Group Leader

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Dr. Richard S. Smith
Group Leader
Phone:+49 221 5062 130
Email:smith@...

MorphoGraphX

Computational modelling of morphogenesis and biomechanics (Richard Smith)

Computational modelling of morphogenesis and biomechanics

Transport-feedback model of auxin transport on a growing leaf. Growth creates space in the leaf margin for new auxin convergence points to emerge, which initiates new veins in the leaf lamina. See Smith and Bayer 2009 Zoom Image
Transport-feedback model of auxin transport on a growing leaf. Growth creates space in the leaf margin for new auxin convergence points to emerge, which initiates new veins in the leaf lamina. See Smith and Bayer 2009 [less]

Our research uses mathematical and computer simulation techniques to investigate questions in plant development. Working in close collaboration with experimental biologists, we develop cellular-level simulation models of hormone signaling and patterning in plant tissue. These models involve a biochemical aspect, genes, proteins, hormones, combined with growing, changing geometry as cells divide and tissues grow. We are interested in the interaction between these two processes. How genes control physical properties of cells resulting in growth, and how the resulting change in geometry and physical forces feeds back on signaling and gene regulation. With this in mind, we are researching methods to quantify mechanical properties in plant tissues, to facilitate the construction of biophysically-based simulation models of plant growth.

We are always looking for motivated students, interns and postdocs that are interested in applying their skills to questions in plant development and simulation modelling. Please contact Richard Smith for more information.

 

 

MorphoGraphX

Screen shot of MorphoGraphX showing two consecutive time points of a tomato shoot meristem taken as confocal image stacks (from Kierzkowski et al. 2012). The curved surface shape is extracted, subdivided, and then segmented into cells, allowing the quantification of shape change at the cellular level. Initially developed as part of the SystemsX.ch Swiss initiative for systems biology Plant Growth RTD. Zoom Image
Screen shot of MorphoGraphX showing two consecutive time points of a tomato shoot meristem taken as confocal image stacks (from Kierzkowski et al. 2012). The curved surface shape is extracted, subdivided, and then segmented into cells, allowing the quantification of shape change at the cellular level. Initially developed as part of the SystemsX.ch Swiss initiative for systems biology Plant Growth RTD. [less]

Much of our research involves the precise tracking of cell shape change, either from growth or elastic deformation. Since plants display symplastic growth, considerable information about morphogenesis can be obtained by looking at shape change in the surface layer of cells. However, in many systems, the surface layer of cells is not flat, and cell shape information is lost when doing max projections of confocal image data onto a plane. To address this problem, we have developed specialized software (www.MorphoGraphX.org) for the quantification of curved surface layers of cells. Working somewhere between 2 and 3D, MorphoGraphX is able to turn 3D confocal image stacks into curved surface images, which are then processed with standard algorithms we have adapted for this purpose. We are now extending our software for full 3D cell segmentation, fluorescence quantification, shape analysis, and other image processing problems as our research demands.

 

 

Cellular Force Microscopy

Cellular Force Microscopy on a mature <i>Arabidopsis</i> Embryo. Color indicates stiffness in N/m. Mature embryo project work done by Anne-Lise Routier-Kierzkowska in collaboration with the Bassel lab, Birmingham. Zoom Image
Cellular Force Microscopy on a mature Arabidopsis Embryo. Color indicates stiffness in N/m. Mature embryo project work done by Anne-Lise Routier-Kierzkowska in collaboration with the Bassel lab, Birmingham. [less]

Cellular force microscopy (CFM) is a new micro-indentation technique (Routier-Kierzkowska et al. 2012) that we have developed in collaboration with the Nelson lab and Femtotools. Sample stiffness is measured by indenting a thin probe connected to a force sensor. The recorded force and displacement are then used to determine the stiffness. Similar to atomic force microscopy (AFM), CFM uses computer controlled actuators to move the probe and can be used to create high-resolution stiffness maps as well as height maps. Some advantages of CFM are the wide range of forces that can be measured, filling the gap between AFM and load cells. CFM also has greater geometrical freedom; it is able to make large movements (up to cm's) and its long slender probe can access areas that a cantilever cannot. The CFM system is also highly flexible and can be used in combination with various optical microscopes, including both upright and inverted confocal systems.

 

 

Morphogenesis during early Arabidopsis embryo development

2D simulation of a growing <i>Arabidopsis </i>embryo with cell division. Specific division rules are required for correct patterning at several key stages. Zoom Image
2D simulation of a growing Arabidopsis embryo with cell division. Specific division rules are required for correct patterning at several key stages. [less]

Early embryo development provides an excellent system to study morphogenesis. In this system cell expansion, cell division, and genetic activity can be followed cell by cell in great detail. In collaboration with the Weijers lab, we use state of the art 3D imaging and molecular techniques to link gene and signaling networks to morphogenesis in plants. We test our hypothesis by using 3D spatial simulation models, developed in collaboration with the Prusinkiewicz lab, that are based on cell shape information extracted from sample tissue using MorphoGraphX. By developing a close integration between our simulation and imaging environments we will be able to use gene expression marker levels as direct input to our models, as well as to test model outputs. Our goal is to move one step closer to a true virtual plant tissue.

 

 

Cell expansion during seed germination

Cortical cells of a mature <i>Arabidopsis</i> embryo colored by cell volume. (lighter cells are larger). Zoom Image
Cortical cells of a mature Arabidopsis embryo colored by cell volume. (lighter cells are larger).

Another great systems for exploring the link between genetics and cell expansion is the mature Arabidopsis embryo. During germination a decision is made based largely on environmental cues to break dormancy and commence growth. Driven by the gibberellic acid (GA) signaling pathway, this binary growth switch represents an ideal system for examining the relationship between the induction of growth promoting gene expression and organ morphogenesis. In collaborating with the Bassel lab, Birmingham, we are developing methods to quantify cell shape change and gene expression in 3D. These data are being used to feed a physically-based finite-element (FEM) simulation model of the embryo that we are using to explore the regulation of cell expansion in a geometrically and mechanically realistic environment.

 
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