Advanced Course Metabolomics for Microbial Systems Biology

Delft University of Technology, Universidade de São Paulo and Universidade de Campinas are pleased to announce the organization of an advanced course oriented to graduate students, young researchers and senior investigators, working in the area of microbial systems biology with interests in methods to determine intracellular metabolite concentrations and fluxes. The course is based on (method) lectures, computer exercises and conference talks showing results from different research groups in Brazil, Netherlands, Germany and United States of America. The official course language is English.

The first two days are mainly dedicated to experimental techniques, including cultivation approaches for steady-state analysis and stimulus response experiments. Proper sampling and sample handling procedures for reliable and reproducible metabolome analysis will be discussed and validation calculations (computer exercise) are performed. The main measurement techniques addressed are based on liquid and gas chromatographic separation, coupled to mass spectrometry. The third and fourth days will be focused on theoretical and modeling aspects of Systems Biology. Approaches from network reconstruction, stoichiometric and thermodynamic network analysis and in-vivo kinetic modeling will be covered. ¹³C tracer methods will be discussed to identify intracellular cycles under stationary state as well as dynamic conditions. The last day will show-case some metabolomics research highlights from Brazil, the Netherlands and USA.

Topics:

• Rapid sampling and quantitative analysis
• Metabolite quantification and validation using
• Isotope Dilution Mass Spectrometry (IDMS)
• Perturbation strategies
• Estimation of extra- and intracellular rates from experimental data
• Kinetic modeling and approaches to handle parameter identification problems

Exercises

Several exercises will be performed to familiarize the participants with the theory and practice and to illustrate the utility and utilization of quantitative metabolomics in modern biotechnology. IDMS calculations will be carried out using Microsoft Excel. Flux analysis and dynamic simulations are performed using the numerical computing environment MATLAB. Prior knowledge of MATLAB is advantageous – a tutorial for learning the required (basic) MATLAB knowledge will be sent prior to the course. In every practice, at least two instructors will be present to help in the solution of eventual problems.

Who should attend?

This Advanced Course is aimed at participants from industry, universities and research institutions who want to update and extend their theoretical knowledge and practical insight in quantitative metabolomics and modeling. The course is intended for graduate students and postgraduates (MSc, PhD), with a sound background in microbiology, microbial physiology, biotechnology, biochemistry or biochemical engineering, with a basic working knowledge in some of the other disciplines and an affinity to applied mathematics. It is our intention to conform a select group of attendants of no more than 36 participants. Our aim is to have a multi-disciplinary group, with people from the industry and the academy.