Notes 20101021 BioCompiler Homework

From SnOwy - Ed's Wiki Notebook

I've finally found some time to type up the audits that I performed -- I only got to three of the seven teams I was assigned; one team audited had two projects, one team had a very incomplete page.

Contents 1 Victoria Australia 1.1 Project: Biological Lighting System 1.1.1 Inputs 1.1.2 Compilation to Solution 1.1.3 Compilation to Protocol 1.1.4 Side Effects 2 Queensland Australia 2.1 Project: Bioprecipitation 2.1.1 Inputs 2.1.2 Compilation to Solution 2.1.3 Side Effects 2.2 Project: Biofiltration 2.2.1 Inputs 2.2.2 Compilation to Solution 2.2.3 Compilation Errors 2.2.4 Side Effects 3 UNAM Mexico 3.1 Project: Turing-like oscillation of pigment morphology 3.1.1 Inputs 3.1.2 Compilation to Solution 3.1.3 Compilation to Circuit 3.1.4 Side Effects

Victoria Australia

http://2009.igem.org/Team:Victoria_Australia

Project: Biological Lighting System

Inputs

• biological lighting system
• must be a cell free extract
• must utilize a generally-regarded-as-safe (GRAS) chasis

Compilation to Solution

• identified protein family: green fluorescent protein (GFP) including those which emit various colours
• identified wheat germ cell extract as GRAS chasis

Compilation to Protocol

• identified: missing biobricks for other colour -FPs
  • solution: quickchange PCR used to create remaining -FPs
• identified: test -FPs in known chasis
  • solution: use E. coli as first chasis

Side Effects

• contribution of BioBricks corresponding to the additional -FPs

Queensland Australia

http://2009.igem.org/Team:UQ-Australia

Project: Bioprecipitation

Inputs

• "optimise ice-nucleative ability of P. syringae."

Compilation to Solution

• identified: P. syringae as organism with natural ability to emit bioprecipitating product -- InaZ
• identified: P. syringae is not viable above 28°C.
• identified: {GroEL}+{GroES} = HSP60-family of heatshock proteins
• identified: {DnaK}+{DnaJ+GrpE} = HSP70-family of heat shock proteins (prokaryote orthologue thereof)

Side Effects

• contribution of BioBricks for the named HSP60-family of heatshock proteins
• contribution of BioBricks for the named HSP70-family of heatshock proteins (prokaryote orthologue)

Project: Biofiltration

Inputs

• "modify the mercury uptake, reduction and efflux system in E. coli."

Compilation to Solution

• identified: E. coli for its Hg⁺⁺ uptake
• identified: history of As uptake in previous project
• identified: bacterial protein Antigen 43 (AG43) used to aggregate cells together

Compilation Errors

• BBa_l76101 is not correct

Side Effects

• contribution of {MerT} biobrick -- facilitates transport of Hg⁺⁺ into bacterial inner membrane

UNAM Mexico

http://2009.igem.org/Team:IPN-UNAM-Mexico

Project: Turing-like oscillation of pigment morphology

Inputs

• demonstrate turing-like behaviour
• create self-emerging morphological patterns with pigment morphology

Compilation to Solution

• Identified: oscillatory model

Compilation to Circuit

• Identified: Self-activating module with Las operon
• Identified: Self-inhibiting module with Lux operon
• Identified: Quorum sensing
• Model: Morphogen action is the diffusion of chemicals in a genetic network

Side Effects

• {LasR+PAI} inducible promoter
• {LuxR+AI → inhibition} + {LasR+PAI → activation} double controlled oscillatory promoter