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Semiotic structures and meaningful information in biological systems

 

fig3



Snapshot from a simulation of the inner kinetochore model. Typical simulation run with all inner kinetochore proteins responsible for building the bridge between two nucleosomes. Kinetochore proteins are labeled in a short form (e.g. K for CenpK). The same structure is rotated 180◦ from left to right.

manyNucSim

Simulations of Chromatin structures : Pairs of nucleosomes are laid parallel with a distance of 85A ̊ between each other. Protein amount was twentyfold. The simulation show seven bridges and some cross connections a long with some proteins were still unbound.


This project is funded within the SPP InKoMBio and performed in collaboration with the Leibniz institute for Age Research in Jena (Prof. Dr. Diekmann).

Team

Peter Dittrich

Bashar Ibrahim

Gerd Grünert

Richard Henze

Sergej Tschernyschkow

Sabine Herda

Abstract

The project aims at the semantic aspect of biological information. We develop novel methods to objectively identify and describe semiotic sub-systems of living cells. The basic idea relies on the identification of organic codes (as recently reviewed by Barbieri, 2008) and on how these codes are physically instantiated. First, we are developing formal concepts and measures that allow to describe and quantify organic codes based on experimental observations. Second, we apply these methods to a concrete biological signalling system in which the codes are difficult to identify: inner and outer kinetochore proteins and their involvement in structure formation and the control of mitosis (especially the spindle assembly checkpoint). The required data are measured in the Diekmann group, while in the Dittrich group the data are modelled in order to theoretically describe cell cycle dependent inner and outer kinetochore assembly and function. As an additional benefit, this project delivers a novel way to describe and understand biological systems from a semantic perspective.


Results

Richard Henze, Jan Huwald, Nelly Fernanda Mostajo Berrospi, Peter Dittrich, Bashar Ibrahim (2015)
Structural analysis of in silico mutant experiments of human inner-kinetochore structure
Biosystems 127, 47-59


Peter Kreyßig, Christian Wozar, Stephan Peter, Tomas Veloz, Bashar Ibrahim, Peter Dittrich (2014)
Effects of Small Particle Numbers on Long-Term Behaviour in Discrete Biochemical Systems
Bioinformatics 2014 Sep;30(17):i475-81


Bashar Ibrahim, Richard Henze, Gerd Grünert, Matthew Egbert, Jan Huwald, Peter Dittrich (2013)
Spatial Rule-Based Modeling: A method and its application to the human mitotic kinetochore
Cells, 2:506-544


Dennis Görlich, Gabi Escuela, Gerd Grünert, Peter Dittrich, Bashar Ibrahim (2013)
Molecular Codes Through Complex Formation in a Model of the Human Inner Kinetochore.
Biosemiotics, pages 223-247, 2013


Sergej Tschernyschkow, Sabine Herda, Gerd Grünert, Volker Döring, Dennis Görlich, Antje Hofmeister, Christian Hoischen, Stephan Diekmann, Peter Dittrich, Bashar Ibrahim (2013)
Rule-based Modeling and Simulations of the Inner Kinetochore Structure
Progress in Biophysics and Molecular Biology, 113(1):33 - 45, 2013


Ayse Koca Caydasi, Maiko Lohel, Gerd Grünert, Peter Dittrich, Gislene Pereira, Bashar Ibrahim (2012)
A Dynamical Model of the Spindle Position Checkpoint
Molecular Systems Biology, 8(582)


Peter Kreyßig, Gabi Escuela, Bryan Reynaert, Tomas Veloz, Bashar Ibrahim, Peter Dittrich (2012)
Cycles and the Qualitative Evolution of Chemical Systems
PLoS ONE, 7(10): e45772




Acknowledgements / Funding

German Research Foundation (DFG) Grant Di 852/10-1/2

Contact

Peter Dittrich
Biosystem Analysis Research Group
Department of Mathematics and Computer Science
Friedrich Schiller University Jena
D-07743 Jena
Germany