Team:Calgary/1 July 2009

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Colony PCR
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WIKI CODING HERE
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* Only one colony was present on plates and continued with colony PCR using forward and reverse gene specific primers.
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* Results showed that colony did not have plasmid because no bands appeared on gel.
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Visualization of Colony PCR
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*Ran colony PCR Product from yesterday on a 1% agarose gel with 1.0kb Generuler DNA Ladder.  See gel below.  Lane 1 is BBK LuxOD47E cut with EcoRI/PstI Colony 4, lane 2 is BBK LuxOD47E cut with XbaI/PstI, lane 3 is LuxOD47E C4-8 TOPO DNA, lane 4 is a negative control, lane 5 is BBK LuxOD47E cut with EcoRI/PstI Colony 4, lane 6 is BBK LuxOD47E cut with XbaI/PstI, Colony 2, lane 7 is a positive control with only the psB1AC3 vector and lane 8 is a second negative control.
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*Analysis:  The negative control lanes are clean, which is a very good sign as this indicates that we have no contamination.  All of the bands are also at the expected sizes.  The first three lanes show (faint) bands around 1.4 kb, which is expected as this is approximately the size of trhe gene of interest (1362 bp).  The fifth lane shows bands.
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Repeat restriction digest of LuxPQ BBK PCR product and psB1AC3
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Purpose: To effectively digest the LuxPQ insert and psB1AC3 vector overnight in order to standardize the genetic part for future construction. The following sets of restriction enzymes were used for overnight digest: XbaI/PstI and EcoRI/PstI. The water bath was set at 37ºC
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None were from bacteria until MpAFP was found
None were from bacteria until MpAFP was found
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Working on Wiki for Canada Day
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The images used in the wiki have been removed as they were hotlinked from other websites. Instead, they have been replaced by those hosted on our photobucket account (still need to figure how much can be uploaded on this wiki here, so just in case, they will be hosted externally for now at least). The menu for the wiki has been updated. I put in a header and transparency coding. I'm learning overlays and positioning to make it look really 'cool'. Eventually the background image of the menu can be changed using scripting which I think will be neat.
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In addition to the menu, image sizing is fixed and an RSS feed for our blog has been added to the wiki. This only shows the last 10 posts, so I will have to convert blog updates to their respective sections so that they remain permanently accessible on this site.
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Working on Canada Day
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I replied back to company emails and tried my best to answer their questions about our project. I researched a few old companies who had declined our proposals and searched new contacts in different departs.  I will call them tomorrow.
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'''In the lab'''
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Shadowed Vicky with Colony PCR of J13002 + JuxOD47A BBk + B0015 on pSB1AK3
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Purpose: The bacterial culture growth is prolific. This will verify if the proper gene constructs are included within.
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Materials an methods:
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* Primers: BBk forward and reverse construction primers
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* Master mix: Use pTaq DNA polymerase. The contents will suffice for 15 tubes, and were prepared in the same fashion as on June 26.
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* PCR conditions: These are also the same as they were on June 26
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Tubes 1/6 were colony 1
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tubes 2/7 were col 2
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tubes 3/8 were col 3
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tubes 4/9 were col 4
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tubes 5/10 were col 5
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The 1% agarose gel is attached below. Lane 1 is a GeneElute 1kb+ DNA ladder; lanes 2-11 are the colony-PCR'd samples of J13002 + LuxOD47A + B0015; lane 12 is a sequenced LuxOD47A + B0015 for a size control; lane 13 is a sequenced LuxOD47A BBk for another size control; and lane 14 is a negative control. Based on a very confusing negative control, this procedure will be repeated tomorrow. We will still progress with a NotI restriction digest of the contents, which will also be done tomorrow.
The 1% agarose gel is attached below. Lane 1 is a GeneElute 1kb+ DNA ladder; lanes 2-11 are the colony-PCR'd samples of J13002 + LuxOD47A + B0015; lane 12 is a sequenced LuxOD47A + B0015 for a size control; lane 13 is a sequenced LuxOD47A BBk for another size control; and lane 14 is a negative control. Based on a very confusing negative control, this procedure will be repeated tomorrow. We will still progress with a NotI restriction digest of the contents, which will also be done tomorrow.
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Latest revision as of 18:42, 20 October 2009

University of Calgary

UNIVERSITY OF CALGARY



THIS MONTH

July
MTWTFSS
    [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
MTWTFSS
        [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
MTWTFSS
[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
MTWTFSS
    [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
MTWTFSS
          [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
MTWTFSS
  [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
MTWTFSS
      [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 1, 2009


CAROL

Colony PCR

  • Only one colony was present on plates and continued with colony PCR using forward and reverse gene specific primers.
  • Results showed that colony did not have plasmid because no bands appeared on gel.


EMILY

Visualization of Colony PCR

  • Ran colony PCR Product from yesterday on a 1% agarose gel with 1.0kb Generuler DNA Ladder. See gel below. Lane 1 is BBK LuxOD47E cut with EcoRI/PstI Colony 4, lane 2 is BBK LuxOD47E cut with XbaI/PstI, lane 3 is LuxOD47E C4-8 TOPO DNA, lane 4 is a negative control, lane 5 is BBK LuxOD47E cut with EcoRI/PstI Colony 4, lane 6 is BBK LuxOD47E cut with XbaI/PstI, Colony 2, lane 7 is a positive control with only the psB1AC3 vector and lane 8 is a second negative control.
  • Analysis: The negative control lanes are clean, which is a very good sign as this indicates that we have no contamination. All of the bands are also at the expected sizes. The first three lanes show (faint) bands around 1.4 kb, which is expected as this is approximately the size of trhe gene of interest (1362 bp). The fifth lane shows bands.


JEREMY

Repeat restriction digest of LuxPQ BBK PCR product and psB1AC3

Purpose: To effectively digest the LuxPQ insert and psB1AC3 vector overnight in order to standardize the genetic part for future construction. The following sets of restriction enzymes were used for overnight digest: XbaI/PstI and EcoRI/PstI. The water bath was set at 37ºC


KEVIN

Other hyperactive antifreeze proteins

  • High Arctic plant rhizosphere(P. putida)
  • Mid-gut of frozen beetle larvae (R. erythropolis)
  • Frozen/chilled pork sausages (M. cryophilus)
  • Antarctic soil (Moraxella sp and P. fluorescens).


None were from bacteria until MpAFP was found


MANDY

Working on Wiki for Canada Day

The images used in the wiki have been removed as they were hotlinked from other websites. Instead, they have been replaced by those hosted on our photobucket account (still need to figure how much can be uploaded on this wiki here, so just in case, they will be hosted externally for now at least). The menu for the wiki has been updated. I put in a header and transparency coding. I'm learning overlays and positioning to make it look really 'cool'. Eventually the background image of the menu can be changed using scripting which I think will be neat.

In addition to the menu, image sizing is fixed and an RSS feed for our blog has been added to the wiki. This only shows the last 10 posts, so I will have to convert blog updates to their respective sections so that they remain permanently accessible on this site.


PRIMA

Working on Canada Day

I replied back to company emails and tried my best to answer their questions about our project. I researched a few old companies who had declined our proposals and searched new contacts in different departs. I will call them tomorrow.

In the lab Shadowed Vicky with Colony PCR of J13002 + JuxOD47A BBk + B0015 on pSB1AK3 Purpose: The bacterial culture growth is prolific. This will verify if the proper gene constructs are included within.

Materials an methods:

  • Primers: BBk forward and reverse construction primers
  • Master mix: Use pTaq DNA polymerase. The contents will suffice for 15 tubes, and were prepared in the same fashion as on June 26.
  • PCR conditions: These are also the same as they were on June 26

Tubes 1/6 were colony 1

tubes 2/7 were col 2

tubes 3/8 were col 3

tubes 4/9 were col 4

tubes 5/10 were col 5


VICKI

Colony PCR of J13002 + JuxOD47A BBk + B0015 on pSB1AK3 that I prepared yesterday

Purpose: The bacterial culture growth is prolific. This will verify if the proper gene constructs are included within.

Materials an methods:

  • Primers: BBk forward and reverse construction primers
  • Master mix: Use pTaq DNA polymerase. The contents will suffice for 15 tubes, and were prepared in the same fashion as on June 26.
  • PCR conditions: These are also the same as they were on June 26

Results:

The 1% agarose gel is attached below. Lane 1 is a GeneElute 1kb+ DNA ladder; lanes 2-11 are the colony-PCR'd samples of J13002 + LuxOD47A + B0015; lane 12 is a sequenced LuxOD47A + B0015 for a size control; lane 13 is a sequenced LuxOD47A BBk for another size control; and lane 14 is a negative control. Based on a very confusing negative control, this procedure will be repeated tomorrow. We will still progress with a NotI restriction digest of the contents, which will also be done tomorrow.



July1.png

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