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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?
Publications:
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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