Team:Cambridge/Notebook/Week1

Decided to concentrate on a pigment output. Wednesday plans involve discussing ideas for pigments, following the same meeting pattern used on Tuesday. Ideally the pigment output would be a new registry part which could then be connected to any input system

Wednesday 14 July

Investigated possible outputs, with a kind of bacterial printer in mind.

Colour Wheels

Primary school style: BLUE, YELLOW, RED
True colour wheel: YELLOW, CYAN, MAGENTA
Autochrome: ORANGE, GREEN, VIOLET

Viable Pigments

In an ideal system, we would have lots of pathways making different coloured pigments from a common precursor. One can dream...

Carotenoids - RED, ORANGE, YELLOW
- Biobricks exist for part of the system
- apparently you can go from yellow to white (cool)

Pseudomons aeruginosa - RED, GREENISH/BLUE
- Pyocyanin is greenish/blue, can be synthesized from chorismic acid, or more simply, from phenazine-1-carboxylic acid (PCA)
- Knocking out one of the genes between PCA and pyocyanin leads to the production of a red pigment

Chromobacterium violacein - VIOLET, CYAN
- Violacein is a violet pigment
- A precursor is cyan.

BROWN
- melanin - easily attainable
- anyway we could make black?

Follow ups for tomorrow

Possible inputs
Population control
bacterial chlorophyll?

Thursday 15 July

Hoping to start wet work on Monday!

Pigments

Duncan has orange and brown bacteria we can start to work with. The melanin gene has been sequenced, has a restriction site we would need to remove to submit it to the registry.
We have the genes for violacein! However there seem to be several internal restriction sites within the plasmid that would need to be removed, with three being within the violacein operon.
Contacted the authors of a paper to get the genes for pyocyanin biosynthesis. Two of them have forbidden restriciton sites, so we'll need to figure out how to remove them.

Inputs

explored the idea of using common repressor / inducer systems - arabinose, lac repressor, and tet repressor - to control pigment production
scourged the registry for lots of different inducible promoters

Population Control

Crispian proposed a growth control dependency pathway that would make the growth of each type of bacterium (red colour-producing, blue colour-producing, yellow colour-producing, for example) dependent on one other using HSLs

Friday 16 July

found where to get PCA, pyocyanin precursor
did an inventory of supplies
familiarized ourselves with protocols and planned for next week's wet work
Thinking about a team logo

Current plans for the wet work involve starting transformation of the bacteria in order to view the pigment colours and intensities. For this we will need to create competant cells and then use Duncan's plasmids to transform the violet and brown and the biobrick registary parts to transform the red and orange.

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-<h1>title</h1>
+== Monday 12 July ==
-text
+Each team member researched their own ideas for our project
+== Tuesday 13 July ===
+Afternoon presentations - possible projects included
+*Bacto-Stat
+*Counterfeit Bill Detector
+*Traffic light-obedient bacteria
+*Light-induced pigment production
+*Predator prey bacteria + a parasite
+*Modelling pesticide resistance
+*Galvanotaxis
+*Wave-pulse bacteria
+*Ai2 quorum sensing system
+'''Conclusions'''
+Decided to concentrate on a pigment output. Wednesday plans involve discussing ideas for pigments, following the same meeting pattern used on Tuesday. Ideally the  pigment output would be a new registry part which could then be connected to any input system
+== Wednesday 14 July ==
+Investigated possible outputs, with a kind of bacterial printer in mind.
+'''Colour Wheels'''
+*Primary school style: BLUE, YELLOW, RED
+*True colour wheel: YELLOW, CYAN, MAGENTA
+*Autochrome: ORANGE, GREEN, VIOLET
+'''Viable Pigments'''
+*In an ideal system, we would have lots of pathways making different coloured pigments from a common precursor.  One can dream...
+*Carotenoids - RED, ORANGE, YELLOW
+**Biobricks exist for part of the system
+**apparently you can go from yellow to white (cool)
+*''Pseudomons aeruginosa'' - RED, GREENISH/BLUE
+**Pyocyanin is greenish/blue, can be synthesized from chorismic acid, or more simply, from phenazine-1-carboxylic acid (PCA)
+**Knocking out one of the genes between PCA and pyocyanin leads to the production of a red pigment
+*''Chromobacterium violacein ''- VIOLET, CYAN
+**Violacein is a violet pigment
+**A precursor is cyan.
+*BROWN
+**melanin - easily attainable
+**anyway we could make black?
+'''Follow ups for tomorrow'''
+*Possible inputs
+*Population control
+*bacterial chlorophyll?
+== Thursday 15 July ==
+Hoping to start wet work on Monday!
+'''Pigments'''
+*Duncan has orange and brown bacteria we can start to work with.  The melanin gene has been sequenced, has a restriction site we would need to remove to submit it to the registry.
+*We have the genes for violacein! However there seem to be several internal restriction sites within the plasmid that would need to be removed, with three being within the violacein operon.
+*Contacted the authors of a paper to get the genes for pyocyanin biosynthesis.  Two of them have forbidden restriciton sites, so we'll need to figure out how to remove them.
+'''Inputs'''
+*explored the idea of using common repressor / inducer systems - arabinose, lac repressor, and tet repressor - to control pigment production
+*scourged the registry for lots of different inducible promoters
+'''Population Control'''
+*Crispian proposed a growth control dependency pathway that would make the growth of each type of bacterium (red colour-producing, blue colour-producing, yellow colour-producing, for example) dependent on one other using HSLs
+== Friday 16 July ==
+*found where to get PCA, pyocyanin precursor
+*did an inventory of supplies
+*familiarized ourselves with protocols and planned for next week's wet work
+*Thinking about a team logo
+Current plans for the wet work involve starting transformation of the bacteria in order to view the pigment colours and intensities. For this we will need to create competant cells and then use Duncan's plasmids to transform the violet and brown and the biobrick registary parts to transform the red and orange.
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