We gratefully acknowledge support from NCBS, TIFR, Infosys-TIFR Leading Edge Research Grant, DST-SERB, and the Royal National Institute for the Deaf. We would like to thank Central Poultry Development Organization and Training Institute, Hesaraghatta, Bengaluru. We are grateful to CIFF and EM facility and lab support at NCBS. We thank Yoshiko Takahashi and Koichi Kawakami for the Tol2-eGFP and T2TP constructs, and Guy Richardson for HCA and G19 Pcdh15 antibody. We are grateful to Earlab members for their constant support and valuable feedback on the protocol.

Protocols involving the procurement, culture, and use of fertilized chicken eggs and unhatched embryos were approved by the Institutional Animal Ethics Committee of the National Centre for Biological Sciences, Bengaluru, Karnataka.
1. In ovo electroporation of chick auditory precursors
<ol>
	<li>sgRNA design and cloning for CRISPR/Cas9 gene knockout
	<ol>
		<li>For creating gene knockouts, design guide RNAs to disrupt the exon regions of the gene, preferably closer ...

<ol>
	<li>Sai, X., Ladher, R. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Early+steps+in+inner+ear+development:+induction+and+morphogenesis+of+the+otic+placode.">Early steps in inner ear development: induction and morphogenesis of the otic placode.</a> Frontiers in Pharmacology. 6, 19 (2015).</li><li>Groves, A. K., Fekete, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Shaping+sound+in+space:+the+regulation+of+inner+ear+patterning.">Shaping sound in space: the regulation of inner ear patterning.</a> Development. 139 (2), 245-257 (2012).</li><li>Driver, E. C., 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=Development+of+the+cochlea.">Development of the cochlea.</a> Development. 147 (12), (2020).</li><li>Richardson, G. P., Petit, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hair-bundle+links:+genetics+as+the+gateway+to+function.">Hair-bundle links: genetics as the gateway to function.</a> Cold Spring Harbor Perspectives in Medicine. 9 (12), 033142 (2019).</li><li>Tilney, L. G., Cotanche, D. A., Tilney, M. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Actin+filaments,+stereocilia+and+hair+cells+of+the+bird+cochlea.+VI.+How+the+number+and+arrangement+of+stereocilia+are+determined.">Actin filaments, stereocilia and hair cells of the bird cochlea. VI. How the number and arrangement of stereocilia are determined.</a> Development. 116 (1), 213-226 (1992).</li><li>Jones, 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=Ciliary+proteins+link+basal+body+polarization+to+planar+cell+polarity+regulation.">Ciliary proteins link basal body polarization to planar cell polarity regulation.</a> Nature Genetics. 40 (1), 69-77 (2008).</li><li>Sipe, C. W., Lu, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Kif3a+regulates+planar+polarization+of+auditory+hair+cells+through+both+ciliary+and+non-ciliary+mechanisms.">Kif3a regulates planar polarization of auditory hair cells through both ciliary and non-ciliary mechanisms.</a> Development. 138 (16), 3441-3449 (2011).</li><li>May-Simera, H. L., 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=Cilia,+Wnt+signaling,+and+the+cytoskeleton.">Cilia, Wnt signaling, and the cytoskeleton.</a> Cilia. 1 (1), 1 (2012).</li><li>Ebrahim, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stereocilia-staircase+spacing+is+influenced+by+myosin+III+motors+and+their+cargos+espin-1+and+espin-like.">Stereocilia-staircase spacing is influenced by myosin III motors and their cargos espin-1 and espin-like.</a> Nature Communications. 7, 10833 (2016).</li><li>Corwin, J. T., Cotanche, D. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regeneration+of+sensory+hair+cells+after+acoustic+trauma.">Regeneration of sensory hair cells after acoustic trauma.</a> Science. 240 (4860), 1772-1774 (1988).</li><li>Collado, M. S., Burns, J. C., Hu, Z., 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=Recent+advances+in+hair+cell+regeneration+research.">Recent advances in hair cell regeneration research.</a> Current Opinion in Otolaryngology &amp; Head and Neck Surgery. 16 (5), 465-471 (2008).</li><li>Edge, A. S., Chen, Z. Y. <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.">Hair cell regeneration.</a> Current Opinion in Neurobiology. 18 (4), 377-382 (2008).</li><li>Atkinson, P. J., Huarcaya Najarro, E., Sayyid, Z. N., Cheng, A. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sensory+hair+cell+development+and+regeneration:+similarities+and+differences.">Sensory hair cell development and regeneration: similarities and differences.</a> Development. 142 (9), 1561-1571 (2015).</li><li>Brignull, H. R., Raible, D. W., 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=Feathers+and+fins:+non-mammalian+models+for+hair+cell+regeneration.">Feathers and fins: non-mammalian models for hair cell regeneration.</a> Brain Research. 1277, 12-23 (2009).</li><li>Rubel, E. W., Furrer, S. A., 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=A+brief+history+of+hair+cell+regeneration+research+and+speculations+on+the+future.">A brief history of hair cell regeneration research and speculations on the future.</a> Hearing Research. 297, 42-51 (2013).</li><li>Stone, J. S., Cotanche, D. A. <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+the+avian+auditory+epithelium.">Hair cell regeneration in the avian auditory epithelium.</a> The International Journal of Developmental Biology. 51 (6-7), 633-647 (2007).</li><li>Roberson, D. W., Alosi, J. A., Cotanche, D. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+transdifferentiation+gives+rise+to+the+earliest+new+hair+cells+in+regenerating+avian+auditory+epithelium.">Direct transdifferentiation gives rise to the earliest new hair cells in regenerating avian auditory epithelium.</a> Journal of Neuroscience Research. 78 (4), 461-471 (2004).</li><li>Fritzsch, B., Beisel, K. W., Pauley, S., Soukup, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+evolution+of+the+vertebrate+mechanosensory+cell+and+ear.">Molecular evolution of the vertebrate mechanosensory cell and ear.</a> The International Journal of Developmental Biology. 51 (6-7), 663-678 (2007).</li><li>Tilney, L. G., DeRosier, D. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Actin+filaments,+stereocilia,+and+hair+cells+of+the+bird+cochlea.+IV.+How+the+actin+filaments+become+organized+in+developing+stereocilia+and+in+the+cuticular+plate.">Actin filaments, stereocilia, and hair cells of the bird cochlea. IV. How the actin filaments become organized in developing stereocilia and in the cuticular plate.</a> Developmental Biology. 116 (1), 119-129 (1986).</li><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> Hearing Research. 70 (1), 85-108 (1993).</li><li>Honda, A., Freeman, S. D., Sai, X., Ladher, R. K., O'Neill, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=From+placode+to+labyrinth:+culture+of+the+chicken+inner+ear.">From placode to labyrinth: culture of the chicken inner ear.</a> Methods. 66 (3), 447-453 (2014).</li><li>Matsunaga, 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=Initiation+of+supporting+cell+activation+for+hair+cell+regeneration+in+the+avian+auditory+epithelium:+an+explant+culture+model.">Initiation of supporting cell activation for hair cell regeneration in the avian auditory epithelium: an explant culture model.</a> Frontiers in Cellular Neuroscience. 14, 583994 (2020).</li><li>Concordet, J. P., Haeussler, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=CRISPOR:+intuitive+guide+selection+for+CRISPR/Cas9+genome+editing+experiments+and+screens.">CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens.</a> Nucleic Acids Research. 46, 242-245 (2018).</li><li>Gandhi, S., Piacentino, M. L., Vieceli, F. M., Bronner, M. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optimization+of+CRISPR/Cas9+genome+editing+for+loss-of-function+in+the+early+chick+embryo.">Optimization of CRISPR/Cas9 genome editing for loss-of-function in the early chick embryo.</a> Developmental Biology. 432 (1), 86-97 (2017).</li><li>Green, M. R., Sambrook, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cloning+and+transformation+with+plasmid+vectors.">Cloning and transformation with plasmid vectors.</a> Cold Spring Harbor Protocols. 2021 (11), (2021).</li><li>Sato, Y., 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=Stable+integration+and+conditional+expression+of+electroporated+transgenes+in+chicken+embryos.">Stable integration and conditional expression of electroporated transgenes in chicken embryos.</a> Developmental Biology. 305 (2), 616-624 (2007).</li><li>Takahashi, Y., Watanabe, T., Nakagawa, S., Kawakami, K., Sato, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transposon-mediated+stable+integration+and+tetracycline-inducible+expression+of+electroporated+transgenes+in+chicken+embryos.">Transposon-mediated stable integration and tetracycline-inducible expression of electroporated transgenes in chicken embryos.</a> Methods in Cell Biology. 87, 271-280 (2008).</li><li>Mashal, R. D., Koontz, J., Sklar, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Detection+of+mutations+by+cleavage+of+DNA+heteroduplexes+with+bacteriophage+resolvases.">Detection of mutations by cleavage of DNA heteroduplexes with bacteriophage resolvases.</a> Nature Genetics. 9 (2), 177-183 (1995).</li><li>Ogier, J. M., Burt, R. A., Drury, H. R., Lim, R., Nayagam, B. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Organotypic+culture+of+neonatal+murine+inner+ear+explants.">Organotypic culture of neonatal murine inner ear explants.</a> Frontiers in Cellular Neuroscience. 13, 170 (2019).</li><li>Davies, S., Forge, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Preparation+of+the+mammalian+organ+of+Corti+for+scanning+electron+microscopy.">Preparation of the mammalian organ of Corti for scanning electron microscopy.</a> Journal of Microscopy. 147, 89-101 (1987).</li><li>Parker, A., Chessum, L., Mburu, P., Sanderson, J., Bowl, M. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Light+and+electron+microscopy+methods+for+examination+of+cochlear+morphology+in+mouse+models+of+deafness.">Light and electron microscopy methods for examination of cochlear morphology in mouse models of deafness.</a> Current Protocols in Mouse Biology. 6 (3), 272-306 (2016).</li><li>Bermingham, N. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Math1:+an+essential+gene+for+the+generation+of+inner+ear+hair+cells.">Math1: an essential gene for the generation of inner ear hair cells.</a> Science. 284 (5421), 1837-1841 (1999).</li><li>Goodyear, R. J., Forge, A., Legan, P. K., Richardson, G. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Asymmetric+distribution+of+cadherin+23+and+protocadherin+15+in+the+kinocilial+links+of+avian+sensory+hair+cells.">Asymmetric distribution of cadherin 23 and protocadherin 15 in the kinocilial links of avian sensory hair cells.</a> The Journal of Comparative Neurology. 518 (21), 4288-4297 (2010).</li><li>Bartolami, S., Goodyear, R., Richardson, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Appearance+and+distribution+of+the+275+kD+hair-cell+antigen+during+development+of+the+avian+inner+ear.">Appearance and distribution of the 275 kD hair-cell antigen during development of the avian inner ear.</a> The Journal of Comparative Neurology. 314 (4), 777-788 (1991).</li><li>Funahashi, J., Nakamura, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Electroporation+in+avian+embryos.">Electroporation in avian embryos.</a> Methods in Molecular Biology. 461, 377-382 (2008).</li><li>Nakamura, H., Funahashi, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Electroporation:+past,+present+and+future.">Electroporation: past, present and future.</a> Development, Growth &amp; Differentiation. 55 (1), 15-19 (2013).</li><li>Olaya-Sanchez, 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=Fgf3+and+Fgf16+expression+patterns+define+spatial+and+temporal+domains+in+the+developing+chick+inner+ear.">Fgf3 and Fgf16 expression patterns define spatial and temporal domains in the developing chick inner ear.</a> Brain Structure &amp; Function. 222 (1), 131-149 (2017).</li><li>Jones, J. M., Warchol, M. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Expression+of+the+Gata3+transcription+factor+in+the+acoustic+ganglion+of+the+developing+avian+inner+ear.">Expression of the Gata3 transcription factor in the acoustic ganglion of the developing avian inner ear.</a> The Journal of Comparative Neurology. 516 (6), 507-518 (2009).</li><li>Serralbo, O., 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=Transgenesis+and+web+resources+in+quail.">Transgenesis and web resources in quail.</a> Elife. 9, 56312 (2020).</li></ol>

The chick is a cost-effective and convenient addition to the model organisms that a lab may use to research the inner ear. The methods described here are routinely used in our lab and complement ongoing research in the mammalian inner ear. In ovo electroporation is used to introduce genetic manipulations into the chick genome. Electroporation can also be used to introduce constructs that encode fluorescent proteins targeted to particular organelles or subcellular structures35,<...

The inner ear of all vertebrates is derived from a simple epithelium known as the otic placode1,2. This will give rise to all the structural elements and the cell types necessary to transduce the mechanosensory information associated with hearing and balance perception. Hair cells (HCs), the ciliated sensor of the inner ear, are surrounded by supporting cells (SCs). HCs relay information to the auditory hindbrain through the neurons of the eighth cranial nerve. These are also generated from the otic placode3. The primary transduction of sound is achieved at the apical surface of the auditory HC, through a mechanically sensitive hair bundle4. This is mediated through modified actin-based protrusions called stereocilia, which are arranged in a graded, staircase pattern5. In addition, a modified primary cilium, called the kinocilium, organizes hair bundle formation and is adjacent to the tallest row of stereocilia6,7,8. The architecture of stereocilia is critical for this role in converting mechanical stimuli derived from acoustic energy to electrical neural signals9. Damage to the auditory HC through ageing, infection, otoacoustic trauma, or ototoxic shock can result in partial or complete hearing loss that, in mammals, is irreversible10.
Cellular replacement therapies have been proposed that might repair such damage11,12. The approach of this research has been to understand the normal development of the mammalian hair cell and ask if development programs can be reinitiated in progenitor-like cells that may exist within the inner ear13. A second approach has been to look outside of mammals, to non-mammalian vertebrates in which robust regeneration of auditory hair cells takes place, such as birds14,15. In birds, hair cell regeneration occurs predominantly through the de-differentiation of a supporting cell to a progenitor-like state, followed by asymmetric&#160;mitotic division to generate a hair cell and supporting cell16. In addition, direct differentiation of a supporting cell to generate a hair cell has also been observed17.
While the mechanisms of avian auditory development do show significant similarities with that of mammals, there are differences18. HC and SC differentiation in the chick BP is apparent from embryonic day (E) 7, becoming more distinct over time. By E12, a well-patterned and well-polarized basilar papilla (BP) can be visualized, and by E17 well-developed hair cells can be seen19. These time points provide windows into the mechanisms of differentiation, patterning, and polarity, as well as hair cell maturation. Understanding whether such mechanisms are conserved or divergent is important, as they provide insights into the deep homology of the origins of mechanosensory hair cells.
Here, we demonstrate an array of techniques performed at early and late embryonic stages to study cellular processes such as proliferation, fate specification, differentiation, patterning, and maintenance throughout the development of the inner ear organ. This complements other protocols on understanding inner ear development in explant culture20,21,22. We first discuss the introduction of exogenous DNA or RNA into BP precursors within the E3.5 otocyst using in ovo electroporation. Although genetic manipulations can provide valuable insights, the phenotypes thus generated can be pleiotropic and consequently confounding. This is particularly true during later inner ear development, where fundamental processes such as cytoskeletal remodeling play multiple roles in cell division, tissue morphogenesis, and cellular specialization. We present protocols for pharmacological inhibition in cultured explants, which offer advantages in controlling dosage and treatment timing and duration, offering precise spatiotemporal manipulation of developmental mechanisms.
Different organ culture methods can be utilized depending on the treatment duration of small inhibitors. Here we demonstrate two methods of organ culture that allow insights into epithelial morphogenesis and cellular specialization. A method for 3D culture using collagen as a matrix to culture the cochlear duct enables robust culturing and live visualization of the developing BP. For understanding the formation of stereocilia, we present a membrane culture method such that epithelial tissue is cultured on a stiff matrix enabling actin protrusions to grow freely. Both methods allow downstream processing such as live-cell imaging, immunohistochemistry, scanning electron microscopy (SEM), cell recording, etc. These techniques provide a roadmap for the effective use of the chick as a model system to understand and manipulate the development, maturation, and regeneration of the avian auditory epithelium.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Alexa Fluor 488 Phalloidin</td>
			<td>Thermo Fisher Scientific</td>
			<td>A12379</td>
			<td></td>
		</tr>
		<tr>
			<td>Alexa Fluor 647 Phalloidin</td>
			<td>Thermo Fisher Scientific</td>
			<td>A22287</td>
			<td></td>
		</tr>
		<tr>
			<td>Alt-R S.p. HiFi Cas9 Nuclease V3</td>
			<td>Integrated DNA Technologies</td>
			<td>1081061</td>
			<td>High fidelity Cas9 protein</td>
		</tr>
		<tr>
			<td>Anti-GFP antibody</td>
			<td>Abcam</td>
			<td>ab290</td>
			<td>Rabbit polyclonal to GFP</td>
		</tr>
		<tr>
			<td>Bovine Serum Albumin</td>
			<td>Sigma-Aldrich</td>
			<td>A9647</td>
			<td></td>
		</tr>
		<tr>
			<td>Calcium Chloride Dihydrate</td>
			<td>Thermo Fisher Scientific</td>
			<td>Q12135</td>
			<td></td>
		</tr>
		<tr>
			<td>Collagen I, rat tail</td>
			<td>Thermo Fisher Scientific</td>
			<td>A1048301</td>
			<td></td>
		</tr>
		<tr>
			<td>Critical Point Dryer Leica EM CPD300</td>
			<td>Leica</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>CUY-21 Electroporator</td>
			<td>Nepagene</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Dimethyl sulfoxide (DMSO)</td>
			<td>Sigma-Aldrich</td>
			<td>D8418</td>
			<td></td>
		</tr>
		<tr>
			<td>DM5000B Widefield Microscope</td>
			<td>Leica</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM, high glucose, GlutaMAX Supplement, pyruvate</td>
			<td>Thermo Fisher Scientific</td>
			<td>10569010</td>
			<td></td>
		</tr>
		<tr>
			<td>Dumont #5 Forceps</td>
			<td>Fine Science Tools</td>
			<td>11251-20</td>
			<td></td>
		</tr>
		<tr>
			<td>Dumont #55 Forceps</td>
			<td>Fine Science Tools</td>
			<td>11255-20</td>
			<td></td>
		</tr>
		<tr>
			<td>Fast Green FCF</td>
			<td>Sigma-Aldrich</td>
			<td>F7252</td>
			<td></td>
		</tr>
		<tr>
			<td>Fluoroshield</td>
			<td>Sigma-Aldrich</td>
			<td>F6182</td>
			<td></td>
		</tr>
		<tr>
			<td>FLUOVIEW 3000 Laser Scanning Microscope</td>
			<td>Olympus</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Glutaraldehyde (25 %)</td>
			<td>Sigma-Aldrich</td>
			<td>340855</td>
			<td></td>
		</tr>
		<tr>
			<td>Goat anti-Mouse IgG Secondary Antibody, Alexa Fluor 488</td>
			<td>Thermo Fisher Scientific</td>
			<td>A-11001</td>
			<td></td>
		</tr>
		<tr>
			<td>Goat anti-Mouse IgG Secondary Antibody, Alexa Fluor 594</td>
			<td>Thermo Fisher Scientific</td>
			<td>A-11032</td>
			<td></td>
		</tr>
		<tr>
			<td>Goat anti-Rabbit IgG Secondary Antibody, Alexa Fluor 488</td>
			<td>Thermo Fisher Scientific</td>
			<td>A-11008</td>
			<td></td>
		</tr>
		<tr>
			<td>Goat Serum Sterile filtered</td>
			<td>HiMedia</td>
			<td>RM10701</td>
			<td>Heat inactivated</td>
		</tr>
		<tr>
			<td>Hanks&#39; Balanced Salt Solution (HBSS)</td>
			<td>Thermo Fisher Scientific</td>
			<td>14025092</td>
			<td></td>
		</tr>
		<tr>
			<td>LSM980 Airyscan Microscope</td>
			<td>Zeiss</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Millicell Cell Culture Insert, 30 mm, hydrophilic PTFE, 0.4 &#181;m</td>
			<td>Sigma-Aldrich</td>
			<td>PICM03050</td>
			<td></td>
		</tr>
		<tr>
			<td>MVX10 Stereo Microscope</td>
			<td>Olympus</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>MYO7A antibody</td>
			<td>DSHB</td>
			<td>138-1</td>
			<td>Mouse monoclonal to Unconventional myosin-VIIa</td>
		</tr>
		<tr>
			<td>MZ16 Dissecting microscope</td>
			<td>Leica</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>N-2 Supplement (100X)</td>
			<td>Thermo Fisher Scientific</td>
			<td>17502048</td>
			<td></td>
		</tr>
		<tr>
			<td>Noyes Scissors, 14cm (5.5&#39;&#39;)</td>
			<td>World Precision Instruments</td>
			<td>501237</td>
			<td></td>
		</tr>
		<tr>
			<td>Osmium tetroxide (4%)</td>
			<td>Sigma-Aldrich</td>
			<td>75632</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraformaldehyde</td>
			<td>Sigma-Aldrich</td>
			<td>158127</td>
			<td></td>
		</tr>
		<tr>
			<td>PC-10 Puller</td>
			<td>Narishige</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>pcU6_1sgRNA</td>
			<td>Addgene</td>
			<td>92395</td>
			<td>Mini vector with modified chicken U6 promoter</td>
		</tr>
		<tr>
			<td>Penicillin G sodium salt</td>
			<td>Sigma-Aldrich</td>
			<td>P3032</td>
			<td></td>
		</tr>
		<tr>
			<td>Phosphate Buffered Saline (PBS)</td>
			<td>Thermo Fisher Scientific</td>
			<td>10010023</td>
			<td></td>
		</tr>
		<tr>
			<td>ProLong Gold Antifade Mountant</td>
			<td>Thermo Fisher Scientific</td>
			<td>P36934</td>
			<td></td>
		</tr>
		<tr>
			<td>SMZ1500 Dissecting microscope</td>
			<td>Nikon</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Cacodylate Buffer, 0.2M</td>
			<td>Electron Microscopy Sciences</td>
			<td>11652</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium chloride</td>
			<td>HiMedia</td>
			<td>GRM853</td>
			<td></td>
		</tr>
		<tr>
			<td>Sputtre Coater K550X</td>
			<td>Emitech</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Standard Glass Capillaries 3 in, OD 1.0 mm, No Filament</td>
			<td>World Precision Instruments</td>
			<td>1B100-3</td>
			<td></td>
		</tr>
		<tr>
			<td>Sucrose</td>
			<td>Sigma-Aldrich</td>
			<td>84097</td>
			<td></td>
		</tr>
		<tr>
			<td>The MERLIN Compact VP</td>
			<td>Zeiss</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Thiocarbohydrazide</td>
			<td>Alfa Aesar</td>
			<td>L01205</td>
			<td></td>
		</tr>
		<tr>
			<td>TWEEN 20</td>
			<td>Sigma-Aldrich</td>
			<td>P1379</td>
			<td></td>
		</tr>
	</tbody>
</table>

in ovo and ex ovo methods to study avian inner ear development

The inner ear perceives sound and maintains balance using the cochlea and vestibule. It does this by using a dedicated mechanosensory cell type known as the hair cell. Basic research in the inner ear has led to a deep understanding of how the hair cell functions, and how dysregulation can lead to hearing loss and vertigo. For this research, the mouse has been the pre-eminent model system. However, mice, like all mammals, have lost the ability to replace hair cells. Thus, when trying to understand cellular therapies for restoring inner ear function, complementary studies in other vertebrate species could provide further insights. The auditory epithelium of birds, the basilar papilla (BP), is a sheet of epithelium composed of mechanosensory hair cells (HCs) intercalated by supporting cells (SCs). Although the anatomical architecture of the basilar papilla and the mammalian cochlea differ, the molecular mechanisms of inner ear development and hearing are similar. This makes the basilar papilla a useful system for not only comparative studies but also to understand regeneration. Here, we describe dissection and manipulation techniques for the chicken inner ear. The technique shows genetic and small molecule inhibition methods, which offer a potent tool for studying the molecular mechanisms of inner ear development. In this paper, we discuss in ovo electroporation techniques to genetically perturb the basilar papilla using CRIPSR-Cas9 deletions, followed by dissection of the basilar papilla. We also demonstrate the BP organ culture and optimal use of culture matrices, to observe the development of the epithelium and the hair cells.

In the electroporation setup, electrode positioning can play a role in the domain of transfection. The positive electrode is placed under the yolk, and the negative above the embryo (Figure 1A). This results in higher GFP expression in much of the inner ear and both vestibular organs (Figure 1B), and auditory basilar papilla (Figure 1C,D), confirming transfection.
In assessing the phenoty...

Watch this Scientific Journal Video about In Ovo and Ex Ovo Methods to Study Avian Inner Ear Development at JoVE.com

In Ovo and Ex Ovo Methods to Study Avian Inner Ear Development

The chick is a cost-effective, accessible, and widely available model organism for a variety of studies. Here, a series of protocols is detailed to understand the molecular mechanisms underlying avian inner ear development and regeneration.

In Ovo and Ex Ovo Methods to Study Avian Inner Ear Development

The inner ear perceives sound and maintains balance using the cochlea and vestibule. It does this by using a dedicated mechanosensory cell type known as ...

Age, infection, and ototoxic drugs can cause degeneration of hair cells of the inner ear, which in us leads to hearing loss. In non-mammalian vertebrates, such as chick, hair cells can be regenerated. The techniques described here make use of the cost effectiveness of working on chick embryos, the ease of obtaining embryos, and good exo development of tissue explants.Understanding avian inner ear hairs development and regeneration can provide important insights into hearing loss and potential therapies, and explant culture can be important for evaluating the ototoxic effects of various drugs. Before starting the experiment, procure freshly laid eggs, and clean them with 70%ethanol to prevent contamination. Incubate the eggs for 3.5 to 4 days, at 37 to 38 degrees Celsius with 45%humidity.After incubation, reposition the embryo to the top of the yolk, by placing an egg on its side for five minutes. Then, use forceps to make a small hole at the top and blunt end of the egg for a 21 gauge needle to pass through. Using a five milliliter syringe and a 21 gauge needle, remove two milliliters of the albumin from a hole at the blunt end of the egg.Cover the hole at the blunt end using clear tape. To make the egg window affix the clear tape to the top of the egg shell. Hold the needles from microinjection from standard glass capillaries using a vertical pipette puller.After pulling, break off the capillary tip using fine forceps to obtain a tip diameter of approximately 50 micrometers with a tapered end. For the gene knockout experiment, mix the three constructs, namely the guide plasmid, pcU6.1sgRNA, T2KeGFP, T2TP in a one-to-one-to-one ratio with one microgram of SP Cas9 protein, 30%sucrose, and 0.1%fast green dye, and a final volume of 10 microliters. While electroporating multiple plasmids, ensure the final concentration of DNA is at least four micrograms per microliter.With the help of springbow scissors cut open around a two centimeter long and 1.5 centimeter wide window, and expose the embryo. Then use forceps to open the chorionic membranes overlying the embryo, allowing access to the embryo. Inject around 200 nanoliter volume of DNA solution mix to fill the otic vesicle.To determine the guide RNA efficiency perform a T7 endonuclease assay. Add 0.719%saline drops to the embryo to lower the electric resistance, and prevent overheating. Next, place the positive electrode through the hole made at the blunt side of the egg, and maneuver the electrode so that it is under the yolk.Place the negative electrode over the filled otocyst. To transfect the plasmid into the otic vesicle with electroporation, use a square pulse generator, and apply five pulses of 25 volts for 100 milliseconds each, 50 milliseconds apart. Determine the conditions empirically based on an individual electroporation set up.After electroporation, hydrate the embryo by adding a few drops of 0.719%saline. Reseal the egg with clear tape, and return to the humidified incubator at 37 to 38 degrees Celsius for further incubation. Disinfect the surgical table, microscope stage, and surrounding area using 70%ethanol and heat, or alcohol sterilize the micro dissection equipment, including minimally springbow scissors, micro curet, and two pairs of fine forceps.Prepare the dissection plates including a glass Petri dish with a black silicone base, a 90 millimeter plastic Petri dish, and a 60 millimeter Petri dish. Keep chilled PBS or Hanks'balanced salt solution also known as HBSS ready for dissections. Gently crack the egg into the 90 millimeter Petri dish.Then identify the outer ear of the chick, and transfer the head to a 60 millimeter Petri dish filled with ice cold PBS. Next, orient the embryo with the top of the beak facing inside, and hold the beak using one of the number five forceps. Scoop out the eyes using the second number five forceps.Then, from rostral to caudal, cut along the skull along its midline, and scoop out the brain. Add more ice cold PBS, or HBSS, and locate the two otoliths of the lagena as shiny structures at the end of the cochlear duct, and close to the midline. To isolate two inner ears, cut between the two lagenas, and well above and below the region.Then under oblique lighting visualize the outline of the inner ear, and remove extraneous tissue and the vestibule. Transfer the isolated cochlea to a black silicone base plate with ice cold PBS. Peel away the cartilaginous cochlear capsule using number five forceps to obtain the cochlear duct.Then locate the undulated layer or tegmentum of the cochlear duct, and remove it using number 55 forceps to expose the basilar papilla or BP.Next, remove the tectorial membrane to expose hair cells and supporting cells using number 55 forceps. For membrane culture of the basilar papilla, take a six well tissue culture plate, and arrange one culture membrane insert per well. Draw up some media in a 200 microliter pipette, and then aspirate the dissected basilar papilla explant with one X HBSS buffer.Transfer the explant onto a membrane, and orient it so that the basilar papilla faces upward, and the hair and support cells are visible from the top. Once the explant is positioned aspirate the HBSS buffer slowly from the culture membrane surface. In this process the explant will attach to the culture membrane.Fill up the well of the six well plate by adding 1.2 milliliters of dulbecco's modified eagle medium, or DMEM culture media, between the membrane insert and the well wall. To prepare the collagen culture of the cochlear duct add three drops of freshly prepared collagen mixture into each well of a four well plate, and transfer dissected cochlear duct to each collagen drop. Incubate the plate for 10 minutes at 37 degrees Celsius, and 5%carbon dioxide to cure the collagen matrix.For a small molecule treatment of the cultures, replace the culture media with 700 microliters of media supplemented with the pharmacological modulator, such as penicillin, and incubate the plates as demonstrated before. Replace 50%of the culture media every day. After appropriate incubation time, remove the culture media, and use the explants for downstream assays.In the electroporation setup the correct electrode positioning resulted in higher GFP expression in the inner ear in both vestibular organs, and auditory basilar papilla confirming transfection. CRISPR Cas9 mediated Atoh1 gene knockout in inner ear, resulted in loss of hair cells. Atoh1 gene knockout via an ovo-electroporation followed by incubation until E10 showed reduced hair cell development compared to empty plasmid control.Although electroporation is mosaic, control electroporated cells were able to form hair cells. In Atoh1 gRNA electroporated samples, green fluorescent protein positive cells never showed the markers of hair cell development. The organ culture of the basilar papilla in a 3D matrix, such as, collagen and stain with antibodies against hair cell antigen provided the excellent preservation of tissue morphology for up to five days.The organization of hair cells and supporting cells were maintained in these culture conditions. The organ cultures on a membrane can be maintained for up to five days while maintaining the hair bundle integrity. This can be seen in the representative image by the localization of the tip link protein, protocadherin 15.For investigating the development of the hair bundle, higher resolution imaging, such as, super resolution microscopy, or scanning electron microscopy can provide more information. Sterile conditions should be maintained throughout the procedure. While electroporating, ensure that the embryos do not dry out.When titrating pharmacological inhibitors, one may reduce the concentration to overcome any lethality. Both embryos and explants can be taken for imaging experiments. Either by performing realtime video microscoping, or static light confocal electron microscoping, as shown in the protocol.Given the ease and accessibility of using chick inner ear explants, we can use medium through proof screening to identify new molecules essential for hair cell regeneration.

in-ovo-and-ex-ovo-methods-to-study-avian-inner-ear-development

Research

JoVE Journal

Developmental Biology

2.0K vistas.  Tata Institute of Fundamental Research. La edad, la infección y los medicamentos ototóxicos pueden causar la degeneración de las células ciliadas del oído interno, lo que en nosotros conduce a la pérdida de audición. En vertebrados no mamíferos, como el pollo, las células ciliadas pueden regenerarse. Las técnicas descritas aquí hacen uso de la rentabilidad de trabajar en embriones de pollo, la facilidad de obtención de embriones y el buen desarrollo exo de los explantes de tejidos.Comprender el desarrollo y la re...