Biology subjects

Pinto, L.

Publications and source records attributed to Pinto, L..

At least 19 recordsLinked to original sources

bioRxiv2026

Simplified model of intrinsically bursting neurons

Rhythmic neural activity underlies essential biological functions such as locomotion, breathing, and feeding. Computational models are widely used to study how such rhythms emerge from interactions between neuron-level and circuit-level dynamics. Intrinsically bursting neurons are key components of many central pattern generators (CPGs), yet existing models span a tradeoff between biological realism and practical usability. Biophysical models involve many parameters that are difficult to tune, whereas abstract models often integrate poorly into neural circuit simulations. We propose a simplified model of intrinsically bursting neurons derived from a reduced non-spiking biophysical formulation. The model integrates readily into neural circuits while enabling direct and independent control of bursting characteristics, including duration, amplitude, and shape. We show that the model reproduces single-unit biophysical responses to diverse stimuli as well as circuit-level activity patterns from crustacean and mammalian CPGs. This model provides a practical tool for studying rhythm generation in neural circuits.

neuroscience↗

bioRxiv2025

A cholinergic mechanism orchestrating task-dependent computation across the cortex

In an ever-changing environment, animals often need to switch between performing different tasks involving distinct sets of cognitive processes. Many such tasks involve neural activity distributed across the cortex, with dynamics that depend on both task demands and behavioral strategy1-17. A fundamental but unanswered question is what circuit mechanisms orchestrate these task-dependent dynamics. Here, we hypothesized that acetylcholine release in the cortex plays a key role. The cortexs only long-range source of this neuromodulator is the basal forebrain cholinergic system, which targets the entire cortical sheet and can individually modulate single regions on sub-second timescales18-26. To test our hypothesis, we first imaged cholinergic axons innervating the cortex while mice switched frequently between two navigational decision-making tasks in virtual reality (VR), only one of which required gradual accumulation of sensory evidence. We found that cholinergic input to the cortex is spatiotemporally heterogeneous and multiplexes sensory, motor, arousal, and cognitive signals in a task- and strategy-dependent fashion, with overall higher activity during evidence accumulation. Crucially, beyond contextual variables, cholinergic activity directly tracked task computations themselves, encoding an evidence-dependent decision variable only in the accumulation task. To test if acetylcholine release is causal to the performance of each task, we optogenetically silenced cholinergic terminals in the cortex while simultaneously imaging excitatory cortical activity. We found that this input is selectively required for evidence accumulation, and for large-scale cortical coding of evidence and choice during the accumulation task. Thus, we have identified a new cholinergic mechanism that orchestrates cortex-wide activity in a task-dependent manner and serves as a key node in the distributed brain network underlying the accumulation of sensory evidence.

neuroscience↗

bioRxiv2025

iPSC derived MSC secretome activates distinct neuroprotective pathways in a preclinical model of Parkinsons disease

Parkinsons disease (PD) is characterized by a progressive loss of dopaminergic neurons, which current therapies fail to address. Mesenchymal stem cells (MSCs) secretome holds promising therapeutic potential; however, the gold standard source - bone marrow (BM) - face scalability limitations. Induced pluripotent stem cells (iPSCs)-derived MSCs (iMSCs) are a rejuvenated and clinically attractive source, yet the effects of their secretome have not been studied in PD. Here, we directly compare the effects of BM-MSCs and iMSCs secretome in a 6-OHDA rat model. Despite few differences in secretome composition, both improved motor function and partially ameliorated anhedonia, but only iMSCs secretome significantly preserved dopaminergic neurons. Proteomic analysis revealed that BM-MSCs secretome activates antioxidant and proteostasis pathways, whereas iMSCs secretome activate broader pro-survival and regenerative pathways, including NRF2-mediated oxidative stress response and mTOR. In addition, iMSC-secretome treatment modulated glutamatergic and GABAergic neurotransmission, suggesting restoration of synaptic homeostasis beyond dopaminergic preservation. These findings demonstrate that iMSCs secretome exerts robust neuroprotective effects and shed light on the mechanisms underlying this scalable and clinically translatable therapy for PD.

neuroscience↗

bioRxiv2025

Working memory expands shared task representations in cortex

Cognition is thought to emerge from the flexible organization of neural activity, yet how this organization reconfigures across behaviors varying in cognitive load remains unclear. We investigated how the structure of working-memory representations in the cortex compares to task representations that do not involve working memory. We used a task-switching paradigm in virtual reality, where mice alternated between a navigation-based working-memory task and a simpler task with matched sensorimotor demands. During behavior, we simultaneously imaged three cortical areas: higher visual area AM, and two association areas--premotor (M2) and retrosplenial cortex. At the single-neuron level, trial-averaged activity appeared similar across tasks. However, pairwise correlations decreased during the working-memory task, particularly in association areas. In addition, the corresponding linear task subspace explained the variance of both tasks equally well, whereas the simpler task subspace failed to do so, suggesting an asymmetric relationship between them. Nonlinear dimensionality reduction revealed a shared low-dimensional structure across tasks. Yet, the organization of neuronal firing fields along this shared structure accounted for the difference in pairwise correlations: in the working-memory task, firing fields were more disjoint, especially among neurons in association areas that formed sequences along the memory dimension. Moreover, the degree of overlap between these firing fields predicted the mices behavioral reliance on working memory. We conclude that behaviors varying in cognitive demands are supported by a single low-dimensional neural structure, which can expand or contract depending on cognitive load. We thus provide a framework for how task representations across the cortex reconfigure to support cognitive processes.

neuroscience↗

bioRxiv2025

Network dynamics underlying activity-timescale differences between cortical regions

Network-level dynamics are thought to be central to computation in the cerebral cortex. Yet, how these dynamics differ across areas remains poorly understood. We leveraged an intrinsic property of cortical regions to tackle this problem -- the timescales over which they spontaneously sustain activity. We first co-registered functional and spatial transcriptomics datasets to show that timescales across the mouse cortex are predicted by many transcript categories, including those that regulate circuit wiring. Next, we used simultaneous two-photon imaging and optogenetics in mice to ask how these putative differences in connectivity lead to distinct network responses to brief, focal excitatory input to a short-timescale visual area, VISp, and a long-timescale frontal area, MOs. MOs neurons were more likely to respond to photostimulation of their neighbors. Moreover, the evoked dynamics of the overall network were much longer lasting in MOs than VISp, due to the more prevalent recruitment of late-responding neurons, which formed reliable activity sequences. Overall, our findings show that, beyond single-neuron timescales, different cortical areas are distinctly wired to sustain input over varying time windows via network dynamics, with important implications for our understanding of cortical computation.

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bioRxiv2025

Cognitive processes are disentangled at cortex-wide scales

Most decisions involve multiple cognitive processes. Recent findings suggest that these processes are distributed across the cortex1-21, but that single regions implement them via orthogonal population-activity patterns14,21-33. How are these local geometries combined across the cortex? Here, we designed a virtual-navigation task for mice that dissociates the accumulation and short-term memory of sensory evidence, and choice. Combining dimensionality reduction and decoding models with cortex-wide widefield Ca2+ imaging, we observed distributed but near-orthogonal coding subspaces for these different cognitive processes, and that this geometry breaks down during erroneous choices. Further, only the memory subspace corresponded to a spontaneous activity-timescale hierarchy, suggesting that it co-opts intrinsic circuit properties. Thus, we reconcile previous findings by showing that cortex-wide dynamics supporting distinct cognitive processes are disentangled.

neuroscience↗

bioRxiv2025

Adaptive changes of cholinergic projections to the nucleus accumbens bidirectionally mediate cocaine reinforcing effects

The laterodorsal tegmentum (LDT) sends critical inputs to distinct reward circuit regions, including the nucleus accumbens (NAc), but their functional role in addiction-related behaviors remains underexplored. Here, we demonstrate that LDT-NAc cholinergic projections undergo cocaine-induced adaptations and modulate cocaine-related behaviors. Using cell type-specific tracing, we show that LDT neurons preferentially innervate NAc medium spiny neurons and cholinergic interneurons. Large-scale in vivo recordings reveal that cocaine pre-exposure induces persistent alterations in both LDT and NAc neuronal dynamics and modifies responses to subsequent cocaine challenge. Remarkably, pre-exposure to cocaine triggers population-specific adaptations in the LDT, selectively enhancing excitability of LDT-NAc-projecting cholinergic neurons while reducing that of non-projecting cholinergic cells. Behaviorally, optogenetic activation of LDT-NAc cholinergic projections enhances cocaine conditioning, whereas their inhibition diminishes cocaines reinforcing effects. Our findings identify LDT-NAc cholinergic inputs as key substrates of cocaine-induced plasticity, and critical mediators of cocaines rewarding properties, introducing a novel component to addiction circuitry.

neuroscience↗

bioRxiv2024

Patterned wireless transcranial optogenetics generates artificial perception

Synthesizing perceivable artificial neural inputs independent of typical sensory channels remains a fundamental challenge in the development of next-generation brain-machine interfaces. Establishing a minimally invasive, wirelessly effective, and miniaturized platform with long-term stability is crucial for creating a clinically meaningful interface capable of mediating artificial perceptual feedback. In this study, we demonstrate a miniaturized fully implantable wireless transcranial optogenetic encoder designed to generate artificial perceptions through digitized optogenetic manipulation of large cortical ensembles. This platform enables the spatiotemporal orchestration of large-scale cortical activity for remote perception genesis via real-time wireless communication and control, with optimized device performance achieved by simulation-guided methods addressing light and heat propagation during operation. Cue discrimination during operant learning demonstrates the wireless genesis of artificial percepts sensed by mice, where spatial distance across large cortical networks and sequential order-based analyses of discrimination performance reveal principles that adhere to general perceptual rules. These conceptual and technical advancements expand our understanding of artificial neural syntax and its perception by the brain, guiding the evolution of next-generation brain-machine communication.

neuroscience↗

bioRxiv2024

Maintenance of taste receptor cell presynaptic sites requires gustatory nerve fibers

The turnover and re-establishment of peripheral taste synapses is vital to maintain connectivity between the primary taste receptor cells and the gustatory neurons which relay taste information from the tongue to the brain. Despite the importance of neuron-taste cell reconnection, mechanisms governing synapse assembly and the specificity of synaptic connections is largely unknown. Here we use the expression of presynaptic proteins, CALHM1 and Bassoon, to probe whether nerve fiber connectivity is an initiating factor for the recruitment of presynaptic machinery in different populations of taste cells. Under homeostatic conditions, the vast majority (>90%) of presynaptic sites are directly adjacent to nerve fibers. In the days immediately following gustatory nerve transection and complete denervation, Bassoon and CALHM1 puncta are markedly reduced. This suggests that nerve fiber innervation is crucial for the recruitment and maintenance of presynaptic sites. In support of this, we find that expression of Bassoon and Calhm1 mRNA transcripts are significantly reduced after denervation. During nerve fiber regeneration into the taste bud, presynaptic sites begin to replenish, but are not as frequently connected to nerve fibers as intact controls ([~]50% compared to >90%). This suggests that gustatory neuron proximity, rather than direct contact, likely drives taste receptor cells to express and aggregate presynaptic proteins at the cell membrane. Together, these data support the idea that trophic factors secreted by gustatory nerve fibers prompt taste receptor cells to produce presynaptic specializations at the cell membrane, which in turn may guide neurons to form mature synapses. These findings provide new insights into the mechanisms driving synaptogenesis and synaptic plasticity within the rapidly changing taste bud environment.

neuroscience↗

bioRxiv2024

Azole resistance: Patterns of amino acid substitutions in Candida sterol 14α-demethylase

The emergence of azole-resistant Candida infections is a major concern. A key mechanism is the gain of resistance through amino acid substitutions in the sterol 14-demethylase, the main target of azole drugs. While numerous resistant substitutions are known, the pattern of such substitutions is unclear. We hypothesized that the resistant substitutions occur disproportionately at the azole-binding sites. We compiled 2,222 instances of azole-resistant substitutions from the literature and performed extensive computational sequence analyses. Altogether there were 169 known substitutions at 133 sites in sterol 14-demethylases of seven Candida species, whereas C. albicans alone had 120 substitutions at 97 sites. Just 10 sites and 18 substitutions (such as Y132F/H, K143R, D116E, and G464S) accounted for 75% of the total instances. Only about 48% of the sites were present within the previously recognized hotspot regions, while just 33% of the known azole-interacting residues had known resistant substitutions, most of them with only a few instances. The literature data on azole-resistant substitutions in Candida appear to be highly biased as a few substitutions such as Y132F/H and K143R were preferentially sought and reported with over 1000 instances, while there were also numerous reports of "resistant" substitutions in azole-susceptible Candida isolates. Our study provides interesting perspectives into azole resistance.

bioinformatics↗

bioRxiv2024

Dynamic representation of appetitive and aversive stimuli in nucleus accumbens shell D1- and D2-medium spiny neurons

The nucleus accumbens (NAc) is a key brain region for motivated behaviors, yet how distinct neuronal populations encode appetitive or aversive stimuli remains undetermined. Using microendoscopic calcium imaging, we tracked NAc shell D1- or D2-medium spiny neurons (MSNs) activity during exposure to stimuli of opposing valence and associative learning. Despite drift in individual neurons coding, both D1- and D2-population activity was sufficient to discriminate opposing valence unconditioned stimuli, but not predictive cues. Notably, D1- and D2-MSNs were similarly co-recruited during appetitive and aversive conditioning, supporting a concurrent role in associative learning. Conversely, when contingencies changed, there was an asymmetric response in the NAc, with more pronounced changes in the activity of D2-MSNs. Optogenetic manipulation of D2-MSNs provided causal evidence of the necessity of this population in the extinction of aversive associations. Our results reveal how NAc shell neurons encode valence, Pavlovian associations and their extinction, and unveil new mechanisms underlying motivated behaviors.

neuroscience↗

bioRxiv2023

Azole resistance: Insights from Y132 substitutions in Candida sterol 14α-demethylase

BackgroundAzole-resistant Candida infections are on the rise. Resistant substitutions at Y132 in sterol 14-demethylase, the key target of azole drugs, are frequent. However, it is unclear why only some Y132 substitutions are favoured or how they exert differential effects on different azoles. Materials and MethodsReported instances of Y132 substitutions were collected from the literature. Extensive molecular dynamics simulations of sterol 14-demethylase bound to fluconazole or VT1161 (VT1) were performed, and the ligand-binding free energies were computed to quantify the effects of various Y132 substitutions on azole binding/interactions. ResultsThree azole-resistant substitutions, Y to C/F/H, were reported at residue position 132 in sterol 14-demethylase. The Y132H was the most common substitution in C. albicans, while it was Y132F in other species. Ligand-binding free energies were -13.81 kcal/mol and -35.04 kcal/mol for fluconazole and VT1, respectively. There were differences in the ligand-binding free energies after substitutions compared to the wild type protein. ConclusionY132F and Y132H were the most frequent substitutions in Candida sterol 14-demethylase. Far higher binding free energy of fluconazole in comparison with VT1 might partly explain its susceptibility to azole-resistant substitutions. The results give key insights into azole resistance, and antifungal drug discovery and optimization.

bioinformatics↗

bioRxiv2023

Gut feeling: Extent of virulence and antibiotic resistance genes in Helicobacter pylori and campylobacteria

BackgroundHelicobacter pylori, a member of campylobacteria, is the leading cause of chronic gastritis and gastric cancer. Virulence and antibiotic resistance of H. pylori are of great concern to public health. However, the relationship between virulence and antibiotic resistance genes in H. pylori in relation to other campylobacteria remains unclear. Materials and MethodsBy using the virulence and comprehensive antibiotic resistance databases, we explored all available 354 complete genomes of H. pylori and compared it with 90 species of campylobacteria for virulence and antibiotic resistance genes/proteins. ResultsOn average, H. pylori had 129 virulence genes, highest among Helicobacter spp. and 71 antibiotic resistance genes, one of the lowest among campylobacteria. Just 2.6% of virulence genes were shared by all campylobacterial members, whereas 9.4% were unique to H. pylori. The cytotoxin-associated genes (cags) seemed to be exclusive to H. pylori. Majority of the isolates from Asia and South America were cag2-negative and many antibiotic resistance genes showed isolate-specific patterns of occurrence. Just 15 (8.8%) antibiotic resistance genes, but 103 (66%) virulence genes including 25 cags were proteomically identified in H. pylori. Arcobacterial members showed large variation in the number of antibiotic resistance genes and there was a positive relation with the genome size. ConclusionLarge repository of antibiotic resistance genes in campylobacteria and a unique set of virulence genes might have important implications in shaping the course of virulence and antibiotic resistance in H. pylori.

bioinformatics↗

bioRxiv2023

Functional network analysis identifies multiple virulence and antibiotic resistance systems in Stenotrophomonas maltophilia

Stenotrophomonas maltophilia, an emerging multidrug-resistant opportunistic bacterium in humans is of major concern for immunocompromised individuals for causing pneumonia and bloodborne infections. This bacterial pathogen is associated with a considerable fatality/case ratio, with up to 100%, when presented as hemorrhagic fever. It is resistant to commonly used drugs as well as to antibiotic combinations. In-silico based functional network analysis is a key approach to get novel insights into virulence and resistance in pathogenic organisms. This study included the protein-protein interaction (PPI) network analysis of 150 specific genes identified for antibiotic resistance mechanism and virulence pathways. Eight proteins, namely, pilL, fliA, Smlt2260, Smlt2267, cheW, Smlt2318, cheZ, and fliM were identified as hub proteins. Further docking studies of selected phytochemicals were performed against the identified hub proteins. Deoxytubulosine and Corosolic acid were found to be potent inhibitors of hub proteins of pathogenic S. maltophilia based on protein-ligand interactive study. Further pharmacophore studies are warranted with these molecules to develop them as novel antibiotics against S. maltophilia.

bioinformatics↗

bioRxiv2023

Astrocytic Foxo1 regulates hippocampal spinogenesis and synaptic plasticity to enhance fear memory

Astrocytes are active players in brain circuits, sensing and responding to neuronal activity, impacting behavior production. Activation of astrocytes triggers intracellular calcium elevations displaying complex spatiotemporal properties. Intracellular calcium activity is thought to underlie synaptic transmission, metabolism, and brain homeostasis modulation. However, the calcium-dependent signaling pathways involved in these processes are poorly understood, representing a critical knowledge gap in this field. To reveal calcium-dependent signaling pathways involved in circuit structure and function, we performed a multi-level analysis of the inositol 1,4,5-triphosphate receptor type 2 knockout (IP3R2 KO) mouse model which lacks somatic calcium elevations specifically in astrocytes. We focused on the hippocampus, a brain region responsible for cognitive function and emotional behaviors. The transcriptomic analysis of hippocampal tissue revealed that the lack of astrocytic somatic calcium causes the differential expression of hundreds of genes. Among these, 76 genes are regulated by the astrocyte-specific Foxo1 transcription factor. This transcription factor is over-expressed in the hippocampal astrocytes of this mouse model and regulates the expression of genes involved in spinogenesis and synaptic coverage. A detailed morphological analysis of hippocampal pyramidal neurons revealed dendrites with a shift to a more immature spine profile. This spine profile shift may underlie previously described a reduction of long-term depression and performance in fear memory tasks observed in this mouse model. Indeed, we confirmed that these mice lacking astrocytic somatic calcium display an enhancement of long-term fear memory. To verify a causal relationship between these structural, synaptic, and behavioral observations, we used a viral approach to induce the over-expression of Foxo1 in hippocampal astrocytes in naive C57BL/6J mice. This viral-driven over-expression of Foxo1 in astrocytes of the stratum radiatum replicated the shift to an immature spine profile in dendrites of pyramidal neurons crossing the territory of these astrocytes and led to a reduction of long-term depression in the same region. Finally, this manipulation was sufficient to enhance long-term fear memory. The detailed characterization of the mouse model lacking astrocytic somatic calcium revealed that astrocytes modulate hippocampal circuit structure and function through Foxo1 signaling to enhance fear memory.

neuroscience↗

bioRxiv2023

Cannabinoid type 2 receptor inhibition enhances the antidepressant and proneurogenic effects of physical exercise after chronic stress

Chronic stress is a major risk factor of neuropsychiatric conditions such as depression. Adult hippocampal neurogenesis (AHN) has emerged as a promising target to counteract stress-related disorders given the ability of newborn neurons to facilitate endogenous plasticity. Recent data sheds light on the interaction between cannabinoids and neurotrophic factors underlying the regulation of AHN, with important effects upon cognitive plasticity and emotional flexibility. Since physical exercise (PE) is known to enhance neurotrophin levels, we hypothesized that PE could engage with cannabinoids to influence AHN and that this would result in beneficial effects under stressful conditions. We therefore investigated the actions of modulating cannabinoid type 2 receptors (CB2R), which are devoid of psychotropic effects, in combination with PE in chronically stressed animals. We found that CB2R inhibition, but not CB2R activation, in combination with PE significantly ameliorated stress-evoked emotional changes and cognitive deficits. Importantly, this combined strategy critically shaped stress-induced changes in AHN dynamics, leading to a significant increase in the rates of cell proliferation and differentiation of newborn neurons, and an overall reduction in neuroinflammation. Together, these results show that CB2Rs are crucial regulators of the beneficial effects of PE in countering the effects of chronic stress. Our work emphasizes the importance of understanding the mechanisms behind the actions of cannabinoids and PE and provides a framework for future therapeutic strategies to treat stress-related disorders that capitalize on lifestyle interventions complemented with endocannabinoid pharmacomodulation.

neuroscience↗

bioRxiv2023

Nucleus accumbens neurons dynamically encode positive and aversive associative learning

To survive, individuals must learn to associate cues in the environment with emotionally relevant outcomes. This association is partially mediated by the nucleus accumbens (NAc), a key brain region of the reward circuit that is mainly composed by GABAergic medium spiny neurons (MSNs), that express either dopamine receptor D1 or D2. Recent studies showed that both populations can drive reward and aversion, however, the activity of these neurons during appetitive and aversive Pavlovian conditioning remains to be determined. Here, we investigated the relevance of D1- and D2-neurons in Pavlovian associations, by measuring calcium transients with fiber photometry during appetitive and aversive Pavlovian tasks. Sucrose was used as a positive unconditioned stimulus (US) and foot shock was used as a negative US. We show that during appetitive Pavlovian conditioning, D1- and D2-neurons exhibit a general decrease in activity in response to CS and to US across learning, with dynamic, and partially overlapping, activity responses to CS and US. During the aversive Pavlovian conditioning, D1- and D2-neurons showed an increase in the activity in response to the CS and to the US (shock). Our data supports a synchronous role for D1- and D2-neurons in appetitive and aversion processing.

neuroscience↗

bioRxiv2022

Modeling communication and switching nonlinear dynamics in multi-region neural activity

Understanding how multiple brain regions interact to produce behavior is a major challenge in systems neuroscience, with many regions causally implicated in common tasks such as sensory processing and decision making. However, a precise description of interactions between regions remains an open problem. Moreover, neural dynamics are nonlinear, non-stationary, and can vary dramatically across sessions, days, and animals. Here, we propose multi-region, switching dynamical systems (MR-SDS), a probabilistic model of multiple latent interacting systems that evolve with switching nonlinear dynamics and communication between regions. MR-SDS includes directed interactions between brain regions, allowing for estimation of state-dependent communication signals, and accounts for sensory inputs effects, history effects, and heterogeneity across days and animals. We show that our model accurately recovers latent trajectories, vector fields underlying switching nonlinear dynamics, and cross-region communication profiles in two simulations. We then apply our method to two large-scale, multi-region neural datasets involving mouse decision making. The first includes hundreds of neurons per region, recorded simultaneously at single-cell-resolution across 3 distant cortical regions. The second is a mesoscale widefield dataset of 8 adjacent cortical regions imaged across both hemispheres. On these multi-region datasets, our model outperforms existing piece-wise linear multi-region models and reveals multiple distinct dynamical states and a rich set of cross-region communication profiles.

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