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From 2013.igem.org

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	{{TeamBYUProvo}}		{{TeamBYUProvo}}
-	==March==	+	{| width="100%"
-	===3/15/13===	+	| colspan="3" | Small Phage (Add formatting)
-	===3/18/13===	+	|-
		+	| style="width: 20%; background-color: transparent;"|
-	===3/20/13===	+	Overview
-	===3/22/13===	+	Winter
-	===3/25/13===	+	[[Team:BYU Provo/Notebook/SmallPhage/Springexp|Spring]]
-	===3/27/13===	+	Summer
-	===3/29/13===	+	Fall
-	===experiment===	+	| style="width: 60%; background-color: transparent;"|
		+	'''add overview'''
-	==April==	+	Description of our purpose and approaches
-	===4/1/13===	+
-	===4/4/13===	+	'''Pages that needs deleting'''
-	===4/5/13===	+	[[Spring]] [[Winter]]
-	===4/8/13===	+	'''Things to figure out'''
-	===4/10/13===	+	How to format table?
-	===4/12/13===	+	How to format text besides default?
-	===4/15/13===	+	Domain/URL?
-	==May==	+	text alignment in table
-	===5/1/13===	+
-	===5/3/13===	+	| style="width: 20%; background-color: transparent;"|
		+	'''add picture'''
-	===5/6/13===	+	|}
-	===5/8/13===
-	===5/10/13===	+	==March==
-	===5/13/13===
-	===5/15/13===	+	==April==
-	===5/17/13===
-	===5/20/13===
-	LP, XL	+	==May==
-	- We performed T7 Mutagen Concentration Test	+
-	- We performed T7 Minor Capsid Protein PCR	+
		+	===5/1/13===
-	----	+	- Commencement of spring!!!
-	'''T7 Minor Capsid Protein PCR'''	+
-	PCR Protocol for T7 Capsid Protein	+	- Discussed goals and outlined plans for spring term
-	1)  Isolating DNA	+	===5/2/13===
-	- 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.	+
-	- Boil for 12 minutes in the PCR machine.	+	- Designed primers for amplifying and sequencing phage capsid protein
-	- Remove the tubes from the PCR machine and shake the tube.  Centrifuge it for 1 minutes at top speed.	+	- Wrote emails inquiring mutagen (NG) and plasmid for in vitro assembly
-	- Keep on ice.  DNA should be in the supernatant.	+	===5/3/13===
-	2) PCR	+	- Performed agar test, focusing primarily on ×8
-	• To a PCR tube, add:	+
-	o 40 ul ddH20	+
-	o 5 ul 10X TAQ buffer	+
-	o 1.5 ul 10mMdNTP’s	+
-	o 1 ul of each primer	+
-	o 1 uL of template DNA (from supernatant of the step 1)	+
-	• Mix well	+
-	• Add 0.5 ul TAQ Polymerase	+
-	• Keep on ice until placed in the PCR machine	+
-	• Create a duplicate as a control, but do not add the template	+
-	• Prewarm the PCR machine to 94 C	+
-	• Run 35-40 cycles with temperatures of 94 C, 50 C, and 72 C and an extension time of 1.5 minutes	+
-	• If left overnight, keep at 4 C	+
-	3)  Check with Agarose Electrophoresis	+
-	• To make a standard 1% gel use 75 ml of 1X TAE and 0.75 grams of agarose (regular agarose, not low melt).  Put it into the microwave for about 90 seconds or until the agarose is completely dissolved.  Pulsing the microwave may be necessary to prevent boiling over	+
-	• Add 12 ul of 1mg/ml ethidium bromide and swirl to mix.  Be sure to wear gloves.	+
-	• Allow flask to cool so that the glass feels warm, not burning hot.  Pour the liquid onto the gel bed and let it cool.  Insert the appropriate sample comb (need 3 slots).	+
-	• Add loading dye to each PCR product.  Do this by adding 6 ul of 10X loading dye to a 50ul PCR.	+
-	• Move the gel into the proper orientation (DNA runs towards the red electrode) in the gel box, cover the gel with 1X TAE buffer and load 4-5 ul of each of the PCR product.  Add a DNA ladder as a reference.  Turn on the power supply and run at 150-175 volts.  It will take about 15-30 to complete.	+
-	• Visualize the gel on the Alphaimager.  Print off the results and log in your notebook.	+
-	===5/22/13===	+	: [[5.3 T7 phage selection method test]]
-	===5/24/13===	+	- Processed phage amplification
-	===5/27/13===	+	: [[5.3 T7 phage amplification/purification]]
-	===5/29/13===	+	===5/4/13===
-	===5/31/13===	+	- Performed dilution series using stock 5.3 (-1 through -11)
-	==June==	+	- Started two 5mL overnights of BL21
-	===6/3/13===	+
-	===6/5/13===	+	===5/5/13===
-	===6/7/13===	+	- Spot test using stock 5.3 and its dilution series (from 5.4)
-	===6/10/13===	+	: [[5.3 T7 phage amplification/purification]]
-	===6/12/13===	+	- Started liquid culture for purification team (at around noon)
-	===6/14/13===	+	: 1mL of BL21 overnight + 4mL of LB + 100μL -2 phage (received stock)
-	===6/17/13===	+	- Started 5.5 amplification from a plaque test
-	===6/19/13===	+	: [[5.5 Amplification from a plaque test]]
-	===6/21/13===	+	===5/6/13===
-	===6/24/13===	+	- Continued [[5.3 T7 phage amplification/purification]]
-	===6/26/13===	+	- Performed liquid culture phage concentration test
-	===6/28/13===	+	: [[5.6 T7+ Liquid Culture Phage Concentration Test]]
-	==July==	+	===5/7/13===
-	===7/1/13===	+
-	===7/3/13===	+	- Started two 5mL of E coli BL21 overnight
-	===7/5/13===	+	- Designed procedure for applying mutagen and selecting for T7
-	===7/8/13===	+	===5/8/13===
-	===7/10/13===	+	- Went over procedure for applying mutagen and PCR with Dr. Grose
-	===7/12/13===	+	- Performed spot tests under [[5.6 T7+ Liquid Culture Phage Concentration Test]]
-	===7/15/13===	+	- Started two 5mL BL21 overnights
-	===7/17/13===	+	- Learned how to create LB plates
-	===7/19/13===	+	===5/9/13===
-	===7/22/13===	+	- Practiced with ×6 and ×8 top agar
-	===7/24/13===	+	: [[5.9 T7 selection method test #2]]
-	===7/26/13===	+	- Started [[5.9 T7+ Liquid Culture Phage Concentration Test #2]]
-	===7/29/13===	+	- Discussed plans and schedule for next week.
-	===7/31/13===	+	===5/20/13===
-	==August==	+	LP, XL
-	===8/2/13===	+
-	===8/5/13===	+	- We performed T7 Mutagen Concentration Test
-	===8/7/13===	+	: [[5.20 Mutagen Concentration Experiment]]
-	===8/9/13===	+	- We performed T7 Minor Capsid Protein PCR
		+	: [[5.20 T7 Minor Capsid Protein PCR]]
-	===8/12/13===	+	===5/21/13===
-	===8/14/13===	+	XL
-	===8/16/13===	+	- started two 5mL E coli BL21 overnight at around 7:00pm
-	===8/19/13===
-	===8/21/13===	+	===5/22/13===
-	===8/23/13===	+	- Continued with [[5.20 Mutagen Concentration Experiment|T7 Mutagen Concentration Test]]
-	===8/26/13===	+	- 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.
-	===8/28/13===	+	==June==
-	===8/30/13===
-	==September==
-	===9/2/13===
-	===9/4/13===	+	==July==
-	===9/6/13===
-	===9/9/13===	+	==August==
-	===9/11/13===
-	===9/13/13===	+	==September==
-		+
-	===9/16/13===	+
-		+
-	===9/18/13===	+
-		+
-	===9/20/13===	+
-		+
-	===9/23/13===	+
-		+
-	===9/25/13===	+
-		+
-	===9/27/13===	+
-	===9/30/13===
	{{TeamBYUProvoFooter}}		{{TeamBYUProvoFooter}}

---

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