Biology subjects

Borges, F. d. S.

Publications and source records attributed to Borges, F. d. S..

4 recordsLinked to original sources

bioRxiv2025

Closed-Loop Connectivity Best Supports Angular Tuning and Sleep Dynamics in a Biophysical Thalamocortical Circuit Model

Despite recent advancements in mapping thalamic and cortical projections, the specific organization of intrathalamic and corticothalamic connectivity remains elusive. Current experimental approaches cannot definitively determine whether these connections are arranged in reciprocal (closed-) or non-reciprocal (open-loop) circuits. We developed a biophysically detailed multi-compartmental model of the mouse whisker pathway, built on anatomical and physiological data. We showed that closed-loop intrathalamic projections between the thalamocortical (TC) relay neurons in the ventral posteromedial nucleus and the inhibitory neurons in the thalamic reticular nucleus (TRN) best reproduce thalamic spiking and local field potential responses across awake and sleep states. Increasing the percentage of closed-loop projections regulates the angular tuning in the awake state, while also supporting spindle oscillations during sleep. We also showed that direct activation of closed-loop corticothalamic feedback (CT[->]TC and CT[->]TRN), simulating TC inputs, sharpens the angular tuning in the thalamus. These results contribute to resolving a long-standing question regarding the organization of intrathalamic projections, offering insights into how thalamo-cortical circuits balance precise sensory tuning with robust oscillatory rhythms across behavioral states. Moreover, all model resources are open-source and available to other researchers interested in studying thalamocortical circuits. Author summaryA long standing question in the study of thalamocortical interactions is whether neurons in the thalamus form so-called open- or closed-loops when they project within the thalamus and to the cortex. In this study, we used a detailed computational model of the thalamic neurons in the whisker pathway of the mouse with realistic biophysics to investigate this question. We evaluated the impact of different connectivity arrangements in reproducing the activity of thalamic neurons observed during wakefulness and sleep. Our results show that a closed-loop circuit arrangement provides the best alternative to reproduce wake and sleep neuronal responses, highlighting the importance of computational modeling as a tool to disentangle thalamic circuit organization. We also showed that closed-loop projections from the cortex to the thalamus help further amplify the selectivity of thalamic neurons, suggesting a similar organization of corticothalamic projections. We hope our predictions can inform future experiments, and elucidate principles of thalamocortical connectivity that can be generalized across other thalamocortical motifs besides the whisker pathway and across species.

neuroscience↗

bioRxiv2023

Leishmania Ribosomal Protein (RP) paralogous genes compensate each others expression maintaining protein native levels

In the protozoan parasite Leishmania, most of the genes encoding for ribosomal proteins (RPs) are present as two or more copies in the genome, their untranslated regions (UTRs) are predominantly divergent, and might be associated with a distinct regulation of the paralogous genes expression. Here, we investigated the expression profiles of two RPs (S16 and L13a) encoded by duplicated genes in Leishmania major. The genes encoding for S16 protein have identical CDSs and divergent UTRs while the L13a CDSs diverge in two amino acids with divergent UTRs. Using CRISPR/Cas9 genomic editing system, we generated knockout ({Delta}) and tagged transfectants for each paralog of L13a and S16. Combining tagged and {Delta} cell lines we show that the expression of both RPS16 and RPL13a isoforms differ throughout the parasite development with one of the isoforms being always more abundant than its respective copy. Additionally, compensatory expression was observed for each paralog when one of the isoforms was deleted, evidencing functional conservation of these proteins. Such phenomenon is related to post-translational processes, since the compensation happened at the protein levels, with no alterations observed at the transcript levels. Ribosomal profiles for RPL13a point out a standard behavior for these paralogues as already reported for other RPs in trypanosomatids, showing its interaction with heavy RNA-protein complexes. The identification of sets of proteins binding specifically to the 3UTRs of either the high or less abundant transcripts suggests a possible role of these proteins to differently control the levels of expression of these RP genes. In addition, conserved cis-elements were identified in the 3UTRs of RPS16 or RPL13a; among these, exclusive cis-elements for the more or for the less expressed transcripts were identified.

molecular biology↗

bioRxiv2023

The Role of Potassium and Calcium Currents in the Bistable Firing Transition

AO_SCPLOWBSTRACTC_SCPLOWHealthy brains display a wide range of firing patterns, from synchronized oscillations during slowwave sleep to desynchronized firing during movement. These physiological activities coexist with periods of pathological hyperactivity in the epileptic brain, where neurons can fire in synchronized bursts. Most cortical neurons are pyramidal regular spiking cells (RS) with frequency adaptation and do not exhibit bursts in current-clamp experiments (in vitro). In this work, we investigate the transition mechanism of spike-to-burst patterns due to slow potassium and calcium currents, considering a conductance-based model of a cortical RS cell. The joint influence of potassium and calcium ion channels on high synchronous patterns is investigated for different synaptic couplings (gsyn) and external current inputs (I). Our results suggest that slow potassium currents play an important role in the emergence of high-synchronous activities, as well as in the spike-to-burst firing pattern transitions. This transition is related to bistable dynamics of the neuronal network, where physiological asynchronous states coexist with pathological burst synchronization. The hysteresis curve of the coefficient of variation of the inter-spike interval demonstrates that a burst can be initiated by firing states with neuronal synchronization. Furthermore, we notice that high-threshold (IL) and low-threshold (IT) ion channels play a role in increasing and decreasing the parameter conditions (gsyn and I) in which bistable dynamics occur, respectively. For high values of IL conductance, a synchronous burst appears when neurons are weakly coupled and receive more external input. On the other hand, when the conductance IT increases, higher coupling and lower I are necessary to produce burst synchronization. In light of our results, we suggest that channel subtype-specific pharmacological interactions can be useful to induce transitions from pathological high bursting states to healthy states.

neuroscience↗

bioRxiv2022

Large-scale biophysically detailed model of somatosensory thalamocortical circuits in NetPyNE

The primary somatosensory cortex (S1) of mammals is critically important in the perception of touch and related sensorimotor behaviors. In 2015, the Blue Brain Project developed a groundbreaking rat S1 microcircuit simulation with over 31,000 neurons with 207 morpho-electrical neuron types, and 37 million synapses, incorporating anatomical and physiological information from a wide range of experimental studies. We have implemented this highly-detailed and complex S1 model in NetPyNE, using the data available in the Neocortical Microcircuit Collaboration Portal. NetPyNE provides a Python high-level interface to NEURON and allows defining complicated multiscale models using an intuitive declarative standardized language. It also facilitates running parallel simulations, automates the optimization and exploration of parameters using supercomputers, and provides a wide range of built-in analysis functions. This will make the S1 model more accessible and simpler to scale, modify and extend in order to explore research questions or interconnect to other existing models. Despite some implementation differences, the NetPyNE model preserved the original cell morphologies, electrophysiological responses and spatial distribution for all 207 cell types; and the connectivity properties of all 1941 pathways, including synaptic dynamics and short-term plasticity (STP). The NetPyNE S1 simulations produced reasonable physiological firing rates and activity patterns across all populations. The network generated a 1 Hz oscillation comparable to the original model in vitro-like state. By then reducing the extracellular calcium concentration, the model reproduced the original S1 in vivo-like states with asynchronous activity. These results validate the original study using a new modeling tool. Simulated local field potentials (LFPs) exhibited realistic oscillatory patterns and features, including distance- and frequency-dependent attenuation. The model was extended by adding thalamic circuits, including 6 distinct thalamic populations with intrathalamic, thalamocortical and corticothalamic connectivity derived from experimental data. The thalamic model reproduced single known cell and circuit-level dynamics, including burst and tonic firing modes and oscillatory patterns, providing a more realistic input to cortex and enabling study of thalamocortical interactions. Overall, our work provides a widely accessible, data-driven and biophysically-detailed model of the somatosensory thalamocortical circuits that can be employed as a community tool for researchers to study neural dynamics, function and disease.

neuroscience↗