Course syllabus for Metabolic engineering

Course syllabus adopted 2021-02-26 by Head of Programme (or corresponding).

Overview

  • Swedish nameMetabolic engineering
  • CodeKKR063
  • Credits7.5 Credits
  • OwnerMPBIO
  • Education cycleSecond-cycle
  • Main field of studyBioengineering
  • DepartmentBIOLOGY AND BIOLOGICAL ENGINEERING
  • GradingTH - Pass with distinction (5), Pass with credit (4), Pass (3), Fail

Course round 1

  • Teaching language English
  • Application code 08133
  • Maximum participants20
  • Minimum participants4
  • Block schedule
  • Open for exchange studentsYes

Credit distribution

0107 Examination 6 c
Grading: TH		 6 c
  • 11 Jan 2022 pm J
  • 12 Apr 2022 am J
  • 18 Aug 2022 am J
0207 Project 1.5 c
Grading: UG		 1.5 c

In programmes

Examiner

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Eligibility

General entry requirements for Master's level (second cycle)
Applicants enrolled in a programme at Chalmers where the course is included in the study programme are exempted from fulfilling the requirements above.

Specific entry requirements

English 6 (or by other approved means with the equivalent proficiency level)
Applicants enrolled in a programme at Chalmers where the course is included in the study programme are exempted from fulfilling the requirements above.

Course specific prerequisites

Basic knowledge in biochemistry, applied microbiology and bioreaction engineering. Students with other background must discuss this with the examiner.

Aim

One of society's major challenges is the transition away from fossil resources, and elementary to this transition are microbial biocatalysts that can convert renewable feedstocks to bio-based chemicals. Metabolic engineering is the emerging field where microbial biocatalysts are designed, genetically engineered and optimized. Metabolic engineering includes microbiology, chemistry, computational biology, systems and synthetic biology. This course aims to provide advanced knowledge in the development of microbial biocatalysts through metabolic engineering by studying the process from design to implementation, with a particular focus on constraint-based modelling of metabolism.

Learning outcomes (after completion of the course the student should be able to)

  • Describe how metabolic engineering can contribute to reaching multiple Sustainable Development Goals.
  • Describe the design-build-test-learn cycle of metabolic engineering.
  • Understand the principles of enzyme function, kinetics and regulation.
  • Describe metabolic physiology in a quantitative manner.
  • Describe metabolic networks computationally as stoichiometric and kinetic models.
  • Perform genome-scale model reconstruction based on genomic and biochemical information.
  • Describe how metabolism is constrained and how biological and physical constraints can be applied for simulating metabolism.
  • Define objective functions for simulating metabolism and how these affect the function of biocatalysts.
  • Quantify the biosynthetic requirements for cellular growth.
  • Describe the concept of equivalent states in cellular metabolism.
  • Apply linear programming to analyse metabolic network properties.
  • Describe the implications of metabolic control analysis on metabolic engineering.
  • Use models of metabolism to predict metabolic engineering strategies.
  • Describe how genetic engineering techniques can be used to implement metabolic engineering strategies.
  • Improve oral and written presentation skills.

    • Content

    In this course, we will follow the design-build-test-learn cycle that is central to modern metabolic engineering. Essential is the ability to describe and analyse metabolic networks, and therefore significant focus will be on the application of computational models of metabolism. We will study both steady-state (stoichiometric) models and dynamic (kinetic) models. The students will get hands-on experience working with both type of models as part of computer exercises, with the ultimate aim to design metabolism for (increased) production of valuable chemicals. 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.

    Organisation

    The course consists of lectures, self-study of the literature, computer exercises, an individual and a group project.

    The individual assignment is on the reconstruction and analysis of a genome-scale model. During the lectures and computer exercises various tools and methods will be introduced that the students will then use in the assignment, to be graded as a written report.

    The aim of the group project is to review the current status of the research field, identify the most pressing challenges and suggest how to move forward. Groups of 2-5 students (size dependent on total number of students) select a topic in consultation with the examinator and will present their results in the form of an oral presentation.

    Literature

    Bernard O Palsson, "Systems Biology: Constraint-Based Reconstruction and Analysis" available as an E-book via the Chalmers library; in addition to literature that will be distributed via the course homepage.

    Examination including compulsory elements

    The individual and group assignments are both compulsory. The final grade is determined by the assignments and a written exam at the end of the course.

    The course examiner may assess individual students in other ways than what is stated above if there are special reasons for doing so, for example if a student has a decision from Chalmers on educational support due to disability.