Biology subjects

Fruleux, A.

Publications and source records attributed to Fruleux, A..

5 recordsLinked to original sources

bioRxiv2025

Inferring diffusion, reaction, and exchange parameters from imperfect FRAP

Fluorescence recovery after photobleaching (FRAP) is broadly used to investigate the dynamics of molecules in cells and tissues, notably to quantify diffusion coefficients. FRAP is based on the spatiotemporal imaging of fluorescent molecules following an initial bleaching of fluorescence in a region of the sample. Although a large number of methods have been developed to infer kinetic parameters from experiments, it is still a challenge to fully characterize molecular dynamics from noisy experiments in which diffusion is coupled to other molecular processes or in which the initial bleaching profile is not perfectly controlled. To address this challenge, we have developed HiFRAP to quantify the reaction-(or exchange-)diffusion kinetic parameters from FRAP under imperfect experimental conditions. HiFRAP is based on a low-rank approximation of a kernel related to the model Greens function and is implemented as an ImageJ/Python macro for (potentially curved) one-dimensional systems and for two-dimensional systems. To the best of our knowledge, HiFRAP offers features that have not been combined together: making no assumption on the initial bleaching profile, which does not need to be known; accounting for the limitation of the optical setup by diffraction; inferring several kinetic parameters from a single experiment; providing errors on parameter estimation; and testing model goodness. In the future, our approach could be applied to other dynamical processes described by linear partial differential equations, which could be useful beyond FRAP, in experiments where the concentration fields are monitored over space and time. SIGNIFICANCEFluorescence recovery after photobleaching (FRAP) is a microscopy approach that is widely used to investigate the diffusion and transport of molecules in life sciences and in material sciences. Numerous methods have been developed to derive kinetic parameters such as diffusion and binding coefficients. However, these methods suffer from limitations associated with experimental constraints, such as technical noise or an imperfectly known initial condition. To circumvent these limitations, we developed a comprehensive approach to estimate several kinetic parameters from a single experiment, to assess the precision of estimation, and to test whether the underlying model is well-suited. We implemented this approach in HiFRAP, an ImageJ/Python macro of broad applicability to one- and two-dimensional systems.

biophysics↗

bioRxiv2023

Growth couples temporal and spatial fluctuations of tissue properties during morphogenesis

Living tissues display fluctuations - random spatial and temporal variations of tissue properties around their reference values - at multiple scales. It is believed that such fluctuations may enable tissues to sense their state or their size. Recent theoretical studies developed specific models of fluctuations in growing tissues and predicted that fluctuations of growth show long-range correlations. Here we elaborated upon these predictions and we tested them using experimental data. We first introduced a minimal model for the fluctuations of any quantity that has some level of temporal persistence or memory, such as concentration of a molecule, local growth rate, or mechanical property. We found that long-range correlations are generic, applying to any such quantity, and that growth couples temporal and spatial fluctuations, through a mechanism that we call fluctuation stretching -- growth enlarges the lengthscale of variation of this quantity. We then analysed growth data from sepals of the model plant Arabidopsis and we quantified spatial and temporal fluctuations of cell growth using the previously developed Cellular Fourier Transform. Growth appears to have long-range correlations. We compared different genotypes and growth conditions: mutants with lower or higher response to mechanical stress have lower temporal correlations and longer-range spatial correlations than wild-type plants. Finally, we used theoretical predictions to merge experimental data from all conditions and developmental stages into an unifying curve, validating the notion that temporal and spatial fluctuations are coupled by growth. Altogether, our work reveals kinematic constraints on spatiotemporal fluctuations that have an impact on the robustness of morphogenesis. Significance StatementHow do organs and organisms grow and achieve robust shapes in the face of subcellular and cellular variability? In order to address this outstanding mystery, we investigated the variability of growth at multiple scales and we analysed experimental data from growing plant tissues. Our results support the prediction that tissue expansion couples temporal memory of growth with spatial variability of growth. Our work reveals a constraint on the spatial and temporal variability of growth that may impact the robustness of morphogenesis.

biophysics↗

bioRxiv2022

Dynamic growth re-orientation orchestrates flatness in the Arabidopsis leaf

The growth and division of cells in plant leaves is highly dynamic in time and space, even though cells cannot move relative to their neighbors. Thus, organ shape must emerge from carefully coordinated growth, especially in leaves that remain relatively flat as they grow. Here we explored the phenotype of the jagged and wavy (jaw-D) mutant in Arabidopsis thaliana, in which the leaves do not remain flat. It has previously been shown that the jaw-D mutant phenotype is caused by the overexpression of miR319, which represses TCP transcription factors, thus delaying maturation of the leaf. We analyzed cell dynamics in wild type and jaw-D by performing time lapse live imaging of developing leaves. We found that the progression of maturation from the tip of the leaf downward was delayed in jaw-D relative to wild type based on several markers of maturation, in agreement with the role of TCP transcription factors in promoting maturation. We further found that these changes in maturation were accompanied by differences in the coordination of growth across the leaf, particularly across the medial-lateral axis, causing growth conflicts that prevent the leaf from remaining flat. Although leaf flatness is often framed as a problem that requires the local synchronization of growth on the abaxial vs adaxial sides of the leaf, our results based on the jaw-D phenotype suggest that wild-type plants also need to coordinate growth more globally across the leaf blade to maintain flatness.

plant biology↗

bioRxiv2022

Spatial consistency of cell growth direction during organ morphogenesis requires CELLULOSE-SYNTHASE INTERACTIVE1

Extracellular matrices generally contain fibril-like polymers that may be organized in parallel arrays. Although their role in morphogenesis has been long recognized, it is still unclear how the subcellular control of fibril synthesis translates into well-defined organ shape. Here, we addressed this question using the Arabidopsis sepal as a model organ. In plants, cell growth is driven by turgor pressure and restrained by the extracellular matrix known as the cell wall. Cellulose is the main load-bearing component of the plant cell wall and cellulose microfibrils are thought to channel growth perpendicularly to their main orientation. Given the key function of CELLULOSE SYNTHASE INTERACTIVE 1 (CSI1) in guidance of cellulose synthesis, we investigated the role of CSI1 in sepal morphogenesis. We observed that sepals from csi1 mutants are shorter, although their newest cellulose microfibrils are more aligned compared to wild type. Surprisingly, cell growth anisotropy was similar in csi1 and wild-type plants. We resolved this apparent paradox using polarized Raman microspectroscopy, live imaging of growing sepals, and bespoke mechanical assays. We found that CSI1 is required for spatial consistency of growth direction across the sepal and for the maintenance of overall organ elongation. Our work illustrates how the subcellular regulation of the extracellular matrix may control morphogenesis at multiple scales.

developmental biology↗

bioRxiv2018

Modulation of tissue growth heterogeneity by responses to mechanical stress

Morphogenesis often yields organs with robust size and shapes, whereas cell growth and deformation feature significant spatio-temporal variability. Here, we investigate whether tissue responses to mechanical signals contribute to resolve this apparent paradox. We built a model of growing tissues made of fiber-like material, which may account for the cytoskeleton, polar cell-cell adhesion, or the extracellular matrix in animals, and for the cell wall in plants. We considered the synthesis and remodeling of this material, as well as the modulation of synthesis by isotropic and anisotropic response to mechanical stress. Formally, our model describes an expanding, mechanoresponsive, nematic, and active fluid. We show that mechanical responses buffer localized perturbations, with two possible regimes - hypo-responsive and hyper-responsive, and the transition between the two corresponds to a minimum value of the relaxation time. Whereas robustness of shapes suggests that growth fluctuations are confined to small scales, our model yields growth fluctuations that have long-range correlations. This indicates that growth fluctuations are a significant source of heterogeneity in development. Nevertheless, we find that mechanical responses may dampen such fluctuations, with a specific magnitude of anisotropic response that minimizes heterogeneity of tissue contours. We finally discuss how our predictions might apply to the development of plants and animals. Altogether, our results call for the systematic quantification of fluctuations in growing tissues.

biophysics↗