slimfast 4c software Search Results


slimfast 4c software  (MathWorks Inc)
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MathWorks Inc slimfast 4c software
( A ) Schematic representation of the system used for sample preparation of stoichiometry experiments in model membranes to determine membrane insertion (mGSDMD(NTD)-mEGFP depicted in pink and green). ( B ) Representative TIRF images of an SLB incubated with 2 nM of full-length mGSDMD-mEGFP (left) or cleaved mGSDMD-mEGFP (right) for 1 h. Scale bars 5 µm. ( C ) Density of detected assemblies on SLB for full-length mGSDMD-mEGFP (GSDMD FL) and active mGSDMD-mEGFP (cleaved GSDMD) at 2 nM. Plotted are values obtained from recordings from three independent experiments with at least ten movies per experiment analyzed ( p = 6.7 × 10 −9 ). Data are presented as box plots with the center line at the median, lower bound at 25th percentile, upper bound at 75th percentile, and whiskers at minimum and maximum values. ( D ) Particle localization analysis by <t>SLIMfast</t> <t>4C.</t> Right: representative image of immobile particles detected in the SLB sample and highlighted by colored ROIs (scale bar 5 µm). Left: Percentage of immobile (I) versus mobile (M) particles detected in the sample. Averages from three independent experiments with a minimum of 10 recordings analyzed per experiment ( p < 0.0001). ( E ) Representative fluorescence distribution of mGSDMD-mEGFP oligomers obtained from preformed SLB incubated with 2 nM mGSDMD-mEGFP activated with 20 nM Caspase 11. The resulting brightness distribution was plotted as a probability distribution function (Pdf, black) and fitted with a mixture of Gaussians to estimate the percentage of occurrence of particles containing n-mer oligomers (color). ( F ) Percentage of occurrence of the different oligomeric species of GSDMD (the color code used for the occurrence graph is the same as for the distributions in ( E )) calculated as the average from seven independent experiments (minimum 2000 particles analyzed per experiment). Data are corrected for GFP partial labeling. Individual experimental data points are indicated as scatter plots in the graph (0 values are not indicated). Error bars correspond to the SD from the different experiments. Statistics were measured by Student’s t-tests with **** for p < 0.0001. .
Slimfast 4c Software, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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( A ) Schematic representation of the system used for sample preparation of stoichiometry experiments in model membranes to determine membrane insertion (mGSDMD(NTD)-mEGFP depicted in pink and green). ( B ) Representative TIRF images of an SLB incubated with 2 nM of full-length mGSDMD-mEGFP (left) or cleaved mGSDMD-mEGFP (right) for 1 h. Scale bars 5 µm. ( C ) Density of detected assemblies on SLB for full-length mGSDMD-mEGFP (GSDMD FL) and active mGSDMD-mEGFP (cleaved GSDMD) at 2 nM. Plotted are values obtained from recordings from three independent experiments with at least ten movies per experiment analyzed ( p = 6.7 × 10 −9 ). Data are presented as box plots with the center line at the median, lower bound at 25th percentile, upper bound at 75th percentile, and whiskers at minimum and maximum values. ( D ) Particle localization analysis by SLIMfast 4C. Right: representative image of immobile particles detected in the SLB sample and highlighted by colored ROIs (scale bar 5 µm). Left: Percentage of immobile (I) versus mobile (M) particles detected in the sample. Averages from three independent experiments with a minimum of 10 recordings analyzed per experiment ( p < 0.0001). ( E ) Representative fluorescence distribution of mGSDMD-mEGFP oligomers obtained from preformed SLB incubated with 2 nM mGSDMD-mEGFP activated with 20 nM Caspase 11. The resulting brightness distribution was plotted as a probability distribution function (Pdf, black) and fitted with a mixture of Gaussians to estimate the percentage of occurrence of particles containing n-mer oligomers (color). ( F ) Percentage of occurrence of the different oligomeric species of GSDMD (the color code used for the occurrence graph is the same as for the distributions in ( E )) calculated as the average from seven independent experiments (minimum 2000 particles analyzed per experiment). Data are corrected for GFP partial labeling. Individual experimental data points are indicated as scatter plots in the graph (0 values are not indicated). Error bars correspond to the SD from the different experiments. Statistics were measured by Student’s t-tests with **** for p < 0.0001. .

Journal: The EMBO Journal

Article Title: Gasdermin D cysteine residues synergistically control its palmitoylation-mediated membrane targeting and assembly

doi: 10.1038/s44318-024-00190-6

Figure Lengend Snippet: ( A ) Schematic representation of the system used for sample preparation of stoichiometry experiments in model membranes to determine membrane insertion (mGSDMD(NTD)-mEGFP depicted in pink and green). ( B ) Representative TIRF images of an SLB incubated with 2 nM of full-length mGSDMD-mEGFP (left) or cleaved mGSDMD-mEGFP (right) for 1 h. Scale bars 5 µm. ( C ) Density of detected assemblies on SLB for full-length mGSDMD-mEGFP (GSDMD FL) and active mGSDMD-mEGFP (cleaved GSDMD) at 2 nM. Plotted are values obtained from recordings from three independent experiments with at least ten movies per experiment analyzed ( p = 6.7 × 10 −9 ). Data are presented as box plots with the center line at the median, lower bound at 25th percentile, upper bound at 75th percentile, and whiskers at minimum and maximum values. ( D ) Particle localization analysis by SLIMfast 4C. Right: representative image of immobile particles detected in the SLB sample and highlighted by colored ROIs (scale bar 5 µm). Left: Percentage of immobile (I) versus mobile (M) particles detected in the sample. Averages from three independent experiments with a minimum of 10 recordings analyzed per experiment ( p < 0.0001). ( E ) Representative fluorescence distribution of mGSDMD-mEGFP oligomers obtained from preformed SLB incubated with 2 nM mGSDMD-mEGFP activated with 20 nM Caspase 11. The resulting brightness distribution was plotted as a probability distribution function (Pdf, black) and fitted with a mixture of Gaussians to estimate the percentage of occurrence of particles containing n-mer oligomers (color). ( F ) Percentage of occurrence of the different oligomeric species of GSDMD (the color code used for the occurrence graph is the same as for the distributions in ( E )) calculated as the average from seven independent experiments (minimum 2000 particles analyzed per experiment). Data are corrected for GFP partial labeling. Individual experimental data points are indicated as scatter plots in the graph (0 values are not indicated). Error bars correspond to the SD from the different experiments. Statistics were measured by Student’s t-tests with **** for p < 0.0001. .

Article Snippet: Movies acquired were cut with Image J, and the first 100 frames were analyzed via tracking analysis by using the SLIMfast 4C software for localization-based imaging in Matlab (Bellón et al, ).

Techniques: Sample Prep, Membrane, Incubation, Fluorescence, Labeling

Reagents and tools table

Journal: The EMBO Journal

Article Title: Gasdermin D cysteine residues synergistically control its palmitoylation-mediated membrane targeting and assembly

doi: 10.1038/s44318-024-00190-6

Figure Lengend Snippet: Reagents and tools table

Article Snippet: Movies acquired were cut with Image J, and the first 100 frames were analyzed via tracking analysis by using the SLIMfast 4C software for localization-based imaging in Matlab (Bellón et al, ).

Techniques: Recombinant, Sequencing, Protease Inhibitor, Membrane, Microscopy, Software, Clinical Proteomics, High Content Screening