Team:TzuChiU Formosa/Notebook/photopaper

From 2011.igem.org

(Difference between revisions)
(2011.09.23)
 
(78 intermediate revisions not shown)
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</html>
</html>
 +
<font color="#228B22" size=6>Photopaper</font>
 +
<br><br><font color="#000080" size=4>Meeting Minutes</font>
 +
<Hr Align="left" width="100%" size=2>
 +
<font color="#000000" size=3><b>2011.02.24</b></font>
 +
<br><font size=2><b>Discussion:</b></font>
-
='''Photopaper'''=
 
-
=='''Meeting Notes'''==
 
-
==='''2011.02.24'''===
 
-
'''Discussion:'''
 
*Team organization[[File:001.jpg|right|500px|caption]]
*Team organization[[File:001.jpg|right|500px|caption]]
*Brain storming
*Brain storming
Line 36: Line 37:
-
==='''2011.03.04'''===
+
 
-
'''Discussion:'''
+
<br><font color="#000000" size=3><b>2011.03.04</b></font>
 +
<br><font size=2><b>Discussion:</b></font>
 +
 
*Team advisory   
*Team advisory   
*Brain storming
*Brain storming
Line 44: Line 47:
-
==='''2011.03.14'''===
+
 
-
'''Discussion:'''
+
 
 +
<br><font color="#000000" size=3><b>2011.03.14</b></font>
 +
<br><font size=2><b>Discussion:</b></font>
 +
 
*Task Allocation
*Task Allocation
*Brain storming
*Brain storming
Line 52: Line 58:
-
==='''2011.03.23'''===
+
 
-
'''Discussion:'''
+
<br><font color="#000000" size=3><b>2011.03.23</b></font>
 +
<br><font size=2><b>Discussion:</b></font>
**Project : paperia  
**Project : paperia  
Line 60: Line 67:
-
==='''2011.03.24'''===
+
 
-
'''Discussion:'''
+
<br><font color="#000000" size=3><b>2011.03.24</b></font>
 +
<br><font size=2><b>Discussion:</b></font>
* Exp. procedure:  
* Exp. procedure:  
Line 68: Line 76:
-
==='''2011.06.22'''===
+
 
-
'''Discussion:'''
+
<br><font color="#000000" size=3><b>2011.06.22</b></font>
 +
<br><font size=2><b>Discussion:</b></font>
 +
 
* Due to some unforseen reason, the team decided to change their project.
* Due to some unforseen reason, the team decided to change their project.
* New project: Biojenny  
* New project: Biojenny  
Line 75: Line 85:
         -yeast to be our host
         -yeast to be our host
-
==='''2011.07.01'''===
+
 
-
'''Discussion:'''
+
 
 +
<br><font color="#000000" size=3><b>2011.07.01</b></font>
 +
<br><font size=2><b>Discussion:</b></font>
* Freeze > grin > genome DNA isolation > Cloning = silk protein gene
* Freeze > grin > genome DNA isolation > Cloning = silk protein gene
-
==='''2011.07.09'''===
+
 
-
'''Discussion:'''
+
<br><font color="#000000" size=3><b>2011.07.09</b></font>
 +
<br><font size=2><b>Discussion:</b></font>
 +
 
* the connections between 3 silk proteins : Fibl Fibh P25
* the connections between 3 silk proteins : Fibl Fibh P25
* major proteins : H-chain, L-chain, P25
* major proteins : H-chain, L-chain, P25
-
==='''2011.07.15'''===
+
 
-
'''Discussion:'''
+
<br><font color="#000000" size=3><b>2011.07.15</b></font>
 +
<br><font size=2><b>Discussion:</b></font>
 +
 
* Due to limited resources and techniques required, the team decided to switch back to the previous project. Paper making !
* Due to limited resources and techniques required, the team decided to switch back to the previous project. Paper making !
* However it would be modified to be more innovative and creative.
* However it would be modified to be more innovative and creative.
-
==='''2011.07.18'''===
+
 
-
'''Discussion:'''
+
<br><font color="#000000" size=3><b>2011.07.18</b></font>
 +
<br><font size=2><b>Discussion:</b></font>
 +
 
* Latest project : Photo paper
* Latest project : Photo paper
* cyanobacteria is designed as the host, cellulose made up of the glucose produced by cyanobacteria could be one of the main attraction of the project.
* cyanobacteria is designed as the host, cellulose made up of the glucose produced by cyanobacteria could be one of the main attraction of the project.
-
==='''2011.07.23'''===
+
 
-
'''Discussion:'''
+
<br><font color="#000000" size=3><b>2011.07.23</b></font>
 +
<br><font size=2><b>Discussion:</b></font>
* system modification to overcome the problems arises during preliminary round
* system modification to overcome the problems arises during preliminary round
Line 108: Line 127:
-
==='''2011.09.15'''===
+
 
 +
<br><font color="#000000" size=3><b>2011.09.15</b></font>
'''Genome miniprep'''<br>
'''Genome miniprep'''<br>
Line 115: Line 135:
-
==='''2011.09.18'''===
+
<br><font color="#000000" size=3><b>2011.09.18</b></font>
'''Gel/PCR DNA extraction'''<br>
'''Gel/PCR DNA extraction'''<br>
Line 122: Line 142:
-
=='''Protocols'''==
+
<font size=4 color="#000080"><b>Protocols</b></font>
 +
<Hr Align="left" width="100%" size=3>
-
==='''2011.09.07'''===
+
<br>[[File:1-20110907.jpg|lefe|650px|caption]][[File:Catt.gif|right|250px|caption]]
-
<br>[[File:Catt.gif|right|250px|caption]]
+
-
'''Rhodobacter rudrum medium'''
+
<br>
<br>
-
<br>K2HPO4                  1g<br>
 
-
<br>NaCl                   0.5g<br>
 
-
<br>FeSO4.7H2O            0.01g<br>
 
-
<br>CaCl2                0.02g<br>
 
-
<br>MnCl2.4H2O              0.002g<br>
 
-
<br>MgSO4.7H2O                        0.2g<br>
 
-
<br>NaMO2O4.2H2O                        0.01g<br>
 
-
<br>ddH2O             998.258ml<br>
 
-
<br>________________________________________
 
-
<br>                1L →take100ml<br>
 
-
 
-
          + 
 
-
 
-
<br>Yeast Extrat                             0.5g<br>
 
-
<br>Sodium malate
 
-
<br>(Sodium succinate dibasic hexohydrate)    5g<br>
 
-
<br>NH4Cl                          1g<br>
 
-
<br>ddH2O                         893.5ml<br>
 
-
<br>_________________________________________________
 
-
<br>                            1L<br>
 
<br>
<br>
<br>
<br>
-
'''Raise E. coli(PSB1C3)'''
+
<br>[[File:2-20110908-13.jpg|lefe|650px|caption]]
<br>
<br>
-
<br>1.50ml LB+500μl CHLORAMPHENICOL
 
-
<br>2.37℃, overnight (14-16hrs)
 
<br>
<br>
<br>
<br>
 +
<br>[[File:3-20110910-11.jpg|lefe|650px|caption]]
<br>
<br>
-
==='''2011.09.08-13'''===
 
<br>
<br>
-
'''Plasmid miniprep kit'''
 
-
<br>PSB1C3 plasmid[[File:Cats.jpg|right|404px|caption]]
 
<br>
<br>
 +
<br>[[File:4-20110912-20.jpg|lefe|650px|caption]]
<br>
<br>
-
'''Raise Rhodobacter rubrum'''
 
<br>
<br>
-
<br>1.50ml LB+500μl CHLORAMPHENICOL
 
-
<br>2.37℃, overnight (14-16hrs)
 
<br>
<br>
 +
<br>[[File:5-20110921.jpg|lefe|550px|caption]][[File:Cats.jpg|right|404px|caption]]
<br>
<br>
<br>
<br>
-
==='''2011.09.09'''===
 
<br>
<br>
-
'''Raise Gluconacetobacter hansenii'''
+
<br>[[File:6-20110922.jpg|lefe|650px|caption]]
<br>
<br>
-
<br>1.50ml LB+500μl CHLORAMPHENICOL
 
-
<br>2.37℃, overnight (14-16hrs)
 
<br>
<br>
<br>
<br>
 +
<br>[[File:7-20110923.jpg|lefe|650px|caption]]
<br>
<br>
-
==='''2011.09.10-11'''===
 
<br>
<br>
-
'''Digestion check of DNA'''
 
<br>
<br>
-
<br>[pSB1C3/EcoRI]
+
<br>[[File:8-20110924.jpg|lefe|550px|caption]][[File:Cats2.gif |right|404px|caption]]
<br>
<br>
-
<br>DNA            500ng<br>
 
-
<br>10×buffer             5μl<br>
 
-
<br>BSA             5μl<br>
 
-
<br>EcoRⅠ            1μl<br>
 
-
<br>ddH2O           29μl<br>
 
-
<br>_______________________________
 
<br>
<br>
-
<br>total           50μl<br>
 
<br>
<br>
 +
<br>[[File:9-20110925.jpg|lefe|650px|caption]]
<br>
<br>
-
<br>[pSB1C3/PstⅠ]
 
<br>
<br>
-
<br>DNA             500ng<br>
 
-
<br>10×buffer           5μl<br>
 
-
<br>BSA               5μl<br>
 
-
<br>pstⅠ              1μl<br>
 
-
<br>ddH2O             29μl<br>                                             
 
-
<br>_________________________________
 
<br>
<br>
-
<br>total             50μl<br>
+
<br>[[File:10-20110926.jpg|lefe|650px|caption]]
<br>
<br>
<br>
<br>
-
'''Digestion of DNA'''
 
<br>
<br>
-
<br>[pSB1C3/EcoRⅠ+PstⅠ]
+
<br>[[File:11-20110927.jpg|lefe|550px|caption]][[File:Cats3.jpg|right|404px|caption]]
<br>
<br>
-
<br>DNA             500ng<br>
 
-
<br>10×buffer           5μl<br>
 
-
<br>BSA               5μl<br>
 
-
<br>EcoRⅠ              1μl<br>
 
-
<br>pstⅠ              1μl<br>
 
-
<br>ddH2O            28μl<br>             
 
-
<br>__________________________________
 
<br>
<br>
-
<br>total            50μl<br>
 
-
<br>→37℃ for 30 mins
 
<br>
<br>
 +
<br>[[File:12-20110928.jpg|lefe|650px|caption]]
<br>
<br>
-
<br>[pSB1C3/XbaⅠ+SpeⅠ]
 
-
<br>
 
-
<br>DNA               10μl<br>
 
-
<br>10×buffer            5μl<br>
 
-
<br>BSA               5μl<br>
 
-
<br>XbaⅠ                1μl<br>
 
-
<br>SpeⅠ               1μl<br>
 
-
<br>ddH2O              28μl<br>
 
-
<br>____________________________________
 
-
<br>
 
-
<br>total              50μl<br>
 
-
<br>→37℃ for 2 hrs
 
-
<br>
 
-
<br>
 
-
<br>[pSB1C3/SpeⅠ+PstⅠ]
 
-
<br>
 
-
<br>DNA               10μl<br>
 
-
<br>10×buffer            5μl<br>
 
-
<br>BSA               5μl<br>
 
-
<br>SpeⅠ              1μl<br>
 
-
<br>pstⅠ               1μl<br>
 
-
<br>ddH2O              28μl<br>
 
-
<br>____________________________________
 
-
<br>
 
-
<br>total              50μl<br>
 
-
<br>→37℃ for 2 hrs
 
-
<br>
 
-
<br>
 
-
<br>[pSB1C3/EcoRⅠ+XbaⅠ]
 
-
<br>
 
-
<br>DNA               10μl<br>
 
-
<br>10×buffer            5μl<br>
 
-
<br>BSA               5μl<br>
 
-
<br>EcoRⅠ              1μl<br>
 
-
<br>XbaⅠ               1μl<br>
 
-
<br>ddH2O              28μl<br>
 
-
<br>____________________________________
 
-
<br>
 
-
<br>total              50μl<br>
 
-
<br>→37℃ for 2 hrs
 
-
<br>
 
-
<br>
 
-
<br>[pSB1A3/EcoRⅠ+PstⅠ]
 
-
<br>
 
-
<br>DNA               10μl<br>
 
-
<br>10×buffer            5μl<br>
 
-
<br>BSA               5μl<br>
 
-
<br>EcoRⅠ              1μl<br>
 
-
<br>PstⅠ               1μl<br>
 
-
<br>ddH2O              28μl<br>
 
-
<br>____________________________________
 
-
<br>
 
-
<br>total              50μl<br>
 
-
<br>→37℃ for 2 hrs
 
-
<br>
 
-
<br>
 
-
'''electroelution Purification'''
 
-
<br>
 
-
<br>[pSB1C3/EcoRⅠ+PstⅠ]
 
-
<br>
 
-
<br>[pSB1C3/XbaⅠ+SpeⅠ]
 
-
<br>
 
-
<br>[pSB1C3/SpeⅠ+PstⅠ]
 
-
<br>
 
-
<br>[pSB1C3/EcoRⅠ+XbaⅠ]
 
-
<br>
 
-
<br>[pSB1A3/EcoRⅠ+PstⅠ]
 
-
<br>
 
-
<br>
 
-
<br>
 
-
 
-
==='''2011.09.12-20'''===
 
-
<br>
 
-
'''PCR'''
 
-
[[File:Cats2.gif |right|404px|caption]]
 
-
<br>[acsAB]
 
-
<br>
 
-
<br>[acsCD]
 
-
<br>
 
-
<br>[cmcax-ccp]
 
-
<br>
 
-
<br>template DNA   1μl<br>
 
-
<br>5×Buffer     4μl<br>
 
-
<br>2.5μM dNTP    1.6μl<br>
 
-
<br>10μM F      1μl<br>
 
-
<br>10μM R      1μl<br>
 
-
<br>Taq        0.2μl<br>
 
-
<br>ddH2O      8.8μl<br>
 
-
<br>_______________________________
 
-
<br>
 
-
<br>total       20μl<br>
 
-
<br>
 
-
<br>
 
-
<br>
 
-
'''electroelution Purification'''
 
-
<br>
 
-
<br>[acsAB]
 
-
<br>
 
-
<br>[acsCD]
 
-
<br>
 
-
<br>[cmcax-ccp]
 
-
<br>
 
-
<br>
 
-
<br>
 
-
 
-
==='''2011.09.21'''===
 
-
<br>
 
-
'''Digestion of DNA'''
 
-
<br>
 
-
<br>[acsAB/ XbaⅠ+SpeⅠ]
 
-
<br>
 
-
<br>DNA           10μl<br>
 
-
<br>10×buffer        5μl<br>
 
-
<br>BSA           5μl<br>
 
-
<br>EcoRⅠ          1μl<br>
 
-
<br>pstⅠ           1μl<br>
 
-
<br>ddH2O          28μl<br>
 
-
<br>____________________________
 
-
<br>
 
-
<br>total             50μl<br>
 
-
<br>→37℃ for 16 hr
 
-
<br>
 
-
<br>
 
-
<br>[acsCD/XbaⅠ+SpeⅠ]
 
-
<br>
 
-
<br>DNA            10μl<br>
 
-
<br>10×buffer         5μl<br>
 
-
<br>BSA             5μl<br>
 
-
<br>XbaⅠ            1μl<br>
 
-
<br>SpeⅠ             1μl<br>
 
-
<br>ddH2O            28μl<br>
 
-
<br>__________________________________
 
-
<br>
 
-
total               50μl<br>
 
-
<br>→37℃ for 16 hr
 
-
<br>
 
-
<br>
 
-
<br>[CMCax/SpeⅠ+AlwNⅠ]
 
-
<br>
 
-
<br>DNA            10μl<br>
 
-
<br>10×buffer         5μl<br>
 
-
<br>BSA             5μl<br>
 
-
<br>SpeⅠ            1μl<br>
 
-
<br>AlwNⅠ             1μl<br>
 
-
<br>ddH2O            28μl<br>
 
-
<br>__________________________________
 
-
<br>
 
-
<br>total               50μl<br>
 
-
<br>→37℃ for 16 hr
 
-
<br>
 
-
<br>
 
-
<br>[Ccp/AlwNⅠ+PstⅠ]
 
-
<br>
 
-
<br>DNA            10μl<br>
 
-
<br>10×buffer         5μl<br>
 
-
<br>BSA             5μl<br>
 
-
<br>AlwNⅠ            1μl<br>
 
-
<br>PstⅠ             1μl<br>
 
-
<br>ddH2O            28μl<br>
 
-
<br>__________________________________
 
-
<br>
 
-
total               50μl<br>
 
-
<br>→37℃ for 16 hr
 
-
<br>
 
-
<br>
 
-
<br>
 
-
 
-
==='''2011.09.22'''===
 
-
'''Ligation of DNA'''
 
-
<br>[pSB1C3-acsAB][[File:Cats3.jpg|right|404px|caption]]
 
-
<br>
 
-
<br>Vector          3μl<br>
 
-
<br>Insert          14μl<br>
 
-
<br>ligase buffer        2μl<br>
 
-
<br>ligase          1μl<br>
 
-
<br>ddH2O           -μl<br>
 
-
<br>________________________________
 
-
<br>
 
-
<br>total          20μl<br>
 
-
<br>→16℃ for 16 hr
 
-
<br>
 
-
<br>
 
-
<br>[pSB1A3-acsCD]
 
-
<br>
 
-
<br>Vector           3μl<br>
 
-
<br>Insert           14μl<br>
 
-
<br>ligase buffer       2μl<br>
 
-
<br>ligase            1μl<br>
 
-
<br>ddH2O             -μl<br>
 
-
<br>_________________________________
 
-
<br>
 
-
<br>total           20μl<br>
 
-
<br>→16℃ for 16 hr
 
-
<br>
 
-
<br>
 
-
<br>[pSB1C3-acsCD]
 
-
<br>
 
-
<br>Vector           3μl<br>
 
-
<br>Insert           14μl<br>
 
-
<br>ligase buffer       2μl<br>
 
-
<br>ligase            1μl<br>
 
-
<br>ddH2O             -μl<br>
 
-
<br>_________________________________
 
-
<br>
 
-
<br>total           20μl<br>
 
-
<br>→16℃ for 16 hr
 
-
<br>
 
-
<br>
 
-
<br>[pSB1C3-CMCax-Ccp]
 
-
<br>
 
-
<br>Vector           3μl<br>
 
-
<br>Insert           14μl<br>
 
-
<br>ligase buffer       2μl<br>
 
-
<br>ligase            1μl<br>
 
-
<br>ddH2O             -μl<br>
 
-
<br>_________________________________
 
-
<br>
 
-
<br>total           20μl<br>
 
-
<br>→16℃ for 16 hr
 
-
<br>
 
-
<br>
 
-
<br>
 
-
 
-
==='''2011.09.23'''===
 
-
<br>
 
-
'''PCR'''
 
-
<br>
 
-
<br>R0011 promoter         1μl<br>
 
-
<br>5×Buffer            4μl<br>
 
-
<br>2.5μM dNTP          1.6μl<br>
 
-
<br>Taq               0.2μl<br>
 
-
<br>ddH2O             13.2μl<br>
 
-
<br>_____________________________________
 
-
<br>
 
-
<br>total              20μl<br>
 
-
<br>
 
-
<br>
 
-
'''Digestion of DNA'''
 
-
<br>
 
-
[R0011 promoter/EcoRⅠ+XbaⅠ]
 
-
<br>
 
-
<br>DNA           10μl<br>
 
-
<br>10×buffer        5μl<br>
 
-
<br>BSA           5μl<br>
 
-
<br>EcoRⅠ          1μl<br>
 
-
<br>XbaⅠ           1μl<br>
 
-
<br>ddH2O          28μl<br>
 
-
<br>____________________________
 
-
 
-
<br>total             50μl<br>
 
-
<br>
 
-
<br>→37℃ for 16 hr
 
-
 
-
==='''2011.09.24'''===
 
-
<br>
 
-
'''Transformation of DNA'''
 
-
<br>
 
-
<br>PSB1C3-acsAB
 
-
<br>Transform into E.coli
 
-
<br>LB+CHLORAMPHENICOL
 
-
 
-
'''Transformation of DNA'''
 
-
<br>
 
-
<br>PSB1A3-acsCD
 
-
<br>Transform into E.coli
 
-
<br>LB+Ampicillin
 
-
 
-
'''Transformation of DNA'''
 
<br>
<br>
-
<br>PSB1C3-acsAB
 
-
<br>PSB1A3-acsCD
 
-
<br>Transform into E.coli
 
-
<br>LB+Ampicillin+CHLORAMPHENICOL
 
<br>
<br>
 +
<br>[[File:13-20110929.jpg|lefe|650px|caption]]
<br>
<br>
<br>
<br>
-
==='''2011.09.24'''===
 
<br>
<br>
-
'''Ligation of DNA'''
+
<br>[[File:14-20111001.jpg|lefe|650px|caption]]
-
<br>[pSB1C3-promoter]
+
<br>
<br>
-
<br>Vector           3μl<br>
 
-
<br>Insert           14μl<br>
 
-
<br>ligase buffer                     2μl<br>
 
-
<br>ligase            1μl<br>
 
-
<br>ddH2O             -μl<br>
 
-
<br>________________________________
 
<br>
<br>
-
<br>total             20μl<br>
 
<br>
<br>

Latest revision as of 02:56, 6 October 2011

Photopaper

Meeting Minutes


2011.02.24
Discussion:

  • Team organization
    caption
  • Brain storming
    • paper made by bacteria with add-ons such as colors, fragrance, etc.
    • "light up" the plants for replacing lamp posts.



2011.03.04
Discussion:

  • Team advisory
  • Brain storming
    • Add-ons: colorful cellulose which produced by bacteria such as beta-carotene
    • information exchange with iGEM 2009 Cambridge team




2011.03.14
Discussion:

  • Task Allocation
  • Brain storming
    • Avatar - "light up" the plants by transfecting symbiotic bacteria which cloned into fluorescence gene
    • Eco-friendly warmer - biotic thermal pad



2011.03.23
Discussion:

    • Project : paperia
    • Option 1 : Culture bacteria which has pigment gene
    • Option 2 : Cellulose-producing bacteria secrete pigment into the medium



2011.03.24
Discussion:

  • Exp. procedure:
    • cloning of cellulose gene’s CDS
    • the product should operate within E. coli.



2011.06.22
Discussion:

  • Due to some unforseen reason, the team decided to change their project.
  • New project: Biojenny

         -economical and humane way to produce paper in large quantities.
         -yeast to be our host



2011.07.01
Discussion:

  • Freeze > grin > genome DNA isolation > Cloning = silk protein gene



2011.07.09
Discussion:

  • the connections between 3 silk proteins : Fibl Fibh P25
  • major proteins : H-chain, L-chain, P25



2011.07.15
Discussion:

  • Due to limited resources and techniques required, the team decided to switch back to the previous project. Paper making !
  • However it would be modified to be more innovative and creative.



2011.07.18
Discussion:

  • Latest project : Photo paper
  • cyanobacteria is designed as the host, cellulose made up of the glucose produced by cyanobacteria could be one of the main attraction of the project.



2011.07.23
Discussion:

  • system modification to overcome the problems arises during preliminary round
  • Biobricks from Tokyo 2010 team will be utilized
    • regulator promoter in order to regulate the secretion of cellulose to solve the aggregation of the bacteria




2011.09.15

Genome miniprep
Gluconacetobacter hansenii



2011.09.18

Gel/PCR DNA extraction
Gluconacetobacter hansenii


Protocols




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