Team:Tokyo-NoKoGen/Diary

From 2013.igem.org

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+
      <h1 id="index_title"></h1>
            <ul id="contents">
            <ul id="contents">
-
                <a href="#april"><li><a href="#diary"><strong>April</a></strong></li></a>
+
                <a href="https://2013.igem.org/Team:Tokyo-NoKoGen/Diary"><li><strong>Diary<strong></li></a>
-
                <a href="#may"><li><strong>May<strong></li></a>
+
                <a href="https://2013.igem.org/Team:Tokyo-NoKoGen/Protocol"><li><strong>Protocol<strong></li></a>
-
                <a href="#june"><li><strong>June</strong></li></a>
+
                <a href="https://2013.igem.org/Team:Tokyo-NoKoGen/Safety"><li><strong>Safety</strong></li></a>
-
                <a href="#july"><li><strong>July</strong></li></a>
+
                <a href="https://2013.igem.org/Team:Tokyo-NoKoGen/Acknowledgement"><li><strong>Acknowledgement</strong></li>
-
<a href="#august"><li><strong>August</strong></li></a>
+
<a href="https://2013.igem.org/Team:Tokyo-NoKoGen/Attribution"><li><strong>Attribution</strong></a></li>
-
<a href="#september"><li><strong>September</strong></li></a>
+
               
-
<a href="#october"><li><strong>October</strong></li></a>
+
-
             
+
            </ul>
            </ul>
-
 
 
               </div>
               </div>
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<p>
<p>
Our first official gathering of Tokyo-NoKoGen 2013! Okay, let’s deicde on what we will do for the project this year.
Our first official gathering of Tokyo-NoKoGen 2013! Okay, let’s deicde on what we will do for the project this year.
 +
<BR>
<BR><strong>25</strong>
<BR><strong>25</strong>
<p>Before we start, we looked up on what projects have been in presented in the past iGEM competitions.  
<p>Before we start, we looked up on what projects have been in presented in the past iGEM competitions.  
Line 532: Line 530:
<BR>
<BR>
<BR>
<BR>
-
<img src=https://static.igem.org/mediawiki/2013/3/35/Line.jpg width=1000>
+
<img src=https://static.igem.org/mediawiki/2013/3/35/Line.jpg>
-
<h1 id="april">May</h1>
+
 
 +
 
 +
<h1 id="may">May</h1>
<BR><strong>1</strong>
<BR><strong>1</strong>
<BR>To understand how iGEM work, we made a seminar to understand the basics, for example how to use restriction enzymes, and how to use the BioBrick parts.
<BR>To understand how iGEM work, we made a seminar to understand the basics, for example how to use restriction enzymes, and how to use the BioBrick parts.
<BR>
<BR>
-
<img src=https://static.igem.org/mediawiki/2013/3/35/Line.jpg>
+
<BR><strong>16</strong>
-
<h1 id="april">June</h1>
+
<BR>Since we are going to present at Tokyo University very very soon, we need to practice and revise our poster presentation...Are we all ready?
-
<BR>
+
<BR><BR><strong>19</strong>
 +
<BR>School festival at Tokyo University! We made a poster presentation to many high school students and parents on our last year's project. It was very interesting to explain about genetic engineering of E. coli to those who are not familiar with them! We also got to know other team members of iGEM Japan, they were people who were fun to be with.
<BR>
<BR>
 +
<BR><strong>25</strong>
 +
<BR>Homework for the next iGEM meeting - each person must look up on a recent paper and make a presentation to the team.
 +
 +
<BR>
<BR>
 +
<img src=https://static.igem.org/mediawiki/2013/3/35/Line.jpg>
<img src=https://static.igem.org/mediawiki/2013/3/35/Line.jpg>
-
<h1 id="april">July</h1>
+
<h1 id="june">June</h1>
-
<BR>
+
<BR><strong>6</strong>
 +
<BR>Brainstorming...production of biodiesel? Make fertilisers using E. coli?
<BR>
<BR>
 +
<BR><strong>20</strong>
 +
<BR>Another brainstorming...shall we make an extended version of lux luminescence? Anyone with good idea? Since we are running out of time, we wil make it a compulsory for each person to come up with at least 3 ideas!
<BR>
<BR>
 +
 +
<img src=https://static.igem.org/mediawiki/2013/3/35/Line.jpg>
<img src=https://static.igem.org/mediawiki/2013/3/35/Line.jpg>
-
<h1 id="april">August</h1>
+
<h1 id="july">July</h1>
 +
<strong>4</strong>
 +
<BR>Everyone came up with many interesting ideas over the past two weeks. Hmmm....which one shall we challenge? Not so much time left.
<BR>
<BR>
 +
<BR><strong>11</strong>
 +
<BR>Brainstorming...Ooo, HHR, RNA oscillator...?
<BR>
<BR>
<BR>
<BR>
<img src=https://static.igem.org/mediawiki/2013/3/35/Line.jpg>
<img src=https://static.igem.org/mediawiki/2013/3/35/Line.jpg>
-
<h1 id="april">September</h1>
+
<h1 id="august">August</h1>
 +
<BR><strong>14</strong>
 +
<BR>Yay, we got BBa_K1053000, our first ribozyme!
<BR>
<BR>
 +
<BR><strong>18</strong>
 +
<BR>Ohki: E-mail was sent to me(Ohki). It said as follows: Oscillator group members are Ito, Sakamoto and Takabayashi (modeling). This was the first time I had to make a simulation for RNA oscillation. Hey, who decided on that?
<BR>
<BR>
 +
<BR><strong>19</strong>
 +
<BR>Ohki: I(Ohki) decided the plan roughly. First of all, I researched what kind of software there are. I also studied how they simulate the entire system, in the protein oscillation article.
<BR>
<BR>
-
<img src=https://static.igem.org/mediawiki/2013/3/35/Line.jpg>
+
<BR><strong>22</strong>
-
<h1 id="april">October</h1>
+
<BR>Akiko, Nana:Plac-RBS, Ptet-RBS, PcI-RBS, tetRllite-DT, λCI-lite-DT, lacI-lite-DT was constructed
<BR>
<BR>
 +
<BR><strong>25</strong>
 +
<BR>iGEM Japan Party (this time, I(Ohki) didnt simulate at all)
<BR>
<BR>
 +
<BR><strong>27</strong>
 +
<BR>Ohki: I installed the cellillustrator. This is the software which enables us to simulate biological phenomenon. But, in this software, I was not able to simulate concisely. For example, I was not able to consider the generation of complex between HHR and taRNA. Because I roughly simulated the system, the oscillation occured. This was an obvious result because it was set to be so.
 +
<BR>
 +
<BR><strong>28</strong>
 +
<BR>We dicided on wiki, poster and oral presentation members
 +
<BR>Ohki: Prof. Sode said to me, "parameter in this model was not enough at all." So, I decided to recreate the simulation and decided that I was going to use other software.
 +
<BR>
 +
<BR><strong>30</strong>
 +
<BR>Ippei, Shunsuke: We got BBa_K1053003 and BBa_K1053004
 +
<BR>Akiko, Nana: We confirmed sequences
 +
<img src=https://static.igem.org/mediawiki/2013/3/35/Line.jpg>
 +
 +
 +
<BR>
 +
<BR>
 +
<h1 id="september">September</h1>
 +
<BR><strong>3</strong>
 +
<BR>Ippei, Shunsuke: Made TOP10 competent cells
 +
<BR>Akiko, Nana: constructed pSB1C3-Plac-RVS-tetR-lite-DT and pSB1C3-PcI-RBS-lacI-lite-DT
 +
<BR>Akiko, Nana:We confirmed sequences of pSB1C3- Plac -RBS -tetR -lite –-DT (BBa_K1053301), pSB1C3- PcI -RBS -lacI -lite –DT (BBa_K1053302).
 +
<BR>
 +
<BR><strong>5</strong>
 +
<BR>Eri, Masaki: Construction of RNA scaffold (containing MS2/PP7 aptamer) BBa_K1053110
 +
<BR>Akiko, Nana: We constructed pSB1C3- Ptet -RBS -λcI -lite –DT.
 +
<BR>
 +
<BR><strong>7</strong>
 +
<BR>Eri, Masaki:Sequence analysis of constructed "RNA scaffold" parts. Okay, the sequence seems fine!
 +
<BR>
 +
<BR><strong>9</strong>
 +
<BR>Ippei, Shunsuke: Construction of pSB3C5-PBAD-HHR-GRP-DT and evaluation. Hopefully it works!
 +
<BR>Akiko, Nana: We confirmed the sequence of PcI -RBS and pSB1C3- Ptet -RBS -cI -lite -DT(BBa_K1053300).
 +
<BR>
 +
<BR><strong>10</strong>
 +
<BR>Get ready for BioBrick submition! Woohoo
 +
<BR>Eri, Masaki: We received our synthesized genes, FA-linker-MS2 and FB-linker-PP7! Yes!
 +
<BR>
 +
<BR><strong>11</strong>
 +
<BR>Eri, Masaki: The three separate fragments were ligated together, however obtained no colonies. We decided to construct using another method.
 +
<BR>Akiko, Nana: We constructed pSB1c3-Plac-RBS-tetR-lite-DT-Pcl-RBS-lacI-lite-DT.
 +
<BR>
 +
<BR><strong>12</strong>
 +
<BR>Ohki: I installed Simbiology and studied how this software works.
 +
<BR>Akiko, Nana: We constructed pSB1c3-Plac-RBS-tetR-lite-DT-Pcl-RBS-lacI-lite-DT-Ptet-RBS-λcI-lite-DT .
 +
<BR>
 +
<BR><strong>13</strong>
 +
<BR>Ippei, Shunsuke: RE-evaluation of pSB3C5-PBAD-HHR-GRP-DT and evaluation. Hopefully it works this time.
 +
<BR>
 +
<BR><strong>16</strong>
 +
<BR>Ippei, Shunsuke: We got three HHRs composing RNA oscillator and HHR fused with RNA scaffold. But oh no...they have extra <i>Xba</I>I :(
 +
<BR>Akiko, Nana: We constructed pSB1A2-PtetO-1-GFPaav-DT, pSB1A2-PtetO-1-GFPlva-DT, however we couldn’t confirm its sequences.
 +
<BR>
 +
<BR><strong>19</strong>
 +
<BR>Ohki: I simulated our RNA oscillator and noticed this system doesn't work by substituting any parameters.
 +
<BR>
 +
<BR><strong>20</strong>
 +
<BR>Ippei, Shunsuke: Evaluation of pSB3C5-PBad-tr(12)-HHR-GFP-DT by taking a time course. When is the optimal time to see the difference?
 +
<BR>Eri: Time to order our T-shirt!
 +
<BR><img src=https://static.igem.org/mediawiki/2013/a/aa/%EF%BC%B4%E3%82%B7%E3%83%A3~1.PNG width=300>
 +
<BR>Ohki: I formularized differential equation to confirm whether oscillation doesn't occur and solve them.
 +
<BR>
 +
<BR><strong>22</strong>
 +
<BR>Eri, Masaki: Construction of split GFP fused with MS2/PP7 proteins, Pconst(w)-RBS-MS2-RBS-PP7-DT
 +
<BR>
 +
<BR><strong>23</strong>
 +
<BR>Eri, Masaki: Evaluated GFP fluorescence in <i>E. coli</i> expressing split GFP fused with proteins and RNA scaffold. But we detected no fluorescence....why?
 +
<BR>Yukimi, Chihiro: Evalution of light sensors. Seems to behave differently under light and under dark!
 +
<BR>Akiko, Nana: We confirmed the sequence of pSB1c3-Plac-RBS-tetR-lite-DT-Pcl-RBS-lacI-lite-DT-Ptet-RBS-λcI-lite-DT, but we found it had a different sequence from other source. We decided to stop this experiment and we will achieve to construct and evaluate the protein oscillator by MOT.
 +
<BR>
 +
<BR><strong>26</strong>
 +
<BR>Evaluation of pSB1A3-PBAD-tr(42)-HHR-taR(12)-DT-Pconst(H)-taR(42)-DT
 +
<BR>Ohki: Time to finish writing the wiki.
 +
<BR>
 +
<BR><strong>27</strong>
 +
<BR>Wiki FREEZE
 +
<BR>
 +
<BR>
 +
<BR><img src=https://static.igem.org/mediawiki/2013/3/35/Line.jpg>
 +
<h1 id="october">October</h1>
 +
<BR><strong>5</strong>
 +
<BR><font size=7 color=red>Asia Regional Jamboree</font>
 +
<BR>
 +
<BR>
 +
<img src=https://static.igem.org/mediawiki/2013/8/81/DSC01616.JPG width=800>
 +
<BR>
 +
<img src=https://static.igem.org/mediawiki/2013/5/59/DSC01611.JPG width=800>
 +
<BR>
               </div>
               </div>

Latest revision as of 02:51, 28 September 2013

Team:Tokyo-NoKoGen - 2013.igem.org


April


18

Our first official gathering of Tokyo-NoKoGen 2013! Okay, let’s deicde on what we will do for the project this year.

25

Before we start, we looked up on what projects have been in presented in the past iGEM competitions. Each one of us picked a team of our interest, and made a presentation to the team.

May


1
To understand how iGEM work, we made a seminar to understand the basics, for example how to use restriction enzymes, and how to use the BioBrick parts.

16
Since we are going to present at Tokyo University very very soon, we need to practice and revise our poster presentation...Are we all ready?

19
School festival at Tokyo University! We made a poster presentation to many high school students and parents on our last year's project. It was very interesting to explain about genetic engineering of E. coli to those who are not familiar with them! We also got to know other team members of iGEM Japan, they were people who were fun to be with.

25
Homework for the next iGEM meeting - each person must look up on a recent paper and make a presentation to the team.

June


6
Brainstorming...production of biodiesel? Make fertilisers using E. coli?

20
Another brainstorming...shall we make an extended version of lux luminescence? Anyone with good idea? Since we are running out of time, we wil make it a compulsory for each person to come up with at least 3 ideas!

July

4
Everyone came up with many interesting ideas over the past two weeks. Hmmm....which one shall we challenge? Not so much time left.

11
Brainstorming...Ooo, HHR, RNA oscillator...?

August


14
Yay, we got BBa_K1053000, our first ribozyme!

18
Ohki: E-mail was sent to me(Ohki). It said as follows: Oscillator group members are Ito, Sakamoto and Takabayashi (modeling). This was the first time I had to make a simulation for RNA oscillation. Hey, who decided on that?

19
Ohki: I(Ohki) decided the plan roughly. First of all, I researched what kind of software there are. I also studied how they simulate the entire system, in the protein oscillation article.

22
Akiko, Nana:Plac-RBS, Ptet-RBS, PcI-RBS, tetRllite-DT, λCI-lite-DT, lacI-lite-DT was constructed

25
iGEM Japan Party (this time, I(Ohki) didnt simulate at all)

27
Ohki: I installed the cellillustrator. This is the software which enables us to simulate biological phenomenon. But, in this software, I was not able to simulate concisely. For example, I was not able to consider the generation of complex between HHR and taRNA. Because I roughly simulated the system, the oscillation occured. This was an obvious result because it was set to be so.

28
We dicided on wiki, poster and oral presentation members
Ohki: Prof. Sode said to me, "parameter in this model was not enough at all." So, I decided to recreate the simulation and decided that I was going to use other software.

30
Ippei, Shunsuke: We got BBa_K1053003 and BBa_K1053004
Akiko, Nana: We confirmed sequences

September


3
Ippei, Shunsuke: Made TOP10 competent cells
Akiko, Nana: constructed pSB1C3-Plac-RVS-tetR-lite-DT and pSB1C3-PcI-RBS-lacI-lite-DT
Akiko, Nana:We confirmed sequences of pSB1C3- Plac -RBS -tetR -lite –-DT (BBa_K1053301), pSB1C3- PcI -RBS -lacI -lite –DT (BBa_K1053302).

5
Eri, Masaki: Construction of RNA scaffold (containing MS2/PP7 aptamer) BBa_K1053110
Akiko, Nana: We constructed pSB1C3- Ptet -RBS -λcI -lite –DT.

7
Eri, Masaki:Sequence analysis of constructed "RNA scaffold" parts. Okay, the sequence seems fine!

9
Ippei, Shunsuke: Construction of pSB3C5-PBAD-HHR-GRP-DT and evaluation. Hopefully it works!
Akiko, Nana: We confirmed the sequence of PcI -RBS and pSB1C3- Ptet -RBS -cI -lite -DT(BBa_K1053300).

10
Get ready for BioBrick submition! Woohoo
Eri, Masaki: We received our synthesized genes, FA-linker-MS2 and FB-linker-PP7! Yes!

11
Eri, Masaki: The three separate fragments were ligated together, however obtained no colonies. We decided to construct using another method.
Akiko, Nana: We constructed pSB1c3-Plac-RBS-tetR-lite-DT-Pcl-RBS-lacI-lite-DT.

12
Ohki: I installed Simbiology and studied how this software works.
Akiko, Nana: We constructed pSB1c3-Plac-RBS-tetR-lite-DT-Pcl-RBS-lacI-lite-DT-Ptet-RBS-λcI-lite-DT .

13
Ippei, Shunsuke: RE-evaluation of pSB3C5-PBAD-HHR-GRP-DT and evaluation. Hopefully it works this time.

16
Ippei, Shunsuke: We got three HHRs composing RNA oscillator and HHR fused with RNA scaffold. But oh no...they have extra XbaI :(
Akiko, Nana: We constructed pSB1A2-PtetO-1-GFPaav-DT, pSB1A2-PtetO-1-GFPlva-DT, however we couldn’t confirm its sequences.

19
Ohki: I simulated our RNA oscillator and noticed this system doesn't work by substituting any parameters.

20
Ippei, Shunsuke: Evaluation of pSB3C5-PBad-tr(12)-HHR-GFP-DT by taking a time course. When is the optimal time to see the difference?
Eri: Time to order our T-shirt!

Ohki: I formularized differential equation to confirm whether oscillation doesn't occur and solve them.

22
Eri, Masaki: Construction of split GFP fused with MS2/PP7 proteins, Pconst(w)-RBS-MS2-RBS-PP7-DT

23
Eri, Masaki: Evaluated GFP fluorescence in E. coli expressing split GFP fused with proteins and RNA scaffold. But we detected no fluorescence....why?
Yukimi, Chihiro: Evalution of light sensors. Seems to behave differently under light and under dark!
Akiko, Nana: We confirmed the sequence of pSB1c3-Plac-RBS-tetR-lite-DT-Pcl-RBS-lacI-lite-DT-Ptet-RBS-λcI-lite-DT, but we found it had a different sequence from other source. We decided to stop this experiment and we will achieve to construct and evaluate the protein oscillator by MOT.

26
Evaluation of pSB1A3-PBAD-tr(42)-HHR-taR(12)-DT-Pconst(H)-taR(42)-DT
Ohki: Time to finish writing the wiki.

27
Wiki FREEZE


October


5
Asia Regional Jamboree



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