Stanford/BIOE44:Module 4:Day1

M4: Day 1 - Baking

Moss

We will learn how to work with Phycomitrella patens. We have 3 main goals:

1. Learn how to culture the moss.
2. Figure out how to transform it.
3. Make freezer stocks for all the future BIOE44 students.

Moss Protocols

Arsenic

Using the Same Language

Please review common symbols for representing your device. http://openwetware.org/wiki/Endy:Notebook/Synthetic_Biology_Open_Language

Current Inventory of Parts

Please enter what you have and indicate the state which it is in.

Part	status	volume	notes	contributor
O/P for ars operon	cPCR, PCR Cleanup, Digested@EcoR:SpeI, Gel Extract	6ul	~200ng/ul	Koshlan
RBS + arsR ORF	cPCR, PCR Cleanup, Digested@XbaI:PstI, Gel Extracted	6ul	~80mg/ul (extra codon flanking ATG)	Koshlan
O/P + RBS + arsR (Combined like the edinburgh part)	cPCR, PCR Cleanup, Digested@EcoR:SpeI, PCR Cleanup	20ul	~40ng/ul questionable quality since no gel extract	Koshlan

Refining our Goals

We need to think about the fundamental relationship between the amount of pollution in our sample and the reporter strength. What will this relationship look like? How can we alter it? Consider the effect of the following.

1. copy number
2. ribosome binding site
3. ratio of ArsR transcription factor to the operator site
4. one plasmid or multiple plasmids
5. what else?

What are our options.

Here are some imaginary curves to stimulate your thinking.

Deconstructing our Device

What do we need? Should we shuffle anything?

Design and Baking