Renowned scientists in the field of synthetic biology from all over Europe present and discuss their latest research results with the participants, inspire and show what is possible.
Dorothy Zhang and Nemanja Stijepovic, iGEM HQ Paris, France
Introduction to iGEM
Thomas Gorochowski, Univeristy of Bristol, UK
Programming biology – controlling the flow of molecular machines empowering life
Thomas Gorochowski is a synthetic biologist and complexity scientist who was originally trained in computer science. In his lab at the University of Bristol he is attempting to develop efficient architectures for cellular information processing using biologically derived parts and principles. He also won Best Model in iGEM 2008, when he participated in iGEM as a student!
Abstract: Synthetic genetic circuits are composed of many interconnected parts that must control the flows of transcriptional and translational machinery such that genes are expressed in the correct way. A major challenge when developing such circuits is that the genetic parts used often display unexpected changes in their behavior when pieced together in new ways. Such changes can arise due to contextual effects or unintended interactions with the host cell. In this talk, I will demonstrate how we have been using a variety of sequencing technologies to create a genetic debugger to pinpoint the root of such failures, as well as our recent efforts to develop “tunable” genetic parts whose functions can be dynamically altered to fix many of these common issues. Taken together, our work provides a more complete and quantitative view of the inner workings of genetic circuits, offers a route to engineering more robust and adaptive functionalities in living cells, and improves our understanding of the rules governing the effective reprogramming of biology.
Nico Claassens, Wageningen University, Netherlands
Towards efficient, synthetic one-carbon metabolism - modular and growth-coupled engineering
Dr. Nico J. Claassens is an assistant professor at the Laboratory of Microbiology in Wageningen. A core occupation of his group is to perform systems-wide metabolic engineering using novel high-throughput genome editing techniques in bacteria. After obtaining his PhD at Wageningen University in 2017, Nico worked as postdoctoral fellow from 2017 till 2019 at the Max Planck Institute Potsdam with Dr. Arren Bar-Even. In 2019 he obtained a prestigious NWO-Veni grant for talented junior researchers.
Vitor Pinheiro, KU Leuven, Belgium
Directed evolution of xenobiotic nucleic acid processing enzymes: polymerases and ligases.
After a PhD in bacterial pathogenesis at University of Cambridge with Prof. David Ellar, he did 7 years of post-doctoral work at the MRC Laboratory of Molecular Biology in Cambridge with Dr. Phil Holliger. In 2013 he started his independent research career at UCL and Birkbeck and moved to KU Leuven in September 2018. His research focuses on all aspects of directed evolution and in its application. Supported by a multidisciplinary approach, Vitor aims to establish a ‘design, build, test, learn’ cycle using directed evolution to engineer new enzymes and to redesign biology.
Abstract: Nucleic acids have long been heralded as programmable biomaterials, given their predictable structure and sub-angstrom precision in the placement of chemical moieties – a consequence of the efficient and unambiguous Watson-Crick base-pairing. Improvements in the chemical synthesis of DNA and RNA oligonucleotides now enable long and more chemically diverse molecules to be synthesized which, coupled to nucleic acid processing enzymes, can deliver a wide range of applications. Nonetheless, their use remains limited in scope due to DNA’s and RNA’s limited chemical and poor biological stability.
Alternative non-biological genetic polymers, also known as xenobiotic nucleic acids (or XNAs), introduce novel base-pairs as well as significant chemical changes to backbone and phosphate that can deliver chemically and biologically stable polymers. However, chemical synthesis of typical XNAs is challenging, lagging decades behind DNA synthesis, and XNA processing enzymes – the needed XNA molecular biology tool kit – often do not exist.
Through directed evolution, it has been possible to isolate nucleic acid processing enzymes for the template-mediated synthesis and reverse transcription of a wide range of XNAs – opening the doors for the directed evolution of XNA aptamers and XNAzymes. However, XNA polymerases are limited to one chemistry per synthesis, and their synthetic precision near the template ends is often poor – leading to XNAs with significant variation in length.
Here, we report on our progress at developing XNA ligases – by enhancing the function of natural ligases, computationally redesigning them and isolating improved ligases through directed evolution. They represent a second essential enzyme for the controlled synthesis and assembly of XNA (or XNA/DNA hybrid) molecules at scale.
Nico Krink, Technical University of Denmark
Solving humankind's challenges with SynBio and MetEng in the ultimate chassis
Nicolas Krink is a successful iGEM Alumni, having won the grand prize 2013 with the iGEM team Paris-Bettencourt. He also co-founded and headed the German Association for Synthetic Biology—GASB. Since 2020 he works as a post-doctoral fellow in Pablo Ivan Nikel’s group in Copenhagen. There he will engineer P. putida as a host to produce new-to-nature long-chain fluorinated molecules.
Anthony Forster, Uppsala University, Sweden
Synthetic translation systems
Anthony C. Forster (Ph.D. Biochem., U. Adelaide; M.D., Harvard U.) researches RNA and protein synthesis. He discovered the hammerhead catalytic RNA structure, invented external guide sequences for ribonuclease P, and created unnatural genetic codes de novo, all of which lead to the foundation of biotech companies. One of his recent research projects aims to improve ribosomal incorporation of unnatural amino acids for investigating the translation mechanism and for applications such as directed evolution of peptidomimetic drugs.
Mirko Himmel, University of Hamburg, Germany
Molecular Infection Biology: Nexus between Basic Research and Biosecurity
Mirko Himmel has been active in the biosecurity community since 2013. Over the years he worked for the Center for Science and Peace Research, as an advisor for the Biological Weapon Convention at the UN and is now a researcher at the Biology department of the University of Hamburg, His research focuses on characterizing CRISPR/Cas in Burkholderia glumae, a pathogen for rice. He also uses his expertise to guide risk assessment for civil security research and peace studies.
