Team:Thessaly/Human Practices
Integrated Human Practices
Once we decided on the problem on which our project would be based on, we immediately started thinking about who can give us more information, where to start and which people did we have to meet to exchange views and adapt the project accordingly. Unfortunately, due to Sars-CoV-2 many conversations took place either on skype or on the phone, as live communication was not possible. In addition, countless emails were sent, because it was the only way to contact with them during this difficult situation. But without these wonderful people, who devoted their time to our team, the result would not be the same!
To begin with, we wanted to know more about IBDs and the treatment that the patients receive. That's why our team attended on March 26, 2020 a virtual webinar “Tyler IBD Education Day” (image 1) organized by Crohn’s and Colitis Foundation.Aaron Duvall discussed about treatment updates for IBD patients and Machelle McDowell told us about health maintenance and what IBD patients can do to stay as healthy as possible.
We decided that our first contact should be with gastroenterologists, as they are at the forefront of the problem. However, our conversation (image 2) with Ioannis Serafetinidis Director Gastroenterologist - ELPIS Clinic – Volos, Scientific collaborator of Athens Hospital & head of polyclinics MEDICAL, YASIS – Athens, really got us into thinking us.
Image 1. Virtual webinar “Tyler IBD Education Day”.
The doctor told us that the symptoms vary (diarrhea, anemia, fever, high heart rate, abdominal pain, discomfort, etc.) and that there is a high probability that the patient does not have any of these symptoms at all. It is common for patients to be referred to a gastroenterologist, after consulting another specialist such as a dermatologist or rheumatologist, as IBDs often cause side-effects that can be seen in different areas of the body. The following procedures are important for doctors to have a clearer view of the situation: endoscopic examination, laboratory examination, and the clinical picture of the patient. Of the indicators available, calprotectin (in the stool) is the best, but also not quite specific. He also pointed out, that they administer a big amount of various drugs, inevitably causing significant nutritional deficiencies to the patients, even to the ones that did not have them before the treatment. He urged us to talk to Clinical Nutritionists and that is exactly what we did!
Meropi Kontogianni, Assistant Professor at Harokopio University of
Athens, Department of Nutrition and Dietetics, Clinical Nutrition, pointed out/underlined that patients are not referred to nutritionists (image 3). She told us about the difference between diagnosing and evaluating the microbiome as it is accomplished by the use of SCFAs. She pointed out/underlined that patients with Crohn’s disease are the ones who face the biggest problem in treatment because there is a lack of data. SCFAs reflect on our diet and therefore, on the nutrient substrates we give to the large intestine. Although they are not specific indicators of IBDs, they do represent the health state of the gut microbiota, so it is beneficial to increase them in the body to have a more healthy and balanced microbiome. Another surprise awaited us when the Clinical Nutritionist referred us to the biotechnologist-molecular biologist Adamantia Kyriakou.
You can read more on our Education and Public Engagement page
One of our initial thoughts was to create a web application for patients, where they could add their symptoms and dietary habits, in order to create a database on IBD, that could eventually hold enough data to provide a first basic diagnosis. That idea was rejected as the doctors and clinical nutritionists told us that it would be dangerous for patients to have a subjective view of their condition from just an app, that can’t accurately diagnose the disease and take into account various factors.
Also, she urged us to contact the Hellenic Society of Crohn’s Disease and Ulcerative Colitis Patients (HELLESCC). That activity is described more thoroughly on our education and public engagement page.
Adamantia Kyriakou, Associate Professor in Microbiology at Department of Nutrition and Dietetics at Harokopio University of Athens, helped us with the biotechnological part of our project (image 4). She considers our subject as the next generation of probiotics. She believed that it will be useful for the evolution of the direction that current treatments have taken. Her advice was to focus more on butyric acid because it is the most important out of all the SCFAs. We thank her very much for her willingness to help us, but also for the bibliography she provided us with and the personal notes she gave us about our work.
But let's see what happened more specifically in the wet lab and dry lab department.
Georgios Skretas has been the Principal Investigator of the Laboratory of Enzyme & Synthetic Biotechnology at the Institute of Biology, Medicinal Chemistry & Biotechnology of the National Hellenic Research Foundation, Greece, where he currently holds the rank of Research Assistant Professor, helped us in several parts of our project. He sent us MC1061 strains for reporter Gene expression and SuptoxD and R plasmids for GPCR expression in bacteria (images 5 and 6). We also thank him as he was one of the speakers at the Big Greek Meetup we organized. The subject of his speech, “Modified bacteria as a platform for discovering potential drugs against problematic protein folding diseases”, was really interesting.
Image 5. MC1061 strains for reporter Gene expression.
Image 6. SuptoxD and R for GPCR expression in bacteria.
Our attempt to contact engineers and scientists to obtain advice around building our capsule did not receive the desired feedback. Although, we were lucky enough to receive a reply from Ashram Bin Islam, from the University of Asia Pacific. Islam was happy to answer any and all questions that we had, specifically our concerns around the operating and transmission frequency, antenna size and power consumption. He also presented us with specifications that we hadn’t thought of at the time. We thank him for his interest and contribution.
Emails from Ashram Bin Islam: First emailSecond email
During our experimental design we had to find out an E. coli strain, BL21 D3, to serve as our chassis. After searching we found that team Bielefeld 2014 had constructed strains including this knock out (image 8). So we contacted them through email and they sent us a plate with their bacteria.
After intragroup and intergroup discussion with the iGEM team from the Ohio State University, and in line with appropriate biosafety guidelines and standards, we have concluded that a two-tier system, utilizing auxotroph bacteria in conjunction with a “kill switch” genetic circuit, would present a viable solution to suppress biosafety concerns. A fruitful collaboration with the IGEM Ohio State University resulted in some interesting alternatives. They suggested that we knock out the alaR and IlvE genes from the bacterias’ genome and add L-alanine, L-valine and leucine inside the capsule for the cells to survive, creating therefore a metabolic auxotroph.
Image 8. Tube and plate with the bacteria that team
Bielefeld 2014 send us.
Back to the beginning again or are they all starting to come together now?
Having learned a lot, we again discussed our initial idea for the web application with the Dietician, Nutritionist in Larissa Mekras Apostolis. So, he suggested we build a web application to monitor patients’ progress. Patients would add their symptoms and dietary habits, to monitor how they react to treatment and extract valuable information from this.
Paroutoglou George, Director of the Infusion Unit of the Gastroenterology Clinic
of the General Hospital of Larissa George Paroutoglou and Helen Papadimitriou
an IBD specialist from the General Hospital of Larissa (image 9), urged us to continue
our research, as the SCFAs do not currently count in patients' examinations. They
consider our project to be a new and promising method, not only because it is a non-
invasive approach, but also because it targets the core of IBD generation which is
disturbances in the gut microbiota. Also, we designed questionnaires that were
distributed to the patients, with the help of Helen Papadimitriou, an IBD
specialist. The questionnaires were about the difficulties that they may experience in
their diagnosis and treatment, and how they believe that our project could help
them.
You can read more on our Education and Public Engagement page.
Furthermore, we met Oikonomou Konstantinos MD, PhD is a gastroenterologist - hepatologist in Larissa who told us of an electronic platform from the University Hospital in Larissa, Thessaly, containing samples and biomarkers of IBDs patients. Next year, maybe we will start from that and try to get access to this data base.
Our team communicated with the European Federation of Crohn´s and Colitis Association (EFCCA). They also told us to contact the Greek IBD patient association HELLESC to establish a dialogue and exchange views directly with patients about what is important and what are their unmet needs. We discussed with them about the mental wellbeing of chronic patients and they told us that it's an important issue for their organization and it will be their priority theme for 2021 (image 10).
Email from EFCCA: Click here
