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• iGEM 2013

Overview March-April May-June July-August September-October	Overview ADD large Phage project overview

Contents 1 March 1.1 3/15/13 1.2 3/18/13 1.3 3/20/13 1.4 3/22/13 1.5 3/25/13 1.6 3/27/13 1.7 3/29/13 2 April 2.1 4/1/13 2.2 4/4/13 2.3 4/5/13 2.4 4/8/13 2.5 4/10/13 2.6 4/12/13 2.7 4/15/13 3 May 3.1 5/1/13 3.2 5/3/13 3.3 5/6/13 3.4 5/8/13 3.5 5/10/13 3.6 5/13/13 3.7 5/15/13 3.8 5/17/13 3.9 5/20/13 3.10 5/22/13 3.11 5/24/13 3.12 5/27/13 3.13 5/29/13 3.14 5/31/13 4 June 4.1 6/3/13 4.2 6/5/13 4.3 6/7/13 4.4 6/10/13 4.5 6/12/13 4.6 6/14/13 4.7 6/17/13 4.8 6/19/13 4.9 6/21/13 4.10 6/24/13 4.11 6/26/13 4.12 6/28/13 5 July 5.1 7/1/13 5.2 7/3/13 5.3 7/5/13 5.4 7/8/13 5.5 7/10/13 5.6 7/12/13 5.7 7/15/13 5.8 7/17/13 5.9 7/19/13 5.10 7/22/13 5.11 7/24/13 5.12 7/26/13 5.13 7/29/13 5.14 7/31/13 6 August 6.1 8/2/13 6.2 8/5/13 6.3 8/7/13 6.4 8/9/13 6.5 8/12/13 6.6 8/14/13 6.7 8/16/13 6.8 8/19/13 6.9 8/21/13 6.10 8/23/13 6.11 8/26/13 6.12 8/28/13 6.13 8/30/13 7 September 7.1 9/2/13 7.2 9/4/13 7.3 9/6/13 7.4 9/9/13 7.5 9/11/13 7.6 9/13/13 7.7 9/16/13 7.8 9/18/13 7.9 9/20/13 7.10 9/23/13 7.11 9/25/13 7.12 9/27/13 7.13 9/30/13

March

3/15/13

3/18/13

3/20/13

3/22/13

3/25/13

3/27/13

3/29/13

April

4/1/13

4/4/13

4/5/13

4/8/13

4/10/13

4/12/13

4/15/13

May

5/1/13

5/3/13

5/6/13

5/8/13

5/10/13

5/13/13

5/15/13

5/17/13

5/20/13

Today we need to run a dilution series to test the titer of our mutated phage stock. We also need to start selecting for small plaques and learning how to pick them and titer them out. We also should run a UV test on the mutated phage stock compared to the normal stock.

We picked one plaque off of the 180 sec UV plate sample. We suspended it in 1 mL of broth, and then UV-ed 20 uL samples at 45 second intervals. The number of plaques decreased the longer the samples sat under UV light. The samples were irradiated from 0 sec to 4 min 30 sec.

As a control, we diluted the T4Do stock to 10^-6 and tested 20 uL at 45 sec intervals (up to 6 min) under UV light.

Also, we diluted the T4 mutagenized stock to 10^-6 and tested 20 uL at 45 sec intervals (up to 4 min 30 sec) under UV light.

UV tests were done by placing 20 uL spots on parafilm and placed in a BSL-2 hood with the UV light turned on.

5/22/13

Results from 5/20/13 - We left the plates in the incubator for 48 hours, which caused contamination on many plates to grow.

When checked at 24 hours, the T4 mutagenized stock had a web plate at 10^-3 and less than 5 plaques at 10^-6. This experiment will need to be redone from 10^0 down through 10^-6. The whole mutagenesis may need to be redone if this only represents a dilution of our titer when we were trying to grow it in liquid culture. (We infected with ___ mL of phage at ___ titer in ____ vol of resuspended bacteria.)

Under UV light, the T4Do stock (diluted to 10^-6) has 19 plaques after being irradiated for six minutes (down from almost cleared at 0 min). Under UV light, the 180 sec UV plate spot (diluted in 1 mL) has a few hundred plaques on it, but the amount dropped significantly at 4 min 30 sec from when it was UV-ed for 0 min.

We will re-titer the T4-Mut stock so we can learn whether it was diluted or whether an infection worked. We will also re-run the UV test comparing the T4-Mut (10^-3) with the T4-Do stock (at 10^-6) for survivability. The mutagenized phage should survive better.

Since the loss of plaques seemed to level off for the T4Do stock at 5:15 (23 plaques) and 6 min (19 plaques), we will test a 7 min and 8 min timepoint to see if it stays level, suggesting these phage have multiple genomes and are severely mutated.

5/24/13

5/27/13

5/29/13

Today we wanted to see if we can transfer our current experiment from using E. coli W3110 as the host to E. coli B as the host. We set up multiple experiments. 1. We spot tested the following phage samples on W3110 and B: T1, T2, T3, T4Do stock, T4 mutated stock, T4-UV one-plaque plate harvest, T4-UV-mutated one-plaque plate harvest. 2. We did a dilution series on the T1 stock to see how concentrated it is. We will need to know the PFUs in order to grow a successful liquid culture and mass produce it for our large phage amplification procedure. 3. We also infected two samples of E. coli B, each with 10 uL of 10^-6 T4Do to observe plaque formation.

5/31/13

June

6/3/13

6/5/13

6/7/13

6/10/13

6/12/13

6/14/13

6/17/13

6/19/13

6/21/13

6/24/13

6/26/13

6/28/13

July

7/1/13

7/3/13

7/5/13

7/8/13

7/10/13

7/12/13

7/15/13

7/17/13

7/19/13

7/22/13

7/24/13

7/26/13

7/29/13

7/31/13

August

8/2/13

8/5/13

8/7/13

8/9/13

8/12/13

8/14/13

8/16/13

8/19/13

8/21/13

8/23/13

8/26/13

8/28/13

8/30/13

September

9/2/13

9/4/13

9/6/13

9/9/13

9/11/13

9/13/13

9/16/13

9/18/13

9/20/13

9/23/13

9/25/13

9/27/13

9/30/13