Team:Aalto-Helsinki/Human Practices

Aalto-Helsinki Team Wiki

Aalto-Helsinki Team Wiki

Integrated Human Practices



The Problem

In European Union (EU) countries, every 25th person is diagnosed with depression and every 20th person with anxiety (Pay up or put it off, 2021) (Figures 1 and 2). The burden of mental disorders continues to grow globally with significant impacts not only on health, but also on human rights and economics (World Health Organization, 2019). It was affirmed in the 36th session of the Human Rights Council (resolution 36/13) that individuals with mental health conditions face widespread discrimination, stigma, prejudice, violence, abuse, social exclusion and segregation, unlawful or arbitrary insitutionalization, over-medicalization and treatment practices that fail to respect their autonomy, will and preferences (United Nations Human Rights Council, 2017). Furthermore, just anxiety disorders and depression alone are estimated to cost the global economy US$ 1 trillion each year (The Lancet Global Health, 2020).

Commission on global mental health and sustainable development, published in 2018, stated that “When it comes to mental health, all countries can be thought of as developing countries.” (The Lancet Commission, 2018). This statement resonates strongly today, as there is an increased clustering of numerous social determinants of mental health. Fear and anxiety about COVID-19, emotional discomfort resulting from illness, bereavement, unemployment, loss of income, and loneliness due to social isolation are just a few of the contributing factors to poor mental health conditions. On a global basis, all of the aforementioned are contributing or exacerbating mental health issues. While we are better informed of mental disorders and are aiming for a healthier future, the complexity of the issue - and even the human mind itself - still remains a major roadblock.

Figure 1. Number of people per 100 diagnosed with depression (Pay up or put it off, 2021).
Figure 2. Average wait times for psychological treatment in months (Pay up or put it off, 2021).

Depression and anxiety disorders are often treated similarly. In many cases, therapies are tailored to an individual to reduce the symptoms of both disorders. Several forms of psychotherapy have been found helpful in treating depression and anxiety disorders. Of these, cognitive-behavioral therapy (CBT) is commonly used when negative and unproductive thought patterns need to be replaced with more realistic and useful ones. Medications can also be useful in some cases. Since depression and anxiety disorders commonly occur together, they can be treated with the same selective serotonin reuptake inhibitor (SSRI) or serotonin norepinephrine reuptake inhibitor (SNRI) drug. Despite the availability of these effective treatment options, about 56 percent of individuals with severe depression receive no therapy at all (Purebl et al., 2017).

Marcin Rodzinka, a spokesperson for NGO Mental Health Europe, lists three main barriers to mental health treatments: i) stigma, ii) waiting times, and iii) user fees (Deutsche Welle (, 2021). There is still a lot of shame and fear associated with the idea of going to a psychologist or a psychiatrist. Even when people overcome stigma, their access to mental health care can be scarce, and the quality of their treatment very unsatisfactory - even in high-income countries with universal health care coverage. In France, for example, only psychiatric therapy is covered, whereas psychologists are not compensated at all under the national health care system (Barbato et al., 2016). Thus, many people who need therapy the most face a number of challenges before receiving treatment - if they ever do.

Finland is making progress on a variety of public health concerns, but despite these gains, the country still faces significant challenges in the treatment of mental disorders, with high waiting times being among the most significant issues. Finnish mental health treatment has a 90-day waiting list, which can be extended to six months in less urgent instances. As a result, there may be a considerable period of time between a person seeking assistance and receiving it. It is critical to begin counseling as soon as possible in order to avoid mental disorders from worsening and becoming chronic. The continuous rise of mental health issues, further exacerbated with the global pandemic and lockdowns, has only highlighted the alarming need for alternative treatment options. According to the U.S. Health Resources and Services Administration/National Center for Health Workforce analysis (2015), there will be a 45,000 to 250,000 mental health professional shortfall by 2025. Thus, our team saw a need to either get people treated faster or find new treatment options.

Our Solution

As many of our team members were interested in the rising popularity of microbiome-based therapies, we wanted to try and tackle the problem utilizing the gut-brain axis, a bidirectional communication pathway between enteric microbiota and the central nervous system. The gut-brain axis, which is influenced by the microbes that reside in our gut, is related to a variety of diseases including depression and anxiety disorders. This led us to hypothesize that this interaction could be utilized as an alternative pathway for faster, more reliable treatment. However, as our project progressed and the ideation process evolved, we realized that many questions about the microbiota-gut-brain axis' involvement in neuropsychiatric disorders remain unknown. To help researchers answer some of these questions and advance the search for alternative treatment options for mental disorders, we have created GutLux, a novel research tool for research of gut microbiota inside the human body.


Human practices have shaped the design and direction of our project from the beginning. To ensure that our idea is relevant and could be utilized in the real world, we consulted a wide range of experts from academics, industry, and legislation. By meeting with various experts from different fields, we received valuable insight into our local community and how our project could be further designed to meet the local requirements. Below you can read the more detailed storyline of GutLux.

Getting Started

To get started with our project, we asked the team to select the Standard Track Awards they were most interested in, based on their academic and personal backgrounds. The following tracks were the most popular among our team: diagnostics, therapeutics, environment, and new application.


During our first meeting, the team agreed to do some individual brainstorming for the following week’s meeting. All the suggestions were written down during the second meeting, with the most promising eight being retained for future investigation. During our third meeting, all ideas were discussed in further details followed by a team vote. The team was asked to vote on which topic they were most interested in so that we could narrow down our options for further, more profound research. The following were the two most voted project ideas that we decided to move forward with: thermo-resistant insulin and gut microbiota and mental health.

We considered some project ideas from our institutions in addition to our own ones. However, after much thought, we came to the conclusion that iGEM is a once-in-a-lifetime opportunity for students to build something from scratch, and we did not want to miss it. Therefore, it was important to the team to compete with a project idea that was entirely our own.

We had a meeting with our principal investigators to consult their opinions after narrowing down our two project topics. After this meeting, we had another team meeting to make the final decision in which we reached a mutual agreement on moving forward with gut microbiota and mental health.

Our team was particularly concerned about the potential consequences of COVID-19 on people's psychological well-being, since we had all experienced social distancing and remote study to be very mentally draining. This worry was supported by studies that have shown the connection between COVID-19 and increased risk for developing anxiety and depression symptoms (Savolainen et al., 2021; Kekäläinen et al., 2021). Furthermore, according to the Finnish Institute of Welfare (THL), the percentage of Finnish people experiencing psychological discomfort after the second wave showed a significant increase compared to the previous years (Finnish Institute for Health and Welfare, 2021).

Thus, after settling on a broad topic of gut microbiota and mental health, the entire team began to investigate how the gut-brain interaction could be used as an alternative treatment route for mental disorders, such as depression and anxiety disorders.

How could this be done?

Project Evolution

From a therapeutic tool to a research tool

Phage therapy and creating a probiotic or bacteria-detecting biosensor to help in mental health diagnosis were two of our initial research ideas. The first meeting we had was with a sleep expert, Henna-Kaisa Wigren. We were interested in the role of sleep in mental health and if there were some studies connecting microbiota, sleep, and mental health. We were very excited about this topic, but struggled to find a way to make it into an iGEM synthetic biology project. Thus, we turned away from sleep and started looking into other options.

The next expert we met up with was a Professor of Research of the National Research Council (CSIC) at the Institute of Agrochemistry and Food Technology (IATA-CSIC), Yolanda Sanz. Her research group ("Microbial Ecology, Nutrition and Health") focuses on human microbiome research, and has greatly contributed to elucidating the role the gut microbiota plays in the transition from health to disease. We were specifically interested in the relationship between microbiota, depression, and anxiety, and in this meeting, Dr. Sanz encouraged us to look more deeply into the tryptophan pathway. She supported the idea of an ingestible biosensor, which we had discussed along with phage therapy, and raised concerns about genetically modified organisms (GMOs). This led us to consider if a cell-free system could be constructed.

After the meeting with Yolanda Sanz, we met with Mikael Skurnik, a professor of bacteriology with extensive experience in phage therapy, and Saija Kiljunen, a human microbiome researcher. They both warned us about the difficulty of phage therapy in our time frame, and how it would not even necessarily be useful for the gut-microbiota studies. To move forward with the phage idea, we would have needed specific bacterial strains, different laboratory facilities, and a lot of help - which was not possible due to the strict timeline of the competition. As a result, we chose to shift away from phages and focus on metabolites.

Next, we wanted to further investigate the feasibility of developing an ingestible biosensor as well as its use in society. We talked to Marko Kalliomäki, a pediatric gastroenterologist, who did not see value in it as a diagnostic or clinical tool. However, he liked the concept of us developing a research tool, as there are not many in vivo research tools currently present. To understand more about the existing models and the process as a whole, Kalliomäki suggested we contact Kaisa Linderborg, who has done research with ingestible biosensors.

Before having a meeting with Kaisa Linderborg, we had three other meetings. One with Merja Penttilä, a research professor from VVT Technical Research Centre of Finland and a part-time synthetic biology professor, another with Per Saris, a microbiome professor, and the last with Kaisa Hiippala, a postdoctoral researcher in human microbiome research. Penttilä encouraged us to start developing the mechanism and begin thinking about how to actually implement our idea. Saris, on the other hand, reaffirmed the biosensor's utility as a research tool. He believed that the measures in the small intestine, which are not routinely collected, would be a benefit of the biosensor. He also emphasized that the host organisms must be able to withstand a wide range of pH. Hiippala challenged us to consider possible safety issues and agreed that a cell free system would be good in the prevention of GMOs.

In the meeting with Kaisa Linderborg, an associate professor in molecular food sciences, Linderborg confirmed the feasibility of an ingestible capsule. She did, however, bring out certain difficulties she experienced with their capsule use, such as signal collection. She also thought it would be great to get some competition in the market, as the existing ingestible capsules are not only costly, but also have some major flaws that could be fixed. As a result, we decided to create an ingestible biosensor that researchers could use to learn more about the gut microbiota in the human body and its links to mental health.

Next: How could this be executed?

From A Vision To Execution

At this point, we had acquired some critical information on the viability of the ingestible biosensor and the need for such a research instrument. There was a clear shift from our initial idea of a diagnostic tool to a research tool, and now all we had to do was start implementing the concept. Based on the meeting with Dr. Sanz and current literature, we decided to look more deeply into the metabolites of the tryptophan pathway. At this point, the help from our PhD mentors (see: Team) was key to guide us in the correct direction.

We first came up with a whole array of possible biological mechanisms that included the use of either enzymes or transcription factors. We soon realized that our focus should be directed towards those tryptophan-derived metabolites which can be found in the lumen of the gut, as our biosensor would not be able to interact with them otherwise. After selecting for these criteria, we were left with a couple of options, whose subsequent research drew us to the conclusion that the best mechanism to be implemented would be the one defined by three proteins: Aryl hydrocarbon Receptor (AhR), Aryl hydrocarbon Receptor Nuclear Translocator (ARNT) and Aryl hydrocarbon Receptor Interacting Protein (AIP). Likewise, after exploring different kinds of biological outputs to be read by the electronic component, we came to the conclusion that coupling the concentration of a given metabolite to the production of green fluorescent protein (GFP) was the most suitable way.

Once the main parts of our biological component were defined, we set up a meeting with Konstantin Kogan, a postdoctoral researcher in the University of Helsinki Institute of Biotechnology, to further discuss the plasmid design logistics. Kogan helped us understand and develop the integral parts of our protein-expression plasmids and assisted us in producing the design according to the cloning method that we had chosen, that is, MoClo. Chris Jonkergouw from Aalto University also assisted us in troubleshooting part of our plasmid design and provided us with compatible plasmid backbones for use during our transformations.

Next, we contacted Marco Casteleijn, a senior scientist at the VTT Technical Research Center of Finland. We discussed with him the benefits and disadvantages to using cell-free protein expression systems. From this meeting, we understood that our main obstacle in using a cell-free system would be the leaking of some small components needed for the synthesis of our green fluorescent protein, such as amino acids or energy-supplying molecules. He said that with a cell based system using our AhR, ARNT, and AIP proteins might be possible, but to his knowledge, not in a cell free system. This opinion was confirmed by a doctoral researcher of the department of bioproducts and biosystems, Bartosz Gabryelczy, who also did not see the cell free systems feasible in our case. Thus, we decided to continue with the whole-cell biosensor as previously theorized.

Our first idea was to use Escherichia coli as the chassis for the biological component. However, as prior literature did not provide information about expressing functional human AhR, ARNT, and AIP proteins in E. coli, and anticipating problems derived from the expression of eukaryotic proteins in a prokaryotic host, we also decided to produce the whole system in parallel using Saccharomyces cerevisiae as chassis. We sought the support of two experts in yeast protein expression, Alexander Kastaniotis from the University of Oulu and Alexander Frey from Aalto University. Alexander Kastaniotis guided us through the basic characteristics of S. cerevisiae and helped us anticipate possible problems derived from its use as a host organism. Alexander Frey supplied us with the necessary strains and yeast expression and integration plasmids for use in our laboratory experiments.

One of the main drawbacks of our chosen mechanism was its low specificity. To improve it, we turned to computational softwares that would help us predict possible mutations in the AhR protein that would favor its affinity to our metabolites of interest while decreasing affinity of other possible ligands. Ville Paavilainen gave us very insightful advice in this matter and guided us into the most suitable option for our purpose, that is, predicting small mutations in silico and then testing them out in vitro.

Next: Creating A Prototype

Prototype Development

Developing Guidelines For Prototype Design

Our first meeting before starting our prototype work was with Quan Zhou, associate professor of automatic control and leader of the Robotic Instruments group at Aalto University, to discuss the design for miniature-scale wireless transmittance system. In this meeting, we learned that the best way to approach our prototype development is to start from the functionality rather than the scale of the device. This way, we can ensure that our design works in the desired way for our application, and later optimize the components to fit our capsule dimensions. In addition to the prototype development plan, we discussed the limitations of our capsule and possibility for incorporating a localization mechanism. In order to implement a localization method, we decided to research further the possible approaches and existing localization solutions, such as magnetic and ultrasonic options. Our major limitation for the capsule design is the power consumption. This is why we decided to first design the capsule using a silver oxide battery, as other ingestible capsules in the market have, and research further the up-and-coming techniques for powering the capsule and their feasibility. More details on our proposed powering solutions can be found in Hardware.

To understand the real-life application of our capsule, we met with Kaisa Linderborg, a researcher with experience of working with ingestible capsules, to discuss how these types of capsules are used in research. During this discussion, we gained a lot of valuable information from the end-user perspective for our product development. We learned that breaking connections from the capsule to the receiver are a great problem that affect the use of the product. The products have been developed so that they can be used in 1-meter range, but if the receiver is not close to the body, significant gapping in the data can be seen later. Another aspect of the receiver was its comfort to use. The receiver was used in a “necklace” and was uncomfortable because it was big and not well supported. Thus, we wanted to focus on the comfort of the receiver and make sure that the strength of the signal is great enough so that there would be no gapping in the data. Instead of having the receiver on a necklace, we wanted to develop it to be worn on the wrist, similar to smartwatches.

To solve the connection issues, we investigated different ways to transmit data and how to develop our product in the future by applying other wireless communication methods, like backscatter communication. To further study wireless communication, we reached out to Riku Jäntti, an Associate Professor in Communications Engineering at Aalto University. We had interesting discussions about how to conduct research to test our capsule and its transmission properties, and which aspects need to be taken into account while working with signal transmittance through the different tissues and orientations of the body.

Next: Future

The Future Of GutLux

In addition to all the steps we took to develop GutLux described in the storyline, we also began to look into its future development. We contacted Rosa Tengvall from Kasve, a business management consulting company specialized in medical devices. She aided us in recognizing the legal requirements needed for a medical device to enter the market. Read more about this meeting on our Implementation page. To find out more on the next steps of GutLux, check out our Future Prospects page.


1. Barbato, A., Vallarino, M., Rapisarda, F., Lora, A., & Caldas De Almeida, J. M. (2016). Access to Mental Health Care in Europe. EU Health Programme. Finnish Institute for Health and Welfare. (2021). Increase in psychological distress during coronavirus second wave. THL.

2. Health Resources and Services Administration/National Center for Health Workforce Analysis; Substance Abuse and Mental Health Services Administration/Office of Policy, Planning, and Innovation. (2015). National Projections of Supply and Demand for Behavioral Health Practitioners: 2013-2025. Rockville, Maryland.

3. Kekäläinen, T., Hietavala, E. M., Hakamäki, M., Sipilä, S., Laakkonen, E. K., & Kokko, K. (2021). Personality Traits and Changes in Health Behaviors and Depressive Symptoms during the COVID-19 Pandemic: A Longitudinal Analysis from Pre-pandemic to Onset and End of the Initial Emergency Conditions in Finland. International Journal of Environmental Research and Public Health, 18(15), 7732.

4. Pay up or put it off: Europe fails to treat mental health. (2021, March 10). Deutsche Welle.

5. Purebl, G., Petrea, I., Shields, L., Tóth, M. D., Székely, A., Kurimay, T., McDaid, D., Arensman, E., Granic, I., & Abello, K. M. (2017). Joint Action on Mental Health and Well-being. European Commission.

6. Savolainen, I., Oksa, R., Savela, N., Celuch, M., & Oksanen, A. (2021). COVID-19 Anxiety—A Longitudinal Survey Study of Psychological and Situational Risks among Finnish Workers. International Journal of Environmental Research and Public Health, 18(2), 794.

7. The Lancet Commission on global mental health and sustainable development. (2018, October 10). The Lancet.

8. The Lancet Global Health. (2020). Mental health matters. The Lancet Global Health, 8(11), e1352.

9. United Nations Human Rights Council (2017, September). 36th session of the Human Rights Council. OHCHR.

10. World Health Organization. (2019, November 28). Mental disorders. World Health Organization.

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