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Unveiling the World of Ovarian Oncology: My HiLIFE Traineeship Journey

Introduction

Let’s begin our journey through the world of Ovarian Oncology with the story of a patient named Maija. A grandmother and avid sportswoman, her life took an unexpected turn when she began experiencing high blood pressure and abdominal discomfort. Misdiagnosed initially, her journey into the realm of ovarian cancer reveals the critical importance of the research conducted during my HiLIFE traineeship.

Maija’s Journey

Maija’s health struggles began with indigestion-like symptoms (pain and discomfort in abdomen) and were initially attributed to common ailments. However, as her symptoms worsened, medical investigations unveiled a more sinister reality. Ascites, fluid accumulation within one’s abdomen, found during ultrasound analysis and elevated cancer antigen levels raised the alarm. A subsequent CT scan revealed possible stage IIIC ovarian cancer, a diagnosis all too common among patients.

The Crucial Surgery

Maija’s journey took a hopeful turn when she underwent primary debulking surgery, a critical procedure to remove cancerous tissues. Although most tissues were successfully removed, one remained elusive due to its location. Post-surgery, her recovery was on track, but the pathology report delivered unsettling news – high-grade serous epithelial ovarian cancer, known for its aggressive nature.

The Treatment and Challenges

Chemotherapy, combined with an anti-VEGF drug, became the next chapter in Maija’s fight. Genetic testing revealed BRCA1/2 mutations, classifying her as homologous recombination deficiency (HRD) positive. Being HRD-positive means cancer cells have a more challenging time repairing themselves after DNA damage. PARP inhibitors further block this repair mechanism, causing more cancer cells to die. However, the treatment journey was not without hurdles, with hemoglobin levels dropping as a side effect of PARP inhibitor therapy. Despite the challenges, the treatment was continued, albeit at a lower dose, in pursuit of extending Maija’s life.

The Heartbreaking Relapse

After three years of battling cancer, Maija experienced a devastating relapse. Multiple rounds of chemotherapy and PARP inhibitors had taken their toll. Left with limited treatment options and a dauntingly radical tumor, Maija confronted the harsh reality that current cancer treatments had little more to offer.

Tailoring Treatment: The Key to Ovarian Cancer Patients’ Survival

 The heart-wrenching journey of patients like Maija underscores the critical importance of ongoing research in the field of ovarian cancer. Statistics reveal that in over 7 out of 10 cases, ovarian cancer returns after the initial treatment1. This sobering fact highlights a pivotal lesson from ongoing research: there is no universal solution when it comes to treating ovarian cancer. Each patient’s experience is unique, and their tumors are characterized by heterogeneity. It is, therefore, imperative to delve into the realm of precision medicine, where treatments are tailored to the individual. The quest for personalized medicine hinges on the discovery of a myriad of biomarkers. These biomarkers serve as keys, unlocking the understanding of how each patient responds uniquely to available treatments and which approach holds the most promise.

The Role of Traineeship in My Journey

At the forefront of the search for answers to these pressing questions stands Färkkilä lab at the University of Helsinki. This laboratory is dedicated to pioneering prognostic and predictive biomarkers, along with innovative therapeutic approaches aimed at elevating the treatment and survival prospects of ovarian cancer patients. And I had the incredible opportunity to be a part of their research. Our project aimed to analyze imaging data to predict cancer cell mutations, seeking out predictive features that could shape future treatments. Throughout this journey, I never felt alone; support was always at hand. From day one, I felt like an integral part of an exceptional team.

During my traineeship, I eagerly embraced Machine Learning tools to unravel the secrets that could serve as predictive markers for cancer mutations. This experience allowed me to immerse myself in cutting-edge technologies for profiling tumors and the intricate process of analyzing the data we received. It was an opportunity to push the boundaries of Machine Learning applications, to turn theory into practice, and to contribute meaningfully to a field that holds the potential to improve people’s lives.

One of the most eye-opening experiences was coming face-to-face with the immense challenge of acquiring sufficient data for effective Machine Learning models. It underscored the monumental collaborative effort required to create a dataset that could be harnessed for Machine Learning analysis.

Beyond the Lab

 My HiLIFE experience extended beyond the laboratory; it was about forming lasting friendships, discovering the artistic side of life, and even indulging in sports. I had the privilege of collaborating with colleagues who not only expanded my knowledge of ovarian cancer challenges but also introduced me to the beauty of Finland and the joy of camaraderie. We organized a fun and educational musical video about our staining procedures, explored the Finnish tradition of berry picking, and even tried our hand at standup paddleboarding.

A Recommendation for All

In closing, I wholeheartedly recommend seizing the opportunity to join the lab of your dreams. It can be a life-changing experience. Remember the old proverb: “If you want to go fast, go alone; if you want to go far, go together.” My journey through Ovarian Oncology taught me the power of collaboration, the significance of research, and the beauty of friendships forged in the pursuit of a common goal.

So, embark on your journey, make a difference, and create lasting memories along the way. Your HiLIFE traineeship could be the start of something truly extraordinary.

References:
  1. Surgery for Recurrent Ovarian Cancer May Help Selected Patients – NCI. https://www.cancer.gov/news-events/cancer-currents-blog/2022/ovarian-cancer-return-surgery-desktop-iii (2022).
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Following the swallows

Ecology field course in Kenya

At the hottest hour, we stop at a cliff for a lunch break. It’s January in Ngangao, one of the few protected montane forests remaining in Eastern Kenya. Everyone finds a rocky seat and starts digging their backbacks for lunchboxes. I have brought fresh avocados, passion fruits and mangos from the market place. This time we found both sweet and sour varieties of passion fruit. Someone asks a half-question about nature and our Professor, Jouko Rikkinen, seizes the moment and starts lecturing about lichens and lichen symbionts. I listen, but mostly for the beauty of it all. View behind him stretches hundreds of kilometers to the lowlands. Wind is soft and Ken, Darius and Mwadime are asleep and snore slowly. Swallows, such as barn swallows (Hirundo rustica), greet us with their spectacular airshow. I wonder if they are the same to which I bid farewell a couple of months back in Finland.

Taita Hills and a happy bunch of biologists

Jambo! I’m Maria Reiman, a Master’s student at the Master’s Programme in Integrative Plant Sciences. With the help of HiLIFE Trainee Conference Grant I was able to participate in Flora and vegetation of East Africa –field course (IPS-175) in Kenya in January 2023. In this blogpost, I’m going to share some of my key learnings as well as plant treasures of Taita Hills.

The course was organized by the University of Helsinki’s Faculty of Biological and Environmental Sciences, and our teachers on the field were Prof. Jouko Rikkinen, Mr. Mwadime Mjomba and Mr. Darius Kimuzi. The aim of the course is to learn about plant biodiversity in the area as well as climatic and environmental factors determining it. The Taita Research Station, established by the University of Helsinki in 2011, served as a base to our field course. It is located at Taita Hills in southeastern Kenya, in the village of Wundanyi. The area has attracted many scientists from different fields but especially biologists and geographers as it is a very unique area biogeographically. Taita Hills are like a miniature of East-Africa with an elevation range from 500 to 2200 meters and ecosystems including dry grasslands to moist montane rainforests.

Learning in the field

Nature was our classroom for the week. Every day, we would go to a different mountain, walk up the slopes and wonder at everything around us. Picture a group of students and teachers walking very slowly, taking pictures, squatting and pointing at something. Our guide and driver Ken was always sighing like “I just can’t with these botanists…”.

Mountains are an exception to Africa’s very flat general landscape. This goes back to 100 million years ago when the ancient supercontinent, Gondwana, broke up. South America, Antarctica, Madagascar, Australia and India separated but the remaining middle part – Africa – didn’t go through massive mountain formations unlike the other continents. However, these movements formed Eastern Arc –mountain chain of Kenya and Tanzania. Taita Hills are the northernmost mountain range of Eastern Arc.

Map of Eastern Arc -mountains on the left (EAMCEF 2014) and map of Taita Hills on the right (Kaasalainen n.d.).

Taita Hills are one of the most important biodiversity hotspots of Africa. They are known for their moist forests and unique flora and fauna. The moist rainforests support high diversity of life. One explanation to this is that because water and temperature are not limiting factors, species can focus on competition with other species, leading to speciation and evolution. For example, in dry and only seasonally warm Finnish forests, there are usually only a few dominant tree species but Kenyan rainforests host tens or even close to a hundred tree species. During the field course, I learned at least 176 new species (or if not learned then at least took notes and pictures).

Rainforest’s canopy is multi-storey as plants compete for light. Taita Hills used to be a vast rainforest area but due to changing climate and its consequence, anthropogenic pressure, there are only a dozen forest patches left. Most are the size of a few hectares and some are 70-190 hectares. Many species have evolved in Taita Hills and are thus so called endemic species. The mountain peaks have acted like islands and some species have their own subspecies for every mountain peak due to diversification.

Plants of East Africa. The strangler fig (Ficus thonningii) uses other plant’s truncks to climb up since the competition for light in the rainforests is though and investing into one’s own truck is very energy-consuming. Impatiens teitensis and the Taita African violet (Saintpaulia teitensis) are endemic to Taita. As visually beautiful species, they are area’s flagship species that are used to spread awereness of area’s biodiversity. African violets are endemic to Eastern Arc –mountains that Taita Hills also belong to. They are popular houseplants as well as Zamioculcas zamiifolia that grows in dry lowlands of Africa and is thus a good houseplant in dry households. Coffea fadenii is also endemic to Taita and is commercial coffee’s wild relative. Crop wild relatives (CWRs) are important for food security.

People’s livelihoods, biodiversity and ecosystem functioning are interdependent

Taita Hills, like all mountains, provide many vital ecosystem services for humans. One of the most important is water. Water’s journey to Taita begins 200 km eastwards from The Indian Ocean. Moist trade winds flow towards Taita and condense to water when they hit the eastern forested slopes of Taita. In this sense, the mountains act as water towers. Montane forests capture and provide water for vast areas and households far below in the lowlands.

Deforestation of montane forests and climate change have led to decreased water security in the area. Clear-cutted forest land doesn’t catch water as well as montane forests and their vegetation would and ‘water tower effect’ is lost. Rains have become unpredictable and sparse. This has devastating consequences for humans and wildlife. When humans struggle, questionable methods are used to meet the living costs. Even more forest is cut to get livelihood from selling timber and firewood. This leads to a vicious circle where water is even scarcer. However, local authorities are taking action to stop the deforestation of remaining forests. These include e.g. guidance of agroforestry methods and reforestation with native tree species.

In Taita Hills, there are some reference areas like Mount Kasigau (1000 m up to 1600m), previously inhabited higher at the hills but people moved downhill when the issue with water arose. Currently, only the lower hills of Mount Kasigau are inhabited and there are no plantations. Mount Vuria (500 m up to 2200m) however, is largely under human pressure and deforestation is ongoing. Optimally, Mount Vuria would look like Mount Kasigau. On our hike at Mount Vuria we witnessed forest cutting and many invasive tree species. Invasive tree species and their plantations are a huge problem in East Africa. For example, Eucalyptus-plantations cause many wildfires because their bark is very fire-prone while the tree itself is very fire-resistant.

Mount Vuria (left) is largely under human pressure and covered with invasive species (pic by Maiju Kupiainen). Mount Kasigau (right) is not and it is covered with native afro-alpine vegetation.

Native and biodiverse montane forests maintain functioning ecosystems which in turn mean secured water supply and livelihoods for people. Nowadays, people are moving downhill to the lowlands which is good in terms of water security. However, this has increased the number of human-wildlife -conflicts when residential areas and wildlife territories overlap. Elephants and baboons can destroy crops but they are undeniably vital for lowland ecosystems and their ecosystem services. As always, the co-existence of humans and the rest of the natural world is complicated but the search for compromise is a necessity.

The joy and anger of finding things out

As botanists, we were of course very interested in individual plant species of Taita Hills. In addition, we gained a lot of insight about ecosystem dynamics and societies of the tropics that could never be learned from the books. We discovered new species, ecosystems and phenomena every day. The more we learned and understood, the wider our view of the natural world got. Access to this type of knowledge is a privilege that correspondingly means responsibility.

Developed countries such as Finland, produce most of the greenhouse gases yet the consequences are currently mostly suffered in the developing countries such as Kenya. Developed countries must learn to live within the planetary boundaries e.g. by carrying their responsibility, reducing emissions and stopping overconsumption. Actors of the developed countries – states, companies and inhabitants – have the resources for these actions and there aren’t any acceptable excuses for not acting. Liveable future for all lifeforms of the Earth is secured and determined only by actions done in this decade (IPCC 2023).

Getting a wider perspective of global change, such as climate change and biodiversity loss, meant anger caused by injustice, lack of actions and already unstoppable consequences such as deaths of people and endemic species. We are devastated by drought and deforestation in the area, which were largely caused by climate change or its consequential human pressure. Defending and fighting for the beautiful but threatened biodiversity and ecosystems of Taita Hills are also our duty. Our realities are linked and swallows migrating from their overwintering sites in Kenya to their breeding grounds in Finland are an evident symbol of that.

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Big thanks to station staff, teachers, faculty, steering board and everybody who made this field course possible. We students really appreciate this as we know that field courses are constantly threatened with tightening budgets. Thank you for understanding that skilled biologists are made in the field, not classrooms!

PS:

  • Fellow students and dear friends of mine have also written HiLIFE-blogposts about Kenya. Gabriela Lemoine wrote a post about her experiences with more reflection e.g. about native and invasive species as well as our teacher’s, Mr. Darius Kimuzi’s, innovative agroforest farm. Lola Fernández Multigner took part in Human-Wildlife Conflicts in East Africa –field course (EEB-306) organized also by the University of Helsinki. She describes the complicated relationship between elephants and humans in this post.
  • Kaisaniemi Botanic Garden has many East African plants. For example, you can find Saintpaulia teitensis in the African Violet Room, Ficus thonningii in the Dry Forest Room and Coffea fadenii in the Rainforest House! Pictures of these are earlier in the text.
  • Water’s Journey, a documentary (2022) about Taita Hills can be found in Yle Areena. Beautiful nature, daily life and current topics are displayed magnificently. Watch Water’s Journey here.

References

EAMCEF. (12.8.2014). Eastern Arc Mountains. The Eastern Arc Mountains Conservation Endowment Fund (EAMCEF). [Webpage]. Available: https://eamcef.wordpress.com/2014/08/12/eastern-arc-mountains/

IPCC. (2023). Climate Change 2023: Synthesis Report. Contribution of Working Groups I, II and III to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change [Core Writing Team, H. Lee and J. Romero (eds.)]. IPCC, Geneva, Switzerland, pp. 35-115, doi: 10.59327/IPCC/AR6-9789291691647

Kaasalainen, Ulla. (No date). Taita Hills and Mt. Kasigau. Lichens from East Africa and elsewhere. [Blog]. Available: https://lichens.academy/taita-hills-and-mt-kasigau-kenya/

Laine, Toni. (2022). Water’s Journey. [Documentary Film]. Helsinki: Wild Heart Productions Oy. Available: https://areena.yle.fi/1-61218224

Niemelä, T. (2011). Vihreä Afrikka: kasveja ja kasvillisuutta. Norrlinia; Vol. 23. Luonnontieteellinen keskusmuseon kasvimuseo.

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From Theory to Practice: Reflections on the Daily Life of Brain Research

Hi everyone! I’m Santeri Lepistö, a master’s student in the neuroscience programme. I conducted my HiLIFE internship in Satu Palva’s research group, part of Palva Lab, at the University of Helsinki. During the trainee period I contributed to a research project that investigates how digital therapeutics can be utilized in the treatment of depression. Next, I will tell you about my thoughts regarding the internship experience!

 

Biological Brains and Digital Treatments 

Since depression is a common and serious mental disorder, causing a significant amount of suffering, there is an evident need to gain new knowledge to understand it and new ways to treat it. During the internship I was involved in a research project that studies how a video game-based intervention can be utilized in the treatment of depression. In the study, the subjects go through an intensive period of video game playing, a training program, that aims to alter operations of the brain underlying cognitive functions. These neurocognitive alterations, in turn, can be linked to changes in the state of depression. In addition to video game-based intervention, the project exploits an extensive repertory of other methodological instruments, including multiple brain imaging methods, behavioral experiments and psychological questionnaires. 

In my case, the internship made it possible to be absorbed in the daily practicalities of the project and participate in organizing and implementing the study – from recruitment to data acquisition. Before all, I focused on conducting magnetoencephalography measurements, behavioral tasks and clinical interviews for the subjects. Since there was diversity in my day-to-day duties, I had a chance to see how different methodological steps are connected in the project and what is the scientific value of some precise part of the study. So, experiencing the same project from many perspectives was informative! Clearly, understanding methodology is not just about putting cables into the right devices (which is indeed relevant), but becoming aware of the theoretical underpinnings how combinations of certain methodological choices serve the goals of study and capture valid information about the world. To take one example from my daily work, in the clinical interviewing – in which I examined subjects’ state of depression – it was essential to evaluate what kind of psychiatric symptoms are concordant with study’s research questions and how subjects’ different psychiatric and neurological conditions might influence to subsequent stages of the project, namely, brain imaging measurements, video game playing and, eventually, data analysis, results and theoretical interpretations. It was therefore necessary to know the specific scientific aims of the project and to keep in mind how one phase could affect another.

Brain’s Information Processing as a Window to Mental Health 

Importantly, the internship gave me an opportunity to deepen my understanding of magnetoencephalography. The facilities of Meilahti Campus and the BioMag Laboratory at Helsinki University Hospital provided an adequate environment to collect magnetoencephalography data and, simultaneously, connect with inspiring people and learn from others. In the lab, it was not only rewarding to learn new but also to notice how the four-month training period made it possible to routinize oneself with many methodological procedures. Daily activities soon became habits. Also, efficient working in the lab is a must, since schedules are limited and each brain imaging session consisted of numerous steps, such as preparations of the lab settings, preparations of the participant, the actual brain imaging measurements and, additionally, use of psychological questionnaires and behavioral tasks. 

What theoretically fascinated me in the utilization of magnetoencephalography was that the neuroimaging method illuminates brain’s architecture and activity from the perspective of information processing. As I contemplated in my previous blogpost, the human brain can be conceived as a complex information processing system that selects, modifies and transmits – or even creates – information. As an astonishing feat, this information processing, shaped by different biological and cultural forces (like natural selection and social conventions of our species cultural niche), orchestrates mental phenomena. Since magnetoencephalography gives an elegant access to brain’s information processing in the form of oscillatory activity, it is consequently possible to investigate what happens to brain’s information processing during depression. 

When looking at the brain’s system-level information-processing in depression, several functional alterations, both increased and decreased connectivity, can be found within and between different neural networks [1, 2]. For instance, in a magnetoencephalography study of large-scale brain dynamics, it was found that central executive network hyper-intertwines with itself, whereas salience network hyper-integrates with other networks in depressed patients [2]. Moreover, the trainee months made me contemplate the heterogeneity of depression. Since varying biopsychological factors and symptoms have been linked to depression, it has been characterized as a heterogeneous clinical syndrome that might be caused by different pathological processes and, possibly, require various treatments. Also, it has been argued that different system-level functional alterations take place in different subtypes of depression. For example, in a fMRI study distinct subtypes were found based on differences in dysfunctional connectivity patterns of the fronto-striatal and limbic networks [3].

Thinking Science: Terms, Tools and Theories 

Working in a scientific project provokes scientific thinking. In addition to learning about digital therapeutics in the treatment of mental disorders, oscillatory activity and subtyping of depression, the internship experience offered a great vantage point to think about scientific inquiry in general. The project, broad in its scale and important in its objective, provided a good impetus to contemplate how novel scientific knowledge comes into existence. To take a Simple View of Scientific Progress (a plain view on a complex process), I often found myself thinking scientific research through three interrelated domains: terms, tools and theories. Terms are the set of conditions where science takes place at a given period of time. Academic research has its surroundings, time and place. It emerges in a sociocultural matrix and is influenced by contemporary ideas, beliefs, values and resources – for instance, shared recognition of the importance of treating depression and other mental health problems. Tools, on the other hand, are the set of methodological ways that are harnessed to acquire scientific information – like magnetoencephalography and other brain imaging methods. Lastly, there are theories: systematically collected data can be transformed into sets of explanations about the world and models that imitate life – for example, more detailed and accurate understanding of depression. These perspectives, three Ts, can be considered tightly connected and guided by each other. 

To sum up, I’m thankful for HiLIFE and Palva Lab for both educative and inspirational internship experience! Not only is science a process of seeking truth but it’s also a source of awe and amazement. It adds beauty to our lives by inviting to appreciate the many and diverse characteristics of reality, like simplicity and elegance, complexity and harmony, and hidden logic and patterns.

 

References

[1] Mulders, P. C., van Eijndhoven, P. F., Schene, A. H., Beckmann, C. F., & Tendolkar, I. (2015). Resting-state functional connectivity in major depressive disorder: a review. Neuroscience & Biobehavioral Reviews, 56, 330-344.

[2] Tian, S., Chattun, M. R., Zhang, S., Bi, K., Tang, H., Yan, R., … & Lu, Q. (2019). Dynamic community structure in major depressive disorder: A resting-state MEG study. Progress in Neuro-Psychopharmacology and Biological Psychiatry, 92, 39-47.

[3] Drysdale, A. T., Grosenick, L., Downar, J., Dunlop, K., Mansouri, F., Meng, Y., … & Liston, C. (2017). Resting-state connectivity biomarkers define neurophysiological subtypes of depression. Nature medicine, 23(1), 28-38.

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Studying an unusual shrub (Eastern leatherwood) and the beginning of my HiLIFE grant

Lignin and its chemical properties are, for the most part, fully taken advantage of in most plant and tree species: it’s a molecule that occurs in the area between neighboring cells, inside the cell wall, and generally provides mechanical support and supports water transport. But this looks a little different in leatherwood, a small, understory shrub that lacks lignin in places where there are normally large amounts in other species, such as silver birch or Norway spruce. This allows its branches to bend well past what would easily break a spruce tree. Interestingly, we still do not understand why leatherwood evolved like this (other than the fact that being extremely bendy is obviously a fun skill).

Lignin, in this sense, can be thought of as one of the many Bermuda triangles of the plant world. While much of plant biology remains unknown, lignin is particularly interesting because how and why lignin is distributed, especially in leatherwood, remains a mystery.

My name is Dayla and, while I’m originally from Austin, Texas in the United States, I have lived in California, West Virginia, New York City, and now Helsinki. One of the reasons that I was drawn to the University of Helsinki is because of the access to plant science research, ranging from stomatal development to lignin formation.

Before entering the master’s program here, I was already considering whether a PhD in plant biology could be the right path for me, but I was scared. Was this really what I wanted? A decade of mass-murdering weeds for the sake of science?

The short answer, I think, is yes. The slightly longer answer is that I have been lucky enough to work with HiLIFE to spend four months exploring lignin and its many roles in leatherwood, poplar and Norway spruce. Over the course of this traineeship, I will have the opportunity to see how trees fit into the wider world of plant biology, learn new techniques (including how to pick up 20 micron thick pieces of wood using only a drop of water), and explore the possibility of a career in research.

In the past, I’ve worked with Arabidopsis roots to investigate genes responsible for growth and development. Now, with Kurt Fagerstedt’s group, I will have the opportunity to study a different facet of plant biology – what happens to a plant when one of its key macromolecules is modified.

However, the real main goal of this traineeship is to resolve the love–hate relationship that I have with lab refrigerators. They smell similar to how it feels to gag – that is to say, I gag every time I open one. Alas, this is where we store the true muscle of developing mutant plants, and the culprit of the smell: E. coli. This bacteria is partially responsible for the transformation of healthy, strong weeds, into sad, small plants that are no longer able to produce lignin properly.

Over the course of the next four months, I hope that I can either a) grow accustomed to the smell in the refrigerator or b) appreciate the importance of E. coli in plant molecular biology enough that it no longer bothers me.

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Field course in the tropical forests of Laos

Sabaidee! My name is Emmi Kaislasalmi, and I am a master´s student in forest ecology at the University of Helsinki. Earlier this year I got the HiLIFE Conference Grant to participate in a three-week intensive field course in Laos called “Tropical Forests and Agroforests”.

Here in this post, I am going to share my experience of the course. Please note that this course is conducted every second year (next time in January 2025), and you might have the chance to also get in if you want to learn more about tropical forests, the problems facing them, and the deep interconnection between forest well-being with societal and economic aspects.

Multicultural experience

The course was conducted by the University of Helsinki in partnership with a local university, Souphanouvong University from Luang Prabang. The course participants, students, and professors were from Finland, Laos, and Thailand.

We started from a UNESCO World Heritage City, Luang Prabang, where we got straight away immersed in the Lao culture as we arrived. Throughout the course, we learned about each other’s cultures and customs as we worked in groups of four, where the participants were at least from three different nationalities. Learning from one another was one of the greatest experiences for me.

On the second day, we headed to Nambak District, famous for its crispy river weed, “kaipen”, which is a delicacy we enjoyed throughout the course.

Pic. 1. Kaipen in making. The river weed is first harvested from the Nambak river floor, them processed, and left under the sun to dry. Usually, kaipen is topped with sesame seeds, tomatoes, and garlic, like in this picture, but other toppings can also be used. Finally, the kaipen is quickly deep fried before its ready to use. ©Field course: tropical forests and agroforests.

Hands-on approach and field research

After a short lecture and introduction on what we were about to do, we left to the field to conduct research. The research had two major parts, one was doing biodiversity research and forest inventory in the tropical forests and agroforests, and the other part was interviewing the locals and trying to understand their relationship with forest and forest products in terms of livelihood and food security in the Nambak District.

Pic. 2. Vieng Hinh Soung Village in Nambak District, one of the study villages in the field course. ©Dipjoy Chakma

In the forest, we learned to use different biodiversity and forest inventory methodologies, identify different tree and herbaceous species, find the indicators for forest disturbance, and how extremely diverse and beautiful the forests in Laos can be. We also learned that some trees make you itchy if you stand underneath them, some smell like cinnamon, and others bleed red sap, that looks like blood, if make a cut on the trunk.

By conducting the interviews, we learned about locals´ perceptions and needs when it comes to forests and forest products. Especially in the more remote villages, where access to stores and markets is not easy, people rely on non-timber forest products (NTFPs) such as bamboo, different wild vegetables and herbs, mushrooms, and bushmeat for sustenance and livelihoods. Firewood is also an everyday necessity for the locals, as cooking is done with using firewood. When building or renovating a house, the timber usually comes from the local community forests, which are cared and managed by the whole community.

What I left the course with

What I truly loved about the experience was that we did not only learn about the ecological and environmental aspects of tropical forests. Instead, the course had an interdisciplinary approach, and we learned about the social and economic realities that affect tropical forests, and how understanding and addressing these issues is key to sustainable forest and land-use management.

Looking ahead, I am convinced that we should have more courses and collaboration between disciplines and departments to address many of the current challenges regarding sustainable development and land-use. This approach is essential to bridge the divide between our current understanding of forests—focusing on their ecological and environmental dimensions—and the broader knowledge we should possess about societal, economic, governmental, and legislative aspects.

This interdisciplinary approach is needed to bring long-term solutions to the many problems facing tropical forests, including the loss of biodiversity, forest degradation, and deforestation. Moreover, it would also address the needs of the local communities and enhance their overall well-being.

Participating in this course was a truly enriching experience, and I am very grateful to HiLIFE for awarding me the HiLIFE Conference Grant since it made the experience accessible to me. My time in Laos was also very meaningful to me because I got insights about the direction in which I want to pursue my future career.

This field course in Laos was an unforgettable journey that deepened my appreciation for tropical forests and the critical importance of their preservation. The experiential learning, combined with theoretical insights and interactions with experts and local communities, enriched my understanding of ecology, research methodologies, and how the welfare of local communities plays a vital role in ensuring the health and prosperity of forests.

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My first-ever academic conference experience in Tromsø, Norway

Hi all! My name is Aliisa Niemelä and I am a freshly graduated M.Sc. (Pharm), also known as proviisori, from the University of Helsinki. I was delighted to receive a HiLIFE Conference Grant to participate in my first-ever academic conference in June 2023. I am here to tell you about my experience!

Tromsø, located in the beautiful Northern Norway above the Arctic Circle, is a scenic and historical city surrounded by the sea, fells and mountains. The scenery was breath-taking and unlike anything I’d ever seen before! I was thrilled.

The scenic view outside Tromsø Airport.

Did you know that Tromsø is often referred to as “Paris of the North”? This nickname speaks for itself – the city has a lively, historical and sophisticated atmosphere. But more importantly for us, the city is home to the world’s northernmost university, University of Tromsø – The Arctic University of Norway. UiT is the only university in Norway to offer both three-year bachelor and two-year master programmes in Pharmacy, which are compliant with the Bologna Process.

7th – 9th of June 2023 UiT and the Department of Pharmacy hosted the 10th Nordic Social Pharmacy Conference (NSPC), a three-day event focusing on “Pharmacist services of tomorrow”. The Nordic Social Pharmacy Conference 2023 brought together researchers and practitioners from Nordic countries and all around the world, even all the way from the US. We discussed and learned about key topics concerning social pharmacy, pharmacy practice and pharmacoepidemiology. In my studies I have focused specifically on social and clinical pharmacy, so NSPC 2023 was an excellent event to deepen my knowledge and to network internationally in my field. The conference included plenary sessions, workshops, poster sessions, oral presentations and pre-conference master classes and was all about sharing experiences and ideas and learning from each other.

The conference had the warmest atmosphere and I felt so welcome to my first-ever conference. And it wasn’t all about sitting in auditoriums – we also enjoyed the nature while climbing up Sherpatrappa (1200 stairs) to Storsteinen mountain 421 meters above sea level. This might have been the most challenging part of the trip! 😀

View from Strosteinen after hiking up Sherpatrappa.

The highlight of the conference for me was getting the opportunity to share the findings of our own research and present our poster entitled “Developing clinical pharmacy expertise with a postgraduate pharmacy programme: Individual interviews with specializing pharmacists and their line-managers” in one of the poster sessions of the conference. This was a great experience for me and I am grateful for all the discussions around this topic.

I will cherish this experience for years to come and look forward to my next scientific conference! I want to thank my dear colleague Raisa Laaksonen, University of Helsinki and HiLIFE for the experience and support received!

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Meet the Aalto-Helsinki iGEM team 2023!

We are the Aalto-Helsinki iGEM team 2023!

We are a very diverse group of 10 students and here you can find about us and our project.

What is iGEM?

Welcome to the exciting world of synthetic biology! At the forefront of this rapidly developing interdisciplinary field is the International Genetically Engineered Machine (iGEM) competition, which originated from the prestigious Massachusetts Institute of Technology (MIT) in Boston, USA. Synthetic biology has enormous potential applications in fields such as medicine, food, agriculture, and energy. iGEM challenges students from around the world to design and implement innovative projects using experimental work, modelling applications, and cutting-edge design techniques, all within a short time frame. To learn more, please visit the official website: https://igem.org/

What is our idea?

Our team was born in February 2023, and shortly thereafter, we initiated our ideation process. Discovering a problem to address in our common interest proved more challenging than expected. Following intense ideation sessions, we came up with two proposals, which we subsequently presented to several experts. Consequently, the team reached a consensus to merge these ideas and address two pressing global challenges: plastic waste, and food scarcity.

The scale of plastic waste pollution is alarming, with over 350 million tons of plastics manufactured annually, and over 70% of plastic waste accumulating in landfills and oceans. This poses a significant environmental threat to ecosystems, marine life, and human health. Without any further changes to current policies, global plastic waste generation is projected to triple to one billion metric tons by 2060. Currently, the goal of plastic recycling is to reduce the need for primary plastic production. The competition between virgin plastics market and recycled plastics make recycling less attractive, since newly produced plastic has a higher relative material efficiency due to the ongoing availability of lower-cost feedstock.

Simultaneously, global food security remains a pressing concern, with over 820 million people undernourished and the need to increase food production by 70% before 2050. Conventional methods are insufficient to meet this growing demand. Focusing on the nordic countries, most of the agricultural activity focuses on meat production, even though it is a well known fact that it has a huge carbon footprint, and takes up double the resources than plant based food production. As the demand for food protein continues to rise, the development of novel and sustainable protein sources becomes environmentally and economically significant. There is great potential for producing protein-rich feed or food additives in the form of algae, yeasts, fungi and plain bacterial cellular biomass. They have a lower environmental footprint compared with other plant or animal-based alternatives.

We are focused on a circular economy system, aiming to reduce waste and utilise resources more efficiently by converting waste into valuable proteins. Our objective is to develop an optimised enzymatic plastic depolymerization system and demonstrate the feasibility of protein production utilising polyethylene terephthalate (PET) as the primary source.

Our project, PET-2-Protein, aims to develop a proof-of-concept approach for converting PET into proteins. Naturally occurring PETase enzymes are able to break down PET plastics into monomers such as terephthalic acid (TPA) and ethylene glycol (EG). Enzymatic degradation of plastic waste is an eco-friendly alternative to chemical plastic recycling. Our research aims to address the fundamental issue of plastic waste by focusing on plastic reduction. Consequently, we do not only design an optimised system for producing plastic-degrading enzymes but also optimise the enzymatic depolymerization of PET into TPA and EG, and finally, the microbial conversion of those monomers into proteins.

More about iGEM

iGEM is not only about designing our project. Using synthetic biology to address real-world problems requires thoughtful engagement with the world. In iGEM, this is referred to as Human Practices: thinking deeply and creatively about whether a synthetic biology project is responsible and good for the world. Throughout our project design we have contacted various experts and companies whose expertise shared similarities with PET-2-Protein, who have helped us to refine protocols and objectives. We have discussed several matters such as practicalities related to our methodology, the different uses that our end product could have and the ethical implications related to our work. Moreover, we are also focused in community outreach and science communication, addressing different audiences so that they can get to know our project, synthetic biology and iGEM. Our team is preparing a “science for children” workshop in Heureka as well as a collaboration with The Science Basement.

If you are interested in knowing more about our project and journey, you can visit our webpage, social media and blog.

Thank you for reading!

Our team wants to thank HiLIFE and the University of Helsinki for supporting the iGEM team and its project. Their support has been essential for us in order to participate in the iGEM program and competition. It has been an amazing experience and opportunity for all of us so far!

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Where passion meets purpose

Hi fellow students!

My name is Aina Rossinyol Fernàndez, and I am a second-year master’s student in the Ecology and Evolutionary Biology Programme here at the University of Helsinki. I am passionate about understanding and preserving the biodiversity of our planet, and I chose this master’s programme to deepen my knowledge of applied biodiversity conservation.

In March 2023, I attended the Student Conference in Conservation Science (SCCS) that took place in Cambridge, UK. SCCS is the only international series of conservation conferences entirely aimed at students. In case it is of your interest, SCCS is yearly conducted in Cambridge (UK), Brisbane (Australia), Beijing (China), Bangalore (India), New York (USA) and Budapest (Hungary).

The conference spanned three days and offered both in-person and online attendance options. Thanks to the HiLIFE Conference Grant, I had the great opportunity of participating in person. As the conference started early on the 28th of March, I decided to get to Cambridge on the 27th. I spent the whole morning exploring the city’s stunning architecture and streets as well as the river Cam. One of the things that surprised me the most was finding colleges all over around (Cambridge has a total of 31 colleges!). My favourite one was Christ’s College, as it is the one Charles Darwin stayed at. In the afternoon, I ended up joining a tour of 11 Indian people – including the guide – about the linkages in the history of Cambridge and India. Even though I was the only non-Indian participant and felt a bit lost in some of the explanations, it was such an interesting tour. This city has so much history to tell!

The conference days were very intense, but I was ready to absorb knowledge like a sponge! The conference included many interesting planetary talks, student oral presentations and poster presentations, as well as activities to facilitate networking and to introduce numerous both national and international institutions and organisations involved in conservation. I was truly admired by the wide range of incredible conservation work being done worldwide! Some of the vast array of topics covered included species distribution in the Anthropocene, human-wildlife conflict, ecosystem services in a changing world and people’s perceptions of nature.

The conference counted with an exciting programme of workshops. I wish I could have attended all of them, as they all seemed very interesting. However, we could just attend two of them. On the first conference day I attended the “Collections-based research” workshop. After discussing the diverse ways that collections can be used in biological research, we had a behind-the-scenes tour of the zoological collections housed in the University Museum of Zoology in Cambridge. The collections harbour over two million zoological specimens. Yes, over two million! The specimens are kept in storerooms at a constant temperature and humidity to avoid pests, such as beetles and moths, as well as to prevent mould formation. And now you may be wondering “Why do they put that much effort in store and catalogue this huge zoological collection?” The answer is easy. All these specimens collected over the past 200 years are a precious record of life on Earth and significantly contribute to scientific knowledge. For example, collections can provide essential data about animal distribution in an ever-changing world. Thousands of researchers from different disciplines from all over the world come along to study the collections to better understand and appreciate our natural world.

I especially enjoyed seeing specimens collected by Darwin. I would have literally spent days exploring these never-ending collections!

Fundraising is essential for conservation projects and thought that having the opportunity to meet face-to-face a donor would be a great opportunity to develop relevant skills on grant applications. That is why on the second day of the conference I attended the workshop entitled “Tips and tricks for writing grant applications: the view from a funder” held by Claire McNulty, the executive director of the National Geographic Society of Europe and the Middle East (Western Asia). For those who don’t know National Geographic Society, it awards grants to people working on conservation projects all over the world. Claire gave us practical and very useful tips, which can also be used in other funding sources, on how to develop a successful grant proposal.

As a young and aspiring conservationist, I believe that the best way to start my professional career is by learning from experienced tutors and experts in tropical conservation as well as from fellow like-minded students. Throughout the conference, I had the opportunity to interact with many enthusiastic students and renowned researchers and professors from all over the world. Speaking about projects, career paths and future plans, while exchanging ideas, was very inspiring to me, and I have no doubt that it will be valuable for my conservation journey. Additionally, getting to know conservation perspectives and practices from cultures all over the world allowed me to become more open-minded.

After those three very inspiring days, which combined learning, forging lifelong connections and overall unforgettable experiences, I can assure you that I left the conference with even more willingness to make a positive impact on tropical conservation.

In-person participants of SCCS 2023

The love for all living creatures is the most noble attribute of man – Charles Darwin

Even though this time I just attended, I can’t wait to present my own work in future SCCS conferences… who knows where! I am very grateful to HiLIFE for awarding me the HiLIFE Trainee Conference Grant and to SCCS Cambridge for organizing such an inspiring conference.

Thanks for reading me!

Aina Rossinyol

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Whether or not obesity pandemic is stopped will define public health globally in the near future

Laitinen seeks to understand hunger-satiety signalling to understand its root causes.

Check the introduction video where she describes her project.

Suvi Laitinen, 21, researcher and MD-PhD-student from the University of Helsinki started meticulously chasing her hypothesis about elevated hunger/decreased satiety in the human brain in 2022. She co-founded the Obesity Curiosity research project with Dr Teemu Aitta-Aho (PI of the Loss of Control Behaviour lab, Department of Pharmacology, University of Helsinki). She explains the big idea behind Obesity Curiosity:

“It seems that this effect [of environmental factor(s)] causes us to eat a tiny bit more every day. I hypothesise people have decreased satiety, increased hunger, or both. Some people seem to be more vulnerable to the effect while others are more resilient. This would explain why weight management is gruelling. The urge to eat is one of the most powerful signals of the body and almost impossible to resist.”

Laitinen’s PhD project is part of Obesity Curiosity and her goal in the first stage, is to develop a human arcuate nucleus model. Then in the second stage, they will use the model to study the effect of factors of interest, such as medications with weight gain as a side effect, on the human brain in vitro.

Currently, Laitinen is completing her research at a scientific collaboration visit in Dr Florian Merkle’s lab at the Institute of Metabolic Science University of Cambridge, funded by the Helsinki Institute of Life Science (HiLIFE) Undergraduate Student Research Trainee Scholarship. “My work here is focused on directed differentiation of human induced pluripotent stem cells (hiPSC) to hypothalamic neural origin cells, including neurons. This way we can generate a model that quite faithfully replicates human physiology without having to deal with the inaccessibility of the human brain otherwise. The hiPSC cells have been generated from volunteer donations of patients in past”, she explains.

“Working in Dr Merkle’s lab allows me to learn their robust methodology of hiPSC-derived 2D hypothalamic cell culture and with his generous support I am highly grateful of, I have expanded into preliminary testing of my own protocol to generate organoids. I hope to be able to establish corresponding cultures when I return to Helsinki. The research methods learnt during the exchange will be the firm foundation of my PhD research project, and forming strong collaboration will be immensely helpful. I am highly enthusiastic about this opportunity!”

Laitinen independently designed her new research opening involving a novel methodology of assembloids based on the literature of the field in 2022 and convinced Dr Aitta-Aho to become her supervising Principal Investigator in October of the same year. She has since executed her research in the Loss of Control Behaviour lab of Dr Aitta-Aho alongside her medical school studies at the University of Helsinki. Obesity Curiosity, the wider project involving multiple approaches to study the root causes of the obesity pandemic is their joint effort.

“To understand obesity, I have started the same way as many scientists before me, by finding special cases and trying to understand the general rule from there. Common clinical knowledge and scientifically proven fact is that many psychiatric drugs statistically cause patients to gain substantial amounts of weight in a relatively short period of time. I want to study this with a novel human brain model. Long-term, I hope to be able to help in improving the treatment and prevention of obesity”

Before founding Obesity Curiosity, Laitinen had close to nine months of full-time biomedical research experience. After winning Millenium Youth Prize 2018 , she worked at Aalto University in the Department of Neuroscience and biomedical engineering rotating between different laboratories in summer 2019, exploring what the work of a researcher is like. Summer of 2020 and the four months between final exams and starting medical school in 2021, she worked at Professor Pekka Katajisto’s lab (HiLIFE Institute, University of Helsinki) in stem cell research.

In Katajisto lab, Laitinen investigated basal mammary gland cell adhesions to EMC proteins in the normal development and the cancer of mammary gland epithelium.

“The experience was amazing! Professor Pekka Katajisto and Dr Johanna Englund, my supervising researcher in the lab, always believed the most and best of me, teaching me to reach my full potential and ask all my questions. They also demonstrated how great supervising at best can be!”

Her work in 2021 also resulted in her first two co-authored publications, an accomplishment she is proud of and grateful for. “In the scientific world, they are proof that I am capable of executing research at the meticulous level, and maybe help to get respected as a fellow researcher regardless of my young age”

In her first year of medical school, she got accepted to the MD-PhD-program at the University of Helsinki, which had been her goal ever since she learnt that it is possible to become physician-doctor. “It was a nerve-wracking process, as one can apply for the program only once [in the first year of medical school] and I had focused my work towards that goal for a long time. Acceptance felt like reaching the top of a mountain – a completion – and a wonderful landscape of the research world opening in front of me!”

Her initial interest in cancer led to her choosing the first rotation lab studying ovarian cancer. She completed 2 months rotation in the Dr Anniina Färkkilä’s lab (Systems Oncology Research Program (ONCOSYS), University of Helsinki) in the summer of 2022 to learn about three cutting-edge methodologies: cyclic immunofluorescence method, patient-donated sample-derived organoids and complex cell typing flow cytometry.“The point of rotation is to get experience that helps with PhD projects, and I strongly believe these methods will help me design my own project and readouts to investigate my research questions”

“The burning question keeping me up at night is What causes the obesity pandemic? Ultimately this is about the health of over 700 million people suffering from obesity already today and countless others to come. Obesity affects everyone, if not directly themselves, their loved ones. I have a hypothesis, so I am trying my best to test it. I am working in molecular neuroscience to hopefully make the world a better place.”

Laitinen was awarded HiLIFE Undergraduate Student Research Trainee Scholarship for international research exchange in November 2022. She secured a position in Dr Merkle’s lab to conduct the research visit between May-August 2023 working on her Obesity Curiosity project.

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European Society of Human Genetics conference 2023

Hi, we are Rafaela, Victoria, and Johanna, and we are all recipients of the HiLIFE conference grant. In June, we travelled to Glasgow, UK to attend the European Society of Human Genetics conference. 

From right to left: Johanna, Victoria, Rafaela, and Maria Francesca, a visiting scientist and medical doctor in our group.

We are all students of Marco Savarese’s lab (Folkhälsan Research Center) studying genotype-phenotype correlations in rare inherited muscle diseases. Thus, ESHG was a great opportunity for us to learn about the newest, most cutting-edge research in genetics, and to start building connections in the field. 

This was the first international scientific conference experience for all of us, and thus it was an extremely valuable opportunity to gain professional experience in networking, poster presenting, and scientific discussion, early on in our careers. 

The conference offered special opportunities for newer members of the human genetics community, including events organized by ESHG Young Geneticist Committee (ESHG-Y). As first-time attendees, their events and workshops felt extremely helpful and informative and provided excellent opportunities to connect with our peers.  

Overall, human genetics is a broad topic, which was reflected in the wide variety of research topics covered at the conference. Some of the reoccurring topics included AI-based solutions for variant interpretation, variant classification methods, and multiomics applications in genetics research. We wanted to highlight a few topics that we found most interesting and relevant in our work with rare genetic muscular diseases.  

Artificial intelligence-based solutions in human genetics 

Implementing AI based solutions is a hot topic in genetics, and many of the conference presentations reflected this excitement. Among the most interesting ones were a talk about the Eye2gene project and a poster about the Gestaltmatcher database.  

The Eye2gene project was inspired by clinicians diagnosing inherited retinal disease from eye scans. The disease causes specific patterns of damage to the eye. For the clinicians, it takes years of experience to be able to recognize these patterns. Thus, there are few doctors capable of reaching such diagnosis, causing delays in patient care. The Eye2gene method uses AI to interpret these eye scans, and the results show reliable performance. This method could not only speed up diagnosis but also reduce human error and variability of analysis from clinician to clinician, making the diagnosis more precise. 

In relation to our work with rare muscular diseases, the Eye2gene project is a great example of how improved understanding of the phenotype can aid with understanding the genetic background of the diseases as well. Although this approach would probably be much more difficult to implement in MRI imaging used in muscular diseases, it is an intriguing potential future application.   

The Gestaltmatcher is a similar AI-based approach to medical imaging analysis. This database allows an authorized user to upload medical images associated with rare diseases. The AI of the database groups similar images together to find groups of patients with common phenotypes. A major challenge in rare genetic diseases is often the small number of patients. Thus, it is extremely valuable to be able to share data and to gather a database as large as possible from the limited number of patients with a similar phenotype. Larger databases allow for better understanding of the disease phenotype and the genetic background of the disease, and ultimately, to develop treatments for even the rarest of genetic diseases. 

Gestaltmatcher showed that AI has an enormous potential in assisting clinicians and researchers in pattern detection in patient cohorts. This is an asset we should consider taking advantage of in our group’s muscle disease patient cohorts to better understand genotype-phenotype relationships in these diseases. 

Improved sequencing methods and multiomics approaches 

Multiomics approaches were a reoccurring topic at ESHG and it was featured in several presentations and posters throughout the event. In the context of genetics, the term multiomics generally refers to the practice of combining genomics, transcriptomics, proteomics, and sometimes epigenomics. Multiomics has many applications: it can be used for interpretation of variant pathogenicity or to uncover novel disease-causing variants, for example. A presentation at the conference revealed a method of combining genome sequencing with proteomics data to help uncover novel causative variants or reach a final classification for variants of uncertain significance. Epigenomic and transcriptomic approaches were also featured.   

The use of newer, more advanced sequencing approaches, such as long-read sequencing, is also growing rapidly, with regards to both DNA and RNA. In particular, targeted long-read sequencing is being used to diagnose specific diseases since it includes only genes that have a known association with a disease, making it cheaper than whole genome long-read sequencing, but more accurate and precise than traditional gene panels.  

The presentations at the conference clearly emphasized the advantages of multiomics approaches and new sequencing methods. Clearly, these are growing topics in human genetics, and thus, it was useful to hear stories of how these methods have been implemented in practice. This helps us to start developing an understanding of how these methods could be most effectively implemented in the context of muscular diseases.  

The conference venue, Scottish Event Campus (SEC) in Glasgow, Scotland.

This conference experience allowed us to learn about many new topics and to broaden our understanding of human genetics. It was inspiring to hear about the outstanding research and the future of genetics. This trip left us inspired and even more excited and motivated to continue working on our projects with newly developed skills, knowledge, and connections. On top of that, we had a wonderful time together in sunny Glasgow. 

We would like to thank HiLIFE for making this trip possible!