(A) Illustration of the adult human inner ear showing cochlea, semicircular canals (SCCs), and endolymphatic duct and sac (ES, red arrowhead) and their organization of tissue (green), endolymph …
(A) ES morphogenesis begins at 36-hr post fertilization (hpf) as an evagination in the dorsal epithelial wall of the otic vesicle (green arrowhead points to nascent ES, see also Video 1). Scale bar …
(A) Illustration of larval zebrafish highlighting sagittal plane of image acquisition (blue square). (B) Time points of individual sagittal slices of raw data from 3D time course (endolymph labeled …
(A) Lateral view of wild-type and lmx1bbjj410/jj410 mutant ears imaged by bright-field microscopy at 80 hpf, asterisk labels greatly enlarged mutant ES. Scale bar, 100 μm. (B) Slices from 3D …
Quantification of segmented ES volumes (primary axis, green) and leak in fluorescence (secondary axis, magenta) from an additional time-lapse of an lmx1bbjj410/jj410 mutant (see Video 6).
(A) Select images from serial-section scanning electron microscopy of a 5.5 dpf zebrafish’s right inner ear. Dorsal is up, lateral left, medial right, ventral down, anterior top, and posterior …
(A) Illustration of AO-LLSM mounting strategy for imaging ES using volcano mount. (B) Representative LLSM images without adaptive optics (AO), with AO, and with AO followed by deconvolution. (C) …
(A) 3D rendering of AO-LLSM data, three sequential time points 30 s apart (membrane citrine depicted in grey, Video 10). Bright patches on surface move (red, blue, green arrows). (B) Consecutive 3D …
(A,C) 3D renderings of segmented cells and ES lumen. (A) Dorsal view. (B) Raw data of membrane citrine AO-LLSM data spanning same time range as in (A). First and last time point are overlaid with …
Video begins with schematic of experimental set-up and context of the presented field of view. Then, an annotated time point is presented of the upcoming video. The presented video is of a sagittal …
Video begins with an illustration depicting the context of the presented field of view, which is a sagittal slice encompassing the developing ES from a 4D time course. Then, an annotated time point …
A video of two time courses, sagittal slices from 4D datasets, quantified in Figure 1—figure supplement 1B (left) and Figure 1—figure supplement 1C (right). Fluorescence from membrane citrine, shown …
Time course of otic vesicle injected with 3 kDa dextran-Texas red at 55 hpf. Panels are transverse volumes of same time course. Left, labeled endolymph presented in yellow. Right, labeled endolymph …
Time course of otic vesicle injected with 3 kDa dextran-Texas red at 55 hpf, and perilymph labeled with 10 kDa dextran- Alexa Fluor 488. First three panels are transverse volumes while the fourth is …
Video of sagittal slice from 4D dataset of lmx1bbjj410/jj410 mutant- quantified in Figure 3D. Fluorescence from membrane citrine shown in green. Perilymph highlighted with fluorescence from 3 kDa …
Video of sagittal slice from 4D dataset of lmx1bbjj410/jj410 mutant- quantified in Figure 3—figure supplement 1. Fluorescence from membrane citrine shown in green. Perilymph highlighted with …
Sections are 60 nm thick and color overlays highlight cells with lamellar barriers or basal lamellae. Second half explores organization of cells in space using cell segmentations.
15 sequential slices (300 nm slice spacing) were combined as a maximum intensity projections (MIP) to make a 4.5 μm slab. 7 sequential 4.5 μm slabs were tiled to consolidate the presentation of a …
An anterior view on the left and dorsal view on the right. Segmented ES lumen is colored magenta. All other objects are ES cells. Labeled cubes indicate body axes. Same time course as Video 9.
The video begins with an annotated time point from the 3D rendering of signal from an AO-LLSM time course. A yellow dotted line highlights the rendered ES, green arrows point to basal lamellae, and …
Seven sequential slices (600 nm slice spacing) were combined as a maximum intensity projections (MIP) to make a 4.2 μm slabs. 4 sequential 4.2 μm slabs, starting with the distal tip of the ES on the …
Embryos were heat shocked at 55 hpf. At 57 hpf, α-bungarotoxin protein and 3 kDa dextran-Texas red were injected into the hearts. Time course began at 58 hpf, membrane citrine is green, perilymph is …
Four embryos with 3 kDa dextran-Texas red injected into the otic vesicle. First three are 3-D rendered volumes from a dorsal view. The fourth fish is 3-D rendered from a transverse view (as in Videos…
Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
---|---|---|---|---|
Strain, strain background (Danio rerio) | AB | ZIRC, Eugene, OR | ZFIN ID: ZDB-GENO-960809–7 | |
Strain, strain background (Danio rerio) | lmx1bb mutant, ale uchu (jj410 allele) | ZIRC, Eugene, OR, PMID: 17574823 | jj410; ZFIN ID: ZDB-ALT-070426–3 | Schibler and Malicki, 2007 |
Strain, strain background (Danio rerio) | Tg(actb2:mem-citrine-citrine)hm30 | Megason lab, PMID: 25303534 | hm30; ZFIN ID: ZDB-ALT-150209–1 | Xiong et al., 2014 |
Strain, strain background (Danio rerio) | Tg(actb2:mem-citrine)/(actb2:Hsa.H2b-tdTomato)hm32 | Megason lab, PMID: 27535432 | hm32; ZFIN ID: ZDB-ALT-161213–1 | Aguet et al., 2016 |
Strain, strain background (Danio rerio) | Tg(actb2:mem-citrine)/(actb2:Hsa.H2b-tdTomato)hm33 | Megason lab, PMID: 27535432 | hm33; ZFIN ID: ZDB-ALT-161213–2 | Aguet et al., 2016 |
Strain, strain background (Danio rerio) | Tg(−5.0lmx1bb:d2eEGFP)mw10 | gift from Brian Link's lab, PMID: 19500562 | mw10; ZFIN ID: ZDB-ALT-091218–2 | McMahon et al., 2009 |
Strain, strain background (Danio rerio) | Tg(actb2:mem-mcherry2)hm29 | Megason lab, PMID: 23622240 | hm29; ZFIN ID: ZDB-ALT-130625–1 | Xiong et al., 2013 |
Strain, strain background (Danio rerio) | Tg(hsp70:rac1_T17N-p2a-mem-cherry2)hm35 | Megason lab, rac1 mutant plasmid gift from Raz lab, this paper | hm35 | Kardash et al., 2010 |
Strain, strain background (Danio rerio) | Tg(elavl3:GCaMP5G)a4598 | gift from Alexander Schier's lab, PMID: 23524393 | a4598; ZFIN ID: ZDB-ALT-130924–1 | Ahrens et al., 2013 |
Strain, strain background (Danio rerio) | Tg(actb2:myl12.1-EGFP)e2212 | gift from C.P. Heisenberg's lab, PMID: 25535919 | e2212; ZFIN ID: ZDB-ALT-130108–2 | Compagnon et al., 2014 |
Strain, strain background (Danio rerio) | Tg(actb2:mCherry-Hsa.UTRN)e119 | gift from C.P. Heisenberg's lab, PMID: 25535919 | e119; ZFIN ID: ZDB-ALT-151029–2 | Compagnon et al., 2014 |
Antibody | mouse anti ZO-1 | Thermo Fisher Scientific, Waltham, MA | ZO1-1A12 | |
Antibody | rabbit anti collagen II | Abcam, Cambridge, United Kingdom | ab209865 | |
Antibody | rabbit anti laminin | Sigma-Aldrich, St. Louis, MO | L9393 | |
Recombinant DNA reagent | pet-28b-Cas9-His | gift from Alexander Schier's lab, PMID: 24873830 | addgene id: 47327 | Gagnon et al., 2014 |
Recombinant DNA reagent | pmtb-t7-alpha-bungarotoxin | Megason lab, PMID: 26244658 | addgene id: 69542 | Swinburne et al., 2015 |
Sequence-based reagent | foxi in situ probes,Danio rerio | PCRtemplate + T7 reaction (Sigma) | RefSeq:NM_181735 | Thisse and Thisse, 2014 |
Sequence-based reagent | bmp4 in situ probes, Danio rerio | PCRtemplate + T7 reaction (Sigma) | RefSeq:NM_131342 | Thisse and Thisse, 2014 |
Sequence-based reagent | lmx1bb sgRNA (exon 2), Danio rerio | annealedoligos + SP6 reaction (NEB) | GenBank:CR376762 | Gagnon et al., 2014 |
Sequence-based reagent | lmx1bb sgRNA (exon 3),Danio rerio | annealed oligos + SP6 reaction (NEB) | GenBank:CR376762 | Gagnon et al., 2014 |
Peptide, recombinant protein | cas9 protein | Megason lab | purification scheme fromGagnon et al., 2014 | |
Peptide, recombinant protein | alpha-bungarotoxin | Tocris Bioscience (Bristol, United Kingdom) | Tocris catalog number 2133 | Swinburne et al., 2015 |
Commercial assay or kit | mMessage mMachine T7 ULTRA kit | Thermo Fisher Scientific, Waltham, MA | AM1345 | |
Chemical compound, drug | Dextran, Texas Red, 3000 MW | Thermo Fisher Scientific, Waltham, MA | D-3329 | |
Chemical compound, drug | Dextran, Alexa Fluor 488, 10000 MW | Thermo Fisher Scientific, Waltham, MA | D-22913 | |
Chemical compound, drug | tricaine methanosulfate | Sigma-Aldrich, St. Louis, MO | E10521 | |
Chemical compound, drug | nonenyl succinic anhydride | Electron Microscopy Sciences, Hatfield, PA | 19050 | |
Chemical compound, drug | DMP-30 | Electron Microscopy Sciences, Hatfield, PA | 13600 | |
Chemical compound, drug | 1,2,7,8-diepoxyoctane (97%) | Sigma-Aldrich, St. Louis, MO | 139564 | |
Chemical compound, drug | Sorensen's Phosphate Buffer | Electron Microscopy Sciences, Hatfield, PA | 11600–10 | |
Chemical compound, drug | glutaraldehyde, EM grade | Electron Microscopy Sciences, Hatfield, PA | 16220 | |
Chemical compound, drug | paraformaldehyde | Electron Microscopy Sciences, Hatfield, PA | 15710 | |
Chemical compound, drug | potassium ferricyanide | Sigma-Aldrich, St. Louis, MO | 702587 | |
Chemical compound, drug | osmium tetroxide | Electron Microscopy Sciences, Hatfield, PA | 19140 | |
Chemical compound, drug | uranyl acetate | Electron Microscopy Sciences, Hatfield, PA | 22400 | |
Chemical compound, drug | maleic acid | Sigma-Aldrich, St. Louis, MO | m5757 | |
Chemical compound, drug | acetronitrile | Electron Microscopy Sciences, Hatfield, PA | 10020 | |
Chemical compound, drug | Taab 812 Resin | Marivac Ltd., Nova Scotia, Canada | ||
Software, algorithm | MovingROIExtract, convertFormat | https://github.com/krm15/AO-LLSM | ||
Software, algorithm | ConvertToMegacapture, GoFigure2ContoursToMeshes | https://github.com/krm15/GF2Exchange | ||
Software, algorithm | Itk-snap | www.itksnap.org PMID: 16545965 | Yushkevich et al., 2006 | |
Software, algorithm | Fluorender | www.sci.utah.edu/software/fluorender.html PMID:23584131 | Wan et al., 2012 | |
Software, algorithm | HandBrake | https://handbrake.fr/ | ||
Software, algorithm | LabVIEW | National Instruments | ||
Software, algorithm | MATLAB (R2014A) | www.mathworks.com | ||
Software, algorithm | ParaView | www.paraview.org | ||
Software, algorithm | GoFigure2 | Xiong et al., 2013 | ||
Software, algorithm | FIJI (imagJ) | www.fiji.sc PMID: 22743772 | Schindelin et al., 2012 | |
Software, algorithm | cellPreprocess, multiscalePlanarityAndVoting3D, DistanceFromMask, resample, MorphologicalErosionOnLabelImageFilter, SizeThreshold, MembraneSegmentation, MembraneSegmentationWithMarkersImageFilter, CellSegmentationStatistics | https://github.com/krm15/ACME/tree/MultithreadLookup | ||
Software, algorithm | Zen software | http://www.zeiss.com/microscopy/us/products/microscope-software/zen-lite.html | ||
Other | Volcano mould,‘frosted extreme detail’ | https://www.shapeways.com/, this paper | Volcano400 | |
Other | FemtoJet 4x | Eppendorf, Hamburg, Germany | 5253000017 | |
Other | Nanoject | Drummond Scientific, Broomall, PA | 3-000-204 | |
Other | Tungsten wire | Sigma-Aldrich, St. Louis, MO | 267554–9.5G |