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| We have decided to prepare a course on 'Introduction on Synthetic Biology'. | | We have decided to prepare a course on 'Introduction on Synthetic Biology'. |
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Revision as of 07:39, 5 February 2008
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
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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:
Communication with environment
- sensors
- extracellular
- intracellular
- signal transducers
- 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
(Basic) Laboratory Techniques (of molecular biology of bacteria)
- cellular culture
- bacterial transformation
- extraction of plasmids
- electrophoresis
- cut and paste DNA: restriction, ligation
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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
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