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:

Journal: Biochemistry

Article Title: Chemometric Approaches for Developing Infrared Nanosensors to Image Anthracyclines

doi: 10.1021/acs.biochem.8b00926

Figure Lengend Snippet: (A) Fluorescence response (F-F0/F0) for spectra of CB13 DNA-SWNTs upon addition of 100 μM DOX. Changing the ratio of SWNT:DNA (w/w) alters both the fluorescence emission intensity and response to DOX. 1 mL samples of 100 μM DNA suspending (i) 1 mg (red), (ii) 3 mg (yellow), or (iii) 5 mg (blue) SWNT. Each spectrum represents the average of 3 technical replicate measurements. (B) Fluorescence emission spectra of CB13-DNA SWNT before addition of (t=0), and after 10 min incubation with (t=10 min) 100 μM DOX. Time series traces of the (C) (6,5) and (D) (7,6) peaks reveal that the peak wavelength (red) shifts continuously over 10 min while the peak intensity (black) for (6,5) plateaus rapidly compared to (7,6). (E, F) Fluorescence response of normalized intensity (E) and wavelength (F) for the (7,6) chirality peak of CB13-DNA-SWNT versus DOX concentration. Triangles (red) and circles (black) represent separate experimental replicates. Each point is the average of 3 technical replicates with standard deviation as error bars. Curve fits were calculated using non-linear least squares. (G) Fluorescence emission spectra of CB13-DNA-SWNT in the presence of 0.1 mM of the anthracyclines doxorubicin (DOX), epirubicin (EPR) and daunorubicin (DAR). (H) Fraction of pristine SWNT (solid lines) and anthracycline-bound SWNT (dotted lines) calculated from fluorescence emission spectra as a function of concentration for the different anthracyclines. (I) Comparison of the fluorescence response of CB13-DNA-SWNT nanosensor to the chemotherapeutics doxorubicin (DOX) and dacarbazine (DTIC) at 0.1 mM concentration.

Article Snippet: 14 For comparison of nanosensor response to doxorubicin (HCl salt, Fisher BioReagents, Fisher Scientific), epirubicin (HCl salt, Selleck Chemical LLC), and daunorubicin (HCl salt, Calbiochem, MilliporeSigma), each emission spectrum was approximated as the linear combination of the spectrum for a bare nanosensor and the spectrum for a nanosensor saturated in anthracycline, S = αS initial + βS saturated The fraction of bare nanosensor ( α ) and anthracycline bound nanosensor ( β ) was was calculated by a least squares method lsqnonneg() in MATLAB (R2017b, The Mathworks, Inc.).

Techniques: Fluorescence, Incubation, Concentration Assay, Standard Deviation, Comparison