Lionel Dupuy
I graduated in Timber Engineering from the École Supérieure du Bois (Nantes, France) in 2000 and was awarded a PhD in 2003 from the University of Bordeaux (School of Physics and Engineering Sciences) where I was developing biomechanical models of tree uprooting at the Laboratoire de Rheologie du Bois de Bordeaux (now Institute of Mechanics and Engineering of Bordeaux). I developed software for digitising the architecture of root systems and constructed finite element models of root soil interactions. In 2005 I took a post-doctoral position in Jim Haseloff's laboratory (University of Cambridge) to work on computational methods to analyse plant cell morphogenesis. I developed image analysis methods to track cell expansion and division from live microscopy data, and used these measurements to construct models that integrated genetic and biomechanical processes into dynamic multicellular architectures.
Current research interests
I develop models that predict how crops utilise environmental resources to grow and produce yield. I design experimental systems where such processes can be observed and quantified. For example, recent work has focused on the development of novel transparent soils that are suitable for the culture and live imaging of soil biological organisms (Helen Downie, co-supervisors Tracy Valentine, Wilfred Otten, Andrew Spiers).
My research also focuses on quantitative imaging to improve data resolution and throughput for models. I use techniques such as Optical Projection Tomography (OPT), Single Plane Illumination Microscopy (SPIM, in collaboration with Mike MacDonald), and Biospeckle Laser (BSL, in collaboration with Roberto Braga), and web-cam and scanner based systems to construct low cost high throughput phenotyping (Michael Adu, co-supervisors Martin Broadley, Malcolm Bennett, Philip White).
The main objective is to construct simple models that can be understood, calibrated easily using available data and integrated with existing software. To achieve this objective, I develop continuous models (PDE) where fundamental growth processes can be incorporated explicitly into conservation equations (in collaboration with Glyn Bengough, Xavier Draye, Tim George and Philip White).
See group pages for more information.
Software development
Archiroot: Software for the acquisition and visualisation of root architecture
BalloonPlugin: Fiji plugin for the segmentation of cell architecture
CellModeller2.0: Software platform for multicellular analysis modelling and computation
SIMUL3R : simulation of root architectures dynamics
More descriptions at: http://www.archiroot.org.uk/doku.php/navigation/architools
Grants and Awards
2012-2015: Root phenotyping (BB/J019631/1), BBSRC
2012-2016: EURoot (KBBE.2011.1.2-05), EU
2011: iGEM Dundee
2011: Wellcome Image Award (Welcome Trust)
Bibliography
- De La Fuente Canto, C.; Kalogiros, D.I.; Ptashnyk, M.; George, T.S.; Waugh, R.; Bengough, A.G.; Russell, J.; Dupuy, L.X., (2018) Morphological and genetic characterisation of the root system architecture of selected barley recombinant chromosome substitution lines using an integrated phenotyping approach., Journal of Theoretical Biology, 447, 84-97.
- Giri, J.; Bhosale, R.; Huang, G.; Pandey, B.K.; Parker, H.; Zappala, S.; Yang, J.; Dievart, A.; Bureau, C.; Ljung, K.; Price, A.; Rose, T.; Larrieu, A.; Mairhofer, S.; Sturrock, C.J.; White, P.; Dupuy, L.; Hawkesford, M.J.; Perin, C.; Liang, W.; Peret, P.; Hodgman, C.T.; Lynch, J.; Wissuwa, M.; Zhang, D.; Pridmore, T.; Mooney, S.J.; Guidordoni, E.; Swarup, R.; Bennet, M.J., (2018) Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate., Nature Communications, 9, Article No. 1408.
- Dupuy L.X.; Mimault, M.; Patko, D.; Ladmiral, V.; Ameduri, B.; MacDonald, M.P.; Ptashnyk, M., (2018) Micromechanics of root development in soil., Current Opinion in Genetics and Development, 51, 18-25.
- Giles, C.D.; Dupuy, L.; Boitt, G.; Brown, L.K.; Condron, L.; Darch, T.; Blackwell, M.S.A.; Menezes-Blackburn, D.; Shand, C.A.; Stutter, M.I.; Lumsdon, D.G.; Wendler, R.; Cooper, P.; Wearing, C.; Zhang, H.; Haygarth, P.M.; George, T.S., (2018) Root development impacts on the distribution of phosphatase activity: Improvements in quantification using soil zymography., Soil Biology and Biochemistry, 116, 158-166.
- O'Callaghan, F.E.; Braga, R.A.; Neilson, R.; MacFarlane, S.A.; Dupuy, L.X., (2018) New live screening of plant-nematode interactions in the rhizosphere., Scientific Reports, 8, Article No. 1440.
- Bizet, F.; Dupuy, L. X.; Bengough, A. G.; Peaucelle, A.; Hummel, I.; Bogeat-Triboulot, M., (2017) Non-invasive protocol for kinematic monitoring of root growth under infrared light., Bio-protocol, 7, Article No. e2390.
- Banerjee, S.; Tawade, B.V.; Ladmiral, V.; Dupuy, L.X.; MacDonald, M.P.; Ameduri, B., (2017) Poly (fluoroacrylate)s with tunable surface hydrophobicity via radical copolymerization of 2, 2, 2-trifluoroethyl a-fluoroacrylate and 2-(trifluoromethyl) acrylic acid., Polymer Chemistry, 8, 1978-1988.
- Dupuy, L.X.; Wright, G.; Thompson, J.A.; Taylor, A.; Dekeyser, S.; White, C.P.; Thomas, W.T.B.; Nightingale, M.; Hammond, J.P.; Graham, N.S.; Thomas, C.L.; Broadley, M.R.; White, P.J., (2017) Accelerating root system phenotyping of seedlings through a computer-assisted processing pipeline., Plant Methods, 13, Article No. 57.
- Adu, M.O.; Yawson, D.O.; Bennett, MJ.; Broadley, M.R.; Dupuy, L.X.; White, P.J., (2017) A scanner-based rhizobox system enabling the quantification of root system development and response of Brassica rapa seedlings to external P availability., Plant Root, 11, 16-32.
- Bizet, F.; Bengough, A.G.; Hummel, I.; Bogeat-Triboulot, M.B.; Dupuy, L.X., (2016) 3D deformation field in growing plant roots reveals both mechanical and biological responses to axial mechanical forces., Journal of Experimental Botany, 67, 5605-5614.
- White, P.J.; Kawachi, T.; Thompson, J.A.; Wright, G.; Dupuy, L.X., (2016) Minimizing the treatments required to determine the responses of different crop genotypes to potassium supply., Communications in Soil Science and Plant Analysis, 47, 104-111.
- Thomas, C.L.; Graham, N.S.; Hayden, R.; Meacham, M.C.; Neugebauer, K.; Nightingale, M.; Dupuy, L.X.; Hammond, J.P.; White, P.J.; Broadley, M.R., (2016) High-throughput phenotyping (HTP) identifies seedling root traits linked to variation in seed yield and nutrient capture in field-grown oilseed rape (Brassica napus L.)., Annals of Botany, 118, 655-665.
- Kalogiros, D.I.; Adu, M.O.; White, P.J.; Broadley, M.R.; Draye, X.; Ptashnyk, M.; Bengough, A.G.; Dupuy, L.X., (2016) Analysis of root growth from a phenotyping data set using a density-based model., Journal of Experimental Botany, 67, 1045-1058.
- Adu, M.O.; Yawson, D.O.; Armah, F.A.; Asare, P.A.; Bennett, M.J.; Broadley, M.R.; White, P.J.; Dupuy, L.X., (2016) Effects of rooting media on root growth and morphology of Brassica rapa seedlings., South African Journal of Plant and Soil, 33, 219-227.
- Dupuy, L.X.; Silk, W.K., (2016) Mechanisms of early microbial establishment on growing root surfaces., Vadose Zone Journal, 15(2). Open access.
- Thomas, C.L.; Alcock, T.D.; Graham, N.S.; Hayden, R.; Matterson, S.; Wilson, L.; Young, S.D.; Dupuy, L.X.; White, P.J.; Hammond, J.P.; Danku, J.M.C.; Salt, D.E.; Sweeney, A.; Bancroft, I.; Broadley, M.R., (2016) Root morphology and seed and leaf ionomic traits in a Brassica napus L. diversity panel show wide phenotypic variation and are characteristic of crop habit., BMC Plant Biology, 16, Article No. 214.
- Downie, H.F.; Adu, M.O.; Schmidt, S.; Otten, W.; Dupuy, L.X.; White, P.J.; Valentine, T.A., (2015) Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis., Plant, Cell and Environment, 38, 1213-1232.
- Adu, M.O.; Wiesel, L.; Bennett, M.J.; Broadley, M.R.; White, P.J.; Dupuy, L.X., (2015) Scanner-based time-lapse root phenotyping., Bio-protocol, 5, Article No. e1424.
- Graham, N.S.; Hammond, J.P.; Lysenko, A.; Mayes, S.; O'Lochlainn, S.; Blasco, B.; Bowen, H.C.; Rawlings, C.J.; Rios, J.J.; Welham, S.; Carion, P.W.C.; Dupuy, L.X.; King, G.J.; White, P.J.; Broadley, M.R., (2014) Genetical and comparative genomics of Brassica under altered Ca supply identifies Arabidopsis Ca-transporter orthologs., The Plant Cell, 26, 2818-2830.
- Downie, H.; Valentine, T.A.; Otten, W.; Spiers, A.J.; Dupuy, L.X., (2014) Transparent soil microcosms allow 3D spatial quantification of soil microbiological processes in vivo., Plant Signaling and Behavior, 9, Article No. e29878.
- Ribeiro, K.M.; Baretto, B.; Pasqual, M.; White, P.J.; Braga, R.A.; Dupuy, L.X., (2014) Continuous, high-resolution biospeckle imaging reveals a discrete zone of activity at the root apex that responds to contact with obstacles., Annals of Botany, 113, 555-563.
- Adu,M.O.; Chatot, A.; Wiesel, L.; Bennett, M.J.; Broadley, M.R.; White, P.J.; Dupuy, L.X., (2014) A scanner system for high-resolution quantification of variation in root growth dynamics of Brassica rapa genotypes., Journal of Experimental Botany, 65, 2039-2048.
- Sargent, F.; Davidson, F.A.; Kelly, C.L.; Binny, R.; Christodoulides, N.; Gibson, D.; Johansson, E.; Kozyrska, K.; Lado, L.L.; MacCallum, J.; Montague, R.; Ortmann, B.; Owen, R.; Coulthurst, S.J.; Dupuy, L.; Prescott, A.R.; Palmer, T., (2013) A synthetic system for expression of components of a bacterial microcompartment., Microbiology-SGM, 159, 2427-2436.
- Brown, L.K.; George, T.S.; Dupuy, L.X.; White, P.J., (2013) A conceptual model of root hair ideotypes for future agricultural environments: what combination of traits should be targeted to cope with limited P availability?, Annals of Botany, 112, 317-330.
- Dresboll, D.B.; Thorup-Kristensen, K.; McKenzie, B.M.; Dupuy, L.X.; Bengough, A.G., (2013) Timelapse scanning reveals spatial variation in tomato (Solanum lycopersicum L.) root elongation rates during partial waterlogging., Plant and Soil, 369, 467-477.
- Yang, Z.; Downie, H.; Dupuy, L.; MacDonald, M., (2013) Light-sheet tomography for in situ imaging of Arabidopsis Thaliana roots., Optics Express, 21, 16239-16247.
- White, P.J.; George, T.S.; Dupuy, L.X.; Karley, A.J.; Valentine, T.A.; Wiesel, L.; Wishart, J., (2013) Root traits for infertile soils., Frontiers in Plant Science, 4, 193.
- Chavarria-Krauser, A.; Dupuy, L.; Ptashnyk, M., (2013) Preface., Mathematical Modelling of Natural Phenoma, 8, 1-4.
- Brown, L.K.; George, T.S.; Thompson, J.A.; Wright, G.M.; Lyon, J.; Dupuy, L.; Hubbard, S.F.; White, P.J., (2012) What are the implications of variation in root hair length on tolerance to phosphorus deficiency in combination with water stress in barley (Hordeum vulgare)?, Annals of Botany, 110, 319-328.
- Dupuy, L.X.; Vignes, M., (2012) An algorithm for the simulation of the growth of root systems on deformable domains., Journal of Theoretical Biology, 310, 164-174.
Scientific posters/conferences
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