18th, Feb

Place: Room 363, Life Science building

Instructor: Mr.Hong

Recordist: Wuyang Chen

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I. Discuss about our project:
1. SNS:
To complete this project is hardly possible. While it is likely to realize part of it, such as a system which is able to create and sense signals. But we need to confer our project some new meanings.
1) About making a signal disappear, according to Mr. Hong, we can add a rapid degradation label onto the signal.
2) We are afraid that the colony is too small to create an appropriate concentration gradient. According to Mr. Hong, it won’t be a big problem.

2. Solve the graph colouring problem using E.coli
1) In fact, we will only use E.coli to emit light in different colors, and all the algorithm for solving graph coloring problem is processed artificially.
2) We need to consult professors in Chemistry Department about constructing structures using ssDNA.
3) The scale of DNA strand is far too small than that of E.coli.
4) The fusion protein of Zn finger and the Ag43 would be very useful. We can think about how to make use of it.

3. Fatigue of specific stimulus
1) comK is a protein produced by bacillus subtilis and “competence” is a state of it. The possibility of turning into competence state is proportional to the amount of comK. We can substitute the protein involved in competence state for the protein we need.
2) The system can be used as a special lock.
3) How to make circuit one recover its function as quick as possible?
a) by means of protease?
b) by means of aptamer?

II. Set up groups to continue brainstorm

III. Make plans for the whole term.

25th, Feb

Place: Room 363, Life Science building

Instructor: Mr.Hong, Yinghong Lan

Recordist: Xingwen Chen

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Continue brainstorming.
I.Three ideas we have put forward before:
1.Bacterio-SNS (Social Networking Services )
problem1.The signal molecules may exist for too long.
solution：Add a degradation tag to the signal protein for the cell to degrade it quickly.
problem2.How to construct a memory system?
There are several ways but which is the most suitable? problem3.Does CDK exist in bacteria?
We can't get it until we find a paper about that.
problem4.We should consider what kinds of result we will achieve.

2.Solve graph coloring problem with DNA and visualize the result with E.coli.
problem1.How to construct the complex DNA structure?
We can ask a professor who are studying this.
problem2.Bacteria are much bigger than DNA,thus the visualization may be impossible.

3.E.coli mimic specific stimulation fatigue
problem1.The idea will actually be quite boring if our purpose is only to mimic.
Think of something new which can apply the system.
problem2.The signal molecules may exist for too long and signals may influence each other.
Change the signal and consider some physical signals such as temperature and light.


II.New Ideas
Zhou Shan says:
1.Bacteriaphage therapy

2.Synthetic biology moving into the clinic

3.improve bacteria tolerance：
a)efflux pump
b)heat shock proteins
c)membrane modification
d)general stress respond
These are mostly achieved by scientists.It is wrong to repeat others unless we can come up with something new.

4.Some thoughts about nucleic acid aptamer
a) Aptamer itself can be substrate.
b) Two aptamers cna be combined on a single bead.


III.Professor Liu suggest we could do something on the basis of our work of iGEM 2011.
Luo Siwei, a team member of iGEM2011,says that if we must do as this,the only thing we can do is to make it more specific,which seems a little boring.And he indicates that the work last year is too complicated and lacking in aesthetics.


IV.About aptamer
We have the technology and we can start the SELEX now.But we have to work out a good application of it.


V.Tasks of the next two weeks
Direction 1.Come up with a new idea on the basis of the work last year.
a)What can we improve?
b)Think about uncompleted work.
c)Try to apply the signal and response system we came up with in the SNS subject.
d)Try to apply the circuits in the specific stimulation fatigue subject.
e)Read more papers,view previous works and get some inspirations.

Direction 2.Bacterio-SNS:
a) Learn more about toggle switch.
b) Find out if there is something similar to CDK complex in E.coli or B.subtilis.
c) Think about what effect shall we get finally.
Direction 3:E.coli mimic specific stimulation fatigue:
Think of an application of it.

3rd,Mar

Place: Room 363, Life Science building

Instructor: Mr.Hong

Recordist: Xi Chen

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I.journal club
Chen Wuyang, who talked firstly, introduced a kind of marine photosynthetic bacterium Rhodulum sulfidophilum which can produces extracellular nucleic acids. These were found to be produced concomitantly with cell growth. However, the mechanism of this phenomenon had not been figured out, instead, someone hypothesised that it is the process of lysis of a subfraction of cells that makes this happen. After that, the speaker addressed that using engineered plasmids and the bacterium can make the production of extracellular nucleic acid under control which had been proved by anther paper.

After that Zheng Xuexuan gave us a presentation about nanorobot. This autonomous DNA nanorobot was controlled by an aptamer-encoded logic gate, enabling it show different function in different cues. What’s more this kind of device can be loaded with a variety of materials in a highly organized fashion.


II.Introduction of SELEX
We invited Chen Liang, a graduate student, to refer us some knowledge about SELEX( Systematic Evolution of Ligands by Exponential Enrichment).In sum, he talked about the definition about this technology and the main round of this method. Additionally, some examples also were taken so that we can comprehend in a deeper degree.

III.Discussion about the probability of the SNS the program someone raised in the previous meeting and proposed more questions remaining fixed.

July 17-July 23

7.18-7.21 ---- ligate the standard part Terminator to the end of toggle switch result: we conduct a enzyme digestion with EcoR1 and Pst1 to the final ligation product and the electrophoresis result shows that the ligation is successful.

July 24-July 30

7.22-7.29 ---- perform the following experiments: PCR of rbs-ci-ter, enzyme digestion(E,S),ligation with LuxPR(standard part from IGEM registry digested by E,X),tranformation,plasmids extraction. result: the concentration of plasmids with ligation gene is as high as ...

July 31-Aug 6

7.30-8.3 ---- PCR of LuxPR-rbs-ci-ter, enzyme digestion(E,S),ligation with LuxPR(standard part from IGEM registry digested by E,X),tranformation,plasmids extraction.

Aug 7-Aug 13

Aug 14-Aug 20