Biology subjects

Milicevic, N.

Publications and source records attributed to Milicevic, N..

7 recordsLinked to original sources

bioRxiv2026

Flavonoid chronotherapy normalizes circadian dynamics and sleep architecture in mice with painful nerve injury

Neuropathic pain (NP) is linked to disrupted sleep and circadian abnormalities upon painful peripheral nerve injury. By performing spared nerve injury (SNI) in circadian reporter PER2::LUC mice, we characterized the real-time changes in rhythmicity of the core clock gene Per2 in the pain-regulating dorsal root ganglia (DRG), and the sleep-wake cycle using wireless EEG/EMG under NP conditions. We further evaluated whether the clock-resynchronizing flavonoids, nobiletin (2 mg/kg/day) and tangeretin (1.8 mg/kg/day), administered continuously via osmotic minipumps for two weeks, could restore circadian dynamics and alleviate pain-related behaviour. Both flavonoids alleviated SNI-induced dynamic hypersensitivity in PER2::LUC mice on post-surgical day 14. SNI increased the amplitude of Per2 rhythms in the DRGs, which was restored to pre-surgical levels by administration of flavonoids. In addition, tangeretin showed sleep-restoring properties upon SNI by alleviating disturbances in NREM sleep and wakefulness. These results support targeting circadian disruption as a potential chronotherapeutic approach to alleviate NP.

neuroscience↗

bioRxiv2025

Shapley Fields Reveal Chemotopic Organization in the Mouse Olfactory Bulb Across Diverse Chemical Feature Sets

Representations of chemical features in the neural activity of the olfactory bulb (OB) are not well-understood, unlike the neural code for stimuli of the other sensory modalities. This is because the space of olfactory stimuli lacks a natural coordinate system, and this significantly complicates characterizing neural receptive fields (tuning curves), analogous to those in the other sensory modalities. The degree to which olfactory tuning is spatially organized across the OB, often referred to as chemotopy, is also not well-understood. To advance our understanding of these aspects of olfactory coding, we introduce an interpretable method of Shapley fields, as an olfactory analog of retinotopic receptive fields. Shapley fields are spatial distributions of chemical feature importance for the tuning of OB glomeruli. We used this tool to investigate chemotopy in the OB with diverse sets of chemical features using widefield epifluorescence recordings of the mouse dorsal OB in response to stimuli across a wide range of the chemical space. We found that Shapley fields reveal a weak chemotopic organization of the chemical feature sensitivity of dorsal OB glomeruli. This organization was consistent across animals and mostly agreed across very different chemical feature sets: (i) the expert-curated PubChem database features and (ii) features derived from a Graph Neural Network trained on human olfactory perceptual tasks. Moreover, we found that the principal components of the Shapley fields often corresponded to single commonly accepted chemical classification groups, that therefore could be "recovered" from the neural activity in the mouse OB. Our findings suggest that Shapley fields may serve as a chemical feature-agnostic method for investigating olfactory perception.

neuroscience↗

bioRxiv2024

Circadian Rhythms in Murine Ocular Tissues including Sclera are affected by Neurobasal A Medium Preincubation, Mouse Strain, but not Sex

PurposeOur understanding of ocular clocks has been profoundly advanced by the development of real-time recording of bioluminescence of PER2::LUC knock-in mouse explants. However, the effect of sex, mouse strain and culturing conditions on ocular clocks remains unknown. Here, we studied the role these variables play on PER2::LUC bioluminescence rhythms of ocular tissues: retinas, corneas and posterior eye cups (PEC). We also tested the hypothesis that the sclera contains a circadian oscillator by using scraped PEC as a proxy. MethodsRetinas, corneas, intact and scraped PECs were obtained from male and female PER2::LUC knock-in mice maintained on either a pigmented C57BL/6J or albino RjOrl:SWISS background. PER2::LUC bioluminescence rhythms in ocular tissues were measured using a Lumicycle(R). ResultsWe compared PER2::LUC bioluminescence rhythms between ocular tissues and found that all ocular tissues oscillated, including the scraped PEC, which was previously not known to oscillate. The rhythms in scraped PECs had lower amplitudes, longer periods and distinct acrophases compared to other ocular tissues. Ocular tissues of RjOrl:SWISS mice oscillated with higher amplitudes compared to the ones of C57BL/6J, with corneal rhythms being most affected by mouse strain. A 24h preincubation with Neurobasal A medium enhanced rhythms of ocular tissues, whereas sex differences were not detected for these rhythms. ConclusionsWe discovered a novel oscillator in the sclera. PER2::LUC bioluminescence rhythms in murine ocular tissues are enhanced by Neurobasal A medium preincubation, mouse strain but not sex.

neuroscience↗

bioRxiv2023

Stereopy: modeling comparative and spatiotemporal cellular heterogeneity via multi-sample spatial transcriptomics

Tracing cellular dynamic changes across conditions, time, and space is crucial for understanding the molecular mechanisms underlying complex biological systems. However, integrating multi-sample data in a unified and flexible way to explore cellular heterogeneity remains a major challenge. Here, we present Stereopy, a flexible and versatile framework for modeling and dissecting comparative and spatiotemporal patterns in multi-sample spatial transcriptomics with interactive data visualization. To optimize this flexible framework, we have developed three key components: a multi-sample tailored data container, a scope controller, and an analysis transformer. Furthermore, Stereopy showcases three transformative applications supported by pivotal algorithms. Firstly, the multi-sample cell community detection (CCD) algorithm introduces an innovative capability to detect specific cell communities and identify genes responsible for pathological changes in comparable datasets. Secondly, the spatially resolved temporal gene pattern inference (TGPI) algorithm represents a notable advancement in detecting important spatiotemporal gene patterns while concurrently considering spatial and temporal features, which enhances the identification of important genes, domains and regulatory factors closely associated with temporal datasets. Finally, the 3D niche-based regulation inference tool, named NicheReg3D, reconstructs the 3D cell niches to enable the inference of cell-gene interaction network within the spatial texture, thus bridging intercellular communications and intracellular regulations to unravel the intricate regulatory mechanisms that govern cellular behavior. Overall, Stereopy serves as both a bioinformatics toolbox and an extensible framework that provides researchers with enhanced data interpretation abilities and new perspectives for mining multi-sample spatial transcriptomics data.

bioinformatics↗

bioRxiv2023

CDK5 activity in retinal pigment epithelium contributes to gap junction dynamics during phagocytosis

Retinal pigment epithelium (RPE) at the back of the eye is a monolayer of cells with an extensive network of gap junctions that contributes to retinal health in a multitude of ways. One of those roles is the phagocytosis of photoreceptor outer segments. This renewal is under circadian regulation and peaks after light onset. Connexin 43 (Cx43) is the most predominantly expressed gap junction protein in RPE. In this study, we examine how gap junctions and specifically, Cx43 phosphorylation, contribute to phagocytosis in both human embryonic stem cell derived RPE and mouse RPE monolayers. We show that both Rac1 and CDK5 have differences in protein localization at different points in phagocytosis, and that by using their effectors, the capability of RPE for phagocytosis changes. CDK5 has not yet been reported in RPE tissue, and here we show that it likely regulates Cx43 localization and resulting electrical coupling. We find that gap junctions in RPE are temporally highly dynamic during phagocytosis and that regulation of gap junctions via phosphorylation is likely critical for maintaining eye health.

cell biology↗

bioRxiv2021

TDAExplore: quantitative image analysis through topology-based machine learning

Machine learning has greatly expanded the ability to classify images. However, many machine learning classifiers require thousands of images for training and lack quantitative descriptors of how images were grouped. We overcome these limitations with a machine learning approach based on topological data analysis, where a data set of 20-30 images is sufficient to accurately train the classifier. Our method quantifies differences between groups and identifies subcellular regions with the largest dissimilarities.

cell biology↗

bioRxiv2020

Core Circadian Clock Genes Per1 and Per2 regulate the Rhythm in Photoreceptor Outer Segment Phagocytosis

Retinal photoreceptors undergo daily renewal of their distal outer segments, a process indispensable for maintaining retinal health. Photoreceptor Outer Segment (POS) phagocytosis occurs as a daily peak, roughly about one hour after light onset. However, the underlying cellular and molecular mechanisms which initiate this process are still unknown. Here we show that, under constant darkness, mice deficient for core circadian clock genes (Per1 and Per2), lack a daily peak in POS phagocytosis. By qPCR analysis we found that core clock genes were rhythmic over 24h in both WT and Per1, Per2 double mutant whole retinas. More precise transcriptomics analysis of laser capture microdissected WT photoreceptors revealed no differentially, expressed genes between time-points preceding and during the peak of POS phagocytosis. By contrast, we found that microdissected WT retinal pigment epithelium (RPE) had a number of genes that were differentially expressed at the peak phagocytic time-point compared to adjacent ones. We also found a number of differentially expressed genes in Per1, Per2 double mutant RPE compared to WT ones at the peak phagocytic time-point. Finally, based on STRING analysis we found a group of interacting genes which potentially drive POS phagocytosis in the RPE. This potential pathway consists of genes such as: Pacsin1, Syp, Camk2b and Camk2d among others. Our findings indicate that Per1 and Per2 are necessary clock components for driving POS phagocytosis and suggest that this process is transcriptionally driven by the RPE. DeclarationsO_ST_ABSFundingC_ST_ABSThis project has been funded with support from the NeuroTime Erasmus+ grant (European Union), Rotterdamse Stichting Blindenbelangen (Netherlands), Nelly Reef fund (Netherlands), Stichting voor Ooglijders (Netherlands), Stichting tot Verbetering van het Lot der Blinden (Netherlands) and Retina France (France). Conflicts of interest/Competing interestsThe authors declare no competing interests. Availability of data and materialData supporting the conclusions of this article are included within the article and are available from the corresponding authors on reasonable request. Code availabilityThe R code for analysis is available from the corresponding authors on reasonable request. Ethics approvalAll experimental procedures were performed in accordance with the Association for Research in Vision and Ophthalmology Statement on Use of Animals in Ophthalmic and Vision Research, as well as with the European Union Directive (2010/63/EU). Consent to participateNot applicable Consent for publicationAll authors read and approve of the contents of this manuscript. Author contributionsN.M. performed experiments, analysis, prepared figures, wrote the manuscript and obtained funding. O.A.-H.H. performed experiments, data analysis, prepared figures and obtained funding. P.D.M. and A.J. performed bioinformatics analysis and edited the manuscript. U.B., J.B.t.B. and C.S. provided technical assistance, performed experiments, prepared figures and edited the manuscript. D.H., A.A.B. and M.-P.F.-S. conceptualized and directed the project, obtained funding, provided resources, performed analysis and edited the manuscript.

neuroscience↗