Team:WHU-China/Criteria
Bronze1.Competition Deliverables
a)Wiki
b)Poster
c)Presentation Video
d)Project Promotion Video
e)Judging Form
All required materials were submitted before deadlines.
2.Attributions
We wouldn’t have accomplished our works without our team members’ efforts and assistance of other people! Special thanks to individuals and groups that have helped us are expressed on this Attributions page.
3.Project Description
Ventilator-Associated Pneumonia (VAP) is threatening thousands of patients’ lives during the COVID-19 pandemic, and our project, the Negotiator, aims to develop an engineered probiotic bacterium to help these patients who suffering from VAP. More detailed background information and project description are available on this Description page.
4.Contribution
We made contributions for future iGEM teams in different aspects: a series of new parts, from BBa_K3562000 to BBa_K3562015, were submitted; supplementary information was added to existing parts, such as BBa_C0179, BBa_C0160, BBa_K2957001; a DIY co-culture device was built; and new thinking of model, HP and entrepreneurship. Detailed contributions are available on this Contribution page.
Silver1.Engineering Success
We have accomplished Design-Build-Test-Learn (DBTL) cycles in Quenching Module, Sensing Module, cell-free quorum sensing and hardware related experiments.
In the Quenching Module, based on the problem “how to choose optimal quenching enzymes”, we selected several acylases and lactonases as options, designed protocols and tested their efficiency; to optimize the final selection of quenching enzymes, we built a model and gathered its preliminary data, aiming to combine our wet lab with this model to gain the ultimate result in the next iGEM season.
In the Sensing Module, to solve the problem “how to deal with G- pathogens”, we designed a chemokine combination to recruit different immune cells, and did a series of experiments to test which chemokine combination is the best. However, these feedbacks reflected another problem: excessive chemokine production will cause a deadly cytokine storm. Thus, we made a further design about controlling chemokine concentration: adding TEV cleavage site on the chemokines. Though not all experiments are completed (because of the limited time), we plan to use our data to guide advanced experiments next year.
In cell-free quorum sensing, we planned to build a work flow that includes establishing an in vitro quorum sensing network, rapid in silico screening QS inhibitor & in vitro testing, and final in vivo test of validation. Though this work flow stopped at step one, we believe that these works will be accomplished next year.
In the hardware-related wet lab, we applied our hardware to evaluate the tolerance of our probiotics when they are exposed to G- pathogens, and what we have learnt will be utilized to improve the application strategy next year.
We have characterized three new parts in engineering this year: BBa_K3562001, BBa_K3562002, and BBa_K3562013. All of them are clearly documented on the Registry.
BBa_K3562001 is a coding sequence of AiiO, an acylase that degrades AHL by hydrolyzing the amide linkage between the acyl side chain and HSL moiety. Though we failed to gather its experimental information, AiiO kinetic data from previous research were contributed on the Registry.
BBa_K3562002 is a regulatory sequence, promoter pLasRV, which was cloned from P. aeruginosa. We documented several sources describing pLasRV properties and designed a protocol for LasRV cell-free biosensor.
BBa_K3562013 is a coding sequence of CCL2, a C-C chemokine receptor that mainly exhibits a chemotactic activity for monocytes and basophils. Our experiments successfully revealed that the monocyte-recruiting efficiency of C-C/CCL2 pairs and determined that C-C/CCL2 is the best option among our chemokine parts.
Detailed Engineering Success in each aspect of our project is displayed here.
2.Collaboration
We have established partnership with different teams and worked as groups. We held meetings, published educational booklets, shared our modeling and hardware, provided mutually novel engineering strategies……we helped each other a lot!
All the Collaborations are shown here.
3.Human Practices
As students from Wuhan University, we witnessed how the COVID-19 pandemic has inflicted people from the beginning—and that is why we decided to help those patients with synthetic biology methods. Our human practices work includes Integrated Human Practices, Education and Inclusivity.
In Integrated Human Practices, we gathered a large spectrum of suggestions form different experts to evaluate and reform our project; in Education, we published popular science booklets as e-books and paper books, and we delivered a lecture about synthetic biology; in Inclusivity, we gained and analyzed pubic concerns about multiple aspects, including the pandemic, probiotics, synthetic biology and our project.
4.Proposed Implementation
The proposed users of our probiotics, the Negotiator, are patients in need of ventilation, who will face high risk of getting ventilator-associated pneumonia (VAP). As a product applied on patients, the safety is a main concern: TEV protease and toxin-antitoxin system are applied to control chemokine secretion and horizonal gene transfer. To implement our project to real world, multiple researches and interviews are done. You can get more information about the application attempt on Entrepreneurship.
Further Implementations can be found on this page.
Gold1.Integrated Human Practices
We interviewed experts of various fields and adjusted our project with their suggestions, which covered a large spectrum from cell-free techniques to entrepreneurship experiences. Full Integrated HP work is shown here.
2.Project Modeling
Our models focus on quorum sensing kinetics and structural biology, aiming to use our wet lab data to select appropriate genes and evaluate our strategy. On another aspect, results of modeling will feedback to our wet lab works and shape our future actions. These are details of our models.
3.Proof of Concept
Our wet lab, hardware and model are combined together firmly in this project.
In the Quenching Module, we did wet lab experiments with our co-cultivation hardware, which data reveals some feasibility of our project. And raw data our model came from our enzymatical experiments while the feedback will further guide our selection of an optimal enzyme.
In the Sensing Module, our microfluidic chip hardware will be utilized to mimic lower respiratory tracts and to evaluate our project.
Detailed Proof-of-Concept is available here.
4.Partnership
We founded (or co-founded) two iGEMer communities: Anti-Biofilm Community (ABC) and China Synthetic Biotic Delta (CSBD), and worked as a leading factor throughout in this season.
In ABC, we published our booklet together as education materials and promoted our works overseas; we shared our biofilm-related hardware, modeling; we benefited mutually in biofilm-related experiment design and implementation; etc.
In CSBD, we provided each other a novel biosafety strategy; we attempted to share human-organ-mimicking microfluidic chips and related models; etc.
For more information about our Partnership, please visit our Partnership page.
5.Science Communication
For the public, we have posted articles and comics on most of popular Chinese social media and published a booklet; for freshmen majored in bioscience, we have delivered a lecture, revealing the beauty of synthetic biology to them. To spread our work to wider audience, we published our booklet as e-books.
You can read more information here.
6.Excellence in Another Area
Lots of efforts must be paid to apply an iGEM project to real world, and one of the points is the commercialization. To overcome this difficulty, we develop an Entrepreneurship plan preliminarily.
