Difference between revisions of "Team:WashU StLouis/Notebook"

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. Performed gel electrophoresis on the digested Dsup[Collin, Micah]
.
• 
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 [Zoe]
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. Skyped with Purdue's iGEM team [Micah, Maddie, Mark, Collin, Alex]
2. Worked on the Arduino for the UV exposure box [Micah]
• Configured the temperature and humidity sensing mechanism
3. 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) into DH5α cells [Zoe}
3. Made LB+CM plates [Mark]

Outside Work / Discussion

1. 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 of Dsup, phrAT, phrAC, and the UV promoter 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

1. 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

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

Friday, July 7

Present: Micah, Maddie, Collin, Zoe, Alex

Lab Work

1. Transformed the UV promoter (BBa_J22106) into DH5α cells and plated them onto a LB + Amp plate [Collin]

Outside Work / Discussion

1. Talked with the University of Iowa iGEM team over Skype
2. Worked on the Monsanto presentation

Saturday, July 8

Present: Collin

Lab Work

1. Checked on the transformation of the UV promoter (BBa_J22106) [Collin]

Outside Work / Discussion

Sunday, July 9

No work done today!

Monday, July 10

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

Lab Work

1. Sent Dsup, phrAC, phrAC, and lac promoter+RBS+GFP (all in pSB1C3 plasmids) for sequencing [Alex]

Outside Work / Discussion

1. Visited the Monsanto and Pfizer campus in Chesterfield, MO [Zoe, Collin, Mark, Maddie, Micah, Alex]

Tuesday, July 11

Present: Maddie, Zoe, Alex, Collin, Mark

Lab Work

1. Prepared 5 mL liquid culture of BBa_J22106 (UV promoter) and incubated at 37°C [Maddie]

Outside Work / Discussion

Wednesday, July 12

Present: Collin, Zoe, Maddie, Alex

Lab Work

1. Miniprepped the overnight culture of BBa_J22106 [Maddie]
2. Prepared BG-11 cyanobacteria media [Maddie, Zoe]
3. Measured OD for an undiluted cyanobacteria (S-6803) solution [Maddie, Zoe]
   • The OD was 0.4519
4. Diluted the cyanobacteria culture to an OD of 0.02 in two 250 mL flasks [Zoe, Maddie]
• The actual OD's after the dilution were 0.0207 (#1) and 0.0209 (#2)
• 

  From left to right: #1, #2

5. Transformed BBa_K592009 (Blue chromoprotein) into DH5α E. coli cells [Alex]
6. Prepared a 20 mL liquid culture of DH5α cells with BBa_J04500 in pSB1C3 [Zoe]

Outside Work / Discussion

1. Skyped with the Peshawar iGEM team [Maddie, Alex, Collin]

Thursday, July 13

Present: Zoe, Mark, Collin, Alex, Maddie

Lab Work

1. Prepared 1600 mL of LB Agar [Maddie, Zoe]
2. Prepared 112 small LB+CM plates [Maddie, Mark, Zoe]
3. Measured the OD of the two cyanobacteria cultures [Zoe]
• 0.0443 (#1), 0.1135 (#2)
• 

  From left to right: #1, #2

4. Transformed BBa_J04500 (Lac promoter + RBS) in DH5α cells [Collin]

Outside Work / Discussion

Friday, July 14

Present: Zoe, Collin, Alex, Maddie, Mark

Lab Work

1. Prepared 800 mL of LB Agar [Mark]
2. Prepared 59 small LB+CM plates [Maddie, Mark, Zoe]
3. Measured the OD of the two cyanobacteria cultures [Zoe]
• 0.0734 (#1), 0.4439 (#2)
• 

  From left to right: #1, #2

4. Prepared two more 50 mL cultures of Synechocystis S-6803 and incubated them in the 30°C room [Maddie, Zoe]
• Starting OD's: 0.0213 <#3), 0.0213 (#4)

Outside Work / Discussion

Saturday, July 15

Present:Zoe

Lab Work

1. Measured the OD of all four cyanobacteria cultures [Zoe]
• 0.1179 (#1), 0.9077 (#2), 0.0592 (#3), 0.0436 (#4)
• 

  From left to right: #1, #2 #3, #4

Outside Work / Discussion

Sunday, July 16

Present:Zoe

Lab Work

1. Measured the OD of the four cyanobacteria cultures [Zoe]
• 0.1791 (#1), 1.3581 (#2), 0.1312 (#3), 0.0799 (#4)
2. Prepared liquid cultures of lac promoter + RBS (BBa_J04500) and Blue chromoprotein (BBa_K592009) [Zoe]

Outside Work / Discussion

Monday, July 17

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

Lab Work

1. Miniprepped 4 E. coli cultures with lac promoter + RBS (BBa_J04500) [Zoe]
2. Miniprepped 1 E. coli culture with blue chromoprotein (BBa_K592009) [Zoe]
3. Digested Dsup, phrAC, phrAT, uvsE, RBS (BBa_B0034), Lac promoter + RBS (BBa_J04500), and Blue Chromoprotein (BBa_K592009) [Collin]
4. Performed gel electrophoresis on the digested Dsup, phrAC, phrAT, uvsE, RBS, Lac promoter + RBS, and blue chromoprotein [Mark, Collin]
5. Measured the OD730 of the 4 cyanobacteria cultures [Zoe]
• 0.2854 (#1), 2.4509 (#2), 0.2725 (#3), 0.1262 (#4)
6. Streaked the 9 strains of E. coli from the BioBuilder iTUNE activity for the Pre-Engineering Institute workshop [Mark, Collin]

Outside Work / Discussion

1. Skyped with Austin Burns, the Regulatory Manager at Monsanto [Alex]
2. Worked on the code for the Environmental Simulation System (ESS) [Micah]

Tuesday, July 18

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

Lab Work

1. Purified uvsE, phrAT, phrAC, Dsup, Lac promoter + RBS, RBS, and blue chromoprotein from their respective gels [Maddie]
2. Ligated uvsE to lac + RBS, phrAT to lac + RBS, phrAC to lac + RBS, Dsup to lac + RBS, and RBS to blue chromoprotein [Maddie]
3. Transformed the ligated plasmids into DH5α E. coli cells [Maddie]
4. Measured the OD730 of the 4 cyanobacteria cultures [Zoe, Mark]
• 0.4047 (#1), 3.2044 (#2), 0.4633 (#3), 0.1951 (#4)
5. Prepared overnight cultures of the 9 strains of E. coli from the Biobuilder iTune activity (for the Pre-Engineering Institute workshop [Alex]

Outside Work / Discussion

1. Worked on the Environmental Simulation System (ESS) [Micah, Collin]
2. Prepared materials for the Pre-Engineering Institute workshop [Mark, Maddie, Alex, Micah]

Wednesday, July 19

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

Lab Work

1. Checked the transformations of lac+RBS+Dsup, lac+RBS+phrAT, lac+RBS+phrAC, lac+RBS+uvsE, and RBS+blue chromoprotein [Alex]
2. Measured the OD730 of the 4 cyanobacteria cultures [Zoe]
• 0.5425 (#1), 3.6448 (#2), 0.7760 (#3), 0.3022 (#4)
3. Transforomed lac+RBS+phrAT into DH5α E. coli cells (again) [Maddie]
4. Prepared overnight cultures for 3 colonies each of lac+RBS+phrAT, lac+RBS+phrAC, lac+RBS+Dsup, lac+RBS+uvsE, and RBS+Blue chromoprotein [Zoe]

Outside Work / Discussion

1. Led a synthetic biology workshop for high school students in the Pre-Engineering Institute Program [Mark, Collin, Zoe, Alex, Maddie, Micah]
2. Worked on the Environmental Simulation System [Micah]

Thursday, July 20

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

Lab Work

1. Prepared LB+CM plates [Mark]
2. Prepared glycerol stocks of lac+RBS+phrAT, lac+RBS+phrAC, lac+RBS+Dsup, lac+RBS+uvsE, and RBS+blue chromoprotein [Alex]
3. Miniprepped each of the overnight cultures of DH5α E. coli cells with lac+RBS+phrAT, lac+RBS+phrAC, lac+RBS+Dsup, lac+RBS+uvsE, and RBS+blue chromoprotein [Alex]
4. Digested the miniprepped lac+RBS+phrAT, lac+RBS+phrAC, lac+RBS+Dsup, lac+RBS+uvsE, and RBS+blue chromoprotein [Mark, Collin]
5. Measured the OD730 of the 4 cyanobacteria cultures [Collin, Mark]
• 0.7062 (#1), 3.9385 (#2), 1.0866 (#3), 0.7098 (#4)
6. Performed gel electrophoresis on the digested lac+RBS+phrAT, lac+RBS+phrAC, lac+RBS+Dsup, lac+RBS+uvsE, and RBS+blue chromoprotein to test if the ligation was correct [Maddie, Zoe]
7. Prepared 3 overnight cultures of DH5α E. coli cells with lac+RBS+phrAT [Alex]

Outside Work / Discussion

1. Presented on our project and the iGEM competition as a whole to high school teachers attending the BioBuilder Professional Development Workshop at Monsanto [Maddie, Zoe, Mark, Collin, Micah]

Friday, July 21

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

Lab Work

1. Miniprepped the three cultures with lac+RBS+phrAT Alex
2. Measured the OD730 of the four cyanobacteria cultures [Maddie]
• 0.9366 (#1), 3.989 (#2), 1.584 (#3), 0.6518 (#4)
3. Measured the amount of light that each cyanobacteria is receiving on average (in micro-molars per meter squared per second) using a FieldScout Quantum Light Meter [Maddie, Zoe]
• 8.4 (#1), 23 (#2), 16.6 (#3), 9.8 (#4)
4. Digested lac+RBS+uvsE, lac+RBS+phrAC, lac+RBS+Dsup, and RBS+blue chromoprotein to determine if the ligations were correct [Alex, Mark]
5. Performed gel electrophoresis on the 3 miniprepped samples (#4, #5, #6) of phrAT and the digested lac+RBS+uvsE, lac+RBS+phrAC, lac+RBS+Dsup, and RBS+blue chromoprotein to test if the ligations were correct [Alex]

Outside Work / Discussion

1. Skyped with Cardiff iGEM to explore potential collaboration scenarios [Alex, Micah, Mark, Zoe, Collin]

Saturday, July 22

No lab work done today!

Sunday, July 23

Present: Maddie

Lab Work

1. Measured the OD730 of the four cyanobacteria cultures [Maddie]
• 1.4122 (#1), 3.965 (#2), 2.3244 (#3), 0.9878 (#4)

Outside Work / Discussion

Monday, July 24

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

Lab Work

1. Digested lac+RBS+uvsE, lac+RBS+phrAC, lac+RBS+Dsup, phrAT, lac+RBS and RBS+blue chromoprotein [Alex]
2. Performed gel electrophoresis for the digested lac+RBS+uvsE, lac+RBS+phrAC, lac+RBS+Dsup, phrAT, lac+RBS and RBS+blue chromoprotein [Alex]
3. Measured the OD730 of the four cyanobacteria cultures [Mark, Micah]
• 1.7252 (#1), 3.884 (#2), 2.8400 (#3), 1.218 (#4)
4. Digested uvsE, phrAC, Dsup, and lac+RBS [Collin, Mark]
5. Performed gel electrophoresis on digested uvsE, phrAC, Dsup, and lac+RBS [Mark, Collin]
6. Performed a PCR gradient test on phrAT, phrAC, Dsup, and uvsE with Golden Gate compatible primers [Maddie, Zoe]
• uvsE and Dsup were successful
7. Prepared three overnight cultures of lac+RBS+phrAC, three cultures of lac+RBS+uvsE, and two cultures of lac+RBS+Dsup [Zoe]

Outside Work / Discussion

1. Practiced our presentation for the EECE poster session [Maddie, Alex, Collin]
2. Met with Dr. Brennan to discuss our progress [Mark, Maddie, Alex, Collin, Zoe, Micah]

Tuesday, July 25

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

Lab Work

1. Made glycerol stocks of three cultures with lac+RBS+phrAC (#4, #5, #6), three cultures with lac+RBS+uvsE (#4, #5, #6), and two cultures with lac+RBS+Dsup (#4, #5) [Alex]
2. Performed gel purification on the Golden Gate (GG) compatible uvsE and Dsup PCR products [Maddie, Mark]
3. Performed gel purification on lac+RBS, phrAC, Dscup, and uvsE [Mark, Maddie]
4. Miniprepped three cultures with lac+RBS+phrAC (#4, #5, #6), three cultures with lac+RBS+uvsE (#4, #5, #6), and two cultures with lac+RBS+Dsup (#4, #5) [Zoe]
5. Measured the OD730 of the four cyanobacteria colonies [Mark, Collin]
• 2.126 (#1), 3.881 (#2), 3.667 (#3), 1.5272 (#4)
6. Transformed BBa_I13521 (RFP with a constitutive promoter) into DH5α E. coli cells [Maddie]
7. Ligated lac+RBS (BBa_J04500) with phrAC, Dsup, phrAT, and uvsE individually in pSB1C3 [Alex, Mark, Collin]
8. Transformed the ligated lac+RBS+Dsup, lac+RBS+phrAT, lac+RBS+phrAC, and lac+RBS+uvsE [Mark, Collin]

Outside Work / Discussion

1. Presented at the EECE summer poster session [Zoe, Maddie, Collin, Alex, Micah, Mark]

Wednesday, July 26

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

Lab Work

1. Measured the OD730 of the four cyanobacteria cultures [Collin, Mark]
• 2.2204 (#1), 3.742 (#2), 3.786 (#3), 1.7132 (#4)
2. Performed gradient PCR on PCV0020 [Zoe, Maddie]
• Did not work
3. Made liquid cultures for 3 colonies each of lac+RBS+uvsE, lac+RBS+Dsup, lac+RBS+phrAC, lac+RBS+phrAT (#7, #8, #9) [Alex]
4. Tested the efficacy of the UV box by exposing plates of DH5α E. coli cells with RFP to UV for different time intervals [Micah, Mark]
5. Plated pDeg+PCPC360 and pDeg+pTrc on Kan plates and PCV0020 on Spec plates [Collin, Mark]

Outside Work / Discussion

1. Met with Dr. Larry Gilbertson, a molecular biologist at Monsanto, and discussed methods of transforming plant cells [Alex, Micah, Mark, Collin, Zoe]

Thursday, July 27

Present: Zoe, Micah, Alex, Collin, Mark

Lab Work

1. Checked the UV-exposed RFP plates [Micah]
2. Made glycerol stocks for three cultures each of lac+RBS+phrAC, lac+RBS+phrAT, lac+RBS+uvsE, and lac+RBS+Dsup (#7, #8, #9) [Alex]
3. Miniprepped the three cultures each of lac+RBS+phrAC, lac+RBS+phrAT, lac+RBS+uvsE, and lac+RBS+Dsup (#7, #8, #9) [Zoe, Mark]
4. Prepared Kanamycin (Kan) and Spectinomycin (Spec) solutions [Mark, Collin]
5. Measured the OD730 of the four cyanobacteria cultures [Mark]
• 2.4388 (#1), 0.3345 (#2), 0.3613 (#3), 1.9760 (#4)
6. Tested the UV box and shaker with two cultures of DH5α E. coli cells with RFP (One inside the box and the other outside the box) [Micah]
7. Prepared three overnight cultures of DH5α E. coli cells with pDeg+PCPC360, pDeg+pTrc, and PCV0020 [Collin]
8. Digested lac+RBS+Dsup #7, lac+RBS+uvsE #7, lac+RBS+phrAC #8, lac+RBS+phrAT #9, and RBS+blue chromoprotein #1 [Alex]
9. Performed gel electrophoresis for the digested lac+RBS+Dsup #7, lac+RBS+uvsE #7, lac+RBS+phrAC #8, lac+RBS+phrAT #9, and RBS+blue chromoprotein #1 [Alex]

Outside Work / Discussion

Friday, July 28

Present: Collin, Mark, Zoe, Alex, Micah

Lab Work

1. Checked the OD600 of the two cultures used to test the UV box and shaker [Micah]
2. Prepared glycerol stocks of DH5α E. coli cells with pDeg+PCPC360, pDeg+pTrc, and PCV0020 [Alex]
3. Miniprepped the DH5α E. coli cells with pDeg+PCPC360, pDeg+pTrc, and PCV0020 [Zoe]
4. Measured the OD730 of the cyanobacteria cultures [Mark, Collin]
• 2.8328 (#1), 3.682 (#2), 3.652 (#3), 2.2800 (#4)
5. Performed a PCR gradient for phrAT and phrAC with GG compatible primers [Alex]
6. Performed gel electrophoresis for the PCR gradient for phrAT and phrAC with GG compatible primers [Alex]

Outside Work / Discussion

Saturday, July 29

Present: Micah, Collin

Lab Work

1. Measured the OD600 of the DH5α E. coli cultures (one inside the box and one in the culture room) for the UV box test [Micah]
2. Measured the OD730 of the four cyanobacteria cultures [Collin]
• 3.0176 (#1), 3.622 (#2), 3.468 (#3), 2.2704 (#4)

Outside Work / Discussion

Sunday, July 30

Lab Work

1. Measured the OD730 of the four cyanobacteria cultures [Mark]
• 3.3316 (#1), 3.489 (#2), 3.314 (#3), 2.7836 (#4)
2. Prepared overnight cultures of DH5α E. coli cells with lac+RBS+Dsup, lac+RBS+phrAT, and RFP individually [Mark]
3. Digested uvsE, phrAT, phrAC, and Dsup from pSB1C3 and digested lac+RBS+psB1A2 to linearize the plasmid [Alex]
4. Performed gel electrophoresis for uvsE, phrAT, phrAC, Dsup, and lac+RBS+psB1A2 [Alex]

Outside Work / Discussion

Monday, July 31

Present: Collin, Micah, Alex, Mark, Zoe

Lab Work

1. Performed a PCR gradient for phrAT and phrAC with GG compatible primers [Mark, Collin]
2. Performed gel electrophoresis for the PCR gradient of phrAT and phrAC (with GG compatible primers) [Mark]
3. Measured the OD730 of the four cyanobacteria cultures [Mark]
• 3.913 (#1), 3.371 (#2), 3.357 (#3), 3.273 (#4)
4. Prepared a liquid culture of DH5α cells wih lac+RBS+phrAT in pSB1C3 [Zoe]
5. Ligated phrAT, Dsup, phrAC, and uvsE into a pSB1A2 backbone with lac+RBS [Zoe]
6. Performed another PCR gradient for phrAT with GG compatible ends [Collin]
7. Performed gel electrophoresis for the PCR gradient of phrAT with GG compatible ends [Collin, Mark]
8. Digested lac+RBS+Dsup+pSB1C3 and lac+RBS+phrAT+pSB1C3 to linearize the plasmids [Micah]
9. Performed gel electrophoresis on the digested lac+RBS+Dsup+pSB1C3 and lac+RBS+phrAT+pSB1C3 plasmids [Mark]

Outside Work / Discussion

Tuesday, August 1

Present: Zoe, Mark, Micah, Collin, Alex

Lab Work

1. Miniprepped lac+RBS+phrAT+pSB1C3 [Zoe]
2. Purified RBS+blue chromoprotein and the linearized lac+RBS+Dsup+pSB1C3 from their respective gels [Mark]
3. Digested PCPC360 and pTrc to linearize both plasmids [Micah]
4. Performed gel electrophoresis on the digested PCPC360 and pTrc [Micah, Mark]
5. Digested lac+RBS+phrAT+pSB1C3 [Micah]
6. Performed gel electrophoresis on the digested lac+RBS+phrAT+pSB1C3 along with undigested PCPC360 and pTrc [Mark]
7. Measured the OD730 of the four cyanobacteria cultures [Micah]
• 4.078 (#1), 3.298 (#2), 3.163 (#3), 3.422 (#4)
8. Ligated RBS+Blue chromoprotein into lac+RBS+Dsup+pSB1C3 [Mark]
9. Transformed the ligated lac+RBS+Dsup+RBS+Blue chromoprotein+psB1C3 into DH5α E. coli cells [Mark, Zoe]
10. Prepared three cultures each of DH5α E. coli cells with lac+RBS+uvsE+psB1A2, lac+RBS+Dsup+psB1A2, lac+RBS+phrAT+pSB1A2, and lac+RBS+phrAC+pSB1A2 (numbered #1, #2, #3) [Micah]
11. Prepared an overnight cultures of DH5α E. coli cells [Collin]

Outside Work / Discussion

Wednesday, August 2

Present: Zoe, Mark, Micah, Collin, Alex

Lab Work

1. Prepared glycerol stocks for each culture of DH5α E. coli cells with lac+RBS+uvsE+psB1A2, lac+RBS+Dsup+psB1A2, lac+RBS+phrAT+pSB1A2, and lac+RBS+phrAC+pSB1A2 (numbered #1, #2, #3) [Mark]
2. Miniprepped each culture of DH5α E. coli cells with lac+RBS+uvsE+psB1A2, lac+RBS+Dsup+psB1A2, lac+RBS+phrAT+pSB1A2, and lac+RBS+phrAC+pSB1A2 (numbered #1, #2, #3) [Zoe]
3. Measured the OD730 of the four cyanobacteria cultures [Mark]
• 4.783 (#1), 3.230 (#2), 3.110 (#3), 4.019 (#4)
4. Prepared an overnight culture of a DH5α E. coli colony with ligated lac+RBS+Dsup+RBS+blue chromoprotein+pSB1C3 [Micah]
5. Digested the previously ligated lac+RBS+phrAT+pSB1A2, lac+RBS+Dsup+pSB1A2, lac+RBS+phrAC+pSB1A2, and lac+RBS+uvsE+pSB1A2 to test if the ligations were correct [Mark, Micah]
6. Performed gel electrophoresis on the digested lac+RBS+phrAT+pSB1A2, lac+RBS+Dsup+pSB1A2, lac+RBS+phrAC+pSB1A2, and lac+RBS+uvsE+pSB1A2 [Mark]

Outside Work / Discussion

Thursday, August 3

Present: Zoe, Mark, Micah, Collin, Alex

Lab Work

1. Miniprepped the lac+RBS+Dsup+RBS+blue chromoprotein+pSB1C3 [Zoe]
2. Digested the pCB3C5 backbone, lac+RBS+Dsup+pSB1A2, lac+RBS+phrAT+pSB1A2, lac+RBS+phrAC+pSB1A2, lac+RBS+uvsE+pSB1A2, and RBS+Blue chromoprotein [Collin]
3. Measured the OD730 of the four cyanobacteria cultures [Mark]
• 5.052 (#1), 3.208 (#2), 3.156 (#3), 4.308 (#4)
4. Performed gel electrophoresis on the digested pCB3C5 backbone, lac+RBS+Dsup+pSB1A2, lac+RBS+phrAT+pSB1A2, lac+RBS+phrAC+pSB1A2, lac+RBS+uvsE+pSB1A2, and RBS+Blue chromoprotein [Mark, Collin]
5. Digested the previously ligated lac+RBS+Dsup+RBS+blue chromoprotein+pSB1C3 to test if the ligation was correct[Alex]
6. Performed gel electrophoresis on the digested lac+RBS+Dsup+RBS+blue chromoprotein+pSB1C3 [Alex]
7. Prepared three overnight cultures of DH5α E. coli cells with lac+RBS+Dsup+RBS+blue chromoprotein+pSB1C3 and with lac+RBS+phrAT+pSB1A2 [Micah]

Outside Work / Discussion

Friday, August 4

Present: Zoe, Mark, Micah, Collin, Alex

Lab Work

1. Miniprepped three cultures of lac+RBS+Dsup+RBS+blue chromoprotein+pSB1C3 (#2, #3, #4) and three cultures of lac+RBS+phrAT+pSB1A2 (#1, #2, #3) [Zoe]
2. Measured the OD730 of the four cyanobacteria cultures [Mark]
• 5.207 (#1), 3.122 (#2), 3.024 (#3), 4.709 (#4)
3. Prepared overnight cultures of DH5α E. coli cells with lac+RBS+uvsE+pSB1A2 and lac+RBS+phrAC+pSB1A2 [Mark]

Outside Work / Discussion

Saturday, August 5

Present: Zoe, Mark, Micah, Collin, Alex

Lab Work

1. Measured the OD730 of the four cyanobacteria cultures [Collin]
• 7.436 (#1), 3.031 (#2), 2.914 (#3), 4.865 (#4)
2. Miniprepped lac+RBS+uvsE+pSB1A2 and lac+RBS+phrAC+pSB1A2 [Collin]
3. Plated DH5α E. coli cells with lac+RBS+Dsup+RBS+Blue chromoprotein+pSB1C3 from its glycerol stock [Collin]

Outside Work / Discussion

Sunday, August 6

Present: Zoe, Mark, Micah, Collin, Alex

Lab Work

1. Measured the OD730 of the four cyanobacteria cultures [Mark]
• 5.473 (#1), 3.029 (#2), 2.650 (#3), 4.676 (#4)
2. Prepared an overnight cultures from the glycerol stock of DH5α E. coli cells with lac+RBS+Dsup+RBS+blue chromoprotein+pSB1C3 [Mark]
3. Digested lac+RBS+phrAC+pSB1A2 (3 samples: #4, #5, and #6), lac+RBS+uvsE+pSB1A2 (3 samples: #4, #5, and #6), lac+RBS+pSB1A2, phrAT+pSB1C3, phrAC+pSB1C3, uvsE+psB1C3, lac+RBS+Dsup+RBS+blue chromoprotein+pSB1C3, pSB4C5, and pSB3C5 [Collin, Mark]
4. Performed gel electrophoresis on the digested lac+RBS+phrAC+pSB1A2 (3 samples: #4, #5, and #6), lac+RBS+uvsE+pSB1A2 (3 samples: #4, #5, and #6), lac+RBS+pSB1A2, phrAT+pSB1C3, phrAC+pSB1C3, uvsE+psB1C3, lac+RBS+Dsup+RBS+blue chromoprotein+pSB1C3, pSB4C5, and pSB3C5 [Collin]

Outside Work / Discussion

Monday, August 7

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

Lab Work

1. Measured the OD730 of the four cyanobacteria cultures [Maddie]
• 5.820 (#1), 2.935 (#2), 2.564 (#3), 4.845 (#4)
2. Purified the digested uvsE, phrAC, lac+RBS+psB1A2, pSB4C5, and phrAT from their respective agarose gels [Collin]
3. Miniprepped lac+RBS+Dsup+RBS+blue chromoprotein+pSB1C3 [Micah]
4. Prepared competent DH5α E. coli cells [Micah, Maddie]
5. Transformed DH5α E. coli cells with RFP (BBa_J00450) [Maddie, Micah]
6. Ligated uvsE to lac+RBS+pSB1A2, phrAC to lac+RBS+pSB1A2, and lac+RBS+Dsup+RBS+blue chromoprotein to pSB4C5 [Collin]
7. Transformed DH5α E. coli cells with the ligated lac+RBS+pSB1A2, lac+RBS+phrAC+pSB1A2, and lac+RBS+Dsup+RBS+blue chromoprotein+pSB4C5 [Collin]
8. Digested phrAT+pSB1C3, lac+RBS+uvsE+pSB1A2 #5, pSB1C3+RBS+blue chromoprotein, and lac+pSB1C3 [Mark]
9. Performed gel electrophoresis on the digested phrAT+pSB1C3, lac+RBS+uvsE+pSB1A2 #5, pSB1C3+RBS+blue chromoprotein, and lac+pSB1C3 [Mark]
10. Prepared LB Media [Maddie]
11. Performed the UV irradiation test on DH5α cells with Dsup (with time intervals of 0, 2, 5, and 15 minutes) [Micah, Alex]

Outside Work / Discussion

Tuesday, August 8

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

Lab Work

1. Purified lac+RBS+uvsE+pSB1A2, RBS+blue chromoprotein, lac+pSB1C3, and lac+RBS+uvsE from their respective agarose gels [Collin]
2. Performed PCR on phrAT with Golden Gate (GG) compatible primers (Step 1) [Maddie]
3. Performed gel electrophoresis on the GG compatible phrAT PCR product [Maddie]
4. Purified the GG compatible phrAT PCR product from its agarose gel [Maddie]
5. Measured the OD730 of two cyanobacteria cultures [Mark]
• 6.465 (#1), 4.660 (#4)
• We decided to only continue measuring the the OD730 of growing cultures. Cultures #2 and #3 seem to have already plateaued
6. Performed Golden Gate assembly to ligate Dsup to pDeg_pTrc, uvsE to pDeg_pTrc, Dsup to pDeg_PCPC, and uvsE to pDeg_PCPC [Alex]
7. Ligated phrAT to lac+RBS+pSB1A2, RBS+blue chromoprotein to lac+RBS+Dsup+pSB1A2, RBS+blue chromoprotein to pSB1C3+lac+RBS+uvsE, and lac+RBS+uvsE to pSB4C5 [Mark]
8. Transformed DH5α E. coli cells with the ligated lac+RBS+phrAT+pSB1A2, lac+RBS+Dsup+RBS+blue chromoprotein+pSB1A2, lac+RBS+uvsE+RBS+blue chromoprotein+pSB1C3, and lac+RBS+uvsE+pSB4C5[Mark, Zoe]
9. Performed the UV irradiation test on DH5α cells with Dsup (with time intervals of 0, 15, 30, and 60 minutes) [Micah, Mark]

Outside Work / Discussion

Wednesday, August 9

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

Lab Work

1. Measured the OD730 of two cyanobacteria cultures [Collin]
• 6.434 (#1), 4.676 (#4)
2. Ligated phrAT to lac+RBS+pSB1A2, RBS+blue chromoprotein to lac+RBS+uvsE+pSB1A2, phrAC to lac+RBS+pSB1A2, and uvsE to lac+RBS+pSB1A2 [Collin]
3. Transformed lac+RBS+phrAT+pSB1A2, lac+RBS+uvsE+RBS+blue chromoprotein+pSB1A2, lac+RBS+phrAC+pSB1A2, and lac+RBS+uvsE+pSB1A2 into DH5α E. coli cells [Collin, Zoe]
4. Performed the UV irradiation test on DH5α cells with Dsup (with time intervals of 0, 30, 60, 90, and 120 minutes) [Micah, Mark, Collin, Zoe, Maddie]

Outside Work / Discussion

Thursday, August 10

Present: Mark, Micah, Maddie, Collin, Alex

Lab Work

1. Measured the OD730 of two cyanobacteria cultures [Maddie]
• 6.254 (#1), 4.047 (#4)
2. Performed gel electrophoresis on lac+RBS+uvsE+RBS+blue chromoprotein+pSB1C3, lac+RBS+Dsup+pSB4C5, Trc+Dsup, PCP+Dsup, Trc+uvsE, and PCP+uvsE [Mark, Collin]
3. Performed PCR to add golden gate ends onto phrAT [Alex]
4. Prepared overnight cultures of lac+RBS+pSB1C3, lac+RBS+uvsE+RBS+blue chromoprotein+pSB1A2 (3 cultures; #1, #2, #3), and lac+RBS+Dsup+RBS+blue chromoprotein+pSB1C3 [Alex]

Outside Work / Discussion

Friday, August 11

Present: Micah, Maddie

Lab Work

1. Miniprepped the 3 cultures with lac+RBS+uvsE+RBS+blue chromoprotein+pSB1A2 [Micah]
2. Digested lac+RBS+pSB1C3, uvsE+pSB1C3, phrAT+pSB1C3, phrAC+pSB1C3, Trc+Dsup, and PCP+uvsE [Maddie]
3. Performed gel electrophoresis on the digested lac+RBS+pSB1C3, uvsE+pSB1C3, phrAT+pSB1C3, phrAC+pSB1C3, Trc+Dsup, and PCP+uvsE [Maddie]
4. Tranformed plac Or2-62 (BBa_I12210) into DH5α E. Coli cells [Micah]

Outside Work / Discussion

Saturday, August 12

Present: Mark, Micah, Collin, Alex

Lab Work

Outside Work / Discussion

1. Met up with the Missouri S&T iGEM Team in Rolla Missouri [Alex, Collin, Mark, Micah]

Sunday, August 13

Present: Maddie, Alex

Lab Work

1. Gel purified lac+RBS+pSB1C3,lac+RBS+phrAC+pSB1C3, and lac+RBS+uvsE+pSB1C3 [Maddie]
2. Ligated lac+RBS+uvsE and lac+RBS+phrAC [Alex]
3. Transformed lac+RBS+uvsE and lac+RBS+phrAC into DH5α E. Coli cells [Alex]

Outside Work / Discussion

Monday, August 14

Present: Mark, Micah, Maddie, Alex

Lab Work

1. Digested phrAT+pSB1C3 [Maddie, Mark]
2. Prepared liquid cultures of lac+RBS+uvsE+pSB1C3 and lac+RBS+phrAC+pSB1C3 (3 cultures of each; #20, #21, #22) [Alex, Mark]
3. Performed the UV irradiation test on DH5α cells with Dsup (with time intervals of 0, 1, 2, 3, and 4 hours) [Micah, Mark, Maddie]
4. Performed PCR to add Golden Braid ends to Dsup [Alex]

Outside Work / Discussion

Tuesday, August 15

Present: Mark, Micah, Maddie, Alex

Lab Work

1. Counted the colonies on the plates from the previous day's UV irradiation test [Micah, Mark, Alex]
2. Miniprepped the overnight cultures of lac+RBS+uvsE+pSB1C3 and lac+RBS+phrAC+pSB1C3 [Maddie]
3. Digested phrAT+pSB1C3, lac+RBS+phrAC+pSB1C3, and lac+RBS+uvsE [Mark]
4. Performed gel electrophoresis on the digested phrAT+pSB1C3, lac+RBS+phrAC+pSB1C3, and lac+RBS+uvsE [Mark]
5. Prepared liquid cultures of induced lac+RBS+Dsup+RBS+Blue chromoprotein+pSB1C3, non-induced lac+RBS+Dsup+RBS+Blue chromoprotein+pSB1C3, control DH5α E. Coli cells and lac+RBS+uvsE [Alex]
6. Performed PCR to add golden gate compatible ends to phrAT [Maddie]
7. Prepared LB+CM mini plates [Mark]

Outside Work / Discussion

Wednesday, August 16

Present: Zoe, Mark, Micah, Maddie, Alex

Lab Work

1. Performed gel purification on phrAT+pSB1C3 [Maddie]
2. Prepared 1200 mL of LB+Agar [Maddie]
3. Performed the UV irradiation test on Dsup and the control [Micah, Mark]
4. Performed restriction digestion on lac+RBS+uvsE+pSB1C3, lac+RBS+phrAC+pSB1C3, and lac+RBS+pSB1C3 [Maddie, Mark]
5. Performed gel electrophoresis on the digested DNA [Mark]
6. Ligated lac+RBS+uvSE+pSB1C3 with lac+RBS+blue chromoprotein, lac+RBS+pSB1C3 with blue chromoprotein, and lac+RBS+pSB1C3 with phrAT [Zoe, Alex]

Outside Work / Discussion

Thursday, August 17

Present: Zoe, Mark, Micah, Maddie, Alex

Lab Work

1. Digested lac+RBS+phrAC+pSB1C3 [Maddie]
2. Counted the colonies on the plates from the previous day's UV irradiation test [Micah, Mark, Alex, Zoe]
3. Performed a PCR gradient of uvsE for GoldenBraid [Maddie]
4. Prepared overnight cultures of Dsup+BCP, lac+RBS+phrAT+pSB1C3, and RBS+BCP+pSB1C3 [Mark]

Outside Work / Discussion

Friday, August 18

Present: Zoe, Mark, Micah, Maddie, Alex

Lab Work

1. Prepared glycerol stocks of DH5α E. coli cells that contained lac+RBS+phrAT+pSB1C3, lac+RBS+BCP+pSB1C3, and lac+RBS+Dsup+RBS+BCP+pSB1C3 [Mark]
2. Miniprepped lac+RBS+phrAT+pSB1C3 [Zoe]
3. Performed a UV irradiation test for Dsup and the Blue chromoprotein control [Micah, Mark]
4. Performed PCR for uvsE [Maddie, Zoe]
5. Digested lac+RBS+phrAT+pSB1C3 [Alex]
6. Ran a gel electrophoresis for the digested lac+RBS+phrAT+pSB1C3 [Mark]

Outside Work / Discussion

Saturday, August 19

Present: Zoe, Maddie, Mark

Lab Work

1. Counted colonies on the plates from the UV irradiation test on Dsup [Zoe, Maddie, Mark]

Outside Work / Discussion

Sunday, August 20

Present: Micah

Lab Work

1. Prepared overnight cultures of DH5α E. coli cells with lac+RBS+blue chromoprotein+pSB1C3, lac+RBS+Dsup+RBS+blue chromoprotein+pSB1C3, and lac+RBS+uvsE+RBS+blue chromoprotein+pSB1C3 (#1) [Micah]

Outside Work / Discussion

Monday, August 21

Present:Mark, Micah

Lab Work

1. Prepared overnight cultures of DH5α E. coli cells with pSB1C3+lac+RBS+phrAC+RBS+blue chromoprotein (2 cultures, #1 and #2), pSB1C3+lac+RBS+blue chromoprotein, and pSB1C3+lac+RBS+Dsup+RBS+blue chromoprotein [Mark]
2. Miniprepped DH5α E. coli cell cultures with lac+RBS+blue chromoprotein+pSB1C3, lac+RBS+Dsup+RBS+blue chromoprotein+pSB1C3, and lac+RBS+uvsE+RBS+blue chromoprotein+pSB1C3 (#1) [Micah]

Outside Work / Discussion

1. Watched the Great American Eclipse of 2017 [Micah, Mark, Zoe, Maddie, Alex, Collin]

Tuesday, August 22

Present: Mark, Zoe, Micah, Alex, Maddie

Lab Work

1. Miniprepped lac+RBS+phrAC+RBS+BCP+pSB1C3 [Zoe]
2. Gel purified lac+RBS+phrAT+pSB1C3 [Maddie]
3. Prepared LB+CM plates [Mark]
4. Performed the UV irradiation test on uvsE, phrAC, and the blue chromoprotein control [Micah, Mark]

Outside Work / Discussion

Wednesday, August 23

Present: Zoe, Maddie, Mark, Alex, Micah

Lab Work

1. Counted the colonies on the plates from the previous day's UV irradiation test [Micah, Alex, Mark, Zoe, Maddie]
2. Streaked lac+RBS+uvsE+RBS+BCP+pSB1C3 and lac+RBS+phrAC+RBS+BCP+pSB1C3 onto LB+CM plates [Micah]
3. Ligated lac+RBS+phrAT+pSB1C3 with RBS+BCP [Micah]
4. Transformed DH5α E. coli cells with lac+RBS+phrAT+RBS+BCP+pSB1C3 [Mark]

Outside Work / Discussion

Thursday, August 24

Present:Micah

Lab Work

1. Prepared overnight cultures of DH5α E. coli cells with lac+RBS+phrAT+RBS+BCP+pSB1C3 {Micah]

Outside Work / Discussion

Friday, August 25

Present: Zoe

Lab Work

1. Miniprepped lac+RBS+phrAT+RBS+BCP+pSB1C3 [Zoe]

Outside Work / Discussion

Saturday, August 26

No work done today!

Sunday, August 27

No work done today!

Monday, August 28

No work done today!

Tuesday, August 29

No work done today!

Wednesday, August 30

No work done today!

Thursday, August 31

Present: Collin

Lab Work

1. Prepared overnight cultures from glycerol stock of lac+RBS+BCP+pSB1C3 [Collin]

Outside Work / Discussion

Friday, September 1

No work done today!

Saturday, September 2

No work done today!

Sunday, September 3

No work done today!

Monday, September 4

No work done today!

Tuesday, September 5

No work done today!

Wednesday, September 6

No work done today!

Thursday, September 7

No work done today!

Friday, September 8

No work done today!

Saturday, September 9

No work done today!

Sunday, September 10

No work done today!

Monday, September 11

No work done today!

Tuesday, September 12

No work done today!

Wednesday, September 13

No work done today!

Thursday, September 14

Present:Mark

Lab Work

1. Transformed Lac+RBS+BCP+pSB1C3 into E.coli cells [Mark]

Outside Work / Discussion

Friday, September 15

No work done today!

Saturday, September 16

Present:Maddie

Lab Work

1. Started a cyanobacteria culture [Maddie]
2. Performed GoldenBraid PCR for uvsE, phrAC, phrAT, and Dsup [Maddie]

Outside Work / Discussion

Sunday, September 17

No work done today!

Monday, September 18

No work done today!

Tuesday, September 19

No work done today!

Wednesday, September 20

No work done today!

Thursday, September 21

No work done today!

Friday, September 22

No work done today!

Saturday, September 23

No work done today!

Sunday, September 24

No work done today!

Monday, September 25

No work done today!

Tuesday, September 26

No work done today!

Wednesday, September 27

No work done today!

Thursday, September 28

Present: Collin

Lab Work

1. Refreshed Cyanobacteria culture [Collin]

Outside Work / Discussion

Friday, September 29

No work done today!

Saturday, September 30

Present:Collin, Micah, Mark

Lab Work

1. Performed PCR on Dsup, uvsE, phrAC, and phrAT for the GoldenBraid assembly [Collin]
2. Performed the UV irradiaton test for uvsE, phrAC, and the control [Micah, Mark, Collin]

Outside Work / Discussion

Sunday, October 1

No work done today!

Monday, October 2

Present: Collin

Lab Work

1. Measured the ODs of the Cyanobacteria culture [Collin]
• 3.413 (#1), 0.1370 (#2)

Outside Work / Discussion

Tuesday, October 3

Present:Maddie

Lab Work

1. Measured the OD of the cyanobacteria culture [Maddie]
• 0.1452 (#2)

Outside Work / Discussion

Wednesday, October 4

Present:Maddie

Lab Work

1. Measured the OD of the cyanobacteria culture [Maddie]
• 0.3725 (#2)

Outside Work / Discussion

Thursday, October 5

Present:Maddie

Lab Work

1. Measured the OD of the cyanobacteria culture [Maddie]
• 0.6746 (#2)

Outside Work / Discussion

Friday, October 6

Present:Mark

Lab Work

1. Prepared LB Media [Mark]

Outside Work / Discussion

Saturday, October 7

Present:Mark, Maddie

Lab Work

1. Prepared LB Agar [Mark]
2. Prepared overnight cultures of BCP, uvsE, and phrAC [Maddie]

Outside Work / Discussion

Sunday, October 8

Present:Mark, Micah

Lab Work

1. Prepared for a UV irradiation test for uvsE, phrAC, and BCP control [Mark, Micah]

Outside Work / Discussion

Monday, October 9

Present: Collin

Lab Work

1. Measured the OD of the cyanobacteria culture [Maddie]
• 3.1760 (#2)

Outside Work / Discussion

Tuesday, October 10

Present: Collin

Lab Work

1. Digested neomycin phosphotransferase (nptII) and pSB1C3 [Colin]
2. Ran a gel electrophoresis for the digested nptII and pSB1C3 [Collin]
3. Transformed uvsE+BCP into E. coli [Collin]

Outside Work / Discussion

Wednesday, October 11

Present: Collin

Lab Work

1. Made Kanamycin plates [Collin]
2. Prepared bacterial stabs of Dsup, phrAC, and phrAT for the UChicago team [Collin]

Outside Work / Discussion

Thursday, October 12

No work done today!

Friday, October 13

No work done today!

Saturday, October 14

No work done today!

Sunday, October 15

No work done today!

Monday, October 16

Present: Mark

Lab Work

1. Gel purified pSB1C3 and nptII [Mark]
2. Ligated pSB1C3 and nptII [Mark]
3. Transformed pSB1C3+nptII [Mark]

Outside Work / Discussion

Tuesday, October 17

No work done today!

Wednesday, October 18

No work done today!

Thursday, October 19

Present: Collin

Lab Work

1. Streaked phrAT, phrAC, BCP, uvsE, and BCP [Collin]

Outside Work / Discussion

Friday, October 20

Present: Collin

Lab Work

1. Transformed lac+RBS+Dsup+BCP into E.coli cells [Collin]
2. Prepared cultures of lac+RBS+Dsup, lac+RBS+BCP, and lac+RBS+uvsE [Collin]

Outside Work / Discussion

Saturday, October 21

Present: Micah

Lab Work

1. Transformed medium promoter+medium RBS (BBa_K608006) into E. coli [Micah]
2. Prepared cultures from previous transformation [Micah]

Outside Work / Discussion

Sunday, October 22

Present:Collin

Lab Work

1. Made glycerol stocks of lac+RBS+Dsup+RBS+BCP+pSB1C3 [Collin]

Outside Work / Discussion

Monday, October 23

Present: Collin

Lab Work

1. Miniprepped lac+RBS+BCP+pSB1C3 [Collin]

Outside Work / Discussion

Tuesday, October 24

Present: Collin, Mark

Lab Work

1. Prepared two overnights of Dsup and one of BCP [Collin]
2. Digested nptII and med promoter + med RBS + pSB1C3 [Mark]
3. Ran gel electrophoresis on the digested DNA [Mark]

Outside Work / Discussion

Wednesday, October 25

Present:Mark, Collin, Micah, Maddie, Zoe

Lab Work

1. Performed the UV irradiation test on Dsup and the control BCP [Micah, Collin, Maddie, Zoe]
2. Gel purified nptII and med promoter + med RBS + pSB1C3 [Mark]
3. Ligated nptII to the med promoter + med RBS + pSB1C3 [Mark, Collin]
4. Transformed the ligated DNA into E. coli cells [Collin, Mark]

Outside Work / Discussion

Thursday, October 26

Present: Micah

Lab Work

1. Prepared an overnight culture of med promoter + med RBS + nptII [Micah]

Outside Work / Discussion

Friday, October 27

Present: Micah, Alex

Lab Work

1. Miniprepped the med promoter + med RBS + nptII [Micah]
2. Prepared the DNA to be sent to the registry [Alex, Micah]

Outside Work / Discussion

Saturday, October 28

No work done today!

Sunday, October 29

No work done today!

Monday, October 30

No work done today!

Tuesday, October 31

No work done today!