Biology subjects

Zardilis, A.

Publications and source records attributed to Zardilis, A..

4 recordsLinked to original sources

bioRxiv2025

Learning a mechanical growth model of flower morphogenesis

Morphogenesis, the process by which organs take their shape, is a fundamental problem in biology and requires a complex combination of genetic, biochemical, and mechanical signals. The data that we collect for this process are usually multi-scale and multi-modal, typically image timeseries of tissue morphology and transcription data. As the data becomes larger and more diverse, the harder it becomes to gain meaningful understanding in terms of theoretical models. Here, and tackling this problem in the developing flower organ, we learn a mechanical model of growth starting from combined morphology and transcription data across the tissue by firstly learning and connecting independent representations for the two spaces and secondly refining the representation using the mechanical state of the tissue to learn a mechanical growth model. This approach can link multiple scales, in this case proposing the physical action of genes, and can act as a vehicle to accommodate diverse data and hypotheses in developmental biology of plants and beyond.

developmental biology↗

bioRxiv2024

Hibiscus bullseyes reveal mechanisms controlling petal pattern proportions that influence plant-pollinator interactions

Colourful patterns on flower corollas are key signals to attract pollinators. The formation of such motifs relies on the establishment of developmental boundaries that partition the growing petal epidermis into different subdomains, where cells can produce specific pigments and acquire distinctive cell shapes and textures. While some of the transcription factors and biosynthetic pathways producing these characteristics as cell differentiate have been extensively studied, the upstream processes restricting the activities of molecular players to specific regions of the petal epidermis remain enigmatic. Here, we unveil that the petal surface of Hibiscus trionum, an emerging model system featuring a bullseye on its corolla, is pre-patterned as the position of the bullseye boundary is specified long before the motif becomes visible to the human eye. Using a 1-D computational model, we explore how a boundary established at such an early stage can be maintained throughout development. Reciprocally, by exploiting transgenic lines and natural variants, we show that plants can regulate the relative position of the boundary during the pre-patterning phase or modulate division and growth on either side of this boundary at later developmental stages to yield variations in final bullseye proportions. Finally, we provide evidence that such modifications in bullseye size have functional significance as buff-tailed bumblebees (Bombus terrestris) can reliably identify a food source based on the size of its bullseye. Notably, we found that individuals exhibit a clear preference for the larger bullseye of H. trionum over the smaller pattern of its close relative, H. richardsonii.

plant biology↗

bioRxiv2020

A multiscale analysis of early flower development in Arabidopsis provides an integrated view of molecular regulation and growth control

The link between gene regulation and morphogenesis of multicellular organisms is a fundamental problem in biology. We address this question in the floral meristem of Arabidopsis, which generates new tissues and organs through complex changes in growth patterns. Starting from high-resolution time-lapse images, we generated a comprehensive 4-D atlas of early flower development including cell lineage, cellular growth rates and the expression patterns of 28 regulatory genes. This information was introduced in MorphoNet, a web-based open-access platform. The application of mechanistic computational models indicated that the molecular network based on the literature only explained a minority of the expression patterns. This was substantially improved by adding single regulatory hypotheses for individual genes. We next used the integrated information to correlate growth with the combinatorial expression of multiple genes. This led us to propose a set of hypotheses for the action of individual genes in morphogenesis, not visible by simply correlating gene expression and growth. This identified the central transcription factor LEAFY as a potential regulator of heterogeneous growth, which was supported by quantifying growth patterns in a leafy mutant. By providing an integrated, multiscale view of flower development, this atlas should represent a fundamental step towards mechanistic multiscale-scale models of flower development.

developmental biology↗

bioRxiv2018

A multi-model Framework for the Arabidopsis life cycle

Linking our understanding of biological processes at different scales is a major conceptual challenge in biology, which is aggravated by differences in research methods. Modelling can be a useful approach to consolidating our understanding across traditional research domains. The laboratory model species Arabidopsis thaliana is very widely used to study plant growth processes and has also been tested more recently in eco-physiology and population genetics. However, approaches from crop modelling that might link these domains are rarely applied to Arabidopsis. Here, we combine plant growth models with phenology models from eco-physiology, using the agent-based modelling language Chromar. We introduce a simpler Framework Model of vegetative growth for Arabidopsis, FM-lite. By extending this model to include inflorescence and fruit growth and seed dormancy, we present a whole-life-cycle, multi-model FM-life, which allows us to simulate at the population level in various genotype x environment scenarios. Environmental effects on plant growth distinguish between the simulated life history strategies that were compatible with previously-described Arabidopsis phenology. Our results simulate reproductive success that is founded on the broad range of physiological processes familiar from crop models and suggest an approach to simulate evolution directly in future.\n\nHighlightA whole-life-cycle multi-model for Arabidopsis thaliana combines phenology and physical growth models to explain reproductive success in different genotype x environment scenarios.

plant biology↗