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

Journal: Nature Communications

Article Title: Translational control by DHX36 binding to 5′UTR G-quadruplex is essential for muscle stem-cell regenerative functions

doi: 10.1038/s41467-021-25170-w

Figure Lengend Snippet: a Gnai2 protein and mRNA were detected in Ctrl and iKO SCs cultured for 48 h. b Gnai2 protein and mRNA were detected in proliferating Ctrl and Dhx36-KO C2C12 cells. c GNAI2 protein was detected in Ctrl, KO, or KO C2C12 cells treated with proteasome inhibitor MG132 for 8 h. d Left: SCs were treated with 2.5 or 5 μM cPDS and GNAI2 protein levels were detected by western blot. The relative intensity of each GNAI2 protein band normalized by α-Tubulin was calculated by ImageJ as the intensity for untreated cells set as 1. Right: Gnai2 mRNA was detected by qRT-PCR in the above cells. Gapdh mRNA was used as a normalization control. e Left: rG4 formation in Ctrl and iKO SCs was detected by QUMA-1 staining. Cells treated with RNase A were used as negative controls. Scale bar = 5 μm. Right: Boxplot of normalized rG4 fluorescence signals which were calculated from the indicated number of cells from three pairs of Ctrl/iKO mice by Matlab R2014b using in-house scripts. The average intensity from Ctrl cells was set as 1. Horizontal lines represent median values. Error bars show the distribution from the minimum to the maximum data points. The boxes extend from the 25th to 75th percentiles. Significance was calculated by Student’s t test (two-tailed unpaired), P = 3.1E-17. f EGFP reporter plasmids harboring WT or Mut full-length 5’ UTR, rG4#1, or rG4#2 were transfected into C2C12 cells and EGFP protein was detected by western blot. α-Tubulin was used as the internal loading control. g EGFP mRNA was detected by qRT-PCR from the above samples. h EGFP reporter plasmids harboring WT full-length 5’ UTR, rG4#1, or rG4#2 were transfected into Ctrl or Dhx36-KO C2C12 cells and EGFP protein was detected by western blot with α-Tubulin used as the internal loading control. i EGFP mRNA was detected by qRT-PCR from the above samples. Data represent the average of three independent experiments ± s.d. in a , b , d , g , and i . Source data are provided as a Source Data file.

Article Snippet: Right: Boxplot of normalized rG4 fluorescence signals which were calculated from the indicated number of cells from three pairs of Ctrl/iKO mice by Matlab R2014b using in-house scripts.

Techniques: Cell Culture, Western Blot, Quantitative RT-PCR, Control, Staining, Fluorescence, Two Tailed Test, Transfection

Journal: iScience

Article Title: Sensory plasticity caused by up-down regulation encodes the information of short-term learning and memory

doi: 10.1016/j.isci.2025.112215

Figure Lengend Snippet:

Article Snippet: The Ca 2+ signals, ΔF , were displayed as the mean values in various colors and SEM in light grey using IGOR Pro 6.10 (WaveMetrics, Inc., Lake Oswego, OR, USA), as heatmap using Matlab-R2019a (MathWorks, Nidec, MA, USA), or boxplot using GraphPad Prism 8 (GraphPad Software, Inc., San Diego, CA, USA).

Techniques: Virus, Recombinant, Agarose Gel Electrophoresis, DNA Extraction, Plasmid Preparation, Cloning, Software