(A) Surface rendering of a 4-day-old zebrafish larva (top) and a zoom-in of the nasal cavity (bottom). (B) A representative example of a left nose marked by a red box in (A). In the maximum …
(A) Top, front and side view of the surface rendering of a zebrafish head at 4dpf (using a transgenic lines expressing Cherry in all cells, ubi:zebrabow). The approximate location of multiciliated …
(A) Schematic spectral analysis of a reference pixel. As cilia move through a pixel (black rectangle), the pixel intensity fluctuates. The Fourier transform of pixel intensity time series (top), …
(A) Ciliary beat frequency of six different fish, for left (top) and right (bottom) noses show high levels of heterogeneity. (B) Ciliary beating remains relatively constant over time. Ciliary beat …
(A–B) Cilia from individual cells beat at a similar frequency. Representative examples of the beating of one cell versus the entire multiciliated epithelium. A hspGGFF19B:UAS:GFP animal, expressing …
A grid of 16 reference pixels with equal spacing across the nose were chosen for systematic analysis. The relationship between coherence and spectral power at the frequency of the reference pixel is …
(A) Schematic representation of the adult brain explant and location of multiciliated cells on the tela choroida. (B) (Top) Peak coherence for three reference pixels (indicated with black crosses) …
(A–B) Ciliary beating frequency decreases under increasing viscosity conditions (0–2% methylcellulose) and partially recovers upon re-exposure to 0% methylcellulose (0%*). (A) Representative example …
(A) Difference probability histograms between the various viscosity conditions for the example shown in Figure 3C. (B) The fraction of synchronized pixels (coherence>0.25) increases with viscosity. …
(A-A’) Metachronal coordination observed using a conventional kymograph-based analysis. (A) A kymograph was drawn (red line in inset, representing transverse cilia beating) on a light transmission …
(A) Wave parameters, wave direction (top), and wavelength (bottom), for a representative fish over the course of 10 min. (B) Wave direction (top), and wavelength (bottom), for a representative fish …
(A–B) Neighboring pixels with similar frequency (beat frequency map, A) are segmented into frequency patches (B). (C) Phase angles are determined from Fourier transforms evaluated at the prominent …
(A–B) Wave direction (top) and wavelength (bottom) for three left (A, red) and three mirrored right (B, green) noses show asymmetry in the wave direction between the left and right noses. …
Wave parameters, including phase angles, wave direction, and wavelength, for all aligned left (A1–A2) and mirrored right (B1–B2) noses. Note that the transparency in wave direction reflects the …
Immunohistochemistry on a left nose stained for gamma-tubulin (basal body marker, red) and glutamylated tubulin (cilia marker, white) for left (n=3) and right (n=2) noses. Ciliary direction measured …
A systematic comparison of left (red) and right (green) noses (A) revealed no significant differences in the median CBF (B; left n=20; right n=24), nose (C; left n=13; right n=12) and cavity size (D;…
(A,D) Light transmission images of 4-day-old zebrafish larva left (A; n=14) or mirrored right (D; n=14) nose at ×63 magnification. Note that the images are rotated to align with the reference left …
(A) Possible traveling wave solutions in a computational model of a cilia carpet. Left: Cilia are arranged on a triangular lattice (gray dots), with three-dimensional cilia beat pattern from Parameci…
(A) Synthetic phase map of a metachronal wave with wave direction of 190º and wavelength 4 µm, represented with pixel resolution of 0.15 µm. Noise was modeled as superposition of independent Fourier …
(A) Histogram representing the CBF for all pixels and their segmentation into high and low CBF. In red are indicated the bottom 33% CBF values and in green the top 33% CBF values. (B) Map showing …
We used a binning of 0.54Hz for all our analysis due to their minimal impact and good coverage of CBF values.
From Reiten et al., 2017.
Note that a binning of 0.54Hz and minimum size of 400 pixels (9 µm2) provides the best segmentation of the ciliated epithelium with a reasonable number of patches.
Note that increasing recording length reduces the background values, but do not changes the overall coherence patterns. We recommend a duration of 30s to increase signal-to-noise ratio of the …
Each frame of the movie represents the analysis of 20s-long sliding windows. The timer indicates the center of the sliding window.
Every frame of the video corresponds to the output of a Fourier Transform calculated over a 30 s timebin.
Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
---|---|---|---|---|
Genetic reagent (zebrafish) | Et(hspGGFF19B:Gal4)Tg(UAS:gfp) | Reiten et al., 2017; Asakawa et al., 2008 | ZDB-ALT-080523–22 | |
Genetic reagent (zebrafish) | Tg(foxj1a:gCaMP6s)nw9 | This study | N/A | Trangenic zebrafish line expressing the calcium indicator GCamp6s in multiciliated cells of the nose, Jurisch-Yaksi lab, NTNU |
Genetic reagent (zebrafish) | Tg(Ubi:zebrabow) | Pan et al., 2013 | ZDB-ALT-130816–1 | |
Genetic reagent (zebrafish) | mitfab692 | Lister et al., 1999 | ZDB-ALT-010919–2 | |
Antibody | Mouse monoclonal glutamylated tubulin (GT335) | Adipogen | Cat#AG-20B-0020-C100; RRID: AB_2490210 | Dilution 1:400 |
Antibody | Rabbit polyclonal Gamma-tubulin | Thermo Fisher | Cat# PA5-34815; RRID: AB_2552167 | Dilution 1:400 |
Antibody | Rabbit Polyclonal anti beta-catenin | Cell Signalling Technologies | Cat#9562; RRID:AB_331149 | Dilution 1:200 |
Antibody | Chicken Polyclonal Anti-GFP | Abcam | Cat#ab13970; RRID:AB_300798 | Dilution 1:1,000 |
Antibody | Goat Polyclonal anti-rabbit IgG (H+L) Highly Cross-adsorbed Alexa Fluor 555 | Thermo Fisher | Cat# A32732; RRID:AB_2633281 | Dilution 1:1,000 |
Antibody | Goat Polyclonal anti-mouse IgG (H+L) Highly Cross-adsorbed Alexa Fluor 647 | Thermo Fisher | Cat#A32728; RRID:AB_2633277 | Dilution 1:1,000 |
Chemical compound, drug | Alpha-bungarotoxin | Invitrogen | Cat#BI601 | |
Chemical compound, drug | Ultrapure LMP agarose | Fisher Scientific | Cat#16520100 | |
Chemical compound, drug | DAPI | Invitrogen | Cat# D1306 | Dilution 1:1,000 |
Software, algorithm | ImageJ/Fiji | Schindelin et al., 2012 | ||
Software, algorithm | Cell counter plugin for Fiji/ImageJ | Kurt De Vos, University of Sheffield | https://imagej.net/Cell_Counter | |
Software, algorithm | BigWarp | Saalfeld lab, Janelia https://imagej.net/BigWarp; Bogovic et al., 2016 | ||
Software, algorithm | Zebrascope software in Labview | Ahrens lab, Janelia Farm; Vladimirov et al., 2014 | ||
Software, algorithm | Manta Controller | Yaksi lab, NTNU; Reiten et al., 2017 | ||
Software, algorithm | Fast Fourier Analysis | MATLAB, this paper; Jurisch-Yaksi, 2023 | https://github.com/Jurisch-Yaksi-lab/CiliaCoordination | |
Software, algorithm | Coherence analysis | MATLAB, this paper; Jurisch-Yaksi, 2023 | https://github.com/Jurisch-Yaksi-lab/CiliaCoordination | |
Software, algorithm | Wave analysis | MATLAB, this paper; Jurisch-Yaksi, 2023 | https://github.com/Jurisch-Yaksi-lab/CiliaCoordination | |
Software, algorithm | Computation model of cilia carpet | Solovev and Friedrich, 2022b; Solovev and Friedrich, 2021a; Solovev and Friedrich, 2021b; Solovev and Friedrich, 2021c | https://github.com/icemtel/reconstruct3d_opt, https://github.com/icemtel/stokes, and https://github.com/icemtel/carpet | |
Software, algorithm | ColorBrewer: Attractive and Distinctive Colormaps | Brewer, 2022; Cynthia Brewer | https://github.com/DrosteEffect/BrewerMap/releases/tag/3.2.3, GitHub. Retrieved December 4, 2022 | |
Software, algorithm | Beeswarm | Stevenson, 2019; Ian Stevenson | https://github.com/ihstevenson/beeswarm GitHub. Retrieved December 4, 2022. | |
Other | Sutter laser puller | Sutter | Model P-200 | pulling needles for injection |
Other | Pressure injector | Eppendorf | Femtojet 4i | injection of bungartoxin for paralysis |
Other | Confocal microscope | Zeiss | Examiner Z1 | confocal imaging |
Other | 20 x water immersion Plan-Apochromat NA 1 | Zeiss | 421452-9880-000 | confocal imaging |
Other | Light-sheet objective | Nikon | 20 x Plan-Apochromat, NA 0.8 | light-sheet imaging |
Other | Transmission microscope | Bresser, Olympus | transmission imaging | |
Other | Transmission microscope objective | Zeiss | 63 X, NA 0.9 | transmission imaging |