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Latest revision as of 14:03, 15 October 2014

Imperial iGEM 2014

The whiteboard after an intense brainstorming session

An intense two weeks of brainstorming yielded a large range of possible projects. These ranged from the amazingly ambitious to the downright infeasible. These sessions were directed by the team. but we had input from some artists as well as our advisors. We’ve documented them here for future teams.

Developed Ideas

Living/active biomaterials

Conventional materials have static bulk properties that cannot adapt to the environment changing. Hybrid materials would allow biological functionality and the variation of properties over time and space. One such implementation would build on Nature Materials 13, 515-523 (2014) and modify E.coli curli fibrils in order to create novel biomaterials. The expression of these could also be induced by external stimuli as desired. This could through producing biofilms that can coat surfaces and confer useful functions. For example the addition of non-living materials such as nanoparticles and quantum dots to confer electrical or optical properties. Possible uses include self healing materials, large scale biosensors as well as solar cells.


The role of microorganisms in the weathering of terrestrial rocks and in the soil formation process has been shown to be significant with respect to physical processes alone. However the specific organism and method of weathering action is dependent on the terrain. This project would aim to engineer an organism that could act as an initial coloniser in a large range of environments, utilising multiple methods to breakdown rocky terrain into a soil. This would effectively kickstart succession, eventually making previously barren land usable for agriculture. This could in principle be used to increase arable land on Earth or even terraform other planets.

Thames water/wastewater treatment - microbial fuel cell

Water treatment coupled with either bioremediation, biomass growth or electricity was considered, particularly cultivating algae in waste water while producing electricity through an integrative co-culture microbial fuel cell. Algae could could be used as fuel or feedstock for farming. Another tangent from this idea was bioremediation of heavy metals using heavy metal-binding bacteria, occurring in conjunction with industrial wastewaters treatment. This would allow us to recollect and reuse these currently wasted metals (eg. platinum from electronics), perhaps for nanoparticle synthesis (Cd, Se, and Si). Maximise electron transfer at the microbe-electrode interface by using nanowires from G.sulfurreducens.

Animal free antibody generation

Forming a stable cell line (eukaryotic or prokaryotic) that can specifically and inducibly generate humanized antibodies. The benefit would be higher and purer production of antibodies, which would in turn allow antibody technology to become more affordable and ethically acceptable for animal activists. Together, these two reasons should allow for more widespread usage in research, particularly as common assays and for disease targeting.

Potsdam 2012 iGEM team have attempted a similar project using CHO (chinese hamster ovary) cells, and imitated the adaptability of the immune system that create a library of antibodies for in vivo clonal selection. They introduced a ‘Mutation Module’ consisting of the AID enzyme (Activation induced Cytidine Deaminase) that can introduce a 106 range of diversity through mutation. Then, in the ‘Selection Module’, they proposed a novel viral selection method where binding against the virus will select the appropriate antibody-matched cell, and will either promote or inhibit growth through signalling.

This idea was extended to perhaps apply a similar synthetic system for antibiotic design to address the antibiotic crisis. Delivery of an adaptable antibiotic or antibody producing biological unit into the gut or bloodstream to markedly improve our medical approach to bacterial and viral infections. We habitually only prescribe one pure form of antibiotic to patients and it is inconclusive whether this worsens the situation by directing and quickening evolution.

Programmable drug patches

Creating a dynamic, controlled, drug delivery system. inspired by the discussion of the low efficiency of the current nicotine patches used by smoking quitters. These provide a steady-state, quite low and constant nicotine supply done via skin absorption.Such a system would consist of three components: drug biosynthesis module, threshold setting module and an oscillatory release module. Such a system could be used to tackle smoking addiction but also other conditions that require an oscillatory drug supply. One example is chronic pain, where increasing tolerance and dependence can lead to serious problems. The advantage of such a system compared to a surgically implanted drug pump is that it is non-invasive and the dose cannot be modified by the patient.

Bio-electronic interfaces - protein nanowires

The advent of the personal computer made accessible the processing power and accuracy of these machines. Without these, significant advances in biology would have been delayed or unrealised due to unfeasible or lengthy data processing and rigidity in modelling capacity. Equally, if we were able to mediate direct signal or data transfer from one to the other, we would reveal wide possibilities that take the best of both worlds.

The biological unit is often better at sensing trace amounts, adapting to conditions, self-sustaining and communicating with other cells. If we could engineer an interface by which biology and computers could talk to each other, we can create bio-electronic sensors where a signal is sensed by the cell and this information is passed onto the computer. In turn, we could also better control biology by sending signals via the interface. The aim would be a quickly and easily programmable cell.

Conductive pilli are found in Geobacter and Shewellena species, and they could be arranged and engineered to be the mentioned interface, where the signal would be electrical. Potentially, this could provide a quantitative biosensor output on the computer. Some bacteria are naturally magnetic. A potential idea would be to align the poles of these bacteria directionally such that their combined magnetic force can induce an electromotive force perpendicular to their direction, according to Faraday’s Law. The idea would then be to read the strength and signal of the induced electricity.

Bacteria Breathalyser

The motivation for this idea was the Longitude Prize and it’s mission to prevent the rise of antimicrobial resistance through the development of a rapid, easy-to-use test for bacterial infections. This would allow health practitioners to use the appropriate antibiotics. Rapid specific detection of bacterial infections could be achieved through analysis of volatile organic compounds. This is already done to an extent using mass spectrometry techniques. A SynBio method would integrate the outputs of a number of biosensors in order to detect a specific strain. In order to do this the VOC profiles of specific species would first have to be identified. An alternative method of identification involves identifying unique molecules for each bacterial strain that are present in breath and using this to form a sensor. To achieve ease of use this would be incorporated into a breathalyser with some simple readout of results. One possible output would be a colour indicator for the most common infections.

Mammalian cell transformation

Mammalian genetic engineering is currently slow and expensive. This hampers research into many areas, including gene therapy, cancer research and fundamental genetics studies. Currently viral vectors and chemical/physical methods are used but these have fundamental problems. A new method that can carry larger payloads and allows easy engineering of genetic constructs is needed. We propose to develop a mammalian specific methods for transforming cells and use this to create induced pluripotent stem cells. Use as a treatment for diabetes would also be possible.

Plant Tumour transformation

Plant galls are usually seen as problematic by farmers as they direct resources away from crop plant development. This reduces yields and so affects the livelihoods of farmers.. It would be useful if these plant tumours could be used as living factories to produce high-value compounds. This would provide farmers with an additional source of income as well as meeting world demands.

Early Discarded Ideas

Lobster repair

Imitate the method crustaceans use for repairing breaks in their exoskeleton, perhaps by installing a biomaterial as a synthetic exoskeleton/clothing for humans that self-initiate repair.

Spy glue

Recent research exploits the protein domains from Streptococcus pyogenes to create a pair of irreversibly binding peptides, called SpyTag and SpyCatcher. We considered their application in modularly binding molecules on membranes and potentially as a Space Elevator.

Synthesizing water

Some areas are water scarce for a variety of reasons: governmental, political, and environmental. If we could synthesize a bacteria that releases water through respiration and could produce water anywhere and from locally available carbon sources, we could improve water distribution and availability in inaccessible areas.

Precious material production - silk, diamond, saffron, graphene

Alleviate the social and unethical consequences involved in the production and sourcing of of certain precious goods, by engineering an alternative method of producing these commodities using biological organisms.

Tasty Algae

Photosynthetic cyanobacteria (algae) are the most efficient fixers of carbon, and eating algae would help reduce energy wasted through transfers in food production (eg. from sun to plants to cattle). They are also highly nutritious (recall Spirulina). Unfortunately, they taste horrid, so engineering taste could be a big step towards energy efficiency in food production.


Detection of biological weapons or agents as a counter-terrorism measure.

RNA sensing

An RNA sensor does not currently exist, but would give vast quantities of data on the happenings of the cell, particularly the metabolic differences in different stages of diseased cells (eg. cancer). We extrapolated using a Cas9 from the CRISPR system to determine specificity using the sensing RNA attached to it.

Food packaging

Use bacteria to secrete a biomaterial that could be used as a biodegradable packaging material. This could also act as a lifetime indicator for the food.

Crop pests

Harness aphids, crown galls and other species commonly considered pests to express a useful and redeeming function, thus creating something of a synthetic symbiosis between crop and pest. Alternatively, we can also develop a more specific pesticide, which would not affect bees and nearby insects.

Car exhaust

Conventional chemical catalytic converters are not as efficient as they could be due to a warm-up period before they become fully functional. A biological catalytic convertor could be engineered that works in the desired temperature range and binds a greater range of pollutants

Oil recycling

Recycling the lubricating oil used in motor vehicles by removing the impurities collected over time.

Dormant triggered antibiotics

Antibiotics are often given to farm animals as a preventative measure. However the majority of the livestock is often healthy and do not require the antibiotics. This contributes to the development of antibiotic resistance. Dormant antibiotics would only be activated when infection is present and so would only be deployed when the greatest effect would be had.

Mouth problems

Design bacteria that can live happily in our mouth and help dental hygiene, maintain tooth enamel, to prevent bad breath, to combat plaque, improve tooth whiteness and strengthen teeth!

Gut bacteria producing vitamins and tackling obesity

Engineer gut bacteria to reuse waste and excess nutrients in order to produce useful products

Tackling addiction

Nicotine binding by nanobody triggers signal transduction for nicotine processing.

Electronics recycling

Breakdown waste electronics and collect the useful metals

CRISPR messaging

Adapt CRISPR systems to use guide RNAs and target transcriptional repressors (or activators) to any sequence. Possibly implement complex gene expression profiles by putting in the right amounts of various RNAs,

Phage therapy

Come up with a workflow for engineering a set of phages that target one or more specific pathogens, with optimised properties (e.g. infectivity, latent period) to most effectively wipe out the pathogen population.

Synthetic peptidoglycans or other ECM components for arthritic treatment

Some forms of arthritis develop due to imbalances in extracellular matrix (ECM) turnover. Synthetic peptidoglycans with long biological half-lives can be used to retain function.

Solving meat problem

Growing meat somehow in a way requiring less resources. Perhaps make a meat-producing plant, by expressing muscle tissue associated proteins in certain plant organs, e.g. fruit.

Project De-extinction

Use an extinct bacterium with a sequenced genome and edit the genome of the closest living relative bacterium in order to recreate the genome of the extinct species. Then insert the new genome into a host bacterium, resurrecting the extinct species.

Cleaning up oil spills

Design a strain which can use the carbohydrates in oil spills as source of energy and can either degrade all of the different compounds fully to CO2 or sequester them somehow into inert substances.

Hybrid system of logic gates

Create a biological OpAmp that could have various applications in SynBio

Orthogonal, light-inducible protein activated by infrared for optogenetics

Evolve a protein to respond to low-wavelength infrared light. This could be used as an orthogonal sensor that is not activated by daylight for optogenetics.

Increase plant stress resistance temporarily by expressing stress-resistance hormones

Use light or sound to induce short-term stress-resistance hormone gene expression prior to stressor (drought, insects, pathogens).

Human decomposition

Using decomposing material as a feedstock for a useful process.

Frog decline - chytrid fungus

Batrachochytrium dendrobatidis (Bd) causes frogs get Chytridiomycosis. This disease is lethal as frogs get hyperkeratosis which is thickening of the skin (high in keratin). This means that they can’t absorb water/electrolytes properly so die from heart failure. This is resulting in a worldwide population decline.We could engineer antifungal symbiotic bacteria or develop a biosensor for Bd.

Milk antibiotics

Detect residual antibiotic levels in milk that exist due to pervasive administration of antibiotics to dairy cows. Extending from this sensor, we could aim to bind the antibiotics specifically using antibodies and extract them somehow, such to prevent discarding milk with unacceptable levels of antibiotics.

Tackling bee decline

Bees and their hives are in danger

Skin microbiome body armour