Biology subjects

Nagy, B.

Publications and source records attributed to Nagy, B..

10 recordsLinked to original sources

bioRxiv2026

SCAMP - an open-source tool for the quantification of calcification in fish larvae

Quantifying skeletal mineralization phenotypes in larval fish is complicated by the natural curvature of the notochord and by sample-to-sample variability in orientation, staining and imaging. Consequently, many studies rely on summary measures such as vertebral counts or total stain intensity. Here we present SCAMP (Spinal Calcification & Mineralization Profiler), an open-source, GUI-based Python tool that computationally straightens the curved notochord of Alizarin Red S-stained fish larvae and generates standardized mineralization profiles along the spinal axis. This approach reduces positional and shape variability, allowing direct, quantitative comparison of calcification patterns within and between experimental cohorts, without requiring programming expertise. We validate SCAMP using a zebrafish model of Pseudoxanthoma elasticum (abcc6aelu15/elu15), recovering genotype-specific differences in the intensity, extent and spatial distribution of ectopic calcification. Using SCAMP, we further show that inorganic pyrophosphate (PPi) supplementation of the medium suppresses ectopic notochord calcification, alters the anterior-posterior distribution of mineralized regions in homozygous mutants, and promotes mineralization at physiological vertebral sites. We also show that methylene blue, a routine antifungal additive in fish medium, reduces baseline calcification, with the most pronounced effects observed in heterozygous controls. SCAMP is freely available and has the potential to be adapted to other fish species used in skeletal and mineralization research.

developmental biology↗

bioRxiv2026

Short-term synaptic plasticity at neuron-OPC synapses in the corpus callosum during postnatal development of mice: experimental and computational study

Neuronal circuits rely on precisely timed synaptic transmission and plasticity, which are established through activity-dependent maturation during development. While these processes are well characterized at neuronal synapses, far less is known about how synaptic communication between neurons and glial cells develops. Pyramidal cortical neurons project axons through white matter where they release glutamate ectopically along their shafts and form glutamatergic synapses with oligodendrocyte precursor cells (OPCs). The functional maturation of these neuron-glia connections remains unknown. Here, using single-cell electrophysiology combined with computational modelling, we show that neuron-OPC synapses in the mouse corpus callosum undergo a pronounced developmental transformation in short-term synaptic plasticity. During the first two postnatal months, these synapses switch from strong synaptic depression to facilitation. This transition is accompanied by a shortening of synaptic delay and a reduction in asynchronous glutamate release, indicating an increase in temporal precision of neurotransmitter signalling in white matter. Computational modelling suggests that both pre- and postsynaptic changes may underlie this functional maturation. Taken together, our findings demonstrate that neuron-OPC synapses in white matter are not static but undergo developmental transition towards facilitation and temporally precise transmission that parallels the maturation trajectory of classical neuronal synapses in cortical grey matter. These results identify neuron-glia synapses in white matter as dynamic elements of developing neural circuits, and suggest that synaptic release machineries at axonal shafts in white matter and synaptic boutons in grey matter mature in a similar fashion.

neuroscience↗

bioRxiv2025

Mammalian PABPC4 is non-essential, but has roles in growth, post-natal survival and haematopoiesis.

Cytoplasmic poly(A)-binding proteins (PABPCs) are multifunctional RNA-binding proteins which play crucial roles in mRNA translation and stability. In mammals, two family members, PABPC1 and PABPC4 appear widely expressed, but the consequences of their loss of function in vivo remain unknown, despite PABPC4 being implicated in a variety of human diseases. We address this knowledge gap using a series of Pabpc4 knock-out mice. Unexpectedly, we reveal that mammalian PABPC4 is not essential for development, contrary to findings in non-mammalian vertebrates. However, its loss affects birth weight, post-natal growth trajectories and survival, although these were not tightly associated. Growth to adulthood was impacted in a sexually dimorphic manner. Viable Pabpc4-deficient mice allowed us to interrogate roles of Pabpc4 that may affect human health. Anaemia represents a large global health burden, and work in a red blood cell (RBC) model suggested a potential role in haemoglobin synthesis. Surprisingly in vivo, we find that Pabpc4 loss did not reduce haemoglobin levels but caused microcytic RBCs and altered RBC distribution width. Moreover, conditional genetic approaches established that this was not a red blood cell intrinsic effect. Taken together, this work provides unprecedented insights into the in vivo functions of mammalian PABPC4, and caution against inferring mammalian PABPC function from work in cell-based models and/or non-mammalian species. The generated mouse lines also form a valuable resource with which to further investigate the roles of PABPC4 in health and disease. Significance StatementRNA-binding protein (RBP)-mediated post-transcriptional regulation is essential for life and life-long health. Cytoplasmic poly(A)-binding proteins are family of RBPs that regulate multiple aspects of cytoplasmic mRNA fate. PABPC4 is an understudied family member, genetically associated with a wide range of human diseases. By creating a series of Pabpc4 knock-out mice, we surprisingly find it is not essential but is required for normal post-natal survival and growth and normal red blood cell development. Our results emphasise the importance of whole organism studies for understanding mammalian PABP function, uncovering differences between function inferred from other vertebrate species and prior cell-based work. The generated mice also provide a valuable resource for exploring its potential broad roles in human disease.

molecular biology↗

bioRxiv2025

BeWo-derived extracellular vesicles downregulate IL-6Rα expression via miRNAs on CD4+ T lymphocytes

Regulatory T lymphocytes are essential for maternal immunotolerance. Their de novo differentiation in the placenta is regulated by local intercellular interactions involving primed uterine immune cells, fetal syncytiotrophoblasts, and the cytokine environment. Trophoblast-derived, HLA-G-positive extracellular vesicles (EVs) can bind to T lymphocytes, thereby influencing their differentiation and cytokine production. Thus, these EVs play a role in establishing and maintaining a tolerogenic environment. In our study, we used the BeWo choriocarcinoma cell line to model the effects of trophoblast-derived EVs. Large EVs derived from BeWo cells (BeWo-12.5K lEVs) reduce IL-6R expression on CD4+ T cells. This modifies the IL-6 pathway by downregulating the transcription factors STAT3 and NFKB1, and PIAS3, while upregulating STAT1. This may be caused by specific microRNAs (miRNAs), such as hsa-mir-92a-3p, hsa-mir-520f-3p, and hsa-mir-25-3p. These microRNAs are present in BeWo-12.5K lEVs and target the IL-6 pathway. BeWo-12.5K lEVs induce phenotypic and functional changes in T cells, enhancing the ratio of CD4+/CD25+ T cells that produce IL-10. Pregnancy-associated IL-6R downregulation has been demonstrated in clinical samples. Significantly lower levels of IL-6R were detected on circulating CD4+CD25+ T cells in healthy pregnant women than in healthy non-pregnant individuals. This finding reflects the in vivo significance of our in vitro studies. Our studies suggest that communication between maternal and fetal cells significantly influences the development and maintenance of local T cell polarity. The microRNA content of HLA-G+ 12.5K lEVs appears to be key to this process, as it alters the IL-6 pathway.

immunology↗

bioRxiv2025

Revisiting object contextual cueing: A replication study on implicit learning

Object contextual cueing is an implicit learning paradigm in which the repeated co-occurrence of certain objects facilitates target detection, even when their spatial arrangement varies. In two experiments - where participants performed a visual search task in which the target was accompanied by either consistently repeated or randomly varying distractors - we attempted to replicate Chun and Jiangs (1999) study. In Experiment 1 (N = 25, M = 20.8 years), although participants became faster and more accurate over time, no significant difference emerged between repeated and new configurations. Thus, using the same experimental design, we were unable to replicate the object contextual cueing effect. In Experiment 2, we tested whether search strategy influences the effect by instructing one group to adopt an active search strategy and another to use a passive one (N = 20 per group, M = 21.8 and 21.7 years, respectively; active: actively search for the target, passive: let the unique item pop out). However, the manipulation had no effect: the contextual cueing effect did not emerge in either group. Importantly, within each group we observed substantial individual differences - some participants showed a facilitation effect, others no effect, and some even showed a reverse pattern. These findings suggest that object contextual cueing may not be a robust or universal phenomenon and may instead depend on individual cognitive styles or learning tendencies. Highlights- Replication of Chun and Jiangs (1999) object cueing study was unsuccessful. - Active vs. passive strategy instructions had no effect on object contextual cueing. - Large individual differences emerged in the contextual cueing effect.

neuroscience↗

bioRxiv2025

Automatic pairing of complex stimuli in younger and older adults: An event-related potential study

Contextual information can influence object perception, even when it is irrelevant to the task. When two unrelated stimuli frequently occur in close temporal succession, they may become associated. This process might be stronger in older adults due to age-related decline in inhibitory control, leading to deeper processing of irrelevant context. Automatic associations and their violations can be studied using visual mismatch negativity (vMMN), an event-related potential component reflecting the detection of violations of regularity in unattended stimuli. In our study, younger (n=18, M=21.2 {+/-} 2.1 yrs) and older (n=17, M=69.8 {+/-} 2.8 yrs) adults viewed pairs of images presented in succession: a scene (forest or street) followed by an emotional face (happy or angry). One scene-emotional face combination occurred frequently, the other rarely, forming a contextual oddball sequence. All individual stimuli appeared equally often. Participants performed an unrelated colour-change detection task, ensuring that the scene-emotional face pairs were unattended. We expected a vMMN to the emotional face in rare pairings, especially in older adults if they formed stronger associations. A control oddball condition with only emotional faces verified automatic emotion discrimination. In the control condition, vMMN emerged for both deviant emotions (in various ranges within the 94-276 ms post-stimulus time window). However, no vMMN was observed in the scene-emotional face pair condition. Instead, younger adults showed an early posterior positivity (90-161 ms) to rare pairings, while older adults exhibited a later negativity (356-384 ms). These results suggest that task-irrelevant, thematically unrelated visual events can become associated through temporal proximity. However, violations of these associations evoke neural responses distinct from vMMN and vary across age groups, with older adults relying on later, potentially semantic-related mechanisms rather than early visual processes to detect the regularity.

neuroscience↗

bioRxiv2025

Cognitive training effects are shaped more by individual brain dynamics than age - Evidence from younger and older women

Given the well-established structural and functional changes in the aging brain, it is widely assumed that cognitive aging is primarily driven by robust group-level differences between young and older adults. However, our individual-level EEG functional connectivity analysis challenges this notion. We investigated the impact of cognitive training on functional brain connectivity using task-switching paradigms in 39 younger (18-25 years) and 40 older (60-75 years) women. Participants were randomly assigned to either a training group, which completed eight individualized one-hour cognitive training sessions, or a no-contact control group. EEG was recorded at both pre- and post-training sessions across three task-switching paradigms (trained and near-transfer versions). Unique functional connectivity of different sources of variation was examined by calculating how much variance was shared across stable traits (e.g., individual, age, and common factors), or dynamic states (e.g., task and training effects). Our results revealed that age accounted for only a modest proportion of variance, whereas self-similarity was a dominant factor - particularly in older adults. Similarly, group-level training effects were small but strongly modulated by individual neural profiles, suggesting person-specific trajectories. Participants recruited distinct neural networks across tasks, and even within the same task engaged unique, individual-specific network configurations, reflecting personalised brain adaptations to cognitive demands. Importantly, older adults displayed a shift from common to individual network patterns, consistent with increased neural specialization and compensatory mechanisms. These findings underscore the importance of moving beyond group-level contrasts toward models that capture the complexity of individual brain dynamics in cognitive aging and training responsiveness. Significance StatementWhy do cognitive training programs work for some individuals but not for others? And is aging really the main factor driving changes in brain function? Using individual-level EEG functional connectivity analyses, we show that individual differences - not chronological age, task, or training - are the primary drivers of similarity in brain connectomes. While training effects are modest on average, their impact strongly depends on the individuals unique neural profile. Older adults, in particular, rely more on personalized brain network configurations. These results help explain why cognitive training studies often yield inconsistent findings and point toward a more individualized approach to understanding and enhancing brain function across the lifespan.

neuroscience↗

bioRxiv2024

Age-related differences in working memory subprocesses decomposed by the reference-back paradigm

We used a data-driven approach to study the electrophysiological correlates of the working memory subprocesses revealed by the reference-back paradigm. In the absence of prior research, we focused on how aging affects the four subprocesses: updating, substitution, gate opening, and gate closing. We conducted our experiment with 25 younger adults (M=20.17{+/-}1.47) and 23 older adults (M=67.35{+/-}4.01) using the reference-back paradigm. Significant reaction time costs were observed for all four subprocesses, but age-related differences were found only in substitution, which was larger in older than younger adults, indicating it as being the most vulnerable subprocess in aging. Using difference waves, we identified event-related potential components that characterize the subprocesses we studied. Regarding updating: three occipital negativities between 80-180 ms, 300-400 ms, and 400-1,000 ms were observed, with only the latter range showing age group differences. Source analysis showed larger activity differences in the right frontal and temporal areas for younger adults. Regarding substitution: a frontal positivity between 250-600 ms emerged in younger adults, while a posterior positivity between 550-750 ms was found in older adults indicating different underlying processes supported by sLORETA results. Regarding gate opening: three parieto-occipital components were identified: a negativity between 150-250 ms, a positivity between 300-500 ms, and a positivity between 500-700 ms, all showing age-related differences. Regarding gate closing: we found an occipital negativity between 150-300 ms and a frontal positivity between 300-600 ms, neither of which changed between the age groups. From our findings, we conclude that the process of protecting information (gate closing) remains stable with age, despite older adults sensitivity to interference. Conversely, gate opening is sensitive to age-related changes, likely to be resulting in different brain activity patterns during substitution being the updating of working memory with new information.

neuroscience↗

bioRxiv2023

Hypoxia-inducible factor (HIF) activation promotes osteogenic transition of valve interstitial cells and accelerates heart valve calcification in chronic kidney disease (CKD)

AimsValve calcification (VC) is a widespread complication in chronic kidney disease (CKD) patients on hemodialysis. VC is an active process with the involvement of in situ osteogenic transition of valve interstitial cells (VICs). VC is accompanied by the activation of hypoxia inducible factor (HIF) pathway, but the role of HIF activation in the calcification process remains undiscovered. Methods and resultUsing in vitro and in vivo approaches we addressed the role of HIF activation in osteogenic transition of VICs and CKD-associated VC. Elevation of osteogenic (Runx2, Sox9) and HIF activation markers (HIF-1 and HIF-2) and VC occurred in adenine-induced CKD mice. High phosphate (Pi) induced upregulation of osteogenic (Runx2, alkaline-phosphatase, Sox9, osteocalcin) and hypoxia markers (HIF-1, HIF-2, Glut-1), and calcification in VICs. Down-regulation of HIF-1 and HIF-2 inhibited, whereas further activation of HIF pathway by hypoxic exposure (1% O2) or hypoxia mimetics (desferrioxamine, CoCl2, Daprodustat (DPD)) promoted Pi-induced calcification of VICs. Pi augmented the formation of reactive oxygen species (ROS) and decreased viability of VICs, whose effects were further exacerbated by hypoxia. N-acetyl cysteine inhibited Pi-induced ROS production, cell death and calcification under both normoxic and hypoxic conditions. DPD treatment corrected anemia but promoted VC in the CKD mice model. ConclusionsHIF activation plays a fundamental role in Pi-induced osteogenic transition of VICs and CKD-induced VC. The cellular mechanism involves stabilization of HIF-1 and HIF-2, increased ROS production and cell death. Targeting the HIF pathways may thus be investigated as a therapeutic approach to attenuate VC. Translational perspectiveOne in four hemodialysis-dependent CKD patients on DPD treatment experience a major cardiovascular event during a 2.5-year follow-up period. This work provides a possible explanation for this phenomenon and should initiate further studies to address whether DPD-mediated acceleration of valve calcification triggers the unbeneficial effect of DPD.

pathology↗

bioRxiv2018

Innovative method for reducing uninformative calls in non-invasive prenatal testing

MotivationNon-invasive prenatal testing or NIPT is currently among the top researched topic in obstetric care. While the performance of the current state-of-the-art NIPT solutions achieve high sensitivity and specificity, they still struggle with a considerable number of samples that cannot be concluded with certainty. Such uninformative results are often subject to repeated blood sampling and re-analysis, usually after two weeks, and this period may cause a stress to the future mothers as well as increase the overall cost of the test.\n\nResultsWe propose a supplementary method to traditional z-scores to reduce the number of such uninformative calls. The method is based on a novel analysis of the length profile of circulating cell free DNA which compares the change in such profiles when random-based and length-based elimination of some fragments is performed. The proposed method is not as accurate as the standard z-score; however, our results suggest that combination of these two independent methods correctly resolves a substantial portion of healthy samples with an uninformative result. Additionally, we discuss how the proposed method can be used to identify maternal aberrations, thus reducing the risk of false positive and false negative calls.\n\nAvailability and ImplementationA particular implementation of the proposed methods is not provided with the manuscript.\n\nContactCorrespondence regarding the manuscript should be directed at Frantisek Duris (fduris@dcs.fmph.uniba.sk).\n\nSupplementary InformationNo additional supplementary information is available.

bioinformatics↗