We would like to thank William A. Eimer for imaging technical assistance. This work was supported by the Cure Alzheimer's Fund [to R.E.T], the National Institute of Health [R01AG014713 and R01MH60009 to R.E.T; R03AR063271 and R15EB019704 to A.L.], and the National Science Foundation [NSF1455613 to A.L.].

1. Experimental Preparation
<ol>
	<li>Prepare the following reagents: Dulbecco&#39;s phosphate buffered saline (PBS); Triton X-100; 0.2% PBST (PBS + 0.2% Triton X-100); 32% paraformaldehyde (PFA), diluted into 4% before use; silicone elastomer base and curing agent; antifade mounting medium (e.g., ProLong Gold); and fingernail polish.</li>
	<li>Prepare the following equipment: dissection microscope, two sharp forceps and a pair of scissors for microdissection, a number of pins for microdissection, a Petri dish...

<ol>
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H., Kim, S., Lee, S. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+cellular+basis+of+dendrite+pathology+in+neurodegenerative+diseases.">The cellular basis of dendrite pathology in neurodegenerative diseases.</a> BMB Rep. 50 (1), 5-11 (2016).</li><li>Baloyannis, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dendritic+pathology+in+Alzheimer's+disease.">Dendritic pathology in Alzheimer's disease.</a> J Neurol Sci. 283 (1-2), 153-157 (2009).</li><li>Masliah, E., Terry, R. D., Alford, M., DeTeresa, R., Hansen, L. 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C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Wnt+signaling+through+Dishevelled,+Rac+and+JNK+regulates+dendritic+development.">Wnt signaling through Dishevelled, Rac and JNK regulates dendritic development.</a> Nat Neurosci. 8 (1), 34-42 (2005).</li><li>Grueber, W. B., Jan, L. Y., Jan, Y. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Different+levels+of+the+homeodomain+protein+cut+regulate+distinct+dendrite+branching+patterns+of+Drosophila+multidendritic+neurons.">Different levels of the homeodomain protein cut regulate distinct dendrite branching patterns of Drosophila multidendritic neurons.</a> Cell. 112 (6), 805-818 (2003).</li><li>Sugimura, K., Satoh, D., Estes, P., Crews, S., Uemura, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+of+morphological+diversity+of+dendrites+in+Drosophila+by+the+BTB-zinc+finger+protein+abrupt.">Development of morphological diversity of dendrites in Drosophila by the BTB-zinc finger protein abrupt.</a> Neuron. 43 (6), 809-822 (2004).</li><li>Jan, Y. N., Jan, L. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Branching+out:+mechanisms+of+dendritic+arborization.">Branching out: mechanisms of dendritic arborization.</a> Nat Rev Neurosci. 11 (5), 316-328 (2010).</li><li>Sears, J. C., Broihier, H. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=FoxO+regulates+microtubule+dynamics+and+polarity+to+promote+dendrite+branching+in+Drosophila+sensory+neurons.">FoxO regulates microtubule dynamics and polarity to promote dendrite branching in Drosophila sensory neurons.</a> Dev Biol. 418 (1), 40-54 (2016).</li><li>Li, 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=Silencing+of+the+Drosophila+ortholog+of+SOX5+leads+to+abnormal+neuronal+development+and+behavioral+impairment.">Silencing of the Drosophila ortholog of SOX5 leads to abnormal neuronal development and behavioral impairment.</a> Hum Mol Genet. 26 (8), 1472-1482 (2017).</li><li>Misra, 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=A+Genome-Wide+Screen+for+Dendritically+Localized+RNAs+Identifies+Genes+Required+for+Dendrite+Morphogenesis.">A Genome-Wide Screen for Dendritically Localized RNAs Identifies Genes Required for Dendrite Morphogenesis.</a> G3 (Bethesda). 6 (8), 2397-2405 (2016).</li><li>Emoto, K., 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=Control+of+dendritic+branching+and+tiling+by+the+Tricornered-kinase/Furry+signaling+pathway+in+Drosophila+sensory+neurons.">Control of dendritic branching and tiling by the Tricornered-kinase/Furry signaling pathway in Drosophila sensory neurons.</a> Cell. 119 (2), 245-256 (2004).</li><li>Olesnicky, E. C., 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=Extensive+use+of+RNA-binding+proteins+in+Drosophila+sensory+neuron+dendrite+morphogenesis.">Extensive use of RNA-binding proteins in Drosophila sensory neuron dendrite morphogenesis.</a> G3 (Bethesda). 4 (2), 297-306 (2014).</li><li>Parrish, J. Z., Xu, P., Kim, C. C., Jan, L. Y., Jan, Y. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+microRNA+bantam+functions+in+epithelial+cells+to+regulate+scaling+growth+of+dendrite+arbors+in+drosophila+sensory+neurons.">The microRNA bantam functions in epithelial cells to regulate scaling growth of dendrite arbors in drosophila sensory neurons.</a> Neuron. 63 (6), 788-802 (2009).</li><li>Schindelin, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fiji:+an+open-source+platform+for+biological-image+analysis.">Fiji: an open-source platform for biological-image analysis.</a> Nat Methods. 9 (7), 676-682 (2012).</li><li>Corty, M. M., Matthews, B. J., Grueber, W. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecules+and+mechanisms+of+dendrite+development+in+Drosophila.">Molecules and mechanisms of dendrite development in Drosophila.</a> Development. 136 (7), 1049-1061 (2009).</li><li>Jinushi-Nakao, 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=Knot/Collier+and+cut+control+different+aspects+of+dendrite+cytoskeleton+and+synergize+to+define+final+arbor+shape.">Knot/Collier and cut control different aspects of dendrite cytoskeleton and synergize to define final arbor shape.</a> Neuron. 56 (6), 963-978 (2007).</li><li>Crozatier, M., Vincent, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Control+of+multidendritic+neuron+differentiation+in+Drosophila:+the+role+of+Collier.">Control of multidendritic neuron differentiation in Drosophila: the role of Collier.</a> Dev Biol. 315 (1), 232-242 (2008).</li><li>Copf, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Importance+of+gene+dosage+in+controlling+dendritic+arbor+formation+during+development.">Importance of gene dosage in controlling dendritic arbor formation during development.</a> Eur J Neurosci. 42 (6), 2234-2249 (2015).</li><li>Rosso, S. B., Inestrosa, N. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=WNT+signaling+in+neuronal+maturation+and+synaptogenesis.">WNT signaling in neuronal maturation and synaptogenesis.</a> Front Cell Neurosci. 7, 103 (2013).</li><li>Engel, T., Hernandez, F., Avila, J., Lucas, J. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Full+reversal+of+Alzheimer's+disease-like+phenotype+in+a+mouse+model+with+conditional+overexpression+of+glycogen+synthase+kinase-3.">Full reversal of Alzheimer's disease-like phenotype in a mouse model with conditional overexpression of glycogen synthase kinase-3.</a> J Neurosci. 26 (19), 5083-5090 (2006).</li><li>Longair, M. H., Baker, D. A., Armstrong, J. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Simple+Neurite+Tracer:+open+source+software+for+reconstruction,+visualization+and+analysis+of+neuronal+processes.">Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes.</a> Bioinformatics. 27 (17), 2453-2454 (2011).</li><li>Pool, M., Thiemann, J., Bar-Or, A., Fournier, A. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=NeuriteTracer:+a+novel+ImageJ+plugin+for+automated+quantification+of+neurite+outgrowth.">NeuriteTracer: a novel ImageJ plugin for automated quantification of neurite outgrowth.</a> J Neurosci Methods. 168 (1), 134-139 (2008).</li></ol>

Dendrites that innervate the epidermis are the input regions of neurons, and their morphologies determine how information is received and processed by individual neurons. Development dendrite morphology reflects gene modulation of dendrite organization. The Drosophila larval da neuron of the peripheral nervous system is an important model for studying dendrite development because of: 1) the functional similarity with mammals11,12; 2) four class distincti...

Dendrites, which are the branched projections of a neuron, cover the field that encompasses the neuron&#39;s sensory and synaptic inputs from other neurons1,2. Dendrites are an important component of synapse formation and play a critical role in integrating synaptic inputs, as well as propagating the electrochemical stimulation in a neuron. Dendritic arborization (da) is a process by which neurons form new dendritic trees and branches to create new synapses. The development and morphology of da, such as branch density and grouping patterns, result from multi-step biological processes and are highly correlated to neuronal function. The goal of this protocol is to provide a method for quantitative analysis of neuronal dendritric arborization complexity in Drosophila. 
The complexity of dendrites determines the synaptic types, connectivity, and inputs from partner neurons. Branching patterns and the density of dendrites are involved in processing the signals that converge onto the dendritic field3,4. Dendrites have the flexibility for adjustment in development. For instance, synaptic signaling has an effect on dendrite organization in the somatosensory neuron during the developmental phase and in the mature nervous system5. The establishment of neuronal connectivity relies on the morphogenesis and maturation of dendrites. Malformation of dendrites is associated with impaired neuronal function. Studies have shown that the abnormality of da neuron morphogenesis might contribute to the etiologies of multiple neurodegenerative diseases, including Alzheimer&#39;s disease (AD), Parkinson&#39;s disease (PD), Huntington&#39;s disease (HD), and Lou Gehrig&#39;s disease/Amyotrophic lateral sclerosis (ALS)6,7,8. Synaptic alterations appear in the early stage of AD, in concert with the decline and impairment of neuron function7,8. However, the specifics of how dendrite pathology contributes to pathogenesis in these neurodegenerative diseases remains elusive.
The development of dendrites is regulated by genes that encode a complex network of regulators, such as the Wnt family of proteins9,10, transcription factors, and ligands on cell surface receptors11,12. Drosophila da neurons consist of four classes (Class I, II III, IV), of which class IV da neurons have the most complex branching patterns and have been employed as a powerful experimental system for better understanding morphogenesis13,14. During early morphogenesis, overexpression and/or RNAi silencing of genes in class IV da neurons result in changes in branching patterns and dendrite pruning13. It is important to develop a practical method for quantitative analysis of the neuronal dendritic arborization.
We have previously shown that silencing of the Drosophila ortholog of SOX5, Sox102F, led to shorter dendrites of da neurons and reduced complexity in class IV da neurons15. Here, we present the procedure of quantitative analysis for the neuronal dendritic arborization complexity (NDAC) in Drosophila. This protocol, adapted from the previous described methodology, provides a brief method to assay the development of da sensory neurons. It illustrates the robust image labeling and the da neuron in the third instar larval body wall16,17,18,19. It is a valuable protocol for researchers who wish to investigate the NDAC and developmental differences in vivo.

<table border="0" cellpadding="0" cellspacing="0" style="width:949px;" width="948">
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	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:363px;">Phosphate buffered saline(PBS)</td>
			<td style="width:223px;">Gibco Life Sciences</td>
			<td style="width:197px;">10010-023</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:363px;">TritonX-100</td>
			<td style="width:223px;">Fisher Scientific</td>
			<td style="width:197px;">9002-93-1</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:22px;width:363px;">Paraformaldehyde(PFA)</td>
			<td style="width:223px;">Electron Microscopy Sciences</td>
			<td style="width:197px;">15714-S</td>
			<td></td>
		</tr>
		<tr height="28">
			<td height="28" style="height:29px;width:363px;">Sylgard 184 silicone elastomer base and curing agent</td>
			<td style="width:223px;">Dow Corning Corportation</td>
			<td style="width:197px;">3097366-0516;3097358-1004</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:25px;width:363px;">ProLong Gold Antifade Mountant</td>
			<td style="width:223px;">Thermo Fisher Scientific</td>
			<td style="width:197px;">P36931</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:363px;">Fingernail polish&#160;</td>
			<td style="width:223px;">CVS</td>
			<td style="width:197px;">72180</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:363px;">Stereo microscope</td>
			<td style="width:223px;">Nikon</td>
			<td style="width:197px;">SMZ800</td>
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			<td height="21" style="height:21px;width:363px;">Confocal microscope</td>
			<td style="width:223px;">Nikon</td>
			<td style="width:197px;">Eclipse Ti-E</td>
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			<td height="21" style="height:21px;width:363px;">Petri dish</td>
			<td style="width:223px;">Falcon</td>
			<td style="width:197px;">353001</td>
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			<td height="21" style="height:21px;width:363px;">Forceps</td>
			<td style="width:223px;">Dumont</td>
			<td style="width:197px;">11255-20</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:363px;">Scissors&#160;</td>
			<td style="width:223px;">Roboz Surgical Instrument Co</td>
			<td style="width:197px;">RS-5611</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:363px;">Insect Pins&#160;</td>
			<td style="width:223px;">Roboz Surgical Instrument Co</td>
			<td style="width:197px;">RS-6082-25</td>
			<td></td>
		</tr>
		<tr height="18">
			<td height="18" style="height:19px;width:363px;">Microscope slides and cover slips</td>
			<td style="width:223px;">Fisher Scientific</td>
			<td style="width:197px;">15-188-52</td>
			<td></td>
		</tr>
	</tbody>
</table>

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.

The dendrites of da neurons were labeled by co-overexpressing GFP (UAS-GFP; ppk-GAL4) in the da neural soma and dendritic arbors for GFP fluorescence imaging analysis. The morphology of da neuron dendrites was imaged by an inverted confocal microscope (Figure 2).
The dendrites of da neurons were traced using Fiji ImageJ software. The file was used to estimate the dendrite length (<strong class="xfig...

Watch this Scientific Journal Video about Quantitative Analysis of Neuronal Dendritic Arborization Complexity in Drosophila at JoVE.com

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.

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. ...

The overall goal of this procedure is to observe the impact of the SOX5 gene on the complexity of the dendritic arborization neurons during the neuronal development in Drosophila. This method can help study morphogenesis of neuro-dendrites, and the gene function in the development of nervous system, to better understand neurodegenerative disease genes. Ultimately this technique provides a quantitative analysis of dendrites complexity, which can be used in many different types of neuro-dendrites.The implications of this technique extend toward genetic mechanism of neuro-degenerative disease, because mutation holds the key to understanding gene function. Set-up crosses of UAS-GFP;ppk-GAL4 with the UAS-Sox102F-RNAi strain flies or W118 controls. Culture the flies under standard conditions at 25 degrees Celsius.In about five to six days, use forceps to carefully collect the third instar larvae for dissection. Place a larva in a dissection dish made of silicon elastomer base, and a tissue-culture Petri dish. Then place the dish under the dissection microscope.Now pin the tail of the larva to expose the midline. Then pin the larva mouth hooks so the larva's dorsal side is up. Now add 200 microliters of PBS to the dish to immerse the larva in solution.Next, cut the tail and mouth of larva with small incisions. Then cut the larva open along the dorsal midline and between the two tracheas, going from caudal to rostral. Then place a pin at each of the four corners of the body so the body lies flat.Now fix the larva body wall in four percent PFA for 25 minutes at room temperature. Then wash the larva with PBS three times for five minutes per wash. After the washes, remove the pins and transfer the tissue onto a glass slide.Then immerse the tissue in antifade mounting medium, and mount it with a cover slip. Allow the mounted tissue to air dry for an hour before sealing on the cover slip with fingernail polish. Store these slides in the dark at four degrees Celsius.Capture z-series images with a confocal microscope using a 20X objective. First, set the range of the z-steps to include all of the DA neurons in the larva body wall, and set the step size to a half micrometer. Then store the images as TIF or ND2 files for processing.Next, evaluate the number and morphology of the dendrites on the DA neurons. Begin with assessing their lengths. First, in Fiji ImageJ, split the images into separate channels if necessary.Only the GFP channel needs to be assessed. Next, make a z-projection. In the new window, select max intensity for projection type, and choose the start and stop slices.Then click OK to produce a z-projection image with clear dendrite projections. Now trace the neurites using the plug-in tool. First, go to the soma of the neuron of interest and click where one dendrite emerges from the cell body.Then click at the tip of this dendrite. If the blue line that connects the two points runs the length of the neurite, press Y for yes. Then if this line fits the complete path of the neurite, click complete path.If the line does not fit the path, then click on points further along this neurite to bend the path into multiple line segments that will fit the length of the neurite. Then, click complete path and proceed with marking the path for the next neurite. After completing all the tracing paths, select the Analysis, Measure Paths option to export the paths to a CSV file.Use this data to calculate and average value of path lengths for analysis. Next, calculate the surface area of the neuron. First, select the free hand drawing tool from the Fiji ImageJ window.Then, connect the end points of the neuron of interest. Then, select the Measure option from the Analyze window. The result appears in a new box with the value for the area selected.Copy this value to the data analysis software. Finally, calculate the total number of branches using the Analyze Skeletonized Paths plugin. The dendrites of DA neurons were labeled by co-overexpressing GFP in their soma and dendrite arbors for GFP florescence imaging analysis.The morphology of dendrites was imaged using an inverted confocal microscope. The dendrites of DA neurons were traced as described. The file was used to estimate the dendrite length.Silencing of Sox102F in DA neurons in the third instar larva led to a significant reduction in the total number of dendrites with about half of the branch length and with a simpler structure, showing only half the number of branches. Logically, this led to reduction in arbor surface area. This protocol provides a quick method to assess development of DA sensory neurons.While attempting this procedure, be sure to take an ample number of images of each group of DA neurons to get a good coverage. Following this procedure, other methods like dendrite analysis can be performed in order to answer additional questions about dendrite development. Since it's development, this technique has helped researchers in the field of neurosciences make inferences into neurodegenerative disease such as Alzheimer's using model systems.

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13.8K ビュー.  Mass General Institute of Neurodegenerative Disease. この手順の全体的な目標は、ショウジョウバエのニューロンの発達中に樹状樹状の樹状樹状ニューロンの複雑さに対するSOX5遺伝子の影響を観察することです。この方法は、神経変性疾患遺伝子をよりよく理解するために、神経デンドライトの形態形成、および神経系の発達における遺伝子機能を研究するのに役立ちます。最終的にこの技術は、多くの異なるタイプの神?...

ビデオ: 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...

assessment of hippocampal dendritic complexity in aged mice using the golgi-cox method

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

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...

assessment of dendritic arborization in the dentate gyrus of the hippocampal region in mice

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

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...

time-lapse imaging of neuronal arborization using sparse adeno-associated virus labeling of genetically targeted retinal cell populations

Time-Lapse Imaging of Neuronal Arborization using Sparse Adeno-Associated Virus Labeling of Genetically Targeted Retinal Cell Populations

Here, we present a method for investigating neurite morphogenesis in postnatal mouse retinal explants by time-lapse confocal microscopy. We describe an approach for sparse labeling and acquisition of retinal cell types and their fine processes using recombinant adeno-associated virus vectors that express membrane-targeted fluorescent proteins in a Cre-dependent manner.

time-lapse live imaging and quantification of fast dendritic branch dynamics in developing drosophila neurons

Time-lapse Live Imaging and Quantification of Fast Dendritic Branch Dynamics in Developing Drosophila Neurons

Here, we describe the method we employed to image highly motile dendritic filopodia in a live preparation of the Drosophila larval brain, and the protocol we developed to quantify time-lapse 3D imaging datasets for quantitative assessments of dendrite dynamics in developing...

Time-lapse Live Imaging and Quantification of Fast Dendritic Branch Dynamics in Developing Drosophila Neurons

analysis of dendritic spine morphology in cultured cns neurons

Analysis of Dendritic Spine Morphology in Cultured CNS Neurons

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...

quantitative analysis of climbing defects in a drosophila model of neurodegenerative disorders

Quantitative Analysis of Climbing Defects in a Drosophila Model of Neurodegenerative Disorders

We present an optimized inexpensive and reliable negative geotaxis assay in Drosophila melanogaster as a model for neurodegenerative disorders. Being more sensitive to mild locomotor defects, this assay will help screen for potential genetic interactions and drug targets.

quantitative cell biology of neurodegeneration in drosophila through unbiased analysis of fluorescently tagged proteins using imagej

Quantitative Cell Biology of Neurodegeneration in Drosophila Through Unbiased Analysis of Fluorescently Tagged Proteins Using ImageJ

We have developed a simple and adaptable workflow to extract quantitative data from fluorescence-imaging-based cell biological studies of protein aggregation and autophagic flux in the central nervous system of Drosophila models of...

Quantitative Cell Biology of Neurodegeneration in Drosophila Through Unbiased Analysis of Fluorescently Tagged Proteins Using ImageJ

analyzing dendritic morphology in columns and layers

Analyzing Dendritic Morphology in Columns and Layers

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...

the analysis of purkinje cell dendritic morphology in organotypic slice cultures

The Analysis of Purkinje Cell Dendritic Morphology in Organotypic Slice Cultures

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...

functional analysis of the larval feeding circuit in drosophila

Functional Analysis of the Larval Feeding Circuit in Drosophila

The feeding circuit in Drosophila melanogaster larvae serves a simple yet powerful model that allows changes in feeding rate to be correlated with alterations in the stomatogastric neural circuitry. This circuit is composed of central serotonergic neurons that send projections to the mouth hooks as well as the...

Functional Analysis of the Larval Feeding Circuit in Drosophila

quantification of macronutrients intake in a thermogenetic neuronal screen using drosophila larvae

Quantification of Macronutrients Intake in a Thermogenetic Neuronal Screen using Drosophila Larvae

Described here is a protocol that enables the colorimetric quantification of the amount of food eaten within a defined interval of time by Drosophila melanogaster larvae exposed to diets of different macronutrient quality. These assays are conducted in the context of a neuronal thermogenetic...

Quantification of Macronutrients Intake in a Thermogenetic Neuronal Screen using Drosophila Larvae

inducing dendritic growth in cultured sympathetic neurons

Inducing Dendritic Growth in Cultured Sympathetic Neurons

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...

automated sholl analysis of digitized neuronal morphology at multiple scales

Automated Sholl Analysis of Digitized Neuronal Morphology at Multiple Scales

We have developed a computer program to analyze neuronal morphology.  In combination with two existing open source analysis tools, our program performs Sholl analysis and determines the number of neurites, branch points, and neurite tips.  The analyses are performed so that local changes in neurite morphology can be...

quantitative measurement of the immune response and sleep in drosophila

Quantitative Measurement of the Immune Response and Sleep in Drosophila

To understand a link between the immune response and behavior, we describe a method to measure locomotor behavior in Drosophila during bacterial infection as well as the ability of flies to mount an immune response by monitoring survival, bacterial load, and real-time activity of a key regulator of innate immunity,...

Quantitative Measurement of the Immune Response and Sleep in Drosophila

novel whole-tissue quantitative assay of nitric oxide levels in drosophila neuroinflammatory response

Novel Whole-tissue Quantitative Assay of Nitric Oxide Levels in Drosophila Neuroinflammatory Response

Levels of the inflammatory cell-signaling molecule nitric oxide (NO) are commonly assayed using Griess reagent. In this protocol, we have created a modified Griess assay utilizing live Drosophila brain tissue in order to detect the secretion of NO in a simple, quantifiable and highly repeatable...

Novel Whole-tissue Quantitative Assay of Nitric Oxide Levels in Drosophila Neuroinflammatory Response

quantitative analysis of chromatin proteomes in disease

Quantitative Analysis of Chromatin Proteomes in Disease

Advances in mass spectrometry have allowed the high throughput analysis of protein expression and modification in a host of tissues. Combined with subcellular fractionation and disease models, quantitative mass spectrometry and bioinformatics can reveal new properties in biological systems. The method described herein analyzes chromatin-associated proteins in the setting of heart disease and is readily applicable to other in vivo models of human...

drosophila optogenetics: a method to manipulate neuronal circuits

Optogenetics enables the use of light to manipulate neurons that are genetically engineered to express specific opsins&#8211;light-sensitive proteins whose light activation triggers a change in the state of the neuron. Here we describe an optogenetic approach in Drosophila using the opsin Channelrhodopsin2. The example protocol features an optogenetics assay set to study the neuronal circuitry behind the fly&#39;s escape...

Drosophila Optogenetics: A Method to Manipulate Neuronal Circuits

preparation of neuronal cultures from midgastrula stage drosophila embryos

Preparation of Neuronal Cultures from Midgastrula Stage Drosophila Embryos

This video demonstrates the preparation of primary neuronal cultures from midgastrula stage Drosophila embryos. Views of live cultures show cells 1 hour after plating and differentiated neurons after 2 days of growth in a bicarbonate-based defined medium. The neurons are electrically excitable and form synaptic...

3d particle tracking for noninvasive in vivo analysis of synaptic microtubule dynamics in dendrites and neuromuscular junctions of drosophila

3D Particle Tracking for Noninvasive In Vivo Analysis of Synaptic Microtubule Dynamics in Dendrites and Neuromuscular Junctions of Drosophila

This study presents a noninvasive intravital neuronal imaging strategy combined with a new software strategy to achieve automated, unbiased tracking and analysis of in vivo microtubule (MT) plus-end dynamics in the sensory dendrites and the neuromuscular junctions of Drosophila.

Neuronal morphology plays a significant role in determining how neurons function and communicate1-3. Specifically, it affects the ability of neurons to receive inputs from other cells2 and contributes to the propagation of action potentials4,5. The morphology of the neurites also affects how information is processed. The diversity of dendrite morphologies facilitate local and long range signaling and allow individual neurons or groups of neurons to carry out specialized functions within the neuronal network6,7. Alterations in dendrite morphology, including fragmentation of dendrites and changes in branching patterns, have been observed in a number of disease states, including Alzheimer's disease8, schizophrenia9,10, and mental retardation11. The ability to both understand the factors that shape dendrite morphologies and to identify changes in dendrite morphologies is essential in the understanding of nervous system function and dysfunction.
Neurite morphology is often analyzed by Sholl analysis and by counting the number of neurites and the number of branch tips. This analysis is generally applied to dendrites, but it can also be applied to axons. Performing this analysis by hand is both time consuming and inevitably introduces variability due to experimenter bias and inconsistency. The Bonfire program is a semi-automated approach to the analysis of dendrite and axon morphology that builds upon available open-source morphological analysis tools. Our program enables the detection of local changes in dendrite and axon branching behaviors by performing Sholl analysis on subregions of the neuritic arbor. For example, Sholl analysis is performed on both the neuron as a whole as well as on each subset of processes (primary, secondary, terminal, root, etc.) Dendrite and axon patterning is influenced by a number of intracellular and extracellular factors, many acting locally. Thus, the resulting arbor morphology is a result of specific processes acting on specific neurites, making it necessary to perform morphological analysis on a smaller scale in order to observe these local variations12.
The Bonfire program requires the use of two open-source analysis tools, the NeuronJ plugin to ImageJ and NeuronStudio. Neurons are traced in ImageJ, and NeuronStudio is used to define the connectivity between neurites. Bonfire contains a number of custom scripts written in MATLAB (MathWorks) that are used to convert the data into the appropriate format for further analysis, check for user errors, and ultimately perform Sholl analysis. Finally, data are exported into Excel for statistical analysis. A flow chart of the Bonfire program is shown in Figure 1.

We have developed a computer program to analyze neuronal morphology. In combination with two existing open source analysis tools, our program performs Sholl analysis and determines the number of neurites, branch points, and neurite tips. The analyses are performed so that local changes in neurite morphology can be observed.

Neuronal morphology plays a significant role in determining how neurons function and communicate1-3.  Specifically, it affects the ability of neurons to ...

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 ...

Optogenetic Perturbation of Neural Activity with Laser Illumination in Semi-intact Drosophila Larvae in Motion

Drosophila larval locomotion is a splendid model system in developmental and physiological neuroscience, by virtue of the genetic accessibility of the underlying neuronal components in the circuits1-6. Application of optogenetics7,8 in the larval neural circuit allows us to manipulate neuronal activity in spatially and temporally patterned ways9-13. Typically, specimens are broadly illuminated with a mercury lamp or LED, so specificity of the target neurons is controlled by binary gene expression systems such as the Gal4-UAS system14,15. In this work, to improve the spatial resolution to "sub-genetic resolution", we locally illuminated a subset of neurons in the ventral nerve cord using lasers implemented in a conventional confocal microscope. While monitoring the motion of the body wall of the semi-intact larvae, we interactively activated or inhibited neural activity with channelrhodopsin16,17 or halorhodopsin18-20, respectively. By spatially and temporally restricted illumination of the neural tissue, we can manipulate the activity of specific neurons in the circuit at a specific phase of behavior. This method is useful for studying the relationship between the activities of a local neural assembly in the ventral nerve cord and the spatiotemporal pattern of motor output.

Optogenetic Perturbation of Neural Activity with Laser Illumination in Semi-intact Drosophila Larvae in Motion

Here we describe a protocol for optogenetic manipulation of motoneuronal activity while monitoring changes in motor output (muscle contraction) in semi-intact Drosophila larvae using lasers within a conventional confocal microscope. This technique enables researchers to achieve local perturbation of neural activity in a few neuromeres to elucidate the dynamics of motor circuits.

Drosophila larval locomotion is a splendid model system in developmental and physiological neuroscience, by virtue of the genetic accessibility of the ...

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 ...

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 ...

Locomotive defects resulting from neurodegenerative disorders can be a late onset symptom of disease, following years of subclinical degeneration, and thus current therapeutic treatment strategies are not curative. Through the use of whole exome sequencing, an increasing number of genes have been identified to play a role in human locomotion. Despite identifying these genes, it is not known how these genes are crucial to normal locomotive functioning. Therefore, a reliable assay, which utilizes model organisms to elucidate the role of these genes in order to identify novel targets of therapeutic interest, is needed more than ever. We have designed a sensitized version of the negative geotaxis assay that allows for the detection of milder defects earlier and has the ability to evaluate these defects over time. The assay is performed in a glass graduated cylinder, which is sealed with a wax barrier film. By increasing the threshold distance to be climbed to 17.5 cm and increasing the experiment duration to 2 min&#160;we have observed a greater sensitivity in detecting mild mobility dysfunctions. The assay is cost effective and does not require extensive training to obtain highly reproducible results. This makes it an excellent technique for screening candidate drugs in Drosophila mutants with locomotion defects.

We present an optimized inexpensive and reliable negative geotaxis assay in Drosophila melanogaster as a model for neurodegenerative disorders. Being more sensitive to mild locomotor defects, this assay will help screen for potential genetic interactions and drug targets.

Locomotive defects resulting from neurodegenerative disorders can be a late onset symptom of disease, following years of subclinical degeneration, and ...

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 ...

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 ...

With the rising prevalence of neurodegenerative diseases, it is increasingly important to understand the underlying pathophysiology that leads to neuronal dysfunction and loss. Fluorescence-based imaging tools and technologies enable unprecedented analysis of subcellular neurobiological processes, yet there is still a need for unbiased, reproducible, and accessible approaches for extracting quantifiable data from imaging studies. We have developed a simple and adaptable workflow to extract quantitative data from fluorescence-based imaging studies using Drosophila models of neurodegeneration. Specifically, we describe an easy-to-follow, semi-automated approach using Fiji/ImageJ to analyze two cellular processes: first, we quantify protein aggregate content and profile in the Drosophila optic lobe using fluorescent-tagged mutant huntingtin proteins; and second, we assess autophagy-lysosome flux in the Drosophila visual system with ratiometric-based quantification of a tandem fluorescent reporter of autophagy. Importantly, the protocol outlined here includes a semi-automated segmentation step to ensure all fluorescent structures are analyzed to minimize selection bias and to increase resolution of subtle comparisons. This approach can be extended for the analysis of other cell biological structures and processes implicated in neurodegeneration, such as proteinaceous puncta (stress granules and synaptic complexes), as well as membrane-bound compartments (mitochondria and membrane trafficking vesicles). This method provides a standardized, yet adaptable reference point for image analysis and quantification, and could facilitate reliability and reproducibility across the field, and ultimately enhance mechanistic understanding of neurodegeneration.

We have developed a simple and adaptable workflow to extract quantitative data from fluorescence-imaging-based cell biological studies of protein aggregation and autophagic flux in the central nervous system of Drosophila models of neurodegeneration.

With the rising prevalence of neurodegenerative diseases, it is increasingly important to understand the underlying pathophysiology that leads to neuronal ...

Imaging and Analysis of Neurofilament Transport in Excised Mouse Tibial Nerve

Neurofilament protein polymers move along axons in the slow component of axonal transport at average speeds of ~0.35-3.5 mm/day. Until recently the study of this movement in situ was only possible using radioisotopic pulse-labeling, which permits analysis of axonal transport in whole nerves with a temporal resolution of days and a spatial resolution of millimeters. To study neurofilament transport in situ with higher temporal and spatial resolution, we developed a hThy1-paGFP-NFM transgenic mouse that expresses neurofilament protein M tagged with photoactivatable GFP in neurons. Here we describe fluorescence photoactivation pulse-escape and pulse-spread methods to analyze neurofilament transport in single myelinated axons of tibial nerves from these mice ex vivo. Isolated nerve segments are maintained on the microscope stage by perfusion with oxygenated saline and imaged by spinning disk confocal fluorescence microscopy. Violet light is used to activate the fluorescence in a short axonal window. The fluorescence in the activated and flanking regions is analyzed over time, permitting the study of neurofilament transport with temporal and spatial resolution on the order of minutes&#160;and microns, respectively. Mathematical modeling can be used to extract kinetic parameters of neurofilament transport including the velocity, directional bias and pausing behavior from the resulting data. The pulse-escape and pulse-spread methods can also be adapted to visualize neurofilament transport in other nerves. With the development of additional transgenic mice, these methods could also be used to image and analyze the axonal transport of other cytoskeletal and cytosolic proteins in axons.

We describe fluorescence photoactivation methods to analyze the axonal transport of neurofilaments in single myelinated axons of peripheral nerves from transgenic mice that express a photoactivatable neurofilament protein.

Neurofilament protein polymers move along axons in the slow component of axonal transport at average speeds of ~0.35-3.5 mm/day. Until recently the study ...