iDEC Cambridge 2026

Archive

This section contains weekly records of our progress.

  1. Project planning and initial work

    • Selected IDP solubility project
    • Worked on directed evolution selection method using β-lactamase
    • Developing and optimising computational programs
    • Investigated reagents
    • Discussion of epPCR and selection method
    • Developed a rough project timeline
    • Began designing primers

  2. Week 1

    • Ordered degenerate and library oligos
    • Determined conditions for epPCR including magnesium and manganese chloride concentrations and choosing taq polymerase enzyme.

  3. Week 2

    • Began first round of epPCR experimentation, made TAE gels and carried out pBAD linearisations and DNA purification of the epPCR and digested pBAD samples and subsequently Dpn1 digestion on linearised and purified pBAD.
    • Carried out troubleshooting on epPCR, Dpn1 digestion and DNA purification.
    • Reached out to companies and discussed sponsorship

  4. Week 3

    • Carried out Mn2+ and Mg2+ ion optimisation experiment for epPCR and checked results with gel electrophoresis.
    • Conducted a desiccation dry-run for the tardigrade pipeline
    • Sent out a sample of of epPCR product for sequencing and concluded that the major smearing on gels is due to GC rich content and started using a GC enhancer.

  5. Week 4

    • Carried out epPCR mispriming troubleshoot
    • Tested how using DMSO or GC enhancer changes the conditions for epPCR
    • Attempted second linearisation of pBAD but will have to troubleshoot
    • Tested if lowering primer concentration would decrease smearing in epPCR

  6. Week 5

    • epPCR round 2 worried after optimised conditions
    • Transformation of Gibson assembly products of De novo, SSB and NEXT tags into DH10β bacteria.

  7. Week 6

    • Started research about target proteins that could be used to test the solubility of our tag product
    • Researched about potential commercially available tags we could use to benchmark our own tag performance against.

  8. Week 7

    • Started liquid batch selection method using carbenicillin for De novo, SSB and NEXT tags
    • Decided antibiotic concentration did not exert enough selection pressure and optimised concentrations
    • 0, 10000, 15000, 30000 and 40000 ug/ml of carbenicillin were used for streaking plates of cultures.

  9. Week 8

    • Carried out gibson assembly for tardigrade library and degenerate oligos.
    • Carried out freeze-thaw tardigrade dry run using an ice bath made with isopropanol plus dry ice.
    • Received back sequencing results, what we thought was SSB library is actually NEXT library

  10. Week 9

    • Compiled all gel images in PNG formats
    • Carried out 6 complete cycles of freeze-thaw selection for the tardigrade pipeline.
    • Conducted another round of liquid batch selection for the other three tags using liquid batch selection
    • Started making buffers for SDS PAGE gels.

  11. Week 10

    • Performed plasmid extraction and sent samples form both tardigrade and the other three tags for sequencing and subsequent analysis
    • Carried out SDS-Page gel for combination of fusion of target protein and tags, which included the combination of hEGF, taCA, and isPETase as target proteins and GB1 and MBP as tags.
    • Carried out protein purification using buffers and protein His-Tag Spin column.