Discussing the necessity of DNA tetrahedron in the whole project.
Exploring methods to demonstrate the success of DNA tetrahedron assembly.
Identifying a peptide that can effectively label circulating tumor cells (CTCs) from references.
Learning the principles of instruments used for observing DNA tetrahedron, including Atomic Force Microscope (AFM) and TEM.
Discussing if PEG linker is necessary for the Folic acid conjugated single-stranded DNA.
Dry Lab
Ensuring that team members are familiar with the assignment of tasks in the hardware process.
Explaining the principle of Ficoll separation of peripheral blood myeloid cells (PBMC).
Determining the type of pump and valves for Circulating Tumor Cells (CTC) detection.
Discussing the storage conditions for fluorescent protein and DNAse.
Draw the prototype of the Main Chamber.
Micro channel design brainstorming - for separating CTCs.
Quantitative Counting Method for fluorescence protein labeled CTCs.
Exploring the principles and applications of Fluorescence Microscopy and Flow Cytometry.
Animating CTC-FAST device model and its principles.
CTC-FAST device prototype.
Calculating the probability of CTC occurrence and the number of macrophages.
Exploring methods to separate CTCs from macrophages
Calculating the minimum volume of the Main Chamber.
Human Practice
Brainstorming for CTC-FAST product promotion.
Conducting the SWOT analysis for CTC-FAST product.
After discussing with Professor Hong Jing, we decided to address the “Uneven Distribution of Medical Resources in Rural Areas" as the motivational direction.
Collecting data on medical resources distribution in Taiwan.
Collecting data on the medical challenges faced by rural patients in Taiwan.
Wiki
Selecting color schemes and designing the concept for the Wiki.
Week 2 (5/7-5/13)
Wet Lab
Learning to use AFM.
Inquiring about PEG-related questions with Dr. Tseng.
Exploring whether mGreen Lantern (mGL) fluorescent protein affects the binding affinity of the CTC-recognining peptide.
Inquiring with Dr. Tseng (with Biochemistry expertise) the pros and cons of PEG linker.
Inquiring with Dr. Tsai about the modeling of mGL and CTC-recognining peptide fusion protein.
Inquiring with Dr. Kan if we could use the AFM for DNA tetrahedron detection.
Learning how to culture cells.
Dry Lab
Estimating the probability of two CTCs being connected together.
Discussing the calculation of flow rate, the probability algorithm, and the calculations involved in main chamber modeling.
Human Practice
Collecting policies related to healthcare in Taiwan rural areas.
Discussing the benefits that CTC-FAST can bring to society.
Brainstorming future lung cancer prevention and awareness events that we can hold.
Wiki
Designing the menu, footer parts of Wiki.
Week 3 (5/14-5/20)
Wet Lab
Discussing how to integrate our project into the society.
Learning how to culture cells.
Organizing the project description and the questions for consulting.
Dry Lab
Estimating the cost of CTC-FAST device.
Finding papers on pressure differences caused by microchannel junctions, and the feasibility of microfluidics and Raman spectroscopy
Human Practice
Inviting the Taiwan Cancer Foundation to co-organize World Lung Cancer Day event.
Wiki
Planning the open lab activities for educating high school students in synthetic biology.
Scheduling future social media post themes and dates.
Week 4 (5/21-5/2)
Wet Lab
Learning how the pET vectors work.
Learning the mechanism of Gibson assembly.
Organizing how the pET-15b vector works.
Discussing the safety form
Dry Lab
Purchasing the materials of CTC-FAST device.
Completing the Summer Personnel Schedule.
Human Practice
Designing the first version of the board game for lung cancer education.
Discussing the necessity of CTC-FAST detectors for rural areas.
Wiki
Designing the appearance of the members page.
Brainstorming the post-crossing activity.
Week 5 (5/28-6/3)
Wet Lab
Planning the experiment of DNA tetrahedron assembly.
Preparing a Glossary for team members without biology expertise.
Dry Lab
Learning 3D Printing machines and Electronics circuitry.
Cold welding the peristaltic pump for pushing buffer in CTC-FAST.
Applying stepper motor to control syringe injection in CTC-FAST.
Human Practice
Listing experts who specialize in research related to healthcare in rural areas, and getting ready to interview them.
Discussing and uploading the project description.
Wiki
Illustrating the portraits of members (Leaders).
Design the style of postcards.
Week 6 (6/4~6/10)
Wet Lab
Designing the ssDNA sequence for DNA tetrahedron.
Dry Lab
Assembling the stepper motors onto the syringe.
Photodiode device assembly.
3D printing of valves and laser placement.
Designing light intensification and filtering device assembly.
Measurement of Voltage and current value.
Wiki
Designing and Coding parts page.
Designing the appearance of Hardware pages of Wiki.
Week 7 (6/11~6/17)
Wet Lab
Organizing the experimental results and write notebooks.
Performing the DNA tetrahedron assembly experiments with one, two, three or four ssDNAs in assembly buffer with 5mM Mg2+. Results examined by agarose gel electrophoresis.
Human Practice
After discussing with the supervisor again, We thought that the original motivation to solve the difficulty of seeking medical treatment in rural areas could not be achieved. Therefore, another meeting was held to discuss a new motivation.
Wiki
Designing the appearance of home page of Wiki.
Week 8 (6/18~6/24)
Wet Lab
Performing DNA tetrahedron assembly experiments again and change the concentration of Mg2+.
Linearizing pET-15b by for restriction enzyme for mGL+peptide or EGFP+peptide protein production.
Performing Gibson assembly to assemble mGL+peptide or EGFP+peptide expressing biobrick into linearized pET-15b.
Performing colony PCR to pick the right clone for sequencing confirmation.
Dry Lab
Basic training for microchannel
Human Practice
Recruitment of openlab apprentices.
Revising and Uploading Description
Discussing the feasibility of incorporating a CTC detection device in the healthcare system with Professor Hong Jing.
Search of Taiwan's National Health Insurance meeting records from 2013 to 2022 and compile favorable conditions for adding CTC-FAST to the insurance.
Collecting global and local statistics about lung cancer death rates.
Wiki
Illustrating the portraits of members (Human Practice).
Week 9 (6/25~7/1)
Wet Lab
Fusion Protein (mGL/eGFP+peptide) induction and SDS-PAGE confirmation.
Optimizing DNA tetrahedron assembly.
Dry Lab
Manufacturing steering engine (examine propulsion and flow control testing).
Designing device for fluorescent detection (light path correction, examination photodiode, data analysis).
Human Practice
Presenting a proposal to the Taiwan Cancer Society for the World Lung Cancer Day event plan.
Making an on-campus fundraising presentation.
Planning fundraising schedule.
Wiki
Coding description page.
Designing and Coding Notebook page.
Week 10 (7/2-7/8)
Wet Lab
Optimization of the first-generation DNA tetrahedron.
mGreen Lantern protein expression and purification (small scale).
Cloning the zinc finger binding protein by Gibson Assembly (pET-15b-PBSII+Zif268).
Initiating the construction of long tetrahedral DNA (pET32a-ssDNA-L-R).
SDS-PAGE confirmation of mGreen Lantern protein expression.
Conjugating folic acid with the NHS.
SDS-PAGE reconfirmation of mGreen Lantern protein expression.
Harvesting the NHS-conjugated folic acid after agitating overnight, and purifying by filtration.
Dry Lab
The assembly of the microcontroller-controlled pumping device.
Adjustion for precise control of the outflow rate and time using the microcontroller-controlled pump (with an allowable error range of ±1ml / ±1s).
The first version of the peristaltic pump power driving device.
Successfully achievement of micro-dosing of liquids with one drop per output using the microcontroller-controlled pump.
Human Practice
Surveying the place for Lung Cancer Day lecture and circulation planning.
Completing documents related to on-campus fundraising (including proposals, speeches and presentations).
Confirmation of World Lung Cancer Day venues.
Consulting with previous team members about their experience in organizing events.
Replan future work based on progress meeting feedback.
Wiki
Surveying the place for Lung Cancer Day lecture and circulation planning.
Completing documents related to on-campus fundraising (including proposals, speeches and presentations).
Organizing Open Lab trial teaching activities.
Designing the appearance of Human Practices.
Week 11 (7/9-7/15)
Wet Lab
Small-scale purification of mGreen Lantern.
Continue cloning the zinc finger binding protein by Gibson Assembly (pET-15b-PBSII+Zif268).
Sequencing the pET-15b-PBSII+Zif268.
Construction of the long tetrahedral DNA (pET32a-ssDNA-L-R).
Discussing the result of NHS-folic acid with Dr. Tseng and revised the protocol.
Activating folic acid again.
Harvesting the NHS-conjugated folic acid after agitating overnight, and purifying by filtration.
Dry Lab
Outsourced the production of the Main chamber to a manufacturer.
Completing the second version of the peristaltic pump power drive device.
Human Practice
Reviewing and Revising the Lung Cancer Day activity plan and flow chart.
Creating a venue map for the World Lung Cancer Day event.
Wiki
Editing the contents of notebook (May) and coding the Notebook page.
Preparing for the trial run of the open lab event.
Week 12 (7/16-7/22)
Wet Lab
SDS-PAGE confirmation of zinc finger binding protein (PBSII+Zif268) expression.
Conjugating folic acid with the NHS again.
SDS-PAGE confirmation of mGreen Lantern protein expression.
Ligation gene blocks of the long tetrahedral DNA (ssDNA-L-R) by ligation PCR.
Cloning the ligated gene block (ssDNA-L-R) into pET32a.
Gel electrophoresis confirming pET32a-ssDNA-L-R by restriction enzyme digestion.
Sequencing confirmation of pET32a-ssDNA-L-R.
mGreen Lantern protein purification (small scale).
Zinc finger binding protein (PBSII+Zif268) expression and purification (small scale).
SDS-PAGE confirmation of mGreen Lantern protein purification.
Dry Lab
Drawing the mold of trident microchannel by Solidwork. The main channel is with a diameter 500 micrometers, and the branch channel is with a diameter 300 micrometers.
Printing and solidifying the mold of trident microchannel by light-curing 3D printer and ultraviolet light, respectively.
Pulling the degased 10:1 mixture of ethylene benzene and PMS into mold to generate trident microchannel.
Placing the mixture filled mold on an electromagnetic heating stirrer, baking it for 4 hours at 85C.
Bonding the trident microchannel to glass slide and subjecting them to ozone for 40 minutes.
Successfully let the Main Chamber shake by a servo motor.
Human Practice
Confirming the speakers with the Taiwan Cancer Foundation for World Lung Cancer Day.
Preparing a budget for the World Lung Cancer Day event.
Confirming the list of staff members for the World Lung Cancer Day event.
Arrangement of on-campus fundraising personnel.
Wiki
Editing the contents of notebook (June) and coding the Notebook page.
Conducting a trial run for the Open Lab event (7/17).
Week 13 (7/23-7/29)
Wet Lab
Analyzing the NHS-folic acid by Thin Layer Chromatography (TLC).
Cloning the long tetrahedral DNA by Gibson Assembly (pET32a-ssDNA-L-R).
Learning large scale purification of mGreen Lantern.
Analyze the NHS-folic acid by Fourier-transform infrared spectroscopy (FTIR).
Gel electrophoresis confirmation pET32a-ssDNA-L-R after restriction enzyme digestion.
Searching the method for crosslinking PBSII+Zif268 to PMMA.
Dry Lab
Improving the skill for trident microchannel production, and generating trident microchannels with main channel of 300 micrometers in diameter and branch channel of 100 micrometers.
Completing the integrated propulsion system to connect with the Main Chamber.
Circuit Amplification Issues and Discussion.
Human Practice
Sending interview invitations to lung cancer specialists and clinics offering CTC testing.
Interviewing Reporter Qiu-Ping Gao from the Formosa Cancer Foundation.
Interviewing Dr. Gi-Ming Lai, the executive director of the Formosa Cancer Foundation, to discuss the experience of lung cancer prevention.
Introducing iGEM competetion in an Instagram post.
Check the draft of on-campus fundraising personnel.
Calling the medical laboratory to invite them for an interview.
Wiki
Coding Human Practices page.
Contacting the manufacturer to order team uniforms and postcards.
Conducting final trial run for Open Lab. (7/24)
Holding the Open Lab event. (7/29)
Week 14 (7/30-8/5)
Wet Lab
Discussing the FA-conjugated DNA purification methods with Dr. Tseng and protocol revison.
Cloning the long tetrahedral DNA by Gibson Assembly (pET32a-ssDNA-L-R).
Gel electrophoresis confirming pET32a-ssDNA-L-R by restriction enzyme digestion.
SDS-PAGE confirmation of zinc finger binding protein (PBSII+Zif268) expression.
SDS-PAGE confirmation of mGreenLantern protein expression.
Large-scale purification of mGreen Lantern.
Discussing the dialysis formulation with Dr. Tseng and protocol revision.
Dry Lab
Discussing how to build the liquid propulsion device for the microchannel.
Experiment proved that mGL can be detected by fluorescent detection under the concentration of 1.83*10^-11 mg/ml.
Improving the wire configuration and voltage issues of the liquid microcontroller.
Human Practice
Introducing synthetic biology concepts on Instagram post.
Venue survey for World Lung Cancer Day.
Organizing World Lung Cancer Day event.
WIki
Editing the contents of notebook (July) and coding the Notebook page.
Editing description page.
Holding the Open Lab event. (8/5)
Contacting the Manufacturer to Order Team merchandising (stickers).
Week 15 (8/6-8/12)
Wet Lab
Initiating the construction of long tetrahedral DNA (pET15b-tetrahedral DNA-RCR).
Cloning the long tetrahedral DNA by Gibson Assembly (pET15B-tetrahedral DNA-RCR).
Gel electrophoresis confirming pET15b-tetrahedral DNA-RCR by restriction enzyme digestion.
Cloning the long tetrahedral DNA by Gibson Assembly (pET15b-SSB-RepA).
mGreen Lantern protein quantification.
mGreen Lantern protein cryopreservation.
First attempt at performing a DNA dialysis experiment.
Harvesting the products of DNA dialysis.
SDS-PAGE confirmation of the products of DNA dialysis.
Second attempt at performing a DNA dialysis experiment.
Harvesting the products of DNA dialysis.
SDS-PAGE confirmation of the products of DNA dialysis.
Re-transformation of the Zinc finger binding protein (PBSII+Zif268).
SDS-PAGE confirmation of zinc finger binding protein (PBSII+Zif268) expression.
Dry Lab
Building the liquid propulsion system of the microchannel.
Detecting the voltage of excitation light generated by laser light from different concentrations of fluorescent substances.
Applying AD620 amplifier to our fluorescent detection system and collect mGL data under different concentrations.
Human Practice
Introducing the work that the CTC-FAST team was engaged in on Instagram.
Fundraising in the College of Science and the College of Social Sciences.
Contact medical laboratories, foundations, and lung cancer associations to invite for interviews, which plays a role in optimizing our product and providing constructive suggestions.
Wiki
Illustrating the portraits of members (Wet Lab).
Designing and Coding protocol and proof of concept page.
Week 16 (8/13-8/19)
Wet Lab
Ligation gene blocks of the long tetrahedral DNA (ssDNA-L-R) by ligation PCR.
Cloning the long tetrahedral DNA by Gibson Assembly (pET32a-ssDNA-L-R).
Gel electrophoresis confirmation pET32a-ssDNA-L-R after restriction enzyme digestion.
Cloning the ligated gene block (ssDNA-L-R) into pET32a.
Gel electrophoresis confirmation pET15b-SBP-RepA after restriction enzyme digestion.
Sequencing confirmation of pET15b-SBP-RepA.
Preservation of mGreen Lantern protein by freeze-drying.
Fluorescence detection confirming the fluorescence intensity of mGreen Lantern.
First attempt at performing a Folic acid conjugate to ssDNA experiment.
Purify FA-ssDNA after dialysis.
SDS-PAGE confirmation of Folic acid conjugate ssDNA (FA-ssDNA).
Research papers on inclusion body solubilization.
Dry Lab
Building the liquid propulsion system of the microchannel.
Using the amplifier module to analyze the data of unpurified mGL.
Human Practice
Hold a video interview with Dr. Huang to gain insights into the current development and Application of CTC detection.
Drafted the interview outline and sent interview invitations to the Taiwan Society of Laboratory Medicine.
Wiki
Editing the content of attributions, filling the attribution form, and coding attribution page.
Designing and Coding Hardware page.
Week 17 (8/20-8/26)
Wet Lab
Sequencing confirmation of pET15b-SSB-RepA.
SDS-PAGE confirmation of pET15b-SSB-RepA expression.
Learning cell culture.
mGreen Lantern protein cryopreservation.
Large-scale purification of mGreen Lantern.
Fluorescence detection confirming the fluorescence intensity of mGreen Lantern.
SDS-PAGE confirmation of mGreen Lantern protein expression.
Cultivating SKOV3 cells for CTC mimic.
Second attempt at performing a Folic acid conjugate to ssDNA experiment.
Analyzing the spectrum of the FA-ssDNA conjugate using NanoDrop.
Collecting reference for inclusion body solubilization.
Dry Lab
Improving the liquid propulsion system of the microchannel.
Discussing the problem of liquid inflow into the microchannel and discuss the solution to it.
Using the amplifier module to detect the data of purified mGL.
Human Practice
Fundraising with the Management College.
Interview Dr. Yao-Lin Tzeng, chairman of the Taiwan Association of Thoracic & Cardiovascular Surgery.
Interviewing Dr. Chih-Ying Liao, founder of Cancell.
Interviewing Dr. Gi-Ming Lai, executive director of the Formosa Cancer Foundation, to gain insights into the current development and Application of CTC detection.
Interviewing Dr. Chia-Jui Yen, director of the National Cheng Kung University Hospital Cancer Center.
Wiki
Illustrating the portraits of members (Dry Lab).
Coding the Safety and Model pages.
Week 18 (8/27-9/2)
Wet Lab
Cloning the long tetrahedral DNA by Gibson Assembly (pET32a-ssDNA-L-R).
Gel electrophoresis confirmation pET32a-ssDNA-L-R after restriction enzyme digestion.
SDS-PAGE confirmation of pET15b-SSB-RepA expression.
Analyzing the spectrum of the FA-ssDNA conjugate using NanoDrop.
Cultivating SKOV3 cells as CTC mimics.
Purification of inclusion bodies (pET-15b-PBSII+Zif268).
Dry Lab
Generating a thicker microchannel with 4 mm thickness.
Making thicker aluminum plates on the microfluidic liquid propulsion system to improve the stability of the propelled liquid.
Trying to solve the liquid exudate problem of the microchannel.
Human Practice
Conducting an interview with a lung cancer patient.
Interview with the case manager.
Interview Dr. Mei-Chia Wang, chief Medical Technologist at Chang Gung Hospital.
Interview Mr. Tsai, Manager at LifeCode Biotech.
Wiki
Designing the appearance of sponsors, and coding Sponsors page.
Designing and coding Implementation page.
Week 19 (9/3-9/9)
Wet Lab
Cloning the long tetrahedral DNA by Gibson Assembly (pET32a-ssDNA-L-R).
Gel electrophoresis confirmation pET32a-ssDNA-L-R after restriction enzyme digestion.
Purification of inclusion bodies (pET-15b-PBSII+Zif268).
Learn to use oxygen plasma to modify NHS on PMMA.
Research papers on refolding of solubilized protein (pET-15b-PBSII+Zif268).
Dry Lab
Finish the Contribution and Hardware writeups for the Wiki.
Human Practice
List of nutrient-rich foods and discussion with school cafeteria about collaborative ‘Healthy bento for healthy lungs’ nutrient lunch box programs.
Fundraising event in Chiayi temple.
Promotion video shooting.
Planning short, medium, and long-term goals for FAST CTC.
Wiki
Editing the contents of notebook (August) and coding the Notebook page.
Designing and coding Contribution page.
Week 20 (9/10-9/16)
Wet Lab
Ligation gene blocks of the long tetrahedral DNA (ssDNA-L-R) by ligation PCR.
Cloning the long tetrahedral DNA by Gibson Assembly (pET32a-ssDNA-L-R).
Gel electrophoresis confirmation pET32a-ssDNA-L-R after restriction enzyme digestion.
Cloning the ligated gene block (ssDNA-L-R) into pET32a.
Fourth attempt at performing a Folic acid conjugate to ssDNA experiment.
Purify FA-ssDNA after dialysis.
Analyze the spectrum of the FA-ssDNA conjugate using NanoDrop.
Treating PMMA with oxygen plasma.
Modifying PMMA with NHS.
Subjecting the activated folic acid to UV-vis spectroscopy.
Learning safranin staining.
Staining PMMA with Safranin O.
Cultivating SKOV3 cells to simulate CTCs.
Purification of inclusion bodies (pET-15b-PBSII+Zif268).
Dry Lab
Drawing CTC-FAST's internal 3D modeling design for Contribution.
Human Practice
Inquire about ISO certification.
Compile and summarizing interview records.
Contact a specialist from the Legal Affairs Department.
Wiki
Illustrating the portraits of members (Investigators and Instructors).
Coding Material page.
Week 21 (9/17-9/23)
Wet Lab
Cloning the long tetrahedral DNA by Gibson Assembly (pET32a-ssDNA-L-R).
Gel electrophoresis confirmation pET32a-ssDNA-L-R after restriction enzyme digestion.
Treating PMMA with oxygen plasma.
Modifying PMMA with NHS.
Staining PMMA with Safranin O.
Subjecting the PMMA to UV-vis spectroscopy.
Dry Lab
Assembling the final overall CTC-FAST device.
Making a video showing how CTC-FAST works.
Human Practice
Composing Wiki education content.
Composing Wiki outreach content.
Composing Wiki Integrated Human Practice content.
Wiki
Illustrating the portraits of members (Wiki and Advisors).
Editing the content of Mempers and coding the Members page.
Week 22 (9/24-9/30)
Wet Lab
Cloning the long tetrahedral DNA by Gibson Assembly (pET32a-ssDNA-L-R).
Gel electrophoresis confirmation pET32a-ssDNA-L-R after restriction enzyme digestion.
Treating PMMA with oxygen plasma.
Modifying PMMA with amino functional groups.
Staining PMMA with Safranin O.
Subjecting the PMMA to UV-vis spectroscopy.
Conjugating PMMA with mGL to verify the successful NHS modification on the PMMA surface.
Human Practice
Editing and uploading IHP, Education, Outreach Wiki content
Wiki
Editing the contents of notebook (September) and coding the Notebook page.
Week 23 (10/1-10/7)
Wiki
Coding the Results and Judging pages.
Check and modify the content and typesetting on wiki.
Week 24 (10/8-10/12)
Wiki
Editing the contents of notebook (October) and coding the Notebook page.
