UNIFIED MODELING OF SEVERAL PERTURBATION EXPERIMENTS IN SYSTEMS BIOLOGY - A Case Study on the Glucose Uptake of Lactococcus Lactis

András Hartmann, Susana Vinga, Joao M. Lemos

Abstract

Dynamic modeling of the metabolism is one of the main research areas of systems biology. A typical but yet unresolved problem is the modeling of glucose uptake of Lactococcus lactis bacteria upon in-vivo NMR measurements in perturbation experiments. Most modelers are focusing on the inverse problem, namely to identify the parameters of a set of differential equations using the available dataset. Majority of the available models suffer from the drawback that even if a perfect fit to a single experiment was achieved, they can not explain the systems’ behavior in different experimental conditions. The aim of this study is to introduce an appropriate method and a model to fit one set of parameters to several different experiments, enabling unify modeling of the glucose decay of the bacteria. With the proposed approach a good overall fit was obtained to the dataset. The results confirm that this could be a future way towards unified modeling of data with heterogeneous experimental conditions.

References

  1. Ashyraliyev, M., Fomekong-Nanfack, Y., Kaandorp, J. a., and Blom, J. G. (2009). Systems biology: parameter estimation for biochemical models. The FEBS journal, 276(4):886-902.
  2. Castro, R., Neves, A. R., Fonseca, L. L., Pool, W. a., Kok, J., Kuipers, O. P., and Santos, H. (2009). Characterization of the individual glucose uptake systems of Lactococcus lactis: mannose-PTS, cellobiose-PTS and the novel GlcU permease. Molecular microbiology, 71(3):795-806.
  3. Daniels, B. C., Chen, Y.-J., Sethna, J. P., Gutenkunst, R. N., and Myers, C. R. (2008). Sloppiness, robustness, and evolvability in systems biology. Current opinion in biotechnology, 19(4):389-95.
  4. Goel, G., Chou, I.-C., and Voit, E. (2008). System estimation from metabolic time-series data. Bioinformatics, 24(21):2505.
  5. Kennedy, J. and Eberhart, R. (1995). Particle swarm optimization. of IEEE international conference on neural, 4:1942-1948.
  6. Naval, P., Sison, L., and Mendoza, E. (2006). Metabolic network parameter inference using particle swarm optimization. In International Conference on Molecular Systems Biology, pages 3-4.
  7. Neves, A. R., Pool, W. a., Kok, J., Kuipers, O. P., and Santos, H. (2005). Overview on sugar metabolism and its control in Lactococcus lactis - the input from in vivo NMR. FEMS microbiology reviews, 29(3):531-54.
  8. Papagianni, M., Avramidis, N., and Filiousis, G. (2007). Glycolysis and the regulation of glucose transport in Lactococcus lactis spp. lactis in batch and fed-batch culture. Microbial cell factories, 6:16.
  9. Srinath, S. and Gunawan, R. (2010). Parameter identifiability of power-law biochemical system models. Journal of biotechnology.
  10. Vilela, M., Vinga, S., Maia, M. a. G. M., Voit, E. O., and Almeida, J. S. (2009). Identification of neutral biochemical network models from time series data. BMC systems biology, 3:47.
  11. Vinga, S., Thomaseth, K., Lemos, J., Neves, A., Santos, H., and Freitas, A. (2008). Structural analysis of metabolic networks: a case study on lactococcus lactis. In 8th Portuguese Conference on Automatic Control (CONTROLO2008), pages 566-571.
  12. Voit, E., Neves, A., and Santos, H. (2006). The intricate side of systems biology. Proceedings of the National Academy of Sciences, 103(25):9452.
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Paper Citation


in Harvard Style

Hartmann A., Vinga S. and M. Lemos J. (2011). UNIFIED MODELING OF SEVERAL PERTURBATION EXPERIMENTS IN SYSTEMS BIOLOGY - A Case Study on the Glucose Uptake of Lactococcus Lactis . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011) ISBN 978-989-8425-36-2, pages 309-312. DOI: 10.5220/0003158103090312


in Bibtex Style

@conference{bioinformatics11,
author={András Hartmann and Susana Vinga and Joao M. Lemos},
title={UNIFIED MODELING OF SEVERAL PERTURBATION EXPERIMENTS IN SYSTEMS BIOLOGY - A Case Study on the Glucose Uptake of Lactococcus Lactis},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011)},
year={2011},
pages={309-312},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003158103090312},
isbn={978-989-8425-36-2},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011)
TI - UNIFIED MODELING OF SEVERAL PERTURBATION EXPERIMENTS IN SYSTEMS BIOLOGY - A Case Study on the Glucose Uptake of Lactococcus Lactis
SN - 978-989-8425-36-2
AU - Hartmann A.
AU - Vinga S.
AU - M. Lemos J.
PY - 2011
SP - 309
EP - 312
DO - 10.5220/0003158103090312