Team:Imperial College/BrainStorm


Manufacturing

Cell-free manufacturing of antimicrobial peptides (AMPs) – Antimicrobial peptides are being sold as the solution to antibiotic resistant bacteria. However, they are currently being harvested from transgenic animals resulting in extremely high production costs. We proposed to develop a cell free system that allows for the quick manufacture of AMPs.

Functional amyloid fibril manufacturing – Amyloid fibrils are nanoscale protein structure that are characterized by their strength and flexibility. In addition to their material properties, they may be functionalized by fusing active protein domains to the amyloid monomers that make up the fibrils. The fibrils can therefore act as a scaffold that can be modified for various purposes. We investigated the possibility of fusing cellulolytic domains to these fibrils to enable cell-free cellulose degradation.

Biosilica – Silica is a common mineral that may be used in a variety of applications. The use of silica in nanotechnology often requires the formation of fine-scale silica structures, which are difficult to achieve using conventional synthesis methods. The aim of this idea was to exploit the naturally-occurring process of biomineralization to produce biosilica nanostructures that could be functionalized for a variety of applications, such as targeted drug delivery.

Food and nutrition

Algae-based food – Current food products created from sustainable ocean-based sources like algae are not particularly appealing to many people’s palettes, both visually and taste-wise. To encourage the widespread adoption of these food sources, we planned to create things such as bacon-flavoured red algae that would likely appeal to wider audiences as a viable staple food.

Fish feed – Aquaculture plays a massive role in feeding the world. However, current aquaculture practices rely on rather unsustainable practices to maintain cultured fish populations. Ironically, aquaculture is sustained on overfishing “feeder fish” populations in the wild to create fish feed to supply the required nutrients required sustain domestic aquaculture populations. The idea we came up with was to use yeast to create an extract that could supply the most costly key nutrients currently supplied by feeder fish. This extract could then be used manufacture fish feed that did not require the overfishing of wild fish populations allowing aquaculture to continue meeting its increasing demand in a sustainable manner.

Diagnostic

Blood coagulation biosensor – Anticoagulant drugs are used to prevent blood clotting. People requiring oral anti-coagulation therapy are part of three categories: those with atrial fibrillation, those with artificial heart valves, and those who are at risk of thrombosis. Today, testing of patients to determine if they are in the therapeutic range of the anticoagulant drug is performed weekly a hospital-based clinic or the physician’s office. The tests require a 24-hour wait before receiving results. Studies have shown that the more regularly patients test their blood, they significantly decrease their risk of heart attack or stroke. Microvisk recently designed an at-home blood coagulation testing electronic device which utilizes vibrating cantilevers to determine blood viscosity. We believed the system could be made more simple, cheaper, and sensitive through cell free patches containing cell derived molecular rotors which fluoresce at different intensities to indicate blood viscosity.

Environment

Abscisic acid production for crop drought protection – Abscisic Acid (ABA) is a plant hormone involved in the environmental stress response mechanism causing the stomata to close in drought conditions but this mechanism can be too slow to preserve the yield. Currently ABA is sprayed onto crops prior to droughts to improve the survival rates however ABA is expensive to produce and deteriorates quickly making the system inefficient. Therefore we devised a mechanism to allow fertilizers to respond to droughts/weather conditions faster than the natural system with a kill switch to ensure the device would not contaminate the surrounding environment.

Information processing

Turing machine – Theorised by Alan Turing in 1936. A Turing machine is a general example of a CPU that controls data manipulation, using sequential memory to store data.

Associative learning – One of the most basic and primitive form of learning is learning by association. The most profound example of such behaviour is Pavlov’s dog. Where the dog associate one stimulus with the onset of another one. We wanted to program this same behaviour into bacterial cell. Computational and some experimental evidences are present that suggest the possibility of such behaviour in E. coli. Various attempts have been made and one research group successfully program pavlovian conditioning in cell using AND gate with a memory component. However, true associative learning with reinforcement and the capability to relearn new information have not been programmed into cell before. Such behaviour could potentially be used to create smarter biosensors and diagnostic tool.

Neural networks – Biomimetic design of the human brain resulted in the development of neural networks. Neural networks are composed of multiple layers of two types: one that performs a turning function (allowing for selectivity to be implemented) and another that performs a MAX function that allows for invariance.

Foundational advances

Sonogenetics – Much like how different frequencies of light can be used to control gene expression via optogenetics, the idea behind sonogenetics is to use different frequencies of sound to do the same. Sound, unlike light, can propagate relatively easily and effectively through solid and liquid media allowing for possibly superior spatiotemporal control over gene expression compared to optogenetics in environments such as the human body.

In vivo optogenetic DNA re-coding – Genetic modifications in synthetic biology generally require the adding the DNA sequence of interest to the target cell via transformation. The aim of this idea was to remove the need for this by linking the target cell’s endogenous mechanisms for DNA synthesis to an engineered light-sensing system. The resulting synthetic system would allow the cell to recognize 4 wavelengths of lights, corresponding to the 4 nucleotide bases of the genetic code. Light pulses of these 4 wavelengths in a particular sequence could subsequently be used to ‘instruct’ the cell to synthesize DNA with the desired sequence in vivo.

Synthetic morphogenesis – In nature, shape defines function. Whether it be plant tissue, human tissue or on biofilms, the higher level structures and morphologies that populations of cells arrange themselves into play a massive role in the function of these cells. By creating biobricks whose function is to create and control 2D spatial arrangements and interactions of populations to form predictable, reusable basic shapes, we hoped to create a library of modular, basic population shape morphologies that could be used to create more complex structures in both 2D and possibly 3D.

Miscellaneous

Tunnel-forming bacteria – Deserts make up around 1/3 of the Earth’s surface. We propose to create create arable land with a micro-irrigation system in those deserted locations by creating a series of micro-tunnels. Bacterias are able to agglomerate sand into stone Ureolytic bacteria use urea has a source of energy. In the presence of high concentration of urea and calcium ions, the bacteria will release carbonate from urea hydrolysis to form calcium carbonate in-situ.They also produce ammonia, causing an increase in pH necessary for the bacteria to promote calcite precipitation. This results in soil solidification and stable microtunnel formation. Could possibly apply this method to create new composite materials (graphene foam).

Swarming bacteria – Engineer spatial control in bacteria for localised drug delivery, creation of complex material structures, bioremediation or localised biosensing. Two bacterial populations are engineered one called leader and the other follower. The Leader population is engineered to target and move towards specific signals in the environment it also produces chemoattractants and chemorepellents in oscillation. The follower population are receptive to the leader population’s chemotaxins. The followers home towards the leader population when they sens chemoattractants and away from the leaders when they sens chemorepellents creating an oscillating swarming behaviour. The follower population are engineered to perform task such as production of a material or drug, bioremediation or biosensing.

Programmable pigments/colour change – Chromatophores are pigment containing, colour changing cells. Their unique cellular structures allow animals such as fish and reptiles to rapidly change the colour and pattern of their skin to camouflage themselves against predators. Chromatophores used cytoskeleton to rapidly distribute pigment sacs across the cell in a process called pigment translocation. We wanted to couple this process to inducible protein receptors in order to create colour changing biomaterials that can respond to a wide range of stimuli.

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