Biology subjects

Parutto, P.

Publications and source records attributed to Parutto, P..

5 recordsLinked to original sources

bioRxiv2025

Endoplasmic Reticulum Geometry Dictates Neuronal Bursting via Calcium Store Refill Rates

The endoplasmic reticulum (ER)s continuous morphology is tightly controlled by ER-shaping proteins, whose genetic or expression defects drive a spectrum of neurodegenerative disorders from Hereditary Spastic Paraplegia to Alzheimers disease. Why perturbations in ER morphology manifest specifically in neurons remains unknown. Here, by coupling visualisation of global sub-Hz firing bursts to ER ultrastructural manipulations in hiPSC-derived cortical neurons, alongside physical simulations, we establish a key ER structure-function principle: neuronal ER architecture dictates Ca2+ replenishment speed. Altering ER structure hinders network ER luminal connectivity and Ca2+ propagation from refill points at plasma membrane contact sites, impairing the ERs capability to supply repetitive Ca2+ bursts. The ER morpho-regulatory control of Ca2+ refill speed thus constitutes a switch on neuronal activity. These results expose the selective vulnerability of Ca2+-firing cells to ER structural disruptions, rationalising ER dysfunction in neurodegeneration. This mechanism could apply universally to Ca2+-firing cells.

cell biology↗

bioRxiv2021

High-throughput super-resolution single particle trajectory analysis reconstructs organelle dynamics and membrane re-organization

Super-resolution imaging can generate thousands of single-particle trajectories. These data can potentially reconstruct subcellular organization and dynamics, as well as measure disease-linked changes. However, computational methods that can derive quantitative information from such massive datasets are currently lacking. Here we present data analysis and algorithms that are broadly applicable to reveal local binding and trafficking interactions and organization of dynamic sub-cellular sites. We applied this analysis to the endoplasmic reticulum and neuronal membrane. The method is based on spatio-temporal time window segmentation that explores data at multiple levels and detects the architecture and boundaries of high density regions in areas that are hundreds of nanometers. By statistical analysis of a large number of datapoints, the present method allows measurements of nano-region stability. By connecting highly dense regions, we reconstructed the network topology of the ER, as well as molecular flow redistribution, and the local space explored by trajectories. Segmenting trajectories at appropriate scales extracts confined trajectories, allowing quantification of dynamic interactions between lysosomes and the ER. A final step of the method reveals the motion of trajectories relative to the ensemble, allowing reconstruction of dynamics in normal ER and the atlastin-null mutant. Our approach allows users to track previously inaccessible large scale dynamics at high resolution from massive datasets. The SPtsAnalysis algorithm is available as an ImageJ plugin that can be applied by users to large datasets of overlapping trajectories and offer a standard of SPTs metrics.

cell biology↗

bioRxiv2021

Endoplasmic Reticulum morphological regulation by RTN4/NOGO modulates neuronal regeneration by slowing luminal transport

Cell and tissue functions rely on an elaborate intracellular transport system responsible for distributing bioactive molecules with high spatiotemporal accuracy. The tubular network of the Endoplasmic Reticulum (ER) constitutes a system for the delivery of luminal solutes it stores, including Ca2+, across the cell periphery. The physical nature and factors underlying the ERs functioning as a fluidics system are unclear. Using an improved ER transport visualisation methodology combined with optogenetic Ca2+ dynamics imaging, we observed that ER luminal transport is modulated by natural ER tubule narrowing and dilation, directly proportional to the amount of an ER membrane morphogen, Reticulon 4 (RTN4). Consequently, the ER morphoregulatory effect of RTN4 defines ERs capacity for peripheral Ca2+ delivery and thus controls axonogenesis. Excess RTN4 limited ER luminal transport, Ca2+ release and iPSC-derived cortical neurons axonal extension, while RTN4 elimination reversed the effects. SummaryIntracellular transport through the lumen of the ER network is modulated through narrowing/dilation of ER tubules by a membrane morphogen - RTN4, a process controlling axonogenesis by limiting the delivery of ER-stored Ca2+.

cell biology↗

bioRxiv2020

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

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 within minutes 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 re-positioning of lysosomes, which leads to both a redistribution of the ER tubules and its global morphology. 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.

cell biology↗

bioRxiv2019

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

Large amount of super-resolution single particle trajectories has revealed that the cellular environment is enriched in heterogenous regions of high density, which remain unexplained. The biophysical properties of these regions are characterized by a drift and their extension (a basin of attraction) that can be estimated from an ensemble of trajectories. We develop here two statistical methods to recover the dynamics and local potential wells (field of force and boundary) using as a model a truncated Ornstein-Ulhenbeck process. The first method uses the empirical distribution of points, which differs inside and outside the potential well, while the second focuses on recovering the drift field. Finally, we apply these two methods to voltage-gated calcium channels and phospholipids moving on the surface of neuronal cells and recover the energy and size of these high-density regions with nanometer precision.

biophysics↗