Team:TzuChiU Formosa/Meeting Minutes

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Revision as of 14:36, 4 August 2010

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: 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: Jul-27, 2010

• Related to the aspect of the adviser:

 The teacher, Jiun Yau Chen went back to school, team leader will make sure whether the teacher would receive
 to guide or not.
 We would like to inquire professor Ji Wei Chen to receive guiding us.

• Team leader would confer on the Cambridge’s project, E-coli with the professor Bing Shiang Wen.
• We should familiar with the lesson of biochemistry and molecular biology, learn how to design primers, and glance at the experiment、material of the Cambridge’s project.
• We decide to get into contact with each other by gmail.
• We hope to finish designing the primer before Thursday.

 (The hypothesis is we could get the promoter sequence from Germany.)

• Shih-shan teach us how to design primer.

 measure the value of Tm
 prefer to clip the front of PCR promoter sequence
 the length is about 2k
 make sure which factor we should use on iGEM website

• To make sure to design the shinedalgarno on the primer directly, there are 78 bases on the primer.
• The problems related to the primer were had to conduct immediately as follows:

 First, decide which vector to connect the restriction site on the primer.
 Second, should we decide to use the AlkG operon? Please review the paper about the genome which was mentioned
 in the reference that Shih-shan sent from.

• Team leader brought up an idea about observing trace elements would let the ecoli change the color.
• If the time were enough to add the gene of brightening, we could know the ocean was polluted or not. (The green light of luciferin system is different from the light of photosynthesis system.)
• Shih-shan illustrated how to find AlkB1 on the nucleotide of NCBI.

• The letter of requesting German to offer us gene had sent out.
• Team leader would send the application document of asking for cyanobacteria to ATCC.
• According to the photosynthesis of cyanobacteria, the reference told the different from the prokaryote and the

 eukaryote photosynthesis system. The reference also told that the thylakoid is better than the chlorophyll,
 and the thylakoid would influence the eukaryote was eaten by it. Yu-jen will continue to search for the paper
 about the photosynthesis of cyanobacteria.

• In National Taiwan Ocean University professor Shiou-mei tries to sift out the gene of oil eating at

 present,she recommended the candidates to us about finding the resources of cyanobacteria, like Mr.Ju from the 
 surroundings research of NTU and Miss.Su from the branch in Dung-guang under the examination of aquatic 
 products research.
 Though Mr.Ju from the environmental engineering research of NTU deals with the problems of environmental 
 engineering but had mentioned to do not do molecular biology.
 Miss.Su or Mr. Jeng from the branch in Dung-guang under the examination of aquatic products research both had 
 mentioned to do not do molecular engineering.

• About inquiring for the marine biogeochemistry laboratory, we discovered three classifications of

 cyanobacteria cultivated in the laboratory are prochlorococcus, synechococcus and trichodesmium.

• At present the iGEM factor wasn’t found yet, Chiau-wen will continue to find out and watch the video of the

 iGEM.

• According to the teacher Yan recommended us to find the CO2 induced gene, Shih-shan didn’t find out yet. We

 hoped to use the chemical way to resolve, how about adding reagent to observe the colors.

• Shih-shan help to design primer and watch the video of iGEM.

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-06, 2010

• Carry out experiment program:

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

• Correct our idea model.
• 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

• 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.

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

Date: Jun-15, 2010

• Discuss everyone’s opinions after read several papers.
• 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.

 Sinceβ-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.

• 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

• Brainstorming.
• Everyone elected 2 ideas and chose 1 idea which they want to follow.
• 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

Date: Jul-19, 2010

• Team leader introduce subgroup project, the project idea from the aromatic which put in bathroom.
• Plan to produce fragrance in E-Coli.
• Current problem: haven't find the sequence and the pathway.
• We have sent several letter toProfessor Hong-Hwa Chen, Institute of Tropical Plant Sciences, NCKU
• Advisor: Professor Woon Peng-Yeong, Institute of Molecular Biology and Human Genetics, Tzu Chi University