Yannis Kalaidzidis - Academia.edu (original) (raw)
Papers by Yannis Kalaidzidis
arXiv (Cornell University), Aug 15, 2023
Zeitschrift für Gastroenterologie, 2018
PLOS Computational Biology, 2020
Can three-dimensional, microvasculature networks still ensure blood supply if individual links fa... more Can three-dimensional, microvasculature networks still ensure blood supply if individual links fail? We address this question in the sinusoidal network, a plexus-like microvasculature network, which transports nutrient-rich blood to every hepatocyte in liver tissue, by building on recent advances in high-resolution imaging and digital reconstruction of adult mice liver tissue. We find that the topology of the three-dimensional sinusoidal network reflects its two design requirements of a space-filling network that connects all hepatocytes, while using shortest transport routes: sinusoidal networks are sub-graphs of the Delaunay graph of their set of branching points, and also contain the corresponding minimum spanning tree, both to good approximation. To overcome the spatial limitations of experimental samples and generate arbitrarily-sized networks, we developed a network generation algorithm that reproduces the statistical features of 0.3-mm-sized samples of sinusoidal networks, using multi-objective optimization for node degree and edge length distribution. Nematic order in these simulated networks implies anisotropic transport properties, characterized by an empirical linear relation between a nematic order parameter and the anisotropy of the permeability tensor. Under the assumption that all sinusoid tubes have a constant and equal flow resistance, we predict that the distribution of currents in the network is very inhomogeneous, with a small number of edges carrying a substantial part of the flow. We quantify network resilience in terms of a permeability-at-risk, i.e. permeability as function of the fraction of removed edges. We find that sinusoidal networks are resilient to random removal of edges, but vulnerable to the removal of high-current edges. Our findings suggest the existence of a mechanism counteracting flow inhomogeneity to balance metabolic load on the liver.
1. Background: Provocation tests are widely used in allergology to objectively reveal patients se... more 1. Background: Provocation tests are widely used in allergology to objectively reveal patients sensitivity to specific allergens. The objective quantification of an allergic reaction is a crucial characteristic of the tests. Due to the absence of objective quantitative measurements the conjunctival provocation test (CPT) is a less frequently used method despite its sensitivity and simplicity. We developed a new method AllergoEye based on AI for quantitative evaluation of conjunctival allergic reactions and validated it in a clinical study. 2. Methods: AllergoEye was implemented as a two component system. The first component is based on an Android smartphone camera for imaging the patients eye and the second one is PC based for image analysis and quantification. For AllergoEye validation an open-label, prospective, monocentric study was carried out on 41 patients. Standardized CPT was performed with sequential titration of grass allergen in 4 dilutions with the reaction evaluated by ...
Three dimensional (3D) geometrical models are not only a powerful tool for quantitatively charact... more Three dimensional (3D) geometrical models are not only a powerful tool for quantitatively characterizing complex tissues but also useful for probing structure-function relationships in a tissue. However, these models are generally incomplete due to experimental limitations in acquiring multiple (>4) fluorescent channels simultaneously. Indeed, predictive geometrical and functional models of the liver have been restricted to few tissue and cellular components, excluding important cellular populations such as hepatic stellate cells (HSCs) and Kupffer cells (KCs). Here, we performed deep-tissue immunostaining, multiphoton microscopy, deeplearning techniques, and 3D image processing to computationally expand the number of simultaneously reconstructed tissue structures. We then generated a spatio-temporal singlecell atlas of hepatic architecture (Hep3D), including all main tissue and cellular components at different stages of post-natal development in mice. We used Hep3D to quantitati...
Journal of Cell Biology
Hepatocytes grow their apical surfaces anisotropically to generate a 3D network of bile canalicul... more Hepatocytes grow their apical surfaces anisotropically to generate a 3D network of bile canaliculi (BC). BC elongation is ensured by apical bulkheads, membrane extensions that traverse the lumen and connect juxtaposed hepatocytes. We hypothesize that apical bulkheads are mechanical elements that shape the BC lumen in liver development but also counteract elevated biliary pressure. Here, by resolving their structure using STED microscopy, we found that they are sealed by tight junction loops, connected by adherens junctions, and contain contractile actomyosin, characteristics of mechanical function. Apical bulkheads persist at high pressure upon microinjection of fluid into the BC lumen, and laser ablation demonstrated that they are under tension. A mechanical model based on ablation results revealed that apical bulkheads double the pressure BC can hold. Apical bulkhead frequency anticorrelates with BC connectivity during mouse liver development, consistent with predicted changes in ...
3D ‘ground truth’ images of idealized models of liver tissue ( 0.3 um x 0.3 um x 0.3u m per voxel
tion in early endosomes, cargo to be recycled (exempli-fied by the transferrin receptor [TFR] or ... more tion in early endosomes, cargo to be recycled (exempli-fied by the transferrin receptor [TFR] or low-density li-poprotein receptor [LDLR]) returns to the cell surface via recycling endosomes, whereas cargo destined for degradation (epidermal growth factor receptor [EGFR] *Correspondence:
Proceedings of the 2019 3rd International Conference on Computational Biology and Bioinformatics - ICCBB '19, 2019
High-content screens (HCS) using chemical and genomic interference based on light microscopy and ... more High-content screens (HCS) using chemical and genomic interference based on light microscopy and quantitative image analysis yielded a large amount of multi-parametric (MP) phenotypic data. Such data-sets hold great promise for the understanding of cellular mechanisms by systems biology. However, extracting functional information from data-sets, such as links between cellular processes and the functions of unknown genes, remains challenging. The limitation of HCS analysis lies in the complexity of cellular organization. Here, we assumed that cellular processes have a modular structure, and deconvolved the MP data into separate signals from different cellular modules by Blind Source Separation. We applied a combination of quantitative MP image analysis (QMPIA) and Independent Component Analysis (ICA) to an image-based HCS of endocytosis, the process whereby cells uptake molecules from the outside and distribute them to different sub-cellular organelles. We named our approach Independ...
1 Center for Information Services and High Performance Computing, Technische Universität Dresden,... more 1 Center for Information Services and High Performance Computing, Technische Universität Dresden, 01062 Dresden, Saxony, Germany 2) Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Saxony, Germany 3) UCSF, Cardiovascular Research Institute, Department of Biochemistry and Biophysics, California, USA 4) Chair of Scientific Computing for Systems Biology, Faculty of Computer Science, Technische Universität Dresden, 01187 Dresden, Saxony, Germany 5) Center for Systems Biology Dresden, 01307 Dresden, Saxony, Germany 6) Cluster of Excellence Physics of Life, Technische Universität Dresden, 01187 Dresden, Saxony, Germany
Journal of Cell Biology, 2021
Lumen morphogenesis results from the interplay between molecular pathways and mechanical forces. ... more Lumen morphogenesis results from the interplay between molecular pathways and mechanical forces. In several organs, epithelial cells share their apical surfaces to form a tubular lumen. In the liver, however, hepatocytes share the apical surface only between adjacent cells and form narrow lumina that grow anisotropically, generating a 3D network of bile canaliculi (BC). Here, by studying lumenogenesis in differentiating mouse hepatoblasts in vitro, we discovered that adjacent hepatocytes assemble a pattern of specific extensions of the apical membrane traversing the lumen and ensuring its anisotropic expansion. These previously unrecognized structures form a pattern, reminiscent of the bulkheads of boats, also present in the developing and adult liver. Silencing of Rab35 resulted in loss of apical bulkheads and lumen anisotropy, leading to cyst formation. Strikingly, we could reengineer hepatocyte polarity in embryonic liver tissue, converting BC into epithelial tubes. Our results s...
Journal of Cell Biology, 2021
Delivery of exogenous mRNA using lipid nanoparticles (LNPs) is a promising strategy for therapeut... more Delivery of exogenous mRNA using lipid nanoparticles (LNPs) is a promising strategy for therapeutics. However, a bottleneck remains in the poor understanding of the parameters that correlate with endosomal escape versus cytotoxicity. To address this problem, we compared the endosomal distribution of six LNP-mRNA formulations of diverse chemical composition and efficacy, similar to those used in mRNA-based vaccines, in primary human adipocytes, fibroblasts, and HeLa cells. Surprisingly, we found that total uptake is not a sufficient predictor of delivery, and different LNPs vary considerably in endosomal distributions. Prolonged uptake impaired endosomal acidification, a sign of cytotoxicity, and caused mRNA to accumulate in compartments defective in cargo transport and unproductive for delivery. In contrast, early endocytic/recycling compartments have the highest probability for mRNA escape. By using super-resolution microscopy, we could resolve a single LNP-mRNA within subendosomal...
The Journal of Cell Biology, 2019
Recycling of MT-MMPs to actin-rich membrane-protrusive structures promotes breast cancer invasion... more Recycling of MT-MMPs to actin-rich membrane-protrusive structures promotes breast cancer invasion. This study shows that SNX27–retromer, an endosomal sorting and recycling machinery, interacts with MT1-MMP and regulates its transport to the cell surface, thus promoting matrix invasive activity of the breast cancer cells.
Many cellular organelles, including endosomes, show compartmentalization into distinct functional... more Many cellular organelles, including endosomes, show compartmentalization into distinct functional domains, which however cannot be resolved by diffraction-limited light microscopy. Single molecule localization microscopy (SMLM) offers nanoscale resolution but data interpretation is often inconclusive when the ultrastructural context is missing. Correlative light electron microscopy (CLEM) combining SMLM with electron microscopy (EM) enables correlation of functional sub-domains of organelles in relation to their underlying ultrastructure at nanometer resolution. However, the specific demands for EM sample preparation and the requirements for fluorescent single-molecule photo-switching are opposed. Here, we developed a novel superCLEM workflow that combines triple-colour SMLM (dSTORM & PALM) and electron tomography using semi-thin Tokuyasu thawed cryosections. We applied the superCLEM approach to directly visualize nanoscale compartmentalization of endosomes in HeLa cells. Internaliz...
Functional tissue architecture originates by self-assembly of distinct cell types, following tiss... more Functional tissue architecture originates by self-assembly of distinct cell types, following tissue-specific rules of cell-cell interactions. In the liver, a structural model of the lobule was pioneered by Elias in 1949. This model, however, is in contrast with the apparent random 3D arrangement of hepatocytes. Since then, no significant progress has been made to derive the organizing principles of liver tissue. To solve this outstanding problem, we computationally reconstructed 3D tissue geometry from microscopy images and analyzed it applying soft-condensed-matter-physics concepts. Surprisingly, analysis of the spatial organization of cell polarity revealed that hepatocytes are not randomly oriented but follow a long-range liquid-crystal order. This does not depend exclusively on hepatocytes receiving instructive signals by endothelial cells as generally assumed, since silencing Integrin-β1 disrupted both liquid-crystal order and organization of the sinusoidal network. Our results...
Journal of Cell Science, 2016
Platelet-derived growth factor receptor β (PDGFRβ) is a receptor tyrosine kinase which upon activ... more Platelet-derived growth factor receptor β (PDGFRβ) is a receptor tyrosine kinase which upon activation by PDGF-BB stimulates cell proliferation, migration and angiogenesis. Ligand binding induces intracellular signaling cascades but also internalization of the receptor, eventually resulting in its lysosomal degradation. However, endocytic trafficking of receptors often modulates their downstream signaling. We previously reported that internalization of PDGFRβ occurs via dynamin-dependent and -independent pathways but their further molecular determinants remained unknown. Here we show that in human fibroblasts expressing endogenous PDGFRβ and stimulated with 50 ng/ml PDGF-BB, ligand-receptor uptake proceeds via parallel routes of clathrin-mediated endocytosis (CME) and clathrin-independent endocytosis (CIE). CME involves the canonical AP2 complex as a clathrin adaptor, while CIE requires RhoA-ROCK, Cdc42 and galectin-3, the latter indicating lectin-mediated internalization via clathr...
Cell Systems, 2017
Highlights d The bile canaliculi network displays geometric heterogeneity within the liver lobule... more Highlights d The bile canaliculi network displays geometric heterogeneity within the liver lobule d Bile flow is driven by osmotic effects and bile canaliculi contractility d A multi-scale model reveals gradients of bile velocity and pressure within the lobule d The multi-scale model predicts drug-induced alterations of bile flow
European Microscopy Congress 2016: Proceedings, 2016
Nature, Sep 24, 2016
An early step in intracellular transport is the selective recognition of a vesicle by its appropr... more An early step in intracellular transport is the selective recognition of a vesicle by its appropriate target membrane, a process regulated by Rab GTPases via the recruitment of tethering effectors. Membrane tethering confers higher selectivity and efficiency to membrane fusion than the pairing of SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) alone. Here we address the mechanism whereby a tethered vesicle comes closer towards its target membrane for fusion by reconstituting an endosomal asymmetric tethering machinery consisting of the dimeric coiled-coil protein EEA1 (refs 6, 7) recruited to phosphatidylinositol 3-phosphate membranes and binding vesicles harbouring Rab5. Surprisingly, structural analysis reveals that Rab5:GTP induces an allosteric conformational change in EEA1, from extended to flexible and collapsed. Through dynamic analysis by optical tweezers, we confirm that EEA1 captures a vesicle at a distance corresponding to its extended conf...
arXiv (Cornell University), Aug 15, 2023
Zeitschrift für Gastroenterologie, 2018
PLOS Computational Biology, 2020
Can three-dimensional, microvasculature networks still ensure blood supply if individual links fa... more Can three-dimensional, microvasculature networks still ensure blood supply if individual links fail? We address this question in the sinusoidal network, a plexus-like microvasculature network, which transports nutrient-rich blood to every hepatocyte in liver tissue, by building on recent advances in high-resolution imaging and digital reconstruction of adult mice liver tissue. We find that the topology of the three-dimensional sinusoidal network reflects its two design requirements of a space-filling network that connects all hepatocytes, while using shortest transport routes: sinusoidal networks are sub-graphs of the Delaunay graph of their set of branching points, and also contain the corresponding minimum spanning tree, both to good approximation. To overcome the spatial limitations of experimental samples and generate arbitrarily-sized networks, we developed a network generation algorithm that reproduces the statistical features of 0.3-mm-sized samples of sinusoidal networks, using multi-objective optimization for node degree and edge length distribution. Nematic order in these simulated networks implies anisotropic transport properties, characterized by an empirical linear relation between a nematic order parameter and the anisotropy of the permeability tensor. Under the assumption that all sinusoid tubes have a constant and equal flow resistance, we predict that the distribution of currents in the network is very inhomogeneous, with a small number of edges carrying a substantial part of the flow. We quantify network resilience in terms of a permeability-at-risk, i.e. permeability as function of the fraction of removed edges. We find that sinusoidal networks are resilient to random removal of edges, but vulnerable to the removal of high-current edges. Our findings suggest the existence of a mechanism counteracting flow inhomogeneity to balance metabolic load on the liver.
1. Background: Provocation tests are widely used in allergology to objectively reveal patients se... more 1. Background: Provocation tests are widely used in allergology to objectively reveal patients sensitivity to specific allergens. The objective quantification of an allergic reaction is a crucial characteristic of the tests. Due to the absence of objective quantitative measurements the conjunctival provocation test (CPT) is a less frequently used method despite its sensitivity and simplicity. We developed a new method AllergoEye based on AI for quantitative evaluation of conjunctival allergic reactions and validated it in a clinical study. 2. Methods: AllergoEye was implemented as a two component system. The first component is based on an Android smartphone camera for imaging the patients eye and the second one is PC based for image analysis and quantification. For AllergoEye validation an open-label, prospective, monocentric study was carried out on 41 patients. Standardized CPT was performed with sequential titration of grass allergen in 4 dilutions with the reaction evaluated by ...
Three dimensional (3D) geometrical models are not only a powerful tool for quantitatively charact... more Three dimensional (3D) geometrical models are not only a powerful tool for quantitatively characterizing complex tissues but also useful for probing structure-function relationships in a tissue. However, these models are generally incomplete due to experimental limitations in acquiring multiple (>4) fluorescent channels simultaneously. Indeed, predictive geometrical and functional models of the liver have been restricted to few tissue and cellular components, excluding important cellular populations such as hepatic stellate cells (HSCs) and Kupffer cells (KCs). Here, we performed deep-tissue immunostaining, multiphoton microscopy, deeplearning techniques, and 3D image processing to computationally expand the number of simultaneously reconstructed tissue structures. We then generated a spatio-temporal singlecell atlas of hepatic architecture (Hep3D), including all main tissue and cellular components at different stages of post-natal development in mice. We used Hep3D to quantitati...
Journal of Cell Biology
Hepatocytes grow their apical surfaces anisotropically to generate a 3D network of bile canalicul... more Hepatocytes grow their apical surfaces anisotropically to generate a 3D network of bile canaliculi (BC). BC elongation is ensured by apical bulkheads, membrane extensions that traverse the lumen and connect juxtaposed hepatocytes. We hypothesize that apical bulkheads are mechanical elements that shape the BC lumen in liver development but also counteract elevated biliary pressure. Here, by resolving their structure using STED microscopy, we found that they are sealed by tight junction loops, connected by adherens junctions, and contain contractile actomyosin, characteristics of mechanical function. Apical bulkheads persist at high pressure upon microinjection of fluid into the BC lumen, and laser ablation demonstrated that they are under tension. A mechanical model based on ablation results revealed that apical bulkheads double the pressure BC can hold. Apical bulkhead frequency anticorrelates with BC connectivity during mouse liver development, consistent with predicted changes in ...
3D ‘ground truth’ images of idealized models of liver tissue ( 0.3 um x 0.3 um x 0.3u m per voxel
tion in early endosomes, cargo to be recycled (exempli-fied by the transferrin receptor [TFR] or ... more tion in early endosomes, cargo to be recycled (exempli-fied by the transferrin receptor [TFR] or low-density li-poprotein receptor [LDLR]) returns to the cell surface via recycling endosomes, whereas cargo destined for degradation (epidermal growth factor receptor [EGFR] *Correspondence:
Proceedings of the 2019 3rd International Conference on Computational Biology and Bioinformatics - ICCBB '19, 2019
High-content screens (HCS) using chemical and genomic interference based on light microscopy and ... more High-content screens (HCS) using chemical and genomic interference based on light microscopy and quantitative image analysis yielded a large amount of multi-parametric (MP) phenotypic data. Such data-sets hold great promise for the understanding of cellular mechanisms by systems biology. However, extracting functional information from data-sets, such as links between cellular processes and the functions of unknown genes, remains challenging. The limitation of HCS analysis lies in the complexity of cellular organization. Here, we assumed that cellular processes have a modular structure, and deconvolved the MP data into separate signals from different cellular modules by Blind Source Separation. We applied a combination of quantitative MP image analysis (QMPIA) and Independent Component Analysis (ICA) to an image-based HCS of endocytosis, the process whereby cells uptake molecules from the outside and distribute them to different sub-cellular organelles. We named our approach Independ...
1 Center for Information Services and High Performance Computing, Technische Universität Dresden,... more 1 Center for Information Services and High Performance Computing, Technische Universität Dresden, 01062 Dresden, Saxony, Germany 2) Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Saxony, Germany 3) UCSF, Cardiovascular Research Institute, Department of Biochemistry and Biophysics, California, USA 4) Chair of Scientific Computing for Systems Biology, Faculty of Computer Science, Technische Universität Dresden, 01187 Dresden, Saxony, Germany 5) Center for Systems Biology Dresden, 01307 Dresden, Saxony, Germany 6) Cluster of Excellence Physics of Life, Technische Universität Dresden, 01187 Dresden, Saxony, Germany
Journal of Cell Biology, 2021
Lumen morphogenesis results from the interplay between molecular pathways and mechanical forces. ... more Lumen morphogenesis results from the interplay between molecular pathways and mechanical forces. In several organs, epithelial cells share their apical surfaces to form a tubular lumen. In the liver, however, hepatocytes share the apical surface only between adjacent cells and form narrow lumina that grow anisotropically, generating a 3D network of bile canaliculi (BC). Here, by studying lumenogenesis in differentiating mouse hepatoblasts in vitro, we discovered that adjacent hepatocytes assemble a pattern of specific extensions of the apical membrane traversing the lumen and ensuring its anisotropic expansion. These previously unrecognized structures form a pattern, reminiscent of the bulkheads of boats, also present in the developing and adult liver. Silencing of Rab35 resulted in loss of apical bulkheads and lumen anisotropy, leading to cyst formation. Strikingly, we could reengineer hepatocyte polarity in embryonic liver tissue, converting BC into epithelial tubes. Our results s...
Journal of Cell Biology, 2021
Delivery of exogenous mRNA using lipid nanoparticles (LNPs) is a promising strategy for therapeut... more Delivery of exogenous mRNA using lipid nanoparticles (LNPs) is a promising strategy for therapeutics. However, a bottleneck remains in the poor understanding of the parameters that correlate with endosomal escape versus cytotoxicity. To address this problem, we compared the endosomal distribution of six LNP-mRNA formulations of diverse chemical composition and efficacy, similar to those used in mRNA-based vaccines, in primary human adipocytes, fibroblasts, and HeLa cells. Surprisingly, we found that total uptake is not a sufficient predictor of delivery, and different LNPs vary considerably in endosomal distributions. Prolonged uptake impaired endosomal acidification, a sign of cytotoxicity, and caused mRNA to accumulate in compartments defective in cargo transport and unproductive for delivery. In contrast, early endocytic/recycling compartments have the highest probability for mRNA escape. By using super-resolution microscopy, we could resolve a single LNP-mRNA within subendosomal...
The Journal of Cell Biology, 2019
Recycling of MT-MMPs to actin-rich membrane-protrusive structures promotes breast cancer invasion... more Recycling of MT-MMPs to actin-rich membrane-protrusive structures promotes breast cancer invasion. This study shows that SNX27–retromer, an endosomal sorting and recycling machinery, interacts with MT1-MMP and regulates its transport to the cell surface, thus promoting matrix invasive activity of the breast cancer cells.
Many cellular organelles, including endosomes, show compartmentalization into distinct functional... more Many cellular organelles, including endosomes, show compartmentalization into distinct functional domains, which however cannot be resolved by diffraction-limited light microscopy. Single molecule localization microscopy (SMLM) offers nanoscale resolution but data interpretation is often inconclusive when the ultrastructural context is missing. Correlative light electron microscopy (CLEM) combining SMLM with electron microscopy (EM) enables correlation of functional sub-domains of organelles in relation to their underlying ultrastructure at nanometer resolution. However, the specific demands for EM sample preparation and the requirements for fluorescent single-molecule photo-switching are opposed. Here, we developed a novel superCLEM workflow that combines triple-colour SMLM (dSTORM & PALM) and electron tomography using semi-thin Tokuyasu thawed cryosections. We applied the superCLEM approach to directly visualize nanoscale compartmentalization of endosomes in HeLa cells. Internaliz...
Functional tissue architecture originates by self-assembly of distinct cell types, following tiss... more Functional tissue architecture originates by self-assembly of distinct cell types, following tissue-specific rules of cell-cell interactions. In the liver, a structural model of the lobule was pioneered by Elias in 1949. This model, however, is in contrast with the apparent random 3D arrangement of hepatocytes. Since then, no significant progress has been made to derive the organizing principles of liver tissue. To solve this outstanding problem, we computationally reconstructed 3D tissue geometry from microscopy images and analyzed it applying soft-condensed-matter-physics concepts. Surprisingly, analysis of the spatial organization of cell polarity revealed that hepatocytes are not randomly oriented but follow a long-range liquid-crystal order. This does not depend exclusively on hepatocytes receiving instructive signals by endothelial cells as generally assumed, since silencing Integrin-β1 disrupted both liquid-crystal order and organization of the sinusoidal network. Our results...
Journal of Cell Science, 2016
Platelet-derived growth factor receptor β (PDGFRβ) is a receptor tyrosine kinase which upon activ... more Platelet-derived growth factor receptor β (PDGFRβ) is a receptor tyrosine kinase which upon activation by PDGF-BB stimulates cell proliferation, migration and angiogenesis. Ligand binding induces intracellular signaling cascades but also internalization of the receptor, eventually resulting in its lysosomal degradation. However, endocytic trafficking of receptors often modulates their downstream signaling. We previously reported that internalization of PDGFRβ occurs via dynamin-dependent and -independent pathways but their further molecular determinants remained unknown. Here we show that in human fibroblasts expressing endogenous PDGFRβ and stimulated with 50 ng/ml PDGF-BB, ligand-receptor uptake proceeds via parallel routes of clathrin-mediated endocytosis (CME) and clathrin-independent endocytosis (CIE). CME involves the canonical AP2 complex as a clathrin adaptor, while CIE requires RhoA-ROCK, Cdc42 and galectin-3, the latter indicating lectin-mediated internalization via clathr...
Cell Systems, 2017
Highlights d The bile canaliculi network displays geometric heterogeneity within the liver lobule... more Highlights d The bile canaliculi network displays geometric heterogeneity within the liver lobule d Bile flow is driven by osmotic effects and bile canaliculi contractility d A multi-scale model reveals gradients of bile velocity and pressure within the lobule d The multi-scale model predicts drug-induced alterations of bile flow
European Microscopy Congress 2016: Proceedings, 2016
Nature, Sep 24, 2016
An early step in intracellular transport is the selective recognition of a vesicle by its appropr... more An early step in intracellular transport is the selective recognition of a vesicle by its appropriate target membrane, a process regulated by Rab GTPases via the recruitment of tethering effectors. Membrane tethering confers higher selectivity and efficiency to membrane fusion than the pairing of SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) alone. Here we address the mechanism whereby a tethered vesicle comes closer towards its target membrane for fusion by reconstituting an endosomal asymmetric tethering machinery consisting of the dimeric coiled-coil protein EEA1 (refs 6, 7) recruited to phosphatidylinositol 3-phosphate membranes and binding vesicles harbouring Rab5. Surprisingly, structural analysis reveals that Rab5:GTP induces an allosteric conformational change in EEA1, from extended to flexible and collapsed. Through dynamic analysis by optical tweezers, we confirm that EEA1 captures a vesicle at a distance corresponding to its extended conf...