Biology subjects

Gil, R.

Publications and source records attributed to Gil, R..

4 recordsLinked to original sources

bioRxiv2024

Activation mapping in multi-center rat sensory-evoked functional MRI datasets using a unified pipeline.

Functional Magnetic Resonance Imaging (fMRI) in rodents is pivotal for understanding the mechanisms underlying Blood Oxygen Level-Dependent (BOLD) signals and phenotyping animal models of disorders, amongst other applications. Despite its growing use, comparing rodent fMRI results across different research sites remains challenging due to variations in experimental protocols. Here, we aggregated and analyzed 22 sensory-evoked rat fMRI datasets from 12 imaging centers, totaling scans from 220 rats, to assess the consistency of results across diverse protocols. We applied a standardized preprocessing pipeline and evaluated the impact of different hemodynamic response function models on group and individual level activity patterns. Our analysis revealed inter-dataset variability attributed to differences in experimental design, anesthesia protocols, and imaging parameters. We identified robust activation clusters in all (22/22) datasets. The comparison between stock human models implemented in software and rat-specific models showed significant variations in the resulting statistical maps. Our findings emphasize the necessity for standardized protocols and collaborative efforts to improve the reproducibility and reliability of rodent fMRI studies. We provide open access to all datasets and analysis code to foster transparency and further research in the field.

neuroscience↗

bioRxiv2024

Evidence for a push-pull interaction between superior colliculi in monocular dynamic vision mode

Visual perception can operate in two distinct vision modes - static and dynamic - that have been associated with different neural activity regimes in the superior colliculus (SC). The static vision mode (low flashing frequencies) is associated with strong SC activation modulated by cortical gain and inhibitory intertectal effects, while the dynamic vision mode (high flashing frequencies) evokes the continuity illusion, with associated suppression of SC neural activity. However, the pathway-wide mechanisms underpinning the dynamic vision mode remain poorly understood, especially in terms of corticotectal and tectotectal feedback. Here, we harness rat functional MRI combined with brain lesions to investigate whole-pathway interactions in the dynamic vision mode. In the SC, we find contralateral suppression of activity opposing positive ipsilateral neural activation upon monocular visual stimulation in the dynamic vision mode. A cortical amplification effect was confirmed for both static and dynamic vision modes through cortical lesions, while further lesioning ipsilateral SC led to a boost in the contralateral negative signals, suggesting an active push-pull interaction between ipsilateral and contralateral SCs during the dynamic vision mode regime. This push-pull interaction is specific to the dynamic vision mode; in the static vision mode, both SCs show similar response polarities. These results highlight hitherto unreported frequency-dependent modulations in the tectotectal pathway and further challenge the contemporary notion that intertectal connections solely serve as reciprocal inhibitory mechanisms for avoiding visual blur during saccade occurrence. One Sentence SummaryOpposing signals between superior colliculi in the dynamic vision mode suggest an active push-pull interaction within the tectotectal commissural pathway.

neuroscience↗

bioRxiv2022

Activation/suppression balances in rat Superior Colliculus encode the visual continuity illusion

When visual stimuli are presented at a sufficiently high temporal frequency, visual perception shifts from the static to dynamic vision mode, thereby facilitating a continuity illusion which is key for correctly identifying continuous and moving objects and placing them in the context of the surrounding environment. However, how this continuity illusion is encoded along the entire visual pathway remains poorly understood, with disparate Flicker Fusion Frequency (FFF) thresholds measured at retinal, cortical, and behavioural levels. Here, we hypothesized that these disparities may suggest that other brain areas may be involved in encoding the shift from static to dynamic vision modes. We employ a comprehensive approach encompassing behavioural measurements, whole brain activation mapping with high fidelity functional MRI (fMRI), and local electrophysiological validation for studying the mechanisms underlying the shift from static to dynamic vision modes in the rat. Our behavioural measurements reported an FFF threshold proxy of 18{+/-}2 Hz. At the network level, functional MRI revealed that the superior colliculus (SC) exhibits marked signal transitions from positive to negative fMRI signal regimes at the behaviourally measured FFF threshold surrogates, with a strong linear correlation between fMRI signal and behaviour, while thalamic and cortical visual areas displayed a significantly poorer correlation with the behaviour. fMRI-driven neurometric curves approximated the behavioural psychometric curve in SC but not in the other visual areas. Electrophysiological recordings in SC suggested that these fMRI signals transitions arise from strong neural activation/suppression at low/high frequency regimes, respectively, and that a transition between these regimes occurs around the measured FFF threshold proxies. Lesions in V1 further reinforced that these transitions originate in SC. Combined, our data suggests a critical role for SC in encoding temporal frequency discriminations, in particular the shifts from the static to the dynamic vision modes.

neuroscience↗

bioRxiv2021

The Thousand Polish Genomes Project- a national database of Polish variant allele frequencies

Although Slavic populations account for over 3.5% of world inhabitants, no centralized, open source reference database of genetic variation of any Slavic population exists to date. Such data are crucial for either biomedical research and genetic counseling and are essential for archeological and historical studies. Polish population, homogenous and sedentary in its nature but influenced by many migrations of the past, is unique and could serve as a good genetic reference for middle European Slavic nations. The aim of the present study was to describe first results of analyses of a newly created national database of Polish genomic variant allele frequencies. Never before has any study on the whole genomes of Polish population been conducted on such a large number of individuals (1,079). A wide spectrum of genomic variation was identified and genotyped, such as small and structural variants, runs of homozygosity, mitochondrial haplogroups and Mendelian inconsistencies. The allele frequencies were calculated for 943 unrelated individuals and released publicly as The Thousand Polish Genomes database. A precise detection and characterisation of rare variants enriched in the Polish population allowed to confirm the allele frequencies for known pathogenic variants in diseases, such as Smith-Lemli-Opitz syndrome (SLOS) or Nijmegen breakage syndrome (NBS). Additionally, the analysis of OMIM AR genes led to the identification of 22 genes with significantly different cumulative allele frequencies in the Polish (POL) vs European NFE population. We hope that The Thousand Polish Genomes database will contribute to the worldwide genomic data resources for researchers and clinicians.

genomics↗