Team:UGent Belgium/LabNotebook

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Lab Notebook

August

  • August 29:
    • We made a strong expression vector (pXS) by restriction of the linearized plasmid backbone pSB1C3 and insertion of gblock made up of promoter-RBS-cloning site-terminator-terminator (cut with EcoRI and PstI). Details
      • Details:

        1. Resuspend gBlocks in Elution Buffer (=TE) to concentration of 50 ng/uL -> 500 ng delivered => 10uL buffer
        2. Linearised PSB1C3: 25ng/uL at 50uL (used 2013 iGEM tubes)
        3. Prepare mixes (enzymes by NEB):

          table1

          table1

          Incubate overnight in 37°C warm water bath (overdigestion because of enzyme expiration date and restriction sites close to fragment termini, especially for the gBlock).

    • Our first attempts to isolate the inaZ gene from P. syringae and the inaX gene from X. campestris failed. Details
      • Details: The inaZ gene was sourced from BBa_K584027 using primers oM7628 and oM7629* (length 3.6 kbp, anneal at 58°C). The plasmid is obtained from KU Leuven (concentration unknown): run PCR (Q5) with 10x and 1000x template dilutions, transform into E. coli DH5a by heatshock, plate on chloramphenicol. The inaX gene was sourced from X. campestris colonies using primers oM7626 and oM7627 (length 4.7 kbp, anneal at 70°C). Cloning overhangs were not included on these primers. The colony was suspended in 1000uL distilled water, vortexed, freezed 30 min. @ -80 deg. C, heated 20 min. @ 95 deg. C, vortexed, and debris spinned down.



  • August 30:
    • We transformed the strong expression vector (cf. 29/08) by electroshock into E. coli Top10, and we plated it on chloramphenicol. Details
      • Details: Test
    • As a backup strategy we also used CPEC with the backbone from the K584027 plasmid to generate a strong expression vector. For this, we used Primestar HS PCR with primers oM7643 and oM7645. Details
      • Details: Test
  • August 31:
    • Second attempt (cf. 29/08) to isolate the inaZ gene from P. syringae and the inaX gene from X. campestris. InaX failed, but inaZ was successful. Annealing temperature was 66.20°C and 61.93°C for respectively both primers for the inaZ gene, 60.96°C and 70.34°C for respectively both primers of the inaX gene. Both Primestar HS and Primestar GXL PCR were used for this. On the gel, lane 4 and 8 are inaX attempts. Details
      • Details: Test



    • Transformation of the strong expression vector by restriction and ligation was not very successful, we only had a few colonies. The backbone amplification using CPEC was successful (see gel, cf. 30/08). Details
      • Details: Test



September

  • September 01:
    • Heatshock transformation of the strong expression vector made with CPEC (cf. 31/08) yielded no colonies.
    • Colony PCR on the colonies with the strong expression vector made with restriction and ligation didn’t show any positive ones (cf. 31/08). As primers, we used BioBrick verification primers (length: 534 bp).
  • September 02:

    Electroshock transformation of the strong expression vector made with CPEC (cf. 31/08) into E. coli Top10 cells.

  • September 04:
    • CPEC using Primestar GXL and an excess of insert. Details
      • Details: Test
    • Via colony PCR we saw that all colonies with the strong expression vector made with CPEC and electroshock transformation were all positive (cf. 02/09). We used BioBrick verification primers for this. Details
      • Details: Test



    • We transformed E. coli Top10 cells with our weak expression vector (pXW), which came in today. Q5 CPEC was used for this with the linearized plasmid backbone pSB1C3, and as insert a gBlock consisting of promoter-RBS-cloning site-terminator-terminator. The promoter is weaker than the promoter of the strong expression vector (cf. 29/08). Details
      • Details: Test
  • September 06:

    Colonies from our strong expression vector made with CPEC (cf. 04/09) are cultured and miniprepped. These are used for following constructs:

    • pXS-INP_WT using the inaZ PCR fragment
    • pXS-INP_NC-mGFPuv
    • pXS-INP_NC-Strep (Strep: regular streptavidin)
    • pXS-INP_NC-mSA2 (mSA2: monomeric streptavidin)
    • pXS-Lpp-ompA-mGFPuv
    • pXS-Lpp-ompA-Strep
    • pXS-Lpp-ompA-mSA2
    All constructs are made by using a Golden Gate reaction mix. Details
    • Details: Test
  • September 07:

    We transformed our Golden Gate reactions (cf. 06/08) into E. coli Top10 cells.

  • September 08:
    • We did a colony PCR of our weak expression vector (cf. 04/09), and of our constructs made with the strong expression vector (cf. 06/09), both using BioBrick verification primers. Details
      • Details: Test
    • We tried to make inaZ Golden Gate safe by removing the internal BsaI sites. To achieve this, we used Primestar HS PCR and cut it into 3 different fragments. This was successful for the separate fragments, but we didn’t succeed to combine them. For the first fragment, this was simply from the original PCR fragment. The second fragment is a new PCR fragment, using oM7658 and oM7629 as primers and the inaZ plasmid as template (length:3039 bp). This band is smeared, probably due to excessive template concentration or annealing time. The third fragment is also a new PCR fragment, using oM7658 and oM7229 as primers and the inaZ plasmid as template (length: 293 bp).


  • September 09:

    The colony PCR of E. coli cells with the constructs with the strong expression vector showed no positive colonies (cf. 06/09). The colony PCR on our cells transformed with the weak expression vector (cf. 04/09), however, did. We repeated the colony PCR under different conditions, but bands were still not of the correct lengths. We therefore tried cloning all our parts into the weak expression vector by using a Golden Gate reaction mix. These Golden Gate reactions were then transformed into E. coli Top10 cells. Incubation was done at 30°C instead of 37°C to repress the plasmid copy number. Details

    • Details: Test

  • September 10:
    • We got our sequencing results: the strong expression vector is good!
    • Colonies with the weak expression vector constructs are still too small to pick up with colony PCR (cf. 09/09).
  • September 11:

    • All our plates with the weak expression vector constructs show colonies! The control reaction has colonies as well, but much fewer, which was to be expected. Fluorescence is seen for the pXW-INP_NC-mGFPuv construct. All Lpp-ompA plates have a mixed phenotype, with 10-20 large colonies (same size as control reaction), and >60 small colonies (see culture picture). Colony PCR was performed using OneTaq at 50°C annealing temperature to proof that the small colonies are the positives ones, the larger ones the negative ones. This theory was confirmed for all colonies (see gel picture).


    • We performed Primestar HS PCR to create following constructs:
      • pXW-Lpp-ompA-mGFPuv-(m)Strep using Lpp-ompA-mGFPuv fragment. As a template, we used the Golden Gate mix for pXW-Lpp-ompA-mGFPuv, and oMEMO7667_Lpp_Fw and oMEMO7663_GFP_Rv-ATCT as primers (expected length:1167).
      • pXW-mGFPuv-m(Strep) using mGFP. As a template, we used a 100x diluted gBlock, and oMEMO7662_GFP_Fw-GATG and oMEMO7663_GFP_Rv-ATCT as primers (expected length: 752 bp).
      • pXS-mGFPuv using mGFP. As a template, we used a 100x diluted gBlock, and oMEMO7662_GFP_Fw-GATG and oMEMO7664_GFP_Rv-TACT as primers (expected length: 752 bp).
      We also repeated previous PCR (cf. 08/09) of the largest piece of inaZ to make it Golden Gate safe. As a template, we used the inaZ plasmid, and oM7658 and oM7629 as primers (expected length: 3039 bp). Because the band was smeared last time, we should either use lower template concentrations or a shorter anneal time.
  • September 12:

    • Miniprep of a number of colony PCR positive colonies (cf. 09/09).
    • Next picture is the gel of the PCR reactions of the previous day (cf. 11/09). inaZ was run 2 times (at 1/100 and 1/1000 dilution), these are the first 2 bands. The next 3 bands are the 3 constructs. PCR using the Golden Gate mix as a template didn’t work very well (two extra bands, lane 3). We therefore repeated this reaction using a pure plasmid.


    • Golden Gate assemblies of:
      • pXW-inaZ_GGsafe
      • pXW-mGFPuv-Strep
      • pXW-mGFPuv-mSA2
      • pXW-mGFPuv
      • pXS-mGFPuv
      Details
      • Details: Test
  • September 13:

    • pXW-Lpp-ompA-mGFPuv miniprep tubes that did not grow yesterday (cf. 12/09) did show growth today, probably through mutations.
    • Transformed Golden Gate assemblies (cf. 12/09) into E. coli Top10 cells.
  • September 14:

    Colony PCR of the transformed Golden Gate assemblies (cf. 13/09): fail for pXW-INP_GGsafe (first 7 lanes), okay for other assemblies. For pXW-INP_GGsafe, we will make a new Golden Gate design.




  • September 15:

    Colony PCR screening of 8 more colonies with pXW-inaZ_GGsafe showed no result (cf. 13/09)

  • September 16:

    • Minipreps of the following plasmids and sequencing with verification primers:
      • pXW-mGFPuv-Strep
      • pXW-mGFPuv-mSA2
      • pXW-mGFPuv
      • pXS-mGFPuv
    • We did a Primestar HS PCR to go from high copy to low copy (LC) backbone, with as backbone pSB3K3 and 4 inserts: INP_NC-Strep, INP_NC-mSA2, Lpp-ompA-Strep and Lpp-ompA-mSA2. For the backbone, we used pSB3K3 as template, with oMEMO7669 & oMEMO 7670 as primers (length: 2790 bp). For the INP_NC-Strep insert, we used pXW-INP_NC-Strep as template, and oMEMO7671 & oMEMO 7672 as primers (length: 1684 bp). pXW-INP_NC-mSA2 is the template used for insert NP_NC-mSA2, and oMEMO7671 & oMEMO 7672 were used as primers. For the Lpp-ompA-Strep, we had pXW-Lpp-ompA-Strep as template, and oMEMO7671 & oMEMO 7672 as primers. For the last insert, Lpp-ompA-mSA2, we used pXW-Lpp-ompA-mSA2 as template, and oMEMO7671 & oMEMO 7672 as primers. The backbone and Lpp-ompA-mSA2 both failed. On the gel, all four inserts are seen. The backbone was run on a different gel not pictured here.


  • September 19:

    • We retried the Primestar HS PCR to go from high to low copy backbone, with now oMEMO7675 & oMEMO7644 as primers for the pSB3K3 backbone, but this again failed. The Lpp-ompA-mSA2 insert was also redone with now the Golden Gate mix as template, which was successful. We also made the ‘new parts’ of inaZ, using the inaZ plasmid as a template. For the first piece, we used oMEMO7628 & oMEMO7673 as primers (length: 634 bp), for the second piece, we used oMEMO7658 & oMEMO7674 as primers (length: 2792 bp), and for the last piece, oMEMO7659 & oMEMO7629 were used as primers (length: 297 bp).


    • Golden gate assembly of pXW-inaZ_GGsafe. Details
      • Details: Test
  • September 21:

    • We did a colony PCR for the Golden Gate assembly of pXW-inaZ_GGsafe (cf. 19/09). Colony 2, 6, 8, and 32 are preculture. 13 also kind off looks okay, but is too small in length (probably due to some failed fragments).


    • We opted for a new backbone for the low copy vector (cf. 19/09): pSC101-Kan vector.
  • September 22:

    • We digested colony PCR samples 2, 6, 8, 13, and 32 (cf. 21/09), and a control with BsaI. If pXW-inaZ_GGsafe is indeed Golden Gate safe, it should not be cut. This was okay! Colony 2 and 6 are plasmid prepped for sequencing. Colony 13 is lane 5, control is lane 6.


    • We again retried the Primestar HS PCR to go from high to low copy backbone. For this, we used the pSC101-Kan vector as backbone to obtain the low copy backbone pSC101 (right gel, lane 1). As primers, we used oMEMO7714 & oMEMO7715 (length: 4034 bp). A new Lpp-ompA-mSA2 insert was also done (left gel, lane 1), with the Golden Gate mix as template, and oMEMO7671 & oMEMO 7672 as primers (length: 1051 bp). A weak expression vector with an empty expression site was also added (left gel, lane 2), with pXW as template, and oMEMO7671 & oMEMO 7672 as primers (length: 224 bp). To obtain inaZ-RC (left gel, lane 3), we used pXW-inaZ_GGsafe as template, and oMEMO7665 & oMEMO7666 as primers (length: 3100 bp). Lane 2 and 3 on the right gel are respectively a control, and backbone pSB1C3 (mSA2-REsafe gBlock assembly).


  • September 26: CPEC assemblies to create:
    • pLC-XW
    • pLC-XW-INP_NC-Strep
    • pLC-XW-INP_NC-mSA2
    • pLC-XW-Lpp-ompA-Strep
    • pLC-XW-Lpp-ompA-mSA2
    • pSB1C3-mSA2
    Details
    • Details: Test
  • September 27:

    Colony PCR of all CPEC assemblies (cf. 26/09) with primers oMEMO3441 + oMEMO1760 for the first 5 assemblies and verification primers for the last assembly. The order of the gel is: pLC-XW-INP_NC-Strep, pLC-XW-INP_NC-mSA2, pLC-XW-Lpp-ompA-Strep, pLC-XW-Lpp-ompA-mSA2, pSB1C3-mSA2, and pLC-XW (only 3 colonies).




  • September 28:

    • Second attempt for CPEC assemblies (cf. 26/09), with increased backbone DNA and an altered backbone/insert ratio. Details
      • Details: Test
    • Primestar HS PCR to create GATG-mGFPuv-ATCT, which is necessary for new attempts for the pXW-mGFPuv-Strep and pXW-mGFPuv-mSA2 constructs, due to mutations in previous versions. For this, we used primers oMEMO7662 + oMEMO7663, and pXS-mGFPuv as template.


    • Golden Gate assemblies to create:
      • pXW-inaZ-RC+Strep
      • pXW-inaZ-RC+mSA2
      • pXW-inaZ-RC+GFP
      • pXW-mGFPuv-Strep
      • pXS-mGFPuv-Strep
      • pXS-mGFPuv-mSA2
      Details
      • Details: Test
    • We also started cultures for the cell binding assay to test the attachment to our filament, and for protein extraction. For the first, we used constructs pXW-INP_NC-Strep + pSC101-RFP, pXW-INP_NC-mSA2 + pSC101-RFP, and pSC101-RFP. For the latter, we used constructs pXW-mGFPuv-mSA2 and pXW-mGFPuv.
  • September 29:

    • Sequenced two new colonies of construct pXW-mGFPuv-Strep (due to mutation in GFP).
    • Created pSB1C3-mGFPuv2 for submission to the parts registry. For this we amplified the backbone from pSB1C3 linear template using primers oM7722 and oM772 (length: 2093 bp), and mGFPuv2 from construct pXW-mGFPuv or pXS-mGFPuv using primers oM7662 and oM7664 (length: 744 bp). Golden Gate assembly was done using BsaI.
  • September 30:

    We did colony PCR on the CPEC assemblies with increased backbone DNA and altered backbone/insert ratio (cf. 28/09), and previous Golden Gate assemblies (cf. 28/09). We found positive colonies for following constructs:

    • pLC-XW
    • pLC-XW-INP_NC-Strep
    • pLC-XW-INP_NC-mSA2
    • pXW-inaZ-RC+mSA2
    • pXW-mGFPuv-Strep
    • pXS-mGFPuv-Strep
    • pXS-mGFPuv-mSA2
    For constructs pXW-inaZ-RC+Strep and pXW-inaZ-RC+GFP, more colonies need testing.


October

  • October 03:

    New colony PCR of 2x14 colonies of constructs pXW-inaZ-RC+Strep and pXW-inaZ-RC+GFP.

  • October 04:

    We found a positive colony for construct pXW-inaZ-RC+GFP (cf. 03/10).




  • October 05:

    Golden Gate assembly of pSB1C3-mGFPuv2, with a shorter protocol (cf. 29/09), and transformation into E. coli Top10 cells. Details

    • Details: Test

  • October 06:

    • Colony PCR on 14 pSB1C3-mGFPuv2 colonies (cf. 05/10). For primers, we used verification primers (length: 1030 bp).


    • Combined pXW-INP_GGsafe with pLC-XW-INP_NC-mSA2 by electroporation (plate on kan+chloramphenicol).