Difference between revisions of "Team:Munich/Attributions"

The iGEM competition demands a lot of work in terms of project planning, research, programming, fundraising, human practices and wet lab experiments. Because we are a team with a diverse background, we divided tasks to best match our members' experience and interests. Sometimes, that meant doing what we do best; other times, it meant learning something new. When difficulties arose, we turned to our supervisors for help and guidance. Here, we would like to credit our team members for the specific roles they played into making CascAID. Also, we would like to thank our supervisors and external helpers for their important contributions to our project.

Organization

As our team was composed of people with different lab experience, there were some members who instructed the others in the use of lab equipment and methods. Our master students, Max, Ludwig and Sven taught the other team members and coordinated work distribution. Our supervisors Lukas and Aurore took over responsibility, supported the team in each point of this project and invested a lot of time in and outside the lab.

Molecular cloning

Due to our biochemistry background, most of us had experience in molecular cloning and thus almost every student helped with it in some way. However, most of the work for the Cas13a cloning was done by Ludwig and Christoph. The BioBricks were done by Rob and Max, who also cloned the constructs needed for the Intein-Extein read-out. The parts for the aeBlue read-out were done by Florian and Christoph. All the genes and primers design were done by the above-mentioned students and reviewed by our supervisor Aurore.

Protein purification

Our three Cas13a proteins: Lsh, Lwa and Lbu, were purified thanks to the hard work of Ludwig, Max, Sven and Milica. Dr. Sandra Sagredo, a postdoc at Prof. Simmel´s group, introduced them to the Äkta Purification System.

Targets

The original idea of using 16S rRNA from E. coli as a target for our initial experiments came from our supervisor Aurore, with the advice from Dr. Pardee. Our pathogen targets were chosen according to the main pathogens recommended by the experts we interviewed and designed by Dawafuti. Kilian Vogele, a PhD student from Prof. Simmel´s group, kindly provided us with the viral target sequences.

RNA extraction

We tried several approaches for extracting RNA: Julian and Patrick did multiple experiments using beads to bind RNA; Jorge experimented with the FINA extraction method (McFall et al., 2015) and tried to adapt it for RNA extraction; and Dawafuti and Julian also experimented with RNA extraction for different targets and purification methods for detection with Cas13a.

Colorimetric read-outs

As we considered colorimetric readouts for CascAID, our supervisor Jeffery helped us brainstorm and suggested two interesting options: aeBlue and the Intein-Extein readout. The initial cloning for the first option was done by Christoph, and Florian performed all main experiments. For the Intein-Extein system, Max, with help from Sven, did most of the cloning and experiments. Rob worked on the Gold Nanoparticles readout with help from Kilian Vogele, a PhD student in Prof. Simmel´s group. Kilian also kindly gave us some linker sequences necessary for testing this readout.

Fluorescence read-out

Igor optimized the RNase Alert system and cleavage assays with the in vitro targets and different Cas13a proteins in the plate reader. Dawafuti did experiments with the different targets and the Cas13a Lbu using the plate reader. She, together with Sven and Rob, tried different targets on paper. Our supervisor Lukas showed them how to use the plate reader and always provided great guidance.

Lyophilization

The lyophilization of both Cas13a and other components was done by Rob, who contacted Christine Braig from the IMETUM for guidance and equipment. With her support, Rob was able to use the lyophilization equipment at the IMETUM to make the lyophilization experiments.

Interlab

Erika and Dawafuti were in charge of the InterLab Study. They received an introduction to the Plate Reader and help setting the protocol for the measurements from our instructor Lukas. They both transformed the devices, did the measurement experiments, and processed the data. Their flow-cytometry experiments were supervised by Aradhana Chopra, a PhD student in Prof. Simmel's group.

Hardware

Our hardware team consisted of four students: Katzi, Matthias, Sven and Max. Our fluorescence detector "Lightbringer" was conceived, designed and built by Katzi and Matthias, while the whole hardware team developed "Heatbringer", the thermocycler. Sven and Max worked on the initial design blueprints, both in design and execution; Matthias and Katzi then develop "Heatbringer" to its final version. Along the way, our supervisors Lukas, Benjamin and Michael gave valuable input and feedback. Julia Müller und Marisa Götzfried, both PhD students in Prof. Simmel's lab, helped our hardware team by giving tips regarding 3D-printing and circuit design. Jerome Lutz, from UnternehmerTUM, also helped us by giving us access to the awesome parts library in UnternehmerTUM's MakerSpace and offering us some courses there.

Software

Jorge worked on the fluorescence detector's software under the instructions of Katzi, who designed the algorithm. Sven and Max wrote most of the thermocycler's software, with support from Igor for the web interface.

Human Practices and outreach

Everyone on the team contributed to human practices by organizing our attendance in one of the many events we went to, representing us there, or reaching out scientists and the community to discuss our project. However, Dawafuti, Rob, Erika, and Benedikt presented our project in most of the fairs and youth educational meet-ups. For outreaching and acquiring sponsors, Matthias coordinated the communication between the different companies and our team. Thanks to Jerome Lutz from UnternehmerTUM for reaching out to for different events like the TECHFEST .

Wiki

Our wiki was a joint effort mainly between Benedikt, who drew all the icons, logos, and designed most of the page, and Jorge, who did most of the coding with help from Milica and Igor. Our supervisor Benjamin provided us with helpful ideas and feedback. All our team members helped writing the wiki content. We would like to thank Team Bristol 2017 for creating and showing us the iGEM IDE which facilitated the work.

Design, Presentation and Poster

As our main art-guy Benedikt created our amazing logo and banner, took pictures, filmed, and styled our presentation. Together with Teeradon, he also was in charge of designing the poster.

Social media

Our Facebook, Instagram, and Twitter accounts were managed mostly by Erika, Benedikt and Dawafuti.

Even though they are not official members of the team, several people helped us to develop our project. We would like to thank them for their help and support; without them CascAID wouldn't have been possible: Thanks to all the people in the Chair of Physics of Synthetic Biology Systems at the TUM for their patience, help and for showing us our way around the lab. Special thanks to Kilian Vogele (PhD Student), Aradhana Chopra (PhD Student), Julia Müller (PhD Student), Marisa Götzfried (PhD Student), and Dr. Sandra Sagredo (Postdoc). Thanks the people at UnternehmerTUM for supporting us along the way with practical courses and ideas. Thanks to Christine Braig for lending us her machine for the lyophilization experiments. And many thanks to all our sponsors for their financial help and contributions.