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From 2010.igem.org

IGEM Workshop Asia in TCU Formosa

Our team has three sub-groups with different projects going on. The final project will be determined latest by August. Here are our meeting minutes starting from July.

Team 1: GoldenLi

Date: Jul-22, 2010

Last meeting, we try to use e-coli to secrete β-carotene, but we found that some biotech company had published this idea already.

So we decide to change our way:

• Use bacteria to deal the sewage problem
  
• Combine two igem biobrick, which are 2008 Chiba time manager and 2009UCSF Motile cellular robots.
  
• Use the system that the bacteria which can secrete the biofilm combined with our original idea that secretβ-carotene.
  
• use nano size silver ion to use at antibacterial
  
• creat a bacteria which could make there own Magnetic field
  

Date: Jul-19, 2010

• Team leader introduce subgroup project, the original idea came from Golden Rice production in Taiwan
• Plan to produce mass volume of beta-carotine in E-Coli to solve the problem of malnutrition in under-develope countries
• Current problem: B-carotine releasing mechanism
• Advisor: [http://www.humangenetics.tcu.edu.tw/new_faculty/wps/wps_basic.html Professor Woon Peng-Yeong, Institute of Molecular Biology and Human Genetics, Tzu Chi University]

Date: Jul-10, 2010

Our idea is using E.coli to synthesis β-carotene and secret it out of E.coli.
There are two main parts we have to do with this idea.

• Synthesisβ-carotene in E.coli. There’s a biobrick, BBa_K274210, which used to synthesize β-carotene is publish by 2009 Cambirdge team.
  
• The most difficult part of this idea is that we have to find the secretion mechanisms of E.coli, so this part divided into two major ways and we have to search for much more detail .
  

(1) Signal peptide: find a meet signal peptide for our idea. And find out where should it be cloned.
(2) E.coli: whether E.coli has the ability to exocytosis? Can it be used in secretion of β-carotene in E.coli?

Team 2: Poseidon - Save the World

Date: Aug-9, 2010

Group presentation

1. Find replacement gene : Oceanicaulis alexandrii & Marinobacter aquaeolei VT8,and read their paper to discuss.

• Conclusion :the first choice to replace Alcanivorax borkumensis SK2 is Marinobacter aquaeolei VT8

2.Study the following publications.

Group discussion

1. We found some new bacterias that have the talent to degrade oil in Taiwan.
2. Everyone to find their paper and relative function individually, and finish a report in Microsoft PowerPoint to present in next meeting.

• Shih Shan : Gordonia alkanivorans
• Chen Jung : Gordonia amicaliskim
• Chau Chieh : Gordonia hirsutacorrig
• Chaio Wen : Gordonia namibiensis
• Ying Yu : Gordonia terraecorrig
• Yu Zhen : Gordonia malaquae
  

3. Guan Nan : contact prof. young at National Chung Hsing University that holds our replacement gene.
4. Chau Chieh : arrange our experiment protocol
5. Next meeting on Wednesday(8/11) 12:00 p.m. at Conference room (E407).

Date: Jul-30, 2010

Project Discussing:

1. Looking for alternatives:
2. Here are two groups:

• Ying Yu、Shih Shan、Chen Jung、Chau Chieh are going to find Marinobacter aquaeolei VT8
• Guan Nan、Chiao Wen and Yu Zhen are going to find Oceaniaulis alexandrii HTCC 2633 in another group

3. Must have to understand the function of how to degrade the oil and how to connect them. Your group have consensus and sent information to Ying Yu in 4th August. On next time meeting (8/9), group have to report what you had find with slides.
4. Please send vector’s map email to us.
5. Translated your record into English.

• Shih Shan and Ying Yu translation the part which before 7/6, send gmail to Chen Jung in 8/4, check and unite the font.

6. Advisor: [http://jhc.tcu.edu.tw/detail.php?recordID=1 Professor Chen Ji-Hshiung, Institute of Molecular Biology and Human Genetics, Tzu Chi University]

Date: Jul-27, 2010

Group Discussing:

1. The candidates of instructor:

• Chun-Yao Chen: Dr. Chen went back to school, team leader will make sure whether the teacher would receive to guide or not.
• Prof. Ji-Hshiung Chen: We would like to inquire Prof. Chen to receive guiding us

2. Team leader would discuss the 2009 iGEM Cambridge’s project and the E.coli they use with the professor Ping-Young Woon.
3. We should review the concepts of biochemistry and molecular biology, learn how to design primers, and glance at the experiments and materials of the 2009 iGEM Cambridge’s project.
4. We decide to contact with each other by gmail.
5. We hope to finish designing the primer before this Thursday. (We assume that we could get the alk operon region from Bielefeld University.)
6. Shih-Shan teach us how to design primer.

• Calculate the value of Tm.
• In prokaryotic genes, they need Shine-Dalgarno sequence to help the RNA polymerase binding, so, the fragments of PCR prefer to include the upstream of alk genes.
• The length of alk fragments are about 2k each.
• Make sure which plasmid backbone we should use on iGEM website.
  

7. We dicided to add the Shine-Dalgarno sequence on the primer directly, there are about 7-8 bases.
8. The problems related to the primer design that have to solve immediately as follows:

• First, decide which expression vector to use, and design the restriction site on the primer.
• Secondly, should we decide to include the alkG gene into our idea model?
• About this question we have to review the papers about the A. borkumensis genome which was mentioned in the reference that Shih-Shan sent from.
  

9. Team leader brought up an idea about observing trace elements would let the e.coli change their color.
10. If the time were enough to add the fluorescence gene, we could know the ocean was polluted or not. (The green light of luciferase system is different from the light of photosynthesis system.)
11. Shih-Shan illustrated how to find alkB1 sequence on the NCBI:.

Progress Report:

1. The e-mail of requesting Bielefeld University to offer us ALK genes had sent out.
2. Team leader would send the application document to buy the cyanobacteria from ATCC.
3. About the photosynthesis of cyanobacteria, the reference states that it is different from the prokaryotic and the plant photosynthesis system. It also states that the photosynthetic efficiency of thylakoid is better than the chlorophyll. Yu-Jen will continue to search for the papers about the photosynthesis of cyanobacteria.
4. The professor of National Taiwan Ocean University, Shiou-mei, tries to sift out the gene of eating oil at present, she recommended the candidates to us about finding the resources of cyanobacteria

• Mr. Ju from the surroundings research of NTU
• Though Mr. Ju from the environmental engineering research of NTU deals with the problems of environmental engineering but had mentioned that he doesn’t focus on the molecular biology field.
  
• Miss. Su from the branch in Dung-guang under the examination of aquatic products research institute
• Miss. Su or Mr. Jeng from the branch in Dung-Guang under the examination of aquatic products research institute both had mentioned that they don’t focus on transgenic cyanobacteria.
  

5. About inquiring for the marine biogeochemistry laboratory, we discovered three strains of cyanobacteria cultivated in the laboratory are Prochlorococcus, Synechococcus and Trichodesmium.
6. At present the iGEM biobrick wasn’t found yet, Chiau-Wen will continue to find out and watch the video of the iGEM Asia workshop.
7. According to the teacher, Jui-HungYen recommended us to find the CO2 induced gene, Shih-Shan didn’t find out yet. We hoped to use the chemical way to resolve. We also think about that adding reagent to observe the colors.
8. Shih-Shan help to design primer and watch the video of iGEM Asia workshop.
9. Schedules:

• 7/28(Wed) 16:00pm taking group photos(wear white clothes)
• 7/29(Thu) 16:30pm meeting with teachers
• 7/30(Fri) 12:10pm team meeting in the committee room on 4th floor
• 8/10(Tue) 12:10pm team meeting in the committee room on 4th floor
  

Date: Jul-19, 2010

• Team leader introduces subgroup project, the project idea came from the recent massive oil leak in Gulf of Mexico
• Project introduction could be found here
• Plan to write to professor in German and Tianjin to obtain cyanobacteria and vectors for the project
  

Date: Jul-19, 2010

Group presentation

1. Find the company of ATCC can buy cynobacteria,and UNION BIOMED INC can purchase for ours ,and we need apply for the cynobacteria to enter our country from COA.We planned to purchase cyanobacteria from ATCC.
2. Letter asking for prof. Liu have been sent to Germany Bielefeld University.
3. Yu Zhen reports the cyanobacteria raise way is to consult ATCC’s protocol.
4. Chiao Wen reports we can use MS analysis and GC to detect long chain alkanes.

Group discussion

1. Find our group instruct professor.
2. Everyone apply for a g-mail account to modify our meeting record.
3. Discuss our experiment protocol.
4. Send draft letter to prof.Liu, before E-mail to prof. Puehler Bielefeld University.
5. Find expression vector, purchase cynobacteria ,and find potential replacement bacteria.
6. Next meeting on Wednesday(7/21) 12:10p.m. at Conference room E407.

Date: Jul-13, 2010

Progress Report:

1. Guan Nan completes introduction in english, and revises.
2. Yu Zhen to everybody report cyanobacteria raise way.
3. Shih Shan obtains with Germany's contact way.
4. Ying Yu approach everybody report about the cyanobacteria biological technology.
5. Chiao Wen approach everybody to report how to confirm tests whether to succeed.
6. Chau Chieh and Chen Jung study homepage manufacture.
7. Divides into two groups in our team.

• Cooperates and the invite gene to Germany.
• Purchase cyanobacteria.

8. Seeks professor

Date: Jul-06, 2010

1. Carry out experiment program:

• Introduction: base on the PPT of first seminar, and do some correction.

2. Methods & materials:

• Oil degradation genes: find out the institute to give us these genes.
• Method of culturing cyanobacteria.
• Method of transformation of cyanobacteria.
• Detection device 1: detect the genes are successfully transform into cyanobacteria.
• Detection device 2: detect if the oil-degraded enzymes are workable.

3. Find an instructor:

• Dr. Chen (department of lifescience)
• Dr. Chang (department of laboratory medicine & biotechnology)

We are so happy that we had overcome our first challenge. After the final exam, joyful summer vacation will come to us!! But experiments are waiting for us to accomplish. So this week, Friday(6/25) 7:00 p.m. in Conference hall (4th), we have to discuss following matters:
1. Discuss our experiment time (and when will we go home in summer vacation).
2. Division work to find the required materials.
3. Who we can invite to be our instructor.
4. Meeting we had scheduled on 6/25 but we change the date to 7/6.

Date: Jun-18, 2010

• Rehearsal for the first idea seminar.
• First idea seminar.

Date: Jun-17, 2010

1. Correct our idea model.
2. List problems which need to be solve:

• Which gene do we want to transform into cyanobacteria? (look up these genes’ name, size, and

function etc.)

• Which strain of cyanobacteria we want to express oil-degraded-enzyme genes?
• Look up the alkane transporter of A. borkumensis.
• Look up the oil degradation enzyme genes.
• Keep correcting the idea model.

Date: Jun-16, 2010

1. Discuss everyone’s opinions after read 3 following papers:

• Proteomic Insights into Metabolic Adaptation in Alcanivorax borkumensis Induced by Alkane Utilization.
• Genome sequence of the ubiquitous hydrocarbondegrading marine bacterium Alcanivorax borkumensis.
• Global features of the Alcanivorax borkumensis SK2 genome.

2. Find useful figures on the internet.
3. Figure out the contents for the first seminar.
4. Compare 2009 iGEM Tianjin University, we found the way to solve the problem of CO2 production.
5. Bring up the model of our idea.

Date: Jun-15, 2010

1. Discuss everyone’s opinions after read several papers.
2. Now, we face some difficult problems:

• Alcanivorax borkumensis is gammaproteobacteria, its gene regulation may be the same with E.coli. So, we have to prove that the A. borkumensis gene can work in e.coli.
• Crude oil is composed of many compounds, are they all took in bacteria via the same transporter?
• A. borkumensis can degrade the long-chain alkanes into “ non-poisonous” carbon chain.
• We have to define what is the “non-pooisonous” carbon chain. However, if the end product of oil degradation is non-polar, it may still destroy the protection ability of bird feather.
• Since β-oxidation is an important metastasis pathway. It is difficult to reduce production of CO2 via inhibit the β-oxidation of A. borkumensis. And it is also hard to application in large scale.
  

3. Focus on 3 following papers:

• Proteomic Insights into Metabolic Adaptation in Alcanivorax borkumensis Induced by Alkane Utilization.
• Genome sequence of the ubiquitous hydrocarbondegrading marine bacterium Alcanivorax borkumensis.
• Global features of the Alcanivorax borkumensis SK2 genome.

Date: Jun-11, 2010

1. Brainstorming.
2. Everyone elected 2 ideas and chose 1 idea which they want to follow.
3. Oil-degradation group reported their progress:

• We found Alcanivorax borkumensis can live in oil polluted sea region and able to degrade the crude oil then turn into energy which it can use.
• We want to find an oil-eating plankton, which with symbiosis bacteria can help it degrade greenhouse gas(CO2).
• Moreover, we want to let the oil-eating plankton radiate fluorescence, so it can be used to determine the oil polluted situation and oil-flowing direction.

Team 3:Saycar sata'os(cymbidium fragrance of Taiwan aboriginal language)

• The last week of May:

a.Ascertained who would take part in this competition, formed the team.
b.Decided the way of discussion and our weekly meeting times.
c.Chose 宏任 to be the leader, and 俊誠 would be the one who make contact with other academic organizations.
d.Separated the team into three groups, and every group should bring up ideas next time.

• The first week of June:

Came out with many ideas-

a. use the bacteria to filter water
b. use the bacteria to produce fiber which can be used on papermaking
c. decrease the content of CO2 by using the bacteria to sedimentate calcium carbonate
d. use the bacteria to pare cornea→to treat myopia
e. use the bacteria to release cool air
f. use the bacteria to decompose the hard-decomposing petrochemicals
g. transform the exhaust gas into non-toxic one
h. use the bacteria to produce fragrance
i. use the bacteria to make cleaning products
j. apply the bacteria to cosmetology
k. use the bacteria to produce water-resisting paint
l. generate electric power by bacteria
m. use the bacteria to probe methane or other poison gas
n. use the bacteria to sublime silicon
o. use the bacteria to make facial masks

• The second week of June:

a. Discussed about the feasibility and originality of every idea
b.俊誠 discussed the questions about fragrance with professors at school

• The third week of June:

a.Chose “using the bacteria to produce fragrance” to be the researching theme of our team

b.Searched for reports about fragrance of plants, and found out that Academia Sinica were making great effort on researching the fragrance of mint. We also heard of that National Cheng Kung University was researching on fragrance of flowers, too.

c.We wanted to choose professor 溫秉祥 to be our instructor, and we decided to request him later.

• The fourth week of June:

a.Made sure that professor 溫秉祥 would be our instructor
b. Joined the primary election at school
c. Sent the first letter to NCKU to ask questions about fragrance molecules.

• Last week of June:

a. Kept in touch with NCKU by e-mails
b. Collected papers
c. iGEM workshop

• The second week of July:

We got the paper which was written by National Cheng Kung University in 2002.They said hat they could give us their papers which was written in 2006 and 2008,too.

• The third week of July:

a.Our leader interpreted the paper to us. We discussed whether to conduct the MVA pathway in this project or not because the MVA pathway is very complex.

b.We designed the primer by using the information which was given by the paper —'Strategies for transgenic manipulation of monoterpene biosynthesis in plants'.

• The fourth week of July:

We discussed with the teacher about whether to take the target DNA from Phalaenopsis bellina by ourselves or not .Considering that we didn't have much time, we thought we should keep in touch with NCKU, trying to get what we want, such as the GDPS gene, plasmid, and restriction enzyme from them.

• The first week of August:

We found out that the bacteria we cultured had MVA pathway itself. Therefore, we only have to conduct IPP and DAMPP pathway from GDPS to produce GPS.After talking with the professor of NCKU on the phone, we realized that we should get the materials of GDPS from their postdoctoral graduate students, so we decided to visit them next week.