This page is how our ideas developed and how we listened and learned from our human practices in the design and implementation of our project.

Project Genesis

Brainstorming

Being inspired at SB6

Sharing ideas at YSB

Brainstorming ideas:

Bacterial Consortia

Control of synthetic microbial consortia is a desirable step in achieving increased potential in the field of synthetic biology. Advantages include the production of more complicated metabolites, the ability to optimize individual pathway production, higher level logic gates and into the future, self regulating communities, approaching the abilities of multicellular organisms. Populations in a community interact in different ways producing mutualisms, commensalisms and parasitisms. In order to rationally control communities we must understand how these different relations can form. Investigations in synthetic systems have focused on mutual dependence through the use of auxotrophic strains, toxin-antitoxin systems and antibiotic resistance modules. Control systems are currently based upon chemically relieved transcriptional repression which is precise in neither time or space. We aim to utilize different light inducible two component systems to control community interactions. We will use this to control the mutual dependency and investigate the conditions under which the above relationships form. We will also disturb the system to investigate the exchange of metabolites as an analogue to a financial system.

Synthesis of a biological scaffold using bacteria

Our project looks at generating self-sustaining Turing patterns from quorum sensing molecule AIP and bacterial swimming in a B. subtilis chassis. Once the Turing patterns are formed, the cells propagate until they reach high density, upon which they begin biosynthesis of two biomolecular polymers: γ-PGA and bacterial collagen. These are secreted into the ECM, forming a biocompatible, non-immunogenic, and bio-degradable matrix that contains pores and is able to absorb water. Removing the bacteria is then achieved in a non-invasive means by using the magnetosome within the bacteria to displace them from the scaffold, which can then be prepared for stem cell seeding or use in addition to this an ECM protein that binds to the matrix and has the capability of augmenting catalytic efficiency.

OR

Our project looks at generating self-sustaining Turing patterns from the use of bioluminescence and bacterial swimming in a B. subtilis chassis. Once the Turing patterns are formed, the cells propagate until they reach high density, upon which they begin biosynthesis of two biomolecular polymers: γ-PGA and bacterial collagen. These are secreted into the ECM, forming a biocompatible, non-immunogenic, and bio-degradable matrix that contains pores and is able to absorb water. Bacteria will not excrete these proteins in the presence of blue light. Removing the bacteria is then achieved in a non-invasive means by using the magnetosome within the bacteria to displace them from the scaffold, which can then be prepared for stem cell seeding or use in addition to this an ECM protein that binds to the matrix and has the capability of augmenting catalytic efficiency.

RNA world: orthogonal system to report on internal environment of E.coli cells in real time

Our system is designed to report the internal metabolic environment of cells through an RNA- only pathway. The advantage for relying on RNA for this signalling process is for speed, rather than relying on the time and resource consuming process of gene expression. The input of this system is the different metabolites within the cell. Different metabolites can bind to different RNA aptamers to induce a conformational change in the RNA and exposure of a sequence which displaces with one strand in an RNA biosensor. The second strand in the biosensor is then free to anneal with and change conformation of other RNAs, in a specific manner. This exposes different RNA-fluorophore aptamers and causes fluorescence. Different metabolites will produce a different palette of fluorescence. After generating a toolbox for this process, we could expand this technology to regulatory functions and utilizing different cell types.

Dopamine Production and Release in E. coli

Our project aims to engineer E. coli to produce a therapeutically important neurotransmitter, dopamine, by rewiring EnvZ-OmpR two-component system. We focus on activating dopamine production from tyrosine in response to a symptom of hypertension. Potential input signals could be concentration changes in oxygen, triglycerides and glucose. Once stimulated, EnvZ-OmpC TCS induces expression of enzymes involved in dopamine synthetic pathway. Therefore, the engineered E .coli forms an automated machine that efficiently controls the blood pressure without the need of frequent blood pressure check.