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	{{TeamBYUProvo}}		{{TeamBYUProvo}}
		+
		+	{| width="100%"
		+	| colspan="3" | Small Phage (Add formatting)
		+
		+	|-
		+	| style="width: 20%; background-color: transparent;"|
		+
		+	Overview
		+
		+	Winter
		+
		+	[[Team:BYU Provo/Notebook/SmallPhage/Springexp|Spring]]
		+
		+	Summer
		+
		+	Fall
		+
		+	| style="width: 60%; background-color: transparent;"|
		+	'''add overview'''
		+
		+	Description of our purpose and approaches
		+
		+	'''Pages that needs deleting'''
		+
		+	[[Spring]] [[Winter]]
		+
		+	'''Things to figure out'''
		+
		+	How to format table?
		+
		+	How to format text besides default?
		+
		+	Domain/URL?
		+
		+	text alignment in table
		+
		+	| style="width: 20%; background-color: transparent;"|
		+	'''add picture'''
		+
		+	|}
		+
	==March==		==March==
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	==May==		==May==
		+	===5/1/13===
-	===5/20/13===	+	- Commencement of spring!!!
-	LP, XL	+	- Discussed goals and outlined plans for spring term
-	- We performed T7 Mutagen Concentration Test [[5.20 Mutagen Concentration Experiment]]	+	===5/2/13===
-	- We performed T7 Minor Capsid Protein PCR ([[5.20 T7 Minor Capsid Protein PCR]])	+	- Designed primers for amplifying and sequencing phage capsid protein
-	===5.20 T7 Minor Capsid Protein PCR===	+	- Wrote emails inquiring mutagen (NG) and plasmid for in vitro assembly
-	'''I) Purpose'''	+	===5/3/13===
-	: To isolate the T7 minor capsid protein	+	- Performed agar test, focusing primarily on ×8
-	'''II) Expected Outcome'''	+	: [[5.3 T7 phage selection method test]]
-	: We expect that we will have isolated the T7 minor capsid protein.  This can be visualized by gel electrophoresis and there should be one band that matches the number of base pairs in the minor capsid protein.	+	- Processed phage amplification
-	'''III) Reagents Used'''	+	: [[5.3 T7 phage amplification/purification]]
-	ADD	+	===5/4/13===
-	'''IV) Procedure'''	+	- Performed dilution series using stock 5.3 (-1 through -11)
-	1)  Isolating DNA	+	- Started two 5mL overnights of BL21
-	- Put 5 ul of phage stock and 45 ul of ddH20 in one PCR tube and 10 ul of phage stock and 40 ul of ddH20 in another PCR tube.	+	===5/5/13===
-	- Boil for 12 minutes in the PCR machine.	+	- Spot test using stock 5.3 and its dilution series (from 5.4)
-	- Remove the tubes from the PCR machine and shake the tube. Centrifuge it for 1 minutes at top speed.	+	: [[5.3 T7 phage amplification/purification]]
		+
		+	- Started liquid culture for purification team (at around noon)
		+
		+	: 1mL of BL21 overnight + 4mL of LB + 100μL -2 phage (received stock)
		+
		+	- Started 5.5 amplification from a plaque test
		+
		+	: [[5.5 Amplification from a plaque test]]
		+
		+	===5/6/13===
		+
		+	- Continued [[5.3 T7 phage amplification/purification]]
		+
		+	- Performed liquid culture phage concentration test
		+
		+	: [[5.6 T7+ Liquid Culture Phage Concentration Test]]
		+
		+	===5/7/13===
		+
		+	- Started two 5mL of E coli BL21 overnight
		+
		+	- Designed procedure for applying mutagen and selecting for T7
		+
		+	===5/8/13===
		+
		+	- Went over procedure for applying mutagen and PCR with Dr. Grose
		+
		+	- Performed spot tests under [[5.6 T7+ Liquid Culture Phage Concentration Test]]
		+
		+	- Started two 5mL BL21 overnights
		+
		+	- Learned how to create LB plates
		+
		+	===5/9/13===
		+
		+	- Practiced with ×6 and ×8 top agar
		+
		+	: [[5.9 T7 selection method test #2]]
		+
		+	- Started [[5.9 T7+ Liquid Culture Phage Concentration Test #2]]
		+
		+	- Discussed plans and schedule for next week.
		+
		+	===5/20/13===
		+
		+	LP, XL
-	- Keep on ice.  DNA should be in the supernatant.	+	- We performed T7 Mutagen Concentration Test
-	2) PCR	+	: [[5.20 Mutagen Concentration Experiment]]
-	- To a centrifuge tube, add	+	- We performed T7 Minor Capsid Protein PCR
-	: 120 ul ddH20	+	: [[5.20 T7 Minor Capsid Protein PCR]]
-	: 15 ul 10X TAQ Buffer	+
-	: 4.5 ul 10mMdNTP's	+
-	: 3 ul of forward primer	+
-	: 3 ul of reverse primer	+
-	- Mix well	+
-	- Label 3 PCR tubes "C" (Control), "5" (5 ul of phage stock), and "10" (10 ul of phage stock).	+	===5/21/13===
-	- Add 2 ul of template DNA from the supernatant of step 1 into their respective tubes (nothing in the control tube).	+	XL
-	- Add 1.5 ul of TAQ Polymerase into the centrifuge tube (master mix).	+	- started two 5mL E coli BL21 overnight at around 7:00pm
-	- Pipette 48 ul of master mix into each PCR tube.
-	- Run 35 cycles with temperatures of 95 C, 50 C, and 72 C with an extension time of 1.5 minutes.	+	===5/22/13===
-	- Leave overnight at 4 C.	+	- Continued with [[5.20 Mutagen Concentration Experiment|T7 Mutagen Concentration Test]]
-	- Remove and place in the freezer.	+	- Continued with [[5.20 T7 Minor Capsid Protein PCR|T7 Minor Capsid Protein PCR ]] by running an agarose gel to confirm that we got the desired PCR product.
	==June==		==June==

---

Latest revision as of 15:06, 24 May 2013

• Home
• Team
  • Overview
  • Official Team Profile
  • Team Video
  • Undergraduates
  • Mentors
• Project
  • Overview
  • Background
  • Experimental Design
• Notebook
  • Overview
  • Phage Team
  • Cholera Team
• Results
  • Overview
  • Judging Criteria
  • Experimental
  • Modeling
  • Parts Submitted to the Registry
  • A Taste of Toronto
• Human Practices
  • Overview
  • Orem Public Library Visit
  • The Adventure of Baxter Bacteria
• Safety
• Attributions & Collaborations
  • Attributions & Acknowledgements
  • Collaborations
• iGEM 2013

Small Phage (Add formatting)
Overview Winter Spring Summer Fall	add overview Description of our purpose and approaches Pages that needs deleting Spring Winter Things to figure out How to format table? How to format text besides default? Domain/URL? text alignment in table	add picture

Contents 1 March 2 April 3 May 3.1 5/1/13 3.2 5/2/13 3.3 5/3/13 3.4 5/4/13 3.5 5/5/13 3.6 5/6/13 3.7 5/7/13 3.8 5/8/13 3.9 5/9/13 3.10 5/20/13 3.11 5/21/13 3.12 5/22/13 4 June 5 July 6 August 7 September

March

April

May

5/1/13

- Commencement of spring!!!

- Discussed goals and outlined plans for spring term

5/2/13

- Designed primers for amplifying and sequencing phage capsid protein

- Wrote emails inquiring mutagen (NG) and plasmid for in vitro assembly

5/3/13

- Performed agar test, focusing primarily on ×8

5.3 T7 phage selection method test

- Processed phage amplification

5.3 T7 phage amplification/purification

5/4/13

- Performed dilution series using stock 5.3 (-1 through -11)

- Started two 5mL overnights of BL21

5/5/13

- Spot test using stock 5.3 and its dilution series (from 5.4)

5.3 T7 phage amplification/purification

- Started liquid culture for purification team (at around noon)

1mL of BL21 overnight + 4mL of LB + 100μL -2 phage (received stock)

- Started 5.5 amplification from a plaque test

5.5 Amplification from a plaque test

5/6/13

- Continued 5.3 T7 phage amplification/purification

- Performed liquid culture phage concentration test

5.6 T7+ Liquid Culture Phage Concentration Test

5/7/13

- Started two 5mL of E coli BL21 overnight

- Designed procedure for applying mutagen and selecting for T7

5/8/13

- Went over procedure for applying mutagen and PCR with Dr. Grose

- Performed spot tests under 5.6 T7+ Liquid Culture Phage Concentration Test

- Started two 5mL BL21 overnights

- Learned how to create LB plates

5/9/13

- Practiced with ×6 and ×8 top agar

5.9 T7 selection method test #2

- Started 5.9 T7+ Liquid Culture Phage Concentration Test #2

- Discussed plans and schedule for next week.

5/20/13

LP, XL

- We performed T7 Mutagen Concentration Test

5.20 Mutagen Concentration Experiment

- We performed T7 Minor Capsid Protein PCR

5.20 T7 Minor Capsid Protein PCR

5/21/13

XL

- started two 5mL E coli BL21 overnight at around 7:00pm

5/22/13

- Continued with T7 Mutagen Concentration Test

- Continued with T7 Minor Capsid Protein PCR by running an agarose gel to confirm that we got the desired PCR product.

June

July

August

September