0000000000072835
AUTHOR
Derek Toomre
showing 9 related works from this author
Fuzzy temporal random sets with an application to cell biology
2007
Total Internal Reflection Fluorescence Microscopy (TIRFM) greatly facilitates to imaging the first steps of endocytosis, a process whereby cells traffic cargo from the cell surface to endosomes. Using TIRFM, fluorescent-tagged endocytic proteins are observed as overlapped areas forming random clumps of different sizes, shapes and durations. A common procedure to segment these objects consists of thresholding the original gray-level images to produce binary sequences in which a pixel is covered or not by a given fluorescent-tagged protein. This binary logic is not appropriate because it leaves a free tuning parameter to be set by the user which can influence on the conclusions of the statist…
Loss of endocytic clathrin-coated pits upon acute depletion of phosphatidylinositol 4,5-bisphosphate.
2007
Phosphatidylinositol 4,5-bisphosphate [PI(4,5) P 2 ], a phosphoinositide concentrated predominantly in the plasma membrane, binds endocytic clathrin adaptors, many of their accessory factors, and a variety of actin-regulatory proteins. Here we have used fluorescent fusion proteins and total internal reflection fluorescence microscopy to investigate the effect of acute PI(4,5) P 2 breakdown on the dynamics of endocytic clathrin-coated pit components and of the actin regulatory complex, Arp2/3. PI(4,5) P 2 breakdown was achieved by the inducible recruitment to the plasma membrane of an inositol 5-phosphatase module through the rapamycin/FRB/FKBP system or by treatment with ionomycin. PI(4,5)…
Measuring Spatiotemporal Dependencies in Bivariate Temporal Random Sets with Applications to Cell Biology
2008
Analyzing spatiotemporal dependencies between different types of events is highly relevant to many biological phenomena (e.g., signaling and trafficking), especially as advances in probes and microscopy have facilitated the imaging of dynamic processes in living cells. For many types of events, the segmented areas can overlap spatially and temporally, forming random clumps. In this paper, we model the binary image sequences of two different event types as a realization of a bivariate temporal random set and propose a nonparametric approach to quantify spatial and spatiotemporal interrelations using the pair correlation, cross-covariance, and the Ripley K functions. Based on these summary st…
Studying endocytosis in space and time by means of temporal Boolean models
2006
Endocytosis is a process by which cells carry traffic from the extracellular space into various intracellular compartments. Visualization of fluorescently tagged clathrin proteins (mediators of endocytosis) allows us to image endocytosis in real time. When imaging the plasma membrane, areas of fluorescence generated by different endocytic processes overlap spatially and temporally, forming random clumps. Here, a sequence of segmented clathrin spots is considered a realization of a non-isotropic 3D Boolean model. Estimates of the intensity, the mean perimeter and the density function of the durations of endocytic events are obtained.
Analyzing Protein-Protein Spatial-Temporal Dependencies from Image Sequences Using Fuzzy Temporal Random Sets
2008
Total Internal Reflection Fluorescence Microscopy (TIRFM) allows us to image fluorescenttagged proteins near the plasma membrane of living cells with high spatial-temporal resolution. Using TIRFM imaging of GFP-tagged clathrin endocytic proteins, areas of fluorescence are observed as overlapping spots of different sizes and durations. Standard procedures to measure protein-protein colocalization of dual labeled samples threshold the original graylevel images to segment areas covered by different proteins. This binary logic is not appropriate as it leaves a free tuning parameter which can influence the conclusions. Moreover, these procedures rely on simple statistical analysis based on corre…
Analysis of Spatially and Temporally Overlapping Events with Application to Image Sequences
2006
Counting spatially and temporally overlapping events in image sequences and estimating their shape-size and duration features are important issues in some applications. We propose a stochastic model, a particular case of the nonisotropic 3D Boolean model, for performing this analysis: the temporal Boolean model. Some probabilistic properties are derived and a methodology for parameter estimation from time-lapse image sequences is proposed using an explicit treatment of the temporal dimension. We estimate the mean number of germs per unit area and time, the mean grain size and the duration distribution. A wide simulation study in order to assess the proposed estimators showed promising resul…
Phosphatidylinositol phosphate kinase type I gamma regulates dynamics of large dense-core vesicle fusion.
2005
Phosphatidylinositol-4,5-bisphosphate was proposed to be an important regulator of large dense-core vesicle exocytosis from neuroendocrine tissues. Here, we have examined the kinetics of secretion in chromaffin cells from mice lacking phosphatidylinositol phosphate kinase type Iγ, the major neuronal phosphatidylinositol-4-phosphate 5-kinase. Absence of this enzyme caused a reduction of the readily releasable vesicle pool and its refilling rate, with a small increase in morphologically docked vesicles, indicating a defect in vesicle priming. Furthermore, amperometry revealed a delay in fusion pore expansion. These results provide direct genetic evidence for a key role of phosphatidylinositol…
Automatic detection of large dense-core vesicles in secretory cells and statistical analysis of their intracellular distribution.
2010
Analyzing the morphological appearance and the spatial distribution of large dense-core vesicles (granules) in the cell cytoplasm is central to the understanding of regulated exocytosis. This paper is concerned with the automatic detection of granules and the statistical analysis of their spatial locations in different cell groups. We model the locations of granules of a given cell as a realization of a finite spatial point process and the point patterns associated with the cell groups as replicated point patterns of different spatial point processes. First, an algorithm to segment the granules using electron microscopy images is proposed. Second, the relative locations of the granules with…
Spatio-Temporal Analysis of Constitutive Exocytosis in Epithelial Cells
2006
Exocytosis is an essential cellular trafficking process integral to the proper distribution and function of a plethora of molecules, including transporters, receptors, and enzymes. Moreover, incorrect protein targeting can lead to pathological conditions. Recently, the application of evanescent wave microscopy has allowed us to image the final steps of exocytosis. However, spatio-temporal analysis of fusion of constitutive vesicular traffic with the plasma membrane has not been systematically performed. Also, the spatial sites and times of vesicle fusion have not yet been analyzed together. In addition, more formal tests are required in testing biological hypotheses, rather than visual insp…