Journal: Virologica Sinica

Article Title: PABP-driven secondary condensed phase within RSV inclusion bodies activates viral mRNAs for ribosomal recruitment

doi: 10.1016/j.virs.2023.12.001

Figure Lengend Snippet: The viral mRNP granules within RSV IBs are secondary biomolecular condensates formed by LLPS. A – C Live imaging of HeLa-GFP-PABP cells infected with RSV. The enlargement of white-framed regions was shown on the right. The time point is indicated at the top right corner of each frame ( A and B ). A The dynamic behavior of viral mRNP granules. Arrowhead indicates a cluster of viral mRNP granules released and diluted into the cytoplasm in a to f order, also referred to Video S1. Scale bar, 5 ​μm. B Representative images showing the fusion of two touching viral mRNP granules (a and b) labeled with GFP-PABP into larger spherical granules. Also referred to as Video S2. Scale bar, 2 ​μm. C Fluorescence recovery after photobleaching (FRAP) analysis of viral mRNP granules labeled with GFP-PABP. The bleached region of interest (ROI) is marked with a white circle. The FRAP data from four distinct granules in four distinct cells were fitted into a single curve (blue) by using R/Rstudio. Also referred to as Video S3. Scale bar, 2 ​μm. D HeLa-GFP-PABP cells were treated with 1.5% 1,6-hexanediol for 5 ​min after being infected with RSV for 36 ​h. IBs were detected by mouse anti-RSV P antibody (red). Arrowhead indicates viral mRNP granules dissolved by 1,6-hexanediol. Nuclei are stained with DAPI (blue in Merge). Scale bar, 10 ​μm.

Article Snippet: The FRAP data from four distinct granules in four distinct cells were fitted into a single curve (blue) by using R/Rstudio.

Techniques: Imaging, Infection, Labeling, Fluorescence, Staining

Journal:

Article Title: The polarity and dynamics of microtubule assembly in the budding yeast Saccharomyces cerevisiae

doi: 10.1038/71357

Figure Lengend Snippet: Statistical analysis of FSM and FRAP marks relative to SPBs

Article Snippet: Statistical analysis of FSM and FRAP data Metamorph software was used to measure selected parameters (distance or fluorescence intensity) from time series that were suitable for analysis.

Techniques:

Journal:

Article Title: The polarity and dynamics of microtubule assembly in the budding yeast Saccharomyces cerevisiae

doi: 10.1038/71357

Figure Lengend Snippet: a, A metaphase spindle in a cell expressing GFP–tubulin that was photobleached in the lower half-spindle and then observed by time-lapse microscopy. The −7 s time point shows the spindle before photobleaching. The laser was targeted to the lower half of the spindle (white arrowhead), which was exposed to the laser for 25 ms. Time point 0 shows that the upper half-spindle is still fluorescent (grey arrowhead) while the lower half has been bleached. Time-lapse analysis for 20 min revealed that the bleached portion of the spindle recovered fluorescence (white arrowhead), while the unbleached portion lost intensity, because of photobleaching by fluorescent exposures for image acquisition and incorporation of bleached tubulin subunits. Time points are given in seconds. b, The graph shows integrated intensity measurements of a 5 pixel × 5 pixel square placed over the bleached region (squares) and the unbleached region (diamonds) over time. These values are corrected for photobleaching that occurred during time-lapse image acquisition; a decrease from the initial value of ~20% had occurred by the 360-s time point. Also plotted are the predicted rates of FRAP for bleached (grey line) and unbleached (black line) half-spindles. These theoretical values were derived using the first-order rate constant k, calculated as described in Methods. Scale bar in a represents 2 μm.

Article Snippet: Statistical analysis of FSM and FRAP data Metamorph software was used to measure selected parameters (distance or fluorescence intensity) from time series that were suitable for analysis.

Techniques: Expressing, Time-lapse Microscopy, Fluorescence, Derivative Assay

Journal: Traffic (Copenhagen, Denmark)

Article Title: Simplified equation to extract diffusion coefficients from confocal FRAP data

doi: 10.1111/tra.12008

Figure Lengend Snippet: List of parameters and their definitions

Article Snippet: Data fitting was carried out for D and M f by a nonlinear least-squares fitting routine (nlinfit.m) available in MATLAB ® (version 7.10, R2010a, The Mathworks, Inc.) minimizing a weighted residual between averaged FRAP data from 10 experiments ( F Data ( t )) and a theoretical FRAP curve ( F ( t ), Eq.

Techniques: Diffusion-based Assay, Fluorescence, Sampling, Protein Concentration

Journal: Traffic (Copenhagen, Denmark)

Article Title: Simplified equation to extract diffusion coefficients from confocal FRAP data

doi: 10.1111/tra.12008

Figure Lengend Snippet: (A) Representative images of Alexa-CTxB on the plasma membrane during a FRAP experiment on either live or fixed cells for rn=1.1μm. Scale bar = 1 μm. (B) Postbleach profiles of Alexa-CTxB on the plasma membranes of live (□, n=12) and fixed (○, n=5) cells. (C) FRAP data of Alexa-CTxB on the plasma membranes of live (□, n=12) and fixed (○, n=5) cells. Since the bleach ROI is slightly off center in our system as seen in the images of (A) at t=0, a correction was made to align the center of the postbleach profile to determine re.

Article Snippet: Data fitting was carried out for D and M f by a nonlinear least-squares fitting routine (nlinfit.m) available in MATLAB ® (version 7.10, R2010a, The Mathworks, Inc.) minimizing a weighted residual between averaged FRAP data from 10 experiments ( F Data ( t )) and a theoretical FRAP curve ( F ( t ), Eq.

Techniques:

Journal: Traffic (Copenhagen, Denmark)

Article Title: Simplified equation to extract diffusion coefficients from confocal FRAP data

doi: 10.1111/tra.12008

Figure Lengend Snippet: Comparison of diffusion coefficients determined by FRAP data fitting (DFitting, Eq. 3), versus the DConfocal equation (Eq. 5), or the Soumpasis equation using either rn (Drn) or re (Dre) in log scale. D’s were found from averaged FRAP curves (N≥12 cells per experiment) for three or more separate experiments (n≥3). Error bars represent standard errors. Dashed boxes show D’s reported in the literature (Table 3). *, p<0.05 compared to DFitting, Student’s t-test.

Article Snippet: Data fitting was carried out for D and M f by a nonlinear least-squares fitting routine (nlinfit.m) available in MATLAB ® (version 7.10, R2010a, The Mathworks, Inc.) minimizing a weighted residual between averaged FRAP data from 10 experiments ( F Data ( t )) and a theoretical FRAP curve ( F ( t ), Eq.

Techniques: Diffusion-based Assay

Journal: Traffic (Copenhagen, Denmark)

Article Title: Simplified equation to extract diffusion coefficients from confocal FRAP data

doi: 10.1111/tra.12008

Figure Lengend Snippet: Diffusion coefficients were determined by FRAP data fitting (DFitting, Eq. 3), by the DConfocal equation (Eq. 5), by the Soumpasis equation using rn (Drn), and by the Soumpasis equation using re (Dre) for individual confocal FRAP curves (N≥6). Dashed box indicates the range of EGFP’s diffusion coefficients in the cytosol reported in the literature. re was measured from an averaged postbleach profile (n=1,N=10 cells) and D’s were obtained from individual FRAP data (n=1, N=8,10,10, and 8 cells). *, p<0.05 compared to DFitting, Student’s t-test.

Article Snippet: Data fitting was carried out for D and M f by a nonlinear least-squares fitting routine (nlinfit.m) available in MATLAB ® (version 7.10, R2010a, The Mathworks, Inc.) minimizing a weighted residual between averaged FRAP data from 10 experiments ( F Data ( t )) and a theoretical FRAP curve ( F ( t ), Eq.

Techniques: Diffusion-based Assay

Journal: Traffic (Copenhagen, Denmark)

Article Title: Simplified equation to extract diffusion coefficients from confocal FRAP data

doi: 10.1111/tra.12008

Figure Lengend Snippet: Comparison of Mean±SE of (A) re, (B) τ1/2, (C) D, and (D) Mf determined using averaged FRAP data from more than three independent experiements with 10 cells (n≥3, N=10) or means from 10 individual FRAP data in a single experiment (N=10). Error bars represent standard errors. p>0.05 Cross comparison, Student’s t-test.

Article Snippet: Data fitting was carried out for D and M f by a nonlinear least-squares fitting routine (nlinfit.m) available in MATLAB ® (version 7.10, R2010a, The Mathworks, Inc.) minimizing a weighted residual between averaged FRAP data from 10 experiments ( F Data ( t )) and a theoretical FRAP curve ( F ( t ), Eq.

Techniques: