Wet Lab Protocols

LB Broth
25g LB Broth, Miller
1L Water
Mix LB powder into water, autoclave for 15 minutes. Supplement with antibiotics
(Chloramphenicol, 35μL/mL) as needed.

LB Agar
25g LB Broth, Miller
15g Granulated Agar
1L Water
Mix LB powder and Agar into water. Heat until agar is dissolved and solution is clear, avoid boiling over. Autoclave for 15 minutes. Supplement with antibiotics (Chloramphenicol, 35μL/mL) as needed. Pour 20mL into sterile culture plates and let cool.

Transformation of Competent Cells

50μL Competent Cells (DH5α E. coli)
10ng Plasmid DNA
450μL LB
LB/Chloramphenicol Plate
Thaw Competent cells on ice and add plasmid DNA. Let sit for 20 minutes on ice. Heat shock cells at 45 o C for 30 seconds and then return to ice for 2 minutes. Add LB and incubate at 37 o C for 2-3 hours. Plate 100μL of the cells on a LB/Chloramphenicol plate and incubate at 37 o C overnight.

Dry Lab Protocols

Protein Reverse Translation
Isolate the protein sequence of interest and reverse translate using the E. coli preferred codon library in SnapGene. After reverse translation, look for out-of- frame coding regions and alter the codons so that no transcription is likely to occur. Finally, run a BLASTX protocol to ensure that the nucleotide sequence still encodes the protein of interest.

Wet Lab Protocols

LSTM model was coded using Tensorflow library and imported to Jupyter notebooks for 3 main experiments.

Artemisinin Binding

Import LSTM model.
Collected and import positive dataset for proteins that bind to Artemisinin and negative dataset for proteins that do not bind to Artemisinin by hand from NCBI and literature.
Establish consistent parameters for learning process (number of proteins per dataset, learning rate, network size, and sub-sequence length viewed).
Run test and repeat to establish consistency.

Artemisinin Consensus Sequence

Homeobox Consensus Sequence