Timeline
Terzoudi Ekaterini
Terzoudi Ekaterini PhD,
Neurologist, Assistant Professor of Neurology
Importance
One of the key foundations of our project revolves around the gut-brain axis. To gain a deeper understanding of its intricacies and to obtain insights from a clinical neurologist's perspective, it was necessary to engage in a conversation with Dr. Terzoudi.
Feedback
Following our presentation of the project, Dr. Terzoudi delved into the intricacies of the gut-brain axis, shedding light on its operational principles. She underscored the dynamic and rapidly evolving nature of research in this field, emphasizing the need for thorough scrutiny of our information sources during our literature review. Furthermore, regarding our project’s app ‘DEPRETECT’, she said that it is vital to use a reliable questionnaire so that the final result is as valid as possible. Lastly, Dr. Terzoudi provided valuable input on how to effectively present our ideas to other experts in the field. Her guidance and advice proved to be exceptionally beneficial to our project.
Ioannis Kourkoutas
Ioanna Prapa
Grigorios Nelios
Ioannis Kourkoutas , PhD
Professor of Molecular Microbiology and Applied Biotechnology in the Department of Molecular Biology and Genetics,
Head of the Laboratory of Applied Microbiology & Biotechnology in the Department of Molecular Biology and Genetics.
Ioanna Prapa , PhD
Candidate in the Department of Molecular Biology and Genetics
Grigorios Nelios , PhD
Candidate in the Department of Molecular Biology and Genetics
Importance
MDr Kourkoutas has more than two decades of experience working with microorganisms and especially with bacteria of the lactobacillus species. He, together with many researchers, PhDs and PhD Candidates, such as Ms Prapa and Mr Nelios, runs the de facto biotechnological lab of our school. Many probiotic patents have come out of this very lab.
Feedback
During our discussions with these experts our project transformed from an abstract idea into an applicable plan with solid foundations. Specifically, they advised us to minimize and simplify as much as possible our experiments in order to catch up with the timeline. Besides that they gave us the criteria in order to select the best for our purpose bacterial strain and prebiotic. Lastly, they helped us in the experimental design (e.g what combination of SCFAs should we use in our cell lines, info about the LGG and more).
Implementation
We carried out a screening test among several Lactobacillus strains in order to select the one that produces the SCFAs we wanted in the preferable concentrations. So we end up selecting LGG as our probiotic and as our prebiotic. Besides that we ended with several controls of our bacterial cultures in order to test the growth rate of the strain and the concentration of SCFAs produced.
Stergios Vradelis
Stergios Vradelis, PhD
Gastroenterologist, Assistant professor in the Department of Medicine
Importance
Dr Stergios Vradelis has a multi-year experience as a clinician gastroenterologist in the General University Hospital of Alexandroupolis. In addition his subject area is pathology with emphasis on the pathophysiological conditions of the digestive system.
Feedback
After leaving our meeting with Dr Vradelis we had gained some very important advice not only for the current stage of our project at the time but also for the latter stages of an approval of a probiotic. To be specific, he informed us about the harsh enteric symptoms that depressed patients develop that could affect the activity of the probiotic. Moreover, he raised us the questions of how other antidepressants could affect the metabolism of a probiotic and to what kind of depressed people our probiotic aims.
Adamantini Kyriakou
Adamantini Kyriakou , Associate Professor
Bacteriology with emphasis on biotechnological applications
Importance
Her research focuses on the study of the intestinal microbiota and the factors that influence it in health and disease and the study of the microbial processes involved in the breakdown of solid organic debris in aerobic (compost) and anaerobic conditions, through the use of both cultural and molecular techniques.
Feedback
Dr. Kyriakou helped us a lot with the technical aspect of our experiments. As we ran our first experiment twice, we took her advice two times; one before starting the experiment for the first time and one after our initial results, to find ways to optimize our results. She shared with us her concerns about using the Caco2 cell line and highlighted the advantages of using the R1N14B cell line, we discussed the SCFAs’ concentrations we should use for our first experiment and she also provided us with technical details for the correct culture of the cell line.
Implementation
After discussing with Dr. Kyriakou, we decided the exact SCFAs’ concentrations we were going to use. However, we could not follow her advice to use the R1N14B cell line, as our lab faculty was experienced and trained in using the Caco2 cell line. For this reason, we took her advice again, in order to minimize the possible negative outcomes from using the Caco2 cell line.
Group of Psychologists and Social Workers
Group of Psychologists and Social Workers of the Society of Social Psychiatry P. Sakellaropoulos
Mademli Kassiani, Psychologist
Papasideri Maria, Psychologist
Athanasia Papadoudi, Psychologist
Papadopoulou Vasiliki, Psychologist
Topali Sarantula, Social Worker
Goutsidou Irini-Korina, Social Worker
Importance
The Society of Social Psychiatry P. Sakellaropoulos, is a scientific, non-profit association, since 1986 and is an official provider of mental health services under the National Plan for Mental Health "Psychargos" of the Ministry of Health. The main purpose of the services is to inform, raise awareness and promote Mental Health through networking and cooperation with agencies and society.
The experienced psychologists and social workers of the association provide prevention, support and treatment services, special home care, psychosocial rehabilitation and community education in cities and hard-to-reach areas.
Feedback
Our team consulted psychologists and social workers who highlighted that neglecting proper nutrition is a symptom of depression. They appreciated the application's feature of providing nutritional advice, recognizing the significance of holistic approaches in treating mental illnesses, incorporating both diet and exercise.
The experts emphasized that the app would resonate well with younger individuals experiencing depression, given their familiarity with technology. They also noted its relevance for people with anxiety disorders, who frequently seek health information online. However, they expressed their concern that, as with most applications, apps that are easy to download are equally easy to uninstall.
They recommended incorporating a feature in the app that displays nearby mental health specialists. This would serve as an encouragement and simplify the process for users seeking professional help.
Furthermore, the expert group reviewed the questionnaire designed for the general public. They proposed modifications to the phrasing of questions and answer options to ensure accuracy. Additionally, they recommended including questions about gender, marital status, education level, and type of residential area at the beginning of the anonymous questionnaire. This addition aims to facilitate a more precise analysis of the collected data.
Implementation
Our discussion with this group proved to be highly valuable and influential in shaping various aspects of the project. Following our meeting, we made adjustments to the questionnaire based on their suggestions. We were now prepared to distribute it to both our contacts and individuals we engaged with during the activities we organized and the events we attended (you can find the questionnaire form and results below). Additionally, we implemented the feature in the app that shows nearby mental health specialists, enhancing the app's comprehensiveness and efficiency.
Georgios Boulougouris
Georgios Boulougouris
Assistant Professor at Department of Molecular Biology and Genetics, Democritus University of Thrace
Importance
Dr. Boulougouris research interests focus on the dynamics of physical-chemistry systems with emphasis on molecular dynamics simulations and statistical learning.
Feedback
He introduced us to metabolic pathway and flux balance analysis concepts. He, in addition, proposed methods and software to explore the dynamics of gut metabolites, to study the relationship between SCFA and the corresponding signal that leads to serotonin production. He also suggested docking specific ligands to our target proteins to see further and unknown stimuli to the system.
Group of Psychiatrists
Group of Psychiatrists of the Society of Social Psychiatry P. Sakellaropoulos
Eleftheriadou Marina, Psychiatrist
Eleuftheriadis Antonis, Psychiatrist
Mpellas Yannis, Psychiatrist
Deligiannis Marinos, Psychiatrist
Importance
The Society of Social Psychiatry P. Sakellaropoulos, is a scientific, non-profit organization association, since 1986 and is an official provider of mental health services under the National Mental Health Plan "Psychargos" of the Ministry of Health. The main purpose of its services is to provide information, awareness and promotion of Mental Health through networking and cooperation with institutions and society.
Feedback
The psychiatrists shared with us their concerns about the use of the DEPRETECT digital application. As their main concern was the reliability of the results offered by the application, they drew our attention to using an approved and tested questionnaire in order to correctly measure depressive symptoms. They also proposed the idea that the users can somehow track their previous data.
Implementation
We completely implemented the psychiatrists’ advice. The chatbot now uses questions from a well-known questionnaire in the field of depression detection and therapy. It is often called QIDS-SR (Quick Inventory of Depressive Symptomatology). Apart from this, the user can select a date and see his past conversations with the chatbot.
Kolovos Petros
Kolovos Petros , PhD, MBA
Assistant professor of Biology Systems in the Department of Molecular Biology and Genetics, at Democritus University of Thrace
Head of the Laboratory of Molecular Regulation and Development of Diagnostic Technology
Importance
Mr. Kolovos has extended knowledge in the subject of Molecular Biology, gene expression and regulation, and the general structure of the genome. He also has a lot of knowledge on CRISPR-Cas9 and the genetic modification of microorganisms. Mr. Kolovos is also engaged with bioinformatics making a high-tech depiction of the biological interactions.
Feedback
After a very interesting conversation with Mr. Kolovos, he suggested that the modification of the genome of Lactobacillus would not be preferable due to the technical and biological difficulties that would come up if we wanted to introduce our whole new gene cassette permanently in the genome. Also, he made a point about the change of a cis-component (e.g. a promoter) that we could change it in a way that it would be stronger and thus lead to higher production of protein.
Implementation
Since modifying an organism and making the changes directly in its genetic makeup poses technical difficulties and threatens the overall quality of expression of our gene cassette, we decided that we would not include any experimental step that performs genetic modification of the genome makeup. So our selection marker for the food-grade plasmid should be dominant and not complementary (like any lac gene). Moreover, we decided to include not only a constitutive promoter but a strong-regulated one as well.
Antigone Oreopoulou
Antigone Oreopoulou, MSc
Biologist-Body Psychotherapist, Communication and Crisis Communication Coach
Fottes Panetsos, PhD
Biologist, Biochemist
Importance
Antigone Oreopoulou graduated from the Biology Department of the Aristotle University of Thessaloniki. She then completed her first M.Sc. in Nutrition at the University of Toronto's Department of Medicine and her second M.A. in Psychology at the University of Indianapolis. Her husband, Fottes Panetsos, graduated from the Biology Department of the Aristotle University of Thessaloniki. He then completed his postgraduate and PhD thesis as a scholarship holder of the Greek Atomic Energy Commission at the Institute of Biochemistry and Biophysics of the Greek Centre for Natural Sciences "DEMOCRITOS" and the University of Athens.
Feedback
After carefully listening to the details of our project, they expressed their concerns about the possible implementation of our project in the real world. They highlighted the importance of the biosafety of our project, expressing their concern that, after genetically engineering L. rhamnosus, it might not be safe to use it as a probiotic. Although our project is for sure not yet ready to be used in the real world, it was still very useful to discuss with them possible solutions to these kinds of problems.
Elpida Papanikolaou
Mr. Elpida Papanikolaou , Νutritionist
Importance
In order to take the project a step further our team took into consideration nutrition as an integral factor that affects the mood through the alteration of intestinal flora. To better understand and implement this idea we contacted Mrs. Elpida Papanikolaou, a dietician specialized in nutritional psychiatry as well as in gut microbiome.
Feedback
During this collaboration, Mrs. Papanikolaou provided us with information about the foods and supplements that help patients with depression, what types of food to avoid and how to approach mentally ill people in order to generate a personalized nutrition plan specifically to the person’s needs.
Implementation
With her assistance, we updated depretect to offer complementary advice to the user on how to maintain a healthy lifestyle.
Ioannis-Alexandros Gampierakis
Ioannis-Alexandros Gampierakis , PhD
Neuroscientist, Postdoctoral Research Fellow, Inflammation and Immunology, Pfizer
Importance
Ioannis-Alexandros Gampierakis is a neuroscientist, currently working as a postdoctoral research fellow in Pfizer. He is researching how the gut communicates with the brain. One of his lifelong research goals is to study the mechanisms of neuroimmune interactions within the Enteric and Central Nervous System in health and disease.
Feedback
Dr. Gabierakis helped us a lot with our project in the beginning, when we were to decide our final project. In the beginning, when we still weren’t sure that there is enough bibliography to base our project on, his research encouraged us a lot. He also helped us a lot with some initial technical details. We talked about the cell line we are going to use in our experiments, its advantages and disadvantages and how we could possibly model the gut-brain axis in vitro. Finally, as he is himself working in a pharmaceutical corporation, we discussed the future directions our project could take and how it could, as a last step, be implemented in the every-day life of patients.
Katerina Palaiologou
Katerina Palaiologou, PhD
Assistant Professor of Molecular Biology in the Department of Molecular Biology and Genetics
Importance
Mrs Katerina Palaiogou is an Assistant Professor teaching neurobiology in our university. Her research interests involve neurodegenerative diseases, such as Pakinson’s and Alzheimer’s disease, focusing on their molecular and genetic basis, as well as their treatment.
Feedback
After presenting to her our project, she helped us identify some parts of our project that we had not considered. For example, we talked about the exact path serotonin follows in the gut-brain axis, the safety of our project, the previous data we are going to base our project on, the long-term effects of our proposed probiotic, etc. She also highlighted the fact that the serotonin produced in the gut is not irrelevant from the rest of the body and it is important to always consider it as part of the bigger picture of the other organic systems.
Konstantinos Anastasiou
Konstantinos Anastasiou , PhD
Assistant Professor of Nutrition and Dietetics at Harokopio University
Importance
Mr. Anastasiou has extended and multi-year experience in subjects including dietary patterns and their relationship to health and disease, energy balance, appetite mechanisms and body weight regulation.
Feedback
Mr. Anastasiou provided us with some highly important information regarding our project. We discussed our aims and the relevant methodology that we should use. He advised us on how to monitor the therapy more effectively through the mobile application that we developed. He proposed that we should include a section in the app where the user can track his dietary habits. He also gave us some really useful insights about the diet that a patient could possibly follow in order to tackle depression.
Implementation
We redesigned and further developed our application so that we include Mr. Anastasiou’s suggestions about dietary tracking. We also implemented a mechanism that gives dietary advice to the users, hoping that this will help them to deal with depression.
Tegopoulos Kostantinos
Tegopoulos Kostantinos , PhD
Candidate at the Department of Molecular Biology & Genetics, Democritus University of Thrace
Importance
Tegopoulos Kostantinos’ contribution to our project was really important, as he is valuable for both our wet and dry lab. At the same time, he is also actively participating in entrepreneurship contests.
Feedback
In his PhD, Tegopoulos Kostantinos is using different strains of Lactobacillus, offering us the chance to discuss the advantages and the disadvantages of the different Lactobacillus strains we could use. Apart from this, he advised us about the type of analysis we should use to analyze the results from our experiments. Lastly, we discussed the different options we have for the delivery of our probiotic.
Implementation
His feedback was implemented in our project in many ways. Firstly, we decided to use Lactobacillus rhamnosus GG, as it is a commonly used and safe probiotic with many advantages. We also decided to administer our probiotic in food, as this would enhance the patient’s experience, while also maximizing the probiotic’s action. Regarding our dry lab, he helped us make our minds into using ANOVA to model our results.
Konstantina Vaitsi
Konstantina Vaitsi, PhD
Candidate at Department of Molecular Biology and Genetics, Democritus University of Thrace
Importance
Dr. Vaitsi , currently doing research on Dr.Boulougouris Lab has similar interests and capabilities in Bioinformatics tasks. She is familiar with various analyses techniques as her MSc focused on big data analytics.
Feedback
She helped us organize the material for our 1st team’s workshop on the 1st Panhellenic Conference Students Bioscientists oriented in mathematical modeling of genetic circuits. She gave us examples of possible circuits in correspondence with their computational logic gates and guided us on how to simulate the systems.
Haris Zafeiropoulos
Haris Zafeiropoulos , PhD
Postdoctoral Researcher at Rega Institute for Medical Research, KU Leuven, Belgium
Importance
Helped us understand the problem of finding differences of the microbiomes between healthy and depressed individuals. Together we designed our dry lab bioinformatics workflow and interpreted the results that were produced.
Feedback
Introduction to microbiome analysis methods and steps from metagenomes to functional enrichment of annotated proteins. He showed us why compositionality and sparsity in microbiome datasets can create problems in analyzing them and proposed specific ways to do so.
He made it clear to us how to use GTDB, Prokka, GMrepo and many other software packages. We also checked if the statistics we used during our analyses were appropriate and gave us correct results.
Implementation
At first we informed him of our intention to create metabolic models and apply flux balance analysis using the micom software package. He advised us to not follow this approach because it makes many assumptions and might produce significant errors. He proposed different methods to study the complexity of microbiome metabolites which was our eventual approach.
We wanted to manually find and download the metagenomes that concerned us but he suggested using the NCBI database package and the API from GTDB database, thus we won valuable time. We wanted to acquire a specific strain for each bacterial species, so he directed us to use representative genomes from the GTDB database. Suggestions for genome annotation software like “Prokka”, “Prodigal” and ”Bakta” were really helpful as we had no previous background experience in genomics analysis.
Raphael Sandaltzopoulos
Raphael Sandaltzopoulos , PhD, MBA
Professor of Molecular Biology in the Department of Molecular Biology and Genetics,
Head of the Laboratory of Gene Expression, Molecular Diagnosis, and Modern Therapeutics in the Department of Molecular Biology and Genetics.
Importance
Mr. Sandaltzopoulos has extended and multi-year experience in subjects including gene expression, plasmid design and transformation, and biochemical knowledge of the different gene cassettes introduced into the host. Also, he has worked with different kinds of bacteria, taxa, and strains, including our target strain Lactobacillus rhamnosus GG. He is also a member of the Omic-Engine research institution, the National Research Foundation of Synthetic Biology.
Feedback
Mr. Sandaltzopoulos provided us with some highly important information regarding our project. Firstly, we evaluated our project and our aims. We examined the metabolic pathway that we wanted to introduce into our host strain. He advised us to ensure that the chemical reaction of each biochemical pathway should be ideally one-directional and be more favored from other biochemical pathways for our final product, butyrate, to be produced.
Subsequently, he proposed that the genes and the sequences overall should be codon-optimized for the hosts that we would use, to have a proper expression. Next, we discussed more in-depth the expression and cis components that we should include on the cassette. He suggested that before every gene we should include a ribosome binding site, after the final gene we should include a terminator compatible with Lactobacillus as well as a promoter in the start that is constitutive and compatible with our genus. Moreover, he was very concerned about the implementation of our project in the real world. He proposed a more compatible by the food regulations way for designing our plasmid. More specifically, he advised us to design a food-grade plasmid, which is different and safer for the human organism, because it is composed of DNA of Generally Recognised as Safe organism (for example L.lactis) and includes a safe marker such as nisin and does not have an antibiotic resistance marker (for no antibiotic resistance gene to crossover another organism in human and end up in antibiotic resistance).
Implementation
We redesigned the part that we would like to improve for the gold criteria, including the aforementioned cis-regulatory components. Also, we changed our minds from ordering a typical plasmid for Lactobacillus to designing one that is food-grade, suitable for Lactobacillus, and compatible with any legislation for genetically modified organisms in foods. We also checked the chemical reactions and interactions that would take place, based on previous similar experiments and bibliography, to form a complete and comprehensive troubleshooting at the end of our experiments.
Galanis Alexis
Galanis Alexis, PhD
Assistant Professor of Molecular Biology with an emphasis on signal transduction in the Department of Molecular Biology and Genetics.
Importance
Mr. Galanis has a long research experience on probiotics and a majority of his experimental work includes probiotics of the Lactobacillus strain, which was our target organism. Also, he and his laboratory staff have a wide knowledge of the techniques of cloning, digesting, and transection of bacteria, since they have an extensive library of plasmids and digestion/transfection protocols.
Feedback
After the presentation of our project to Mr. Galanis and his laboratory’s staff, he first warned us about the safety issues that might come up. He advised us to create a food-grade system that includes the proper design of the plasmid and the correct selection of the probiotic host. Also, he provided us with some extremely useful protocol tips which made us redesign some of our sequences.
Implementation
As we were told about the safety pylons that should be established we designed a food-grade system accordingly. Also, we changed the sequence of our last gene in the butyrate-producing gene complex, so that it can be fused with GFP protein and detect more easily the presence of the plasmid inside the transformed cells. Also, he proposed a different food-graded plasmid to use in place of the one that we already designed due to some technical difficulties.
Zoe Vogiatzaki
Zoe Vogiatzaki
Clinical Psychologist, Group Psychoanalyst, Family Therapist
Importance
Our discussion with Ms. Zoe Vogiatzaki held significant importance, because she is a clinical psychologist and at the same time she is actively researching the link between mental health and diet, a topic directly directly to our project.
Feedback
Following our project presentation, Mrs. Vogiatzaki expressed her overall enthusiasm for the integration of artificial intelligence in psychotherapy. She shared that psychologists utilize specialized questionnaires and personality tests when necessary, and she displayed a positive outlook on our application concept. She suggested a future enhancement for the app, proposing the inclusion of a list of emergency hotlines that users could access. Additionally, she highlighted the tendency for individuals in distress to turn to comfort food, often neglecting their diet. Furthermore, Mrs. Vogiatzaki noted that many individuals visiting her office are dealing with irritable bowel syndrome.
DOUNI HEALTH PRODUCTS A.E.
DOUNI HEALTH PRODUCTS A.E.
Name
Importance
DOUNI HEALTH PRODUCTS A.E. is a Greek company specializing in the distribution of natural health care products for more than 40 years, including a variety of nutritional supplements with probiotics.
In particular, we spoke with Mrs. Ioanna Antoniadou, Marketing director at DOUNI HEALTH PRODUCTS A.E. and with Mrs. Kalozoumi Vally, Homeopath who works at DOUNI HEALTH PRODUCTS A.E.
Feedback
After our project presentation, Mrs. Antoniadou and Mrs. Kalozoumi talked to us about the process of marketing nutritional supplements. However, according to legislation in Greece, it is not allowed to make health claims about probiotics. In other words, a nutritional supplement package containing probiotics cannot attribute specific actions to the probiotic, even if it is the main active component. In addition, they talked to us about the advantages of encapsulating the probiotic. They explained that inside a capsule, it is easy to maintain an adequate amount of probiotic, and if the capsule is enteric soluble, the risk of destroying a portion of the probiotic due to the acidic environment of the stomach is reduced.
Implementation
After this meeting, we decided to propose an additional method of administering our probiotic, apart from incorporating it into fermented foods. The probiotic can be taken as a dietary supplement, available in various forms such as capsules and tablets, with a preference for capsules.
Questionnaire
In collaboration with the Group of Psychologists and Social Workers of the Society of Social Psychiatry P. Sakellaropoulos, we created a questionnaire addressed to the general public.To obtain diverse opinions and feedback, we distributed this questionnaire to both our friends and families, as well as during conferences and outreach events that we organized. This approach ensured that we received feedback from individuals of various ages and academic backgrounds, each with different experiences and perspectives. You can find more information about these initiatives in the Education and Public Engagement Page. Through this questionnaire, we were able to evolve and add additional features to make the application more user-friendly. This process also ensured that the user is using a trusted and secure environment:
After analyzing feedback from the graph above, it became clear that a significant number of participants are hesitant to seek help from a mental health expert. In response to this, we have decided to introduce an additional feature in our application that encourages users to consider consulting a mental health professional. This new feature allows users to share their chatbot conversations with experts.
Also,one of the survey questions asked participants what they expect from our application, and many expressed concerns about the accuracy of our machine learning model. To address this concern, we have significantly improved our model's training by utilizing a large dataset sourced from various scientific references, encompassing both depressive and non-depressive texts.
Moreover, addressing worries about personal data security, we have taken measures to safeguard user data. Instead of storing their responses in a cloud-based system, we have developed a local database for secure data storage. Additionally, to ensure the utmost data privacy, we have chosen to deploy our neural network locally, avoiding the use of any cloud platforms and thus making any potential data leaks impossible.
Closing the Loop
Throughout our project's lifecycle, we carefully considered its ethical implications and responsibility to society. Our Human Practices efforts influenced the project's purpose, design, and execution, with a focus on responsible and reflective implementation. We integrated personal reflections, extensive research, and stakeholder feedback into our decision-making, aligning our project with the needs of the community. Beyond theoretical considerations, we took concrete actions, providing a pioneering therapeutic solution with minimal side-effects, improving the app as much as possible to be user-friendly, safe and work as an effective tool for both the patient and the mental health professional, demonstrating our commitment to responsible implementation. Our project evolved significantly due to the insights gained from our Human Practices activities. You can read more in the Implementation page.