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First Meet Up of the Greek iGEM teams

iGEM Thessaly: The research team from the University of Thessaly organized the First Meet Up of all the Greek iGEM teams at the city of Larissa on Saturday 13 July. 



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The students of the iGEM Thessaly team conducted from 12 to 14 of July a meeting with the Greek teams iGEM Athens and Thessaloniki that are also taking part in the iGEM competition this year at the city of Larissa, Thessaly. 

iGEM is an international completion taking place in Boston on October. It started in 2004 at MIT with only a few teams participating, exclusively from the United States. Today, there are more than 300 teams competing from all over the world. 

One of iGEM’s main goals is to promote collaboration among the iGEM teams and, as an extension, to society. In this context, iGEM Thessaly hosted the First Greek Meet Up and invited iGEM Athens and Thessaloniki to Larissa. The aim of this meet-up was for every team to present their project to the rest and receive useful feedback, comments, and ideas. The conference that was held on Saturday 13th of July.Apart from the teams’ presentations, an iGEM Alumni panel (consisting of exceptional guests with great experience in the iGEM competition) initiated  a constructive discussion with and filled a lot of gaps for the students that are making their first attempt to participate in something this big. 

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The conference was enriched by interesting talks by postdoctoral researchers of the Department of Biochemistry and Biotechnology. The invited speakers  were Constantine Garagounis, from the Laboratory of Plant and Environmental Biotechnology, and Konstantina Tsoumani , from the Laboratory of Molecular Biology and Genomics., We were also happy to host the coordinator of Academia and Research Committee of After iGEM Thea Chrysostomou, the iGEM Sheffield supervisor Dimitris Michailidis, and Giannis Ntekas, iGEM Athens 2018 team leader. Finally,  it was a great honor that our PI Papadopoulou Kalliope, who has been supporting as from the beginning, attended our meet up. 

We wish good luck to all the Greek iGEM teams! 


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iGEM Thessaly’s research project is being supported by the research infrastructure Omic- Engine, States Scholarship Foundation (ΙΚΥ), Research Committee of the University of Thessaly, Hellenic Petroleum, and ELPEN. 


Contact

iGEM Thessaly

e-mail: igem.thessaly@gmail.com 

website: http://igem-thessaly.uth.gr 

Facebook: https://www.facebook.com/igemthessaly 

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Twitter: https://twitter.com/igemthessaly 

YouTube: https://www.youtube.com/channel/UCBHXzFL7r9xxHxqQICznphA 

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.

SynBioS - towards stronger international connections in synthetic biology

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Accompanying adolescence of the discipline of synthetic biology, the past five years have seen many local, national, and supranational synthetic biology groups founded around the globe. United in the aims of promoting synthetic biology research as well as professional and policy development, the associations can benefit substantially from forging and maintaining strong horizontal connections.

On October 23rd, representatives from six national and supranational synthetic biology associations - EUSynBioS (Europe), SynBio UK (United Kingdom), GASB (Germany), SynBio  Australasia (Oceania), SynBio Canada (Canada), and EBRC SPA (United States of America) came together at the 2018 EUSynBioS Symposium Toulouse to set the foundation for a new international collaborative effort, the SynBioS Consortium. The representatives introduced their history, activities, and future plans through short presentations and discussed various topics of mutual interest, such as funding, social media, and science policy.

Concluding the workshop, the representatives confirmed their interest in continuing discussions as part of the future SynBioS Consortium, which will include regular online meetings focused on exchanging advice, coordinating initiatives, and reviewing progress.

We are looking forward to advancing synthetic biology together and encourage other national synthetic biology associations to join our endeavour.

  • EUSynBioS, SynBio UK, GASB, SynBio Australasia, SynBio Canada, EBRC SP

iGEM Paris Bettencourt 2018: STAR CORES - Protein scaffolds for star-shaped AMPs

iGEM Paris Bettencourt Team (2018) group photo. Left to right: Maksim Baković, Juliette Delahaye, Annissa Améziane, Santino Nanini, Elisa Sia (Team leader), Antoine Levrier, Jake Wintermute (Secondary P.I.), Ariel Lindner (Primary P.I.), Darshak Bhatt (Team leader), Oleksandra Sorokina (Advisor). Bottom row: Anastasia Croitoru, Camille Lambert, Naina Goel. Missing from the photo are Shubham Sahu, Alexis Casas, Haotian Guo (Mentor), Ana Santos (Mentor), and Gayetri Ramachandran (Mentor)

iGEM Paris Bettencourt Team (2018) group photo. Left to right: Maksim Baković, Juliette Delahaye, Annissa Améziane, Santino Nanini, Elisa Sia (Team leader), Antoine Levrier, Jake Wintermute (Secondary P.I.), Ariel Lindner (Primary P.I.), Darshak Bhatt (Team leader), Oleksandra Sorokina (Advisor). Bottom row: Anastasia Croitoru, Camille Lambert, Naina Goel. Missing from the photo are Shubham Sahu, Alexis Casas, Haotian Guo (Mentor), Ana Santos (Mentor), and Gayetri Ramachandran (Mentor)

Microorganisms such as bacteria and yeasts are fascinating! They are both beneficial and harmful to us. Over the decades, we have been using antibiotics to kill such harmful, disease-causing bacteria. With time, over-prescription and misuse of these drugs have made bacteria resistant to them; thus, evolving into what we call “superbugs”. This is a global health crisis that we currently face where simple and treatable bacterial infections have become incurable.
Recent statistics have shown that antibiotic resistance is responsible for an estimate of 25,000 deaths per year in the European Union (EU). More importantly, it is predicted to be responsible for up to 700,000 deaths each year, which is expected to rise – overtaking cancer by 2050. Not only does it take many lives but it also has a huge economic impact. In 2009, the cost of treating multidrug-resistant bacterial infections amounted to € 1.5 million in the EU alone. Likewise, according to a CDC report in 2013 entitled, “Antibiotic Resistance Threats in the United States”, antibiotic resistance was responsible for $20 billion in direct health-care costs in the United States.

In order to fight this catastrophe, many strategies have been developed but are primarily focused on humans. Thus, the World Health Organization (WHO) has come up with a more holistic approach to deal with this problem - One health concept. This states that the dispersal of resistance genes is not only limited to human species but it also spread through animals and the environment. Given the complex interactions between different sectors, one has to expand our focus to other areas like animal farming, agricultural industries, hospitals, urban and rural sectors to curb the spread of this man-made problem.
    
In response, the iGEM Paris Bettencourt 2018 team has decided to concentrate on animal-husbandry. According to Agence nationale de sécurité sanitaire de l’alimentation, de l’environnement et du travail (ANSES), the pig and pork industry consumed the highest amount of farm antibiotics in the year 2015 (129 kg/PCU), making the situation worse, while the European Food and Safety Authority (EFSA) stated that it is time to Reduce, Replace, and Re-think the use of antimicrobials given to animals. Thus, our team chose to work for a possible replacement for antibiotics for reared pigs, along with engaging the public to increase awareness of the misuse of antibiotics.

After doing some intensive research, we came across a promising alternative to antibiotics which is called antimicrobial peptides (AMPs), a diverse class of naturally occurring proteins. AMPs have a broad host range and are highly efficient: since they target the bacterial membranes, resistance to AMPs evolves at a much slower rate. Despite their great potential, there are some limitations for clinical usage including their potential toxicity, susceptibility to protease degradation, and high cost of production.

Considering the prospects of using AMPs and to overcome their drawbacks, we have proposed to employ an E. coli-based cell-free expression platform to produce naturally occurring or artificially designed AMPs (Fig. 1, step 2). These AMPs have been fused to self-assembling scaffold proteins to improve their bactericidal efficiency. We started with screening the best possible AMPs and scaffold protein complexes, in terms of their bactericidal property and biocompatibility (Fig. 1, step 1), which will followed by their production in cell-free systems. Then, we would test their mechanism of action by liposome leakage assay and microscopy. In addition, we want to mathematically model the influence of the charge distribution on the efficacy of the AMPs. To achieve this aim, we have generated 12,000 variants from 5 native sequences which were suitable candidates for designing our library. Lastly, the selected AMPs fused with the scaffold proteins would be tested for their efficacy via killing kinetics experiment in which the minimum inhibitory concentration was also determined (Figure 1, Step 3). We also check for any resistance development after exposure to the controls and our experimental product. Finally, we would determine their toxicity on mammalian cell lines.

Figure 1. The three core components of the project. Step 1: Screening of the AMPs and scaffold protein complexes. Step 2: Production of the selected AMPs and scaffold protein via E. coli-based cell-free expression. Step 3: Test for the efficacy and safety of the AMPs fused with the scaffold protein produced via cell-free synthesis.

Figure 1. The three core components of the project. Step 1: Screening of the AMPs and scaffold protein complexes. Step 2: Production of the selected AMPs and scaffold protein via E. coli-based cell-free expression. Step 3: Test for the efficacy and safety of the AMPs fused with the scaffold protein produced via cell-free synthesis.

Our battle against antibiotic resistance bugs has just started, and if you would like to join us on our journey to save the planet, please do follow us on our social media portals (Facebook, Instagram, Twitter, and our YouTube channel). Feel free to message us via email or any of our social media accounts. We are open to questions, suggestions, collaborations, and monetary support.


By Nympha Elisa M. Sia and Gayetri Ramachandran - iGEM Paris Bettencourt 2018

iGEM TU Delft 2018: Advanced Detection of Performance Enhancement

Left to right:  Lisbeth Schmidtchen; Timmy Paez; Gemma van der Voort; Lisa Büller; Jard Mattens; Janine Nijenhuis; Alex Armstrong; Nicole Bennis; Kavish Kohabir; Venda Mangkusaputra; Susan Bouwmeester; Monique de Leeuw

Left to right:

Lisbeth Schmidtchen; Timmy Paez; Gemma van der Voort; Lisa Büller; Jard Mattens; Janine Nijenhuis; Alex Armstrong; Nicole Bennis; Kavish Kohabir; Venda Mangkusaputra; Susan Bouwmeester; Monique de Leeuw

Doping has been an issue for fair sports for many years. Lance Armstrong for example won the Tour the France seven times before he was caught for the use of doping. At the end of 2012 all these seven victories were taken. The cycling world was shocked.

Lisa Büller

Lisa Büller

Athletes are constantly searching for new types of performing enhancement. Rapid advances in gene therapy enable athletes nowadays to inject themselves with performance enhancing genes, like Erythropoietin (EPO) and insulin-like growth factor 1 (IGF-1), in an almost undetectable process called gene doping. The big advantage of the use of gene doping is the easy bypassing of current detection methods. The World Anti-Doping Agency (WADA) is taking the possibility of gene doping seriously. Sooner or later, the sporting world has to deal with the phenomenon of gene doping to control athletic performance enhancement. The big problem is that no suitable detection method has been accepted for official use so far.

The TU Delft iGEM team is trying to tackle this problem by designing a suitable detection method for gene doping. In October our concept will be presented at the biggest international competition on synthetic biology, iGEM (international Genetically Engineered Machine competition). In this competition over 340 teams compete. All teams try to solve a world problem with the use of synthetic biology. This year the TU Delft is designing an efficient, secure and versatile method for the detection of gene doping.

Venda Mangkusaputra

Venda Mangkusaputra

Our novel detection method uses a dxCas9-Transposase fusion protein to target and tag the specific gene doping DNA with adapters. Only the genes with the adaptor will be sequenced with Oxford Nanopore Technologies’ next generation sequencing. With this method we create a method for targeted sequencing, which can be an efficient, secure and versatile for the detection of gene doping.

Currently, it is most likely that for the administration of gene doping, an adenovirus or a plasmid is used. Both methods bring the doping gene in the cell nucleus, where the gene will be expressed. The inserted genes however, do differ from the regular EPO genes present. Because of the size of the gene, introns must be taken out. We therefore search for the exon-exon junctions, which we do using a dxCas9 with a library of different gRNA sequences that cover all different gene doping changes. When the dxCas9 finds an exon-exon junction, the Tn5 transposase will cut the doping gene and add the sequencing adapters (Figure 1). This method for targeted sequencing will make sure that only gene doping DNA will be sequenced.

Figure 1      Schematic project overview

Figure 1 Schematic project overview

Do you want to know more about our project? Please visit our website for more information and sign up for our newsletter. We are always happy to answer questions via e-mail. You can follow us on Facebook and Twitter to stay in touch with our last sprint to the competition in October.

Get on your marks, get set and join us in the fight against gene doping.