We appreciate the support provided by William Archer and the Notre Dame Integrated Imaging Facility. Special thanks are directed to the Freimann Life Sciences technicians for their continuous help and their care and husbandry of the zebrafish. This study was supported by grants from the National Eye Institute of NIH to DRH (R01-EY018417, R01-EY024519) and the Center for Zebrafish Research, University of Notre Dame, Notre Dame, IN.

Note: Zebrafish were raised and maintained in the Notre Dame Zebrafish facility in the Freimann Life Sciences Center. The methods described in this manuscript are approved by the University of Notre Dame Animal Care and Use Committee and are in compliance with the statement for the use of animals in vision research by the Association for Research in Vision and Ophthalmology.
1. Solutions
<ol>
	<li>Prepare 70% ethanol to sterilize the tissue culture hood and any equipment/reagents that are transferred into the tissue culture hood.</li>
	<li>Add 2 mL of 2-phenoxyethanol to 1 L of system water (1:500 2-phenoxyethanol).</li>
	<li>Prepare 0.1 mM NaHCO3, pH 8.0. Use a 10 mL&#160;syringe and a 0.2 &#181;m pore-size syringe filter to sterilize the solution in a sterilized tissue culture hood. 
	NOTE: NaHCO3 is used to efficiently spread the cell and tissue adhesive across the coverslip surface of fluorodishes (see step 3.2).</li>
	<li>Prepare 1.0 M CaCl2 and 1.0 M MgCl2. Sterilize with a 10 mL syringe and 0.2 &#181;m pore-size syringe filter in a sterilized tissue culture hood.</li>
	<li>To prepare Hank&#39;s-balanced Salt Solution (HBSS), add sterile CaCl2 and sterile MgCl2 to 1x HBSS without Ca2+/Mg2+, without phenol red at a final concentration of 1 mM each. Work in a sterile environment.</li>
	<li>To prepare culture medium, mix 50% 1x Minimum Essential Medium (MEM) without phenol red, 25% HBSS containing CaCl2 and MgCl2 (see section 1.4), 25% Horse Serum (HS), 10 units/mL penicillin, and 10 &#181;g/mL streptomycin. Work in a sterile environment. 
	NOTE: Avoid medium containing phenol red as it autofluoresces, thereby affecting signal to noise ratios.23</li>
	<li>Prepare 10 mL&#160;of 1% low melting point agarose in 1x MEM without phenol red. Melt agarose/1x MEM using a microwave. Prepare small volumes of agarose (e.g., 10 mL)&#160;as repetitive reheating will change ion concentrations due to fluid evaporation.</li>
	<li>Prior to culturing, sterilize 1.5 mL microcentrifuge tubes by autoclaving.</li>
</ol>
2. Light-damage Paradigm
<ol>
	<li>Dark-adaptation
	<ol>
		<li>Place 2 - 3&#160;Tg[gfap:nGFP]mi2004 zebrafish (or other transgenic zebrafish of interest) at 6 - 14 months of age into an environment devoid of light for 14 d. For further detail see reference2, 6, 24, 25.</li>
	</ol>
	</li>
	<li>Position the tank containing 2 - 3 dark-adapted transgenic zebrafish in system water between two fluorescent lamps that emit light of 2,800 lux2, 6, 24, 25.</li>
	<li>Expose zebrafish to constant intense light for 35 h. During the light exposure, assure that the water temperature is maintained between 31 - 33 &#176;C.</li>
</ol>
3. Preparation for Culturing (On the Day of Retinal Isolation)
<ol>
	<li>Using 70% ethanol, sterilize the tissue culture hood and the components/tools that are transferred into the tissue culture hood (e.g., flasks containing MEM and HBSS, pipettes, sterile pipette tips, etc.).</li>
	<li>Preparation of fluorodishes
	<ol>
		<li>Coat one fluorodish for each retina with cell and tissue adhesive (see Table of Materials).</li>
		<li>Dilute the cell and tissue adhesive in 0.1 mM NaHCO3 to a final concentration of 70 &#181;g/mL, add 50 &#181;L to each fluorodish and spread the solution across the center of the fluorodish with a 200 &#181;L pipette tip (approximately 1 - 1.2 cm diameter).</li>
		<li>Incubate the coated fluorodishes for 1 - 3 h at RT&#160;(alternatively, incubate O/N at 4 &#176;C).</li>
		<li>Remove the solution and rinse 3x with 500 &#181;L of 1x MEM for each wash. To avoid the coated fluorodishes from drying out, maintain them in MEM until retinal explants are mounted.</li>
	</ol>
	</li>
	<li>Prepare culture medium as described in step 1.6. The culture medium can be stored for up to 1 week at 4 &#176;C.</li>
</ol>
4. Isolation and Culturing of Retinal Explants
NOTE: The protocol outlined below is for the isolation of the dorsal retina, which is the retinal region that is predominantly lesioned by the described light-damage paradigm. Therefore, damage-induced proliferation and the associated event of interkinetic nuclear migration occur in the dorsal retina. However, the isolation procedure can be adjusted to yield retinal regions according to the specific requirements of the researcher/research question.
<ol>
	<li>Euthanize one light-damaged transgenic zebrafish at a time in 1:500 2-phenoxyethanol.</li>
	<li>Remove MEM from one fluorodish with a 1,000 &#181;L pipette so that only a thin film of fluid remains.</li>
	<li>Transfer the zebrafish onto a dry paper towel, remove the eye with a curved pair of Dumont forceps (forceps #5, 45&#176; angle) and transfer it onto the fluorodish.</li>
	<li>Using a stereomicroscope, orient the eye with the pupil onto the cover slip of the fluorodish so that the back of the eye with the optic nerve is visible (Figure 1D).</li>
	<li>With a pair of McPherson-Vannas scissors remove the optic nerve, cutting close to the back of the eye. In addition, remove connective tissue lining the outside of the eye.</li>
	<li>Hold the eye between its nasal and temporal side with a pair of #5 forceps while making an incision at the optic stalk by piercing with one scissor blade through the lamina cribrosa and cutting along both the nasal and temporal sides of the eye (see Figure 1E, segmented line).</li>
	<li>Using two pairs of #5 forceps, one for holding the dorsal side of the retina and the other pair to separate the ventral from the dorsal retina, pull the tissue. 
	NOTE: It is advisable to orient the dorsal retina so that the lens and the ganglion cell layer face the coverslip while the sclera is facing upwards.</li>
	<li>Remove the sclera from the dorsal retina with one pair of #5 forceps, while holding the lens that is connected to the retina with a second pair of #5 forceps (Figure 1H, I).</li>
	<li>To remove the lens, use McPherson-Vannas scissors and cut behind the lens without damaging the retina (Figure 1I, J). Sometimes, the lens separates in step 4.7. In this case, remove the sclera carefully with forceps by holding the retina at a cut edge with a second pair of #5 forceps.</li>
	<li>Remove the vitreous while removing the lens without damaging the retina. Flatten the retina with the ganglion cell layer facing the cover slip of the fluorodish (Figure 1L, M).</li>
	<li>Surround the retina with 10 &#181;L of 1% low melting point agarose and let the agarose solidify.</li>
	<li>Watch that the liquid agarose does not lift the retina as even a slight elevation might affect the ability to focus deeply into the tissue. If lifting is observed, use a pipette to remove agarose. Let residual agarose set before attempting to add more.</li>
	<li>Repeat step 4.12 several times before adding 1% low melting point agarose to cover the entire fluorodish. Once the agarose has solidified, add 1.5 mL culture medium.</li>
	<li>Maintain the retinal explant culture in a 5% CO2/air environment set at 32 &#176;C for approximately 12 h to allow the retina to recover from the stress incurred by the isolation procedure. Set the temperature to 32 &#176;C to maintain retinas at the same temperature as light-treated zebrafish (see step 2.3).</li>
</ol>
5. Multiphoton Microscopy
NOTE: The experiments performed in this manuscript were optimized for a multiphoton microscope equipped with an infrared laser (see Table of Materials), a 40X Apo long distance water immersion objective (N.A. 1.15), a galvanometer scanner and an environmental chamber that contains an insert for four 35 mm Petri dishes. The images were acquired with a non-descanned detector (R-NDD).
<ol>
	<li>Prior to imaging, equilibrate the environmental chamber to achieve a 5% CO2/air atmosphere. Make sure that empty Petri dishes are inserted into the holder to avoid leakage of gas into the room.</li>
	<li>Turn on the microscopy system.</li>
	<li>Once the environmental chamber is equilibrated, add refractive index liquid onto the 40X Apo long distance water immersion objective (N.A. 1.15). 
	NOTE: The refractive index liquid with optical properties similar to water is used to avoid evaporation of water during long-term imaging.</li>
	<li>Place fluorodishes with retinal explants into the chamber. Using brightfield light, position the specimen into the light path and bring the midregion of the dorsal retina into the plane of focus.</li>
	<li>Use GFP epifluorescent light to focus on gfap:nGFP-positive M&#252;ller glia nuclei (Figure 2A, C). 
	NOTE: If explants are not mounted flat or agarose accumulated under the explant, it will be difficult to focus onto the gfap:nGFP-positive nuclei or they will fluoresce dimly.
	<ol>
		<li>Check whether moving to a different region within the same retinal explant will overcome the focusing issue. Otherwise move to a different retinal explant.</li>
	</ol>
	</li>
	<li>In the image acquisition software, open the &#39;A1 MP GUI&#39;, the &#39;TiPad&#39;, the &#39;A1 Compact GUI&#39; and the &#39;ND acquisition&#39; windows. For multiphoton imaging, ensure that the &#39;IR NDD&#39; option is chosen in the &#39;A1 Compact GUI&#39;.</li>
	<li>In the &#39;setting&#39; field, select IR-DM for the 1st dichroic mirror and choose the band pass filter 525/50 to acquire GFP fluorescence.</li>
	<li>Switch on the IR laser in the window labeled &#39;A1MP GUI&#39;. It will take a few minutes for the laser to be ready. Set the wavelength to 910 nm to excite GFP fluorescence and align the laser by clicking the &#39;Auto alignment&#39; button in the &#39;A1 MP GUI&#39; window.</li>
	<li>Ensure that room and equipment lights are switched off or covered before opening the shutter in the &#39;A1 MP GUI&#39; to avoid overexposure of the photomultiplier tube. To reduce noise levels, house the microscope in a darkened environment.</li>
	<li>Acquire images of a field of view of 300 x 300 pixels, at a zoom of two, and a pixel dwelling time of 4.8 &#181;s/pixel. Roughly set up the laser power by changing the &#39;acquisition area&#39; in the &#39;A1MP GUI&#39; and the gain in the &#39;A1 Compact GUI&#39; window.</li>
	<li>Setting up the z-stack
	<ol>
		<li>Focus on the ganglion cell layer to set the top focal plane of the z-stack in the &#39;z&#39;-subwindow within the &#39;ND acquisition&#39; window. Some gfap:nGFP-positive cells are typically located in the ganglion cell layer, which helps to identify the basal limit of the retina (Figure 2A, D).</li>
		<li>Move the focal plane through the level of the ONL (Figure 2A, B), which is characterized by the presence of dimly labeled gfap:nGFP-positive cells that are round and enlarged relative to their counterparts in the INL (Figure 2A, C).</li>
		<li>Set this plane as the bottom of the z-stack. Ensure that the entire ONL will be imaged (Figure 2A, B).</li>
		<li>When experiencing focal plane shifts that require re-adjusting during the imaging period, double-click on the middle position in the &#39;z&#39; subwindow to assign it as the &#39;home&#39; position. Change to &#39;symmetric mode defined&#39; and click &#39;relative&#39;.</li>
		<li>Set the z-step size between 0.7 to 1 &#181;m.</li>
	</ol>
	</li>
	<li>Z-intensity correction:
	<ol>
		<li>Apply z-intensity corrections to compensate for loss of pixel intensity due to light scattering when imaging in deep layers of the tissue.</li>
		<li>To set up the correction, open the &#39;z-intensity correction&#39; window. To set the &#39;z-stack range&#39;, choose &#39;From ND&#39;.</li>
		<li>Click on the bottom focal plane in the &#39;z-intensity correction&#39; window (in this case, corresponds to the ganglion cell layer) and set the laser intensity (&#39;acquisition area&#39; in the &#39;A1MP GUI&#39;) and gain (A1 Compact GUI).</li>
		<li>Click the arrow next to the &#39;z-values&#39; in the &#39;z-intensity correction&#39; window to confirm the settings that are subsequently shown under &#39;device settings&#39; in the &#39;z-intensity correction&#39; window for the chosen focal plane.</li>
		<li>Repeat the process for the middle and top planes, increasing the laser power and gain. Additional focal planes can be added if necessary. See Table 1 for specific laser and gain settings for experiments in Figures 2 - 4.</li>
		<li>Set the &#39;acquisition area&#39; in the &#39;A1 MP GUI&#39; window. Avoid selecting an acquisition area larger than 15 and a gain higher than 126 at the start of imaging to circumvent photobleaching and increased noise levels. 
		NOTE: As lasers and photomultiplier tubes differ between microscopy systems, test laser and gain settings to obtain optimal imaging conditions for the microscope set up while avoiding photobleaching.</li>
		<li>Choose &#39;relative intensity correction&#39; in the &#39;z-intensity correction&#39; window.</li>
	</ol>
	</li>
	<li>In the &#39;timeseries&#39; subwindow in the &#39;ND acquisition&#39; window, set the duration to 8 h and the interval to &#39;no delay&#39;. Then, make sure to click the &#39;Run z-correction&#39; in the &#39;z-stack&#39; sub window in the &#39;ND acquisition&#39; window button to acquire the 3-D timeseries.</li>
	<li>Maintain retinal explants at a temperature of 27 - 29 &#176;C throughout the duration of image acquisition.</li>
	<li>Throughout the image acquisition period, if necessary, readjust the power level and gain in order to maintain image quality for post-imaging analysis. For adjustments perform steps 5.11.2 - 5.11.4.</li>
	<li>If the focal plane shifts, pause or stop the run and perform step 5.11 again. 
	NOTE: If &#39;relative z-correction&#39; was chosen in step 5.12.7 and step 5.11.4 was performed it should not be necessary to readjust power and gain levels, unless extensive photobleaching occurred.</li>
</ol>
6. Analysis of Velocity
<ol>
	<li>Extract the time, setting a &#39;region of interest&#39; on the image. Use the &#39;time measurement&#39; tool and export the time values to a spreadsheet.</li>
	<li>Crop a region that contains a dividing gfap:nGFP-positive nucleus.</li>
	<li>Choose the cropped region so that it contains at least one nucleus that does not undergo INM in order to set a reference point to subsequently measure the distances that the dividing nucleus migrated in relation to the basal INL.&#160;NOTE: To choose a nucleus that remains in the basal INL, it helps to prepare a 3-D reconstruction of the timeseries.</li>
	<li>Alternatively, if a gfap:nGFP-positive cell is observed in the ONL throughout the acquisition period, use a vertical line of fixed length spanning from the ONL nucleus to the basal INL in order to identify a reference point.</li>
	<li>Using the &#39;show slices view&#39; function, generate orthogonal projections. Subsequently, change the mode from &#39;slice&#39; to &#39;maximum intensity projection&#39;.</li>
	<li>Turn off the &#39;xy&#39; view of the orthogonal maximum projection. Depending on the orientation at which the migrating/dividing nucleus is best visible, also turn off either the &#39;xz&#39;- or the &#39;yz&#39;-view.</li>
	<li>Click on the remaining image with the right mouse button and extract the &#39;xz&#39; or &#39;yz&#39;-image series with the &#39;Create new document from this view&#39; function. If necessary, rotate the image.</li>
	<li>Using the &#39;manual measurement&#39; function, draw a horizontal line across the image at the bottom level of the nucleus that remains in the basal INL and does not undergo INM (= reference point; Figure 4A - E, red horizontal line).</li>
	<li>Measure the distance between the reference line and the basal point of the migrating nucleus for the timeseries using the &#39;line measurement&#39; tool in the analysis software (see Figure 4A - E).</li>
	<li>Once the nuclear envelope breaks down, measure the basal position of the soma if it is identifiable following the diffusion of GFP into the entire cell.</li>
	<li>Using a spreadsheet software, plot the distance a nucleus migrated against the time passed (Figure 4F).
	<ol>
		<li>To determine the apical migration velocity (va), graph the distances traveled for the period before nuclear envelope breakdown occurs (Figure 4G).</li>
		<li>Select the data series within the chart, right-click the mouse and insert a linear regression curve including the corresponding function &#39;y=mx+c&#39;. The slope &#39;m&#39; in the function represents the velocity, va (Figure 4G).</li>
		<li>Repeat steps 6.11.1 and 6.11.2 for the first phase of rapid basal migration to determine the basal migration velocity, vb (Figure 4H).</li>
	</ol>
	</li>
</ol>

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R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Use+of+an+adult+rat+retinal+explant+model+for+screening+of+potential+retinal+ganglion+cell+neuroprotective+therapies.">Use of an adult rat retinal explant model for screening of potential retinal ganglion cell neuroprotective therapies.</a> Invest.Ophthalmol.Vis.Sci. 52 (6), 3309-3320 (2011).</li><li>Kustermann, S., Schmid, S., Biehlmaier, O., Kohler, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Survival,+excitability,+and+transfection+of+retinal+neurons+in+an+organotypic+culture+of+mature+zebrafish+retina.">Survival, excitability, and transfection of retinal neurons in an organotypic culture of mature zebrafish retina.</a> Cell Tissue Res. 332 (2), 195-209 (2008).</li><li>Williams, P. R., Morgan, J. L., Kerschensteiner, D., Wong, R. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vitro+imaging+of+retinal+whole+mounts.">In vitro imaging of retinal whole mounts.</a> Cold Spring Harb Protoc. 2013, (2013).</li><li>Johnson, T. V., Oglesby, E. N., Steinhart, M. R., Cone-Kimball, E., Jefferys, J., Quigley, H. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Time-Lapse+Retinal+Ganglion+Cell+Dendritic+Field+Degeneration+Imaged+in+Organotypic+Retinal+Explant+Culture.">Time-Lapse Retinal Ganglion Cell Dendritic Field Degeneration Imaged in Organotypic Retinal Explant Culture.</a> Invest.Ophthalmol.Vis.Sci. 57 (1), 253-264 (2016).</li><li>Roehlecke, C., Schumann, U., Ader, M., Knels, L., Funk, R. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Influence+of+blue+light+on+photoreceptors+in+a+live+retinal+explant+system.">Influence of blue light on photoreceptors in a live retinal explant system.</a> Mol.Vis. 17, 876-884 (2011).</li><li>Coutu, D. L., Schroeder, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Probing+cellular+processes+by+long-term+live+imaging--historic+problems+and+current+solutions.">Probing cellular processes by long-term live imaging--historic problems and current solutions.</a> J.Cell.Sci. 126 (Pt 17), 3805-3815 (2013).</li><li>Thomas, J. L., Thummel, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+novel+light+damage+paradigm+for+use+in+retinal+regeneration+studies+in+adult+zebrafish.">A novel light damage paradigm for use in retinal regeneration studies in adult zebrafish.</a> J.Vis.Exp. 80, e51017 (2013).</li><li>Conner, C., Ackerman, K. M., Lahne, M., Hobgood, J. S., Hyde, D. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Repressing+notch+signaling+and+expressing+TNFalpha+are+sufficient+to+mimic+retinal+regeneration+by+inducing+Muller+glial+proliferation+to+generate+committed+progenitor+cells.">Repressing notch signaling and expressing TNFalpha are sufficient to mimic retinal regeneration by inducing Muller glial proliferation to generate committed progenitor cells.</a> J.Neurosci. 34 (43), 14403-14419 (2014).</li><li>Nelson, C. M., Gorsuch, R. A., Bailey, T. J., Ackerman, K. M., Kassen, S. C., Hyde, D. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stat3+defines+three+populations+of+Muller+glia+and+is+required+for+initiating+maximal+muller+glia+proliferation+in+the+regenerating+zebrafish+retina.">Stat3 defines three populations of Muller glia and is required for initiating maximal muller glia proliferation in the regenerating zebrafish retina.</a> J.Comp.Neurol. 520 (18), 4294-4311 (2012).</li><li>Gorsuch, R. A., Hyde, D. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulation+of+Muller+glial+dependent+neuronal+regeneration+in+the+damaged+adult+zebrafish+retina.">Regulation of Muller glial dependent neuronal regeneration in the damaged adult zebrafish retina.</a> Exp.Eye Res. 123, 131-140 (2014).</li><li>Zhao, X. F., Wan, J., Powell, C., Ramachandran, R., Myers, M. G., Goldman, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Leptin+and+IL-6+family+cytokines+synergize+to+stimulate+Muller+glia+reprogramming+and+retina+regeneration.">Leptin and IL-6 family cytokines synergize to stimulate Muller glia reprogramming and retina regeneration.</a> Cell.Rep. 9 (1), 272-284 (2014).</li><li>Wan, J., Ramachandran, R., Goldman, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=HB-EGF+is+necessary+and+sufficient+for+Muller+glia+dedifferentiation+and+retina+regeneration.">HB-EGF is necessary and sufficient for Muller glia dedifferentiation and retina regeneration.</a> Dev.Cell. 22 (2), 334-347 (2012).</li><li>Lenkowski, J. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Retinal+regeneration+in+adult+zebrafish+requires+regulation+of+TGFbeta+signaling.">Retinal regeneration in adult zebrafish requires regulation of TGFbeta signaling.</a> Glia. 61 (10), 1687-1697 (2013).</li><li>Weber, I. P., Ramos, A. P., Strzyz, P. J., Leung, L. C., Young, S., Norden, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitotic+position+and+morphology+of+committed+precursor+cells+in+the+zebrafish+retina+adapt+to+architectural+changes+upon+tissue+maturation.">Mitotic position and morphology of committed precursor cells in the zebrafish retina adapt to architectural changes upon tissue maturation.</a> Cell.Rep. 7 (2), 386-397 (2014).</li><li>Magidson, V., Khodjakov, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Circumventing+photodamage+in+live-cell+microscopy.">Circumventing photodamage in live-cell microscopy.</a> Methods Cell Biol. 114, 545-560 (2013).</li><li>Bailey, T. J., Fossum, S. L., Fimbel, S. M., Montgomery, J. E., Hyde, D. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+inhibitor+of+phagocytosis,+O-phospho-L-serine,+suppresses+Muller+glia+proliferation+and+cone+cell+regeneration+in+the+light-damaged+zebrafish+retina.">The inhibitor of phagocytosis, O-phospho-L-serine, suppresses Muller glia proliferation and cone cell regeneration in the light-damaged zebrafish retina.</a> Exp.Eye Res. 91 (5), 601-612 (2010).</li><li>Lee, J. E., Liang, K. J., Fariss, R. N., Wong, W. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ex+vivo+dynamic+imaging+of+retinal+microglia+using+time-lapse+confocal+microscopy.">Ex vivo dynamic imaging of retinal microglia using time-lapse confocal microscopy.</a> Invest.Ophthalmol.Vis.Sci. 49 (9), 4169-4176 (2008).</li><li>Zhao, L., 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=Microglial+phagocytosis+of+living+photoreceptors+contributes+to+inherited+retinal+degeneration.">Microglial phagocytosis of living photoreceptors contributes to inherited retinal degeneration.</a> EMBO Mol.Med. 7 (9), 1179-1197 (2015).</li><li>Peri, F., Nusslein-Volhard, C. <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+neuronal+degradation+by+microglia+reveals+a+role+for+v0-ATPase+a1+in+phagosomal+fusion+in+vivo.">Live imaging of neuronal degradation by microglia reveals a role for v0-ATPase a1 in phagosomal fusion in vivo.</a> Cell. 133 (5), 916-927 (2008).</li><li>Morsch, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vivo+characterization+of+microglial+engulfment+of+dying+neurons+in+the+zebrafish+spinal+cord.">In vivo characterization of microglial engulfment of dying neurons in the zebrafish spinal cord.</a> Front.Cell.Neurosci. 9, 321 (2015).</li></ol>

The authors have nothing to disclose.

Studies investigating the mechanisms governing regeneration of the damaged adult zebrafish retina predominantly used immunocytochemical methods5,25,26,27,28,29,30. Establishing conditions to culture retinal explants and to perform live-cell imaging on phenomena, such as INM, provide us a tec...

Unlike humans, zebrafish (Danio rerio) exhibit a robust regeneration response upon cell death of retinal neurons1,2,3,4. Tumor necrosis factor &#945;, a signaling molecule that is released from dying retinal neurons induces M&#252;ller glia residing in the basal Inner Nuclear Layer (INL) of the retina, to proliferate5 and produce neuronal progenitor cells that continue to proliferate before differentiating into the neuronal cell types that died2,3,4. During the proliferative phase of the regeneration response, the nuclei of M&#252;ller glia and their derived neuronal progenitor cells undergo a repetitive migratory pattern in phase with the cell cycle (Interkinetic Nuclear Migration, INM)6,7. Nuclei positioned in the basal INL replicate their DNA before migrating to the Outer Nuclear Layer (ONL) where they divide before the arising nuclei return basally to the INL. This process was first described during neuroepithelial development using histological methods, while live-cell imaging approaches later confirmed the interpretation by Sauer8,9,10,11,12. Both histochemical and live-cell imaging approaches have been used to determine mechanisms underlying INM and its function in developing neuroepithelia including the retina9,11,12,13. However, the mechanisms governing INM in the adult regenerating retina have not been studied in much detail6,7. Live-cell imaging will be an invaluable approach to advance our knowledge of the signaling pathways that control INM in the adult regenerating retina.
Until recently, live-cell imaging of INM in the retina was limited to either live zebrafish embryos or to embryonic chick or postnatal mouse retinal explants9,10,11,12,14,15,16. While retinal explants from adult animals of a variety of species including mouse, rat and zebrafish have been utilized for different cell biological approaches17,18,19,20, live-cell imaging experiments using retinal explants have been restricted to brief periods of time and have not been executed continuously over several hours21,22. Here, we describe a detailed protocol to culture light-damaged adult zebrafish retinas to perform live-cell imaging experiments monitoring INM using multi-photon microscopy6. Live-cell imaging approaches are advantageous over immunohistochemical methods when investigating the mechanisms controlling INM, as the dynamics of INM, e.g., velocities might be affected rather than the location of mitosis, which would potentially not be detected using immunocytochemistry.
In the future, this method has also the potential to be modified to study other dynamic processes during retinal regeneration, such as phagocytosis of dying photoreceptors by M&#252;ller glia or the behavior of microglia.

<table border="0" cellpadding="0" cellspacing="0" width="876">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:491px;">Dumont forceps size #5</td>
			<td style="width:201px;">World precision instruments</td>
			<td align="right" style="width:113px;">14098</td>
			<td style="width:72px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Dumont forceps size #5, 45&#176; angle</td>
			<td>World precision instruments</td>
			<td align="right">14101</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">McPherson-Vannas scissors</td>
			<td>World precision instruments</td>
			<td align="right">501233</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Fluordishes</td>
			<td>World precision instruments</td>
			<td>FD35-100</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Stereomicroscope</td>
			<td>Nikon&#160;</td>
			<td>SMZ-1B</td>
			<td>similar type of dissection stereomicroscope will work</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Biological Safety Cabinet class type A2</td>
			<td>Labconco</td>
			<td></td>
			<td>equivalent type will work</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">tissue culture incubator</td>
			<td>Thermoscientific</td>
			<td>HEPA-class 100</td>
			<td>equivalent type will work</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Sylvania fluorescent lamps OSFP5835HOECO</td>
			<td>Bulbtronics</td>
			<td align="right">31850</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">0.2 &#181;m pore-size Acrodisc syringe filter</td>
			<td>VWR</td>
			<td align="right">4192</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">10 ml Luer-lok syringe</td>
			<td>VWR</td>
			<td>BD309604</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">60 ml Luer-lok syringe</td>
			<td>VWR</td>
			<td>BD309653</td>
			<td></td>
		</tr>
		<tr height="25">
			<td height="25" style="height:25px;">NaHCO3</td>
			<td>FischerScientific</td>
			<td>S233-500</td>
			<td></td>
		</tr>
		<tr height="25">
			<td height="25" style="height:25px;">CaCl2</td>
			<td>ThermoScientific</td>
			<td>C79-500</td>
			<td></td>
		</tr>
		<tr height="25">
			<td height="25" style="height:25px;">MgCl2</td>
			<td>EMD Millipore</td>
			<td align="right">5980</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">HBSS w/o Ca2+/Mg2+, w/o phenol red, Gibco</td>
			<td>ThermoScientific</td>
			<td>14175-095</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">MEM w/o phenol red, Gibco</td>
			<td>ThermoScientific</td>
			<td>5100-038</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Horse serum, heat-inactivated</td>
			<td>ThermoScientific</td>
			<td>26050-070</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">penicillin/streptomycin</td>
			<td>VWR</td>
			<td>16777-164</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Ultrapure low melting point agarose</td>
			<td>ThermoScientific</td>
			<td>16520-100</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">ethanol, absolute</td>
			<td>ThermoScientific</td>
			<td>BP2818-4</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">2-phenoxyethanol</td>
			<td>Sigma</td>
			<td align="right">77699</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Corning Cell-Tak cell and tissue adhesive&#160;</td>
			<td>VWR</td>
			<td align="right">354240</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">refractive index liquid&#160;</td>
			<td>Cargille Lab</td>
			<td>1803Y</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Nikon A1 multiphoton microscope equipped with a MaiTai infrared laser</td>
			<td>Nikon</td>
			<td></td>
			<td>equivalent system will work</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">40x Apo long-distance water immersion objective (N.A. 1.15)</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">environmental chamber equipped with insert for 35 mm petridishes</td>
			<td>Okolab</td>
			<td></td>
			<td>equivalent system will work</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">NIS analysis software</td>
			<td>Nikon</td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

culture of adult transgenic zebrafish retinal explants for live-cell imaging by multiphoton microscopy

An endogenous regeneration program is initiated by M&#252;ller glia in the adult zebrafish (Danio rerio) retina following neuronal damage and death. The M&#252;ller glia re-enter the cell cycle and produce neuronal progenitor cells that undergo subsequent rounds of cell divisions and differentiate into the lost neuronal cell types. Both M&#252;ller glia and neuronal progenitor cell nuclei replicate their DNA and undergo mitosis in distinct locations of the retina, i.e. they migrate between the basal Inner Nuclear Layer (INL) and the Outer Nuclear Layer (ONL), respectively, in a process described as Interkinetic Nuclear Migration (INM). INM has predominantly been studied in the developing retina. To examine the dynamics of INM in the adult regenerating zebrafish retina in detail, live-cell imaging of fluorescently-labeled M&#252;ller glia/neuronal progenitor cells is required. Here, we provide the conditions to isolate and culture dorsal retinas from Tg[gfap:nGFP]mi2004 zebrafish that were exposed to constant intense light for 35 h. We also show that these retinal cultures are viable to perform live-cell imaging experiments, continuously acquiring z-stack images throughout the thickness of the retinal explant for up to 8 h using multiphoton microscopy to monitor the migratory behavior of gfap:nGFP-positive cells. In addition, we describe the details to perform post-imaging analysis to determine the velocity of apical and basal INM. To summarize, we established conditions to study the dynamics of INM in an adult model of neuronal regeneration. This will advance our understanding of this crucial cellular process and allow us to determine the mechanisms that control INM.

The isolation of the retina according to the procedure outlined in the schematic in Figure 1 allows the culturing of a flattened dorsal retina from light-damaged adult Tg[gfap:nGFP]mi2004 zebrafish over a period of at least 24 h in a 5% CO2/air environment. These flat-mounted retinal explants can be used to image focal planes at deep tissue levels. An example is M&#252;ller glia/neuronal progenitor cell nuclei labeled with GFP from the M&#25...

Watch this Scientific Journal Video about Culture of Adult Transgenic Zebrafish Retinal Explants for Live-cell Imaging by Multiphoton Microscopy at JoVE.com

Culture of Adult Transgenic Zebrafish Retinal Explants for Live-cell Imaging by Multiphoton Microscopy

Zebrafish retinal regeneration has mostly been studied using fixed retinas. However, dynamic processes such as interkinetic nuclear migration occur during the regenerative response and require live-cell imaging to investigate the underlying mechanisms. Here, we describe culture and imaging conditions to monitor Interkinetic Nuclear Migration (INM) in real-time using multiphoton microscopy.

An endogenous regeneration program is initiated by M&#252;ller glia in the adult zebrafish (Danio rerio) retina following neuronal damage and death. The ...

culture-adult-transgenic-zebrafish-retinal-explants-for-live-cell

Research

JoVE Journal

Developmental Biology

8.5K Views.  University of Notre Dame. Zebrafish retinal regeneration has mostly been studied using fixed retinas. However, dynamic processes such as interkinetic nuclear migration occur during the regenerative response and require live-cell imaging to investigate the underlying mechanisms. Here, we describe culture and imaging conditions to monitor Interkinetic Nuclear Migration (INM) in real-time using multiphoton microscopy.

Video: Culture of Adult Transgenic Zebrafish Retinal Explants for Live-cell Imaging by Multiphoton Microscopy

Kidney Regeneration in Adult Zebrafish by Gentamicin Induced Injury

The kidney is essential for fluid homeostasis, blood pressure regulation and filtration of waste from the body. The fundamental unit of kidney function is the nephron. Mammals are able to repair existing nephrons after injury, but lose the ability to form new nephrons soon after birth. In contrast to mammals, adult fish produce new nephrons (neonephrogenesis) throughout their lives in response to growth requirements or injury. Recently, lhx1a has been shown to mark nephron progenitor cells in the adult zebrafish kidney, however mechanisms controlling the formation of new nephrons after injury remain unknown. Here we show our method for robust and reproducible injury in the adult zebrafish kidney by intraperitoneal (i.p.) injection of gentamicin, which uses a noninvasive visual screening process to select for fish with strong but nonlethal injury. Using this method, we can determine optimal gentamicin dosages for injury and go on to demonstrate the effect of higher temperatures on kidney regeneration in zebrafish.

Here we present a reliable method to study adult kidney regeneration by inducing acute kidney injury by gentamicin injection. We show that injury is dependent on gentamicin dosage and environmental temperature using in situ hybridization to label lhx1a+ developing new nephrons.

The kidney is essential for fluid homeostasis, blood pressure regulation and filtration of waste from the body. The fundamental unit of kidney function is ...

Culture of Embryonic Mouse Cochlear Explants and Gene Transfer by Electroporation

Auditory hair cells located within the mouse organ of Corti detect and transmit sound information to the central nervous system. The mechanosensory hair cells are aligned in one row of inner hair cells and three rows of outer hair cells that extend along the basal to apical axis of the cochlea. The explant culture technique described here provides an efficient method to isolate and maintain cochlear explants from the embryonic mouse inner ear. Also, the morphology and molecular characteristics of sensory hair cells and nonsensory supporting cells within the cochlear explant cultures resemble those observed in vivo and can be studied within its intrinsic cellular environment. The cochlear explants can serve as important experimental tools for the identification and characterization of molecular and genetic pathways that are involved in cellular specification and patterning. Although transgenic mouse models provide an effective approach for gene expression studies, a considerable number of mouse mutants die during embryonic development thereby hindering the analysis and interpretation of developmental phenotypes. The organ of Corti from mutant mice that die before birth can be cultured so that their in vitro development and responses to different factors can be analyzed. Additionally, we describe a technique for electroporating embryonic cochlear explants ex vivo which can be used to downregulate or overexpress specific gene(s) and analyze their potential endogenous function and test whether specific gene product is necessary or sufficient in a given context to influence mammalian cochlear development1-8.

We present a method that describes isolation and culture of cochlear explants from embryonic mouse inner ear. We also demonstrate a method for gene transfer into cochlear explants via square-wave electroporation. The in vitro explant culture coupled with gene transfer technique enables researchers to study the effects of altering gene expression during development.

Auditory hair cells located within the mouse organ of Corti detect and transmit sound information to the central nervous system. The mechanosensory hair ...

Whole Retinal Explants from Chicken Embryos for Electroporation and Chemical Reagent Treatments

The retina is a good model for the developing central nervous system. The large size of the eye and most importantly the accessibility for experimental manipulations in ovo/in vivo makes the chicken embryonic retina a versatile and very efficient experimental model. Although the chicken retina is easy to target in ovo by intraocular injections or electroporation, the effective and exact concentration of the reagents within the retina may be difficult to fully control. This may be due to variations of the exact injection site, leakage from the eye or uneven diffusion of the substances. Furthermore, the frequency of malformations and mortality after invasive manipulations such as electroporation is rather high.
This protocol describes an ex ovo technique for culturing whole retinal explants from chicken embryos and provides a method for controlled exposure of the retina to reagents. The protocol describes how to dissect, experimentally manipulate, and culture whole retinal explants from chicken embryos. The explants can be cultured for approximately 24 hr and be subjected to different manipulations such as electroporation. The major advantages are that the experiment is not dependent on the survival of the embryo and that the concentration of the introduced reagent can be varied and controlled in order to determine and optimize the effective concentration. Furthermore, the technique is rapid, cheap and together with its high experimental success rate, it ensures reproducible results. It should be emphasized that it serves as an excellent complement to experiments performed in ovo.

This protocol describes a method to dissect, experimentally manipulate and culture whole retinal explants from chicken embryos. The explant cultures are useful when high success rate, efficacy and reproducibility are needed to test the effects of plasmids for electroporation and/or reagent substances, i.e., enzymatic inhibitors.

The retina is a good model for the developing central nervous system. The large size of the eye and most importantly the accessibility for experimental ...

Tracking Cells in GFP-transgenic Zebrafish Using the Photoconvertible PSmOrange System

The rapid development of transparent zebrafish embryos (Danio rerio) in combination with fluorescent labelings of cells and tissues allows visualizing developmental processes as they happen in the living animal. Cells of interest can be labeled by using a tissue specific promoter to drive the expression of a fluorescent protein (FP) for the generation of transgenic lines. Using fluorescent photoconvertible proteins for this purpose additionally allows to precisely follow defined structures within the expression domain. Illuminating the protein in the region of interest, changes its emission spectrum and highlights a particular cell or cell cluster leaving other transgenic cells in their original color. A major limitation is the lack of known promoters for a large number of tissues in the zebrafish. Conversely, gene- and enhancer trap screens have generated enormous transgenic resources discretely labeling literally all embryonic structures mostly with GFP or to a lesser extend red or yellow FPs. An approach to follow defined structures in such transgenic backgrounds would be to additionally introduce a ubiquitous photoconvertible protein, which could be converted in the cell(s) of interest. However, the photoconvertible proteins available involve a green and/or less frequently a red emission state1 and can therefore often not be used to track cells in the FP-background of existing transgenic lines. To circumvent this problem, we have established the PSmOrange system for the zebrafish2,3. Simple microinjection of synthetic mRNA encoding a nuclear form of this protein labels all cell nuclei with orange/red fluorescence. Upon targeted photoconversion of the protein, it switches its emission spectrum to far red. The quantum efficiency and stability of the protein makes PSmOrange a superb cell-tracking tool for zebrafish and possibly other teleost species.

We established the photoconvertible PSmOrange system as a powerful, straight-forward and cost inexpensive tool for in vivo cell tracking in GFP transgenic backgrounds. This protocol describes its application in the zebrafish model system.

The rapid development of transparent zebrafish embryos (Danio rerio) in combination with fluorescent labelings of cells and tissues allows visualizing ...

Isolation and Culture of Adult Zebrafish Brain-derived Neurospheres

The zebrafish is a highly relevant model organism for understanding the cellular and molecular mechanisms involved in neurogenesis and brain regeneration in vertebrates. However, an in-depth analysis of the molecular mechanisms underlying zebrafish adult neurogenesis has been limited due to the lack of a reliable protocol for isolating and culturing neural adult stem/progenitor cells. Here we provide a reproducible method to examine adult neurogenesis using a neurosphere assay derived from zebrafish whole brain or from the telencephalon, tectum and cerebellum regions of the adult zebrafish brain. The protocol involves, first the microdissection of zebrafish adult brain, then single cell dissociation and isolation of self-renewing multipotent neural stem/progenitor cells. The entire procedure takes eight days. Additionally, we describe how to manipulate gene expression in zebrafish neurospheres, which will be particularly useful to test the role of specific signaling pathways during adult neural stem/progenitor cell proliferation and differentiation in zebrafish.

Here we provide a reproducible method to examine adult neurogenesis using a neurosphere assay derived from the whole brain or from either the telencephalic, tectal or cerebellar regions of the adult zebrafish brain. Additionally, we describe the procedure to manipulate gene expression in zebrafish neurospheres.

The zebrafish is a highly relevant model organism for understanding the cellular and molecular mechanisms involved in neurogenesis and brain regeneration ...

Analysis of Zebrafish Kidney Development with Time-lapse Imaging Using a Dissecting Microscope Equipped for Optical Sectioning

In order to understand organogenesis, the spatial and temporal alterations that occur during development of tissues need to be recorded. The method described here allows time-lapse analysis of normal and impaired kidney development in zebrafish embryos by using a fluorescence dissecting microscope equipped for structured illumination and z-stack acquisition. To visualize nephrogenesis, transgenic zebrafish (Tg(wt1b:GFP)) with fluorescently labeled kidney structures were used. Renal defects were triggered by injection of an antisense morpholino oligonucleotide against the Wilms tumor gene wt1a, a factor known to be crucial for kidney development.
The advantage of the experimental setup is the combination of a zoom microscope with simple strategies for re-adjusting movements in x, y or z direction without additional equipment. To circumvent focal drift that is induced by temperature variations and mechanical vibrations, an autofocus strategy was applied instead of utilizing a usually required environmental chamber. In order to re-adjust the positional changes due to a xy-drift, imaging chambers with imprinted relocation grids were employed.
In comparison to more complex setups for time-lapse recording with optical sectioning such as confocal laser scanning&#160;or light sheet microscopes, a zoom microscope is easy to handle. Besides, it offers dissecting microscope-specific benefits such as high depth of field and an extended working distance.
The method to study organogenesis presented here can also be used with fluorescence stereo microscopes not capable of optical sectioning. Although limited for high-throughput, this technique offers an alternative to more complex equipment that is normally used for time-lapse recording of developing tissues and organ dynamics.

The method described here allows time-lapse analysis of organ development in zebrafish embryos by using a fluorescence dissecting microscope capable of performing optical sectioning and simple strategies of readjustment to correct focal and planar drift.

In order to understand organogenesis, the spatial and temporal alterations that occur during development of tissues need to be recorded. The method ...

In Vivo Imaging of Transgenic Gene Expression in Individual Retinal Progenitors in Chimeric Zebrafish Embryos to Study Cell Nonautonomous Influences

The genetic and technical strengths have made the zebrafish vertebrate a key model organism in which the consequences of gene manipulations can be traced in vivo throughout the rapid developmental period. Multiple processes can be studied including cell proliferation, gene expression, cell migration and morphogenesis. Importantly, the generation of chimeras through transplantations can be easily performed, allowing mosaic labeling and tracking of individual cells under the influence of the host environment. For example, by combining functional gene manipulations of the host embryo (e.g., through morpholino microinjection) and live imaging, the effects of extrinsic, cell nonautonomous signals (provided by the genetically modified environment) on individual transplanted donor cells can be assessed. Here we demonstrate how this approach is used to compare the onset of fluorescent transgene expression as a proxy for the timing of cell fate determination in different genetic host environments.
In this article, we provide the protocol for microinjecting zebrafish embryos to mark donor cells and to cause gene knockdown in host embryos, a description of the transplantation technique used to generate chimeric embryos, and the protocol for preparing and running in vivo time-lapse confocal imaging of multiple embryos. In particular, performing multiposition imaging is crucial when comparing timing of events such as the onset of gene expression. This requires data collection from multiple control and experimental embryos processed simultaneously. Such an approach can easily be extended for studies of extrinsic influences in any organ or tissue of choice accessible to live imaging, provided that transplantations can be targeted easily according to established embryonic fate maps.

In Vivo Imaging of Transgenic Gene Expression in Individual Retinal Progenitors in Chimeric Zebrafish Embryos to Study Cell Nonautonomous Influences

Live tracking of individual WT retinal progenitors in distinct genetic backgrounds allows for the assessment of the contribution of cell non-autonomous signaling during neurogenesis. Here, a combination of gene knockdown, chimera generation via embryo transplantation and in vivo time-lapse confocal imaging was utilized for this purpose.

The genetic and technical strengths have made the zebrafish vertebrate a key model organism in which the consequences of gene manipulations can be traced ...

Live Imaging of Mouse Secondary Palate Fusion

The fusion of the secondary palatal shelves to form the intact secondary palate is a key process in mammalian development and its disruption can lead to cleft secondary palate, a common congenital anomaly in humans. Secondary palate fusion has been extensively studied leading to several proposed cellular mechanisms that may mediate this process. However, these studies have been mostly performed on fixed embryonic tissues at progressive timepoints during development or in fixed explant cultures analyzed at static timepoints. Static analysis is limited for the analysis of dynamic morphogenetic processes such a palate fusion and what types of dynamic cellular behaviors mediate palatal fusion is incompletely understood. Here we describe a protocol for live imaging of ex vivo secondary palate fusion in mouse embryos. To examine cellular behaviors of palate fusion, epithelial-specific Keratin14-cre was used to label palate epithelial cells in ROSA26-mTmGflox reporter embryos. To visualize filamentous actin, Lifeact-mRFPruby reporter mice were used. Live imaging of secondary palate fusion was performed by dissecting recently-adhered secondary palatal shelves of embryonic day (E) 14.5 stage embryos and culturing in agarose-containing media on a glass bottom dish to enable imaging with an inverted confocal microscope. Using this method, we have detected a variety of novel cellular behaviors during secondary palate fusion. An appreciation of how distinct cell behaviors are coordinated in space and time greatly contributes to our understanding of this dynamic morphogenetic process. This protocol can be applied to mutant mouse lines, or cultures treated with pharmacological inhibitors to further advance understanding of how secondary palate fusion is controlled.

Here, we present a protocol for live imaging of mouse secondary palate fusion using confocal microscopy. This protocol can be used in combination with a variety of fluorescent reporter mouse lines, and with pathway inhibitors for mechanistic insight. This protocol can be adapted for live imaging in other developmental systems.

The fusion of the secondary palatal shelves to form the intact secondary palate is a key process in mammalian development and its disruption can lead to ...

Multimodal Hierarchical Imaging of Serial Sections for Finding Specific Cellular Targets within Large Volumes

Targeting specific cells at ultrastructural resolution within a mixed cell population or a tissue can be achieved by hierarchical imaging using a combination of light and electron microscopy. Samples embedded in resin are sectioned into arrays consisting of ribbons of hundreds of ultrathin sections and deposited on pieces of silicon wafer or conductively coated coverslips. Arrays are imaged at low resolution using a digital consumer like smartphone camera or light microscope (LM) for a rapid large area overview, or a wide field fluorescence microscope (fluorescence light microscopy (FLM)) after labeling with fluorophores. After post-staining with heavy metals, arrays are imaged in a scanning electron microscope (SEM). Selection of targets is possible from 3D reconstructions generated by FLM or from 3D reconstructions made from the SEM image stacks at intermediate resolution if no fluorescent markers are available. For ultrastructural analysis, selected targets are finally recorded in the SEM at high-resolution (a few nanometer image pixels). A ribbon-handling tool that can be retrofitted to any ultramicrotome is demonstrated. It helps with array production and substrate removal from the sectioning knife boat. A software platform that allows automated imaging of arrays in the SEM is discussed. Compared to other methods generating large volume EM data, such as serial block-face SEM (SBF-SEM) or focused ion beam SEM (FIB-SEM), this approach has two major advantages: (1) The resin-embedded sample is conserved, albeit in a sliced-up version. It can be stained in different ways and imaged with different resolutions. (2) As the sections can be post-stained, it is not necessary to use samples strongly block-stained with heavy metals to introduce contrast for SEM imaging or render the tissue blocks conductive. This makes the method applicable to a wide variety of materials and biological questions. Particularly prefixed materials e.g., from biopsy banks and pathology labs, can directly be embedded and reconstructed in 3D.

This protocol targets specific cells in tissue for imaging at nanoscale resolution using a scanning electron microscope (SEM). Large numbers of serial sections from resin-embedded biological material are first imaged in a light microscope to identify the target and then in a hierarchical manner in the SEM.

Targeting specific cells at ultrastructural resolution within a mixed cell population or a tissue can be achieved by hierarchical imaging using a ...

Live Cell Imaging of Chromosome Segregation During Mitosis

Chromosomes must be reliably and uniformly segregated into daughter cells during mitotic cell division. Fidelity of chromosomal segregation is controlled by multiple mechanisms that include the Spindle Assembly Checkpoint (SAC). The SAC is part of a complex feedback system that is responsible for prevention of a cell progress through mitosis unless all chromosomal kinetochores have attached to spindle microtubules. Chromosomal lagging and abnormal chromosome segregation is an indicator of dysfunctional cell cycle control checkpoints and can be used to measure the genomic stability of dividing cells. Deregulation of the SAC can result in the transformation of a normal cell into a malignant cell through the accumulation of errors during chromosomal segregation. Implementation of the SAC and the formation of the kinetochore complex are tightly regulated by interactions between kinases and phosphatase such as Protein Phosphatase 2A (PP2A). This protocol describes live cell imaging of lagging chromosomes in mouse embryonic fibroblasts isolated from mice that had a knockout of the PP2A-B56&#947; regulatory subunit. This method overcomes the shortcomings of other cell cycle control imaging techniques such as flow cytometry or immunocytochemistry that only provide a snapshot of a cell cytokinesis status, instead of a dynamic spatiotemporal visualization of chromosomes during mitosis.

This protocol describes an easy and convenient method to label and visualize live chromosomes in mitotic cells using Histone2B-GFP BacMam 2.0 label and a spinning disc confocal microscopy system.

Chromosomes must be reliably and uniformly segregated into daughter cells during mitotic cell division. Fidelity of chromosomal segregation is controlled ...