Intertech:Synthetic Biology course: Difference between revisions
(New page: 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 ...) |
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**extracellular | **extracellular | ||
**intracellular | |||
signal transducers | *signal transducers | ||
**phosphorylations | |||
actuators | *actuators | ||
**transcription factors | |||
**quorum sensing | |||
**polymerase’s sigma factor | |||
- Kinetic Chemistry | - Kinetic Chemistry |
Revision as of 06:58, 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
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.