We thank Michael Rosbash for his mentorship and support during the initial phase of the development of this method. This work was funded by the JST PRESTO program, the Swiss National Science Foundation (31003A_149893 and 31003A_169548), the European Research Council (ERC-StG-311194), Novartis Foundation for Medical-Biomedical Research (13A39) and the University of Geneva.

1. Preparation of Stock Solutions Under a Culture Hood
<ol>
	<li>Prepare 400 mL of 1x Schneider Active Medium (SAM) optimized for ex vivo culture of larval brains (modified from reference24,25) (Table 1). Aliquot to 5 mL and flash freeze in liquid nitrogen (LN2), store at - 80 &#176;C.</li>
	<li>Prepare 1x Dissecting Saline Solution (DSS) by diluting 10x stock solution (modified from reference26) (Table 2).</li>
	<li>Aliquot fibrinogen to 10 mg and store at 4 &#176;C for a single use. 
	Caution: Weigh fibrinogen under laminar flow, wearing gloves, as it is harmful.</li>
	<li>Prepare thrombin stock solution in SAM (1500 NIH unit/mg) and aliquot to 10 &#181;L, flash freeze in LN2 and keep at -80 &#176;C. 
	Caution: Wear gloves when handling thrombin as it is harmful.</li>
	<li>Aliquot stock solution of 100x Penicillin-Streptomycin. Keep at -20 &#176;C.</li>
	<li>Cut circles of polytetrafluoroethylene (PTFE) membrane (see Materials Table) to the size that fits the inside of a glass bottom dish. Rinse them in 70% EtOH and then in autoclaved dH2O. Sterilize and dry under laminar flow with UV. Keep in a sterile Petri dish. Single use. 
	NOTE: PTFE is a porous flexible membrane that allows gas exchange and prevents medium from evaporating during long-term recording.</li>
</ol>
2. Time-lapse Microscopy Setup
NOTE: The following setup is for a tandem scanner inverted confocal microscope (see Materials Table) equipped with a resonant scanner (8,000 Hz). The system includes a highly sensitive photo-multiplier detector, which together with the resonant scanner prevents phototoxicity and photobleaching. Temperature and humidity are controlled within a microscope environmental chamber (see Materials Table) that covers most of the microscope.
<ol>
	<li>Place a stage-top humidity chamber.</li>
	<li>Turn on the temperature and humidity controllers to equilibrate the microscope chamber to 25 &#176;C and 80% humidity.</li>
	<li>To perform experiments in constant darkness (DD), cover the microscope environmental chamber with an opaque cloth (unless the microscope chamber is made of an opaque material).</li>
	<li>If using a water-immersion objective, position a Water Immersion Micro Dispenser on top of the objective and program a protocol with the Autoimmersion Objective Controller software to dispense water at a constant rate during time-lapse imaging. 
	NOTE: Water-immersion objectives together with a water dispenser or dry objective lens are recommended for long-term live imaging, as other type of immersion medium would dry out.</li>
	<li>Place a Petri dish holder on the stage, inside of the humidity chamber.</li>
	<li>Launch the microscope software and select the resonant scanner mode from the first dialogue box. Select OK to initialize the stage when prompted. Go to Configuration tab and to Hardware configuration to switch on the relevant laser lines.</li>
	<li>Go to Acquire tab and to XY panel to select bidirectional mode and set image acquisition parameters. 
	NOTE: The described imaging setup presented here (Figure 2, Figure 3 and Movie 1) is optimized to observe circadian expression of specific fluorescent reporters. The following parameters were chosen to best fit our specifications: 40X water immersion objective, 8X line average with 512 &#215; 512 image resolution. For multicolor imaging, sequential image acquisition is required when the emission wavelength of one fluorophore and the excitation wavelength of another overlap (here, wavelengths of Yellow Fluorescent Protein (YFP) emission and Tomato excitation overlap). Choose the sequential mode &#34;in between stack&#34; as it is the fastest and the movement of clock neurons is negligible during the acquisition of a Z-stack. Microscopy settings should be adapted to suit the aim of each experiment.</li>
</ol>
3. Setup of Larval Brain Explant Culture
NOTE: The whole procedure from dissection to embedding of brain explants takes ~30 min.
<ol>
	<li>Preparation of reagents under a culture hood.
	<ol>
		<li>Thaw an aliquot of thrombin and keep at room temperature until the embedding step (step 3.3). Single use.</li>
		<li>Thaw quickly an aliquot of SAM at 37 &#176;C and keep on ice for a single use.</li>
		<li>Add SAM to a 10 mg aliquot of fibrinogen to 10 mg/mL, flick gently and incubate at 37 &#176;C for at least 30 min and during the embedding step (step 3.3). Single use. 
		NOTE: Do not incubate the fibrinogen solution more than 2 h as it starts to polymerize.</li>
		<li>Thaw an aliquot of 100x stock Penicillin-Streptomycin. Prepare 2.5 mL of SAM containing 1x Penicillin-Streptomycin (SAM/antibiotics). Keep at room temperature. 
		NOTE: Store the remaining 100x stock Penicillin-Streptomycin at 4 &#176;C up to 1 month.</li>
		<li>Prepare an aliquot of 500 &#181;L from the remaining SAM. Keep on ice.</li>
		<li>For long-term imaging, apply autoclaved vacuum grease to the plastic part of the bottom of the glass bottom dish (Figure 1A) and sterilize under laminar flow with UV.</li>
	</ol>
	</li>
	<li>Dissection of the central nervous system and ventral nerve cord.
	<ol>
		<li>Clean the forceps and 2 x three-well glass dissection dishes with 70% EtOH. Pour 400 &#181;L of DSS into 4 wells and 400 &#181;L of SAM in one well. Keep on ice.</li>
		<li>Scoop out fly medium containing larvae and pick non-wandering 3rd instar larvae (L3) with forceps. Rinse them successively in 2 DSS-filled wells. Keep them in the 3rd DSS-filled well on ice that anesthetizes the larvae. 
		NOTE: L3 lasts approximately 2 days at 25 &#176;C. To observe the brain in physiologically relevant timeframe we chose to use non-wandering L3 larvae. Other subgroups of clock neurons, such as l-LNvs and DN3s, start to be formed at wandering L3 stage but they are not necessarily cycling yet (data not shown). Therefore, although it is possible to image cycling clock neurons at this stage (data not shown), it is important to carefully distinguish the already functional larval clock neurons from developing ones for data analysis. Non-wandering L3 appear approximately 4 to 4.5 days after egg laying at 25 &#176;C. To use this protocol for studying circadian rhythms, synchronize (entrain) the developing larvae in 12 h/12 h LD cycles at 25 &#176;C for 3 days before collecting L3 larvae.</li>
		<li>Dissect larval brains with fine forceps in the 4th DSS-filled well, which has not been used for rinsing larvae, using the inside-out method27.
		<ol>
			<li>Briefly, cut the larva in two, gently pinch the mouth hooks with a pair of forceps and roll up inside-out the body wall using the other pair of forceps, thus exposing the brain. Free the brain by cutting out all the trachea and nerves that attach it to the rest of the body.</li>
			<li>Aspirate the brain in about 3 &#181;L of DSS with a 20 &#181;L pipette (pre-rinsed with DSS) and dispense in the SAM-filled well. Repeat the procedure for up to 7 brains. 
			NOTE: Dissection should be performed on a cold surface to keep the larvae anesthetized and the brain chilled. For example, place the dissection dish on a cooling block connected to a pump to circulate ice-chilled water. The dissection procedure takes ~30 s per brain. It is important to keep the eye/antennal imaginal discs attached to the brains and the ventral nerve cord intact. Tearing off these parts will damage the brain and reduce the quality of the culture. Also, avoid exposing the brains to the air. Before aspirating the first brain, pipette up and down the DSS containing parts of the dissected larvae, as it prevents the brains from sticking to the wall of the tip.</li>
		</ol>
		</li>
	</ol>
	</li>
	<li>Embedding of brain explants in a 3D matrix and mounting (~20 min).
	<ol>
		<li>Submerge a dissected brain in fibrinogen working solution (fibrinogen final concentration ~3.3 mg/mL, 10.5 &#181;L per brain) as follows:</li>
		<li>Aspirate 3.5 &#181;L of SAM/antibiotics (with the same tip used in section 3.2.3). Aspirate a dissected brain from the dissection well into the same pipette tip without dispensing the SAM/antibiotics medium in the tip.</li>
		<li>Dispense the brain and the medium on the lid of a sterile Petri dish. Add another 3.5 &#181;L of SAM/antibiotics and 3.5 &#181;L of warm fibrinogen/SAM 10 mg/mL solution on the drop containing the brain. Mix the solution around the brain gently by pipetting with a 20 &#181;L pipette tip. 
		NOTE: Using a pipette rather than forceps in this step avoids stressing the brain.</li>
		<li>Take 2 &#181;L of the fibrinogen working solution from the drop and apply it on the coverslip of the glass bottom dish as a small circle. Add 0.8 &#181;L of thrombin and mix very quickly with a pipette tip. The fibrinogen is converted to fibrin and starts to polymerize.</li>
		<li>Take the brain that sits in the fibrinogen working solution (step 3.3.1) between a pair of forceps and position it on the matrix once a white matrix of fibrin is visible. Orient the brain anterior side down (for imaging clock neurons). Push it down as close as possible to the cover glass. Fibrin clot is composed of layers of fibrin. Pick one layer and fold it on top of the brain with small and gentle movements without detaching the matrix.
		<ol>
			<li>Repeat 2 to 3 times from different parts of the clot to stabilize the brain. 
			NOTE: When handling the brain with forceps, be careful not to dry it or impose it a physical stress.</li>
		</ol>
		</li>
		<li>Add 20 &#181;L of SAM/antibiotics on top of the embedded brain to stop the action of thrombin.</li>
		<li>Repeat the procedure to mount the remaining brains. It is possible to embed up to 5 to 6 brains on a glass bottom dish.</li>
		<li>For long-term live imaging, add 600 &#181;L of SAM/antibiotics in the inner well (the glass part). Position a pre-cut PTFE membrane on top of the medium and stick it to the vacuum grease applied on the plastic part of the bottom (3.1.5) (Figure 1A).</li>
		<li>For pharmacological assays, fill the dish with 2 mL of SAM/antibiotics (Figure 1B). 
		NOTE: It is very important to avoid evaporation of the medium, as the osmolality of the medium is critical to the viability of neurons. Therefore, for long-term imaging experiments, it is necessary to seal the culture dish with PTFE membrane. Whereas for short-term experiments, sealing membrane is not required as long as the dish is filled with 2 mL of medium and monitored in a humidified chamber.</li>
	</ol>
	</li>
</ol>
4. Time-lapse Image Acquisition
<ol>
	<li>Place the glass bottom dish on the Petri dish holder inside the stage-top humidity chamber.</li>
	<li>Go to z-stack panel in the Acquire tab and set the z-section steps from the microscope software (2 &#181;m &#215; ~40 in the experiments shown in Figure 2 and Figure 3, and Movie 1). Set the beginning of a z-stack at the plane farthest from the coverslip and the end at the surface of the brain explant, close to the coverslip. Though brain movements are negligible, add extra z-sections at the beginning and end of the z-stack.</li>
	<li>Go to Mark &#38; Find panel and set-up multi-position image acquisition. With a 40X objective, 1 brain hemisphere can be captured within a field of view</li>
	<li>Go to Acquisition mode panel and select xyzt (z-stack time-lapse). Go to Time Acquisition panel and set the preferred time interval and frequency parameters. 
	NOTE: Acquire time-lapse images with desired frequency. Note that long-term live imaging (24-72 h) with time lapse interval shorter than 2 h tends to results in fewer cycling neurons, probably because it reduces the viability of neurons. The data volume expands as the rate of image acquisition increases, which makes data analysis and storage more challenging.</li>
</ol>
5. Pharmacological Treatment of brain Explants with Short-term Live Imaging
NOTE: The following procedure is essentially the same as that for long-term imaging but does not require a PTFE membrane. To avoid exposing the brains to blue light when the chemical is added to the culture, the microscope should be placed in the dark room with red light.
<ol>
	<li>Go to Time Acquisition panel and set the desired time interval and number of scan to obtain the baseline data before drug application. Start Scan.</li>
	<li>After the baseline scan is completed, lift the scan head of the microscope system. Remove the lid of the stage-top humidity controller and very carefully remove the lid of the glass bottom dish without moving it.</li>
	<li>Remove the appropriate amount of culture medium if necessary. Add the experimental solution in the medium and, carefully and very gently, mix with a sterile Pasteur pipette without touching the brain explants. 
	NOTE: For bath application of PDF, use 2 &#181;M PDF stock solution (in 10% DMSO).</li>
	<li>Replace the lids of the glass bottom dish and the humid chamber, and the scan head. If using, reposition the black opaque cloth around the microscope chamber.</li>
	<li>Check if the brains are at their original positions in live scan mode. Adjust if necessary.</li>
	<li>Go to Time Acquisition panel and set the desired time interval and number of scan. Start Scan. 
	NOTE: Here we tested time-lapse images acquired every hour for up to 10 h.</li>
</ol>

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D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cytochalasin+D+and+latrunculin+affect+chromosome+behaviour+during+meiosis+in+crane-fly+spermatocytes.">Cytochalasin D and latrunculin affect chromosome behaviour during meiosis in crane-fly spermatocytes.</a> Chromosome Res. 6 (7), 533-549 (1998).</li><li>Lukinavi&#269;ius, G., 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=SiR-Hoechst+is+a+far-red+DNA+stain+for+live-cell+nanoscopy.">SiR-Hoechst is a far-red DNA stain for live-cell nanoscopy.</a> Nature Communications. 6, 8497 (2015).</li><li>Medioni, C., Ephrussi, A., Besse, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Live+imaging+of+axonal+transport+in+Drosophila+pupal+brain+explants.">Live imaging of axonal transport in Drosophila pupal brain explants.</a> Nat Protoc. 10 (4), 574-584 (2015).</li><li>Enoki, R., Ono, D., Hasan, M. T., Honma, S., Honma, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-cell+resolution+fluorescence+imaging+of+circadian+rhythms+detected+with+a+Nipkow+spinning+disk+confocal+system.">Single-cell resolution fluorescence imaging of circadian rhythms detected with a Nipkow spinning disk confocal system.</a> J Neurosci Methods. 207 (1), 72-79 (2012).</li><li>Ozel, M. N., Langen, M., Hassan, B. A., Hiesinger, P. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Filopodial+dynamics+and+growth+cone+stabilization+in+Drosophila+visual+circuit+development.">Filopodial dynamics and growth cone stabilization in Drosophila visual circuit development.</a> Elife. 4, (2015).</li><li>Yao, Z., Macara, A. M., Lelito, K. R., Minosyan, T. Y., Shafer, O. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+functional+neuronal+connectivity+in+the+Drosophila+brain.">Analysis of functional neuronal connectivity in the Drosophila brain.</a> J Neurophysiol. 108 (2), 684-696 (2012).</li></ol>

The authors have nothing to disclose.

Here we described the method for long-term fluorescence time-lapse microscopy of cultured larval brains. The success of this type of experiments depends on multiple factors, such as the health of the culture, method for immobilization of the brain explant, fluorescence intensity and signal-to-noise ratio of the reporter, temporal and spatial resolution, and accessibility to the explant. These factors can be mutually exclusive. For example, increasing time-lapse frequency affects the health of the culture, and the immobil...

Circadian clocks help organisms to adapt to the periodic environmental changes generated by the 24 h rotation of the Earth. The interlocked transcriptional-translational feedback loops commonly underlie the molecular machinery of circadian clocks across species1. The circadian pacemaker circuit composed of clock-containing neurons integrates time-of-day information conveyed by the environmental cues, such as light/dark (LD) and temperature cycles, to orchestrate the rhythms of a plethora of daily physiological and behavioral processes2,3. The coordination of molecular rhythms with neuronal inputs and outputs is critically important for the operation of the circadian circuit but remains only partially understood.
In Drosophila, at the core of the molecular clock, the CLOCK/CYCLE (CLK/CYC) heterodimer activates the transcription of period (per) and timeless (tim). PER and TIM form a complex and enter the nucleus, where they inhibit transcriptional activity of CLK/CYC and consequently their own transcription. Post-transcriptional and post-translational regulations cause delays between CLK/CYC-mediated transcription and repression by PER/TIM, ensuring the generation of circa 24-h molecular oscillations1,3,4. About 150 neurons containing these molecular clocks form a circuit to control circadian behavior of adult flies5. A much simpler yet fully functional circadian circuit consisting of 3 groups of clock neurons - 5 ventral Lateral Neurons (LNvs; 4 PDF-positive LNvs and one PDF-negative LNv, see below), 2 Dorsal Neuron 1s (DN1s) and 2 Dorsal Neuron 2s (DN2s) - is present in the larval brain6,7.
The simple larval circadian circuit offers an excellent model to study the interactions between inter-neuronal communication and the molecular clockwork. Using our newly developed fluorescent reporter PER-TDT, which mimics the levels of PER protein and its subcellular location, we sought to characterize the dynamics of the molecular clockwork in different clock neuron subgroups in the larval circadian circuit8. Furthermore, knowing the key role of the neuropeptide pigment-dispersing factor (PDF) produced by 4 LNvs in regulating circadian rhythms at the neuronal level9,10,11, we wanted to examine the direct effect of PDF on the molecular clocks. To this end, we developed a method to monitor circadian gene expression rhythms in larval brain explant over multiple days by time-lapse confocal microscopy. The protocol was also adapted for pharmacological assays to test the effect of PDF or other compounds on the level of PER-TDT. Thus, the adaptation consists of making the brain explant culture accessible to drug application, increasing temporal resolution and imaging for a shorter duration.
Ex vivo culture of Drosophila brains of different developmental stages have been previously established12,13,14,15,16,17,18. Whereas these protocols have been used for imaging various biological phenomena, some of them are not compatible with imaging at single-cell resolution or do not support the culture for more than several hours. Alternative methods to perform long-term live imaging of circadian neurons in Drosophila include bioluminescence imaging of molecular rhythms19,20,21 and fluorescence imaging of calcium indicator with light sheet microscopy22,23. Although bioluminescence imaging can achieve higher temporal resolution and light sheet microscopy can be adaptable for in vivo imaging, they are limited on the spatial resolution and require specialized microscope systems.
The method described here is tailored to visualize fluorescent signals in the whole brain culture at single-cell resolution over multiple days. This facile and versatile method could be adapted to image cultured adult fly brains and for pharmacological experiments to study many different problems in Drosophila neurobiology.

<table>
	<tbody>
		<tr>
			<td>KH2PO4</td>
			<td>Sigma-Aldrich</td>
			<td>P5655</td>
			<td>I am not sure they are exactly the same ones we have in the lab. I chose &#34;suitable for insect cell culture&#34; whenever available</td>
		</tr>
		<tr>
			<td>CaCl2</td>
			<td>Sigma-Aldrich</td>
			<td>C7902</td>
			<td></td>
		</tr>
		<tr>
			<td>MgSO4.7H2O</td>
			<td>Sigma-Aldrich</td>
			<td>230391</td>
			<td></td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Sigma-Aldrich</td>
			<td>S5886</td>
			<td></td>
		</tr>
		<tr>
			<td>NaHCO3</td>
			<td>Sigma-Aldrich</td>
			<td>S5761</td>
			<td></td>
		</tr>
		<tr>
			<td>D-(+) Glucose</td>
			<td>Sigma-Aldrich</td>
			<td>G7021</td>
			<td></td>
		</tr>
		<tr>
			<td>Yeast extract</td>
			<td>Sigma-Aldrich</td>
			<td>Y1000</td>
			<td></td>
		</tr>
		<tr>
			<td>Insulin</td>
			<td>Sigma-Aldrich</td>
			<td>I0516-5ML</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin</td>
			<td>Sigma-Aldrich</td>
			<td>P4333</td>
			<td></td>
		</tr>
		<tr>
			<td>BIS-TRIS</td>
			<td>Sigma-Aldrich</td>
			<td>B4429</td>
			<td></td>
		</tr>
		<tr>
			<td>L-(&#8722;)-Malic acid</td>
			<td>Sigma-Aldrich</td>
			<td>M7397</td>
			<td></td>
		</tr>
		<tr>
			<td>D-(+)-Trehalose dihydrate</td>
			<td>Sigma-Aldrich</td>
			<td>T0167</td>
			<td></td>
		</tr>
		<tr>
			<td>Succinic acid</td>
			<td>Sigma-Aldrich</td>
			<td>S9512</td>
			<td></td>
		</tr>
		<tr>
			<td>Fumaric acid</td>
			<td>Sigma-Aldrich</td>
			<td>F8509</td>
			<td></td>
		</tr>
		<tr>
			<td>&#945;-Ketoglutaric acid</td>
			<td>Sigma-Aldrich</td>
			<td>K1128</td>
			<td></td>
		</tr>
		<tr>
			<td>Non-heat-inactivated, Foetal Calf Serum (FCS) Mycoplasma and Virus screened</td>
			<td>BioConcept Ltd. Amimed</td>
			<td>2-01F30-I</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES-KOH, pH 7.4</td>
			<td>E&#38;K Scientific Products</td>
			<td>EK-654011</td>
			<td></td>
		</tr>
		<tr>
			<td>KCl</td>
			<td>Sigma-Aldrich</td>
			<td>P5405</td>
			<td></td>
		</tr>
		<tr>
			<td>NaH2PO4</td>
			<td>Sigma-Aldrich</td>
			<td>S5011</td>
			<td></td>
		</tr>
		<tr>
			<td>Sucrose</td>
			<td>Sigma-Aldrich</td>
			<td>S7903</td>
			<td></td>
		</tr>
		<tr>
			<td>Fibrinogen from bovine plasma</td>
			<td>Calbiochem (Merck)</td>
			<td>341573-1GM</td>
			<td>CAUTION: Harmful by inhalation, in contact with skin and if swallowed. Manipulate under laminar flow</td>
		</tr>
		<tr>
			<td>Thrombin from bovine plasma</td>
			<td>Sigma-Aldrich</td>
			<td>T9549</td>
			<td>CAUTION: Health Hazard, use gloves</td>
		</tr>
		<tr>
			<td>PDF, NH2-NSELINSLLSLPKNMNDA-OH</td>
			<td>Chi Scientific</td>
			<td>custom made</td>
			<td></td>
		</tr>
		<tr>
			<td>Vaccum grease</td>
			<td>Sigma-Aldrich</td>
			<td>18405</td>
			<td></td>
		</tr>
		<tr>
			<td>35 mm Dish, No. 1.5 Coverslip, 20 mm Glass Diameter, Uncoated</td>
			<td>MatTek</td>
			<td>P35G-1.5-20-C</td>
			<td></td>
		</tr>
		<tr>
			<td>Corning Falcon Easy-Grip Tissue Culture Dishes</td>
			<td>fisherscientific</td>
			<td>08-772A</td>
			<td></td>
		</tr>
		<tr>
			<td>Sterile 500 mL Steritop-GP 33 mm threaded bottle top filter, 0.22 &#956;m</td>
			<td>Millipore</td>
			<td>SCGPS05RE</td>
			<td></td>
		</tr>
		<tr>
			<td>Polytetrafluoroethylene (PTFE) film</td>
			<td>Dupont</td>
			<td>200A Teflon FEP Film</td>
			<td></td>
		</tr>
		<tr>
			<td>Millex-HV Syringe Filter Unit, 0.45&#160;&#181;m, PVDF, 33&#160;mm, gamma sterilized</td>
			<td>Millipore</td>
			<td>SLHV033RS</td>
			<td></td>
		</tr>
		<tr>
			<td>Millex-GV Syringe Filter Unit, 0.22&#160;&#181;m, PVDF, 33&#160;mm, gamma sterilized</td>
			<td>Millipore</td>
			<td>SLGV033RS</td>
			<td></td>
		</tr>
		<tr>
			<td>Three-well glass dissection dish</td>
			<td>Any company</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Fine forceps, size 5, Dumont</td>
			<td>Fine Science Tools</td>
			<td>11254-20</td>
			<td></td>
		</tr>
		<tr>
			<td>Tandem scanner inverted TCS SP5 confocal microscope, with resonant scanner and HyD photo-multiplier detectors</td>
			<td>Leica microsystem CMS GmbH</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Temperature control chamber</td>
			<td>Life Imaging Services</td>
			<td>The CUBE &#38; BOX temperature control system, custom designed</td>
			<td></td>
		</tr>
		<tr>
			<td>Stage-top humidity controller</td>
			<td>Life Imaging Services</td>
			<td>custom made</td>
			<td></td>
		</tr>
		<tr>
			<td>Water Immersion Micro Dispenser: dispenser, extended micro-pump MP6 series and Autoimmersion Objective Controller software</td>
			<td>Leica microsystem CMS GmbH</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>SUM-stack creation and 3D correction drift plugin</td>
			<td>ImageJ software</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>10x iterative deconvolution</td>
			<td>AutoQuant and Imaris software</td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

single-cell resolution fluorescence live imaging of drosophila circadian clocks in larval brain culture

The circadian pacemaker circuit orchestrates rhythmic behavioral and physiological outputs coordinated with environmental cues, such as day/night cycles. The molecular clock within each pacemaker neuron generates circadian rhythms in gene expression, which underlie the rhythmic neuronal functions essential to the operation of the circuit. Investigation of the properties of the individual molecular oscillators in different subclasses of pacemaker neurons and their interaction with neuronal signaling yields a better understanding of the circadian pacemaker circuit. Here, we present a time-lapse fluorescent microscopy approach developed to monitor the molecular clockwork in clock neurons of cultured Drosophila larval brain. This method allows the multi-day recording of the rhythms of genetically encoded fluorescent circadian reporters at single-cell resolution. This setup can be combined with pharmacological manipulations to closely analyze real-time response of the molecular clock to various compounds. Beyond circadian rhythms, this multipurpose method in combination with powerful Drosophila genetic techniques offers the possibility to study diverse neuronal or molecular processes in live brain tissue.

Here, we show the representative results of the long-term recording of a circadian fluorescent reporter in ex vivo larval brain culture, and the live imaging results of PDF bath application on reporter expression.
Non-wandering L3 larvae expressing the molecular clock reporter PER-TDT and UAS-mCD8::YFP driven by a clock neuron driver Clk(856)-gal4 (Figure 1C) were entrained in LD. ...

Watch this Scientific Journal Video about Single-cell Resolution Fluorescence Live Imaging of Drosophila Circadian Clocks in Larval Brain Culture at JoVE.com

Single-cell Resolution Fluorescence Live Imaging of Drosophila Circadian Clocks in Larval Brain Culture

The goal of this protocol is to establish ex vivo Drosophila larval brain culture optimized to monitor circadian molecular rhythms with long-term fluorescence time-lapse imaging. The application of this method to pharmacological assays is also discussed.

Single-cell Resolution Fluorescence Live Imaging of Drosophila Circadian Clocks in Larval Brain Culture

The circadian pacemaker circuit orchestrates rhythmic behavioral and physiological outputs coordinated with environmental cues, such as day/night cycles. ...

single-cell-resolution-fluorescence-live-imaging-drosophila-circadian

Research

JoVE Journal

Neuroscience

7.5K Views.  University of Geneva. The goal of this protocol is to establish ex vivo Drosophila larval brain culture optimized to monitor circadian molecular rhythms with long-term fluorescence time-lapse imaging. The application of this method to pharmacological assays is also discussed.

Video: Single-cell Resolution Fluorescence Live Imaging of Drosophila Circadian Clocks in Larval Brain Culture

Magnetic Resonance Spectroscopy of live Drosophila melanogaster using Magic Angle Spinning

High-Resolution Magic Angle Spinning (HRMAS) proton magnetic resonance spectroscopy (1H-MRS) is a novel non-destructive technique that improves spectral line-widths and allows high-resolution spectra to be obtained from extracts, intact cells, cell cultures, and more importantly intact tissue to investigate relationships between metabolites and cellular processes. In vivo HRMAS 1H-MRS studies have yet to be reported in the live fruit fly Drosophila melanogaster. Drosophila, as a simpler genetic organism, allows the multiple biological functions and various evolutionarily conserved signaling pathways to be examined at the whole organism level and it is a useful model for investigating genetics and physiology. To this end, we developed and implemented an in vivo HRMAS 1H-MRS method to investigate live Drosophila at 14.1 T. Here, we outline an HRMAS 1H-MRS protocol for the molecular characterization of Drosophila with a conventional MR spectrometer equipped with an HRMAS probe. This technique is a novel, in vivo, non-destructive Drosophila metabolite measurement approach, which enables the identification of disease biomarkers and thus may contribute to novel therapeutic development.

Magnetic Resonance Spectroscopy of live Drosophila melanogaster using Magic Angle Spinning

This technique enables the use of high-resolution magic angle spinning proton MR spectroscopy (HRMAS 1H-MRS) for molecular characterization of live Drosophila melanogaster with a conventional 14.1 tesla spectrometer equipped with an HRMAS probe.

High-Resolution Magic Angle Spinning (HRMAS) proton magnetic resonance spectroscopy (1H-MRS) is a novel non-destructive technique that improves spectral ...

Visualization of Larval Segmental Nerves in 3rd Instar Drosophila Larval Preparations

Drosophila melanogaster is emerging as a powerful model system for studying the development and function of the nervous system, particularly because of its convenient genetics and fully sequenced genome. Additionally, the larval nervous system is an ideal model system to study mechanisms of axonal transport as the larval segmental nerves contain bundles of axons with their cell bodies located within the brain and their nerve terminals ending along the length of the body. Here we describe the procedure for visualization of synaptic vesicle proteins within larval segmental nerves. If done correctly, all components of the nervous system, along with associated tissues such as muscles and NMJs, remain intact, undamaged, and ready to be visualized. 3rd instar larvae carrying various mutations are dissected, fixed, incubated with synaptic vesicle antibodies, visualized and compared to wild type larvae. This procedure can be adapted for several different synaptic or neuronal antibodies and changes in the distribution of a variety of proteins can be easily observed within larval segmental nerves.

Visualization of Larval Segmental Nerves in 3rd Instar Drosophila Larval Preparations

Drosophila melanogaster larvae provide an ideal model system to investigate the mechanisms of axonal transport within larval segmental nerves. Using this procedure, 3rd instar larvae carrying various mutations can be compared to wild type larvae.

Drosophila melanogaster is emerging as a powerful model system for studying the development and function of the nervous system, particularly because of ...

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 ...

A Rapid Approach to High-Resolution Fluorescence Imaging in Semi-Thick Brain Slices

A fundamental goal to both basic and clinical neuroscience is to better understand the identities, molecular makeup, and patterns of connectivity that are characteristic to neurons in both normal and diseased brain. Towards this, a great deal of effort has been placed on building high-resolution neuroanatomical maps1-3. With the expansion of molecular genetics and advances in light microscopy has come the ability to query not only neuronal morphologies, but also the molecular and cellular makeup of individual neurons and their associated networks4. Major advances in the ability to mark and manipulate neurons through transgenic and gene targeting technologies in the rodent now allow investigators to 'program' neuronal subsets at will5-6. Arguably, one of the most influential contributions to contemporary neuroscience has been the discovery and cloning of genes encoding fluorescent proteins (FPs) in marine invertebrates7-8, alongside their subsequent engineering to yield an ever-expanding toolbox of vital reporters9. Exploiting cell type-specific promoter activity to drive targeted FP expression in discrete neuronal populations now affords neuroanatomical investigation with genetic precision.
Engineering FP expression in neurons has vastly improved our understanding of brain structure and function. However, imaging individual neurons and their associated networks in deep brain tissues, or in three dimensions, has remained a challenge. Due to high lipid content, nervous tissue is rather opaque and exhibits auto fluorescence. These inherent biophysical properties make it difficult to visualize and image fluorescently labelled neurons at high resolution using standard epifluorescent or confocal microscopy beyond depths of tens of microns. To circumvent this challenge investigators often employ serial thin-section imaging and reconstruction methods10, or 2-photon laser scanning microscopy11. Current drawbacks to these approaches are the associated labor-intensive tissue preparation, or cost-prohibitive instrumentation respectively.
Here, we present a relatively rapid and simple method to visualize fluorescently labelled cells in fixed semi-thick mouse brain slices by optical clearing and imaging. In the attached protocol we describe the methods of: 1) fixing brain tissue in situ via intracardial perfusion, 2) dissection and removal of whole brain, 3) stationary brain embedding in agarose, 4) precision semi-thick slice preparation using new vibratome instrumentation, 5) clearing brain tissue through a glycerol gradient, and 6) mounting on glass slides for light microscopy and z-stack reconstruction (Figure 1).
For preparing brain slices we implemented a relatively new piece of instrumentation called the 'Compresstome' VF-200 (http://www.precisionary.com/products_vf200.html). This instrument is a semi-automated microtome equipped with a motorized advance and blade vibration system with features similar in function to other vibratomes. Unlike other vibratomes, the tissue to be sliced is mounted in an agarose plug within a stainless steel cylinder. The tissue is extruded at desired thicknesses from the cylinder, and cut by the forward advancing vibrating blade. The agarose plug/cylinder system allows for reproducible tissue mounting, alignment, and precision cutting. In our hands, the 'Compresstome' yields high quality tissue slices for electrophysiology, immunohistochemistry, and direct fixed-tissue mounting and imaging. Combined with optical clearing, here we demonstrate the preparation of semi-thick fixed brain slices for high-resolution fluorescent imaging.

Here we describe a rapid and simple method to image fluorescently labeled cells in semi-thick brain slices. By fixing, slicing, and optically clearing brain tissue we describe how standard epifluorescent or confocal imaging can be used to visualize individual cells and neuronal networks within intact nervous tissue.

A fundamental goal to both basic and clinical neuroscience is to better understand the identities, molecular makeup, and patterns of connectivity that are ...

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 ...

High-resolution Live Imaging of Cell Behavior in the Developing Neuroepithelium

The embryonic spinal cord consists of cycling neural progenitor cells that give rise to a large percentage of the neuronal and glial cells of the central nervous system (CNS). Although much is known about the molecular mechanisms that pattern the spinal cord and elicit neuronal differentiation1, 2, we lack a deep understanding of these early events at the level of cell behavior. It is thus critical to study the behavior of neural progenitors in real time as they undergo neurogenesis.
In the past, real-time imaging of early embryonic tissue has been limited by cell/tissue viability in culture as well as the phototoxic effects of fluorescent imaging. Here we present a novel assay for imaging such tissue for long periods of time, utilizing a novel ex vivo slice culture protocol and wide-field fluorescence microscopy (Fig. 1). This approach achieves long-term time-lapse monitoring of chick embryonic spinal cord progenitor cells with high spatial and temporal resolution.
This assay may be modified to image a range of embryonic tissues3, 4 In addition to the observation of cellular and sub-cellular behaviors, the development of novel and highly sensitive reporters for gene activity (for example, Notch signaling5) makes this assay a powerful tool with which to understand how signaling regulates cell behavior during embryonic development.

Imaging embryonic tissue in real-time is challenging over long periods of time. Here we present an assay for monitoring cellular and sub-cellular changes in chick spinal cord for long periods with high spatial and temporal resolution. This technique can be adapted for other regions of the nervous system and developing embryo.

The embryonic spinal cord consists of cycling neural progenitor cells that give rise to a large percentage of the neuronal and glial cells of the central ...

Ex vivo Live Imaging of Single Cell Divisions in Mouse Neuroepithelium

We developed a system that integrates live imaging of fluorescent markers and culturing slices of embryonic mouse neuroepithelium. We took advantage of existing mouse lines for genetic cell lineage tracing: a tamoxifen-inducible Cre line and a Cre reporter line expressing dsRed upon Cre-mediated recombination. By using a relatively low level of tamoxifen, we were able to induce recombination in a small number of cells, permitting us to follow individual cell divisions. Additionally, we observed the transcriptional response to Sonic Hedgehog (Shh) signaling using an Olig2-eGFP transgenic line 1-3 and we monitored formation of cilia by infecting the cultured slice with virus expressing the cilia marker, Sstr3-GFP 4. In order to image the neuroepithelium, we harvested embryos at E8.5, isolated the neural tube, mounted the neural slice in proper culturing conditions into the imaging chamber and performed time-lapse confocal imaging. Our ex vivo live imaging method enables us to trace single cell divisions to assess the relative timing of primary cilia formation and Shh response in a physiologically relevant manner. This method can be easily adapted using distinct fluorescent markers and provides the field the tools with which to monitor cell behavior in situ and in real time.

Ex vivo Live Imaging of Single Cell Divisions in Mouse Neuroepithelium

Here we develop the tools necessary for ex vivo live imaging to trace single cell divisions in the mouse E8.5 neuroepithelium

We developed a system that integrates live imaging of fluorescent markers and culturing slices of embryonic mouse neuroepithelium. We took advantage of ...

Live Imaging of Mitosis in the Developing Mouse Embryonic Cortex

Although of short duration, mitosis is a complex and dynamic multi-step process fundamental for development of organs including the brain. In the developing cerebral cortex, abnormal mitosis of neural progenitors can cause defects in brain size and function. Hence, there is a critical need for tools to understand the mechanisms of neural progenitor mitosis. Cortical development in rodents is an outstanding model for studying this process. Neural progenitor mitosis is commonly examined in fixed brain sections. This protocol will describe in detail an approach for live imaging of mitosis in ex vivo embryonic brain slices. We will describe the critical steps for this procedure, which include: brain extraction, brain embedding, vibratome sectioning of brain slices, staining and culturing of slices, and time-lapse imaging. We will then demonstrate and describe in detail how to perform post-acquisition analysis of mitosis. We include representative results from this assay using the vital dye Syto11, transgenic mice (histone H2B-EGFP and centrin-EGFP), and in utero electroporation (mCherry-&#945;-tubulin). We will discuss how this procedure can be best optimized and how it can be modified for study of genetic regulation of mitosis. Live imaging of mitosis in brain slices is a flexible approach to assess the impact of age, anatomy, and genetic perturbation in a controlled environment, and to generate a large amount of data with high temporal and spatial resolution. Hence this protocol will complement existing tools for analysis of neural progenitor mitosis.

Neural progenitor mitosis is a critical parameter of neurogenesis. Much of our understanding of neural progenitor mitosis is based on analysis of fixed tissue. Live imaging in embryonic brain slices is a versatile technique to assess mitosis with high temporal and spatial resolution in a controlled environment.

Although of short duration, mitosis is a complex and dynamic multi-step process fundamental for development of organs including the brain. In the ...

Super-resolution Imaging of Neuronal Dense-core Vesicles

Detection of fluorescence provides the foundation for many widely utilized and rapidly advancing microscopy techniques employed in modern biological and medical applications. Strengths of fluorescence include its sensitivity, specificity, and compatibility with live imaging. Unfortunately, conventional forms of fluorescence microscopy suffer from one major weakness, diffraction-limited resolution in the imaging plane, which hampers studies of structures with dimensions smaller than ~250 nm. Recently, this limitation has been overcome with the introduction of super-resolution fluorescence microscopy techniques, such as photoactivated localization microscopy (PALM). Unlike its conventional counterparts, PALM can produce images with a lateral resolution of tens of nanometers. It is thus now possible to use fluorescence, with its myriad strengths, to elucidate a spectrum of previously inaccessible attributes of cellular structure and organization.
Unfortunately, PALM is not trivial to implement, and successful strategies often must be tailored to the type of system under study. In this article, we show how to implement single-color PALM studies of vesicular structures in fixed, cultured neurons. PALM is ideally suited to the study of vesicles, which have dimensions that typically range from ~50-250 nm. Key steps in our approach include labeling neurons with photoconvertible (green to red) chimeras of vesicle cargo, collecting sparsely sampled raw images with a super-resolution microscopy system, and processing the raw images to produce a high-resolution PALM image. We also demonstrate the efficacy of our approach by presenting exceptionally well-resolved images of dense-core vesicles (DCVs) in cultured hippocampal neurons, which refute the hypothesis that extrasynaptic trafficking of DCVs is mediated largely by DCV clusters.

We describe how to implement photoactivated localization microscopy (PALM)-based studies of vesicles in fixed, cultured neurons. Key components of our protocol include labeling vesicles with photoconvertible chimeras, collecting sparsely sampled raw images with a super-resolution microscopy system, and processing the raw images to produce a super-resolution image.

Detection of fluorescence provides the foundation for many widely utilized and rapidly advancing microscopy techniques employed in modern biological and ...

Live Imaging of Drosophila Larval Neuroblasts

Stem cells divide asymmetrically to generate two progeny cells with unequal fate potential: a self-renewing stem cell and a differentiating cell. Given their relevance to development and disease, understanding the mechanisms that govern asymmetric stem cell division has been a robust area of study. Because they are genetically tractable and undergo successive rounds of cell division about once every hour, the stem cells of the Drosophila central nervous system, or neuroblasts, are indispensable models for the study of stem cell division. About 100 neural stem cells are located near the surface of each of the two larval brain lobes, making this model system particularly useful for live imaging microscopy studies. In this work, we review several approaches widely used to visualize stem cell divisions, and we address the relative advantages and disadvantages of those techniques that employ dissociated versus intact brain tissues. We also detail our simplified protocol used to explant whole brains from third instar larvae for live cell imaging and fixed analysis applications.

Live Imaging of Drosophila Larval Neuroblasts

This protocol details a streamlined method used to conduct live cell imaging in the context of an intact larval brain. Live cell imaging approaches are invaluable for the study of asymmetric neural stem cell divisions as well as other neurogenic and developmental processes, consistently uncovering mechanisms that were previously overlooked.

Stem cells divide asymmetrically to generate two progeny cells with unequal fate potential: a self-renewing stem cell and a differentiating cell. Given ...