Anderson GA , Gelens L , Baker JC , Ferrell JE .

P50 GM107615 NIGMS NIH HHS , R01 GM103787 NIGMS NIH HHS , R01 GM110564 NIGMS NIH HHS , R01 HD076839 NICHD NIH HHS

	Figure 1. Waves in Early Xenopus laevis Development The Xenopus laevis embryo undergoes multiple spatially organized and dynamic events in its early development. Sperm entry point (SEP) denotes the sperm entry point, and mpf is minutes post-fertilization. Adapted from Nieuwkoop and Faber (1994).
	Figure 2. Cell Division Waves in Three Dimensions The first 12 divisions of the X. laevis embryo are regular in time and nearly synchronous within a round of division. Deviations from synchrony take the form of a wave of divisions. (A) Top view of X. laevis embryos at the 1-, 2-, 4-, and 8-cell stage, 18°C. (B) Cell cycle periods in the top view as a function of time at 18°C. The first cell cycle is much longer and was omitted for clarity. Cell cycle periods shortened slightly through division six and then began lengthening around division 9 or 10, followed by an increase in period at divisions 11 and 12. Error bands are ± one SD. (C) Top-down view of cell division waves at 18°C. Cell division waves originated opposite the SEP and terminated near the SEP. Color scale denotes the timing of cell division, with cooler colors being earlier divisions. Contours are at two-minute intervals. (D) Top view of cell division as a function of position and time at 18°C. Lines were fit to rounds of division to illustrate their progression across the surface of the embryo in spatial waves. Centroids of parent cells were projected onto a line that runs along the direction of the division wave and plotted on the y axis. (E) Side view of X. laevis embryos at the 1-, 2-, 4-, and 8-cell stage. (F) Cell cycle periods in the side view as a function of time at 18°C. The second division is difficult to accurately score in the side view and is omitted along with the first for clarity. Trend of cell cycle periods is similar to the top view in (B) but with more variation. Error bands are ± one SD. (G) Side view of cell division waves at 18°C. Color scale and contours are as in (C). (H) Side view of cell division as a function of position and time at 18°C. Centroids of parent cells are projected onto a line that runs along the animal-vegetal axis. (I) The direction of the first cleavage plane correlates with the direction of the post-fertilization wave. (J) Cell division waves anti-correlate with the direction of the post-fertilization wave. The post-fertilization wave begins near the sperm entry point and progresses away from it. The cell division wave begins opposite the SEP and progresses toward it. A total of 47 embryos were analyzed in (I) and 92 in (J).
	Figure 3. A Temperature Gradient Reveals Lack of Coupling in Cell Divisions (A) Temperature gradient device. (B) Desynchronizing cell divisions. Embryo was initially maintained at 23°C and then a temperature gradient of 11°C–25°C was applied during the time marked by the horizontal red bar, from 70 mpf to 107 mpf. The second round of cell divisions was desynchronized as a result, with the two divisions occurring approximately 15 min apart. Temperature was then uniformly set to 18°C for the remainder of time. Subsequent divisions were labeled red (descendants of the warmed cell) and blue (descendants of the cooled cell). Vertical lines indicate average division time of each group, and gray regions indicate the difference in average division time between the groups. (C) Cell divisions in a mock-treated control embryo at 18°C. (D) The difference in average division time between descendants of cooled cells and descendants of warmed cells. These values correspond to the width of gray regions in (B). The error band is ±1 SD of the timing difference. (E) Average periods in lineages descended from the cooled cell (blue) and warmed cell (red) at the two-cell stage. Error bands are ±1 SD of the period. (F) Comparison of early- and late-division timing. Average timing differences measured at divisions two and three were compared with average timing differences measured at divisions seven and eight. For gradient embryos, timing differences were between descendants of warmed and cooled cells, and the temperature gradient was applied with different durations, ranging from 37 to 57 min (always starting at 70 mpf). For control embryos, timing differences were between descendants of the two-cell stage. Red point is the embryo in (B), (D), and (E).
	Figure 4. A Simple Model Accounts for Cell Division Waves (A) Cell-cycle periods for cells in the animal half (blue) and vegetal half (red) of nine unperturbed embryos at 18°C. Black bars are medians, and the shaded boxes indicate 25th and 75th percentiles. (B) The first six simulated divisions of a cubic space representing the embryo. (C–F) Simulated cell division waves in the side view (C) and top view (E). (D) and (F) are experimentally measured cell division waves at 18°C for comparison. See also Figure S1.
	Figure 5. A Side-to-Side Temperature Gradient Leads to Asynchronous MBT Entry (A) Snapshots of embryo at 23°C at three different time points after it has experienced a side-to-side temperature gradient (11°C–25°C) from 1:10 hpf to 5:45 hpf. Two regions of equal size have been selected on the previously cold and previously warm side. (B) Number of visible cells in the previously cold region (blue) and the previously warm region (red) as indicated in (A). The number of visible cells has been calculated by taking the initial number of cells and then increasing it by one every time a cell division is observed. The black lines show a smoothed fit using the “robust LOESS” (quadratic fit) option in MATLAB. (C) The average division rate of the visible cells as calculated from the fitted curves in (B). The time of maximal average division rate is taken as a measure for MBT onset. MBT is found to occur ∼60 min later in the previously cold region than in the previously warm region (with a SD of 16 min; 3 analyzed embryos).
	Figure 6. A Long Temperature Gradient Induces a Mesodermal Induction Defect and Reveals a Resynchronizing Mechanism (A) Xbra expression after MBT. Time course of Xbra expression in gradient embryos treated in the side to side and top to bottom directions. Unstained and mock-treated control embryos are shown for comparison. (B and C) Phenotype and survival of embryos two weeks after treatment with a side-to-side (B) or top-to-bottom (C) gradient. “Alive” includes embryos that survived with a generally normal phenotype, and “abnormal” includes embryos that did not survive and embryos that experienced clear developmental defects, such as dorsalization, ventralization, and bent body axes.
	Figure S1, Related to Figure 4. Model Validation (A) Varying the spatial heterogeneity along simulated embryonic axes results in simulated cell division waves with fit lines of varying slope. Simulation results were compared to experimentally measured slopes ± 1 standard deviation to yield a range of heterogeneities. The predicted heterogeneity for the animal-vegetal axis was used to calculate an expected difference in period between the animal and vegetal halves of an embryo. (B) Average slopes ± 1 standard deviation fit to experimentally measured data. Divisions four, five, and six contain comparatively less variation and contribute uniformly to wave development. Division 8 served as a benchmark for model calibration. (C) Predicted difference in average period between vegetal and animal cells matches with average measured period difference between these two hemispheres.
	Figure S2, Related to Figure 5. Evolution of the Xbra Phenotype (A) Onset of Xbra expression in untreated embryos. Each time point is five images of the same stained embryo. (B) Quantification of Xbra expression pattern after MBT. N.S. = No staining, A. = Asymmetric staining, S. = Symmetric staining. Each set of control embryos was collected from the same fertilization as the set of gradient-treated embryos below. (C) Mock-treated control and desynchronized embryos. Temperature gradient treatment (initial 23°C followed by 11°C-25°C gradient from 1:10 hpf – 5:36 hpf) of embryos in the side-to-side direction from the one-cell stage to just before mid-blastula transition resulted in severely desynchronized embryos compared to controls. (D) Mock-treated control and desynchronized embryos. Temperature gradient applied in the top to-bottom direction (initial 23°C followed by 18°C at the animal pole and 24°C at the vegetal pole from 1:10 hpf to 8:55 hpf) reversed the usual direction of the cell division wave and produced embryos with larger animal cells and smaller vegetal cells compared to controls. (E) Side-to-side gradient-treated embryo stained for Xbra but not bleached. Pigmentation and Xbra staining are both visible.
	Graphical Abstract.

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