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Abenza, J. F., Couturier, E., Dodgson, J., Dickmann, J., Chessel, A., Dumais, J., et al. (2015). Wall mechanics and exocytosis define the shape of growth domains in fission yeast. Nat. Commun., 6, 13 pp.
Abstract: The amazing structural variety of cells is matched only by their functional diversity, and reflects the complex interplay between biochemical and mechanical regulation. How both regulatory layers generate specifically shaped cellular domains is not fully understood. Here, we report how cell growth domains are shaped in fission yeast. Based on quantitative analysis of cell wall expansion and elasticity, we develop a model for how mechanics and cell wall assembly interact and use it to look for factors underpinning growth domain morphogenesis. Surprisingly, we find that neither the global cell shape regulators Cdc42-Scd1-Scd2 nor the major cell wall synthesis regulators Bgs1-Bgs4-Rgf1 are reliable predictors of growth domain geometry. Instead, their geometry can be defined by cell wall mechanics and the cortical localization pattern of the exocytic factors Sec6-Syb1-Exo70. Forceful re-directioning of exocytic vesicle fusion to broader cortical areas induces proportional shape changes to growth domains, demonstrating that both features are causally linked.
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Azeem, M., Guérin, A., Dumais, T., Caminos, L., Goldstein, R. E., Pesci, A. I., et al. (2020). Optimal Design of Multilayer Fog Collectors. ACS Appl. Mater. Interfaces, 12(6), 7736–7743.
Abstract: The growing concerns over desertification have spurred research into technologies aimed at acquiring water from nontraditional sources such as dew, fog, and water vapor. Some of the most promising developments have focused on improving designs to collect water from fog. However, the absence of a shared framework to predict, measure, and compare the water collection efficiencies of new prototypes is becoming a major obstacle to progress in the field. We address this problem by providing a general theory to design efficient fog collectors as well as a concrete experimental protocol to furnish our theory with all the necessary parameters to quantify the effective water collection efficiency. We show in particular that multilayer collectors are required for high fog collection efficiency and that all efficient designs are found within a narrow range of mesh porosity. We support our conclusions with measurements on simple multilayer harp collectors.
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Besson, S., & Dumais, J. (2014). Stochasticity in the symmetric division of plant cells: when the exceptions are the rule. Front. Plant Sci., 5, 4 pp.
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Campas, O., Rojas, E., Dumais, J., & Mahadevan, L. (2012). Strategies For Cell Shape Control In Tip-Growing Cells. Am. J. Bot., 99(9), 1577–1582.
Abstract: Premise of the study: Despite the large diversity in biological cell morphology, the processes that specify and control cell shape are not yet fully understood. Here we study the shape of tip-growing, walled cells, which have evolved a polar mode of cell morphogenesis leading to characteristic filamentous cell morphologies that extend only apically. Methods: We identified the relevant parameters for the control of cell shape and derived scaling laws based on mass conservation and force balance that connect these parameters to the resulting geometrical phenotypes. These laws provide quantitative testable relations linking morphological phenotypes to the biophysical processes involved in establishing and modulating cell shape in tip-growing, walled cells. Key results and conclusions: By comparing our theoretical results to the observed morphological variation within and across species, we found that tip-growing cells from plant and fungal species share a common strategy to shape the cell, whereas oomycete species have evolved a different mechanism.
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Campos, J. L., Dumais, J., Pavissich, J. P., Franchi, O., Crutchik, D., Belmonte, M., et al. (2019). Predicting Accumulation of Intermediate Compounds in Nitrification and Autotrophic Denitrification Processes: A Chemical Approach. Biomed Res. Int., 2019, 9 pp.
Abstract: Nitrification and sulfur-based autotrophic denitrification processes can be used to remove ammonia from wastewater in an economical way. However, under certain operational conditions, these processes accumulate intermediate compounds, such as elemental sulphur, nitrite, and nitrous oxide, that are noxious for the environment. In order to predict the generation of these compounds, an analysis based on the Gibbs free energy of the possible reactions and on the oxidative capacity of the bulk liquid was done on case study systems. Results indicate that the Gibbs free energy is not a useful parameter to predict the generation of intermediate products in nitrification and autotrophic denitrification processes. Nevertheless, we show that the specific productions of nitrous oxide during nitrification, and of elemental sulphur and nitrite during autotrophic denitrification, are well related to the oxidative capacity of the bulk liquid.
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Couturier, E., Dumais, J., Cerda, E., & Katifori, E. (2013). Folding of an opened spherical shell. Soft Matter, 9(34), 8359–8367.
Abstract: Thin, doubly curved shells occur commonly in nature and their mechanical properties and modes of deformation are very important for engineering structures of all scales. Although there has been substantial work on the stability and modes of failure of thin shells, relatively little work has been done to understand the conditions that promote continuous large scale deformations. A major impediment to progress in this direction is the inherent difficulty in obtaining analytical expressions for the deformed shapes. In this work we propose a new integrable solution which describes the behavior under load of a thin spherical shell with an opening (aperture) of n-fold axial symmetry. We derive a two-parameter family of approximately isometric, constant positive Gaussian curvature shapes that is in excellent agreement with our experimental results of deformed shells (3D scans of compressed ping-pong balls) and simulations (tethered membrane simulations minimizing the stretching and bending energy). The integrable solutions that describe those shapes have n symmetrically arranged curvature singularities which correspond to cusps of the folded shape. We examine the properties of the folded shells and observe that in the analytic solutions isometric closure is more easily achieved when the singularities lie away from the center of the aperture. We find that when allowed by the geometry of the aperture and the nature of the load, physical shells expel the curvature singularities into the aperture.
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Dumais, J. (2013). Modes of deformation of walled cells. J. Exp. Bot., 64(15), 4681–4695.
Abstract: The bewildering morphological diversity found in cells is one of the starkest illustrations of lifes ability to self-organize. Yet the morphogenetic mechanisms that produce the multifarious shapes of cells are still poorly understood. The shared similarities between the walled cells of prokaryotes, many protists, fungi, and plants make these groups particularly appealing to begin investigating how morphological diversity is generated at the cell level. In this review, I attempt a first classification of the different modes of surface deformation used by walled cells. Five modes of deformation were identified: inextensional bending, equi-area shear, elastic stretching, processive intussusception, and chemorheological growth. The two most restrictive modesuinextensional and equi-area deformationsuare embodied in the exine of pollen grains and the wall-like pellicle of euglenoids, respectively. For these modes, it is possible to express the deformed geometry of the cell explicitly in terms of the undeformed geometry and other easily observable geometrical parameters. The greatest morphogenetic power is reached with the processive intussusception and chemorheological growth mechanisms that underlie the expansive growth of walled cells. A comparison of these two growth mechanisms suggests a possible way to tackle the complexity behind wall growth.
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Dumais, J. (2021). Mechanics and hydraulics of pollen tube growth. New Phytol., 232(4), 1549–1565.
Abstract: All kingdoms of life have evolved tip-growing cells able to mine their environment or deliver cargo to remote targets. The basic cellular processes supporting these functions are understood in increasing detail, but the multiple interactions between them lead to complex responses that require quantitative models to be disentangled. Here, I review the equations that capture the fundamental interactions between wall mechanics and cell hydraulics starting with a detailed presentation of James Lockhart's seminal model. The homeostatic feedbacks needed to maintain a steady tip velocity are then shown to offer a credible explanation for the pulsatile growth observed in some tip-growing cells. Turgor pressure emerges as a central variable whose role in the morphogenetic process has been a source of controversy for more than 50 yr. I argue that recasting Lockhart's work as a process of chemical stress relaxation can clarify how cells control tip growth and help us internalise the important but passive role played by turgor pressure in the morphogenetic process.
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Gole, C., Dumais, J., & Douady, S. (2016). Fibonacci or quasi-symmetric phyllotaxis. Part I: why? Acta Soc. Bot. Pol., 85(4), 34 pp.
Abstract: The study of phyllotaxis has focused on seeking explanations for the occurrence of consecutive Fibonacci numbers in the number of helices paving the stems of plants in the two opposite directions. Using the disk-accretion model, first introduced by Schwendener and justified by modern biological studies, we observe two distinct types of solutions: the classical Fibonacci-like ones, and also more irregular configurations exhibiting nearly equal number of helices in a quasi-square packing, the quasi-symmetric ones, which are a generalization of the whorled patterns. Defining new geometric tools allowing to work with irregular patterns and local transitions, we provide simple explanations for the emergence of these two states within the same elementary model. A companion paper will provide a wide array of plant data analyses that support our view.
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Gravelle, S., & Dumais, J. (2020). A multi-scale model for fluid transport through a bio-inspired passive valve. J. Chem. Phys., 152(1), 10 pp.
Abstract: Tillandsia landbeckii is a rootless plant thriving in the hyper-arid Atacama Desert of Chile. These plants use unique cellulose-based microscopic structures called trichomes to collect fresh water from coastal fog. The trichomes rely on a passive mechanism to maintain an asymmetrical transport of water: they allow for the fast absorption of liquid water deposited by sporadic fog events while preventing evaporation during extended drought periods. Inspired by the trichome's design, we study fluid transport through a micrometric valve. Combining Grand Canonical Monte Carlo with Non-Equilibrium Molecular Dynamics simulations, we first analyze the adsorption and transport of a fluid through a single nanopore at different chemical potentials. We then scale up the atomic results using a lattice approach, and simulate the transport at the micrometric scale. Results obtained for a model Lennard-Jones fluid and TIP4P/2005 water were compared, allowing us to identify the key physical parameters for achieving a passive hydraulic valve. Our results show that the difference in transport properties of water vapor and liquid water within the cellulose layer is the basis for the ability of the Tillandsia trichome to function as a water valve. Finally, we predict a critical pore dimension above which the cellulose layer can form an efficient valve.
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Guerin, A., Gravelle, S., & Dumais, J. (2016). Forces behind plant cell division. Proc. Natl. Acad. Sci. U. S. A., 113(32), 8891–8893.
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Hamant, O., Inoue, D., Bouchez, D., Dumais, J., & Mjolsness, E. (2019). Are microtubules tension sensors? Nat. Commun., 10, 12 pp.
Abstract: Mechanical signals play many roles in cell and developmental biology. Several mechan-otransduction pathways have been uncovered, but the mechanisms identified so far only address the perception of stress intensity. Mechanical stresses are tensorial in nature, and thus provide dual mechanical information: stress magnitude and direction. Here we propose a parsimonious mechanism for the perception of the principal stress direction. In vitro experiments show that microtubules are stabilized under tension. Based on these results, we explore the possibility that such microtubule stabilization operates in vivo, most notably in plant cells where turgor-driven tensile stresses exceed greatly those observed in animal cells.
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Jarur, M. C., Dumais, J., & Rica, S. (2019). Limiting speed for jumping. C. R. Mec., 347(4), 305–317.
Abstract: General mechanical considerations provide an upper bound for the take-off velocity of any jumper, animate or inanimate, rigid or soft body, animal or vegetal. The take-off velocity is driven by the ratio of released energy to body mass. Further, the mean reaction force on a rigid platform during push-off is inversely proportional to the characteristic size of the jumper. These general considerations are illustrated in the context of Alexander's jumper model, which can be solved exactly and which shows an excellent agreement with the mechanical results. (C) 2019 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved.
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Llorens, C., Argentina, M., Rojas, N., Westbrook, J., Dumais, J., & Noblin, X. (2016). The fern cavitation catapult: mechanism and design principles. J. R. Soc. Interface, 13(114), 13 pp.
Abstract: Leptosporangiate ferns have evolved an ingenious cavitation catapult to disperse their spores. The mechanism relies almost entirely on the annulus, a row of 12-25 cells, which successively: (i) stores energy by evaporation of the cells' content, (ii) triggers the catapult by internal cavitation, and (iii) controls the time scales of energy release to ensure efficient spore ejection. The confluence of these three biomechanical functions within the confines of a single structure suggests a level of sophistication that goes beyond most man-made devices where specific structures or parts rarely serve more than one function. Here, we study in detail the three phases of spore ejection in the sporangia of the fern Polypodium aureum. For each of these phases, we have written the governing equations and measured the key parameters. For the opening of the sporangium, we show that the structural design of the annulus is particularly well suited to inducing bending deformations in response to osmotic volume changes. Moreover, the measured parameters for the osmoelastic design lead to a near-optimal speed of spore ejection (approx. 10 m s(-1)). Our analysis of the trigger mechanism by cavitation points to a critical cavitation pressure of approximately -100 +/- 14 bar, a value that matches the most negative pressures recorded in the xylem of plants. Finally, using high-speed imaging, we elucidated the physics leading to the sharp separation of time scales (30 versus 5000 μs) in the closing dynamics. Our results highlight the importance of the precise tuning of the parameters without which the function of the leptosporangium as a catapult would be severely compromised.
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Raux, P. S., Gravelle, S., & Dumais, J. (2020). Design of a unidirectional water valve in Tillandsia. Nat. Commun., 11(1), 7 pp.
Abstract: The bromeliad Tillandsia landbeckii thrives in the Atacama desert of Chile using the fog captured by specialized leaf trichomes to satisfy its water needs. However, it is still unclear how the trichome of T. landbeckii and other Tillandsia species is able to absorb fine water droplets during intermittent fog events while also preventing evaporation when the plant is exposed to the desert's hyperarid conditions. Here, we explain how a 5800-fold asymmetry in water conductance arises from a clever juxtaposition of a thick hygroscopic wall and a semipermeable membrane. While absorption is achieved by osmosis of liquid water, evaporation under dry external conditions shifts the liquid-gas interface forcing water to diffuse through the thick trichome wall in the vapor phase. We confirm this mechanism by fabricating artificial composite membranes mimicking the trichome structure. The reliance on intrinsic material properties instead of moving parts makes the trichome a promising basis for the development of microfluidics valves.
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Rojas, E. R., & Dumais, J. (2019). A Mechanical Cusp Catastrophe Imposes a Universal Developmental Constraint on the Shapes of Tip-Growing Cells. In Biophysical Journal (Vol. 116, p. 121A). Cell Press.
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Valenzuela-Heredia, D., Panatt, C.:, Belmonte, M., Franchi, O., Crutchik, D., Dumais, J., Vazquez-Padin, J. R., et al. (2022). Performance of a two-stage partial nitritation-anammox system treating the supernatant of a sludge anaerobic digester pretreated by a thermal hydrolysis process. Chem. Eng. J., 429, 131301.
Abstract: A two-stage system (partial nitritation (PN) and anammox processes) was used to remove nitrogen from the dewatering liquor originating from the thermal hydrolysis/anaerobic digestion (THP/AD) of municipal WWTP sludge. Two strategies were tested to start up the PN reactor: 1) maintaining a fixed hydraulic retention time (HRT) and increasing the ammonium loading rate (ALR) by decreasing the feeding dilution ratio and 2) feeding undiluted dewatering liquor and gradually decreasing the HRT. With diluted feeding, the reactor performance had destabilization episodes that were statistically correlated with the application of high specific ammonium (> 0.6 g NH4+-N/(g TSS.d)) and organic (> 0.7 g COD/(g TSS.d)) loading rates. The second strategy allowed stable PN reactor operation while treating ALR up to 4.8 g NH4+-N/(L.d) and demonstrating that dilution of THP/AD effluents is not required. The operating conditions promoted the presence of free nitrous acid levels (> 0.14 mg HNO2-N/L) inside the PN reactor that inhibited the proliferation of nitrite oxidizing bacteria.
Batch activity tests showed that the inhibitory effects of organic compounds present in the THP/AD dewatering liquor on the ammonia oxidizing bacteria activity can be removed in the PN reactor. Thus, aerobic pretreatment would not be necessary when two-stage systems are used. The PN reactor effluent was successfully treated by an anammox reactor.
An economic analysis showed that using two-stage systems is advantageous for treating THP/AD dewatering liquor. The implementation of an aerobic pre-treatment unit is recommended for WWTPs capacities higher than 5.10(5) inhabitants equivalent when one-stage systems are used.
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Van Hemelryck, M., Bernal, R., Ispolatov, Y., & Dumais, J. (2018). Lily Pollen Tubes Pulse According to a Simple Spatial Oscillator. Sci Rep, 8, 10 pp.
Abstract: Polar growth is a fundamental mode of cell morphogenesis observed in nearly all major groups of organisms. Among polarly growing cells, the angiosperm pollen tubes have emerged as powerful experimental systems in large part because of their oscillatory growth, which provides a window into the network of interactions regulating morphogenesis. Empirical studies of oscillatory pollen tubes have sought to uncover the temporal sequence of cellular and molecular events that constitutes an oscillatory cycle. Here we show that in lily pollen tubes the distance or wavelength (lambda = 6.3 +/- 1.7 μm) over which an oscillatory cycle unfolds is more robust than the period of oscillation (tau = 39.1 +/- 17.6 s) (n = 159 cells). Moreover, the oscillatory cycle is divided into slow and fast phases, with each phase unfolding over precisely one half of the wavelength. Using these observations, we show that a simple spatial bi-oscillator predicts the most common modes of oscillation observed in pollen tubes. These results call into question the traditional view of pollen tube morphogenesis as a temporal succession of cellular events. Space, not time, may be the most natural metric to inteprete the morphogenetic dynamics of these cells.
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