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Talk:Team:Cambridge/Project
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| - | + | == '''Brainstorming''' == | |
| - | + | ||
| - | + | *'''Mood lighting:''' | |
| + | *'''Bacterial PCB:'''Bacteria are amazing at sensing chemical signals. However, because they lack internal compartments, their internal logic tends to be poor due to lack of specificity of signals and a limited set of different signalling pathways that cannot be spatially segregated. Nevertheless, individual cells are capable of acting as individual signal modifiers, capable of integrating or processing various chemical signals in a simple fashion fairly reliably. | ||
| + | |||
| + | Taking advantage of this fact, several different constructs would have been made. Once transformed into e.coli, these would have been permanently inducable by a substance which could have been painted onto the surface of a bacterial lawn. This would allow the differentiation of several different cell types, each with different logic processing properties. For example, it may be possible to create a cell type that can propogate a chemical signal in a simelar fashion to a neuronal action potential. See the image for how this might work. | ||
| + | |||
| + | By using several different substances, each causing induction of a single cell type, it would be possible to create fairly complex circuits upon a single agar plate, without the need for potentially interfering protein based signal processing within a single cell. The eventual aim would have been to create a kit which could be sent out to end users, who could use bacteria with a standardized output as a biosensor linked up to an input cell type. The user could then define the exact output properties they desired the circuit to have by painting their own circuits. For example, integration of two signal with an AND gate would be quite simple, as shown in the image. | ||
| + | |||
| + | It was felt that, though this project was highly modular, the individual modules were too ambitious and there were too many of them. The creation of a chemical action potential would have been excellent, but it would also have required some extremely fine tuning. Given the time span we had to work in, there seemed to be far too much to do. | ||
| + | |||
| + | *'''Inversion based devices:''' Endy et al. were able to create a system that was able to cause repeated inversion of a section of DNA. The ability to invert DNA creates a form of cellular memory, and this advance by Endy may allow for the creation of rewritable cellular memory. Rewritable memory is one of the components of a Turing complete machine, and when combined with the systems already characterized in e.coli and beyond may allow for extremely powerful microcomputing devices. Kyoto 2010 tapped into some small portion of this with their Sudoku solving bacteria that relied upon excision of DNA - non-rewritable memory. Adding rewritability could considerably extend the possibilities of bacteria. | ||
| + | |||
| + | This project would have involved obtaining the construct from the Endy lab and using it in some sort of bacterial logic system - potentially something as interesting as the Sudoku system. Additionally, the ability to use inversion based systems (even if non-rewritable) means we would be able to create a bacterium that was capable of maintaining a memory of what chemical environments it had encountered and in what order (similar to what Wisconson-Madison proposed but did not complete in 2010). This would have many potential bio-medical applications, from determining the location of gastrointestinal disease to working out the degree of pulmonary shunt a patient had, something that is only presently possible to determine by indirect methods. | ||
| + | |||
| + | As well as these, there is the possibility to create a new kind of biosensor that was capable of working out the concentration of substances at very low levels in the medium. As shown in the image '''(need to draw that image)''', inversion upon encountering a region of high concentration of a substance (due to induction of a specific recombinase) would result in a permanent change in DNA structure. Induction of a second recombinase could then indicate that a second substance was encountered later, causing one promoter to be bought into the correct orientation to drive expression of one reporter gene, here GFP. Multiple versions of these cassettes could be used to determine the differential experiences of many different bacteria - for example, substance A could cause expression of recombinase A, substance B recombinase B etc. As shown in the second image, many different reporter genes could be used for specific sequences of substances encountered. e.g, GFP could be expressed if B was encountered before A, but RFP if A was encountered before B. | ||
| + | |||
| + | Given that soluble substances will occasionally form tiny pockets of high concentration despite this being thermodynamically unfavourable, | ||
| + | *'''Speakoli:''' | ||
| + | *'''Piezoelectric mechanosensor:''' | ||
| + | *'''DNA localized protease signalling:''' | ||
| + | *'''Fire retardant biofilm:''' | ||
| + | *'''Tunable biosensor:''' | ||
| + | *'''Recombination based devices:''' | ||
| + | *'''Soil enrichment:''' One of the key issues facing the world in the 21st century is an increasingly strained water supply. From aquifer depletion in many wet areas, to encroaching desertification in drier areas, the accessibility of fresh water for drinking and food production will become a considerable point of strain for many countries in the coming years. | ||
| + | |||
| + | The idea behind this potential project was to introduce bacteria that produce bacterial cellulose into the soil of dry areas. Cellulose is a humectant, a substance which absorbs water from its surroundings and which releases it slowly upon drying of the surrounding environment. Hygroscopic polymers are already used in the growth of crops in dry soils, allowing crop growth in many areas where growth was originally unfeasible. Use of synthetic biology to create a more intelligent and environmentally friendly system could have a large impact in the world of low water agriculture. | ||
| + | |||
| + | It has the potential to be highly modular in design. In particular, the following ideas could be implemented: | ||
| + | |||
| + | *Chemotaxis towards roots. | ||
| + | |||
| + | *'Intellegent' production of cellulose upon prediction of drought conditions. | ||
| + | |||
| + | *Creation of an appropriate cellulose network within the soil. | ||
| + | |||
| + | *Appropriate termination of biosynthesis upon rainfall. | ||
| + | |||
| + | *Possible design of symbiotic relationship between plant and bacteria - provision of raw materials for bacterial cellulose by plant. | ||
| + | |||
| + | Bacterial cellulose network may also help block soil erosion, along with the increased water content of the soil. | ||
| + | |||
| + | Decided that project too closely resembles a combination of the Imperial 2011 project and the Osaka 2010 project. Additionally, many of the modules may be too ambitious to be realistic in the ten week time frame. | ||
| + | |||
| + | '''What do people think about aptamers? - JM''' | ||
Latest revision as of 09:25, 17 July 2012
Brainstorming
- Mood lighting:
- Bacterial PCB:Bacteria are amazing at sensing chemical signals. However, because they lack internal compartments, their internal logic tends to be poor due to lack of specificity of signals and a limited set of different signalling pathways that cannot be spatially segregated. Nevertheless, individual cells are capable of acting as individual signal modifiers, capable of integrating or processing various chemical signals in a simple fashion fairly reliably.
Taking advantage of this fact, several different constructs would have been made. Once transformed into e.coli, these would have been permanently inducable by a substance which could have been painted onto the surface of a bacterial lawn. This would allow the differentiation of several different cell types, each with different logic processing properties. For example, it may be possible to create a cell type that can propogate a chemical signal in a simelar fashion to a neuronal action potential. See the image for how this might work.
By using several different substances, each causing induction of a single cell type, it would be possible to create fairly complex circuits upon a single agar plate, without the need for potentially interfering protein based signal processing within a single cell. The eventual aim would have been to create a kit which could be sent out to end users, who could use bacteria with a standardized output as a biosensor linked up to an input cell type. The user could then define the exact output properties they desired the circuit to have by painting their own circuits. For example, integration of two signal with an AND gate would be quite simple, as shown in the image.
It was felt that, though this project was highly modular, the individual modules were too ambitious and there were too many of them. The creation of a chemical action potential would have been excellent, but it would also have required some extremely fine tuning. Given the time span we had to work in, there seemed to be far too much to do.
- Inversion based devices: Endy et al. were able to create a system that was able to cause repeated inversion of a section of DNA. The ability to invert DNA creates a form of cellular memory, and this advance by Endy may allow for the creation of rewritable cellular memory. Rewritable memory is one of the components of a Turing complete machine, and when combined with the systems already characterized in e.coli and beyond may allow for extremely powerful microcomputing devices. Kyoto 2010 tapped into some small portion of this with their Sudoku solving bacteria that relied upon excision of DNA - non-rewritable memory. Adding rewritability could considerably extend the possibilities of bacteria.
This project would have involved obtaining the construct from the Endy lab and using it in some sort of bacterial logic system - potentially something as interesting as the Sudoku system. Additionally, the ability to use inversion based systems (even if non-rewritable) means we would be able to create a bacterium that was capable of maintaining a memory of what chemical environments it had encountered and in what order (similar to what Wisconson-Madison proposed but did not complete in 2010). This would have many potential bio-medical applications, from determining the location of gastrointestinal disease to working out the degree of pulmonary shunt a patient had, something that is only presently possible to determine by indirect methods.
As well as these, there is the possibility to create a new kind of biosensor that was capable of working out the concentration of substances at very low levels in the medium. As shown in the image (need to draw that image), inversion upon encountering a region of high concentration of a substance (due to induction of a specific recombinase) would result in a permanent change in DNA structure. Induction of a second recombinase could then indicate that a second substance was encountered later, causing one promoter to be bought into the correct orientation to drive expression of one reporter gene, here GFP. Multiple versions of these cassettes could be used to determine the differential experiences of many different bacteria - for example, substance A could cause expression of recombinase A, substance B recombinase B etc. As shown in the second image, many different reporter genes could be used for specific sequences of substances encountered. e.g, GFP could be expressed if B was encountered before A, but RFP if A was encountered before B.
Given that soluble substances will occasionally form tiny pockets of high concentration despite this being thermodynamically unfavourable,
- Speakoli:
- Piezoelectric mechanosensor:
- DNA localized protease signalling:
- Fire retardant biofilm:
- Tunable biosensor:
- Recombination based devices:
- Soil enrichment: One of the key issues facing the world in the 21st century is an increasingly strained water supply. From aquifer depletion in many wet areas, to encroaching desertification in drier areas, the accessibility of fresh water for drinking and food production will become a considerable point of strain for many countries in the coming years.
The idea behind this potential project was to introduce bacteria that produce bacterial cellulose into the soil of dry areas. Cellulose is a humectant, a substance which absorbs water from its surroundings and which releases it slowly upon drying of the surrounding environment. Hygroscopic polymers are already used in the growth of crops in dry soils, allowing crop growth in many areas where growth was originally unfeasible. Use of synthetic biology to create a more intelligent and environmentally friendly system could have a large impact in the world of low water agriculture.
It has the potential to be highly modular in design. In particular, the following ideas could be implemented:
- Chemotaxis towards roots.
- 'Intellegent' production of cellulose upon prediction of drought conditions.
- Creation of an appropriate cellulose network within the soil.
- Appropriate termination of biosynthesis upon rainfall.
- Possible design of symbiotic relationship between plant and bacteria - provision of raw materials for bacterial cellulose by plant.
Bacterial cellulose network may also help block soil erosion, along with the increased water content of the soil.
Decided that project too closely resembles a combination of the Imperial 2011 project and the Osaka 2010 project. Additionally, many of the modules may be too ambitious to be realistic in the ten week time frame.
What do people think about aptamers? - JM
