# Team:Buenos Aires/Results/BBsTesting

(Difference between revisions)
 Revision as of 17:48, 26 October 2012 (view source)Vparasco (Talk | contribs)m (→Secretion Rate of Trp as a function of culture growth)← Older edit Revision as of 18:15, 26 October 2012 (view source)Vparasco (Talk | contribs) m (→Experimental determination of K death)Newer edit → Line 95: Line 95: === Strain characterization === === Strain characterization === - ==== Experimental determination of K death ==== + ==== Experimental determination of strains' death rate==== - In order to determinate the K death used in the modeling section of our wiki, we set cultures of the two auxotrophic strains without being transformed (TCY3081 and TCY3128) in medium –HT at an initial OD of 0.01. + We set out to determine how long can auxotrophic cells[link] survive in media that lacks both TRP and HIS. These values are the'''death''' parameters for strains CFP_HIS and YFP_TRP used in our model[link]. They 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 ''the feasability of our system''. + + , we set cultures of the two auxotrophic strains without being transformed (TCY3081 and TCY3128) in medium –HT at an initial OD of 0.01. Taking into account that an OD:1 is approximately 3.10 7 cells/ml, we plated 133 µl in order to have around 200 colonies in the first day. Each following 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. Taking into account that an OD:1 is approximately 3.10 7 cells/ml, we plated 133 µl in order to have around 200 colonies in the first day. Each following 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.

# 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

Plasmids

 YFP_TRP+++_TRPZipper details YFP_TRP+_TRPZipper details YFP_TRP+++_PoliWb details YFP_TRP+_PoliWb details CFP_HIS+_PoliHa details CFP_HIS+_PoliHb details

## Week 3: synthetic Ecology Characterization

xxoo

### BB characterization

xxoo

#### 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_TRP+++_TRPZipper
• YFP_TRP+++_PolyWb
• YFP_TRP+++
• YFP_TRP+_TRPZipper
• YFP_TRP+_PolyWb
• YFP_TRP+
• YFP

Protocol

• 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
```

#### Trp Secretion at different His concentrations in medium and His secretion at different Trp concentrations in medium

We started cultures in -T of the following strains:

i. strain TCY3081+pCM185 containing device2 ii. strain TCY3081+pCM185 containing device4 iii. strain TCY3081+pCM185 (empty plasmid)

We measured the OD of the cultures after 12 hs. We prepared cultures with increasing concentrations of His in medium (1X, 1/4; 1/8; 0X)and set cultures at initial OD: 0.1. After 5 hours we measured the final OD and Trp in medium.

### 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 TRP and HIS. These values are thedeath parameters for strains CFP_HIS and YFP_TRP used in our model[link]. They 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 the feasability of our system.

```, we set cultures of the two auxotrophic strains without being transformed (TCY3081 and TCY3128) in medium –HT at an initial OD of 0.01.
```

Taking into account that an OD:1 is approximately 3.10 7 cells/ml, we plated 133 µl in order to have around 200 colonies in the first day. Each following 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
TCY 3128 1 260 320 285
TCY 3128 2 267 314 76
TCY 3128 3 413 362 278
TCY 3081 1 230 316 688
TCY 3081 2 291 194 524
TCY 3081 3 449 344 725

Table: Number of colonies counted per plate.

We observed that the size of the colonies was smaller everyday, as can be seen in the following pictures:

FOTOS DROPBOX

#### Growth rate in function of the concentration of Trp and His

ESTO NO DEBE SER UNA SECCION DE ACA, SINO DE STRAIN CHARACTERIZATION, COMO UNA CONTINUACIÒN DEL EXPERIMENTO DE ALAN

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 TCY3081 (non transformed)in each Trp concentration (dilutions 1/32; 1/16; 1/8; 1/4; 1/2; 1x)

Series 2: strain TCY3128 (non transformed)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.

RESULTADOS:

ANALISIS DE VERO

### Co-Culture of strains

We proceeded then to test the coculture growth of transformed strains with devices vs transformed strains with empty devices and non transformed strains.

Table: Coculture planification. Number indicates level of priority of the experiment for characterization of devices. Due to a time constrain, we ordered the experiments by level of priority and proceeded to test our devices by cocultures 1 and 2.

Starters of each strain were done in medium complementary to the auxotrophy of the strain so that they would maintain their plamids (medium –H for pEG202; medium –T for pCM182/5 and medium SC for cells without plasmid), then sonicated briefly in low power and then washed with medium –H-T . When they are in exponential phase, we set the coculture of strains was at OD 600: 0.02 (Total, 1:1), in 5 ml of medium –H-T.

We used epifluorescence microscope in order to determinate the strain proportion of each coculture. We used a 384 wells plate , with 20 µl of cyclohexamide 2x (CHX 2x) in each of the wells where we placed a sample. 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.