Biology subjects

Zagorski, M.

Publications and source records attributed to Zagorski, M..

6 recordsLinked to original sources

bioRxiv2026

Aggregation dynamics of terrestrial isopods under extended Vicsek model

Terrestrial isopods display a rich behavioral repertoire, including fast escape responses and aggregation dynamics. Their response to environmental stimuli such as artificial light, humidity, vibration, heat and predation stress has been documented, but research highlights a variability in these responses, depending on the studied species and the different ecological niches they inhabit. The Vicsek model is widely used in the study of collective behavior and has been adapted multiple times to model different biological phenomena. In this work, we exposed terrestrial isopod Porcellionides pruinosus to different combinations of vibration and light stimuli within a circular enclosure and used the resulting experimental observations to extend the Vicsek model to account for aggregation dynamics and speed variability. To this end, we modeled aggregation dynamics using local group size and edge proximity to modulate aggregation probability. Our experimental results suggest that the combined effect of light and vibration increases the speed of isopods more than light or vibration alone. Additionally, the speed relaxation also occurs later when exposed to the combined stimuli. Interestingly, the classic Vicsek model correctly predicted the motion of isopods only within a few seconds under stimuli presence, indicating the isopods move in a collective fashion at short time scales. In contrast, the results of simulating swarms with the extended Vicsek model were consistent with the mean square displacement of the experimentally tracked isopods over longer times and also, depending on the stimuli, for the short times. This extension of the Vicsek model provides a framework that can be used for multi-modal stimuli testing of terrestrial collective and aggregation invertebrate behavior, thus providing a platform to understand better the variability of the responses of these valuable members of the ecosystem.

animal behavior and cognition↗

bioRxiv2026

Enhancer-mediated metabolic pre-patterning defines trabecular cardiomyocyte identity prior to morphogenesis

Cardiac trabeculae are essential structures of the vertebrate heart critical for ventricular wall integrity and contractility. Despite their importance, the transcriptional regulatory program defining trabecular cardiomyocyte identity and driving their development remains poorly understood. We identify a novel enhancer, -6.8got2b, that drives gene expression specifically in the trabecular myocardium of the zebrafish heart. Functional analyses revealed that - 6.8got2b is required for trabeculae formation, likely acting through its target gene, got2b, which encodes a mitochondrial enzyme. We delineated a 166bp core region responsible for restricting gene expression to trabecular cardiomyocytes, harboring binding motifs for multiple transcription factors (TFs), including Tbx20, whose motif deletion abolished trabeculae-specific expression. A human genomic region sharing partial sequence similarity and TF motifs with -6.8got2b was found near GOT2P4 - a pseudogene related to the human GOT2 gene. Strikingly, the human sequence drove expression in the zebrafish trabeculae and ventricular myocardium, indicating partial but functionally relevant conservation. Using - 6.8got2b as a molecular marker, we transcriptionally profiled trabecular cardiomyocytes and show that, compared to compact layer cardiomyocytes, they exhibit distinct gene signatures indicative of transcriptional priming for elevated energy metabolism prior to the formation of overt trabecular structure. Our findings reveal a conserved -6.8got2b-got2b regulatory axis driving trabecular cardiomyocyte development downstream of Tbx20, establishing a new layer of transcriptional regulation in heart morphogenesis.

developmental biology↗

bioRxiv2024

Dynamics of morphogen source formation in a growing tissue

A tight regulation of morphogen production is key for morphogen gradient formation and thereby for reproducible and organised organ development. Although many genetic interactions involved in the establishment of morphogen production domains are known, the biophysical mechanisms of morphogen source formation are poorly understood. Here we addressed this by focusing on the morphogen Shh in the vertebrate neural tube. Shh is produced by the adjacently located notochord and by the floor plate of the neural tube. Using a data-constrained computational screen, we identified different possible mechanisms by which floor plate formation can occur, only one of which is consistent with experimental data. In this mechanism, the floor plate is established rapidly in response to Shh from the notochord and the dynamics of regulatory interactions within the neural tube. In this process, uniform activators and Shh-dependent repressors are key for establishing the floor plate size. Subsequently, the floor plate becomes insensitive to Shh and increases in size due to tissue growth, leading to scaling of the floor plate with neural tube size. In turn, this results in scaling of the Shh amplitude with tissue growth. Thus, this mechanism ensures a separation of time scales in floor plate formation, so that the floor plate domain becomes growth dependent after an initial rapid establishment phase. Our study raises the possibility that the time scale separation between specification and growth might be common strategy for scaling the morphogen gradient amplitude in growing organs. The model that we developed provides a new opportunity for quantitative studies of morphogen source formation in growing tissues.

systems biology↗

bioRxiv2023

scRNA-seq reveals the diversity of the developing cardiac cell lineage and molecular building blocks of the primary pacemaker

The heart is comprised of a variety of specialized cell types that work in unison to maintain blood flow. Here we utilized scRNA-seq analysis to delineate the diversity of cardiac cell types in the zebrafish. With the growing use of the zebrafish to model human heart biology, a deeper insight into its complex cellular composition is critical for a better understanding of heart function, development, and associated malformations. We present a high resolution atlas of zebrafish heart single cells transcriptomics, consisting of over 50 000 cells representing the building blocks of the zebrafish heart at 48 and 72 hpf. We defined 18 discrete cell populations comprising major cell lineages and sublineages of the developing heart. We pinpointed a population of cells likely to be the primary pacemaker and identified the transcriptome profile defining this critical cell type. Our analyses identified two genes, atp1b3b and colec10, which were enriched in the sinoatrial pacemaker cells. CRISPR/Cas9-mediated knockout of these two genes significantly reduced heart rate which is accompanied by arrhythmia or morphological defects, suggesting their novel function in cardiac development and conduction. Additionally, we describe other subpopulations of cardiac cell lineages, including the endothelial and neural cells, whose expression profiles we provide as a resource for further investigations into the cellular and molecular mechanisms of this organ.

developmental biology↗

bioRxiv2022

Cell cycle dynamics controls fluidity of the developing mouse neuroepithelium

As organs are remodelled by morphogenetic changes and pattern formation during development, their material properties may change. To address whether and how this occurs in the mouse neural tube, we combined highly resolved mosaic analysis, biophysical modelling and perturbation experiments. We found that at early developmental stages the neuroepithelium surprisingly maintains both high junctional tension and high fluidity. This is achieved via a previously unrecognized mechanism in which interkinetic nuclear movements generate cell area dynamics that drive extensive cell rearrangements. Over time, the proliferation rate declines, effectively solidifying the tissue. Thus, unlike well-studied jamming transitions, the solidification we uncovered resembles a glass transition that depends on the dynamics of stresses generated by proliferation and differentiation. This new link between epithelial fluidity, interkinetic movements and cell cycle dynamics has implications for the precision of pattern formation and could be relevant to multiple developing tissues.

developmental biology↗

bioRxiv2019

Neuronal differentiation affects tissue mechanics and progenitor arrangement in the vertebrate neuroepithelium

Cell division, movement and differentiation contribute to pattern formation in developing tissues. This is the case in the vertebrate neural tube where neurons differentiate in a characteristic pattern from a highly dynamic proliferating pseudostratified epithelium. To investigate how progenitor proliferation and differentiation affect cell arrangement and growth of the neural tube, we use experimental measurements to develop a mechanical model of the apical surface of the neuroepithelium that incorporates inter-kinetic nuclear movement and spatially varying rates of neuronal differentiation. Simulations predict that tissue growth and the shape of lineage-related clones of cells differ with the rate of differentiation. Growth is isotropic in regions of high differentiation, but dorsoventrally biased in regions of low differentiation. This is consistent with experimental observations. The absence of directional signalling in the simulations indicates that global mechanical constraints are sufficient to explain the observed differences in anisotropy. This provides insight into how the tissue growth rate affects cell dynamics and growth anisotropy and opens up possibilities to study the coupling between mechanics, pattern formation and growth in the neural tube.

developmental biology↗