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KKR063 Metabolic Engineering: design of microbial metabolism

Course objectives
The objective of the course is to provide the students with an overview of the different tools available to analyze metabolism and enable them to propose strategies to meet a metabolic design objective. In this course, the students will be presented with several models of microbial metabolism and the advantages and disadvantages of each kind of model will be discussed extensively. Broadly, two kinds of metabolic models will be addressed in this course – steady-state models (stoichiometric models, elementary flux modes, etc) and dynamic models (kinetic models). The students will also get a hands-on experience working with each of the models as part of their assignments, which will be used to design metabolism for selected applications. The assignments are geared to help the student understand metabolism, rather than on model development. Consequently, there will be a strong emphasis on interpreting the results obtained from the models. The overall aim of the course is to train the students such that they will be capable of working independently in the area of metabolic engineering.

Learning objectives
At the end of the course, the students should be able to:

  • Understand the principles of enzyme function and kinetics
  • Describe physiology in a quantitative manner
  • Learn stoichiometry and energetics of metabolism
  • Extend stoichiometric analysis of metabolism to mass balancing
  • Learn the basics about the techniques used to construct engineered strains
  • Learn to apply concepts of linear programming to metabolic models
  • Understand the use of radiolabeled tracers in metabolic studies
  • Learn the basics of metabolic control analysis
  • Learn the concept of elementary flux modes
  • Learn how to apply thermodynamics to metabolic engineering problems
  • Learn how to gather and summarize information related to real research projects

Course prerequisites
Students interested in taking this course are expected to have basic knowledge of biology and algebra. Programming skills in any language are not required, but will be useful.

The medium of instruction, assignments and examination will be in English. The course will be held every Monday (from 13:00 to 17:00) and Thursday, (from 08:00 to 12:00).
Detailed information on the course, hand-outs for the lectures, assignments, etc will be available from the website www.sysbio.se/teaching/2013_KKR063/kkr063.html. The username and password will be given to course participants on the first meeting time.

The final grade will depend on a project that is worth 25% and an examination, 75%. Some voluntary assignments can help to improve the final grade. The project will consist in a written report about one of the research topics that will be presented in class.

Teaching material
The relevant reading material will be posted as lecture notes on the course website. Frequently, references will be made to the textbook Metabolic Engineering that is available in electronic form from the Chalmers library. The slides used during the lecture will also be made available on the website. Additional literature pertaining to the specific lecture will also be mentioned.

Jens Nielsen: nielsenj@chalmers.se
Sergio Bordel: velasco@chalmers.se



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