Team:TzuChiU Formosa/Notebook

From 2011.igem.org

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Revision as of 03:48, 13 September 2011

Photopaper

2011.02.24

Discussion:

Team organization
Brain storming
- paper making by bacteria with other manufactures such as colors, fragrance, etc.
- "light up" the plants for replacing streetlamps.

2011.03.04

Discussion:

Deciding the guiding teacher (Dr. Chen, Dr. Jung, Dr. Liu, or Dr. Yen?)
Brain storming
- to make colorful cellulose which produce by bacteria. We may choose pigments such as beta-carotene
- Planning to get informations of pigments by iGEM 2010 teams

2011.03.14

Discussion:

Division of work
Brain storming
- paper making by bacteria with other manufactures such as colors, fragrance, etc.
- "light up" the plants by transfecting symbiotic bacteria which is cloned in fluorescence gene
- biotic thermal pads

2011.03.23

Discussion:

still cannot decide which teacher will our team choose to be our guiding

teacher(Dr. Yen?)

two ways that we may use to proceed our project-
- Culturing bacteria which has pigment gene
- Let the cellulose-producing bacteria secrete pigment into the medium

2011.03.24

Discussion:

Deciding the guiding teacher (Dr. Chen, Dr. Jung, Dr. Liu, or Dr. Yen?)
about our project: Wanna find out the cellulose gene’s CDS, clone it out, then clone the cellulose gene and pigment gene into E. coli.

2011.04.08

Discussion:

about our project-

Maybe we’ll change our project if it’s not innovate enough

mentioning that every team member should follow the iGEM 2011

website so that we won’t miss important notices

2011.06.22

Discussion:

a new project- Biojenny(to produce silk protein)
the next step is to find out the detailed compositions of silk
maybe we’ll choose yeast to be our host

2011.07.01

Discussion:

How to get silkworms?
discussed about the methods that we can get silk proteins

2011.07.09

Discussion:

discussion about the connections between four silk proteins
get clearer informations about silk proteins by reading papers
make sure what the major proteins are(H-chain, L-chain, P25)

2011.07.15

Discussion:

after having discussion with our guiding teacher, we find out the project may not be finished with technology and ime limitations (one of the silk protein size is too big for cloning)
we decided to change the project back to the one before: to produce cellulose for paper-making by bacteria.

2011.07.18

Discussion:

planning to choose cyanobacteria to be our host
discussion about the presentation contents of semi-final

2011.07.23

Discussion:

clearer explanation of our project
system designing
How to solve the problems that the judges of semi-final just asked?
- We plan to use regulator promoter to regulate the secretion of cellulose; and we’ll use biobricks that the Tokyo team designed last year.

==='''2011.09.06'''===

'''revive Rhodobacter rubrum'''


==='''2011.09.07'''===

'''R. rudrum medium'''
K2HPO4 					1g
NaCl					0.5g
FeSO4．7H2O				0.01g
CaCl2 					0.02g
MnCl2．4H2O 				0.002g
MgSO4．7H2O				0.2g
NaMO2O4．2H2O				0.01g
ddH2O					998.258 ml
                                                   （＋
______________________________________________________
                                        1L→take100ml

		＋
Yeast Extrat				0.5g
Sodium malate
(Sodium succinate dibasic hexohydrate)	5g
NH4Cl 					1g
ddH2O 					893.5ml
                                                  （＋
______________________________________________________
                                        1L

'''Raise E. coli(PSB1C3)'''
1.50ml LB+500μl CHLORAMPHENICOL
2. 37℃, overnight (14-16hrs)


==='''2011.09.08'''===

'''Plasmid miniprep kit'''
PSB1C3 plasmid


==='''2011.09.10'''===

'''Digestion check of DNA'''　
PSB1C3 DNA (control)			3μl
PSB1C3/ EcoR
DNA					10μl
10×buffer				5μl
BSA					5μl
EcoRⅠ					1μl
ddH2O					29μl
                                                  （＋
______________________________________________________
                                        50μl

PSB1C3/ pstⅠ
DNA					10μl
10×buffer				5μl
BSA					5μl
pstⅠ					1μl
ddH2O					29μl
                                                  （＋
______________________________________________________
                                        50μl

PSB1C3/ EcoRⅠ+pstⅠ
DNA					10μl
10×buffer				5μl
BSA					5μl
EcoRⅠ					1μl
pstⅠ					1μl
ddH2O					28μl

                                                  （＋
______________________________________________________
                                        50μl
→37℃ for 30 mins


==='''2011.09.11'''===

'''Digestion of DNA'''
PSB1C3/ EcoRⅠ+pstⅠ
DNA					10μl

10×buffer				5μl
BSA					5μl
EcoRⅠ					1μl
pstⅠ					1μl
ddH2O					28μl
                                                  （＋
______________________________________________________
                                        50μl
→37℃ for 2 hrs

'''electroelution Purification'''
PSB1C3 backbone


==='''2011.09.13'''===

'''Raise Rhodobacter rubrum'''
1.50ml LB+500μl CHLORAMPHENICOL
2.37℃, overnight (14-16hrs)

File:.jpg

CO killer

2011.07.04

Today we had our meeting in the afternoon. The weather is so hot. It was like barbeque ourselves under the sun so we decided not to have meeting in the afternoon anymore. The topic today is the oxidation of CO to CO2 – we found out that Rhodospirillum rubrum can undergo Calvin Cycle to obtain their energy from sunlight and use CO2 as their carbon source, however cyanobacteria or other bacteria is needed for CO2 fixation and production of biofuels. But it would be much more sophiscated if we add on the cyanobacteria into the system. Hmmm … looks like we have to improve more on our system design !

2011.07.05

We talked to the microbiologist Prof. Chen CY yesterday evening and stunned us with 3 questions. The time factor, the mutation factor and the gene expression rate. The experiment of CO2 fixation requires at least half a year to complete so we probably couldn’t just simply add in our project. Besides that, we also have to think of the mutation of the gene. If the gene mutated then the product would be useless. And the most important is the rate of the protein to turn fluorescent. Lastly, if the gene size is getting bigger it would be more difficult to insert into the plasmid. Consequently, we would need more time in cloning and that would be time-costing. Uhh … we really need to find the resolution soon ! Any way, Prof. Ingrid is really very busy. We have not see her for the past 2 weeks. Gotta check out with her lab assistant.

2011.07.06

Today we had meeting in the afternoon again. Thanks god the weather is windy. We downloaded all the sequences and CDS of the gene we need. On the other hand we also search the sources of R. Rubrum which we planned to use in our project. There is a few proffesor in taiwan doing the research about R.Rubrum. So Joanne will help the letter to them to request a sample of it. And the worst case we can buy it from biotech corporation. Steven need somebody to be the in-charge of wikipedia. Leo volunteered. Found out that 2 enzymes are available : CODH–Nickel, OM5 –Molybdenum; CODH is has a higher rate of binding with CO, but OM5 can bind with CO in enormous amount at one time. Say no to procrastination ! Next meeting on Friday. A day off tomorrow =D

2011.07.09

Discussion regarding the presentation slide during the preliminary round. Task allocated to all the members. While Joanne and Steven had to write the project proposal ASAP. Not much were done today. But TGIF !! Had some photo session after the meeting. Joanne go crazy with the effect thingy on the MacBook. Stressed up after one week of intensive meeting.

==='''2011.09.08'''===

'''Raise E. coli(K325903&K325229) from CAMBRIDGE'''
1.50ml LB+500μl CHLORAMPHENICOL
2.37℃, overnight (14-16hrs)
3.L-arabinose test

Neither of the two E. coli is feasible.

File:.jpg

Helmersi Codon

2011.02.13

Let the participants to propose some ideas:

To make the waste become ink after bacterial reaction.
Make the bacteria to produce combustible materials.
Make the bacteria to emit different light.
Edible bacteria.
To control the shape of bacterial.
To make the bacteria a fat eater.
Glowing mushrooms.
Make the bacteria to stick with dust.

Poll result:

Top three projects:

Edible bacteria.
Glowing mushrooms.
Combustible bacteria.

Conclusion:

Let all participants to choose their project and make a group then check the extent of implementation.

2011.03.12

Discuss the problem between the team members:

The rule of conference:
- We can choose a chairman.
- We can take turns by seat number then everyone has a chance to practice how to speak stable on the stage.

Group report & Vote:

Edible bacteria had become our determined project.

Conclusion:

To make three groups and search the information of soy protein, milk protein and yeast.

2011.03.21

Group report:

Soy protein: There have people inject a piece of soy protein, but can’t find out the sequence.
The relation between milk protein and probiotics: There is both good and bad relation between milk protein and probiotics.
Yeast:

Pai: Maybe we can search other organisms which have essential amino acids. Then we can complement the lack of essential amino acids in the yeast.

The application on the internet of iGEM:

Huang and Celia will teach other team members how to apply it.

The schedule of iGEM:

2011.05.23:Preliminary

The registration of iGEM:

Registration fee: Give it to Celia
Deadline: 2011.03.23 12:10-13:30

2011.04.12

Celiahas explain the competition system to other team members:

Everybody needs to create a new idea and search its extent of implementation. Then design the experiment.
On May 23, everyone has to introduce and explain the idea through the power point.

Discussion:

How to handle with our original project?
- We can process this project and our own project at the same time.
- We can give the project to one of the team member.

Conclusion:

We decided to give the project to Jin, but we still can process two projects at the same time if he needs our help.
In order to help each other and solve the problems with our ideas, we still have discussion every week.

2011.05.06

Share the ideas:

Sea water purification
Purification of factory water use
Bacteria for wound
Glowing mushroom

Suggestion:

Celia: Maybe you use plant can be easier to get the same purpose.
Huang: Maybe you can use symbiotic bacteria of plant and inject the glowing gene into it.

2011.05.10-2011.05.12

Progress report:

Huanghas changed her idea and is still searching the information.
Tsai has an idea is about bio-battery. To create the ion concentration difference by bacteria and produce the electricity.
- Questions:
  - Celia: If you can produce this project successfully, how do you convince the public to use your product?
  - Huang: Do you have any certification to proof that you can make this project by yeast or bacteria?
Zou has a new idea: To clean up our teeth by bacteria. She had find out the gene of decomposition of tartar and has the conception of teeth whitening.
Ting find the element that both petroleum and oil has contained.
Paiput out a new idea is odorless sweat. He chooses Helicobacter pylori and Proteus mirabilis as host.
Jinfind the information of how Staphylococcus aureus maintain its electricity.
Dorrie is still searching the experiment and being revised the idea.
Yu has a new idea: Rust proof bacteria. She wanted to injected the gene into aerobic bacteria.

2011.05.25

Progress report:

Jin: Because we have figured out the gene then we have to ask Pr. Woon to contact with the author of that paper and get the gene sequence.

Homework:

To find the…
- The performance of E.coli and Lactobacillus.
- Protein purification.
- The plasmid of Lactobacillus.
- TA-cloning
Huang: Send the paper to team members and ask Pr. Woon help us to get the sequence.
Celia: Translate the conference record and store them.

2011.06.26

Progress report:

Experiment design:Jinwill discuss with Pr. Woon and set for the primer.

Homework:

To find the farming methods of lactobacillus.
To find the plasmid is used by Cambridge in 2010.
To understand the design methods of primer.

Team:TzuChiU Formosa/Notebook

From 2011.igem.org

Revision as of 03:48, 13 September 2011

Contents

Photopaper

2011.02.24

2011.03.04

2011.03.14

2011.03.23

2011.03.24

2011.04.08

2011.06.22

2011.07.01

2011.07.09

2011.07.15

2011.07.18

2011.07.23

CO killer

2011.07.04

2011.07.05

2011.07.06

2011.07.09

Helmersi Codon

2011.02.13

2011.03.12

2011.03.21

2011.04.12

2011.05.06

2011.05.10-2011.05.12

2011.05.25

2011.06.26

2011.09.08