Team:Toulouse/Result/experimental-results

Figure 2 : Scheme of the tubes system

As we did previously, we tested this new system with fuchsin. This experiment was made with WT Bacillus subtilis and N-Acetylglucosamine.

NB: We could not see the diffusion from one tube to the other. We made the hypothesis that it was not visible by sight because of by the small diameter of the capillary.

The following strategy was used to avoid disturbance due to pressure and liquid movement through the capillary:
- The first step was the addition of Wash Buffer until the capillary was full to avoid the presence of air bubbles which could lead to diffusion problems.
- Then, the tube 2 was plugged with the thumb while another person was adding the bacteria solution of WT Bacillus subtilis in the tube 1.
- The tube 1 was also plugged and only after the thumb could be removed of the tube 2.
- In the same way, the N-Acetylglucosamine was added in the tube 2.
- The same process was made with a xylose positive control.

NB: According to the article Chemotaxis towards sugars by Bacillus subtilis, (George W. Ordal et al., 1979), glucose and xylose have the same attractant power. We prefer a positive control instead of a negative because we were not sure that this system was efficient.

- The system was kept straight for 2hours. Every 40 minutes, we took a sample of each tube and spread it on an agar plate (dilution 1/1,000).

Figure 3 : Photography of the tubes system

Unfortunately, the dilution was too high to detect any chemotaxis movement and the time was too short. We did not find any information in the literature.
As we did not have the time to optimize this protocol we preferred using the protocol of the Imperial college iGEM team 2011: the tips capillary test.

3. Tips capillary system

First tips capillary system

This protocol comes from Imperial College iGEM team 2011 and was adapted by our team in several steps (See chemotaxis protocol).

First of all, parafilm was used to close the tips:
- 15µL of each chemo-attractant was then pipetted.
- The tips with the pipette were then put on a piece of parafilm and the pipette was removed from the tip.
- The tip was sealed with a piece of parafilm. By this way, the sterility can be assured and the liquid stays inside the tip.
- To finish, the level of the solution in the tip was marked.

Figure 4 : Sealing of a tip with parafilm

- After all the chemo-attractants were added in the tips, we put them on a green base to carry them. The whole process can be seen on Figure 5.
- Each tip was put in 300 µL of a bacteria solution in the wells of an Elisa plate.

Figure 5 : First tips capillary system

NB: the yellow carton was used to stabilize the system and keep it straight.

- After one hour, the tips were removed from the bacteria solutions and the content of the tips was observed with Thoma cell under the microscope.

We had several problems with this system:
- The liquid level decreased during the experiment and we did not have enough liquid to fill the Thoma cell. Thus, it was not possible to count.
- The bacteria were moving and therefore, we could not proceed to a bacteria count.

Regarding these observations we decided to spread the tips content on agar plate instead of using Thoma cell and microscopy.

Second tips capillary system

Figure 6 : Second tips capillary system

Improvement of the second tips capillary system

However this system was not optimal it is why we decided to use blu tack instead of parafilm:

Figure 7 : Improvement of the second tips capillary system

At that point, the protocol was approved and the final test could finally start! :-)

There was just one tiny problem… we did not have our optimized bacterium with the chemotaxis gene… That is why we concentrated our efforts on WT Bacillus subtilis strain.

The main goal was to find an optimized control and to analyze the eventual chemotaxis of the WT strain. To avoid osmolarity bias, we wanted to find a molecule which was non-attractant and with a similar molecular weight than the N-Acetylglucosamine (221.21 g/mol). Our first idea was to use fuchsin (Molecular weight: 337.85 g/mol).

The experiment was conducted with fuchsin as a negative control and was tested with different positive controls: glucose (25mM) and xylose (25mM).

We obtained the following result with NAG at different concentrations: 25mM, 250mM and 500mM. The tested strain was Bacillus subtilis 168:

Figure 8 : Fuchsin - negative control (dilution 1/50)	Figure 9 : NAG (25mM) (dilution 1/50)

The average number of colonies with the negative control is 121. On the contrary, a cell layer is observed for the NAG plates with every concentration.

Thus, we assumed that WT Bacillus subtilis was more attracted by NAG than fuchsin. Indeed we can neglect the bacterial growth because the test only lasts one hour. We also neglect diffusion and osmolality phenomena for the previous reasons.

Unfortunately for us we forgot one major effect… Can you believe that fuchsin solution contains about 15% of ethanol?!!! This concentration can lead to the death of some cells which probably happened to our results.

This incredible discovery destroyed all of our hopes about the God of chemotaxis! :-(

However, our team did not give up on synthetic biology and on our strength! Indeed, after days of disappointment and no time left for lab work, we raised from ashes and tried to find another negative control.

We finally used galactose (25mM) as a negative control. The article Chemotaxis towards sugars by Bacillus subtilis (George W. Ordal et al., 1979) proved that it was a poor attractant.

We made our tests again with this new molecule and glucose (25mM) as positive control.

Figure 10 : Final results (dilution : 1/10,000)

NB: It was our last experiment. Unfortunately we were running out of time and we could not do much more test. We would like to do the experiment with a lower dilution and repeat it several times.

Our results are not statistically significant however this result has been proved in literature.

Binding module

1. Preliminary experiments

Purpose

The first experiment deals with the culture conditions to see if Bacillus subtilis can resist to a low temperature and with the CBB buffer. To do that, several bacterial concentrations have been tested starting with an OD of 0.1 and diluting this solution to get estimated ODs of 0.05, 0.025, 0.01. These different Bacillus subtilis solutions were incubated 1 hour at 4°C with 500µL of CBB or water. Finally a cell count on Thoma cell counting chamber was performed.

Results

The bacterial solutions could not be counted because of two main problems: the too high number of bacteria with the 0.1 OD or the too low number of bacteria with the 0.01 OD. Thus, the study is mostly focused on the intermediate values (Figure 1).
First of all, a same cell concentration can be noticed with the presence of CBB or water with estimated ODs of 0.05 or 0.025. Moreover, twice less cells can be found in the lowest concentrations in bacteria comparing to the 0.05 OD concentration which is in agreement with the dilution ratio.
Thus, the experimental conditions regarding the presence of CBB and the incubation temperature at 4°C do not harm the cell surviving.

Figure 1: CBB presence has no effect on bacteria. The bacterial concentration was measured regarding the presence or the absence of CBB for the observed OD (0.1) or estimated ODs (0.05, 0.025, 0.01).

2. Binding test using engineered B. subtilis

Purpose

Transformed Bacillus subtilis with the binding module is able to produce a protein composed of the bacterial peptidoglycan bonding of LycT and the GbpA 4th domain of Vibrio cholerae allowing the chitin bonding. The synthetic bacterium is put with special beads composed of the polymer miming the fungal pathogen wall. After several washes, bacteria specifically attached to the chitin are put on plates and counted.

Results

The first observation is that both bacterial solutions of wild type Bacillus subtilis and SubtiTree have the same concentration : 105 bacteria/mL (Figure 2). Even though there is no significant difference between both strains after the first wash, the second wash has a major effect since it allows 40 times more Wild Type bacteria to come off the beads. This result correlates with the number of bacteria binded to the beads for the synthetic strain with the binding module.
Thus, the binding system seems to function correctly and leads to the bacterial attachment on the chitin.

Figure 2: Attachment of Bacillus subtilis with binding module to chitin. The WT bacteria or the bacteria with the binding system concentration has been determined during the different steps of the binding test. The stars represent a significant difference observed with a Student test with p < 0.05.

3. Microscopic observations

Purpose

We want to observe the SubtiTree's binding on beads coated with chitin. In order to perform a 3D reconstruction showing this interaction, we use confocal laser scanning microscope. Through the use of a fluorochrome (Syto9), we can highlight the presence of bacteria on the surface of the beads (individualized by phase-contrast). A first calibration step determine the minimum threshold to remove the background noise and the natural fluorescence.

Results

First, we note the great bacterial presence on the surface of beads coated with chitin. These images seem to highlight their interactions.
Using ImageJ software, we are able to create 3D pictures and movies of those comments.
Finally we want to observe the bacteria after the second wash. When our bacterium has the binding module, results suggest a lower number of bacteria in the washing solution. SubtiTree is retained by the beads.
Finally, overall results are consistent with the presence of functional binding system.

Fungicides module

1. Preliminary experiments

Tests with commercial peptides and controls

The first tests were accomplished with commercial GAFP-1 and D4E1 peptides at different concentrations (12,5µM/25µM/100µM). These tests were performed on different fungal strains sharing the same phylum with Ceratocystis Platani. As Ceratocystis Platani is pathogenic, we could not perform tests directly with this fungus.
After several days at 30°C, the PDA (Potato Dextrose Agar) plates couvered with fungus and commercial peptides were analyzed.

An inhibition halo was noticeable with commercial D4E1 peptide at 100µM on Aspergillus brasiliensis. Less bright halos were also present with lower concentrations. Concerning commercial GAFP-1, we did not notice any effect in the tested conditions.As positive control, a well-known chemical fungicide was used: the Copper Sulfate. The inhibition of the fungal growth was complete at 20mg/ml, and at 10mg/ml a darker halo appeared around the pad filled with Copper Sulfate as we can see on the figure below. This corresponds to a sporing halo in response to the stress generated by the fungicide.

Given these results, we concluded that very high fungicide concentrations are required to inhibit the fungal growth. Following these tests, new conditions were adopted in order not to encourage too much fungal growth over bacterial growth. The culture medium was adjusted to fit our objective and to approximate the conditions found in the trees: a 'sap-like' medium was elaborated. The incubations were then carried at room temperature.

2. Test with SubtiTree

In order to test Bacillus subtilis mutants, it was essential to find the right balance between the fungal growth and the bacterial one. This condition was necessary to get a high concentration of peptides. In our genetic constructions, these peptides are designed to be exported in the extracellular medium.

The transformed Bacillus subtilis strains were grown at 37°C during 72h and tested. After centrifugation, the supernatant and the resuspended pellet were placed on pads and disposed on plates previously seeded with a defined number of conidia (see protocols to have more details). After several days at room temperature, an inhibition halo of Trichoderma reesei's growth was clearly observable for the strain expressing D4E1 gene. The inhibition was even more noticeable with the strain carrying the operon GAFP-1 + D4E1 (see the photos below).
However, no effect was detected for the strain expressing the GAFP-1 gene, supposing a synergistic effect between these two peptides.
Regarding EcAMP and the triple-fungicides operon, no effect has been detected on the fungal growth. Several factors can explain these results: a number of post-transcriptional modifications are required to have a functional EcAMP and in addition to that, sequencing results of these constructs showed some differences with the original designed sequence.

Inhibition halos are not visible with supernatants, probably because of their low concentrations in the extracellular medium. Another effect was noted with the same strains expressing D4E1 and GAFP-1 + D4E1 on another fungus Aspergillus brasiliansis. This effect is comparable to the one previously noted with low concentration of sulfate copper.

The choice of our chassis appears to be optimal as we noted that wild type Bacillus subtilis disturbs the hyphae growth of the fungi. Some strains of Bacillus subtilis (qst 713) are already used as Biofungicides for use on several minor crops to treat a variety of plant diseases and fungal pathogens.
After this set of experiments, the strains expressing D4E1 and expressing GAFP-1 + D4E1 have shown to be the best candidates to play a major role in the fight against fungal diseases such as Canker stain. Keeping in mind our objective, we decided to tests these strains in model plants : Nicotiana benthamiana and Arabidopsis thaliana.
These tests were performed in the National Institute for the Agronomic Research by experts in this domain.

3. In planta tests with SubtiTree

Twenty-four hours after SubtiTree inoculation, no phenotypic modification of the leaves can be detected. We can conclude that our bacterium, its introduction and the fungicides production in plants don't have deleterious effects.
Without proper treatment, the drop of the pyhtopathogenic fungus on Nicotiana benthamiana's leaves causes a necrosis halo which can be measured after 40h. The lesion size and the number of inoculated sites seem reduced by B. subtilis expressing DE41 or GAFP1-D4E1, unlike with the WT bacterium. A second set of experiments is expected to be more statistically precise.
We did not observe any significant results for Arabidopsis thaliana because of the use of two plants batches with different ages.
We can therefore conclude that when SubtiTree is in plant physiological conditions, it is harmless to the plant, and that the production of fungicides is effective, reducing the leaves' necrosis .

Thanks to the diversity of anti-fungal peptides, this strategy can be adapted to different types of diseases, with different degree of specifity, etc.

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