Periodic Reporting for period 2 - OrganellenanoComp (Computational methods and modeling to decipher organelle nanophysiology)
Période du rapport: 2022-09-01 au 2024-02-29
What is the problem/issue being addressed?
Nanophysiology of dendritic spines, synapses, nanodomains remains unclear: we reconstructed the flow and trafficking inside organelles, based on novel SPTs analysis and characterize nanoregions of ~80nm to identify their role (Parutto et al 2019 and 2022). This project bridges the molecular level (calcium dynamics), nano-compartments, organelle interactions, cellular interactions, synaptic circuits.
As calcium regulation in mitochondria remains unknown, we studied in L Kushnireva, etal International journal of molecular sciences 23 (20), 12321, Dynamic Regulation of Mitochondrial [Ca2+] in Hippocampal Neurons, showing calcium dynamics interaction with organelles (WP1.1). Many key physiological functions are played by mitochondria such as regulation of Ca2+ signaling that requires specialized structural and functional contacts with the smooth endoplasmic reticulum (ER), observed in immature neurons and astrocytes in vivo.
Why is it important for society?
This research bring
1-new understanding for fundamental processes of brain function at subcellular level
2- new mathematical analysis, modeling and simulations of calcium in nanodomains
3-novel algorithm that can be used by the community.
4-this research wll bring novel concepts that inlage our knowledge of science.
What are the overall objectives?
By developing computational methods, data analysis, stochastic simulations and algorithms, we unravel the physiology of nanodomains in neurons. The models are diffusion and electro-diffusion in complex structures. We have explored how the local organization can sustain several physiological functions, such as Ca2+ homeostasis and voltage regulation in neurons and astrocytes, between various organelles such as ER. Deriving biological functions from structures was one of our main purposes.
We developed novel approaches to extract features from large numbers of SPTs and retrieve parameters and information such as residence times of Ca2+ in nanodomains.
We developed mathematical analysis (singular perturbation methods), especially in the context of electrodiffusion.
By adopting a multidisciplinary approach combining data originating from SPTs, electrophysiology using nanopipettes and voltage dyes, our goal was to
1) Decipher the properties of neuronal, located between or inside ER and mitochondria organelles, based on diffusion. I investigated Ca2+ exchange in physiological conditions, such as spontaneous activity in neurons;
2) Analyze and model voltage sensitive indicators and nanopipettes data using electrodiffusion model;
3) Reconstruct flow and trafficking inside organelles, based on novel SPTs analysis and characterize nanoregions of ~80nm to identify their role.
Nanophysiology of dendritic spines, synapses, nanodomains remains unclear: we reconstructed the flow and trafficking inside organelles, based on novel SPTs analysis and characterize nanoregions of ~80nm to identify their role (Parutto et al 2019 and 2022). This project bridges the molecular level (calcium dynamics), nano-compartments, organelle interactions, cellular interactions, synaptic circuits.
As calcium regulation in mitochondria remains unknown, we studied in L Kushnireva, etal International journal of molecular sciences 23 (20), 12321, Dynamic Regulation of Mitochondrial [Ca2+] in Hippocampal Neurons, showing calcium dynamics interaction with organelles (WP1.1). Many key physiological functions are played by mitochondria such as regulation of Ca2+ signaling that requires specialized structural and functional contacts with the smooth endoplasmic reticulum (ER), observed in immature neurons and astrocytes in vivo.
Why is it important for society?
This research bring
1-new understanding for fundamental processes of brain function at subcellular level
2- new mathematical analysis, modeling and simulations of calcium in nanodomains
3-novel algorithm that can be used by the community.
4-this research wll bring novel concepts that inlage our knowledge of science.
What are the overall objectives?
By developing computational methods, data analysis, stochastic simulations and algorithms, we unravel the physiology of nanodomains in neurons. The models are diffusion and electro-diffusion in complex structures. We have explored how the local organization can sustain several physiological functions, such as Ca2+ homeostasis and voltage regulation in neurons and astrocytes, between various organelles such as ER. Deriving biological functions from structures was one of our main purposes.
We developed novel approaches to extract features from large numbers of SPTs and retrieve parameters and information such as residence times of Ca2+ in nanodomains.
We developed mathematical analysis (singular perturbation methods), especially in the context of electrodiffusion.
By adopting a multidisciplinary approach combining data originating from SPTs, electrophysiology using nanopipettes and voltage dyes, our goal was to
1) Decipher the properties of neuronal, located between or inside ER and mitochondria organelles, based on diffusion. I investigated Ca2+ exchange in physiological conditions, such as spontaneous activity in neurons;
2) Analyze and model voltage sensitive indicators and nanopipettes data using electrodiffusion model;
3) Reconstruct flow and trafficking inside organelles, based on novel SPTs analysis and characterize nanoregions of ~80nm to identify their role.
We study Ca2+ equilibrium in mitochondria and also in the ER, using the store-operated Ca2+ entry (SOCE) machinery.
WP1.1: We also revelaed a new model of ER reffiling, based on STIM protein as the intra-store calcium sensor and Orai as the plasma membrane Ca2+ channel, activated by STIM. We modeled ER refilling by a Poissonian slow time scale of ~100ms (dissimiated in Basnayake et al, Sc Adv 2021). Results were reported in 2022 Meditarneen meeting in dubrovnik.
WP1.2: Calcium spontaneous activity driven by extreme statistic diffusion. We obtain novel computation (K. Basnayake, Plos Biology 2019, Toste et al, Euro. Phys B, 2021).We simulated Brownian trajectories in the vicinity of channels and use classical Markov chain to estimate the opening probability.
WP2.1: We recently simulated voltage dynamics in nonadomains such as dendritic spine. Voltage distribution in nanodomains remained poorly understood, despite several theoretical efforts, which has used the electroneutrality assumption in very simplified geometry such as cylinder.
We developed approaches to study voltage distribution and electro-diffusion using Poisson-Nernst Planck (PNP) in complex nanodomains: we found novel result about voltage distribution with non-local electroneutrality (Tricot et al, J. Math Bio 2021).
WP 2.3 We recently study the voltage distribution in spines and glia protrusions revealed by nanopipettes. we develop a deconvolution method to recover the time scale and voltage from the signal changes during several electrophysiological protocols ( Coll. with Rouach lab.). We found novel electrophyiological motifs in dendrites (aritlce in revision in journal called Small) .
WP1.1: We also revelaed a new model of ER reffiling, based on STIM protein as the intra-store calcium sensor and Orai as the plasma membrane Ca2+ channel, activated by STIM. We modeled ER refilling by a Poissonian slow time scale of ~100ms (dissimiated in Basnayake et al, Sc Adv 2021). Results were reported in 2022 Meditarneen meeting in dubrovnik.
WP1.2: Calcium spontaneous activity driven by extreme statistic diffusion. We obtain novel computation (K. Basnayake, Plos Biology 2019, Toste et al, Euro. Phys B, 2021).We simulated Brownian trajectories in the vicinity of channels and use classical Markov chain to estimate the opening probability.
WP2.1: We recently simulated voltage dynamics in nonadomains such as dendritic spine. Voltage distribution in nanodomains remained poorly understood, despite several theoretical efforts, which has used the electroneutrality assumption in very simplified geometry such as cylinder.
We developed approaches to study voltage distribution and electro-diffusion using Poisson-Nernst Planck (PNP) in complex nanodomains: we found novel result about voltage distribution with non-local electroneutrality (Tricot et al, J. Math Bio 2021).
WP 2.3 We recently study the voltage distribution in spines and glia protrusions revealed by nanopipettes. we develop a deconvolution method to recover the time scale and voltage from the signal changes during several electrophysiological protocols ( Coll. with Rouach lab.). We found novel electrophyiological motifs in dendrites (aritlce in revision in journal called Small) .
We developed a new ImageJ software published in Parutto et al, Cell Methods Reports, 2022
We expect to increase the quality of the software.
We expect to increase the quality of the software.