Paul Southam

Generation of Leaf Shape Through Early Patterns of Growth and Tissue Polarity

Shape-Shifting Signals Although orthogonal signaling systems seem to direct various developmental processes, few tissues remain in the same shape as they are at initiation to that of the final form. Arabidopsis leaves are free of the cell migrations that complicate animal development, and thus allowed Kuchen et al. (p. 1092) to track and model the trajectory of leaf growth under a variety of perturbations. Varying the values of parameters in their model produced outputs of different leaf shapes ranging from obcordate, ovate, and oval to elliptic, and offered predictions for genes that regulate the developmental process. The meristem at the growing tip of plants is home to stem cells and is the source of newly differentiating shoots and leaves. New leaves make their first appearance as bulges at the side of the dome-shaped meristem. Although these developmental events are under hormonal control, they also seem to be constrained by the physical properties of the meristem. Kierzkowski et al. (p. 1096) tested physical effects acting on the shoot apical meristem of growing tomato shoots that alter turgor pressure. Again, mathematical modeling combined with observations of plant tissue helped to define the different zones in the meristem that respond to diverse mechanical stimuli. A model for the development of leaf shape describes how it arises through oriented growth and tissue deformation. A major challenge in biology is to understand how buds comprising a few cells can give rise to complex plant and animal appendages like leaves or limbs. We address this problem through a combination of time-lapse imaging, clonal analysis, and computational modeling. We arrive at a model that shows how leaf shape can arise through feedback between early patterns of oriented growth and tissue deformation. Experimental tests through partial leaf ablation support this model and allow reevaluation of previous experimental studies. Our model allows a range of observed leaf shapes to be generated and predicts observed clone patterns in different species. Thus, our experimentally validated model may underlie the development and evolution of diverse organ shapes.

JAGGED Controls Growth Anisotropy and Coordination between Cell Size and Cell Cycle during Plant Organogenesis

Summary Background In all multicellular organisms, the links between patterning genes, cell growth, cell cycle, cell size homeostasis, and organ growth are poorly understood, partly due to the difficulty of dynamic, 3D analysis of cell behavior in growing organs. A crucial step in plant organogenesis is the emergence of organ primordia from the apical meristems. Here, we combined quantitative, 3D analysis of cell geometry and DNA synthesis to study the role of the transcription factor JAGGED (JAG), which functions at the interface between patterning and primordium growth in Arabidopsis flowers. Results The floral meristem showed isotropic growth and tight coordination between cell volume and DNA synthesis. Sepal primordia had accelerated cell division, cell enlargement, anisotropic growth, and decoupling of DNA synthesis from cell volume, with a concomitant increase in cell size heterogeneity. All these changes in growth parameters required JAG and were genetically separable from primordium emergence. Ectopic JAG activity in the meristem promoted entry into S phase at inappropriately small cell volumes, suggesting that JAG can override a cell size checkpoint that operates in the meristem. Consistent with a role in the transition from meristem to primordium identity, JAG directly repressed the meristem regulatory genes BREVIPEDICELLUS and BELL 1 in developing flowers. Conclusions We define the cellular basis for the transition from meristem to organ identity and identify JAG as a key regulator of this transition. JAG promotes anisotropic growth and is required for changes in cell size homeostasis associated with accelerated growth and the onset of differentiation in organ primordia.

Theoretical and experimental comparison of different approaches for color texture classification

Color texture classification has been an area of intensive research activity. From the very onset, approaches to combining color and texture have been the subject of much discussion, and in particular, whether they should be considered joint or separately. We present a comprehensive comparison of the most prominent approaches both from a theoretical and experimental standpoint. The main contributions of our work are: (i) the establishment of a generic and extensible framework to classify methods for color texture classification on a mathematical basis, and (ii) a theoretical and experimental comparison of the most salient existing methods. Starting from an extensive set of experiments based on the Outex dataset, we highlight those texture descriptors that provide good accuracy along with low dimensionality. The results suggest that separate color and texture processing is the best practice when one seeks for optimal compromise between accuracy and limited number of features. We believe that our work may serve as a guide for those who need to choose the appropriate method for a specific application, as well as a basis for the development of new methods.

Generation of shape complexity through tissue conflict resolution

Out-of-plane tissue deformations are key morphogenetic events during plant and animal development that generate 3D shapes, such as flowers or limbs. However, the mechanisms by which spatiotemporal patterns of gene expression modify cellular behaviours to generate such deformations remain to be established. We use the Snapdragon flower as a model system to address this problem. Combining cellular analysis with tissue-level modelling, we show that an orthogonal pattern of growth orientations plays a key role in generating out-of-plane deformations. This growth pattern is most likely oriented by a polarity field, highlighted by PIN1 protein localisation, and is modulated by dorsoventral gene activity. The orthogonal growth pattern interacts with other patterns of differential growth to create tissue conflicts that shape the flower. Similar shape changes can be generated by contraction as well as growth, suggesting tissue conflict resolution provides a flexible morphogenetic mechanism for generating shape diversity in plants and animals. DOI: http://dx.doi.org/10.7554/eLife.20156.001

Towards Texture Classification in Real Scenes

Two new texture features, based on morphological scale-space processors are introduced. The new methods are shown to have good performance over a variety of tests. We demonstrate that if texture classifies are to be used in real world scenes, then the choice of test is critical and that Brodatz-like tests are unlikely to represent reality.

Texture granularities

We introduce three new texture features that are based on the morphological scale-space operator known as the sieve. The new features are tested on two databases. The first, the Outex texture database, contains Brodatz-like textures captured under constant illumination, scale and rotation. The second, the Outex natural scene database, contains images of real-world scenes taken under variable conditions. The new features are compared to univariate granulometries, with which they have some similarities, and to the dual-tree complex wavelet transform, local binary patterns and co-occurrence matrices. The features based upon the sieve are shown to have the best overall performance.

Oriented clonal cell dynamics enables accurate growth and shaping of vertebrate cartilage

Cartilaginous structures are at the core of embryo growth and shaping before the bone forms. Here we report a novel principle of vertebrate cartilage growth that is based on introducing transversally-oriented clones into pre-existing cartilage. This mechanism of growth uncouples the lateral expansion of curved cartilaginous sheets from the control of cartilage thickness, a process which might be the evolutionary mechanism underlying adaptations of facial shape. In rod-shaped cartilage structures (Meckel, ribs and skeletal elements in developing limbs), the transverse integration of clonal columns determines the well-defined diameter and resulting rod-like morphology. We were able to alter cartilage shape by experimentally manipulating clonal geometries. Using in silico modeling, we discovered that anisotropic proliferation might explain cartilage bending and groove formation at the macro-scale. DOI: http://dx.doi.org/10.7554/eLife.25902.001

Fruit shape diversity in the Brassicaceae is generated by varying patterns of anisotropy

Fruits exhibit a vast array of different 3D shapes, from simple spheres and cylinders to more complex curved forms; however, the mechanism by which growth is oriented and coordinated to generate this diversity of forms is unclear. Here, we compare the growth patterns and orientations for two very different fruit shapes in the Brassicaceae: the heart-shaped Capsella rubella silicle and the near-cylindrical Arabidopsis thaliana silique. We show, through a combination of clonal and morphological analyses, that the different shapes involve different patterns of anisotropic growth during three phases. These experimental data can be accounted for by a tissue-level model in which specified growth rates vary in space and time and are oriented by a proximodistal polarity field. The resulting tissue conflicts lead to deformation of the tissue as it grows. The model allows us to identify tissue-specific and temporally specific activities required to obtain the individual shapes. One such activity may be provided by the valve-identity gene FRUITFULL, which we show through comparative mutant analysis to modulate fruit shape during post-fertilisation growth of both species. Simple modulations of the model presented here can also broadly account for the variety of shapes in other Brassicaceae species, thus providing a simplified framework for fruit development and shape diversity. Summary: The diversity of fruit shape in the Brassicaceae family is based on local variation of directional growth that alters during developmental phases.

Texture classification via morphological scale-space: Tex-Mex features

We consider the problem of classifying textures. First, we consider images where the orientation of the texture is known. Then, we consider the classification of textures where the orientation is unknown. Last, classification in real scenes is considered. A wide variety of techniques are tested using the Outex framework. We introduce a new grayscale multiscale texture classification method based on a class of morphological filters called sieves. The method, denoted Tex-Mex because it extracts TEXture features using Morphological EXtrema filters, is shown to be among the best performing texture feature extraction methods. Tex-Mex features can be computed rapidly and are shown to be more robust and compact than the alternatives. Furthermore, they may be applied over windows of arbitrary size and orientation, a useful attribute when classifying texture in real scenes.

Compact rotation-invariant texture classification

This paper constructs a texture feature extractor based on a morphological scale-space. It produces features that are invariant to rotation of the texture. The features are used with a very simple k-nearest neighbour classifier and tested using the Outex methodology. The classifier has comparable performance to a number of benchmark classifiers but uses fewer features. The algorithm is quick to compute and provides insight into the underlying structure of texture.