We thank Shigeo Okabe and Hitomi Matsuno for the low-density culture of hippocampal neurons, Masayoshi Mishina for TLCN-deficient mice, Sachiko Mitsui and Momoko Shiozaki for technical assistance, and members of the Yoshihara laboratory for helpful discussions. This work was supported by JSPS KAKENHI Grant Nos. JP20700307, JP22700354, and JP24500392 and MEXT KAKENHI Grant Nos. JP23123525 to YF and JP20022046, JP18H04683, and JP18H05146 to YY.

All methods described here have been approved by the Institutional Animal Care and Use Committee of RIKEN Wako.
1. Culture of Hippocampal Neurons
<ol>
	<li>Preparation of culture medium
	<ol>
		<li>Preparation of 200x Vitamin mix. Dissolve 100 mg of D-pantothenic acid hemicalcium salt, 100 mg of choline chloride, 100 mg of folic acid, 180 mg of i-inositol, 100 mg of niacinamide, 100 mg of pyridoxal HCl, and 100 mg of thiamine HCl in 500 mL of ultrapure water using a magnetic stirrer. The solution is not completely dissolved. Carefully mix, aliquot in 50 mL tubes and store at -20 &#176;C.</li>
		<li>Preparation of Riboflavin solution. Dissolve 100 mg of Riboflavin in 500 mL of ultrapure water using a magnetic stirrer. The solution is not completely dissolved. Carefully mix, aliquot in 50 mL tubes and store at -20 &#176;C.</li>
		<li>Preparation of 1 M CaCl2. Dissolve 7.35 g of CaCl2&#183;2H2O in 50 mL of ultrapure water using a magnetic stirrer.</li>
		<li>Preparation of Minimum essential medium (MEM). Dissolve 400 mg of KCl, 6800 mg of NaCl, 2,200 mg of NaHCO3, 158 mg of NaH2PO4&#183;2H2O, 7000 mg of D-glucose, and 200 mg of MgSO4-7H2O in 950 mL of ultrapure water using a magnetic stirrer.</li>
		<li>Titrate 1.8 mL of 1 M CaCl2 to the MEM in a drop-by-drop manner using a 1 mL pipet with a constant agitation on a magnetic stirrer. Adjust the pH of the MEM to pH 7.25 with 1 mol/L HCl.</li>
		<li>Add 5 mL of 200x Vitamin mix and 200 &#956;L of Riboflavin solution to the MEM. Adjust the volume of the solution to 1,000 mL with ultrapure water. Filter the solution using a 0.22 &#956;m filter system and store it at 4 &#176;C.</li>
		<li>Preparation of 10x DNase-I stock solutions. Dissolve 100 mg of DNase-I in 12.5 mL of Hanks&#39; Balanced Salt Solution (HBSS), filter through a 0.22 &#956;m filter, aliquot in 1.5 mL tubes, and store the tubes at -20 &#176;C.</li>
		<li>Preparation of cytosine &#946;-D-arabinofuranoside (Ara-C) stock solution. Dissolve 25 mg of Ara-C in 8.93 mL of ultrapure water (final concentration of 10 mM), filter through a 0.22 &#956;m filter, aliquot in 1.5 mL tubes and store at -20 &#176;C</li>
		<li>Preparation of Plating medium. Mix 1 mL of MEM amino acid solution, 750 &#956;L of 1 M HEPES, 1 mL of B27, 125 &#956;L of 200 mM glutamine, 250 &#956;L of penicillin/streptomycin, 2.5 mL of fetal bovine serum (FBS), and 44.375 mL of MEM in a 50 mL tube.</li>
		<li>Preparation of Stop medium. Mix 1 mL of MEM amino acid solution, 750 &#956;L of 1 M HEPES, 5 mL of FBS (final 10%), and 43.25 mL of MEM in a 50 mL tube.</li>
	</ol>
	</li>
	<li>Preparation of poly-L-Lysine-coated dishes
	<ol>
		<li>Coat 35 mm plastic cell culture dishes with 0.2 mg/mL of poly-L-lysine hydrobromide for 1 day at 25 &#176;C. 
		NOTE: Poly-L-lysine should not be used instead of poly-L-lysine hydrobromide.</li>
		<li>Wash the dishes with 2 mL of ultrapure water 3 times. Incubate the dishes with 1.5 mL of Stop medium at 25 &#176;C until use.</li>
	</ol>
	</li>
	<li>Dissection of hippocampal neurons from mouse embryo
	<ol>
		<li>Tissue source of hippocampal neurons. Dissect the hippocampus from wild-type and TLCN-deficient C57BL6/J mice on the embryonic days 16-17 according to the method of Lu et al.19.</li>
		<li>Incubate dissected hippocampi in 0.25% trypsin and 1x DNaseI in HBSS containing 15 mM HEPES, pH 7.2 for 15 min at 37 &#176;C with agitation every 3 min. Remove the solution. Incubate the hippocampi in 10 mL of STOP medium to inactivate trypsin at 4 &#176;C for 5 min.</li>
		<li>Move the hippocampi into 10 mL of fresh STOP medium and incubate at 4 &#176;C for 5 min. Move the hippocampi into 10 mL of fresh STOP medium and incubate at 4 &#176;C for another 5 min. Move the hippocampi into 900 &#956;L of STOP medium and 100 &#956;L of 10x DNaseI in a 15 mL tube. Dissociate the hippocampi into isolated neurons by pipetting 20 times using a 1 mL pipet. 
		NOTE: The tip of the 1 mL pipet slightly touches the bottom of the 15 mL tube during dissociation of the hippocampi.</li>
		<li>Add 9 mL of plating medium, and filter through a 70 &#956;m cell strainer into a 50 mL tube. Count the number of cells using a hemocytometer and adjust to 3.5 x 104 cells/mL in plating medium.</li>
		<li>Aspirate STOP medium from poly-L-lysine-coated dishes. Plate the cells on poly-L-Lysine-coated dishes at 7 x 104 cells/dish (2 mL/dish).</li>
		<li>After 60-64 h of incubation under 5% CO2 at 37 &#176;C, add 2 &#956;L of Ara-C stock solution (final 10 &#956;M) to the neurons, and shake the dish slowly. Keep the culture dishes in a humidified box without changing the culture medium under 5% CO2 at 37 &#176;C.</li>
	</ol>
	</li>
</ol>
2. Purification of Dendritic Filopodia-rich Fraction
<ol>
	<li>After 13 days in vitro (DIV), add magnetic polystyrene microbeads (3 x 106 particles/dish) to 20 dishes containing the cultured neurons. After 1 day, wash the neurons in 1 mL of PBS with agitation 3 times to remove the medium and unbound microbeads. After removing PBS, lyse the neurons with 500 &#956;L/dish of lysis buffer (PBS containing 0.01% Triton X-100, EDTA-free protease inhibitor cocktail, and phosphatase inhibitor cocktail).</li>
	<li>Collect the lysate with a cell scraper and move the lysate to low protein-binding microtubes (10 tubes). Set the tubes on a magnet separator and wait for 1 min. Collect the supernatant and use it as the unbound fraction for silver staining and Western blot analysis.</li>
	<li>Transfer the beads to a new low-protein-binding microtube, set on a magnetic separator, and completely remove the supernatant. Add 500 &#956;L of lysis buffer and wash the beads using a vortex mixer for 15 s. Set the tube on a magnet separator, wait for 1 min, remove the supernatant, and add 500 &#956;L of lysis buffer. Repeat the washing of the beads 10 times and remove the supernatant.</li>
	<li>Elute proteins bound to the beads (the bound fraction) by the addition of 50 &#956;L of 1x SDS sample buffer (62.5 mM Tris HCl, pH 6.8, 2.5% SDS, and 10% glycerol) and boil the tube at 98 &#176;C for 5 min. Centrifuge the tube at 860&#160;x g for 10 s and set the tube on a magnetic separator for 1 min. Collect the supernatant and use it as the bound fraction. 
	NOTE: The protocol can be paused here.</li>
	<li>Measure protein concentrations of the unbound and bound fractions by the BCA protein assay. Visualize protein solutions with bromophenol blue and adjust the concentration to 5 ng/&#956;L for SDS-PAGE.</li>
</ol>
3. Silver Staining and Western Blot Analysis
<ol>
	<li>Separate the bound and unbound fractions (50 ng) by SDS-PAGE using a 5-20% gradient gel. Silver-stain the gel.</li>
	<li>Western blot using anti-TLCN-C (1/3,000), anti-bovine vitronectin (1/5,000), anti-actin (1/1,000), and anti-&#945;-tubulin (1/1,000) as primary antibodies and HRP-conjugated goat anti-rabbit IgG (1/5,000) as the secondary antibody. Visualize the antigens using chemiluminescent Western Blotting Detection Reagent and a chemiluminescence imager.</li>
</ol>

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J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evidence+for+a+role+of+dendritic+filopodia+in+synaptogenesis+and+spine+formation.">Evidence for a role of dendritic filopodia in synaptogenesis and spine formation.</a> Neuron. 17 (1), 91-102 (1996).</li><li>Lohmann, C., Bonhoeffer, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+role+for+local+calcium+signaling+in+rapid+synaptic+partner+selection+by+dendritic+filopodia.">A role for local calcium signaling in rapid synaptic partner selection by dendritic filopodia.</a> Neuron. 59 (2), 253-260 (2008).</li><li>Yoshihara, Y., De Roo, M., Muller, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dendritic+spine+formation+and+stabilization.">Dendritic spine formation and stabilization.</a> Current Opinion in Neurobiology. 19 (2), 146-153 (2009).</li><li>Bayes, 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=Comparative+study+of+human+and+mouse+postsynaptic+proteomes+finds+high+compositional+conservation+and+abundance+differences+for+key+synaptic+proteins.">Comparative study of human and mouse postsynaptic proteomes finds high compositional conservation and abundance differences for key synaptic proteins.</a> PLoS One. 7 (10), e46683 (2012).</li><li>Bayes, 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=Characterization+of+the+proteome,+diseases+and+evolution+of+the+human+postsynaptic+density.">Characterization of the proteome, diseases and evolution of the human postsynaptic density.</a> Nature Neuroscience. 14 (1), 19-21 (2011).</li><li>Furutani, Y., 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=Interaction+between+telencephalin+and+ERM+family+proteins+mediates+dendritic+filopodia+formation.">Interaction between telencephalin and ERM family proteins mediates dendritic filopodia formation.</a> Journal of Neuroscience. 27 (33), 8866-8876 (2007).</li><li>Mao, Y. 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The authors have nothing to disclose.

We developed a purification method for the dendritic filopodia-rich fraction using affinity between the cell adhesion molecule TLCN and the extracellular matrix protein vitronectin. Compared to PSD fraction, it could be possible to identify the synaptic proteins acting on the immature synapse from the dendritic filopodia-rich fraction. Thus, the constituents of the dendritic filopodia-rich fraction are different from those of the PSD fraction by 74%. Different from PSD fraction, we used cultured hippocampal neurons to actively form phagocytic cups, and the cells need to be alive. To form the phagocytic cup, we used the interaction between TLCN and vitronectin. TLCN expression is limited in the telencephalon. Thus, we cannot use cultured neurons derived from the cerebellar. However, if we coat the beads with different proteins, this activity-dependent purification method could be applied to cerebellar neurons. For example, when the N-terminal domain of glutamate receptor delta2-coated microbeads are applied to cerebellar granule cells, presynaptic neurexin and cbln1 were identified from the binding proteins. Therefore, this activity-dependent method could be used, if the coating proteins are changed. Since the access of vitronectin-coated microbeads is limited to the brain slice and brain tissue, phagocytic cups are not formed efficiently. Thus, future tasks include developing the purification method of the dendritic filopodia-rich fraction from brain slice and tissue.
In this protocol, low-density culture condition is used for hippocampal neurons, and the growth of glial cells are inhibited by the addition of Ara-C10,20,21. Hippocampal neurons are cultured in MEM prepared by ourselves, but not in neurobasal medium, which is widely used for the culture of hippocampal neurons. Hippocampal neurons often die by 14 DIV when cultured on neurobasal medium, which indicates that the neurobasal medium is not suitable for our low-density culture condition. In addition, an important aspect of low-density culture is coating the dish with poly-L-lysine hydrobromide, which cannot be replaced with poly-L-lysine.
To obtain sufficient amount of proteins from the dendritic filopodia-rich fraction, the numbers of hippocampal neurons and magnetic microbeads are important factors. For immunostaining dendritic filopodia, hippocampal neurons were plated on a 35 mm dish at 5.6 x&#215; 104 cells/dish, while the neurons were plated at 7.0 x 104 cells/dish for purification of the dendritic filopodia-rich fraction. At 14 DIV, almost no hippocampal neurons overlapped at 5.6 x 104 cells/dish for immunostaining, while many of hippocampal neurons partly overlapped with the other neurons at 7.0 x 104 cells/dish for purification of the dendritic filopodia-rich fraction. However, dendritic filopodia were abundantly present at both densities of hippocampal neurons. High-density cultures of hippocampal neurons often mature faster than low-density cultured hippocampal neurons; thus, adjusting the density of hippocampal neurons to low-density culture is indispensable to obtain the dendritic filopodia-rich fraction. Microbeads were added at 1 x 106 microbeads/dish for immunostaining and at 3 x 106 microbeads/dish for purification of the dendritic filopodia-rich fraction. For purification of the fraction, once a sufficient amount of beads was added, the unbound beads were washed out from hippocampal neurons.
In this protocol, microbeads were automatically coated with VN, which is present in the culture medium. However, microbeads can be coated with recombinant VN and added to hippocampal neurons. Because VN is a very sticky protein, VN-coated microbeads easily form aggregates. Thus, VN-coated microbeads are sonicated and pipetted to dissociate from each other just before addition to hippocampal neurons.
We previously showed that VN-coated microbeads induces phosphor-ERM, PI(4,5)P2, and F-actin together with TLCN accumulation15. When the dendritic filopodia-rich fraction was analyzed by Western blotting, phospho-ERM was not detected by anti-phospho-ERM polyclonal antibody and was slightly detected by anti-ezrin and anti-moesin monoclonal antibodies. It appears that the sensitivity of the monoclonal antibodies was higher than the anti-phospho-ERM polyclonal antibody. In addition, ERM proteins were localized to almost all regions of the hippocampal neurons, but phospho-ERM proteins were only localized to the tip of the dendritic filopodia and the phagocytic cup. It is considered that the amount of phospho-ERM binding to TLCN is limited compared to the amount of nonphosphorylated ERM. Thus, detection of phospho-ERM in the dendritic filopodia-rich fraction appears to be difficult.
To detach the microbeads from the cell membrane, we used a weak detergent, 0.01% Triton X-100. TLCN is linked to actin filament through phospho-ERM in the dendritic filopodia and phagocytic cup structures. To purify proteins indirectly linked to TLCN through the actin filament, we used a weak detergent in this protocol. However, the concentration of Triton X-100 could be changed to a higher concentration depending on the purpose of the experiment.
Esselens et al. has shown that the phagocytic uptake of microbeads induced TLCN, PIP2, and F-actin accumulation in cultured hippocampal neurons17. According to our analysis via confocal microscopy after 24 h of incubation with microbeads, the microbeads were not completely taken up into the cytoplasm. TLCN and PIP2, which are localized to the cell membrane, were localized around beads, especially on the bottom of the microbeads. In addition, 319 proteins identified from the dendritic filopodia-rich fraction were analyzed using the KEGG pathway analysis. Phagocytosis and autophagy pathways were not detected, but cytoskeleton organization, exocytosis, actin-filament-based process, and microtubule-based process were significantly enriched in the fraction18.
The molecular mechanism of dendritic filopodia formation remains largely unknown. Analysis of the phagocytic cup structure could help understand the molecular constituents and dynamic functions of dendritic filopodia. It would be interesting to analyze the dendritic filopodia-rich fraction prepared from mouse models of neurodevelopmental and neuropsychiatric disorders.

Dendritic filopodia are thought to be precursors of spines. Actin filaments in the dendritic filopodia regulate their extension and retraction1,2,3. After contacting with an axon, selected dendritic filopodia begin their maturation into spines, and a synapse is formed4,5. Components of spines have been determined from comprehensive analysis of postsynaptic density fractions6,7, while components of dendritic filopodia remain largely unknown. It has been shown that telencephalin (TLCN), ERM, SynGAP, Ras, PI3 kinase, Akt, mTOR, polo-like kinase 2, CaMKII, syndecan-2, paralemin-1, ARF6, and EphB regulate dendritic filopodia formation5,8,9,10,11, while a method has not been developed for the comprehensive analysis of molecules present in the dendritic filopodia.
TLCN (ICAM-5) is specifically expressed by spiny neurons in the most rostral brain segment, the telencephalon12. TLCN has 9 Ig-like domains in its extracellular region, a transmembrane region, and a cytoplasmic tail13. TLCN binds to vitronectin (VN) and LFA-1 integrin in its extracellular region, to presenilin in its transmembrane region, and to phospho-ERM and &#945;-actinin in its cytoplasmic region5,8,14,15,16. TLCN binds to the actin cytoskeleton through phospho-ERM at the tips of dendritic filopodia and &#945;-actinin in spines and dendritic shafts8,16.
We showed that overexpression of TLCN enhanced dendritic filopodia formation and induced the reversion of spines to filopodia10. The constitutive active form of ezrin bound to the TLCN cytoplasmic region and enhanced dendritic filopodia formation8. Thus, TLCN regulates dendritic filopodia formation through actin-binding proteins. Esselens et al. demonstrated that microbeads induced TLCN accumulation on cultured neurons17. We showed that phagocytic cup structures were formed on neuronal dendrites around VN-coated microbeads in a TLCN-dependent manner15. Constituents of dendritic filopodia are similar to those of the phagocytic cup. It is difficult to collect dendritic filopodia, but it is relatively easier to collect the phagocytic cup using magnetic microbeads. Thus, we developed a method to purify the phagocytic cup instead of dendritic filopodia18. Here, we describe the purification method for the dendritic filopodia-rich fraction.

<table>
	<tbody>
		<tr>
			<td>1 M HEPES</td>
			<td>Gibco</td>
			<td>15630-080</td>
			<td></td>
		</tr>
		<tr>
			<td>1.7 ml Low Binding MCT</td>
			<td>Sorenson BioScience</td>
			<td>39640T</td>
			<td></td>
		</tr>
		<tr>
			<td>200 mM L-Glutamine</td>
			<td>Gibco</td>
			<td>2530149</td>
			<td></td>
		</tr>
		<tr>
			<td>35-mm plastic cell culture dishes</td>
			<td>Corning</td>
			<td>430165</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-actin</td>
			<td>Sigma-Aldrich</td>
			<td>A-5060</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-alpha-Actinin</td>
			<td>Sigma-Aldrich</td>
			<td>A-5044</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-alpha-tubulin</td>
			<td>Sigma-Aldrich</td>
			<td>T-9026</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-Ezrin</td>
			<td>Sigma-Aldrich</td>
			<td>clone3C12, SAB4200806</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-Galphaq</td>
			<td>Santacruz</td>
			<td>sc-393</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-MAP2</td>
			<td>Chemicon</td>
			<td>clone AP20, MAB3418</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-Moesin</td>
			<td>Sigma-Aldrich</td>
			<td>clone 38/87, M7060</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-PLCbeta1</td>
			<td>Santacuz</td>
			<td>sc-5291</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-PSD95</td>
			<td>MA2</td>
			<td>ABR</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-Spectrin beta</td>
			<td>Chemicon</td>
			<td>MAB1622</td>
			<td></td>
		</tr>
		<tr>
			<td>B27</td>
			<td>Gibco</td>
			<td>0080085SA</td>
			<td></td>
		</tr>
		<tr>
			<td>BCA protein assay kit</td>
			<td>Thermo</td>
			<td>23227</td>
			<td></td>
		</tr>
		<tr>
			<td>Bromophenol blue</td>
			<td>Merck</td>
			<td>1.08122.0005</td>
			<td></td>
		</tr>
		<tr>
			<td>calcium chrolide, hydrous</td>
			<td>Wako</td>
			<td>038-19735</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell scraper</td>
			<td>Falcon</td>
			<td>353085</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell strainer</td>
			<td>Falcon</td>
			<td>352350</td>
			<td></td>
		</tr>
		<tr>
			<td>Choline chloride</td>
			<td>Sigma-Aldrich</td>
			<td>C7527</td>
			<td></td>
		</tr>
		<tr>
			<td>Complete EDTA free protease inhibitor cocktail</td>
			<td>Roche</td>
			<td>11873580001</td>
			<td></td>
		</tr>
		<tr>
			<td>Cytosine beta-D-arabinofuranoside</td>
			<td>Sigma-Aldrich</td>
			<td>C-6645</td>
			<td></td>
		</tr>
		<tr>
			<td>DNase-I</td>
			<td>Sigma-Aldrich</td>
			<td>DN-25</td>
			<td></td>
		</tr>
		<tr>
			<td>D-Pantothenic acid hemicalcium salt</td>
			<td>Sigma-Aldrich</td>
			<td>P5155</td>
			<td></td>
		</tr>
		<tr>
			<td>DynaMag-2 Magnet</td>
			<td>Thermo</td>
			<td>12321D</td>
			<td></td>
		</tr>
		<tr>
			<td>ECL Prime Western Blotting Detection Reagent</td>
			<td>GE</td>
			<td>RPN2232</td>
			<td></td>
		</tr>
		<tr>
			<td>e-PAGEL 5-20% SDS-PAGE gradient gel</td>
			<td>ATTO</td>
			<td>E-T520L</td>
			<td></td>
		</tr>
		<tr>
			<td>Folic acid</td>
			<td>Sigma-Aldrich</td>
			<td>F8758</td>
			<td></td>
		</tr>
		<tr>
			<td>HBSS</td>
			<td>Gibco</td>
			<td>14175095</td>
			<td></td>
		</tr>
		<tr>
			<td>HRP-conjugated anti-rabbit IgG</td>
			<td>Jackson ImmunoResearch</td>
			<td>111-035-144</td>
			<td></td>
		</tr>
		<tr>
			<td>i-Inositol</td>
			<td>Sigma-Aldrich</td>
			<td>I7508</td>
			<td></td>
		</tr>
		<tr>
			<td>LAS-1000 mini</td>
			<td>Fuji Film</td>
			<td>LAS-1000 mini</td>
			<td>For detection of luminescence from WB membrane</td>
		</tr>
		<tr>
			<td>Magnetic polystyrene microbeads</td>
			<td>Sperotech</td>
			<td>PM-20-10</td>
			<td></td>
		</tr>
		<tr>
			<td>MEM amino acid solution</td>
			<td>Gibco</td>
			<td>11130-051</td>
			<td>30 mM L-Arginine hydrochloride, 5 mM L-Cystine, 10 mM L-Histidine hydrochloride-H2O, 20 mM L-Isoleucine, 20 mM L-Leucine, 19.8 mM L-Lysine hydrochloride, 5.1 mM L-Methionine, 10 mM L-Phenylalanine, 20 mM L-Threonine, 2.5 mM L-Tryptophan, 10 mM L-Tyrosine, and 20 mM L-Valine</td>
		</tr>
		<tr>
			<td>Mini-slab size electrophoresis system</td>
			<td>ATTO</td>
			<td>AE-6530</td>
			<td></td>
		</tr>
		<tr>
			<td>Niacinamide</td>
			<td>Sigma-Aldrich</td>
			<td>N0636</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicilin / Streptomycin</td>
			<td>Gibco</td>
			<td>15070063</td>
			<td></td>
		</tr>
		<tr>
			<td>PhosSTOP phosphatase inhibitor cocktail</td>
			<td>Roche</td>
			<td>4906845001</td>
			<td></td>
		</tr>
		<tr>
			<td>Poly-L-lysine hydrobromide</td>
			<td>Nacali</td>
			<td>28360-14</td>
			<td></td>
		</tr>
		<tr>
			<td>Pyridoxal HCl</td>
			<td>Sigma-Aldrich</td>
			<td>P6155</td>
			<td></td>
		</tr>
		<tr>
			<td>Riboflavin</td>
			<td>Sigma-Aldrich</td>
			<td>R9504</td>
			<td></td>
		</tr>
		<tr>
			<td>Silver Stain 2 Kit wako</td>
			<td>Wako</td>
			<td>291-5031</td>
			<td></td>
		</tr>
		<tr>
			<td>Thiamine HCl</td>
			<td>Sigma-Aldrich</td>
			<td>T1270</td>
			<td></td>
		</tr>
		<tr>
			<td>Trans-Blot SD Semi-Dry Transfer Cell</td>
			<td>Bio-rad</td>
			<td>1703940JA</td>
			<td></td>
		</tr>
		<tr>
			<td>Ultra pure water</td>
			<td>MilliQ</td>
			<td></td>
			<td>For production of ultra pure water</td>
		</tr>
	</tbody>
</table>

purification of the dendritic filopodia-rich fraction

Dendritic filopodia are thin and long protrusions based on the actin filament, and they extend and retract as if searching for a target axon. When the dendritic filopodia establish contact with a target axon, they begin maturing into spines, leading to the formation of a synapse. Telencephalin (TLCN) is abundantly localized in dendritic filopodia and is gradually excluded from spines. Overexpression of TLCN in cultured hippocampal neurons induces dendritic filopodia formation. We showed that telencephalin strongly binds to an extracellular matrix molecule, vitronectin. Vitronectin-coated microbeads induced phagocytic cup formation on neuronal dendrites. In the phagocytic cup, TLCN, TLCN-binding proteins such as phosphorylated Ezrin/Radixin/Moesin (phospho-ERM), and F-actin are accumulated, which suggests that components of the phagocytic cup are similar to those of dendritic filopodia. Thus, we developed a method for purifying the phagocytic cup instead of dendritic filopodia. Magnetic polystyrene beads were coated with vitronectin, which is abundantly present in the culture medium of hippocampal neurons and which induces phagocytic cup formation on neuronal dendrites. After 24 h of incubation, the phagocytic cups were mildly solubilized with detergent and collected using a magnet separator. After washing the beads, the binding proteins were eluted and analyzed by silver staining and Western blotting. In the binding fraction, TLCN and actin were abundantly present. In addition, many proteins identified from the fraction were localized to the dendritic filopodia; thus, we named the binding fraction as the dendritic filopodia-rich fraction. This article describes details regarding the purification method for the dendritic filopodia-rich fraction.

In cultured hippocampal neurons, TLCN was abundantly localized to the dendritic filopodia, shaft, and soma and colocalized with F-actin (Figure 1A, B). When polystyrene microbeads were added to cultured hippocampal neurons, the beads were automatically coated with vitronectin (VN) derived from fetal bovine serum (FBS) in the culture medium; they were mainly bound to dendrites, and they induced the formation of phagocytic cups (Figure 1B-E). Phagocytic cups were based on sheet-shaped actin filaments around microbeads on dendrites. TLCN, phospho-ERM, and PI(4,5)P2, which are markers for dendritic filopodia, are highly accumulated around beads (Figure 1D)8,15. Phagocytic cups were only formed on wild-type hippocampal neurons, but not on TLCN-deficient hippocampal neurons (Figure 2A-D). Thus, the phagocytic cup formation was crucially dependent on the presence of TLCN in dendrites.
Constituents of the dendritic filopodia appeared similar to those of phagocytic cups. Next, we purified phagocytic cups instead of dendritic filopodia. The protocol for the purification of phagocytic cups is schematically shown in Figure 3. Magnetic microbeads were added to wild-type cultured hippocampal neurons, which induces the formation of phagocytic cup structures. The phagocytic cup structures were lysed with a weak detergent. The microbeads were collected after the lysis using a magnet separator. After washing of the beads, their binding proteins were boiled and eluted in an SDS sample buffer.
The amount of proteins in the bound and unbound fraction was measured using the BCA protein assay kit. The same amount of proteins in the unbound and bound fractions was separated by SDS-PAGE and stained by silver staining (Figure 4A). The protein band patterns were almost the same for the unbound and bound fractions, but the intensities at 50 and 70 kDa in the bound fraction were lower than those in the unbound fraction. However, the band intensity was not obviously different between the unbound and bound fractions prepared from TLCN-deficient culture hippocampal neurons. To confirm the purification of phagocytic cup structures, we performed Western blotting using anti-TLCN-C, anti-bovine vitronectin, anti-actin, and anti-&#945;-tubulin (Figure 4B). TLCN and VN were mainly detected in the bound fraction. Actin, ezrin, G&#945;q, PLC&#946;1, MAP-2, and spectrin were detected in both the bound and unbound fractions. Moesin, PSD-95, &#945;-actinin, and &#945;-tubulin were detected in the unbound fraction.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/59292/59292fig1.jpg" /> 
Figure 1: Localization of TLCN and F-actin in dendritic filopodia and phagocytic cups. (A) Immunofluorescence staining of dendrites of a cultured hippocampal neuron expressing gapVenus with anti-GFP antibody (blue in a merged image), anti-TLCN antibody (red in a merged image), and phalloidin (green in a merged image). TLCN and F-actin are abundantly observed in dendritic filopodia. (B, C) Formation of phagocytic cup structures on neuronal dendrites. Fluorescent microbeads (blue in merged images of B, C) added to cultured hippocampal neurons strongly adhere onto dendrites and induce the accumulation of TLCN (red in merged images of B, C) and F-actin (green in merged images of B, C). (D) A lateral view of a dendritic phagocytic cup reconstructed from confocal images reveals TLCN (red in merged images of D) surrounding the fluorescent bead (blue in merged images of D). (E) A dendritic phagocytic cup induced by a magnetic microbead attached onto a neuronal dendrite and immunostained with anti-VN antibody (blue in merged images of E), anti-TLCN antibody (red in merged images of E), and phalloidin (green in merged images of E). Scale bars = 1 &#956;m in (D); 2 &#956;m in (A), (C), and (E); and 20 &#956;m in (B). This figure has been modified from a previous study18. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/59292/59292fig1large.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/59292/59292fig2.jpg" /> 
Figure 2: TLCN-dependent formation of phagocytic cup-like structure. (A-D) Triple fluorescence images of wild-type (WT; A, C) and TLCN-deficient (KO; C, D) neurons treated with VN-coated fluorescent beads (red in merged images of A, B, C, D) and labeled with anti-TLCN antibody (green in merged images of A, B, C, D) and anti-phospho-ERM antibody (blue in merged images of A, B) or Alexa488-phalloidin (blue in merged images of C, D). Scale bars = 5 &#956;m. This figure has been modified from a previous study15. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/59292/59292fig2large.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/59292/59292fig3.jpg" /> 
Figure 3: A schematic diagram illustrating the purification procedure of the dendritic filopodia-rich fraction. Magnetic microbeads were added onto cultured hippocampal neurons to induce the formation of dendritic phagocytic cups. After 1 day of incubation, the neurons were solubilized with lysis buffer containing 0.01% Triton X-100. The beads were separated from the unbound fraction using a magnetic separator. After washing, the bound proteins were eluted with SDS sample buffer and used as the bound fraction. Red: VN, green: TLCN, other colors: bound proteins. This figure has been modified from a previous study18. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/59292/59292fig3large.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/59292/59292fig4.jpg" /> 
Figure 4: Confirmation of phagocytic cup fraction. (A) Silver staining of proteins in the unbound and bound fractions of the microbeads. The same amount (50 ng) of proteins in the unbound and bound fractions purified from wild-type (WT) and TLCN-deficient (TLCN KO) hippocampal neurons were separated by SDS-PAGE and visualized with silver staining. (B) Western blot analysis of the unbound and bound fractions. The same amount (50 ng) of proteins were separated by SDS-PAGE and subjected to Western blot analysis using anti-TLCN, anti-VN, anti-actin, anti-ezrin, anti-moesin, anti-G&#945;q, anti-PLC&#946;1, anti-MAP-2, anti-spectrin, anti-PSD-95, anti-&#945;-actinin, and anti-&#945;-tubulin antibodies. Note that TLCN, VN, actin, ezrin, PLC&#946;1, MAP-2, and spectrin are observed in the dendritic filopodia-rich fraction. This figure has been modified from a previous study18. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/59292/59292fig4large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Purification of the Dendritic Filopodia-rich Fraction at JoVE.com

Purification of the Dendritic Filopodia-rich Fraction

In this protocol, we introduce a method for purifying the dendritic filopodia-rich fraction from the phagocytic cup-like protrusion structure on cultured hippocampal neurons by taking advantage of the specific and strong affinity between a dendritic filopodial adhesion molecule, TLCN, and an extracellular matrix molecule, vitronectin.

Dendritic filopodia are thin and long protrusions based on the actin filament, and they extend and retract as if searching for a target axon. When the ...

purification-of-the-dendritic-filopodia-rich-fraction

Nanyang Technological University

Research

JoVE Journal

Neuroscience

5.2K Views.  RIKEN Brain Science Institute. In this protocol, we introduce a method for purifying the dendritic filopodia-rich fraction from the phagocytic cup-like protrusion structure on cultured hippocampal neurons by taking advantage of the specific and strong affinity between a dendritic filopodial adhesion molecule, TLCN, and an extracellular matrix molecule, vitronectin.

Video: Purification of the Dendritic Filopodia-rich Fraction

Analysis of Dendritic Spine Morphology in Cultured CNS Neurons

Dendritic spines are the sites of the majority of excitatory connections within the brain, and form the post-synaptic 
compartment of synapses. These structures are rich in actin and have been shown to be highly dynamic. In response to classical Hebbian plasticity 
as well as neuromodulatory signals, dendritic spines can change shape and number, which is thought to be critical for the refinement of neural 
circuits and the processing and storage of information within the brain. Within dendritic spines, a complex network of proteins link extracellular 
signals with the actin cyctoskeleton allowing for control of dendritic spine morphology and number. Neuropathological studies have demonstrated that 
a number of disease states, ranging from schizophrenia to autism spectrum disorders, display abnormal dendritic spine morphology or numbers. 
Moreover, recent genetic studies have identified mutations in numerous genes that encode synaptic proteins, leading to suggestions that these 
proteins may contribute to aberrant spine plasticity that, in part, underlie the pathophysiology of these disorders. In order to study the potential 
role of these proteins in controlling dendritic spine morphologies/number, the use of cultured cortical neurons offers several advantages. Firstly, 
this system allows for high-resolution imaging of dendritic spines in fixed cells as well as time-lapse imaging of live cells. Secondly, this in 
vitro system allows for easy manipulation of protein function by expression of mutant proteins, knockdown by shRNA constructs, or pharmacological 
treatments. These techniques allow researchers to begin to dissect the role of disease-associated proteins and to predict how mutations of these 
proteins may function in vivo.

Numerous recent studies have identified mutations in synaptic proteins associated with brain pathologies. Primary cultured cortical neurons offer great flexibility in examining the effects of these disease-associated proteins on dendritic spine morphology and motility.

Dendritic spines are the sites of the majority of excitatory connections within the brain, and form the post-synaptic 
compartment of synapses. These ...

Inducing Dendritic Growth in Cultured Sympathetic Neurons

The shape of the dendritic arbor determines the total synaptic input a neuron can receive 1-3, and influences the types and distribution of these inputs 4-6. Altered patterns of dendritic growth and plasticity are associated with impaired neurobehavioral function in experimental models 7, and are thought to contribute to clinical symptoms observed in both neurodevelopmental disorders 8-10 and neurodegenerative diseases 11-13. Such observations underscore the functional importance of precisely regulating dendritic morphology, and suggest that identifying mechanisms that control dendritic growth will not only advance understanding of how neuronal connectivity is regulated during normal development, but may also provide insight on novel therapeutic strategies for diverse neurological diseases.
Mechanistic studies of dendritic growth would be greatly facilitated by the availability of a model system that allows neurons to be experimentally switched from a state in which they do not extend dendrites to one in which they elaborate a dendritic arbor comparable to that of their in vivo counterparts. Primary cultures of sympathetic neurons dissociated from the superior cervical ganglia (SCG) of perinatal rodents provide such a model. When cultured in defined medium in the absence of serum and ganglionic glial cells, sympathetic neurons extend a single process which is axonal, and this unipolar state persists for weeks to months in culture 14,15. However, the addition of either bone morphogenetic protein-7 (BMP-7) 16,17 or Matrigel 18 to the culture medium triggers these neurons to extend multiple processes that meet the morphologic, biochemical and functional criteria for dendrites. Sympathetic neurons dissociated from the SCG of perinatal rodents and grown under defined conditions are a homogenous population of neurons 19 that respond uniformly to the dendrite-promoting activity of Matrigel, BMP-7 and other BMPs of the decapentaplegic (dpp) and 60A subfamilies 17,18,20,21. Importantly, Matrigel- and BMP-induced dendrite formation occurs in the absence of changes in cell survival or axonal growth 17,18.
Here, we describe how to set up dissociated cultures of sympathetic neurons derived from the SCG of perinatal rats so that they are responsive to the selective dendrite-promoting activity of Matrigel or BMPs.

We describe a protocol for using bone morphogenetic protein-7 (BMP-7) or Matrigel to selectively induce dendritic growth in primary sympathetic neurons dissociated from the superior cervical ganglia (SCG) of perinatal rats.

The shape of the dendritic arbor determines the total synaptic input a neuron can receive 1-3, and influences the types and distribution of these inputs ...

The Analysis of Purkinje Cell Dendritic Morphology in Organotypic Slice Cultures

Purkinje cells are an attractive model system for studying dendritic development, because they have an impressive dendritic tree which is strictly oriented in the sagittal plane and develops mostly in the postnatal period in small rodents 3. Furthermore, several antibodies are available which selectively and intensively label Purkinje cells including all processes, with anti-Calbindin D28K being the most widely used. For viewing of dendrites in living cells, mice expressing EGFP selectively in Purkinje cells 11 are available through Jackson labs. Organotypic cerebellar slice cultures cells allow easy experimental manipulation of Purkinje cell dendritic development because most of the dendritic expansion of the Purkinje cell dendritic tree is actually taking place during the culture period 4. We present here a short, reliable and easy protocol for viewing and analyzing the dendritic morphology of Purkinje cells grown in organotypic cerebellar slice cultures. For many purposes, a quantitative evaluation of the Purkinje cell dendritic tree is desirable. We focus here on two parameters, dendritic tree size and branch point numbers, which can be rapidly and easily determined from anti-calbindin stained cerebellar slice cultures. These two parameters yield a reliable and sensitive measure of changes of the Purkinje cell dendritic tree. Using the example of treatments with the protein kinase C (PKC) activator PMA and the metabotropic glutamate receptor 1 (mGluR1) we demonstrate how differences in the dendritic development are visualized and quantitatively assessed. The combination of the presence of an extensive dendritic tree, selective and intense immunostaining methods, organotypic slice cultures which cover the period of dendritic growth and a mouse model with Purkinje cell specific EGFP expression make Purkinje cells a powerful model system for revealing the mechanisms of dendritic development.

We present a protocol that permits to view and to quantitatively asses the morphology of the dendritic tree of individual Purkinje cells grown in organotypic cerebellar slice cultures. This protocol is intended to promote studies on the mechanisms of Purkinje cell dendritic development.

Purkinje cells are an attractive model system for studying dendritic development, because they have an impressive dendritic tree which is strictly ...

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

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

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

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

Assessment of Dendritic Arborization in the Dentate Gyrus of the Hippocampal Region in Mice

Dendritic arborization has been shown to be a reliable marker for examination of structural and functional integrity of neurons. Indeed, the complexity and extent of dendritic arborization correlates well with the synaptic plasticity in these cells. A reliable method for assessment of dendritic arborization is needed to characterize the deleterious effects of neurological disorders on these structures and to determine the effects of therapeutic interventions. However, quantification of these structures has proven to be a formidable task given their complex and dynamic nature. Fortunately, sophisticated imaging techniques can be paired with conventional staining methods to assess the state of dendritic arborization, providing a more reliable and expeditious means of assessment. Below is an example of how these imaging techniques were paired with staining methods to characterize the dendritic arborization in wild type mice. These complementary imaging methods can be used to qualitatively and quantitatively assess dendritic arborization that span a rather wide area within the hippocampal region.

We describe two methods for visualization and quantification of dendritic arborization in the hippocampus of mouse models: real-time and extended depth of field imaging. While the former method allows sophisticated topographical tracing and quantification of the extent of branching, the latter allows speedy visualization of the dendritic tree.

Dendritic arborization has been shown to be a reliable marker for examination of structural and functional integrity of neurons. Indeed, the complexity ...

Purification of Mouse Brain Vessels

In the brain, most of the vascular system consists of a selective barrier, the blood-brain barrier (BBB) that regulates the exchange of molecules and immune cells between the brain and the blood. Moreover, the huge neuronal metabolic demand requires a moment-to-moment regulation of blood flow. Notably, abnormalities of these regulations are etiological hallmarks of most brain pathologies; including glioblastoma, stroke, edema, epilepsy, degenerative diseases (ex: Parkinson&#8217;s disease, Alzheimer&#8217;s disease), brain tumors, as well as inflammatory conditions such as multiple sclerosis, meningitis and sepsis-induced brain dysfunctions. Thus, understanding the signaling events modulating the cerebrovascular physiology is a major challenge. Much insight into the cellular and molecular properties of the various cell types that compose the cerebrovascular system can be gained from primary culture or cell sorting from freshly dissociated brain tissue. However, properties such as cell polarity, morphology and intercellular relationships are not maintained in such preparations. The protocol that we describe here is designed to purify brain vessel fragments, whilst maintaining structural integrity. We show that isolated vessels consist of endothelial cells sealed by tight junctions that are surrounded by a continuous basal lamina. Pericytes, smooth muscle cells as well as the perivascular astrocyte endfeet membranes remain attached to the endothelial layer. Finally, we describe how to perform immunostaining experiments on purified brain vessels.

We describe a protocol allowing the purification of the mouse brain's vascular compartment. Isolated brain vessels include endothelial cells linked by tight junctions and surrounded by a continuous basal lamina, pericytes, vascular smooth muscle cells, as well as perivascular astroglial membranes.

In the brain, most of the vascular system consists of a selective barrier, the blood-brain barrier (BBB) that regulates the exchange of molecules and ...

Analyzing Dendritic Morphology in Columns and Layers

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

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

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

Assessment of Hippocampal Dendritic Complexity in Aged Mice Using the Golgi-Cox Method

Dendritic spines are the protuberances from the neuronal dendritic shafts that contain&#160; excitatory synapses. The morphological and branching variations of the neuronal dendrites within the hippocampus are implicated in cognition and memory formation. There are several approaches to Golgi staining, all of which have been useful for determining the morphological characteristics of dendritic arbors and produce a clear background. The present Golgi-Cox method, (a slight variation of the protocol that is provided with a commercial Golgi staining kit), was designed to assess how a relatively low dose of the chemotherapeutic drug 5-flurouracil (5-Fu) would affect dendritic morphology, the number of spines, and the complexity of arborization within the hippocampus. The 5-Fu significantly modulated the dendritic complexity and decreased the spine density throughout the hippocampus in a region-specific manner. The data presented show that the Golgi staining method effectively stained the mature neurons in the CA1, the CA3, and the dentate gyrus (DG) of the hippocampus. This protocol reports the details for each step so that other researchers can reliably stain tissue throughout the brain with high quality results and minimal troubleshooting.

Here we present a Golgi-Cox protocol in extensive detail. This reliable tissue stain method allows for a high-quality assessment of the cytoarchitecture in the hippocampus, and throughout the entire brain, with minimal troubleshooting.

Dendritic spines are the protuberances from the neuronal dendritic shafts that contain&#160; excitatory synapses. The morphological and branching ...

Real-time Iontophoresis with Tetramethylammonium to Quantify Volume Fraction and Tortuosity of Brain Extracellular Space

This review describes the basic concepts and protocol to perform the real-time iontophoresis (RTI) method, the gold-standard to explore and quantify the extracellular space (ECS) of the living brain. The ECS surrounds all brain cells and contains both interstitial fluid and extracellular matrix. The transport of many substances required for brain activity, including neurotransmitters, hormones, and nutrients, occurs by diffusion through the ECS. Changes in the volume and geometry of this space occur during normal brain processes, like sleep, and pathological conditions, like ischemia. However, the structure and regulation of brain ECS, particularly in diseased states, remains largely unexplored. The RTI method measures two physical parameters of living brain: volume fraction and tortuosity. Volume fraction is the proportion of tissue volume occupied by ECS. Tortuosity is a measure of the relative hindrance a substance encounters when diffusing through a brain region as compared to a medium with no obstructions. In RTI, an inert molecule is pulsed from a source microelectrode into the brain ECS. As molecules diffuse away from this source, the changing concentration of the ion is measured over time using an ion-selective microelectrode positioned roughly 100 &#181;m away. From the resulting diffusion curve, both volume fraction and tortuosity can be calculated. This technique has been used in brain slices from multiple species (including humans) and in vivo to study acute and chronic changes to ECS. Unlike other methods, RTI can be used to examine both reversible and irreversible changes to the brain ECS in real time.

This protocol describes real-time iontophoresis, a method that measures physical parameters of the extracellular space (ECS) of living brains. The diffusion of an inert molecule released into the ECS is used to calculate the ECS volume fraction and tortuosity. It is ideal for studying acute reversible changes to brain ECS.

This review describes the basic concepts and protocol to perform the real-time iontophoresis (RTI) method, the gold-standard to explore and quantify the ...

Quantitative Analysis of Neuronal Dendritic Arborization Complexity in Drosophila

Dendrites are the branched projections of a neuron, and dendritic morphology reflects synaptic organization during the development of the nervous system. Drosophila larval neuronal dendritic arborization (da) is an ideal model for studying morphogenesis of neural dendrites and gene function in the development of nervous system. There are four classes of da neurons. Class IV is the most complex with a branching pattern that covers almost the entire area of the larval body wall. We have previously characterized the effect of silencing the Drosophila ortholog of SOX5 on class IV neuronal dendritic arborization complexity (NDAC) using four parameters: the length of dendrites, the surface area of dendrite coverage, the total number of branches, and the branching structure. This protocol presents the workflow of NDAC quantitative analysis, consisting of larval dissection, confocal microscopy, and image analysis procedures using ImageJ software. Further insight into da neuronal development and its underlying mechanisms will improve the understanding of neuronal function and provide clues about the fundamental causes of neurological and neurodevelopmental disorders.

Quantitative Analysis of Neuronal Dendritic Arborization Complexity in Drosophila

This protocol focuses on quantitative analysis of neuronal dendritic arborization complexity (NDAC) in Drosophila, which can be used for studies of dendritic morphogenesis.

Dendrites are the branched projections of a neuron, and dendritic morphology reflects synaptic organization during the development of the nervous system. ...

Purification of the Dendritic Filopodia-rich Fraction

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Real-time Iontophoresis with Tetramethylammonium to Quantify Volume Fraction and Tortuosity of Brain Extracellular Space

Quantitative Analysis of Neuronal Dendritic Arborization Complexity in Drosophila