Team:TU Eindhoven/Society/Synenergene/Application Scenario

Application Scenario

Bacteria will be able to solve some of the biggest problems humans have to face currently. Some caused by us directly some indirectly. They can provide us with cures and treatments for diseases that most of us come in contact with during our lifetime. For example, bacteria that can function as a pancreas: sensing glucose and producing insulin within a human body. Alternatively, bacteria that can clean up leaked oil in an oil spill are a possibility. The possibilities are endless; to a certain extend.

Nowadays, the biggest constraint genetically modified bacteria encounter is their limited ability to survive under non-natural conditions, such as the harsh conditions in industrial reactors and the immune system in the human body. Since early 2014, it has been iGEM team Eindhoven’s goal to tackle this constraint. They aspire to deliver a system that would allow Synthetic Biology to fulfil its dreams; to be able to apply the great ideas in the real world.

We started out by developing a “plug-and-play” system, Click Coli, for bacteria by designing a Clickable Outer Membrane Protein (COMP). In the fall of 2014, the functionality of the system has been proven: using the COMP, any DBCO-functionalized molecule can be clicked onto the outer membrane of the bacteria. This opens up a whole new world of coating bacteria in a desired material or immobilizing the bacteria onto a desired material.

This is a great new addition to the chemical toolbox used for altering bacteria, but alone it does not solve a fundamental problem in utilizing bacteria. Many materials have to be tested on their compatibility and functionality before practical application of the Click Coli system outside of the lab environment. Furthermore, a kill switch has to be implemented for teams using Click Coli so that the coated, and thus extra resilient, bacteria can be controllably killed. Lastly, more tests have to be done on how a clicked on material affects the internal homeostasis of bacteria.

Before making the Click Coli system public property, team Eindhoven has decided to perfect the Click Coli system first. We made this choice because we did not want to take unnecessary risks by presenting to the world an incomplete system that enhances the resilience of bacteria. Also, we expect that our idea is more appealing if the Click Coli system comes along with its own safety measures. Luckily, the Technical University of Eindhoven sees the potential of our project and decided to sponsor our research. Furthermore, we wrote to several institutes, such as the RSC (Royal Society of Chemistry), to collect small grants. Using this and the facilities the university already offers us, we will be able to prolong our research.

We expect the research phase to be finished early 2016. The Click Coli system will then be finished: its functionality is proven and perfected, there is a broad knowledge on how a coating affects bacterial homeostasis and using that knowledge, procreation of the bacteria has been permanently halted. Furthermore, the genetic code of a kill switch is inherently linked to the system itself, so the risks are mitigated. We are convinced that now, the Click Coli system is ready to be released free to use for anyone.

We hope that many research groups will pick up at this point and will begin testing their own materials. At this point, team Eindhoven will leave its current formation and split up into daughter companies. These companies, as the name implies, are commercial institutes that will begin to develop their own product. Naturally, as they go into a commercial formation, they will lose the privilege of funding by the Technical University of Eindhoven. They will have to find their own capital through funding. In this paper, three possible daughter companies will be discussed, which are as follows:

The program has the following steps: find and count the droplets, then find and count the cells in the droplets and finally create a histogram of the results (number of droplets with 0 cells, with 1 cell, with 2 et cetera). By adding up the histograms of multiple images you get a view of how the cells are divided over the droplets.

Droplet Detection

To detect the cells EdgeDetect (a function of Mathematica using gradient methods) is used followed by a dilation to make the edges clearer (Figure 2).

This results in clusters of pixels, all the pixels that are connected with only black pixels. The program then looks for the clusters bigger than 2000 pixels and smaller than 6000 pixels (Figure 3).

Parameters of Droplets Detection

The parameters of this function are chosen so they have a very low false positive, because a false positive means a non-existing droplet and thus false data. A false negative only lowers the sample size, which can be increased by analyzing more images.

Bacterial Cell Detection

The program is now at the point where it has to count the number of cells in the droplets. Using the droplets from the edgedetect picture, erosion with value 1 is performed (resulting with the deletion of before in closing of the image). This makes sure the cells connected to the borders of the droplet are loose, the program deletes the border components so it only finds cells. The program uses EnclosingComponentCount instead of count now because a lot of cells became empty circles to get the results.

The results for this image are 9 false positives and 11 false negatives on a total of 93 cell in 126 droplets. Because some droplets had multiple false positives or false negatives the next step to improve this number is selecting to droplets better.
Click here to download the code