Team:BYU Provo/Notebook/SmallPhage/Summerexp/Period4/Dailylog

From 2013.igem.org

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: [[Team:BYU_Provo/Small_Phage|Overview]]
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: <u> '''Small Phage''' </u> </font>
: [[Team:BYU Provo/Notebook/SmallPhage/Winterexp|March-April]]
: [[Team:BYU Provo/Notebook/SmallPhage/Winterexp|March-April]]
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<font size="4"> '''8/17/13''' </font>
<font size="4"> '''8/17/13''' </font>
-
- Started characterizing post-CsCl phage in [[Team:BYU_Provo/Notebook/SmallPhage/Summerexp/8.14_Mutagen_Concentration_Test_-_Seventh_Protocol|8.14 Mutagen Concentration Test - Seventh Protocol]].
+
* Started characterizing post-CsCl phage in [[Team:BYU_Provo/Notebook/SmallPhage/Summerexp/8.14_Mutagen_Concentration_Test_-_Seventh_Protocol|8.14 Mutagen Concentration Test - Seventh Protocol]].
-
- Started approximately 10mL of E coli B liquid culture overnight.
+
* Started approximately 10mL of E coli B liquid culture overnight.
-
- Streaked out E coli B.
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* Streaked out E coli B.
<br>
<br>
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<font size="4"> '''8/2/13''' </font>
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<font size="4"> '''8/18/13''' </font>
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- Because the top agar used in yesterday's spot was contaminated, we decided to redo this step. Also, because most of the spot tests went down to -6, we performed further dilution for the next testing to get a more accurate idea of phage concentration.
+
* Continued characterization of post-CsCl phage in [[Team:BYU_Provo/Notebook/SmallPhage/Summerexp/8.14_Mutagen_Concentration_Test_-_Seventh_Protocol|8.14 Mutagen Concentration Test - Seventh Protocol]].
-
- Discussed modeling options: model phage plaque size against various variables including phage particle size, agar concentration, and bacterial concentration.
+
* Started approximately 20mL of E coli B liquid culture overnight.
-
 
+
-
- Streaked E coli W3110 and K12 from frozen stock in preparation for the viability test in [[Team:BYU Provo/Notebook/SmallPhage/Summerexp/8.2 Modeling phage plaque size|8.2 Modeling Phage Plaque Sizes - Preliminary Experiments]].
+
<br>
<br>
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<font size="4"> '''8/3/13''' </font>
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<font size="4"> '''8/19/13''' </font>
 +
 
 +
* Plaque test of post-CsCl phage in [[Team:BYU_Provo/Notebook/SmallPhage/Summerexp/8.14_Mutagen_Concentration_Test_-_Seventh_Protocol|8.14 Mutagen Concentration Test - Seventh Protocol]].
 +
 
 +
* Discussed modeling result of [[Team:BYU Provo/Notebook/SmallPhage/Summerexp/8.16 Modeling phage plaque size|8.16 Modeling Phage Plaque Sizes - Experiment One]] with Dr. Grose -> need to repeat for T1 and T2 starting from dilution series and spot test.
-
- E coli W3110 streak worked, but K12 did not survive. Thus, we tried to amplify K12 using liquid culture. For specifics, please consult [[Team:BYU Provo/Notebook/SmallPhage/Summerexp/8.2 Modeling phage plaque size|8.2 Modeling Phage Plaque Sizes - Preliminary Experiments]].
+
* Started approximately 30 mL of E coli B liquid culture overnight.
<br>
<br>
-
<font size="4"> '''8/4/13''' </font>
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<font size="4"> '''8/20/13''' </font>
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- Started E coli liquid culture over night
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* Selected for 12 small plaques (S1-S12, relatively large phage) and 12 big plaques (B1-B12, relatively small phage) at respective end of spectrum for [[Team:BYU_Provo/Notebook/SmallPhage/Summerexp/8.14_Mutagen_Concentration_Test_-_Seventh_Protocol|8.14 Mutagen Concentration Test - Seventh Protocol]]. Spectrum ends were chosen because the likelihood of contamination between different layers of CsCl during the extraction process.
-
* 10mL of BL21 for spot test in [[Team:BYU Provo/Notebook/SmallPhage/Springexp/Period3/Exp/7.29 Mutagen Concentration Test - Sixth Protocol|7.29 Mutagen Concentration Test - Sixth Protocol]].
+
-
* 2mL each of BL21, W3110, and B for phage viability and infection test in [[Team:BYU Provo/Notebook/SmallPhage/Summerexp/8.2 Modeling phage plaque size|8.2 Modeling Phage Plaque Sizes - Preliminary Experiments]].
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-
<br>
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* Performed dilution series and spot test for T1, T2 (from stock), and T7.
-
<font size="4"> '''8/5/13''' </font>
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* Started approximately 30 mL of E coli B liquid culture overnight.
-
- Performed Phage viability/infection test for [[Team:BYU Provo/Notebook/SmallPhage/Summerexp/8.2 Modeling phage plaque size|8.2 Modeling Phage Plaque Sizes - Preliminary Experiments]].
 
-
 
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- Discussed ideas for modeling phage plaque sizes
 
-
 
<br>
<br>
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<font size="4"> '''8/6/13''' </font>
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<font size="4"> '''8/21/13''' </font>
-
- Check up on the phage viability/infection test for [[Team:BYU Provo/Notebook/SmallPhage/Summerexp/8.2 Modeling phage plaque size|8.2 Modeling Phage Plaque Sizes - Preliminary Experiments]].
+
* Spot test for T7 only showed plaques up to -5. Might not be high enough for mutagenesis. Need to propagate.
 +
 +
* Plated the S1-S12 and B1-B12 samples in [[Team:BYU_Provo/Notebook/SmallPhage/Summerexp/8.14_Mutagen_Concentration_Test_-_Seventh_Protocol|8.14 Mutagen Concentration Test - Seventh Protocol]].
-
- Started 5mL of E coli B liquid culture overnight.
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* Started approximately 6 mL of E coli B liquid culture overnight
<br>
<br>
-
<font size="4"> '''8/7/13''' </font>
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<font size="4"> '''8/22/13''' </font>
-
- Performed spot test to estimate phage titerfor [[Team:BYU Provo/Notebook/SmallPhage/Summerexp/8.2 Modeling phage plaque size|8.2 Modeling Phage Plaque Sizes - Preliminary Experiments]].
+
* Nothing showed on the S1-S12 and B1-B12 plates. Wildtype had too many plaques (T7 at -4).  
-
- Phage Purification Group started the purification process with CsCl gradient.
+
* T7 propagation for [[Team:BYU Provo/Notebook/SmallPhage/Summerexp/8.26 Mutagen Concentration Test|8.26 Mutagen Concentration Test - Eighth Protocol]].
 +
 
 +
* Started approximately 20 mL of E coli liquid culture overnight.
<br>
<br>
-
<font size="4"> '''8/8/13''' </font>
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<font size="4"> '''8/23/13''' </font>
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- Started approximately 15mL of E coli B liquid culture overnight.
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- Repeated plating of S1-S12 and B1-B12 in [[Team:BYU_Provo/Notebook/SmallPhage/Summerexp/8.14_Mutagen_Concentration_Test_-_Seventh_Protocol|8.14 Mutagen Concentration Test - Seventh Protocol]].
<br>
<br>
-
<font size="4"> '''8/9/13''' </font>
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<font size="4"> '''8/24/13''' </font>
-
- Performed Preliminary Titer for [[Team:BYU Provo/Notebook/SmallPhage/Summerexp/8.2 Modeling phage plaque size|8.2 Modeling Phage Plaque Sizes - Preliminary Experiments]].
+
- Still no bacteria or phage plaques showed up for S1-S12 and B1-B12 in [[Team:BYU_Provo/Notebook/SmallPhage/Summerexp/8.14_Mutagen_Concentration_Test_-_Seventh_Protocol|8.14 Mutagen Concentration Test - Seventh Protocol]] -> We decided to focus on [[Team:BYU Provo/Notebook/SmallPhage/Summerexp/8.26 Mutagen Concentration Test|8.26 Mutagen Concentration Test - Eighth Protocol]] instead
-
<br>
+
- Purified T7 phage propagation and performed a spot test to estimate the titer of this fresh stock (8.24).
-
<font size="4"> '''8/11/13''' </font>
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- Started approximately 10mL of E coli B liquid culture overnight
-
 
+
-
- Started approximately 20mL of E coli B liquid culture overnight.
+
<br>
<br>
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<font size="4"> '''8/12/13''' </font>
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<font size="4"> '''8/25/13''' </font>
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- Performed titer - repeat for [[Team:BYU Provo/Notebook/SmallPhage/Summerexp/8.2 Modeling phage plaque size|8.2 Modeling Phage Plaque Sizes - Preliminary Experiments]] based on the results from 8.10 preliminary titer test.
+
- Titer was performed for T7 phage 8.24 stock at -6 and -7 to gain a more accurate estimate of phage concentration.
-
- Started T1 propagation.
+
- Started approximately 10mL of E coli B liquid culture overnight.
-
 
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-
- Made accurate x2 top agar as preparation for [[Team:BYU Provo/Notebook/SmallPhage/Summerexp/8.16 Modeling phage plaque size|8.16 Modeling Phage Plaque Sizes - Experiment One]].
+
<br>
<br>
-
<font size="4"> '''8/13/13''' </font>
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<font size="4"> '''8/26/13''' </font>
 +
 
 +
- Performed the actual mutagenesis procedure in [[Team:BYU Provo/Notebook/SmallPhage/Summerexp/8.26 Mutagen Concentration Test|8.26 Mutagen Concentration Test - Eighth Protocol]].
 +
 
 +
- Phage Purification Team was able to run the CsCl gradient right after the completion of mutagenesis.
- Started approximately 20mL of E coli B liquid culture overnight.
- Started approximately 20mL of E coli B liquid culture overnight.
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<br>
<br>
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<font size="4"> '''8/14/13''' </font>
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<font size="4"> '''8/27/13''' </font>
-
 
+
-
- Performed mutagenesis and spot test for [[Team:BYU_Provo/Notebook/SmallPhage/Summerexp/8.14_Mutagen_Concentration_Test_-_Seventh_Protocol|8.14 Mutagen Concentration Test - Seventh Protocol]].
+
-
- Performed spot test for T1 propagation. Spotted 5uL of -2 through -7 dilutions.
+
- Spot test was performed for the post CsCl aliquots (for both control and mutated group) to estimate phage concentration in each. For specific procedure please refer to [[Team:BYU Provo/Notebook/SmallPhage/Summerexp/8.26 Mutagen Concentration Test|8.26 Mutagen Concentration Test - Eighth Protocol]].
<br>
<br>
-
<font size="4"> '''8/15/13''' </font>
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<font size="4"> '''8/30/13''' </font>
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- T1 propagation revealed plaques on each of the tested dilutions, suggesting that this propagated T1 phage stock has a titer of at least 10<sup>9</sup> pfu/mL -> more accurate spot test / titer needed to determine the exact phage concentration.
+
- Started approximately 20mL of E coli B liquid culture overnight.
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- Started approximately 30mL of E coli B liquid culture overnight.
+
- Worked on editing the abstract for submission.
<br>
<br>
-
<font size="4"> '''8/16/13''' </font>
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<font size="4"> '''8/31/13''' </font>
-
- Started [[Team:BYU Provo/Notebook/SmallPhage/Summerexp/8.16 Modeling phage plaque size|8.16 Modeling Phage Plaque Sizes - Experiment One]].
+
- Further dilution series and spot test was performed to gain a more accurate idea of phage distribution in CsCl gradient. Specific procedures can be found at [[Team:BYU Provo/Notebook/SmallPhage/Summerexp/8.26 Mutagen Concentration Test|8.26 Mutagen Concentration Test - Eighth Protocol]].
-
- Phage Purification team performed the CsCl gradient for [[Team:BYU_Provo/Notebook/SmallPhage/Summerexp/8.14_Mutagen_Concentration_Test_-_Seventh_Protocol|8.14 Mutagen Concentration Test - Seventh Protocol]].
+
- Started approximately 10mL of E coli B liquid culture overnight.
<br>
<br>
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|}
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{{TeamBYUProvoFooter}}
{{TeamBYUProvoFooter}}

Latest revision as of 20:02, 4 September 2013


Small Phage July - August Notebook: August 17 - August 31 Daily Log



Small Phage
March-April
May-June
July-August
September-October

8/17/13

  • Started approximately 10mL of E coli B liquid culture overnight.
  • Streaked out E coli B.


8/18/13

  • Started approximately 20mL of E coli B liquid culture overnight.


8/19/13

  • Started approximately 30 mL of E coli B liquid culture overnight.


8/20/13

  • Selected for 12 small plaques (S1-S12, relatively large phage) and 12 big plaques (B1-B12, relatively small phage) at respective end of spectrum for 8.14 Mutagen Concentration Test - Seventh Protocol. Spectrum ends were chosen because the likelihood of contamination between different layers of CsCl during the extraction process.
  • Performed dilution series and spot test for T1, T2 (from stock), and T7.
  • Started approximately 30 mL of E coli B liquid culture overnight.


8/21/13

  • Spot test for T7 only showed plaques up to -5. Might not be high enough for mutagenesis. Need to propagate.
  • Started approximately 6 mL of E coli B liquid culture overnight


8/22/13

  • Nothing showed on the S1-S12 and B1-B12 plates. Wildtype had too many plaques (T7 at -4).
  • Started approximately 20 mL of E coli liquid culture overnight.


8/23/13

- Repeated plating of S1-S12 and B1-B12 in 8.14 Mutagen Concentration Test - Seventh Protocol.


8/24/13

- Still no bacteria or phage plaques showed up for S1-S12 and B1-B12 in 8.14 Mutagen Concentration Test - Seventh Protocol -> We decided to focus on 8.26 Mutagen Concentration Test - Eighth Protocol instead

- Purified T7 phage propagation and performed a spot test to estimate the titer of this fresh stock (8.24).

- Started approximately 10mL of E coli B liquid culture overnight


8/25/13

- Titer was performed for T7 phage 8.24 stock at -6 and -7 to gain a more accurate estimate of phage concentration.

- Started approximately 10mL of E coli B liquid culture overnight.


8/26/13

- Performed the actual mutagenesis procedure in 8.26 Mutagen Concentration Test - Eighth Protocol.

- Phage Purification Team was able to run the CsCl gradient right after the completion of mutagenesis.

- Started approximately 20mL of E coli B liquid culture overnight.


8/27/13

- Spot test was performed for the post CsCl aliquots (for both control and mutated group) to estimate phage concentration in each. For specific procedure please refer to 8.26 Mutagen Concentration Test - Eighth Protocol.


8/30/13

- Started approximately 20mL of E coli B liquid culture overnight.

- Worked on editing the abstract for submission.


8/31/13

- Further dilution series and spot test was performed to gain a more accurate idea of phage distribution in CsCl gradient. Specific procedures can be found at 8.26 Mutagen Concentration Test - Eighth Protocol.

- Started approximately 10mL of E coli B liquid culture overnight.


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