Projects
Ion and solute homeostasis in enteric bacteria: an integrated view generated from the interface of modelling and biological experimentation
A programme involving seven research groups in UK, Netherlands, Germany and Spain.
Aberdeen leaders: Ian R Booth, Samantha Miller, Celso Grebogi and Alessandro Moura.
The principal research objective is to understand, via molecular analysis and predictive modelling, the regulation of ionic homeostasis in bacteria and its role in regulating the integration of gene expression and metabolism. Bacterial cells attempt to regulate the cytoplasmic constitution close to an optimum for cell growth – pH ~7.8, ~0.3 M K+ and ~0.2 M anions, principally glutamate. This is effected by environmentally driven regulation of the activity and expression of a group of solute transporters and ion channels. Modification of the cytoplasmic constitution plays a key role in modulating the topology of DNA, the activity of RNA polymerase subunits augmented by very specific effects on regulatory transcription factors. The effects of these integrated elements are not only the potentiation of growth, but also the modulation of the survival potential of pathogenic organisms since many of the environmental cues perceived for cytoplasmic homeostasis are also signals for the expression of pathogenicity determinants. The core molecular biology of many of the regulatory elements is known making this a tractable problem for systems analysis and modelling. Moreover, the understanding provided by an in-depth insight into cytoplasmic homeostasis offers the missing link that perturbs many attempts at modelling cell function. The specific aims of this programme are: (a) Analysis of K+ homeostasis in E. coli including stimulus perception, signal transduction and integration, response and adaptation of all K+ uptake systems. (b) Analysis of the control over glutathione adduct regulated KefB K+ efflux systems that responds to chemical cues in E. coli. (c) Protein diffusion and folding in the cytoplasm: the role of ionic strength and osmoprotectants. (d) An integrated model for the regulation of cytoplasmic constitution and of the role of cytoplasmic ionic strength in regulating gene expression.
Articular cartilage damage and cellular responses following controlled impact loading
Richard M. Aspden
Impact loads due to trauma are a known cause of secondary osteoarthritis. However, the processes resulting in articular cartilage breakdown following injury and the capabilities of the tissue to repair are little understood. This project is studying two models of traumatic injury to cartilage: excessive loading at slow rates of loading and a true impact load. Results are strongly indicating these are not equivalent. Intercellular signalling via ERK/bFGF and IL-1b/COX-2/PGE2 is also being studied. Because damaged tissue in vivo is still subjected to loading during everyday activities, we are applying cyclic loading to impacted explants to investigate how this might affect these signalling pathways and subsequent tissue degeneration or attempts to repair. Together these data will provide information on the likely responses of articular cartilage to trauma and indicate how pharmaceutical intervention may be able to delay or prevent subsequent degeneration.
Stresses analysis of the human proximal femur and the role of ligaments and muscles
Richard M. Aspden, Jude R. Meakin.
Trabeculae in the proximal femur are organised broadly into two groups; commonly termed the principle compressive and the principle tensile groups. These names derive from the superficial observation that, with the distal femur fixed, a load applied to the superior femoral head would generate a bending moment in the femoral neck, leading to these stresses. However, the literature, and our pilot studies, lead us to hypothesize that (a) if muscle and ligamentous forces are included, and (b) the femur is constrained by its seating in the acetabulum and in equilibrium with the forces then all these trabeculae will be found to placed into compression, not tension. We are developing 3D finite element models of the femur and pelvis to test this hypothesis in various postures. Establishing this hypothesis would correct a 150 year-old misconception in the literature and may lead to novel designs for implants and fixation devices.
Modelling translational feedback loops in the yeast Saccharomyces
Ian Stansfield, J. Krishnan (Imperial College, London)
Gene expression is regulated at a number of levels, including at the level of translation, governing how and when the mRNA is translated to make protein. This form of control can operate at the level of translation initiation, elongation or termination, and employ a variety of mechanisms. One frequently employed regulatory motif is the negative feedback loop, in which the protein product specified by an mRNA serves to feedback inhibit its own mRNA translation. In this project the aims are to model a negative feedback loop operating in the yeast Saccharomyces cerevisiae at the level of translation termination, in order to model and test the functions of a number of different translation factors participating in termination, as well as to define the competitive interaction between termination and translation elongation.
Post-transcriptional feedback control of polyamine metabolism in yeast: an integrated modelling and experimental investigation
Ian Stansfield, Heather Wallace, Declan Bates (University of Leicester)
Polyamines are small polycationic molecules essential for life in eukaryotes and eubacteria. Among a wide diversity of roles, they bind DNA and RNA, regulate transcriptional silencing, and protect membranes from oxidative damage. While the polyamine biosynthesis pathway is relatively simple, its control mechanisms are remarkably complex and interlocking. They include examples of feedback inhibition of enzyme activity by pathway intermediates, as well as a unique negative feedback mechanism regulating the levels of the enzyme ornithine decarboxylase (ODC), which combines elements of translational and post-translational control. Although the control network is qualitatively understood, it is unclear how it operates as a complete system to dynamically regulate polyamine synthesis, what its control properties are, how robust the control system is to perturbation, and finally, which control elements are crucial for accurate and robust regulation. This research project employs an integrated modelling and experimentation approach to dissect these polyamine regulatory mechanisms.
Nonlinear dynamics in flow abnormalities related to cardiovascular pathology
Celso Grebogi, Nuala Booth
We are funded by the MRC (Discipline Hopping Award, 2006-2007) to model the abberant flow that occurs in blood vessels in which there is a surface irregularity, occurring because of pathologies like atherosclerosis or the insertion of a stent. This project is giving us new insights into how components of the blood, for instance platelets, behave under different conditions.
Modelling the amino acid starvation response (the GCN System) in yeast
George M Coghill, Tao You and Alistair JP Brown
The yeast, Saccharomyces cerevisiae responds to histidine starvation by activating the amino acid biosynthesis in general. This phenomenon is called the General Control of Amino Acid Synthesis (or the GCN System). We are generating a quantitative mathematical model that accurately describes the kinetic behaviour of the GCN System in S. cerevisiae. This complex model integrates modules describing the initial sensing events, Gcn2-mediated signal transduction, the transcriptional and translational regulation of the GCN4 gene, the general effects upon mRNA translation, the destabilisation of the Gcn4 transcription factor, the transcriptional regulation of amino acid biosynthetic genes by Gcn4, and amino acid synthesis. Our short term aim is to complete this model of the yeast GCN System and to test specific predictions of this model experimentally. Already the model has highlighted unexpected properties of the GCN System such as: (a) probable changes in ribosome scanning rates during translation initiation under amino acid replete and starvation conditions; and (b) additional layers of regulation, possibly at the level of Gcn4 protein stability. Our long term aim is to compare the behaviour of the GCN system in other fungi with a view to highlighting evolutionary changes in the kinetic properties of this conserved system.
CRISP (Combinatorial Responses In Stress Signalling)
A collaborative programme involving the University of Aberdeen and Imperial College London, funded by the BBSRC under the SABR (Systems Approaches to Biological Research) Initiative.
Aberdeen PIs: Al Brown, Celso Grebogi, George Coghill, Alessandro Moura, Marco Thiel, Maria Carmen Romano and Neil Gow.
Imperial PIs: Jaroslav Stark, Ken Haynes, Michael Stumpf and Ivana Gugelj
Life on this planet is dependent upon environmental adaptation. Biological systems function in constantly changing complex environments, where they are subject to wide ranging perturbations. To fully understand such systems it is necessary to experimentally perturb them, measure the resulting dynamic responses, and account for these responses mechanistically. Most researchers dissect specific environmental perturbations in isolation. Whilst this can yield major new biological insights, most organisms are often simultaneously exposed to combinations of several stimuli. This is particularly true for pathogens. Understanding and predicting the responses of biological systems to such combinatorial perturbations is a difficult but essential challenge for Systems Biology. We will tackle this challenge in the context of an important biological problem - the responses of the major fungal pathogens Candida albicans and Candida glabrata to the combinatorial stresses that they encounter in their human host. The virulence of these pathogens depends upon these stress responses. The comparative modelling of these divergent pathogens will provide important clues about the extent to which the strategies for dealing with combinatorial perturbations have been conserved during evolution.
Our objectives are to:
- Develop and validate tools and approaches that predict the molecular and cellular responses of Candida albicans and Candida glabrata to the combination of stresses they encounter during disease progression in the host.
- Compare the dynamic behaviour of stress regulatory networks in these two pathogens to determine the extent to which cross species comparisons can be made, and to highlight common points of system fragility that rep-resent potential targets for pharmaceutical intervention.
- Assess the utility of existing data and models from S. cerevisiae in understanding the response of pathogenic fungi to host defences.
- Evaluate the possibility of extending the tools developed in this project to other biological systems subject to combinatorial stimuli.
- Provide young scientists with a multidisciplinary training in Integrative Systems Biology.