Team:WashU StLouis/Notebook

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Notebook

Click on a date to see what we did on that day!

June 2017
Sunday Monday Tuesday Wednesday Thursday Friday Saturday
1 2 3
4 5 6 7 8 9 10
11 12 13 14 15 16 17
18 19 20 21 22 23 24
25 26 27 28 29 30

Thursday, June 1

Present: Micah, Maddie, Alex

Lab Work

  1. Prepared LB Media [Micah, Maddie, Alex]
  2. Re-suspended DNA (D. Radiodurans Uracil DNA Glycosylate 2) from iGEM kit [Micah, Maddie, Alex]
  3. Transformed Uracil DNA Glycosylate 2 in psB1C3 plasmid into MHD42 competent cells (Practice transformation) [Micah, Maddie, Alex]
  4. Prepared LB Agar [Micah, Maddie, Alex]
  5. Prepared overnight culture to make competent cells (MHD42) [Micah, Maddie, Alex]

Outside Work / Discussion

Friday, June 2

Present: Micah, Maddie

Lab Work

  1. Prepared MHD42 competent cells [Micah, Maddie]
  2. Checked on transformed MHD42 cells with Uracil DNA Glycosylate 2 [Micah, Maddie]
    • Transformation was a success with 100 colonies
    • Plate was stored in 4 deg. Celsius for future use
  3. Prepared TSS Buffer [Micah, Maddie]

Outside Work / Discussion

Saturday, June 3

No work done today!

Sunday, June 4

No work done today!

Monday, June 5

Present: Micah, Maddie, Alex, Mark, Collin

Lab Work

  1. Prepared LB + Chloramphenicol (CM) plates [Micah, Maddie, Mark, Collin]
  2. Prepared Ampicillin solution to be used for plates in the future [Micah, Maddie, Mark, Collin]
  3. Made more LB Agar [Alex]

Outside Work / Discussion

  1. Discussed shifting focus from Dsup gene to a variety of UV radiation resistance gene [Micah, Maddie, Mark, Collin, Alex]
  2. Found more genes to compare to Dsup (i.e. phrA in tardigrades and cyanobacteria) [Micah, Maddie, Mark, Collin, Alex]
  3. Met with Dr. Brennan to discuss updates [Micah, Maddie, Mark, Collin, Alex]

Tuesday, June 6

Present: Micah, Maddie, Alex, Mark, Collin

Lab Work

  1. Prepared DH5α competent cells [Micah, Maddie, Mark, Collin, Alex]
  2. Tested MHD42 cells for competency [Micah, Maddie, Mark, Collin, Alex]
  3. Tested DH5α cells for competency [Micah, Maddie, Mark, Collin, Alex]

Outside Work / Discussion

  1. Fleshed out project and decided specific parts to transform [BBa_B0034 (RBS), BBa_R0010 (lac promoter), and BBa_K1499200 (uvsE gene)] into MHD42 cells during the next day [Micah, Maddie, Mark, Collin, Alex]
    • The Deinococcus radiodurans UV DNA damage endonuclease (uvsE) gene is a UV radiation damage repair gene from the Stanford-Brown-Spelman 2014 team. We plan to use this to compare to other UV radiation repair genes.
  2. Planned out more long-term goals such as collaborations with other teams (especially those in the Midwest) [Micah, Maddie, Mark, Collin, Alex]

Wednesday, June 7

Present: Micah, Maddie, Mark, Collin, Alex

Lab Work

  1. Checked competency test for MHD42 cells [Micah, Maddie, Mark, Collin, Alex]
    • Test was successful!
  2. Checked competency test for DH5α [Micah, Maddie, Mark, Collin, Alex]
    • Test showed that the cells were competent but had a low transformation efficiency
  3. Prepared LB + Ampicillin (Amp) plates [Micah, Mark, Collin]
  4. Resuspeded parts BBa_B0034, BBa_R0010, and BBa_K1499200 from current and past distribution kits [Maddie, Alex]
  5. Transformed part BBa_B0034 (with plasmid psB1A2) into MHD42 competent cells [Maddie, Alex]
  6. Transformed part BBa_R0010 (with plasmid psB1C3) into MHD42 competent cells [Maddie, Alex]
  7. Transformed part BBa_K1499200 (with plasmid psB1C3) into MHD42 competent cells [Maddie, Alex]
  8. Prepared overnight culture of DH5α competent cells [Mark, Collin]

Outside Work / Discussion

  1. Discussed modelling ideas [Micah, Maddie, Mark, Collin]
  2. Learned how to design primers from Eugene [Micah, Maddie, Mark, Collin, Alex]

Thursday, June 8

Present: Alex, Maddie, Micah, Collin, Mark, Zoe

Lab Work

  1. Checked the results of the transformations of BBa_B0034, BBa_R0010, and BBa_K1499200 into MHD42 cells [Alex, Micah, Zoe]
  2. Made 900 mL of LB media [Collin, Mark, Zoe]
  3. Prepared DH5α competent cells [Micah, Zoe, Collin, Mark]
  4. Tested competency of the prepared DH5 [Maddie, Zoe, Mark]
  5. Prepared three separate overnight cultures of MHD42 cells with parts BBa_B0034, BBa_R0010, and BBa_K1499200 [Alex, Zoe]

Outside Work / Discussion

  1. Attended Energy, Environmental, and Chemical Engineering (EECE) summer interns orientation [Collin, Mark, Maddie, Zoe, Alex, Micah]
  2. Discussed each member's designated role and plans for the future [Collin, Mark, Maddie, Zoe, Alex, Micah]
  3. Made a team calendar [Collin, Mark, Maddie, Zoe, Alex, Micah]

Friday, June 9

Present: Maddie, Zoe, Micah, Mark, Collin, Alex

Lab Work

  1. Checked results for competency of DH5α cells [Alex, Mark, Micah, Maddie, Zoe, Collin}
    • Test was successful! The cells had a moderate transformation efficiency.
  2. Began the Interlab study by transforming the parts into DH5α cells [Maddie, Zoe, Mark]
    • Parts: Postive control (BBa_I20270), Negative control (BBa_R0040), Test device 1 (BBa_J364000), Test device 2 (BBa_J364001), Test device 3 (BBa_J364002), Test device 4 (BBa_J364003), Test device 5 (BBa_J364004), Test device 6 (BBa_J364005)
  3. Made 400 mL of LB Agar [Zoe]
  4. Made 11 Chloramphenicol (CM) + LB plates [Collin, Mark, Alex]

Outside Work / Discussion

  1. Researched modelling ideas [Micah]

Saturday, June 10

Present: Zoe

Lab Work

  1. Checked on the transformations for the interlab study [Zoe]
    • Colonies existed on all plates. Only a few colonies appeared on the plate with Test Device 1 (BBa_J364000)
    • Top (from left to right): Postive control (BBa_I20270), Negative control (BBa_R0040), Test device 1 (BBa_J364000), Test device 2 (BBa_J364001) Bottom (from left to right): Test device 3 (BBa_J364002), Test device 4 (BBa_J364003), Test device 5 (BBa_J364004), Test device 6 (BBa_J364005)

Outside Work / Discussion

Sunday, June 11

Present: Alex

Lab Work

  1. Prepared inoculated overnight cultures of the DH5α cells with BBa_B0034, BBa_R0010, and BBa_K1499200 in chloramphenicol [Alex]

Outside Work / Discussion

Monday, June 12

Present: Micah, Zoe, Mark, Collin, Maddie, Alex

Lab Work

  1. Transformed part BBa_E004 (GFP) into MHD42 competent cells [Zoe, Micah]
  2. Miniprepped the 3 separate cultures of MHD42 cells that contained BBa_R0010, BBa_B0034, and BBa_K1499200 [Alex, Collin]
  3. Measured concentration of DNA using the NanoDrop [Alex, Collin]
  4. Performed the Calibration Protocol for the Interlab study by measuring the absorbances of distilled water and Ludox HS-40 [Maddie, Mark]
  5. Measured the fluorescence of fluorescein serial dilutions for the Interlab study [Mark, Maddie]

Outside Work / Discussion

  1. Filled out Forms 1 and 2 for the Interlab study [Maddie, Mark]
  2. Studied BioBrick assembly methods [Alex, Micah]
  3. Met with Dr. Brennan and discussed our project thus far with her [Micah, Collin, Alex, Maddie, Mark, Zoe]

Tuesday, June 13

Present: Zoe, Mark, Collin, Alex, Maddie, Micah

Lab Work

  1. Checked for the transformation of part BBa_E0040 (GFP) into MHD42 competent cells [Micah]
  2. Miniprepped the DNA for parts BBa_R0010 and BBa_B0034 from the MHD42 cells that were cultured overnight [Zoe, Micah]
  3. Measured concentration of DNA using the NanoDrop [Micah, Zoe]
  4. Performed cell measurements for the Interlab study (Day 3) [Maddie, Mark]
    • Measured the OD of the each of the 16 cultures (2 colonies per control and test device) and diluted each so that the OD of each would be approximately 0.02
    • Measured the OD of samples of each diluted culture after 0, 2, 4, and 6 hours
  5. Prepared overnight culture of the MHD42 cells with BBa_E0040 (GFP) [Micah, Zoe]

Outside Work / Discussion

  1. Discussed how perform restriction digest and ligation using the BioBrick kit with Dr. Brennan [Alex, Collin]

Wednesday, June 14

Present: Zoe, Collin, Micah, Alex, Mark, Maddie

Lab Work

  1. Miniprepped 4 tubes of part BBa_E0040 (GFP) [Zoe, Micah]
  2. Measured concentration of DNA using the NanoDrop [Micah, Mark, Zoe]
  3. Performed restriction digest of parts BBa_B0034 and BBa_R0010 [Alex, Collin]
  4. Performed gel electrophoresis of digested BBa_B0034 and BBa_R0010 [Alex, Collin]
  5. Prepared LB + Ampicillin plates [Zoe, Micah, Mark]

Outside Work / Discussion

Thursday, June 15

Present: Mark, Zoe, Alex, Maddie, Collin, Micah

Lab Work

  1. Purified the digested BBa_R0010 and BBa_B0034 from the agarose gel [Collin, Alex, Zoe]
  2. Ligated the lac promoter from BBa_R0010 to the RBS and pSB1A2 backbone of BBa_B0034 [Alex]
  3. Performed restriction digest of parts BBa_B0034 and BBa_R0010 [Zoe, Collin]
  4. Prepared LB Agar [Zoe]

Outside Work / Discussion

  1. Researched modelling ideas [Micah, Maddie]
  2. Researched possible parts in the registry to improve [Mark]
  3. Met with Dr. Brennan to discuss progress done so far [Mark, Zoe, Maddie, Alex, Collin, Micah]

Friday, June 16

Present: Zoe, Maddie, Micah, Alex, Mark

Lab Work

  1. Checked on the transformation of the MHD42 E. coli cells with ligated plasmid consisting of RBS (from Part BBa_B0034) and the lac promoter (from Part BBa_R0010) [Micah]
    • Prepared lab materials (reagents, E. coli strains) for our lesson to the students part of WashU's Pre-Engineering Institute [Zoe, Mark, Maddie, Micah, Alex]

Outside Work / Discussion

  1. Identified composite part in registry (BBa_J04500) that already consists of BBa_B0034 [Micah, Alex]
  2. Planned out presentation and lab for the Pre-Engineering Institute students on June 20 [Micah, Mark, Alex, Zoe, Maddie]
    • Set up lab stations with vortex machines, pipet tips, and micropipettors

Saturday, June 17

Present: Micah

Lab Work

  1. Transformed composite part BBa_J04500 into MHD42 E. coli cells [Micah]

Outside Work / Discussion

Sunday, June 18

Present: Micah, Mark

Lab Work

  1. Checked the plate of MHD42 cells transformed with BBa_J04500 [Micah]
    • Prepared an overnight culture of the cells transformed with BBa_J04500 [Mark]

Outside Work / Discussion

Monday, June 19

Present: Zoe, Mark, Micah, Alex, Maddie, Collin

Lab Work

  1. Miniprepped part BBa_J04500 (lac promoter + RBS) [Maddie,Zoe]
  2. Performed restriction digest on parts BBa_J04500 and BBa_E0040 [Maddie, Zoe]
  3. Performed gel electrophoresis on parts BBa_J04500 and BBa_E0040 [Maddie, Zoe, Collin]
  4. Prepared overnight cultures of 9 E. Coli strains for the Pre-Engineering Institute workshop [Mark, Collin, Micah]

Outside Work / Discussion

  1. Discussed how to build an apparatus to expose cell cultures to UV-B radiation [Alex, Micah, Mark, Collin, Maddie, Zoe]
  2. Researched cyanobacteria transformations [Alex, Micah, Mark, Collin, Maddie, Zoe]
  3. Met with Dr. Brennan to give her updates and prepare for the Pre-Engineering Institute event [Alex, Micah, Mark, Collin, Maddie, Zoe]

Tuesday, June 20

Present: Micah, Alex, Collin, Zoe, Maddie, Mark

Lab Work

  1. Performed gel purification on parts BBa_J04500 and BBa_E0040

Outside Work / Discussion

  1. Led a three hour synthetic biology workshop for the WashU Pre-Engineering Institute summer program [Micah, Mark, Zoe, Maddie, Collin, Alex]
    • Presented on the field of synthetic biology and the iTune BioBuilder lab activity
    • Led the iTune BioBuilder lab activity

Wednesday, June 21

Present: Alex, Zoe, Maddie, Collin, Micah, Mark

Lab Work

  1. Ligated BBa_J04500 and BBa_E0040 and transformed the composite plasmid into DH5α E. coli cells [Maddie, Zoe]
  2. Transformed BBa_I13500 into DH5α E. coli cells [Alex]

Outside Work / Discussion

  1. Purchased materials for the UV-B radiation box [Micah, Collin, Mark]

Thursday, June 22

Present: Alex, Zoe, Maddie, Mark, Micah, Collin

Lab Work

  1. Prepared 50% glycerol stock [Alex, Zoe]
  2. Prepared six overnight cultures for the DH5α cells transformed with ligated parts BBa_J04500 and BBa_E0040 [Alex, Mark]
  3. Prepared overnight culture for the DH5α cells transformed with part BBa_I13500 [Alex, Mark]

Outside Work / Discussion

  1. Purchased more materials for the UV-B radiation box [Micah, Collin, Mark]

Friday, June 23

Present: Zoe, Mark, Alex, Maddie, Collin, Micah

Lab Work

  1. Miniprepped the DNA from the six DH5α cultures with BBa_J04500 and BBa_E0040 ligated together [Mark, Zoe]
  2. Miniprepped the DNA from the DH5α culture with BBa_I13500 [Zoe, Mark]
  3. Performed restriction digest on the plasmids consisting of BBa_J04500 and BBa_E0040 ligated together. [Alex, Mark]
  4. Performed gel electrophoresis to separate the backbone and the ligated insert (BBa_J04500 and BBa_BBa_E0040) in order to check if the parts were ligated correctly [Mark, Alex]

Outside Work / Discussion

Saturday, June 24

Present: Micah, Collin, Zoe, Mark

Lab Work

Outside Work / Discussion

  1. Purchased more materials for the UV exposure box [Micah, Collin, Zoe, Mark]
  2. Began the construction of the UV exposure box [Micah, Collin, Zoe, Mark]

Sunday, June 25

No work done today!

Monday, June 26

Present: Zoe, Micah, Collin, Alex, Maddie, Mark

Lab Work

  1. Resuspended the Dsup DNA from IDT [Collin, Micah]
  2. Digested the Dsup DNA [Collin, Micah]
  3. Digested the pSB1A2 plasmids with ligated BBa_J04500 (lac promoter + RBS) and BBa_E0040 (GFP) [Alex, Mark]
  4. Performed gel electrophoresis on the digested pSB1A2 plasmids with ligated BBa_J04500 and BBa_E0040 [Alex, Mark]
    5. .
  5. Performed gel electrophoresis on the digested Dsup[Collin, Micah]
    6. .
  6. Transformed the pSB1A2 with BBa_J04500 and BBa_E0040 into DH5α E. coli cells [Alex, Maddie]
  7. Transformed the pSB3C5 plasmid into DH5α E. coli cells [Maddie]

Outside Work / Discussion

  1. Finished constructing the UV exposure box [Zoe, Collin, Micah]

Tuesday, June 27

Present: Zoe, Mark, Micah, Maddie, Collin, Alex

Lab Work

  1. Checked for the transformation of DH5α cells with expression plasmid pSB3C5 [Alex]
  2. Checked for the transformation of DH5α cells with the ligated parts, BBa_J04500 (lac promoter + RBS) and BBa_E0040 (GFP) [Alex}
  3. Purified Dsup from its gel [Collin, Micah]
  4. Digested the phrA (from Tardigrade species, Ramazzottius varieornatus), phrA (from cyanobacteria), and BBa_R0010 (lac promoter) [Zoe, Maddie]
    • We digested BBa_R0010 to obtain its pSB1C3 backbone
  5. Performed gel electrophoresis on the digested phrA from tardigrades, phrA from cyanobacteria, and BBa_R0010 (lac promoter) [Mark, Zoe]
  6. Performed a PCR gradient test on Dsup, phrA (from tardigrades), and phrA (from cyanobacteria) [Maddie, Zoe]
  7. Performed gel electrophoresis for the PCR gradient test [Maddie, Zoe]

    • left to right:Dsup, phrA (from tardigrades), phrA (from cyanobacteria)

    • The gel pattern shows that the gradient test failed and that we need to design better primers
  8. Evaluated the efficacy of the UV exposure box [Collin, Micah]
    • Transformed pSB1C3 with RFP into MHD42 E. coli cells
    • Plated the transformation on two plates and incubated one in the UV box and the other outside of the box overnight
  9. Transformed pSB4C5 into DH5α E. coli cells [Alex]
  10. Transformed the ligated BBa_E0040 (GFP), BBa_J04500 (lac promoter + RBS), and pSB1C3 plasmid into DH5α E. coli cells [Alex]
  11. Prepared an inoculated overnight culture of DH5α cells with pSB3C5 expression plasmids [Alex]

Outside Work / Discussion

Wednesday, June 28

Present: Mark, Alex, Maddie, Zoe, Micah, Collin

Lab Work

  1. Checked for the transformation of pSB4C5 into DH5α cells [Alex]
  2. Checked for the transformation of the ligated parts, BBa_J04500, BBa_E0040, and pSB1C3, into DH5α cells [Alex]
  3. Miniprepped the pSB3C5 expression plasmids [Zoe]
  4. Transformed MHD42 and DH5α E. coli cells with BBa_J04450 (RFP plasmid) to test the efficacy of the UV box [Collin, Micah]
    • Placed two plates of the transformation inside the UV box and two plates outside of the box
  5. Purified pSB1C3, phrA (from tardigrades), and phrA (from cyanobacteria) from their respective gels [Mark]
  6. Ligated Dsup, phrA (from tardigrades), and phrA (from cyanobacteria) into pSB1C3 backbones [Mark, Zoe]
  7. Transformed each of the ligations into DH5α E. coli cells [Zoe, Mark]
  8. Prepared LB + Chloramphenicol (CM) plates [Mark]

Outside Work / Discussion

  1. Worked on modeling growth curves [Micah]

Thursday, June 29

Present: Collin, Micah, Maddie, Zoe, Mark, Alex

Lab Work

  1. Checked on the transformations of Dsup, phrA (from tardigrades), and phrA (from cyanobacteria), all of which were ligated into pSB1C3 plamids previously [Alex]
  2. Compared the plates of cells transformed with BBa_J04450 (RFP) that were stored in the UV box with the plates that were stored outside of the box [Micah]
  3. Prepared LB Agar [Mark]
  4. Prepared overnight cultures of the cells with Dsup, phrA (from tardigrades), phrA (from cyanobacteria), pSB4C5, and the ligated BBa_J04500 and BBa_E0040 (which is lac promoter + RBS + GFP altogether) [Zoe, Alex]

Outside Work / Discussion

  1. Met with Sarah Rommelfanger to discuss our plans of transforming cyanobacteria in the near future [Zoe, Alex, Maddie, Mark, Micah, Collin]
  2. Met with Dr. Brennan to update her on our progress [Alex, Mark, Zoe, Maddie, Collin, Micah]

Friday, June 30

Lab Work

  1. Miniprepped 4 cultures with phrA (from tardigrades), 3 cultures with phrA (from cyanobacteria), 3 cultures with Dsup, 1 culture with the ligated BBa_j04500 and BBa_E0040 (which is lac promoter + RBS + GFP altogether), and 4 cultures with pSB4C5 [Alex, Zoe, Maddie]
  2. Digested phrA (from tardigrades), phrA (from cyanobacteria), and Dsup to remove the genes from their pSB1C3 backbones [Zoe]
  3. Performed gel electrophoresis on these three digestions [Alex, Collin, Mark]

    • phrA from tardigrades (aka phrAT)

    • left 3 lanes: phrA from cyanobacteria (aka phrAC) ; right 3 lanes: Dsup

  4. Performed a PCR gradient test on Dsup, phrA (from tardigrades), and phrA (from cyanobacteria) [Maddie, Zoe]
  5. Performed gel electrophoresis for the PCR gradient test [Maddie, Zoe, Mark]

    • Top: phrAT ; Bottom: phrAC

    • Dsup

Outside Work / Discussion

  1. Worked on the Arduino for the UV exposure box [Micah]
    • Configured the temperature and humidity sensing mechanism
  2. Worked on the style of the wiki's menu and updated several pages [Mark]

Saturday, July 1

No work done today!

Sunday, July 2

No work done today!

Monday, July 3

Present: Micah, Mark, Zoe, Alex

Lab Work

  1. Transformed UV promoter on an Amp plate into DH5α cells [Zoe]
  2. Transformed Dsup #3, phrAC #1, and phrAT #4 (pSB1C3) on Cm plates DH5α cells [Zoe}
  3. Made LB+Cm plates [Mark]

Outside Work / Discussion

  • Started working on Arduino and designing code for the "To-Grow Box" [Micah, Zoe]

    • Tuesday, July 4

    Present: Alex

    Lab Work

    1. Checked the transformations and moved them to the cold room [Alex]

    Outside Work / Discussion

    Wednesday, July 5

    Present: Mark, Micah, Alex, Maddie, Zoe

    Lab Work

    1. Transformation of Lac+RBS+GFP (pSB1A2) on Amp plates into DH5α cells [Alex]
    2. Prepared 5mL liquid cultures from transformations done on Monday: Dsup#3, phrAC #1, phrAT #4 (all with Cm), and UV promoter (with Amp) [Zoe]

    Outside Work / Discussion

  • Started working on our presentation for our July 10th Monsanto tour [Micah, Maddie, Alex, Mark, Zoe]

    • Thursday, July 6

    Present: Micah, Maddie, Collin, Zoe, Alex

    Lab Work

    1. Made glycerol stocks of Dsup, phrAT, and phrAC in pSB1C3 from liquid cultures [Alex]
    2. Preparation of 21 Amp plates [Alex]
    3. Miniprepped UV promoter [Maddie]
    4. Transformation of Lac+RBS+GFP (pSB1A2) on Amp plates into DH5α cells [Zoe]

    Outside Work / Discussion

  • Went to hardware store and bought more materials for "To-Grow Box" [Collin, Micah]
  • Designed and started 3D printing parts for the mini shaker for the "To-Grow Box" [Collin, Micah]

    • Friday, July 7

    Lab Work

    Outside Work / Discussion

    Saturday, July 8

    Lab Work

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    Sunday, July 9

    Lab Work

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    Monday, July 10

    Lab Work

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    Tuesday, July 11

    Lab Work

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    Wednesday, July 12

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    Thursday, July 13

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    Friday, July 14

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    Saturday, July 15

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    Sunday, July 16

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    Monday, July 17

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    Tuesday, July 18

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    Wednesday, July 19

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    Thursday, July 20

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    Friday, July 21

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    Saturday, July 22

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    Sunday, July 23

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    Monday, July 24

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    Tuesday, July 25

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    Wednesday, July 26

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    Thursday, July 27

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    Friday, July 28

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    Saturday, July 29

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    Sunday, July 30

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    Monday, July 31

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    Tuesday, August 1

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    Wednesday, August 2

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    Thursday, August 3

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    Friday, August 4

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    Saturday, August 5

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    Sunday, August 6

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    Monday, August 7

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    Tuesday, August 8

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    Wednesday, August 9

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    Thursday, August 10

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    Friday, August 11

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    Saturday, August 12

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    Sunday, August 13

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    Monday, August 14

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    Tuesday, August 15

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    Wednesday, August 16

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    Thursday, August 17

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    Friday, August 18

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    Saturday, August 19

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    Sunday, August 20

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    Monday, August 21

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    Tuesday, August 22

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    Wednesday, August 23

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    Thursday, August 24

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    Friday, August 25

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    Saturday, August 26

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    Sunday, August 27

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    Monday, August 28

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    Tuesday, August 29

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    Wednesday, August 30

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    Thursday, August 31

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    Friday, September 1

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