Publications

Abstract

Not specified

Authors: Dmitry Devetyarov, Ilia Nouretdinov

Date Published: 2010

Journal: Artificial Intelligence Applications and Innovations

Abstract

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Author: Wolfgang Müller

Date Published: 2017

Journal: Research and Advanced Technology for Digital Libraries

Abstract

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Authors: Sebastian Schmelzle, Thomas van de Kamp, Michael Heethoff, Vincent Heuveline, Philipp Lösel, Jürgen Becker, Felix Beckmann, Frank Schluenzen, Jörg U. Hammel, Andreas Kopmann, Wolfgang Mexner, Matthias Vogelgesang, Nicholas T. Jerome, Oliver Betz, Rolf Beutel, Benjamin Wipfler, Alexander Blanke, Steffen Harzsch, Marie Hörnig, Tilo Baumbach

Date Published: 7th Sep 2017

Journal: Developments in X-Ray Tomography XI

Abstract (Expand)

UNLABELLED: In an accompanying paper [du Preez et al., (2012) FEBS J279, 2810-2822], we adapt an existing kinetic model for steady-state yeast glycolysis to simulate limit-cycle oscillations. Here we validate the model by testing its capacity to simulate a wide range of experiments on dynamics of yeast glycolysis. In addition to its description of the oscillations of glycolytic intermediates in intact cells and the rapid synchronization observed when mixing out-of-phase oscillatory cell populations (see accompanying paper), the model was able to predict the Hopf bifurcation diagram with glucose as the bifurcation parameter (and one of the bifurcation points with cyanide as the bifurcation parameter), the glucose- and acetaldehyde-driven forced oscillations, glucose and acetaldehyde quenching, and cell-free extract oscillations (including complex oscillations and mixed-mode oscillations). Thus, the model was compliant, at least qualitatively, with the majority of available experimental data for glycolytic oscillations in yeast. To our knowledge, this is the first time that a model for yeast glycolysis has been tested against such a wide variety of independent data sets. DATABASE: The mathematical models described here have been submitted to the JWS Online Cellular Systems Modelling Database and can be accessed at http://jjj.biochem.sun.ac.za/database/dupreez/index.html.

Authors: F. B. du Preez, D. D. van Niekerk, Jacky Snoep

Date Published: 13th Jun 2012

Journal: FEBS J

Abstract

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Authors: K. S. Bose, R. H. Sarma

Date Published: 27th Oct 1975

Journal: Biochem Biophys Res Commun

Abstract

Not specified

Author: Alan Williams

Date Published: 16th Jan 2019

Journal: Not specified

Abstract (Expand)

UNLABELLED: Oscillations are widely distributed in nature and synchronization of oscillators has been described at the cellular level (e.g. heart cells) and at the population level (e.g. fireflies). Yeast glycolysis is the best known oscillatory system, although it has been studied almost exclusively at the population level (i.e. limited to observations of average behaviour in synchronized cultures). We studied individual yeast cells that were positioned with optical tweezers in a microfluidic chamber to determine the precise conditions for autonomous glycolytic oscillations. Hopf bifurcation points were determined experimentally in individual cells as a function of glucose and cyanide concentrations. The experiments were analyzed in a detailed mathematical model and could be interpreted in terms of an oscillatory manifold in a three-dimensional state-space; crossing the boundaries of the manifold coincides with the onset of oscillations and positioning along the longitudinal axis of the volume sets the period. The oscillatory manifold could be approximated by allosteric control values of phosphofructokinase for ATP and AMP. DATABASE: The mathematical models described here have been submitted to the JWS Online Cellular Systems Modelling Database and can be accessed at http://jjj.mib.ac.uk/webMathematica/UItester.jsp?modelName=gustavsson5. [Database section added 14 May 2014 after original online publication].

Authors: A. K. Gustavsson, D. D. van Niekerk, C. B. Adiels, B. Kooi, M. Goksor, Jacky Snoep

Date Published: No date defined

Journal: FEBS J

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