Team:CCU Taiwan/Notebook

Notebook

Week1 (04/05-04/11)

WL

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Understand the project and discuss the procedures of experiment.

DL

---

Search for the principles and materials of the NS1 detection kits on the market.

HP

---

Schedule the progress of HP.

Week2 (04/12-04/18)

WL

---

1. Find the principle of LAE and experimental procedures.
2. Confirm the interaction between the CLEC5A and E protein. (in progress)

DL

---

1. Search for the structures and binding regions of the envelope protein (E protein) and CLEC5A.
2. Learn how to use Chimera.

HP

---

Search for the current products on market.

Week3 (04/19-04/25)

WL

---

1. Optimize the experimental procedure of LAE.
2. Confirm the sequence and structure of E protein and design the procedure of CLEC5A expression.

DL

---

Use Chimera to simulate the docking of E protein and CLEC5A.

HP

---

Analyze the pros and cons between our product and the current products.

Week4 (04/26-05/02)

WL

---

1. Design the TR-PCR primers. (in progress)
2. Confirm the interaction between the CLEC5A and E protein. (done)

DL

---

1. Analyze the results of Chimera.
2. Learn how to use Rosetta.

HP

---

Virtual meetup with NCTU_Formosa iGEM.

Week5 (05/03-05/09)

WL

---

1. Design the TR-PCR primers and choose the plasmid for expression.
2. Design the procedure of E protein expression, E protein and CELC5A’s primers and choose the plasmid for expression. (in progress)

DL

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1. Search for the principles of the NS1 antigen test and pregnancy test and design our detection kit.
2. Try to use the ab initio method to produce the peptides and the FlexPepDock method to simulate peptide and protein docking by using Rosetta.

HP

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Fund raising for project.

Week6 (05/10-05/16)

WL

---

1. Design the TR-PCR, E protein and CLEC5A primers. (done)
2. Choose the plasmid for E protein and CLEC5A expression. (E protein-pET-29a (+), CLEC5A-pET-29b (+))

DL

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1. Design each component of the detection pads.
2. Practice the FlexPepDock method to simulate peptide and protein docking.
3. Generate fragments which is the input of producing the peptides.

HP

---

Conduct the survey on dengue.

Week7 (05/17-05/23)

WL

---

1. Practice the instrument operating.
2. Culture the DH5α-pET29b, DH5α-pCMV6-CLEC5A and DH5α-pKz-V5 tag-C-CI-prM-E-(HA tag)2

DL

---

1. Search for the concentration of each stage of dengue virus viremia.
2. Use the ab initio method to produce the peptides.

HP

---

Conduct the survey on dengue.

Week8 (05/24-05/30)

WL

---

1. Culture DH5A-pCMV6-CLEC5A.
2. Extract the pET-29b (+) & pCMV6-CLEC5A & pKz-V5 tag-C-CI-prM-E-(HA tag)2.

DL

---

1. Discuss the production of the detection kit with Professor Chau, Lai-Kwan.
2. Search for the nature of gold nanoparticles and how to attach gold nanoparticles to the peptides.
3. Use the ab initio method to produce the peptides.
4. Utilize the Mutation method to produce E protein (PL046).

HP

---

1. Build the lesson plan of synthetic biology on podcast.
2. Contact department of health in Kaohsiung city government.

Week9 (05/31-06/06)

WL

---

1. TR-PCR 110 & design the AD-primers.
2. Plasmid extraction of pCMV6-CLEC5A.

DL

---

1. Discuss how to attach gold nanoparticles to the peptides, the size of gold nanoparticles and nonspecific adsorption of the reagent with Postdoctor Tseng, Yen-Ta.
2. Fill in the biosafety form.
3. Use the ab initio method to produce the peptides.
4. Utilize the Mutation method to produce E protein (PL046).

HP

---

1. Contact Dr.Jiang, Yi-huah.
2. Contact Center for Dengue Prevention and Control, Tainan City Government.

Week10 (06/07-06/13)

WL

---

Design the AD-primers. (done)

DL

---

1. Use the ab initio method to produce the peptides.
2. Utilize the Mutation method to produce E protein (PL046).

HP

---

Visit Dr.Jiang, Yi-huah.

Week11 (06/14-06/20)

WL

---

Optimize the conditions of TR-PCR.

DL

---

1. Use the ab initio method to produce the peptides.
2. Utilize the Mutation method to produce E protein (PL046).

HP

---

Contact Department of Health, Kaohsiung City Government.

Week12 (06/21-06/27)

WL

---

Optimize the conditions of TR-PCR.

DL

---

1. Use the ab initio method to produce the peptides.
2. Utilize the Mutation method to produce E protein (PL046).

HP

---

1. Contact Center for Dengue Fever Control and Research, Kaohsiung Medical University Chung-Ho Memorial Hospital.
2. Contact National Mosquito-Borne Diseases Control Research Center.

Week13 (06/28-07/04)

WL

---

1. TR-PCR 151(done) & TR-PCR 110.
2. Amplify the CLEC5A and E protein.

DL

---

1. Confirm the source of the materials of the detection kit.
2. Design the home page of wiki.
3. Use the ab initio method to produce the peptides.
4. Utilize the RosettaCM method to produce E protein (PL046).
5. Deal with the carbohydrate on the E protein.

HP

---

1. Record the first episode of podcast.
2. Build the lesson plan of education on Mingyang High School.

Week14 (07/05-07/11)

WL

---

1. TR-PCR 151(done), TR-PCR 110. (done) and AD-PCR 151 and AD-PCR 110 (done).
2. TA-CLEC5A cloning.

DL

---

1. Modify the component of the control line.
2. Use the ab initio method to produce the peptides.
3. Utilize the RosettaCM method to produce E protein (PL046).
4. Deal with the carbohydrate on the E protein.

HP

---

Virtual meetup with NCTU _Formosa iGEM.

Week15 (07/12-07/18)

WL

---

1. TA-110, TA-151, TA-151R cloning and TA-110, TA-151, TA-151R colony PCR.
2. TA-CLEC5A colony PCR & plasmid extraction (TA-CLEC5A) & DNA sequencing. (M13F(R)-TA-CLEC5A)

DL

---

1. Search for the ways of modeling by 3D printer.
2. Confirm the component of the control line.
3. Use the ab initio method to produce the peptides.
4. Utilize the RosettaCM method to produce E protein (PL046).
5. Deal with the carbohydrate on the E protein.

HP

---

1. Visit TFDA.
2. Visit Center for Dengue Prevention and Control, Tainan City Government.
3. Visit National Mosquito-Borne Diseases Control Research Center.
4. Education at Cheng-He Confucian Academic Center.

Week16 (07/19-07/25)

WL

---

1. TR-PCR 110R. (done)
2. Sequencing M13F(R)TA-151 and M13F(R)TA-151R.
3. Digest TA-CLEC5A, ligate CLEC5A to pET-29b (+) and transform pET-29b (+)-CLEC5A into DH5α.
4. pET-29b (+)-CLEC5A colony PCR, TA-E protein cloning and cultivatepET-29a (+).

DL

---

1. Design the layout of wiki.
2. Design the project promotion video.
3. Arrange the content of the poster.
4. Use the ab initio method to produce the peptides.
5. Utilize the RosettaCM method to produce E protein (PL046).
6. Use the Protein-protein Docking method to simulate peptide and E protein docking.

HP

---

1. Visit Department of Health, Kaohsiung City Government.
2. Visit Center for Dengue Fever Control and Research, Kaohsiung Medical University Chung-Ho Memorial Hospital.
3. Virtual meetup with iGEM CSMU Taiwan.
4. Virtual meetup with Team iGEM IISER Berhampur

Week17 (07/26-08/01)

WL

---

1. AD-PCR 110R& AD-PCR TA-151R (done), TA-110R cloning & TA-110R colony PCR.
2. Transform pET-29b (+)-CLEC5A into BL21(DE3) and sequencing (M13F(R)-TA-E protein).

DL

---

1. Design the home page of wiki.
2. Design the project promotion video.
3. Arrange the content of the poster.
4. Use the ab initio method to produce the peptides.
5. Utilize the RosettaCM method produce E protein (PL046).
6. Use the Protein-protein Docking method to simulate peptide and E protein docking.

HP

---

1. Design the project logo.
2. Record the second episode of podcast.
3. Compose the children storybook.

Week18 (08/02-08/08)

WL

---

1. Digest TA-110 and TA-151 & ligate 110 & 151 to pET-29b (+).
2. Sequencing (M13F(R)TA-110R) and AD-PCR TA-151R (done).
3. Express CLEC5A with 1μM IPTG and run SDS-PAGE.

DL

---

1. Design the layout of the poster.
2. Shoot the member introduction of the project promotion video.
3. Calculate the force between gold nanoparticles.
4. Use the ab initio method to produce the peptides (110-3 and 151-8).
5. Use the Protein-protein Docking method to simulate peptide (110-3) and E protein (PL046) docking.

HP

---

1. Virtual meetup with Dr.Liang, Shih-Yuan.
2. Taiwan National Education Radio interview.
3. Visit senior citizen service center for dengue fever informational audio recording in Taiwanese Hokkien.

Week19 (08/09-08/15)

WL

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1. Culture DH5A-pET-29b-110 & DH5A-pET-29b (+)-151.
2. Run the CLEC5A western blot.

DL

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1. Make the poster.
2. Shoot and edit the member introduction of the project promotion video.
3. Print the model for NCTU and the detection kit by using a 3D printer.
4. Calculate the force between gold nanoparticles.
5. Use the Protein-protein Docking method to simulate peptide (110-3) and E protein (PL046) docking.

HP

---

Education at Cheng-He Confucian Academic Centre.

Week20 (08/16-08/22)

WL

---

1. pET-29b (+)-110 colony PCR & pET-29b-151 colony PCR.
2. Ligate E protein into pET-29a (+) & transform pET-29a (+)-E protein into DH5α and pET-29a (+)-E protein colony PCR.

DL

---

1. Shoot and edit the member introduction and the beginning of the project promotion video.
2. Calculate the force between gold nanoparticles.
3. Done the template of wiki.
4. Print the team name by using a 3D printer.
5. Use the Clustering method to deal with the result of the peptide.
6. Use the Protein-protein Docking method to simulate peptide (151-8) and E protein (PL046) docking.

HP

---

1. Record the third episode of podcast.
2. Taiwan iGEM conference.

Week21 (08/23-08/29)

WL

---

1. Optimize the procedure from digestion of TA-110 to pET-29b(+)-110 colony PCR.
2. Express the CLEC5A in large scale and find that protein was expressed in the pellet.

DL

---

1. Done the member introduction and the beginning of the project promotion video.
2. Code the home page.
3. Use the Clustering method to deal with the result of the peptide.
4. Use the Protein-protein Docking method to simulate protein and protein docking for NYMU.

HP

---

1. Contact with Mingyang High School.
2. Virtual meetup with Team iGEM IISER Berhampur.
3. Virtual meetup with NYMU Taipei.

Week22 (08/30-09/05)

WL

---

1. Ligate 151R to pET-29b (+).
2. Optimize the procedure of TA-110 with pET-29b ligation and the procedure from transformation pET-29a (+)-E protein into DH5A to protein colony PCR.

DL

---

1. Code the wiki page of safety and sponsors.
2. Use the Clustering method to deal with the result of the peptide.
3. Use the Protein-protein Docking method to simulate peptides and E protein (PL046) docking.
4. Shoot and edit the project promotion video.
5. Do the gold nanoparticles liquidity experiment.

HP

---

Contact with glove puppetry show troupe.

Week23 (09/06-09/12)

WL

---

Optimize the condition of IPTG induction in CLEC5A expression.

DL

---

1. Shoot and edit the project promotion video.
2. Code the wiki page of description, notebook and team members.
3. Design and do the experiment of modifying gold nanoparticles and glass fiber.
4. Analysis the result of the clustering result.

HP

---

1. Record the fourth episode of podcast.
2. Mentoring Mingdao High School.

Week24 (09/13-09/19)

WL

---

1. Culture DH5α-pET-29b(+)-110 & DH5A-pET-29b (+)-151.
2. pET-29b (+)-110 colony PCR & pET-29b (+)-151 colony PCR.

DL

---

1. Shoot and edit the project promotion video.
2. Code the wiki page of notebook and team members.
3. Design and do the experiment of modifying gold nanoparticles and glass fiber.

HP

---

1. Record the fifth episode of podcast.
2. Mentoring Mingdao High School.

Week25 (09/20-09/26)

WL

---

1. Culture DH5α-pET-29b(+)-110 & DH5A-pET-29b (+)-151.
2. pET-29b (+)-110 colony PCR & pET-29b (+)-151 colony PCR.
3. Do the digest and ligation again, transform to DH5α and do the colony PCR.

DL

---

1. Edit the project promotion video.
2. Do the experiment of modifying gold nanoparticles and glass fiber.

HP

---

1. Contact with glove puppetry show troupe.
2. Glove puppetry show filming.

Week26 (09/27-10/03)

WL

---

1. Optimize the procedure from digestion of TA-151 to pET-29b(+)-151 colony PCR.
2. Do the digest and ligation again, transform to DH5α and do the colony PCR.

DL

---

1. Code the wiki page of contribution, parts and collaborations.
2. Changing from MUA/MCH to MHA/SBSH & EDC to DCC.

HP

---

1. SDG panel discussion.
2. Education at Mingyang High School.
3. Record the sixth episode of podcast.

Week27 (10/04-10/10)

WL

---

1. Optimize the procedure from digestion of TA-151 to pET-29b(+)-151 colony PCR.
2. Optimize the procedure from digestion of TA-110 to pET-29b(+)-110 colony PCR.
3. Culture DH5α-pET-29b(+) and optimize the quality of plasmid pET-29b(+).
4. Do the digest and ligation again, transform to DH5α and do the colony PCR.

DL

---

1. Code the wiki page of design and model.
2. Design the narrative thread of the presentation video.

HP

---

1. Education at Mingyang High School.
2. Record the seventh episode of podcast.

Week28 (10/11-10/17)

WL

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Do the digest and ligation again, transform to DH5α and do the colony PCR.

DL

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1. Code the wiki page of education, implementation and protocols.
2. Revise the script of the presentation video.
3. Design the storyboard of the presentation video.

HP

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