Team:Cambridge/Brainstorm

The Brainstorming Process

Coming up with an actual 'big idea' was exceptionally difficult - we went through a plethora of different ideas, which we narrowed down (with a great deal of difficulty) to 'Bactiridescence' over the course of three weeks. That was over a quarter of our project time! Here we outline the key considerations we had to bear in mind throughout the process, some highlighted projects that came to mind during this period, and the reasons why we dismissed them. We discuss them here in the hope of inspiring future iGEM teams and other researchers in the field of synthetic biology, as well as hopefully setting an example in terms of biosafety responsibility.

Responsibilities when working with GMOs

In our brainstorming we considered safety from the start. Working with genetically modifies organisms (GMOs) poses potential risks -- not just to ourselves -- in a number of ways. Here are some potential 'dangerous experiments':

• Demonstrate how to render a vaccine ineffective
• Confer resistance to clinically useful antibiotics or antivirals
• Enhance virulence of a pathogen or activate a non-pathogen
• Increase transmissability of a pathogen
• Alter the host range of a pathogen
• Enable the evasion of a diagnostic technique
• Develop a biological agent that has potential to be used as a weapon

In our project work we only used strains of E. coli that were multiply disabled and non-pathogenic. However, highly virulent strains of E. coli do exist and so the concerns outlined above are especially relevant, and led us to reject a number of project proposals.

Ideas on the longlist

Radiation detection/scrubbing - This idea was rapidly discarded because the team did not want to work in a radioactive environment over the summer!

Removal of poison in catalytic converters - Although we thought this was a great application, heavy metal detection and removal have already been done many times in iGEM so we wanted to go instead for a more original idea.

Water treatment/filtration - Again, a common topic in iGEM, that we couldn’t find a sufficiently original angle to approach for our project

Fertiliser production on demand - something we thought would be too similar to Bristol 2010’s project.

Disease detection from blood serum - although we thought this would be a great achievement if we managed it, there weren’t many parallel lines of enquiry that we could branch off to if we couldn’t achieve the main aim.

Generic disease diagnosis paradigm - inspired by Imperial College 2010, but unfortunately our research didn’t get anywhere.

Drug delivery transport mechanism - the idea was to use tissue recognition to target drugs to the relevant region in the body. Unfortunately, not only was the project difficult, but we did not want to release live bacteria within the human body (outside the gut). The patient would be likely to have a strong immune response to the bacteria as well, which would be extremely difficult to avoid.

Curing cholera - we were thinking of trying to counteract the ion leakage associated with cholera, but it turns out that the simplest way to cure cholera is abundant hydration (with clean water), which is more likely to be available than GM bacteria, in general!

Insulin implant for diabetics - a bacterial implant that releases insulin on demand based on blood sugar levels. This idea was discarded because of the immune response triggered when bacteria enter the bloodstream, as well as the potentially harmful technology of having bacteria that can live in your bloodstream, if we succeed in overcoming the immune mechanism.

Scent detection - although this is highly applicable (for biosensing at a distance), we couldn’t find enough information in the literature to pursue this idea.

Hormone releaser - in particular, adrenaline synthesis really caught our imagination, but we didn’t want to create E. coli (that originally could survive in the human gut) that produced chemicals that can interfere with human physiology - dangerous ground!

Eutrophication prevention/reversal - the main issues here were the unpredictable effects of introducing a GM foreign species into the local ecosystem, and the fact that nitrate removal had been attempted before, so our project wouldn’t be very original.

Purification of salt water - distillation just seemed a lot easier than introducing bacteria into the water and then removing them (completely) before the water can be drunk.

Control of fruit ripening - something which could absorb ethene and hence prevent fruit ripening was the idea, but we realised that fruits would have to be individually shielded in order for this to work; hardly feasible if we want to be economical and avoid contamination of the fruit with bacteria.

Application of PACE - we were all enthused by this novel technology, but we found out that it was more difficult than we thought initially to harness. We decided to pick a more focussed project and use PACE as a tool, rather than using PACE as the starting point.

Smart bandage - despite the fact that biofilms have been shown to ‘protect’ wounds, the problems of containment and medical approval would be insurmountable.

Removal of mucus/toxins from the lungs - discarded because we don’t want to release GM bacteria in the body.

Leak detection - we thought this would be quite feasible, but perhaps not ambitioous enough given that it has been attempted before and could be done entirely with existing parts.

Bio-scaffolds - we didn’t think we’d be able to have much success in this area, the technology seems a bit too far off to do anything that would give us a substantial sense of achievement.

Lab on a chip - we wanted to harness microfluidics in this project, and really take miniaturisation of, for example, blood tests, to a new level. However, it was too ambitious to be attempted in a summer project.

Bacterial hand warmer - dropped when we saw that chemical versions exist, which we didn’t think we could beat.

Inner city air scrubbing - we thought that it would not be possible to make a significant difference in open spaces, since the volume of air would be too large. It would take a lot of bacteria, and probably completely uncontained - not a good idea!

Bacterial battery - this was considered infeasible because the bacteria with the most interesting behaviour (including ‘’Rhodoferax ferrireducens’’ which produces conducting nanowire filaments) are anaerobic, and hence difficut to work with in the lab. We think that the production of ions in such bacteria is likely also to be linked to their anaerobic environment, which means that any bacterial battery would need to be kept in anaerobic conditions; not a convenient arrangement.

Asbestos degradation - asbestos toxicity doesn’t seem to be fully understood, so we couldn’t find any strong goals to target in this area.

Hydrogen production - the sheer amount of hydrogen that we would have to produce makes bacterial production very inefficient. In addition many relevant genes have been patented, limiting our research freedom.

Disruption of biofilms - This idea looked very interesting until we saw that British Columbia 2010 had had exactly the same idea, and were (very nearly) successful. We wished to pursue a project that was more original, ideally.

Vitamin-secreting bacteria - the idea being that they would stay in the gut and secrete exactly the right amount whenever there was a deficiency detected. the complexity of making sure that the bacteria would produce exactly the right amount of vitamins for the body seemed almost insurmountable, and the idea of having bacteria that could permanently live in the gut was not desirable, either.

Sugar substitute creator - we became interested when some proteins were identified that were a lot sweeter than glucose by mass, but we then saw that aspartame is already produced by bacteria commercially; this would render the project unoriginal.

Plastic and crude oil degradation - we didn’t think that we could add much new to this area that hadn’t already been done before; in particular we thought that TU Delft 2010 did an excellent job with alkane degradation last year. We considered expanding their work to degrade aromatic hydrocarbons too, but we thought that squid was more interesting to work with in the end!

Ideas on the shortlist

Pathogen detection - The application we had in mind was detection of pathogenic contamination in food; we wanted to develop a biosensor (which must be highly sensitive) and assay that would allow us to detect the contamination in food before it reached consumers. One idea was to put a sample of the food onto a petri dish containing a GM phage that was specific to a particular pathogen, and which caused its host to produce a specific chemical. Some GM E.coli (also on the dish) would move towards the pathogens by chemotaxis and become pigmented in response to the chemical, reporting the presence of the pathogen. We dropped the idea because we though it would be too ambitious to complete within 10 weeks.

Carbon sequestration and bioplastics - We considered various possible approaches, including photosynthesis using cyanobacteria, and producing bioplastics from carbon dioxide, but all had either already been attempted industrially with much greater success (with time and funding!) than we could ever achieve, or were infeasible to work with in the lab (cyanobacteria).

Exploit iron chelating siderophores - we were really keen on exploiting the iron chelating and transport mechanisms in E. coli, which we found to be extremely extensive. However, we simply couldn’t think of a useful and interesting application, so we dropped the idea.

Scent production - we thought of using this as a reporter system for a biosensor, and even came up with a couple of synthesis pathways that looked feasible, but we just couldn’t find a good application area in which the use of a scent would be a better reporter than light or colour output (or electronic alarms).

Magnetic bacteria - although we found this highly interesting, and of undoubtable utility, we believed that there was very little we could do beyond making magnetic nanoparticles within the bacteria, which has already been done by other research teams, and trying to make the nanoparticles equally sized. unfortunately, we would need to perform a large amount of research using electron microscopy in order to investigate the nanoparticle sizes in detail, which we couldn’t afford under our research budget.

Production of quantum dots - we were really interested in developing this technology for biological tagging, which has extensive medical applications. However, all quantum dots that we found that we thought could be plausibly produced in E. coli required heavy metals that are highly toxic, and so health and safety prevented us from going further.

Ice-nucleating biosensor - in literature, it has been claimed that ice nucleating bacteria can be used as an assay for chemicals/pathogens with a sensitivity 10 times better than GFP. We thought that this was a technology that had a lot of scope, but ultimately we thought that reflectins were simply more interesting to work with.

The final cut - reflectin

In the end, we finally chose to try to produce structural colour and iridescence by expressing reflectin proteins in E. coli. The main attraction of pursuing this project lay in both its novelty and its potential impact, particularly since reflectin has only recently been identified no one has ever tried to explore its potential in the context of synthetic biology before. Although this makes the project very challenging, in the sense that we have very little groundwork in the literature to build on, the potential applications - including use in real-time response biosensors and structurally coloured commercial display screens - could be groundbreaking. The openness of the field also gives us an opportunity to delve into the unknown and even participate in primary research. We think it's worth the risk!