SSB-50806 Systems and Synthetic Biology

Course

Credits 6.00

Teaching methodContact hours
Lecture24
Tutorial34
Independent study0
Course coordinator(s)prof. dr. VAP Martins dos Santos
dr. E Saccenti
Lecturer(s)prof. dr. VAP Martins dos Santos
dr. E Saccenti
Examiner(s)prof. dr. VAP Martins dos Santos
dr. E Saccenti

Language of instruction:

English

Assumed knowledge on:

Basic knowledge in biological sciences; Mathematics 2 and 3 (MAT-14903, MAT-15003) or equivalent.

Contents:

Although many important components and interactions in biology have been discovered, biological complexity (the emergence of non-trivial behaviour from the connections between biological components) remains largely unexplored: Amsterdam cannot be understood from a list of its bricks. Recently, several systematic approaches aim to make complex biological mechanisms easier to understand and to engineer.
Firstly, systems biology aims to contribute to the elucidation of universal mechanisms underlying basic biological processes by studying how higher-level properties emerge from the complex interactions among individual components of biological systems. The representation of biological interactions in terms of networks plays a central role in understanding how molecular mechanisms, cells, organisms and even ecosystems behave. Through a mathematical and computational description of dynamic networks, which allows analysis of their often unexpected properties, this course introduces the basic principles and concepts in systems biology. We emphasize the integrative perspective on biology (i.e. that the whole is more than the sum of the parts) and the intertwining between modelling and effective experimentation. Network motif analysis (for motifs involved in e.g. positive and negative auto-regulation, feed forward, feed backward loops) as well as metabolic modelling (such as mass balances and metabolic flux analyses) will be exercised.
Secondly, this course introduces the principles of synthetic biology, a technology infrastructure to translate systems knowledge into biological engineering. The fundamental principles that should make up this infrastructure include automated DNA writing technologies (i.e., DNA synthesis), standardization of modular DNA parts, and the theoretical analysis and design of biochemical and genetic interaction circuits. In addition, for synthetic circuits to function properly, stable host organisms need to be selected. Further, this course discusses the scientific literature on biological circuit design.

Learning outcomes:

After successful completion of this course students are expected to be able to:
- understand basic concepts of systems biology;
- understand fundamental principles of synthetic biology;
- understand different types of networks;
- design a basic model with each of the types of networks exemplified;
- understand the properties of the components of a network;
- analyse network behaviour under various conditions;
- integrate network information and use adequate bottom-up vs top-down approaches with respect to biological questions.

Activities:

- computer assisted practicals;
- tutorials;
- study of relevant literature.

Examination:

- assessment of practical assignments (20%);
- written exam with open questions (80%).

Literature:

Literature will be provided during the course.

MinorPeriod
Compulsory for: WUSYBBSc Minor Systems Biology1AF