ARTICLE Cell Mass and Cell Cycle Dynamics of an Asynchronous Budding Yeast Population: Experimental Observations, Flow Cytometry Data Analysis, and Multi-Scale Modeling Rita Lencastre Fernandes, 1 Magnus Carlquist, 2,3 Luisa Lundin, 4 Anna-Lena Heins, 2 Abhishek Dutta, 5 Søren J. Sørensen, 4 Anker D. Jensen, 6 Ingmar Nopens, 5 Anna Eliasson Lantz, 2 Krist V. Gernaey 1 1 Center for Process Engineering and Technology, Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark; telephone: þ45 45 25 29 70; fax: þ45 45 93 29 06; e-mail: kvg@kt.dtu.dk 2 Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark 3 Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden 4 Molecular Microbial Ecology Group, Department of Biology, University of Copenhagen, Copenhagen, Denmark 5 BIOMATH, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium 6 Center for Combustion and Harmful Emission Control, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kongens Lyngby, Denmark ABSTRACT: Despite traditionally regarded as identical, cells in a microbial cultivation present a distribution of pheno- typic traits, forming a heterogeneous cell population. More- over, the degree of heterogeneity is notably enhanced by changes in micro-environmental conditions. A major devel- opment in experimental single-cell studies has taken place in the last decades. It has however not been fully accompanied by similar contributions within data analysis and mathe- matical modeling. Indeed, literature reporting, for example, quantitative analyses of experimental single-cell observa- tions and validation of model predictions for cell property distributions against experimental data is scarce. This study focuses on the experimental and mathematical description of the dynamics of cell size and cell cycle position distribu- tions, of a population of Saccharomyces cerevisiae, in re- sponse to the substrate consumption observed during batch cultivation. The good agreement between the proposed multi-scale model (a population balance model [PBM] coupled to an unstructured model) and experimental data (both the overall physiology and cell size and cell cycle distributions) indicates that a mechanistic model is a suit- able tool for describing the microbial population dynamics in a bioreactor. This study therefore contributes towards the understanding of the development of heterogeneous popu- lations during microbial cultivations. More generally, it consists of a step towards a paradigm change in the study and description of cell cultivations, where average cell behaviors observed experimentally now are interpreted as a potential joint result of various co-existing single-cell behaviors, rather than a unique response common to all cells in the cultivation. Biotechnol. Bioeng. 2013;110: 812–826. ß 2012 Wiley Periodicals, Inc. KEYWORDS: population balance model (PBM); multiscale modeling; flow cytometry; standardized data analysis; Saccharomyces cerevisiae; total protein content; cell cycle Introduction Cells in a cultivation are traditionally regarded as identical, though microbial populations are most often heteroge- neous. As such, distributions of phenotypic traits such as cell Correspondence to: K.V. Gernaey Contract grant sponsor: Danish Council for Strategic Research Contract grant number: 09-065160 Contract grant sponsor: ERA-IB (ERA-NET Industrial Biotechnology) Contract grant number: EIB.08.031 Additional supporting information may be found in the online version of this article. Received 24 August 2012; Accepted 5 October 2012 Accepted manuscript online 10 October 2012; Article first published online 12 November 2012 in Wiley Online Library (http://onlinelibrary.wiley.com/doi/10.1002/bit.24749/abstract) DOI 10.1002/bit.24749 812 Biotechnology and Bioengineering, Vol. 110, No. 3, March, 2013 ß 2012 Wiley Periodicals, Inc.