Model Development and Investigations on Ion Homeostasis

Abstract

The environment surrounding an organism, a cell and an organelle is constantly changing. To keep organisms functioning there is an everlasting need to regulate and adapt in order to keep the internal environment relatively constant. Homeostasis is the term used to describe this ability of a system to regulate and stabilize its environment. Different processes and compensatory mechanisms are employed to do this. Homeostasis is also the overall theme binding this thesis together, spanning from iron regulation in plants to the regulation of calcium (Ca2+) in humans. Ever since the term emerged, scientists have been searching for answers on how biological control mechanisms function and how they are able to maintain homeostasis. The work presented in this thesis is based on a computational approach using systems biology and control mechanisms like negative feedback and integral control. Controller motifs based on negative feedback loops between a controlled and manipulated/compensatory variable was previously identified by the research group, and has been used as a basis for the computational calculations and models. Plants need iron for their growth and development, and even though this essential nutrient is difficult to access through the soil due to its availability. In the soil iron is strongly bound as Fe2O3, and plants have developed different strategies for iron uptake. Iron is also of great importance for human nutrition. Iron deficiency is one of the major causes of anaemia. Anaemia is a world wide problem and is a condition with too few red bloods cells or where the haemoglobin level within these is lower than usual. Iron regulation and homeostasis was modeled for non-graminaceous plants, with Arabidopsis thaliana as a model species. Since iron is toxic for plants at high levels it needs to be under homeostatic control. A model in agreement with experimental observations was developed. Iron-dependent degradation of the high-affinity transporter IRT1 was included in agreement with experimental findings, as well as the importance of the transcription factor FIT for the regulation of cytosolic iron. Auxiliary feedback was also introduced and investigated in the model. The role of such feedback is to help improve adaptation kinetics without an influence to the set-point, resulting in a significant improvement of the system response time. Homeostasis was also explored in order to see whether oscillatory conditions, which are common in biological systems, could show robust homeostasis. Homeostatic oscillators were identified, where compensatory frequency or amplitude levels lead to the average level corresponding to the set-point. This indicates that even during sustained oscillatory conditions homeostasis can be observed, suggesting an extension of the concept. Frequency control with the frequency being homeostatically regulated have also been described by us. Cytosolic calcium (Ca2+) is a biological example of one of these conditions where oscillations, transients etc. take place even though Ca2+ is under strict homeostatic control. Dysregulation of cytosolic Ca2+ is critical as it will affect cellular signaling and promote apoptosis at high levels. A simple initial model of oscillating Ca2+ regulation was used as an example of oscillatory homeostats, which spiked the interest to investigate Ca2+ homeostasis on a cellular level. Thus started the approach on building a model on cytosolic Ca2+ homeostasis and regulatory mechanisms in non-excitable cells. The work was started from an initial simple model based on erythrocytes with few organelles by studying the inflow and outflow mechanisms through the plasma membrane. Hysteretic properties in the plasma membrane Ca2+ ATPase (PMCA) was studied and identified, and compared well with experimental results. We also suggest that the inflow of Ca2+ could be inhibited by carboxyeosin which was used as an inhibitor in experimental research based on model calculations fitting well with these. For the Ca2+ induced Ca2+ release mechanism through the inositol 1,4,5-trisphosphate receptor (IP3R) a dicalcic model has been presented. Comparing theoretical calculations with experimental bell-shaped curves of the Ca2+ dependency of the IP3R channel at different IP3 levels, a cooperativity of 2 has been suggested in the inhibition by Ca2+. Cooperativity in the capacitative Ca2+ entry was also investigated and compared to experiments. Finally, even though oscillations was not the focus of this latest project, the cellular model can show sustained Ca2+ oscillations with period length ranging from a few seconds up to 30 hours!