All Outputs (43)

Plant phenotyping: an active vision cell for three-dimensional plant shoot reconstruction (2018)
Journal Article
Gibbs, J., Pound, M., French, A. P., Wells, D. M., Murchie, E., & Pridmore, T. (2018). Plant phenotyping: an active vision cell for three-dimensional plant shoot reconstruction. Plant Physiology, 178(2), 524-534. https://doi.org/10.1104/pp.18.00664

© 2018 American Society of Plant Biologists. All rights reserved. Three-dimensional (3D) computer-generated models of plants are urgently needed to support both phenotyping and simulation-based studies such as photosynthesis modeling. However, the co... Read More about Plant phenotyping: an active vision cell for three-dimensional plant shoot reconstruction.

Uncovering the hidden half of plants using new advances in root phenotyping (2018)
Journal Article
Atkinson, J. A., Pound, M. P., Bennett, M. J., & Wells, D. M. (2019). Uncovering the hidden half of plants using new advances in root phenotyping. Current Opinion in Biotechnology, 55, 1-8. https://doi.org/10.1016/j.copbio.2018.06.002

© 2018 The Authors Major increases in crop yield are required to keep pace with population growth and climate change. Improvements to the architecture of crop roots promise to deliver increases in water and nutrient use efficiency but profiling the r... Read More about Uncovering the hidden half of plants using new advances in root phenotyping.

Erratum: Author Correction: A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate (Nature communications (2018) 9 1 (1409)) (2018)
Journal Article
Bhosale, R., Giri, J., Pandey, B. K., Giehl, R. F. H., Hartmann, A., Traini, R., …Swarup, R. (2018). Erratum: Author Correction: A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate (Nature communications (2018) 9 1 (1409)). Nature Communications, 9(1), 1818. https://doi.org/10.1038/s41467-018-04281-x

The original version of this Article omitted the following from the Acknowledgements: 'We also thank DBT-CREST BT/HRD/03/01/2002.'This has been corrected in both the PDF and HTML versions of the Article.

Root gravitropism: quantification, challenges, and solutions (2018)
Journal Article
Muller, L., Bennett, M. J., French, A., Wells, D. M., & Swarup, R. (2018). Root gravitropism: quantification, challenges, and solutions. Methods in Molecular Biology, 1761, 103-112. https://doi.org/10.1007/978-1-4939-7747-5_8

© 2018, Springer Science+Business Media, LLC. Better understanding of root traits such as root angle and root gravitropism will be crucial for development of crops with improved resource use efficiency. This chapter describes a high-throughput, autom... Read More about Root gravitropism: quantification, challenges, and solutions.

An updated protocol for high throughput plant tissue sectioning (2017)
Journal Article
Atkinson, J. A., & Wells, D. M. (2017). An updated protocol for high throughput plant tissue sectioning. Frontiers in Plant Science, 8, https://doi.org/10.3389/fpls.2017.01721

Quantification of the tissue and cellular structure of plant material is essential for the study of a variety of plant sciences applications. Currently, many methods for sectioning plant material are either low throughput or involve free-hand section... Read More about An updated protocol for high throughput plant tissue sectioning.

Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large-scale genetic studies (2017)
Journal Article
Atkinson, J. A., Lobet, G., Noll, M., Meyer, P. E., Griffiths, M., & Wells, D. M. (2017). Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large-scale genetic studies. GigaScience, 6(10), https://doi.org/10.1093/gigascience/gix084

Genetic analyses of plant root systems require large datasets of extracted architectural traits. To quantify such traits from images of root systems, researchers often have to choose between automated tools (that are prone to error and extract only a... Read More about Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large-scale genetic studies.

Linear discriminant analysis reveals differences in root architecture in wheat seedlings related to nitrogen uptake efficiency (2017)
Journal Article
Kenobi, K., Atkinson, J. A., Wells, D. M., Gaju, O., deSilva, J. G., Foulkes, M. J., …Bennett, M. J. (2017). Linear discriminant analysis reveals differences in root architecture in wheat seedlings related to nitrogen uptake efficiency. Journal of Experimental Botany, 68(17), 4969-4981. https://doi.org/10.1093/jxb/erx300

© The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. Root architecture impacts water and nutrient uptake efficiency. Identifying exactly which root architectural properties influence these agronom... Read More about Linear discriminant analysis reveals differences in root architecture in wheat seedlings related to nitrogen uptake efficiency.

Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large scale genetic studies (2017)
Other
Atkinson, J. A., Lobet, G., Noll, M., Meyer, P. E., Griffiths, M., & Wells, D. M. (2017). Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large scale genetic studies

Background: Genetic analyses of plant root system development require large datasets of extracted architectural traits. To quantify such traits from images of root systems, researchers often have to choose between automated tools (that are prone to e... Read More about Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large scale genetic studies.

Quiescent center initiation in the Arabidopsis lateral root primordia is dependent on the SCARECROW transcription factor (2016)
Journal Article
Goh, T., Toyokura, K., Wells, D. M., Swarup, K., Yamamoto, M., Mimura, T., …Guyomarc'h, S. (2016). Quiescent center initiation in the Arabidopsis lateral root primordia is dependent on the SCARECROW transcription factor. Development, 143(18), 3363-3371. https://doi.org/10.1242/dev.135319

Lateral root (LR) formation is an important determinant of root system architecture. In Arabidopsis, LRs originate from pericycle cells, which undergo a programme of morphogenesis to generate a new LR meristem. Despite its importance for root meriste... Read More about Quiescent center initiation in the Arabidopsis lateral root primordia is dependent on the SCARECROW transcription factor.

Approaches to three-dimensional reconstruction of plant shoot topology and geometry (2016)
Journal Article
Gibbs, J., Pound, M. P., French, A. P., Wells, D. M., Murchie, E. H., & Pridmore, T. P. (2016). Approaches to three-dimensional reconstruction of plant shoot topology and geometry. Functional Plant Biology, 44(1), 62-75. https://doi.org/10.1071/FP16167

There are currently 805 million people classified as chronically undernourished, and yet the World’s population is still increasing. At the same time, global warming is causing more frequent and severe flooding and drought, thus destroying crops and... Read More about Approaches to three-dimensional reconstruction of plant shoot topology and geometry.

Characterization of pearl millet root architecture and anatomy reveals three types of lateral roots (2016)
Journal Article
Passot, S., Gnacko, F., Moukouanga, D., Lucas, M., Guyomarc’h, S., Ortega, B. M., …Laplaze, L. (2016). Characterization of pearl millet root architecture and anatomy reveals three types of lateral roots. Frontiers in Plant Science, 7(June2016), https://doi.org/10.3389/fpls.2016.00829

© 2016 Passot, Gnacko, Moukouanga, Lucas, Guyomarc’h, Moreno Ortega, Atkinson, Belko, Bennett, Gantet, Wells, Guédon, Vigouroux, Verdeil, Muller and Laplaze. Pearl millet plays an important role for food security in arid regions of Africa and India.... Read More about Characterization of pearl millet root architecture and anatomy reveals three types of lateral roots.

Three-dimensional reconstruction of plant shoots from multiple images using an active vision system (2015)
Journal Article
Gibbs, J., Pound, M. P., Wells, D. M., Murchie, E. H., French, A. P., & Pridmore, T. P. (2015). Three-dimensional reconstruction of plant shoots from multiple images using an active vision system

The reconstruction of 3D models of plant shoots is a challenging problem central to the emerging discipline of plant phenomics – the quantitative measurement of plant structure and function. Current approaches are, however, often limited by the use o... Read More about Three-dimensional reconstruction of plant shoots from multiple images using an active vision system.

The circadian clock rephases during lateral root organ initiation in Arabidopsis thaliana (2015)
Journal Article
Voß, U., Wilson, M. H., Kenobi, K., Gould, P. D., Robertson, F. C., Peer, W. A., …Bennett, M. J. (2015). The circadian clock rephases during lateral root organ initiation in Arabidopsis thaliana. Nature Communications, 6, Article 7641. https://doi.org/10.1038/ncomms8641

The endogenous circadian clock enables organisms to adapt their growth and development to environmental changes. Here we describe how the circadian clock is employed to coordinate responses to the key signal auxin during lateral root (LR) emergence.... Read More about The circadian clock rephases during lateral root organ initiation in Arabidopsis thaliana.

Multi-omics analysis identifies genes mediating the extension of cell walls in the Arabidopsis thaliana root elongation zone (2015)
Journal Article
Wilson, M. H., Holman, T. J., Sørensen, I., Cancho-Sanchez, E., Wells, D. M., Swarup, R., …Hodgman, T. C. (2015). Multi-omics analysis identifies genes mediating the extension of cell walls in the Arabidopsis thaliana root elongation zone. Frontiers in Cell and Developmental Biology, 3(FEB), Article 10. https://doi.org/10.3389/fcell.2015.00010

Plant cell wall composition is important for regulating growth rates, especially in roots. However, neither analyses of cell wall composition nor transcriptomes on their own can comprehensively reveal which genes and processes are mediating growth an... Read More about Multi-omics analysis identifies genes mediating the extension of cell walls in the Arabidopsis thaliana root elongation zone.

Phenotyping pipeline reveals major seedling root growth QTL in hexaploid wheat (2015)
Journal Article
Atkinson, J. A., Wingen, L. U., Griffiths, M., Pound, M. P., Gaju, O., Foulkes, M. J., …Wells, D. M. (2015). Phenotyping pipeline reveals major seedling root growth QTL in hexaploid wheat. Journal of Experimental Botany, 66(8), 2283-2292. https://doi.org/10.1093/jxb/erv006

Seedling root traits of wheat (Triticum aestivum L.) have been shown to be important for efficient establishment and linked to mature plant traits such as height and yield. A root phenotyping pipeline, consisting of a germination paper-based screen c... Read More about Phenotyping pipeline reveals major seedling root growth QTL in hexaploid wheat.

Quantification of Fluorescent Reporters in Plant Cells (2014)
Book Chapter
Pound, M., French, A. P., & Wells, D. M. (2015). Quantification of Fluorescent Reporters in Plant Cells. In J. M. Estevez (Ed.), Plant Cell Expansion: Methods and Protocols (123-131). Springer. https://doi.org/10.1007/978-1-4939-1902-4_11

© Springer Science+Business Media New York 2015. Fluorescent reporters are powerful tools for plant research. Many studies require accurate determination of fluorescence intensity and localization. Here, we describe protocols for the quantification o... Read More about Quantification of Fluorescent Reporters in Plant Cells.

Quantification of fluorescent reporters in plant cells (2014)
Book Chapter
Pound, M., French, A. P., & Wells, D. M. (2014). Quantification of fluorescent reporters in plant cells. In Plant Cell Expansion: Methods and Protocols (123--131). Springer. https://doi.org/10.1007/978-1-4939-1902-4

Branching out in roots: uncovering form, function, and regulation (2014)
Journal Article
Atkinson, J. A., Rasmussen, A., Traini, R., Voss, U., Sturrock, C., Mooney, S. J., …Bennett, M. J. (2014). Branching out in roots: uncovering form, function, and regulation. Plant Physiology, 166(2), 538-550. https://doi.org/10.1104/pp.114.245423

Root branching is critical for plants to secure anchorage and ensure the supply of water, minerals, and nutrients. To date, research on root branching has focused on lateral root development in young seedlings. However, many other programs of postemb... Read More about Branching out in roots: uncovering form, function, and regulation.

Systems Analysis of Auxin Transport in the Arabidopsis Root Apex (2014)
Journal Article
Band, L. R., Wells, D. M., Fozard, J. A., Ghetiu, T., French, A. P., Pound, M. P., …Bennett, M. J. (2014). Systems Analysis of Auxin Transport in the Arabidopsis Root Apex. Plant Cell, 26(3), 862-875. https://doi.org/10.1105/tpc.113.119495

Auxin is a key regulator of plant growth and development. Within the root tip, auxin distribution plays a crucial role specifying developmental zones and coordinating tropic responses. Determining how the organ-scale auxin pattern is regulated at the... Read More about Systems Analysis of Auxin Transport in the Arabidopsis Root Apex.

From jellyfish to biosensors: the use of fluorescent proteins in plants (2013)
Journal Article
Voss, U., Larrieu, A., & Wells, D. M. (2013). From jellyfish to biosensors: the use of fluorescent proteins in plants. International Journal of Developmental Biology, 57(6-7-8), 525-533. https://doi.org/10.1387/ijdb.130208dw

The milestone discovery of green fluorescent protein (GFP) from the jellyfish Aequorea victoria, its optimisation for efficient use in plantae, and subsequent improvements in techniques for fluorescent detection and quantification have changed plant... Read More about From jellyfish to biosensors: the use of fluorescent proteins in plants.