[Show abstract][Hide abstract] ABSTRACT: title>Author Summary
Although plants are mostly seen as static, they are constantly moving to adapt to changes in their stature and to their environment. Gravity and light, among others, are major factors that sculpt the shapes of plants. Plants tend to grow in the direction of the light to get access to their energy resource. At the same time, however, they need to maintain their balance and control their posture. In a recent study, we showed that postural control is regulated by two types of perception: graviception and proprioception. We extend that study to include light perception in order to obtain a unified description of plant tropism. As the system is highly dynamic, a model is required in order to evaluate hypotheses against experimental data. Our results show that the direction of plant growth is determined by the combined influence of light and gravity, whereas postural control is still regulated by gravity and proprioception.</p
Preview · Article · Feb 2015 · PLoS Computational Biology
[Show abstract][Hide abstract] ABSTRACT: This research proposed a new model to differentiate leaf venation topology patterns using Multiscale Fractal Dimension. Identification of medicinal plants is important considering wide
range of biodiversity in Indonesia and significant role of medicinal plants in Indonesia. Plants
identification can be performed with shape analysis using plant leaf venation as a feature. Multiscale Fractal Dimension is a shape analysis method that analyze shapes through its complexity. In this research three Indonesian medicinal plants species has their leaf venation topologies modelled with Multiscale Fractal Dimension. The result shows that while the difference is not remarkably clear, there are irregularities that can be made more evident with multiscale analysis. Future works can include Multiscale Fractal Dimension as one technique to identify plants.
[Show abstract][Hide abstract] ABSTRACT: Gravitropism, the slow reorientation of plant growth in response to gravity, is a major determinant of the form and posture of land plants. Recently a universal model of shoot gravitropism, the AC model, was presented, in which the dynamics of the tropic movement is only determined by the conflicting controls of (1) graviception that tends to curve the plants toward the vertical, and (2) proprioception that tends to keep the stem straight. This model was found to be valid for many species and over two orders of magnitude of organ size. However, the motor of the movement, the elongation, was purposely neglected in the AC model. If growth effects are to be taken into account, it is necessary to consider the material derivative, i.e., the rate of change of curvature bound to expanding and convected organ elements. Here we show that it is possible to rewrite the material equation of curvature in a compact simplified form that directly expresses the curvature variation as a function of the median elongation and of the distribution of the differential growth. By using this extended model, called the ACĖ model, growth is found to have two main destabilizing effects on the tropic movement: (1) passive orientation drift, which occurs when a curved element elongates without differential growth, and (2) fixed curvature, when an element leaves the elongation zone and is no longer able to actively change its curvature. By comparing the AC and ACĖ models to experiments, these two effects are found to be negligible. Our results show that the simplified AC mode can be used to analyze gravitropism and posture control in actively elongating plant organs without significant information loss.
[Show abstract][Hide abstract] ABSTRACT: Gravitropism, the slow reorientation of plant growth in response to gravity, is a key determinant of the form and posture of land plants. Shoot gravitropism is triggered when statocysts sense the local angle of the growing organ relative to the gravitational field. Lateral transport of the hormone auxin to the lower side is then enhanced, resulting in differential gene expression and cell elongation causing the organ to bend. However, little is known about the dynamics, regulation, and diversity of the entire bending and straightening process. Here, we modeled the bending and straightening of a rod-like organ and compared it with the gravitropism kinematics of different organs from 11 angiosperms. We show that gravitropic straightening shares common traits across species, organs, and orders of magnitude. The minimal dynamic model accounting for these traits is not the widely cited gravisensing law but one that also takes into account the sensing of local curvature, what we describe here as a graviproprioceptive law. In our model, the entire dynamics of the bending/straightening response is described by a single dimensionless "bending number" B that reflects the ratio between graviceptive and proprioceptive sensitivities. The parameter B defines both the final shape of the organ at equilibrium and the timing of curving and straightening. B can be estimated from simple experiments, and the model can then explain most of the diversity observed in experiments. Proprioceptive sensing is thus as important as gravisensing in gravitropic control, and the B ratio can be measured as phenotype in genetic studies.
Preview · Article · Dec 2012 · Proceedings of the National Academy of Sciences
[Show abstract][Hide abstract] ABSTRACT: Branching morphogenesis is a widely spread phenomenon in nature. In organogenesis, it results from the inhomogeneous growth of the epithelial sheet, leading to its repeated branching into surrounding mesoderm. Lung morphogenesis is an emblematic example of tree-like organogenesis common to most mammals. The core signalling network is well identified, notably the Fgf10/Shh couple, required to initiate and maintain branching. In a previous study, we showed that the restriction by SHH of Fgf10 expression domain to distal mesenchyme spontaneously induces differential epithelial proliferation leading to branching. A simple Laplacian model qualitatively reproduced FGF10 dynamics in the mesenchyme and the spontaneous self-avoiding branching morphogenesis. However, early lung geometry has several striking features that remain to be addressed. In this paper, we investigate, through simulations and data analysis, if the FGF10-diffusion scenario accounts for the following aspects of lung morphology: size dispersion, asymmetry of branching events, and distal epithelium-mesothelium equilibrium. We report that they emerge spontaneously in the model, and that most of the underlying mechanisms can be understood as dynamical interactions between gradients and shape. This suggests that specific regulation may not be required for the emergence of these striking geometrical features.
No preview · Article · Nov 2012 · Physical Biology
[Show abstract][Hide abstract] ABSTRACT: Calibration curves used to measure the intracellular pH. (A) Background corrected 485/436 ratios of BCECF. The in vitro calibration corresponds to BCECF-free acid (5 µM) in a wide range of pH buffer values. Mean and SD correspond to three independent experiments and from 8 to 30 measures. (B) In situ calibration of BCECF-AM (5 µM) loaded cells after cells had been treated with ionophores to equilibrate the intracellular and extracellular H+-concentrations. The data correspond to two independent experiments, with 11≤n≤21 measures.
[Show abstract][Hide abstract] ABSTRACT: Influence of the environmental pH on valve morphology. We used TEM images at resolution level from the nanometer to the micron-scale to test the impact of the environmental pH on morphometric traits of the valve. (A) The width (W) of the valve (10≤n≤21). (B) The number (N) of central fultoportulae per cell (10≤n≤22). (C) The minimum distance between fultoportulae present in the central region (cp) cell (35≤n≤82). (D) Distance between two adjacent rimoportulae (rp) (28≤n≤128). (E) The distance (d1) between two adjacent pores (54,842≤n≤78,374). (F) The width of branching ribs (d2) (54,842≤n≤78,374). (G) The distance between the ribs (D) (6,378≤n≤15,038). The representations from A to D correspond to boxplots, and in E to G only the mean and the standard deviation are presented.
[Show abstract][Hide abstract] ABSTRACT: Dynamics of frustule formation in T. weissflogii. This real-time movie shows the evolution of the fluorescence of the dye used to follow valve formation in diatoms. The entire movie corresponds to 31 images acquired at 3.33 mHz, and the quantification of the HCK-123 is presented in Figure 4A. The left panel corresponds to the quantification and the right panel to the images of the HCK-123 fluorescence.
[Show abstract][Hide abstract] ABSTRACT: Calibration of the fluorescence intensity as a concentration of HCK-123.
In situ determination of the fluorescence signal for 9 different concentrations (between 0 and 62.5 µM) of HCK-123. The method used was the same method as the one used to determine the signal inside T. weissflogii cells. The data that correspond to 3 independent experiments from 36 to 150 measurements were fitted to a linear curve.
[Show abstract][Hide abstract] ABSTRACT: Step by step image analyses for the extraction of several valve morphometric traits. (A) Original TEM image. The scale bar corresponds to 100 nm. (B) The same image after noise reduction. (C) Image after binarization. (D) Determination of the circular regions which correspond to the valve pores (in green), directly allowed us to determine the pore radius (r) and the valve porosity (r). It also allows to compute the corresponding Voronoi diagram (blue lines). (E) Histogram of distances between two neighbors (d) in the Voronoi diagram. (F) Determination of points defining the fingers (yellow crosses). (G) Determination of the second Voronoi diagram. (H) Measurement of distance D, across fingers. (I) Histogram of the distance D.
[Show abstract][Hide abstract] ABSTRACT: Influence of the external pH on valves morphometry. The eight morphometric traits measured on purified valves from T. weissflogii cells grown at the different pHs are: the average cell width and the number (N) of central fultoportulae, the minimum distance (l) between two adjacent central fultoportulae, the minimum distance (L) between two adjacent rimoportulae, the radius (R) of the pores, the distance (d1) between two adjacent pores, the width of semi-continuous cribra (D), the width of radial ribs (d2), and the valve porosity.
[Show abstract][Hide abstract] ABSTRACT: Scanning electron micrographs of the centric diatom Thalassiosira weissflogii. (A) View of the valve exterior showing the network on loculate areola. Note the presence of central fultoportulae, and of rimoportulae. (B) Semicontinuous cribra are present on the valve face. The interior opening of rimoportulae and the fultoportulae is visible. The scale bar corresponds to 5 µm.
[Show abstract][Hide abstract] ABSTRACT: Diatoms, the major contributors of the global biogenic silica cycle in modern oceans, account for about 40% of global marine primary productivity. They are an important component of the biological pump in the ocean, and their assemblage can be used as useful climate proxies; it is therefore critical to better understand the changes induced by environmental pH on their physiology, silicification capability and morphology. Here, we show that external pH influences cell growth of the ubiquitous diatom Thalassiosira weissflogii, and modifies intracellular silicic acid and biogenic silica contents per cell. Measurements at the single-cell level reveal that extracellular pH modifications lead to intracellular acidosis. To further understand how variations of the acid-base balance affect silicon metabolism and theca formation, we developed novel imaging techniques to measure the dynamics of valve formation. We demonstrate that the kinetics of valve morphogenesis, at least in the early stages, depends on pH. Analytical modeling results suggest that acidic conditions alter the dynamics of the expansion of the vesicles within which silica polymerization occurs, and probably its internal pH. Morphological analysis of valve patterns reveals that acidification also reduces the dimension of the nanometric pores present on the valves, and concurrently overall valve porosity. Variations in the valve silica network seem to be more correlated to the dynamics and the regulation of the morphogenesis process than the silicon incorporation rate. These multiparametric analyses from single-cell to cell-population levels demonstrate that several higher-level processes are sensitive to the acid-base balance in diatoms, and its regulation is a key factor for the control of pattern formation and silicon metabolism.
[Show abstract][Hide abstract] ABSTRACT: Fluorescence properties of the Lysotracker HCK-123. Influence of the pH on the maximum emission of 1 µM HCK-123 in either 100 mM potassium hydrogen phosphate buffer or in 20 mM phosphate/citrate buffer. The intensity was normalized to the value obtained at pH = 7.0.
[Show abstract][Hide abstract] ABSTRACT: The supplemental methods contains: assessment of the use of HCK-123 as a reporter for valve formation, image analyses, morphometric analyses, modeling, and additional references.
[Show abstract][Hide abstract] ABSTRACT: Boxplots showing the fluorescence intensity of cells labeled with different concentrations of HCK-123.
T. weissflogii cells grown for 24 hours in the presence of HCK-123 were analyzed by flow cytometry, with a total of 3,800 to 5,800 analyzed cells. These results support the idea that HCK-123 is quantitative incorporated into the newly synthesized silica frustules.
[Show abstract][Hide abstract] ABSTRACT: Duration of the initial phases of valve formation. The duration of the two initial periods of valve formation was determined from cells grown at different pHs. (A) Length of the exponential phase (tExp). (B) Length of the decay phase (tDec). The data that correspond to 3 to 9 independent experiments were extracted from the recording of 8 to 92 individual cell kinetics.