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Boston Calling – Potsdam students take part in an international biotechnology competition

Students of the iGEM-Team. Photo: Thomas Roese.

Students of the iGEM-Team. Photo: Thomas Roese.

They establish their own research team, set themselves an ambitious goal and meticulously plan extensive experiments. Students of the University of Potsdam spare no effort to participate in a large international synthetic biology competition.

Bryan Nowack, Lukas Golombek, and Robin Michael have a common goal: They want to go to Boston. They are students at the University of Potsdam studying life sciences, computer science, biochemistry, and molecular biology. In addition to their studies, the 21-, 22- and 24-year old students are already engaged in research. Right now they are in the middle of preparing for a competition that demands a lot from them: it takes time, money, and enthusiasm to participate in the iGEM Competition. In the fall of 2019, the team will travel to Boston to showcase the results of a year’s hard work and compete with hundreds of other research teams from around the world.

Until then, there is still a lot to do. For half a year, the students have been revising and refining their ideas, forging plans for the upcoming work and putting together a team of students, scientists, and professors. In the end, about 40 students from different disciplines will belong to the team. Natural and life scientists are as much involved in the project as computer scientists, philosophers, and psychologists. The team will be supervised and advised by about 20 PhD students, postdocs, professors, and technical assistants. In addition to scientists from the University of Potsdam, the team is also supported by the Potsdam Max Planck and Fraunhofer Institutes and the Leibniz Institute for Zoo and Wildlife Research.

Biotechnology on the computer

Robin Michael and Bryan Nowack are at the center of the project. This isn’t Nowack’s first time at the iGEM Competition; he already led a team two years ago. “It was a lot of fun,” he explains. But that is not the only reason to plunge into the iGEM adventure again; his first time around sparked his ambition. “We did not achieve our goal at that time. In the end, time was too short.” That's what happens to most of the teams in the competition, but for the Potsdam students it is going to be different this year. “Now more than ever” is their motto.

The iGEM team has lofty aims again this year. “We want to change a protein, which is normally active at temperatures of 20- 45 °C, so that it becomes thermostable and remains active at higher temperatures,” Michael explains. Industrially used proteins – such as enzymes in the food industry – could be used in completely new areas without losing their stability and function. To achieve their goal, the students will perform conventional experiments in the laboratory and also work with neural networks on the computer.

The approach is called “in silico”. It is based on experiments with computer simulations. The structure of the protein, which the young researchers want to use for their investigations, is already known. They gather additional information from databases. An artificial neural network can then be used to create a digital model of the protein that features the desired thermostability. The decisive factors are the protein’s proper folding, how the amino acids are arranged relative to one another, and which bonds exist between the individual atoms. Thousands of combinations are possible. It is a gigantic task that requires enormous computing resources, so the Institute of Computer Science is supporting the iGEM team. “The training data for the neural network are a crucial point,” explains Lukas Golombek. The IT team will primarily work on researching appropriate data and feeding it into the neural network so that this network can learn to predict probabilities for mutations and create the optimal protein model.

Optimized proteins from the lab

They are starting laboratory work at the same time. The team is able to use laboratories at the German Institute of Human Nutrition (DIfE) and the Max Planck Institute (MPI) of Colloids and Interfaces. Here, the researchers want to induce random mutations in gene segments that carry the code for the protein. As the genetic information changes, the resulting protein takes on new properties. Subsequently, the students select and screen the resulting molecules and mutants for higher thermostability.
“The biggest challenge will be the screening,” says Robin Michael, because thousands of mutants will be created in the lab, which need to be analyzed as soon as possible. The young researchers hope that at least one of these mutations will have the desired characteristics and carries the information for a protein that is thermostable and functional at the same time. With this method, known among experts as “directed evolution,” proteins can be specifically optimized and improved.

The iGEM team is looking forward to the laboratory test results but also to the computer experiments, because the neural network develops in parallel the sequence for a protein that has the desired properties – without any laboratory work. The big goal is to combine both approaches to replace part of the lab work with computer work, making the overall process more efficient and cost effective.

A question of time – and money

“It is extremely time-consuming” says Michael. Until October 2019, the team members will have little free time. The lab will be staffed daily – in four-hour shifts during the lecture period, and even eight hours during the semester break. Every ten days, the team members, who are working in different groups, meet to discuss important results and upcoming work. “It's a full-time job, in addition to studying,” says Robin Michael, who knows what he has to expect. Before graduating, he completed training as a biological-technical assistant and worked in molecular biology labs in Berlin and Ireland. These experiences are good starting conditions for him and his team for the competition.

Time isn’t the only pressure facing the team; they also have to raise funds. “It's a very expensive project that we have to fund entirely by donations,” Michael explains. “The registration for the competition alone costs several thousand euros.” Finding sponsors is therefore one of the next key tasks. At least some of the material for the work in the lab has already received funding: the companies Eppendorf, ZymoResearch, and Promega are providing support.

At the end of the project, which will continue until October 2019, the team will take part in the big event in Boston – the “Giant Jamboree.” Thousands of students, scientists, and jurors will spend four days watching presentations and research results from over 300 teams. The Potsdam team will then have 20 minutes to present their results. They do not care about a place in the first ranks. What matters are the results, and having fun.


iGEM stands for international Genetically Engineered Machine. The competition was initially organized by the Massachusetts Institute of Technology (MIT), but it is now an autonomous event supported by an independent foundation. It has been held since 2003 and primarily targets students who can submit synthetic biology projects. This discipline combines molecular biology, nanotechnology, organic chemistry, engineering, and information technology. The goal is to create biological systems with new properties that are not found in nature. Novel enzymes, therapeutic substances, materials and even fuels can be produced using synthetic biology.

www.igem.org

The Students

Bryan Nowack is 21 years old and is in his first semester of a Master’s degree in microbiology.
Lukas Golombek is 24 years old and is in his ninth semester of studying computational science.
Robin Michael is 22 years old and is in his third semester of studying life sciences after his training to become a biological-technical assistant.
igem.up@gmail.nomorespam.com

Film: iGEM@UP 2019

Text: Heike Kampe
Translation: Susanne Voigt
Published online by: Alina Grünky
Contact to the online editorial office: onlineredaktion@uni-potsdam.nomorespam.de