Lab training for all members. Lab meeting entails biosafety training, lab emergency prevention measures, machine operation protocols, and biological waste management.
We designed a device that can detect changes in fluorescent intensity.
We discussed our approach and plan for human practice.
In preparation for designing our wiki website, we learned CSS coding format.
We reviewed papers on how to regulate the electron transfer system and evaluated the possibility of constructing conductive E-pili in E. coli.
We retrieved the plasmid for the promoter phla and the two-component gene saeRS from Professor Bae and transformed them into E. coli DH5a.
We designed a device that can transduce the signal of changes in fluorescent intensity detected by our device to the computer.
We decided on the list of teams we wanted to collaborate with. Meanwhile, we worked on fundraising for our team.
In preparation for designing our wiki website, we learned the HTML5 coding format.
We combed through the chemical biomarkers from the database markerDB, and narrowed it down by nonhereditary diseases. We then searched every biomarker for detection pathways.
We looked for methods to construct Extracellular Electron Transfer pathway into E. coli.
We extracted plasmids which the genes two-component system saeRS, the fluorescent protein mCerulean, and the promoter phla are on.
We built an Arduino code for the control panel of our fluorescent detection device.
We designed a device that can detect electric signals from extracellular electron transfer signaling pathways.
We visited the Asian Biotechnology Exhibition and interviewed biotechnology companies about probiotic bacteria and diagnostic biomarkers.
In preparation for designing our wiki website, we learned JavaScript and ECMAScript coding format.
We narrowed down to 33 biomarkers from the database markerDB.
We prepared competent cells and solutions for our experiments.
S.avermitilis has the gene to produce rhamnosidase. We tried using liquid culture to extract the genomic DNA of S.avermitilis to clone the gene for Rhamnosidase.
We used PCR to amplify and retrieve the DNA sequence we needed from the plasmids' DNA. The genes we retrieved include gene saeRS, promoter p3, promoter phla, and gene mCerulean. We modified the program of the PCR until desired results were produced.
We learned how to operate a 3D printing machine. And we created a 3D model of the device and configured the parameters based on the material we used, the machine specifications, and our device design.
We decided to interview two expert physicians: one specialized in immuno-rheumatology, Dr. Chang Yen-An, and the other, Dr. Hsih Mo-Song, in neurology.
In preparation for designing our wiki website, we learned the Document Object Model (DOM), the Browser Object Model (BOM), AJAX (Asynchronous JavaScript and XML), and how to use jQuery.
We narrowed down to 5 biomarkers from the database markerDB.
We extracted the plasmids of mtrCAB.
We measured the growth curve of the engineered E. coli carrying the mCerulean fluorescent gene.
We failed repeatedly because of the excessive amount of starch in the culture broth used in culturing S.avermitilis. So we switched over to solid media to culture S.avermitilis. However, we encountered another issue with extracting the genomic DNA of S.avermitilis, the DNA we managed to extract was broken into small fragments. To solve this problem, we changed the experiment protocol to using phenol and chloroform to purify the genomic DNA instead of using the Presto™ Mini gDNA Bacteria Kit.
We used PCR to amplify and retrieve the DNA sequence we needed from the plasmids' DNA. The genes we retrieved include saeRS, promoter p3, promoter phla, and gene mCerulean. We modified the program of the PCR until desired results were produced.
We worked on optimizing our printing results and assembled our device. We also built a function-fitting Matlab code for our device modeling.
We designed an electrical circuit for our EET detection device.
We implemented a responsive layout and set up a two-column layout pattern for our wiki website. In these two weeks, we also decided on our color scheme and created templates for our wiki website's homepage, members, and timeline pages.
We decided on L-Tyrosine as a new biomarker.
To construct the EET reporting system into our E. coli, we extracted the genomic DNA of MG1655 for the gene ccmA-H and constructed a plasmid with it.
We measured the growth curve of the engineered E. coli carrying the mCerulean fluorescent gene.
We ligated the genes we needed for our construct design with Gibson Assembly, adjusting the proportion of each part until we succeeded in cloning our genes into an assembled plasmid.
To optimize our fluorescent detection device, we visited TamKang University to discuss with Professor Hsu, Chun-Fei, who specializes in digital integrated circuit design. We modified our fluorescent detection device based on the professor’s advice.
We visited Professor Ta-Chung Liu from NYCU, who specializes in electrochemistry, to figure out the specifications of what circuit design and material would work best for our EET detection device.
We attended the clubs and students’ association expo to share knowledge about synthetic biology and our project. We also visited Dr. Chang Yen-An, a physician specializing in immuno-rheumatology from Taipei Veterans General Hospital, about the clinical demand for the type of diagnostic tool our team aims to make.
We produced the promotion video for our team project.
We ligated the mtrCAB gene after the two-component system saeRS genes.
We transformed the engineered plasmid into our E. coli. Then we extracted the proteins that were produced by the E. coli and performed SDS-PAGE to check if the gene of interest is expressed. We also constructed two plasmid that contain the phla promoter and the p3 promoter, both followed by the mCerulean gene, respectively.
We built a new, modified version of our fluorescent detection device. We tested its function and ability and further modified the device accordingly. Also, we started collecting data for our device model.
We designed a 3D model of the EET detection device.
We transformed the engineered plasmid into our E. coli. Then we extracted the proteins that were produced by the E. coli and performed SDS-PAGE to check if the gene of interest is expressed. We also constructed two plasmid that contain the phla promoter and the p3 promoter, both followed by mCerulean, respectively.
We collaborated with the iGEM team from Chung Cheng University of Taiwan, UGM of Indonesia, and UNC-Chapel Hill of the USA. We also visited Dr. Hsih Mo-Song, a neurologist physician from Chang Gung Memorial Hospital, about the clinical demand for the type of diagnostic tool our team aims to make. During this period, we held a 17th-anniversary concert for all the NYCU-Taipei iGEM alumni. We also held a synthetic biology seminar for NYCU undergraduates.
We purified the proteins from our engineered E. coli and ran the SDS-PAGE to make sure the plasmid was constructed correctly. We also went to Tunghai University to visit Professor Li Shiue-Lin who specializes in electrochemistry and electromicrobiology to discuss the construction design and detection capability of our device.
We performed functional assay on our engineered E. coli to test the correlation between the concentration of zinc ions and the intensity of fluorescent protein produced by the E. coli.
We tested our fluorescent detection device’s function and ability and modified the device accordingly. We also collected data to train our device model.
We 3D printed our EET detection device and tested it with wet lab experiments.
We organized, summarized, and reviewed the results of our year doing human practice.
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