Difference between revisions of "Team:Duesseldorf/Kaethe"
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<h2>The Challanges</h2> | <h2>The Challanges</h2> | ||
<p class=details> Before starting research, first the safety must be ensured. But this is a self solving problem, since the organisms are only able to live in a community that is designed by the researcher itself. That includes a detailed control of the microorganisms, the cell density, their behavior and environmental conditions. For industrial usage the production must be scalable and high throughput must be guaranteed as well. Furthermore, general technologies for a normed use for research projects that are also easily applicable for large scale production must be achieved<sup>4</sup>. One goal would be the reduction and simplification of processing steps and easy-to-use protocols for stable co-cultures to make cultivation and production faster and cheaper. Other requirements for making co-cultures a profitable alternative to isolated culturing are big product diversity and efficient extraction of them. For scientists the possibility to build complex systems and methods for big data collection are desirable and highly demanded. | <p class=details> Before starting research, first the safety must be ensured. But this is a self solving problem, since the organisms are only able to live in a community that is designed by the researcher itself. That includes a detailed control of the microorganisms, the cell density, their behavior and environmental conditions. For industrial usage the production must be scalable and high throughput must be guaranteed as well. Furthermore, general technologies for a normed use for research projects that are also easily applicable for large scale production must be achieved<sup>4</sup>. One goal would be the reduction and simplification of processing steps and easy-to-use protocols for stable co-cultures to make cultivation and production faster and cheaper. Other requirements for making co-cultures a profitable alternative to isolated culturing are big product diversity and efficient extraction of them. For scientists the possibility to build complex systems and methods for big data collection are desirable and highly demanded. | ||
Revision as of 12:27, 23 August 2018
PROJECT DESCRIPTION
The Challanges
Before starting research, first the safety must be ensured. But this is a self solving problem, since the organisms are only able to live in a community that is designed by the researcher itself. That includes a detailed control of the microorganisms, the cell density, their behavior and environmental conditions. For industrial usage the production must be scalable and high throughput must be guaranteed as well. Furthermore, general technologies for a normed use for research projects that are also easily applicable for large scale production must be achieved4. One goal would be the reduction and simplification of processing steps and easy-to-use protocols for stable co-cultures to make cultivation and production faster and cheaper. Other requirements for making co-cultures a profitable alternative to isolated culturing are big product diversity and efficient extraction of them. For scientists the possibility to build complex systems and methods for big data collection are desirable and highly demanded.
The Project
Since our co-cultures should be universally usable for laboratories all over the world, we plan to design it as easy and modular as possible. Therefore, the Golden Gate modular cloning standard techniques (MoClo) were used besides Gibson Assembly for our cloning steps, which allows exchange of all parts to adjust the co-culture to every possible condition5,6. We envision a standardised system, a three-way co-culture with a selection of organisms and regulations. `Trinity` is going to incorporate different dependencies between the organisms in order to control their growth and enable them to adjust each others behaviour. Project Trinity is divided into three systems. Our system 1 deals with the dependence of the organisms Escherichia coli, Saccharomyces cerevisiae and Synechococcus elongatus sp. PCC 7942 based on the availability of essential nutrients such as nitrogen7, phosphate8 and carbon9. The aim of system 2 is the dependency of E.coli, S. cerevisiae and S. elongatus , achieved through the exploitation of auxotrophies. S. cerevisiae is in our case auxotrophic for lysine which is produced by E.coli10(. At the same time, E.coli has an auxotrophy for leucine, which, in turn, is provided by S. cerevisiae. S. elongatus shows no auxotrophy and enriches the media with the monosaccharides glucose and fructose. This way E.coli and S. cerevisiae are regulating each other and do not overgrow S. elongatus. Each organism is responsible for the production of one substance, amino acid or glucose, and thus makes the other organism dependent on it. System 3 is utilising the quorum sensing mechanism to regulate cell density in the population by using bacterial communication molecules. E.coli regulates its own cell density by expressing a lysis gene after induction by AHL1 quorum sensing molecules11. For S. cerevisiae two different systems were introduced. The first one utilises the fact that upon recognition of the complementary mating type factor pheromone (MAT `a` for `alpha` yeast) yeast cells go into a cell cycle arrest and stop growing12. The second system depends on the design of a synthetic promoter that activates another lysis gene after the recognition of AHL2 molecules13. The following box provides a graphical overview as well as a summery of the role of each organism in the system for each Level: .
Our Trinity
Since our co-cultures should be universally usable for laboratories all over the world, we plan to design it as easy and modular as possible. Therefore, the Golden Gate modular cloning standard techniques (MoClo) were used besides Gibson Assembly for our cloning steps, which allows exchange of all parts to adjust the co-culture to every possible condition5,6. We envision a standardised system, a three-way co-culture with a selection of organisms and regulations. `Trinity` is going to incorporate different dependencies between the organisms in order to control their growth and enable them to adjust each others behaviour. Project Trinity is divided into three systems. Our system 1 deals with the dependence of the organisms Escherichia coli, Saccharomyces cerevisiae and Synechococcus elongatus sp. PCC 7942 based on the availability of essential nutrients such as nitrogen7, phosphate8 and carbon9. The aim of system 2 is the dependency of E.coli, S. cerevisiae and S. elongatus , achieved through the exploitation of auxotrophies. S. cerevisiae is in our case auxotrophic for lysine which is produced by E.coli10(. At the same time, E.coli has an auxotrophy for leucine, which, in turn, is provided by S. cerevisiae. S. elongatus shows no auxotrophy and enriches the media with the monosaccharides glucose and fructose. This way E.coli and S. cerevisiae are regulating each other and do not overgrow S. elongatus. Each organism is responsible for the production of one substance, amino acid or glucose, and thus makes the other organism dependent on it. System 3 is utilising the quorum sensing mechanism to regulate cell density in the population by using bacterial communication molecules. E.coli regulates its own cell density by expressing a lysis gene after induction by AHL1 quorum sensing molecules11. For S. cerevisiae two different systems were introduced. The first one utilises the fact that upon recognition of the complementary mating type factor pheromone (MAT `a` for `alpha` yeast) yeast cells go into a cell cycle arrest and stop growing12. The second system depends on the design of a synthetic promoter that activates another lysis gene after the recognition of AHL2 molecules13.