This project was supported by grant MOP62827 from the Canadian Institutes of Health Research.

NOTE: The following procedures are in accordance with guidelines approved by the Canadian Council of Animal Care. All efforts are made to minimize pain and distress of animals during procedures.
1. Coating of Filters
NOTE: When culture filter inserts are placed in wells of multi-well plates, two compartments are defined: the top compartment is the region above the insert and the bottom compartment is the one below the insert Figure 1A.a-b. Explants ar...

<ol>
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Q., 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+functional+role+for+intra-axonal+protein+synthesis+during+axonal+regeneration+from+adult+sensory+neurons.">A functional role for intra-axonal protein synthesis during axonal regeneration from adult sensory neurons.</a> J. Neurosci. 21, 9291-9303 (2001).</li><li>Willis, 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=Differential+transport+and+local+translation+of+cytoskeletal,+injury-response,+and+neurodegeneration+protein+mRNAs+in+axons.">Differential transport and local translation of cytoskeletal, injury-response, and neurodegeneration protein mRNAs in axons.</a> J. Neurosci. 25, 778-791 (2005).</li><li>Poon, M. M., Choi, S. H., Jamieson, C. A., Geschwind, D. H., Martin, K. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+process-localized+mRNAs+from+cultured+rodent+hippocampal+neurons.">Identification of process-localized mRNAs from cultured rodent hippocampal neurons.</a> J. Neurosci. 26, 13390-13399 (2006).</li><li>Schoenmann, 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=Axonal+degeneration+is+regulated+by+the+apoptotic+machinery+or+a+NAD+-sensitive+pathway+in+insects+and+mammals.">Axonal degeneration is regulated by the apoptotic machinery or a NAD+-sensitive pathway in insects and mammals.</a> J. Neurosci. 30, 6375-6386 (2010).</li><li>Unsain, N., Higgins, J. M., Parker, K. N., Johnstone, A. D., Barker, P. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=XIAP+regulates+caspase+activity+in+degenerating+axons.">XIAP regulates caspase activity in degenerating axons.</a> Cell Rep. 4, 751-763 (2013).</li><li>Ure, D. R., Campenot, R. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Retrograde+transport+and+steady-state+distribution+of+125I-nerve+growth+factor+in+rat+sympathetic+neurons+in+compartmented+cultures.">Retrograde transport and steady-state distribution of 125I-nerve growth factor in rat sympathetic neurons in compartmented cultures.</a> J. Neurosci. 17, 1282-1290 (1997).</li><li>Taylor, A. 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=Axonal+mRNA+in+uninjured+and+regenerating+cortical+mammalian+axons.">Axonal mRNA in uninjured and regenerating cortical mammalian axons.</a> J. Neurosci. 29, 4697-4707 (2009).</li><li>Minis, 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=Subcellular+transcriptomics-Dissection+of+the+mRNA+composition+in+the+axonal+compartment+of+sensory+neurons.">Subcellular transcriptomics-Dissection of the mRNA composition in the axonal compartment of sensory neurons.</a> Dev. Neurobiol. , (2013).</li><li>Niekerk, E. 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=Sumoylation+in+axons+triggers+retrograde+transport+of+the+RNA-binding+protein+La.">Sumoylation in axons triggers retrograde transport of the RNA-binding protein La.</a> Proc. Natl. Acad. Sci. U. S. A. 104, 12913-12918 (2007).</li><li>Huang, E. J., Reichardt, L. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neurotrophins:+roles+in+neuronal+development+and+function.">Neurotrophins: roles in neuronal development and function.</a> Annu. Rev. Neurosci. 24, 677-736 (2001).</li><li>Vargas, M. E., Barres, B. 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The authors have nothing to disclose.

Important parameters to take into account when adapting this technique include the neuronal population that will be studied, the substrate, pore size of the filter and surface area. All these parameters will impact the specificity, quality and quantity of the neurite preparation obtained, and must be considered carefully by the end user. In the examples presented in this protocol, the use of DRG neurons has the advantage of extending only axons, thus giving a pure (specific) axonal preparation.
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The axonal compartment of neurons shows a large degree of functional independence from the somato-dendritic compartment. In projection neurons, axons contain most of the neuronal protein1,2. The study of the physiology and pathophysiology of axons has gained momentum in the neuroscience community because recent studies have shown that early axonal dysfunction appears to be a common feature of neurodegenerative diseases and neuropsychiatric disorders3. It seems likely that a better understanding of axonal-exclusive mechanisms under normal and pathological conditions will shed light on the early events that drive dysfunction.
The present protocol describes how to use culture inserts bearing a porous membrane (filter) to obtain large amounts of pure axonal material that is suitable for biochemical and immunocytochemical analyses. The use of filter inserts to study axonal biology was first implemented by Steward and colleagues4 and further developed by Twiss and colleagues5 to its present configuration. The technique is now in current use by groups studying different aspects of axonal and dendrite biology, with slight modifications in each case to accommodate for the population of neurons studied, the treatments performed and the type of biochemical analyses used6-9. The present protocol does not intend to accommodate all the alternatives for such a variety of applications, but rather provide a simple approach that is suitable for most applications. In particular, the protocol described here uses a triple coating that maximizes axonal yield for biochemical analyses and is most suitable to study axonal degeneration &#8211;other coatings described in the literature produced less axons that retract and degenerate faster when deprived from trophic factors9.
In this procedure, neuronal cell bodies remain isolated atop the filter while axons pass through the pores and grow along its bottom surface. Pure axons (free of glia and neuronal cell body contaminants) that grow on the bottom surface of the filter can be collected for biochemical analyses or can be fixed in situ and examined by immunocytochemical techniques9. The procedure relies on the use of embryonic sensory neurons from the dorsal root ganglia (DRG). Embryonic DRGs are widely used to study axonal biology because neurites from these cells undergo fast and robust growth in vitro when maintained in nerve growth factor (NGF), and because they rapidly undergo degeneration when deprived of this factor. Also, DRG neurons lack dendrites, so that all the neurites collected by this method are purely axons.
Filter inserts represent a great advantage compared to other approaches used to study axons. Studies relying on the use of microscopy to differentiate processes occurring in the cell soma from those in axons provide limited biochemical information. As another example, compartmentalized culture systems (e.g., Campenot chambers10 or microfluidic devices11) are useful for imaging approaches and for differential treatment of cell compartments but provide only small amounts of axonal material, precluding the use of these techniques for biochemical analyses which require relatively large amounts of sample. Further, their use requires significant training as well as specialized devices, and they are time consuming. Another approach often used to isolate axons from explants is to manually remove an explant center (containing neuronal cell bodies) before axonal sample collection. Although this can produce large quantities of axon-enriched preparations, axons in this preparation can be enveloped in glia and rapidly removing 20 explant&#8217;s bodies consecutively from 6 wells (as an example of a minimal experiment) is time-consuming and at the limit of feasibility.
In contrast, the method presented here produces abundant and pure axonal preparations that can then be analyzed by virtually any biochemical technique that is commonly used to analyze whole-cell lysates, like western blot, immunoprecipitation6, northern blot5 mass spectrometry6, RNA purification7,12,13, among others. Moreover, the protocol can be applied to immunofluorescence (IF) techniques, as it is possible to fix axons growing in the bottom side of the filter to further examine them by IF. This approach greatly facilitates the analysis of axonal-specific processes since there are no cell bodies in the final preparation. This is a significant advantage since a high immunofluorescent signal from cell bodies often undermines examination and analysis of a weaker signal originating from thin structures such as axons.
Two applications of the culture method to study axonal degeneration are described; a model of developmental pruning and a model of injury-induced degeneration (commonly referred to as Wallerian degeneration). The modeling of developmental pruning is based on the fact that sensory neurons in vivo compete for limiting amounts of target-derived NGF and those failing to receive enough neurotrophic support degenerate14. This phenomenon can be mimicked in embryonic DRG cultures by withdrawing NGF from the culture media, which, as happens in vivo, initiates axonal degeneration followed by cell body destruction. To model Wallerian degeneration, the top side of the filter with the cell bodies is scraped away. The axons that had grown onto the bottom side of the filter become physically separated from the cell bodies and thereafter undergo the rapid and stereotypic degenerative process known as Wallerian degeneration15, named after A. Waller who first reported the phenomenon in 185016.

<table border="0" cellpadding="0" cellspacing="0" width="972">
	<tbody>
		<tr height="40">
			<td height="40" style="height:40px;width:297px;">CD-1 mouse, E13 timed pregnancy</td>
			<td style="width:140px;">Charles River</td>
			<td style="width:119px;"></td>
			<td style="width:416px;">In house timed pregnancies can be done by mating mice and checking for vaginal plugs (Day E0)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Falcon Cell Culture Inserts</td>
			<td>Corning</td>
			<td>353102</td>
			<td>1 &#181;m pore size, fits 6-well receiving plate</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Falcon Cell Culture Companion Plates</td>
			<td>Corning</td>
			<td>353502</td>
			<td>Receiving plates for inserts</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Poly-D-Lysine</td>
			<td>Sigma-Aldrich</td>
			<td>P6407</td>
			<td>Used at 1 mg/ml in water. Can re-use once.</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Laminin</td>
			<td>Sigma-Aldrich</td>
			<td>L2020</td>
			<td style="width:416px;">Used at 10 ug/ml in water. Take 100X stock from -80 &#176;C and thaw overnight at 4 &#176;C&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">PureCol Bovine Collagen Solution</td>
			<td>Advanced Biomatrix</td>
			<td>5005-B</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Leibovitz&#39;s L-15 Medium</td>
			<td>Invitrogen</td>
			<td>11415-064</td>
			<td>Can be replaced by DMEM.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Neurobasal Medium</td>
			<td>Invitrogen</td>
			<td>21103-049</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">B-27 Serum-Free Supplement</td>
			<td>Invitrogen</td>
			<td>17504-044</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">5-Fluoro-2&#8242;-deoxyuridine (FDU)</td>
			<td>Sigma-Aldrich</td>
			<td>F0503</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">NGF (2.5S, beta subunit)</td>
			<td>Cedarlane</td>
			<td>CLMCNET-001</td>
			<td></td>
		</tr>
		<tr height="88">
			<td height="109" rowspan="2" style="height:109px;width:297px;">Anti-NGF Antibody</td>
			<td style="width:140px;">Prepared in-house</td>
			<td>-</td>
			<td style="width:416px;">As described in: Acheson, A., Barker, P.A., Alderson, R.F., Miller, F.D. &#38; Murphy, R.A. Detection of brain-derived neurotrophic factor-like activity in fibroblasts and Schwann cells: inhibition by antibodies to NGF. Neuron.7, 265-75, (1991)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Alomone Labs</td>
			<td style="width:119px;">AN-240</td>
			<td>Commercial option</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Anti-Tubulin Antibody</td>
			<td>Millipore</td>
			<td>MAB5564</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Alexa Fluor 488 Goat Anti-Mouse Antibody</td>
			<td>Invitrogen</td>
			<td>A-11029</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;"></td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">DRG culture medium</td>
		</tr>
		<tr height="126">
			<td height="126" style="height:126px;width:297px;">Neurobasal Medium 
			2 % B27 Neurobasal Supplement 
			2 mM l-Glutamine 
			1 % Penicillin-Streptomysin 
			10 &#181;M FDU 
			15 ng/ml NGF (bottom compartment only)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">1X Laemmli Sample Buffer</td>
		</tr>
		<tr height="105">
			<td height="105" style="height:105px;width:297px;">10 % SDS 
			0.5 M DTT 
			0.5 M Tris (pH 6.8) 
			5 % Glycerol 
			0.01 % (w/v) Bromophenol blue</td>
		</tr>
	</tbody>
</table>

production and isolation of axons from sensory neurons for biochemical analysis using porous filters

Neuronal axons use specific mechanisms to mediate extension, maintain integrity, and induce degeneration. An appropriate balance of these events is required to shape functional neuronal circuits. The protocol described here explains how to use cell culture inserts bearing a porous membrane (filter) to obtain large amounts of pure axonal preparations suitable for examination by conventional biochemical or immunocytochemical techniques. The functionality of these filter inserts will be demonstrated with models of developmental pruning and Wallerian degeneration, using explants of embryonic dorsal root ganglion. Axonal integrity and function is compromised in a wide variety of neurodegenerative pathologies. Indeed, it is now clear that axonal dysfunction appears much earlier in the course of the disease than neuronal soma loss in several neurodegenerative diseases, indicating that axonal-specific processes are primarily targeted in these disorders. By obtaining pure axonal samples for analysis by molecular and biochemical techniques, this technique has the potential to shed new light into mechanisms regulating the physiology and pathophysiology of axons. This in turn will have an impact in our understanding of the processes that drive degenerative diseases of the nervous system.

Dorsal root ganglion explants from E13.5 mice grow extensively on filters coated sequentially with poly-D-lysine, laminin and collagen (Figure&#160;1B, left), reaching up to 2 mm within 2 days in culture. This substrate combination yields particularly exuberant growth; other combinations yield axons that are considerably shorter (Figure&#160;1B, right). Moreover, DRGs maintained on filters extend more and longer axons than DRGs grown on plastic Figure&#160;1C.
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Watch this Scientific Journal Video about Production and Isolation of Axons from Sensory Neurons for Biochemical Analysis Using Porous Filters at JoVE.com

Production and Isolation of Axons from Sensory Neurons for Biochemical Analysis Using Porous Filters

This article describes a neuronal culture system that can be used to obtain large quantities of pure axonal samples for biochemical and immunocytochemical analyses. This technique will allow an improved understanding of normal axonal physiology and signaling pathways leading to neurodegeneration.

Neuronal axons use specific mechanisms to mediate extension, maintain integrity, and induce degeneration. An appropriate balance of these events is ...

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Neuroscience

14.1K Görüntüleme.  Montreal Neurological Institute, McGill University. This article describes a neuronal culture system that can be used to obtain large quantities of pure axonal samples for biochemical and immunocytochemical analyses. This technique will allow an improved understanding of normal axonal physiology and signaling pathways leading to neurodegeneration. 