Current research interests
- Imaging and analysis of plant roots and root particle interactions in 3D.
- Optical projection tomography (OPT) and confocal microscopy.
- Development of novel imaging and 3D image analysis approaches to study biological and physical processes which control root growth in heterogeneous media.
Root systems are essential in allowing uptake of water and nutrients from soil. However, root systems and other soil biological processes are inherently difficult to study because they are concealed within soil.
Destructive approaches for studying roots have provided the greatest insight into the architecture and growth of root systems, but have numerous limitations and compromise the resolution and accuracy of information collected. There have recently been huge developments in optical imaging techniques to allow the detailed study of live biological activity and so I am interested in applying these techniques to the study of soil biology.
To use high resolution imaging and visualization techniques to track root trajectories in heterogeneous soil and artificial granular media to enable generation of detailed numerical descriptions of root growth. This will involve:
- Creating reconstituted, isorefractive, heterogeneous medium for OPT microscopy of plant roots, using refractive index matching techniques.
- To mimic soil characteristics by controlling the properties of the growth medium (e.g. particle size, surface chemistry).
- Use of image analysis techniques to obtain numerical descriptions of the evolution of root geometry in relation to the distribution of particles.
- Downie, H., Holden, N., Otten, W., Spiers, A.J., Valentine, T.A., Dupuy, L.X. 2012. Transparent Soil for Imaging the Rhizosphere. PLoS ONE 7(9): e44276.
- Fisher, M., Downie, H., Welten, M. C. M., Delgado, I., Bain, A., Planzer, T., Sherman, A., Sang, H. and Tickle, C. 2011. Comparative Analysis of 3D Expression Patterns of Transcription Factor Genes and Digit Fate Maps in the Developing Chick Wing. PLoS ONE 6, e18661.
- Bangs, F., Welten, M., Davey, M. G., Fisher, M., Yin, Y., Downie, H., Paton, B., Baldock, R., Burt, D. W. and Tickle, C. 2010. Identification of genes downstream of the Shh signalling in the developing chick wing and syn-expressed with Hoxd13 using microarray and 3D computational analysis. Mechanisms of Development 127, 428-41.
- Towers, M., Signolet, J., Downie, H., Delgado, I., Sherman, A., Sang, H. and Tickle, C. 2009. 13-P056 Contributions of polarizing region cells to digit pattern. Mechanisms of Development 126, S211-S212.
- Fisher, M.E., Clelland, A.K., Bain, A., Baldock, R.A., Murphy, P., Downie, H., Tickle, C., Davidson, D.R., Buckland, R.A. 2008. Integrating technologies for comparing 3D gene expression domains in the developing chick limb. Developmental Biology 317(1), 13-23.
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