Thursday, April 17, 2014
Spalding Laboratory 106 (Hartley Memorial Seminar Room) – Eudora Hull Spalding Laboratory of Engineering
Chemical Engineering Seminar
Using MetRxn for metabolic model reconstruction, flux elucidation and strain redesign
Costas D. Maranas, Donald B. Broughton Professor, Chemical Engineering, The Pennsylvania State University
MetRxn is a standardized, non-redundant, searchable collection of published metabolic models and databases from a wide variety of organisms. The current MetRxn 2.0 update includes recently published metabolic data for a total of 112 metabolic models and 8 metabolic databases spanning over 44K metabolites and 35K reactions. In this talk, we will elaborate on new features of MetRxn 2.0 (http://www.metrxn.che.psu.edu/) including atom mapping information across all reactions and enhanced integration with other databases. We will describe how this resource can impact genome-scale metabolic model reconstruction by providing curated reaction and metabolite content. Progress towards the rapid generation of microbial models, multi-tissue models for maize, and multi-organism models for microbial communities will be briefly highlighted. We will discuss how reaction atom mapping information in MetRxn can be used to construct isotope mapping models for metabolic flux elucidation, classify reactions and contrast pathways across organisms. Finally, we will present computational tools for strain optimization leading to the microbial overproduction of target biomolecules. Experimental results for a number of collaborative projects will be highlighted and the integration of kinetic information will be detailed.