Team:Tuebingen/HP/Silver
Human Practice
Introduction
The research environment in Tübingen has a strong orientation on clinical research, microbiology and biochemistry and chemical analytics. For this reason, especially life science students come in touch with the latest developments and the present problems in this research fields. Some of us came across the particular research field of antibiotic research where many projects seem on hold or stopped. When we took a closer look and discovered that many team members shared the interest in this topic, we decided to take on this problem as our challenge. Our vision was to find a project which both has the potential for significant advancement in the field of antibiotic research and at the same time animates other scientists to contribute to research in the field. Even more, we aimed to show the public why research and advances in the area of antibiotics is inevitable to tackle evolving problems of resistant pathogens.
Project idea
When we were able to express our vision we presented our ideas to PD Dr. Gust. His experience with cloning and antibiotic production in streptomyces fits our project's needs perfectly. He knows everything about the current state of art techniques and provided us with important know-how concerning the practicability of our project idea. We included his valuable input about chemical and biochemical synthesis of our antibiotic and presented our cloning strategy to him. Additionally, he gave us some tips on working with Streptomyces. Furthermore, Dr. Gust offered us some of the materials and chemicals from his lab. This enabled us to proceed with our lab work in a safe and sustainable environment on our own.
Modelling our project idea
Our project includes the development of a new antibiotic. Antibiotics, in general, interact with structures of targeted bacteria to disrupt their cellular and vital functions. Before starting off with our laboratory work, we had the idea to model the interaction of our newly developed and optimized antibiotic. We estimated through a variety of docking techniques whether our compound - and its different stereo versions - would fit into the binding pocket of the enzyme. Moreover, we also wanted to know, whether the binding affinity to the human topoisomerase II decreases due to our modifications, as this is one of the main problems with the unmodified Clorobiocin.
This docking experiment confirmed that the included modification changed the interaction pattern accordingly, which gave us a better understanding of reaction patterns of troiacin.
Safety considerations
Working with genetically engineered organisms calls for special awareness of safety for humans and environment. Therefore, we had to assess possible risks while working in the lab. We had to constantly rethink assumptions we made during the project to ensure the safety of all people working on our project, affected by our work or our environment. This included the necessity of planning every step of our research ahead of time and coordinating the work, respectively. To follow Good Scientific Practice and federal regulations, we profoundly researched all available information about our used gene blocks and possible complications we might face in the course of our work with genetically modified organisms. To minimize evolving risks, we decided to limit ourselves to tools, parts, and organisms within the Biosafety level 1 and therefore also to limit our work to a BSL 1 laboratory.
Before we started our work, we contacted the representative for biological safety and security of the University of Tuebingen, Dr. Kittel, to confirm that we follow all necessary provisions and keep our work at BSL1. We took a comprehensive safety instruction by our technical officer Dr. Möschel and our PI PD Dr. Gust.
Working in lab
Our project demanded all kinds of diverse expertise. As our team consists of different backgrounds and very individual talents, we decided to allocate the different tasks respectively. We did not only rely on the expertise of our group members but also contacted and cooperated with various professors and workgroups. The cooperation started with providing materials and lab space and included support for both theoretical and practical procedures. Luckily, we could organize different parts of the project in separate labs to react on different needs according to the subprojects. For our chemical synthesis, we joined the Lab of AG Schwarzer located in the Inerfacultrary Institute of Biochemistry in Tübingen. They provided us with analytical facilities such as HPLC, MALDI-TOF, LC-MS (ESI-Quadrupole) and all required equipment for our chemical synthesis. In addition, we were pleased about our close cooperation with the Gust lab.
