iGEM 2019

ODYSSEE: A modular platform for field diagnosis of Tuberculosis

By iGEM Thessaly 2019

 

Can you imagine a world where everyone has unlimited access to healthcare? A world where equal opportunities are guaranteed, despite economic, social or political status, through the collaboration among countries?

 

Well, this is just not wishful thinking. These are some of the goals set by the UN (Sustainable Development Goals) for a better world by 2030. iGEM Thessaly decided to work on contributing to the effort made for the achievement of these goals.

 

iGEM Thessaly is the first team from the Thessaly area of central Greece to participate in the iGEM competition.  We are ten students from different Departments of the University of Thessaly. Our project “OdysSEE” aims for the fight against the communicable disease Tuberculosis (TB), a major threat for populations affected by crises such as refugees.

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Refugees and migrants are entitled to the same universal human rights and fundamental freedoms as all people, which must always be respected, protected, and fulfilled. More than 85% of refugees flee from and stay in countries with a high burden of TB (Kimbourgh et al, 2012). 

 

Despite increases in notifications of TB, progress in closing detection and treatment gaps is slow and large gaps remain. The goals of the World Health Organization’s End TB strategy will not be achieved without new tools to fight TB. 

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For this reason, we are developing “OdysSEE”, a rapid, reliable and safe test for early diagnosis of Tuberculosis that would be applied in refugee camps in Greece, as well as worldwide, wherever is needed. OdysSEE reflects the challenging journey that refugees are going through and our logo contains a migratory bird every piece of which represents a unique part of our project.

 

The test will work on urine samples. Once the Mycobacterium tuberculosis, that causes the disease, dies in a patient’s lung, it releases DNA fragments (cell-free DNA - cfDNA) into the blood as it breaks down. cfDNA’s small size allows for it to cross the kidney barrier and appear in the urine (Fernαndez-Carballo et al., 2018). The biomarker we selected is the IS6110 gene (1355 bp), which is located in the genome of the Mycobacterium Tuberculosis (MTB) and encodes for a putative transposase. IS6110 belongs to the family of insertion sequences (IS) of the IS3 category and is most commonly used for the detection of MTB because it is highly conserved (Thierry et al., 1990, Thabet S. & Souissi N., 2016).

 

The detection workflow contains 4 steps of amplification of the target gene. It begins with isothermal DNA amplification of the MTB DNA fragment, with the incorporation of two universal sequences, at 5’ and 3’ end respectively. An in vitro transcription of the amplicon follows with the combination of these two steps enabling addition and amplification of a universal trigger sequence, which is transcribed to RNA.

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This trigger RNA enables the in vitro translation of a toehold switch, a biosensor that encodes for a b-lactamase. b-lactamase is an enzyme that hydrolizes cephalosporins including nitrocefin, which then turns from yellow to red. The colorimetric readout will enable naked eye detection of the result. 


Tuberculosis detection is just the beginning. We aim to create a universal tool able to identify other communicable diseases as well. The key component to achieve this is the trigger RNA that is designed by the team’s wet lab and added to the reverse primer for the first step amplification. This can be achieved by just changing the primer set, while keeping the overhangs that contain the universal trigger, as well as the following path the same, thus targeting different pathogenic agents.

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The ultimate goal is to supplement conventional diagnostics by providing a modular, universal diagnostic platform for various diseases so that all patients have access to innovative tools and services for rapid diagnosis and care.

Join our journey and stay in touch with us and our project by following us on Facebook, Instagram and Twitter and also by visiting our website. Any feedback for our project is welcomed and can be addressed to us via email at igem.thessaly@gmail.com.

You can support our effort through our crowdfunding platform here.

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

  

References

Kimbrough, W., Saliba, V., Dahab, M., Haskew, C., & Checchi, F. (2012). The burden of tuberculosis in crisis-affected populations: A systematic review. The Lancet Infectious Diseases, 12(12), 950–965.

D Thierry, A Brisson-Noël, V Vincent-Lévy-Frébault, S Nguyen, J L Guesdon, B Gicquel, Characterization of a Mycobacterium tuberculosis insertion sequence, IS6110, and its application in diagnosis (1990), Journal of Clinical Microbiology

Thabet, S., & Souissi, N. (2016). Transposition mechanism, molecular characterization and evolution of IS6110, the specific evolutionary marker of Mycobacterium tuberculosis complex. Molecular Biology Reports, 44(1), 25–34.

Fernández-Carballo, B. L., Broger, T., Wyss, R., Banaei, N., & Denkinger, C. M. (2018). Toward the development of a circulating free DNA-Based in vitro diagnostic test for infectious diseases: A review of evidence for tuberculosis. Journal of Clinical Microbiology, 57(4), 1–9.

 

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 

Ιnstagram: https://www.instagram.com/igemthessaly 

Twitter: https://twitter.com/igemthessaly 

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

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