Difference between revisions of "Team:WashU StLouis/Notebook"
| Line 873: | Line 873: | ||
<p><strong> Lab Work </strong></p> | <p><strong> Lab Work </strong></p> | ||
<ol> | <ol> | ||
| − | <li> 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)</li> | + | <li> 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) <em>[Micah]</em></li> |
| − | <li> Prepared lab materials ( | + | <ul> |
| + | <li><img src="https://static.igem.org/mediawiki/2017/1/12/T--WashU_StLouis--2017-06-16_Transformation_of_ligated_BBa_B0034_and_BBa_R0010.jpg" style="height:11vw;width:11vw"/></li> | ||
| + | <li> Prepared lab materials (reagents, E. coli strains) for our lesson to the students part of WashU's Pre-Engineering Institute </li> | ||
</ol> | </ol> | ||
<p><strong> Outside Work / Discussion </strong><p> | <p><strong> Outside Work / Discussion </strong><p> | ||
| Line 880: | Line 882: | ||
<li> Identified composite part in registry (BBa_J04500) that already consists of BBa_B0034 </li> | <li> Identified composite part in registry (BBa_J04500) that already consists of BBa_B0034 </li> | ||
<li> Planned out presentation and lab for the Pre-Engineering Institute students on June 20 </li> | <li> Planned out presentation and lab for the Pre-Engineering Institute students on June 20 </li> | ||
| + | <ul> | ||
| + | <li>Set up lab stations with vortex machines, pipet tips, and micropipettors </li> | ||
| + | </ul> | ||
</div> | </div> | ||
</div> | </div> | ||
Revision as of 21:26, 18 June 2017
Notebook
Click on a date to see what we did on that day!
| June 2017 | ||||||
|---|---|---|---|---|---|---|
| Sunday | Monday | Tuesday | Wednesday | Thursday | Friday | Saturday |
| 1 | 2 | 3 | ||||
| 4 | 5 | 6 | 7 | 8 | 9 | 10 |
| 11 | 12 | 13 | 14 | 15 | 16 | 17 |
| 18 | 19 | 20 | 21 | 22 | 23 | 24 |
| 25 | 26 | 27 | 28 | 29 | 30 | |
Thursday, June 1
Present: Micah, Maddie, Alex
Lab Work
- Prepared LB Media [Micah, Maddie, Alex]
- Re-suspended DNA (D. Radiodurans Uracil DNA Glycosylate 2) from iGEM kit [Micah, Maddie, Alex]
- Transformed Uracil DNA Glycosylate 2 in psB1C3 plasmid into MHD42 competent cells (Practice transformation) [Micah, Maddie, Alex]
- Prepared LB Agar [Micah, Maddie, Alex]
- Prepared overnight culture to make competent cells (MHD42) [Micah, Maddie, Alex]
Outside Work / Discussion
Friday, June 2
Present: Micah, Maddie
Lab Work
- Prepared MHD42 competent cells [Micah, Maddie]
- 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
- Prepared TSS Buffer [Micah, Maddie]
Outside Work / Discussion
Saturday, June 3
No Work!
Sunday, June 4
No Work!
Monday, June 5
Present: Micah, Maddie, Alex, Mark, Collin
Lab Work
- Prepared LB + Chloramphenicol (CM) plates [Micah, Maddie, Mark, Collin]
- Prepared Ampicillin solution to be used for plates in the future [Micah, Maddie, Mark, Collin]
- Made more LB Agar [Alex]
Outside Work / Discussion
- Discussed shifting focus from Dsup gene to a variety of UV radiation resistance gene [Micah, Maddie, Mark, Collin, Alex]
- Found more genes to compare to Dsup (i.e. phrA in tardigrades and cyanobacteria) [Micah, Maddie, Mark, Collin, Alex]
- Met with Dr. Brennan to discuss updates [Micah, Maddie, Mark, Collin, Alex]
Tuesday, June 6
Present: Micah, Maddie, Alex, Mark, Collin
Lab Work
- Prepared DH5α competent cells [Micah, Maddie, Mark, Collin, Alex]
- Tested MHD42 cells for competency [Micah, Maddie, Mark, Collin, Alex]
- Tested DH5α cells for competency [Micah, Maddie, Mark, Collin, Alex]
Outside Work / Discussion
- 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.
- 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
- Checked competency test for MHD42 cells [Micah, Maddie, Mark, Collin, Alex]
- Test was successful!
-
- Checked competency test for DH5α [Micah, Maddie, Mark, Collin, Alex]
- Test showed that the cells were competent but had a low transformation efficiency
-
- Prepared LB + Ampicillin (Amp) plates [Micah, Mark, Collin]
- Resuspeded parts BBa_B0034, BBa_R0010, and BBa_K1499200 from current and past distribution kits [Maddie, Alex]
- Transformed part BBa_B0034 (with plasmid psB1A2) into MHD42 competent cells [Maddie, Alex]
- Transformed part BBa_R0010 (with plasmid psB1C3) into MHD42 competent cells [Maddie, Alex]
- Transformed part BBa_K1499200 (with plasmid psB1C3) into MHD42 competent cells [Maddie, Alex]
- Prepared overnight culture of DH5α competent cells [Mark, Collin]
Outside Work / Discussion
- Discussed modelling ideas [Micah, Maddie, Mark, Collin]
- Learned how to design primers from Eugene [Micah, Maddie, Mark, Collin, Alex]
Thursday, June 8
Present: Alex, Maddie, Micah, Collin, Mark, Zoe
Lab Work
- Checked the results of the transformations of BBa_B0034, BBa_R0010, and BBa_K1499200 into MHD42 cells [Alex, Micah, Zoe]
-
- Made 900 mL of LB media [Collin, Mark, Zoe]
- Prepared DH5α competent cells [Micah, Zoe, Collin, Mark]
- Tested competency of the prepared DH5 [Maddie, Zoe, Mark]
- Prepared three separate overnight cultures of MHD42 cells with parts BBa_B0034, BBa_R0010, and BBa_K1499200 [Alex, Zoe]
Outside Work / Discussion
- Attended Energy, Environmental, and Chemical Engineering (EECE) summer interns orientation [Collin, Mark, Maddie, Zoe, Alex, Micah]
- Discussed each member's designated role and plans for the future [Collin, Mark, Maddie, Zoe, Alex, Micah]
- Made a team calendar [Collin, Mark, Maddie, Zoe, Alex, Micah]
Friday, June 9
Present: Maddie, Zoe, Micah, Mark, Collin, Alex
Lab Work
- Checked results for competency of DH5α cells [Alex, Mark, Micah, Maddie, Zoe, Collin}
- Test was successful! The cells had a moderate transformation efficiency.
-
- 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)
- Made 400 mL of LB Agar [Zoe]
- Made 11 Chloramphenicol (CM) + LB plates [Collin, Mark, Alex]
Outside Work / Discussion
- Researched modelling ideas [Micah]
Saturday, June 10
Present: Zoe
Lab Work
- 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
- 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
- Transformed part BBa_E004 (GFP) into MHD42 competent cells [Zoe, Micah]
- Miniprepped the 3 separate cultures of MHD42 cells that contained BBa_R0010, BBa_B0034, and BBa_K1499200 [Alex, Collin]
- Measured concentration of DNA using the NanoDrop [Alex, Collin]
- Performed the Calibration Protocol for the Interlab study by measuring the absorbances of distilled water and Ludox HS-40 [Maddie, Mark]
- Measured the fluorescence of fluorescein serial dilutions for the Interlab study [Mark, Maddie]
Outside Work / Discussion
- Filled out Forms 1 and 2 for the Interlab study [Maddie, Mark]
- Studied BioBrick assembly methods [Alex, Micah]
- 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
- Checked for the transformation of part BBa_E0040 (GFP) into MHD42 competent cells [Micah]
- Miniprepped the DNA for parts BBa_R0010 and BBa_B0034 from the MHD42 cells that were cultured overnight [Zoe, Micah]
- Measured concentration of DNA using the NanoDrop [Micah, Zoe]
- 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
- Prepared overnight culture of the MHD42 cells with BBa_E0040 (GFP) [Micah, Zoe]
Outside Work / Discussion
- 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
- Miniprepped 4 tubes of part BBa_E0040 (GFP) [Zoe, Micah]
- Measured concentration of DNA using the NanoDrop [Micah, Mark, Zoe]
- Performed restriction digest of parts BBa_B0034 and BBa_R0010 [Alex, Collin]
- Performed gel electrophoresis of digested BBa_B0034 and BBa_R0010 [Alex, Collin]
- Prepared LB + Ampicillin plates [Zoe, Micah, Mark]
Outside Work / Discussion
Thursday, June 15
Present: Mark, Zoe, Alex, Maddie, Collin, Micah
Lab Work
- Purified the digested BBa_R0010 and BBa_B0034 from the agarose gel [Collin, Alex, Zoe]
- Ligated the lac promoter from BBa_R0010 to the RBS and pSB1A2 backbone of BBa_B0034 [Alex]
- Performed restriction digest of parts BBa_B0034 and BBa_R0010 [Zoe, Collin]
- Prepared LB Agar [Zoe]
Outside Work / Discussion
- Researched modelling ideas [Micah, Maddie]
- Researched possible parts in the registry to improve [Mark]
- 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
- 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
Outside Work / Discussion
- Identified composite part in registry (BBa_J04500) that already consists of BBa_B0034
- Planned out presentation and lab for the Pre-Engineering Institute students on June 20
- Set up lab stations with vortex machines, pipet tips, and micropipettors
Saturday, June 17
Lab Work
Outside Work / Discussion
Sunday, June 18
Lab Work
Outside Work / Discussion
Monday, June 19
Lab Work
Outside Work / Discussion
Tuesday, June 20
Lab Work
Outside Work / Discussion
Wednesday, June 21
Lab Work
Outside Work / Discussion
Thursday, June 22
Lab Work
Outside Work / Discussion
Friday, June 23
Lab Work
Outside Work / Discussion
Saturday, June 24
Lab Work
Outside Work / Discussion
Sunday, June 25
Lab Work
Outside Work / Discussion
Monday, June 26
Lab Work
Outside Work / Discussion
Tuesday, June 27
Lab Work
Outside Work / Discussion
Wednesday, June 28
Lab Work
Outside Work / Discussion
Thursday, June 29
Lab Work
Outside Work / Discussion
Friday, June 30
Lab Work
Outside Work / Discussion
Saturday, July 1
Lab Work
Outside Work / Discussion
Sunday, July 2
Lab Work
Outside Work / Discussion
Monday, July 3
Lab Work
Outside Work / Discussion
Tuesday, July 4
Lab Work
Outside Work / Discussion
Wednesday, July 5
Lab Work
Outside Work / Discussion
