I'm working with oscillations in glycolysis in intact yeast cells.
But bacterial pattern-formation is also of great interest to me.

Glycolytic Oscillations

Glycolytic oscillations in yeast cells
During glycolysis, oscillations in the concentrations of key metabolites is seen in intact, living yeast cells (Saccharomyces cerevisiae). 
By studying these oscillations, we want to introduce new ways of thinking about the dynamics of biological systems, and to learn more about biological oscillations.

In my experiments, I want to describe this system in the context of nonlinear dynamics. To do this, it is essential to maintain the yeast cells in the same, well-defined state away from equilibrium. This is done by using a CSTR setup.
The oscillations are monitored by measuring the fluorescence of the intracellular redox-carrier NADH.

What makes the metabolites oscillate?
Why are oscillations interesting?
Why bother?


  • Sune Danø, Preben Graae Sørensen and Finn Hynne: Sustained oscillations in living cells, Nature 402: 320-322, 1999.
  • Master Thesis : Glycolytic Oscillations in Yeast Cells. [gzip'ed PostScript] [PDF]
  • S. Danø, F. Hynne and P. G. Sørensen: Dynamics of Yeast Cell Populations, Proceedings of the 5th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Belgrade, Yugoslavia (2000) 12-19 [gzip'ed PostScript] [PDF] 
  • S. Danø, F. Hynne and P. G. Sørensen: Hopf Dynamics in a Suspension of Yeast Cells, Proceedings of the 2nd Workshop on Computation of Biochemical Pathways and Genetic Networks, Heidelberg, Germany, (2001) 101-106.
  • F. Hynne,S. Danø and P. G. Sørensen: Full-scale model of glycolysis in Saccharomyces cerevisiae, Biophysical Chemistry 94 (2001) 121-163. Preprint: [gzip'ed PostScript] [PDF]. Poster: [EPS, 4.6 MB] [gzipped EPS, 1 MB]. Model description file for chem: [glycolysis.des]. Run the model from the Java Web Simulation (JWS) database of kinetic models.
  • S. Danø, F. Hynne, S. De Monte, F. d'Ovidio, P. G. Sørensen and H. Westerhoff: Synchronization of glycolytic oscillations in a yeast cell population, Faraday Discussions 120 (2001) 261-275. [link].
  • F. Hynne, S. Danø and P. G. Sørensen: A functional dynamics approach to modelling of glycolysis, in Function and regulation of cellular systems: experiments and models (eds. A. Deutsch, M. Falcke, J. Howard, W. Zimmermann), Birkhauser, Basel, 2004. Book available at amazon.com. Preprint of chapter: [gzip'ed PostScript] [PDF].
  • Ph.D. Thesis : Functional Dynamics: The relations between function and dynamics studied in yeast cells and bacterial colonies. [gzip'ed PostScript] [PDF].
  • S. Danø, M.F. Madsen and P. G. Sørensen: Chemical interpretation of oscillatory modes at a Hopf bifurcation, Phys. Chem. Chem. Phys. 7 (2005) 1674-1679. [Reprint, further redistribution is not allowed].
  • M.F. Madsen, S. Danø and P. G. Sørensen: On the mechanisms of glycolytic oscillations in yeast, FEBS Journal 272 (2005) 2648-2660. [PDF at FEBS J.] [PubMed].
  • G. Cedersund, S. Danø, P.G. Sørensen and M. Jirstrand: From in vitro biochemistry to in vivo understanding of the glycolytic oscillations in Saccharomyces cerevisiae, Proceedings of the BioMedSim conference, Linkoping, Sweden, pp. 105-114, 2005.
  • S. Danø, M.F. Madsen, H. Schmidt and G. Cedersund: Reduction of a biochemical model with preservation of its basic dynamic properties, FEBS Journal, 273 (2006) 4862-4877. [PDF at FEBS J.] [PubMed].
  • S. Danø, M.F. Madsen and P.G. Sørensen: Quantitative characterization of cell synchronization in yeast, PNAS, 104 (2007) 12732-12736. [PNAS] [PubMed].
  • S. De Monte, F. d'Ovidio, S. Danø, M.F. Madsen and P.G. Sørensen: Dynamical quorum sensing: Population density encoded in cellular dynamics, PNAS, 104 (2007) 18377-18381. [PNAS] .
  • H. Schmidt, M.F. Madsen, S. Danø, and G. Cedersund: Complexity reduction of biochemical rate expressions, Bioinformatics 24 (2008) 848-854.

    Articles in Danish:

  • Robin Engelhardt: Da livet lærte at gå i takt. Dagbladet Information den 22. november 1999, side 6.
  • Sune Danø og Henrik Skødt: Heraklit i kemien. Dagbladet Information den 14. december 1998 , 1. sektion side 6.
  • Gode historier fra forskningens verden: Speciale i Nature. Redegørelse fra Det naturvidenskabelige Fakultet, Københavns Universitet til Forskningsministeren og Undervisningsministeren. Bilag B: Succeshistorier, 1. december 1999, side 22.


    Programs for fitting and data acquisition

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    Bacterial Pattern-formation

    The pattern formation of bacterial colonies has a broad interest, because it is one of the simplest examples of a biological cell organisation. The hope is, that the understanding of the bacterial pattern formation will be an important step towards understanding of the morphogenesis in plants, animals and human beings.

    Together with J.A. Shapiro and K. Dyring-Andersen, I work with the gram negative, motile bacterium Proteus mirabilis. The bacterium is well-known for the patterns, formed by its colonies on agar plates. They consist of extremely circular, concentric rings. These rings are formed as the bacteria change their cellular morphology back and forth between two different cell types.

    We explain how colonies of Proteus mirabilis can become so perfectly circular, and investigate how changes in the bacterial environment changes the morphology of the bacterial colony. Some of this work can be found in chapter 8 of my Ph.D. thesis.

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