Team:SouthBend-Mishawaka-HS-2/Notebook

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[[Image:SouthBend-Mishawaka-HS-2_logo.png|200px|center|frame]]
[[Image:SouthBend-Mishawaka-HS-2_logo.png|200px|center|frame]]
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[[Image:SouthBend-Mishawaka-HS-2_team.png|right|frame|Your team picture]]
 
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!align="center"|[[Team:SouthBend-Mishawaka-HS-2|Home]]
!align="center"|[[Team:SouthBend-Mishawaka-HS-2|Home]]
!align="center"|[[Team:SouthBend-Mishawaka-HS-2/Team|Team]]
!align="center"|[[Team:SouthBend-Mishawaka-HS-2/Team|Team]]
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!align="center"|[https://igem.org/Team.cgi?year=2010&team_name=SouthBend-Mishawaka-HS-2 Official Team Profile]
+
!align="center"|[https://igem.org/Team.cgi?year=2011&team_name=SouthBend-Mishawaka-HS-2 Official Team Profile]
!align="center"|[[Team:SouthBend-Mishawaka-HS-2/Project|Project]]
!align="center"|[[Team:SouthBend-Mishawaka-HS-2/Project|Project]]
!align="center"|[[Team:SouthBend-Mishawaka-HS-2/Parts|Parts Submitted to the Registry]]
!align="center"|[[Team:SouthBend-Mishawaka-HS-2/Parts|Parts Submitted to the Registry]]
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</tr><tr>
</tr><tr>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">23</font><br><br><br><br></TD>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">23</font><br><br><br><br></TD>
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<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">24  [[:05/24/11 Agenda: Establishment of the K346002 Hg Sensitive Promotor]]</font><br><br><br><br></TD>
+
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">24  [[:Agenda: Establishment of the K346002 Hg Sensitive Promoter]]</font><br><br><br><br></TD>
-
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">25</font><br><br><br><br></TD>
+
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">25 [[Agenda: Examining Results of Establishment of the K346002 Hg Sensitive Promoter]]</font><br><br><br><br></TD>
-
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">26</font><br><br><br><br></TD>
+
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">26 [[Agenda: Examining Results of Establishment of the K346002 Hg Sensitive Promoter Round II]] 
 +
 
 +
 
 +
[[ Agenda: Transforming Top 10 cells to Establish Hg sensitive promoter part K346002]]</font><br><br><br><br></TD>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">27</font><br><br><br><br></TD>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">27</font><br><br><br><br></TD>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">28</font><br><br><br><br></TD>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">28</font><br><br><br><br></TD>
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<TD vAlign=top align=left width="14%" >&nbsp;<br><br><br><br></TD>
<TD vAlign=top align=left width="14%" >&nbsp;<br><br><br><br></TD>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">1</font><br><br><br><br></TD>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">1</font><br><br><br><br></TD>
-
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">2</font><br><br><br><br></TD>
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<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">2 [[Agenda: Transformation of promoter part K346002 in E.Coli Bacteria]]</font><br><br><br><br></TD>
-
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">3</font><br><br><br><br></TD>
+
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">3 [[Agenda: No Growth of E.col with K346002]]</font><br><br><br><br></TD>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">4</font><br><br><br><br></TD>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">4</font><br><br><br><br></TD>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">5</font><br><br><br><br></TD>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">5</font><br><br><br><br></TD>
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</tr><tr>
</tr><tr>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">13</font><br><br><br><br></TD>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">13</font><br><br><br><br></TD>
-
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">14</font><br><br><br><br></TD>
+
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">14[[Agenda: A3 Assembly]] </font><br><br><br><br></TD>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">15</font><br><br><br><br></TD>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">15</font><br><br><br><br></TD>
-
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">16</font><br><br><br><br></TD>
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<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">16 [[Agenda:  Added Enzymes to E0840, J45119, and PSB1T3]]</font><br><br><br><br></TD>
-
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">17</font><br><br><br><br></TD>
+
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">17[[Agenda:  Change in Promoter from Hg detection to As Detection]]</font><br><br><br><br></TD>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">18</font><br><br><br><br></TD>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">18</font><br><br><br><br></TD>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">19</font><br><br><br><br></TD>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">19</font><br><br><br><br></TD>
</tr><tr>
</tr><tr>
-
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">20</font><br><br><br><br></TD>
+
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">20 [[Agenda:  K190015 (ArsR regulated promoter) Transformed]]</font><br><br><br><br></TD>
-
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">21</font><br><br><br><br></TD>
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<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">21 [[Agenda:  K190015 (ArsR regulated promoter) No Growth]]</font><br><br><br><br></TD>
-
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">22</font><br><br><br><br></TD>
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<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">22 [[Agenda:  Began powerpoint presentation]]</font><br><br><br><br></TD>
-
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">23</font><br><br><br><br></TD>
+
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">23[[Agenda:  Continued working on powerpoint presentation and Ligation]]</font><br><br><br><br></TD>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">24</font><br><br><br><br></TD>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">24</font><br><br><br><br></TD>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">25</font><br><br><br><br></TD>
<TD vAlign=top align=left width="14%" ><font size="3" face="Verdana">25</font><br><br><br><br></TD>
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-
==='''Agenda:Transformation Test Run'''===
+
==='''05/19/11 Agenda: Transformation Test Run'''===
   
   
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  (2) Added 50 microliters of BIO-RAD transformation solution  
  (2) Added 50 microliters of BIO-RAD transformation solution  
-
     (Control number 31000008916 recd 1-17-11 GT)
+
     (Control number 31000008916 rec'd 1-17-11 GT)
  (3) Added 2 microliters of DNA from Registry plate 2  well 5b
  (3) Added 2 microliters of DNA from Registry plate 2  well 5b
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  (8) Plate 100 microliters and 25 microliters of transformed cells on LB-AMP (5-19-11 "who")
  (8) Plate 100 microliters and 25 microliters of transformed cells on LB-AMP (5-19-11 "who")
-
 
+
===''' 05/24/11 Agenda: Establishment of the K346002 Hg Sensitive Promoter'''===
-
===''' 05/24/11 Agenda: Establishment of the K346002 Hg Sensitive Promotor'''===
+
  (1)Electroporation of K346002 into Top 10 cells.  
  (1)Electroporation of K346002 into Top 10 cells.  
Line 172: Line 173:
-
===''' 05/25/11 Agenda: Examining Results of Establishment of the K346002 Hg Sensitive Promotor'''===
+
===''' 05/25/11 Agenda: Examining Results of Establishment of the K346002 Hg Sensitive Promoter'''===
  (1) Examined results from yesterday: Lawn of bacteria!
  (1) Examined results from yesterday: Lawn of bacteria!
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-
===''' 05/26/11 Agenda: Examining Results of Establishment of the K346002 Hg Sensitive Promotor Round II'''===
+
===''' 05/26/11 Agenda: Examining Results of Establishment of the K346002 Hg Sensitive Promoter Round II'''===
  (1) Results: NO GROWTH!
  (1) Results: NO GROWTH!
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  (5) Placed in ice bath for 5 minutes.
  (5) Placed in ice bath for 5 minutes.
-
  (6) 1 microliter of SOB buffer at rrom temperature added to broth  
+
  (6) 1 microliter of SOB buffer at room temperature added to broth  
     (in order to close plasmid channels).  
     (in order to close plasmid channels).  
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  Expected: 10 to 50 colonies projected to grow.
  Expected: 10 to 50 colonies projected to grow.
-
 
===''' 06/02/11 Agenda: Transformation of promoter part K346002 in E.Coli Bacteria'''===
===''' 06/02/11 Agenda: Transformation of promoter part K346002 in E.Coli Bacteria'''===
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  (1)105 E.col: calls were added to 100ul BioRad Transformation Solution.
  (1)105 E.col: calls were added to 100ul BioRad Transformation Solution.
-
  (2)1ul of each part of DNA from the Registery was added to the cells which were incubated  
+
  (2)1ul of each part of DNA from the Registry was added to the cells which were incubated  
     30min on ice.
     30min on ice.
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  (5)100ul of the transformed cells were plated on a fresh LB/AMP plate.
  (5)100ul of the transformed cells were plated on a fresh LB/AMP plate.
 +
 +
===''' 06/03/11 Agenda: No Growth of E.col with K346002'''===
 +
The E.col that was transformed on 6/02/11 did not have any growth.
 +
 +
==='''06/14/11 Agenda: A3 Assembly'''===
 +
 +
Today, we put together our entire part. We used the A3 assembly, as explained on the [[Team:SouthBend-Mishawaka-HS-2/Model|<font color=#99FFFF>Model</font>]] page.<br> We then poured plates of our assembled plasmid. We hope for 10 to 50 colonies of transformed colonies.<br>
 +
 +
==='''06/16/11 Agenda:  Added Enzymes to E0840, J45119, and PSB1T3'''===
 +
 +
 +
(1)Vortex E0840, J45119, and PSB1T3.
 +
 +
(2)Add 1 uL of SpeI enzyme and 1 uL of PstI enzyme to 8 uL of E0840 in order to cut both ends of the wanted DNA.<br> Also add .5 uL of BSA and 5 uL.
 +
 +
(3)Add 1 uL of EcoRI enzyme and 1 uL of XbaI enzyme to J45119 in order to cut both ends of the wanted DNA.<br> Also add .5 microliters of BSA and 5 microliters.
 +
 +
(4)Add 1 uL of EcoRI enzyme and 1 uL of PstI enzyme to PSB1T3 in order to cut both ends of the wanted DNA.
 +
 +
(5)Place E0840, J45119, and PSB1T3 in a water bath at 37 degrees C for 20 minutes so that all the parts are<br> sufficiently cut.
 +
 +
(6)Assemble the new plasmid by combining 2 uL of E0840, 2 uL J45119, and 2 uL PSB1T3 plasmids in one container.<br> Also add 2 micro liters of buffer and 1 microliter of ligase.
 +
 +
(7)Place the new assembly of E0840, J45119, and PSB1T3 in the water bath at 37 degrees C for 20 minutes.
 +
 +
Ligation
 +
 +
(1)Incubate at room temperature for 10 minutes and then heat inactive at 80 degrees C for 20 min.
 +
 +
(2)Transform 2 uL of the ligation product into 50 uL of competent ''E. coli'' cells.
 +
 +
==='''06/17/11 Agenda:  Change in Promoter from Hg detection to As Detection'''===
 +
 +
Because of many failed attempts with the Hg promoter, we will be changing our project to a device that detects<br> Arsenic with a promoter that is activated with the presents of arsenic.
 +
 +
==='''06/20/11 Agenda:  K190015 (ArsR regulated promoter) Transformed'''===
 +
 +
==='''06/21/11 Agenda:  K190015 (ArsR regulated promoter) No Growth'''===
 +
==='''06/22/11 Agenda:  Began powerpoint presentation'''===
 +
To view the power point presentation click [https://docs.google.com/leaf?id=1qhQSJj4KF1CyB8f-d5UELRZgZgZZQ9jN9IPd4HsFTvuEP7GqBROFzr1CP6il&hl=en_US Here] and Download!
 +
 +
===''' 06/23/11 Agenda:  Continued working on powerpoint presentation and Ligation'''===
 +
Continued working on [https://docs.google.com/leaf?id=1qhQSJj4KF1CyB8f-d5UELRZgZgZZQ9jN9IPd4HsFTvuEP7GqBROFzr1CP6il&hl=en_US power point] and began ligating parts K190015 to J45119 and K190015 to E0840.

Latest revision as of 17:16, 24 June 2011

SouthBend-Mishawaka-HS-2 logo.png


Home Team Official Team Profile Project Parts Submitted to the Registry Modeling Notebook Safety Attributions


Contents

Notebook

May 2011

Mon Tues Wed Thur Fri Sat Sun
 



 



 



 



 



 



1



2



3



4



5



6



7



8



9



10



11



12



13



14



15



16



17



18



19 Agenda:Transformation Test Run



20



21



22



23



24 Agenda: Establishment of the K346002 Hg Sensitive Promoter



25 Agenda: Examining Results of Establishment of the K346002 Hg Sensitive Promoter



26 Agenda: Examining Results of Establishment of the K346002 Hg Sensitive Promoter Round II


Agenda: Transforming Top 10 cells to Establish Hg sensitive promoter part K346002




27



28



29



30



31



 

 

 

 

 


June 2011

Mon Tues Wed Thur Fri Sat Sun
 



 



1



2 Agenda: Transformation of promoter part K346002 in E.Coli Bacteria



3 Agenda: No Growth of E.col with K346002



4



5



6



7



8



9



10



11



12



13



14Agenda: A3 Assembly



15



16 Agenda: Added Enzymes to E0840, J45119, and PSB1T3



17Agenda: Change in Promoter from Hg detection to As Detection



18



19



20 Agenda: K190015 (ArsR regulated promoter) Transformed



21 Agenda: K190015 (ArsR regulated promoter) No Growth



22 Agenda: Began powerpoint presentation



23Agenda: Continued working on powerpoint presentation and Ligation



24



25



26



27



28



29



30



 

 

 





05/19/11 Agenda: Transformation Test Run

(1) Obtained a vial of 2mL of TOP-10 electro competent E. coli cells 3-16-11 (44-0003/793762)
(2) Added 50 microliters of BIO-RAD transformation solution 
   (Control number 31000008916 rec'd 1-17-11 GT)
(3) Added 2 microliters of DNA from Registry plate 2  well 5b
(4) Incubate on ice 5 minutes.
(5) Heat shocked 40 degrees C for 50 seconds
(6) Incubated 4 degrees C for 50 seconds
(7) Added 1mL LB 5-17-11 D.G.
(8) Plate 100 microliters and 25 microliters of transformed cells on LB-AMP (5-19-11 "who")

05/24/11 Agenda: Establishment of the K346002 Hg Sensitive Promoter

(1)Electroporation of K346002 into Top 10 cells. 
(2)40 microliters of Top 10 cells (JH 5-23-10)10E9 + 2 microliters K346002 DNA from Registry.
(3)Parameters of electroporation: not recorded.
(4)Added 1 microliter of SOB media (JH 2-11-11)immediately after electroporation.
(5)Incubated tube at 37 degrees Celsius for 30 minutes.
(6)Plated 200 microliters of transformation mixture on LB Agar AMP 5 micrograms/microliter 
  (4-21-10).Stored mixture at 4 degrees Celsius. 
 Expected: 10 to 50 colonies projected to grow.


05/25/11 Agenda: Examining Results of Establishment of the K346002 Hg Sensitive Promoter

(1) Examined results from yesterday: Lawn of bacteria!
(2) Conclusion: No selection either due to inconclusive AMP or fabulous transformation.
(3) Replated 100 microliters  K346002 on LB AMP Agar (AM 5-19-11)
  Expected: 10 to 50 colonies projected to grow.


05/26/11 Agenda: Examining Results of Establishment of the K346002 Hg Sensitive Promoter Round II

(1) Results: NO GROWTH!
(2) Conclusion: Perhaps no transformation and bad AMP on 4-21-10 plate. However, could still
    be some transformants present.
(3) Q-tip swabbed up lawn and resuspended in AMP LB broth. Resuspension fluid placed in 
    photospectrometer.
(4) Photospectrometer results for K346002:
Time         A600 nm
 0 hr.            .315
 1 hr.            .148
 2.5 hr.          .133
(5) Results: absorbance is declining meaning cells are dying, thus no transformation 
    has resulted. Will leave in incubator overnight to see if transformants grow out.


05/26/11 Agenda: Transforming Top 10 cells to Establish Hg sensitive promoter part K346002

(1) 5 microliters of transformation media (BIO RAD Catalogue 166-0409 received 1-17-11 GT) 
    added to 40 microliters of competent cells in LB broth.
(2) 2 microliters of K346002 DNA added to broth.
(3) Solution was placed in ice bath for 5 minutes.
(4) Placed in 44.7 degree Celsius water for 50 seconds.
(5) Placed in ice bath for 5 minutes.
(6) 1 microliter of SOB buffer at room temperature added to broth 
   (in order to close plasmid channels). 
(7) PLated 100 microliters of cells on LB AMP plates (5-26-11 AM). 
Expected: 10 to 50 colonies projected to grow.

06/02/11 Agenda: Transformation of promoter part K346002 in E.Coli Bacteria

  Decided to Transform E.col: three transformations with the E080 part, the J45004 part, 
  and the K346002 part. We follow this procedure.
(1)105 E.col: calls were added to 100ul BioRad Transformation Solution.
(2)1ul of each part of DNA from the Registry was added to the cells which were incubated 
   30min on ice.
(3)Cells were heat shocked by swirling in water at 42 degree water bath for 2min. Then 
   return to ice for 30min.
(4)1ml 50B buffer was added to the cells and they were incubated for 2 hrs. at room temp.
(5)100ul of the transformed cells were plated on a fresh LB/AMP plate.

06/03/11 Agenda: No Growth of E.col with K346002

The E.col that was transformed on 6/02/11 did not have any growth.

06/14/11 Agenda: A3 Assembly

Today, we put together our entire part. We used the A3 assembly, as explained on the Model page.
We then poured plates of our assembled plasmid. We hope for 10 to 50 colonies of transformed colonies.

06/16/11 Agenda: Added Enzymes to E0840, J45119, and PSB1T3

(1)Vortex E0840, J45119, and PSB1T3.
(2)Add 1 uL of SpeI enzyme and 1 uL of PstI enzyme to 8 uL of E0840 in order to cut both ends of the wanted DNA.
Also add .5 uL of BSA and 5 uL.
(3)Add 1 uL of EcoRI enzyme and 1 uL of XbaI enzyme to J45119 in order to cut both ends of the wanted DNA.
Also add .5 microliters of BSA and 5 microliters.
(4)Add 1 uL of EcoRI enzyme and 1 uL of PstI enzyme to PSB1T3 in order to cut both ends of the wanted DNA.
(5)Place E0840, J45119, and PSB1T3 in a water bath at 37 degrees C for 20 minutes so that all the parts are
sufficiently cut.
(6)Assemble the new plasmid by combining 2 uL of E0840, 2 uL J45119, and 2 uL PSB1T3 plasmids in one container.
Also add 2 micro liters of buffer and 1 microliter of ligase.
(7)Place the new assembly of E0840, J45119, and PSB1T3 in the water bath at 37 degrees C for 20 minutes.
Ligation
(1)Incubate at room temperature for 10 minutes and then heat inactive at 80 degrees C for 20 min.
(2)Transform 2 uL of the ligation product into 50 uL of competent E. coli cells.

06/17/11 Agenda: Change in Promoter from Hg detection to As Detection

Because of many failed attempts with the Hg promoter, we will be changing our project to a device that detects
Arsenic with a promoter that is activated with the presents of arsenic.

06/20/11 Agenda: K190015 (ArsR regulated promoter) Transformed

06/21/11 Agenda: K190015 (ArsR regulated promoter) No Growth

06/22/11 Agenda: Began powerpoint presentation

To view the power point presentation click Here and Download!

06/23/11 Agenda: Continued working on powerpoint presentation and Ligation

Continued working on power point and began ligating parts K190015 to J45119 and K190015 to E0840.