We thank Dr. Gary Banker for suggestion on neuronal culture protocol. This work is supported by the Howard Hughes Medical Institute, a grant from NIH, and a George Barth Geller endowed professorship (V.B.).

NOTE: This culture method of hippocampal neurons from postnatal 0-day ANK3-E22/23f/f mice is adapted from Gary Banker&#8217;s glia/neuron co-culture system. Therefore, it is critical to perform all steps after dissection in a clean hood using sterilized tools. This protocol takes up to 1 month. The workflow is displayed in Figure 3. The protocol follows the animal guidelines of Duke University.
1. Preparing of coverslips and neuronal plating dishes
<ol>
	<li>At least one week before culture day, load coverslips on coverslip rack and soak it in nitric acid (70% W/W) overnight (could be extended for days).</li>
	<li>Wash nitric acid treated coverslips with distilled water on a low speed shaker in a glass jar 2 times, 1 hour each.</li>
	<li>Incubate coverslips in saturated KOH dissolved in 100% ethanol overnight. Add KOH into ethanol till it is no longer dissolved.</li>
	<li>Repeat the wash step with distilled water. Rinse coverslips with 100% ethanol once for 10 minutes.</li>
	<li>Transfer coverslips from the rack to a glass beaker. Cover the beaker with aluminum foil. Bake coverslips in a 225 &#176;C oven overnight to sterilize the coverslips. (Coverslips could be stored in the beaker for weeks).</li>
	<li>Place coverslips in a Petri dish and then apply 3-4 wax dots on the coverslip to serve as feet. Use a Pasteur pipette to dip into boiled wax in a glass bottle. Then quickly touch the coverslip to create a dot. A 60 mm Petri dish can hold 4 coverslips. A 10 mm Petri dish can hold ~10 coverslips.</li>
	<li>2 days before culture day, coat coverslips (the side with the wax dots) with filter sterilized 1 mg/mL poly-L-lysine in 0.1 M boric acid (pH 8.5) for a minimum of 6 hours and rinse with water 2 times, 1 hour each time. Coverslips remain in the same Petri dish.</li>
	<li>Add plating medium (MEM supplemented with glucose 0.6% (wt/vol) and 10% (vol/vol) horse serum) to plates slowly without disturbing coverslips. Put plates in the incubator till the culture day to seed neurons.</li>
</ol>
2. Preparing glia cell feeder dishes (2 weeks before culture day)
<ol>
	<li>Dissect the cortex from a postnatal 1-day old mice brain and peel off the meninges.</li>
	<li>Chop the cortex tissue as finely as possible with a clean scissors in a clean Petri dish in a clean bench.</li>
	<li>Transfer the chopped tissue into 12 mL of HBSS and add 1.5 mL of 2.5% trypsin and 1% (wt/vol) DNase. Incubate in a 37 &#176;C water bath for 15 min, swing every 5 min. Well digested tissue become sticky and form a big cluster. Triturate 10-15 times with a 10 mL pipette to break the tissue down and get better digestion.</li>
	<li>Triturate the well digested tissue 10-15 times with a 5 mL pipette till most chunks disappear and the medium turns to cloudy. Pass through a cell strainer to remove remaining chunks and add 15 mL of glia medium (Minimal essential medium (MEM) supplemented with glucose (0.6% wt/vol), 10% (vol/vol) horse serum and Penicillin-Streptomycin (1x) to stop the digestion.</li>
	<li>Centrifuge the cells at 120 x g for 5 minutes and aspirate the supernatant. Resuspend the cell pellet with fresh glia medium and seed in cell culture dishes (about 105 cells/cm2).</li>
	<li>Replace medium with fresh glia medium the next day to remove unattached cells.</li>
	<li>Feed the glia dishes every 3-4 days with fresh glia medium. Slap the flask 5-10 times with a hand to dislodge loosely attached cells before changing medium.</li>
	<li>After 10 days of culture, glia cells should be nearly confluent. Detach glia cells with 0.25% trypsin-EDTA and seed about 105 cells in a new 60 mm cell culture dish. Remaining cells could be frozen for future use.</li>
	<li>3 days before the culture day, change the glia medium to neuronal culture medium (Neurobasal-A Medium with 1x GlutaMAX-I and 1x B27 supplement).</li>
</ol>
3. Culture hippocampal neurons
NOTE: All steps are performed at room temperature.
<ol>
	<li>Dissect 6-8 hippocampi from postnatal 1-day old pups from ANK3-E22/23f/f mice with HBSS medium in a Petri dish at room temperate. Chop the hippocampi with dissection scissors to smaller pieces. Transfer hippocampi from the Petri dish to a 15 mL tube.</li>
	<li>Wash hippocampi 2x with 5 mL of HBSS in the tube. Leave the hippocampi in 4.5 mL of 1x HBSS after wash.</li>
	<li>Add 0.5 mL of 2.5% trypsin into 4.5 mL of HBSS and incubate in a 37 &#176;C water bath for 15 minutes. Invert the tube every 5 minutes. Well digested hippocampi should become sticky and form a cluster. If needed, extend the digestion for 5 more minutes.</li>
	<li>Wash hippocampi with HBSS 3 times for 5 minutes each. Do not use a vacuum to remove the HBSS. It is very easy to remove the hippocampi.</li>
	<li>Add 2 mL of HBSS after the wash and pipette the hippocampi up and down with a Pasteur pipette 15 times.</li>
	<li>Triturate the tissue with a fire-polished Pasteur pipette (the diameter of the open is narrowed by half) 10 times. Do not go beyond 10 times even if there are still chunks remaining. Overshearing kills neurons.</li>
	<li>Rest the tube for 5 minutes till all chunks set to the bottom. Gently use a 1 mL pipette tip to transfer the supernatant containing the dissociated neurons to plating dishes (105 cells/60 mm dish). Add it directly to the pre-incubated plating medium and shake the plate gently.</li>
	<li>Repeat step 3.6-3.7 with the remaining chunks till most of the chunks have disappeared.</li>
	<li>2-4 hours after seeding, check the plating dishes with a light microscope. The majority of neurons should have attached to the coverslip. Attached cells are round and bright. Flip coverslips using a fine tip forceps to the glia cell feeder dishes with preconditioned neuronal culture medium with the wax dots side facing downwards.</li>
	<li>Neurons can grow in the glia cell feeder dishes for up to 1 month. Feed neurons every 7 days with 1 mL of fresh neuronal culture medium.</li>
	<li>Optional step: 1 week after seeding, add cytosine arabinoside (1-&#946;-D-arabinofuranosylcytosine) to a final concentration of 5 &#956;M to curb glial proliferation.</li>
</ol>
4. Disruption of AIS by Knockout of Ankyrin-G at earlier stage of neuron development
<ol>
	<li>On 3 div (day in vitro), flip the coverslips with wax dots side facing up to a glia cell feeder dish with conditioned neuronal culture medium.</li>
	<li>Mix 0.25 &#956;g of Cre-BFP DNA with 0.5 &#956;g of ankyrin-G-GFP (WT/mutant) DNA in a 1.7 mL tube to transfect 4 coverslips (~ 2:1 ratio of DNA copy number). Add 100 &#956;L of culture medium (e.g., Opti-MEM), mix and rest on a rack. If only Cre-BFP is transfected, the GFP plasmid backbone is used to match the total amount of DNA.</li>
	<li>Mix 3 &#956;L of transfection reagent (e.g., Lipofectamine 2000) (~ 3 times of DNA) with 100 &#956;L culture medium in a new 1.7 mL tube. Incubate for 5 minutes at RT.</li>
	<li>Mix 100 &#956;L of DNA solution from step 4.2 with 100 &#956;L of transfection reagent from step 4.3. Rest for 5-10 minutes on a rack.</li>
	<li>Add 50 &#956;L of DNA mix from step 4.4 right on top of each coverslip by inserting the tip just below the medium without touching the coverslips. Pipette slowly to avoid spreading of DNA mix.</li>
	<li>Slowly bring the dish back to the incubator and incubate for 30-45 minutes.</li>
	<li>Flip the coverslips back to the home glia feeder dish with wax dots side facing down and put the plate back to the incubator.</li>
</ol>
5. Quantification of axon initial segment
<ol>
	<li>Fix neurons on 7-10 div and stain with AIS marker following the standard immunocytochemistry protocol for the protein of interesting.</li>
	<li>Collect fluorescent pictures with desired microscopy.
	<ol>
		<li>Take Z-series sections to collect the signal of the entire AIS. Keep the same Z-depth for all pictures.</li>
		<li>Adjust the laser intensity to reach the best pixel intensity dynamic range.</li>
		<li>Make sure all AIS pictures are taken on the same microscope setup.</li>
		<li>Always check the signal of Cre-BFP.</li>
	</ol>
	</li>
	<li>AIS quantification
	<ol>
		<li>Open picture with Fiji (https://fiji.sc).</li>
		<li>Generate maximum projection of Z-series images.</li>
		<li>Subtract the empty coverslip background signal from the image.</li>
		<li>Draw a line along the AIS. The width of the line should fully cover the AIS. Start the line before the AIS signal is raised above the background and stop after it drops to the background.</li>
		<li>Measure the mean pixel intensity alone the line and export to a spreadsheet (~10-15 AISs are needed).</li>
		<li>Generate the average intensity curve of AIS using the MATLAB script adapted from Berger et al.15.</li>
		<li>For each experiment, include Cre only and Cre plus wildtype 480 kDa ankyrin-G transfected neurons as negative and positive controls to make sure that the knockout of AIS is efficiency and the rescue is successful.</li>
	</ol>
	</li>
</ol>

<ol>
	<li>Nelson, A. 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=Correction:+Ankyrin-G+regulates+forebrain+connectivity+and+network+synchronization+via+interaction+with+GABARAP.">Correction: Ankyrin-G regulates forebrain connectivity and network synchronization via interaction with GABARAP.</a> Molecular Psychiatry. , (2019).</li><li>Tseng, W. C., Jenkins, P. M., Tanaka, M., Mooney, R., Bennett, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Giant+ankyrin-G+stabilizes+somatodendritic+GABAergic+synapses+through+opposing+endocytosis+of+GABAA+receptors.">Giant ankyrin-G stabilizes somatodendritic GABAergic synapses through opposing endocytosis of GABAA receptors.</a> Proceedings of the National Academy of Sciences of the U S A. 112 (4), 1214-1219 (2015).</li><li>Tai, Y., Gallo, N. B., Wang, M., Yu, J. R., Van Aelst, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Axo-axonic+Innervation+of+Neocortical+Pyramidal+Neurons+by+GABAergic+Chandelier+Cells+Requires+AnkyrinG-Associated+L1CAM.">Axo-axonic Innervation of Neocortical Pyramidal Neurons by GABAergic Chandelier Cells Requires AnkyrinG-Associated L1CAM.</a> Neuron. 102 (2), 358-372 (2019).</li><li>Hofflin, F., 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=Heterogeneity+of+the+Axon+Initial+Segment+in+Interneurons+and+Pyramidal+Cells+of+Rodent+Visual+Cortex.">Heterogeneity of the Axon Initial Segment in Interneurons and Pyramidal Cells of Rodent Visual Cortex.</a> Frontiers in Cellular Neuroscience. 11, 332 (2017).</li><li>Schluter, 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=Structural+Plasticity+of+Synaptopodin+in+the+Axon+Initial+Segment+during+Visual+Cortex+Development.">Structural Plasticity of Synaptopodin in the Axon Initial Segment during Visual Cortex Development.</a> Cerebral Cortex. 27 (9), 4662-4675 (2017).</li><li>Kuba, H., Oichi, Y., Ohmori, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Presynaptic+activity+regulates+Na(+)+channel+distribution+at+the+axon+initial+segment.">Presynaptic activity regulates Na(+) channel distribution at the axon initial segment.</a> Nature. 465 (7301), 1075-1078 (2010).</li><li>Grubb, M. S., Burrone, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Activity-dependent+relocation+of+the+axon+initial+segment+fine-tunes+neuronal+excitability.">Activity-dependent relocation of the axon initial segment fine-tunes neuronal excitability.</a> Nature. 465 (7301), 1070-1074 (2010).</li><li>Pan, Z., 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=A+common+ankyrin-G-based+mechanism+retains+KCNQ+and+NaV+channels+at+electrically+active+domains+of+the+axon.">A common ankyrin-G-based mechanism retains KCNQ and NaV channels at electrically active domains of the axon.</a> Journal of Neuroscience. 26 (10), 2599-2613 (2006).</li><li>Cooper, E. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Made+for+"anchorin":+Kv7.2/7.3+(KCNQ2/KCNQ3)+channels+and+the+modulation+of+neuronal+excitability+in+vertebrate+axons.">Made for "anchorin": Kv7.2/7.3 (KCNQ2/KCNQ3) channels and the modulation of neuronal excitability in vertebrate axons.</a> Seminars in Cell &amp; Developmental Biology. 22 (2), 185-192 (2011).</li><li>Zhou, 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=AnkyrinG+is+required+for+clustering+of+voltage-gated+Na+channels+at+axon+initial+segments+and+for+normal+action+potential+firing.">AnkyrinG is required for clustering of voltage-gated Na channels at axon initial segments and for normal action potential firing.</a> The Journal of Cell Biology. 143 (5), 1295-1304 (1998).</li><li>Kordeli, E., Lambert, S., Bennett, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=AnkyrinG.+A+new+ankyrin+gene+with+neural-specific+isoforms+localized+at+the+axonal+initial+segment+and+node+of+Ranvier.">AnkyrinG. A new ankyrin gene with neural-specific isoforms localized at the axonal initial segment and node of Ranvier.</a> Journal of Biological Chemistry. 270 (5), 2352-2359 (1995).</li><li>Jenkins, P. M., 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=Giant+ankyrin-G:+a+critical+innovation+in+vertebrate+evolution+of+fast+and+integrated+neuronal+signaling.">Giant ankyrin-G: a critical innovation in vertebrate evolution of fast and integrated neuronal signaling.</a> Proceedings of the National Academy of Sciences of the U S A. 112 (4), 957-964 (2015).</li><li>Jenkins, P. M., 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=E-cadherin+polarity+is+determined+by+a+multifunction+motif+mediating+lateral+membrane+retention+through+ankyrin-G+and+apical-lateral+transcytosis+through+clathrin.">E-cadherin polarity is determined by a multifunction motif mediating lateral membrane retention through ankyrin-G and apical-lateral transcytosis through clathrin.</a> Journal of Biological Chemistry. 288 (20), 14018-14031 (2013).</li><li>Kaech, S., Banker, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Culturing+hippocampal+neurons.">Culturing hippocampal neurons.</a> Nature Protocol. 1 (5), 2406-2415 (2006).</li><li>Berger, S. L., 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=Localized+Myosin+II+Activity+Regulates+Assembly+and+Plasticity+of+the+Axon+Initial+Segment.">Localized Myosin II Activity Regulates Assembly and Plasticity of the Axon Initial Segment.</a> Neuron. 97 (3), 555-570 (2018).</li><li>Yang, R., 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=Neurodevelopmental+mutation+of+giant+ankyrin-G+disrupts+a+core+mechanism+for+axon+initial+segment+assembly.">Neurodevelopmental mutation of giant ankyrin-G disrupts a core mechanism for axon initial segment assembly.</a> Proceedings of the National Academy of Sciences of the U S A. 116 (39), 19717-19726 (2019).</li></ol>

The authors have nothing to disclose.

The assembly of AIS is organized by 480 kDa ankyrin-G. However, ankyrin-G has shorter isoforms that can target to the AIS of wildtype neurons, which may lead to difficulty in interpretation of structure-function analyses of AIS assembly. Here we present a method using neurons from ANK3-E22/23-flox mice that allows study of de novo assembly of the AIS. By transfecting with Cre-BFP at 3 div, we eliminate the all endogenous isoforms of ankyrin-G. We could also co-transfect 480 kDa ankyrin-G to rescue the f...

The axon initial segment is located at the proximal axon in most vertebrate neurons. Functionally, AIS is where action potentials are initiated due to the high-density of voltage-gated sodium channels in this region. AIS of some excitatory neurons are also targeted by inhibitory interneurons through forming GABAergic synapses1,2,3. Therefore, AIS is a critical site to integrate cell signaling and modulate the excitability of neurons. AIS is normally 20-60 &#956;m in length and located within 20 &#956;m of the cell body. The length and position of AIS varies in neurons across brain regions, as well as in different developmental stages of the same neuron4,5. Accumulated evidence suggested that the composition and position of AIS are dynamic in responding to the change of neuronal activity4,5,6,7.
480 kDa ankyrin-G is the master organizer of AIS. 480 kDa ankyrin-G is a membrane associated adaptor protein that directly binds to voltage gated sodium channels as well as other major AIS proteins including beta4-spectrin, KCNQ2/3 channels that modulate sodium channel activity8,9, and 186 kDa neurofascin, a L1CAM that directs GABAergic synapses to the AIS2,10. 480 kDa ankyrin-G shares canonical ankyrin domains found in the short 190 kDa ankyrin-G isoform (ANK repeats, spectrin binding domain, regulatory domain), but are distinguished by a giant exon that is found only in vertebrates and is specifically expressed in neurons (Figure 1A)11,12. The 480 kDa ankyrin-G neuron specific domain (NSD) is required for AIS formation12. The 190 kDa ankyrin-G does not promote AIS assembly or target AIS in ankyrin-G-null neurons12. However, 190 kDa ankyrin-G is concentrated at the AIS containing 480 kDa ankyrin-G12. This ability of the 190 kDa ankyrin-G to target pre-assembled AIS of wildtype neurons has been a source of confusion in the literature and has slowed appreciation of the critical specialized functions of the 480 kDa ankyrin-G in AIS assembly. Therefore, it is critical to study AIS assembly in ankyrin-G-null neurons that lack a pre-assembled AIS.
Here, we present a method to study the assembly and structure of the AIS using cultured hippocampal neurons from ANK3-E22/23-flox mice that eliminates all isoforms of ankyrin-G13 (Figure 1B). By transfecting neurons with a Cre-BFP construct before AIS is assembled, we generated ankyrin-G-deficient neurons completely lacking an AIS (Figure 1B, Figure 2). The assembly of AIS is fully rescued following co-transfection of 480 kDa ankyrin-G-GFP plasmid with a Cre-BFP plasmid. This method provides a way to study the AIS assembly in a non-pre-assembled AIS environment. We also modified the glia-neuron co-culture system from Gary Banker without using antibiotics, previously designed for embryonic day 18 neurons, for application to postnatal mouse neurons and adapted a AIS quantitation method to average AIS measurements from multiple neurons to normalize the variation of AIS14,15.

<table>
	<tbody>
		<tr>
			<td>10xHBSS</td>
			<td>Thermo Fisher Scientific</td>
			<td>14065-056</td>
			<td></td>
		</tr>
		<tr>
			<td>18mm coverglass (1.5D)</td>
			<td>Fisher Scientific</td>
			<td>12-545-84-1D</td>
			<td></td>
		</tr>
		<tr>
			<td>190kDa ankyrin-G-GFP</td>
			<td>Addgene</td>
			<td>#31059</td>
			<td></td>
		</tr>
		<tr>
			<td>2.5% Tripsin without phenol red</td>
			<td>Thermo Fisher Scientific</td>
			<td>14065-056</td>
			<td></td>
		</tr>
		<tr>
			<td>480kDa ankyrin-G-GFP</td>
			<td>lab made</td>
			<td>Provide upon request</td>
			<td></td>
		</tr>
		<tr>
			<td>ANK3-E22/23f/f mice</td>
			<td>JAX</td>
			<td>Stock No: 029797</td>
			<td>B6.129-Ank3tm2.1Bnt/J;</td>
		</tr>
		<tr>
			<td>B27 serum-free supplement</td>
			<td>Thermo Fisher Scientific</td>
			<td>A3582801</td>
			<td></td>
		</tr>
		<tr>
			<td>Boric acid</td>
			<td>Sigma-Aldrich</td>
			<td>B6768</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell strainer with 70-mm mesh</td>
			<td>BD Biosciences</td>
			<td>352350</td>
			<td></td>
		</tr>
		<tr>
			<td>Ceramic coverslip-staining rack</td>
			<td>Thomas Scientific</td>
			<td>8542E40</td>
			<td></td>
		</tr>
		<tr>
			<td>Cre-BFP</td>
			<td>Addgene</td>
			<td>#128174</td>
			<td></td>
		</tr>
		<tr>
			<td>D-Glucose</td>
			<td>Sigma-Aldrich</td>
			<td>G7021</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM</td>
			<td>Thermo Fisher Scientific</td>
			<td>11995073</td>
			<td></td>
		</tr>
		<tr>
			<td>GlutaMAX-I supplement</td>
			<td>Thermo Fisher Scientific</td>
			<td>A1286001</td>
			<td></td>
		</tr>
		<tr>
			<td>Lipofectamine 2000</td>
			<td>Thermo Fisher Scientific</td>
			<td>11668030</td>
			<td></td>
		</tr>
		<tr>
			<td>MEM with Earle&#8217;s salts and L-glutamine</td>
			<td>Thermo Fisher Scientific</td>
			<td>11095-080</td>
			<td></td>
		</tr>
		<tr>
			<td>Neurobasal Medium</td>
			<td>Thermo Fisher Scientific</td>
			<td>21103-049</td>
			<td></td>
		</tr>
		<tr>
			<td>Nitric acid 70%</td>
			<td>Sigma-Aldrich</td>
			<td>225711</td>
			<td></td>
		</tr>
		<tr>
			<td>Opti-MEM I Reduced Serum Medium</td>
			<td>Thermo Fisher Scientific</td>
			<td>31985062</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraformaldehyde</td>
			<td>Sigma-Aldrich</td>
			<td>P6148</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin-streptomycin</td>
			<td>Thermo Fisher Scientific</td>
			<td>15140122</td>
			<td></td>
		</tr>
		<tr>
			<td>Poly-L-lysine hydrochloride</td>
			<td>Sigma-Aldrich</td>
			<td>26124-78-7</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium hydroxide</td>
			<td>Sigma-Aldrich</td>
			<td>1310-58-3</td>
			<td></td>
		</tr>
	</tbody>
</table>

use of primary cultured hippocampal neurons to study the assembly of axon initial segments

Neuronal axon initial segments (AIS) are sites of initiation of action potentials and have been extensively studied for their molecular structure, assembly and activity-dependent plasticity. Giant ankyrin-G, the master organizer of AIS, directly associates with membrane-spanning voltage gated sodium (VSVG) and potassium channels (KCNQ2/3), as well as 186 kDa neurofascin, a L1CAM cell adhesion molecule. Giant ankyrin-G also binds to and recruits cytoplasmic AIS molecules including beta-4-spectrin, and the microtubule-binding proteins, EB1/EB3 and Ndel1. Giant ankyrin-G is sufficient to rescue AIS formation in ankyrin-G deficient neurons. Ankyrin-G also includes a smaller 190 kDa isoform located at dendritic spines instead of the AIS, which is incapable of targeting to the AIS or rescuing the AIS in ankyrin-G-deficient neurons. Here, we described a protocol using cultured hippocampal neurons from ANK3-E22/23-flox mice, which, when transfected with Cre-BFP exhibit loss of all isoform of ankyrin-G and impair the formation of AIS. Combined a modified Banker glia/neuron co-culture system, we developed a method to transfect ankyrin-G null neurons with a 480 kDa ankyrin-G-GFP plasmid, which is sufficient to rescue the formation of AIS. We further employ a quantification method, developed by Salzer and colleagues to deal with variation in AIS distance from the neuronal cell bodies that occurs in hippocampal neuron cultures. This protocol allows quantitative studies of the de novo assembly and dynamic behavior of AIS.

A complete set of experiment should include Cre-BFP only transfection as negative control, Cre-BFP plus 480 kDa ankyrin-G co-transfection as positive control and a non-transfected condition as technique control. In Cre-BFP only control, transfected neurons lack the accumulation of AIS markers, including ankyrin-G (ankG), beta4-spectrin (&#946;4), neurofascin (Nf) and voltage gated sodium channels (VSVG) (Figure 4A)16. In contrast, Cre and 480 kDa ankyrin-G co-transfec...

Watch this Scientific Journal Video about Use of Primary Cultured Hippocampal Neurons to Study the Assembly of Axon Initial Segments at JoVE.com

Use of Primary Cultured Hippocampal Neurons to Study the Assembly of Axon Initial Segments

Here, we described a protocol to quantitatively study the assembly and structure of the axon initial segments (AIS) of hippocampal neurons that lack pre-assembled AIS due to the absence of a giant ankyrin-G.

Neuronal axon initial segments (AIS) are sites of initiation of action potentials and have been extensively studied for their molecular structure, ...

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JoVE Journal

Neuroscience

4.9K Views.  Xi'an Jiaotong University. Here, we described a protocol to quantitatively study the assembly and structure of the axon initial segments (AIS) of hippocampal neurons that lack pre-assembled AIS due to the absence of a giant ankyrin-G.

Video: Use of Primary Cultured Hippocampal Neurons to Study the Assembly of Axon Initial Segments

Genetic Study of Axon Regeneration with Cultured Adult Dorsal Root Ganglion Neurons

It is well known that mature neurons in the central nervous system (CNS) cannot regenerate their axons after injuries due to diminished intrinsic ability to support axon growth and a hostile environment in the mature CNS1,2. In contrast, mature neurons in the peripheral nervous system (PNS) regenerate readily after injuries3. Adult dorsal root ganglion (DRG) neurons are well known to regenerate robustly after peripheral nerve injuries. Each DRG neuron grows one axon from the cell soma, which branches into two axonal branches: a peripheral branch innervating peripheral targets and a central branch extending into the spinal cord. Injury of the DRG peripheral axons results in substantial axon regeneration, whereas central axons in the spinal cord regenerate poorly after the injury. However, if the peripheral axonal injury occurs prior to the spinal cord injury (a process called the conditioning lesion), regeneration of central axons is greatly improved4. Moreover, the central axons of DRG neurons share the same hostile environment as descending corticospinal axons in the spinal cord. Together, it is hypothesized that the molecular mechanisms controlling axon regeneration of adult DRG neurons can be harnessed to enhance CNS axon regeneration. As a result, adult DRG neurons are now widely used as a model system to study regenerative axon growth5-7.
Here we describe a method of adult DRG neuron culture that can be used for genetic study of axon regeneration in vitro. In this model adult DRG neurons are genetically manipulated via electroporation-mediated gene transfection6,8. By transfecting neurons with DNA plasmid or si/shRNA, this approach enables both gain- and loss-of-function experiments to investigate the role of any gene-of-interest in axon growth from adult DRG neurons. When neurons are transfected with si/shRNA, the targeted endogenous protein is usually depleted after 3-4 days in culture, during which time robust axon growth has already occurred, making the loss-of-function studies less effective. To solve this problem, the method described here includes a re-suspension and re-plating step after transfection, which allows axons to re-grow from neurons in the absence of the targeted protein. Finally, we provide an example of using this in vitro model to study the role of an axon regeneration-associated gene, c-Jun, in mediating axon growth from adult DRG neurons9.

An in vitro model for genetic study of axon regeneration using cultured adult mouse dorsal root ganglion neurons is described. The method includes a re-suspension/re-plating step to allow axon re-growth from neurons undergoing genetic manipulation. This approach is especially useful for loss-of-function studies of axon regeneration using RNAi-based protein knockdown.

It is well known that mature neurons in the central nervous system (CNS) cannot regenerate their axons after injuries due to diminished intrinsic ability ...

Imaging pHluorin-tagged Receptor Insertion to the Plasma Membrane in Primary Cultured Mouse Neurons

A better understanding of the mechanisms governing receptor trafficking between the plasma membrane (PM) and intracellular compartments requires an experimental approach with excellent spatial and temporal resolutions. Moreover, such an approach must also have the ability to distinguish receptors localized on the PM from those in intracellular compartments. Most importantly, detecting receptors in a single vesicle requires outstanding detection sensitivity, since each vesicle carries only a small number of receptors. Standard approaches for examining receptor trafficking include surface biotinylation followed by biochemical detection, which lacks both the necessary spatial and temporal resolutions; and fluorescence microscopy examination of immunolabeled surface receptors, which requires chemical fixation of cells and therefore lacks sufficient temporal resolution1-6 . To overcome these limitations, we and others have developed and employed a new strategy that enables visualization of the dynamic insertion of receptors into the PM with excellent spatial and temporal resolutions 7-17 . The approach includes tagging of a pH-sensitive GFP, the superecliptic pHluorin 18, to the N-terminal extracellular domain of the receptors. Superecliptic pHluorin has the unique property of being fluorescent at neutral pH and non-fluorescent at acidic pH (pH &lt; 6.0). Therefore, the tagged receptors are non-fluorescent when within the acidic lumen of intracellular trafficking vesicles or endosomal compartments, and they become readily visualized only when exposed to the extracellular neutral pH environment, on the outer surface of the PM. Our strategy consequently allows us to distinguish PM surface receptors from those within intracellular trafficking vesicles. To attain sufficient spatial and temporal resolutions, as well as the sensitivity required to study dynamic trafficking of receptors, we employed total internal reflection fluorescent microscopy (TIRFM), which enabled us to achieve the optimal spatial resolution of optical imaging (~170 nm), the temporal resolution of video-rate microscopy (30 frames/sec), and the sensitivity to detect fluorescence of a single GFP molecule. By imaging pHluorin-tagged receptors under TIRFM, we were able to directly visualize individual receptor insertion events into the PM in cultured neurons. This imaging approach can potentially be applied to any membrane protein with an extracellular domain that could be labeled with superecliptic pHluorin, and will allow dissection of the key detailed mechanisms governing insertion of different membrane proteins (receptors, ion channels, transporters, etc.) to the PM.

By tagging the extracellular domains of membrane receptors with superecliptic pHluorin, and by imaging these fusion receptors in cultured mouse neurons, we can directly visualize individual vesicular insertion events of the receptors to the plasma membrane. This technique will be instrumental in elucidating the molecular mechanisms governing receptor insertion to the plasma membrane.

A better understanding of the mechanisms governing receptor trafficking between the plasma membrane (PM) and intracellular compartments requires an ...

Detection of Protein Palmitoylation in Cultured Hippocampal Neurons by Immunoprecipitation and Acyl-Biotin Exchange (ABE)

Palmitoylation is a post-translational lipid modification involving the attachment of a 16-carbon saturated fatty acid, palmitate, to cysteine residues of substrate proteins through a labile thioester bond [reviewed in1]. Palmitoylation of a substrate protein increases its hydrophobicity, and typically facilitates its trafficking toward cellular membranes. Recent studies have shown palmitoylation to be one of the most common lipid modifications in neurons1, 2, suggesting that palmitate turnover is an important mechanism by which these cells regulate the targeting and trafficking of proteins. The identification and detection of palmitoylated substrates can therefore better our understanding of protein trafficking in neurons.
Detection of protein palmitoylation in the past has been technically hindered due to the lack of a consensus sequence among substrate proteins, and the reliance on metabolic labeling of palmitoyl-proteins with 3H-palmitate, a time-consuming biochemical assay with low sensitivity. Development of the Acyl-Biotin Exchange (ABE) assay enables more rapid and high sensitivity detection of palmitoylated proteins2-4, and is optimal for measuring the dynamic turnover of palmitate on neuronal proteins. The ABE assay is comprised of three biochemical steps (Figure 1): 1) irreversible blockade of unmodified cysteine thiol groups using N-ethylmaliemide (NEM), 2) specific cleavage and unmasking of the palmitoylated cysteine's thiol group by hydroxylamine (HAM), and 3) selective labeling of the palmitoylated cysteine using a thiol-reactive biotinylation reagent, biotin-BMCC. Purification of the thiol-biotinylated proteins following the ABE steps has differed, depending on the overall goal of the experiment.
Here, we describe a method to purify a palmitoylated protein of interest in primary hippocampal neurons by an initial immunoprecipitation (IP) step using an antibody directed against the protein, followed by the ABE assay and western blotting to directly measure palmitoylation levels of that protein, which is termed the IP-ABE assay. Low-density cultures of embryonic rat hippocampal neurons have been widely used to study the localization, function, and trafficking of neuronal proteins, making them ideally suited for studying neuronal protein palmitoylation using the IP-ABE assay. The IP-ABE assay mainly requires standard IP and western blotting reagents, and is only limited by the availability of antibodies against the target substrate. This assay can easily be adapted for the purification and detection of transfected palmitoylated proteins in heterologous cell cultures, primary neuronal cultures derived from various brain tissues of both mouse and rat, and even primary brain tissue itself.

Detection of Protein Palmitoylation in Cultured Hippocampal Neurons by Immunoprecipitation and Acyl-Biotin Exchange ABE

The reversible addition of palmitate to proteins is an important regulator of intracellular protein trafficking. This is of particular interest in neurons where many synaptic proteins are palmitoylated. We utilize a simple biochemical method to detect palmitoylated proteins in cultured neurons, which can be adapted for multiple cell types and tissues.

Palmitoylation is a post-translational lipid  modification involving the attachment of a 16-carbon saturated fatty acid,  palmitate, to cysteine residues ...

Calcium Phosphate Transfection of Primary Hippocampal Neurons

Calcium phosphate precipitation is a convenient and economical method for transfection of cultured cells. With optimization, it is possible to use this method on hard-to-transfect cells like primary neurons. Here we describe our detailed protocol for calcium phosphate transfection of hippocampal neurons cocultured with astroglial cells.

Calcium phosphate precipitation is a convenient and economical method for transfection of cultured cells. With optimization, it is possible to use this ...

Imaging Dendritic Spines of Rat Primary Hippocampal Neurons using Structured Illumination Microscopy

Dendritic spines are protrusions emerging from the dendrite of a neuron and represent the primary postsynaptic targets of excitatory inputs in the brain. Technological advances have identified these structures as key elements in neuron connectivity and synaptic plasticity. The quantitative analysis of spine morphology using light microscopy remains an essential problem due to technical limitations associated with light's intrinsic refraction limit. Dendritic spines can be readily identified by confocal laser-scanning fluorescence microscopy. However, measuring subtle changes in the shape and size of spines is difficult because spine dimensions other than length are usually smaller than conventional optical resolution fixed by light microscopy's theoretical resolution limit of 200 nm.
Several recently developed super resolution techniques have been used to image cellular structures smaller than the 200 nm, including dendritic spines. These techniques are based on classical far-field operations and therefore allow the use of existing sample preparation methods and to image beyond the surface of a specimen. Described here is a working protocol to apply super resolution structured illumination microscopy (SIM) to the imaging of dendritic spines in primary hippocampal neuron cultures. Possible applications of SIM overlap with those of confocal microscopy. However, the two techniques present different applicability. SIM offers higher effective lateral resolution, while confocal microscopy, due to the usage of a physical pinhole, achieves resolution improvement at the expense of removal of out of focus light. In this protocol, primary neurons are cultured on glass coverslips using a standard protocol, transfected with DNA plasmids encoding fluorescent proteins and imaged using SIM. The whole protocol described herein takes approximately 2 weeks, because dendritic spines are imaged after 16-17 days in vitro, when dendritic development is optimal. After completion of the protocol, dendritic spines can be reconstructed in 3D from series of SIM image stacks using specialized software.

This article describes a working protocol to image dendritic spines from hippocampal neurons in vitro using Structured Illumination Microscopy (SIM). Super-resolution microscopy using SIM provides image resolution significantly beyond the light diffraction limit in all three spatial dimensions, allowing the imaging of individual dendritic spines with improved detail.

Dendritic spines are protrusions emerging from the dendrite of a neuron and represent the primary postsynaptic targets of excitatory inputs in the brain. ...

Stripe Assay to Study the Attractive or Repulsive Activity of a Protein Substrate Using Dissociated Hippocampal Neurons

Growing axons develop a highly motile structure at their tip, termed the growth cone. The growth cone contacts extracellular environmental cues to navigate axonal growth. Netrin, slit, semaphorin, and ephrins are known guidance molecules that can attract or repel axons upon binding to receptors and co-receptors on the axon. The activated receptors initiate various signaling molecules in the growth cone that alter the structure and movement of the neuron. Here, we describe the detailed protocol for a stripe assay to assess the ability of a guidance molecule to attract or repel neurons. In this method, dissociated hippocampal neurons from E15.5 mice are cultured on laminin-coated dishes processed with alternating stripes of ectodomain of fibronectin and leucine-rich transmembrane protein-2 (FLRT2) and control immunoglobulin G (IgG) fragment crystallizable region (Fc) protein. Both axons and cell bodies were strongly repelled from the FLRT2-coated stripe regions after 24 h of culture. Immunostaining with tau1 showed that ~90% of the neurons were distributed on the Fc-coated stripes compared to the FLRT2-Fc-coated stripes (~10%). This result indicates that FLRT2 has a strong repulsive effect on these neurons. This powerful method is applicable not only for primary cultured neurons but also for a variety of other cells, such as neuroblasts.

Axon guidance molecules regulate neuronal migration and targeted growth-cone navigation. We present a powerful method, the stripe assay, to assess the ability of guidance molecules to attract or repulse neurons. In this protocol, we demonstrate the stripe assay by showing FLRT2's ability to repel cultured hippocampal neurons.

Growing axons develop a highly motile structure at their tip, termed the growth cone. The growth cone contacts extracellular environmental cues to ...

Measuring Synaptic Vesicle Endocytosis in Cultured Hippocampal Neurons

During endocytosis, fused synaptic vesicles are retrieved at nerve terminals, allowing for vesicle recycling and thus the maintenance of synaptic transmission during repetitive nerve firing. Impaired endocytosis in pathological conditions leads to decreases in synaptic strength and brain functions. Here, we describe methods used to measure synaptic vesicle endocytosis at the mammalian hippocampal synapse in neuronal culture. We monitored synaptic vesicle protein endocytosis by fusing a synaptic vesicular membrane protein, including synaptophysin and VAMP2/synaptobrevin, at the vesicular lumenal side, with pHluorin, a pH-sensitive green fluorescent protein that increases its fluorescence intensity as the pH increases. During exocytosis, vesicular lumen pH increases, whereas during endocytosis vesicular lumen pH is re-acidified. Thus, an increase of pHluorin fluorescence intensity indicates fusion, whereas a decrease indicates endocytosis of the labelled synaptic vesicle protein. In addition to using the pHluorin imaging method to record endocytosis, we monitored vesicular membrane endocytosis by electron microscopy (EM) measurements of Horseradish peroxidase (HRP) uptake by vesicles. Finally, we monitored the formation of nerve terminal membrane pits at various times after high potassium-induced depolarization. The time course of HRP uptake and membrane pit formation indicates the time course of endocytosis.

Synaptic vesicle endocytosis is detected by light microscopy of pHluorin fused with synaptic vesicle protein and by electron microscopy of vesicle uptake.

During endocytosis, fused synaptic vesicles are retrieved at nerve terminals, allowing for vesicle recycling and thus the maintenance of synaptic ...

Use of Pre-Assembled Plastic Microfluidic Chips for Compartmentalizing Primary Murine Neurons

Microfabricated methods to compartmentalize neurons have become essential tools for many neuroscientists. This protocol describes the use of a commercially available pre-assembled plastic chip for compartmentalizing cultured primary rat hippocampal neurons. These plastic chips, contained within the footprint of a standard microscope slide, are compatible with high-resolution, live, and fluorescence imaging. This protocol demonstrates how to retrograde label neurons via isolated axons using a modified rabies virus encoding a fluorescent protein, create isolated microenvironments within one compartment, and perform axotomy and immunocytochemistry on-chip. Neurons are cultured for &gt;3 weeks within the plastic chips, illustrating the compatibility of these chips for long-term neuronal cultures.

This protocol describes the use of plastic chips to culture and compartmentalize primary murine neurons. These chips are preassembled, user-friendly, and compatible with high-resolution, live, and fluorescence imaging. This protocol describes how to plate rat hippocampal neurons within these chips and perform fluidic isolation, axotomy and immunostaining.

Microfabricated methods to compartmentalize neurons have become essential tools for many neuroscientists. This protocol describes the use of a ...

An Antibody Feeding Approach to Study Glutamate Receptor Trafficking in Dissociated Primary Hippocampal Cultures

Cellular responses to external stimuli heavily rely on the set of receptors expressed at the cell surface at a given moment. Accordingly, the population of surface-expressed receptors is constantly adapting and subject to strict mechanisms of regulation. The paradigmatic example and one of the most studied trafficking events in biology is the regulated control of the synaptic expression of glutamate receptors (GluRs). GluRs mediate the vast majority of excitatory neurotransmission in the central nervous system and control physiological activity-dependent functional and structural changes at the synaptic and neuronal levels (e.g., synaptic plasticity). Modifications in the number, location, and subunit composition of surface expressed GluRs deeply affect neuronal function and, in fact, alterations in these factors are associated with different neuropathies. Presented here is a method to study GluR trafficking in dissociated hippocampal primary neurons. An &#34;antibody-feeding&#34; approach is used to differentially visualize GluR populations expressed at the surface and internal membranes. By labeling surface receptors on live cells and fixing them at different times to allow for receptors endocytosis and/or recycling, these trafficking processes can be evaluated and selectively studied. This is a versatile protocol that can be used in combination with pharmacological approaches or overexpression of altered receptors to gain valuable information about stimuli and molecular mechanisms affecting GluR trafficking. Similarly, it can be easily adapted to study other receptors or surface expressed proteins.

This article presents a method to study glutamate receptor (GluR) trafficking in dissociated primary hippocampal cultures. Using an antibody-feeding approach to label endogenous or overexpressed receptors in combination with pharmacological approaches, this method allows for the identification of molecular mechanisms regulating GluR surface expression by modulating internalization or recycling processes.

Cellular responses to external stimuli heavily rely on the set of receptors expressed at the cell surface at a given moment. Accordingly, the population ...

Super-Resolution Imaging to Study Co-Localization of Proteins and Synaptic Markers in Primary Neurons

Synapses are the functional elements of neurons and their defects or losses are at the basis of several neurodegenerative and neurological disorders. Imaging studies are widely used to investigate their function and plasticity in physiological and pathological conditions. Because of their size and structure, localization studies of proteins require high-resolution imaging techniques. In this protocol, we describe a procedure to study in primary neurons the co-localization of target proteins with synaptic markers at a super-resolution level using structured illumination microscopy (SIM). SIM is a patterned-light illumination technique that doubles the spatial resolution of wide-field microscopy, reaching a detail of around 100 nm. The protocol indicates the required controls and settings for robust co-localization studies and an overview of the statistical methods to analyze the imaging data properly.

This protocol shows how to employ super-resolution microscopy to study protein co-localization in primary neuronal cultures.

Synapses are the functional elements of neurons and their defects or losses are at the basis of several neurodegenerative and neurological disorders. ...