Team:NCKU Tainan/Notebook


Notebook

Notebook

Weekly journal of wet, dry, and HP

This is not just a journal, it is the history of iGEM NCKU Tainan.

 

Week 1 5/31-6/6

Wet

  1. Do the PCR to copy bsNOS gene from bacillus subtilis.

  2. Basic lab skills.

  3. First attempt to make the competent cell of DH5α and BL21.

  4. Design the primer of IDT fragment.

Dry

  1. Test the different solution ratio of contact lenses.

  2. Looking for current model simulating ocular drug delivery system.

  3. Device brainstorming - looking for relevant information.

  4. Design Wiki page structure.

HP

  1. Establish the future plan of HP events.

  2. Contact with Camax Optical Corp.

Week2 6/7-6/13

Wet

  1. Culture the competent cell of DH5α and BL21.

  2. Clone bsNOS into DH5α.

  3. Design the functional test for NOS production.

Dry

  1. Trial production of contact lenses by using glass plates.

  2. Discussing about how to modified current model to fit our situation.

  3. Discuss with a professor about the device.

  4. Design Wiki layout.

HP

  1. Preparation of Tainan First High School education event.

Wet

  1. Culture different competent cell for csgD functional test.

  2. Freeze the engineered bacteria.

Dry

  1. Trial production of contact lenses by using the mold from CAMAX

  2. Establishing our own models.

  3. Design the first version of the device.

  4. Design the basic page.

HP

  1. 6/16: Meetup with president.

Wet

  1. Finalize the primer design.

  2. Design for the kill switch functional test.

  3. Establish the protocol of biofilm assay.

Dry

  1. Design our mold of the contact lens by solidwork.

  2. Looking for parameters.

  3. Go to Prof. Huang laboratory to do porcine eye experiment.

  4. Making the basic page.

HP

  1. 6/24: Tainan First High School education event.

Week5 6/28-7/4

Wet

  1. Establish the protocol of functional test for NOS production.

  2. Transform plasmid with csgD gene into bacteria.

  3. Amplify the product we got from IDT synthesized with PCR.

Dry

  1. Print the mold by 3D-printing.

  2. Looking for parameters.

  3. Test 40kHz transducer and design the prototype.

  4. Modify the design of the basic page.

HP

  1. 6/29: Glaucoma awareness week online education event

  2. Preparation of visiting Camax Optical Corp.

Wet

  1. Double Digest the gene fragment.

  2. Extract the pSB1C3 from the plate.

Dry

  1. Making the contact lenses by our mold.

  2. Confirming the parameters that cannot be found in current research, and try to estimate them.

  3. Arduino learning.

  4. Discuss main page design.

HP

  1. 7/10: Visit Camax Optical Corp.

Week7 7/12-7/18

Wet

  1. Culture IDT fragment into different bacteria.

  2. Use the three fragment assembly to clone NOS gene, csgD, and csgA together on psb1C3.

  3. Change the plasmid that with EcorV for kill switch.

  4. Do the congo red asset for testing csgD and csgA gene’s function.

Dry

  1. Improve the contact lens

  2. Confirming all the compartment’s conditions

  3. The first porcine eye experiment, guided by a Dr. Hung.

  4. Design the main page.

HP

  1. 7/15 Meetup with Ming-Dao High School.

  2. Preparation of Synthetic biology in Five levels video.

  3. Preparation of Read for Love Summer Camp education event.

Week8 7/19-7/25

Wet

  1. Clone both csgD, csgA, and also NOS successfully into DH5α.

  2. Redo the csgD functional test with different control, we use PCA24N instead of pSB1C3.

  3. Run SDS PAGE for csgD.

Dry

  1. Assemble device of Digital Image Correlation.

  2. Looking for theories that can describe our equations’ boundary conditions, and ask wet team to do necessary experiments in order to obtain some critical parameters and conditions.

  3. Test arduino to read high frequency signal.

  4. Design the main page.

HP

  1. 7/20: Take Synthetic biology in Five levels video.

  2. 7/21: Release survey.

  3. 7/25: Read for Love Summer Camp education event.

Week9 7/26-8/1

Wet

  1. Clone both csgD, csgA and also NOS into BL21.

  2. Do the congo red assay.

  3. Clone hicB, FLP represently intoDH5α.

Dry

  1. Calibration of VIC-3D (software of strain analysis)

  2. Solving the partial differentiation equations we established.

  3. Design the function generator and draw the schematic circuit diagram with DXP.

  4. Drawing the basic page picture.

HP

  1. 7/31: Discussion with NarLab.

  2. 8/1: I’ve Gotta PhD announcement with CSMU.

  3. Preparation of Taiwan iGEM conference.

Wet

  1. Run the SDS PAGE for NOS.

  2. Do the heat-inactivated test to test the efficiency of heat-inactivated chlortetracycline in pTet-GFP-pBAD-TetR with 2% arabinose.

  3. Use CI857 to replace EL222 gene, change the design of growth switch.

  4. Analyze the data of congo red assay.

Dry

  1. Familiar with the operation process of DIC.

  2. Solving the partial differentiation equations we established.

  3. Design and test the amplifying circuit, and continue to draw circuit diagrams.

  4. Populating Wiki for basic page.

HP

  1. Preparation of The Something Podcast.

  2. Preparation of YMCA education event.

Week11 8/9-8/15

Wet

  1. Do the NOS assay to test the efficiency of NO producing.

  2. Use new strain WM3064 in DAP deficient functional test.

  3. Do the heat-inactivated test to test the efficiency of heat-inactivated chlortetracycline in pTet-GFP-pBAD-TetR with 2% arabinose.

  4. Do the three fragment assembly with CI857, FRT, OFP and GFP.

Dry

  1. Perform porcine eyes experiments for five-time.

  2. Solving the partial differentiation equations we established.

  3. The second porcine eye experiment.

  4. Make the basic page picture.

HP

  1. W8/10: YMCA education event.

  2. 8/13: Molecularcloud live stream.

  3. 8/15 Online meet up with iGEM iBowu China.

Week12 8/16-8/22

Wet

  1. Update the newest result from congo red assay

  2. Improve the protocol in NOS assay.

  3. Do the kill switch functional test.

  4. Do heat-inactivated chlortetracycline in pTet-GFP-pBAD-TetR and tetracycline with 0.2% arabinose.

  5. Freeze current bacteria.

Dry

  1. Data analysis and processing.

  2. Solving the partial differentiation equations we established.

  3. Design and test the envelope detector, and order the designed PCB board.

  4. .Make the basic page picture.

HP

  1. 8/17, 18: Taiwan iGEM conference.

Week13 8/23-8/29

Wet

  1. Do heat-inactivated chlortetracycline in pTet-GFP-pBAD-TetR and tetracycline with 0.02% arabinose.

  2. Knockout DapA gene from BL21.

  3. Change growth switch design and test that it can work.

  4. Test NOS kinetic.

Dry

  1. Perform porcine eyes experiments for five-time.

  2. Analyze the datas from the DIC experiment and wet team experiment to fit our model results, and adjust the parameters and conditions.

  3. Envelope Circuit Ver.2

  4. Design the HP page picture.

HP

  1. Preparation of Undergraduate research presentation.

Week14 8/30-9/5

Wet

  1. Do heat-inactivated chlortetracycline in pTet-GFP-pBAD-TetR and tetracycline with 0.02% arabinose.

  2. Do the NO assay.

  3. Biofilm assay with hand.

Dry

  1. Data analysis and processing.

  2. Analyze the datas from the DIC experiment and wet team experiment to fit our model results, and adjust the parameters and conditions.

  3. Soldering the PCB board and integrate the Arduino program.

  4. Design the HP page picture.

HP

  1. 8/31: Undergraduate research presentation.

  2. 9/05: Releasing The Something Podcast.

  3. 9/5,6: Online meet up iGEMeetParis.

  4. Preparation of Into the darkness LARP event.

Week15 9/6-9/12

Wet

  1. Do heat-inactivated chlortetracycline in pTet-GFP-pBAD-TetR and tetracycline with 0.002% arabinose.

  2. IPTG concentration and time difference.

  3. Biofilm assay with book.

Dry

  1. Analyze the datas from the DIC experiment and wet team experiment to fit our model results, and adjust the parameters and conditions.

  2. The third porcine eye experiment.

  3. Make the HP page picture.

HP

  1. 9/8: Meet up with NCKU College X.

  2. 9/12, 13: Into the darkness LARP event.

Week16 9/12-9/20

Wet

  1. Test the best concentration of arabinose to induce pBAD promoter.

  2. Biofilm assay with book.

Dry

  1. Analyze the datas from the DIC experiment and wet team experiment to fit our model results, and adjust the parameters and conditions.

  2. DDesign the app and combine the whole system

  3. Populating Wiki for HP page.

HP

  1. 9/17: NCKU Club Festival.

  2. 9/20: Contact lens recycling week.

Week17 9/21-9/27

Wet

  1. Do heat-inactivated chlortetracycline in pTet-GFP-pBAD-TetR and tetracycline with 0.002% arabinose.

  2. Porcine eye NO penetration.

Dry

  1. Comparing MATLAB simulation results with wet and dry experimental datas, adn try to adjust our models..

  2. Test the entire system and make improvements.

  3. Check for every pages.

HP

  1. Preparation of SDGs Panel discussion.

  2. Preparation of collaboration with NYMU.

Week18 9/28-10/3

Wet

  1. Do heat-inactivated chlortetracycline in pTet-GFP-pBAD-TetR and tetracycline with 0.0002% arabinose.

  2. Do kanamycin resistance gene deletion experiments.

  3. Biofilm SDS PAGE.

Dry

  1. Comparing MATLAB simulation results with wet and dry experimental datas, adn try to adjust our models.

  2. Device appearance design.

  3. Team page coding.

HP

  1. 9/29: SDGs Panel discussion with Taiwan iGEM team.

  2. 10/3: Collaboration with NYMU.

  3. Preparation of visiting TWBIO.

Week19 10/4-10/10

Wet

  1. Do heat-inactivated chlortetracycline in pTet-GFP-pBAD-TetR with 0.0001% arabinose.

  2. IPTG induces NOS SDS PAGE.

Dry

  1. Documenting our results on the wiki page.

  2. Printed and assembled device.

  3. Finish all wiki page design.

HP

  1. 10/4: Online meet up cGEM.

  2. 10/8: Visit TWBIO.

  3. Preparation of discussion with AIESEC.

Week20 10/11-10/17

Wet

  1. Wrinting wiki page.

Dry

  1. Writing software (computational method) page, documenting double laplace transform (the method we use to solve our models) as a new tool to help future iGEMers.

  2. Complete device and demo.

  3. Wiki content submission.

HP

  1. 10/11: Discussion with AIESEC.