Stanford/BIOE44:Module 4:Day1: Difference between revisions
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''' M4: Day 1 - "Baking is a Busy Time" ''' | |||
=Introduction= | |||
=Team Moss= | |||
[[Image:Moss5.jpg|300px|thumb|right|Moss]] | [[Image:Moss5.jpg|300px|thumb|right|Moss]] | ||
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</biblio> | </biblio> | ||
=Team Arsenic= | |||
==Using the Same Language== | |||
Please review common symbols for representing your device. | Please review common symbols for representing your device. | ||
http://openwetware.org/wiki/Endy:Notebook/Synthetic_Biology_Open_Language | 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. | Please enter what you have and indicate the state which it is in. | ||
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|} | |} | ||
==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. | 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. | ||
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[[Image:Imaginary_Curve1.jpg|thumb|center]] | [[Image:Imaginary_Curve1.jpg|thumb|center]] | ||
==Deconstructing our Device== | |||
What do we need? Should we shuffle anything? | What do we need? Should we shuffle anything? | ||
[[Image:Deconstruction2.jpg]] | [[Image:Deconstruction2.jpg]] | ||
==Design and Baking== | |||
Revision as of 09:25, 6 May 2010
M4: Day 1 - "Baking is a Busy Time"
Introduction
Team Moss
We will learn how to work with Phycomitrella patens. We have 3 main goals:
- Learn how to culture the moss.
- Figure out how to transform it.
- Make freezer stocks for all the future BIOE44 students.
None of us has ever worked with moss before so we will all be figuring it out together. Here are some resources we can start from:
References
- Hohe A, Egener T, Lucht JM, Holtorf H, Reinhard C, Schween G, and Reski R. An improved and highly standardised transformation procedure allows efficient production of single and multiple targeted gene-knockouts in a moss, Physcomitrella patens. Curr Genet. 2004 Jan;44(6):339-47. DOI:10.1007/s00294-003-0458-4 |
- Horstmann V, Huether CM, Jost W, Reski R, and Decker EL. Quantitative promoter analysis in Physcomitrella patens: a set of plant vectors activating gene expression within three orders of magnitude. BMC Biotechnol. 2004 Jul 7;4:13. DOI:10.1186/1472-6750-4-13 |
Team 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.
- copy number
- ribosome binding site
- ratio of ArsR transcription factor to the operator site
- one plasmid or multiple plasmids
- 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?
