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

From 2013.igem.org

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{| width="100%"
{| width="100%"
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| colspan="3" | <font color="#333399" size="5" font face="Calibri"> '''Small Phage Spring Notebook: May 27 - June 9 Daily Log'''</font>
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| colspan="3" | <font color="#333399" size="5" font face="Calibri"> '''Small Phage May - June Notebook: May 27 - June 16 Daily Log'''</font>
<br>
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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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<font size = "4">
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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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- Prepared sample for sequencing. This is done as part of [[Team:BYU Provo/Notebook/SmallPhage/Springexp/Period2/Exp/5.20 T7 Minor Capsid Protein PCR|5.20 T7 Minor Capsid Protein PCR]]
- Prepared sample for sequencing. This is done as part of [[Team:BYU Provo/Notebook/SmallPhage/Springexp/Period2/Exp/5.20 T7 Minor Capsid Protein PCR|5.20 T7 Minor Capsid Protein PCR]]
-
- Dr. Studier responded to our email today! We also received the E coli stains containing plasmids with clone T7 genes. WE CAN START SITE DIRECTED MUTAGENESIS SOON!
+
- Dr. Studier responded to our email today! We also received the E coli stains containing plasmids with clone T7 genes.  
<br>
<br>
-
<font size="4"> '''5/15/13''' </font>
+
<font size="4"> '''5/30/13''' </font>
-
- Completed [[Team:BYU Provo/Notebook/SmallPhage/Springexp/Period1/Exp/5.9 T7+ Liquid Culture Phage Concentration Test|5.9 T7+ Liquid Culture Phage Concentration Test #2]] by doing the spot test
+
- Plates from yesterday are taken out of incubation at around 4:00pm
-
- Performed [[Team:BYU Provo/Notebook/SmallPhage/Springexp/Period2/Exp/5.15 Titer Test on 5.3 T7 new Phage Stock|5.15 Titer Test on 5.3 T7 new Phage Stock]] to determine phage concentration and estimate dilution for applying mutagen
+
<br>
-
- Sorted LB plates made on May 8 and threw away the ones with obvious contamination
+
<font size="4"> '''5/31/13''' </font>
-
<br>
+
- Discussed results for [[Team:BYU Provo/Notebook/SmallPhage/Springexp/Period2/Exp/5.20 Mutagen Concentration Experiment|5.20 Mutagen Concentration Experiment]] -> will need to try this one more time with minor adjustment to experimental design: plate -4 dilution using x6 and x8 top agar.
-
<font size="4"> '''5/16/13''' </font>
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- Discussed plans for next week.
-
- Took plates from 5.15 out of incubation at around 4:00pm
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- Made new LB and x6 top agar.
<br>
<br>
-
<font size="4"> '''5/17/13''' </font>
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<font size="4"> '''6/2/13''' </font>
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- Determined that all LB plates from 5.8 had contamination
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- Made about 20ml of BL21 overnight
-
- Poured new LB plates
+
<br>
-
- Made x8 top agar
+
<font size="4"> '''6/3/13''' </font>
 +
 
 +
- Made new LB plates
 +
 
 +
- Plated -4 titer on x6 and x8 plates for [[Team:BYU Provo/Notebook/SmallPhage/Springexp/Period2/Exp/5.20 Mutagen Concentration Experiment|5.20 Mutagen Concentration Experiment]]
<br>
<br>
-
<font size="4"> '''5/18/13''' </font>
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<font size="4"> '''6/5/13''' </font>
 +
 
 +
- Discussed plans for the selection process of [[Team:BYU Provo/Notebook/SmallPhage/Springexp/Period2/Exp/5.20 Mutagen Concentration Experiment|5.20 Mutagen Concentration Experiment]] and calculated the needed volume of agar, overnight, and phage
-
- Stacked up the LB plates made yesterday. No obvious sign of contamination seen.
+
- Made 500mL x8 agar
-
- Threw away the 5.8 LB plates (the ones with contamination).
+
- Performed dilution series to generate enough 200ug -4 phage stock for selection.
<br>
<br>
-
<font size="4"> '''5/19/13''' </font>
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<font size="4"> '''6/6/13''' </font>
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- Started two 5mL of E coli BL21 overnight
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- Started approximately 50mL of BL21 liquid culture overnight.
-
 
+
-
- Designed procedure for applying mutagen and selecting for T7
+
<br>
<br>
-
<font size="4"> '''5/20/13''' </font>
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<font size="4"> '''6/7/13''' </font>
-
- Performed T7 Mutagen Concentration Test
+
- Performed the selection process of  [[Team:BYU Provo/Notebook/SmallPhage/Springexp/Period2/Exp/5.20 Mutagen Concentration Experiment|5.20 Mutagen Concentration Experiment]]. Specifically, we plated 45 plates of 200ug mutagen, -4 phage dilution using x8 agar. 5 plates of 0ug, -3 phage dilution were also done a control.
-
: [[Team:BYU Provo/Notebook/SmallPhage/Springexp/Period2/Exp/5.20 Mutagen Concentration Experiment|5.20 Mutagen Concentration Experiment]]
+
<br>
-
- Performed T7 Minor Capsid Protein PCR
+
<font size="4"> '''6/9/13''' </font>
-
: [[Team:BYU Provo/Notebook/SmallPhage/Springexp/Period2/Exp/5.20 T7 Minor Capsid Protein PCR|5.20 T7 Minor Capsid Protein PCR]]
+
- Started 21mL of BL21 overnight.
<br>
<br>
-
<font size="4"> '''5/21/13''' </font>
+
<font size="4"> '''6/10/13''' </font>
-
- Started two 5mL E coli BL21 overnight at around 7:00pm
+
- Made 1250mL of x8 top agar
 +
 
 +
- Attempted to amplify phage from larger plaques in [[Team:BYU Provo/Notebook/SmallPhage/Springexp/Period2/Exp/5.20 Mutagen Concentration Experiment|5.20 Mutagen Concentration Experiment]]
<br>
<br>
-
<font size="4"> '''5/22/13''' </font>
+
<font size="4"> '''6/11/13''' </font>
 +
 
 +
- Started approximately 70mL of BL21 liquid culture overnight
 +
 
 +
<br>
-
- Performed spot test for [[Team:BYU Provo/Notebook/SmallPhage/Springexp/Period2/Exp/5.20 Mutagen Concentration Experiment|5.20 Mutagen Concentration Experiment]]
+
<font size="4"> '''6/12/13''' </font>
-
- Ran agarose gel to confirm PCR product
+
- Perfected protocol for applying mutagen to phage
-
: [[Team:BYU Provo/Notebook/SmallPhage/Springexp/Period2/Exp/5.20 T7 Minor Capsid Protein PCR|5.20 T7 Minor Capsid Protein PCR]]
+
- Started [[Team:BYU Provo/Notebook/SmallPhage/Springexp/Period3/Exp/6.12 Mutagen Concentration Test - Perfected Protocol|6.12 Mutagen Concentration Test - Second Protocol]]
<br>
<br>
-
<font size="4"> '''5/23/13''' </font>
+
<font size="4"> '''6/13/13''' </font>
-
- Started two 25mL E coli BL21 liquid culture over night at around 6:00pm
+
- Started approximately 30mL of BL21 liquid culture overnight.
<br>
<br>
-
<font size="4"> '''5/24/13''' </font>
+
<font size="4"> '''6/14/13''' </font>
-
- Proceeded with [[Team:BYU Provo/Notebook/SmallPhage/Springexp/Period2/Exp/5.20 Mutagen Concentration Experiment|5.20 Mutagen Concentration Experiment]] by performing preliminary selection using x8 top agar
+
- Titered the mutagenesis product from Wednesday as part of [[Team:BYU Provo/Notebook/SmallPhage/Springexp/Period3/Exp/6.12 Mutagen Concentration Test - Perfected Protocol|6.12 Mutagen Concentration Test - Second Protocol]]
<br>
<br>
-
<font size="4"> '''5/25/13''' </font>
+
<font size="4"> '''6/16/13''' </font>
-
- Took pictures in preparation for [[Team:BYU Provo/Notebook/SmallPhage/Springexp/Period2/PR|Progress Report]]
+
- Started approximately 100mL of BL21 liquid culture overnight.
<br>
<br>
 +
 +
</font>
</font>

Latest revision as of 15:30, 9 September 2013


Small Phage May - June Notebook: May 27 - June 16 Daily Log



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

5/28/13

- Started three 8mL E coli BL21 liquid culture at around 4pm.


5/29/13

- Continued 5.20 Mutagen Concentration Experiment

- Prepared sample for sequencing. This is done as part of 5.20 T7 Minor Capsid Protein PCR

- Dr. Studier responded to our email today! We also received the E coli stains containing plasmids with clone T7 genes.


5/30/13

- Plates from yesterday are taken out of incubation at around 4:00pm


5/31/13

- Discussed results for 5.20 Mutagen Concentration Experiment -> will need to try this one more time with minor adjustment to experimental design: plate -4 dilution using x6 and x8 top agar.

- Discussed plans for next week.

- Made new LB and x6 top agar.


6/2/13

- Made about 20ml of BL21 overnight


6/3/13

- Made new LB plates

- Plated -4 titer on x6 and x8 plates for 5.20 Mutagen Concentration Experiment


6/5/13

- Discussed plans for the selection process of 5.20 Mutagen Concentration Experiment and calculated the needed volume of agar, overnight, and phage

- Made 500mL x8 agar

- Performed dilution series to generate enough 200ug -4 phage stock for selection.


6/6/13

- Started approximately 50mL of BL21 liquid culture overnight.


6/7/13

- Performed the selection process of 5.20 Mutagen Concentration Experiment. Specifically, we plated 45 plates of 200ug mutagen, -4 phage dilution using x8 agar. 5 plates of 0ug, -3 phage dilution were also done a control.


6/9/13

- Started 21mL of BL21 overnight.


6/10/13

- Made 1250mL of x8 top agar

- Attempted to amplify phage from larger plaques in 5.20 Mutagen Concentration Experiment


6/11/13

- Started approximately 70mL of BL21 liquid culture overnight


6/12/13

- Perfected protocol for applying mutagen to phage

- Started 6.12 Mutagen Concentration Test - Second Protocol


6/13/13

- Started approximately 30mL of BL21 liquid culture overnight.


6/14/13

- Titered the mutagenesis product from Wednesday as part of 6.12 Mutagen Concentration Test - Second Protocol


6/16/13

- Started approximately 100mL of BL21 liquid culture overnight.



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