Intertech:iSB2008:Materials

Syllabus

Syllabus of this course is divided in three parts. There is a group of topics that need to be known by biologists (or 'life science' people), then a bunch of topics that need to be known by engineers (or 'technical' people) and, finally, some lectures on 'what' is syntehtic biology and some examples of it.

Part 1 Training for biologists Ordinary differential equations Introduction Basic concepts to understand an ODE Description and properties of ODE Solving ODE Vector spaces Dynamic systems Control theory Introduction Types od controllers Block diagram Example of control Laplace transform and transfer function Frequency domain Examples Electronics Introduction Boolean algebras Logical gates Representation of boolean functions Karnaugh maps Error Theory Introduction to measurement theory Error theroy description Types of errors Evaluation of the error in an experimental measurement Minimal square fit Obtaining relations from experimental data Programming in Matlab Introduction to programming languages Basic MatLab operations Programming in Matlab Solving ODE with Matlab

Part 2 Training for engineers Cell Cell, definition Basic elements Eukaryotes Prokaryotes Metabolism Flow of genetic information Elements Nucelic acid – DNA and RNA Amino acid – proteins Central Dogma of Molecular Biology Dogma, revisited Horizontal transference Genetic regulation DNA regulation RNA regulation Protein regulation Global regulatory mechanisms: Communication with environment Signal transduction Signal Receptor Transducer Actuator Examples Kinetic Chemistry Definitions Law of mass action Enzyme-catalyzed reactions Hill equation: allosterism Hill equation in gene modelling (Basic) Laboratory Techniques (of molecular biology) DNA cloning Polymerase Chain Reaction Gel electrophoresis Reading and writing DNA Molecular hybridization rewriting DNA: mutations arrays

Part 3 Training in Synthetic Biology

Introduction to Synthetic Biology Introduction Synthetic Biology evolution Some examples Biology and Engineering: the paradigm of Synthetic biology Systems Biology work Synthetic gene regulatory systems Standards Building a composable DNA library Registry Parts Signal carrier Modularity Looking for abstraction Abstraction hierarchy

Basic Synthetic Biology Circuits Synthetic Biology works Toggle switch Repressilator Counting machine - ETH iGEM 2005 Memory device - ETH iGEM 2007 Cell free system - Imperial iGEM 2007 Synthetic pattern formation Artifitial quorum sensing Artemisinin production

Reference materials

1. Goldbeter A and Koshland DE Jr. An amplified sensitivity arising from covalent modification in biological systems. Proc Natl Acad Sci U S A. 1981 Nov;78(11):6840-4. DOI:10.1073/pnas.78.11.6840 |
2. JACOB F and MONOD J. Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol. 1961 Jun;3:318-56. DOI:10.1016/s0022-2836(61)80072-7 |
3. ISBN:0879697164