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 model

- 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 oscillation.