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A predictive model for ethylene-mediated auxin and cytokinin patterning in the Arabidopsis root (2024)
Journal Article
Moore, S., Jervis, G., Topping, J., Chen, C., Liu, J., & Lindsey, K. (2024). A predictive model for ethylene-mediated auxin and cytokinin patterning in the Arabidopsis root. Plant communications, 5(7), Article 100886. https://doi.org/10.1016/j.xplc.2024.100886

The interaction between auxin and cytokinin is important in many aspects of plant development. Experimental measurements of both auxin and cytokinin concentration and reporter gene expression clearly show the coexistence of auxin and cytokinin concen... Read More about A predictive model for ethylene-mediated auxin and cytokinin patterning in the Arabidopsis root.

Putrescine depletion affects Arabidopsis root meristem size by modulating auxin and cytokinin signaling and ROS accumulation (2021)
Journal Article
Hashem, A., Moore, S., Chen, S., Hu, C., Zhao, Q., IE Elasawi, I., Feng, Y., Topping, J., Liu, J., Lindsey, K., & Chen, C. (2021). Putrescine depletion affects Arabidopsis root meristem size by modulating auxin and cytokinin signaling and ROS accumulation. International Journal of Molecular Sciences, 22(8), Article 4094. https://doi.org/10.3390/ijms22084094

Polyamines (PAs) dramatically affect root architecture and development, mainly by unknown mechanisms; however, accumulating evidence points to hormone signaling and reactive oxygen species (ROS) as candidate mechanisms. To test this hypothesis, PA le... Read More about Putrescine depletion affects Arabidopsis root meristem size by modulating auxin and cytokinin signaling and ROS accumulation.

Understanding hormonal crosstalk in Arabidopsis root development via emulation and history matching (2020)
Journal Article
Jackson, S., Vernon, I., Liu, J., & Lindsey, K. (2020). Understanding hormonal crosstalk in Arabidopsis root development via emulation and history matching. Statistical Applications in Genetics and Molecular Biology, 19(2), Article 20180053. https://doi.org/10.1515/sagmb-2018-0053

A major challenge in plant developmental biology is to understand how plant growth is coordinated by interacting hormones and genes. To meet this challenge, it is important to not only use experimental data, but also formulate a mathematical model. F... Read More about Understanding hormonal crosstalk in Arabidopsis root development via emulation and history matching.

Design principles for decoding calcium signals to generate specific gene expression via transcription (2019)
Journal Article
Liu, J., Lenzoni, G., & Knight, M. R. (2020). Design principles for decoding calcium signals to generate specific gene expression via transcription. Plant Physiology, 182(4), 1743-1761. https://doi.org/10.1104/pp.19.01003

The second messenger calcium plays a key role in conveying specificity of signalling pathways in plant cells. Specific calcium signatures are decoded to generate correct gene expression responses and amplification of calcium signatures is vital to th... Read More about Design principles for decoding calcium signals to generate specific gene expression via transcription.

Bayesian uncertainty analysis for complex systems biology models: emulation, global parameter searches and evaluation of gene functions (2018)
Journal Article
Vernon, I., Liu, J., Goldstein, M., Rowe, J., Topping, J., & Lindsey, K. (2018). Bayesian uncertainty analysis for complex systems biology models: emulation, global parameter searches and evaluation of gene functions. BMC systems biology, 12, Article 1. https://doi.org/10.1186/s12918-017-0484-3

Many mathematical models have now been employed across every area of systems biology. These models increasingly involve large numbers of unknown parameters, have complex structure which can result in substantial evaluation time relative to the needs... Read More about Bayesian uncertainty analysis for complex systems biology models: emulation, global parameter searches and evaluation of gene functions.

Predicting plant immunity gene expression by identifying the decoding mechanism of calcium signatures (2017)
Journal Article
Lenzoni, G., Liu, J., & Knight, M. (2018). Predicting plant immunity gene expression by identifying the decoding mechanism of calcium signatures. New Phytologist, 217(4), 1598-1609. https://doi.org/10.1111/nph.14924

Calcium plays a key role in determining the specificity of a vast array of signalling pathways in plants. Cellular calcium elevations with different characteristics (calcium signatures) carry information on the identity of the primary stimulus, ensur... Read More about Predicting plant immunity gene expression by identifying the decoding mechanism of calcium signatures.

Crosstalk complexities between auxin, cytokinin and ethylene in Arabidopsis root development: from experiments to systems modelling, and back again (2017)
Journal Article
Liu, J., Moore, S., Chen, C., & Lindsey, K. (2017). Crosstalk complexities between auxin, cytokinin and ethylene in Arabidopsis root development: from experiments to systems modelling, and back again. Molecular Plant, 10(12), 1480-1496. https://doi.org/10.1016/j.molp.2017.11.002

Understanding how hormones and genes interact to coordinate plant growth in a changing environment is a major challenge in plant developmental biology. Auxin, cytokinin and ethylene are three important hormones that regulate many aspects of plant dev... Read More about Crosstalk complexities between auxin, cytokinin and ethylene in Arabidopsis root development: from experiments to systems modelling, and back again.

A recovery principle provides insight into auxin pattern control in the Arabidopsis root (2017)
Journal Article
Moore, S., Liu, J., Zhang, X., & Lindsey, K. (2017). A recovery principle provides insight into auxin pattern control in the Arabidopsis root. Scientific Reports, 7, Article 43004. https://doi.org/10.1038/srep43004

Regulated auxin patterning provides a key mechanism for controlling root growth and development. We have developed a data-driven mechanistic model using realistic root geometry and formulated a principle to theoretically investigate quantitative auxi... Read More about A recovery principle provides insight into auxin pattern control in the Arabidopsis root.

The POLARIS Peptide: Role in Hormone Signalling and Root Growth (2016)
Book Chapter
Mehdi, S., Mudge, A., Rowe, J., Liu, J., Topping, J., & Lindsey, K. (2016). The POLARIS Peptide: Role in Hormone Signalling and Root Growth. In A. Huffaker, & G. Pearce (Eds.), Annual Plant Reviews: Peptide Signals in Plants. Wiley

Abscisic acid regulates root growth under osmotic stress conditions via an interacting hormonal network with cytokinin, ethylene and auxin (2016)
Journal Article
Rowe, J., Topping, J., Liu, J., & Lindsey, K. (2016). Abscisic acid regulates root growth under osmotic stress conditions via an interacting hormonal network with cytokinin, ethylene and auxin. New Phytologist, 211(1), 225-239. https://doi.org/10.1111/nph.13882

Understanding the mechanisms regulating root development under drought conditions is an important question for plant biology and world agriculture. We examine the effect of osmotic stress on abscisic acid (ABA), cytokinin and ethylene responses and h... Read More about Abscisic acid regulates root growth under osmotic stress conditions via an interacting hormonal network with cytokinin, ethylene and auxin.

Some fundamental aspects of modelling auxin patterning in the context of auxin-ethylene-cytokinin crosstalk (2015)
Journal Article
Moore, S., Zhang, X., Liu, J., & Lindsey, K. (2015). Some fundamental aspects of modelling auxin patterning in the context of auxin-ethylene-cytokinin crosstalk. Plant Signaling & Behavior, 10(10), Article e1056424. https://doi.org/10.1080/15592324.2015.1056424

The activities of hormones in the Arabidopsis root depend on cellular context and exhibit either synergistic or antagonistic interactions. Patterning in Arabidopsis root development is coordinated via a localized auxin concentration maximum in the ro... Read More about Some fundamental aspects of modelling auxin patterning in the context of auxin-ethylene-cytokinin crosstalk.

Combining modelling and experimental approaches to explain how calcium signatures are decoded by calmodulin-binding transcription activators (CAMTAs) to produce specific gene expression responses (2015)
Journal Article
Liu, J., Whalley, H., & Knight, M. (2015). Combining modelling and experimental approaches to explain how calcium signatures are decoded by calmodulin-binding transcription activators (CAMTAs) to produce specific gene expression responses. New Phytologist, 208(1), 174-187. https://doi.org/10.1111/nph.13428

Experimental data show that Arabidopsis thaliana is able to decode different calcium signatures to produce specific gene expression responses. It is also known that calmodulin-binding transcription activators (CAMTAs) have calmodulin (CaM)-binding do... Read More about Combining modelling and experimental approaches to explain how calcium signatures are decoded by calmodulin-binding transcription activators (CAMTAs) to produce specific gene expression responses.

Spatiotemporal modelling of hormonal crosstalk explains the level and patterning of hormones and gene expression in Arabidopsis thaliana wildtype and mutant roots (2015)
Journal Article
Moore, S., Zhang, X., Mudge, A., Rowe, J., Topping, J., Liu, J., & Lindsey, K. (2015). Spatiotemporal modelling of hormonal crosstalk explains the level and patterning of hormones and gene expression in Arabidopsis thaliana wildtype and mutant roots. New Phytologist, 207(4), 1110-1122. https://doi.org/10.1111/nph.13421

Patterning in Arabidopsis root development is coordinated via a localized auxin concentration maximum in the root tip, requiring the regulated expression of specific genes. However, little is known about how hormone and gene expression patterning is... Read More about Spatiotemporal modelling of hormonal crosstalk explains the level and patterning of hormones and gene expression in Arabidopsis thaliana wildtype and mutant roots.

Dissecting the regulation of pollen tube growth by modeling the interplay of hydrodynamics, cell wall and ion dynamics (2014)
Journal Article
Liu, J., & Hussey, P. (2014). Dissecting the regulation of pollen tube growth by modeling the interplay of hydrodynamics, cell wall and ion dynamics. Frontiers in Plant Science, 5, Article 392. https://doi.org/10.3389/fpls.2014.00392

Hydrodynamics, cell wall and ion dynamics are all important properties that regulate pollen tube growth. Currently, the two main pollen tube growth models, the cell wall model and the hydrodynamic model do not appear to be reconcilable. Here we devel... Read More about Dissecting the regulation of pollen tube growth by modeling the interplay of hydrodynamics, cell wall and ion dynamics.

Hormonal crosstalk for root development: a combined experimental and modeling perspective (2014)
Journal Article
Liu, J., Rowe, J., & Lindsey, K. (2014). Hormonal crosstalk for root development: a combined experimental and modeling perspective. Frontiers in Plant Science, 5, Article 116. https://doi.org/10.3389/fpls.2014.00116

Plants are sessile organisms and therefore they must adapt their growth and architecture to a changing environment. Understanding how hormones and genes interact to coordinate plant growth in a changing environment is a major challenge in development... Read More about Hormonal crosstalk for root development: a combined experimental and modeling perspective.

Elucidating the regulation of complex signalling systems in plant cells (2014)
Journal Article
Liu, J., Lindsey, K., & Hussey, P. J. (2014). Elucidating the regulation of complex signalling systems in plant cells. Biochemical Society Transactions, 42(1), 219-223. https://doi.org/10.1042/bst20130090

The pollen tube represents a model system for the study of tip growth, and the root provides a valuable system to study gene and signalling networks in plants. In the present article, using the two systems as examples, we discuss how to elucidate the... Read More about Elucidating the regulation of complex signalling systems in plant cells.

POLARIS. (2013)
Book Chapter
Lindsey, K., Mehdi, S., Casson, S., Mudge, A., Topping, J., & Liu, J. (2013). POLARIS. In A. Kastin (Ed.), The Handbook of Biologically Active Peptides, 2nd Edition (40-45). (2nd.). Academic Press

Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development (2013)
Journal Article
Liu, J., Mehdi, S., Topping, J., Friml, J., & Lindsey, K. (2013). Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development. Frontiers in Plant Science, 4, Article 75. https://doi.org/10.3389/fpls.2013.00075

Understanding how hormones and genes interact to coordinate plant growth is a major challenge in developmental biology. The activities of auxin, ethylene, and cytokinin depend on cellular context and exhibit either synergistic or antagonistic interac... Read More about Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development.