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| - | Went through Other Team Wiki's to look for what they did with modelling
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| | Today we did a Polymerase Chain Reaction (PCR) with P Taq. The purpose of this experiment was to amplify LuxOD47E . Gene specific LuxO forward and reverse primers were used. Conditions used were: Denature (94 Degrees Celsius, 3 minutes), 36 cycles (Denature (94 Degrees Celsius, 45 Seconds), Anneal (55 Degrees Celsius, 45 Seconds), Extend (72 Degrees Celsius, 2 minutes)), Final Extension (72 Degrees Celsius, 10 minutes), and hold at 4 Degrees Celsius overnight. | | Today we did a Polymerase Chain Reaction (PCR) with P Taq. The purpose of this experiment was to amplify LuxOD47E . Gene specific LuxO forward and reverse primers were used. Conditions used were: Denature (94 Degrees Celsius, 3 minutes), 36 cycles (Denature (94 Degrees Celsius, 45 Seconds), Anneal (55 Degrees Celsius, 45 Seconds), Extend (72 Degrees Celsius, 2 minutes)), Final Extension (72 Degrees Celsius, 10 minutes), and hold at 4 Degrees Celsius overnight. |
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| + | Purpose: Amplify LuxO D47A with pTaq PCR. LuxO-F/R primers were used fwith the following conditions: 94ºC for 3 minutes; 36 X (94ºC for 30 seconds; 55ºC for 45 seconds; 72ºC for 4 minutes); 72ºC for 10 minutes; held at 4ºC overnight. |
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| | LB agar plates with different antibiotics were made for later use. | | LB agar plates with different antibiotics were made for later use. |
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| - | WIKI CODING HERE
| + | We got together and made our project proposal, outlining the three areas of the island we wanted to develop, and a general idea of what would be in each. Katie and I are working on the Virtual Lab :). I walked through a couple more scripting tutorials and then did a lot of lab equipment building: shelves, tables, fridges, etc. |
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| | None to offer here – the PCR tubes had mysteriously vanished from the PCR machine when I returned to collect them after the PCR had finished. | | None to offer here – the PCR tubes had mysteriously vanished from the PCR machine when I returned to collect them after the PCR had finished. |
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CAROL
Amplification of luxCDABE using Taq polymerase
The purpose of this experiment was to amplify luxCDABE with Taq polymerase. Gene specific luxCDABE forward and reverse primers were used. Conditions used were: Denature (94 Degrees Celsius, 3 minutes), 30 cycles (Denature (94 Degrees Celsius, 45 Seconds), Anneal (52 Degrees Celsius, 45 Seconds), Extend (72 Degrees Celsius, 6 minutes)), Final Extension (72 Degrees Celsius, 10 minutes), and hold at 4 Degrees Celsius overnight.
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CHINMOYEE
Past Teams' Modelling
Went through Other Team Wiki's to look for what they did with modelling
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EMILY
Amplification of LuxOD47E
Today we did a Polymerase Chain Reaction (PCR) with P Taq. The purpose of this experiment was to amplify LuxOD47E . Gene specific LuxO forward and reverse primers were used. Conditions used were: Denature (94 Degrees Celsius, 3 minutes), 36 cycles (Denature (94 Degrees Celsius, 45 Seconds), Anneal (55 Degrees Celsius, 45 Seconds), Extend (72 Degrees Celsius, 2 minutes)), Final Extension (72 Degrees Celsius, 10 minutes), and hold at 4 Degrees Celsius overnight.
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JEREMY
Amplification of LuxOD47A
Purpose: Amplify LuxO D47A with pTaq PCR. LuxO-F/R primers were used fwith the following conditions: 94ºC for 3 minutes; 36 X (94ºC for 30 seconds; 55ºC for 45 seconds; 72ºC for 4 minutes); 72ºC for 10 minutes; held at 4ºC overnight.
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KATIE
Planning the Second Life Project
Project Proposal was made and it appears the island will consist of three domains:
- Biobrick Simulator
- Synthetic Kingdom
- Virtual Lab
I have been assigned to the virtual lab and it will be mainly my responsibility to organize the activities that can be done in the building. A layout for the island is also in the process of being made.
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KEVIN
Making of different LB agar plates
LB agar plates with different antibiotics were made for later use.
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MANDY
Second Life Project Proposal
We got together and made our project proposal, outlining the three areas of the island we wanted to develop, and a general idea of what would be in each. Katie and I are working on the Virtual Lab :). I walked through a couple more scripting tutorials and then did a lot of lab equipment building: shelves, tables, fridges, etc.
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VICKI
PCR Amplification of LuxPQ
Purpose:
To amplify LuxPQ on TOPO II Blunt on a PCR and verify that the sample really does consist of LuxPQ.
Materials and methods:
- DNA template: LuxPQ on TOPO II blunt
- Forward primer: LuxPQ forward (T_m = 60 degrees Celsius)
- Reverse primer: LuxPQ reverse (T_m = 60 degrees Celsius)
- Expected PCR product size: 3855 bp
- DNA template concentration:
- Colony 1: 254.7 ng/uL
- Colony 9: 168.7 ng/uL
2 amplification tubes were made for each colony, in addition to a negative control tube (for a total of 5 tubes)
Master Mix contents (for 5 tubes):
- 10X PCR Buffer minus Mg 2+ (25 uL)
- 10mM dNTPs mixture (5 uL)
- 50mM MgCl2 (7.5 uL)
- Forward primer [10 uM] (7.5 uL)
- Reverse primer [10 uM] (7.5 uL)
- Taq DNA polymerase [5 units/uL] (2.0 uL)
- Autoclaved distilled HOH (190.5 uL)
TOTAL: 245 uL of Master Mix, for 5 tubes of 49 uL each.
Each PCR tube requires between 100-200 ng of template DNA. Accordingly, the Colony 1 sample was diluted to 200 ng/uL. 1 uL of DNA template was added to the following tubes:
- Tube 1: Colony 1
- Tube 2: Colony 1
- Tube 3: Colony 9
- Tube 4: Colony 9
- Tube 5: dd HOH (negative control).
PCR steps:
- Denaturation: 94 degrees C, 3 minutes
- Amplification: 36 cycles of:
- Denaturation (94 degrees C, 45 seconds);
- Annealing (55 degrees C, 45 seconds);
- Extension (72 degrees C, 4 minutes)}
- Final extension: 72 degrees C, 10 minutes
- Hold temperature: 4 degrees C
Results:
None to offer here – the PCR tubes had mysteriously vanished from the PCR machine when I returned to collect them after the PCR had finished.
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