Team:Cambridge/Brainstorm

From 2011.igem.org

(Difference between revisions)
(→Responsibilities when working with GMOs)
 
(12 intermediate revisions not shown)
Line 3: Line 3:
==The Brainstorming Process==
==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 all the considerations we had to bear in mind throughout the process, all the projects that came to mind during this period, and the reasons why we dismissed them.  
+
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.
-
==Working with GMOs==
+
==Responsibilities when working with GMOs==
In our brainstorming we considered [[Team:Cambridge/Safety | 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':
In our brainstorming we considered [[Team:Cambridge/Safety | 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
*Demonstrate how to render a vaccine ineffective
Line 14: Line 14:
*Enable the evasion of a diagnostic technique
*Enable the evasion of a diagnostic technique
*Develop a biological agent that has potential to be used as a weapon
*Develop a biological agent that has potential to be used as a weapon
-
In our preliminary work we used E. coli strain K12, which is 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.
+
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.
-
==Cool Ideas==
+
==Ideas on the longlist==
-
'''Bacteria as indicators of specific pathogens''' -  
+
'''Radiation detection/scrubbing''' - This idea was rapidly discarded because the team did not want to work in a radioactive environment over the summer!
-
A project proposal:
+
'''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.
-
How about this triggering system for high sensitivity bioluminescence detection of pathogens:
+
-
Bacteria type A detects pathogen, ideally binds to it, triggering (continual) release of autoinducers (as used in quorum sensing). Chemotaxis will hopefully also take place.
+
-
Bacteria type B detects autoinducers, triggering bioluminescence (and ideally the production of more autoinducers). Of course, we’ll also try to implement all the techniques described in the literature for ways which they have managed to increase the sensitivity of the detection.
+
-
The ‘autoinducer’ could actually be any chemical; in the ‘cell-cell signalling’ section of the registry there are a number of different chemicals we could try.
+
'''Water treatment/filtration''' - Again, a common topic in iGEM, that we couldn’t find a sufficiently original angle to approach for our project
-
If we try to employ as many sensitivity-increasing techniques as possible, then that provides us with a ‘multi-step’ project. We can try different chemical signals, etc. as far as I’ve seen, this ‘chain reaction’ triggering system doesn’t seem to have been employed before, and particularly not in iGEM, although many usable parts (poorly characterised, though!) already exist in the registry.  
+
'''Fertiliser production on demand''' - something we thought would be too similar to Bristol 2010’s project.
-
Researched so far:
+
'''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.
-
Original inspiring paper (bioluminscent and fluorescent detection were the most interesting in my opinion): http://cau.ac.kr/~jjang14/BioMEMS/Ivnitski_BSBE_Bacteria_Detection_Bio_Sensors_Review_1999.pdf
+
'''Generic disease diagnosis paradigm''' - inspired by Imperial College 2010, but unfortunately our research didn’t get anywhere.
-
Many more papers come up if you look up something like “bioluminescence detect salmonella” in google; some highlights of my research so far:
+
'''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.
-
http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2672.1998.00393.x/pdf a detailed study
+
'''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!
-
http://www.sciencedirect.com/science/article/pii/S0009912097001367#toc10
+
'''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.
-
Very high sensitivity achieved!
+
-
“In this study, however, approximately 104–105 cells grown in culture were required to produce a significant luciferase signal with the reporter phages. This means that luciferase production is poor and, as a result, more cells are needed to produce enough light to quantify. Moreover, light emission was not constant following infection, and declined 2–3 h after phage addition, probably because of cell lysis (see Fig. 2). To overcome these problems and improve the sensitivity of the assay, Sarkis et al. [27] used the well-characterized mycobacteriophage L5, a temperate phage that is able to form stable lysogens when propagated on M. smegmatis. Recombinant phages were obtained by insertion of the FFlux gene into a portion of the genome highly expressed early during lytic phage development. Upon infection of M. smegmatis with some of these reporters, light production was indeed five-fold greater than that measured from TM4 derived phages, a result that was shown to be a consequence of lysogeny. The development of such lysogenic reporter phages introduces considerable flexibility into the assay of bacteria, as light output can be measured any time after infection, and longer incubation will reveal the presence of only a few bacteria. The L5 derived reporter phages allowed the detection of only a hundred cells in a few hours and as little as ten cells in 2 days, still less time than is required for conventional solid media assays.”
+
-
http://onlinelibrary.wiley.com/doi/10.1111/j.1472-765X.2005.01783.x/full
+
'''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.
-
This team quantified sensitivity and specificity of their detection of salmonella
+
-
Also, http://www.sciencedirect.com/science/article/pii/S0963996902000947
+
'''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!
-
Ice nucleation protein biosensor for bacteria? Triggers chain reaction of ice formation in supercooled water. They have managed to express this in E. coli ...
+
-
https://2008.igem.org/Team:Heidelberg/Project/Sensing : iGEM team Heidelburg investigated something similar, except they wanted to kill the target gene instead of simply detecting it; their sensing mechanism could be good to look at though...
+
'''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.
-
Pathogen detection using ‘sonar’, as exhibited by E. faecalis:
+
'''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.
-
http://www.livescience.com/111-bacteria-sonar-strategy-probe-environment.html news
+
'''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.
-
http://www.sciencemag.org/content/306/5705/2202.full original paper
+
-
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC257833/ genetic structure
+
-
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC197123/?tool=pubmed genetic structure
+
-
+
-
http://onlinelibrary.wiley.com/doi/10.1046/j.1462-5822.2003.00310.x/full#b8
+
-
Nucleotide sequence determination, transposon muta- genesis, site-specific mutagenesis and intracellular and extracellular complementation studies identified eight open reading frames within the cytolysin operon and, together with results from the purification and characterization of each of the cytolysin components, elucidated the functional role of each gene (Gilmore et al., 1990; 1994; Ike et al., 1990; Segarra et al., 1991; Coburn et al., 1999; Haas et al., 2002). The eight cytolysin operon genes are termed cylR1, cylR2, cylLL, cylLS, cylM, cylB, cylA and cylI (Fig. 1). The cylLL and cylLS genes encode a large and a small peptide, respectively, that together constitute the lytic component, and cylA encodes the activator component originally observed by Granato and Jackson (1969).
+
-
http://www.nature.com/nature/journal/v415/n6867/full/415084a.html reporter gene assay used, and primers described in ‘supplementary information’
+
-
Unfortunately we had to abandon this idea - the toxin released could potentially be harmful to humans, and although we could try to remove the toxicity by disabling certain genes, we  cannot be sure that the bacteria we produce are not harmful to humans. Once again, safety has to take precedence!
+
 +
'''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.
-
Radiation:
+
'''Smart bandage''' - despite the fact that biofilms have been shown to ‘protect’ wounds, the problems of containment and medical approval would be insurmountable.
-
radiation-sensitive bacteria (existing radiation detection technology is quite cheap and convenient, why use bacteria?)
+
-
radiation scrubbing using bacteria
+
 +
'''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.
-
Carbon Sequestration
+
'''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.
-
Felix: Potential idea - look into  a) a cycle process that we can develop for formation of ethylene from CO2, allowing us to test multicellular/ differentiated processes, and b) potential solar source of energy if we use cyanobacteria as products of photosynthesis
+
'''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.
-
Can we work with cyanobacteria? -Haydn: to paraphrase Jim, no.
+
'''Bacterial hand warmer''' - dropped when we saw that chemical versions exist, which we didn’t think we could beat.
-
Can we process fixed carbon into something else, like a biopolymer?  - Felix: I assume this mean bioplastic as biopolymer is anything that contains C-H groups with more than one unit...
+
'''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!
-
reference is http://en.wikipedia.org/wiki/Bioplastic
+
'''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.
-
Current bioplastics are:
+
'''Asbestos degradation''' - asbestos toxicity doesn’t seem to be fully understood, so we couldn’t find any strong goals to target in this area.
-
starch based - constitute 50% of bioplastic mkt - starch is made of glucose molecules which i believe is a product of photosynthesis?
+
-
cellulose based - mainly cellulose esters
+
-
polylactic acid - produced from cane sugar/glucose - so again bacteria producing glucose is good
+
-
Poly-3-hydroxybutyrate (PHB) - produced by certain bacteria with glucose
+
-
Polyamide 11 (PA 11) - derived natural oil
+
-
Bio-derived polyethylene - this one is the most interesting , uses ethylene which comes from ethanol which is a fermentation process which produces CO2?  C6H12O6 + Zymase → 2C2H5OH + 2CO2
+
-
So the plan is: bacteria use CO2 to photsynthesise glucose - glucose with zymase to produce ethanol, then produce ethylene for polyethylene. But this is the same as normal polyethylene so it doesn’t biodegrade, however plastic is recyclable...
+
-
Specifically talking about cyanobacteria
+
'''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.
-
http://en.wikipedia.org/wiki/Cyanobacteria
+
-
it seems these bacteria ‘utilize the energy of sunlight to drive photosynthesis, a process where the energy of light is used to split water molecules into oxygen, protons, and electrons’
+
-
Thus I would very much try to look at this bacteria as a way of potentially creating an energy supply? Especially if we can stick some probe into it? Or silicon? We could also look at it as an expandable battery too, as they reproduce?
+
'''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.
-
A simpler suggest is: (but seems lame compared to above?)
+
'''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.
-
- Store up carbon, maybe similarly to chloroplasts? Could we also make use of carboxysomes for increased uptake?
+
-
- Ca(OH)2 + CO2 → CaCO3 + H2O
+
-
- the Ca(OH)2 comes readily from CaO + H2O → Ca(OH)2 and CaO; a by-product of the Solvay process to produce sodium carbonate.
+
 +
'''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.
-
Catalytic Converters / Removing chemicals from emissions
+
'''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!
-
Poisoning or recovery?
+
==Ideas on the shortlist==
-
Current catalytic converters use a platinum catalysts - quite expensive.
+
'''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.
-
http://mic.sgmjournals.org/content/156/9/2630
+
-
http://libsta28.lib.cam.ac.uk:2087/doi/10.1002/jctb.928/full (behind Raven login)
+
-
http://www.sciencedirect.com/science/article/pii/S016816560600976X
+
-
All modern catalytic converters are 3-way:
+
'''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).
-
A three-way catalytic converter has three simultaneous tasks:
+
-
Reduction of nitrogen oxides to nitrogen and oxygen: 2NOx → xO2 + N2
+
-
Oxidation of carbon monoxide to carbon dioxide: 2CO + O2 → 2CO2
+
-
Oxidation of unburnt hydrocarbons (HC) to carbon dioxide and water: CxH2x+2 + [(3x+1)/2]O2 → xCO2 + (x+1)H2O
+
-
Point 2 is performed by methanogenic bacteria, e.g. http://www.ebi.ac.uk/2can/genomes/archaea/Methanobacterium_thermoautotrophicum.html
+
'''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.
-
see paper http://www.ncbi.nlm.nih.gov/pmc/articles/PMC221834/pdf/jbacter00299-0130.pdf which has some rate data (quite a gem, from my experience lately!)
+
-
Felix : - perhaps consider it from the perspective of removing catalyst posioning? Or finding better catalytic methods? - maybe carboxysomes? These seem to have a large surface area - however this project seems potentially difficult since enzymes seem to catalyse most reactions
+
'''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).
-
Another perspective to approach is that since the products are carbon dioxide + nitrides, we could do well to send in bacteria to eat or store them? Though I can see this is hard due to sheer volume...
+
'''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.
-
Water Treatment / Filtration
+
'''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.
-
Or even a way of detecting whether water is contaminated or not. - what criteria? use of thresholding? I remember in GCSE geography measuring levels of nitrate, oxygen, etc....
+
==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!
-
Contaminant testing seems to have been done a lot - mainly heavy metals etc.  Water treatment through microbes is the way sewage treatment works at the moment - we could possibly look at optimising that? - this is probably difficult, and filtering with coarse and fine sands seem very effective anyway
+
-
 
+
-
http://microbewiki.kenyon.edu/index.php/Candidatus_Accumulibacter_Phosphatis seems to be the big one in preventing eutrophication, but it was only discovered through metagenomics - not sure if anyone’s managed to culture it yet even, so it’s not that well characterised. 
+
-
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC124021/ suggests that E.coli could do it
+
-
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC182526/ shows some steps towards it
+
-
https://2008.igem.org/Team:NYMU-Taipei/Project/Phosphate seem to have done most of the characterisation for phosphate absorbtion - some optimisation work left for water reclaimation but not a whole project. --Cat
+
-
Soil Fertilisation / Monitoring
+
-
 
+
-
Release of Nitrogen when necessary
+
-
Malaria Diagnosis (or other diseases)
+
-
 
+
-
Can we optimise existing techniques
+
-
 
+
-
Good outline of existing http://cmr.asm.org/cgi/content/full/15/1/66
+
-
 
+
-
Felix - ‘ My vote is probably a no; working with diseases is dangerous, and work done may not be very general. However, generic methods of diagnosis and treatment by a bacteria could potentially be groudbreaking!!!’
+
-
Joe - We don’t need samples of the disease! If our method relies on detecting an antigen, we only need samples of that antigen. We might even come up with something else.
+
-
 
+
-
Many diseases are hard to diagnose in the field - they require at least rudimentary lab skills & equipment. EDIT: for Malaria, devices exist for use in the field but they are not very sensitive
+
-
 
+
-
More generally: detection of disease from blood serum
+
-
https://2008.igem.org/Team:NYMU-Taipei/Project/Urea have a brick for a Urea sensor.  Could create biosensor to illustrate normal/potentially toxic levels, but is there enough here for a whole project?  What else could be detected? Any parasite that inhabits blood or releases antigens into the blood, for instance:
+
-
Chaga’s disease - difficulty is, procuring specimens of this disease to test would be potentially dangerous? Imperial only needed to procure one protein (an antigen displayed by the parasite and harmless on its own) to prove that their concept was sound.
+
-
 
+
-
In the case of malaria, it seems like the consensus is how to improve the production of artemisin which is the most effective cure to date... - may be quite difficult and seems like lots of work has been done - but Gos thinks it’s possible.  Perhaps induce expression of artemisinic acid and chemically modifying the enzyme - novel drug?
+
-
 
+
-
Generic Diagnosis Paradigm?
+
-
- We all felt that the detection mechanism used by the Imperial team last year for tropical disease was very novel, which begs the question: is there a neat way to isolate and diagnose diseases generically? - Maybe expand on their mechanism?
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Drug Delivery Transport Mechanism - tissue recognition?
+
-
- A lot of systems have been engineered which deliver drugs when they reach the target destination, but not many address the issue of how the bacteria manage to identify the target site.... - is there a way to flexibly code a destination site?
+
-
Curing Cholera
+
-
 
+
-
The cause of cholera is excessive Cl ion leak from the GIT epithelium - the cholera toxin causes this by raising cellular cAMP ( I think). E. coli populate the GIT in humans and therefore there may be a way to stop Cl ion leaking (which draws excessive water out) if E. coli are used to deliver a prevention.
+
-
(Curing cholera is simple - abundant rehydration - but it’s just often hard to deliver so much clean water in remote places and/or when epidemics involve such huge numbers that the resources are insufficient)
+
-
Diabetes
+
-
 
+
-
Implant to release insulin on demand based on blood sugar levels. According to Gos, putting bacteria inside a person is currently a long way from being feasible due to an inflammation response.  Insulin production has been done - doubtful we could add anything to the current recombinant technology there.
+
-
 
+
-
Magnetic Bacteria
+
-
Quality and size -- enzymatic biosensors
+
-
 
+
-
Potential excellent method for gathering in bacteria dispersed for a task - eg. cleaning nitrates from a lake.
+
-
Found perfect review: http://www.ncbi.nlm.nih.gov/pubmed/21171958
+
-
A summary of the aspects relavent to our work:
+
-
Certain bacterial species have an unusual internal membrane system: a magnetite particle surrounded by a lipid bilayer - the magnetosome (MS).  The MS is 50-100nm in diameter - possible nanophotonic properties?  Producing fusion proteins with endogenous (native to the magnetic bacteria) magnetosome-targeted proteins allows display of proteins on the MS outer surface.  Nothing particularly interesting seems to have been done with this technique.
+
-
 
+
-
No useful magnetic parts are present in the registry. There’s an opportunity to contribute a huge amount!
+
-
From Wikipedia, it seems like many possible applications of magnetic bacteria are already in people’s minds, the only barrier to mass commercial production is that naturally magnetotactic bacteria are expensive to produce - simply putting the characteristic into E.Coli would open up a world of possibility within industry. I’m very interested in perhaps focussing very simply on just giving E.Coli magnetic properties, and amplifying them as much as possible. This would follow in a similar vein to last year’s team, who focussed on just amplifying fluorescence as much as possible, except that magnetic characteristics are probably far more useful (and difficult to produce!). Some useful links from brainstorming sessions of previous teams: Bristol, Brown.
+
-
Cambridge 2008 seriously considered it, but discounted it in favour of the iBrain...it’ll be worth asking Jim why. I just saw that Toronto also looks like they’ll be attempting it this year.
+
-
We could perhaps distinguish our work by linking it with the iron absorption idea below...and submit for the environmental track? And combine this with pigments to make it change colour depending on how much iron it absorbs/is around?
+
-
Even got a potential project name - E. GEM - E.coli:Genetically Engineered Magnet!
+
-
Some genomic information about a specific species: http://microbewiki.kenyon.edu/index.php/Magnetospirillum_magneticum
+
-
Some success in getting compatible genes from magnetotactic bacteria into E.coli - also aiding iron absorption
+
-
http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.1991.tb02156.x/abstract
+
-
A study which claims to have found a potential “magnetosome genomic island”, and is generally about magnetosome production in prokaryotes:
+
-
http://www.nature.com/nrmicro/journal/v2/n3/abs/nrmicro842.html
+
-
Identification and functional characterization of liposome tubulation protein from magnetotactic bacteria(initiating magnetosome production: http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2010.07117.x/full
+
-
 
+
-
Felix - potentially groundbreaking stuff, as described, however a lot of bacteria would be required and concentrating iron could be difficult, though quite a lot of methods have been tried (like optimising the promoter, or changing the choice of anchor gene). Potentially we could try tackling this by means of something structural?  there are also worries about over-expression leading to cytotoxicity, and I thought that high levels of Fe is bad for bacteria? hm....
+
-
Functional magnetic particles have been produced by the genetic engineering of magnetotactic bacteria e.g. M. magneticum AMB-1 - so there seems to be a starting point however I don’t know how easy these things are to engineer - and can we get some of these bacteria?
+
-
 
+
-
 
+
-
Nutrient fixation in soil
+
-
Felix - I don’t think there’s much to be done and not much new to gain from re-engineering this?
+
-
 
+
-
Bacteria that naturally fix nitrogen already exist (Diazotrophs , cyanobacteria) - I’m not sure if we could beat their design!
+
-
- but if nitrogen-fixing bacteria require specific environmental conditions, maybe it would be possible to create an E.coli/ Bacillus with the nitrogen-fixing pathway that could survive more unfavourable conditions - e.g. considering pH, temperature, or higher levels of harmful chemicals?
+
-
 
+
-
Removal of heavy metal particles from lungs (bacteria removed from lung in normal fashion...)-
+
-
 
+
-
Heavy metal absorbtion (As, Ca) has been done by a few groups.  Could look at other lung stuff, like the mucus removal idea?
+
-
 
+
-
Chocolate-scented poo dangerous - probably safe to say this idea is eliminatable :P
+
-
 
+
-
Highly sensitive olfactory indicator, or detect source of chemical contaminant
+
-
Detection of explosives? No - explosive ‘smell’ is too varied; and so bacterial sensors are too specific for this application.
+
-
Not much in the registry. Not much research success in the literature, either.
+
-
 
+
-
 
+
-
 
+
-
Hormone sensors/releasers
+
-
 
+
-
Hormone-biosynthesis
+
-
The hormone production idea could have some scope; Human growth hormone and some plant hormones have already been produced by GM bacteria, and the benefits are substantial...
+
-
 
+
-
http://en.wikipedia.org/wiki/Alpha_subunit_of_glycoprotein_hormones might be an interesting starting point - hormones used in IVF treatment etc share a subunit.  Bacteria which can produce any one of these hormones in response to different stimuli?
+
-
 
+
-
Adrenaline biosynthesis: useful, given that chemical synthesis requires the separation of a racemic mixture.  4 enzymes in the pathway http://upload.wikimedia.org/wikipedia/commons/0/08/Catecholamines_biosynthesis.svg
+
-
Useful in emergency medicine etc.  Can’t see it in the registry either...
+
-
Also a promising project since every intermediate product is medically useful:
+
-
Start: produce tyrosine amino acid - codons known to be UAC, UAU
+
-
 
+
-
Enzyme 1: Tyrosine hydroxylase (TH gene in humans) sequenced in rats:
+
-
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC397092/
+
-
http://www.genecards.org/cgi-bin/carddisp.pl?id_type=entrezgene&id=7054
+
-
 
+
-
expressed in high yield in E. coli! http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1991.tb16133.x/pdf
+
-
 
+
-
-> produce Levodopa (clinically useful for Parkinson’s treatment)
+
-
 
+
-
Enzyme 2: aromatic L-amino acid decarboxylase
+
-
The gene encoding the enzyme is referred to as DDC and located on chromosome 7 in humans.[3]
+
-
 
+
-
->Produce dopamine (many medical applications)
+
-
 
+
-
Enzyme 3: Dopamine beta hydroxylase (Dbh)
+
-
2003: “Recently, two polymorphisms (DBH5'-Ins/del and DBH 444 g/a) of the Dopamine Beta Hydroxylase (DBH) gene were isolated”
+
-
Dbh “activity requires ascorbate as a cofactor.[1]” (i.e. vit C)
+
-
http://www.genecards.org/cgi-bin/carddisp.pl?gene=DBH
+
-
 
+
-
 
+
-
->Produce norepinephrine, used to treat life-threatening low blood pressure (hypotension) that can occur with certain medical conditions or surgical procedures. This medication is often used during CPR (cardio-pulmonary resuscitation).
+
-
 
+
-
enzyme 4: phenylethanolamine N-methyltransferase
+
-
 
+
-
-> produces adrenaline.
+
-
 
+
-
E. coli thrive with such chemicals:
+
-
http://iai.asm.org/cgi/content/abstract/70/11/5913
+
-
 
+
-
Unfortunately, we don’t want to tamper with making bacteria that could live in the human gut that can affect human physiology - it’s outside containment level 1!
+
-
 
+
-
 
+
-
Bacteria to recognise and disable/remove eutrophying bacteria
+
-
 
+
-
Tricky to do - as I understand it the main problem is algal blooms etc - it’s not so much the bacteria as the size of the population, which is difficult to judge in order to model the right amount of our killer bug to add etc. Possibly looking at nitrogen scrubbing from water is the better angle.
+
-
 
+
-
Purification of salt water
+
-
 
+
-
Intelligent food packaging and Control of fruit ripening (potential)
+
-
http://en.wikipedia.org/wiki/Ethylene#Ethylene_biosynthesis_in_plants suggests that there are only 3 enzymes in the pathway, and it uses Methionine which will definitely be found in bacteria. EDIT-
+
-
https://2010.igem.org/Team:Monash_Australia/Parts appear to have done this and made bricks for the enzymes, though based more around plastic production.
+
-
 
+
-
perhaps not the most original of ideas:
+
-
http://www.juiceland.co.uk/item--Ethylene-Gas-Guardian--OT002.html
+
-
http://www.dixellasia.com/s0218/index.php?pgid=0508
+
-
 
+
-
If we could get this to work, then we would need to think about the wider implications of such technology. We’d need to think about how to contain the bacteria (there was a team which developed beads as a containment method, these guys)
+
-
 
+
-
Plastic or metal degradation
+
-
there’re certainly some bacteria that have been proven to aid the degradation of plastic (several different kinds of plastic actually, e.g. polythene
+
-
however, those bacteria are of different strains(by Phanerochaete and Streptomyces Species in one paper), not sure if there are biobricks for E.Coli.
+
-
 
+
-
pros: the application is direct, and addresses an important environmental issue
+
-
 
+
-
http://www.ots.ac.cr/tropiweb/attachments/volumes/vol51-3-4/03-Kathiresan-Polythene.pdf
+
-
http://www.ncbi.nlm.nih.gov/pubmed/16419620
+
-
http://green-plastics.net/features/64-guest/93-plastic-biodegradation-in-landfills
+
-
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC182779/
+
-
 
+
-
Stanford 2009 have looked at this a bit.
+
-
 
+
-
 
+
-
Crude oil degradation
+
-
Interesting paper - “Microbial degradation of hydrocarbons in the environment” - enough said! (paper published in 1990, a bit dated)
+
-
It is known that they improve their degradation properties a lot with evolution - a good example to experiment with phage-assisted continuous evolution (PACE, see here). This isn't related to phage display; instead it's a really interesting way of speeding up evolution drastically. It relies on having a certain gene (pIII) in the bacteria; this gene already exists in the Registry (BBa_K415108) which is good. We then need to devise a way to link the gene we want to evolve to the rate of production of pIII. (Courtesy of Edinbourgh 2011 :P)
+
-
PACE: http://www.nature.com/nature/journal/v472/n7344/full/nature09929.html
+
-
EDIT - ‘oil-eating bacteria’ have already been patented. COUNTER-EDIT: “natural oil eaters” exist and are there for us to exploit
+
-
 
+
-
 
+
-
Heather (5 Jul)
+
-
very interesting paper  on polycyclic aromatic hydrocarbon degradationgenes. polycyclic aromatic hydrocarbons are widespread important pollutants in the environment with known or suspected toxic, mutagenic and carcinogenic properties.
+
-
 
+
-
    http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6968.1999.tb13510.x/full
+
-
a few biobricks  from alkB1GHJ operon of a hydrocarbone-degrating marine bacterium, Alcanivorax Borkumensis SK2.    Part:BBa_K419008
+
-
 
+
-
these biobricks were produced by the 2010 TU_Delft team https://2010.igem.org/Team:TU_Delft#page=Home
+
-
 
+
-
alkane breaking enzyme and corresponding gene identified. solvent tolerance sub-project is well-linked to real application
+
-
http://www.springerlink.com/content/x5q267pcmmkj3nd7/fulltext.pdf
+
-
The metabolism of Mycobacterium gilvum can break down polycyclic aromatic hydrocarbons, including pyrene, via the dioxygenase NidAB enzyme.
+
-
 
+
-
            http://www.asknature.org/strategy/4167cd6828a6d8853562a84aa53ef1a3
+
-
much potential in bioremediation!
+
-
 
+
-
 
+
-
 
+
-
Potential applications of PACE
+
-
 
+
-
Smart bandage
+
-
Despite the fact that biofilms have been shown to ‘protect’ wounds from the outside world (PMID: 18211576) (in this case by increasing the resistance to antibiotics), the problem of containment and medical approval are insurmountable.
+
-
 
+
-
Removal of mucus from lungs of cystic fibrosis sufferers - better yet gene therapy?
+
-
No - we want to avoid any application which involves getting GM bacteria in the body!
+
-
 
+
-
Synchronised swimming (multi cellular signalling)
+
-
 
+
-
Leak detection (most applicable when the pipe is hard to access)
+
-
 
+
-
Could be done with a bacterial coat or whatever on the outside of the pipe: run a signalling compound through the liquid inside the pipe, use a reporter mechanism (e.g. lux) to highlight any leaked signal.  Basically an extension of the biosensor idea, would be more sensitive than current dye-based detection methods due to amplification if we included a positive feedback loop.  Seems straightforward to do, but it could be done with existing parts.
+
-
 
+
-
Smart coating on windows, bacterial ‘curtains’
+
-
 
+
-
Bio-scaffolds
+
-
 
+
-
Bacterial Solar panel
+
-
 
+
-
Gecko gloves
+
-
 
+
-
Microfluidics control -- “Lab on a chip”
+
-
Alex Kabla
+
-
Applications of microfluidics in designing precise tools for bio -- side project?
+
-
 
+
-
Bacterial electronics and electron transport
+
-
Bacterial battery?
+
-
Rhodoferax ferrireducens - key bacteria!
+
-
Other members of the plant sciences department have just returned from a seminar where one group was trying to do something a lot like this: transfer electrons from a plant cell to a bacterium (I think)
+
-
I read about microbial fuel cells - it seems that quite a lot of people are working on ‘batteries’ with Geobacter bacteria - about 0.3 volts.http://www.geobacter.org/Microbial_Fuel_Cells
+
-
But these bacteria also produce nanowires - conductive filaments, and these “may have applications in the development of nanoelectronic devices, sensors, and microbially based fuel cells”. http://www.geobacter.org/Nanowires
+
-
 
+
-
Bacterial heater
+
-
 
+
-
Inner-city air scrubbing
+
-
 
+
-
Asbestos removal (infeasible)
+
-
Can’t be degraded in-situ - needs high temperatures.
+
-
Mitigating toxicity is feasible, at least.
+
-
However, after researching into what makes asbestos dangerous, it seems that people are not even sure what causes their toxicity...hard to target.
+
-
 
+
-
 
+
-
Hydrogen production
+
-
Key genes may be being patented, but there is a lot of potential there too. Some of the difficulties in hydrogen production in E. coli have been recently solved. Worth considering what we could do differently to this start up. Perhaps try and follow the Bristol 2010 model and mock up our designs as commericial products?  Or perhaps focus on utility in the developing world? It is worth bearing in mind that hydrogen has a low energy density, so it would take a lot of hydrogen production to manage to power anything particularly large - a vehicle, for example, is out of the question.
+
-
 
+
-
Disruption of biofilms
+
-
A potentially good idea. A biofilm is made of of many bacteria (usually of different species) which secrete ‘Extracellular Polymeric Substance’ (EPS), aka slime, which protects them from antibiotics & disinfectant (think dental plaque, Legionnaire's disease & gonorrhoea).
+
-
An enzyme, dispersinB has been shown to disperse these bacteria (PMIDs: 15215120, 16339929). Also, cis-2-decenoic acid reduced biofilm growth and also causes dispersal.
+
-
A previous iGEM team, British Columbia 2010, had the idea of getting E. coli to detect biofilms (quorum sensing) and release dispersinB. While they did not clearly demonstrate a working prototype, they did a lot of the leg-work, so we’d pretty much just be mopping up their left overs.
+
-
The metabolic pathway for cis-2-decenoic acid is not well understood. It looks like something of a mammoth task to try something along that route.
+
-
 
+
-
Stress sensor
+
-
 
+
-
Metal fatigue detection
+
-
 
+
-
Self-healing surface protection / scratch-proofing/ self cleaning
+
-
Effects of micro- and nano-structures on the self-cleaning behaviour of lotus leaves - Science a review article surveying different methods of self cleaning coatings
+
-
A summary of natural self cleaning:
+
-
- due to two levels of surface structure: micro-scale mound-like structures of several micrometres tall protruding from the leaf and nanoscale hair-like structures covering the leaf surface acting in conjunction with the leaf’s waxy surface composition.
+
-
- the overall effect is that the water accumulates and rolls off the leaf collecting up the dirt etc..
+
-
- the key idea in developing this strand/track is to basically prevent the sticking of grease etc... by engineering such a repellant surface. - perhaps using detergent as a model?
+
-
 
+
-
Light-emitting biofilms
+
-
- sounds like an light emitting screen which is a past iGEM project
+
-
- the challenge would be to create one whose lighting levels can be dimmed actively..
+
-
- However, surely last year’s bricks could just be expressed under controllable promoters?
+
-
 
+
-
Combined `light sensor and light emitter
+
-
 
+
-
Reclaim nitrate from eutrophied water
+
-
Denitrifying bacteria have already been identified that convert nitrate into nitrogen in aerobic conditions - these are already thought to be useful in waste water systems: they are already at home in rice paddy sediment in Taiwan: http://www.sciencedirect.com/science/article/pii/S0960852498001400
+
-
http://mic.sgmjournals.org/content/129/9/2847.full.pdf+html
+
-
And also in the 1970s: http://books.google.co.uk/books?id=D-Syvg2TEJQC&pg=PA394&lpg=PA394&dq=nitrate+content+sludge&source=bl&ots=5iJ_aE6ldL&sig=skMpfFhBEqDx-xpkOus-NBvJv8k&hl=en&ei=b3wLTq7SIMaBhQf-s9zlDw&sa=X&oi=book_result&ct=result&resnum=4&ved=0CDcQ6AEwAw#v=onepage&q=nitrate%20content%20sludge&f=false
+
-
We could attempt to optimise the pathways?
+
-
 
+
-
According to Wikipedia, it’s phosphates that are the main problem in freshwater lakes/rivers; nitrates is more limiting and so will produce bigger blooms in the sea.  Reclaiming nitrates from water more generally is already an important part of sewage treatment (done by fermenting with random colonies) and for cleaning fishtanks, apparently. 
+
-
 
+
-
 
+
-
Vitamin-secreting bacteria, smart food supplements
+
-
+
-
Once again, we’d rather avoid having bacteria in the body...
+
-
 
+
-
Artificial organelles or compartmentalisation
+
-
 
+
-
Remote control bacteria
+
-
 
+
-
Sugar substitute creator
+
-
Already done very successfully (aspartame), with very bad press! Not much point effectively repeating what others have done already... Aspartame has a bad press because it was alleged to be unsafe, not because it is a sweetener. Perhaps we could introduce sweet proteins (or this) to E. coli?
+
-
 
+
-
Bread and beer making
+
-
Beer flavouring
+
-
How about a real “floral peach” aroma when you drink Golden Glory?
+
-
Wine making
+
-
- kombucha - a new drink fad made via fermentation&biofilm http://www.getkombucha.com/reforkotea.html
+
-
How about improving fermentation processes? Different temporal patterns?
+
-
This is also relevant to cellulose breakdown for biofuels (producing ethanol from glucose)
+
-
 
+
-
IRON
+
-
Extracting Iron from Iron ore at room temperature
+
-
-remove a particularly dull part of the A-level chemistry course for good, and potentially reduce material costs
+
-
 
+
-
Rust-eating or rust-preventing bacteria
+
-
The reason rust is bad is because it flakes off, exposing the surface underneath it to the air, which then begins to rust (cf. aluminium, which has a more physically stable oxide which protects the metal underneath it).
+
-
A common protection method is to introduce a barrier between the iron/steel and the air, either by paint or by coating it with a layer of plastic / something unreactive. If bacteria could be manipulated into reducing the rust and then laying down a layer of protective material, this may help solve the problem, but I imagine it would be difficult to be better than existing solutions, especially given the containment issues.
+
-
- maybe it could be useful in cases when you can’t conserve iron elements regularly, because they are difficult to reach?
+
-
 
+
-
Siderophores for iron absorption
+
-
Seems like an original idea - no other iGEM team has worked with iron, as far as I’ve seen
+
-
From Wikipedia: “the siderophore desferrioxamine B gaining widespread use in treatments for iron poisoning and thalassemia.”
+
-
One of the most powerful siderophores is naturally produced by E.coli when they are iron deficient - we can exploit this! http://en.wikipedia.org/wiki/Enterobactin
+
-
For general information about enterobactin:
+
-
http://biocyc.org/ECOLI/substring-search?type=NIL&object=enterobactin&quickSearch=Quick+Search
+
-
Enterobactin is also “An archetype for microbial iron transport“, “perhaps the best understood of the siderophore-mediated iron uptake systems” - http://www.pnas.org/content/100/7/3584.short
+
-
Chemical synthesis of enterobactin has also failed to exceed a yield of 50% due to production of racemate - all the more reason for biological research...
+
-
Some genetic analysis for other  gram-negative bacteria http://www.ncbi.nlm.nih.gov/pubmed/20585060
+
-
Biobrick relevant to siderophore production in E.Coli: http://partsregistry.org/Part:BBa_K259001
+
-
Relevant gene: http://pubs.acs.org/doi/pdf/10.1021/bi00458a012
+
-
 
+
-
Iron pollution is significant in soil and aqueous environments: e.g. “A fish that could tolerate water with a pH less than 5 will die at a pH of 5.5 if the water contains as little as 1.0 parts per million (ppm) of iron. (“http://www.fish.state.pa.us/anglerboater/2001/jf2001/wpollbas.htm”)
+
-
 
+
-
Iron supplement tablets - since Fe2+ (ferrous) is easier to absorb than Fe3+ (ferric), and enterobactin reduces iron from 3+ to 2+, they could be used to turn ferric into ferrous compounds for absorption in humans.
+
-
Slow release of the iron would be preferable to avoid side effects - this is the downside of commercially available ferrous tablets.
+
-
 
+
-
Peter from last year’s team pointed out that iron deficiency is a problem with quite a lot of crops, and plants have evolved to “steal” iron chelated by bacterial siderophores - mass production of the chelators could have applications in fertilisers? 
+
-
 
+
-
From what I can see there are chemical chelators available that are generally used a foliar sprays, but it may be that bacteria could make cheaper ones/ones better suited to soil application?  Iron precipitates as a hydroxide at higher pHs (which are often created by addition of phosphate fertilisers) , but an Fe3+ chelator will stop this.  Not found any info on whether plants can take up enterobactin specifically though.  If we went down this route we may have to look at plant chelators or chelators which plants have been shown to exploit. 
+
-
http://onlinelibrary.wiley.com/doi/10.1111/j.1747-0765.2005.tb00001.x/pdf seems to have some pertinent content (search for ‘enterobactin’)
+
-
 
+
-
Also, it’s not only enterobactin that seems to be plausibly compatible with an E. coli chassis - I quote:
+
-
“E coli produces and transports the catechol-siderophore, entrobactin, but also has at least four other separate receptor/transport sustems for iron citrate, FC, FOV, and other hudroxamate siderophores produced by soil bacteria and fungi.”
+
-
http://www.jstor.org/stable/pdfplus/4271457.pdf?acceptTC=true
+
-
“Escherichia coli, in which iron metabolism is particularly well understood, contains at least 7 iron-acquisition systems encoded by 35 iron-repressed genes.” and furthermore:
+
-
“Our macroarray-based global analysis of iron- and Fur-dependent gene expression in E.coli has revealed 14 new genes likely to specify at least three additional iron-transport pathways”.
+
-
http://www.ncbi.nlm.nih.gov/pubmed/12746439
+
-
 
+
-
====Carbon Sequestration====
+
-
i.e Removing carbon from the atmosphere
+
-
 
+
-
a) a cycle process developable for formation of ethylene from CO2 and allows us to test multicellular/ differentiated processes and b) potential solar source of energy if we use cyanobacteria as products of photosynthesis here is protons and electrons.
+
-
 
+
-
====Catalytic Converters / Removing chemicals from emissions====
+
-
Current catalytic converters use a platinum catalysts - quite expensive.
+
-
perhaps consider it from the perspective of removing catalyst posioning or finding better catalytic methods.
+
-
 
+
-
====Water Treatment / Filtration====
+
-
Or even a way of detecting whether water is contaminated or not.
+
-
 
+
-
====Soil Fertilisation / Monitoring====
+
-
Release of Nitrogen when necessary
+
-
 
+
-
====Plastic degradation====
+
-
decompose plastic bags/speed up the degradation process
+
-
 
+
-
====Hydrogen producing bacteria====
+
-
 
+
-
====Malaria Diagnosis (or other diseases)====
+
-
Many diseases are hard to diagnose in the field - they require at least rudimentary lab skills & equipment.
+
-
EDIT: for Malaria, devices exist for the use in the field but are not very sensitive
+
-
 
+
-
====Curing Cholera====
+
-
<i>(I may have to leave this explanation to a biologist.)</i>
+
-
 
+
-
====Diabetes====
+
-
Implant to release insulin on demand based on blood sugar levels.
+
-
 
+
-
====Drug Delivery Mechanism/Tissue Recognition====
+
-
A lot of systems have been engineered which deliver the drugs when it reaches the target destination but not many address the issue of how does the bacteria identify the target site. Is there a way to flexibly code a destination site?
+
-
 
+
-
====Magnetic Bacteria====
+
-
Quality and size -- enzymatic biosensers
+
-
 
+
-
====Highly Sensitive Olfactory Indicator====
+
-
Look at this from another angle? Detection of explosives? No - explosive ‘smell’ is too varied; and so bacterial sensors are too specific for this application.
+
-
 
+
-
 
+
-
 
+
-
{{Template:Team:Cambridge/CAM_2011_TEMPLATE_FOOT}}
+

Latest revision as of 19:06, 16 August 2011

Loading...
OVERVIEW
home

Contents

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!

Retrieved from "http://2011.igem.org/Team:Cambridge/Brainstorm"