We thank Dr. A. Jacobo, Dr. J. Salvi, and A. Petelski for their contributions to the original research on which this protocol is based. We also thank J. Llamas and W. Makmura for technical assistance and animal husbandry. We acknowledge NIDCD Training grant T32 DC009975, NIDCD grant R01DC015530, Robertson Therapeutic Development Fund, and the Caruso Family Foundation for funding. Finally, we acknowledge support from Howard Hughes Medical Institute, of which Dr. Hudspeth is an Investigator.

All methods described here have been approved by the Animal Care and Use Committees of Rockefeller University and of the University of Southern California.
1. (Optional) Preparation of Collagen I Solution from Mouse-tail Tendons
Note: Collagen I solutions are available commercially. Follow the manufacturer&#39;s instructions for gel preparation.
<ol>
	<li>Euthanize 5 - 10 young adult (3 - 5 weeks old) mice of any wild type strain with carbon dioxide in accordance with the protocol approved by the relevant Institutional Animal Care and Use Committee16. Collect the tails and disinfect them by submerging in 70% ethanol for a minimum of 4 h at room temperature. 
	Note: Incubation for over 48 h should be avoided, as it results in excessive tissue dehydration and impedes the tendon extraction process.</li>
	<li>Remove the skin from each tail by introducing a longitudinal cut with a scalpel blade and retracting the whole skin with forceps. Transfer the skinned tails to a 100-mm Petri dish filled with clean 70% ethanol and cut them into 10-mm segments. 
	Note: Discard the thinnest parts of the tails, which are difficult to manipulate.</li>
	<li>Using forceps, secure each segment of the tail to the bottom of the Petri dish and use a second pair of fine forceps to extract the tendons from the tail one at a time. Individual tendon fibers should emerge with minimal resistance. 
	Note: Old, dull #5 forceps work well for this step.</li>
	<li>Prepare 100 mL of a 0.1% solution (by volume) of acetic acid in sterile, molecular-grade water and add 10 mL of that solution to a sterile 100-mm Petri dish. Transfer the tendons to the Petri dish and leave for 1 h at room temperature to denature the collagen I.</li>
	<li>Use a sterile scalpel or iridectomy scissors with blunt, curved tips to mince the tendon into 1 - 2 mm fragments. Transfer the minced tendons to a sterile 50-mL tube and add 0.1% acetic acid to bring the volume to 50 mL. 
	Note: Use four or five tails for each 50 mL of acid to achieve a collagen I concentration of 2.0 - 2.5 mg/mL.</li>
	<li>Refrigerate the collagen I solution at 4 &#176;C for a minimum of 48 h to facilitate complete protein denaturation. Vortex with a tabletop vortex set to the maximal speed for 1 min twice a day.</li>
	<li>Measure the protein concentration of the solution using the bicinchoninic acid assay, adjust the collagen I concentration to 2.0 - 2.5 mg/mL by adding 0.1% solution of acetic acid, and store at 4 &#176;C. 
	Note: Collagen I solution can be stored for one to two years.</li>
	<li>(Optional) Centrifuge the collagen I solution at 2,000 x g for 1 h at 4 &#176;C and use the translucent top fraction (approximately half of the volume), to achieve optically clear collagen gels in Section 4.</li>
</ol>
2. Dissection of Vestibular and Auditory Organs
<ol>
	<li>Euthanize pregnant mice of any strain with carbon dioxide in accordance with the protocol approved by the relevant Institutional Animal Care and Use Committee16. Extract and decapitate the embryos. 
	Note: Lfng-CreERT2/tdTomato mice can be used to allow permanent labeling of supporting cells upon exposure to 4-hydroxytamoxifen17.</li>
	<li>Sterilize all the working surfaces and dissection instruments, including two pairs of #5 forceps and a hair knife18, by cleaning them with 70% ethanol.</li>
	<li>Split each head in two halves by introducing a longitudinal cut with a sterile scalpel blade or by using two pairs of #5 forceps. Extract the temporal bones, which contain the inner ears19, and place them into 15 mL of ice-cold Hank&#39;s balanced salt solution (HBSS) in a 60-mm Petri dish. Keep the dish on ice. 
	Note: Embryos at a range of stages from E13.5 to E18.5 have been used successfully.</li>
	<li>(Optional) Wash the inner ears by gently shaking them in a 50 mL conical tube containing 30 mL ice-cold HBSS and replacing the HBSS three or four times. Keep the tube on ice. 
	Note: This step limits possible contamination of the tissue culture and quickly brings the temperature to 4 &#176;C, which prevents tissue degradation and cell death.</li>
	<li>Using two pairs of fine #5 forceps, separate the inner ears from the temporal bone and transfer the ears, three or four at a time, into a 60-mm Petri dish filled with ice-cold HBSS.</li>
	<li>Dissect the vestibular sensory organs.
	<ol>
		<li>Orient the ears medial side up and locate the utricle. With two pairs of #5 forceps, remove the cartilage surrounding the vestibular organs. Gently sever the vestibular nerve, the connection between the utricle and saccule, and the semicircular canals, as shown in Figure 1. Gently pull the utricle and the attached ampullae of the superior and horizontal semicircular canals from the ear. 
		Note: This method can be used on inner ears of stages E16.5 - E18.5. Preserve the cartilage fragments for Section 3 below.</li>
	</ol>
	</li>
	<li>Dissect the cochlea.
	<ol>
		<li>Remove the cartilaginous tissue surrounding the hearing organ with two pairs of #5 forceps. Gently sever the connection between the cochlear base and the saccule as shown in Figure 1. 
		Note: For stages E13.5 - E14.5, soften the cartilage prior to dissection by treating the inner ears with 0.25% collagenase I in phosphate-buffered saline (PBS) solution for 5 min at room temperature. Preserve the cartilage fragments for Section 3 below.</li>
	</ol>
	</li>
	<li>Using a 200-&#181;L pipet fitted with a wide nonstick tip, transfer the utricles and cochleae to a 30-mm Petri dish filled with growth medium comprising DMEM/F12 supplemented with 33 mM Dglucose, 19 mM sodium bicarbonate, 15 mM 4(2hydroxyethyl)-1piperazineethanesulfonic acid (HEPES), 1 mM glutamine, 1 mM nicotinamide, 20 mg/L epidermal growth factor, 20 mg/L fibroblast growth factor, 10 mg/L insulin, 5.5 mg/L transferrin, and 5 &#181;g/L sodium selenite.</li>
	<li>Maintain the utricle preparations for up to 3 h at 37 &#176;C in a tissue-culture incubator gassed with 5% carbon dioxide to allow healing of the cuts in the epithelium introduced during the dissection. Cochlea preparations should be transferred to the collagen gel 10 min after the dissection. 
	Note: Because the dissection is performed in ice-cold HBSS, there is no need to pre-warm the growth medium to 37 &#176;C.</li>
</ol>
3. (Optional) Adjust Collagen I Gel Stiffness by Adding Varying Concentrations of Chondrocytes
Note: The method for chondrocyte isolation was modified from Gosset et al.20
<ol>
	<li>Prepare a 1% solution of collagenase I in sterile 1x PBS and store 100 - 200 &#181;L aliquots at -80 &#176;C. Defrost on ice when needed, avoiding multiple freeze-thaw cycles.</li>
	<li>Use fine forceps to collect the pieces of cartilage left over from the dissection of the vestibular and auditory organs from 10 - 12 ears. Separate connective and inner ear tissues from the cartilage. Transfer the cartilage to a 30-mm Petri dish and add 300 &#181;L of sterile growth medium.</li>
	<li>Use a sterile scalpel blade or iridectomy scissors with blunt curved tips to mince the tissue to achieve cartilage pieces approximately 0.5 mm in length.</li>
	<li>Add collagenase I to the medium with cartilage to achieve a final enzyme concentration of 0.25%. Transfer the dish to a tissue-culture incubator at 37 &#176;C gassed with 5% carbon dioxide. Pipet vigorously using a 1,000 &#181;L pipet every 20 min until pieces of cartilage dissociate and are no longer distinguishable in the solution, then incubate for an additional 20 min. 
	Note: In case of the utricle preparations, chondrocyte isolation can be performed during step 2.9; it takes approximately 2 h (3 - 4 pipetting rounds).</li>
	<li>Collect the cell suspension in a 15 mL conical tube and adjust the volume to 10 mL with sterile 1x PBS. Centrifuge at 800 x g for 5 min at 4 &#176;C. Remove the supernatant and resuspend the cells in 10 mL of sterile 1x PBS. Centrifuge at 800 x g for 5 min at 4 &#176;C and remove the supernatant. 
	Note: It is critical to wash the cells twice; any remaining collagenase I will digest the collagen I gel.</li>
	<li>Using a 200-&#181;L pipet, add 100 &#181;L of culture medium to the cell pellet and pipet gently to resuspend. Count the cells using a hemocytometer and maintain them on ice prior to use.</li>
	<li>To increase gel stiffness, add chondrocytes to the neutralized collagen I gel solution (Section 1) and mix rapidly to distribute the cells throughout the gel prior to solidification. 
	Note: The elastic modulus of the collagen I gel (a measure of stiffness), increases linearly with the number of chondrocytes added11. The relationship is described by the experimentally determined linear function E = 206&#183;Nc + 15, in which E is the elastic modulus in Pascals and Nc is the number of chondrocytes in millions. For a detailed protocol for gel stiffness measurements please refer to the original article11.</li>
</ol>
4. Place the Vestibular or Auditory Sensory Organ in a Collagen I Gel
<ol>
	<li>In a sterile 1.5-mL tube, prepare collagen I polymerization solution by mixing 160 &#181;L of 10x PBS with phenol red pH indicator, 133 &#181;L of 0.34 M sodium hydroxide, 70 &#181;L of 0.9 M sodium bicarbonate, and 40 &#181;L of 1 M HEPES. Keep the tube on ice. 
	Note: This recipe provides the polymerization solution needed to prepare 2 mL of collagen I gel, but can be scaled as needed.</li>
	<li>Mix 100 &#181;L of polymerization solution and 400 &#181;L of collagen I solution on ice by gently pipetting up and down in a chilled 1.5-mL tube. To increase gel stiffness, add 50 &#181;L of growth medium containing chondrocytes and mix gently as described in Section 3.</li>
	<li>Transfer 500 &#181;L of the neutralized collagen I solution to a chilled 30-mm Petri dish with a 10-mm glass-bottom insert or to a well of a four-well plate. 
	Note: It is critical to keep all the reagents on ice to prevent rapid and uneven polymerization of the collagen I.</li>
	<li>Quickly transfer the cochleae or utricles to the neutralized collagen I solution and adjust the organs to their desired positions with a sterile hair knife18 or pair of fine forceps. 
	Note: Collagen I polymerization becomes noticeable after 1 - 2 min as the solution becomes turbid.</li>
	<li>After the solution around the tissue has polymerized, place the Petri dish or four-well plate for 20 min at 37 &#176;C in a tissue-culture incubator gassed with 5% carbon dioxide to ensure complete polymerization.</li>
	<li>Add 3 mL of growth medium supplemented with 0.5% fetal bovine serum (FBS) per Petri dish or 500 &#181;L of the same medium per well of a four-well plate. Maintain the culture at 37 &#176;C in a tissue-culture incubator gassed with 5% carbon dioxide. If desired, supplement the growth medium with 10 &#181;M 5-ethynyl-2&#180;-deoxyuridine (EdU) to label proliferating cells. 
	Note: Higher FBS concentrations can be used if desired.</li>
</ol>
5. Viral Injections in Three-dimensional Cultures of Vestibular and Auditory Sensory Organs
<ol>
	<li>Defrost the desired virus on ice and mix with trypan blue solution in a 0.5 mL conical tube to achieve a final dye concentration of 0.05%. Use 10 - 20x dye to avoid substantial dilution of the virus. Keep on ice. 
	Note: Adenovirus serotype 5 works best for infecting supporting cells in the utricle19, whereas adeno-associated virus Anc80 can infect both hair cells and supporting cells in the utricle and the cochlea21.</li>
	<li>Break the tip of a glass needle prepared on a micropipette puller with clean fine forceps while observing it at the highest magnification of a binocular dissecting microscope. 
	Note: It is important to optimize the settings on the needle puller. Needles with 9 - 12-mm shanks and 20 - 30-&#181;m openings work best.</li>
	<li>Remove a sensory-organ culture from the incubator. Attach the needle to the microinjector and fill it with 2 - 3 &#181;L of dye and virus mixture. Advance the needle into the sensory organ while observing it under the binocular dissecting microscope.</li>
	<li>Gently drive the needle tip through mesenchymal and epithelial layers of the roof of a three-dimensional utricular culture. Inject the viral mixture until the cavities of the utricle and ampullae fill with the blue dye. 
	Note: Because it allows easy access to sensory organs, a 10-mm glass-bottom Petri dish is optimal for the injections.</li>
	<li>Incubate at 37 &#176;C in a tissue-culture incubator gassed with 5% carbon dioxide. 
	Note: When green or red fluorescent protein is used in the viral construct, the fluorescence is apparent 24 h after viral transduction.</li>
</ol>

<ol>
	<li>Oesterle, E. C., Tsue, T. T., Reh, T. A., Rubel, E. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hair-cell+regeneration+in+organ+cultures+of+the+postnatal+chicken+inner+ear.">Hair-cell regeneration in organ cultures of the postnatal chicken inner ear.</a> Hear Res. 70 (1), 85-108 (1993).</li><li>Meyers, J. R., Corwin, J. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Shape+change+controls+supporting+cell+proliferation+in+lesioned+mammalian+balance+epithelium.">Shape change controls supporting cell proliferation in lesioned mammalian balance epithelium.</a> J Neurosci Off J Soc Neurosci. 27 (16), 4313-4325 (2007).</li><li>Cunningham, L. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+adult+mouse+utricle+as+an+in+vitro+preparation+for+studies+of+ototoxic-drug-induced+sensory+hair+cell+death.">The adult mouse utricle as an in vitro preparation for studies of ototoxic-drug-induced sensory hair cell death.</a> Brain Res. 1091 (1), 277-281 (2006).</li><li>Warchol, M. E., Lambert, P. R., Goldstein, B. J., Forge, A., Corwin, J. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regenerative+proliferation+in+inner+ear+sensory+epithelia+from+adult+guinea+pigs+and+humans.">Regenerative proliferation in inner ear sensory epithelia from adult guinea pigs and humans.</a> Science. 259 (5101), 1619-1622 (1993).</li><li>Lin, V., Golub, J. S., Nguyen, T. B., Hume, C. R., Oesterle, E. C., Stone, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Inhibition+of+Notch+activity+promotes+nonmitotic+regeneration+of+hair+cells+in+the+adult+mouse+utricles.">Inhibition of Notch activity promotes nonmitotic regeneration of hair cells in the adult mouse utricles.</a> J Neurosci Off J Soc Neurosci. 31 (43), 15329-15339 (2011).</li><li>Wu, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Co-regulation+of+the+Notch+and+Wnt+signaling+pathways+promotes+supporting+cell+proliferation+and+hair+cell+regeneration+in+mouse+utricles.">Co-regulation of the Notch and Wnt signaling pathways promotes supporting cell proliferation and hair cell regeneration in mouse utricles.</a> Sci Rep. 6, 29418 (2016).</li><li>Chai, 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=Wnt+signaling+induces+proliferation+of+sensory+precursors+in+the+postnatal+mouse+cochlea.">Wnt signaling induces proliferation of sensory precursors in the postnatal mouse cochlea.</a> Proc Natl Acad Sci U S A. 109 (21), 8167-8172 (2012).</li><li>Wang, T., 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=Lgr5++cells+regenerate+hair+cells+via+proliferation+and+direct+transdifferentiation+in+damaged+neonatal+mouse+utricle.">Lgr5+ cells regenerate hair cells via proliferation and direct transdifferentiation in damaged neonatal mouse utricle.</a> Nat Commun. 6, 6613 (2015).</li><li>Doetzlhofer, A., White, P. M., Johnson, J. E., Segil, N., Groves, A. K. <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+growth+and+differentiation+of+mammalian+sensory+hair+cell+progenitors:+a+requirement+for+EGF+and+periotic+mesenchyme.">In vitro growth and differentiation of mammalian sensory hair cell progenitors: a requirement for EGF and periotic mesenchyme.</a> Dev Biol. 272 (2), 432-447 (2004).</li><li>White, P. M., Stone, J. S., Groves, A. K., Segil, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=EGFR+signaling+is+required+for+regenerative+proliferation+in+the+cochlea:+conservation+in+birds+and+mammals.">EGFR signaling is required for regenerative proliferation in the cochlea: conservation in birds and mammals.</a> Dev Biol. 363 (1), 191-200 (2012).</li><li>Gnedeva, K., Jacobo, A., Salvi, J. D., Petelski, A. A., Hudspeth, A. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Elastic+force+restricts+growth+of+the+murine+utricle.">Elastic force restricts growth of the murine utricle.</a> eLife. 6, (2017).</li><li>Aragona, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+mechanical+checkpoint+controls+multicellular+growth+through+YAP/TAZ+regulation+by+actin-processing+factors.">A mechanical checkpoint controls multicellular growth through YAP/TAZ regulation by actin-processing factors.</a> Cell. 154 (5), 1047-1059 (2013).</li><li>Dong, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Elucidation+of+a+universal+size-control+mechanism+in+Drosophila+and+mammals.">Elucidation of a universal size-control mechanism in Drosophila and mammals.</a> Cell. 130 (6), 1120-1133 (2007).</li><li>Low, B. C., Pan, C. Q., Shivashankar, G. V., Bershadsky, A., Sudol, M., Sheetz, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=YAP/TAZ+as+mechanosensors+and+mechanotransducers+in+regulating+organ+size+and+tumor+growth.">YAP/TAZ as mechanosensors and mechanotransducers in regulating organ size and tumor growth.</a> FEBS Lett. 588 (16), 2663-2670 (2014).</li><li>Zhao, B., 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=Inactivation+of+YAP+oncoprotein+by+the+Hippo+pathway+is+involved+in+cell+contact+inhibition+and+tissue+growth+control.">Inactivation of YAP oncoprotein by the Hippo pathway is involved in cell contact inhibition and tissue growth control.</a> Genes Dev. 21 (21), 2747-2761 (2007).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> AVMA Guidelines for the Euthanasia of Animals: 2013 Edition. , (2013).</li><li>Semerci, F., 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=Lunatic+fringe-mediated+Notch+signaling+regulates+adult+hippocampal+neural+stem+cell+maintenance.">Lunatic fringe-mediated Notch signaling regulates adult hippocampal neural stem cell maintenance.</a> eLife. 6, (2017).</li><li>Tuan, R. S., Lo, C. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Developmental+biology+protocols.">Developmental biology protocols.</a> Methods in molecular biology. , 137 (2000).</li><li>Brandon, C. S., Voelkel-Johnson, C., May, L. A., Cunningham, L. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dissection+of+adult+mouse+utricle+and+adenovirus-mediated+supporting-cell+infection.">Dissection of adult mouse utricle and adenovirus-mediated supporting-cell infection.</a> J Vis Exp JoVE. (61), (2012).</li><li>Gosset, M., Berenbaum, F., Thirion, S., Jacques, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Primary+culture+and+phenotyping+of+murine+chondrocytes.">Primary culture and phenotyping of murine chondrocytes.</a> Nat Protoc. 3 (8), 1253-1260 (2008).</li><li>Landegger, L. D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+synthetic+AAV+vector+enables+safe+and+efficient+gene+transfer+to+the+mammalian+inner+ear.">A synthetic AAV vector enables safe and efficient gene transfer to the mammalian inner ear.</a> Nat Biotechnol. 35 (3), 280-284 (2017).</li><li>Burns, J. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reinforcement+of+cell+junctions+correlates+with+the+absence+of+hair+cell+regeneration+in+mammals+and+its+occurrence+in+birds.">Reinforcement of cell junctions correlates with the absence of hair cell regeneration in mammals and its occurrence in birds.</a> J Comp Neurol. 511 (3), 396-414 (2008).</li><li>Wang, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulation+of+polarized+extension+and+planar+cell+polarity+in+the+cochlea+by+the+vertebrate+PCP+pathway.">Regulation of polarized extension and planar cell polarity in the cochlea by the vertebrate PCP pathway.</a> Nat Genet. 37 (9), 980-985 (2005).</li><li>Chacon-Heszele, M. F., Ren, D., Reynolds, A. B., Chi, F., Chen, P. <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+cochlear+convergent+extension+by+the+vertebrate+planar+cell+polarity+pathway+is+dependent+on+p120-catenin.">Regulation of cochlear convergent extension by the vertebrate planar cell polarity pathway is dependent on p120-catenin.</a> Dev Camb Engl. 139 (5), 968-978 (2012).</li><li>Yamamoto, N., Okano, T., Ma, X., Adelstein, R. S., Kelley, M. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Myosin+II+regulates+extension,+growth+and+patterning+in+the+mammalian+cochlear+duct.">Myosin II regulates extension, growth and patterning in the mammalian cochlear duct.</a> Dev Camb Engl. 136 (12), 1977-1986 (2009).</li><li>Tada, M., Heisenberg, C. -. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Convergent+extension:+using+collective+cell+migration+and+cell+intercalation+to+shape+embryos.">Convergent extension: using collective cell migration and cell intercalation to shape embryos.</a> Dev Camb Engl. 139 (21), 3897-3904 (2012).</li></ol>

The authors have nothing to disclose.

The molecular signals that mediate growth and differentiation in the inner ear during development have been studied extensively5,6,7,8,9,10. However, evidence obtained from the utricular model system suggests that mechanical cues, sensed through cell junctions and the activation of Hippo signaling, also play an important role...

The study of most aspects of mammalian organ development has been facilitated by in vitro systems. Two principal methods are now used for the culture of vestibular sensory organs: free-floating1 and adherent2 preparations. Both methods permit the investigation of hair cell vulnerabilities3 and regeneration1,4&#160;in vitro. In addition, the developmental roles of the Notch5,6, Wnt7,8, and epidermal growth factor receptor (EGFR)9,10 signaling cascades in the inner ear have been established, in part, through the use of in vitro cultures of sensory epithelia. However, cell growth and differentiation are controlled, not only through signaling by morphogens, but also through physical and mechanical cues such as intercellular contacts, the stiffness of extracellular matrix, and mechanical stretching or constriction. The role of such mechanical stimuli is challenging to investigate in the developing inner ear in vivo. Moreover, existing free-floating and adherent culture methods are not suitable for such studies in vitro. Here we describe a method for three-dimensional organotypic culture in collagen I gels of varying stiffness. This method largely preserves the in vivo architecture of the vestibular and cochlear sensory organs and allows investigation of the effects of mechanical force on growth and differentiation11.
Because mechanical stimuli are known to activate downstream molecular events, such as the Hippo signaling pathway12,13,14,15, it is important to be able to combine mechanical stimulation with biochemical and genetic manipulations. The culture method described here permits virus-mediated gene delivery and can therefore be used to study both mechanical and molecular signaling during inner ear development11.

<table border="0" cellpadding="0" cellspacing="0" style="width:749px;" width="750">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:252px;">#10 Surgical Blades</td>
			<td style="width:212px;">Miltex</td>
			<td style="width:119px;">4-110</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:252px;">#5 Forceps</td>
			<td style="width:212px;">Dumont</td>
			<td style="width:119px;">11252-20</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:252px;">100 mm Petri dish</td>
			<td style="width:212px;">Sigma</td>
			<td style="width:119px;">P5856-500EA</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:252px;">250 uL large orifice pipette tips</td>
			<td style="width:212px;">USA Scientific</td>
			<td style="width:119px;">1011-8406</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:252px;">30 mm glass-bottom Petri dish</td>
			<td style="width:212px;">Matsunami Glass USA Corporation</td>
			<td style="width:119px;">D35-14-1.5-U</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:252px;">4 well plate</td>
			<td style="width:212px;">Thermo Fisher Scientific</td>
			<td style="width:119px;">176740</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">4-Hydroxytamoxifen&#160;</td>
			<td style="width:212px;">Sigma</td>
			<td style="width:119px;">H7904</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">60&#160;mm Petri dish</td>
			<td style="width:212px;">Thermo Fisher Scientific</td>
			<td style="width:119px;">123TS1</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Acetic acid&#160;</td>
			<td style="width:212px;">Sigma</td>
			<td style="width:119px;">537020</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:252px;">Ad-GFP</td>
			<td style="width:212px;">Vector Biolabs</td>
			<td style="width:119px;">1060</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:252px;">Anti-GFP, chicken IgY fraction</td>
			<td style="width:212px;">Invitrogen</td>
			<td style="width:119px;">A10262&#160;</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:252px;">Anti-Myo7A</td>
			<td style="width:212px;">Proteus Biosciences</td>
			<td style="width:119px;">25-6790</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:252px;">Anti-Sox2 Antibody (Y-17)</td>
			<td style="width:212px;">Santa Cruz</td>
			<td style="width:119px;">sc-17320</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Bicinchoninic acid assay</td>
			<td style="width:212px;">Thermo Fisher Scientific</td>
			<td style="width:119px;">23225</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:252px;">Click-iT EdU Alexa Fluor 647 Imaging Kit</td>
			<td style="width:212px;">Thermo Fisher Scientific</td>
			<td style="width:119px;">C10340</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Collagenase I</td>
			<td style="width:212px;">Gibco</td>
			<td style="width:119px;">17100017</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">D-glucose</td>
			<td style="width:212px;">Sigma</td>
			<td style="width:119px;">G8270</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">DMEM/F12&#160;</td>
			<td style="width:212px;">Gibco</td>
			<td style="width:119px;">11320033</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Epidermal growth factor</td>
			<td style="width:212px;">Sigma</td>
			<td style="width:119px;">E9644</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:252px;">Fetal Bovine Serum (FBS)</td>
			<td style="width:212px;">Thermo Fisher Scientific</td>
			<td style="width:119px;">16140063</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Fibroblast growth factor</td>
			<td style="width:212px;">Sigma</td>
			<td style="width:119px;">F5392</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Flaming/Brown Micropipette Puller</td>
			<td style="width:212px;">Sutter Instrument</td>
			<td style="width:119px;">P-97</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Glutamine</td>
			<td style="width:212px;">Sigma</td>
			<td style="width:119px;">G8540</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">HBSS</td>
			<td style="width:212px;">Gibco</td>
			<td style="width:119px;">14025092</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:252px;">Hemocytometer&#160;</td>
			<td style="width:212px;">Daigger</td>
			<td style="width:119px;">EF16034F</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:252px;">HEPES</td>
			<td style="width:212px;">Sigma</td>
			<td style="width:119px;">H4034</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:252px;">Insulin</td>
			<td style="width:212px;">Sigma</td>
			<td style="width:119px;">I3536</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Iridectomy scissors&#160;</td>
			<td style="width:212px;">Zepf Medical Instruments</td>
			<td style="width:119px;">08-1201-10&#160;&#160;</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:252px;">Microinjector</td>
			<td style="width:212px;">Narishige</td>
			<td style="width:119px;">IM-6</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Nicotinamide</td>
			<td style="width:212px;">Sigma</td>
			<td style="width:119px;">N0636</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:252px;">PBS (10X), pH 7.4</td>
			<td style="width:212px;">Gibco</td>
			<td style="width:119px;">70011044</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">PBS (1X), pH 7.4</td>
			<td style="width:212px;">Gibco</td>
			<td style="width:119px;">10010023</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:252px;">Phenol Red pH indicator&#160;</td>
			<td style="width:212px;">Sigma</td>
			<td style="width:119px;">P4633&#160;</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:252px;">Pure Ethanol, 200 Proof</td>
			<td style="width:212px;">Decon Labs&#160;</td>
			<td style="width:119px;">2716</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:252px;">RFP antibody</td>
			<td style="width:212px;">ChromoTek</td>
			<td style="width:119px;">&#160;5F8</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:252px;">Sodium bicarbonate</td>
			<td style="width:212px;">Sigma</td>
			<td style="width:119px;">S5761</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:252px;">Sodium hydroxide</td>
			<td style="width:212px;">Sigma</td>
			<td style="width:119px;">S8045</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Sodium selenite</td>
			<td style="width:212px;">Sigma</td>
			<td style="width:119px;">S5261</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:252px;">Tabletop vortex&#160;</td>
			<td style="width:212px;">VWR</td>
			<td style="width:119px;">97043-562</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:252px;">Transferrin</td>
			<td style="width:212px;">Sigma</td>
			<td style="width:119px;">T8158</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Trypan blue&#160;</td>
			<td style="width:212px;">Sigma</td>
			<td style="width:119px;">T6146</td>
			<td></td>
		</tr>
	</tbody>
</table>

three-dimensional organotypic cultures of vestibular and auditory sensory organs

The sensory organs of the inner ear are challenging to study in mammals due to their inaccessibility to experimental manipulation and optical observation. Moreover, although existing culture techniques allow biochemical perturbations, these methods do not provide a means to study the effects of mechanical force and tissue stiffness during development of the inner ear sensory organs. Here we describe a method for three-dimensional organotypic culture of the intact murine utricle and cochlea that overcomes these limitations. The technique for adjustment of a three-dimensional matrix stiffness described here permits manipulation of the elastic force opposing tissue growth. This method can therefore be used to study the role of mechanical forces during inner ear development. Additionally, the cultures permit virus-mediated gene delivery, which can be used for gain- and loss-of-function experiments. This culture method preserves innate hair cells and supporting cells and serves as a potentially superior alternative to the traditional two-dimensional culture of vestibular and auditory sensory organs.

Vestibular and auditory sensory organs from embryonic ears, cultured in 40-Pa collagen I gels mimicking low stiffness embryonic conditions11, retain relatively normal three-dimensional structures (Figure 1) and maintain hair cells and supporting cells (Figure 2 and Figure 3). Although supporting cell density decreases by over 30% (Student&#39;s t-test: n = 4, p</e...

Watch this Scientific Journal Video about Three-dimensional Organotypic Cultures of Vestibular and Auditory Sensory Organs at JoVE.com

Three-dimensional Organotypic Cultures of Vestibular and Auditory Sensory Organs

Three-dimensional organotypic cultures of the murine utricle and cochlea in optically clear collagen I gels preserve innate tissue morphology, allow for mechanical stimulation through adjustment of matrix stiffness, and permit virus-mediated gene delivery.

The sensory organs of the inner ear are challenging to study in mammals due to their inaccessibility to experimental manipulation and optical observation. ...

three-dimensional-organotypic-cultures-vestibular-auditory-sensory

Research

JoVE Journal

Developmental Biology

8.1K Views.  Keck School of Medicine of the University of Southern California. Three-dimensional organotypic cultures of the murine utricle and cochlea in optically clear collagen I gels preserve innate tissue morphology, allow for mechanical stimulation through adjustment of matrix stiffness, and permit virus-mediated gene delivery.

Video: Three-dimensional Organotypic Cultures of Vestibular and Auditory Sensory Organs

Organotypic Slice Cultures for Studies of Postnatal Neurogenesis

Here we describe a technique for studying hippocampal postnatal neurogenesis in the rodent brain using the organotypic slice culture technique. This method maintains the characteristic topographical morphology of the hippocampus while allowing direct application of pharmacological agents to the developing hippocampal dentate gyrus. Additionally, slice cultures can be maintained for up to 4 weeks and thus, allow one to study the maturation process of newborn granule neurons. Slice cultures allow for efficient pharmacological manipulation of hippocampal slices while excluding complex variables such as uncertainties related to the deep anatomic location of the hippocampus as well as the blood brain barrier. For these reasons, we sought to optimize organotypic slice cultures specifically for postnatal neurogenesis research.

Here we describe a technique for studying hippocampal postnatal neurogenesis using the organotypic slice culture technique. This method allows for in vitro manipulation of adult neurogenesis and allows for the direct application of pharmacological agents to the cultured hippocampus.

Here we describe a technique for studying hippocampal postnatal neurogenesis in the rodent brain using the organotypic slice culture technique. This ...

Differentiation of a Human Neural Stem Cell Line on Three Dimensional Cultures, Analysis of MicroRNA and Putative Target Genes

Neural stem cells (NSCs) are capable of self-renewal and differentiation into neurons, astrocytes and oligodendrocytes under specific local microenvironments. In here, we present a set of methods used for three dimensional (3D) differentiation and miRNA analysis of a clonal human neural stem cell (hNSC) line, currently in clinical trials for stroke disability (NCT01151124 and NCT02117635, Clinicaltrials.gov). HNSCs were derived from an ethical approved first trimester human fetal cortex and conditionally immortalized using retroviral integration of a single copy of the c-mycERTAMconstruct. We describe how to measure axon process outgrowth of hNSCs differentiated on 3D scaffolds and how to quantify associated changes in miRNA expression using PCR array. Furthermore we exemplify computational analysis with the aim of selecting miRNA putative targets. SOX5 and NR4A3 were identified as suitable miRNA putative target of selected significantly down-regulated miRNAs in differentiated hNSC. MiRNA target validation was performed on SOX5 and NR4A3 3&#8217;UTRs by dual reporter plasmid transfection and dual luciferase assay.

With the intent of characterizing changes in miRNAs on differentiated human neural stem cells (hNSCs) we describe hNSC differentiation on a three dimensional system,the evaluation of changes in microRNA expression by miRNA PCR array, and computational analysis for miRNA target prediction and its validation by dual luciferase assay.

Neural stem cells (NSCs) are capable of self-renewal and differentiation into neurons, astrocytes and oligodendrocytes under specific local ...

Three-dimensional Quantification of Dendritic Spines from Pyramidal Neurons Derived from Human Induced Pluripotent Stem Cells

Dendritic spines are small protrusions that correspond to the post-synaptic compartments of excitatory synapses in the central nervous system. They are distributed along the dendrites. Their morphology is largely dependent on neuronal activity, and they are dynamic. Dendritic spines express glutamatergic receptors (AMPA and NMDA receptors) on their surface and at the levels of postsynaptic densities. Each spine allows the neuron to control its state and local activity independently. Spine morphologies have been extensively studied in glutamatergic pyramidal cells of the brain cortex, using both in vivo approaches and neuronal cultures obtained from rodent tissues. Neuropathological conditions can be associated to altered spine induction and maturation, as shown in rodent cultured neurons and one-dimensional quantitative analysis 1. The present study describes a protocol for the 3D quantitative analysis of spine morphologies using human cortical neurons derived from neural stem cells (late cortical progenitors). These cells were initially obtained from induced&#160;pluripotent stem cells. This protocol allows the analysis of spine morphologies at different culture periods, and with possible comparison between induced&#160;pluripotent stem cells obtained from control individuals with those obtained from patients with psychiatric diseases.

Dendritic spines of pyramidal neurons are the sites of most excitatory synapses in mammalian brain cortex. This method describes a 3D quantitative analysis of spine morphologies in human cortical pyramidal glutamatergic neurons derived from induced&#160;pluripotent stem cells.

Dendritic spines are small protrusions that correspond to the post-synaptic compartments of excitatory synapses in the central nervous system. They are ...

Using Ex Vivo Upright Droplet Cultures of Whole Fetal Organs to Study Developmental Processes during Mouse Organogenesis

Investigating organogenesis in utero is a technically challenging process in placental mammals due to inaccessibility of reagents to embryos that develop within the uterus. A newly developed ex vivo upright droplet culture method provides an attractive alternative to studies performed in utero. The ex vivo droplet culture provides the ability to examine and manipulate cellular interactions and diverse signaling pathways through use of various blocking and activating compounds; additionally, the effects of various pharmacological reagents on the development of specific organs can be studied without unwanted side effects of systemic drug delivery in utero. As compared to other in vitro systems, the droplet culture not only allows for the ability to study three-dimensional morphogenesis and cell-cell interactions, which cannot be reproduced in mammalian cell lines, but also requires significantly less reagents than other ex vivo and in vitro protocols. This paper demonstrates proper mouse fetal organ dissection and upright droplet culture techniques, followed by whole organ immunofluorescence to demonstrate the effectiveness of the method. The ex vivo droplet culture method allows the formation of organ architecture comparable to what is observed in vivo and can be utilized to study otherwise difficult-to-study processes due to embryonic lethality in in vivo models. As a model application system, a small-molecule inhibitor will be utilized to probe the role of vascularization in testicular morphogenesis. This ex vivo droplet culture method is expandable to other fetal organ systems, such as lung and potentially others, although each organ must be extensively studied to determine any organ-specific modifications to the protocol. This organ culture system provides flexibility in experimentation with fetal organs, and results obtained using this technique will help researchers gain insights into fetal development.

Using Ex Vivo Upright Droplet Cultures of Whole Fetal Organs to Study Developmental Processes during Mouse Organogenesis

The&#160;ex vivo&#160;upright droplet culture is an alternative to current&#160;in vitro&#160;and&#160;in vivo&#160;experimental techniques. This protocol is easy to perform and requires smaller amounts of reagent, while permitting the ability to manipulate and study fetal vascularization, morphogenesis, and organogenesis.

Investigating organogenesis in utero is a technically challenging process in placental mammals due to inaccessibility of reagents to embryos that develop ...

Generation of Genetically Modified Organotypic Skin Cultures Using Devitalized Human Dermis

Organotypic cultures allow the reconstitution of a 3D environment critical for cell-cell contact and cell-matrix interactions which mimics the function and physiology of their in vivo tissue counterparts. This is exemplified by organotypic skin cultures which faithfully recapitulates the epidermal differentiation and stratification program. Primary human epidermal keratinocytes are genetically manipulable through retroviruses where genes can be easily overexpressed or knocked down. These genetically modified keratinocytes can then be used to regenerate human epidermis in organotypic skin cultures providing a powerful model to study genetic pathways impacting epidermal growth, differentiation, and disease progression. The protocols presented here describe methods to prepare devitalized human dermis as well as to genetically manipulate primary human keratinocytes in order to generate organotypic skin cultures. Regenerated human skin can be used in downstream applications such as gene expression profiling, immunostaining, and chromatin immunoprecipitations followed by high throughput sequencing. Thus, generation of these genetically modified organotypic skin cultures will allow the determination of genes that are critical for maintaining skin homeostasis.

The goal of this paper is to provide a comprehensive and detailed protocol on how to generate genetically modified human organotypic skin from epidermal keratinocytes and devitalized human dermis.

Organotypic cultures allow the reconstitution of a 3D environment critical for cell-cell contact and cell-matrix interactions which mimics the function ...

Gene Transfer into the Chicken Auditory Organ by In Ovo Micro-electroporation

Chicken embryos are ideal model systems for studying embryonic development as manipulations of gene function can be conducted with relative ease in ovo. The inner ear auditory sensory organ is critical for our ability to hear. It houses a highly specialized sensory epithelium that consists of mechano-transducing hair cells (HCs) and surrounding glial-like supporting cells (SCs). Despite structural differences in the auditory organs, molecular mechanisms regulating the development of the auditory organ are evolutionarily conserved between mammals and aves. In ovo electroporation is largely limited to early stages at E1 - E3. Due to the relative late development of the auditory organ at E5, manipulations of the auditory organ by in ovo electroporation past E3 are difficult due to the advanced development of the chicken embryo at later stages. The method presented here is a transient gene transfer method for targeting genes of interest at stage E4 - E4.5 in the developing chicken auditory sensory organ via in ovo micro-electroporation. This method is applicable for gain- and loss-of-functions with conventional plasmid DNA-based expression vectors and can be combined with in ovo cell proliferation assay by adding EdU (5-ethynyl-2&#180;-deoxyuridine) to the whole embryo at the time of electroporation. The use of green or red fluorescent protein (GFP or RFP) expression plasmids allows the experimenter to quickly determine whether the electroporation successfully targeted the auditory portion of the developing inner ear. In this method paper, representative examples of GFP electroporated specimens are illustrated; embryos were harvested 18 - 96 hr&#160;after electroporation and targeting of GFP to the pro-sensory area of the auditory organ was confirmed by RNA in situ hybridization. The method paper also provides an optimized protocol for the use of the thymidine analog EdU to analyze cell proliferation; an example of an EdU based cell proliferation assay that combines immuno-labeling and click EdU chemistry is provided.

Gene Transfer into the Chicken Auditory Organ by In Ovo Micro-electroporation

The auditory organ mediates hearing. Here we present a modified in ovo micro-electroporation method optimized for studying auditory progenitor cell proliferation and differentiation in the developing chicken auditory organ.

Chicken embryos are ideal model systems for studying embryonic development as manipulations of gene function can be conducted with relative ease in ovo. ...

A Novel Use of Three-dimensional High-frequency Ultrasonography for Early Pregnancy Characterization in the Mouse

High-frequency ultrasonography (HFUS) is a common method to non-invasively monitor the real-time development of the human fetus in utero. The mouse is routinely used as an in vivo model to study embryo implantation and pregnancy progression. Unfortunately, such murine studies require pregnancy interruption to enable follow-up phenotypic analysis. To address this issue, we used three-dimensional (3-D) reconstruction of HFUS imaging data for early detection and characterization of murine embryo implantation sites and their individual developmental progression in utero. Combining HFUS imaging with 3-D reconstruction and modeling, we were able to accurately quantify embryo implantation site number as well as monitor developmental progression in pregnant C57BL6J/129S mice from 5.5 days post coitus (d.p.c.) through to 9.5 d.p.c. with the use of a transducer. Measurements included: number, location, and volume of implantation sites as well as inter-implantation site spacing; embryo viability was assessed by cardiac activity monitoring. In the immediate post-implantation period (5.5 to 8.5 d.p.c.), 3-D reconstruction of the gravid uterus in both mesh and solid overlay format enabled visual representation of the developing pregnancies within each uterine horn. As genetically engineered mice continue to be used to characterize female reproductive phenotypes derived from uterine dysfunction, this method offers a new approach to detect, quantify, and characterize early implantation events in vivo. This novel use of 3-D HFUS imaging demonstrates the ability to successfully detect, visualize, and characterize embryo-implantation sites during early murine pregnancy in a non-invasive manner. The technology offers a significant improvement over current methods, which rely on the interruption of pregnancies for gross tissue and histopathologic characterization. Here we use a video and text format to describe how to successfully perform ultrasounds of early murine pregnancy to generate reliable and reproducible data with reconstruction of the uterine form in mesh and solid 3-D images.

Mice are widely used to study gestational biology. However, pregnancy termination is required for such studies which precludes longitudinal investigations and necessitates the use of large numbers of animals. Therefore, we describe a non-invasive technique of high-frequency ultrasonography for early detection and monitoring of post-implantation events in the pregnant mouse.

High-frequency ultrasonography (HFUS) is a common method to non-invasively monitor the real-time development of the human fetus in utero. The mouse is ...

Whole-mount Clearing and Staining of Arabidopsis Flower Organs and Siliques

Due to its formidable tools for molecular genetic studies, Arabidopsis thaliana is one of the most prominent model species in plant biology and, especially, in plant reproductive biology. However, plant morphological, anatomical, and ultrastructural analyses traditionally involve time-consuming embedding and sectioning procedures for bright field, scanning, and electron microscopy. Recent progress in confocal fluorescence microscopy, state-of-the-art 3-D computer-aided microscopic analyses, and the continuous refinement of molecular techniques to be used on minimally processed whole-mount specimens, has led to an increased demand for developing efficient and minimal sample processing techniques. In this protocol, we describe techniques for properly dissecting Arabidopsis flowers and siliques, basic clearing techniques, and some staining procedures for whole-mount observations of reproductive structures.

Whole-mount Clearing and Staining of Arabidopsis Flower Organs and Siliques

In this protocol, we describe techniques for the proper dissection of Arabidopsis flowers and siliques, some basic clearing techniques, and selected staining procedures for whole-mount observations of reproductive structures.

Due to its formidable tools for molecular genetic studies, Arabidopsis thaliana is one of the most prominent model species in plant biology and, ...

Three-dimensional Rendering and Analysis of Immunolabeled, Clarified Human Placental Villous Vascular Networks

Nutrient and gas exchange between mother and fetus occurs at the interface of the maternal intervillous blood and the vast villous capillary network that makes up much of the parenchyma of the human placenta. The distal villous capillary network is the terminus of the fetal blood supply after several generations of branching of vessels extending out from the umbilical cord. This network has a contiguous cellular sheath, the syncytial trophoblast barrier layer, which prevents mixing of fetal blood and the maternal blood in which it is continuously bathed. Insults to the integrity of the placental capillary network, occurring in disorders such as maternal diabetes, hypertension and obesity, have consequences that present serious health risks for the fetus, infant, and adult. To better define the structural effects of these insults, a protocol was developed for this study that captures capillary network structure on the order of 1 - 2 mm3 wherein one can investigate its topological features in its full complexity. To accomplish this, clusters of terminal villi from placenta are dissected, and the trophoblast layer and the capillary endothelia are immunolabeled. These samples are then clarified with a new tissue clearing process which makes it possible to acquire confocal image stacks to z- depths of ~1 mm. The three-dimensional renderings of these stacks are then processed and analyzed to generate basic capillary network measures such as volume, number of capillary branches, and capillary branch end points, as validation of the suitability of this approach for capillary network characterization.

This study presents a protocol for the reversible tissue clearing, immunostaining, 3D-rendering and analysis of vascular networks in human placenta villi samples on the order of 1 - 2 mm3.

Nutrient and gas exchange between mother and fetus occurs at the interface of the maternal intervillous blood and the vast villous capillary network that ...

Three-dimensional Inflammatory Human Tissue Equivalents of Gingiva

Periodontal diseases (such as gingivitis and periodontitis) are the leading causes of tooth loss in adults. Inflammation in gingiva is the fundamental physiopathology of periodontal diseases. Current experimental models of periodontal diseases have been established in various types of animals. However, the physiopathology of animal models is different from that of humans, making it difficult to analyze cellular and molecular mechanisms and evaluate new medicines for periodontal diseases. Here, we present a detailed protocol for reconstructing human inflammatory tissue equivalents of gingiva (iGTE) in vitro. We first build human tissue equivalents of gingiva (GTE) by utilizing two types of human cells, including human gingival fibroblasts (HGF) and human skin epidermal keratinocytes (HaCaT), under three-dimensional conditions. We create a wound model by using a tissue puncher to punch a hole in the GTE. Next, human THP-1 monocytes mixed with collagen gel are injected into the hole in the GTE. By adimistration of 10 ng/mL phorbol 12-myristate 13-acetate (PMA) for 72 h, THP-1 cells differentiated into macrophages to form inflammatory foci in GTE (iGTE) (IGTE also can be stumilated with 2 &#181;g/mL of lipopolysaccharides (LPS) for 48 h to initiate inflammation). IGTE is the first in vitro model of inflammatory gingiva using human cells with a three-dimensional architecture. IGTE reflects major pathological changes (immunocytes activition, intracellular interactions among fibryoblasts, epithelial cells, monocytes and macrophages) in periodontal diseases. GTE, wounded GTE, and iGTE can be used as versatile tools to study wound healing, tissue regeneration, inflammation, cell-cell interaction, and screen potential medicines for periodontal diseases.

The goal of the protocol is to build an inflammatory human gingiva model in vitro. This tissue model co-cultivates three types of human cells, HaCaT keratinocytes, gingival fibroblasts, and THP-1 macrophages, under three-dimensional conditions. This model can be applied to investigating periodontal diseases, such as gingivitis and periodontitis.

Periodontal diseases (such as gingivitis and periodontitis) are the leading causes of tooth loss in adults. Inflammation in gingiva is the fundamental ...