iGEM 2011 — Team SouthBend-Mishawaka-HS-2

[![](/wiki/skins/common/images/wiki.png)"](/Main_Page "Main Page")

* [Page](/Team%3ASouthBend-Mishawaka-HS-2/Notebook)
* [Discussion](/wiki/index.php?title=Talk:Team:SouthBend-Mishawaka-HS-2/Notebook&action=edit&redlink=1)
* [View source](/wiki/index.php?title=Team:SouthBend-Mishawaka-HS-2/Notebook&action=edit)
* [History](/wiki/index.php?title=Team:SouthBend-Mishawaka-HS-2/Notebook&action=history)
* teams

* [Log in](/wiki/index.php?title=Special:UserLogin&returnto=Team:SouthBend-Mishawaka-HS-2/Notebook "You are encouraged to log in; however, it is not mandatory [o]")

# Team:SouthBend-Mishawaka-HS-2/Notebook

### From 2011.igem.org

[![SouthBend-Mishawaka-HS-2 logo.png](/wiki/images/7/76/SouthBend-Mishawaka-HS-2_logo.png)](/File%3ASouthBend-Mishawaka-HS-2_logo.png)

| [Home](/Team%3ASouthBend-Mishawaka-HS-2 "Team:SouthBend-Mishawaka-HS-2") | [Team](/Team%3ASouthBend-Mishawaka-HS-2/Team "Team:SouthBend-Mishawaka-HS-2/Team") | [Official Team Profile](https://igem.org/Team.cgi?year=2011&team_name=SouthBend-Mishawaka-HS-2) | [Project](/Team%3ASouthBend-Mishawaka-HS-2/Project "Team:SouthBend-Mishawaka-HS-2/Project") | [Parts Submitted to the Registry](/Team%3ASouthBend-Mishawaka-HS-2/Parts "Team:SouthBend-Mishawaka-HS-2/Parts") | [Modeling](/Team%3ASouthBend-Mishawaka-HS-2/Modeling "Team:SouthBend-Mishawaka-HS-2/Modeling") | **Notebook** | [Safety](/Team%3ASouthBend-Mishawaka-HS-2/Safety "Team:SouthBend-Mishawaka-HS-2/Safety") | [Attributions](/Team%3ASouthBend-Mishawaka-HS-2/Attributions "Team:SouthBend-Mishawaka-HS-2/Attributions") |
| --- | --- | --- | --- | --- | --- | --- | --- | --- |

|  |
| --- |
| Contents   * [1 Notebook](#Notebook)   + [1.1 05/19/11 Agenda: Transformation Test Run](#05.2F19.2F11_Agenda:_Transformation_Test_Run)   + [1.2 05/24/11 Agenda: Establishment of the K346002 Hg Sensitive Promoter](#05.2F24.2F11_Agenda:_Establishment_of_the_K346002_Hg_Sensitive_Promoter)   + [1.3 05/25/11 Agenda: Examining Results of Establishment of the K346002 Hg Sensitive Promoter](#05.2F25.2F11_Agenda:_Examining_Results_of_Establishment_of_the_K346002_Hg_Sensitive_Promoter)   + [1.4 05/26/11 Agenda: Examining Results of Establishment of the K346002 Hg Sensitive Promoter Round II](#05.2F26.2F11_Agenda:_Examining_Results_of_Establishment_of_the_K346002_Hg_Sensitive_Promoter_Round_II)   + [1.5 05/26/11 Agenda: Transforming Top 10 cells to Establish Hg sensitive promoter part K346002](#05.2F26.2F11_Agenda:_Transforming_Top_10_cells_to_Establish_Hg_sensitive_promoter_part_K346002)   + [1.6 06/02/11 Agenda: Transformation of promoter part K346002 in E.Coli Bacteria](#06.2F02.2F11_Agenda:_Transformation_of_promoter_part_K346002_in_E.Coli_Bacteria)   + [1.7 06/03/11 Agenda: No Growth of E.col with K346002](#06.2F03.2F11_Agenda:_No_Growth_of_E.col_with_K346002)   + [1.8 06/14/11 Agenda: A3 Assembly](#06.2F14.2F11_Agenda:_A3_Assembly)   + [1.9 06/16/11 Agenda: Added Enzymes to E0840, J45119, and PSB1T3](#06.2F16.2F11_Agenda:_Added_Enzymes_to_E0840.2C_J45119.2C_and_PSB1T3)   + [1.10 06/17/11 Agenda: Change in Promoter from Hg detection to As Detection](#06.2F17.2F11_Agenda:_Change_in_Promoter_from_Hg_detection_to_As_Detection)   + [1.11 06/20/11 Agenda: K190015 (ArsR regulated promoter) Transformed](#06.2F20.2F11_Agenda:_K190015_.28ArsR_regulated_promoter.29_Transformed)   + [1.12 06/21/11 Agenda: K190015 (ArsR regulated promoter) No Growth](#06.2F21.2F11_Agenda:_K190015_.28ArsR_regulated_promoter.29_No_Growth)   + [1.13 06/22/11 Agenda: Began powerpoint presentation](#06.2F22.2F11_Agenda:_Began_powerpoint_presentation)   + [1.14 06/23/11 Agenda: Continued working on powerpoint presentation and Ligation](#06.2F23.2F11_Agenda:_Continued_working_on_powerpoint_presentation_and_Ligation) |

## 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](/Agenda%3ATransformation_Test_Run "Agenda:Transformation Test Run") | 20 | 21 | 22 |
| 23 | 24 [Agenda: Establishment of the K346002 Hg Sensitive Promoter](/wiki/index.php?title=Agenda:_Establishment_of_the_K346002_Hg_Sensitive_Promoter&action=edit&redlink=1 "Agenda: Establishment of the K346002 Hg Sensitive Promoter (page does not exist)") | 25 [Agenda: Examining Results of Establishment of the K346002 Hg Sensitive Promoter](/wiki/index.php?title=Agenda:_Examining_Results_of_Establishment_of_the_K346002_Hg_Sensitive_Promoter&action=edit&redlink=1 "Agenda: Examining Results of Establishment of the K346002 Hg Sensitive Promoter (page does not exist)") | 26 [Agenda: Examining Results of Establishment of the K346002 Hg Sensitive Promoter Round II](/wiki/index.php?title=Agenda:_Examining_Results_of_Establishment_of_the_K346002_Hg_Sensitive_Promoter_Round_II&action=edit&redlink=1 "Agenda: Examining Results of Establishment of the K346002 Hg Sensitive Promoter Round II (page does not exist)")   [Agenda: Transforming Top 10 cells to Establish Hg sensitive promoter part K346002](/Agenda%3A_Transforming_Top_10_cells_to_Establish_Hg_sensitive_promoter_part_K346002 "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](/Agenda%3A_Transformation_of_promoter_part_K346002_in_E.Coli_Bacteria "Agenda: Transformation of promoter part K346002 in E.Coli Bacteria") | 3 [Agenda: No Growth of E.col with K346002](/Agenda%3A_No_Growth_of_E.col_with_K346002 "Agenda: No Growth of E.col with K346002") | 4 | 5 |
| 6 | 7 | 8 | 9 | 10 | 11 | 12 |
| 13 | 14[Agenda: A3 Assembly](/wiki/index.php?title=Agenda:_A3_Assembly&action=edit&redlink=1 "Agenda: A3 Assembly (page does not exist)") | 15 | 16 [Agenda: Added Enzymes to E0840, J45119, and PSB1T3](/Agenda%3A_Added_Enzymes_to_E0840%2C_J45119%2C_and_PSB1T3 "Agenda: Added Enzymes to E0840, J45119, and PSB1T3") | 17[Agenda: Change in Promoter from Hg detection to As Detection](/Agenda%3A_Change_in_Promoter_from_Hg_detection_to_As_Detection "Agenda: Change in Promoter from Hg detection to As Detection") | 18 | 19 |
| 20 [Agenda: K190015 (ArsR regulated promoter) Transformed](/Agenda%3A_K190015_%28ArsR_regulated_promoter%29_Transformed "Agenda: K190015 (ArsR regulated promoter) Transformed") | 21 [Agenda: K190015 (ArsR regulated promoter) No Growth](/Agenda%3A_K190015_%28ArsR_regulated_promoter%29_No_Growth "Agenda: K190015 (ArsR regulated promoter) No Growth") | 22 [Agenda: Began powerpoint presentation](/Agenda%3A_Began_powerpoint_presentation "Agenda: Began powerpoint presentation") | 23[Agenda: Continued working on powerpoint presentation and Ligation](/Agenda%3A_Continued_working_on_powerpoint_presentation_and_Ligation "Agenda: 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.
```

Retrieved from "[http://2011.igem.org/Team:SouthBend-Mishawaka-HS-2/Notebook](http://2011.igem.org/Team%3ASouthBend-Mishawaka-HS-2/Notebook)"

[![Powered by MediaWiki](/wiki/skins/common/images/poweredby_mediawiki_88x31.png)](https://www.mediawiki.org/)

[![Attribution 3.0 Unported](https://i.creativecommons.org/l/by/3.0/88x31.png)](https://creativecommons.org/licenses/by/3.0/)

* [Recent changes](/Special%3ARecentChanges "Recent changes")
* [What links here](/Special%3AWhatLinksHere/Team%3ASouthBend-Mishawaka-HS-2/Notebook "List of all wiki pages that link here [j]")
* [Related changes](/Special%3ARecentChangesLinked/Team%3ASouthBend-Mishawaka-HS-2/Notebook "Recent changes in pages linked from this page [k]")
* [Special pages](/Special%3ASpecialPages "List of all special pages [q]")
* [My preferences](/Special%3APreferences)

* [Printable version](/wiki/index.php?title=Team:SouthBend-Mishawaka-HS-2/Notebook&printable=yes "Printable version of this page [p]")
* [Permanent link](/wiki/index.php?title=Team:SouthBend-Mishawaka-HS-2/Notebook&oldid=19132 "Permanent link to this revision of the page")
* [Privacy policy](/2011.igem.org%3APrivacy_policy "2011.igem.org:Privacy policy")
* [Disclaimers](/2011.igem.org%3AGeneral_disclaimer "2011.igem.org:General disclaimer")