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One of the problems we had to face when dealing with unnatural bases was how to detect them in sequence analysis. However, there were many different sequencing methods that we had to consider. One of these is the single molecule real time sequencing that e.g. pacific biosciences is offering. For this purpose, we invited representatives of the company to introduce the method as well as data analysis patterns to us. So, on tuesday, the 5th of September, 2017, at 5pm,  Mr. Cong Luan Nguyen as well as Mr. David Stucki gave a talk on “Single Molecule Real Time Sequencing with the Sequel System and an outlook in data analysis”. This talk was attended by our team as well as many interested members of the CeBiTec and Bielefeld University. It was concluded with interesting discussion featuring different aspects of the technology. Some of the topics were possible uses of the system with unnatural base pairs as well as the advantadges of a general usage for the CeBiTec.
 
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Therefore, all in all, we gained some more insights into sequencing with the new technology and possible usages for our project.
 
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Revision as of 14:50, 31 October 2017

Human Practice Silver

Biosafety Report

Many teams need to deal with biosafety issues during the competition. Is our organism hazardous? What will happen if it escapes from lab? For this reason the iGEM HQ offers various opportunities to obtain information like the safety policies, safe lab work guidelines or the white list of allowed organisms. Further, many teams are working on the development of multilateral biosafety systems to prevent the release or at least the survival of genetically modified organisms (GMOs) in the environment. With the intention to summarize all relevant levels of biosafety systems, we worked on our biosafety review article: Auxotrophy to Xeno-DNA: An Exploration of Combinatorial Mechanisms for a High-Fidelity Biosafety System for Synthetic Biology Applications. Biosafety can begin on different levels, starting from a bioreactor to a complete synthetic DNA. In our review, we describe different containment approaches previously attempted by former iGEM teams. As the report is currently under peer review, it cannot be printed here. Instead, we composed a shortened version of its content, which can be accessed here.

ChImp Report

Research on genetics and related topics has been a topic of discussion and concern for more than a century, especially with regards to the ethics of using the genetic code as a tool. In recent years, the emergence of synthetic biology offers solutions to many world problems, while also raising questions about its responsible use. Researchers in the field aim at developing novel biological systems not found in nature by changing, removing, or adding genetic information, or creating entire organisms synthetically. Most recently, these methods have been applied, for example in the George Church lab, to incorporate non-canonical amino in order to create organisms with novel features. To assess chances and implications of such an expanded genetic code, we interviewed experts from the scientific, philosophical, and religious field, and surveyed the public on their opinions with regards to this topic. Building upon our research, we developed practical guidelines for research projects concerning synthetic biology, some of which we ourselves applied during our iGEM project. From the scientific point of view, incorporating unnatural components to the genetic code still lies within the scientific definition of life as long as the organism can still preserve itself. While stating that synthetic biology is well covered by current biotechnology laws, interviewees name biosecurity and dual use concerns as the most important factors with regards to responsible research. From the philosophical point of view, expanding the genetic code by means of synthetic biology does not change the definition of life for the most part. Specifically, experts in the field state that synthetic biology will most likely not incite new discussions about bioethics, but rather extent existing debates and concerns. With regards to applications, they stressed environmental risks as most important factors to consider. From the religious point of view, expanding the genetic code by incorporating novel components does not in turn lead to a new form of life, and creating such new life should not be pursued as an end in itself. While it is not unethical to carry out this research in order to benefit humanity, the main concern is that the research could lead to reducing humans to objects that can be expanded and recoded, thus robbing humanity of negative experiences such as suffering, which are nevertheless a necessary part of life. The survey of the public’s point of view shows that having prior experiences with synthetic biology is linked to a more favorable attitude towards the research field. Regardless of presence or absence of prior experiences, however, our project was generally perceived as useful and unobjectionable. Evaluating all perspectives, we developed flexible and easily applicable multi-faceted guidelines for research concerning synthetic biology. These guidelines contain for example the incorporation of expert committees relevant for the project, as well as possible dual use concerns and a self-assessment. Over the course of our iGEM project, the experts’ opinions and recommendations have continuously shaped our work, and we were able to already apply most of our guidelines for our own project. The full report can be found here.

Literature Workshop

On the 14th and 22th of January 2017, we organized our own literature workshop to facilitate in depth discussion about synthetic biology projects. The entire iGEM Team Bielefeld-CeBiTec 2017 as well as additional students with a strong interest in synthetic biology participated successfully. Everyone presented an iGEM project to inform us about previous projects and the possibilities the iGEM competition provides. Additionally, presentations about current research were given to enhance discussions about novel projects. By analyzing and discussing former iGEM projects we gained great insight in the structure and the requirements of iGEM. Among other projects like “The Transformers – from Carbon Dioxide to Biofuel” from the iGEM Team Bielefeld-CeBiTec 2014 and “MARSS - Modulated Acetosyringon Receptor Sensor System” from the iGEM Team Bielefeld-CeBiTec 2010 have been presented. The projects demonstrated that neither the fixation of carbon dioxide, producing the biofuel isobutanol from carbon dioxide nor a sensor for capsaicin have an innovative character anymore, which is a critical criterion for any successful iGEM project. Already at the beginning of our project phase, we kept the giant jamboree and our final presentation in mind. Therefore, each team member prepared two presentations in English, to improve our presentation and communication skills in front of a bigger audience. Several scientific discussions had a great impact on our project. The presentation about the minimal genome promoted the work on our biosafety report. One talk described the application of a FRET system to investigate quorum sensing. This inspired us to utilize FRET for one application in our project. During the entire weekend, there was one topic that always recurred: CRISPR/Cas9. Due to the very broad range of applications, we identified its huge benefit for our own project. CRISPR/Cas9 is critical for our retention system, to ensure that the unnatural bases are preserved in the genome. Since this literature workshop contributed significantly to the development of our project, we recommend it to other teams. Looking at previous project is very helpful to identify a novel topic for the next iGEM participation.

Figure 1: Some impressions of our literature workshop.