Report Snythetic Biology III
by Tobias Härtel
International conference “Synthetic Biology III” at Sparkassenakademie Bayern, Landshut
Embedded in the picturesque landscape of Lower Bavaria, the „Synthetic Biology III“ Conference took place in the Sparkassenakademie Landshut from 23-25 July 2018, where 160 scientists met to present their results and exchange ideas in the field of Synthetic Biology. The conference covered a wide range of topics. In the first lectures Ned Budisa (TU Berlin), Kathrin Lang (TU Munich), Michael Hecht (Princeton University) and Tobias Erb (MPI Marburg) presented impressive examples on genetic code engineering, the incorporation of unnatural amino acids into proteins, synthetic proteins and synthetic CO2 fixation. Translational aspects of synthetic biology were highlighted by Pamela Silver (Harvard Medical School), Roy Bar-Ziv (Weizmann Institute of Science), Eriko Takano (University of Manchester) and Jerome Bonnet (CBS Montpellier). They discussed the construction of bacterial biosensors, synthetic approaches to promote sustainability, programmable on-chip DNA compartments as "artificial cells," and the optimization of secondary metabolite pathways. |
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Group photo by Helen Hauber |
| In the session “Metabolic Engineering” Dario Leister (LMU Munich), Poul Erik Jensen (University of Copenhagen) and James Murray (Imperial College London) gave new insights into their work on synthetic photosynthesis, photosynthetic electron transport and alternative ways of carbon fixation.
Synthetic switches, modeling and computer-based design was the topic of the third session with exciting lectures by Naama Barkai (Weizmann Institute of Science), Erwin Frey (LMU Munich), Joseph Loparo (Harvard Medical School), Chase Broedersz (LMU Munich) and Nikta Fakhri (MIT). Their talks addressed robust biological timers, cellular self-organization, protein patterns and their dynamics as well as the mechanics of living cells. Genome Editing was discussed in interesting lectures by Neil St. John Forbes (University of Massachusetts), Arne Skerra (TU Munich) and Simon Elsässer (Karolinska Institutet). They gave new insights into the development of Salmonella strains for cancer therapy, novel synthetic protein-based therapeutics, and the extension of the genetic code in mammalian cells. Last, but not least, Jörg Stülke (University of Göttingen) gave an impressive lecture on the minimal genome of Bacillus subtilis.
The program also included eleven excellent short presentations and 42 poster contributions. The poster prizes were won by Carina Sommer (group A. Skerra) and Kilian Vogele (group F. Simmel). Finally, four invited iGEM teams (Göttingen, Bielefeld, Vilnius and Munich) presented their amazing projects from 2017 and 2018, respectively. In summary, this was a very successful and stimulating conference.
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GRK2062 Publications
Physical Review X, accepted for publication
Two-species active transport along cylindrical biofilaments is limited by emergent topological hindrance
Patrick Wilke, Emanuel Reithmann, and Erwin Frey
Abstract
Active motion of molecules along filamentous structures is a crucial feature of cell biology and is often modeled with the paradigmatic asymmetric simple exclusion process. Motivated by recent experimental studies that have addressed the stepping behavior of kinesins on microtubules, we investigate a lattice gas model for simultaneous transport of two species of active particles on a cylinder. The species are distinguished by their different gaits: While the first species moves straight ahead, the second follows a helical path. We show that the collective properties of such systems critically differ from those of one-species transport in a way that cannot be accounted for by standard models. This is most evident in a jamming transition far below full occupation, as well as in non-equilibrium pattern formation. The altered behavior arises because -- unlike the case in single-species transport -- any given position may be targeted by two particles from different directions at the same time. However, a particle can leave a given position only in one direction. This simple change in connectivity significantly amplifies the impact of steric interactions and thus becomes a key determinant of mixed species transport. We computationally characterize this type of hindrance and develop a comprehensive theory for collective two-species transport along a cylinder. Our observations show high robustness against model extensions that account for additional biomolecular features and demonstrate that even small fractions of a second species can significantly alter transport. This suggests that our analysis is also relevant in a biological context.
Full text https://arxiv.org/abs/1807.02410
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Farewells
Francesca Paieri defended her PhD thesis in July 2018 and started already in June her new job as sales representative of BIOTREND Chemikalien GmbH. Francesca was working as PhD-student in the Leister lab. We wish her all the best for her future career and of course we stay in touch! |
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Events
Upcoming Transferable Skills Courses
Effective Visual Communication for Scientists, by Seyens
If created properly, graphics are the most effective way to explain complex ideas in the shortest amount of time, attract audience and raise credibility. Nevertheless, researchers aren't trained in visual communication in the traditional PhD curricula and are supposed to acquire these skills by themselves. This workshop uses a hands-on approach to help researchers visually present their own research through various means of scientific communication. More details
Date: 20th and 21st of September, 2018
Participation will be awarded with 1.0 ECTS.
Registration: Please write an e-mail to GRK2062
Selfmarketing for women by Sabine Walter and Greta Wonneberger
For a full description please click here. Participation will be awarded with 1.0 ECTS.
Date: 8th and 9th of November, 2018
Registration: Please write an e-mail to GRK2062
Presentation skills by Sabine Walter and Tim Wagner
Unfortunately, only 3% of presentations captivate their audiences, while more than 80% are dull and boring.
Our aim is to ensure that your presentations are among the 3% that captivate and engage their audiences. During the 2-day workshop you will learn how to efficiently prepare a presentation and tailor it to specific audiences. You will overcome your stage fright and learn how to enjoy giving presentations. In short: you captivate your audience and win them over not only with what you are saying but also with how you are saying it.
For a full description please click here. Participation will be awarded with 1.0 ECTS.
Date: 3th and 4th of April, 2019
Registration: Please write an e-mail to GRK2062
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Journal Club
Science 25 May 2018: Vol. 360 no. 6391 p. 915-918
An ingestible bacterial-electronic system to monitor gastrointestinal health
Mark Mimee, Phillip Nadeau, Alison Hayward, Sean Carim, Sarah Flanagan, Logan Jerger, Joy Collins, Shane McDonnell, Richard Swartwout, Robert J. Citorik, Vladimir Bulović, Robert Langer, Giovanni Traverso, Anantha P. Chandrakasan and Timothy K. Lu
Abstract
Biomolecular monitoring in the gastrointestinal tract could offer rapid, precise disease detection and management but is impeded by access to the remote and complex environment. Here, we present an ingestible micro-bio-electronic device (IMBED) for in situ biomolecular detection based on environmentally resilient biosensor bacteria and miniaturized luminescence readout electronics that wirelessly communicate with an external device. As a proof of concept, we engineer heme-sensitive probiotic biosensors and demonstrate accurate diagnosis of gastrointestinal bleeding in swine. Additionally, we integrate alternative biosensors to demonstrate modularity and extensibility of the detection platform. IMBEDs enable new opportunities for gastrointestinal biomarker discovery and could transform the management and diagnosis of gastrointestinal disease.
Full text: http: //dx.doi.org/10.1126/science.aas9315
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