Team:SJTU-Software/Collaborations
Major achivements
In order to make the combination of drylab and wetlab, we collaborated with
1.SYSU-CHINA; our software evaluated the grade of their devices and it was also meaningful for them to evaluate the circuits with software.
2.SJTU-BioX-Shanghai; we evaluated their biobricks; worked together with our brother team in their verification part.
3.China-Tongji; we helped their team find the similar biobricks which could indicate their biobricks with hidden function in the database.
It can be seen from the result that our score is positively correlated to their experiment satisfaction.
According to this result, the comparison of our software score and their experiment results, our software successfully test the parallel experiment and it is also meaningful for them to evaluate the circuits with software, which would be beneficial to improve their future experiments.
This year, SYSU-CHINA develops a plug-in for microbes, a system that can build up a living clock for microbes and guide them to live regularly as well as to work efficiently. Also, microbes with the system inserted acquire the concept of life span so that some dangerous bacterias will come to death in time before they cause any biohazard.
We cooperate with SYSU on the project of experiment grading and result predicting. We would evaluate multiple parallel experiment groups in the construction and testing of inverted components from their team. These groups are comparable between our designs and results, which would become one of the pivotal parts of SYSU project, and the data extracted from which would meet our needs.
Through our cooperation, we got 5 biobricks which were evaluated by their experiment experience; according to our software, each biobricks also got a score. Here are the results.
| Biobrick | Satisfaction | Scored from our software（BLAST first） |
|---|---|---|
| BBa_K1641023 | 95 | 8.1585 |
| BBa_K1641024 | 93 | 8.1581 |
| BBa_K1641025 | 95 | 8.1585 |
| BBa_K1641026 | 85 | 8.1581 |
| BBa_K1641027 | 95 | 8.1585 |
This year, their team is going to engineer a recombinant cyanobacteria to achieve "biodesalination", which means to extract sodium chloride from seawater through biological membranes. Many cyanobacteria possess salt-tolerance mechanisms, among which sodium export is the most important one. Halorhodopsin is a light-driven inward-directed chloride pump from halobacteria. They functionally expressed it in cyanobacteria to drive the influx of chloride together with sodium, thus conferring cyanobacteria the ability to absorb salts to a significant degree. And the biobrick they used in their program is to control the expression quantity of HR protein which served as the pump.
Our goal is to evaluate their biobrick by scoring two parallel experiment results.
we got the new devices and its structure from SJTU-BioX-Shanghai and noticed that the parts was built by themselves not long ago. when we download the database data, they had not upload their new biobrick. So we could not find the parts' ID from the new devices in our database.
In order to evaluate the new parts, we use the blastn to find the parts in our database with most similar sequence compared to the new parts. Then we use the parts found in our database to evalue the the new devices. We found the coding parts in the device is most important,
so our algorithm give the coding part a highest weight.
And the consequence of this collaboration is very ideal. The two devices got two disparate scores, one of which is scored 32.98 and the other is 3.542. In addition, this difference is also reflected by their experiment result that the one with the higher score is chosen as their final biobrick to control the expression of the iron pump.
so this collaboration prove that our algorithm can evaluate new device roughly on the base of existing part.
This year, China-Tongji used the optogenetics technology to control the simple movement of nematodes. In the pathognostic motoneuron and muscles of nematodes, the opsin will be expressed, which is a type of photosensitive channel protein that will be activated at a specific wavelength of light. Then it will stimulate some neurons and ultimately achieve the purpose of nematode movement control.
However, during the evaluation, we found that some of their biobricks are so new that we nearly couldn't find them in our database which covered the data in the iGEM official website. The result showed that those biobricks were never synthesized before.
Beyond that, we also found the regulator BBa_K1634003 is almost 80% similar to BBa_K309026 which is made by a team from Canada. This result might be used to compare the function of their biobricks with the other team, and explored more useful information from the similar one.