Intertech:Synthetic Biology course

We have decided to prepare a course on 'Introduction on Synthetic Biology'.

The aim of this course is diverse.

• First, is a way to organize the series of talks and lectures that we think should be taken by a given iGEM participant.
• Second, is a way to gather educational material focused on people that want to have a broader perspective of Synthetic Biology.
• Third, is a perfect starting point to whoever wants to take a step on this field.

The 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 Definition y clasification of the differential equations Mathematical model formulation First order diferencial equation solution Existence and unicity of the solution Solving differential equations with matlab Electronics Analogic elements basis Logic gates Boolean algebras Practical examples of applications Control theory What is this? Open and closed control loops PID Estability and equilibrium Sensibility and perturbations Homeostasis Error Theory Clasification Error of a magnitud measured directly and indirectly Direct problem Semidirect problem Inverse problem Obtaining data from tables and plots Minimal square fit Modelling systems

Part 2 Training for engineers Cell definition basic elements two tipes: eukaryotes & prokaryotes metabolism Information pathways elements n.a. – DNA and RNA a.a. – proteins structure and organization: “dogma”: DNA → RNA → proteins dogma revisited dogma’s pace special in prokaryotes: horizontal transference Genetic regulation regulation of DNA typical structure of a gene and its surroundings (promoter, operator, RBS) transcription factors regulation of RNA regulación of protein Global regulatory mechanisms: SOS termal shock Communication with environment sensors extracellular intracellular signal transducers phosphorylations actuators transcription factors quorum sensing polymerase’s sigma factor Kinetic Chemistry Definitions: Substrate, Product, Enzyme Michaelis-Menten’s equation Vmax, v0, kcat, k1, k-1, km Hill’s equation activation repression (Basic) Laboratory Techniques (of molecular biology of bacteria) cellular culture bacterial transformation extraction of plasmids electrophoresis cut and paste DNA: restriction, ligation

Part 3 Training in Synthetic Biology

Synthetic Biology (Description)

• What is synthetic biology?
• Synthetic biology from the point of view of engineering

Design

• Modelling biology and types of models

Definition of Standards

• How to make a reusable part
• Registry of parts
• Biobricks and Standard Assembly

Examples of systems in synthetic biology (To be developed in silico by the students)

• Toggle switch
• Repressilator
• Vanillin sensor
• Molecular Predator oscillator