Team:WashU StLouis/Notebook

Notebook

Reading about labwork is almost as fun as doing labwork

June
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5 6 7 8 9 10 11
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19 20 21 22 23 24 25
26 27 28 29 30


No lab work done



No lab work done



  • First day in lab!
  • Made 1L of LB Media


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  • Performed gDNA Extraction on E. Coli MG1655 and Synechocystis 6803


  • Designed PCR primers for pgk, pck, fldA, petF, ATP Synthase 1, and ATP Synthase 2


No lab work done



  • Primers Arrived
  • Ran PCR on ATP Synthase 2 , pgk, fldA, petF, and pdCas9 plasmid
  • Ran all PCR products on gel and recovered ATP Synthase 2, fldA, and petF
  • Ran gradient PCR on pdCas9 plasmid


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  • Made and ran gel for pdCas9
  • Ran PCR on ATP Synthase 1, pgk, and pck
  • Performed gel extraction on yesterday’s ATP Synthase 2
  • Ran pck, pgk, and yesterday’s gradient pdCas9 PCR products on gel and recovered all genes
  • Performed gel extraction on pdCas9, fldA, petF
  • Ran PCR on psc101 and psc102 plasmid
  • Ran psc101 and psc102 PCR products on gel - were recovered
  • Ran gradient PCR on ATP Synthase 1
  • Made agar plates (forgot the antibiotic)
  • Ran golden gate one pot assembly for fldA petF genes and the pdCas9 plasmid


  • Ran ATP Synthase 1 PCR products on gel - no bands seen
  • Gel Extraction for pgk, pck, psc101, and psc102 plasmid
  • Ran PCR on ATP Synthase 1 (3rd times the charm)
  • Ran PCR products on gel - WE SAW BANDS! ATP SYNTHASE 1 RECOVERED
  • Reran PCR on pgk, pck, psc101, and psc102 plasmid because we did not get high enough concentration during gel Extraction
  • Made new agar plates (with the chloramphenicol)
  • Transformed the petF, fldA plasmids into competent cells
  • Plated colonies on agar plates and set in incubator


  • Checked for colonies (both genes were successful)
  • Picked colonies and incubated overnight
  • Ran yesterday’s PCR products on gel - bands were light but all were recovered
  • Gel Extraction for pgk, pck, psc101, and psc102 plasmid
  • Reran PCR on pgk, pck, psc101, and psc102 plasmid because we did not get high enough concentration during gel extraction
  • Ran PCR products on gel - all were recovered
  • Gel Extraction for pgk, pck, psc101, and psc102 plasmid


  • Miniprepped plasmids for fldA, petF
  • Ran sequence PCR on both plasmids
  • Ran PCR product on gel to confirm
  • Clean and Concentrated PCR product
  • Reran PCR on pgk, pck, psc101, and psc102 plasmid because we did not get high enough concentration during gel extraction (for the fourth time)


  • Prepared DNA for sequencing
  • Delivered DNA to WashU Med School
  • Added DPnI to psc101 and psc102 gel extract products, incubated for an hour, did Clean and Concentrate, measured conc
  • Ran Golden Gate assembly on pck, pgk, and ATP Synthase


  • Electroporation with golden gate products
  • Redid golden gate for pck, pgk, ATP synthase (did not run properly first time)


  • Electroporation with better golden gate products
  • Picked colonies for worse golden gate for pck, pgk, ATP synthase


  • Miniprep worse ATP, pck, pgk golden gate
  • Seq PCR worse ATP, pck, pgk golden gate
  • Picked colonies for better golden gate for pck, pgk, ATP synthase


  • Made frozen stock of better golden gate pck, pgk, ATP synthase
  • Miniprepped better golden gate pck, pgk, ATP synthase (low concentration)


  • Ran sequencing PCR for pgk, pck (4 colonies each)
  • Gel Extraction for pgk, pck PCR product (no bands)


  • Ran sequencing PCR for pck and pgk on a gradient
  • Gel Extraction for pck PCR product was successful, not pgk


  • Ran sequencing PCR for pgk on a different gradient
  • Gel Extraction for pgk PCR product was not successful


No lab work done



  • Picked four new colonies of pgk
  • Started 4 new cultures from frozen stock


  • Made frozen stock of the 4 new colonies
  • Miniprepped all 8 pgk cultures and measured concentrations
  • Ran gradient PCR on all 8 pgk plasmids
  • Prepped and sent ATP synthase and pck in for sequencing


No lab work done



  • Mixed new pgk sequencing primers


  • Ran gradient PCR on all 8 pgk plasmids


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No lab work done



4th of July!



No lab work done



  • Sequencing results for ATP and pck were not good
  • Reran seq PCR on ATP Synthase (bad results)
  • Picked new ATP colonies


  • Miniprepped overnight cultures of ATP 5-8 and forgot to make frozen stock
  • Ran PCR on ATP plasmids 5-8
  • PCR for pgk with new primers with gradient
  • Ran pgk PCR product on gels
  • Ran golden gate on pgk PCR gel extract


  • Electroporation with golden gate pgk product


  • Picked 4 pgk products and inoculated them overnight


  • Made frozen stock of new 4 pgk cultures
  • Miniprepped cultures
  • Seq PCR on new cultures
  • All 4 cultures showed correct bands
  • Clean and Concentrate pgk PCR product
  • Prepped pgk for sequencing


  • Delivered pgk for sequencing


  • New ATP synthase sequencing primers and pck regular primers came in
  • Seq PCR of ATP synthase plasmids with new sequencing primers. No bands
  • Picked 4 new ATP synthase colonies (again)
  • Inoculated MG1655 from frozens stock to make more genomic DNA


  • Extracted genomic DNA from MG1655
  • Miniprepped new ATP cultures
  • Ran sequencing PCR on new ATP and got no bands at all. Will use newly transformed cells tomorrow
  • Ran PCR with pck primers, got light bands
  • Reran PCR with pck products


  • Ran pck on gel
  • Gel extracted pck and combined gel extracts to improve concentration
  • Golden gate ligation on pck
  • Ran ATP sequencing PCR again with different backbone primers


  • Ran gel from yesterday’s ATP PCR. No bands
  • Ran PCR for pfo
  • Incubated pck and BioBrick cells


  • Miniprepped pck and biobrock genes (HSP)


No lab work done



  • Ran ATP seq PCR gradient again. No bands. Done with ATP
  • BioBrick digestion, ligation, transformation with HSP and GFP
  • Ran PCR seq for pck and gel extract


  • Delivered pck sequence to med school
  • Ligated backbone for BioBrick
  • Extracted more genomic DNA from MG1655
  • Gradient PCR on pfo
  • Received 𝛥aceE cells from Yale
  • Rehydrated and incubated 𝛥aceE cells


  • Ran PCR and gel extract for fldA backbone and petF backbone
  • DPn1 the two backbones
  • golden gate ligation on pfo gene and two backbones
  • Streaked colony from 𝛥aceE plate onto LB/kan plate


  • Making media for competent cell protocol
  • Made new LB with MgSO4 for chemical transformation


  • Digested BioBrick miniprep to check length


  • Chemically competent cell protocol with 𝛥aceE
  • Miniprepped pfo-petF and fldA-petF
  • Seq PCR miniprepped pfo-petF and fldA=petF
  • Remade LB with MgSO4 with correct concentration


No lab work done



  • Restarted comp cell protocol (3rd times the charm)
  • Clean and Concentrate junction 2 for pfo-fldA
  • Conducted HSP test in LB


  • Redid HSP test in minimal media M9
  • Recultured BioBrick and DH10B control


  • Reset up BioBrick experiment but grew diluted cells with LB instead of M9, so we have to do it again


  • Redid HSP test in minimal media M9


No lab work done



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  • Chemical transformation of pfo-petF, pfo-fldA, petF, fldA into knockout strain, plated 80 and 240 ul, also control
  • Part 1 of interlab study (LUDOX)
  • Transforming 5 interlab plasmids


  • Picked and incubated electron donor colonies plated yesterday
  • Picked and incubated interlab colonies plated yesterday (2 per construct)


  • Made frozen stock of incubated colonies and interlab parts
  • Redid BioBrick experiment at 37C



No lab work done



No lab work done



No lab work done



  • Started induction but had to stop bc no frozen stock of fldA-pfo or petF-fldA in DH10B
  • Transformed fldA-pfo and petF-pfo into DH10B


  • Made frozen stock of 𝛥aceE
  • Made 60% ethanol
  • Incubated 8 constructs for biotin assay w/ methanol extraction (4 constructs and blank in DH10B and 𝛥aceE)


  • Methanol extraction assay (grew cells and froze pellets)


  • Assayed petF-aceE cells. Absorbance was too low to be meaningful


  • Ran preliminary sonication test
  • Incubated large volume of DH10B


  • Ran large sonication test on DH10B to decide protocol


  • Incubated large volume of DH10B


  • More sonication tests


  • Made ATP standards from assay instructions


  • Made more LB


  • Inoculated pgk, pck, DH10B for assay tomorrow


  • ATP luminescence assay
  • Inoculated 4 constructs and blank in 𝛥aceE cells for tomorrow


  • Nothing grew, couldn’t do induction


  • Inoculated DH10B constructs and control from frozen stock


  • DH10B electron donor induction, froze pellets, measured OD600
  • Re-transformed constructs into 𝛥aceE cells


  • Sonicated and assayed pellets for biotin (1 minute, 40 amp, 1mL PBS)
  • Reinoculated 𝛥aceE constructs in all antibiotic combinations to determine problem, in LB and plates


  • Visited Monsanto


  • Measured absorbance data from biotin in DH10B cells
  • Did ATP Assay and got luminescence data
  • Incubated all four 𝛥aceE electron donor constructs from frozen stock plates and original plates and incubated 𝛥aceE and DH10B


  • Nothing grew from yesterday's inoculations
  • Interlab study


  • Remade competent cells
  • Finished interlab study (FITC) and sent to iGEM HQ


No lab work done



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  • Picked colonies from 4 new 𝛥aceE plates and incubated


  • 𝛥aceE cell induction


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No lab work done



  • Incubated pck, pgk, DH10B from frozen stock


  • Ran ATP assay
  • BioBrick digestion and ligation
  • Sonicated 𝛥aceE pellets
  • Ran 𝛥aceE cell absorbance scan
  • Ran biotin assay on 𝛥aceE cells


No lab work done



No lab work done



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No lab work done



  • Transformed ligated petF and pck BioBrick plasmids into DH10B (wrong antibiotic)


No lab work done



  • Transformed ligated petF and pck BioBrick plasmids into DH10B (kan = right)
  • Wrapped pck and pgk plasmids to be sent to Cardiff University iGEM


  • Small colonies grew on all plates
  • Picked colonies and inoculated
  • Sent plasmids to Cardiff University iGEM


  • Miniprep on pck and petF BioBrick
  • Reusupended TetR-pTet gBlocks


  • Digestion/Ligation/Transformation of pSB1C3 and tetr-ptet BioBrick


  • TetR-pTet colonies grew, picked colonies


  • Miniprepped TetR-pTet BioBrick


  • digested BioBricks to check bands sizes


No lab work done



No lab work done



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  • Ran PCR on BioBrick plasmids


  • Ran PCR products on gel
  • Only petF showed up


  • digestion of pck, TetR-pTet, and pSB1C3 with EcoRI


  • Digestion of pck, TetR-pTet, and pSB1C3 with PstI
  • Ligated pck and TetR-pTet to pSB1C3
  • Transformed into DH10B


  • Only TetR-pTet grew
  • Ran colony PCR with 8 pck colonies and 8 TetR-pTet colonies


  • Ran colony PCR products on a gel but got no bands
  • Miniprepped pTet1-8
  • Ran PCR on pTet 1-8 plasmids to check if insert was present
  • Ran PCR product on gel, got the band!
  • Prepped petF, pck, and TetR-pTet to be sent to iGEM HQ


  • Last day in lab!
  • Sent parts to iGEM!


WIKIFREEZE



Done in lab



Prepping for Jamboree



Prepping for Jamboree



Prepping for Jamboree



Prepping for Jamboree



Prepping for Jamboree



Prepping for Jamboree



Fly to Boston for Jamboree



GIANT JAMBOREE



GIANT JAMBOREE



PRESENTATION



Fly back to St. Louis

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