Team:WashU StLouis/Daily

June 2018
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Friday, June 1

No work done today!

Saturday, June 2

No work done today!

Sunday, June 3

No work done today!

Monday, June 4

Present: Cam, Diva, Elizabeth, Havisha, Kyle

  • Researched different resistance genes to identify ones that are sequenced and applicable to the project [Elizabeth, Diva, Cam]
  • Studied glucosamine detection mechanisms to signal the presence the presence of fungi [Havisha]
  • Planned trip to Uganda and human practices potential abroad [Kyle]

Tuesday, June 5

Present: Cam, Diva, Elizabeth, Havisha, Kyle

  • Researched different resistance genes to identify ones that are sequenced and applicable to the project [Elizabeth, Diva]
  • Compared different aspects of Sr genes [Cam]
  • Examined a protocol for rapid cloning of plant disease resistance genes [Diva]
  • Studied glucosamine detection mechanisms to signal the presence the presence of fungi [Havisha, Diva]
  • Planned trip to Uganda and potential human practices abroad [Kyle]

Wednesday, June 6

Present: Cam, Diva, Elizabeth, Havisha, Kyle

  • Examined lengths of resistance gene sequences to begin ordering material [Elizabeth]
  • Studied fungal spore traps to limit specificity to Puccinia graminis [Havisha]
  • Investigated different detection and reporting mechanisms for reporting information with a device [Cam, Diva]
  • Planned trip to Uganda and potential human practices abroad [Kyle]

Thursday, June 7

Present: Cam, Diva, Elizabeth, Havisha, Kyle

  • Met with Dr. Brennan to redefine project goals and timeline [Cam, Diva, Elizabeth, Havisha, Kyle]
  • Reviewed videos from the BGRI to determine locations of wheat rust fungus prevalence [Elizabeth]
  • Prepared presentation for Microsoft partnership meeting and consulted Dr. Brennan on areas for improvement [Cam]
  • Studied fungal spore traps to limit specificity to Puccinia graminis [Havisha]
  • Continued research on various detection mechanisms [Diva]
  • Planned trip to Uganda and potential human practices abroad [Kyle]

Friday, June 8

Present: Cam, Diva, Elizabeth, Havisha

  • Met with a representative from Microsoft to establish a technology partnership [Cam]
  • Reviewed papers regarding resistance gene interactions (Sr35, Sr22, and Sr45) [Elizabeth]
  • Considered phage related detection mechanisms, alongside the use of CRISPR/CAS9 [Diva]
  • Studied fungal spore traps to select only ones of Puccinia graminis [Havisha]

Saturday, June 9

No work done today!

Sunday, June 10

No work done today!

Monday, June 11

Present: Cam, Diva, Elizabeth, Havisha

  • Prepared a summary of the global impact of rust for Microsoft [Cam]
  • Planned for the use of Sr33 and Sr13 [Elizabeth]
  • Studied compounds unique to germinated P. graminis and infectious structures [Havisha]
  • Investigated the DNA repair mechanism of eukaryotes (fungi in particular) [Diva]

Tuesday, June 12

Present: Cam, Diva, Elizabeth, Havisha

  • Revised our project abstract to incorporate changes made over the past week [Cam, Diva, Elizabeth, Havisha]
  • Conducted a marketing brainstorming session [Cam, Diva, Elizabeth, Havisha]
  • Researched Sr50 and truncating resistance genes [Elizabeth]
  • Compiled a research summary for Microsoft [Cam]
  • Examined different detection mechanisms for ribitol [Havisha]
  • Investigated the DNA repair mechanism of eukaryotes (fungi in particular) [Diva]

Wednesday, June 13

Present: Cam, Diva, Elizabeth, Havisha, Kyle

  • Met with Dr. Brennan to assess abstract and project design in preparation to meet with Monsanto [Cam, Diva, Elizabeth, Kyle, Havisha]
  • Compiled gene sequences needed for the project [Elizabeth]
  • Began developing the wiki [Havisha]
  • Identified the sequence for a gene induced by ribotin to transfer into a plasmid and transform E. coli with [Havisha]
  • Investigated the DNA repair mechanism of eukaryotes (fungi in particular) [Diva]
  • Planned trip to Uganda and potential human practices abroad [Kyle]

Thursday, June 14

Present: Cam, Diva, Elizabeth, Havisha

  • Connected with many iGEM teams through social media [Elizabeth, Cam]
  • Developed the wiki template and daily notebook log pages [Havisha]
  • Attempted to identify promoter sequences induced by ribotin [Diva]
  • Investigated truncating Sr50 and fusion proteins [Elizabeth]

Friday, June 15

Present: Cam, Diva, Elizabeth, Havisha

  • Developed footer and human practices page of the wiki [Havisha]
  • Conducted a call with a grain farmer for fundraising and human practices efforts [Cam]
  • Organized presentation in preparation for a meeting with Monsanto [Cam]
  • Investigated Sr35 and fusion proteins [Elizabeth]
  • Met with Jeff to discuss logistics of project [Havisha, Elizabeth]

Saturday, June 16

No work done today!

Sunday, June 17

No work done today!

Monday, June 18

Present: Cam, Diva, Elizabeth, Havisha

  • Worked on presentation in preparation for meeting with Monsanto [Cam, Diva, Elizabeth, Havisha]
  • Prepared PBS buffer and LB Agar plates in preparation for interlab [Cam, Diva, Elizabeth, Havisha]
  • Developed technology partnership with Microsoft. [Cam]

Tuesday, June 19

Present: Cam, Diva, Elizabeth, Havisha

  • Met with Dr. Brennan to prepare for Monsanto presentation. [Cam, Diva, Elizabeth, Havisha]
  • Prepared LB buffer and began overnight culture. [Cam, Diva, Elizabeth, Havisha]

Control agar + CM plates made on 6/18

Wednesday, June 20

Present: Cam, Diva, Elizabeth, Havisha

  • Prepared chemically competent DH5α E. coli cells [Cam, Diva, Elizabeth, Havisha]
  • Developed list of protocols for the wiki [Havisha, Diva]

Thursday, June 21

Present: Cam, Diva, Elizabeth, Havisha

  • Toured Monsanto and Pfizer facilities [Cam, Diva, Elizabeth, Havisha]
  • Presented to Monsanto researchers to solicit advice and feedback from people in the field [Cam, Diva, Elizabeth, Havisha]

Friday, June 22

Present: Cam, Diva, Elizabeth, Havisha

  • Identified gene sequences for ribitol metabolism [Havisha]
  • Began investigating LAMP and primers [Diva]
  • Studied protein-protein interactions of CC-NLR proteins [Diva, Elizabeth]
  • Continued with fundraising efforts and coordinating partnership with Monsanto [Cam]

Saturday, June 23

No work done today!

Sunday, June 24

No work done today!

Monday, June 25

Present: Cam, Diva, Havisha

  • Worked on Day 1 of the interlab study protocol [Cam, Diva, Havisha]

Tuesday, June 26

Present: Cam, Diva, Havisha

  • Troubleshooted problems with Day 1 transformation [Cam, Diva, Havisha]
  • Corresponded with Microsoft regarding digital lab notebook [Cam]
  • Solidified gene sequences needed for general detection mechanism [Havisha]
  • Began filling out iGEM safety form part 1 [Diva]

Transformed DH5α from interlab studies day one on 6/25

Wednesday, June 27

Present: Cam, Diva, Havisha

  • Wrote project overview, background, and general detection mechanism summary for wiki [Havisha]
  • Completed safety form [Diva, Havisha]
  • Made LB Agar Media [Diva, Havisha]
  • Started an overnight culture of DH5α [Diva, Havisha]

Thursday, June 28

Present: Diva, Elizabeth, Havisha

  • Submitted safety form [Diva]
  • Plated LB Agar plates [Diva, Elizabeth, Havisha]
  • Made chemically competent DH5α [Diva, Elizabeth, Havisha]
  • Developed banners for wiki pages [Havisha]

Friday, June 29

Present: Diva, Elizabeth, Havisha

  • Worked on members’ introductions for the wiki [Diva, Elizabeth, Havisha]
  • Tested competency of cells prepared on 6/28 [Diva, Elizabeth, Havisha]

Control agar plate made on 6/28

Saturday, June 30

No work done today!

Sunday, July 1

Present: Diva, Havisha

  • Performed calibration protocol for interlab study [Diva, Havisha]
  • Made LB Agar + CM plates [Diva, Havisha]

Control agar plate with non-transformed competent cells plated on 6/29

Agar + CM plates with cells transformed with iGEM test kit from 6/29

Monday, July 2

Present: Diva, Elizabeth, Havisha

  • ploop

Tuesday, July 3

Present: Diva, Elizabeth, Havisha

  • ploop

Wednesday, July 4

Present: Cam, Diva, Elizabeth

  • ploop

Thursday, July 5

Present: Cam, Diva, Elizabeth

  • ploop

Friday, July 6

Present: Cam, Diva, Elizabeth, Kyle

  • ploop

Saturday, July 7

No work done today!

Sunday, July 8

No work done today!

Monday, July 9

Present: Cam, Diva, Elizabeth, Havisha, Kyle

  • ploop

Tuesday, July 10

Present: Cam, Diva, Elizabeth, Havisha, Kyle

  • ploop

Wednesday, July 11

Present: Cam, Diva, Elizabeth, Havisha, Kyle

  • ploop

Thursday, July 12

Present: Cam, Diva, Elizabeth, Havisha, Kyle

  • ploop

Friday, July 13

Present: Cam, Diva, Elizabeth, Kyle

  • ploop

Saturday, July 14

No work done today!

Sunday, July 15

No work done today!

Monday, July 16

Present: Cam, Diva, Elizabeth, Havisha, Kyle

  • ploop

Tuesday, July 17

Present: Cam, Diva, Elizabeth, Havisha, Kyle

  • ploop

Wednesday, July 18

Present: Cam, Diva, Elizabeth, Havisha, Kyle

  • ploop

Thursday, July 19

Present: Cam, Diva, Elizabeth, Havisha, Kyle

  • ploop

Friday, July 20

Present: Cam, Diva, Elizabeth, Havisha, Kyle

  • ploop

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!