machine learning toolbox  (MathWorks Inc)

Journal: bioRxiv

Article Title: Hollow condensates emerge from gelation-induced spinodal decomposition

doi: 10.1101/2025.06.25.661497

Figure Lengend Snippet: ( a ) Droplet-like DPICs were initially formed by mixing 20 μM ATTO565-labeled p53 4M ΔTAD with 0.6 μM ATTO488-labeled Random DNA and incubating for 30 minutes at room temperature. Subsequently, Cy5-labeled p21 DNA was added at varying concentrations and incubated for an additional 120 minutes: (i) 0.15 μM; (ii) 0.225 μM; (iii) 0.3 μM; (iv) 0.45 μM; (v) 0.6 μM; (vi) 0.75 μM; (vii) 0.9 μM. Representative fluorescence images at incubation time t = 4-min and t = 120-min are shown. Independent in vitro droplet experiments were repeated three times (n = 3). ( b ) Boxplot of characteristic time constants τ 1 and τ 2 for p21 DNA concentrations ranging from 0.3 to 0.9 μM. N indicates the number of individual biomolecule-rich condensates analyzed under each condition. In box plots, the black line denotes the median, box edges represent the 25 th and 75 th percentiles, whiskers indicate the range excluding outliers, and outliers are shown as individual dots (•). ( c ) Phase diagram showing normalized fluorescence intensities of ATTO565-labeled p53 4M ΔTAD and ATTO488-labeled Random DNA at the center of condensates under increasing concentrations of p21 DNA (0.3, 0.45, 0.6, and 0.75 μM). Values are shown both before p21 DNA addition and at the end of Stage I. Control experiments in which Random DNA was used in place of p21 DNA are also included. Error bars indicate mean ± s.d. Green dashed lines mark the estimated binodal boundary, and purple dashed lines represent the spinodal boundary, as confirmed by our phase-field model (see – ).

Article Snippet: The function of “boxplot” in MATLAB software (R2015a, 64-bit, February 12, 2015) was used to plot the boxplots in , , and Supplementary Fig. 3.

Techniques: Labeling, Incubation, Fluorescence, In Vitro, Control