IGEM:MIT/2006/Notebook/2006-6-14

06/14/06 Lab

1. Made 2 glycerols of each of 9 liquid cultures (18 total) from 6-13-06 (BAMT,SAMT,BSMT [A,B,C])
   • Added one ml of culture to each 1ml tube of glycerol
2. Made 9 minipreps of the 9 (BAMT,SAMT,BSMT [A,B,C]) (method outlined 6-13-06)
   • note: while centrifuging (after adding N3), the lid of the tube containing the lysed BAMT-A cells fell off and the tub got stuck in the centrifuge. We pulled it out with tweezers and kept going, but if something goes wrong with this sample later, this might be why...
3. Ran experiment to determine if the cells that grew w/ BAMT last night will express the enzyme and produce methyl benzoate.

Control (use LB)	BAMT (use LB w/ KAN)
**	not induced
induced	induced
**	SA, not induced
SA, induced	SA, induced
**	BA, not induced
BA, induced	BA, induced

• split BAMT culture in a 1:10 dilution to make 6 50mL cultures.

To do

1. Start tests of smell systems including controls
   • Dilute back cultures
   • +/- IPTG, +/- benzoic acid/salicylic acid, and BL21DE3 cells only
2. Read up on characterization of scent compounds
   • I've contacted User:Curt about use of GC. -Austin
3. Project summary?
4. I think there is more?!?

Applications Research

Light Sensor

The light sensing device is a combination of four parts, I15008, I15009, I15010, and R0082. The device is on the featured parts page below:

http://parts.mit.edu/registry/index.php/Featured_Parts:Light_Sensor

Also in the registry is M30109, which would make up strictly the light sensing device of the system. However, no physical DNA is listed as being present in this part's entry in the registry. The part description is below:

<bbpart>BBa_M30109</bbpart>

• RS 09:09, 14 June 2006 (EDT): Natalie got this part synthesized by DNA2.0. It probably hasn't been submitted to the registry yet. She'd likely be happy to give it to us. Note that I think this part has an additional inverter in it. It is not clear if this inverter works.

Heat Sensor

There are two kinds of heat-sensitive promoters that are well described in openwetware: cold shock and heat shock promoters. Here is a description of some of them characterized by the UCSF team last year:

"Only four promoters (barely) survived the screen. By far, the best promoter is hybB, which controlls the hydrogenase II operon. It is clearly active at temperatures lower than 30oC and is off at temperatures higher than 30oC. Two other cold-shock promoters also showed a T-dependent response: ansB and cspA_x. AnsB controls an asparginase operon. CspA is part of the classical cold shock response. It's mRNA has a toxic leader, which is also supposed to participate in adaptation. We removed this sequence, which we denote with an 'x.' Finally, we have had mixed success with the heat-shock htpG promoter, which is part of the classical heat-shock response. It is known to produce a pulse first, but it is unique in that it (in the literature) comes to a T-dependent steady-state."

Although I did not find which parts they are in the registry, I am fairly certain that the parts are in the registry. This device would probably be the easiest to get working since the each device (cold sensor and hot sensor) merely consist of one part, a promoter.

• Austin 10:20, 14 June 2006 (EDT): As of the end of Fall 2005, these parts were not in the registry (the Harvard MCB100 class wanted to use them). I asked Chris Voigt and he seemed to indicate they wouldn't be put in and we should synthesize them (they are really short anyway).

Quorum Sensor

F1610 coupled with F2621 or F2622 can act as a quorum-sensing device. I do not believe that this is the easiest way to develop the quorum sensing system, but it is well-characterized. I thought that there were quorum promoters which would make the construction of such a system easier, but I am not sure.