Team:Vanderbilt/Project/Achievements
Demons in the Code
Sequence
- Invented an innovative software tool for minimizing any gene’s susceptibility to mutation
- Validated rapid spread of mutants in a genetically modified population by mathematical and empirical techniques
- Experimentally validated decreased mutation in optimized sequences with
- Multiple mutagen types (UV radiation, oxidation)
- Multiple quantification protocols (Alkaline gel, plasmid conformation, PCR inhibition)
- Established high expression of optimized sequences
- Modeling and computational strategies for further improvements and expansion of software
- Investigated potential for nanopore sequencing to become next-generation of ultra high-throughput DNA damage detection
Circuit
- Introduced quantitative metric of expected evolutionary stability and computationally modeled simple circuits
- Invented software tool to analyze circuit designs, calculate stability, and suggest modifications to improvements
- Developed software for minimizing sequence homology between synthesized genes
- Designed assay for quantifying the effect of lowering homology on rates of unwanted recombination
- Constructed optimized circuit to demonstrate improved stability with VERT technique
- Validated bidirectional promoter for use with an antibiotic system to select against promoter mutation
Organism
- Verified modeling predictions about population growth with simulated mutant cells
- Calculated the selective pressure against transgene expression by comparing experimental data with the Price equation
- Cloned five exogenous DNA repair enzymes
- Incorporated KIKO vector for genomic integration and simultaneous knock-out
- Designed “Incorruptible Cell” that commits suicide instead of passing on mutations
