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  • 1
    Keywords: CELL ; Germany ; MICROSCOPY ; MODEL ; PATHWAY ; SITE ; SITES ; PROTEIN ; PROTEINS ; COMPONENTS ; RESOLUTION ; COMPLEXES ; DOMAIN ; DYNAMICS ; BINDING ; BIOLOGY ; TRANSPORT ; MEMBRANE ; NUMBER ; PREDICTION ; KINETICS ; LIVING CELLS ; systems biology ; FLUORESCENCE ; SPATIAL-ORGANIZATION ; ORGANIZATION ; DOMAINS ; ENDOPLASMIC-RETICULUM ; ER ; RE ; PATTERN ; VESICLES ; INCREASE ; LEADS ; FLUORESCENCE MICROSCOPY ; COPII ; endoplasmic reticulum ; EXPORT ; PREDICTS ; ENGLAND ; PREDICT ; AGREEMENT ; PICHIA-PASTORIS ; TURNOVER ; SECRETORY PATHWAY ; CELL BIOLOGY ; biophysical modelling ; COOPERATIVE BINDING ; COPII-COATED VESICLE ; domain formation ; membrane traffic
    Abstract: Exit sites (ES) are specialized domains of the endoplasmic reticulum (ER) at which cargo proteins of the secretory pathway are packaged into COPII-coated vesicles. Although the essential COPII proteins (Sar1p, Sec23p-Sec24p, Sec13p-Sec31p) have been characterized in detail and their sequential binding kinetics at ER membranes have been quantified, the basic processes that govern the self-assembly and spatial organization of ERES have remained elusive. Here, we have formulated a generic computational model that describes the process of formation of ERES on a mesoscopic scale. The model predicts that ERES are arranged in a quasi-crystalline pattern, while their size strongly depends on the cargo-modulated kinetics of COPII turnover - that is, a lack of cargo leads to smaller and more mobile ERES. These predictions are in favorable agreement with experimental data obtained by fluorescence microscopy. The model further suggests that cooperative binding of COPII components, for example mediated by regulatory proteins, is a key factor for the experimentally observed organism-specific ERES pattern. Moreover, the anterograde secretory flux is predicted to grow when the average size of ERES is increased, whereas an increase in the number of (small) ERES only slightly alters the flux
    Type of Publication: Journal article published
    PubMed ID: 18073241
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  • 2
    Keywords: MICROSCOPY ; IMAGES ; imaging ; QUANTIFICATION ; segmentation ; 3D ; USA ; MEDICAL IMAGES ; SUBCELLULAR STRUCTURES
    Abstract: We introduce a model-based approach for segmenting and quantifying GFP-tagged subcellular structures of the Golgi apparatus in 2D and 3D microscopy images. The approach is based on 2D and 3D intensity models, which are directly fitted to an image within 2D circular or 3D spherical regions-of-interest (ROIs). We also propose automatic approaches for the detection of candidates, for the initialization of the model parameters, and for adapting the size of the ROI used for model fitting. Based on the fitting results, we determine statistical information about the spatial distribution and the total amount of intensity (fluorescence) of the subcellular structures. We demonstrate the applicability of our new approach based on 2D and 3D microscopy images.
    Type of Publication: Journal article published
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