Biology subjects

Elices, I.

Publications and source records attributed to Elices, I..

4 recordsLinked to original sources

bioRxiv2022

An electrophysiological and behavioral model of Paramecium, the "swimming neuron"

Paramecium is a large unicellular organism that swims in fresh water using cilia. When stimulated by various means (mechanically, chemically, optically, thermally), it often swims backward then turns and swims forward again in a new direction: this is called the avoiding reaction. This reaction is triggered by a calcium-based action potential. For this reason, several authors have called Paramecium the "swimming neuron". Here we present an empirically constrained model of its action potential based on electrophysiology experiments on live immobilized paramecia, together with simultaneous measurement of ciliary beating using particle image velocimetry. Using these measurements and additional behavioral measurements of free swimming, we extend the electrophysiological model by coupling calcium concentration to kinematic parameters, turning it into a swimming model. In this way, we obtain a model of autonomously behaving Paramecium. Finally, we demonstrate how the modeled organism interacts with an environment, can follow gradients and display collective behavior. This work provides a modeling basis for investigating the physiological basis of autonomous behavior of Paramecium in ecological environments. Author SummaryBehavior depends on a complex interaction between a variety of physiological processes, the body and the environment. We propose to examine this complex interaction in an organism consisting of a single excitable and motile cell, Paramecium. The behavior of Paramecium is based on trial and error: when it encounters an undesirable situation, it backs up and changes direction. This avoiding reaction is triggered by an action potential. Here we developed an empirically constrained biophysical model of Parameciums action potential, which we then coupled to its kinematics. We then demonstrate the potential of this model in investigating various types of autonomous behavior, such as obstacle avoidance, gradient-following and collective behavior.

neuroscience↗

bioRxiv2018

RTHybrid: a standardized and open-source real-time software model library for experimental neuroscience

Closed-loop technologies provide novel ways of online observation, control and bidirectional interaction with the nervous system, which help to study complex non-linear and partially observable neural dynamics. These protocols are often difficult to implement due to the temporal precision required when interacting with biological components, which in many cases can only be achieved using real-time technology. In this paper we introduce RTHybrid (www.github.com/GNB-UAM/RTHybrid), a free and open-source software that includes a neuron and synapse model library to build hybrid circuits with living neurons in a wide variety of experimental contexts. In an effort to encourage the standardization of real-time software technology in neuroscience research, we compared different open-source real-time operating system patches, RTAI, Xenomai 3 and Preempt-RT, according to their performance and usability. RTHybrid has been developed to run over Linux operating systems supporting both Xenomai 3 and Preempt-RT real-time patches, and thus allowing an easy implementation in any laboratory. We report a set of validation tests and latency benchmarks for the construction of hybrid circuits using this library. With this work we want to promote the dissemination of standardized, user-friendly and open-source software tools developed for open- and closed-loop experimental neuroscience.

neuroscience↗

bioRxiv2018

Automatic adaptation of model neurons and connections to build hybrid circuits with living networks

Hybrid circuits built by creating mono- or bi-directional interactions among living cells and model neurons and synapses are an effective way to study neuron, synaptic and neural network dynamics. However, hybrid circuit technology has been largely underused in the context of neuroscience studies mainly because of the inherent difficulty in implementing and tuning this type of interactions. In this paper, we present a set of algorithms for the automatic adaptation of model neurons and connections in the creation of hybrid circuits with living neural networks. The algorithms perform model time and amplitude scaling, drift compensation, goal-driven synaptic and model tuning/calibration and also automatic parameter mapping. These algorithms have been implemented in RTHybrid, an open-source library that works with hard real-time constraints. We provide validation examples by building hybrid circuits in a central pattern generator. The results of the validation experiments show that the proposed dynamic adaptation facilitates building hybrid circuits and closed-loop communication among living and artificial model neurons and connections. Furthermore contributes to characterize system dynamics, achieve control, automate experimental protocols and extend the lifespan of the preparations.

neuroscience↗

bioRxiv2018

Robust dynamical invariants in sequential neural activity

By studying different sources of temporal variability in central pattern generator circuits, in this paper we unveil distinct aspects of the instantaneous balance between flexibility and robustness in sequential dynamics -a property that characterizes many systems that display neural rhythms. The level of irregularity and coordination was characterized using intrinsic time references and intervals in long recordings of the pyloric central pattern generator. The analysis demonstrated strong robustness of transient dynamics in keeping not only the activation sequences but also specific cycle-by-cycle temporal relationships in the form of dynamical invariants. The rich dynamics of neurons and connections balance flexibility and coordination to readily negotiate the interactions between neurons and produce the resultant rhythm. In particular, two dynamical invariants were identified between time intervals that build the sequence, existing even outside steady states. We suggest that invariant temporal sequence relationships could be present in other networks, including those related to brain rhythms, and underlie rhythm programming and functionality.

neuroscience↗