- Email: [email protected]
Modelling and simulation of a Ca2+-based feedback loop in the circadian clock of Arabidopsis
Abstracts / Comparative Biochemistry and Physiology, Part A 150 (2008) S42–S48
CSS.11 Differences in sensitivity to waterborne Cu in three freshwater fish: Effects on oxidative stress and ion regulation M. Eyckmans, G. De Boeck, R. Blust (University of Antwerp)
Among species, a clear difference in metal handling can occur. We've investigated the differences between rainbow trout (Oncorhynchus mykiss), carp (Cyprinus carpio) and gibel carp (Carassius auratus gibelio) in dealing with the effects of copper exposure. Fish have been exposed to two sublethal exposure-conditions; one similar concentration (50 μg/l) for every fish species and one concentration which is the 10% LC50 96 h value for each fish species (20 μg/l for rainbow trout, 65 μg/l for carp and 150 μg/l for gibel carp). After 1 h, 12 h, 24 h, 3 days, 1 week and 1 month, gill and plasma samples were collected and Na+/K+-ATPase activity, SOD-, Gr- and CAT activity, as well as GSH-en Ascorbate concentrations in gill tissue were determined. In plasma, ion concentration, cortisol and thyroid concentration were investigated. Most of these physiological parameters were influenced and showed clear differences between fish species. Rainbow trout, the most sensitive fish species used in this experiment, experienced more and earlier effects then the sturdier carp and more resistant gibel carp.
S45
We are investigating the nature of the signalling networks by which the circadian clock regulates cell physiology. We will present models which describe the diurnal and circadian regulation of cytosolic free Ca2+ ([Ca2+]cyt), based on expression data for CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), a gene required for circadian oscillations of [Ca2+]cyt. We show that a fast light-dependent pathway in addition to a slow circadian-dependent Pathway contribute to the daily control of [Ca2+]cyt. We will also describe how systems approaches combined with transcriptomic, physiological, imaging and genetic tools have identified a new arm of the circadian clock in the cytosol containing circadian oscillations of cytosolic free [Ca2+]cyt and cyclic ADP ribose (cADPR). Artificially manipulating [cADPR] leads to large changes in the abundance of clock-associated transcripts. We show how mathematical simulations of the potential effects of altered cADPR can lead to non-intuitive predictions of the regulation of the circadian signalling network by cADPR. Through simulation and experimentation, we have compelling evidence that cADPR forms a feedback loop with the central oscillator. doi:10.1016/j.cbpa.2008.04.021
doi:10.1016/j.cbpa.2008.04.019
CSS.14 Adopting an integrative systems biology approach to study root growth and development
CSS.12 Modelling the mutual support of differential cell fates in the Arabidopsis root epidermis
M. Bennett (University of Nottingham); A. French (University of Nottingham); C. Hodgman (University of Nottingham); P. Hedden (Rothamsted Research); T. Holman (University of Nottingham); A. Middleton (University of Nottingham); J. King (University of Nottingham); M. Owen (University of Nottingham); T. Pridmore (University of Nottingham); R. Swarup (University of Nottingham); S. Thomas (Rothamsted Research); S. Ubeda-Thomas (University of Nottingham); M. Wilson (University of Nottingham)
N. Monk (University of Nottingham) The patterning of the Arabidopsis root epidermis depends on a genetic regulatory network that operates both within and between cells. Genetic studies have identified a number of key components of this network, but the functional logic of the network has remained unclear. In this talk, I will show how the genetic and biochemical data can be integrated in a novel modelling formalism that allows an exploration of both the sufficiency of known network interactions and the extent to which additional assumptions about the model can account for wild type and mutant data. Our new model shows that an existing hypothesis concerning the auto-regulation of WEREWOLF does not account fully for the expression patterns of components of the network, a prediction that we have confirmed experimentally in transgenic plants. Rather, our modelling suggests that patterning depends critically on the directed movement of the CAPRICE and GLABRA3 transcriptional regulators between epidermal cells. These movements underlie a novel mechanism for pattern formation in planar groups of cells, centred on mutual support of two cell fates rather than diffusion-driven local activation and lateral inhibition. doi:10.1016/j.cbpa.2008.04.020
CSS.13 Modelling and simulation of a Ca2+-based feedback loop in the circadian clock of Arabidopsis
The Centre for Plant Integrative Biology (CPIB) at the University of Nottingham aims to create a virtual root which will serve as an exemplar for using Integrative Systems Biology (ISB) to model multicellular systems. CPIB brings together biologists, engineers, mathematicians and computer scientists to generate new data, biological resources and virtual models of plant roots that will aid understanding of how they grow and develop. The 5 year research programme (started in March 2007) involves multidisciplinary teams working simultaneously in sub-programmes at the molecular, sub/cellular, tissue and organ levels. The research activities are structured as three overlapping 3-year strands of increasing sophistication. Strand 1 focuses on hormone regulated cell elongation during radicle emergence and primary root growth. Strand 2 will focus on the root apical meristem, whilst Strand 3 will examine the initiation, patterning and emergence of lateral roots. I will review recent progress made in Strand 1, highlighting how the adoption of a multiscale ISB approach has helped provide new insight into how the plant hormones auxin (1) and gibberellic acid (2) coordinate organ growth. References Swarup, et al. (2005) Nature Cell Biology 7, 1057–1065. Ubeda-Tomas, A. et al. (2008) Nature Cell Biology, in press.
N. Dalchau, J. Gonçalves, A. Webb (University of Cambridge) The Arabidopsis circadian clock is an internal time keeper essential for the coordination of cellular activities and photoperiodic sensing.
doi:10.1016/j.cbpa.2008.04.022
CSS.11 Differences in sensitivity to waterborne Cu in three freshwater fish: Effects on oxidative stress and ion regulation M. Eyckmans, G. De Boeck, R. Blust (University of Antwerp)
Among species, a clear difference in metal handling can occur. We've investigated the differences between rainbow trout (Oncorhynchus mykiss), carp (Cyprinus carpio) and gibel carp (Carassius auratus gibelio) in dealing with the effects of copper exposure. Fish have been exposed to two sublethal exposure-conditions; one similar concentration (50 μg/l) for every fish species and one concentration which is the 10% LC50 96 h value for each fish species (20 μg/l for rainbow trout, 65 μg/l for carp and 150 μg/l for gibel carp). After 1 h, 12 h, 24 h, 3 days, 1 week and 1 month, gill and plasma samples were collected and Na+/K+-ATPase activity, SOD-, Gr- and CAT activity, as well as GSH-en Ascorbate concentrations in gill tissue were determined. In plasma, ion concentration, cortisol and thyroid concentration were investigated. Most of these physiological parameters were influenced and showed clear differences between fish species. Rainbow trout, the most sensitive fish species used in this experiment, experienced more and earlier effects then the sturdier carp and more resistant gibel carp.
S45
We are investigating the nature of the signalling networks by which the circadian clock regulates cell physiology. We will present models which describe the diurnal and circadian regulation of cytosolic free Ca2+ ([Ca2+]cyt), based on expression data for CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), a gene required for circadian oscillations of [Ca2+]cyt. We show that a fast light-dependent pathway in addition to a slow circadian-dependent Pathway contribute to the daily control of [Ca2+]cyt. We will also describe how systems approaches combined with transcriptomic, physiological, imaging and genetic tools have identified a new arm of the circadian clock in the cytosol containing circadian oscillations of cytosolic free [Ca2+]cyt and cyclic ADP ribose (cADPR). Artificially manipulating [cADPR] leads to large changes in the abundance of clock-associated transcripts. We show how mathematical simulations of the potential effects of altered cADPR can lead to non-intuitive predictions of the regulation of the circadian signalling network by cADPR. Through simulation and experimentation, we have compelling evidence that cADPR forms a feedback loop with the central oscillator. doi:10.1016/j.cbpa.2008.04.021
doi:10.1016/j.cbpa.2008.04.019
CSS.14 Adopting an integrative systems biology approach to study root growth and development
CSS.12 Modelling the mutual support of differential cell fates in the Arabidopsis root epidermis
M. Bennett (University of Nottingham); A. French (University of Nottingham); C. Hodgman (University of Nottingham); P. Hedden (Rothamsted Research); T. Holman (University of Nottingham); A. Middleton (University of Nottingham); J. King (University of Nottingham); M. Owen (University of Nottingham); T. Pridmore (University of Nottingham); R. Swarup (University of Nottingham); S. Thomas (Rothamsted Research); S. Ubeda-Thomas (University of Nottingham); M. Wilson (University of Nottingham)
N. Monk (University of Nottingham) The patterning of the Arabidopsis root epidermis depends on a genetic regulatory network that operates both within and between cells. Genetic studies have identified a number of key components of this network, but the functional logic of the network has remained unclear. In this talk, I will show how the genetic and biochemical data can be integrated in a novel modelling formalism that allows an exploration of both the sufficiency of known network interactions and the extent to which additional assumptions about the model can account for wild type and mutant data. Our new model shows that an existing hypothesis concerning the auto-regulation of WEREWOLF does not account fully for the expression patterns of components of the network, a prediction that we have confirmed experimentally in transgenic plants. Rather, our modelling suggests that patterning depends critically on the directed movement of the CAPRICE and GLABRA3 transcriptional regulators between epidermal cells. These movements underlie a novel mechanism for pattern formation in planar groups of cells, centred on mutual support of two cell fates rather than diffusion-driven local activation and lateral inhibition. doi:10.1016/j.cbpa.2008.04.020
CSS.13 Modelling and simulation of a Ca2+-based feedback loop in the circadian clock of Arabidopsis
The Centre for Plant Integrative Biology (CPIB) at the University of Nottingham aims to create a virtual root which will serve as an exemplar for using Integrative Systems Biology (ISB) to model multicellular systems. CPIB brings together biologists, engineers, mathematicians and computer scientists to generate new data, biological resources and virtual models of plant roots that will aid understanding of how they grow and develop. The 5 year research programme (started in March 2007) involves multidisciplinary teams working simultaneously in sub-programmes at the molecular, sub/cellular, tissue and organ levels. The research activities are structured as three overlapping 3-year strands of increasing sophistication. Strand 1 focuses on hormone regulated cell elongation during radicle emergence and primary root growth. Strand 2 will focus on the root apical meristem, whilst Strand 3 will examine the initiation, patterning and emergence of lateral roots. I will review recent progress made in Strand 1, highlighting how the adoption of a multiscale ISB approach has helped provide new insight into how the plant hormones auxin (1) and gibberellic acid (2) coordinate organ growth. References Swarup, et al. (2005) Nature Cell Biology 7, 1057–1065. Ubeda-Tomas, A. et al. (2008) Nature Cell Biology, in press.
N. Dalchau, J. Gonçalves, A. Webb (University of Cambridge) The Arabidopsis circadian clock is an internal time keeper essential for the coordination of cellular activities and photoperiodic sensing.
doi:10.1016/j.cbpa.2008.04.022