Biology subjects

DeSimone, A.

Publications and source records attributed to DeSimone, A..

5 recordsLinked to original sources

bioRxiv2025

Cooperative mixing through hydrodynamic interactions in Stylonychia lemnae

Aquatic microorganisms typically inhabit a heterogeneous resource landscape, composed of localized and transient patches. To effectively exploit these resources, they have evolved a wide range of feeding strategies that combine chemotactic motility with active feeding flows. However, there is a notable lack of experimental studies that examine how these active flows shape resource fields to optimize feeding. In particular, the suspected cooperative hydrodynamics provided by groups of cells remains largely unexplored due to the difficulties in visualizing these dynamic three-dimensional flows. Here, we experimentally investigate how Stylonychia lemnae ciliates form feeding clusters of independent cells around food patches. Individual feeding flows interact hydrodynamically to create a chaotic collective flow at the population scale. Using a combination of experimental and numerical techniques, we measure and predict the entire collective flow, enabling us to assess its outstanding mixing and dispersion properties. We show that the active spreading of the food patch accelerates its detection by starving cells. As many additional fitness advantages provided by collective flows can be envisioned, we propose that this feeding cluster represents a form of intra-specific by-product cooperative behavior.

biophysics↗

bioRxiv2021

Contact guidance as a consequence of coupled morphological evolution and motility of adherent cells

Adherent cells seeded on substrates spread and evolve their morphology while simultaneously displaying motility. Phenomena such as contact guidance viz. the alignment of cells on patterned substrates, are strongly linked to the coupling of morphological evolution with motility. Here we employ a recently developed statistical thermodynamics framework for modelling the non-thermal fluctuating response of the cells to probe this coupling. This thermodynamic framework is first extended to predict temporal responses via a Langevin style model. The Langevin model is then shown to not only predict the different experimentally observed temporal scales for morphological observables such as cell area and elongation but also the interplay of morphology with motility that ultimately leads to contact guidance. Author SummaryThe evolution of cellular morphology and organization plays a crucial role in the micro-architecture of tissues and dictates their biological and mechanical functioning. Despite the importance of cellular organization in all facets of tissue biology, the fundamental question of how a cell organizes itself in an anisotropic environment is still poorly understood. We demonstrate, using a Langevin style model, that non-thermal fluctuations fuelled by nutrient exchanges between the cell and its environment are critical in allowing cells to explore their surroundings. The biochemical changes, associated with non-thermal fluctuations, drive cell motility and morphological changes and the interplay between these two emerging dynamics ultimately leads to contact guidance, a critical component for tissue morphogenesis.

biophysics↗

bioRxiv2020

How Euglena gracilis swims: flow field reconstruction and analysis

Euglena gracilis is a unicellular organism that swims by beating a single anterior flagellum. We study the nonplanar waveforms spanned by the flagellum during a swimming stroke, and the three-dimensional flows that they generate in the surrounding fluid. Starting from a small set of time-indexed images obtained by optical microscopy on a swimming Euglena cell, we construct a numerical interpolation of the stroke. We define an optimal interpolation (which we call synthetic stroke) by minimizing the discrepancy between experimentally measured velocities (of the swimmer) and those computed by solving numerically the equations of motion of the swimmer driven by the trial interpolated stroke. The good match we obtain between experimentally measured and numerically computed trajectories provides a first validation of our synthetic stroke. We further validate the procedure by studying the flow velocities induced in the surrounding fluid. We compare the experimentally measured flow fields with the corresponding quantities computed by solving numerically the Stokes equations for the fluid flow, in which the forcing is provided by the synthetic stroke, and find good matching. Finally, we use the synthetic stroke to derive a coarse-grained model of the flow field resolved in terms of a few dominant singularities. The far field is well approximated by a time-varying Stresslet, and we show that the average behavior of Euglena during one stroke is that of an off-axis puller. The reconstruction of the flow field closer to the swimmer body requires a more complex system of singularities. A system of two Stokeslets and one Rotlet, that can be loosely associated with the force exerted by the flagellum, the drag of the body, and a torque to guarantee rotational equilibrium, provides a good approximation.

biophysics↗

bioRxiv2020

Nutations in plant shoots: Endogenous and exogenous factors in the presence of mechanical deformations

AbstractWe present a three-dimensional morphoelastic rod model capable to describe the morphogenesis of growing plant shoots, as driven by differential growth at the tip. We discuss the evolution laws for endogenous oscillators, straightening mechanisms and reorientations to directional cues, such as phototropic responses to a far light source and gravitropic reactions governed by the statoliths avalanche dynamics. We use this model to investigate the role of elastic deflections due to gravity loading in circumnutating plant shoots. We show that, in the absence of endogenous cues, pendular and circular oscillations arise as a critical length is attained, thus suggesting the occurrence of a Hopf bifurcation reminiscent of flutter instabilities exhibited by structural systems under nonconservative loads. When also oscillations due to endogenous cues are present, their weight relative to those associated with the Hopf instability varies in time as the shoot length and other biomechanical properties change. Thanks to the simultaneous occurrence of these two oscillatory mechanisms, we are able to reproduce a variety of complex behaviors, including trochoid-like patterns, which evolve into circular orbits as the shoot length increases, and the amplitude of the flutter induced oscillations becomes dominant. Our findings suggest that the relative importance of the two mechanisms is an emergent property of the system that is affected by the amplitude of elastic deformations, and highlight the crucial role of elasticity in the analysis of circumnutations.Competing Interest StatementThe authors have declared no competing interest.View Full Text

biophysics↗

bioRxiv2020

The biomechanical role of extra-axonemal structures in shaping the flagellar beat of Euglena

We propose and discuss a model for flagellar mechanics in Euglena gracilis. We show that the peculiar non-planar shapes of its beating flagellum, dubbed "spinning lasso", arise from the mechanical interactions between two of its inner components, namely, the axoneme and the paraflagellar rod. The spontaneous shape of the axoneme and the resting shape of the paraflagellar rod are incompatible. The complex non-planar configurations of the coupled system emerge as the energetically optimal compromise between the two antagonistic components. The model is able to reproduce the experimentally observed flagellar beats and their characteristic spinning lasso geometric signature, namely, travelling waves of torsion with alternating sing along the length of the flagellum.

biophysics↗