Team:Calgary/27 July 2009

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University of Calgary

THIS MONTH

July
M	T	W	T	F	S	S
		[http://2009.igem.org/Team:Calgary/1_July_2009 1]	[http://2009.igem.org/Team:Calgary/2_July_2009 2]	[http://2009.igem.org/Team:Calgary/3_July_2009 3]	[http://2009.igem.org/Team:Calgary/4_July_2009 4]	[http://2009.igem.org/Team:Calgary/5_July_2009 5]
[http://2009.igem.org/Team:Calgary/6_July_2009 6]	[http://2009.igem.org/Team:Calgary/7_July_2009 7]	[http://2009.igem.org/Team:Calgary/8_July_2009 8]	[http://2009.igem.org/Team:Calgary/9_July_2009 9]	[http://2009.igem.org/Team:Calgary/10_July_2009 10]	[http://2009.igem.org/Team:Calgary/11_July_2009 11]	[http://2009.igem.org/Team:Calgary/12_July_2009 12]
[http://2009.igem.org/Team:Calgary/13_July_2009 13]	[http://2009.igem.org/Team:Calgary/14_July_2009 14]	[http://2009.igem.org/Team:Calgary/15_July_2009 15]	[http://2009.igem.org/Team:Calgary/16_July_2009 16]	[http://2009.igem.org/Team:Calgary/17_July_2009 17]	[http://2009.igem.org/Team:Calgary/18_July_2009 18]	[http://2009.igem.org/Team:Calgary/19_July_2009 19]
[http://2009.igem.org/Team:Calgary/20_July_2009 20]	[http://2009.igem.org/Team:Calgary/21_July_2009 21]	[http://2009.igem.org/Team:Calgary/22_July_2009 22]	[http://2009.igem.org/Team:Calgary/23_July_2009 23]	[http://2009.igem.org/Team:Calgary/24_July_2009 24]	[http://2009.igem.org/Team:Calgary/25_July_2009 25]	[http://2009.igem.org/Team:Calgary/26_July_2009 26]
[http://2009.igem.org/Team:Calgary/27_July_2009 27]	[http://2009.igem.org/Team:Calgary/28_July_2009 28]	[http://2009.igem.org/Team:Calgary/29_July_2009 29]	[http://2009.igem.org/Team:Calgary/30_July_2009 30]	[http://2009.igem.org/Team:Calgary/31_July_2009 31]

NOTEBOOK PAGE INDEX

Carol
Chinmoyee
Emily
Fahd
Iman
Jamie
Jeremy
Katie
Kevin
Mandy
Patrick
Prima
Stefan
Vicki

CALENDAR

May
M	T	W	T	F	S	S
				[http://2009.igem.org/Team:Calgary/1_May_2009 1]	[http://2009.igem.org/Team:Calgary/2_May_2009 2]	[http://2009.igem.org/Team:Calgary/3_May_2009 3]
[http://2009.igem.org/Team:Calgary/4_May_2009 4]	[http://2009.igem.org/Team:Calgary/5_May_2009 5]	[http://2009.igem.org/Team:Calgary/6_May_2009 6]	[http://2009.igem.org/Team:Calgary/7_May_2009 7]	[http://2009.igem.org/Team:Calgary/8_May_2009 8]	[http://2009.igem.org/Team:Calgary/9_May_2009 9]	[http://2009.igem.org/Team:Calgary/10_May_2009 10]
[http://2009.igem.org/Team:Calgary/11_May_2009 11]	[http://2009.igem.org/Team:Calgary/12_May_2009 12]	[http://2009.igem.org/Team:Calgary/13_May_2009 13]	[http://2009.igem.org/Team:Calgary/14_May_2009 14]	[http://2009.igem.org/Team:Calgary/15_May_2009 15]	[http://2009.igem.org/Team:Calgary/16_May_2009 16]	[http://2009.igem.org/Team:Calgary/17_May_2009 17]
[http://2009.igem.org/Team:Calgary/18_May_2009 18]	[http://2009.igem.org/Team:Calgary/19_May_2009 19]	[http://2009.igem.org/Team:Calgary/20_May_2009 20]	[http://2009.igem.org/Team:Calgary/21_May_2009 21]	[http://2009.igem.org/Team:Calgary/22_May_2009 22]	[http://2009.igem.org/Team:Calgary/23_May_2009 23]	[http://2009.igem.org/Team:Calgary/24_May_2009 24]
[http://2009.igem.org/Team:Calgary/25_May_2009 25]	[http://2009.igem.org/Team:Calgary/26_May_2009 26]	[http://2009.igem.org/Team:Calgary/27_May_2009 27]	[http://2009.igem.org/Team:Calgary/28_May_2009 28]	[http://2009.igem.org/Team:Calgary/29_May_2009 29]	[http://2009.igem.org/Team:Calgary/30_May_2009 30]	[http://2009.igem.org/Team:Calgary/31_May_2009 31]

June
M	T	W	T	F	S	S
[http://2009.igem.org/Team:Calgary/1_June_2009 1]	[http://2009.igem.org/Team:Calgary/2_June_2009 2]	[http://2009.igem.org/Team:Calgary/3_June_2009 3]	[http://2009.igem.org/Team:Calgary/4_June_2009 4]	[http://2009.igem.org/Team:Calgary/5_June_2009 5]	[http://2009.igem.org/Team:Calgary/6_June_2009 6]	[http://2009.igem.org/Team:Calgary/7_June_2009 7]
[http://2009.igem.org/Team:Calgary/8_June_2009 8]	[http://2009.igem.org/Team:Calgary/9_June_2009 9]	[http://2009.igem.org/Team:Calgary/10_June_2009 10]	[http://2009.igem.org/Team:Calgary/11_June_2009 11]	[http://2009.igem.org/Team:Calgary/12_June_2009 12]	[http://2009.igem.org/Team:Calgary/13_June_2009 13]	[http://2009.igem.org/Team:Calgary/14_June_2009 14]
[http://2009.igem.org/Team:Calgary/15_June_2009 15]	[http://2009.igem.org/Team:Calgary/16_June_2009 16]	[http://2009.igem.org/Team:Calgary/17_June_2009 17]	[http://2009.igem.org/Team:Calgary/18_June_2009 18]	[http://2009.igem.org/Team:Calgary/19_June_2009 19]	[http://2009.igem.org/Team:Calgary/20_June_2009 20]	[http://2009.igem.org/Team:Calgary/21_June_2009 21]
[http://2009.igem.org/Team:Calgary/22_June_2009 22]	[http://2009.igem.org/Team:Calgary/23_June_2009 23]	[http://2009.igem.org/Team:Calgary/24_June_2009 24]	[http://2009.igem.org/Team:Calgary/25_June_2009 25]	[http://2009.igem.org/Team:Calgary/26_June_2009 26]	[http://2009.igem.org/Team:Calgary/27_June_2009 27]	[http://2009.igem.org/Team:Calgary/28_June_2009 28]
[http://2009.igem.org/Team:Calgary/29_June_2009 29]	[http://2009.igem.org/Team:Calgary/30_June_2009 30]

July
M	T	W	T	F	S	S
		[http://2009.igem.org/Team:Calgary/1_July_2009 1]	[http://2009.igem.org/Team:Calgary/2_July_2009 2]	[http://2009.igem.org/Team:Calgary/3_July_2009 3]	[http://2009.igem.org/Team:Calgary/4_July_2009 4]	[http://2009.igem.org/Team:Calgary/5_July_2009 5]
[http://2009.igem.org/Team:Calgary/6_July_2009 6]	[http://2009.igem.org/Team:Calgary/7_July_2009 7]	[http://2009.igem.org/Team:Calgary/8_July_2009 8]	[http://2009.igem.org/Team:Calgary/9_July_2009 9]	[http://2009.igem.org/Team:Calgary/10_July_2009 10]	[http://2009.igem.org/Team:Calgary/11_July_2009 11]	[http://2009.igem.org/Team:Calgary/12_July_2009 12]
[http://2009.igem.org/Team:Calgary/13_July_2009 13]	[http://2009.igem.org/Team:Calgary/14_July_2009 14]	[http://2009.igem.org/Team:Calgary/15_July_2009 15]	[http://2009.igem.org/Team:Calgary/16_July_2009 16]	[http://2009.igem.org/Team:Calgary/17_July_2009 17]	[http://2009.igem.org/Team:Calgary/18_July_2009 18]	[http://2009.igem.org/Team:Calgary/19_July_2009 19]
[http://2009.igem.org/Team:Calgary/20_July_2009 20]	[http://2009.igem.org/Team:Calgary/21_July_2009 21]	[http://2009.igem.org/Team:Calgary/22_July_2009 22]	[http://2009.igem.org/Team:Calgary/23_July_2009 23]	[http://2009.igem.org/Team:Calgary/24_July_2009 24]	[http://2009.igem.org/Team:Calgary/25_July_2009 25]	[http://2009.igem.org/Team:Calgary/26_July_2009 26]
[http://2009.igem.org/Team:Calgary/27_July_2009 27]	[http://2009.igem.org/Team:Calgary/28_July_2009 28]	[http://2009.igem.org/Team:Calgary/29_July_2009 29]	[http://2009.igem.org/Team:Calgary/30_July_2009 30]	[http://2009.igem.org/Team:Calgary/31_July_2009 31]

August
M	T	W	T	F	S	S
					[http://2009.igem.org/Team:Calgary/1_August_2009 1]	[http://2009.igem.org/Team:Calgary/2_August_2009 2]
[http://2009.igem.org/Team:Calgary/3_August_2009 3]	[http://2009.igem.org/Team:Calgary/4_August_2009 4]	[http://2009.igem.org/Team:Calgary/5_August_2009 5]	[http://2009.igem.org/Team:Calgary/6_August_2009 6]	[http://2009.igem.org/Team:Calgary/7_August_2009 7]	[http://2009.igem.org/Team:Calgary/8_August_2009 8]	[http://2009.igem.org/Team:Calgary/9_August_2009 9]
[http://2009.igem.org/Team:Calgary/10_August_2009 10]	[http://2009.igem.org/Team:Calgary/11_August_2009 11]	[http://2009.igem.org/Team:Calgary/12_August_2009 12]	[http://2009.igem.org/Team:Calgary/13_August_2009 13]	[http://2009.igem.org/Team:Calgary/14_August_2009 14]	[http://2009.igem.org/Team:Calgary/15_August_2009 15]	[http://2009.igem.org/Team:Calgary/16_August_2009 16]
[http://2009.igem.org/Team:Calgary/17_August_2009 17]	[http://2009.igem.org/Team:Calgary/18_August_2009 18]	[http://2009.igem.org/Team:Calgary/19_August_2009 19]	[http://2009.igem.org/Team:Calgary/20_August_2009 20]	[http://2009.igem.org/Team:Calgary/21_August_2009 21]	[http://2009.igem.org/Team:Calgary/22_August_2009 22]	[http://2009.igem.org/Team:Calgary/23_August_2009 23]
[http://2009.igem.org/Team:Calgary/24_August_2009 24]	[http://2009.igem.org/Team:Calgary/25_August_2009 25]	[http://2009.igem.org/Team:Calgary/26_August_2009 26]	[http://2009.igem.org/Team:Calgary/27_August_2009 27]	[http://2009.igem.org/Team:Calgary/28_August_2009 28]	[http://2009.igem.org/Team:Calgary/29_August_2009 29]	[http://2009.igem.org/Team:Calgary/30_August_2009 30]
[http://2009.igem.org/Team:Calgary/31_August_2009 31]

September
M	T	W	T	F	S	S
	[http://2009.igem.org/Team:Calgary/1_September_2009 1]	[http://2009.igem.org/Team:Calgary/2_September_2009 2]	[http://2009.igem.org/Team:Calgary/3_September_2009 3]	[http://2009.igem.org/Team:Calgary/4_September_2009 4]	[http://2009.igem.org/Team:Calgary/5_September_2009 5]	[http://2009.igem.org/Team:Calgary/6_September_2009 6]
[http://2009.igem.org/Team:Calgary/7_September_2009 7]	[http://2009.igem.org/Team:Calgary/8_September_2009 8]	[http://2009.igem.org/Team:Calgary/9_September_2009 9]	[http://2009.igem.org/Team:Calgary/10_September_2009 10]	[http://2009.igem.org/Team:Calgary/11_September_2009 11]	[http://2009.igem.org/Team:Calgary/12_September_2009 12]	[http://2009.igem.org/Team:Calgary/13_September_2009 13]
[http://2009.igem.org/Team:Calgary/14_September_2009 14]	[http://2009.igem.org/Team:Calgary/15_September_2009 15]	[http://2009.igem.org/Team:Calgary/16_September_2009 16]	[http://2009.igem.org/Team:Calgary/17_September_2009 17]	[http://2009.igem.org/Team:Calgary/18_September_2009 18]	[http://2009.igem.org/Team:Calgary/19_September_2009 19]	[http://2009.igem.org/Team:Calgary/20_September_2009 20]
[http://2009.igem.org/Team:Calgary/21_September_2009 21]	[http://2009.igem.org/Team:Calgary/22_September_2009 22]	[http://2009.igem.org/Team:Calgary/23_September_2009 23]	[http://2009.igem.org/Team:Calgary/24_September_2009 24]	[http://2009.igem.org/Team:Calgary/25_September_2009 25]	[http://2009.igem.org/Team:Calgary/26_September_2009 26]	[http://2009.igem.org/Team:Calgary/27_September_2009 27]
[http://2009.igem.org/Team:Calgary/28_September_2009 28]	[http://2009.igem.org/Team:Calgary/29_September_2009 29]	[http://2009.igem.org/Team:Calgary/30_September_2009 30]

October
M	T	W	T	F	S	S
			[http://2009.igem.org/Team:Calgary/1_October_2009 1]	[http://2009.igem.org/Team:Calgary/2_October_2009 2]	[http://2009.igem.org/Team:Calgary/3_October_2009 3]	[http://2009.igem.org/Team:Calgary/4_October_2009 4]
[http://2009.igem.org/Team:Calgary/5_October_2009 5]	[http://2009.igem.org/Team:Calgary/6_October_2009 6]	[http://2009.igem.org/Team:Calgary/7_October_2009 7]	[http://2009.igem.org/Team:Calgary/8_October_2009 8]	[http://2009.igem.org/Team:Calgary/9_October_2009 9]	[http://2009.igem.org/Team:Calgary/10_October_2009 10]	[http://2009.igem.org/Team:Calgary/11_October_2009 11]
[http://2009.igem.org/Team:Calgary/12_October_2009 12]	[http://2009.igem.org/Team:Calgary/13_October_2009 13]	[http://2009.igem.org/Team:Calgary/14_October_2009 14]	[http://2009.igem.org/Team:Calgary/15_October_2009 15]	[http://2009.igem.org/Team:Calgary/16_October_2009 16]	[http://2009.igem.org/Team:Calgary/17_October_2009 17]	[http://2009.igem.org/Team:Calgary/18_October_2009 18]
[http://2009.igem.org/wiki/index.php?title=Team:Calgary/19_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 19]	[http://2009.igem.org/wiki/index.php?title=Team:Calgary/20_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 20]	[http://2009.igem.org/wiki/index.php?title=Team:Calgary/21_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 21]	[http://2009.igem.org/wiki/index.php?title=Team:Calgary/22_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 22]	[http://2009.igem.org/wiki/index.php?title=Team:Calgary/23_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 23]	[http://2009.igem.org/wiki/index.php?title=Team:Calgary/24_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 24]	[http://2009.igem.org/wiki/index.php?title=Team:Calgary/25_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 25]
[http://2009.igem.org/wiki/index.php?title=Team:Calgary/26_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 26]	[http://2009.igem.org/wiki/index.php?title=Team:Calgary/27_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 27]	[http://2009.igem.org/wiki/index.php?title=Team:Calgary/28_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 28]	[http://2009.igem.org/wiki/index.php?title=Team:Calgary/29_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 29]	[http://2009.igem.org/wiki/index.php?title=Team:Calgary/30_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 30]	[http://2009.igem.org/wiki/index.php?title=Team:Calgary/31_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 31]

JULY 27, 2009

CAROL

Finishing Modeling Paper

Finished writing modeling paper that summarizes what we will be doing once the circuit is completed. The experiments should not take long to accomplished and these results can be tabulated in Matlab quickly.
Plated the week-long ligation of the promoter library in both XL Gold Ultra competent cells and Top 10 cells, but there is no growth.
A reason that we thought of that might have caused minimal colonies is the phosphatase step. The 32 primers that we have synthesized does not have 5' phosphates. If we phosphatase the vector, that might result in no ligation.
Re-started restriction enzyme digestion on vector pCS26 with XhoI and BamHI at 37^oC for 4 hours. Then I ligated the promoter with the vector with Quick Ligase for 5 minutes. Then I transformed the plasmids into both XL Gold Ultracompetent cells and Top 10 cells. Incubate at 37^oC for 16 hours.

CHINMOYEE

Descriptive Title of What You're Doing

WIKI CODING HERE

EMILY

Descriptive Title of What You're Doing

WIKI CODING HERE

FAHD

Descriptive Title of What You're Doing

WIKI CODING HERE

IMAN

Descriptive Title of What You're Doing

WIKI CODING HERE

JAMIE

Descriptive Title of What You're Doing

WIKI CODING HERE

JEREMY

Colony PCR of LuxPQ-B0015-R0040-LuxOU-B0015 construct in psB1AC3 using BBK CP F/R and LuxPQ F/LuxOU R primers

Colony PCR of LuxPQ-B0015-R0040-LuxOU-B0015 construct in psB1AC3 using BBK CP F/R and LuxPQ F/LuxOU R primers
Purpose: To verify the presence of LuxPQ-B0015-R0040-LuxOU-B0015 construct in psB1AC3.

Protocol

	MM1 (6x) (μL)	MM2 (6x) (μL)
10X PCR buffer minus MgCl₂	30	30
10mM dNTPs	6	6
50mM MgCl₂	9	9
F primer	6 (BBK CP F)	6 (LuxPQ F)
R primer	6 (BBK CP R)	6 (LuxOU R)
ddH₂O	241.8	241.8
pTaq	1.2	1.2

Positive control = LuxPQ-B0015-R0040-LuxOU-B0015 in AK3

PCR conditions

# of cycles	Temp (ºC)	Time
1	94	6 min
36	94	30sec
	55	45sec
	72	6min 20sec
1	72	10min
	4	hold

Result: the only bands that appeared on the gel were those of the ladders. Therefore, start new construction.

Colony PCR of ∆LuxPQ in psB1AC3 using BBK CP F/R and LuxPQ F/R primers
Purpose: To verify the presence of ∆LuxPQ in psB1AC3 (to verify a successful plasmid switch)
Protocol

	MM1 (8x) (μL)	MM2 (6x) (μL)
10X PCR buffer minus MgCl₂	40	40
10mM dNTPs	8	8
50mM MgCl₂	12	12
F primer	8 (LuxPQ F)	8 (BBK CP F)
R primer	8 (LuxPQ R)	8 (BBK CP R)
ddH₂O	322.4	322.4
pTaq	1.6	1.6

Positive control = ∆LuxPQ in psB1AK3

PCR conditions

# of cycles	Temp (ºC)	Time
1	94	6 min
36	94	30sec
	55	45sec
	72	6min 20sec
1	72	10min
	4	hold
pTaq	1.6	1.6

Isolating plasmid from LuxPQ-B0015-R0040-LuxOU-B0015 (AC) and LuxPQ (in AC)
Purpose: isolate and measure concentrations of pure plasmids.

DNA	260/280	260/230	Conc. [ng/μL]
∆LuxPQ in AC3 C1	1.83	2.23	146.8
∆LuxPQ in AC3 C2	1.81	2.19	112.6
∆LuxPQ in AC3 C3	1.8	2.27	145.8
∆LuxPQ in AC3 C4	1.78	2.09	96.6
∆LuxPQ in AC3 C5	1.81	2.25	115.3
∆LuxPQ in AC3 C6	1.79	2.17	44.8
PQ-B-R-OU-B in AC3 C1	1.76	1.86	29.4
PQ-B-R-OU-B in AC3 C2	1.59	1.44	20.1
PQ-B-R-OU-B in AC3 C3	1.7	2.27	16.3
PQ-B-R-OU-B in AC3 C4	1.71	1.79	17

Construction of LuxPQ-B0015-R0040-LuxOU-B0015 by inserting B0015-R0040-LuxOU-B0015 (AK) into LuxPQ (in AC)

Purpose: To construct LuxPQ-B0015-R0040-LuxOU-B0015 by inserting B0015-R0040-LuxOU-B0015 (AK) into LuxPQ (in AC)
Protocol
Recipient

Recipient 1	Recipient 2
2μL REact 4	2μL REact 4
0.75 μL SpeI	0.75 μL SpeI
0.75 μL PstI	0.75 μL PstI
2 μL of ∆LuxPQ in AK3 C2 [112.6ng/μL]	2 μL of ∆LuxPQ in AK3 C5 [115.3ng/μL]
14.5 μL ddH2O	14.5 μL ddH2O

Insert

2μL REact 2
0.75 μL XbaI
0.75 μL PstI
2 μL of LuxPQ-B0015-R0040-LuxOU-B0015 in AK3 C1 [156.3ng/μL]
12.5 μL ddH2O

Put in the incubator at 37ºC overnight.

KATIE

Descriptive Title of What You're Doing

WIKI CODING HERE

KEVIN

Descriptive of What You're Doing

WIKI CODING HERE

MANDY

Descriptive Title of What You're Doing

WIKI CODING HERE

PATRICK

Descriptive Title of What You're Doing

WIKI CODING HERE

PRIMA

Descriptive Title of What You're Doing

WIKI CODING HERE

STEFAN

Descriptive Title of What You're Doing

WIKI CODING HERE

VICKI

Descriptive Title of What You're Doing

WIKI CODING HERE