Team:ZJU-China/Notebook - 2015.igem.org

8.25.2015

The sequence of ermE+plasmid, Frr+plasmid and plu1537+plasmid were confirmed, which marked the success in standardization of 3 parts!!

8.24.2015

Bacteria solution PCR: metK and OrfX. Only negative clone. DNA sequencing: ermE+plasmid, Frr+plasmid, plu1537+plasmid.
Extraction of plasmid mCherry and double enzyme digestion.
Selected from single colonies of plu1537.

Power cut. We played table tennis near our lab.

8.23.2015

Selected from single colonies of metK and OrfX.
Transformed standard plu1537 plasmid into BL-21.
Bacterium solution PCR: ermE and Frr.

We kept a Madagascar cockroach as our pet~

8.22.2015

Selected from single colonies of ermE and Frr. Extraction of plasmid (standard plu1537).
Bacterium solution PCR: standard plu1537.

8.21.2015

DNA sequencing. Seamless assembly: plasmid+1537, plasmid+tcdA1-L+ tcdA1-M+ tcdA1-R, plasmid+ermE, plasmid+Frr.
Seamless assembly: plasmid+metK, plasmid+OrfX.
Successfully booked the HI-Boston Hostel and paid the full payment~

38th Group meeting

8.20.2015

Introduced a software named Mou which could enhance the efficiency of writing wiki. Discussed the business planning of our product and the photos on the wiki.

8.20.2015

Extraction of plasmid mCherry and double enzyme digestion. Seamless assembly: plasmid+1537, plasmid+tcdB1. PCR: ermE, Frr, metK and OrfX. Clean up and DNA gel extraction.
Capsulated Streptomyces Avermitilis toxicity test. TT01 toxicity verification.
PCR: ermE, Frr, metK and OrfX. Clean up and DNA gel extraction.
Again used flow cytometry to check the diameter of the embedded E.coli and tried to count the E.coli which were successfully embedded. The results were not that ideal again.

8.19.2015

Finished the background of avermectin and toxic protein. Sent bacterium sample to BNU and we would continue to help them.
PCR: ermE, Frr, metK and OrfX. Clean up and DNA gel extraction.

8.18.2015

PCR: CDS tcdB1, CDS 1537, tcdA1-L, mcherry. DNA sequencing.
Half-done the model of degration of toxic protein. Got the kit for detection avermectin.

8.17.2015

PCR: CDS tcdB1, CDS plu1537 and mCherry.
DNA gel extraction: tcdA1-L and plu0840L.
Seamless assembly: plasmid+pBad+plu1537.
Detected the relationship between distance of food source and food consumption.
Designed the primers for Frr, metK, OrfX and ermE again because the need for standardization.

37th Group meeting

8.16.2015

Built the framework for wiki. Discussed the Syn-bio talks on next Saturday.

8.16.2015

Preparation of competent cells.DNA gel extraction.
Verification of the bait attractiveness.

8.15.2015

PCR: pBad, tcdA1-L, tcdB1, plu0840L and plu1537.
Purchased E.coli BL21.
The experiment concerning Streptomyces avermitilis finished 80%.
Lovely poppy~

8.14.2015

Test the Avermectin detection kit with pure Ivermectin.
Designed the primers for plu0840, plu1537, tcdA1 and tcdB1 again bucause of the need for standardization.
PCR and clean up. Concluded the successful PCR parameters of different gene clusters.

8.13.2015

Overlap: pBad and tcdA1-L, pBad and tcd-B1, pBad and plu1537. Extraction of plasmid mCherry and enzyme digestion.
Completed wiki page for 2nd model. Drew the 3D ball-and-stick models for CNC with Solidworks. Completed the device for killing termites.
Completed the SCM program for HAZU and they affirmed our help.

Yummy hotpot~

8.12.2015

Overlap: 0840L and 0840R.
Tried to purify the embedded E.coli with the E.coli which were able to express RFP.
Used flow cytometry to check the diameter of the embedded E.coli and tried to count the E.coli which were successfully embedded. The results were not that ideal.

8.11.2015

PCR: pBad, tcdA1-L, tcdA1-M, tcdA1-R, tcdB1, 0840L, 0840R, 1537, GFP.
PCR: ligated product. Optimized the PCR program. Cleaned up. PCR again.
Fed the termites with Photorhabdus luminescens TT01 bacterium cells.
SEM scanned our samples to verify whether Streptomyces avermitilis were successfully embedded with CNC.

8.10.2015

PCR: pBad, tcdA1-L and GFP.
Used Bgl2 and EcoR1 digested inserted fragment and cleaned up the product. Ligating fragment into plasmid with T4 ligase.
Mixed blue-stained termites with red-stained termites to verify trophallaxis.
Specified the standardization requirements and laid the foundation for primer designing.

35th Group meeting

8.9.2015

Planned to hold a seminar for freshmen. Tried to design a device for attracting and killing termites.

8.9.2015

PCR: tcdA1-M, tcdA1-R, tcdB1, plu0840L, plu0840R and plu1537.
Extracted the plasmid containing RFP from DH5α. PCR: RFP and confirmed by gel electrophoresis.
Completed our framework and philosophy of safety.

8.8.2015

Visited Shanghai Science&Technology Museum and promoted our Synbio-cards(Polypoly card).

8.7.2015

One step cloning protocol finished.

8.7.2015-8.8.2015

PCR: pBad, GFP, tcdA1-M, tcdA1-R.

34th Group meeting

8.6.2015

Communicated with 2 members of SJTU in our lab. Began to write wiki. Attached more importance to safety.

8.6.2015

Stained 50 termites in blue and 50 in red for trophallaxis experiments.
Drawing plasmid circuits in snapgene.(toxic protein)

8.5.2015

Decided to give up confocol because we couldn't find the specific dye for CNC.
Discussed the circuit construction and experiments planning of toxic protein.

8.4.2015

Completed the One Step Cloning protocol.

33rd Group meeting

8.2.2015

33rd Group meeting. Began to build framework for wiki. Introduced the habits and characteristics of termites.

32nd Group meeting

7.30.2015

32nd Group meeting. Planned to promote synthetic biology and our project in Shanghai Science & Technology Museum. Polished up the Synbio-cards(Polypoly card).

7.28.2015-8.4.2015

PCR: pBad, tcdA1-L, tcdA1-M, tcdA1-R, tcdB1, plu0840L, plu0840R, plu1537 and GFP.

7.28.2015

Giant Jamboree registration completed.

7.26.2015

Listed 15 main problems we were confronted with, including safety, communication between dry group and wet groups.
Designed a new method to embed the bacterium with CNC.

7.25.2015

Designed the primers for plu0840, plu1537, tcdA1 and tcdB1 again bucause of the bug of extra RBS.

7.24.2015

Discussed helping BNU and HUST. Designed and alpha tested the Synbio-cards. Improved the modeling.

7.19.2015-7.24.2015

Attended NCTU meetup in Taiwan. Present our half-done project and communicated with other teams. Decided to help BNU and HUST.

7.18.2015

Listed and detailed the wiki requirements.
Fed the termites with Streptomyces Avermitilis bacterium cells.

7.16.2015

Prepared the home page and member page of our wiki. Prepared the poster for NCTU meetup.

7.15.2015

Designed the primers for Frr, metK, OrfX and ermE again. Got our name card~
Used confocal to verify the successful package of E.coli with CNC. However, the result appeared not ideal and we couldn't find appropriate dye of CNC.

7.14.2015

Prepared for the souvenirs for NCTU meetup.

31st Group meeting

7.12.2015

31st Group meeting. Reviewed the medal requirement and all the rules in lab.

7.11.2015

Mark-recapture method failed because we failed to recapture enough stained termites.

7.3.2015-7.11.2015

Exams of summer semester.

30th Group meeting

6.25.2015

30th Group meeting. Planned to verify the package of CNC with confocal. Continued to prepare for the presentation and application scenario.

6.24.2015

Completed 2 safety questionaires.
Prepared to learn confocol to verify the CNC package for E.coli.

6.22.2015

Put 150 blue stained termites back into the nest for mark-recapture method.

29th Group meeting

6.21.2015

29th Group meeting. Discussed the application scenario for the 5000€ additional sponsership of SYNENERGENE.

6.21.2015

Contacted with Björn and he would help us animate the process of crystallization.

6.20.2015

TEM scanned our samples.

6.19.2015

Fed the termites with Photorhabdus luminescens TT01 bacterium solution to test the natural toxicity. Stained 150 termites in blue for future experiment.

28th Group meeting

6.18.2015

28th Group meeting. 2nd modeling half done. Discussed the results of the SEM.

6.17.2015

TEM and SEM scanned our samples.

6.15.2015

Fed the termites with Streptomyces Avermitilis bacterium solution to test the natural toxicity.

27th Group meeting

6.14.2015

Rearranged all the events with four quadrant method. Checked everything we have had.

6.14.2015

Solved the diffusion equation.

6.13.2015

Extracted the genome of Streptomyces avermitilis.

6.12.2015

Went to shanghai for the interview of visa. 12 members successfully passed the interview.

26th Group meeting

6.11.2015

26th Group meeting. Discussed the half-done presentation and Skype conference with SYNENERGENE. Prepared for the visa.

6.11.2015

PCR: plu1537, with the template of the genome of TT01.

6.10.2015

Paid for the air tickets.
Got the primers of toxic protein.

6.8.2015

Optimization of the model of termites finding food.

25th Group meeting

6.7.2015

25th Group meeting. Polished up the previous modeling. Protocols about the experiments concerning bacterium. A member quit.

6.7.2015

Extracted the genome of TT01.

6.6.2015

Frozen the spores of Streptomyces avermitilis.

24th Group meeting

6.4.2015

24th Group meeting. Brainstormed the Synbio-cards and Synbio-workshops. Listed the datailed personal scheme about the time arrangement before summer holiday.

6.3.2015

Discussed the characterization of E.coli embedded in CNC, including TEM, SEM, confocal, FTIR and flow cytometry.
Our proposal had been accepted and our team would be awarded financial support from SYNENERGENE! Cheers~

Brainstormed how to do human practice and use the €5000. We came up with the Synbio-cards and Synbio-workshops.

6.2.2015

Began to book the air tickets.

6.1.2015

SEM scanned our samples again. Debugged the first modeling.

23rd Group meeting

5.31.2015

Discussed the half-done modeling.

5.31.2015

Built up the model of termites finding food.

5.31.2015

Taught high school students to do experiment to extract DNA from epithelial cell of mouth.

5.29.2015

Repeated the cellulase activity detection experiment. Meanwhile we measured the lysozyme activity in different parts of termites guts.
22nd Group meeting. Specified the medal requirement. Began to prepare for the NCTU meetup.
SEM scanned our samples.

5.28.2015

Completed a model of a cartoon termite holding a sword. Cleaned up our lab and rearranged all the experiment materials we would need.

5.26.2015

Built the framework of the first web page.

5.25.2015

Learned the skills of culturing Streptomyces avermitilis in the professor's lab.

21st Group meeting

5.24.2015

Began to prepare for the presentation.

5.22.2015

iGEM Shanghai Tour. Took part in the conference held in NYU. Visited FDU and communicated with them.

5.21.2015

Chosen the certain toxic protein which we would transfer into E.coli: tcdA1, tcdB1,plu0840 and plu1537.

5.21.2015

Discussed the medal requirements and collaboration among groups.

5.20.2015

Finished the protocol about TT01.
Measured the cellulase activity in termites head, forgut, midgut and hindgut.

5.19.2015

Detailed the medal requirements depending on our project.

5.18.2015

Got the E.coli strain ET12567 from Professor Li's Lab. Began the experiment about Streptomyces avermitilis.

18th Group meeting

5.17.2015

Emphasized the lab safety.

5.17.2015

Did experiments(rainbow kit)related to synthetic biology in Zhejiang Science&Technology Museum with high school students and by this way promoted syn-bio.

5.15.2015

Read paper and discussed how to enhance the efficiency of Avermectin in Streptomyces avermitilis.

17th Group meeting

5.14.2015

Discussed the results of the TEM. Tried to contact with a judge from PKU.

5.14.2015

TEM scanned our samples: using CNC to pack the Bacillus subtilis.
Completed the cover and comic of our proposal which would be handed in to SYNENERGENE.
Contacted with Hangzhou Termites control Institute.

5.14.2015

TEM scanned our samples: using CNC to pack the Bacillus subtilis.

5.13.2015

Got the genome of tcdA1 and tcdB1 in NCBI.
Got TT01(a species of Photorhabdus luminescens) which could produce toxic protein. It would play an important role in our plan B.

5.12.2015

Successfully checked in termites and tc protein family.

16th Group meeting

5.10.2015

Communication between dry group and 3 wet groups. Arranged time for experiments.

15th Group meeting

5.7.2015

Further discussed the proposal and allocated the tasks. Continued to consult professors about several species of bacterium.

5.6.2015

Gave up synthesizing avermectin in Bacillus subtilis. Tried to overexpress avermectin in E.coli and then transformed its plasmid into Streptomyces avermitilis.

5.6.2015

Successfully got the solution of CNC!! And it appeared Tyndall effect.

5.4.2015-5.6.2015

Exams of spring semester.

5.3.2015

Our termite nest was sent out from Guangdong Province.

14th Group meeting

4.29.2015

10 members would go to Taiwan for NCTU meetup.

4.28.2015

Discussed the plan for embedding baterium with CNC and the self-assembly of CMC and chitosan on the surface of baterium.
Debugged the problem of synthesizing avermectin in Streptomyces avermitilis. Consulted professors specialized in synthesizing avermectin in Streptomyces avermitilis.

4.27.2015

Consulted professors specialized in termites and Bacillus subtilis.

13th Group meeting

4.26.2015

Discussed something important: the proposal for the 5000€ additional sponsership of SYNENERGENE and visa. A new mamber joined our team. Specified the problem remaining to be solved of each group.

4.25.2015

Discussd the advantage of Bacillus subtilis campared with E.coli and the utilization of spore of Bacillus subtilis.

12th Group meeting

4.23.2015

Debugged the previous package plan and decided to pack bacterium with CNC. Planned to buy a nest of termites from Guangdong Province. Discussed several demensions of modeling in this project.

4.22.2015

Consulted professors specialized in termites.

4.21.2015

Consulted professors about directly embedding baterium with CNC rather than with the aid of protein domain. Our idea was confirmed and praised.

4.20.2015

Communication with our instructor. Searched for information about cellulose binding domain (CBDs) and overexpression of ivermectin and avermectin.

11th Group meeting

4.19.2015

Decided our project: termite terminator. Allocated all members into 4 groups. Each group was responsible for a part of our project.

10th Group meeting

4.16.2015

Decided to participate in NCTU meetup in summer holiday and apply for the 5000€ additional sponsership of SYNENERGENE. Discussed 3 existing ideas.

4.14.2015

Preliminarily designed the circuit in Streptomyces avermitilis.

9th Group meeting

4.12.2015

Kept 3 ideas and the final idea would derive from them. Detailed these 3 ideas from all the aspects.

8th Group meeting

4.9.2015

Continued to kill unappropriate ideas. Recalled the aim of participating iGEM and reached a consensus.

7th Group meeting

4.6.2015

Began to kill some undoable ideas and further dug the existing ideas, such as biological enigma machine and killing termites.

6th Group meeting

4.2.2015

Developed several new ideas, including bio-SCM, biological enigma machine and slow release of certain chemical. Talked about their feasibility.

5th Group meeting

3.29.2015

Dug previous ideas and considered their safety and feasibility.

4th Group meeting

3.26.2015

Continued to share and improve our ideas, such as bio-lens, detection of schistosomiasis and killing termites.

3.25.2015

Team registration completed.

3rd Group meeting

3.22.2015

Discussed some ideas about modeling. Shared new ideas.

3.21.2015

Communicate with Zhejiang Science&Technology Museum.

2nd Group meeting

3.19.2015

Built up several rules and principles. Tried to make the most of our BBS.

1st Group meeting

3.16.2015

1st Group meeting. Everyone was assigned with his/her own mission. Brainstorm began.

3.15.2015

Visited the AST space of Zhejiang Science&Technology Museum. Decided to collaborate with.

3.13.2015

Concluded the winter project.

2.1.2015-3.13.2015

Everyone read wikis, learned something from previous projects and attempted to come up with new ideas.

1.31.2015

1st meetup. Had a nice meal~

1.30.2015

15 members was picked out. ZJU-China 2015 team was set up~ Our story began.