This work was supported by grants from the Israel Science foundation (ISF, 561/11) and the European Research Council (ERC, 309377).

The care and treatment of animals in this protocol were performed under the supervision and approval of the Tel Aviv University Committee for Animal Ethics.
1. MFC preparation
<ol>
	<li>PDMS casting in primary molds (Figure 1)
	<ol>
		<li>Purchase or create primary molds (wafers) following a detailed protocol9.</li>
		<li>Use pressurized air to remove any type of dirt from the wafer platform before proceeding to the coating step. The surf...

<ol>
	<li>Misgeld, T., Schwarz, T. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitostasis+in+Neurons:+Maintaining+Mitochondria+in+an+Extended+Cellular+Architecture.">Mitostasis in Neurons: Maintaining Mitochondria in an Extended Cellular Architecture.</a> Neuron. 96, 651-666 (2017).</li><li>Devine, M. J., Kittler, J. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitochondria+at+the+neuronal+presynapse+in+health+and+disease.">Mitochondria at the neuronal presynapse in health and disease.</a> Nature Reviews Neuroscience. 19, 63-80 (2018).</li><li>Gibbs, K. L., Kalmar, B., Sleigh, J. N., Greensmith, L., Schiavo, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vivo+imaging+of+axonal+transport+in+murine+motor+and+sensory+neurons.">In vivo imaging of axonal transport in murine motor and sensory neurons.</a> Journal of Neuroscience Methods. 257, 26-33 (2016).</li><li>Mandal, A., Drerup, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Axonal+Transport+and+Mitochondrial+Function+in+Neurons.">Axonal Transport and Mitochondrial Function in Neurons.</a> Frontiers in Cellular Neuroscience. 13, 373 (2019).</li><li>Magran&#233;, J., Cortez, C., Gan, W. B., Manfredi, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Abnormal+mitochondrial+transport+and+morphology+are+common+pathological+denominators+in+SOD1+and+TDP43+ALS+mouse+models.">Abnormal mitochondrial transport and morphology are common pathological denominators in SOD1 and TDP43 ALS mouse models.</a> Human Molecular Genetics. 23, 1413-1424 (2014).</li><li>Anderson, R. G. W., Orci, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+view+of+acidic+intracellular+compartments.">A view of acidic intracellular compartments.</a> Journal of Cell Biology. 106, 539-543 (1988).</li><li>Kiral, F. R., Kohrs, F. E., Jin, E. J., Hiesinger, P. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rab+GTPases+and+Membrane+Trafficking+in+Neurodegeneration.">Rab GTPases and Membrane Trafficking in Neurodegeneration.</a> Current Biology. 28, R471-R486 (2018).</li><li>Ya-Cheng Liao, 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=RNA+Granules+Hitchhike+on+Lysosomes+for+Long-Distance+Transport,+Using+Annexin+A11+as+a+Molecular+Tether.">RNA Granules Hitchhike on Lysosomes for Long-Distance Transport, Using Annexin A11 as a Molecular Tether.</a> Cell. 179, 147-164 (2019).</li><li>Gluska, S., Chein, M., Rotem, N., Ionescu, A., Perlson, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tracking+Quantum-Dot+labeled+neurotropic+factors+transport+along+primary+neuronal+axons+in+compartmental+microfluidic+chambers.">Tracking Quantum-Dot labeled neurotropic factors transport along primary neuronal axons in compartmental microfluidic chambers.</a> Methods in Cell Biology. 131, 365-387 (2016).</li><li>Gershoni-Emek, N., 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=Localization+of+RNAi+Machinery+to+Axonal+Branch+Points+and+Growth+Cones+Is+Facilitated+by+Mitochondria+and+Is+Disrupted+in+ALS.">Localization of RNAi Machinery to Axonal Branch Points and Growth Cones Is Facilitated by Mitochondria and Is Disrupted in ALS.</a> Frontiers in Molecular Neuroscience. 11, 311 (2018).</li><li>Neto, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Compartmentalized+Microfluidic+Platforms:+The+Unrivaled+Breakthrough+of+In+Vitro+Tools+for+Neurobiological+Research.">Compartmentalized Microfluidic Platforms: The Unrivaled Breakthrough of In Vitro Tools for Neurobiological Research.</a> Journal of Neuroscience. 36 (46), 11573-11584 (2016).</li><li>Ionescu, A., Zahavi, E. E., Gradus, T., Ben-Yaakov, K., Perlson, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Compartmental+microfluidic+system+for+studying+muscle-neuron+communication+and+neuromuscular+junction+maintenance.">Compartmental microfluidic system for studying muscle-neuron communication and neuromuscular junction maintenance.</a> European Journal of Cell Biology. 95, 69-88 (2016).</li><li>Zahavi, E. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+compartmentalized+microfluidic+neuromuscular+co-culture+system+reveals+spatial+aspects+of+GDNF+functions.">A compartmentalized microfluidic neuromuscular co-culture system reveals spatial aspects of GDNF functions.</a> Journal of Cell Science. 128, 1241-1252 (2015).</li><li>Altman, T., Geller, D., Kleeblatt, E., Gradus-Perry, T., Perlson, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+in+vitro+compartmental+system+underlines+the+contribution+of+mitochondrial+immobility+to+the+ATP+supply+in+the+NMJ.">An in vitro compartmental system underlines the contribution of mitochondrial immobility to the ATP supply in the NMJ.</a> Journal of Cell Science. 132 (23), (2019).</li><li>Schaller, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Novel+combinatorial+screening+identifies+neurotrophic+factors+for+selective+classes+of+motor+neurons.">Novel combinatorial screening identifies neurotrophic factors for selective classes of motor neurons.</a> Proceedings of the National Academy of Sciences USA. 114, E2486-E2493 (2017).</li><li>Ionescu, 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=Targeting+the+Sigma-1+Receptor+via+Pridopidine+Ameliorates+Central+Features+of+ALS+Pathology+in+a+SOD1G93A+Model.">Targeting the Sigma-1 Receptor via Pridopidine Ameliorates Central Features of ALS Pathology in a SOD1G93A Model.</a> Cell Death &amp; Disease. 10 (3), 210 (2019).</li><li>Zahavi, E. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+compartmentalized+microfluidic+neuromuscular+coculture+system+reveals+spatial+aspects+of+GDNF+functions.">A compartmentalized microfluidic neuromuscular coculture system reveals spatial aspects of GDNF functions.</a> Journal of Cell Science. 128, 1241-1252 (2015).</li><li>Maimon, 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=Mir126-5p+downregulation+facilitates+axon+degeneration+and+nmj+disruption+via+a+non-cell-autonomous+mechanism+in+ALS.">Mir126-5p downregulation facilitates axon degeneration and nmj disruption via a non-cell-autonomous mechanism in ALS.</a> Journal of Neuroscience. 38, 5478-5494 (2018).</li></ol>

The authors declare no conflict of interest.

In this protocol, we describe a system to track axonal transport of mitochondria and acidic compartments in motor neurons. This simplified in vitro platform allows precise control, monitoring, and manipulation of subcellular neuronal compartments, enabling experimental analysis of motor neuron local functions. This protocol can be useful for studying MN diseases such as ALS, to focus on understanding the underlying mechanism of axonal transport dysfunction in the disease10,<sup class="x...

MNs are highly polarized cells with long axons, reaching up to one meter long in adult humans. This phenomenon creates a critical challenge for the maintenance of MN connectivity and function. Consequently, MNs depend on proper transport of information, organelles, and materials along the axons from their cell body to the synapse and back. Various cellular components, such as proteins, RNA, and organelles are shuttled regularly through the axons. Mitochondria are important organelles that are routinely transported in MNs. Mitochondria are essential for proper activity and function of MNs, responsible for ATP provision, calcium buffering, and signaling processes1,2. The axonal transport of mitochondria is a well-studied process3,4. Interestingly, defects in mitochondrial transport were reported to be involved in several neurodegenerative diseases and specifically in MN diseases5. Acidic compartments serve as another example for intrinsic organelles that move along MN axons. Acidic compartments include lysosomes, endosomes, trans-Golgi apparatus, and certain secretory vesicles6. Defects in the axonal transport of acidic compartments were found in several neurodegenerative diseases as well7, and recent papers highlight their importance in MN diseases8.
To efficiently study axonal transport, microfluidic chambers that separate somatic and axonal compartments are frequently used9,10. The two significant advantages of the microfluidic system, and the compartmentalization and the isolation of axons, render it ideal for the study of subcellular processes11. The spatial separation between the neuronal cell bodies and axons can be used to manipulate the extracellular environments of different neuronal compartments (e.g., axons vs. soma). Biochemical, neuronal growth/degeneration, and immunofluorescence assays all benefit from this platform. MFCs can also assist in studying cell-to-cell communication by coculturing neurons with other cell types, such as skeletal muscles12,13,14.
Here, we describe a simple yet precise protocol for monitoring mitochondria and acidic compartment transport in motor neurons. We further show the use of this method by comparing the relative percentage of retrograde and anterograde moving organelles, as well as the distribution of transport velocity.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>35mm Fluodish &#8211; glass bottom dish</td>
			<td>World Precision Instruments WPI</td>
			<td>FD35-100</td>
			<td></td>
		</tr>
		<tr>
			<td>50mm Fluodish &#8211; glass bottom dish</td>
			<td>World Precision Instruments WPI</td>
			<td>FD5040-100</td>
			<td></td>
		</tr>
		<tr>
			<td>Andor iXon DU-897 EMCCD camera</td>
			<td>Andor</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>ARA-C (Cytosine &#946;-D-arabinofuranoside)</td>
			<td>Sigma-Aldrich</td>
			<td>C1768</td>
			<td>stock of 2mM in filtered DDW</td>
		</tr>
		<tr>
			<td>B-27 Supplement (50X)</td>
			<td>Thermo Fisher</td>
			<td>17504044</td>
			<td></td>
		</tr>
		<tr>
			<td>BDNF</td>
			<td>Alomone Labs</td>
			<td>B-250</td>
			<td>Dilute to 10 &#181;g/mL in filtered ddw with 0.01% BSA)</td>
		</tr>
		<tr>
			<td>Biopsy punch 1.25mm</td>
			<td>World Precision Instruments WPI</td>
			<td>504530</td>
			<td>For preperation of large MFC</td>
		</tr>
		<tr>
			<td>Biopsy punch 6mm</td>
			<td>World Precision Instruments WPI</td>
			<td>504533</td>
			<td>For preperation of small MFC</td>
		</tr>
		<tr>
			<td>Biopsy punch 7mm</td>
			<td>World Precision Instruments WPI</td>
			<td>504534</td>
			<td>For preperation of large MFC</td>
		</tr>
		<tr>
			<td>Bitplane Imaris software - version 8.4.1</td>
			<td>Imaris</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Bovine Serum Albumine (BSA)</td>
			<td>Sigma-Aldrich</td>
			<td>#A3311-100G</td>
			<td>5% w/v in ddw</td>
		</tr>
		<tr>
			<td>Chlorotrimetylsilane</td>
			<td>Sigma-Aldrich</td>
			<td>#386529-100ML</td>
			<td></td>
		</tr>
		<tr>
			<td>CNTF</td>
			<td>Alomone Labs</td>
			<td>C-240</td>
			<td>Dilute to 10 &#181;g/mL in filtered ddw with 0.01% BSA)</td>
		</tr>
		<tr>
			<td>Density Gradient Medium - Optiprep</td>
			<td>Sigma-Aldrich</td>
			<td>D1556</td>
			<td></td>
		</tr>
		<tr>
			<td>Deoxyribonuclease I (DNAse) from bovine pancreas</td>
			<td>Sigma-Aldrich</td>
			<td>DN-25</td>
			<td>stock 10mg/mL in neurobasal</td>
		</tr>
		<tr>
			<td>Dow Corning High-vacuum silicone grease</td>
			<td>Sigma-Aldrich</td>
			<td>Z273554-1EA</td>
			<td>For epoxy mold preperation</td>
		</tr>
		<tr>
			<td>DPBS 10X</td>
			<td>Thermo Fisher</td>
			<td>#14200-067</td>
			<td>dilute 1:10 in ddw</td>
		</tr>
		<tr>
			<td>Dumont fine forceps #55 0.05 &#215; 0.02 mm</td>
			<td>F.S.T</td>
			<td>1125520</td>
			<td></td>
		</tr>
		<tr>
			<td>Epoxy Hardener</td>
			<td>Trias Chem S.R.L</td>
			<td>IPE 743</td>
			<td>For epoxy mold preperation</td>
		</tr>
		<tr>
			<td>Epoxy Resin</td>
			<td>Trias Chem S.R.L</td>
			<td>RP 026UV</td>
			<td>For epoxy mold preperation</td>
		</tr>
		<tr>
			<td>FIJI software</td>
			<td>ImageJ</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>GDNF</td>
			<td>Alomone Labs</td>
			<td>G-240</td>
			<td>Dilute to 10 &#181;g/mL in filtered ddw with 0.01% BSA)</td>
		</tr>
		<tr>
			<td>Glutamax 100X</td>
			<td>Thermo Fisher</td>
			<td>#35050-038</td>
			<td></td>
		</tr>
		<tr>
			<td>HB9:GFP mice strain</td>
			<td>Jackson Laboratories</td>
			<td>005029</td>
			<td></td>
		</tr>
		<tr>
			<td>HBSS 10X</td>
			<td>Thermo Fisher</td>
			<td>#14185-045</td>
			<td>Dilute 1:10 in ddw with addition of 1% P/S and filter</td>
		</tr>
		<tr>
			<td>iQ software</td>
			<td>Andor</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Iris scissors, curved, 10 cm</td>
			<td>AS Medizintechnik</td>
			<td>11-441-10</td>
			<td></td>
		</tr>
		<tr>
			<td>Iris scissors, straight, 9 cm</td>
			<td>AS Medizintechnik</td>
			<td>11-440-09</td>
			<td></td>
		</tr>
		<tr>
			<td>Laminin</td>
			<td>Sigma-Aldrich</td>
			<td>#L-2020</td>
			<td></td>
		</tr>
		<tr>
			<td>Leibovitz&#39;s L-15 Medium</td>
			<td>Thermo Fisher</td>
			<td>11415064</td>
			<td></td>
		</tr>
		<tr>
			<td>LysoTracker Red</td>
			<td>Thermo Fisher</td>
			<td>L7528</td>
			<td></td>
		</tr>
		<tr>
			<td>Mitotracker Deep-Red FM</td>
			<td>Thermo Fisher</td>
			<td>M22426</td>
			<td></td>
		</tr>
		<tr>
			<td>Neurobasal medium</td>
			<td>Thermo Fisher</td>
			<td>21103049</td>
			<td></td>
		</tr>
		<tr>
			<td>Nikon Eclipse Ti micorscope</td>
			<td>Nikon</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin (P/S) Solution</td>
			<td>Biological Industries</td>
			<td>03-031-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Poly-L-Ornithin (PLO)</td>
			<td>Sigma-Aldrich</td>
			<td>#P8638</td>
			<td>Dilute 1:1000 in flitered 1X PBS</td>
		</tr>
		<tr>
			<td>Sylgard 184 silicone elastomer kit</td>
			<td>DOW Corning Corporation</td>
			<td>#3097358-1004</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypsin from bovine pancreas</td>
			<td>Sigma-Aldrich</td>
			<td>T1426</td>
			<td>stock 25 mg/mL in 1XPBS</td>
		</tr>
		<tr>
			<td>Vannas spring microdissection scissors, 3 mm blade</td>
			<td>F.S.T</td>
			<td>15000-00</td>
			<td></td>
		</tr>
		<tr>
			<td>Yokogawa CSU X-1</td>
			<td>Yokogawa</td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

axonal transport of organelles in motor neuron cultures using microfluidic chambers system

Motor neurons (MNs) are highly polarized cells with very long axons. Axonal transport is a crucial mechanism for MN health, contributing to neuronal growth, development, and survival. We describe a detailed method for the use of microfluidic chambers (MFCs) for tracking axonal transport of fluorescently labeled organelles in MN axons. This method is rapid, relatively inexpensive, and allows for the monitoring of intracellular cues in space and time. We describe a step by step protocol for: 1) Fabrication of polydimethylsiloxane (PDMS) MFCs; 2) Plating of ventral spinal cord explants and MN dissociated culture in MFCs; 3) Labeling of mitochondria and acidic compartments followed by live confocal imagining; 4) Manual and semiautomated axonal transport analysis. Lastly, we demonstrate a difference in the transport of mitochondria and acidic compartments of HB9::GFP ventral spinal cord explant axons as a proof of the system validity. Altogether, this protocol provides an efficient tool for studying the axonal transport of various axonal components, as well as a simplified manual for MFC usage to help discover spatial experimental possibilities.

Following the described protocol, mouse embryonic HB9::GFP spinal cord explants were cultured in MFC (Figure 4A). Explants were grown for 7 days, when axons fully crossed into the distal compartment. Mitotracker Deep Red and Lysotracker Red dyes were added to the distal and proximal compartments in order to label the mitochondria and acidic compartments (Figure 4C). Axons in the distal grooves we...

Watch this Scientific Journal Video about Axonal Transport of Organelles in Motor Neuron Cultures using Microfluidic Chambers System at JoVE.com

Axonal Transport of Organelles in Motor Neuron Cultures using Microfluidic Chambers System

Axonal transport is a crucial mechanism for motor neuron health. In this protocol we provide a detailed method for tracking the axonal transport of acidic compartments and mitochondria in motor neuron axons using microfluidic chambers.

Motor neurons (MNs) are highly polarized cells with very long axons. Axonal transport is a crucial mechanism for MN health, contributing to neuronal ...

Axonal transport is vital for neuronal health and viability. Our protocol describes an elegant method for monitoring and analyzing axonal transport. And can be adapted for various neuronal disease models.The use of microfluidic chambers enable precise spatial temporal control, which is crucial for studying axonal biology. Axonal transport abnormalities are implicated with several neurodegenerative disease such as ALS. The microfluidic platform enables study of basic mechanisms as well as testing therapies to repair axonal transport defects.The microfluidic chamber platform can be easily adapted to suit different aspects of axonal research, including axonal growth and degeneration of various neural subtypes. This method is complex and usually taught hands-on. The visual demonstration will increase the accessibility of this procedure to any scientist interested in studying axonal transport.Begin by casting PDMS in primary molds. Use pressurized air to remove any dirt from the wafer platform, making sure that the wafers look smooth and clear before proceeding. Next, fill a container with liquid nitrogen and prepare a 10 milliliter syringe with a 23 gauge needle.In a chemical fume hood, place the wafer containing plate in a sealable container, and fill the syringe with two milliliters of liquid nitrogen per each wafer containing plate. Open a chlorotrimethylsilane bottle. Pierce the rubber cap with the syringe and inject the nitrogen into the bottle.Without pulling out the needle, Turn the bottle upside down and drawback two milliliters of chlorotrimethylsilane for each wafer containing plate. Spread the chlorotrimethylsilane in the container, but not directly on the wafer containing plate. Close the container.And incubate it for five minutes per wafer. Next weigh 47.05 grams of PDMS base in a 50 milliliter tube, and add PDMS curing agent at a ratio of 16 to 1 base to curing agent for a total of 50 grams. Mix the PDMS for 10 minutes on a low speed rotator, then pour it into each wafer containing plate to the desired height.Place the plates inside of a vacuum desiccator for two hours. Which will remove air trapped within the PDMS, and form a clear uniform mold. Afterwards incubate the plates in an oven for three hours or overnight at 70 Celsius.To create the microfluidic chamber or MFC. Cut and remove the PDMS molds from the plate with a scalpel, making sure not to force the molds because they're fragile. Follow the instructions in the text manuscript to punch and cut the chambers, depending on the experimental setup.For spinal cord explant culture, punch two seven millimeter wells in the distal side of a large MFC, making sure that they will overlap with the channel edges. On the proximal side, punch one seven millimeter well in the middle of the channel with minimal overlap, so that sufficient space is left for the explants. Punch two additional one millimeter holes in the two edges of the proximal channel.And cut the PDMS into single chambers. Then turn the MFC facing upwards, and use a 20 gauge needle to carve at three small explant caves on the punched seven millimeter well. For dissociated motor neuron culture, punch four six millimeter wells, in the edges of the two channels of a small MFC and cut the PDMS into single chambers.To sterilize the MFC, spread 50 centimeter long sticky tape bands on the bench. Then press both faces of the chamber on the tape and pull it back. Place the clean chambers in a new plate and incubate them in analytical grade, of 70%ethanol for 10 minutes on an orbital shaker.Dispose of the ethanol and dry the chambers in a tissue culture hood or in an oven at 70 degrees Celsius. Then place the chamber in the center of a tissue culture grade glass bottom ditch, and apply minor force on the edges to bind the PDMS to the dish bottom. Incubate the dish for 10 minutes at 70 degrees Celsius.Then press on the chambers to strengthen the adherence. Incubate the dish under UV for 10 minutes, then proceed to coding the MFC. Add 1.5 nanograms per milliliter PLO to both compartments.Making sure that the PLO is running through the channels. By pipetting the coating media directly in the channel entrance. Examine the MFC under a light microscope, to check for bubbles.If air bubbles are blocking the micro grooves, place the MFC in a vacuum desiccators for two minutes. Remove excess air from the MFC channels. Then incubate it overnight with PLO.Replace the PLO with laminin and incubate the MFC for an additional night. Prior to plating, wash the laminin with culture medium. Dissect an ICR E12.5 pregnant mouse, and separate the embryos from the amniotic sac.Put the embryo in HBSS Silicon dish. Remove the head and tail and flip it onto his belly. Gently peel off superficial skin from the embryos back, exposing the spinal cord.Separate the spinal cord from the body from head to tail, using gentle tweezers. Remove the meninges, then remove the dorsal horns and cut the spinal cord into one millimeter thick transverse sections. Dispose of all medium from the proximal compartment of the MFC.Pick up a single spinal cord explant with a pipette, in a total volume of four microliters. And inject it as close as possible to the cave. Draw out any excess liquid from the proximal well via the lateral outlets.Repeat the previous step two more times and make sure that the explants are embedded in the proximal channel. Slowly add 150 microliters of SCEX medium, to the proximal well. One day after plating.Replaced the SCEX medium in the proximal compartment and add rich SCEX medium to the distal compartment. Maintaining a volume gradient of at least 15 microliters per well between the distal and proximal wells. After four to six days, the axons should cross to the distal compartment and be ready for axonal transport imaging.To label the mitochondria and acidic compartments, prepare fresh SCEX medium with 100 nanomolar MitoTracker Deep Red FM, and 100 nanomolar LysoTracker Red. And add it to the microfluidic chambers. Incubate them for 30 to 60 minutes at 37 degrees Celsius.Then wash three times with warm SCEX medium. Proceed with live imaging of axonal transport. Acquiring a 100 time lapse image series at three second intervals.With a total of five minutes per movie. After seven days in microfluidic chambers. Mouse embryonic HB9 GFP spinal cord explants.We're stained with MitoTracker Deep Red and LysoTracker Red dyes. To label the mitochondria and acidic compartments. Axons in the distal grooves were imaged and Kymograph analysis was used to determine the general movement distribution.This revealed a bias in the retrograde direction only in acidic city compartments, but not in mitochondrial transport. The particle density was also quantified, revealing a higher number of mitochondrial particles compared to acidic compartments in the HB9 GFP spinal cord explant axons. Next, single particle transport analysis was conducted using semi-automated software followed by in-house code.This analysis revealed that acidic components and mitochondria have similar particle velocities. But only acidic compartments display a bias towards retrograde movement. Isolating the embryonic spinal cord can be difficult at first.Practice this procedure several times, making sure to use the correct embryonic age and the appropriate dissection tools. The use of microfluidic chambers changes the way we study axonal biology. It allows us to visualize localized axonal processes, which we're once hypothesized to occur only in the cell body.

axonal-transport-organelles-motor-neuron-cultures-using-microfluidic

Research

JoVE Journal

Neuroscience

9.8K Views.  Tel Aviv University. Axonal transport is vital for neuronal health and viability. Our protocol describes an elegant method for monitoring and analyzing axonal transport. And can be adapted for various neuronal disease models.The use of microfluidic chambers enable precise spatial temporal control, which is crucial for studying axonal biology. Axonal transport abnormalities are implicated with several neurodegenerative disease such as ALS. The microfluidic platform enables study of basic mechanisms as well ...