Achievements

Policies and Practices:

• Thoroughly researched our target markets and differing legislations that could affect our system
• Connected with many different experts in the fields of infectious diseases, anti-malarial medications and public health to truly understand the needs and feasibility of the project
• Connected with the foremost authority in low cost diagnostics, Foundation for Innovative New Diagnostics (FIND), to discuss the viability of our design and concept
• Connected with a small village clinic in rural Uganda, which gave an opportunity to see the facility as well as discuss the topic with local physicians
• Featured iGEM and our project on a global stage at the United Nations, in Geneva, and created discussion regarding the advancement of synthetic biology

Modelling:

• Designed and manufactured a prototype of informed design based on our biological system
• Cost analysis of our prototype and system to ensure that this project is feasible in developing nations
• Quantified the visible threshold of detection for several reporters using time-lapsed cell count and absorbance readings, as well as a programmed colour sensor
• Programmed an Arduino UNO microcontroller, colour sensor, and LCD screen to detect colour change among detection chambers, allowing for quantification of the colour
• Applied circuitry of a heating pad/temperature considerations for ideal isothermal PCR conditions
• Used Autodesk Maya Software to visually model and represent our system
• Used Solid-works Software to model fluid flow analysis for different prototype designs

Transformation:

• Transformed B. subtilis with a primer product containing 125 bp of homologous sequence flanking our gene of interest
• Modified and optimized general transformation: characterized effect of changing xylose concentrations, temperature, and shaking?
• Optimization of transformation in small, liquid volume
• Sporulated B. subtilis
• Activated B. subtilis spores back to vegetative state

Detectives:

• Constructed a reporter operon consisting of a constitutive promoter (Pveg), ribosome binding site, operator (C1434) and reporter (LacZ/RFP).
• Constructed a complementary repressor operon consisting of a constitutive promoter (Pveg), ribosome binding site, and repressor pertaining to the operator. Repressor was also flanked with regions homologous to certain sequences within our pathogens of interest.
• Isolated the comK gene from the genome of B. subtilis using PCR and inserted it into a Biobrick vector for future application as an iGEM standard part. The vast majority of my work was on the genetic circuit, which was done under Dan. You should probably ask him about the specifics since he spearheaded it throughout the summer and concluded it in October.

Sample Preparation:

• Demonstrated efficacy of isothermal PCR to amplify DNA sequences without the need of a thermocycler, using freeze-dried components
• Demonstrated ability to amplify target DNA sequence from whole E. coli cells in a blood mixture
• Obtained specificity in target sequence primers - specific to numerous strains of N. meningititis but not other pathogens including a commensal strain of N. meningititis

Detection/Genetic circuit

• Designed composite regulatory promoter sequences - used to allow repression of a downstream reporter with a specific repressor. Includes 5 variants of repressible promoters in either single or triplicate repeats for variation in strength of repression
• Demonstrated interaction (i.e. repression) between the reporter gene and repressor gene in E. coli
• Demonstrated the efficacy of homologous recombination in B. subtilis and showed the minimum length of flanking sequences
• Biobricked and submitted the full-length lacZ gene, previously non-existant in the latest distribution plates