Biology subjects

Picioreanu, C.

Publications and source records attributed to Picioreanu, C..

5 recordsLinked to original sources

bioRxiv2023

Modeling the radiative, thermal and chemical microenvironment of 3D scanned corals

O_LIReef building corals are efficient biological collectors of solar radiation and consist of a thin stratified tissue layer spread over a light scattering calcium carbonate skeleton surface that together construct complex three dimensional (3D) colony structures forming the foundation of coral reefs. They exhibit a vast diversity of structural forms to maximize photosynthesis of their dinoflagellate endosymbionts (Symbiodiniaceae), while simultaneously minimizing photodamage. The symbiosis takes place in the presence of dynamic gradients of light, temperature and chemical species that are affected by the interaction of incident irradiance and water flow with the coral colony. C_LIO_LIWe developed a multiphysics modelling approach to simulate microscale spatial distribution of light, temperature and O2 in coral fragments with accurate morphology determined by 3D scanning techniques. C_LIO_LIModel results compared well with spatial measurements of light, O2 and temperature under similar flow and light conditions. The model enabled us to infer the effect of coral morphology and light scattering in tissue and skeleton on the internal light environment experienced by the endosymbionts, as well as the combined contribution of light, water flow and ciliary movement on O2 and temperature distributions in the coral. C_LIO_LIThe multiphysics modeling approach is general enough to enable simulation of external and internal light, O2 and temperature microenvironments in 3D scanned coral species with varying degrees of branching and morphology under different environmental conditions. This approach is also relevant for simulating structure-function relationships in other benthic systems such as photosynthetic biofilms and aquatic plant tissue, and can also be adapted to other sessile organisms such as symbiont-bearing giant clams, ascidians, jellyfish or foraminifera. The model could also be useful in more applied research such as optimization of 3D bioprinted constructs where different designs can be evaluated and optimized. C_LI

biophysics↗

bioRxiv2020

Effects of light/dark diel cycles on the photoorganoheterotrophic metabolism of Rhodopseudomonas palustris for differential electron allocation to PHAs and H2

Light/dark cycles can impact the electron distribution in Rhodopseudomonas palustris, a hyperversatile photoorganoheterotrophic purple non-sulfur bacterium (PNSB). Dynamic conditions during diel cycles are important for the physiology of PNSB, but the coupling between illumination patterns and redox balancing has not been extensively studied. For survival and growth, Rhodopseudomonas has developed different mechanisms to allocate electrons under dynamic growth conditions. Products such as hydrogen and poly-{beta}-hydroxyalkanoates (PHAs) can form alternative electron sinks. A continuous culture, fed with a balanced nutrients medium, was exposed to three different conditions: 24 h continuous infrared illumination, 16h light/8h dark, and 8h light/16h dark. Light and dark phase durations in a cycle determined the energy availability level (light) and the attainment of a stationary state. Under long dark phases, the acetate substrate accumulated to levels that could not be depleted by growth in the light. Under short dark phases, acetate was rapidly consumed in the light with most of the phototrophic growth occurring under acetate-limiting conditions. Under diel cycles, substrate uptake and growth were unbalanced and Rhodopseudomonas shunted the excess of carbon and electron flow first toward PHAs production. Only secondarily, when PHA storage got saturated, the electron excess was redirected toward H2. A numerical model described well the dynamics of biomass and nutrients during the different light/dark cycle regimes. The model simulations allowed determination of stoichiometric and kinetic parameters for conversion by Rhodopseudomonas. Understanding the inherent process dynamics of diel light cycles in purple sulfur bacteria cultures would enable optimization procedures for targeted bioproduct formation. ImportancePurple non-sulfur bacteria (PNSB) are important anoxygenic phototrophic microorganisms that take part in numerous environmental processes, based on their metabolic versatility. Rhodopseudomonas palustris is a model photosynthetic bacterium of the PNSB guild. Light cycles influence deeply its physiology. Poly-{beta}-hydroxyalkanoates (PHAs) and biohydrogen are two of the most studied metabolic products of Rhodopseudomonas, because of their biotechnology potential besides involvement in carbon and electron allocations in its metabolism. Their production mechanisms have often been described as competitive, but the rationale behind the production of one or the other compound has not been elucidated. Here, we found that under light / dark cycles an excess of organic substrate was first directed toward PHAs production, and only when this pathway was saturated H2 was produced. Understanding the dynamics of carbon and electron allocation under intermittent light cycles enhances our knowledge on PNSB metabolisms and paves ways to manage the formation of targeted bioproducts.

microbiology↗

bioRxiv2020

Microbial competition reduces interaction distances to the low {micro}m-range

Metabolic interactions between cells affect microbial community compositions and hence their function in ecosystems. It is well-known that under competition for the exchanged metabolite, concentration gradients constrain the distances over which interactions can occur. However, interaction distances are typically quantified in two-dimensional systems or without accounting for competition or other metabolite-removal, conditions which may not very often match natural ecosystems. We here analyze the impact of cell-to-cell distance on unidirectional cross-feeding in a three-dimensional system with competition for the exchanged metabolite. Effective interaction distances were computed with a reaction-diffusion model and experimentally verified by growing a synthetic consortium of 1 {micro}m-sized metabolite producer, receiver and competitor cells in different spatial structures. We show that receivers cannot interact with producers [~]15 {micro}m away from them, as product concentration gradients flatten close to producer cells. We developed an aggregation protocol and created variants of the receiver cells import system, to show that within producer-receiver aggregates even low affinity receiver cells could interact with producers. These results show that competition or other metabolite-removal of a public good in a three-dimensional system reduces the interaction distance to the low micrometer-range, highlighting the importance of concentration gradients as physical constraint for cellular interactions.

microbiology↗

bioRxiv2019

Computational and experimental investigation of biofilm disruption dynamics induced by high velocity gas jet impingement

Experimental data showed that high-speed micro-sprays can effectively disrupt biofilms on their support substratum, producing a variety of dynamic reactions such as elongation, displacement, ripples formation and fluidization. However, the mechanics underlying the impact of high-speed turbulent flows on biofilm structure is complex in such extreme conditions, since direct measurements of viscosity at these high shear rates are not possible using dynamic testing instruments. Here we used computational fluid dynamics simulations to assess the complex fluid interactions of ripple patterning produced by high-speed turbulent air jets impacting perpendicular to the surface of Streptococcus mutans biofilms, a dental pathogen causing caries, captured by high speed imaging. The numerical model involved a two-phase flow of air over a non-Newtonian biofilm, whose viscosity as a function of shear rate was estimated using the Herschel-Bulkley model. The simulation suggested that inertial, shear and interfacial tension forces governed biofilm disruption by the air jet. Additionally, the high shear rates generated by the jet impacts coupled with shear-thinning biofilm property resulted in rapid liquefaction (within milliseconds) of the biofilm, followed by surface instability and travelling waves from the impact site. Our findings suggest that rapid shear-thinning in the biofilm reproduces dynamics under very high shear flows that elasticity can be neglected under these conditions, behaving the biofilm as a Newtonian fluid. A parametric sensitivity study confirmed that both applied force intensity (i.e. high jet-nozzle air velocity) and biofilm properties (i.e. low viscosity, low air-biofilm surface tension and thickness) intensify biofilm disruption, by generating large interfacial instabilities.\n\nIMPORTANCEKnowledge of mechanisms promoting disruption though mechanical forces is essential in optimizing biofilm control strategies which rely on fluid shear. Our results provide insight into how biofilm disruption dynamics is governed by applied forces and fluid properties, revealing a mechanism for ripples formation and fluid-biofilm mixing. These findings have important implications for the rational design of new biofilms cleaning strategies with fluid jets, such as determining optimal parameters (e.g. jet velocity and position) to remove the biofilm from a certain zone (e.g. in dental hygiene or debridement of surgical site infections), or using antimicrobial agents which could increase the interfacial area available for exchange, as well as causing internal mixing within the biofilm matrix, thus disrupting the localized microenvironment which is associated with antimicrobial tolerance. The developed model also has potential application in predicting drag and pressure drop caused by biofilms on bioreactor, pipeline and ship hull surfaces.

microbiology↗

bioRxiv2017

Noise-driven Cell Differentiation and the Emergence of Organization

One of the major transitions in evolution is the step from unicellularity into the brave new world of multicellularity. To understand this feat, one has to fathom two main characteristics of multicellular organisms: differentiation and self-organization. Any explanation concerning this major transition should involve mechanisms that can simultaneously explain the marvellous intricacies manifest in the aforementioned characteristics, and an account of the evolution of such traits. Here we propose a noise-driven differentiation (NDD) model. The reliance on noise, in place of a more mechanistic approach, makes the NDD model a more suitable approach to explain differentiation and self-organization. Furthermore, our model sheds some light on the possible evolutionary origins of these biological innovations. To test the NDD model, we utilize a model of cell aggregation. The behavior of this model of cell aggregation is in concert with the NDD model.

cell biology↗