Computation of forces from deformed visco-elastic biological tissues

We present a least-squares based inverse analysis of visco-elastic biological tissues. The proposed method computes the set of contractile forces (dipoles) at the cell boundaries that induce the observed and quantified deformations. We show that the computation of these forces requires the regularisation of the problem functional for some load configurations that we study here. The functional measures the error of the dynamic problem being discretised in time with a second-order implicit time-stepping and in space with standard finite elements. We analyse the uniqueness of the inverse problem and estimate the regularisation parameter by means of an L-curved criterion. We apply the methodology to a simple toy problem and to an in vivo set of morphogenetic deformations of the Drosophila embryo.Peer ReviewedPostprint (author's final draft

Truss model for stress controlled morphogenesis

We resort to the usual decomposition of the deformation gradient into an active and a passive component, and deduce the constitutive law and equilibrium equations when the two components are not independent. In the model described here the active of the deformation is related to the hyperelastic passive part through a control function that simulates a feedback mechanism that has been experimentally observed during embryo development. Using a variational approach, we first write the equations for continua and study the effects of the control function in these equations. We particularise the results for a system of trusses, which allows us to obtain a simplified set of equations. In our derivations, we apply special attention to the conditions that a thermodynamically complaint formulation should satisfy. We particularise these equations and conditions for the relevant elements of the cytoskeleton, namely, microfilaments and microtubules. We apply the model to simulate the shape changes observed during invagination of the Drosophila Melanogaster embryo. As a salient result, the model reveals that the incompressibility constraint of the yolk furnishes a necessary pressure on the epithelium that eventually eases its internalisation.Postprint (published version

Improvement of physical, chemical and biochemical proprieties of a salt affected Alfisol by addition of biochar and gypsum

Salinization is one of the major environmental problems threatening agricultural productivity. Soil salinization is defined as an excessive accumulation of salts within the soil profile. It negatively affects soil physical and chemical properties, as well as the biochemical ones. Reclamation of salt affected soils requires removal of soluble salts and Na+ from the soil exchange sites. Subsequently, salts are leached out the root zone by irrigation water when available. Gypsum (CaSO4·2H2O) is the most commonly used chemical amendment for reclamation of salt affected soils since it provides Ca2+ that replaces Na+ on the exchange sites and improves soil structure. Also organic amendments have been considered, but not extensively studied, for reclamation of salt affected soils. Recent studies have reported that biochar can be rich in nutrients like Ca2+ and Mg2+ and may enhance their availability in soil when added as amendment. Therefore, addition of biochar to a salt affected soil could aid in its remediation by supplying Ca2+ and Mg2+, and replacing Na+, improving aggregate stability and hydraulic conductivity. The objective of this study was to evaluate the effects of gypsum and biochar for the reclamation of a saline-sodic soil on some physical, chemical and biological properties. The topsoil of an Alfisol, about fifty meters far from the foreshore in the Petrosino coast (Sicily, Italy), was used for this experiment. The soil was air-dried and sieved at 2 mm. The main physical and chemical properties of the soil were: pH 7.3, clay 23 %, total carbonates 50.9 %, electrical conductivity 0.81 dS m-1 (1:5, w/v), total organic C 11.0 g kg-1, cation exchange capacity 24.8 cmol(+) kg-1, exchangeable sodium percentage 35 %. Two doses of gypsum (2.6 and 5.1 g kg-1 of soil) and two doses of biochar (4.2 and 8.3 g kg-1) were tested. The two doses of gypsum were calculated in order to decrease ESP from 35% to 25% and to 15%, respectively, whereas biochar was added in order to achieve an amount of 10 and 20 Mg ha-1. Following addition of gypsum and biochar, either alone or in combination, 100 g of soil were incubated at room temperature in 150 mL plastic pots and maintained at 50% of soil water holding capacity during all the duration of the experiment (22 days). One week after the incubation, three horse-radish seeds were sown. Then, after 13 days, plants were removed, oven dried at 60°C for 48 hours and weighed. The soils were analyzed to determine porosity, CEC, ESP, ECe, microbial biomass C, soil respiration and microbial community structure. The experiment was carried out in octuplicate. In this work, the results are reported and discusse

Quantifying forces in cell biology

Cells exert, sense, and respond to physical forces through an astounding diversity of mechanisms. Here we review recently developed tools to quantify the forces generated by cells. We first review technologies based on sensors of known or assumed mechanical properties, and discuss their applicability and limitations. We then proceed to draw an analogy between these human-made sensors and force sensing in the cell. As mechanics is increasingly revealed to play a fundamental role in cell function we envisage that tools to quantify physical forces may soon become widely applied in life-sciences laboratories

Computational tools for multicellular systems

Macroscopic deformations in embryonic soft tissues are due to the intra-cellular remodelling and cell intercalation. We here present a computational approach that can handle the two types of deformations, and also take into account the active cell response. The model resorts to cell centred techniques, where particles represent cell nuclei, and to vertex models, where the vertices represent cell boundaries. This hybrid approach allows to consider separately intra-cellular and inter-cellular forces, and at the same time impose cell incompressibility. The model is applied to simulate the active stretching of epithelium

Anticipating New Treatments for Cystic Fibrosis: A Global Survey of Researchers

Cystic fibrosis is a life-threatening disease that affects at least 100,000 people worldwide. It is caused by a defect in the cystic fibrosis transmembrane regulator (CFTR) gene and presently, 360 CFTR-causing mutations have been identified. Since the discovery of the CFTR gene, the expectation of developing treatments that can substantially increase the quality of life or even cure cystic fibrosis patients is growing. Yet, it is still uncertain today which developing treatments will be successful against cystic fibrosis. This study addresses this gap by assessing the opinions of over 524 cystic fibrosis researchers who participated in a global web-based survey. For most respondents, CFTR modulator therapies are the most likely to succeed in treating cystic fibrosis in the next 15 years, especially through the use of CFTR modulator combinations. Most respondents also believe that fixing or replacing the CFTR gene will lead to a cure for cystic fibrosis within 15 years, with CRISPR-Cas9 being the most likely genetic tool for this purpose

A 3D finite element model of ventral furrow invagination in the Drosophila melanogaster embryo

The paper describes a mechanical model of epithelial tissue development in Drosophila embryos to investigate a buckling phenomenon called invagination. The finite element method is used to model this ventral furrow formation in 3D by decomposing the total deformation into two parts: an imposed active deformation, and an elastic passive deformation superimposed onto the latter. The model imposes as boundary conditions (i) a constant yolk volume and (ii) a sliding contact condition of the cells against the vitelline membrane, which is interpolated as a B-Spline surface. The active deformation simulates the effects of apical constriction and apico-basal elongation of cells. This set of local cellular mechanisms leads to global shape changes of the embryo which are associated with known gene expressions. Using the model we have tested different plausible hypotheses postulated to account for the mechanical behaviour of epithelial tissues. In particular, we conclude that only certain combinations of local cell shape change can successfully reproduce the invagination process. We have quantitatively compared the model with a 2D model and shown that it exhibits a more robust invagination phenomenon. The 3D model has also revealed that invagination causes a yolk flow from the central region to the anterior and posterior ends of the embryo, causing an accordion-like global compression and expansion wave to move through the embryo. Such a phenomenon cannot be described by 2D models

Computation of forces from deformed visco-elastic biological tissues

We present a least-squares based inverse analysis of visco-elastic biological tissues. The proposed method computes the set of contractile forces (dipoles) at the cell boundaries that induce the observed and quantified deformations. We show that the computation of these forces requires the regularisation of the problem functional for some load configurations that we study here. The functional measures the error of the dynamic problem being discretised in time with a second-order implicit time-stepping and in space with standard finite elements. We analyse the uniqueness of the inverse problem and estimate the regularisation parameter by means of an L-curved criterion. We apply the methodology to a simple toy problem and to an in vivo set of morphogenetic deformations of the Drosophila embryo

SHORT-TERM RESPONSE OF SOIL MICROORGANISMS TO ESSENTIAL OILS WITH ALLELOPATHIC POTENTIAL EXTRACTED FROM MEDITERRANEAN PLANTS

Essential oils (EOs) with allelopathic compounds have been used to reduce or avoid weed germination and growth. The aim of this study was to evaluate the potential phytotoxic effects of EOs extracted from different Mediterranean plants on soil microbial biomass and activity. EOs were extracted from leaves of Eucalyptus camaldulensis Dehnh (EUC); Eriocephalus africanus L. (ERI); Thymus capitatus (L.) Hoffmanns. & Link (TCP); Citrus reticulata Blanco var. ‘Clemenules’ (TAN) and Citrus limon (L.) Osbeck var. ‘Eureka’ (LEM). Each EO was supplied to pots containing 560 g of soil at three different doses (low, medium, high). After 15, 30, 90, 120 days the supply of EOs, soils were destructively analyses for microbial biomass carbon (MBC) and microbial respiration. EOs extracted from E. camaldulensis (EUC), C. limon (LEM) and T. capitatus (TCP), at the highest concentration decreased MBC up to 30 days since their addition, with no further effects at two last samplings. EOs extracted from ERI and TAN did not affect MBC. Soil respiration was not affected by any experimental factor, whereas the metabolic quotient was increased by EO extracted from TCP. Our results suggested that essential oils with allelopathic potential extracted from mediterranean plants can negatively affect soil microorganisms and, consequently, their use as herbicides should take into account these findings