Biology subjects

Ghezzi, D.

Publications and source records attributed to Ghezzi, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Comparable phosphene size and contrast properties, but differing detection reliability for optogenetic versus electrical stimulation of macaque V1

Cortical visual prostheses aim to restore vision by stimulating primary visual cortex (V1) to evoke artificial percepts (phosphenes). Electrical stimulation has long served this purpose, and optogenetic approaches promise higher spatial resolution via cell-type specificity. Recent investigations have demonstrated localized behavioral responses to optogenetic V1 stimulation (1--3), but the applied perimetry paradigms cannot dissociate a genuine percept from a reflexive oculomotor response, leaving the perceptual character of optogenetic phosphenes unresolved. To address this gap, two macaques received optogenetic V1 injections guided by laminar electrophysiology and performed detection and discrimination tasks under interleaved electrical, optogenetic, and visual stimulation, enabling direct within-subject comparison. Electrical stimulation reliably evoked detectable percepts (positive d' in 100% of sessions), with thresholds scaling with current, resembling visual contrast-response functions. Optogenetic stimulation was far less reliable, with positive d' in only ~50% of sessions, despite confirmed V1 activation. Despite this reliability difference, optogenetically evoked percepts closely resembled electrically and visually evoked percepts in perceptual character: perceived size (~1{degrees} of visual angle) was comparable across conditions and scaled similarly with eccentricity. Similarly, perceived contrast equivalents (5%-11% visual-contrast equivalent) were broadly comparable across stimulation approaches. These findings indicate that successful optogenetic activation engages the same perceptual encoding mechanisms as electrical and natural vision, but that reliable detection may additionally depend on circuit-level mechanisms not consistently engaged by current optogenetic parameters. The comparable percept size further suggests optogenetic stimulation may not confer the enhanced spatial resolution often proposed as its key advantage.

neuroscience↗

bioRxiv2025

nAPOGEE: A machine-learning platform for clinically actionable pathogenicity assessment of all mitochondrial noncoding variants

Mitochondrial noncoding variants, particularly those in tRNA and rRNA genes, pose significant challenges for clinical interpretation due to heteroplasmy, broad phenotypic heterogeneity where symptoms can overlap with other conditions, and the limited availability of well-established genotype-phenotype correlations. Despite their central role in mitochondrial translation, these variants have remained largely unexplored by the existing variant-effect predictors. Here, we present nAPOGEE, a novel machine-learning framework specifically designed to assess the pathogenicity of all possible single-nucleotide variants in human mitochondrial noncoding RNAs. nAPOGEE integrates two specialized predictors: tAPOGEE, which outperforms existing tools for tRNAs, and rAPOGEE, the first dedicated classifier for mitochondrial rRNA variants. Using curated training datasets, phylogenetic conservation metrics, secondary structure modeling, RNA-specific embeddings, and thermodynamic features, nAPOGEE provides biologically interpretable predictions and posterior probabilities aligned with the ACMG/AMP guidelines. Applied to both curated variant sets and population-scale data, nAPOGEE revealed consistent spatial correlation of the predicted pathogenicity, reflecting underlying structural and evolutionary constraints. This study addresses a longstanding gap in mitochondrial genomics and offers a clinically applicable tool for variant prioritization, reclassification, and research into mitochondrial disease mechanisms.

bioinformatics↗

bioRxiv2025

Genomic evidence for atmospheric chemosynthesis as a defining trait of Ktedonobacteria inhabiting subterranean environments

Members of the class Ktedonobacteria (phylum Chloroflexota) are widespread across a variety of terrestrial environments. They are particularly enriched in silica-rich oligotrophic caves, where they may act as early colonizers, but the genomic bases supporting this pioneering capacity are still unclear. Here, we present a systematic genomic analysis of Ktedonobacteria from diverse ecosystems, with a focus on oligotrophic caves. Cave Ktedonobacteria belong to novel genera of Ktedonobacteraceae and harbor genes supporting a mixotrophic metabolism that combines the use of organic and inorganic substrates as energy and carbon sources. Comparative analyses of all available Ktedonobacteria genomes from diverse environments showed that most metabolic traits, including those enabling atmospheric gas oxidation, are primarily driven by taxonomy. In contrast, genes involved in CO2 fixation are enriched in Ktedonobacteria inhabiting caves. Phylogenetic analysis showed that the RuBisCO of Ktedonobacteria likely represents a novel Form I subtype, which we designate as BAK, reflecting its wide occurrence in thermophilic and acidophilic Bacillota and Actinomycetota inhabiting similar extreme environments. The presence of this subtype across distinct lineages in comparable habitats suggests that it may confer a selective advantage in nutrient-poor settings (like caves) and that its distribution may be subject to horizontal gene transfer. This autotrophic capacity relies on a transaldolase variant of the Calvin-Benson-Bassham cycle that was previously described only in one Firmicutes species. Overall, this study provides genetic evidence supporting the combination of atmospheric gas oxidation with dark CO2 fixation in Ktedonobacteria, highlighting their role as primary producers in oligotrophic ecosystems, including caves.

microbiology↗

bioRxiv2025

Wide visual angle enhances social interaction in a realistic virtual reality environment under simulated artificial vision

Objective. Social interaction largely relies on visual perception. Yet artificial vision research has primarily focused on navigation and object recognition while assessment of social interaction remains scarce. This study investigates how the visual field size in simulated artificial vision impacts social perception in a virtual reality setting. Approach. We assessed the impact of visual field size in sighted participants experiencing simulated artificial vision in a medical practice across three social task categories: indoor identification (searching for an empty chair, identification of body orientation, body appearance, facial expressions, relationship type, role and interpretation of body language), locomotion (tracking and following a moving person), and outdoor observation (person recognition in a cluttered outdoor environment). Main Results. A wide range of social perception and locomotion tasks in structured indoor environments can be completed with a 45{degrees} field of view in simulated artificial vision. Compared to 20{degrees}, the broader visual field not only enhances accuracy but also enables faster task execution and a more precise assessment of ones own performance. Although the benefits of an expanded visual field are limited in cluttered environments, a 45{degrees} visual field represents a clear advantage in social contexts. Significance. These findings highlight the importance of an expanded visual field for artificial vision users in social settings, reinforcing its role in enhancing social cue processing and the ability to follow people. By integrating simulated artificial vision within an immersive virtual reality framework, this study bridges the gap between controlled experimental paradigms and real-world needs and challenges.

bioengineering↗

bioRxiv2023

An actor-model framework for visual sensory encoding

A fundamental challenge in neuroengineering is determining a proper input to a sensory system that yields the desired functional output. In neuroprosthetics, this process is known as sensory encoding, and it holds a crucial role in prosthetic devices restoring sensory perception in individuals with disabilities. For example, in visual prostheses, one key aspect of image encoding is to down-sample the images captured by a camera to a size matching the number of inputs and resolution of the prosthesis. Here, we show that down-sampling an image using the inherent computation of the retinal network yields better performance compared to a learning-free down-sampling encoding. We validated a learning-based approach (actor-model framework) that exploits the signal transformation from photoreceptors to retinal ganglion cells measured in explanted retinas. The actor-model framework generates down-sampled images eliciting a neuronal response in-silico and ex-vivo with higher neuronal reliability to the one produced by original images compared to a learning-free approach (i.e. pixel averaging). In addition, the actor-model learned that contrast is a crucial feature for effective down-sampling. This methodological approach could serve as a template for future image encoding strategies. Ultimately, it can be exploited to improve encoding strategies in visual prostheses or other sensory prostheses such as cochlear or limb.

bioengineering↗

bioRxiv2022

E4F1 COORDINATES PYRUVATE METABOLISM AND THE ACTIVITY OF THE ELONGATOR COMPLEX TO ENSURE PROTEIN TRANSLATION FIDELITY DURING NEURONAL DEVELOPMENT

Pyruvate metabolism defects lead to severe neuropathies such as the Leigh syndrome (LS) but the molecular mechanisms underlying neuronal cell death remain poorly understood. Here, we unravel a connection between pyruvate metabolism and the regulation of the epitranscriptome that is relevant to LS pathogenesis. We identified the transcription factor E4F1 as a key coordinator of AcetylCoenzyme A (AcCoA) production by the pyruvate dehydrogenase complex (PDC) and its utilization as an essential co-factor by the Elongator complex to acetylate tRNAs at the wobble position uridine 34 (U34). E4F1-mediated direct transcriptional regulation of Dlat and Elp3, two genes encoding key subunits of the PDC and of the Elongator complex, respectively, ensured proper translation fidelity and cell survival in the central nervous system (CNS) during mouse embryonic development. Furthermore, analysis of PDH-deficient cells highlighted a crosstalk linking the PDC to ELP3 expression that is perturbed in LS patients.

developmental biology↗

bioRxiv2022

Conformable neural interface based on off-stoichiometry thiol-ene-epoxy thermosets

Off-stoichiometry thiol-ene-epoxy (OSTE+) thermosets have recently gained attention for the rapid prototyping of microfluidic chips because they show low permeability to gases and little absorption of dissolved molecules, they allow direct low-temperature dry bonding without surface treatments, they have a low Youngs modulus, and they can be manufactured via UV polymerisation. The compatibility with standard clean-room processes and the outstanding mechanical properties make OSTE+ an excellent candidate as a novel material for neural implants. Here we exploit OSTE+ to manufacture a conformable multilayer micro-electrocorticography array with 16 platinum electrodes coated with platinum black. The mechanical properties allow device conformability to curved surfaces such as the brain. The low permeability and strong adhesion between layers improve the stability of the device. Acute experiments in mice show the multimodal capacity of the array to record and stimulate the neural tissue by smoothly conforming to the mouse cortex. Devices are not cytotoxic, and immunohistochemistry stainings reveal only modest foreign body reaction after two and six weeks of implantation. This work introduces OSTE+ as a promising material in the field of implantable neural interfaces.

bioengineering↗

bioRxiv2022

Three-dimensional multilayer concentric bipolar electrodes enhance the selectivity of optic nerve stimulation

ObjectiveIntraneural nerve interfaces often operate in a monopolar configuration with a common and distant ground electrode. This configuration leads to a wide spreading of the electric field. Therefore, this approach is suboptimal for intraneural nerve interfaces when selective stimulation is required. ApproachWe designed a multilayer electrode array embedding three-dimensional concentric bipolar electrodes. First, we validated the higher stimulation selectivity of this new electrode array compared to classical monopolar stimulation using simulations. Next, we compared them in-vivo by intraneural stimulation of the rabbit optic nerve and recording evoked potentials in the primary visual cortex. Main resultsSimulations showed that three-dimensional concentric bipolar electrodes provide a high localisation of the electric field in the tissue so that electrodes are electrically independent even for high electrode density. Experiments in-vivo highlighted that this configuration leads to evoked responses with lower amplitude and more localised cortical patterns due to the fewer fibres activated by the electric stimulus in the nerve. SignificanceHighly focused electric stimulation is crucial to achieving high selectivity in fibre activation. The multilayer array embedding three-dimensional concentric bipolar electrodes improves selectivity in optic nerve stimulation. This approach is suitable for other neural applications, including bioelectronic medicine.

bioengineering↗

bioRxiv2021

Virtual reality validation of naturalistic modulation strategies to counteract fading in retinal stimulation

ObjectiveTemporal resolution is a key challenge in artificial vision. Several prosthetic approaches are limited by the perceptual fading of evoked phosphenes upon repeated stimulation from the same electrode. Therefore, implanted patients are forced to perform active scanning, via head movements, to refresh the visual field viewed by the camera. However, active scanning is a draining task, and it is crucial to find compensatory strategies to reduce it. ApproachTo address this question, we implemented perceptual fading in simulated prosthetic vision using virtual reality. Then, we quantified the effect of fading on two indicators: the time to complete a reading task and the head rotation during the task. We also tested if stimulation strategies previously proposed to increase the persistence of responses in retinal ganglion cells to electrical stimulation could improve these indicators. Main resultsThis study shows that stimulation strategies based on interrupted pulse trains and randomisation of the pulse duration allows significant reduction of both the time to complete the task and the head rotation during the task. SignificanceThe stimulation strategy used in retinal implants is crucial to counteract perceptual fading and to reduce active head scanning during prosthetic vision. In turn, less active scanning might improve the patients comfort in artificial vision.

bioengineering↗

bioRxiv2021

A machine-learning algorithm correctly classifies cortical evoked potentials from both natural retinal stimulation and electrical stimulation of the optic nerve

ObjectiveOptic nerves intraneural stimulation is an emerging neuroprosthetic approach to provide artificial vision to totally blind patients. An open question is the possibility to evoke individual non-overlapping phosphenes via selective intraneural optic nerve stimulation. To begin answering this question, first, we aim at showing in preclinical experiments with animals that each intraneural electrode could evoke a distinguishable activity pattern in the primary visual cortex. ApproachWe performed both patterned visual stimulation and patterned electrical stimulation in healthy rabbits while recording evoked cortical activity with an electrocorticogram array in the primary visual cortex. Electrical stimulation was delivered to the optic nerve with the intraneural array OpticSELINE. We used a support vector machine algorithm paired to a linear regression model to classify cortical responses originating from visual stimuli located in different portions of the visual field and electrical stimuli from the different electrodes of the OpticSELINE. Main resultsCortical activity induced by visual and electrical stimulation could be classified with nearly 100% accuracy relative to the specific location in the visual field or electrode in the array from which it originated. For visual stimulation, the accuracy increased with the separation of the stimuli and reached 100% for separation higher than 7 degrees. For electrical stimulation, at low current amplitudes, the accuracy increased with the distance between electrodes, while at higher current amplitudes, the accuracy was nearly 100% already for the shortest separation. SignificanceOptic nerves intraneural stimulation with the OpticSELINE induced discernible cortical activity patterns. These results represent a leap forward for intraneural optic nerve stimulation towards artificial vision.

bioengineering↗

bioRxiv2021

Degradable endovascular neural interface for minimally invasive neural recording and stimulation

Neural recording and stimulation have been widely used to mitigate traumatic injuries, neurodegenerative diseases or mental disorders. Most neural interfaces commonly require invasive surgery, potentially entailing both transient and permanent complications. A promising strategy designed to overcome these risks involves exploiting the cerebrovascular system as an access route to the neural tissue. Here we present a novel endovascular neural interface for neural recording and stimulation, fully polymeric and degradable. This concept might allow for better integration of the device in the body, reduced inflammatory reaction, the possibility of replacing the implant after degradation, and avoiding removal surgeries. The vasculatures strategic distribution and the use of soft polymers for the devices fabrication will permit targeting both the brain vasculature and the peripheral system. Therefore, this novel endovascular neural interface will broaden the range of applications from neurological diseases and mental disorders to bioelectronics medicine.

bioengineering↗

bioRxiv2021

All-polymeric transient neural probe for prolonged in-vivo electrophysiological recordings

Transient bioelectronics has grown fast, opening possibilities never thought before. In medicine, transient implantable devices are interesting because they could eliminate the risks related to surgical retrieval and reduce the chronic foreign body reaction. However, despite recent progress in this area, the short functional lifetime of devices due to short-lived transient metals, which is typically a few days or weeks, still limits the potential of transient medical devices. We report that a switch from transient metals to an entirely polymer-based approach allows for a slower degradation process and a longer lifetime of the transient probe, thus opening new possibilities for transient medical devices. As a proof-of-concept, we fabricated all-polymeric transient neural probes that can monitor brain activity in mice for a few months rather than a few days or weeks. Also, we extensively evaluated the foreign body reaction around the implant during the probes degradation. This kind of devices might pave the way for several applications in neuroprosthetics.

bioengineering↗

bioRxiv2020

Naturalistic spatiotemporal stimulus modulation during epiretinal stimulation increases the persistence of retinal ganglion cell responsivity

ObjectiveRetinal stimulation in blind patients evokes the sensation of discrete points of light called phosphenes, which allows them performing visual guided tasks, such as orientation, navigation, object recognition, object manipulation and reading. However, the clinical benefit of artificial vision in profoundly blind patients is still tenuous, as several engineering and biophysical obstacles keep it away from natural perception. The relative preservation of the inner retinal neurons in hereditary degenerative retinal diseases, such as retinitis pigmentosa, supports artificial vision through the network-mediated stimulation of retinal ganglion cells. However, the response of retinal ganglion cells to repeated electrical stimulation rapidly declines, primarily because of the intrinsic desensitisation of their excitatory network. In patients, upon repetitive stimulation, phosphenes fade out in less than half of a second, which drastically limits the understanding of the percept. ApproachA more naturalistic stimulation strategy, based on spatiotemporal modulation of electric pulses, could overcome the desensitisation of retinal ganglion cells. To investigate this hypothesis, we performed network-mediated epiretinal stimulations paired to electrophysiological recordings in retinas explanted from both male and female retinal degeneration 10 mice. Main resultsThe results showed that the spatial and temporal modulation of the network-mediated epiretinal stimulation prolonged the responsivity of retinal ganglion cells from 400 ms up to 4.2 s. SignificanceA time-varied, non-stationary and interrupted stimulation of the retinal network, mimicking involuntary microsaccades, might reduce the fading of the visual percept and improve the clinical efficacy of retinal implants.

bioengineering↗

bioRxiv2020

Single-pixel epiretinal stimulation with a wide-field and high-density retinal prosthesis for artificial vision

Retinal prostheses hold the promise of restoring artificial vision in profoundly and totally blind people. However, a decade of clinical trials highlighted quantitative limitations hampering the possibility to reach this goal. A key obstacle to suitable retinal stimulation is the ability to independently activate retinal neurons over a large portion of the subjects visual field. Reaching such a goal would significantly improve the perception accuracy in the users of retinal implants, along with their spatial cognition, attention, ambient mapping and interaction with the environment. Here we show a wide-field, high-density and high-resolution photovoltaic epiretinal prosthesis for artificial vision. The prosthesis embeds 10,498 physically and functionally independent photovoltaic pixels allowing for both wide retinal coverage and high-resolution stimulation. Single-pixel illumination reproducibly induced network-mediated responses from retinal ganglion cells at safe irradiance levels. Furthermore, the prosthesis enables a sub-receptive field response resolution for retinal ganglion cells having a dendritic tree larger than the pixels pitch. This approach could allow the restoration of mid-peripheric artificial vision in patients with retinitis pigmentosa.

bioengineering↗

bioRxiv2020

Virtual reality simulation of epi-retinal prosthetic vision highlights the relevance of the visual angle

ObjectiveRetinal prostheses hold the potential to restore artificial vision in blind patients suffering from outer retinal dystrophies. The optimal number, density, and coverage of the electrodes that a retinal prosthesis should have to provide adequate artificial vision in daily activities is still an open question and an important design parameter needed to develop better implants. ApproachTo address this question, we investigated the interaction between the visual angle, the pixel number and the pixel density without being limited by a small electrode count, as in previous research reports. We implemented prosthetic vision in a virtual reality environment in order to simulate the real-life experience of using a retinal prosthesis. We designed four different tasks simulating: object recognition, word reading, perception of a descending step and crossing a street. Main resultsThe results of our study showed that in all the tasks the visual angle played the most significant role in improving the performance of the participant. SignificanceThe design of new retinal prostheses should take into account the relevance of the restored visual angle to provide a helpful and valuable visual aid to profoundly or totally blind patients.

bioengineering↗

bioRxiv2020

Tailored polymeric, photovoltaic, and near-infrared-responsive neuroprosthesis

Organic materials, such as conjugated polymers, are attractive building blocks for bioelectronic interfaces. In particular, organic semiconductors showed excellent performances in light-mediated excitation and silencing of neuronal cells and tissues. However, the main challenges of these organic photovoltaic interfaces compared to inorganic prostheses are the limited stability of conjugated polymers in the aqueous environment and the exploitation of materials only responsive in the visible spectrum. In this report, we show a new photovoltaic organic interface tailored for neuronal stimulation in the near-infrared spectrum. Also, we adjusted the organic materials by chemical modification in order to improve the stability in aqueous environment and to modulate the photoelectrical stimulation efficiency. As proof of principle, we tested this interface for retinal stimulation. Our results provide an efficient, reliable, and stable implant applicable for neural stimulation.

bioengineering↗

bioRxiv2019

Photovoltaic stimulation efficiently evokes network-mediated activity of retinal ganglion cells

ObjectivePhotovoltaic retinal prostheses theoretically offer the possibility of standalone high-resolution electrical stimulation of the retina. However, in artificial vision, achieving locally selective epiretinal stimulation is particularly challenging, on the grounds of axonal activation and electrical cell coupling.\n\nApproachHere we show that electrical and photovoltaic stimulation of dystrophic retinal circuits with capacitive-like pulses leads to a greater efficiency for indirect network-mediated activation of retinal ganglion cells. In addition, a biophysical model of the inner retina stimulation is proposed to investigate the waveform and duration commitments in the genesis of indirect activity of retinal ganglion cells.\n\nMain resultsBoth in-vitro and in-silico approaches suggest that the application of long voltage pulses or gradual voltage changes are more effective to sustainably activate the inner excitatory and inhibitory layers of the retina, thus leading to a reproducible indirect response. The involvement of the inhibitory feedback from amacrine cells in the forming of indirect patterns represents a novel biological tool to locally cluster the response of the retinal ganglion cells.\n\nSignificanceThese results demonstrate that recruiting inner retina cells with epiretinal stimulation enables not only to bypass axonal stimulation but also to obtain a more focal activation thanks to the natural lateral inhibition. In this perspective, the use of capacitive-like waveforms generated by photovoltaic prostheses may allow improving the neural response resolution while standing high-frequency stimulation.

neuroscience↗

bioRxiv2019

Gene editing preserves visual function in a mouse model of retinal degeneration

Inherited retinal dystrophies are a large and heterogeneous group of degenerative diseases caused by mutations in various genes. Given the favourable anatomical and immunological characteristics of the eye, gene therapy holds great potential for their treatment. We used a tailored CRISPR/Cas9-based gene editing system to prevent retinal photoreceptor death in the Rd10 mouse model of retinitis pigmentosa. We tested the gene editing tool in vitro and then used in vivo subretinal electroporation to deliver it to one of the retinas of mouse pups at different stages of photoreceptor differentiation. Three months after gene editing, the treated eye exhibited a higher visual acuity compared to the untreated eye. Moreover, we observed preservation of light-evoked responses both in explanted retinas and in the visual cortex of treated animals. Our study validates a CRISPR/Cas9-based therapy as a valuable new approach for the treatment of retinitis pigmentosa caused by autosomal recessive loss-of-function point mutations.

neuroscience↗