Wet Lab

Experimental design on the run!

Dry Lab

We gave TAS students lectures on arduino applications, deep learning, 3D printer, and modeling knowledge; Teaching group members deep learning background knowledge.

Human Practices

The Taipei American School Summer Internship Program started on July 4th. Throughout the first week, we taught them safety training and basic techniques applied in a microbiological laboratory.

Wet Lab

Experimental design on the run!

Dry Lab

We teached TAS students to practice modeling 3D products with CREO, building linebot account and deep learning environment.

Human Practices

We gave TAS students lectures on synthetic biology, and assisted them in brainstorming the topic of their summer synbio project.

Wet Lab

We receive the plasmid of fluorescent protein (mCerulean and mCherry) combined with a constitutive promoter (BBa_J23100) and double terminator (BBa_B0015) from our advisor, Dr. Jane. The plasmid are transformed into DH5α for future need, and checked with the enzymes digestion method.

The primer for cloning promoter from gDNA are designed.

Dry Lab

We teach TAS students to practice the application with arduino, and practice the basic program with python.

Human Practices

We shared our project design with the students and invited them to join in our lab meeting. TAS students were encouraged to participate in our troubleshooting sessions, and all members had live discussion on the experimental design of our project.

All team members worked together for the application of the iGEM 2022 Impact Grant. We had a deep discussion regarding the potential impact of our project on the community and world.

Wet Lab

We receive the plasmid of fluorescent protein (YPet and AmilCP) combined with a constitutive promoter (BBa_J23100) and double terminator (BBa_B0015) from our advisor, Dr. Jane. The plasmid are transformed into DH5α for future need, and checked with the enzymes digestion method.

The primer for appending overlapping region to promoter are designed.

Dry Lab

Let TAS students hands-on 3D printing.

Human Practices

Members of the dry lab group instructed the TAS students by giving lectures on machine learning, 3D printing and modeling. During this week, they gained many useful dry lab core skills.

We visited Dr. Yu-Ling Shih, whose advice increased our awareness of potential problems we might face. Consultation with Dr. Ting-Jen Cheng and Dr. Wei-Chieh Cheng enhanced our understanding on the measurement of fluorescence and detection of colonies on agar plates.

Wet Lab

We extract gDNA from E. coli K12 MG1655 for cloning the promoter we needed. The different amounts of gDNA are loaded for electrophoresis to check the quality. Also, we use dreamtaq to check the function of the primer, and use KOD plus to successfully clone part of the promoters from the gDNA. the primer for vector1 and vector2 are designed.

Dry Lab

We collected more than 200 pictures and labeled them into two categories(colony、wcolony), and finished our device prototype. We also tested our ESP32 module and adjusting parameters. Testing the formula for growth model and tuning the total errors down.

Human Practices

The students demonstrated results of their small synthetic biology project. Happy ending of the TAS Summer Internship Program.

We visited Prof. Cheng-Yen Kao and asked for his advice on potential project applications in the clinical field.

We were delighted to hear from the iGEM headquarters that our team has been selected for the 2022 Impact Grant.

Wet Lab

We clone the remaining promoter from the gDNA, and append overlapping sites to dusB promoter, cyoA promoter, and glpABC promoter for Gibson assembly. Other promoters are not yet appended with overlapping sites since the primer hasn't arrived. At the end of the week, we extract gDNA again in case something goes wrong.

Dry Lab

We trained our first Yolov5s model (adjusting parameters and dataset )and fixed Google API problems. By building a fluorescence intensity plotting model, we want to figure out the relation between the simulated and experimental data.

Human Practices

We held a collaboration meetup with team HKUST, where both teams shared their projects and discussed the use of degradation tags. We contacted Dr. Rainer Nikolay to request for the MCrg reporter strain.

We held a virtual meeting with our partnership team Wego_Taipei. Both teams shared their experimental progress and exchanged thoughts about their project.

Wet Lab

We append overlapping sites to all of the promoters besides slp and rmf since the gel extraction for slp continues to fail and rmf shows the unexpected band size. Also, we clone the vector 1 and vector 2 from mCherry for Gibson assembly.

Dry Lab

We abandoned the idea of using ESP32 since the camera module has low resolution; kept collecting more solid culture plate pictures for deep learning model training. Combining new and old growth models, we were trying to find out which model is more precise to fit our data.

Human Practices

Our first education post is written and posted on both our Facebook and Instagram webpage. Fluotato teaches: Episode I explains the growth characteristics of E. coli.

We arranged another meetup event with our partnership team Wego_Taipei, and reached consensus on working together on a functional test which involves transforming the AsPhoU vector into our engineered fluorescent DH5α strain.

Wet Lab

We successfully construct the glpABC-mCherry combination and test its function. The construct is checked by restriction enzyme digestion method. Besides, we cloned the remaining vector 2 from AmilCP and mCerulean for other phase indicators. Then, the dusB-mCerulean and hchA-mCerulean are also successfully cloned and tested with its function. The restriction enzyme digestion method is also performed to check our construct.

We provided team Wego_Taipei with E. coli Nissle 1917 strain.

Dry Lab

We collected 30+ more pictures for model training, and labeled them. As for the low resolution results from the esp32 cam module, we tried to use a webcam as our picture source. We were still proceeding on plotting more diagrams to help us find the best parameters for each data, and progressing on the model for the relation between initial value of bacteria and the time we collected bacteria to the maximum value respectively.

Human Practices

We attended the Taiwan synbio alliance from August 23th-24th and had active communication with other iGEM teams.

We participated in the “iGEM MAP-Navigation of Synthetic Biology” collaboration project held by team NTHU_Taiwan.

Wet Lab

We successfully constructed the remaining nir-mCerulean and hchA-AmilCP combination, checked the construct with restriction enzyme digestion method, and tested its function. The ligation is performed but continuously fails.

We provided team Wego_Taipei with 5ul of BamHI restriction enzyme.

Dry Lab

We tried Yolov5m model and also adjusting Yolov5s parameters to test if the accuracy is better or not. Coding on Arduino turnplate, adjusting its rotation speed and making stopping angle more accurate. Using Excel solver with GRG nonlinear regression to find the best solution for each fitting data.

Human Practices

Our second education post is written and posted on both our Facebook and Instagram webpage. In Fluotato teaches: Episode II, we introduced the importance of monitoring bacterial growth status, as well as common methods used for detection.

We collaborated with team Wego_Taipei in their Podcast series- “Eutro in Vitro”, and shared our project goals and implementation. We were honored to be the first guest of this Podcast project.

Wet Lab

We mutate the mCherry stop codon for tag appending, and then perform the restriction enzyme digestion method to search for the successful colony. Also, we receive the MCrg, which we will use for validation of growth phase indicator, as the generous gifts from Dr. Nikolay.

Dry Lab

We fixed some model output upload to Google sheet problems(google api upload limitation 、RGB accuracy problems), waiting on the 360 rotation motor arriving and graphing the turnplate by Creo.

Human Practices

We made a product questionnaire and invited researchers and all potential users to fill in the survey. We posted the survey on social media and the online website of 2022 Taiwan Bacteriology Conference.

Wet Lab

We combined glp-mCherry-mut with a tag using the ligation method. The confirmation is done by colony PCR. However, we keep failing to search for a successful colony. Also, the ligation of the growth phase indicator is still failing.

Dry Lab

We found that with 200+ pictures, Yolov5m have better accuracy them Yolov5s model(91% v.s. 85%). 3d printing the turnplate by cura and testing the motor if it is eligible for our need.

Human Practices

An English version of our product questionnaire is made. We continued to propagate the survey on social platforms by inviting graduate students and professors to fill in the survey. We also sent out mails to other iGEM teams, and collected feedback from all the respondents.

Wet Lab

The ligation of glp-mCherry-mut and tag are successfully constructed, and verified by PCR. We then performed the OD and fluorescent intensity measurement between both glp-mCherry and glp-mCherry-mut plus tag to test its function. Also, we successfully construct the growth phase indicator with a ligation method. The verifications are done by PCR with primer located at three promoters. The competent cells of MCrg are made but fail to express competency.

Dry Lab

We added more parameters to Google sheet(phase、colony type), improved program process speed by reducing code number. Final testing on all device parts to check if there is any problem during the process.

Human Practices

We held an On-Campus Synthetic Biology Seminar for undergraduate students in NYCU in order to promote education on synthetic biology-related topics.

Wet Lab

we perform the competent cell preparation again and still fail to express competency. On the other hand, the ligation constructs are tested by OD measurement and fluorescence intensity measurement, the photos are taken as well.

Dry Lab

We finished our device and recorded demo video, check model and upload functions worked well.

Human Practices

We cooperated with NYCU Tai-Gi on a special educational project: “Science spoken in traditional language”.

We contacted GeneFerm Biotechnology Co., Ltd. and consulted them on the use of microbiological vectors for recombinant protein expression in the industrial field. They gave us plenty of advice on the microbial fermentation process, and reminded us of safety considerations.