Biology subjects

Mateus, J. C.

Publications and source records attributed to Mateus, J. C..

5 recordsLinked to original sources

bioRxiv2026

Closed-loop control of in vitro neuronal activity using reinforcement learning after in silico pre-training

Controlling specific neuronal dynamics with electrical stimulation is critical for therapeutic neuromodulation, yet deriving optimal control policies remains challenging due to the complex and non-stationary nature of biological neuronal networks. While reinforcement learning (RL) offers a powerful closed-loop control framework, its reliance on prolonged stimulus-driven exploration is difficult to reconcile with the physiological limits of living tissue. Here, we demonstrate an in silico-to-in vitro transfer strategy that achieves efficient state-dependent control of network bursting in cultured neurons. The transferred policy outperforms heuristic controls, while maintaining constrained stimulation usage. Concurrent calcium imaging reveals the mechanistic basis of the learned policy: the agent optimizes stimulation spatially and temporally, exploiting local network topology and intrinsic physiological temporal dynamics. These results establish in vitro brain-on-chip cultures as a tractable stepping stone for RL-based neuromodulation and demonstrate that effective control policies can be derived in biophysically calibrated digital twins and transferred directly to living networks.

neuroscience↗

bioRxiv2024

Stress-actuated Flexible Microelectrode Arrays for Activity Recording in 3D Neuronal Cultures

Microelectrode arrays (MEAs) are instrumental in monitoring electrogenic cell populations, such as neuronal cultures, allowing high precision measurements of electrical activity. Although three-dimensional neuronal cultures replicate the behavior of in vivo systems better than two-dimensional models, conventional planar MEAs are not well suited to capture activity within such networks. Novel MEA geometries can overcome this difficulty, but often at the cost of increased fabrication complexity. Here, we used the stress mismatch between thin film layers to fabricate MEAs with vertical electrodes, using methods compatible with established microfabrication protocols. A micrometric SiO2 hinge enables control over the bending angle of flexible polyimide structures with embedded electrodes. The performance of the patterned electrodes was assessed before and after stress actuation, through impedance measurements, voltage noise mapping, and neuronal activity recordings. 3D MEAs with 30x30 {micro}m2 electrodes showed an impedance of 0.96 {+/-} 0.07 M{Omega} per electrode and detected neuronal activity spikes with amplitudes as high as 400 {micro}V. These results demonstrate the potential of the developed methods to provide a scalable approach to fabricate 3D MEAs, enabling enhanced recording capabilities for in vitro neuronal cultures.

bioengineering↗

bioRxiv2024

Influence of asymmetric microchannels in the structure and function of engineered neuronal circuits

Understanding the intricate structure-function relationships of neuronal circuits is crucial for unraveling how the brain sustains efficient information transfer. In specific brain regions, like the hippocampus, neurons are organized in layers and form unidirectional connectivity, which is thought to help ensure controlled signal flow and information processing. In recent years, researchers have tried emulating these structural principles by providing cultured neurons with asymmetric environmental cues, namely microfluidics microchannels that promote directed axonal growth. Even though a few reports have claimed achieving unidirectional connectivity of in vitro neuronal circuits, given the lack of functional characterization, whether this structural connectivity correlates with functional connectivity remains unknown. We have replicated and tested the performance of asymmetric microchannel designs previously reported in the literature to be successful in the promotion of directed axonal growth, as well as other custom variations. A new variation of "Arrowhead", termed "Rams", was the best-performing motif with a [~]76% probability per microchannel of allowing strictly unidirectional connections at 14 days in vitro. Importantly, we assessed the functional implications of these different asymmetric microchannel designs. For this purpose, we combined custom microfluidics with microelectrode array (MEA) technology to record the electrophysiological activity of two segregated populations of hippocampal neurons ("Source" and "Target"). This functional characterization revealed that up to [~]94% of the spiking activity recorded along microchannels with the "Rams" motif propagates towards the "Target" population. Moreover, our results indicate that these engineered circuits also tended to exhibit network-level synchronizations with defined directionality. Overall, this characterization of the structure-function relationships promoted by asymmetric microchannels has the potential to provide insights into how neuronal circuits use specific network architectures for effective computations. Moreover, the here-developed devices and approaches may be used in a wide range of applications, such as disease modeling or preclinical drug screening.

neuroscience↗

bioRxiv2021

Nanoscale patterning of in vitro neuronal circuits

Methods for patterning neurons in vitro have gradually improved and are used to investigate questions difficult to address in or ex vivo. Though these techniques guide axons between groups of neurons, multiscale control of neuronal connectivity, from circuits to synapses, is yet to be achieved in vitro. As studying neuronal circuits with synaptic resolution in vivo poses significant challenges, an in vitro alternative could serve as a testbed for in vivo experiments or as a platform for validating biophysical and computational models. In this work we use a combination of electron beam and photolithography to create polydimethylsiloxane (PDMS) structures with features ranging from 150 nanometers to a few millimeters. Leveraging the difference between average axon and dendritic spine diameters, we restrict axon growth while allowing spines to pass through nanochannels to guide synapse formation between small groups of neurons (i.e. nodes). We show this technique can be used to generate large numbers of isolated feed-forward circuits where connections between nodes are restricted to regions connected by nanochannels. Using a genetically encoded calcium indicator in combination with fluorescently tagged post synaptic protein, PSD-95, we demonstrate functional synapses can form in this region. Although more work needs to be done to control connectivity in vitro, we believe this is a significant step in that direction.

neuroscience↗

bioRxiv2021

Topologically controlled circuits of human iPSC-derived neurons for electrophysiology recordings

Bottom-up neuroscience, which consists of building and studying controlled networks of neurons in vitro, is a promising method to investigate information processing at the neuronal level. However, in vitro studies tend to use cells of animal origin rather than human neurons, leading to conclusions that might not be generalizable to humans and limiting the possibilities for relevant studies on neurological disorders. Here we present a method to build arrays of topologically controlled circuits of human induced pluripotent stem cell (iPSC)-derived neurons. The circuits consist of 4 to 50 neurons with mostly unidirectional connections, confined by microfabricated polydimethylsiloxane (PDMS) membranes. Such circuits were characterized using optical imaging and microelectrode arrays (MEAs). Electrophysiology recordings were performed on circuits of human iPSC-derived neurons for at least 4.5 months. We believe that the capacity to build small and controlled circuits of human iPSC-derived neurons holds great promise to better understand the fundamental principles of information processing and storing in the brain.

neuroscience↗