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		+	The digestion mixes were incubated for 1 hr. at 37 degrees and partially loaded onto a 1% agaros gel:

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Revision as of 09:13, 31 August 2010

Software development

By Jelmer

Part of the dry lab work involves developing an application that can suggest possible interactions between the newly introduced proteins, and the existing E. coli proteome. This page will be updated with the application, documentation and results of applying it to our biobricks.

The basic idea is to look for interactions of the proteins within their own organism, and map those interactions by looking at homologs in E. coli:

The resulting list of interactions might be usable to 'debug' the resulting bacteria, i.a.w. suggest reasons why the system is not working like it should. Even though there would be no time to fix those problems, it could still help teams in following years that want to take another stab at solving the problem.

Today the work on this application resulted in the first list of some potentially interacting proteins. A locally running version of the [http://string-db.org STRING protein database] (~150 gb PostgreSQL database) was used to look for interactions and homologs . Ideally however, this application would work using existing biological databases. I'm still looking for the right webservices to accomplish this, they might not exist.

Alkane Degradation

Digestion

The results from sequencing are in! It appears that K398013 is not exactly as we expected it to be. A new method of making 013 (however without the terminator region) will be attempted by ligating 009 and 010 digestion products:

The digestion mixes were incubated for 1 hr. at 37 degrees and partially loaded onto a 1% agaros gel:

#	Sample	Enzyme 1	Enzyme 2	Enzyme 3	Buffer	BSA	Needed fragment
1	009A	SpeI	PstI	None	NEBuffer 2	✓	‘S - J23100-J61100-RubA4-pSB1A2 - P’
2	010A	XbaI	PstI	AseI	NEBuffer 3	✓	‘X - J61100-RubR - P’