Team:Leiden/HP/Gold

Human Practices

Human Practices

Safe by Design

During our project, we got into contact with National Institute for Public Health and the Environment (in Dutch: RIVM). This institute challenged us to get engaged and discover the possibilities to implement safety in our synthetic biology design.

The National Institute for Public Health and the Environment challenged us to shape and present our vision on how to make synthetic biology safe for the outside world. Therefore, we had different meetings with the institute and other iGEM teams, finally resulting in a special conference where people from science, business and politics could come together to share their thoughts.

We investigated the subject “Safe by Design” thoroughly and got many bright discussions, learning about new concepts and taking into account the considerations of other people, scientific and non-scientific, present. In this way, we were able to aggregate the following measures we would like to implement in our design to make our bacterium safe.

A bioreactor on Mars

In short, our bacterium would be able to convert a toxic substance found in Martian soil into useful oxygen and harmless chloride. But how do you make sure your organism keeps doing the job you designed it for?

First, one would not want Mars’ surface to be fully covered in bacteria. That’s why we decided very early in the process that the conversion of perchlorate should be performed in a closed environment: a lightweight bioreactor should be taken to Mars. In this way, the reaction but also the conditions needed for the organisms can be closely monitored.

Besides, we would consider to build in a kill switch. This introduces a need for a certain inducer or repressor for the bacterium to survive. When the bacteria find themselves in an area where there no such a substance is present, a killing mechanism will be activated from the inside. This way, the bacteria will only occur in places that we want them to be.

However, it also got mentioned to us that the harsh conditions on Mars can be used as a kill switch. The bioreactor itself should shield the bacteria inside from the changes in temperature and intense radiation so they can perform their task, but UV radiation is also on Earth often used to sterilize a wide variety of products and objects. For example, the water recovered from the bioreactor can be led through an unshielded pipe to kill any bacteria still present after treatment.

We will deliberately not make our bacterium resistant to Mars’ harsh conditions. We can implement measures to give our bacterium radiation and temperature resistance, but we choose not to do so for safety reasons. Further research has to reveal whether E. coli will survive the journey to Mars and how this will affect its metabolism, but if it is not necessary to add these elements, it is in our opinion safer to do not so.

More information on the design of the bioreactor system can be found here.

Regulating the reaction

Then about the removal and degradation of perchlorate. This process can be done chemically, but it is highly explosive and thereby with high risk. Our bacterium provides us with the process in a much more controllable way, via biochemical reduction. However, there’s still oxygen produced in this reaction. This is highly useful, since we also have to breathe when we’re on Mars, but when reaching high concentrations explosion of the gas mixture is imminent.

Strict regulation of the reaction should thus be achieved, for example by implementing feedback-loops in the synthetic biology circuits used. The circuit we would prefer makes use of an oxygen-dependent promotor, which represses the production of our enzymes of interest when a certain oxygen concentration has been exceeded. Thereby, quick degradation of the mRNA for the oxygen producing enzymes can be achieved when a degradation tag, like SsrA or AAV, is added to the end of the transcripts, so that repression of transcription also quickly results in a lowered enzyme production.

Sequencing in space

Only recently it has been proven by NASA that DNA sequencing in space is one of the tools we can take with us. In this way, we can keep track of the possible evolution of our organism, and the mutations involved. Although this doesn’t make the design of the organism itself any safer, it provides us with tools to monitor unwanted changes in our organisms. Besides, we can learn more about bacterial evolution and physiology in space, which will be invaluable to make future synthetic biology designs even safer.

We presented our first findings, in combination with a definition for safety in general, in the shape of a short clip. The National Institute for Public Health and the Environment was very satisfied, and invited us to present our findings at the conference “Veilig verder met synthetische biologie” on September 20th, 2016, where lively discussions led to even deeper insights, which were also included in the section above.

integrated human practices

In our project, we have encountered a large spectrum of interested people. They raised very interesting questions. An example is: “Would you want to be responsible for planting life on Mars?”. Other people wondered why we would even want to go to Mars. Through this dialogue we had, we were able to implement feedback of people into our project, to create an even better design. In the following examples, we want to represent some of the feedback that we have integrated into the design of our project.

The first question related to recycling water to be used for the bioreactor on Mars. We wanted to know how to be able to assure the purity of the water. We were especially interested in keeping GMO’s out of the water we want to store. To solve this issue, we spoke with a professor in biotechnology from the university of Delft. This professor had done research regarding biotechnology under Martian conditions. In terrestrial biotechnology, UV-radiation is used to kill bacteria in water. Through his research, he discovered that the radiation on Mars’ surface easily kills bacteria, as long as they are not extremophiles. We adjusted our designs to be able to integrate this feedback into our system. The result is shown in figure 1.

Figure 1. Radiation killing bacteria

The second improvement we made, was suggested to us by the same professor in Delft. Perchlorate is highly toxic, making its reduction very favourable. In its stead, chloride and oxygen are released. Whilst chloride is only harmful in very high concentrations ([Cl] > 1M), it will accumulate over time. We want to filter out salts formed by chloride. The professor had another idea of using Mars’ conditions to do our work for us. The temperature of the surface of Mars can reach temperatures as low as minus 153 degrees Celcius. The solvability of salts decreases at lower temperatures. If we expose a part of our bioreactor to these extremely low temperatures, a big part of the salts will precipitate. Because the salt than forms a relatively large structure, we can easily filter them. This way, we remove the risk of any dangerous chemical ending up in the water.

Figure 2.

The final refinement of our system, has to do with the bacterium itself. We had already thought of the implementation of a killswitch. In other words, a mechanism in the bacterium that will cause its own death upon a certain change in its environment. Specifically speaking, we wanted to be able to kill the bacterium by introducing a certain type of sugar into its environment. Around this time, the Dutch National Institute for Public Health and the Environment (RIVM) got into contact with us. We agreed to fulfil an assignment for them, in which we would display our idea of safety. For more information, see ‘Safe by Design’. As a result of multiple meetings and an ensuing conference, they inspired us to make a safer killswitch. This entails the bacterium dying upon the lack of a substance in its environment. In this case, it is a sugar that is not easily found in nature. This way, there can be no unpredictable spread of bacteria, in case of a leakage.

In our project, we were very concerned with our outreach. We are very much aware of the implications our work can have on our environments. Especially when it comes to a different planet, the consequences can be miraculous or disastrous. Through the surveys we took, the conversations we had and especially the conferences, we were able to drastically improve our idea. We are very grateful to all the people who were willing to help us.
Thanks!