Metabolic Systems Biology

Systems biology is an integrated approach of experimental and mathematical methods that aims a comprehensive understanding of how biological functions arise and how they are regulated. We will focus on different levels of cellular regulation in bacteria: metabolism, gene expression, and global physiology, while emphasizing interconnections between the regulatory levels to illustrate how stable cellular phenotypes occur, and how these interconnections give rise to seemingly-miraculous properties, like growth rate maximization. The course will consist of a mixture of lectures and student presentations and discussions of current literature. Experimental and modelling approaches will be discussed.

For unravelling how cell functions are regulated, different platforms have been developed, among which are techniques named omics technologies, e.g. metabolomics, transcriptomics, genomics and proteomics. However, data alone are insufficient for understanding how a metabolic pathway or a signaling cascade gives rise to different phenotypes. Using literature presentations and discussion, this course introduces the use of measurement technologies for the purpose of:

- Quantifying metabolites within bacteria

- Quantifying genetic regulation in bacteria

- Quantifying single-cell gene expression

- Identification of interactions between genes and metabolism

The course presents:

- Principles and functions of gene expression networks, emphasizing autoregulation and regulatory dynamics

- Using modelling at different levels of detail to explain cellular behaviors and adaptive advantages

- Using modelling to identify sites of regulation in metabolic pathways

- Measurement techniques and data interpretation for protein and transcript levels at both ensemble and single-cell level

Note that classroom attendance is mandatory at all sessions.

- Computer Exercise (20 %)

- Literature case study: Oral presentation of one journal article and leading a classroom discussion, either alone or as part of a group (50%)

- Participation in classroom discussion (15%)

- 3 short written analyses of assigned reading and classroom discussion (1 paper per week) (15%)

There will be no final exam.

Resits: students will be given one resit opportunity consisting of an oral presentation of a new journal article within 3 weeks of the final student presentation and according to the examiner's schedule. When course is not offered during alternate years, students must request a resit no later than week 3 of Q3 by contacting the teacher. The resit will be scheduled according to examiner's schedule no later than week 9 of Q3.