Research record
Lab Notebook
Wet-lab and dry-lab entries in chronological order — protocols, observations, computational analyses, and results as they happened. Negative and inconclusive results are preserved honestly.
Confirmed In progress Pending
View the original handwritten pages → — a parallel record; the two don't fully cover each other
Week of 15 June 2026
Mon 15 Jun
Competent cell prep — first attempt (unused)
Tue 16 Jun
GH10 & GH1 catalytic residue analysis; cellobiose docking
Tue 16 Jun
CxnA transformation & Gel #1 (inconclusive)
Wed 17 Jun
Interaction analysis — PLIP, PoseView & Notenboom cross-check
Wed 17 Jun
Miniprep setup & Gel #2 (inconclusive)
Thu 18 Jun
AlphaFold3 validation — RMSD = 0.293 Å vs 1FHD
Thu 18 Jun
Miniprep completion, Gel #3 & sequencing
Fri 19 Jun
Binding affinity analysis (Vina) & MSA planning
Week of 22 June 2026
Mon 22 Jun
HotSpot Wizard — mutagenesis target identification
Mon 22 Jun
Media preparation — M9, cellobiose & selection plates
Tue 23 Jun
Selection plate pouring — conditions B, C, D
Wed 24 Jun
CxnA activity assay setup; CMC & MUC plate prep
Thu 25 Jun
FoldX stability analysis — candidate mutations ranked
Thu 25 Jun
Positive control transformation & activity results
Fri 26 Jun
Activity assay analysis
Week of 29 June 2026
Week of 6 July 2026
Mon 6 Jul
GC-rich PCR optimisation and M9 plate prep
Tue 7 Jul
Transforming BL21 with beta-glucosidase plasmid
Wed 8 Jul
Mutant sequences back; BL21 re-transformation; M9 control plates browned
Thu 9 Jul
Redo M9 plates, faithful PCR, and cellobiose selection plates
Fri 10 Jul
Primer mix-up blocks gene PCR; M9 plate dilution-factor correction
Week of 13 July 2026
Week of 20 July 2026
Week of 10 August 2026
Mon 10 Aug
Overnight CxnA culture started for M9 growth-curve work
Tue 11 Aug
M9 growth-curve screen — testing supplement essentiality
Wed 12 Aug
M9 growth-curve screen repeated for consistency
Thu 13 Aug
Cellobiose vs glucose comparison — CxnA and beta-glucosidase strains
Fri 14 Aug
24h culture OD600 readings and CFU serial dilution plating
Week of 17 August 2026
Mon 17 Aug
CFU counts from the cellobiose/glucose comparison
Tue 18 Aug
MUC assay setup — CxnA baseline (lysis, protein quant, plate loading)
Wed 19 Aug
MUC assay Run 1 — first plate, standard curve inverted
Thu 20 Aug
Q5 backbone PCR — template titration
Fri 21 Aug