Difference between revisions of "Team:LMU-TUM Munich/Attributions"

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[[File:Muc16_Attribution.png|400px|right]]
 
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Attribution is an important point of any iGEM project as it is necessary to set the results a team obtained into the context of the support they obtained. Thus, we'll try to describe honestly how our project evolved, which student was responsible for which sub-project and who supported our project with a scientific or non-scientific contribution.
+
Attributions are an important point of any iGEM project as it is necessary to put the results obtained by the team into the context of individual responsibilities. Thus, we will attempt to candidly describe how our project evolved, which student was responsible for which sub-project, and who supported our project with scientific or non-scientific contributions.
 
</div>
 
</div>
  
 
=Finding the biotINK project=
 
=Finding the biotINK project=
 
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For the history about how we found our project it is somehow important to know that there was no iGEM team from TUM or LMU in 2015 and no team in 2014 at TUM. Thus there were in each year students that wanted to participate in the iGEM competition but there was no hosting lab that offered the support necessary to make the "iGEM experience". Thus there has been a long time in which students have brainstormed to find some interesting ideas that they could convert into an iGEM project. Also our bioprinting project is far older than this year, at least in theory. The life science students finally found together approximetely in February at at this time point they had already few promising iGEM projects in mind. The project ideas that were developed the most were i) transforming of the planet mars with bacteria, ii) creating a vegan substitution product for milk and iii) bioprinting. Initially the bioprinting project was seen as the most interesting project-idea. Unfortunately, there has been a really nice project on bioprinting with bacteria by the TU Delft iGEM team in the last year and thus the team has discussed a long time if it is a good idea to participate with another bioprinting project. In the end we agreed that that there will most probably a bioprinting track will be established in the next years and that this topic has very high potential. By the way was it really encouraging when we listened to Randy in Paris when he described the potential of SynBio and used bioprinting of organs as his example of choice! At this point we were totally confident that our project choice has been totally right.
+
For the story of finding our project, it is essential to know that there was no iGEM team from either TUM or LMU in 2015 and no team at TUM in 2014. Thus, each of these years saw students wanting to participate in the iGEM competition but facing the bleak perspective that there was no hosting lab that offered the support necessary to make the "iGEM experience". For this long a time, students have brainstormed in order to find interesting ideas that they could convert into an iGEM project. Likewise, the idea for our bioprinting project is far older than just this year &ndash; at least in theory. The life science students finally assembled around last February, eagerly suggesting various ideas for several promising potential iGEM projects that they had in mind. The project ideas that were developed most involved i) transforming the planet Mars with bacteria, ii) creating a vegan substitution product for milk, and iii) bioprinting. While we considered the bioprinting project to be the most intriguing idea, last year's TU Delft iGEM team had unfortunately already developed an excellent project on bioprinting. Thus began a long discussion of whether it would be in our team's best interests to participate with another bioprinting project. In the end, however, we agreed that the next years of iGEM will most likely witness the establishment of a separate bioprinting track and that this topic has extraordinary potential. By the way, it was much encouraging to listen to Randy in Paris when he described the potential of SynBio and chose bioprinting of organs for an example! At this point, our last doubts melted, and we were wholly confident that our project choice was just right.
 
</div>
 
</div>
  
 
=Our prinicpal investigators (PIs)=
 
=Our prinicpal investigators (PIs)=
 
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As I told you in the last paragraph it has been very difficult to convince a professor at TUM and also at LMU it was difficult to find a PI that is enthusiastic about iGEM after Prof. Mascher has left Munich. The initial spark for the foundation of the iGEM team was given by the Graduate Center GRK 2062: Molecular principles of synthetic biology that wanted to reestablish an iGEM team in Munich.  
+
As implied above, it was very difficult to convince a professor at TUM of an iGEM participation, and at LMU as well it was cumbersome to find a PI enthusiastic about iGEM now that Prof. Mascher has left Munich. The initial motivation to found this year's iGEM team was sparked by the Graduate Center GRK 2062: Molecular principles of synthetic biology, which desired to re-establish the iGEM competition in Munich.  
* '''Prof. Dr. Jung '''(one of our secondary PIs, LMU) is the head of this graduate center and thus initially started the team by recruiting students. But she did not want to hast the project fully at her lab and so she (and the GRK) looked for a lab participating in the graduate center that could host the iGEM team as a main lab. In the end we got a small lab space in her lab in which we could do cloning work as the distance between LMU and TUM at Weihenstephan Campus is more than 2 h with public transportation. We are grateful for Prof. Jung support offering us labspace but in the end we decided to do all work in Weihenstephan as it turned out to be difficult to separate a project into two labs. Prof. Jung was not at all involved into the science of the iGEM project.
+
* '''Prof. Dr. Jung '''(one of our secondary PIs, LMU) is the head of this graduate center and thus initially started the team in recruiting students. However, she was reluctant to host the project entirely at her lab, and thus she (and the GRK) sought a lab participating in the graduate center that could play main host to the iGEM team. In the end, we were given a small lab space at her facility, where we conducted cloning work, the traveling time between LMU and TUM at Weihenstephan Campus being more than 2 h with public transportation. We are grateful to Prof. Jung for supporting us and offering us lab space, even though we eventually decided to finish our entire work in Weihenstephan as it was tedious to separate a coherent project into two labs. Prof. Jung was not involved in scientific planning of the iGEM project.
* '''Prof. Dr. Skerra''' (our main PI, TUM) has already been the main PI of the iGEM teams from TU Munich in 2012 and 2013 and already had some experiences of how it can be to host an iGEM team. In the beginning he did not want to host another iGEM team at his lab but in the end we could convince him that he participates another time in iGEM. He is a well known expert on the field of protein desing, especially for therapeutic proteins and also foundet two successful companies. For this reason he is quite busy and could not invest too much time for the iGEM competition. In this year he joined our weekly team meeting only once, when we had decided on our project. In this session he gave us several very valuable hints, what components we could integrate and what aspects we should focus on in order to get a proof-of-principle in the end. Besides this discussion session with him it is his philosophy that iGEM is a students competition and that the students should design and create the project. He generously offered everything of the resources available at his chair together with the excellent analytical equipment but let us the freedom to plan the project on our own - and we are really grateful that he gave us this opporthunity!
+
* '''Prof. Dr. Skerra''' (our main PI, TUM) already filled the role of main PI of TUM's 2012 and 2013 iGEM teams and thus had first-hand experience on what it means to host an iGEM team. Initially, he was disinclined to host yet another iGEM team at his lab, but finally we could convince him of this. He is a renowned expert in the field of protein design, especially for therapeutic proteins, and has also founded two successful companies. For this reason, he is quite busy and unable invest great amounts of time in the iGEM competition. He joined our weekly team meeting once after we had decided on our project, giving us several invaluable tips concerning what components to integrate and what aspects to focus on in order to arrive at a proof of principle in the end. Apart from this session with him, it is his philosophy that iGEM is an all-students' competition and that the students themselves should design and create the project. He generously offered all of the resources available at his chair together with the excellent analytical equipment, while letting us free rein to plan and execute the project on our own &ndash; and we are very grateful that he provided us with this opportunity!
*'''Prof. Dr. Westmeyer '''(secondary PI, TUM, Helmholtz center) was asked to join the team in the middle of the project when we realized that we needed some expertise in the field of fluorescence microscopic imaging. He supported us especially in the last weeks with cellbiological reagents for stainings and transfection and with the analytical instrumentation of his lab. As he has spent the last years in Boston at the MIT and at Harvard he is very openmindet concerning the potential and possible applications of SynBio in the future.
+
*'''Prof. Dr. Westmeyer '''(secondary PI, TUM, Helmholtz center) was asked to join the team halfway through the project when we realized that we required his expertise in the field of fluorescence microscopic imaging. He supported us, especially in the final weeks, with cell-biological reagents for staining and transfection as well as with the analytical instrumentation of his lab. As he spent the last years in Boston at the MIT and at Harvard, he is very openminded concerning the potential and possible applications of SynBio in the future.
 
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During the course of our project we have met many nice people willing to help and support us with lab space, knowledge or materials. Below you can find all the stations we took throughout our journey to the final result of our project.
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In the course of our project, we have met many nice people willing to help and support us with lab space, knowledge, or materials. Below you can find all the stations we stopped by throughout our journey up to the outcome of our project.
  
  
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=Attribution sorted by methods=
+
=Attributions sorted by methods=
All work associated with planing, conducting and the evaluation of experiments was done by student-members of our team. Instructors have assisted the students in the planing of their experiments, have introduced molecularbiological and chemical techniques to the students when they performed a specific experiment for the first time. Also the evaluation of the experiments was done by the students (after an introduction to the theory and some hints what to do and what to avoid). After a preliminary evaluation of the results, data were discussed in the weekly team meeting where our two instructors Andreas and Volker (both PhD students at the lab of Prof. Skerra) were present to reflect our project. Here we mention for every technique performed during our project to allow the judged to directly contact the student that has performed the specific task they are interested in.
+
All work associated with planning, conducting, and evaluating experiments was performed by student members of our team. Instructors assisted the students in planning their experiments, introducing relevant molecular-biological and chemical techniques to the students when they performed a specific experiment for the first time. Moreover, the students evaluated the experiments themselves after an introduction to the theory and advice on what to do and what to avoid. After this preliminary evaluation, all data were accumulated and discussed in the weekly team meeting, at which our two instructors Andreas and Volker (both PhD students at the lab of Prof. Skerra) were present to reflect on our project. Here we enumerate the specific tasks as well as the student(s) who performed them in order to allow the judges to directly contact the student responsible for a topic of interest.
  
 
==Protein Production and Purification==
 
==Protein Production and Purification==
 
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As we produced, purified, conjugated an analyzed many different protein samples different team members were involved, including Niklas, Jan and Julian. Shaker flask productions were done totally independent of the lab members, for fermentation (which turned out to be a bit more difficult than explained in lectures) one of our Instuctors had a look on the whole production.
+
As we produced, purified, conjugated, and analyzed many different protein samples, several team members were involved, including Niklas, Jan and Julian. Shaker flask productions were conducted independently of other lab members; for fermentation (which turned out to be a somewhat more difficult than explained in lectures), one of our instuctors had an eye on the whole production.
Purification with normal columns was done alone, as soon as a Äkta-purifier was involved we had to have someone from the lab who had a look on our handling for the first 3 to 5 chromatographies.
+
Purification with normal columns was performed independently; for those involving the Äkta purifier, a lab member supervised our handling for the first 3 to 5 chromatographies.
 
</div>
 
</div>
  
 
==Molecular Cloning==
 
==Molecular Cloning==
 
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In the first week we had an introduction to molecular cloning, afterwards we worked independently from our Instructors and only asked them from time to time if some problem occured. The gene design for all BioBricks we made by a student member (often Clemens or Christoph) and was then reviewed by our Instructor Volker.
+
In the first week, we received an introduction to molecular cloning. Afterwards, we worked independently of our instructors and only asked them from time to time whenever a problem occurred. The gene design for all BioBricks was conceptualized by a student member (often Clemens or Christoph) and then reviewed by our instructor Volker.
 
</div>
 
</div>
  
 
==Western Blot==
 
==Western Blot==
 
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All Western Blots were done by Luisa and she got an intoduction to blotting and staining from Fabian Rodewald and Christian Deuschle.
+
All Western Blots were done by Luisa, and she received an introduction to blotting and staining from Fabian Rodewald and Christian Deuschle.
 
</div>
 
</div>
  
 
==Mass spectrometric measurements==
 
==Mass spectrometric measurements==
 
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The coretness of recombinant proteins before and after conjugation was analyzed by ESI-TOF mass spectrometry. Sample preparation was done by student members of the team, the actual measurement was done by a technical asistant (but also the PhD student do not have to measure themselves).
+
The correctness of recombinant proteins before and after conjugation was analyzed by ESI-TOF mass spectrometry. Samples were prepared by student members of the team, the actual measurement was performed by a technical assistant (which is also true for PhD students).
 
</div>
 
</div>
  
 
==Incubation facility==
 
==Incubation facility==
 
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The hypoxia experiments could only be performed thanks to the support of the '''Schwille Group''' at the Max-Planck Intitute of Biochemistry in Martinsried, that kindly provided the required incubation facility. In this context we are really thankful towards '''Tobias Härtel''' and '''Bea''', who always offered their very valuable advice and help. The hypoxia experiments were performed by Jan and Elena, who were ready to take samples every 12 hours.
+
The hypoxia experiments could only be performed thanks to the support of the '''Schwille Group''' at the Max-Planck Institute of Biochemistry in Martinsried, which kindly provided the required incubation facility. In this context, we are indebted to '''Tobias Härtel''' and '''Bea''', who always offered their invaluable advice and help. The hypoxia experiments were performed by Jan and Elena, who were ready to take samples every 12 hours.
 
</div>
 
</div>
  
 
==Flow Cytometry==
 
==Flow Cytometry==
 
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The flow cytometry experiments were all performed by Luisa as she has spent 18 month in a research group in Hamburg before she started her studies in Munich. Thus she already brought all the skills to measure all our cells in FACS.
+
The flow cytometry experiments were all performed by Luisa as she spent 18 months in a research group in Hamburg before she started her studies in Munich, thus already versed in all skills necessary to measure our cells in FACS.
 
</div>
 
</div>
  
 
==Fluorescence Microscopy==
 
==Fluorescence Microscopy==
 
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The fluorescence microscopy at the lab of Prof. Skerra was performed by various different people as it was necessary for many different sub-projects. The high resolution confocal fluorescence microscopy was done at the Helmholtz Center in Munich in the Lab of Prof. Westmeyer by Christoph as he will also do his master's thesis in this lab. He got the introduction into staining cells and performing confocal imaging experiments from our external Instructor Jeff.
+
Fluorescence microscopy at the lab of Prof. Skerra was performed by different people as it was necessary for many different sub-projects. High-resolution confocal fluorescence microscopy was conducted at the Helmholtz Center in Munich in the lab of Prof. Westmeyer by Christoph as he will also do his master's thesis in this lab. He received the introduction into staining cells and performing confocal imaging experiments from our external Instructor Jeff.
 
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Our colorful ''Scanning Electron Microscopy'' images were done by '''Prof. Dr. Wanner''' from the Plant Science Department of the Ludwig-Maximilians University. Elena approached him to support our project in terms of a collaboration providing us some impressive electron microscopy images of cells. Prof. Wanner facilitated all required reagents for the sample preparation such as microscopic slides, glutaraldehyde, transport boxes, ...! The sample preparation was performed by Clemens late in the evening, thus being ''a bit improvised''. The samples were then transported and picked up by Jan and Elena, bringing them to the SEM facility.  Afterwards, the remaining sample preparation steps after the fixation were carried out by Prof. Wanner and his coworkers. We are sincerely grateful for his support!
+
Our colorful ''Scanning Electron Microscopy'' images were shot by '''Prof. Dr. Wanner''' from the Plant Science Department of the Ludwig-Maximilians University. Elena approached him to support our project in terms of a collaboration to provide us impressive electron microscopy images of cells. Prof. Wanner supplied all reagents required for sample preparation, such as microscopic slides, glutaraldehyde, transport boxes, and many more! Clemens was in charge of preparing the samples late in the evening, which were thus ''slightly improvised''. The samples were then picked up and transported by Jan and Elena to the SEM facility.  Afterwards, the remaining sample preparation steps after the fixation were carried out by Prof. Wanner and his coworkers. We are sincerely grateful for his support!
  
 
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[[File:Muc16_bloodsamples.png|thumb|right|200px|'''Figure 1:''' Vivien holding freshly centrifuged tubes of blood, ready to isolate the supernatant plasma!]]
 
[[File:Muc16_bloodsamples.png|thumb|right|200px|'''Figure 1:''' Vivien holding freshly centrifuged tubes of blood, ready to isolate the supernatant plasma!]]
 
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For our "linker chemistry" subproject, we needed fresh blood samples that contained human biotinidase. For this purpose Vivien, the student who performed all the chemistry experiments, went to PD Dr. med. Thomas Skurk who helped us out by taking blood samples.
+
For our "linker chemistry" subproject, we needed fresh blood samples as a readily available source of human biotinidase in the form of plasma. For this purpose, Vivien, the student who performed the chemical experiments, utilized her own blood graciously drawn by PD Dr. med. Thomas Skurk, a medical doctor at the Institute for Food & Health.
 
</div>
 
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==Chemical synthesis of the Biotin-NHS compounds==
+
==Chemical synthesis of Biotin-NHS active esters==
 
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Chemical synthesis was done by Vivien as she has already done here Bachelor's thesis at the Chair for Organic Chemistry at TUM. The initial synthesis plan was discussed with Dr. Martin Dauner, who is the chemist in the lab of Prof. Skerra. Vivien worked alone after during the preparation of the compound and the subsequent analysis of their properties. The NMR measurement were then measured at the chemical faculty in Garching. The evaluation of all results was done by Vivien (including NMR evalution).
+
Chemical synthesis was performed by Vivien, as she wrote her bachelor's thesis at the Chair of Organic Chemistry at TUM. The initial synthesis plan was discussed with Dr. Martin Dauner, who is the chemist in the lab of Prof. Skerra. Vivien worked alone afterwards in synthesizing the target compounds and subsequently analyzing their properties. The NMR experiments were then measured at the Faculty of Chemistry in Garching. Vivien evaluated all results (including NMR).
 
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</div>
  
 
==Maya Video==
 
==Maya Video==
 
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To be honest we are very proud that the Maya Video Vivien made looks so great in the end. In the beginning the first renderings she showed were fare more simple than what it looks now. She has already had some experiences in the field as she has done graphical design with blender as a kind of hobby before and this helped her to understand the Maya software faster (which is really not that intuitive). She also put up a How-To Video in which she explains the creation of the video in app. on hour. If you are interested in the video, please ask her as she really did it on her own ;)
+
To be honest, we are very proud that the Maya Video Vivien built looks so great in the end. Initial renderings that she showed to the team were far more simple than the final product. She had already gathered some experience in 3D animating, having regularly worked with Blender as a hobby before; this helped her very much in understanding the Maya software faster (which is really not that intuitive). She also compiled a How-To Video in which she explains the creation of the video in just short of one hour. If you are interested in the video, please ask her, as she really did it on her own ;)
 
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[[File:Muc16_Mikromanipulator.jpg|thumb|300px| '''Figure 1:''' Javier operating the micromanipulator]]
 
[[File:Muc16_Mikromanipulator.jpg|thumb|300px| '''Figure 1:''' Javier operating the micromanipulator]]
We have to thank '''Professor Dr. Schnieke''' and her [http://btn.wzw.tum.de/ Chair of Livestock Biotechnology] at the WZW (''TUM School of Life Sciences Weihenstephan'') for so generously providing us with the possibility to use the micromanipulator at the chair's laboratory and allowing us to conduct some very specific experiments with our bioink. With the extensive help and instructions of '''Dr. Nicolas Ortega''',  researcher at the lab with a lot of experience with the device, we were able to plan experiments and test our bioprinting technique on a very tiny scale. Thereby our team members '''Julian''' and '''Javier''' were able to observe the ejection process under controlled conditions in great detail and document the behavior of our modified HEK cells containing ink. Thanks to this opportunity we could obtain [[Team:LMU-TUM_Munich/Proof|useful and valuable visual material]] as well as a better understanding of our '''biotINK''' concept.
+
We thank '''Professor Dr. Schnieke''' and her [http://btn.wzw.tum.de/Chair of Livestock Biotechnology] at the WZW (''TUM School of Life Sciences Weihenstephan'') for so generously providing us with the opportunity to use the micromanipulator at the chair's laboratory and allowing us to conduct several highly specific experiments with our bioink. With the extensive help and instructions of '''Dr. Nicolas Ortega''',  a researcher at the lab having much experience with the device, we were able to plan experiments and test our bioprinting technique on a minuscule scale. In the process, our team members '''Julian''' and '''Javier''' were able to observe the ejection process under controlled conditions in great detail and document the behavior of our modified HEK cells containing ink. Thanks to this opportunity we could obtain [[Team:LMU-TUM_Munich/Proof|useful and valuable visual material]] as well as a better understanding of our '''biotINK''' concept.
 
</div>
 
</div>
  
 
==Business plan==
 
==Business plan==
 
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The Businessplan was done by Christoph as he also sudies TUM-Economics besides his studies in Molecular Biotechnology.
+
The business plan was written by Christoph as he also studies TUM Economics besides his studies in Molecular Biotechnology.
 
</div>
 
</div>
  
 
==Survey: "Supporting Entrepreneurship"==
 
==Survey: "Supporting Entrepreneurship"==
 
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For the creation of this survey we had a special Instructor, Philipp. He is a PhD student an the Chair of Technology- and  Innovationmanagement. He supervised Hallie who is a US-american exchange student who joined our team to create this survey and find out how we can make iGEM more productive concerning it's output in successful start-up companies.
+
For the creation of this survey, we had a special Instructor, Philipp. He is a PhD student an the Chair of Technology and  Innovations Management. He supervised Hallie, an exchange student from the USA who joined our team to create this survey and elucidate how we can make iGEM more productive concerning its output in successful start-up companies.
 
</div>
 
</div>
  
 
==The Wiki==
 
==The Wiki==
The wiki was programmed by Peter who is a student in medical informatics (LMU). As he had some problems finding someone who can programm the wiki he joined the team 4 weeks before wiki freeze. As he is also working in the field of webdesign and also completed his Bachelor's thesis he was quite busy all the time and had not that much time for our wiki (which is why we fixed our CSS the last evening). But in the end he completed the work on the wiki.  
+
The Wiki was programmed by Peter, a student in Media Informatics (LMU). As we encountered some problems finding someone to program the Wiki, he joined the team 4 weeks before wiki freeze. As he also works in web design and completed his bachelor's thesis in parallel, he was quite busy and did not have overly much time (which is why we finalized our CSS on the last evening). In the end, though, he successfully completed the work.  
  
 
==Video cutting==
 
==Video cutting==

Revision as of 01:55, 20 October 2016

Attribution

Muc16 Attribution.png

Attributions are an important point of any iGEM project as it is necessary to put the results obtained by the team into the context of individual responsibilities. Thus, we will attempt to candidly describe how our project evolved, which student was responsible for which sub-project, and who supported our project with scientific or non-scientific contributions.

Finding the biotINK project

For the story of finding our project, it is essential to know that there was no iGEM team from either TUM or LMU in 2015 and no team at TUM in 2014. Thus, each of these years saw students wanting to participate in the iGEM competition but facing the bleak perspective that there was no hosting lab that offered the support necessary to make the "iGEM experience". For this long a time, students have brainstormed in order to find interesting ideas that they could convert into an iGEM project. Likewise, the idea for our bioprinting project is far older than just this year – at least in theory. The life science students finally assembled around last February, eagerly suggesting various ideas for several promising potential iGEM projects that they had in mind. The project ideas that were developed most involved i) transforming the planet Mars with bacteria, ii) creating a vegan substitution product for milk, and iii) bioprinting. While we considered the bioprinting project to be the most intriguing idea, last year's TU Delft iGEM team had unfortunately already developed an excellent project on bioprinting. Thus began a long discussion of whether it would be in our team's best interests to participate with another bioprinting project. In the end, however, we agreed that the next years of iGEM will most likely witness the establishment of a separate bioprinting track and that this topic has extraordinary potential. By the way, it was much encouraging to listen to Randy in Paris when he described the potential of SynBio and chose bioprinting of organs for an example! At this point, our last doubts melted, and we were wholly confident that our project choice was just right.

Our prinicpal investigators (PIs)

As implied above, it was very difficult to convince a professor at TUM of an iGEM participation, and at LMU as well it was cumbersome to find a PI enthusiastic about iGEM now that Prof. Mascher has left Munich. The initial motivation to found this year's iGEM team was sparked by the Graduate Center GRK 2062: Molecular principles of synthetic biology, which desired to re-establish the iGEM competition in Munich.

  • Prof. Dr. Jung (one of our secondary PIs, LMU) is the head of this graduate center and thus initially started the team in recruiting students. However, she was reluctant to host the project entirely at her lab, and thus she (and the GRK) sought a lab participating in the graduate center that could play main host to the iGEM team. In the end, we were given a small lab space at her facility, where we conducted cloning work, the traveling time between LMU and TUM at Weihenstephan Campus being more than 2 h with public transportation. We are grateful to Prof. Jung for supporting us and offering us lab space, even though we eventually decided to finish our entire work in Weihenstephan as it was tedious to separate a coherent project into two labs. Prof. Jung was not involved in scientific planning of the iGEM project.
  • Prof. Dr. Skerra (our main PI, TUM) already filled the role of main PI of TUM's 2012 and 2013 iGEM teams and thus had first-hand experience on what it means to host an iGEM team. Initially, he was disinclined to host yet another iGEM team at his lab, but finally we could convince him of this. He is a renowned expert in the field of protein design, especially for therapeutic proteins, and has also founded two successful companies. For this reason, he is quite busy and unable invest great amounts of time in the iGEM competition. He joined our weekly team meeting once after we had decided on our project, giving us several invaluable tips concerning what components to integrate and what aspects to focus on in order to arrive at a proof of principle in the end. Apart from this session with him, it is his philosophy that iGEM is an all-students' competition and that the students themselves should design and create the project. He generously offered all of the resources available at his chair together with the excellent analytical equipment, while letting us free rein to plan and execute the project on our own – and we are very grateful that he provided us with this opportunity!
  • Prof. Dr. Westmeyer (secondary PI, TUM, Helmholtz center) was asked to join the team halfway through the project when we realized that we required his expertise in the field of fluorescence microscopic imaging. He supported us, especially in the final weeks, with cell-biological reagents for staining and transfection as well as with the analytical instrumentation of his lab. As he spent the last years in Boston at the MIT and at Harvard, he is very openminded concerning the potential and possible applications of SynBio in the future.

Our Journey Through Munich

In the course of our project, we have met many nice people willing to help and support us with lab space, knowledge, or materials. Below you can find all the stations we stopped by throughout our journey up to the outcome of our project.


Attributions sorted by methods

All work associated with planning, conducting, and evaluating experiments was performed by student members of our team. Instructors assisted the students in planning their experiments, introducing relevant molecular-biological and chemical techniques to the students when they performed a specific experiment for the first time. Moreover, the students evaluated the experiments themselves after an introduction to the theory and advice on what to do and what to avoid. After this preliminary evaluation, all data were accumulated and discussed in the weekly team meeting, at which our two instructors Andreas and Volker (both PhD students at the lab of Prof. Skerra) were present to reflect on our project. Here we enumerate the specific tasks as well as the student(s) who performed them in order to allow the judges to directly contact the student responsible for a topic of interest.

Protein Production and Purification

As we produced, purified, conjugated, and analyzed many different protein samples, several team members were involved, including Niklas, Jan and Julian. Shaker flask productions were conducted independently of other lab members; for fermentation (which turned out to be a somewhat more difficult than explained in lectures), one of our instuctors had an eye on the whole production. Purification with normal columns was performed independently; for those involving the Äkta purifier, a lab member supervised our handling for the first 3 to 5 chromatographies.

Molecular Cloning

In the first week, we received an introduction to molecular cloning. Afterwards, we worked independently of our instructors and only asked them from time to time whenever a problem occurred. The gene design for all BioBricks was conceptualized by a student member (often Clemens or Christoph) and then reviewed by our instructor Volker.

Western Blot

All Western Blots were done by Luisa, and she received an introduction to blotting and staining from Fabian Rodewald and Christian Deuschle.

Mass spectrometric measurements

The correctness of recombinant proteins before and after conjugation was analyzed by ESI-TOF mass spectrometry. Samples were prepared by student members of the team, the actual measurement was performed by a technical assistant (which is also true for PhD students).

Incubation facility

The hypoxia experiments could only be performed thanks to the support of the Schwille Group at the Max-Planck Institute of Biochemistry in Martinsried, which kindly provided the required incubation facility. In this context, we are indebted to Tobias Härtel and Bea, who always offered their invaluable advice and help. The hypoxia experiments were performed by Jan and Elena, who were ready to take samples every 12 hours.

Flow Cytometry

The flow cytometry experiments were all performed by Luisa as she spent 18 months in a research group in Hamburg before she started her studies in Munich, thus already versed in all skills necessary to measure our cells in FACS.

Fluorescence Microscopy

Fluorescence microscopy at the lab of Prof. Skerra was performed by different people as it was necessary for many different sub-projects. High-resolution confocal fluorescence microscopy was conducted at the Helmholtz Center in Munich in the lab of Prof. Westmeyer by Christoph as he will also do his master's thesis in this lab. He received the introduction into staining cells and performing confocal imaging experiments from our external Instructor Jeff.

Scanning Electron Microscopy

Our colorful Scanning Electron Microscopy images were shot by Prof. Dr. Wanner from the Plant Science Department of the Ludwig-Maximilians University. Elena approached him to support our project in terms of a collaboration to provide us impressive electron microscopy images of cells. Prof. Wanner supplied all reagents required for sample preparation, such as microscopic slides, glutaraldehyde, transport boxes, and many more! Clemens was in charge of preparing the samples late in the evening, which were thus slightly improvised. The samples were then picked up and transported by Jan and Elena to the SEM facility. Afterwards, the remaining sample preparation steps after the fixation were carried out by Prof. Wanner and his coworkers. We are sincerely grateful for his support!

Blood samples

Figure 1: Vivien holding freshly centrifuged tubes of blood, ready to isolate the supernatant plasma!

For our "linker chemistry" subproject, we needed fresh blood samples as a readily available source of human biotinidase in the form of plasma. For this purpose, Vivien, the student who performed the chemical experiments, utilized her own blood graciously drawn by PD Dr. med. Thomas Skurk, a medical doctor at the Institute for Food & Health.

Chemical synthesis of Biotin-NHS active esters

Chemical synthesis was performed by Vivien, as she wrote her bachelor's thesis at the Chair of Organic Chemistry at TUM. The initial synthesis plan was discussed with Dr. Martin Dauner, who is the chemist in the lab of Prof. Skerra. Vivien worked alone afterwards in synthesizing the target compounds and subsequently analyzing their properties. The NMR experiments were then measured at the Faculty of Chemistry in Garching. Vivien evaluated all results (including NMR).

Maya Video

To be honest, we are very proud that the Maya Video Vivien built looks so great in the end. Initial renderings that she showed to the team were far more simple than the final product. She had already gathered some experience in 3D animating, having regularly worked with Blender as a hobby before; this helped her very much in understanding the Maya software faster (which is really not that intuitive). She also compiled a How-To Video in which she explains the creation of the video in just short of one hour. If you are interested in the video, please ask her, as she really did it on her own ;)

Micromanipulator experiments at the Chair of Livestock Biotechnology of Professor Dr. Schnieke

Figure 1: Javier operating the micromanipulator

We thank Professor Dr. Schnieke and her [http://btn.wzw.tum.de/Chair of Livestock Biotechnology] at the WZW (TUM School of Life Sciences Weihenstephan) for so generously providing us with the opportunity to use the micromanipulator at the chair's laboratory and allowing us to conduct several highly specific experiments with our bioink. With the extensive help and instructions of Dr. Nicolas Ortega, a researcher at the lab having much experience with the device, we were able to plan experiments and test our bioprinting technique on a minuscule scale. In the process, our team members Julian and Javier were able to observe the ejection process under controlled conditions in great detail and document the behavior of our modified HEK cells containing ink. Thanks to this opportunity we could obtain useful and valuable visual material as well as a better understanding of our biotINK concept.

Business plan

The business plan was written by Christoph as he also studies TUM Economics besides his studies in Molecular Biotechnology.

Survey: "Supporting Entrepreneurship"

For the creation of this survey, we had a special Instructor, Philipp. He is a PhD student an the Chair of Technology and Innovations Management. He supervised Hallie, an exchange student from the USA who joined our team to create this survey and elucidate how we can make iGEM more productive concerning its output in successful start-up companies.

The Wiki

The Wiki was programmed by Peter, a student in Media Informatics (LMU). As we encountered some problems finding someone to program the Wiki, he joined the team 4 weeks before wiki freeze. As he also works in web design and completed his bachelor's thesis in parallel, he was quite busy and did not have overly much time (which is why we finalized our CSS on the last evening). In the end, though, he successfully completed the work.

Video cutting

All work associated with recording as well as processing auto and video files was done by Julian.

References


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LMU & TUM Munich

Technische Universität MünchenLudwig-Maximilians-Universität München

United team from Munich's universities

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iGEM Team TU-Munich
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