We thank Gary Laevsky for helpful discussions on microscopy. This work was funded by NIH grants R01GM061107 and R01GM067758 to E.R.G.

Note: The procedure for muscle removal (Figure 1) is a modification of previously described methods for preparing larval fillets. The steps that precede and follow muscle removal are outlined briefly and the reader is referred to previous work 10, 11 for more detailed descriptions.
1. Dissect Larva in Cold Saline
<ol>
	<li>Prepare a working dilution of cold HL3.1 saline15 or cold Ca2+-free HL3.1 saline11 (Table 1). Place the larva in a silicone elastomer dish with just enough cold saline to cover the bottom of the dish. 
	NOTE: See Discussion regarding the choice of saline.</li>
</ol>
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1x HL3.1 saline (pH 7.2)</td>
		</tr>
		<tr>
			<td>&#160;&#160;&#160; 5 mM HEPES</td>
		</tr>
		<tr>
			<td>&#160;&#160;&#160; 70 mM NaCl</td>
		</tr>
		<tr>
			<td>&#160;&#160;&#160; 5 mM KCl</td>
		</tr>
		<tr>
			<td>&#160;&#160;&#160; 1.5 mM CaCl2&#160;&#160; (omit for Ca2+-free saline)</td>
		</tr>
		<tr>
			<td>&#160;&#160;&#160; 4 mM MgCl2</td>
		</tr>
		<tr>
			<td>&#160;&#160;&#160; 10 mM NaHCO3</td>
		</tr>
		<tr>
			<td>&#160;&#160;&#160; 5 mM trehalose</td>
		</tr>
		<tr>
			<td>&#160;&#160;&#160; 115 mM sucrose</td>
		</tr>
		<tr>
			<td></td>
		</tr>
		<tr>
			<td>Filter sterilize and store at 4 &#176;C</td>
		</tr>
		<tr>
			<td>Note: Composition mimics insect hemolymph</td>
		</tr>
	</tbody>
</table>
Table 1. Composition of Cold Saline.
<ol start="2">
	<li>Position the larva with the ventral side up. The ventral surface of the larva can be identified by the abdominal dentical belts and the dorsal side by the primary larval tracheal tubes running from anterior to posterior. Stretch the larva in the anterior-posterior direction and pin the head and tail to a silicone elastomer dissecting dish using insect pins. Use fine dissecting scissors to cut along the ventral midline, beginning at one end and progressing toward the other. 
	NOTE: This orientation preserves the commonly studied dorsal cluster of da neurons.</li>
	<li>After the larva is cut open, pin the four corners to the dissecting dish as though opening a book. Use forceps to grab and remove internal organs including the CNS, gut, and trachea. Adjust insect pins so that the fillet is taut but not maximally stretched. 
	NOTE: Muscles are anchored to the body wall at segmental boundaries. Although muscles cover most of the body wall, they are absent in a narrow region near the dorsal midline.</li>
</ol>
2. Muscle Removal
<ol>
	<li>Locate the dorsal midline of the larva, where muscle tissue is absent. Position a single forceps prong such that it can be inserted underneath the muscle tissue in the flattest possible orientation.</li>
	<li>Starting at the dorsal midline, near the anterior boundary of the segment, carefully slide the forceps prong between the muscle and epidermis, taking care to minimize contact between the forceps and epidermis.</li>
	<li>Pull the forceps upwards to break the attachment of the muscle to the body wall at one anchor point. Repeat this process for the remaining hemi-segment(s) of interest. 
	NOTE: This protocol optimizes preservation of the posterior of each da neuron dendrite field. To preserve the anterior part of the dendrite field, it is best to insert the forceps prong at the posterior end of each segment.</li>
	<li>Re-adjust insect pins such that the larval fillet is maximally stretched in all directions.</li>
	<li>Fix the fillet while it is still pinned to the dissecting dish using cold, freshly prepared 4% formaldehyde in PBS for 25 min.</li>
	<li>Rinse 5 times in PBS.</li>
	<li>Use forceps to carefully pull away muscle tissue from the remaining anchor points, taking care to minimize contact with the epidermis.</li>
	<li>Unpin and remove the fillet from the dissecting dish to a 1.5 ml microcentrifuge tube. Perform all subsequent washing, blocking, and immunofluorescence staining steps, as previously described11.</li>
</ol>
3. Mount the Larval Fillet
<ol>
	<li>First remove the head and tail using fine dissecting scissors in order to make the sample as flat as possible. Mount the fillet on a coverslip in antifade mountant with the inner surface of the fillet facing the coverslip.</li>
	<li>Place a microscope slide on the coverslip and press gently to disperse the mounting medium. Flip the microscope slide over and seal the coverslip on the slide using nail polish. Slides can be stored at -20 &#176;C for at least one month.</li>
</ol>

<ol>
	<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>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>Parrish, J. Z., Emoto, K., Kim, M. D., 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=Mechanisms+that+regulate+establishment,+maintenance,+and+remodeling+of+dendritic+fields.">Mechanisms that regulate establishment, maintenance, and remodeling of dendritic fields.</a> Annu Rev Neurosci. 30, 399-423 (2007).</li><li>Kim, M. E., Shrestha, B. R., Blazeski, R., Mason, C. A., 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=Integrins+establish+dendrite-substrate+relationships+that+promote+dendritic+self-avoidance+and+patterning+in+Drosophila+sensory+neurons.">Integrins establish dendrite-substrate relationships that promote dendritic self-avoidance and patterning in Drosophila sensory neurons.</a> Neuron. 73 (1), 79-91 (2012).</li><li>Han, 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=Integrins+regulate+repulsion-mediated+dendritic+patterning+of+Drosophila+sensory+neurons+by+restricting+dendrites+in+a+2D+space.">Integrins regulate repulsion-mediated dendritic patterning of Drosophila sensory neurons by restricting dendrites in a 2D space.</a> Neuron. 73 (1), 64-78 (2012).</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>Jiang, N., Soba, P., Parker, E., Kim, C. C., Parrish, J. Z. <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+regulates+a+developmental+transition+in+epithelial+cells+that+restricts+sensory+dendrite+growth.">The microRNA bantam regulates a developmental transition in epithelial cells that restricts sensory dendrite growth.</a> Development. 141 (13), 2657-2668 (2014).</li><li>Meltzer, 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=Epidermis-derived+Semaphorin+promotes+dendrite+self-avoidance+by+regulating+dendrite-substrate+adhesion+in+Drosophila+sensory+neurons.">Epidermis-derived Semaphorin promotes dendrite self-avoidance by regulating dendrite-substrate adhesion in Drosophila sensory neurons.</a> Neuron. 89 (4), 741-755 (2016).</li><li>Han, 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=Epidermal+cells+are+the+primary+phagocytes+in+the+fragmentation+and+clearance+of+degenerating+dendrites+in+Drosophila.">Epidermal cells are the primary phagocytes in the fragmentation and clearance of degenerating dendrites in Drosophila.</a> Neuron. 81 (3), 544-560 (2014).</li><li>Brent, J. R., Werner, K. M., McCabe, B. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Drosophila+larval+NMJ+dissection.">Drosophila larval NMJ dissection.</a> J Vis Exp. (24), (2009).</li><li>Karim, M. R., Moore, A. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Morphological+analysis+of+Drosophila+larval+peripheral+sensory+neuron+dendrites+and+axons+using+genetic+mosaics.">Morphological analysis of Drosophila larval peripheral sensory neuron dendrites and axons using genetic mosaics.</a> J Vis Exp. (57), e3111 (2011).</li><li>Gustafsson, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Surpassing+the+lateral+resolution+limit+by+a+factor+of+two+using+structured+illumination+microscopy.">Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy.</a> J Microscopy. 198 (2), 82-87 (2000).</li><li>Ashdown, G. W., Cope, A., Wiseman, P. W., Owen, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+flow+quantified+beyond+the+diffraction+limit+by+spatiotemporal+image+correlation+of+structured+illumination+microscopy+data.">Molecular flow quantified beyond the diffraction limit by spatiotemporal image correlation of structured illumination microscopy data.</a> Biophys J. 107 (9), L21-L23 (2014).</li><li>Zhang, W., Yan, Z., 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=Sound+response+mediated+by+the+TRP+channels+NOMPC,+NANCHUNG,+and+INACTIVE+in+chordotonal+organs+of+Drosophila+larvae.">Sound response mediated by the TRP channels NOMPC, NANCHUNG, and INACTIVE in chordotonal organs of Drosophila larvae.</a> PNAS. 10 (33), 13612-13617 (2013).</li><li>Feng, Y., Ueda, A., Wu, C. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+modified+minimal+hemolymph-like+solution,+HL3.1,+for+physiological+recordings+at+the+neuromuscular+junctions+of+normal+and+mutant+Drosophila+larvae.">A modified minimal hemolymph-like solution, HL3.1, for physiological recordings at the neuromuscular junctions of normal and mutant Drosophila larvae.</a> J Neurogenet. 18 (2), 377-402 (2004).</li><li>Babcock, D. T., Landry, C., Galko, M. 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The authors have nothing to disclose.

Here a protocol is described for manual removal of muscle tissue from Drosophila larval fillets. This protocol modifies previously described larval dissection techniques10,11. After the larva is dissected in a silicone elastomer dish, the dorsal midline is located. A single forceps prong, in its flattest possible orientation, is carefully inserted between the muscle tissue and the epidermis, near the dorsal midline. The forceps are gently pulled upwards to separate muscle tissue from one anchor point in each larval segment of interest. The larval fillet is then fixed in cold formaldehyde after which forceps are used again to pull away muscle from the remaining anchor points.
While it is tempting to perform the entirety of the muscle removal procedure post-fixation, we find that stretched muscle, once fixed, remains flattened and closely apposed to the epidermis even after detachment from an anchor point, rendering it difficult to manipulate without damaging the underlying tissue. Additionally, in our experience, fixed muscle tissue is brittle and tears easily, preventing its complete removal from the body wall. In contrast, when muscle is detached from one anchor point prior to fixation, it will contract towards the remaining anchor point during fixation, leaving tissue stubs that can be more easily grabbed by forceps and pulled from the larval body wall.
In order to best preserve samples, considerable care must be taken to minimize contact between the forceps and the epidermis during the muscle removal procedure. As a result, our protocol may add several minutes to previously described dissection techniques10,11. To avoid tissue degradation, the number of larvae that are dissected prior to fixation should be limited such that elapsed time is no more than 25 minutes. Additionally, we recommend testing multiple pairs of forceps &#8212; forceps of the same model may vary considerably in shape and sharpness&#160;&#8212; and adjusting the extent to which fillets are stretched prior to muscle removal in order to improve tissue preservation and dissection speed.
Lastly, we recommend experimenting with the use of Ca2+-free HL3.1 saline versus standard HL3.1 saline during larval dissection. In the absence of calcium, larval muscle contractions are greatly reduced. Thus, larval fillets may be easier to manipulate when dissected in Ca2+-free HL3.1 saline. However, we find that muscle contraction creates space between the muscle and epidermis and this can facilitate the insertion of forceps between these tissues while minimizing risk of damage to the epidermis. As a result, standard HL3.1 may be preferable for preserving the integrity of the epidermis and da neurons. We obtain good results with either saline and the choice is left to the user.
While our protocol increases the duration and complexity of previously described dissection techniques10,11, it offers several improvements that are useful for imaging larval sensory neurons and epidermal cells. First, it permits imaging of neuronally and epidermally expressed proteins that are otherwise obscured by muscle tissue. Second, it improves the fluorescence signal to noise ratio. Lastly, it enables use of super-resolution microscopy for superior discrimination of protein spatial relationships in da neurons and the epidermis. The improved imaging quality that we observe following muscle removal is likely the result of reduced photon absorption and scattering as well as reduced distance between the sample and the coverslip. Although not demonstrated here, muscle removal likely also improves antibody access to the epidermis and da neurons, improving the quality of immunofluorescence. Greater antibody accessibility may be particularly useful for immunofluorescence protocols performed in the absence of a tissue permeabilizing agent4.
The improvements gained by use of this protocol are likely to benefit studies of the neuronal and epidermal factors that regulate dendrite morphogenesis in sensory neurons. Furthermore, muscle removal has previously facilitated electrophysiological study of sensory neurons in the larval body wall and a modified version of this protocol may be useful for future studies that employ neurophysiological manipulation of larval sensory neurons. Lastly, a modified version of this protocol may be useful towards other applications such as the isolation of single da neurons for gene expression profiling.

Drosophila larval dendritic arborization (da) neurons provide a valuable model for studying neuronal development due to their amenability to genetic manipulation and the ease with which they can be imaged. These sensory neurons have been instrumental in the identification of numerous pathways that control dendrite morphogenesis1-3.
Four classes of da neurons (class I - IV) innervate the larval epidermis. These neurons lie between the basement membrane and the epidermis, with their dendrites forming largely two-dimensional arrays4,5. Of the four classes, class IV da neurons have the most highly branched arbors and, like sensory neurons of other animals, the elaboration of these arbors requires intrinsic factors as well as cues from neighboring tissues, particularly the epidermis, for their development6-9.
Studies to determine how such neuronal and extra-neuronal factors control dendrite morphogenesis benefit from the ability to detect protein expression in situ by immunofluorescence. The outer cuticle of the larva is impenetrable to antibodies, but this impediment is easily overcome by the preparation of larval fillets through well-established dissection methods10,11. However, the body wall muscle tissue that lies just interior to the basement membrane presents several challenges towards visualization of da neurons and epidermal cells. First, the muscle tissue, which lines most of the body wall, greatly obscures fluorescent signals emanating from neuronal or epidermal tissue. This substantially reduces the signal to noise ratio in the sample. Second, many relevant proteins may be expressed in the muscle tissue as well as in the neurons or epidermis. This muscle-derived fluorescence signal is likely to further obscure detection of a fluorescence signal from the neuron or epidermis. Finally, advances in microscopy technologies now permit imaging of samples at sub-diffraction resolution and may be especially helpful in discerning the localization of proteins that are expressed in neurons and surrounding epidermal cells12,13. However, imaging via super-resolution microscopy benefits from a strong signal to noise ratio and close proximity of the sample to the coverslip. In addition to reducing the signal to noise ratio, the larval body wall muscle distances da neurons from the coverslip, thereby limiting the improved image resolution that can be achieved with super-resolution microscopy methods. Besides challenges for immunofluorescence analysis, muscle tissue presents a barrier to electrophysiological recording from sensory neurons in the larval body wall. Its removal therefore benefits neurophysiological manipulation of sensory neurons14.
Here a method for manual removal of Drosophila larval muscle tissue is described. We demonstrate that our protocol permits immunofluorescence imaging of proteins that are otherwise obscured by muscle tissue, improves the signal to noise ratio for visualization of class IV da neurons, and enables the use of super-resolution microscopy to better discriminate spatial relationships of proteins and cellular structures in da neurons and the epidermis.

<table border="0" cellpadding="0" cellspacing="0" width="1299">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:413px;">Dumont #5 tweezers</td>
			<td style="width:304px;">Electron Microscopy Sciences</td>
			<td style="width:151px;">72701-D</td>
			<td style="width:432px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Micro Scissors, 8 cm, straight, 5 mm blades, 0.1 mm tips</td>
			<td>World Precision Instruments</td>
			<td>14003</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Sylgard 184 silicone elastomer kit</td>
			<td>Dow Corning</td>
			<td>3097358-1004</td>
			<td>for dissecting plates</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Austerlitz insect pins, 0.1 mm</td>
			<td>Fine Science Tools</td>
			<td>26002-10</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Fostec 8375 light source</td>
			<td>Artisan Technology Group</td>
			<td>62792-4</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Zeiss Stemi 2000</td>
			<td>Carl Zeiss Microscopy</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Vectashield antifade mounting medium</td>
			<td>Vector Laboratories</td>
			<td>H-1000</td>
			<td>for confocal microscopy</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Prolong Diamond antifade mountant</td>
			<td>Life Technologies</td>
			<td>P36970</td>
			<td>for structured illumination microscopy</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Micro cover glass, 22x22 mm, No. 1.5</td>
			<td>VWR</td>
			<td>48366-227</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Superfrost Plus microscope slides, 25 x 75 x 1.0 mm</td>
			<td>Fisherbrand</td>
			<td>12-550-15</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Mouse anti-Coracle antibody</td>
			<td>Developmental Studies Hybridoma Bank</td>
			<td>C615.16</td>
			<td>supernatant, dilute 1:50</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Mouse anti-Discs large antibody</td>
			<td>Developmental Studies Hybridoma Bank</td>
			<td>4F3</td>
			<td>supernatant, dilute 1:50</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Rabbit anti-dsRed antibody</td>
			<td>Clontech</td>
			<td>632496</td>
			<td>dilute 1:1000</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Goat anti-rabbit antibody, Alexa Fluor 568 conjugated</td>
			<td>ThermoFisher Scientific</td>
			<td>A-11011</td>
			<td>dilute 1:1000</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Goat anti-mouse antibody, Alexa Fluor 488 conjugated</td>
			<td>ThermoFisher Scientific</td>
			<td>A-11001</td>
			<td>dilute 1:500</td>
		</tr>
	</tbody>
</table>

removal of drosophila muscle tissue from larval fillets for immunofluorescence analysis of sensory neurons and epidermal cells

Drosophila larval dendritic arborization (da) neurons are a popular model for investigating mechanisms of neuronal morphogenesis. Da neurons develop in communication with the epidermal cells they innervate and thus their analysis benefits from in situ visualization of both neuronally and epidermally expressed proteins by immunofluorescence. Traditional methods of preparing larval fillets for immunofluorescence experiments leave intact the muscle tissue that covers most of the body wall, presenting several challenges to imaging neuronal and epidermal proteins. Here we describe a method for removing muscle tissue from Drosophila larval fillets. This protocol enables imaging of proteins that are otherwise obscured by muscle tissue, improves signal to noise ratio, and facilitates the use of super-resolution microscopy to study da neuron development.

We demonstrate the utility of the muscle removal procedure for improving signal to noise ratio in immunofluorescence experiments to co-visualize the septate junction proteins Coracle (Cora) and Discs-large (Dlg) together with class IV da neurons labeled with the membrane marker CD4-tdTomato.
Cora has been previously used to identify tracts where da neuron dendrites are enclosed by epidermal cells and is one of many identified epidermal factors that have been studied in association with the morphogenesis and function of da neuron dendrites4,6-9,16. Immunostaining with anti-DsRed to detect the neurons (red) and anti-Cora antibody (green) was performed on larval fillets with muscle removed (muscle-off) and with muscle intact (muscle-on). For each condition, the posterior dendrite field of the class IV da neuron was imaged using a laser scanning confocal microscope. Images were obtained using identical imaging parameters for both conditions. We additionally imaged muscle-on fillets using increased laser power to compensate for interference from the muscle tissue.
In muscle-off samples, Cora could be clearly detected at epidermal cell boundaries, in intermittent tracts along class IV da neuron dendrites, and outlining the class IV da neuron soma (Figure 2C). In contrast, its localization to these domains was largely obscured in muscle-on samples, even when laser power was increased (Figure 2A-2B). In muscle-on samples, Cora was primarily visualized in muscle, trachea, and at the neuromuscular junction (NMJ), which become separated from the body wall as a result of the muscle removal procedure. The fluorescence signal emanating from these tissues obscured most of the Cora that localizes to epidermal cell boundaries and to dendrite tracts, except for in the narrow strip of the body wall near the dorsal midline, where muscle is absent. Cora that outlines the class IV da neuron soma was not visualized in muscle-on samples (Figure 2A-2B). Visualization of epidermally expressed proteins that also have high muscle expression, such as Dlg, is particularly problematic. In muscle-on samples, the distribution of Dlg in the epidermis was almost completely obscured by fluorescence from the muscle and NMJ (Figure 2D). After muscle removal, Dlg is readily detected at epidermal cell boundaries, in intermittent tracts along da neuron dendrites, and outlining the class IV da neuron soma (Figure 2E). Thus, muscle removal enables visualization of epidermally and neuronally expressed proteins otherwise obscured by muscle and associated tissues.
In addition, it was observed that the fluorescence intensity of the class IV da neuron marker appeared reduced in muscle-on fillets as compared to muscle-off fillets when imaging parameters were held constant between the two sample preparations (Figure 2A, 2C). With increased laser power, the apparent fluorescence intensity of the class IV da neuron marker could be matched to muscle-off samples but background noise was increased (Figure 2B, 2C). Therefore, muscle removal improves the signal to noise ratio in our samples.
Lastly, we tested whether the improvements gained by removing muscle tissue could be applied to imaging of class IV da neurons at sub-diffraction resolution. To do this, 3D structured illumination microscopy (SIM) imaging was performed, which achieves approximately 120 nm lateral resolution13. As with confocal imaging, we compared muscle-on and muscle-off fillets immunostained for Cora and class IV da neurons, first under identical imaging conditions and then after optimizing laser power, exposure time, and image processing for muscle-on samples. Similarly to confocal microscopy, a substantially reduced signal to noise ratio in muscle-on was observed as compared to muscle-off fillets (Figure 3A-3C). Additionally, image reconstruction appeared sharper in muscle-off samples. Compared to muscle-on samples, fewer apparent artifacts were observed and Cora dendrite tracts were more readily resolved (Figure 3B, 3C). Dendrite membranes could be measured at approximately 114 nm in width in muscle-off fillets but appeared to be 272 nm wide in muscle-on fillets (Figure 3D, 3E). Thus, our protocol enables the application of super-resolution microscopy to visualization of class IV da neurons.
<img alt="Figure 1" src="/files/ftp_upload/54670/54670fig1.jpg" /> 
Figure 1. Overview of Muscle Removal Procedure.&#160;A larva is dissected and pinned to a silicone elastomer dissecting dish. To remove muscle tissue, one forceps prong is inserted between the muscle and epidermal cell layer, starting from the dorsal midline near a segment boundary (2.2). The forceps is pulled upwards to break the attachment between the muscle and body wall (2.3). This is repeated for segments of interest and then the larva is fixed in formaldehyde (2.5). After fixation, forceps are used to separate the remaining muscle tissue from the body wall (2.7 - 2.8) The larval cuticle and epidermis are depicted in orange, class IV da neurons in green, and muscles in red. Insets in (2.2) and (2.7) represent cross-sectional views of a single larval hemi-segment. <a href="https://www.jove.com/files/ftp_upload/54670/54670fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" src="/files/ftp_upload/54670/54670fig2.jpg" /> 
Figure 2. Muscle Removal Improves Confocal Imaging of da Neurons and the Epidermis.&#160;Immunofluorescence of Cora (green; A-C) or Dlg (green; D-E) was detected with muscle tissue (A, B, D) and without muscle tissue (C, E). Class IV da neurons were labeled using the GAL4&#39;477 driver to express UAS-CD4:tdTomato and detected with an anti-dsRed antibody (red). Muscle-on and muscle-off samples labeled for Cora were first imaged with a confocal microscope under identical conditions (A, C) and then with increased laser power to compensate for muscle interference (B). Muscle-on and muscle-off samples labeled for Dlg were imaged under individually optimized conditions. All images are confocal Z-projections. The middle (green) and bottom (red) panels show individual channels; the top panels are the merged channels. The boundary of the muscle tissue (dashed lines), the class IV da neuron soma (cyan arrows), Cora and Dlg dendrite tracts (white arrows), epidermal cell boundaries (magenta arrows), NMJ (yellow arrows), and trachea (orange arrows) are indicated. Scale bar = 20 &#181;m. <a href="https://www.jove.com/files/ftp_upload/54670/54670fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" src="/files/ftp_upload/54670/54670fig3.jpg" /> 
Figure 3. Muscle Removal Enables Super-resolution of Imaging of da Neurons and Epidermal Cells.&#160;Immunofluorescence detection of Cora (green) in class IV da neurons with muscle intact (A, B) and after muscle removal (C). Class IV da neurons were labeled as in Figure 2. Muscle-on and muscle-off samples were imaged with a structured illumination microscope first under identical conditions (A, C); the muscle-on sample in (A) was then re-imaged with increased laser power and exposure times to compensate for muscle interference (B). All images are Z-projections. The middle (green) and bottom (red) panels of A-C show individual channels. The top panel of A-C is a merge. Epidermal cell boundaries (magenta arrows), Cora dendrite tracts (white arrows), and an image reconstruction artifact (yellow arrowhead) are indicated. Insets in the bottom panels of B and C correspond to D and E, respectively. The apparent width of the dendrite membrane is shown in muscle-on (D) and muscle-off (E) samples. Scale bars = 3 &#181;m (A-C) and 0.5 &#181;m (D, E). <a href="https://www.jove.com/files/ftp_upload/54670/54670fig3large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Removal of Drosophila Muscle Tissue from Larval Fillets for Immunofluorescence Analysis of Sensory Neurons and Epidermal Cells at JoVE.com

Removal of Drosophila Muscle Tissue from Larval Fillets for Immunofluorescence Analysis of Sensory Neurons and Epidermal Cells

Studies of neuronal morphogenesis using Drosophila larval dendritic arborization (da) neurons benefit from in situ visualization of neuronal and epidermal proteins by immunofluorescence. We describe a procedure that improves immunofluorescence analysis of da neurons and surrounding epidermal cells by removing muscle tissue from the larval body wall.

Removal of Drosophila Muscle Tissue from Larval Fillets for Immunofluorescence Analysis of Sensory Neurons and Epidermal Cells

Drosophila larval dendritic arborization (da) neurons are a popular model for investigating mechanisms of neuronal morphogenesis. Da neurons develop in ...

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8.9K Views.  Princeton University. Studies of neuronal morphogenesis using Drosophila larval dendritic arborization (da) neurons benefit from in situ visualization of neuronal and epidermal proteins by immunofluorescence. We describe a procedure that improves immunofluorescence analysis of da neurons and surrounding epidermal cells by removing muscle tissue from the larval body wall.

Video: Removal of Drosophila Muscle Tissue from Larval Fillets for Immunofluorescence Analysis of Sensory Neurons and Epidermal Cells

Live-imaging of PKC Translocation in Sf9 Cells and in Aplysia Sensory Neurons

Protein kinase Cs (PKCs) are serine threonine kinases that play a central role in regulating a wide variety of cellular processes such as cell growth and learning and memory. There are four known families of PKC isoforms in vertebrates: classical PKCs (&alpha;, &beta;I, &beta;II and &gamma;), novel type I PKCs (&#949; and &eta;), novel type II PKCs (&delta; and &theta;), and atypical PKCs (&zeta; and &iota;). The classical PKCs are activated by Ca2+ and diacylclycerol (DAG), while the novel PKCs are activated by DAG, but are Ca2+-independent. The atypical PKCs are activated by neither Ca2+ nor DAG. In Aplysia californica, our model system to study memory formation, there are three nervous system specific PKC isoforms one from each major class, namely the conventional PKC Apl I, the novel type I PKC Apl II and the atypical PKC Apl III. PKCs are lipid-activated kinases and thus activation of classical and novel PKCs in response to extracellular signals has been frequently correlated with PKC translocation from the cytoplasm to the plasma membrane. Therefore, visualizing PKC translocation in real time in live cells has become an invaluable tool for elucidating the signal transduction pathways that lead to PKC activation. For instance, this technique has allowed for us to establish that different isoforms of PKC translocate under different conditions to mediate distinct types of synaptic plasticity and that serotonin (5HT) activation of PKC Apl II requires production of both DAG and phosphatidic acid (PA) for translocation 1-2. Importantly, the ability to visualize the same neuron repeatedly has allowed us, for example, to measure desensitization of the PKC response in exquisite detail 3. In this video, we demonstrate each step of preparing Sf9 cell cultures, cultures of Aplysia sensory neurons have been described in another video article 4, expressing fluorescently tagged PKCs in Sf9 cells and in Aplysia sensory neurons and live-imaging of PKC translocation in response to different activators using laser-scanning microscopy.

In this video, we demonstrate visualization of PKC translocation in living cells using fluorescently tagged PKCs.

Protein kinase Cs (PKCs) are serine threonine kinases that play a central role in regulating a wide variety of cellular processes such as cell growth and ...

Live-cell Imaging of Sensory Organ Precursor Cells in Intact Drosophila Pupae

Since the discovery of Green Fluorescent Protein (GFP), there has been a revolutionary change in the use of live-cell imaging as a tool for understanding fundamental biological mechanisms. Striking progress has been particularly evident in Drosophila, whose extensive toolkit of mutants and transgenic lines provides a convenient model to study evolutionarily-conserved developmental and cell biological mechanisms. We are interested in understanding the mechanisms that control cell fate specification in the adult peripheral nervous system (PNS) in Drosophila. Bristles that cover the head, thorax, abdomen, legs and wings of the adult fly are individual mechanosensory organs, and have been studied as a model system for understanding mechanisms of Notch-dependent cell fate decisions. Sensory organ precursor (SOP) cells of the microchaetes (or small bristles), are distributed throughout the epithelium of the pupal thorax, and are specified during the first 12 hours after the onset of pupariation. After specification, the SOP cells begin to divide, segregating the cell fate determinant Numb to one daughter cell during mitosis. Numb functions as a cell-autonomous inhibitor of the Notch signaling pathway.
Here, we show a method to follow protein dynamics in SOP cell and its progeny within the intact pupal thorax using a combination of tissue-specific Gal4 drivers and GFP-tagged fusion proteins 1,2.This technique has the advantage over fixed tissue or cultured explants because it allows us to follow the entire development of an organ from specification of the neural precursor to growth and terminal differentiation of the organ. We can therefore directly correlate changes in cell behavior to changes in terminal differentiation. Moreover, we can combine the live imaging technique with mosaic analysis with a repressible cell marker (MARCM) system to assess the dynamics of tagged proteins in mitotic SOPs under mutant or wildtype conditions. Using this technique, we and others have revealed novel insights into regulation of asymmetric cell division and the control of Notch signaling activation in SOP cells (examples include references 1-6,7 ,8).

Live-cell Imaging of Sensory Organ Precursor Cells in Intact Drosophila Pupae

In this video, we describe a method for live cell imaging of asymmetrically dividing sensory organ progenitor cells and epidermal cells in intact Drosophila pupae

Since the discovery of Green Fluorescent Protein (GFP), there has been a revolutionary change in the use of live-cell imaging as a tool for understanding ...

Morphological Analysis of Drosophila Larval Peripheral Sensory Neuron Dendrites and Axons Using Genetic Mosaics

Nervous system development requires the correct specification of neuron position and identity, followed by accurate neuron class-specific dendritic development and axonal wiring. Recently the dendritic arborization (DA) sensory neurons of the Drosophila larval peripheral nervous system (PNS) have become powerful genetic models in which to elucidate both general and class-specific mechanisms of neuron differentiation.
There are four main DA neuron classes (I-IV)1. They are named in order of increasing dendrite arbor complexity, and have class-specific differences in the genetic control of their differentiation2-10. The DA sensory system is a practical model to investigate the molecular mechanisms behind the control of dendritic morphology11-13 because: 1) it can take advantage of the powerful genetic tools available in the fruit fly, 2) the DA neuron dendrite arbor spreads out in only 2 dimensions beneath an optically clear larval cuticle making it easy to visualize with high resolution in vivo, 3) the class-specific diversity in dendritic morphology facilitates a comparative analysis to find key elements controlling the formation of simple vs. highly branched dendritic trees, and 4) dendritic arbor stereotypical shapes of different DA neurons facilitate morphometric statistical analyses.
DA neuron activity modifies the output of a larval locomotion central pattern generator14-16. The different DA neuron classes have distinct sensory modalities, and their activation elicits different behavioral responses14,16-20. Furthermore different classes send axonal projections stereotypically into the Drosophila larval central nervous system in the ventral nerve cord (VNC)21. These projections terminate with topographic representations of both DA neuron sensory modality and the position in the body wall of the dendritic field7,22,23. Hence examination of DA axonal projections can be used to elucidate mechanisms underlying topographic mapping7,22,23, as well as the wiring of a simple circuit modulating larval locomotion14-17.
We present here a practical guide to generate and analyze genetic mosaics24 marking DA neurons via MARCM (Mosaic Analysis with a Repressible Cell Marker)1,10,25 and Flp-out22,26,27 techniques (summarized in Fig. 1).

Morphological Analysis of Drosophila Larval Peripheral Sensory Neuron Dendrites and Axons Using Genetic Mosaics

The dendritic arborization sensory neurons of the Drosophila larval peripheral nervous system are useful models to elucidate both general and neuron class-specific mechanisms of neuron differentiation. We present a practical guide to generate and analyze dendritic arborization neuron genetic mosaics.

Nervous system development requires the correct specification of neuron position and identity, followed by accurate neuron class-specific dendritic ...

Dissection and Immunohistochemistry of Larval, Pupal and Adult Drosophila Retinas

The compound eye of Drosophila melanogaster consists of about 750 ommatidia (unit eyes). Each ommatidium is composed of about 20 cells, including lens-secreting cone cells, pigment cells, a bristle cell and eight photoreceptors (PRs) R1-R8 2. The PRs have specialized microvillar structures, the rhabdomeres, which contain light-sensitive pigments, the Rhodopsins (Rhs). The rhabdomeres of six PRs (R1-R6) form a trapezoid and contain Rh1 3 4. The rhabdomeres of R7 and R8 are positioned in tandem in the center of the trapezoid and share the same path of light. R7 and R8 PRs stochastically express different combinations of Rhs in two main subtypes5: In the 'p' subtype, Rh3 in pR7s is coupled with Rh5 in pR8s, whereas in the 'y' subtype, Rh4 in yR7s is associated with Rh6 in yR8s 6 7 8.
Early specification of PRs and development of ommatidia begins in the larval eye-antennal imaginal disc, a monolayer of epithelial cells. A wave of differentiation sweeps across the disc9 and initiates the assembly of undifferentiated cells into ommatidia10-11. The 'founder cell' R8 is specified first and recruits R1-6 and then R7 12-14. Subsequently, during pupal development, PR differentiation leads to extensive morphological changes 15, including rhabdomere formation, synaptogenesis and eventually rh expression.
In this protocol, we describe methods for retinal dissections and immunohistochemistry at three defined periods of retina development, which can be applied to address a variety of questions concerning retinal formation and developmental pathways. Here, we use these methods to visualize the stepwise PR differentiation at the single-cell level in whole mount larval, midpupal and adult retinas (Figure 1).

Dissection and Immunohistochemistry of Larval, Pupal and Adult Drosophila Retinas

The Drosophila retina is a crystal-like lattice composed of a small number of cell types that are generated in a stereotyped manner 1. Its amenability to sophisticated genetic analysis allows the study of complex developmental programs. This protocol describes dissections and immunohistochemistry of retinas at three discrete developmental stages, with a focus on photoreceptor differentiation.

The compound eye of Drosophila melanogaster consists of about 750 ommatidia (unit eyes). Each ommatidium is composed of about 20 cells, including ...

Functional Analysis of the Larval Feeding Circuit in Drosophila

The serotonergic feeding circuit in Drosophila melanogaster larvae can be used to investigate neuronal substrates of critical importance during the development of the circuit. Using the functional output of the circuit, feeding, changes in the neuronal architecture of the stomatogastric system can be visualized. Feeding behavior can be recorded by observing the rate of retraction of the mouth hooks, which receive innervation from the brain. Locomotor behavior is used as a physiological control for feeding, since larvae use their mouth hooks to traverse across an agar substrate. Changes in feeding behavior can be correlated with the axonal architecture of the neurites innervating the gut. Using immunohistochemistry it is possible to visualize and quantitate these changes. Improper handling of the larvae during behavior paradigms can alter data as they are very sensitive to manipulations. Proper imaging of the neurite architecture innervating the gut is critical for precise quantitation of number and size of varicosities as well as the extent of branch nodes. Analysis of most circuits allow only for visualization of neurite architecture or behavioral effects; however, this model allows one to correlate the functional output of the circuit with the impairments in neuronal architecture.

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 foregut.

The serotonergic  feeding circuit in Drosophila  melanogaster larvae can be used to investigate neuronal substrates of  critical importance during the ...

Whole Mount Immunolabeling of Olfactory Receptor Neurons in the Drosophila Antenna

Odorant molecules bind to their target receptors in a precise and coordinated manner. Each receptor recognizes a specific signal and relays this information to the brain. As such, determining how olfactory information is transferred to the brain, modifying both perception and behavior, merits investigation. Interestingly, there is emerging evidence that cellular transduction and transcriptional factors are involved in the diversification of olfactory receptor neuron. Here we provide a robust whole mount immunological labeling method to assay in vivo olfactory receptor neuron organization. Using this method, we identified all olfactory receptor neurons with anti-ELAV antibody, a known pan-neural marker and Or49a-mCD8::GFP, an olfactory receptor neuron specifically expressed in Nba neuron using anti-GFP antibody.

Whole Mount Immunolabeling of Olfactory Receptor Neurons in the Drosophila Antenna

Herein we describe the process of whole mount immunostaining of Drosophila antennae, which enables us to better understand the molecular mechanisms involved in the diversification of olfactory receptor neurons (ORN)s.

Odorant molecules bind to their target receptors in a precise and coordinated manner. Each receptor recognizes a specific signal and relays this ...

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.

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 ...

Isolation and Culture of Dissociated Sensory Neurons From Chick Embryos

Neurons are multifaceted cells that carry information essential for a variety of functions including sensation, motor movement, learning, and memory. Studying neurons in vivo can be challenging due to their complexity, their varied and dynamic environments, and technical limitations. For these reasons, studying neurons in vitro can prove beneficial to unravel the complex mysteries of neurons. The well-defined nature of cell culture models provides detailed control over environmental conditions and variables. Here we describe how to isolate, dissociate, and culture primary neurons from chick embryos. This technique is rapid, inexpensive, and generates robustly growing sensory neurons. The procedure consistently produces cultures that are highly enriched for neurons and has very few non-neuronal cells (less than 5%). Primary neurons do not adhere well to untreated glass or tissue culture plastic, therefore detailed procedures to create two distinct, well-defined laminin-containing substrata for neuronal plating are described. Cultured neurons are highly amenable to multiple cellular and molecular techniques, including co-immunoprecipitation, live cell imagining, RNAi, and immunocytochemistry. Procedures for double immunocytochemistry on these cultured neurons have been optimized and described here.

Cell culture models provide detailed control over environmental conditions and thus provide a powerful platform to elucidate numerous aspects of neuronal cell biology. We describe a rapid, inexpensive, and reliable method to isolate, dissociate, and culture sensory neurons from chick embryos. Details of substrata preparation and immunocytochemistry are also provided.

Neurons are multifaceted cells that carry information essential for a variety of functions including sensation, motor movement, learning, and memory. ...

Physiological Preparation of Hair Cells from the Sacculus of the American Bullfrog (Rana catesbeiana)

The study of hearing and balance rests upon insights drawn from biophysical studies of model systems. One such model, the sacculus of the American bullfrog, has become a mainstay of auditory and vestibular research. Studies of this organ have revealed how sensory cells hair can actively detect signals from the environment. Because of these studies, we now better understand the mechanical gating and localization of a hair cell&#39;s transduction channels, calcium&#39;s role in mechanical adaptation, and the identity of hair cell currents. This highly accessible organ continues to provide insight into the workings of hair cells. Here we describe the preparation of the bullfrog&#39;s sacculus for biophysical studies on its hair cells. We include the complete dissection procedure and provide specific protocols for the preparation of the sacculus in specific contexts. We additionally include representative results using this preparation, including the calculation of a hair bundle&#39;s instantaneous force-displacement relation and measurement of a bundle&#39;s spontaneous oscillation.

Physiological Preparation of Hair Cells from the Sacculus of the American Bullfrog Rana catesbeiana

The American bullfrog&#39;s (Rana catesbeiana) sacculus permits direct examination of hair-cell physiology. Here the dissection and preparation of the bullfrog&#39;s sacculus for biophysical studies is described. We show representative experiments from these hair cells, including the calculation of a bundle&#39;s force-displacement relation and measurement of its unforced motion.

The study of hearing and balance rests upon insights drawn from biophysical studies of model systems. One such model, the sacculus of the American ...

Tracking Drosophila Larval Behavior in Response to Optogenetic Stimulation of Olfactory Neurons

The ability of insects to navigate toward odor sources is based on the activities of their first-order olfactory receptor neurons (ORNs). While a considerable amount of information has been generated regarding ORN responses to odorants, the role of specific ORNs in driving behavioral responses remains poorly understood. Complications in behavior analyses arise due to different volatilities of odorants that activate individual ORNs, multiple ORNs activated by single odorants, and the difficulty in replicating naturally observed temporal variations in olfactory stimuli using conventional odor-delivery methods in the laboratory. Here, we describe a protocol that analyzes Drosophila larval behavior in response to simultaneous optogenetic stimulation of its ORNs. The optogenetic technology used here allows for specificity of ORN activation and precise control of temporal patterns of ORN activation. Corresponding larval movement is tracked, digitally recorded, and analyzed using custom written software. By replacing odor stimuli with light stimuli, this method allows for a more precise control of individual ORN activation in order to study its impact on larval behavior. Our method could be further extended to study the impact of second-order projection neurons (PNs) as well as local neurons (LNs) on larval behavior. This method will thus enable a comprehensive dissection of olfactory circuit function and complement studies on how olfactory neuron activities translate in to behavior responses.

Tracking Drosophila Larval Behavior in Response to Optogenetic Stimulation of Olfactory Neurons

This protocol analyzes navigational behavior of Drosophila larva in response to simultaneous optogenetic stimulation of its olfactory neurons. Light of 630 nm wavelength is used to activate individual olfactory neurons expressing a red-shifted channel rhodopsin. Larval movement is simultaneously tracked, digitally recorded, and analyzed using custom-written software.