The author would like to thank Matthew Kelley, Tiziana Cogliati, Jessica Gumerson, Uwe Wolfrum, Rivka Levron, Viola Kretschmer and Zoe Mann and for their critical evaluation of the manuscript. This work was funded by the Sofja Kovalevskaya Award (Humbodlt Foundation) and the Johannes-Gutenberg University, Mainz, Germany.

Use and euthanize all animals in accordance with institutional and governmental guidelines and regulations, most commonly via CO2 inhalation and cervical dislocation.
1. Preparation of Reagents
NOTE: Prior to beginning, prepare all reagents using analytical grade chemicals. Make solutions using molecular grade distilled and deionized water unless otherwise specified.
<ol>
	<li>Phosphate buffered saline (1x&#160;PBS): Make 1 L of 1x PBS by dissolving 8g NaCl, 0.2g KCl, 1.44g Na2HPO<su...

<ol>
	<li>Waters, A. M., Beales, P. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ciliopathies:+an+expanding+disease+spectrum.">Ciliopathies: an expanding disease spectrum.</a> Pediatr Nephrol. 26, 1039-1056 (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, 7 (2012).</li><li>Ross, A. 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=Disruption+of+Bardet-Biedl+syndrome+ciliary+proteins+perturbs+planar+cell+polarity+in+vertebrates.">Disruption of Bardet-Biedl syndrome ciliary proteins perturbs planar cell polarity in vertebrates.</a> Nat Genet. 37, 1135-1140 (2005).</li><li>Ezan, J., Montcouquiol, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Revisiting+planar+cell+polarity+in+the+inner+ear.">Revisiting planar cell polarity in the inner ear.</a> Seminars in cell &amp; developmental biology. 24, 499-506 (2013).</li><li>Semenov, M. V., Habas, R., Macdonald, B. T., He, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SnapShot:+Noncanonical+Wnt+Signaling+Pathways.">SnapShot: Noncanonical Wnt Signaling Pathways.</a> Cell. 131, 1378 (2007).</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, 980-985 (2005).</li><li>Montcouquiol, 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=Identification+of+Vangl2+and+Scrb1+as+planar+polarity+genes+in+mammals.">Identification of Vangl2 and Scrb1 as planar polarity genes in mammals.</a> Nature. 423, 173-177 (2003).</li><li>May-Simera, H. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ciliary+proteins+Bbs8+and+Ift20+promote+planar+cell+polarity+in+the+cochlea.">Ciliary proteins Bbs8 and Ift20 promote planar cell polarity in the cochlea.</a> Development. 142, 555-566 (2015).</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> Nat Genet. 40, 69-77 (2008).</li><li>Lim, 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=Functional+structure+of+the+organ+of+Corti:+a+review.">Functional structure of the organ of Corti: a review.</a> Hearing research. 22, 117-146 (1986).</li><li>Nayak, G. D., Ratnayaka, H. S., Goodyear, R. J., 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=Development+of+the+hair+bundle+and+mechanotransduction.">Development of the hair bundle and mechanotransduction.</a> The International journal of developmental biology. 51, 597-608 (2007).</li><li>Denman-Johnson, K., 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=Establishment+of+hair+bundle+polarity+and+orientation+in+the+deveoping+vestibular+system+of+the+mouse.">Establishment of hair bundle polarity and orientation in the deveoping vestibular system of the mouse.</a> J. Neurocytol. , 821-835 (1999).</li><li>Sobkowicz, H. M., Slapnick, S. M., August, B. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+kinocilium+of+auditory+hair+cells+and+evidence+for+its+morphogenetic+role+during+the+regeneration+of+stereocilia+and+cuticular+plates.">The kinocilium of auditory hair cells and evidence for its morphogenetic role during the regeneration of stereocilia and cuticular plates.</a> Journal of neurocytology. 24, 633-653 (1995).</li><li>Denman-Johnson, K., 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=Establishment+of+hair+bundle+polarity+and+orientation+in+the+developing+vestibular+system+of+the+mouse.">Establishment of hair bundle polarity and orientation in the developing vestibular system of the mouse.</a> Journal of neurocytology. 28, 821-835 (1999).</li><li>van Dam, T. 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=The+SYSCILIA+gold+standard+(SCGSv1)+of+known+ciliary+components+and+its+applications+within+a+systems+biology+consortium.">The SYSCILIA gold standard (SCGSv1) of known ciliary components and its applications within a systems biology consortium.</a> Cilia. 2, 7 (2013).</li><li>Blacque, O. E., Sanders, A. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Compartments+within+a+compartment:+what+C.+elegans+can+tell+us+about+ciliary+subdomain+composition,+biogenesis,+function,+and+disease.">Compartments within a compartment: what C. elegans can tell us about ciliary subdomain composition, biogenesis, function, and disease.</a> Organogenesis. 10, 126-137 (2014).</li><li>Wallingford, J. B., Mitchell, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Strange+as+it+may+seem:+the+many+links+between+Wnt+signaling,+planar+cell+polarity,+and+cilia.">Strange as it may seem: the many links between Wnt signaling, planar cell polarity, and cilia.</a> Genes &amp; development. 25, 201-213 (2011).</li><li>Borovina, A., Ciruna, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=IFT88+plays+a+cilia-+and+PCP-independent+role+in+controlling+oriented+cell+divisions+during+vertebrate+embryonic+development.">IFT88 plays a cilia- and PCP-independent role in controlling oriented cell divisions during vertebrate embryonic development.</a> Cell reports. 5, 37-43 (2013).</li><li>Huang, P., Schier, A. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dampened+Hedgehog+signaling+but+normal+Wnt+signaling+in+zebrafish+without+cilia.">Dampened Hedgehog signaling but normal Wnt signaling in zebrafish without cilia.</a> Development. 136, 3089-3098 (2009).</li><li>Ocbina, P. J., Tuson, M., Anderson, K. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Primary+cilia+are+not+required+for+normal+canonical+Wnt+signaling+in+the+mouse+embryo.">Primary cilia are not required for normal canonical Wnt signaling in the mouse embryo.</a> PloS one. 4, e6839 (2009).</li><li>Jones, C. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Scanning+electron+microscopy:+preparation+and+imaging+for+SEM.">Scanning electron microscopy: preparation and imaging for SEM.</a> Methods Mol Biol. 915, 1-20 (2012).</li><li>Curtin, J. 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=Mutation+of+Celsr1+disrupts+planar+polarity+of+inner+ear+hair+cells+and+causes+severe+neural+tube+defects+in+the+mouse.">Mutation of Celsr1 disrupts planar polarity of inner ear hair cells and causes severe neural tube defects in the mouse.</a> Current biology : CB. 13, 1129-1133 (2003).</li><li>Wang, Y., Guo, N., Nathans, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+role+of+Frizzled3+and+Frizzled6+in+neural+tube+closure+and+in+the+planar+polarity+of+inner-ear+sensory+hair+cells.">The role of Frizzled3 and Frizzled6 in neural tube closure and in the planar polarity of inner-ear sensory hair cells.</a> The Journal of neuroscience : the official journal of the Society for Neuroscience. 26, 2147-2156 (2006).</li><li>Montcouquiol, M., Jones, J. M., Sans, N. <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+planar+polarity+proteins+in+mammalian+cochlea.">Detection of planar polarity proteins in mammalian cochlea.</a> Methods Mol Biol. 468, 207-219 (2008).</li><li>May-Simera, H., 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=Examining+planar+cell+polarity+in+the+mammalian+cochlea.">Examining planar cell polarity in the mammalian cochlea.</a> Methods Mol Biol. 839, 157-171 (2012).</li><li>Yin, H., Copley, C. O., Goodrich, L. V., Deans, 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=Comparison+of+phenotypes+between+different+vangl2+mutants+demonstrates+dominant+effects+of+the+Looptail+mutation+during+hair+cell+development.">Comparison of phenotypes between different vangl2 mutants demonstrates dominant effects of the Looptail mutation during hair cell development.</a> PloS one. 7, e31988 (2012).</li><li>Rachel, R. 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=Combining+Cep290+and+Mkks+ciliopathy+alleles+in+mice+rescues+sensory+defects+and+restores+ciliogenesis.">Combining Cep290 and Mkks ciliopathy alleles in mice rescues sensory defects and restores ciliogenesis.</a> J Clin Invest. 122, 1233-1245 (2012).</li><li>Jagger, 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=Alstrom+Syndrome+protein+ALMS1+localizes+to+basal+bodies+of+cochlear+hair+cells+and+regulates+cilium-dependent+planar+cell+polarity.">Alstrom Syndrome protein ALMS1 localizes to basal bodies of cochlear hair cells and regulates cilium-dependent planar cell polarity.</a> Human molecular genetics. 20, 466-481 (2011).</li><li>Collin, G. 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=The+Alstrom+Syndrome+Protein,+ALMS1,+Interacts+with+alpha-Actinin+and+Components+of+the+Endosome+Recycling+Pathway.">The Alstrom Syndrome Protein, ALMS1, Interacts with alpha-Actinin and Components of the Endosome Recycling Pathway.</a> PloS one. 7, e37925 (2012).</li><li>Copley, C. O., Duncan, J. S., Liu, C., Cheng, H., Deans, 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=Postnatal+refinement+of+auditory+hair+cell+planar+polarity+deficits+occurs+in+the+absence+of+Vangl2.">Postnatal refinement of auditory hair cell planar polarity deficits occurs in the absence of Vangl2.</a> The Journal of neuroscience : the official journal of the Society for Neuroscience. 33, 14001-14016 (2013).</li><li>Sorusch, N., Wunderlich, K., Bauss, K., Nagel-Wolfrum, K., Wolfrum, U. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Usher+syndrome+protein+network+functions+in+the+retina+and+their+relation+to+other+retinal+ciliopathies.">Usher syndrome protein network functions in the retina and their relation to other retinal ciliopathies.</a> Advances in experimental medicine and biology. 801, 527-533 (2014).</li><li>Hebert, J. M., McConnell, S. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Targeting+of+cre+to+the+Foxg1+(BF-1)+locus+mediates+loxP+recombination+in+the+telencephalon+and+other+developing+head+structures.">Targeting of cre to the Foxg1 (BF-1) locus mediates loxP recombination in the telencephalon and other developing head structures.</a> Dev Biol. 222, 296-306 (2000).</li><li>Willott, J. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chapter+8,+Measurement+of+the+auditory+brainstem+response+(ABR)+to+study+auditory+sensitivity+in+mice.">Chapter 8, Measurement of the auditory brainstem response (ABR) to study auditory sensitivity in mice.</a> Current protocols in neuroscience. , Unit8 21B (2006).</li><li>Martin, G. K., Stagner, B. B., Lonsbury-Martin, B. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chapter+8,+Assessment+of+cochlear+function+in+mice:+distortion-product+otoacoustic+emissions.">Chapter 8, Assessment of cochlear function in mice: distortion-product otoacoustic emissions.</a> Current protocols in neuroscience. , Unit8 21C (2006).</li><li>Finetti, 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=Intraflagellar+transport+is+required+for+polarized+recycling+of+the+TCR/CD3+complex+to+the+immune+synapse.">Intraflagellar transport is required for polarized recycling of the TCR/CD3 complex to the immune synapse.</a> Nature cell biology. 11, 1332-1339 (2009).</li><li>Sedmak, T., Wolfrum, U. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Intraflagellar+transport+molecules+in+ciliary+and+nonciliary+cells+of+the+retina.">Intraflagellar transport molecules in ciliary and nonciliary cells of the retina.</a> J Cell Biol. 189, 171-186 (2010).</li><li>Yuan, S., Sun, Z. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Expanding+horizons:+ciliary+proteins+reach+beyond+cilia.">Expanding horizons: ciliary proteins reach beyond cilia.</a> Annual review of genetics. 47, 353-376 (2013).</li><li>Tarchini, B., Jolicoeur, C., Cayouette, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+molecular+blueprint+at+the+apical+surface+establishes+planar+asymmetry+in+cochlear+hair+cells.">A molecular blueprint at the apical surface establishes planar asymmetry in cochlear hair cells.</a> Developmental cell. 27, 88-102 (2013).</li><li>Ezan, 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=Primary+cilium+migration+depends+on+G-protein+signalling+control+of+subapical+cytoskeleton.">Primary cilium migration depends on G-protein signalling control of subapical cytoskeleton.</a> Nature cell biology. 15, 1107-1115 (2013).</li></ol>

The author declares no competing financial interests.

When preparing cochlear tissue for analysis, there are a few key points to bear in mind. Firstly, differences in genetic background can modify the cochlear phenotype, making it necessary to analyze and compare only littermate controls. Secondly, complete removal of the tectorial membrane is required to obtain the best images with immunohistochemistry and is essential for SEM. The tectorial membrane is an opaque structure and can obscure the cells of the sensory epithelium directly beneath it, making imaging more challeng...

Primary cilia are long microtubule-based appendages that extend from the surface of most mammalian cells. Primary cilia are often confused with motile cilia, of which there are always multiple per cell, and whose purpose is to move fluid across membrane surfaces. Primary cilia, in contrast, adopt sensory roles and are consequently also referred to as sensory cilia. Once long forgotten, this organelle has recently been &#39;rediscovered&#39; as a result of its association with a multitude of human genetic diseases1. Ideally positioned as a signaling organelle, the primary cilium has been shown to regulate numerous signaling pathways, many of which are important not only in tissue homeostasis and disease, but also during development2.
One of the first signaling pathways shown to be associated with cilia dysfunction was the non-canonical Wnt signaling pathway, known also as the planar cell polarity (PCP) pathway3. This signaling cascade initially identified in Drosophila, is critical for embryogenesis; in particular for convergence and extension processes and for the correct orientation of cells in the plane of epithelia4. The sequential signaling of a core set of regulatory proteins translates directional cues which ultimately lead to cytoskeletal rearrangements and result in the coordinated polarization of epithelial cells in a plane5. The process of convergence and extension is absolutely required for the cochlear duct to elongate and for correct cellular patterning6. As this is regulated via activation of the PCP pathway, one of the most striking phenotypes of cochlea PCP mutants is a shortened cochlear duct with disorganized sensory epithelia7. Similarly, mouse mutants, which lack cilia, also exhibit such a convergence and extension phenotype8,9, though precisely how this is regulated remains to be elucidated.
Because convergence and extension processes are critical for the outgrowth of the cochlear duct, and cellular patterning of the sensory epithelia within the cochlear duct, the developing cochlea is an ideal organ in which to examine PCP signaling during vertebrate development. The organ of Corti, the term given to the specialized sensory epithelium that lines the cochlear duct, is comprised of non-sensory supporting cells and mechanosensory hair cells which must be uniformly oriented for the cochlea to function10. The mechanosensory hair cells are so called because of the stereociliary bundles that extend from the cuticular plate (apical surface) of each sensory hair cell11. These act as primary transducers of mechanosensation and despite their nomenclature as stereocilia, are actually comprised of modified actin filament-based microvilli. Within each chevron-shaped hair bundle, three rows of stereocilia are organized in a highly ordered and regular pattern in a stair case-like manner. Real microtubule-based cilia, termed kinocilia, are required for the development and orientation of the stereociliary bundles12. Upon each hair cell, one single kinocilium is physically attached to the stereocilia bundle, located centrally adjacent to the tallest row of stereocilia. The precise function of the kinocilium is unclear, and one hypothesis is that the kinocilium &#39;pulls&#39; the stereocilia into shape as they mature from microvilli12. In vertebrates, kinocilia in the cochlea are only present transiently and retract from the hair cells in mice prior to the onset of hearing11,13,14.
Complete loss of cilia in the developing cochlea results in severely shortened cochlear ducts, mis-formed and mis-oriented stereociliary bundles, as well as mis-positioned basal bodies8,9. A functional cilium is not just comprised of the ciliary axoneme. Many proteins associated with cilia function occur in complexes localized to cilia-related subdomains such as the basal body, transition zone, or ciliary axoneme15. The basal body, derived from the mother centriole of the centrosome, is also a microtubule-organizing center for microtubules extending away from the cilium into the cell body and can regulate intracellular trafficking as well as ciliary trafficking. The ciliary transition zone is another region where ciliary function is regulated in terms of organizing import and export of ciliary compounds16.
Multiple studies have identified a connection between cilia and non-canonical Wnt (PCP signaling), though the precise mechanism is unclear17. Redundancy of ciliary and PCP genes and the sensitivity of cell polarity to generalized cellular abnormalities, make it difficult to directly link a mutation to PCP-specific deficits. One of the read outs of PCP signaling is the positioning of the basal body and primary cilium, therefore segregating the primary from the secondary defects is challenging. Some studies in zebrafish and mouse mutants have suggested no connection between cilia and Wnt signaling18-20. Discrepancies in the data may reflect species, tissue, or temporal-dependent differences in ciliary contributions towards Wnt signaling. Furthermore, normal Wnt responsiveness might be retained if basal bodies remain functional. A deeper insight into the role of ciliary proteins in cellular signaling pathways and other biological phenomena is crucial for our understanding of cellular and developmental biology, as well as for the development of targeted treatment strategies.

<table>
	<tbody>
		<tr>
			<td>Tools/Equipment</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Silicone elastomere - Sylgard 184</td>
			<td>Sigma-Aldrich</td>
			<td>761028-5EA</td>
			<td>See Note 2</td>
		</tr>
		<tr>
			<td>Micro dissecting scissors-straight blade</td>
			<td>Various</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Fine forceps (no. 5 and 55) and blunt forceps</td>
			<td>Various</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Dissecting microscope.</td>
			<td>Various</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Uncoated glass microscope slides</td>
			<td>Various</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Microscope cover slips (22 mm &#215; 40 mm &#215; 0.15 mm)</td>
			<td>Various</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Transfer pipettes</td>
			<td>Various</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Minutien pins</td>
			<td>&#160;Fine Science Tools</td>
			<td>26002-10</td>
			<td></td>
		</tr>
		<tr>
			<td>SEM sample holder</td>
			<td>tousimis</td>
			<td>8762</td>
			<td></td>
		</tr>
		<tr>
			<td>Scanning electron microscopy studs</td>
			<td>TED PELLA</td>
			<td>16111</td>
			<td></td>
		</tr>
		<tr>
			<td>PELCO Tabs: Carbon adhesive</td>
			<td>TED PELLA</td>
			<td>16084-3</td>
			<td></td>
		</tr>
		<tr>
			<td>Fluorescent Microscope</td>
			<td>Various</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Critical Point Dryer</td>
			<td>Various</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Scanning Electron Microscope</td>
			<td>Various</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Glass microscope slides</td>
			<td>Various</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Glass coverslips</td>
			<td>Various</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Kimwipe Tissue&#160;</td>
			<td>Various</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Fine Paint Brush</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Reagents</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>1&#215; Phosphate buffered saline (PBS)</td>
			<td>Gibco/Life Technologies</td>
			<td>10010023</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraformaldehyde&#160; (PFA) (EM Grade Required for EM)</td>
			<td>Various</td>
			<td></td>
			<td>Prepare a 4% solution in 1&#215; PBS made fresh each time. EM Grade Required for EM.</td>
		</tr>
		<tr>
			<td>2.5% Glutaraldehyde Grade1</td>
			<td>Sigma-Aldrich</td>
			<td>G5882</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris-HCl (pH 7.5)</td>
			<td>Various</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Various</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>CaCl 2</td>
			<td>Various</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Triton X-100</td>
			<td>Various</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Normal Goat Serum</td>
			<td>Various</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>AffiniPure Fab Fragment Donkey Anti-Mouse IgG (H+L)</td>
			<td>Jackson ImmunoResearch</td>
			<td>715-007-003</td>
			<td></td>
		</tr>
		<tr>
			<td>Fluoromount-G Mounting media</td>
			<td>SouthernBiotech</td>
			<td>0100-01</td>
			<td></td>
		</tr>
		<tr>
			<td>10&#215; Hanks&#8217; Balanced Salt Solution (HBSS)</td>
			<td>Gibco/Life Technologies</td>
			<td>14065</td>
			<td></td>
		</tr>
		<tr>
			<td>Hepes</td>
			<td>Gibco/Life Technologies</td>
			<td>15630-080</td>
			<td></td>
		</tr>
		<tr>
			<td>Osmium tetroxide (OsO4 )</td>
			<td>Sigma-Aldrich/Fluka Analytical</td>
			<td>75632</td>
			<td></td>
		</tr>
		<tr>
			<td>Tannic acid</td>
			<td>Sigma-Aldrich</td>
			<td>403040</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethanol 200 proof</td>
			<td>Various</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Antibodies</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>anti Arl13b</td>
			<td>Protein Tech</td>
			<td>17711-1-AP</td>
			<td>Suggested concentration 1:1000</td>
		</tr>
		<tr>
			<td>anti acetylated tubulin (611-B1)</td>
			<td>Sigma-Aldrich</td>
			<td>T6793</td>
			<td>Suggested concentration 1:800</td>
		</tr>
		<tr>
			<td>anti gamma tubulin (GTU-88)</td>
			<td>Sigma-Aldrich</td>
			<td>T6557</td>
			<td>Suggested concentration 1:200</td>
		</tr>
		<tr>
			<td>anti Zo_1&#160;</td>
			<td>Invitrogen</td>
			<td>40-2300</td>
			<td>Suggested concentration 1:500</td>
		</tr>
		<tr>
			<td>Myosin VI</td>
			<td>Proteus Biosciences</td>
			<td>25-6791</td>
			<td>Suggested concentration 1:1000</td>
		</tr>
		<tr>
			<td>Myosin VIIa</td>
			<td>Proteus Biosciences</td>
			<td>25-6790</td>
			<td>Suggested concentration 1:1000</td>
		</tr>
		<tr>
			<td>anti Vangl2</td>
			<td>Merk Millipore</td>
			<td>ABN373</td>
			<td>Suggested concentration 1:250</td>
		</tr>
		<tr>
			<td>anti G&#945;i3</td>
			<td>Sigma-Aldrich</td>
			<td>G4040</td>
			<td>Suggested concentration 1:250</td>
		</tr>
		<tr>
			<td>Alexa Fluor&#174; 488 Phalloidin</td>
			<td>Invitrogen/Life Technologies</td>
			<td>A12379</td>
			<td>Suggested concentration 1:300-1000</td>
		</tr>
		<tr>
			<td>Alexa Fluor&#174; 568 Phalloidin</td>
			<td>Invitrogen/Life Technologies</td>
			<td>A12380</td>
			<td>Suggested concentration 1:300-1000</td>
		</tr>
	</tbody>
</table>

evaluation of planar-cell-polarity phenotypes in ciliopathy mouse mutant cochlea

In recent years, primary cilia have emerged as key regulators in development and disease by influencing numerous signaling pathways. One of the earliest signaling pathways shown to be associated with ciliary function was the non-canonical Wnt signaling pathway, also referred to as planar cell polarity (PCP) signaling. One of the best places in which to study the effects of planar cell polarity (PCP) signaling during vertebrate development is the mammalian cochlea. PCP signaling disruption in the mouse cochlea disrupts cochlear outgrowth, cellular patterning and hair cell orientation, all of which are affected by cilia dysfunction. The goal of this protocol is to describe the analysis of PCP signaling in the developing mammalian cochlea via phenotypic analysis, immunohistochemistry and scanning electron microscopy. Defects in convergence and extension are manifested as a shortening of the cochlear duct and/or changes in cellular patterning, which can be quantified following dissection from developing mouse mutants. Changes in stereociliary bundle orientation and kinocilia length or positioning can be observed and quantitated using either immunofluorescence or scanning electron microscopy (SEM). A deeper insight into the role of ciliary proteins in cellular signaling pathways and other biological phenomena is crucial for our understanding of cellular and developmental biology, as well as for the development of targeted treatment strategies.

Cochlea Dissection and Tissue Preparation
After removal of the brain, post mid-line sagittal dissection of a P0 mouse head, the bony labyrinth, seen from behind, can be visualized (Figure 1A, white arrow) and removed. Figure 1B shows the isolated bony labyrinths with the cochlear hair facing upwards, ventral, (left) and from behind, dorsal (right). The white arrow points to the ...

Watch this Scientific Journal Video about Evaluation of Planar-Cell-Polarity Phenotypes in Ciliopathy Mouse Mutant Cochlea at JoVE.com

Evaluation of Planar-Cell-Polarity Phenotypes in Ciliopathy Mouse Mutant Cochlea

Primary cilia influence various signaling pathways. The mammalian cochlea is ideal for examining planar cell polarity (PCP) signaling. Cilia dysfunction affects cochlear outgrowth, cellular patterning and hair cell orientation, readouts of PCP. Our goal is to analyze PCP signaling in mouse cochlea via phenotypic analysis, immunohistochemistry and scanning electron microscopy.

In recent years, primary cilia have emerged as key regulators in development and disease by influencing numerous signaling pathways. One of the earliest ...

The overall goal of this protocol is to examine ciliary mutant mouse cochlea for planar-cell-polarity phenotypes. These techniques allow for an extensive detailing of the cochlear phenotype, which will lead to a more precise understanding of the ciliary involvement in establishing vertebrate PCP signaling. The main advantage of this protocol is that once mastered, the dissected cochlear epithelia can be used for a variety of different types of phenotypic analysis.After preparing reagents and tissue from experimental animals, at developmental stage E16.5 to p3, use a scalpel blade or a small pair of scissors to dissect the head along the sagittal midline beginning at the nose and extending cotyle. Remove the brain from each half of the skull with a pair of forceps. Then, identify the temporal bones which contain the developing bony labyrinths of the inner ear.While working with the sample under a dissection microscope, use a pair of forceps to prize the bony labyrinths away from the skull by running the forceps gently underneath the bony labyrinths. Following dissection, use the tip of the dissecting forceps to clear the oval and round windows and make a small hole in the apex of the cochlear spiral. Next, fix the bony labyrinths in 1.5 milliliters of 4%paraformaldehyde for five minutes on ice to allow for easy removal of the tectorial membrane.Now, place the bony labyrinths in a black silicone elastomer-coated dissecting dish containing PBS to facilitate dissection. Use number five forceps to remove the outer cartilage, exposing the cochlear duct. Start at the oval window, insert the bottom tip of the forceps into the oval window, and gently pry open the cartilage, slowly moving upwards towards the apex.Next, use a fine pair of forceps to pinch the Reissner's membrane at the base of the cochlear duct, and peel it off in an upward motion. Visualize the dorsal aspect of the cochlear duct, including the sensory epithelium. Then, use number 55 forceps to pinch the tectorial membrane at the base of the cochlea, and peel upwards towards the apex.Complete removal of the tectorial membrane is required to obtain the best images with immunohistochemistry, and is essential for scanning electron microscopy. After exposing the organ of Corti, further fix the tissue and perform immunohistochemistry, or prepare for scanning electron microscopy, as detailed in the written portion of the protocol. After the tissue has been stained, place the sample in a black silicone elastomer dish, containing PBS.Using fine forceps, remove the vestibular region from the cochlear spiral. Then, very carefully remove the underlying cartilage and mesenchyme from the cochlear spiral. The remaining cochlear spiral contains the inner sulcus, organ of Corti, and outer sulcus.Transfer the cochlear spiral into a drop of PBS placed on a microscope slide. Wick away the PBS with an absorbent tissue or piece of filter paper, and gently re-position the cochlear spiral if the epithelia has shifted and overlaps onto itself. Add a drop of mounting media directly onto the cochlea sample, and gently place a cover slip directly onto the sample, taking care to avoid air bubbles.Use an epifluorescent or laser scanning confocal microscope equipped with high magnification and high numerical aperture objectives, to capture images of the apical surface of the cochlear hair cell. Use lower objectives to take overlapping images of the cochlear spiral to quantify the length of the cochlear duct. The following images show immunofluorescent staining of basal turn, post-natal day one type cochlea.Phalloidin labels filamentous actin in stereocilia, and cortical actin at the cell periphery. Myosin VIIA is a marker for inner and outer hair cells. ZO_1 labels the tight junctions in between cells, making it a great marker to distinguish cell boundaries.Acetylated alpha-tubulin is used as a marker for the kinocilium at the vertex of the bundle, as indicated by the white arrow. Internal microtubules are also labeled by acetylated alpha-tubulin, which are particularly abundant in pillar cells, as indicated by the white asterisks. This image of dissected cochlear ducts at E18.5, stained with acetylated tubulin, demonstrates marked shortening of IFT20 conditional knockout cochlear ducts compared to control.The following image is a whole-mount preparation of basal cochlear turn, in a BBS8 knockout mice, at post natal day zero. Stereociliary bundles in BBS8 knockout cochleae are variably rotated, as indicated by the right arrow, or flattened and mis-localized, as indicated the middle arrow. The kinocilia are mis-localized, or axonemes are missing, as indicated by the left arrow.When preparing cochlear phenotype for analysis, it's important to remember that differences in genetic background can modify the cochlear phenotype. Therefore, it's important to use littermate controls for analysis. Further analyses include audiometric testing and culturing of cochlear explants, which allows for treatment with various signaling activators or inhibitors, thereby contributing to mechanistic understanding of developmental processes involved.After watching this video, you should have a good understanding of how to prepare cochlear tissue for analyzing the role of ciliary components and their distinct effects on PCP signaling.

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10.3K Görüntüleme.  Johannes Gutenberg-Universität Mainz. The overall goal of this protocol is to examine ciliary mutant mouse cochlea for planar-cell-polarity phenotypes. These techniques allow for an extensive detailing of the cochlear phenotype, which will lead to a more precise understanding of the ciliary involvement in establishing vertebrate PCP signaling. The main advantage of this protocol is that once mastered, the dissected cochlear epithelia can be used for a variety of different types of phenotypic analysis.After preparing reagen...