Team:Imperial College London/Brainstorming

Quite early in the project the idea of water sanitation was put forward. We initially collected ideas about different substances, such as heavy metals, and pathogens we might be able to detect using relatively simple biosensors. In this list different parasites and bacteria were included.

Pathogen detection via quorum sensing

We later considered detecting the quorum sensing molecule N-acyl homoserine lactone produced by V. cholera for example. This molecule could than activate a simple colour output in our bacteria and thus exploit pathogen functions for detection. We later dropped this idea because, although it has a powerful application, it was too similar in design to biosensors that had been designed previously in iGEM projects. There were also a number of additional problems with this idea that made us not pursue it further.

Detection via receptors for bacteria-parasite interactions

A step further towards our final project was the idea to detect water borne parasites. Initially we did much research on parasite-bacteria interactions in order to find a sound mechanism we could implement in our system and link to an output. Even though we found some bacteria that interact with parasites, such as Salmonella with Schistosoma in the human gut, these we more often than not non-specific interactions and thus could give rise to false positive activations of our system.

Population control

This concept aimed to keep the total number of bacteria in equilibrium below the number they would naturally achieve, making the population number oscillate around this arbitrary threshold. This might be done by some clever use of quorum sensing systems acting on survival, growth or resistance genes to influence the performance of bacteria depending on the population density. However this construct would be evolutionarily unstable, as bacteria that lost the ability to self regulate growth would inevitably proliferate and out compete the functional bacteria.

Safe biofilms

We came up with similar approaches to making biofilms safer, for example by making the bacteria interdependent. This might be done by promoting cell survival via quorum sensing systems, so bacteria that become detached from the biofilm would die shortly after. This might make them safer for the environment, limiting their spread, as well as for use in medicine, preventing tissue invasion.

Cell state reporters

This idea was to monitor cell activity which might be useful for scientists in many situations. We proposed the use of cell state reporters to quickly give visual information of the activities or phase the cells are undergoing. This might help to maintain a healthy population and to determine whether population grows anaerobically or aerobically. Furthermore it could be used as a warning signal when cells undergo undesired/stressful phases and to examine if the cells grow in synchrony. Many different regulon systems could potentially exploited for this purpose including without limitation:

• Ntr and Nif system that detect ammonia limitation
• Arc and Fnr system that detect anaerobic conditions
• The SOS and response to UV light
• Sporulation in response to starvation and the heat shock response

Use of system specific promoter, enhancer or repressor elements could be used to create a system that gives feed back in the form of different fluorescent proteins to the degree to which the system is activated and by extension about the environment the cell is in.

Biofuels

We spent some time thinking about new ways in which bacteria could be used to produce biofuels, as well as trying to come up with more substances that could be used as biofuels, rather than relying on petrol, ethanol and simple sugars too much. Initial ideas included without limitation the use of octopine or nopaline from the T-DNA of Argobacterium. However ultimately we did not find this an exciting enough project to pursue.

TV screen

We thought about enhancing the iGEM project of the Valencia team 2008 who built a black and white bioscreen using yeast cells with voltage gated ion channels to produce a colour change. We considered implementing colour in this system to create a simple bio-TV. However the project would have been too similar to the original project so we dropped it quite early through our project development process.

Rhyzobium bacteria

We considered engineering Rhyzobium bacteria to fix nitrogen in larger quantities so they could be used more easily as fertilizer. Furthermore, but almost more importantly, we wanted to manipulate them to interact with a greater number of plant species, as to enhance the range of crops that could benefit from our project. However this would have been a very complex process that would probably not have fit into the time and labour constraints of an iGEM project.

Logic gates

Extending the logic gate concept developed in previous iGEM competitions, we considered whether a cell could have its logical state altered by an external input, for example frequency or intensity of light. This would in effect create a biological multiplexer with every input being a different logic gate, and the multiplexer stage being defined by a third input.

Rapid response system

Another idea that continued to keep our attention was the concept of a fast response. Most products of synthetic biology require a long time for gene expression until an output such as a pigment can be seen. We considered many different approaches, basically all involving an input to stimulate a two component system. The signal transducer was to activate a previously inactive enzyme and act on a substrate. The substrate was either to be colourless and only become visible after the enzyme acted on it, or be concentrated, such as a tight chain of pigments, that are than cleaved apart to colour the whole cell. We later settled for a more simplified, yet still highly efficient variant of this system to make our sensor more robust.

Fv-fragment guided input module

In order to detect molecules for which no natural receptor exists, we considered using antibody based receptors, either fused to the signal transduction portions of bacterial receptors, or by introducing the whole Fc-binding receptor of the mammalian immune system into bacteria and combining it with whole antibodies. However antibodies are complex, glycosylated proteins that cannot be expressed by bacteria easily and supplying antibodies to each detection kit would be very expensive. Furthermore introducing genes essential to the human immune system into bacteria, such as E. coli was considered a very risky idea and the human practices side of our project would be weakened.