal resolution of the time-lapse allows measurement of axon elongation speed for 2 h (Figure 6A). Furthermore, the variation of growth cone volume over time-a measure of general growth cone dynamic activity-can be easily obtained, in this case with licensed software (Figure 6B and Figure 6E,F). This can be used to evaluate the speed of actin treadmilling and the balance of filopodia/lamellipodia during growth cone exploring activity.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/63068/63068fig01.jpg" /> 
Figure 1: Schemes of the plasmids used in the protocol. (A) pCAG-lox-STOP-lox-Lyn-mNeonGreen. (B) p-Tub-alpha-1-LifeAct-GFP. (C) pCAG-lox-rox-STOP-rox-tRFP-pA-lox-ZsGreen-pA. Relevant information regarding plasmid components and fluorophore&#39;s origin is found in the boxes. <a href="https://www.jove.com/files/ftp_upload/63068/63068fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/63068/63068fig02.jpg" /> 
Figure 2: Workflow of ex utero and in utero electroporation of E15.5 mice. (A) Set up of surgery station for ex utero electroporation. (B) Set up of surgery station for in utero electroporation. (C) Uterine horns pulled outside the abdominal cavity of the anesthetized mouse. (D) Extraction of an embryo from the uterine sack. (E) Embryo sacrifice by complete spinal cord transection via a diagonal incision; note that beheading was avoided. (F) Placement of embryo in the holder and injected with DNA/Fast Green mixture into the left lateral ventricle. (G,H) Position the embryo&#39;s head between platinum tweezer electrodes with the cathode (red arrow) over the cortex at a 60&#176; angle. (I) Placement of embryo&#39;s arms (black arrows) outside the holder to prevent sliding of the embryo during the procedure. (J) Rotation of the embryo inside the uterine sack to expose the head. (K,L) Injection of DNA/Fast Green mixture into embryo&#39;s lateral ventricles through the uterine wall. (M) Position the embryo&#39;s head between platinum tweezer electrodes with a cathode (red arrow) over the cortex at a 60&#176; angle. (N) Sutured muscle incision via running locking suture. (O) Sutured skin incision via an interrupted suture. (P) Securing of the wound using surgical wound clips and disinfection using betadine. (Q) Placement of the mouse in the recovery cage with far infrared warming light. <a href="https://www.jove.com/files/ftp_upload/63068/63068fig02large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/63068/63068fig03.jpg" /> 
Figure 3: Extraction of E15.5 and E12.5 brains and organotypic slice culture procedure. (A) Tools used for the brain extraction procedure. (B) Set up of organotypic culture station. (C-F) Extraction of E15.5 brain. (G-J) Extraction of E12.5 brain. Dotted lines highlight the location of incisions. Red arrows are pointing out the direction of pulling by forceps. (K) Embedding the brain in a 3 cm dish containing 3% low melt agarose, leaving a 1-2 mm agarose spacing gap under the brain. (L) Collection of 150 &#181;m brain slice. (M) Placement of brain slices on PTFE membrane inserts immobilized in a 35 mm dish using paraffin film (blue arrow). Red star marking indicates a given brain slice collection from vibratome (L) and its transfer to PTFE membrane (M). <a href="https://www.jove.com/files/ftp_upload/63068/63068fig03large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/63068/63068fig04.jpg" /> 
Figure 4: Conserved radial glial cell structure in healthy organotypic slices. Confocal images of E17.5 brain slices revealing RG array (vimentin; green) and overall cell organization (DAPI; magenta) following IUE (A) and EUE (B,C). Note the strong disturbances in the RG array that may occasionally result from EUE (C). Magnifications correspond to the red dotted frames in the main figure: scale bars, 10 &#181;m. <a href="https://www.jove.com/files/ftp_upload/63068/63068fig04large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 5" class="xfigimg" src="/files/ftp_upload/63068/63068fig05.jpg" /> 
Figure 5: In situ visualization of the growth cone dynamics in acute organotypic slices. (A,B) Neurons and their corresponding growth cones labeled with Lyn-mNeonGreen and LifeAct-GFP, respectively. Red star marking growth cone of Lyn-mNeonGreen expressing neuron. Blue asterisk marking growth cone of LifeAct-GFP expressing neuron. (C) Neighboring neurons labeled with the dual plasmid system containing tRFP (magenta) and ZsGreen (green) and their corresponding growth cones. Growth cones imaged (right) were outside the captured frame (left), obtained shortly after acquiring the growth cone time-lapse; scale bars, 5 &#181;m. <a href="https://www.jove.com/files/ftp_upload/63068/63068fig05large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 6" class="xfigimg" src="/files/ftp_upload/63068/63068fig6v2.jpg" /> 
Figure 6: Analysis of axon growth speed and growth cone volume. (A) Axon tracing on a neuron expressing Lyn-mNeonGreen (top) and its corresponding kymograph (below) generated using ImageJ. (B) Reconstruction of z-stack video of growth cone using the image analysis software (top) and the same growth cone highlighted using the surfaces measurement tool (below). (C) Graphs showing changes in growth speed over time for several axons. (D) The average growth speed of axons is quantified in (C). (E) Graph showing the changes in the growth cone volume over time. (F) The average volume of growth cones is quantified in (E); scale bar, 5 &#181;m. <a href="https://www.jove.com/files/ftp_upload/63068/63068fig6v2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 7" class="xfigimg" src="/files/ftp_upload/63068/63068fig07.jpg" /> 
Figure 7: Radial migration and neuronal polarization of pyramidal cortical neurons. Diagram illustrating developing pyramidal cortical neurons (pink) migrating radially from the germinal ventricular zone (VZ) toward the pia surface. Guided by radial glia processes (gray), migrating polarized neurons establish a leading process, future dendrite, and trailing process, future axon, that continue to extend downward toward the intermediate zone (IZ). Dashed red boxes represent the cortical areas where growth cones were imaged. Specifically in the IZ, subventricular zone (SVZ), or joining axon bundles (green). The illustration was created with a web-based tool, BioRender.com. <a href="https://www.jove.com/files/ftp_upload/63068/63068fig07large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Plasmid</td>
			<td>Concentration (&#181;g/&#181;L)</td>
			<td>Intended use</td>
		</tr>
		<tr>
			<td>pCAG-lox-STOP-lox-Lyn-mNeonGreen</td>
			<td>0.25</td>
			<td rowspan="3">Labelling of membrane targeted protein (Lyn)</td>
		</tr>
		<tr>
			<td>+</td>
			<td>+</td>
		</tr>
		<tr>
			<td>p-Tub-alpha-1-iCre</td>
			<td>0.08</td>
		</tr>
		<tr>
			<td>p-Tub-alpha-1-LifeAct-GFP</td>
			<td>0.125</td>
			<td>Filamentous actin (F-actin) labelling in growth cones</td>
		</tr>
		<tr>
			<td>pCAG-lox-rox-STOP-rox-tRFP-lox-Lyn-ZsGreen</td>
			<td>1</td>
			<td rowspan="5">Independent labelling of two populations of neighboring neurons</td>
		</tr>
		<tr>
			<td>+</td>
			<td>+</td>
		</tr>
		<tr>
			<td>p-Tub-alpha-1-iCre</td>
			<td>0.004</td>
		</tr>
		<tr>
			<td>+</td>
			<td>+</td>
		</tr>
		<tr>
			<td>p-Tub-alpha-1-Dre</td>
			<td>0.2</td>
		</tr>
	</tbody>
</table>
Table 1: List of plasmids used in the Protocol. Name, concentration, and intended use of each utilized plasmid.
Supplementary Video 1: In situ visualization of the growth cone dynamics in acute organotypic slices. Dynamics of growth cones labeled with Lyn-mNeonGreen (top left) and LifeAct-GFP (bottom left). Neighboring growth cones are differentially labeled with the dual plasmid system containing tRFP (magenta; top right) and ZsGreen (green; bottom right). Imaging interval, 2.5 s. Scale bars, 5 &#181;m. <a href="https://www.jove.com/files/ftp_upload/63068/Supplementary_Video_1.mp4" target="_blank">Please click here to download this File.</a>

Watch this Scientific Journal Video about In Situ Visualization of Axon Growth and Growth Cone Dynamics in Acute Ex Vivo Embryonic Brain Slice Cultures at JoVE.com

In Situ Visualization of Axon Growth and Growth Cone Dynamics in Acute Ex Vivo Embryonic Brain Slice Cultures

This protocol demonstrates a straightforward and robust method to study in situ axon growth and growth cone dynamics. It describes how to prepare ex vivo physiologically relevant acute brain slices and provides a user-friendly analysis pipeline.

In Situ Visualization of Axon Growth and Growth Cone Dynamics in Acute Ex Vivo Embryonic Brain Slice Cultures

During neuronal development, axons navigate the cortical environment to reach their final destinations and establish synaptic connections. Growth cones ...

in-situ-visualization-axon-growth-growth-cone-dynamics-acute-ex-vivo

Research

JoVE Journal

Neuroscience

3.2K Views.  Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE). This protocol demonstrates a straightforward and robust method to study in situ axon growth and growth cone dynamics. It describes how to prepare ex vivo physiologically relevant acute brain slices and provides a user-friendly analysis pipeline.

Video: In Situ Visualization of Axon Growth and Growth Cone Dynamics in Acute Ex Vivo Embryonic Brain Slice Cultures

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 ...

Methods for Study of Neuronal Morphogenesis: Ex vivo RNAi Electroporation in Embryonic Murine Cerebral Cortex

The cerebral cortex directs higher cognitive functions. This six layered structure is generated in an inside-first, outside-last manner, in which the first born neurons remain closer to the ventricle while the last born neurons migrate past the first born neurons towards the surface of the brain1. In addition to neuronal migration2, a key process for normal cortical function is the regulation of neuronal morphogenesis3. While neuronal morphogenesis can be studied in vitro in primary cultures, there is much to be learned from how these processes are regulated in tissue environments.
We describe techniques to analyze neuronal migration and/or morphogenesis in organotypic slices of the cerebral cortex4,6. A pSilencer modified vector is used which contains both a U6 promoter that drives the double stranded hairpin RNA and a separate expression cassette that encodes GFP protein driven by a CMV promoter7-9. Our approach allows for the rapid assessment of defects in neurite outgrowth upon specific knockdown of candidate genes and has been successfully used in a screen for regulators of neurite outgrowth8. Because only a subset of cells will express the RNAi constructs, the organotypic slices allow for a mosaic analysis of the potential phenotypes. Moreover, because this analysis is done in a near approximation of the in vivo environment, it provides a low cost and rapid alternative to the generation of transgenic or knockout animals for genes of unknown cortical function. Finally, in comparison with in vivo electroporation technology, the success of ex vivo electroporation experiments is not dependant upon proficient surgery skill development and can be performed with a shorter training time and skill.

Methods for Study of Neuronal Morphogenesis: Ex vivo RNAi Electroporation in Embryonic Murine Cerebral Cortex

To conduct a rapid assessment of the function of genes in the development of cerebral cortex, we describe methods involving the ex vivo electroporation of plasmids co-expressing inhibitory RNA (RNAi) and GFP in murine embryonic cortex. This protocol is amenable to the study of various aspects of neurodevelopment such as neurogenesis, neuronal migration and neuronal morphogenesis including dendrite and axon outgrowth.

The cerebral cortex directs higher cognitive functions. This six layered structure is generated in an inside-first, outside-last manner, in which the ...

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

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

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

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

Brain Slice Biotinylation: An Ex Vivo Approach to Measure Region-specific Plasma Membrane Protein Trafficking in Adult Neurons

Regulated endocytic trafficking is the central mechanism facilitating a variety of neuromodulatory events, by dynamically controlling receptor, ion channel, and transporter cell surface presentation on a minutes time scale.&#160;There is a broad diversity of mechanisms that control endocytic trafficking of individual proteins. Studies investigating the molecular underpinnings of trafficking have primarily relied upon surface biotinylation to quantitatively measure changes in membrane protein surface expression in response to exogenous stimuli and gene manipulation.&#160;However, this approach has been mainly limited to cultured cells, which may not faithfully reflect the physiologically relevant mechanisms at play in adult neurons.&#160;Moreover, cultured cell approaches may underestimate region-specific differences in trafficking mechanisms.&#160;Here, we describe an approach that extends cell surface biotinylation to the acute brain slice preparation.&#160;We demonstrate that this method provides a high-fidelity approach to measure rapid changes in membrane protein surface levels in adult neurons.&#160;This approach is likely to have broad utility in the field of neuronal endocytic trafficking.

Brain Slice Biotinylation: An Ex Vivo Approach to Measure Region-specific Plasma Membrane Protein Trafficking in Adult Neurons

Neuronal membrane trafficking dynamically controls plasma membrane protein availability and significantly impacts neurotransmission.&#160;To date, it has been challenging to measure neuronal endocytic trafficking in adult neurons.&#160;Here, we describe a highly effective, quantitative method to measure rapid changes in surface protein expression ex vivo in acute brain slices.

Regulated endocytic trafficking is the central mechanism facilitating a variety of neuromodulatory events, by dynamically controlling receptor, ion ...

Ex Vivo Preparations of the Intact Vomeronasal Organ and Accessory Olfactory Bulb

The mouse accessory olfactory system (AOS) is a specialized sensory pathway for detecting nonvolatile social odors, pheromones, and kairomones. The first neural circuit in the AOS pathway, called the accessory olfactory bulb (AOB), plays an important role in establishing sex-typical behaviors such as territorial aggression and mating. This small (&#60;1 mm3) circuit possesses the capacity to distinguish unique behavioral states, such as sex, strain, and stress from chemosensory cues in the secretions and excretions of conspecifics. While the compact organization of this system presents unique opportunities for recording from large portions of the circuit simultaneously, investigation of sensory processing in the AOB remains challenging, largely due to its experimentally disadvantageous location in the brain. Here, we demonstrate a multi-stage dissection that removes the intact AOB inside a single hemisphere of the anterior mouse skull, leaving connections to both the peripheral vomeronasal sensory neurons (VSNs) and local neuronal circuitry intact. The procedure exposes the AOB surface to direct visual inspection, facilitating electrophysiological and optical recordings from AOB circuit elements in the absence of anesthetics. Upon inserting a thin cannula into the vomeronasal organ (VNO), which houses the VSNs, one can directly expose the periphery to social odors and pheromones while recording downstream activity in the AOB. This procedure enables controlled inquiries into AOS information processing, which can shed light on mechanisms linking pheromone exposure to changes in behavior.

Ex Vivo Preparations of the Intact Vomeronasal Organ and Accessory Olfactory Bulb

The mouse accessory olfactory bulb (AOB) has been difficult to study in the context of sensory coding. Here, we demonstrate a dissection that produces an ex vivo preparation in which AOB neurons remain functionally connected to their peripheral inputs, facilitating research into information processing of mouse pheromones and kairomones.

The mouse accessory olfactory system (AOS) is a specialized sensory pathway for detecting nonvolatile social odors, pheromones, and kairomones. The first ...

Organotypic Slice Cultures to Study Oligodendrocyte Dynamics and Myelination

NG2 expressing cells (polydendrocytes, oligodendrocyte precursor cells) are the fourth major glial cell population in the central nervous system. During embryonic and postnatal development they actively proliferate and generate myelinating oligodendrocytes. These cells have commonly been studied in primary dissociated cultures, neuron cocultures, and in fixed tissue. Using newly available transgenic mouse lines slice culture systems can be used to investigate proliferation and differentiation of oligodendrocyte lineage cells in both gray and white matter regions of the forebrain and cerebellum. Slice cultures are prepared from early postnatal mice and are kept in culture for up to 1 month. These slices can be imaged multiple times over the culture period to investigate cellular behavior and interactions. This method allows visualization of NG2 cell division and the steps leading to oligodendrocyte differentiation while enabling detailed analysis of region-dependent NG2 cell and oligodendrocyte functional heterogeneity. This is a powerful technique that can be used to investigate the intrinsic and extrinsic signals influencing these cells over time in a cellular environment that closely resembles that found in vivo.

A technique to study NG2 cells and oligodendrocytes using a slice culture system of the forebrain and cerebellum is described. This method allows examination of the dynamics of proliferation and differentiation of cells within the oligodendrocyte lineage where the extracellular environment can be easily manipulated while maintaining tissue cytoarchitecture.

NG2 expressing cells (polydendrocytes, oligodendrocyte precursor cells) are the fourth major glial cell population in the central nervous system. During ...

Slice It Hot: Acute Adult Brain Slicing in Physiological Temperature

Here we present a protocol for preparation of acute brain slices. This procedure is a critical element for electrophysiological patch-clamp experiments that largely determines the quality of results. It has been shown that omitting the cooling step during cutting procedure is beneficial in obtaining healthy slices and cells, especially when dealing with highly myelinated brain structures from mature animals. Even though the precise mechanism whereby elevated temperature supports neural health can only be speculated upon, it stands to reason that, whenever possible, the temperature in which the slicing is performed should be close to physiological conditions to prevent temperature related artifacts. Another important advantage of this method is the simplicity of the procedure and therefore the short preparation time. In the demonstrated method adult mice are used but the same procedure can be applied with younger mice as well as rats. Also, the following patch clamp experiment is performed on horizontal cerebellar slices, but the same procedure can also be used in other planes as well as other posterior areas of the brain.

In this paper we show a method for preparing acute brain slices in physiological temperature, using a conventional physiological solution without special modifications for the cutting (such as adding sucrose) and without intracardial perfusion of the animal before slice preparation.

Here we present a protocol for preparation of acute brain slices. This procedure is a critical element for electrophysiological patch-clamp experiments ...

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

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

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

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

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

Imaging Ca2+ Dynamics in Cone Photoreceptor Axon Terminals of the Mouse Retina

Retinal cone photoreceptors (cones) serve daylight vision and are the basis of color discrimination. They are subject to degeneration, often leading to blindness in many retinal diseases. Calcium (Ca2+), a key second messenger in photoreceptor signaling and metabolism, has been proposed to be indirectly linked with photoreceptor degeneration in various animal models. Systematically studying these aspects of cone physiology and pathophysiology has been hampered by the difficulties of electrically recording from these small cells, in particular in the mouse where the retina is dominated by rod photoreceptors. To circumvent this issue, we established a two-photon Ca2+ imaging protocol using a transgenic mouse line that expresses the genetically encoded Ca2+ biosensor TN-XL exclusively in cones and can be crossbred with mouse models for photoreceptor degeneration. The protocol described here involves preparing vertical sections (&#8220;slices&#8221;) of retinas from mice and optical imaging of light stimulus-evoked changes in cone Ca2+ level. The protocol also allows &#8220;in-slice measurement&#8221; of absolute Ca2+ concentrations; as the recordings can be followed by calibration. This protocol enables studies into functional cone properties and is expected to contribute to the understanding of cone Ca2+ signaling as well as the potential involvement of Ca2+ in photoreceptor death and retinal degeneration.

Imaging Ca2+ Dynamics in Cone Photoreceptor Axon Terminals of the Mouse Retina

We describe a protocol to monitor Ca2+ dynamics in the axon terminals of cone photoreceptors using an ex-vivo&#160;slice preparation of the mouse retina. This protocol allows comprehensive studies of cone Ca2+ signaling in an important mammalian model system, the mouse.

Retinal cone photoreceptors (cones) serve daylight vision and are the basis of color discrimination. They are subject to degeneration, often leading to ...

Simultaneous ex vivo Functional Testing of Two Retinas by in vivo Electroretinogram System

An In vivo electroretinogram (ERG) signal is composed of several overlapping components originating from different retinal cell types, as well as noise from extra-retinal sources. Ex vivo ERG provides an efficient method to dissect the function of retinal cells directly from an intact isolated retina of animals or donor eyes. In addition, ex vivo ERG can be used to test the efficacy and safety of potential therapeutic agents on retina tissue from animals or humans. We show here how commercially available in vivo ERG systems can be used to conduct ex vivo ERG recordings from isolated mouse retinas. We combine the light stimulation, electronic and heating units of a standard in vivo system with custom-designed specimen holder, gravity-controlled perfusion system and electromagnetic noise shielding to record low-noise ex vivo ERG signals simultaneously from two retinas with the acquisition software included in commercial in vivo systems. Further, we demonstrate how to use this method in combination with pharmacological treatments that remove specific ERG components in order to dissect the function of certain retinal cell types.

Simultaneous ex vivo Functional Testing of Two Retinas by in vivo Electroretinogram System

Ex vivo ERG can be used to record electrical activity of retinal cells directly from isolated intact retinas of animals or humans. We demonstrate here how common in vivo ERG systems can be adapted for ex vivo ERG recordings in order to dissect the electrical activity of retinal cells.

An In vivo electroretinogram (ERG) signal is composed of several overlapping components originating from different retinal cell types, as well as noise ...