Team:Buenos Aires/Results/BBsTesting


Revision as of 22:29, 26 October 2012 by Manugimenez (Talk | contribs)


After the Jamboree!

When we returned from the Latin America Jamboree we focused all our efforts on completing the neccesary transformations to test our devices and our projet as a whole.

We devided this task in three sections

Week 1&2 : Yeast expression vectors & Transformations


YFP_TRPb_TRPZipper2 details


YFP_TRPa_TRPZipper2 details


YFP_TRPb_PoliWb details


YFP_TRPa_PoliWb details


CFP_HIS_PoliHa details


CFP_HIS_PoliHb details


Week 3: Synthetic Ecology Characterization


BB characterization


Secretion Rate of Trp as a function of culture growth

The first step was to actually check if the construct works: do the transformed yeast strains - with the TRP BB - actually secrete TRP into the medium?

To test this we used the following strains:

  • YFP_TRPb_TRPZipper2
  • YFP_TRPb_PolyWb
  • YFP_TRPb
  • YFP_TRPa_TRPZipper2
  • YFP_TRPa_PolyWb
  • YFP_TRPa
  • YFP


  • We started 5ml cultures with 3 replica until they reached exponential phase, overnight, using a -T medium.
  • Starting OD for the assay 0.1 (exponential phase).
  • We measured OD every hour until they reached an OD: 0.8 (5 hs approximately).
  • We measured the Trp signal for each culture medium using the spectrofluorometer.

We used a simple model to measure the export rate for all the strains. Since the cultures are in exponential phase, we take


After a few calculations, we find that


Next we show the average temporal evolution for each strains used,


Figure X. check


Tryptophan secretion at increasing histidine concentrations

We asked ourselves which was the dependance of tryptophan secretion on the amount of histidine in medium. We carried on this test in order to determine if wether the secretion of tryptophan depends of the concentretation of another amino acid in media, such as histidine, or not. ¿the necessary amount of histidine in medium for the start of our system?


  1. We started cultures of strains YFP transformed with the tryptophan devices (YFP_TRPa_TRPZipper2 and YFP_TRPb_TRPZipper2) and with an empty plasmid(YFP_TRPa) as a control, in -T media.
  2. After 12 hs, we replaced the medium in each tube for one with increasing concentrations of histidine (0X, 1X, 1/4 and 1/8). We afterwards set cultures at an initial OD: 0.1.
  3. We left the cultures in shaker at 30ºC for 5 hours. After that time, we measured the final OD reached by cultures with the use of a spectrophotometer and the amount of tryptophan present in medium with a spectrofluorometer.

Strain characterization

Experimental determination of strains death rate

We set out to determine how long can auxotrophic cells[link] survive in media that lacks both Trytophan and Histidine. These values are the death parameters for CFP and YFP strains used in our model[link]. These were taken as equal in the mathematical analysis for simplicity, we'll test whether this approximation is accurate.

Given that our system most likely will present a lag phase until a certain amount of both AmioAcids is accumulated in the media, will the cells be viable until this occurs? This is a neccesary check of our system's feasability.


  • We set cultures of the two auxotrophic strains without being transformed (YFP and CFP) in medium –HT at an initial OD of 0.01.
  • Each day we plated the same amount of µl of the culture and counted the number of colonies obtain in each plate. We set 3 replica of each strain.
Strain Replica Monday Tuesday Wednesday
CFP 1 260 320 285
CFP 2 267 314 76
CFP 3 413 362 278
YFP 1 230 316 688
YFP 2 291 194 524
YFP 3 449 344 725

Table: Number of colonies counted per plate.

We expect to see a decrease in the number of colonies - because of cell death. We found that this was not the case, in the experiment's time lapse. However we observed that the size of the colonies was smaller everyday. We can infer from this data that though they have not died, they may have enter into a ...Alan state.

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Growth rate in function of the concentration of Trp and His

We aimed to test the growth of the strains in different concentrations of external Trp and His in order to determine the amount of aminoacid at which the culture reaches half of the maximum growth (parameter K in the modeling of our system).

We therefore made a series of cultures with increasing concentrations of Trp (Series 1)and His (Series 2). We set the cultures of the different strains at a low initial OD:0.001 with the following scheme:

Series 1: strain YFP in each Trp concentration (dilutions 1/32; 1/16; 1/8; 1/4; 1/2; 1x)

Series 2: strain CFP in each His concentration (dilutions 1/32; 1/16; 1/8; 1/4; 1/2; 1x)

Controls: As control we started cultures of each strain in complete medium.

Cultures were left overnight (12 hs) and we measured OD reached with the use of spectrophotometer.



Coculture of transformed strains

We did the first experiment to test whether our system works and how two transformed strains grow together.

We designed an assay to do so; following the growth of these strains:

Treatment Strain A Strain B
1 YFP_TRPb_TRPZipper2 CFP_HIS_PolyHa
3 YFP_TRPb_TRPZipper2
5 CFP_HIS_PolyHa

Table 1: Transformed cells' coculture and controls. Manu formato!


  1. Starters of strains were grown over night at 30°C, according the following scheme:
Strain Media
YFP_TRPb_TRPZipper2 -T
  1. Cultures were sonicated briefly in low power, and OD was measured in order to check they were in exponential phase.
  2. Cells were centrifugated and then washed with medium –HT.
  3. We set the culture of strains at OD: 0.02 in 5 ml of medium –HT with 3 replica, according to Table 1.
  4. At 0, 1, 2, 3, 4, 5, 6, 7, 8 and 22 hours we took samples of 20 µl.
  5. Samples were placed in a 384 wells plate, with 20 µl of cyclohexamide 2x (final concentration 1x) in each of the wells.

We used epifluorescence microscope in order to determinate the strain proportion of each coculture. The density of the culture was calculated based on the cell density at in each wells.


Graph: 384 wells plate to be used for epifluorescence microscope.


Table: Coculture planification for number 1.


Table: Coculture planification. Color indicates level of priority of the experiment.