Difference between revisions of "Team:Toulouse/Design"

TrApiColi has been designed in order to take into account ethical reflection, safety and ease of use for beekeepers. The use of genetically modified organisms in a field, and because our project is associated with edible products, underlies both applying of regulations and public interest. In this context, as explain above, we searched a solution being able to isolate our engineered bacteria from the environment, but allowing its growth, metabolism and gas diffusion. We found the project of the iGEM Groeningen 2012 team which used the polymer TPX® in order to contain their bacteria separated of the meat [1]. Thus, we decided to ask them TPX® characteristics. We finally contacted the TPX® supplier Mitsui Chemicals. We obtained some samples of TPX® by contacting the company MitsuiChemicals. TPX®, Polymethylpentene (4-methylpentene-1 based polyolefin, Mitsui Chemicals, Inc.), is a polymer.

To check if our device can be safe and feasible, several tests have been performed:

The second step was to know if bacteria can grow inside a small bag of TPX®. Thus, the strain E. coli BW 25113 has been inoculated in a small bag and disposed inside a biological sample tube which has been incubate at 37 °C. The monitoring of OD at 600 nm has been performed over 10 days.

Figure 1: Growth test of E. coli BW 25113 inside a small bag of TPX® (Tubes n°1 and n°2).
Both tubes contain a small bag of TPX® in which bacteria are growing (t = 17 hours, 37 °C).

Figure 2: Growth test of E. coli BW 25113 in a culture tube (Tube 3).
The culture tube, contains bacteria which are growing (t = 17 hours, 37 °C, 130 rpm) in parallel of biological sample tubes shown above. It represents the control: E. coli BW 25113 are growing under aerobic condition with agitation.

The graph below shows the monitoring of OD at 600 nm. The strain E. coli BW 25113 is growing over 10 days (Tube n°1') in the TPX® bag .

Figure 3: Growth test in TPX® bag by monitoring OD at 600 nm over 7 days (tubes n°1 and 2) over 10 days (tube n°1').

The picture below represents the strain of E. coli BW25113 that grow, previously identified as Tubes n°1', n°1, n°2 and n°3 after 10 days of culture for tube 1' and 7 days for tubes 1, 2 and 3.

Figure 4: Colonies of E. coli BW 25113 on Petri dishes after an overnight incubation at 37°C.

Bacteria are still alive after 10 days or 7 days depending on the tube while growing in TPX® bags. In all the culture tubes, the number of cells is about 4.10⁶. Thus, the strain can survive over 10 days in the TPX® bag.

In order to know if our test that we described in “Protocol” test functions, we made a control with acids solutions in a Falcon and we sample gas in balance.

For butyric acid we did not detect gas butyric acid by NMR, the solution we used to solubilize gas should be not basic enough. So we made a test with a TPX® bag containing butyric acid into a solution of sodium bicarbonate. As a control we sampled directly a solution of 4% (V/V) of butyric acid.

Figure 1: NMR Spectrum of butyric acid liquid control in red and butyric acid liquid which passed through TPX bag in blue. ^* Blue curve is zoomed 1340 times more than red curve. Each condition was tested in two replicates.

Table 1: Concentrations of butyric acid corresponding to NMR spectrum

Thanks to these results, TPX® allows butyric acid to pass outside the bag. We detect only a small quantity but an optimization of test could be made or a plastic with bigger porous could be use.

For formic acid we were able to detect it in gas, probably because its pka is lower than butyric acid.

Figure 2: NMR spectrum of formic acid gas control in red and formic acid gas which passed through TPX bag in blue. At the left top internal standard shows that it is the same scale for both curves. Each condition was tested in two replicates.

Table 2: Concentrations of formic acid corresponding to NMR spectrum

According to these results, TPX® allows 56% of formic acid to pass outside the bag in gas phase. We show that formic acid can go through TPX plastic. And with a better test, as we proposed above this percentage could increase.

Based on the protocol specified in here, the bacteria’s impermeability of TPX®, has been tested inoculating the strain E. coli BW 25113 in M9 defined medium. To summarize, the strain (in M9 medium) has been inoculated inside the small bag of TPX®. Then, the inoculated bag has been immersed in a glass measuring cylinder containing M9 medium. The OD600 nm monitoring of the external medium has been performed.

Figure 1: Measuring cylinders used for the safety test of the TPX® polymer.
The first cylinder, on the right contains the small TPX® bag with E. coli BW 25113 after 27 hours of growth at 37 °C. On the right, the negative control cylinder contains a small bag of TPX® without bacteria and immersed in M9 medium after 27 hours of growth at 37 °C.

Over this time, no bacteria went out of the bag, so the sterility has been conserved over 27 hours.

In the end, our objective is to have a bag which contains bacteria to produce alternately butyric acid and formic acid during at least ten days in order to be practical for beekeeper.
So we faced with some biological questions as:

In order to know better the E.coli strain we would use for our project, we made a culture in aerobic and micro-aerobic conditions. We sampled OD and supernatant as it is explained here to see what happen in it.

Micro-aerobic condition is obtained thanks to cultivation in specific falcons with holes recovered by a membrane into the plug which let pass oxygen without opening the falcon. They were incubated at 37 °C without agitation to best correspond to our real condition.

For the medium, we use a minimal medium M9 because we want to follow acids production by NMR. And we choose a standard glucose concentration, 15mM.

In order to plot biomass concentration it is necessary to convert the OD measured.
This equation was used:

$$ X=OD_{600nm}\times 0,4325 $$

For substrate and products concentration we plotted peak area of each molecule on NMR spectrum.
Then, we calculated concentration with this equation:

$$[A]=\frac{Area_{molecule}}{Area_TSP} \times [TSP] \times \frac{\textrm{TSP proton number}}{\textrm{A proton number}} \times DF $$

Glucose is consumed approximately at the same rate for both conditions but it is not use for the same thing at all. In aerobic condition biomass reaches 3 g/L whereas in micro-aerobic condition there is six times less biomass. Inversely, there are far less products in aerobic conditions, and bacteria consume them when there is not glucose anymore, than in micro-aerobic condition.

For our objective to produce acids in a microporous bag, it is a really interesting results to have naturally bacteria which have slow growth and fermentation products.

We can convert formate concentration into formic acid to know how much more we will have to produce to kill varroa. Indeed, the bacteria produce a base but it is the acid that interests us.
The formula below is used:

$$ pH=pKa+log \left(\frac{C_{b}}{C_{a}} \right) $$

As it is said in the “Eradicate” part, our goal is to produce 50 µM of formic acid to kill varroa, thanks to the equation (3) we know it corresponds to 77,7 mM of formate.

At the maximum the bacteria produces 32mmol/L of formate. It is necessary to add genes involved in formate production to regulate production and multiply it by 2.4. For a perfect regulation it would be necessary to delete pfl-B in E.coli genome not to have formate production during the day.

As it is explained here we plated bacteria on Petri dish to know if they were alive or not because OD measure cannot discriminate alive bacteria from dead. This test show us that wild type bacteria can easily survive during at least 15 days. So if we bring them a carbon source during this period they should survive even better.

Figure 3: Bacteria survival results from culture test with BW25113 on M9 with 15mM of glucose during 15 days to mime real survival condition.

En Presso B is a technology which permits to produce a lot of recombinant proteins thanks to a low substrate delivering during 24 hours. This technology is based on polymer degradation by an enzyme which permits to have the right quantity of substrate at each moment. We would like to use this technology to cultivate our cells during one or two weeks in good conditions in order to produce butyrate and formate. The medium with the polymer is solid and contained in separate bags. To know which quantity of butyrate and formate we can produce, we have to know the quantity of substrate we could obtain with the polymer so we made a kinetic test with a high enzyme concentration (50 U/L).

Figure 4: Kinetic test of enzyme which degrades polymer from Biosilta kit. [Enzyme] = 50 U/L in order to have a complete degradation of polymer.

$$ v_{glucose1}=\frac{[glucose]}{time}=\frac{11.1}{3.97}=2.80 g.L^{-1}.h^{-1} , for [E]_{1}=50 U.L^{-1} (4) $$

$$ v_{glucose2}=\frac{13}{13 days}=\frac{13}{322 hours}=0.0403 g.L^{-1}.h^{-1} (5) $$

$$ RF=\frac{v_{glucose1}}{v_{glucose2}}=\frac{2.8}{0.0403}=69.44 (6)$$

$$ [E]_{2}=\frac{[E]_{1}}{RF}=\frac{50}{69.44}=0.72 U.L^{-1} (7)$$

As we do not know any growth characteristic with Biosilta medium we tested different enzyme concentrations and not only the one which allow growth during 13 days. We made acquisition in two times because of software constraints, this is why there is a break at 5 days:

Except for 1.5 U/L enzyme, OD increase during 12 days so glucose releasing seems to function well. At the beginning there is exponential growth because some glucose is directly available on medium. Since 2 days until the end growth is linear, only the slope change. It is higher between 2 and 4 days than after probably because bacteria were in worse condition after few days so they are not able anymore to consume all glucose available.

Thanks to those results we know it is possible to have continuous growth during at least 12 days. The only problem is that our control, without enzyme, grows also so either another substrate is available or bacteria could able to degrade polymer that could be a problem.

In order to answer these questions we did culture in falcon in order to analyze products and to see evolution of polymer quantity. We made culture without enzyme and we test concentration of enzyme of 0.72 U/L because it this one which allows to reach the highest OD in figure 5 and it is the one we calculated above to have glucose releasing during 13 days.

Figure 6 shows that polymer is not degraded, so it is only enzyme of Biosilta kit which releases glucose. Enzyme concentration could be correlate to glucose rate releasing for further modelling. So bacteria find another carbon source in Biosilta medium but we were not able to determine which one. Products concentrations are nearly identical to those in M9 medium.

In figure 7, polymer area decreases, so enzyme degrades it well. At the beginning, glucose concentration is almost constant so bacteria consumed it directly when enzyme releases it. At the end glucose concentration increases a bit, bacteria either did not consume it as fast as the beginning or they consumed formate because its concentration decreases. This could be a problem for us because we look for produce more formate so we would have to think about it.

Fermentation products have high concentrations in comparison to culture in M9 with 15mM of glucose, around 20 times more for lactate, 3 times more for acetate and 2 times more for ethanol. So if we delete production ways for lactate, acetate and ethanol and degradation way of formate we would able to produce enough formate and butyrate.

With the rate of glucose calculated above, an FBA and FVA simulation were launched as explained in “Modelling” part. Some conversion between the model and the real condition are necessary and they are explain in “Modelling” part.

In order to model production in the most similar conditions to fit real experiment we chose a glucose rate of 0.0403 g.L-1.h-1 that correspond to 0.72 U/L of enzyme.

To convert formate production into formic acid concentration we use equation (3).

Our goal is to produce at least 50µmol/L and with this graph the maximum production could be 6µmol/L. So we have to produce nearly 10 times more formic acid. In order to reach our goal we could see which rate of glucose we needed with a reverse thought.

To produce 50 µmol/L of formic acid different strategies are available. Either a low growth rate is chosen so a low glucose rate would be necessary or a high growth rate is chosen and a high glucose rate would be necessary. As bacteria have to live during at least ten days it will be better to have a continuous slow growth rate. Moreover, it will consume less glucose per hour so we would need a lower polymer concentration in our bag at the beginning. So, we chose a growth rate of 0.2h-1, and we can determine rate of glucose needed.

[Formic acid] (μmol.L^-1 )=166.88 ×[Glucose] (g.L^-1.h^-1 ) (9) $$ [Glucose] = \frac{50}{166.88}=0.3 g.L^{-1}.h^{-1} (10) $$

According to modelling results in figure 10, we would be able to produce around 100µmol/L of butyric acid that correspond to 0.0092% (V/V). As we explained in “Results” part, "attract" section, our objective is to produce at least 0.00001%, so with modelling we reach it.

Nevertheless, in order to have this right glucose rate it is necessary to calculate how much polymer is needed at the beginning and which enzyme concentration.

With the same equations as we used in “Characteristics of Biosilta kit” we can determine which quantity of glucose is needed in total during a fortnight.

$$[Glucose]=v_{glucose}\times time=0.3\times 322=96.6 g.L^{-1} (11)$$

Knowing that one Biosilta kit contains the equivalence of 13 g/L of glucose, we have to concentrate the medium 7 times. Concerning the glucose rate, the 0.3 g.L-1.h-1 value correspond to 5 U/L of enzyme. Thus, we tested different concentrations of Biosilta medium with different enzyme concentrations.

As we do not know the exact composition of Biosilta medium, we are not able to say if there is a molecule which could be toxic at high concentrations. We could only have a global analysis on our results :

There is hardly any growth during three first days, bacteria probably adapt themselves to the medium. Since 3 days until the end, OD increases up to 1 for 1.5 U/L enzyme but it is still slow. Moreover, bacteria grow better with 0.72 and 1.5 U/L than with 3 or 4 U/L. It could be explained by an excess of glucose that inhibits bacteria growth. Indeed, enzyme could release too much glucose that bacteria would not consume as fast, then glucose accumulated itself in medium. We tested with a less concentrated medium in order to see if latency period could be reduce.

With a 4 times concentrated medium, there is no latency period anymore but enzyme concentration seem not to affect bacteria growth. Bacteria probably consume all free glucose in medium and then enzyme does not have enough time to degrade polymer. A longer period test would be necessary to know if bacteria were able to consume glucose as fast as enzyme released it. Maybe by testing a twice concentrated medium, we would be able to answer it.

Decline of curve for 0.72U/L was not expected because in “normal” Biosilta medium, figure 5, bacteria grew during 12 days. We cannot explain this result, but it shows that it is complicated to work with a medium with an unknown composition.

Curves for 3 and 4 U/L enzyme or very similar so it seems that bacteria are not able to consume all glucose released by enzyme. As we only measured OD we do not know if bacteria would assimilate glucose for another way that growth metabolism.

Thanks to figure 11, 12 and 13 we know that it would not be possible to have enough polymer in our medium. As a solution we think to use a dialysis system: in one side there will be bacteria and in the other side there will be the polymer with enzyme. Membrane which separates them will allow only small molecules to pass like glucose. Thanks to this system our device will have enough substrate for two weeks.

Regarding the rate of glucose assimilation we could do additional tests where we would measure glucose in medium to determine maximum rate of assimilation. An optimization of this assimilation could be essential.

In order to optimize resistance of BW25113 to different acids concentrations we tested two medium: LB and M9 with 15mM of glucose.

In M9 medium, growth is slower at the beginning in both figures but OD max is almost the same for both medium.

For formic acid, the only significant difference is for 10mM with a slower growth in LB than in M9. For butyric acid the difference is stronger because in LB bacteria do not grow anymore with 109mM whereas in M9 there is growth.

In fact, M9 is buffered and not LB so we measured pH in both medium with different acids concentrations in order to see if there were a correlation.

It is clear that in M9 medium pH stay at pH 7 for higher acids concentrations than LB medium. Moreover, thanks to previous figures, it is possible to see that bacteria do not grow anymore when pH is around 5. This results show that bacteria are sensitive to acid pH, but they may resist to higher acids concentrations if the medium was better buffered. We will now see if it would be interesting or not to buffer better our medium.

Figure 17 shows a dose/response relationship between formic acid concentration and bacteria growth. We would like to produce at least 50µmol/L of formic acid in order to kill varroas and bacteria growth normally up to 1mM. So we should not have toxicity problem during the treatment.

The higher is butyric concentration, the less is bacteria growth, as our previous results with formic acid. However we have an intermediate result with 109mM of butyric acid. We do not have a specific butyric acid concentration to produce and modelling show us that we could produce around 15mM with all optimizations so we would not have any butyric acid toxicity during our treatment.

Nota Bene: For our conclusions about acids toxicity, we consider that acids evaporate during day for formic acid and night for butyric acid, so there would not be a lot of acid accumulation.