Biology subjects

Mochulska, V.

Publications and source records attributed to Mochulska, V..

4 recordsLinked to original sources

bioRxiv2026

Cycles upon cycles - Temperature Scaling of Medaka Development

How organisms develop in dynamic environmental conditions is a fundamental question. We asked how day-night temperature cycles impact embryonic axis elongation and segmentation, itself a cyclic process linked to the segmentation clock, using the Japanese rice fish medaka. We developed an unbiased dimensional reduction approach, based on Singular Value Decomposition (SVD), to reliably identify the dynamic modes of segmentation clock oscillations across all temperature conditions. We reveal that the two major dynamic modes show opposite temperature sensitivities: while the temporal oscillation (mode 1) varies strongly with temperature, the spatial phase gradient (mode 2) appears largely temperature invariant. In addition, we found developmental parameters with intermediate, sub-scaled temperature responses, such as axis elongation. We used theoretical modeling to understand how dynamic modes emerge from the underlying local oscillation dynamics and axis elongation. We then exposed embryos to circadian and ultradian temperature cycles to reveal dynamic response patterns of oscillations and axis elongation, and found how these responses are integrated into morphological features. Combined, our theoretical-experimental results support a model in which the dynamic integration of temporal (i.e. segmentation clock related) and spatial (i.e. axis elongation) processes, in particular their sub-scaled temperature response patterns, quantitatively compensate each other to yield a robust, temperature-invariant axis patterning outcome.

developmental biology↗

bioRxiv2025

Dynamical model and geometric insights in the discontinuity theory of immunity

The immune systems most basic task is to decide what is "self" and "non-self", but a precise definition of self versus non-self remains challenging. According to the discontinuity theory of immunity, effector responses depend on how quickly an antigenic stimulus changes: rapid change triggers an immune response, whereas gradual change fosters tolerance. We present a model of adaptive immune dynamics including T cells, Tregs and cytokines that reproduces the hallmarks of the discontinuity theory. The model allows for sharp discrimination between acute and chronic infections based on the growth rate of the immune challenge, and vaccination-like acute dynamics upon presentation of a bolus of immune challenge. We further show that the model behavior only depends on a handful of testable assumptions that we map to geometric constraints in phase space. This suggests that the model properties are generic and robust across alternative mechanistic details. We also examine the impact of multiple concurrent immune challenges in this model, and demonstrate the occurrence of dynamical antagonism, wherein, in some parameter regimes, slow-growing challenges hinder acute responses to fast-growing ones, with further counter-intuitive behaviors for sequential co-infections. Together, these results place the discontinuity theory on firm mathematical footing and encourage further investigation of interferences of multi-agent immune challenges, from chronic viral co-infections to cancer immunoediting.

systems biology↗

bioRxiv2025

Generative epigenetic landscapes map the topology and topography of cell fates

Epigenetic landscapes were proposed by Waddington as the central concept to describe cell fate dynamics in a locally low-dimensional space. In modern landscape models, attractors represent cell types, and stochastic jumps and bifurcations drive cellular decisions, allowing for quantitative and predictive descriptions. However, given a biological problem of interest, we still lack tools to infer and build possible Waddington landscapes systematically. In this study, we propose a generative model for deriving epigenetic landscapes compatible with data. To build the landscapes, we combine gradient and rotational vector fields composed of locally weighted elements that encode valleys of the Waddington landscape, resulting in interpretable models. We optimize landscapes through computational evolution and illustrate our approach with two developmental examples: metazoan segmentation and neuromesoderm differentiation. In both cases, we obtain ensembles of solutions that reveal both known and novel landscapes in terms of topology and bifurcations. Conversely, topographic features appear strongly constrained by dynamical data, which suggests that our approach can generically derive interpretable and predictive epigenetic landscapes.

developmental biology↗

bioRxiv2021

Arnold tongue entrainment reveals dynamicalprinciples of the embryonic segmentation clock

Living systems exhibit an unmatched complexity, due to countless, entangled interactions across scales. Here we aim to understand a complex system, i.e. segmentation timing in mouse embryos, without a reference to these detailed interactions. To this end, we develop a coarse-grained approach, in which theory guides the experimental identification of the segmentation clock entrainment responses. We demonstrate period- and phase-locking of the segmentation clock across a wide range of entrainment parameters, including higher-order coupling. These quantifications allow to derive the phase response curve (PRC) and Arnold tongues of the segmentation clock, revealing its essential dynamical properties. Our results indicate that the somite segmentation clock has characteristics reminiscent of a highly non-linear oscillator close to an infinite period bifurcation and suggests the presence of long-term feedbacks. Combined, this coarse-grained theoretical-experimental approach reveals how we can derive simple, essential features of a highly complex dynamical system, providing precise experimental control over the pace and rhythm of the somite segmentation clock.

developmental biology↗