Team:BOKU-Vienna/Collaborations

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Collaborations

Thanks to the many teams which collaborated with us:

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iGEM Vienna - 6 Pics Challenge "comic book"

We have launched our very own challenge to integrate arts, science communication and international collaborations into a tangible output: a comic book full of stories about iGEM projects. 10 teams have provided short and easy to understand illustrations explaining their iGEM projects, and we have added a glossary to overcome the boundaries between non-expert readers and the scientists involved in the projects. The feedback we received for the booklet was positive and incorporated in later versions. Thank you to all participants in this collaboration and for making this a great success, a wonderful piece of art and a useful tool to communicate and celebrate synthetic biology to the world!
Attributions:
Each team sent us 6 illustrations, an abstract, their team- and project logo, their official team name, names of the team members and links to their social media platforms.

iGEM Pasteur Paris 2019
iGEM Munich 2019
iGEM Vitrum (UCSC 2019)
iGEM IONIS Paris 2019
iGEM Tartu_TUIT 2019
iGEM KU_Leuven 2019
iGEM Athens 2019
iGEM GO Paris Saclay
iGEM ULaval
iGEM Erlangen

We, the iGEM team BOKU-Vienna, then designed the comic book, put together all of the materials into one document, wrote a glossary, proofread the texts and illustrations and conveyed a survey to improve the comic book.
For more details on this project please visit Public Engagement

To download the comic book for free, please visit our main page

iGEM Athen - Aptamer Hub

Aptamer sequences as regulators of gene expression – INTRINSIC TERMINATION

iGEM Aptamers Hub
While doing our research for our project, we many times wished for there to be a more formal platform for anybody working with aptamers to be able to share ideas, advice, and feedback. For this reason, most of the teams working with aptamers this year created the iGEM Aptamers Hub. The iGEM Aptamers Hub aims to enable the use of aptamers during the iGEM competition and encourage their use in laboratories worldwide. We curate an ‘’aptamer registry’’, create a network with aptamer researchers, and provide the community with useful resources to facilitate their research.
The iGEM Team BOKU-Vienna is using a riboswitch to diagnose the neglected tropical disease Buruli Ulcer. The riboswitch consists of an RNA-aptamer sequence, a spacer sequence, a terminator structure and an Uracil-stretch.
Aptamer sequences are usually around 80 basepairs long. The spacer sequence that follows the aptamer can vary in length, stretching over 6 to up to 16 basepairs, depending on the switch sensitivity. If the spacer is longer, the intrinsic termination will be stronger. A shorter spacer sequence leads to more upstream expression in the presence of the ligand because the binding of the ligand will occur on the aptamer sequence and not on the spacer sequence. This increases the likelihood of conformational change. The terminator sequence is complementary to the aptamer sequence and should be between 5 and 15 basepairs long. GC-rich regions are preferred in these sequences due to their strong binding capability.
For spacer sequences, GAAA is often found in natural terminators. GC-binding between the spacer sequence and the terminator structure will ensure stability (GGAAAC) and lead to stem loop formation. In the absence of the aptamer-specific ligand, the aptamer structure binds to the terminator sequence, forming a hairpin with the spacer sequence which is present as a tetraloop. This structure is followed by a Uracil-stretch which can be between 6 and 12 basepairs long. During transcription, a protein subunit of the RNA-polymerase (NusA) binds to the hairpin loop described above, forcing the RNA-polymerase to stop transcription. Further, due to the weak interactions between the RNA-polymerase and the Uracil-stretch, the RNA-polymerase dissociates.
This means that on a transcriptional level, ligand-dependent aptamers with intrinsic termination properties can induce the expression of downstream genes if placed between the promoter and ribosome binding site.
The proper hairpin formation in the proposed design may be predicted with the ViennaRNA Web Service. As a side note, due to these strong cross-linking abilities of spacer, terminator and aptamer, it is recommended to order any aptamer with intrinsic termination properties in two separate parts for synthesis: The promoter with the aptamer and the spacer sequence as one part, and the terminator sequence, the Uracil-stretch and the ribosome binding site as a second part.

iGEM Lab Pats (US AFRL Virginia) - Participation in their Wikiguide

After initial problems with the iGEM Wikipage I consulted the Internet and found a Wikiguide from US_AFRL_CarrollHS. I checked out their guide and was very lucky to find many solutions for my problems. But their page wasn’t perfected so I send them an addition which can now be found on their page.

iGEM Düsseldorf - postcards

We have participated in the postcard challenge organized by iGEM Düsseldorf. For this challenge, we have designed a postcard with bacteria explaining that they can be taught to solve problems, and on the back, a more detailed yet easy to understand description of our own project and a promotion to check out the iGEM website for other cool projects. We were very happy to receive all the postcards from all over the world and be part of this cool collaboration!

iGEM Washington – Synthetic biology game

We used the synbiogame of the iGEM washington team 2019 for our presentations at schools. Our first try wasn’t received very well (Verlinken zu Public education and engagement – Francisco Josephinum Wieselburg) the game down to just finding the pros and cons and brainstorming a new way to solve the problems given, it was very well received. As you can see in our graphifcs and figures (Verlinken zu Public education and engagement – Bernoulligym) most of the students from the Bernoulligymansium loved it.

Paris-Saclay: Haikus “poetry collab”

iGEM GO Paris Saclay - Haiku: a synthetic poetry

We collaborated with the GO Paris Saclay iGEM Team on their Project: Haiku: a synthetic poetry
It is about writing Haikus - Japanese poems consisting of a 3 line Format with 17 syllables in a 5-7-5 pattern. They classically reflect the fleeting beauty of life, expressing strong ephemeral feelings. The GO Paris Saclay Team decided to produce Haikus illustrating their experiments in an unconventional and unique way. They also decided to let other teams join in on this challenge. While contacting the team to ask whether they would like to participate in our Six Pics collaboration (what they did), they informed us about this art project.
A team member then wrote these 2 poems and submitted them to GO Paris Saclay:


                        The synthetic cell 
                        Risen from Fantasy, forged
                        Into existence
                        
                        Michaela Mechura
                        
                        Gone, my DNA,
                        When my shift is over
                        I am no longer
                        
                        Michaela Mechura

We are looking forward to reading the poems submitted by other iGEM teams.

Marburg: Bilder von E.Coli

We had one of our first collaborations with the iGEM team from Marburg, which we met during a meet-up in Erlangen (Germany). This project is about the team Marburg trying to create a computer algorithm to automate the counting of colonies on agar plates. In order to have enough material for the tests, the Marbug team called for collaboration. We are happy that we have been able to make a small contribution to the success of the iGEM Marburg project by sending some pictures of our well grown E. Coli plates.

iGEM Marburg - Golden-Gate-Webinar

The Lab-team successfully attended the Golden Gate webinar from iGEM Marburg on July 30th, 2019. We are very grateful for the opportunity, since we also used the golden gate cloning method in our project it was very helpful to get such a great introduction to this topic. The protocols and the documents on the google drive, that were also accessible after the webinar, proved to come in handy as well.
Thank you to the iGEM Marburg for the great webinar!

Bead Homogenizer Survey

We participated in the Bead Homogenizer Survey from the iGEM Team Lambert GA by filling out their questionnaire.

iGEM Erlangen - Poster

Together with iGEM Marburg, iGEM Strasbourg and iGEM Tuebingen we participated in a collaboration organised by iGEM Erlangen. For the day of immunology, iGEM Erlangen decided to present 5 different iGEM projects to the public to demonstrate how diverse the field of application for synthetic biology can be. For this, we designed a poster summarizing our project idea and a little bit of background information about the disease Buruli Ulcer.