In the presence of cyanide, populations of yeast cells can exhibit sustained oscillations in the concentration of glycolytic metabolites, NADH and ATP. This study attempts to answer the long-standing question of whether and how oscillations of individual cells are synchronized. It shows that mixing two cell populations that oscillate 180" out of phase only transiently abolishes the macroscopic oscillation. After a few minutes, NADH fluorescence of the mixed population resumes oscillations up to the original amplitude. At low cell densities, addition of acetaldehyde causes transient oscillations. At higher cell densities, where the oscillations are autonomous, 70 pM acetaldehyde causes phase shifts. Extracellular acetaldehyde is shown to oscillate around the 70 pM level. We conclude that acetaldehyde synchronizes the oscillations of the individual cells.Keywords: cell-cell communication; signalling; control ; dynamics; self-organisation.It is becoming clear that the function of thc living cell extends beyond the steady state 11, 21. Of general interest are the states that derive from the non-linear properties of intracellular regulation and lead to oscillations i n important signallers such as the calcium ion (Ca") 13, 41. The oscillations become even more intriguing when they involve the dynamic interaction of individual cells such as in Dictyosteliunz differentiation [5]. Glycolytic oscillations in yeast are an example of the coupling of the dynamics of metabolism across cell boundaris [6, 7 I.Transient glycolytic oscillations can be induced by adding glucose followed by cyanide to a suspension of starved yeast [ 8-1 1 1. The oscillations last longer at higher cell densities [ 12, 131. This has been interpreted as being due to a synchronization mcchanism which prevents individually oscillating cells from becotning out of phase 1141. Under certain conditions sustained oscillations can be observed with populations of cells 16, 151.Although various substances have been considered to be the intercellular signaller, conclusive evidence for any onc of them has bccn elusive for 25 years 17, 13, 16, 171. In this report we identify and circumvent a complication precluding the measurement of acetaldehyde concentrations in the presence of cyanide. This allows us to demonstrate that the extracellular acetaldehyde concentration oscillates at the frequency of the intracellular glycolytic oscillations. The dependence of the phase shift on the acetaldehyde concentration and on the phase of acetaldehyde addition validates acetaldehyde as the elusive synchronizing agent. MATERIALS AND METHODSStrain and preparation of cells. on glucose as described in 161. At the diauxic shift, i.e. just after the glucose in the medium had been depleted, the cells were harvested by filtration, washed with 100 mM potassium phosphate, pH 6.8, resuspended and starved in the same buffer for 3 h at 30°C. The cells were then collected by filtration, resuspended in the same phosphate buffer and placed on ice until use. The protein concentration was d...

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction‐based models and packages that extend the core with features suited to other model types including constraint‐based models, reaction‐diffusion models, logical network models, and rule‐based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single‐cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution.

In Saccharomyces cerevisiae cells exhibiting high-affinity glucose transport, the glucose consumption rate at extracellular concentrations above 10 mM was only half of the zerotrans-influx rate. To determine if this regulation of glucose transport might be a consequence of intracellular free glucose we developed a new method to measure intracellular glucose concentrations in cells metabolizing glucose, which compares glucose stereoisomers to correct for adhering glucose. The intracellular glucose concentration was 1.5 mM, much higher than in most earlier reports. We show that for the simplest model of a glucose carrier, this concentration is sufficient to reduce the glucose influx by 50%. We conclude that intracellular glucose is the most likely candidate for the observed regulation of glucose import and hence glycolysis. We discuss the possibility that intracellular glucose functions as a primary signal molecule in these cells.

In a population of intact cells of the yeast Saccharomyces cerevisiae the dynamics of glycolytic metabolism were investigated under the condition of sustained oscillations. At 5‐s intervals cells were quenched in −40°C methanol, extracted and the intracellular concentrations of glycolytic metabolites, adenine nucleotides and phosphate were analysed. Oscillations were found for the glycolytic intermediates glucose 6‐phosphate, fructose 6‐phosphate and fructose 1,6‐bisphosphate. At variance with earlier reports on transient glycolytic oscillations, some intermediates further down the glycolytic pathway did not oscillate significantly, even though NADH did. In addition, the adenylate energy charge and the free energy of ATP hydrolysis oscillated significantly. Dynamic coupling through the latter may be responsible for this effective compartmentation of glycolytic dynamics.