Team:Buenos Aires/Results/Strains

From 2012.igem.org

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Revision as of 02:47, 27 September 2012


Contents

Description of strains

Through our experiments we worked with the following strains kindly provided by [http://www.ifibyne.fcen.uba.ar/new/temas-de-investigacion/laboratorio-de-fisiologia-y-biologia-molecular-lfbm/biologia-de-sistemas/dr-alejandro-colman-lerner/ Alejandro Colman-Lerner's] Lab:

Strain ID Relevant Auxotrophies Fluorescence Used as
TCY 3043 (-H-T) No fluorescence Negative control
TCY 3190 (+H-T) YFP + (Induced CFP) For coculture
TCY 3265 (-H+T) CFP For coculture
TCY 3154 (+H+T) CFP +(induced YFP) Positive Control
Bsas2012-strains-figura1.jpg

In the table we can see Hystidine (H) and Tryptophane (T) auxotrophies per strain, type of fluorescence and description of most common utilization during the experiments.

Nearly 15 other similar strains were evaluated and discarded due to several reasons (low screening potentiality; requirement of hormones for fluorescence induction; high reverting rate of auxotrophies, among others)

Fluorescence screening

We measured Strains 3281 (YFP) and 3265 (CFP) and got a spectrum of each one prooving that these strains can be distinguished by their fluorescence in culture.

Reference graph Image: YFP and CFP Emission and Absorption Spectra. Obtained from http://flowcyt.salk.edu/fluo.html

Bsas2012-strains-Refefluro.png


Results

Bsas2012-strains-Yfp.png Bsas2012-strains-grafico2.png
YFP Fluorescence Screening CFP Fluorescence Screening

When measuring YFP Strain 3281, we can see a clear peak around 530 while when measuring CFP Strain 3265, we can see a clear peak around 500, as expected.


Discussion

We were able to measure fluorescence in strains 2181 and 3265 using the espectrofluorometer. However, we considered it would not be precise enough for the purposes of measuring cocultures at different proportions. We also noticed a high background noise produced by dead yeast cells at high concentrations, which would make it possible to measure in this way only at a short range of OD while the culture is at exponential phase.

Screening of strain proportion

A more precise way of measuring the proportion of the strains, is with a epifluorescence microscope.

We mixed strains 3281 (expresses YFP) and 3265 (expresses CFP) in different proportions and analized the images obtained in the microscope, where we counted cells with different fluorescences. We also did a negative control with a non fluorescent strain (TCY 379).

Description of Mixtures

Mix 1: Negative Control

Mix 2: 80% CFP; 20%YFP

Mix 3: 60% CFP; 40%YFP

Mix 4: 50% CFP; 50%YFP

Mix 5: 40% CFP; 60%YFP

Mix 6: 20% CFP; 80%YFP

Results


Montage-annotated.jpg
Mixtures showing YFP and CFP fluorescence.


As shown by images 1-6, cells showing different fluorescences can be count and distinguished from each other in a mixture of strains, and this could be used to measure strains proportion in a coculture.


Counting of cells


Fluorescence Mix 1 Mix 2 Mix 3 Mix 4 Mix 5 Mix 6
YFP 0 23 67 115 135 110
CFP 0* 235 82 107 99 78

The table shows the number of cells counted by expression of fluorescence YFP and CFP in the different mixtures 1-6. I can be observed that the amount of cells is near the proportion stablished by OD measures when preparing the mixtures. This results confirms that epifluorescence measures are reliable and suitable for our research.

Auxotrophy confirmation

Several times during the experiments we control and checked if the auxotrophies in the selected strain were functional by plating all of them in medium deficient in aminoacids (-H; -T; -H-T and control +H+T). We observed differential growth according to expected due to the description of each strain in point a)

Auxotrophies check
Bsas2012-strains-figura3.jpg Bsas2012-strains-figura2.png
Medium complete Medium without H
Bsas2012-strains-figura4.png Bsas2012-strains-figura5.png
Medium without T Medium without H and T

We observed all the strains grew in Plate a and only 3154 (+H+T) grew in Plate c. In plate B, only those strains able to synthesize T grew (3265 and 3154) and in Plate d, only those able to produce H grew (3190 and 3154), as expected. This means our strains work according to their description. We did this several times during the months to check for reversions or contaminations.

Coculture in liquid medium

We used for these experiment TCY3190(H+T-) and TCY3265(H-T+) Positive control: TCY3154 (H+T+) and negative control TCY3043(H-T-)

At different initial OD and proportions

Cultures were set at different initial concentrations (0.25, 0.1 and 0.01) and proportions (1:1; 1:9; 9:1). After 24 hs, we measured OD with the use of a spectrophotometer (two replicas) and we calculated the mean OD and a Growth factor (as Mean OD en time 1 over Initial OD time 0).


Coculture at different initial OD and proportions (Days 0 and 1)
Coculture Proportion (H+T-):(H-T+) Initial OD(t=0) OD1 (t=1) OD2 (t=1) dilution used for measure t=1 Mean OD Growth Factor
01:01 0,25 0,32 0,314 10 3,17 12,68
09:01 0,25 0,148 0,144 10 1,46 5,84
01:09 0,25 0,138 0,189 10 1,635 6,54
01:01 0,1 0,109 0,169 10 1,39 13,9
09:01 0,1 0,04 0,045 10 0,425 4,25
01:09 0,1 0,067 0,053 10 0,6 6
01:01 0,01 0,067 0,061 1 0,064 6,4
09:01 0,01 0,056 0,05 1 0,053 5,3
01:09 0,01 0,074 0,073 1 0,0735 7,35


Bsas2012-strain-Grafale2.png


Bsas2012-strains-Grafale1.png Bsas2012-strains-grafico5.png



As shown in graphs there is a basal growth that does not depend on the initial OD or strain proportion, of a growth factor of 6 approximately. However we observed a much higher growth at the proportion 1:1 when the initial OD 0.25 and 0.1. Therefore we can assume that at these proportions there is a natural cooperation between the strains and that should be the level of growth that we would like to assess through our bioengineering. Besides we would like to be able in the future to tune the strains in order to be able to obtain in the proportions 9:1 and 1:9 similar results to those obtained in the 1:1, at our own will.

At the same initial OD: 0.2, followed over time

We set the same cultures and cocultures as in point i), but starting all of them at the same OD: 0.2 and we followed them over 2 days. At day 1 we took pictures of them and at day 2 we measured the final OD.

Cultures set at initial OD: 0.2 and measured over time (Days 0 and 2)
Strain Day 0 Day 2
TCY 3190 (-H+T) 0,2 2,92
TCY 3265 (+H-T) 0,2 0,19
Coculture of strains (TCY 3190- TCY 3265) 0,2 2,76
Negative control (TCY 3043 / -H-T) 0,2 0,6
Positive Control (TCY 3154/ +H+T) 0,2 2,54


Bsas2012-strains-wednesday.png
Picture: Day 1 after starting cultures, shows different OD reached by strains.

We repeated this experiment 4 times with different modifications: increasing the amount of days for up to a week, measuring every 12 hs instead of every 24 hs and using different strains. However, bacterial contaminations and the high rate of revertants prevented us from getting to a valid results in those cases, whereas the experiment up to day 2 always worked correctly. This denotes that we should assess the problem of contamination (for example including ampicilin in the cultures) and revertant rate (revising the design of the experiment or looking for more stable strains) as the impossibility to go further than day 2 may put limitations to some applications of the Synthetic Community.

Coculture in Agar and Revertant mutation control

Through this experiment we aim to quantify the rate of revertants of each strain.

We used Petri dishes with agar medium with (+) and without (-) Trp and His as shown in the following table.

We started a culture of each strain in synthetic complete medium, measured its OD 24 hs after the culture initiated, replaced the synthetic complete medium for one lacking both H and T (to avoid residual growth) and plated 10 6 cel or 102 cel as shown by the following table (we considered OD600: 1 represents 3.10 7 cells). At the same time, 3 controls (one for each strain) were carried in YPD complete medium to check the viability of each strain separately.

Medium H Medium T Grass (10 6 cel) Seed (102 cel) Description of experiment Results after 3 days - Replica 1 Results after 3 days - Replica 2
(-) (+) (-) Strain –H+T Control of His revertants 7 7
(+) (-) (-) Strain +H-T Control of Trp revertants 2 7
(-) (-) Strain +H-T Strain –H+T Coculture; we expect to see natural cooperation 960 800
(-) (-) Strain –H+T Strain +H-T Coculture; we expect to see natural cooperation 500 712
(-) (-) (-) Strain +H+T Viability of yeasts in medium 171 (-)

Table: Shows description of each plate content and results in number of colonies counted by plate at day 3. YPD control results plates are not shown in the table.

Bsas2012-strains-placas2.jpg Bsas2012-strains-placas1.jpg
Petri Dishes With marks of the counting of colonies


Results

The viability of the strains was high as expected as well as the viability of a control positive strain in the –H-T medium. As shown in Table, we have a very low, but existent, number of revertants from both his and trp auxotrophy strains. This number should be taken into account when seeing results from coculture growth after several days, given that the rate of revertants in liquid medium may as well be of the same numerical order. Growth in coculture was high and near to the number we expected as result of natural cooperation, which confirms that there is a natural way in which the strains cooperate by sharing each other´s missing aminoacids. This is encouraging since we know confirmed that each strain is able to see and relate with each other and therefore we have an open communication way over which to work and control with engineering.

Measurement of Trp in medium and Basal Production

To check the efectiveness of our biobricks, we must first determine the ammount of tryptophan excreted by natural strains to the medium, so we can compare. With that end in mind, we designed a protocol for measurement of tryptophan in medium, based in its fluorescense at 350nm, when excited with 295nm light. As a previous step, we checked that none of the other aminoacids used in the medium interferes, by graphically comparing the spectres for uncomplemented medium and medium complemented with leucine, uracile and histidine, at an appropiate range.

To determine Trp concentration, we must first have a way to transform our readings (intensity) to a more useful output, so we made a calibration curve, through serialized 1:2 dilutions of our medium, which Trp's concentration is 50mg/mL, until approximately constant intensity.

The procedure to measure secretion rates will be growing the strain from a known OD in exponential growth phase in -T medium and plotting it's OD over time, spin-drying at time=t, retrieving the supernatant's Trp concentration and dividing it by the integral of OD vs. time between time=0 and time=t, so we get to a rate which will be proportional to the number of cells in the culture, which means we can actually compare between different strains. Since our medium is free from Trp, all of it should come from within the cells, and if the culture is growing at exponential rates, lysis should be negligible, so the only explanation would be cells exporting their own Trp.


Bsas2012-strains-Trpmario.png
Graph:Tryptophan calibration curve


Results

As can be seen from the graph the screening of the concentration of the Trp in medium describes an almost lineal function. Through this experiment we can be sure that we would be able to measure increase of Trp in medium as it is exported from the cells, within the biological range of export. The sensitivity of this method seems to be enough to detect concentrations as low as ~0.02mg/mL, and as high as 50mg/mL, maybe more. Since our medium is 50mg/mL, we assume that's the saturation point of the curve. If we get bigger intensities than the one corresponding to it, we will dilute the sample.

Because of time constraints, we haven't been able to check the method with either our designed strains nor the non-exporting ones.

Growth dependence on the Trp and His concentrations

A important thing to characterize of the system is the dependence of the growth rate of the culture with the concentration of the crossfeeding aminoacids, tryptophane (Trp) and histidine (His). To do this we measured the final OD after an overnight growth in medium with different concentrations of Trp and His.

We used strain ACL-379, that is auxotroph for both Trp and His. We prepared serial dilutions of SC medium in –T and –H medium, therefore creating two curves: one with decreasing concentrations of Trp and the other with decreasing concentrations of His. We then inoculated equal amounts of ACL-379 in each tube and incubated them overnight at 30°C with agitation. We took a picture of each tube and measured the OD600 reached by each culture.

Growth of ACL-379 as a function of Trp and His concentration
Medium OD Replica 1 OD Replica 2
SC 0,001 (-0,0036)
HLC (-0,003) (-0,019)
S1 HLC (1:10) 0,256 0,217
S2 HLC (1:10) 0,301 0,311
S3 HLC (1:10) 0,154 0,155
S4 HLC 0,393 0,409
S5 HLC 0,013 0,003
TLC (-0,008) (-0,012)
S1 TLC (1:10) 0,368 0,384
S2 TLC (1:10) 0,207 0,2
S3 TLC (1:10) 0,117 0,097
S4 TLC 0,47 0,432
S5 TLC 0,238 0,257
HTLC (1:10) 0,488 0,491

Results

As expected the growth has a sigmoidal relationship with the concentration of Trp and His, when plotted in semilogarithmic scale. We call EC50 the effective concentration of each aminoacid at which the culture reaches 50% of the maximal growth. We considered these values as proxies of the Khis and Ktrp parameters of the mathematical model, which can be used to estimate the secretion rate of each aminoacid needed to get effective crossfeeding.

These results can also be observed by comparison of images that show the tubes at different OD.

Bsas2012-strains-alan1.png Bsas2012-strains-ultima.jpg
Images from HLC series Images from TLC series

Notes: SC: Synthetic complete medium with all the aminoacids. It was used as a blank for the spectrofluorometer.

HTLC is the culture in the medium with all the required aminoacids.

S(Number) are the serial dilutions of HTLC with medium that lacks Histidine (HLC) and Tryptophane (TLC.

HLC and TLC are mediums without cells.