At September 20th ‘18 we, iGEM Team Utrecht, organised the iGEM Biotechnology Conference in collaboration with iGEM Team Aachen. This collaboration was initiated at the European iGEM Meetup in Germany, organised by iGEM Team Munich this summer. The conference consisted of three lectures from experts in the biotechnology field: Dr. Silvia Mihaila (UMC Utrecht), Dr. Mauro Muraro (Hubrecht Institute), Dr. Aljoscha Wahl and Dr. Karel Olavarria Gamez (TU Delft). Furthermore three iGEM Teams presented their project and there was a musical performance by pianist and computer science student Mark de Blecourt. During the break and after the lectures, a networking moment was organised with stands from several biotech companies and different research groups. Students and other interested parties from the Netherlands as well as other European countries were invited to listen and network with scientists and companies during this day.
Audience reached via Social Media
Speakers
Conference Host: Dr. Maarten Flinkenflögel
Maarten Flinkenflögel was the host of our conference.
Maarten worked on the interface between research and industry for most of his career. He is currently working as a Policy Advisor on impact and valorization at Utrecht University. He obtained his master’s degree in Biomedical Sciences in 2006 at Utrecht University. For his Master thesis he studied the use of Danio rerio (zebrafish) as a model system for research on the immune system at the Hubrecht institute. For the following 5 years he worked at Crossbeta Bioscience as a Science & Business Consultant. In 2013 he started at Leiden University where he worked as Funding and Research advisor and Managing Director for the Netherlands Research School of Chemical Biology (NRSCB). Furthermore, he focused on the financial and legal management of the NWO Gravitation program ‘Institute for Chemical Immunology’ (ICI).
Valorisation by Dr. Louis Penning
The overall theme of our conference was valorisation: ‘putting knowledge into action’. In order to explain what this term exactly entailed, Dr. Penning gave an introductory talk about his own experiences and failures in the research field.
As Louis Penning puts it, he did not follow a straightforward career path. Louis: "I simply followed my heart and I always make sure to do what I love." He studied Biology at the University of Leiden and the University of Autonoma, Madrid. In 1993, he performed his PhD research again in Leiden, where he studied light sensitive antitumor agents. After that, Dr. Louis Penning did his Post-Doc in Gent, Leiden and Nijmegen. In 2002, he came to Utrecht to start his research at the faculty of Veterinary Medicine. He is currently working as associate professor, where he studies stem cells in the digestive system of companion animals.
Lecture 1: Disease Modelling and Regenerative Medicine (Nephro)Pharmacology by Dr. Silvia Mihaila
Dr. Silvia Mihaila is currently working on a bioartificial kidney, a kidney-on-a-chip device, at UMC Utrecht guided by Prof. Dr. R. Masereeuw. This was also the main topic of her lecture. She was born in Romania, did her PhD in the USA followed by a post-doc in the Netherlands. As a globe-trotter she encountered a lot of differences in these various education systems.
The goal of the Masereeuw group is to develop novel therapeutic strategies to accelerate organ function recovery during renal failure. Besides that, they are developing novel interventions for renal disease by gaining insight in processes that determine the excretion of metabolic wastes and drugs by the kidneys. Dr. Mihaila’s work covers the optimization and upscaling of the bioartificial kidney system, including in vitro evaluation of long-term function and stability, and subsequently, the in vivo validation of efficacy and tolerability.
Lecture 2: Single Cell Sequencing by Dr. Mauro Muraro
Dr. Mauro Muraro is the CEO and founder of Single Cell Discoveries. During his lecture he explained how he set up his own company and why single cell sequencing is very beneficial.
Dr. Muraro Muraro did his masters in Molecular BioSciences at the University of Amsterdam and Mount Sinai hospital in New York City. This year, he completed his PhD at the van Oudenaarden lab at Hubrecht Institute, where he worked on experimental and analytical pipelines for single-cell sequencing. During his PhD, Dr. Muraro Muraro applied single-cell sequencing to characterize human pancreatic cells to determine genes expressed by each individual cell. Nowadays he is the co-founder and CEO of Single Cell Discoveries B.V., where scientists can order customized Single Cell Sequencing assays.
Lecture 3: Sucrose2PHB - Optimization of Biobased Polymer production by Dr. Aljoscha Wahl & Dr. Karel Olavarria Gamez
The third lecture was presented by two professors: Dr. Aljoscha Wahl and Dr. Karel Olavarria Gamez. They talked about the biochemical engineering process of Sucrose2PHB for the optimization of bio-based polymer production.
Dr. Aljoscha Wahl holds an MSc degree in biochemical engineering from TU Dresden (Germany) and a PhD degree (biotechnology) from Forschungszentrum Jülich and Siegen University in Germany. Since 2008 he is assistant professor TU Delft in ‘Metabolic Systems Engineering’. His research group focuses on systems biology, i.e. identification of metabolic network interactions (kinetics and regulation) in different model organisms. Dr. Wahl collaborates with several leading European universities as well as international companies. In his teaching Dr. Wahl trains students in systems analysis – he teaches master (and post-master) courses for network analysis as well as systems biology. In the bachelor courses include programming and application of linear algebra to biotechnology.
Dr. Karel Olavarria Gamez studied Biology at the University of Havana before achieving his PhD in Molecular and Cellular Biology, and Neurosciences at the University of Chile, in 2012. The focus of his research is Bacterial metabolism, studying Pseudomonas putida and Escherichia coli. He has been working in different academic institutions in Cuba, Chile, Brazil and The Netherlands. At the moment, he combines metabolic modelling with genetic modifications in E. coli to understand and manipulate the catabolism of sugars under (an)aerobic conditions. The immediate applied outcome of his research could be the production of polyhydroxyalkanoates from sucrose in collaboration with Brazilian partners.
iGEM Presentations
iGEM Team Aachen 2018
In total a number of three iGEM teams gave a presentation about their project. At first, this years’ iGEM Team from Aachen explained what iGEM is, followed by a short presentation about their own iGEM project. They are developing a new biosensor to detect the sleeping hormone melatonin. The presenters: Henri Lila and Jan Biederbeck.
iGEM Team Utrecht 2017
Ouafa Dahri and Giel Scheepers of last years’ iGEM Team from Utrecht elaborated on their iGEM adventure and project. Their team has developed an easy-to-use and cheap DNA detection kit for disease diagnosis in areas of the world where advanced diagnostic technologies are unavailable. They call their system ‘OUTCASST’, which stands for ‘Out-of-cell Crispr-Activated Sequence-specific Signal Transducer’.
iGEM Team Utrecht 2018
Last but not least, our team members Pim Swart and Jolijn Govers presented our iGEM project. They especially elaborated on the overall goal of our project including human practices and social relevance. They explained how we are using the chemotaxis pathway of E. coli to build a biosensor to measure the concentration and source of surface water contaminants due to an increased medicine intake.
Network Market
At the networking market, several companies, research groups, and this years’ iGEM teams from Aachen and Utrecht presented themselves and their projects.
Mimetas: Eline van Zutphen
Eline van Zutphen represented MIMETAS - The Organ on a Chip Company at the networking market. She showed what they do and why single cell sequencing can be very applicable.
In 2010, Paul Vulto and Jos Joore came together and started brainstorming on creating a device that could be used for massive parallel testing of individual therapies. The same day Paul Vulto called Prof. Thomas Hankemeier to discuss the potential of starting a new Organ-on-a-Chip Company, now known as MIMETAS. The Organ-on-a-Chip Company offers OrganoPlates® and develops human tissue and disease models for tomorrow's medicines, chemicals and food. MIMETAS’ vision is to develop an easy-to-use 3D device that will help the development for better medicines. With the OrganoPlate®, that vision is now here. OrganoPlate® is the future for 3D tissue models! MIMETAS has currently three offices, with its headquarters located in Leiden. In Leiden, The Netherlands, they perform most of the biological model development work, as well as development of novel hardware and assays. Their manufacturing site is located in Enschede, in the eastern part of The Netherlands. Here they produce OrganoPlates® under strictly controlled clean room conditions. In Gaithersburg (MD) in the USA, and in Tokyo, Japan, MIMETAS has subsidiaries involved in selected R&D, customer support and business development.
Single Cell Discoveries: Dr. Mauro Muraro and Dr. Judith Vivié
Just 2 weeks after the official launch of their company Dr. Mauro Muraro ad Dr. Judith Vivié, co-founders of Single Cell Discoveries, represented their company on the networking market at our conference.
On the 11th September 2018, the official launch of Single Cell Discoveries was celebrated. Just 9 days later, they have presented themselves at the networking market of the iGEM Biotechnology Conference! Single Cell Discoveries was founded as a spin-off from the KNAW’s Hubrecht Institute. Both founders worked there as single cell facility manager (Judith) and PhD researcher (Mauro). In these capacities, they collaborated with many scientists from different backgrounds to set-up and analyze single-cell sequencing experiments. Noticing the common problems many researchers faced when setting up single-cell experiments, they decided to join forces and start Single Cell Discoveries, a one-stop-shop for single cell sequencing.
Veterinary Medicine, companion animal: Dr. Louis C. Penning
Veterinary Medicine is more and more an integrated part of biomedicine. The One Medicine concept appreciates the large similarities in disease causes and treatment options in human and animal medicine. Therefore large animals, like horses and dogs, are regained value as predictive models for human medicine, as these animal were in the past. Pavlov reflexes and insulin, are well known examples of “first in dogs” measurements. My group exploits the downside of inbreeding to dissect genetic background or (rare) diseases in men, and uses relevant dog models as pre-clinical models. A exciting examples of this is the dog model for the rare human diseases called Wilson’s disease. Currently we are transplanting autologous and genetically engineered organoids into the liver of the animals in order to achieve functional liver recovery. The fasten implementation we consults liver patient organIsations on a regular base.
Link to poster
Metagenomics research group (MGX): Dr. Bas E. Dutilh
Metagenomics is an approach to investigate the combined genetic material of an entire microbial community at once. This technology has completely changed the way we view the world, revealing microbes in just about any possible environment on earth. For example, the human body is a complex super-organism that contains more bacteria than human cells, and about ten times more viruses! Most of those viruses infect the abundant bacteria, but we have very little idea how this ecosystem works, how it stays stable, and what happens if the stability is lost. In my group, we develop innovative bioinformatic tools to study metagenomes, and apply them to big datasets to investigate microbes in all natural habitats, including the human body, the global oceans, soils, etc. We collaborate with many international researchers on fascinating questions that we hope to answer with our computational techniques.
Link to poster
Chemical Biology & Drug Discovery: Dr. Seino Jongkees
Complex chains of sugars called glycans are present on the outside of all cells, and the various patterns of their building blocks are vital for cellular communication. For example, cancer cells can signal to the immune system to leave them alone by changing the sugar molecules on their surface. If we could change the ‘sugar code’ of these cells, it would allow the immune system to clear the tumour. The way these molecules interact with protein receptors means that they often bind very weakly, and so it can be very difficult to find drug leads that act on them. In my group we are applying a technology for small cyclic peptide discovery to try and find drug leads that target the enzymes that build up and remodel these glycans, as well as the receptors that recognise them.
Link to poster
Musical Intermezzo
In order to appeal a greater audience for the conference, we invited a pianist who studies at Utrecht University to play during the musical intermezzo.
Mark de Blecourt is a computer science student at Utrecht University. At an early age he already had a gift for music, and he started playing the piano 8 years ago. He played the following songs for us:
