Team:BYU Provo/Notebook/SmallPhage/Summerexp/Period3/Dailylog

From 2013.igem.org

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<font color="#333399" size="3" font face="Calibri">
<font color="#333399" size="3" font face="Calibri">
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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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- Discussed modeling options: model phage plaque size against various variables including phage particle size, agar concentration, and bacterial concentration.
- Discussed modeling options: model phage plaque size against various variables including phage particle size, agar concentration, and bacterial concentration.
-
- 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 - Experiment 1]].
+
- 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>
<font size="4"> '''8/3/13''' </font>
-
- 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 - Experiment 1]].
+
- 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]].
<br>
<br>
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- Started E coli liquid culture over night
- Started E coli liquid culture over night
* 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]].
* 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 - Experiment 1]].
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* 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]].
<br>
<br>
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<font size="4"> '''7/26/13''' </font>
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<font size="4"> '''8/5/13''' </font>
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- Designed protocols for [[Team:BYU Provo/Notebook/SmallPhage/Springexp/Period3/Exp/7.29 Mutagen Concentration Test - Sixth Protocol|7.29 Mutagen Concentration Test - Sixth Protocol]] and decided to conduct an experiment to verify bacteria growth curve (specifics see [[Team:BYU Provo/Notebook/SmallPhage/Summerexp/Period2/Exp/7.27 Bacteria Growth Curve After Dilution|7.27 Bacteria Growth Curve After Dilution]])
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- 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]].
 +
 +
- Discussed ideas for modeling phage plaque sizes
 +
 +
<br>
 +
 
 +
<font size="4"> '''8/6/13''' </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]].
-
- Started 3mL of BL21 liquid culture overnight.
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- Started 5mL of E coli B liquid culture overnight.
<br>
<br>
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<font size="4"> '''7/27/13''' </font>
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<font size="4"> '''8/7/13''' </font>
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- Conducted [[Team:BYU Provo/Notebook/SmallPhage/Summerexp/Period2/Exp/7.27 Bacteria Growth Curve After Dilution|7.27 Bacteria Growth Curve After Dilution]]
+
- 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]].
 +
 
 +
- Phage Purification Group started the purification process with CsCl gradient.
<br>
<br>
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<font size="4"> '''7/28/13''' </font>
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<font size="4"> '''8/8/13''' </font>
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 +
- Started approximately 15mL of E coli B liquid culture overnight.
 +
 
 +
<br>
-
- Started 15mL of BL21 liquid culture overnight.
+
<font size="4"> '''8/9/13''' </font>
-
- Started phage liquid culture to test for superinfection.
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- Performed Preliminary Titer for [[Team:BYU Provo/Notebook/SmallPhage/Summerexp/8.2 Modeling phage plaque size|8.2 Modeling Phage Plaque Sizes - Preliminary Experiments]].
<br>
<br>
-
<font size="4"> '''7/29/13''' </font>
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<font size="4"> '''8/11/13''' </font>
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- Performed part 1 of [[Team:BYU Provo/Notebook/SmallPhage/Springexp/Period3/Exp/7.29 Mutagen Concentration Test - Sixth Protocol|7.29 Mutagen Concentration Test - Sixth Protocol]].
+
- Started approximately 20mL of E coli B liquid culture overnight.
-
- Did a spot test to determine the concentration phage in yesterday's liquid culture (We couldn't test for superinfection because all the bacteria were lysed.)
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<br>
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<font size="4"> '''8/12/13''' </font>
 +
 
 +
- 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.
 +
 
 +
- Started T1 propagation.
 +
 
 +
- 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"> '''7/31/13''' </font>
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<font size="4"> '''8/13/13''' </font>
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- Started 8mL BL21 liquid culture overnight and performed dilution series for the spot test procedure in [[Team:BYU Provo/Notebook/SmallPhage/Springexp/Period3/Exp/7.29 Mutagen Concentration Test - Sixth Protocol|7.29 Mutagen Concentration Test - Sixth Protocol]].
+
- Started approximately 20mL of E coli B liquid culture overnight.
<br>
<br>
 +
 +
<font size="4"> '''8/14/13''' </font>
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 +
- 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.
 +
 +
<br>
 +
 +
<font size="4"> '''8/15/13''' </font>
 +
 +
- 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 30mL of E coli B liquid culture overnight.
 +
 +
<br>
 +
 +
<font size="4"> '''8/16/13''' </font>
 +
 +
- Started [[Team:BYU Provo/Notebook/SmallPhage/Summerexp/8.16 Modeling phage plaque size|8.16 Modeling Phage Plaque Sizes - Experiment One]].
 +
 +
- 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 10 mL of E coli B liquid culture overnight.
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 +
<br>
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|}
|}
{{TeamBYUProvoFooter}}
{{TeamBYUProvoFooter}}

Latest revision as of 15:37, 9 September 2013


Small Phage July - August Notebook: August 1 - August 16 Daily Log



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

8/1/13

- Performed the spot test in 7.29 Mutagen Concentration Test - Sixth Protocol.


8/2/13

- 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.

- Discussed modeling options: model phage plaque size against various variables including phage particle size, agar concentration, and bacterial concentration.

- Streaked E coli W3110 and K12 from frozen stock in preparation for the viability test in 8.2 Modeling Phage Plaque Sizes - Preliminary Experiments.


8/3/13

- E coli W3110 streak worked, but K12 did not survive. Thus, we tried to amplify K12 using liquid culture. For specifics, please consult 8.2 Modeling Phage Plaque Sizes - Preliminary Experiments.


8/4/13

- Started E coli liquid culture over night


8/5/13

- Performed Phage viability/infection test for 8.2 Modeling Phage Plaque Sizes - Preliminary Experiments.

- Discussed ideas for modeling phage plaque sizes


8/6/13

- Check up on the phage viability/infection test for 8.2 Modeling Phage Plaque Sizes - Preliminary Experiments.

- Started 5mL of E coli B liquid culture overnight.


8/7/13

- Performed spot test to estimate phage titerfor 8.2 Modeling Phage Plaque Sizes - Preliminary Experiments.

- Phage Purification Group started the purification process with CsCl gradient.


8/8/13

- Started approximately 15mL of E coli B liquid culture overnight.


8/9/13

- Performed Preliminary Titer for 8.2 Modeling Phage Plaque Sizes - Preliminary Experiments.


8/11/13

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


8/12/13

- Performed titer - repeat for 8.2 Modeling Phage Plaque Sizes - Preliminary Experiments based on the results from 8.10 preliminary titer test.

- Started T1 propagation.

- Made accurate x2 top agar as preparation for 8.16 Modeling Phage Plaque Sizes - Experiment One.


8/13/13

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


8/14/13

- Performed mutagenesis and spot test for 8.14 Mutagen Concentration Test - Seventh Protocol.

- Performed spot test for T1 propagation. Spotted 5uL of -2 through -7 dilutions.


8/15/13

- T1 propagation revealed plaques on each of the tested dilutions, suggesting that this propagated T1 phage stock has a titer of at least 109 pfu/mL -> more accurate spot test / titer needed to determine the exact phage concentration.

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


8/16/13

- Started 8.16 Modeling Phage Plaque Sizes - Experiment One.

- Phage Purification team performed the CsCl gradient for 8.14 Mutagen Concentration Test - Seventh Protocol.

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



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