iGEM Aachen 2019: Plastractor

by Alina Egger and Yasmin Kuhn

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Currently everybody talks about environmental pollution by plastic. But not only big plastic waste, like plastic bottles, are a problem for us, but also microplastic, which e.g. was found in drinking water. Microplastics, particles smaller than 5mm, generated by degradation via wave motion and UV radiation, can work their way into the marine food chain and eventually into the human body.

With our project, we want to approach the microplastic problem. On the one hand we want to produce an easy way to detect micro- and nanoplastics in fluids and differ between different polymers. On the other hand, our project should create an easy way to extract them. Magnetic purification seemed to fit, as it doesn’t require any chemicals or elevated equipment.

Currently there are known magnetic bacteria existing, e.g. Magnetpospirillum gryphiswaldense, which thrive in the sediments of freshwater streams or marine sediments in very low oxygen environments. The most fascinating ability of these bacteria is their capability to produce so called magnetosomes, spherical vesicle-like structures of membrane-coated, biomineralized ferrite monocrystals with an approximate diameter of 45 nm. These are aligned by special cytoskeletal proteins inside the cell body to form little compass needles, which allow the bacteria to orient themselves along the earth’s magnetic field.

We want to develop novel fusion proteins embedded into the vesicular membrane of magnetosomes being able to specifically bind certain polymers, for example polypropylene (PP). They are consisting of a transmembrane domain as well as a variable linker domain and a domain for binding the polymer.

Figure 1: Schematic binding of polypropylene (PP) to the magnetosome mebrane (right) via the constructed fusion protein (left).

Figure 1: Schematic binding of polypropylene (PP) to the magnetosome mebrane (right) via the constructed fusion protein (left).

Figure 2: Fluorescent detection of the bound plastic particle with bound fluorescent markers.

Figure 2: Fluorescent detection of the bound plastic particle with bound fluorescent markers.

Novel fusion proteins embedded into the vesicular membrane of magnetosomes can be developed, able to specifically bind certain polymers, for example polypropylene (PP). For detection purposes there is a fluorescent protein marker inside the fusion protein that marks the polymer particle for fluorescent detection.

Our project aims to make the world a little less “plastic”. We don’t want to build up new plastic but to remove the one already present. Join the fight against microplastic and support us by visiting our website. You can ask us anything via e-mail (igem@rwth-aachen.de) and also follow us on Facebook, Instagram and Twitter to stay in touch with us and our journey to the competition in October.

The 2019 Aachen iGEM team

The 2019 Aachen iGEM team

Keynote speaker confirmed: Jakob Schweizer

We are happy to announce Jakob Schweizer as second keynote speaker for the 2019 EUSynBioS symposium!

Jakob Schweizer received his PhD at the Technical University in Dresden under the supervision of Petra Schwille. During that time he held a scholarship of the German Research Foundation and was involved in research coordination as well as public relations. Since 2014 he has been the Scientific Coordinator of MaxSynBio, the Max Planck Research Network for Synthetic Biology.

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Modularity, functionality and rational design are properties that constitute the essence of synthetic biology. However, these properties and goals are not unique to synthetic biology research alone. Jakob Schweizer will draw in his talk the unexpected comparison to the architectural style of Bauhaus, which marks the 100th anniversary of its creation this year. Bauhaus is characteristic for its minimalism and functionalism, and common grounds and boundaries will be discussed in Brno, a city hosting Villa Tugendhat, one of the most prototypical and at the same time outstanding examples of Bauhaus architecture in Europe.

Stay tuned, more speakers to be announced in the next few days! And don’t forget to register to the EuSynBioS 2019 symposium!

Playing Lego with Terpene Biosynthesis

by Laura Drummond

The smell of orange, lemon and grapefruit, the fresh scent of pine trees during a walk in the forest. The taste of mint in toothpastes, the camphor in pain-relief sprays and even the bitter notes of hops in certain types of beer. Terpenes are more present in our lives than we account for, and yet most of us do not know them by name.

 Terpenes are a class of organic compounds, produced by many different types of organisms, but mostly by plants. They are responsible for severalvolatile aroma compounds that we know, but are also involved in the formation larger molecules likecarotenoids and cholesterol, as well as some very important pharmaceuticals like the anti-malarial drug artemisinin and the anti-cancer medicine taxol.

 When it comes to their biosynthesis, terpenoids always form from two universal precursors: IPP (isopentenyl pyrophosphate) and DMAPP (dimethylallyl pyrophosphate), which are isomers from each other. These two molecules have 5 carbon atomseach, and therefore moleculesdownstream normally have a multiple of 5 carbon atoms in their structures. Terpene biosynthesis is modular, with precursors of fixed size and an almost constant count of carbon atoms, which increases in blocks of five as molecules get bigger

Biosynthesis of terpenoids. The pathways have been conceptually separated into four modules. Image:  Vavitsas et al 2018  (CC BY 4.0)

Biosynthesis of terpenoids. The pathways have been conceptually separated into four modules. Image: Vavitsas et al 2018 (CC BY 4.0)

Isopentenyl pyrophosphate (IPP), the universal precursor of Terpenes, and the different precursor molecules that can be formed using a newly discovered methyltransferase.

Isopentenyl pyrophosphate (IPP), the universal precursor of Terpenes, and the different precursor molecules that can be formed using a newly discovered methyltransferase.

In our recent paper, published in ACS synthetic biology, we found a way to challenge this ‘multiples of 5’ rule. We discovered an enzyme, hidden in the genome of Streptomyces monomycini, which is able to add one or two methyl groups (CH3) to the universal precursor of terpenes IPP, creating precursors with 6 or 7 carbon atoms in their structure. The discovery brings an additional piece for the biosynthetical pathway of these compounds, which is highly modular and resembles a game of lego. We also demonstrated the formation of larger molecules, with added methyl groups, showing that natural enzymes from the pathway can accept the different versions of IPP, taking advantage of their promiscuity.

 The findings open new possibilities for the biosynthesis of compounds so far unknown, by the addition of a new piece to the lego-like terpene biosynthetical pathway.

 

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 Laura Drummond is a PhD student at the Industrial Biotechnology Department of DECHEMA Research Institute in Frankfurt, Germany. She has a BSc in Biological Sciences from the University of Sao Paulo and a MSc in Entomology from the Luiz de Queiroz College of Agriculture in Brazil.

Twitter:  @drumm34

Linkedin: https://www.linkedin.com/in/laura-drummond-dechema/

Young PIs in action: Interview with Iro Tsipa

In our next post of our young PI series, I had the pleasure to interview Iro Tsipa, who will shortly start in her new role as as a Lecturer in Environmental Biotechnology at the University of Cyprus.

Kostas Vavitsas: You recently moved to Cyprus from the UK and you are going to start your own lab very soon. What are the most striking differences between the two research environments?

Iro Tsipa: In the UK, I was working in a world-leading institution, Imperial College London, and in a cutting-edge research centre, SynbiCITE. So, the research could run smoothly in terms of support in equipment and consumables, communicating ideas, being able to attend and participate in conferences.  In Cyprus, these are not for granted, I had to prioritize the tasks in the projects I participate in, as the budgets are much lower. I feel more responsible for the choices I make. This was quite challenging in the beginning but now I understand better the priorities of a lab and a project and it helped a lot to be prepared for my next job.

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Kostas: Do you feel prepared to start your new role?

Iro: I’m very excited to start working as a PI, have my lab and contribute to realistic solutions for environmental bioremediation and bioprocessing. I feel prepared about that. It seems like a natural next step to my academic career. The main challenges are: (i) get funded to be able to have the necessary equipment and working environment, (ii) find young people who share the same passion for environmental biotechnology to make a strong team and (iii) make a multi-disciplinary network of partners and collaborators who appreciate science to share ideas and try to answer key scientific questions.

 

Kostas: What is the true potential of environmental biotechnology and synthetic biology? Any interesting application that came up recently or will be out soon?

Iro: Environmental sustainability is at the core of the challenges of synthetic biology community. Engineered microbes and synthetic microbial consortia can substantially assist in limiting CO2 levels, recovering phosphorus, bioremediating and biodegrading resistant and toxic compounds that natural strains cannot process (yet)… Plastics and micropollutants biodegradation assisted by engineered microbes is an interesting field of emerging concern, which has attracted attention in recent years. Further, bioprocessing is a bottleneck in synthetic biology. We recently submitted a paper with my academic mentor, Sakis Mantalaris, and close collaborator, Gizem Buldum, of a kinetic model of synthetic genetic circuits predicting product formation towards microbial cell factories bioprocessing. I hope that this project will provide a different point of view of mathematical modelling and process intensification in synthetic biology.

Kostas: What is the single most important piece of advice you would give to an early career researcher in synthetic biology?

Iro: I would say ‘follow your own path’, find what fascinates you the most based on your background and knowledge, do your own research in the literature and start building on. Also, perform a thorough research of which groups work on similar projects and try to be inspired. Research and science are based on team efforts which can result in a great individual result.



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In August 2019, Argyro (Iro) Tsipa will start working as a Lecturer in Environmental Biotechnology in the Department of Civil and Environmental Engineering and Nireas International Research Centre, at University of Cyprus.Currently, she has been a Senior Researcherin the Department of Environmental Science and Technologyat Cyprus University of Technology. She obtained a Diploma in Chemical Engineering from the National Technical University of Athens, an MSc in Chemical Engineering with Biotechnology from Imperial College London where she also got her PhD in Bioprocess Systems Engineering. Before her current appointment, she worked as a Research Associate at the UK’s National Innovation and Knowledge Centre for Synthetic Biology (SynbiCITE) and the London DNA Foundry. Iro is considered as an expert in transcriptomics and proteomics. She has been instrumental in developing an integrated experimental-modelling framework to design optimal bioprocesses with applications in Industrial and Environmental Biotechnology, and Synthetic Biology. She developed and is responsible for the molecular biology facility of her current lab and the OzoneBioPro project developing a hybrid ozonation-bioremediation treatment of drill cuttings of the drilling operations in Cyprus.

 

The First Synthetic Biology Conference in Cyprus

AfteriGEM, the University of Nicosia, The Cyprus Institute of Neurology and Genetics, the Cyprus School of Molecular Medicine and the European University of Cyprus joined together to make the first SynBio Conference in Cyprus reality on the 29th and 30th of March, 2019. The conference scope was dedicated to the advancement of synthetic biology, education, and the development of an open community

by Thea Chrysostomou

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Synthetic biology as an emerging interdisciplinary field that focuses on the design and creation of new biological components, as well as the reprogramming of already existing biological systems to function as optimized entities, served as a catalyst and started the national and academic conversation on the possible benefits it can bring to the island. This conference helped us understand the benefits and implications of this encounter between technology and biology, and how SynBio can add value to all aspects of Cyprus and global society in medicine, technology, research, education, environment, economy, agriculture and even art.

Results are so far promising; new biological parts and systems such as tumor-seeking microbes for cancer treatment and photosynthetic systems for fuel production are only the beginning of a series of in-progress developments which have the potential to positively reshape everyday life. 

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Through panel discussions and talks of 25 speakers from around the world, this event gave the Cypriot scientific and business ecosystem the opportunity to push the boundaries of synthetic biology and through the starting line of this movement - the intersection between biology and technology - in the island as well.

After the introduction for the conference in the local TV by the former minister of health, Dr. Stavros Malas and Thea Chrysostomou (EU iGEM Ambassador), the first day of the conference started with Thea and Representatives of Ministry of Health and Ministry of Education addressing the audience, followed by panel discussions.

Dr. Tuck Seng Wong from the University of Sheffield in UK, Dr. Lital Alfonta from the Ben Gurion University in Israel, Dr. Vassily Hadjimanikatis from Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland, Dr. Konstantinos Vavitsas from the University of Queensland, Australia, and Dr. Kostas Mathiopoulos from the University of Thessaly gave us some insights on SynBio communities and iGEM teams regionally, their experiences, educational hubs and what could be some differentiating factors to bring constituents such as academia, research, industry, government involvement for the ecosystem of Cyprus to thrive on this field and be part of this movement.

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Meagan Lizarazo, the Vice President of the iGEM foundation gave a very interesting talk on the history of iGEM and SynBio, vision for the future, startups, success stories in a global level (eg. PvP Biologics, Bluepha).

Prof. Lital Alfonta talked more about her research on “Genetic Code expansion for improved electron transfer”, Prof. Philippos Patsalis about his company NIPD Genetics on “Non-invasive Genetic Tests for Reproductive Medicine and Oncology”, Dr. Yiannis Sarigiannis on “Synthetic Biology as a useful tool in antimicrobial drug discovery”, Dr. George M. Spyrou on “ Systems Bioinformatics and Network Rewiring towards Precision Medicine”,  Dr Margarita Zachariou on “Computational Modelling of Brain/Neural Plasticity”, Dr. Vasiliki Gkretsi on “Targeting metastasis: could Ras Suppressor-1 be the key?”Dr. Kyriaki Michailidou “Large Scale genomics association studies in breast cancer”, Dr. Tuck Seng Wong on “Biological carbon dioxide capture and utilization(bioCCU)”, DR. Vasilly Hatzimanikatis on “What do we need from nature’s chemical toolbox for Synthetic Metabolism?”, Dr. Kostas Mathiopoulos on “Enginnering insects for pest control” and Dr Konstantinos Vavitsas on “ Driving synthetic Biology on with sunlight”.

We also had some after iGEMers and current iGEM teams presenting their experience in iGEM, how it shaped their career, what effect it has on their lives being part of this ecostystem and their research projects. Yiannis Ntekas from the National Technical University of Athens from iGEM 2018 talked about “Toehold switch enabled viral detection via routine glucose monitoring technology”, Fran Quero from the Complutense Univeristy of Madrid, iGEM 2018 and 2019 talked about “ From DIYBio to iGEM. The Spanish example.” Alexis Casas and Antoine Levrier from Bettencourt iGEM team 2018 in Paris on “Cell- free expression platforms enable ne possibilitis at iGEM and beyond”. Chris Graham from the University of Nottingham, iGEM 2017 on “Synthetic Biology in UK, a biological key and how iGEM changes a young scientist’s perspective”. Athina Milona and Thodori Kontogiannis represented iGEM Thessaly 2019 on “ Spot the iGEM impact; a Greek aspect of a worldwide phenomenon”. Dimitrios Michailidis from the University of Sheffield talked about Life after University. My colleague Will Wright talked about afteriGEM and entrepreneurial opportunities in iGEM and Thomas Landrain on his startups: La Paillasse, PILI, and cJOGL.

It is my conviction that the projects presented during this conference have made all of us wealthier in knowledge, ideas, and inspiration.

It is my conviction that the projects presented during this conference have made all of us wealthier in knowledge, ideas, and inspiration.

iGEM Cyprus will participate in 2020 as a research team representing the island in Boston with all the major Unis in the country involved.

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Thea Chrysostomou is currently working for the iGEM Foundation as the European Ambassador. At the same time she is continuing her research on Machine Learning and Biophysics in Paris. She has graduated from the University of Sheffield as a Biomedical Scientist.