Reconstructing wells from high density regions extracted from super-resolution single particle trajectories

Parutto, Pierre; Heck, Jennifer; Heisenberg, Martin; Holcman, David

doi:10.1101/642744

Cited by 2 publications

(3 citation statements)

References 25 publications

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“…From this local map, we kept only the ensemble that has a density of >80% of the central bin value. We collected the trajectory points falling into these bins and from which we computed the corresponding ellipse through their covariance matrix (41). Last, when ellipses overlap, we applied an iterative procedure that merges two overlapping ellipses by computing the ellipse based on the ensemble of points falling in each ellipse.…”

Section: Lysosome Velocitymentioning

confidence: 99%

The structure and global distribution of the endoplasmic reticulum network are actively regulated by lysosomes

et al. 2020

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The endoplasmic reticulum (ER) comprises morphologically and functionally distinct domains: sheets and interconnected tubules. These domains undergo dynamic reshaping in response to changes in the cellular environment. However, the mechanisms behind this rapid remodeling are largely unknown. Here, we report that ER remodeling is actively driven by lysosomes, following lysosome repositioning in response to changes in nutritional status: The anchorage of lysosomes to ER growth tips is critical for ER tubule elongation and connection. We validate this causal link via the chemo- and optogenetically driven repositioning of lysosomes, which leads to both a redistribution of the ER tubules and a change of its global morphology. Therefore, lysosomes sense metabolic change in the cell and regulate ER tubule distribution accordingly. Dysfunction in this mechanism during axonal extension may lead to axonal growth defects. Our results demonstrate a critical role of lysosome-regulated ER dynamics and reshaping in nutrient responses and neuronal development.

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Section: Lysosome Velocitymentioning

confidence: 99%

The structure and global distribution of the endoplasmic reticulum network are actively regulated by lysosomes

et al. 2020

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“…Data from SPT allowed us to reconstruct the lysosome motion density. The high-density regions were extracted from the trajectories using a procedure derived from ( 34 ): the number of points falling into square bins of width Δx = 480 nm was counted to construct the density map. From this map, high-density regions, called seeds, were defined as the fraction with 5% higher-density bins.…”

Section: Methodsmentioning

confidence: 99%

“…From this local map, we kept only the ensemble that have a density > 80% of the central bin value. We collected the trajectory points falling into these bins and from which we computed the corresponding ellipse through their covariance matrix ( 34 ). Finally, when ellipses overlap, we applied an iterative procedure that merge two overlapping ellipses by computing the ellipse based on the ensemble of points falling in each ellipse.…”

Section: Methodsmentioning

confidence: 99%

The structure and global distribution of the endoplasmic reticulum network is actively regulated by lysosomes

Lü

Tartwijk

Lin

et al. 2020

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28The endoplasmic reticulum (ER) comprises morphologically and functionally distinct domains, 29 sheets and interconnected tubules. These domains undergo dynamic reshaping, in response to 30 changes in the cellular environment. However, the mechanisms behind this rapid remodeling 31 within minutes are largely unknown. Here, we report that ER remodeling is actively driven by 32 lysosomes, following lysosome repositioning in response to changes in nutritional status. The 33 anchorage of lysosomes to ER growth tips is critical for ER tubule elongation and connection. We 34 validate this causal link via the chemo-and optogenetically driven re-positioning of lysosomes, 35 which leads to both a redistribution of the ER tubules and its global morphology. Lysosomes sense 36 metabolic change in the cell and regulate ER tubule distribution accordingly. Dysfunction in this 37 mechanism during axonal extension may lead to axonal growth defects. Our results demonstrate a 38 critical role of lysosome-regulated ER dynamics and reshaping in nutrient responses and neuronal 39 development. 40 41 Main text 42 43The structure of the ER is constantly adapted for the particular needs of the cell (1): the dynamic 44 transitions between ER sheets and tubules allow it to rapidly respond to the changing cellular 45 environment. A group of ER-shaping proteins have been identified as maintaining ER morphology 46 (1), mutations in which are linked to diseases such as hereditary spastic paraplegias (HSPs) (2). 47 (3, 4). Previous work has shown that ER tubule elongation can be driven by three mechanisms: 1/ 50 force generation by motors moving along microtubules (5), which can be classified as sliding, 2/ 51 coupling to microtubule growth using a tip assembly complex (TAC), and 3/ hitchhiking by 52 connecting to other organelles. Whether such reshaping in local domains of the ER tubules could 53 lead to the global reorganization and redistribution of ER remains an open question, and, if this is 54 the case, how is this process regulated? The ER is known to contact other motile organelles, 55 including endosomes, lysosomes, mitochondria, peroxisomes et cetera (6). Among these, 56 lysosomes are particularly interesting, as they make a great number of contacts with the ER (7) 57 and their positioning is regulated by different nutritional status (8). Although ER has been reported 58 to regulate lysosome motions (9), it is not clear whether lysosomes can modulate ER reshaping 59 and distribution, for example via coupled motion (4). We hypothesized that a causal link exists 60 between lysosome motion and ER redistributing and asked whether this provides a mechanism for 61 ER morphological response to nutritional status, given that lysosomes are known to act as signaling 62 hubs for metabolic sensing (10). 63 We first investigated the correlation of motions between lysosomes and the ER network by rapid 64 live-cell imaging. We visualized ER with GFP-tagged vesicle-associated membrane protein-65 associated protein A (VAP...

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Reconstructing wells from high density regions extracted from super-resolution single particle trajectories

Cited by 2 publications

References 25 publications

The structure and global distribution of the endoplasmic reticulum network are actively regulated by lysosomes

The structure and global distribution of the endoplasmic reticulum network are actively regulated by lysosomes

The structure and global distribution of the endoplasmic reticulum network is actively regulated by lysosomes

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