Periodic Reporting for period 2 - SALAMANDRA (Decoding the organization and regeneration of locomotor neuronal networks in tetrapods by integrating genomics, systems neuroscience, numerical modeling, and biorobotics)
Reporting period: 2023-03-01 to 2024-08-31
The goals of this project are (1) to decipher how the interplay between central and peripheral mechanisms controls locomotion in four legged animals (tetrapods) and (2) to delineate the reorganization of motor circuits linked to functional regeneration after spinal cord lesion. We take advantage of the evolutionarily conserved traits of neural structures in vertebrates to address these two fundamental questions by using salamanders as model organisms. Salamanders are best suited to these aims for two main reasons: First, because they have an anatomically simplified nervous system, which yet possesses the main features of all tetrapods; second, because they have unique regeneration abilities among vertebrates and can functionally repair their spinal cord after full transection. Taking an interdisciplinary approach, we investigate the dynamic interactions between the nervous system, the body, and its environment before and after spinal cord lesion. We combine numerical models of locomotor neural circuits, robotics, and advanced functional analyses in genetically modified salamanders in a way that allows us to test biological data in neuromechanical models (simulations and robots) and, conversely, to validate model-based predictions in animals. Through the concerted and tightly collaborative activities in our laboratories, implementing state of the art assays ranging from the molecular to the organism level, we expect to create a blueprint of tetrapod locomotion control: how appropriate movements are generated in response to various environmental or intrinsic stimuli, and how such function can be recovered after injury. The synergy between our groups of complementary expertise will boost scientific research at multiple levels, not only in the field of neuroscience but also in regeneration research, robotics, and numerical modeling.
At EPFL, the team of Auke Ijspeert has made good progress on computational modeling and robotic experiments. They have developed a simulation framework called FARMS (Framework for Animal and Robot Modeling and Simulation) with biomechanical models of the salamander in different environments (abstract presentations at Society of Neuroscience (SfN) meeting 2022, and Arreguit et al. BioRxiv 2023). Ijspeert’s team has also developed different types of models of the locomotor circuits, ranging from coupled oscillator circuits to integrate-and-fire neural networks (abstract presentations at SfN 2022, Adaptive Motion in Animals and Machines conference (AMAM), Motor Control in Spinal Circuits and Beyond meeting 2023). Finally, his team has tested some of these circuits on amphibious robots (abstract at AMAM 2023), and is finalizing the construction of a new salamander robot with more sensors than previous versions. A review article of the integration of feedforward and feedback control in the neuromechanics of vertebrate locomotion has also been published (Ijspeert and Daley, JEB 2023).
At Karolinska Institute, the team of Andras Simon has started generating genetically modified Pleurodeles for the visualization, recording and manipulation of neuronal activity. They are now testing and validating the first generations of these animals together with the Ryczko’s lab. To facilitate genome modifications and to characterize neuronal subtypes, Simon’s team obtained a high-quality genome assembly and several transcriptome sets (Brown et al. BioRxiv 2022). The transcriptome dataset has already proved itself instrumental to classify neurons in the Pleurodeles brain (Woych et al. Science 2022), and these tools will also be used to further characterize the cellular composition of the locomotor circuitry. They have established and characterized a spinal cord transection injury model that leads to impaired locomotion and subsequent recovery of walking and swimming (presentations at SfN 2022, Salamandra workshop 2023, ISRB 2023). They have collected videos of walking and swimming salamanders in the context of this experimental paradigm that are being analyzed by Ryczko’s team using deep learning (presentations at SfN 2022, Salamandra workshop 2023, ISRB 2023). The team also established preclinical MRI methods that allowed them to image longitudinally the nervous system of the same animals non-invasively (presentations at SfN 2022, Salamandra workshop 2023, ISRB 2023). To characterize the cellular substrates of natural locomotion and functional regeneration after spinal cord injury, they have generated single nucleus RNA sequencing data of key timepoints along the regeneration process (presentations at SfN 2022, Salamandra workshop 2023, ISRB 2023).
At Université de Sherbrooke, the team of Dimitri Ryczko has successfully developed the use of deep learning to analyze motor behaviors in salamanders before and after spinal cord injury (abstract presentations at FENS 2022, SfN 2022). The team also provided an anatomical and electrophysiological characterization of brainstem neurons that send the locomotor commands to the spinal cord (abstract presentations at FENS 2022, SfN 2022). The team has worked with Simon’s team to validate the Pleurodeles transgenic lines experimentally (presentations at Salamandra workshop 2023, Evolution of Motor Circuits Across Vertebrate Species meeting 2022 France, AMAM 2023 Japan). His lab also published reviews about the locomotor system in Journal of Neurophysiology and the Neuroscientist.
A list of publications and conference participations (oral presentations and posters) is available on the Salamandra project website: https://salamandra.org/(opens in new window)
At Karolinska Institute, the team of Andras Simon has started generating genetically modified Pleurodeles for the visualization, recording and manipulation of neuronal activity. They are now testing and validating the first generations of these animals together with the Ryczko’s lab. To facilitate genome modifications and to characterize neuronal subtypes, Simon’s team obtained a high-quality genome assembly and several transcriptome sets (Brown et al. BioRxiv 2022). The transcriptome dataset has already proved itself instrumental to classify neurons in the Pleurodeles brain (Woych et al. Science 2022), and these tools will also be used to further characterize the cellular composition of the locomotor circuitry. They have established and characterized a spinal cord transection injury model that leads to impaired locomotion and subsequent recovery of walking and swimming (presentations at SfN 2022, Salamandra workshop 2023, ISRB 2023). They have collected videos of walking and swimming salamanders in the context of this experimental paradigm that are being analyzed by Ryczko’s team using deep learning (presentations at SfN 2022, Salamandra workshop 2023, ISRB 2023). The team also established preclinical MRI methods that allowed them to image longitudinally the nervous system of the same animals non-invasively (presentations at SfN 2022, Salamandra workshop 2023, ISRB 2023). To characterize the cellular substrates of natural locomotion and functional regeneration after spinal cord injury, they have generated single nucleus RNA sequencing data of key timepoints along the regeneration process (presentations at SfN 2022, Salamandra workshop 2023, ISRB 2023).
At Université de Sherbrooke, the team of Dimitri Ryczko has successfully developed the use of deep learning to analyze motor behaviors in salamanders before and after spinal cord injury (abstract presentations at FENS 2022, SfN 2022). The team also provided an anatomical and electrophysiological characterization of brainstem neurons that send the locomotor commands to the spinal cord (abstract presentations at FENS 2022, SfN 2022). The team has worked with Simon’s team to validate the Pleurodeles transgenic lines experimentally (presentations at Salamandra workshop 2023, Evolution of Motor Circuits Across Vertebrate Species meeting 2022 France, AMAM 2023 Japan). His lab also published reviews about the locomotor system in Journal of Neurophysiology and the Neuroscientist.
A list of publications and conference participations (oral presentations and posters) is available on the Salamandra project website: https://salamandra.org/(opens in new window)
Three main achievements of the project so far are the following. First, the high-quality genome assembly and transcriptome obtained by the team of Simon (Brown et al. BioRxiv 2022) is essential to identify the cell types in the nervous system, but also to generate transgenic lines. The transcriptome dataset uncovered neuron classes in the Pleurodeles brain (Woych et al. Science 2022). By the end of the project we expect to generate atlases of cell types and states in the newt spinal cord and hindbrain.
Second, the new transgenic lines developed by the team of Simon and validated experimentally by the team of Ryczko should allow us to bridge the gap between genetically defined cell types and behavior, as done in other species such as mice or zebrafish. Understanding the injury response and regenerative tissue substrate at multiple levels including locomotion analyses will help in the understanding of locomotion.
Third, an important achievement is the development of the Framework for Animal and Robot Modeling and Simulation (FARMS) (Arreguit et al. BioRxiv 2023). This accessible and user-friendly platform is a key tool for our neuromechanical modeling work, and will help us as well as other researchers to easily explore the complex interactions between the nervous system, musculoskeletal structures, and their environment in animals and robots.
Second, the new transgenic lines developed by the team of Simon and validated experimentally by the team of Ryczko should allow us to bridge the gap between genetically defined cell types and behavior, as done in other species such as mice or zebrafish. Understanding the injury response and regenerative tissue substrate at multiple levels including locomotion analyses will help in the understanding of locomotion.
Third, an important achievement is the development of the Framework for Animal and Robot Modeling and Simulation (FARMS) (Arreguit et al. BioRxiv 2023). This accessible and user-friendly platform is a key tool for our neuromechanical modeling work, and will help us as well as other researchers to easily explore the complex interactions between the nervous system, musculoskeletal structures, and their environment in animals and robots.