Beneath the surface: Unveiling the hidden dynamics of a Baltic ringed seal population


I’m Murat, a second year student in the Master’s programme in Life Science Informatics at the University of Helsinki, specializing in Biomathematics and Biostatistics. Last summer I embarked on a 4-month internship with the Environmental and Ecological Statistics group that was funded by HiLIFE, where I was able to apply my quantitative skills to a field I have been passionate about since I was a child: wildlife conservation. And what a journey it has been! Although my internship officially ended in September, I have kept working on the project until now.

My mission was to develop a Bayesian state-space model to help monitor Baltic ringed seals, a sub-species of ringed seals that was once on the verge of extinction due to unsustainable hunting practices and large-scale reproductive failure caused by pollution. Thankfully, the population has been recovering during the last few decades, at least in the northern region of the Baltic Sea¹. However, highly dynamic conditions brought on by changing sea ice patterns, decreasing pollution levels and the recent re-introduction of seal hunting have made reliable population monitoring increasingly difficult, and assessments of population status have not been possible for over a decade. The inability to estimate population size and growth rate has been a major obstacle in determining sustainable management practices.

During the summer and fall, ringed seals spend most of their time feeding out at sea, trying to accumulate fat reserves for the winter (foraging period). It is common for young seals to accidentally become entangled in fishing gear during this time. As the Baltic sea begins to freeze over, seals construct snow lairs on the sea ice for protection from harsh weather and predators (subnivean period). Adult females give birth to a single pup inside the snow lair. Once the snow and ice begin to melt, seals move out of their lairs and spend most of their time molting on the ice under the sun (molting period). This is the only time when ringed seals are easily visible, and aerial surveys are conducted each year in the spring to count the number of seals basking on ice. [2] (The illustration was created with the aid of DALL-E 3.)
My challenge was to create and parametrize a model that could accommodate all of these changing factors as well as the uncertainties associated with them, something conventional monitoring methods fell short of. Instead of analyzing different data sources separately, I integrated them into a single, unified model of ringed seal population dynamics – a method that is often called integrated population modeling³. By analyzing all available data holistically, integrated population models can exploit synergies between different data sources, making it possible to parametrize detailed and mechanistic population models.

The results we obtained with this approach were as exciting as they were important. For example, we discovered that the reproductive rates of seals might have fully recovered from the effects of past pollution, and the population may have increased from less than 5,000 to nearly 30,000 individuals! We also discovered that the recent re-introduction of seal hunting has had a notable impact on population growth, though not critical enough to ring any alarm bells for the seal population—yet. Another interesting finding was that seals may be behaving differently during years with low sea ice cover, hauling-out on ice in larger numbers during their annual molt in the spring. Since hauled-out ringed seals are counted each year during this time, population counts after warm winters may be significantly higher! This means that as sea ice patterns are altered due to climate change, reliably estimating the population size could become increasingly more difficult.

A photo of my research group on a beautiful summer day, after an all-day boat party with swimming, sauna and other fun activities.

During the time I was working on this project, every day brought new and diverse challenges – a rich blend of mathematics, statistics, and ecology. Collaboration with researchers from other fields was not just helpful, but essential, making my days anything but repetitive. A year of hard work has finally culminated in a manuscript that is ready to be submitted for publication at a scientific journal! Reflecting back at the journey, it is amazing to see how much I have learned. I started my internship with many doubts – unsure whether I would enjoy doing research, and whether I had what it takes. I am now seriously considering a PhD, confident that a career in research is right for me. As I near the end of this project, I am filled with gratitude for the opportunity to have played a role in preserving these amazing animals, and I eagerly anticipate my next endeavor in the world of research.


¹Sundqvist, L., Harkonen, T., Svensson, C. J., and Harding, K. C. (2012). Linking climate trends to population dynamics in the Baltic ringed seal: Impacts of historical and future winter temperatures. Ambio, 41:865–872.

²Kelly, B. P., Bengtson, J. L., Boveng, P. L., Cameron, M. F., Dahle, S. P., Jansen, J. K., Logerwell E.A., Overland J.E., Sabine C.L., Waring G.T., & Wilder, J. M. (2010). Status review of the ringed seal (Phoca hispida).

³Schaub, M. and Abadi, F. (2011). Integrated population models: a novel analysis framework for deeper insights into population dynamics. Journal of Ornithology, 152:227–237.

The Decorated Cloverleaves in our cells

Transfer RNAs (tRNAs) are often described as humble, clover shaped molecular servants. They participate in protein synthesis by performing codon recognition on messenger RNAs (mRNAs) and by delivering amino acids necessary for translation. Despite technically being an accurate description, it underestimates the profound intricacies of the tRNAs. Humans have around 600 tRNA genes in the genome, and when expressed and processed, the beautiful clover leaf tRNA is reshaped to an L-shaped configuration and will acquire variable chemical modifications, increasing the diversity of tRNAs (Lant et al., 2019). Altogether, the modified L-shaped tRNAs comprise 15% of the total RNA found in the cell, whilst mRNA only comprises 1-5 % (Delaunay et al., 2024). Disruptions in tRNA expression, regulation and mutations have been linked with neurological and metabolic disorders and cancer (Lant et al., 2019). tRNAs are found in all forms of life (Delaunay et al., 2024), underscoring their fundamental role in biology. Understanding tRNAs is essential for understanding life: after all, would life even exist without the humble tRNA?

Modification of cellular macromolecules is crucial for accurate and efficient gene regulation. Many are familiar with DNA modifications, such as cytosine methylation, which may affect gene activity and chromatin structure (Liyanage et al., 2014). Cellular RNAs are also targets of post-transcriptional modifications (PTMs) with the N6-Methyladenosine (m6A) modification being one of the most widely studied (Lauman & Garcia, 2020). RNA modifications have essential regulatory implications: in mRNAs, certain modifications can affect transcript stability, localisation, splicing patterns, and translation (Delaunay et al., 2024). PTMs can be found in ribosomal RNA, long non-coding RNAs, and small non-coding RNAs (Delaunay et al., 2024). Unsurprisingly, PTMs are also seen in tRNAs. In fact, tRNAs are the most abundantly modified RNA species in the cell (Zhang et al., 2022). Our understanding of their effects is still limited but we know that the modifications can affect tRNA stability, tRNA-RNA interactions, tRNA-protein interactions, folding and mRNA decoding (Delaunay et al., 2024). Over 150 tRNA modifications have been identified (Delaunay et al., 2024) and as tRNAs are abundant in the cells, studying tRNA modifications becomes a very intriguing area of research.

Adenosine and N6-Methyladenosine. Created with

During my time as a HiLIFE trainee I had the opportunity to delve into the science of tRNA modifications at the RNAcious laboratory, University of Helsinki. I participated in two projects, one where the aim was to produce hypomodified tRNAs and another where the aim was to determine the tRNA modification landscapes in different mouse tissues. You can find my first blog post here:

The making of plain cloverleaves: Hypomodified tRNAs

Modifications on tRNAs are so abundant that it would be difficult, or maybe even impossible, to extract hypomodified tRNAs from the cell: you see, in eukaryotes there are on average 13 modifications on each ~80nt long tRNA (Zhang et al., 2022). For methylations alone, there are around 40 proteins, known as modification writers (e.g. methyltransferases) and erasers (e.g. demethylases), which moderate tRNA modifications (Delaunay et al., 2024). One way to produce hypomodified tRNAs is through in vitro transcription (IVT), which essentially is a cell free transcription system. As IVT is cell free, it lacks the writer and eraser enzymes which modify the modification profile. My task was to develop a method to produce and isolate hypomodified tRNAs utilizing IVT, ribozyme- and MS2 based techniques.

Differentially decorated cloverleaves: tRNA modifications in different organs

We know that there are different tRNA modification landscapes in different organs (de Crécy-Lagard et al., 2019) but they have not yet been studied extensively. A tRNA modification landscape is the entire modification profile of the tRNAs of a specific organ. Uncovering the modification landscape would offer valuable insights into both the frequency and positional distribution of specific modifications within the tRNAs across various organs. Mass spectrometry is an effective tool to identify and study the location of modifications on single nucleotides (Lauman & Garcia, 2020), and certain reverse transcriptases can be used to study the location of modifications on the tRNA molecule (Zhang et al., 2022).

After my time as a HiLIFE trainee, I’ve truly gained a deep appreciation for the complexities of the humble tRNA. While I metaphorically refer to tRNA modifications as “decorations”, in reality, these modifications play essential roles in biological processes. Learning about them has been truly fascinating.

To end this journey, I would like to express my gratitude to Docent Peter Sarin and his group of bright researchers, especially my supervisor Jenni Pedor, who always supported me during my time in the research laboratory. The pioneering and motivational environment provided an invaluable experience and an inspiration for my career moving forward. I would encourage anyone interested in expanding their understanding of tRNA modifications and tRNA biology to explore the research conducted at RNAcious laboratory.



de Crécy-Lagard, V., Boccaletto, P., Mangleburg, C. G., Sharma, P., Lowe, T. M., Leidel, S. A., & Bujnicki, J. M. (2019). Matching tRNA modifications in humans to their known and predicted enzymes. Nucleic acids research, 47(5), 2143–2159.

Delaunay, S., Helm, M., & Frye, M. (2024). RNA modifications in physiology and disease: towards clinical applications. Nature reviews. Genetics25(2), 104–122.

Lant, J. T., Berg, M. D., Heinemann, I. U., Brandl, C. J., & O’Donoghue, P. (2019). Pathways to disease from natural variations in human cytoplasmic tRNAs. The Journal of biological chemistry, 294(14), 5294–5308.

Lauman, R., & Garcia, B. A. (2020). Unraveling the RNA modification code with mass spectrometry. Molecular omics, 16(4), 305–315.

Liyanage, V. R., Jarmasz, J. S., Murugeshan, N., Del Bigio, M. R., Rastegar, M., & Davie, J. R. (2014). DNA modifications: function and applications in normal and disease States. Biology, 3(4), 670–723.

Zhang, W., Foo, M., Eren, A. M., & Pan, T. (2022). tRNA modification dynamics from individual organisms to metaepitranscriptomics of microbiomes. Molecular cell, 82(5), 891–906.

Paving a route for the PhD project “Obesity Curiosity” – reflections on a traineeship in Dr Merkle’s lab

Photo: Our world in Data map (cc) about Obesity in adults, full access:

Suvi Laitinen, 21, researcher and MD-PhD-student left for a research exchange right after completing her second year of medical school and returned to Finland to start her third year in mid-August. Her grant was awarded exceptionally for 2.5 months, taking into consideration the attendance requirements of her medical school. She completed an international exchange in Dr Florian Merkle’s lab at the Institute of Metabolic Science (IMS) at the University of Cambridge. Her project Obesity Curiosity is focused on understanding the relationship between hunger, satiety and obesity (Project introduction video here: )

Laitinen worked in biosafety level 2 stem cell culture, learning Dr Merkle’s lab neuron differentiation protocol and testing her differentiation protocol for organoids built on existing protocols. Dr Merkle has pioneered in differentiating human induced pluripotent stem cell-derived functional human neurons. “That work has been a game changer – thanks to his work efficient production and the study of the live human brain is possible for hypothalamic key neurons – and his team has continued the work towards applications with stunning results!”, Laitinen describes with visible enthusiasm.

She praises the supervision she received: “In addition to innovative and supportive supervision from Dr Merkle, I had the honour to learn from the brilliant postdoctoral researcher Dr Cortina Chen. Her precision, efficiency and ability to handle multiple projects at the same time is astonishing. Moreover, she welcomed me and my questions warmly to her busy schedule, took time to teach me and helped further develop the methodology for my project. I am very grateful for Dr Chen – not only was she a fabulous immediate supervisor with great leadership skills, she made me feel supported and well on track every day – and also a kind and relaxed person from whom I learnt immensely. It was wonderful to work with her!”

Results from Laitinen’s work were living organoids that then were collected as samples that are the base for her PhD project. “I am immensely grateful to Dr Merkle for warmly welcoming me into his lab and for his ongoing advice and support which has been highly impactful for my project. I have now an idea of how to continue with my research when I return to Finland. The exchange has been a wonderful experience and will stay with me for all my life!”

Laitinen reminds all aspiring young researchers to pay attention to the institute as well when thinking about where to apply: “I was so happy to have both amazing lab and institute. IMS is an amazing place – brilliant, passionate people all working in the same field in the same laboratories. The institute is indeed one of the hot spots of obesity research, and they have amazing internal and external speakers with a full auditorium almost every week. The institute also excelled beyond the academic measures, everyone was welcoming and helpful. Huge thanks to all PhD and Masters students I met, you are amazing and your great team spirit is something I am gonna miss. It was a huge privilege to be part of the community for a short period”.

During her stay, she also had the opportunity to build connections with and seek advice from the other lead scientists in the field. “I want to express my deep gratitude to Dr Madeline Lanchaster, Professor Sir Shankar Balasubramanian and Professor Sir David Klenerman for taking time from their undoubtedly very busy schedule to meet me and answer my questions”.

Dr Madeline Lanchaster pioneered by publishing first brain organoid protocol in 2014 and now leads a lab in the MRC Laboratory of Molecular Biology on brain development in cerebral organoids. Laitinen visited her lab and had a deeply impactful discussion on different approaches in brain modelling. “Dr Lanchaster’s insight into deciding between gardening and engineering approach for brain model composition was eye-opening for me and I believe her advice will benefit the project for a long time”.

Professor Sir Shankar Balasubramanian and Professor Sir David Klenerman won the Millenium Prize in 2020 for Next Generation DNA Sequencing, awarded by the Technology Academy of Finland (TAF), which also awarded Laitinen and Maula Millenium Youth Prize 2019 for their project proposing a solution that could theoretically slow down Alzheimer’s disease.

Professor Balasubramanian leads world-class research on unconventional DNA complexes and the start-up branched from their research is currently investigating those as a treatment for human diseases. “Professor Balasubramanian had amazingly organized an exciting half a day for me to meet both his lab members in Cancer Research UK (CRUK) and at the Department of Chemistry and I met so many exciting people and changed ideas. His advice for me on how to build a research program in a smaller country like Finland and his supportive approach was incredibly helpful!”

Professor Sir David Klenerman leads a research program on imaging single molecules with complex microscopy techniques. In his lab, Laitinen saw first-hand imaging of single protein aggregates associated with neurodegenerative diseases. “I can only try to describe the awe I experienced looking at the microscope capable (with physics I am not able to explain) of visualizing individual protein complexes. Those are on a nanometer scale and it is wonderful that they have stretched the capability of technology to this level! Professor Klenerman also gave useful advice on how to bounce back after mistakes and unsuccessful events that are inevitable in science despite our best efforts especially when trying to do something completely new. Most of the time things don’t work out the way we expect them to just because they are so new”.

Laitinen describes how the research exchange in an international lab was a formative experience for her. “Traveling to Cambridge enabled me to take my project to the next level and strengthen our scientific collaboration with Dr Merkle’s lab. I learnt about exciting research done in the lab and IMS as well as other labs that welcomed me to visit. Joining one of the forefronts of my research field has been incredible and I cannot emphasise enough how impactful meeting all these brilliant people from all career stages joined in Cambridge from around the with the common goal of the best possible science has been”.

Laitinen points out how crucial the support of Helsinki Institute of Life Science (HiLIFE), an independent life sciences research institute within University of Helsinki was for her experience. “HiLIFE supported me with my ambitious idea to explore something that nobody has investigated this way before. In the interview part of the multi-step application process – which by the way I think is an amazing investment of theirs to teach young scientists how to present their ideas and take that challenge of answering to a whole board of experts – I was asked if I could acquire another funding for the summer exchange. As I told them, I am fighting with all my effort for my project, still without preliminary data and restricted funding opportunities for this early career stage, I don’t think it would have been possible. HiLIFE Undergraduate Student Research trainee Scholarship is a unique opportunity and for me, it was impactful beyond measure. I think the exchange set me well for the coming years of PhD research and given me skills that I will be able to use long in my efforts to build my research program in Finland. I humbly thank you for this opportunity”.

On how to teach a man to fish: experiences of my journey as a HiLIFE trainee

As a new year starts and new students are getting the opportunity to become HiLIFE trainees, I have been reflecting about what I did, learned and achieved during my own experience through this program.

I am Adrián Colino Barea, a (now) second year Master’s student of Ecology and Evolutionary Biology.  On March 2023, I was lucky enough to join the Integrative Evolutionary Biology (IntEvoBio) lab to answer what I first thought could be a trivial question that popped in my mind. Claudius Kratochwil, the PI of the group, helped me to plan a small project aiming to determine how light depletion determines sexual choice and preference in colorful cichlid fishes from the African Great Lakes. You can learn more about it reading my previous post, by clicking here.

Males of the fish I use for my experiment show yellow egg-shaped dots in their anal fin. Females lay eggs on the ground and brood them in their mouth cavities. When the ladies lay, the lads display their egg spots close to the ground. Females, confused, try to swallow the egg spots as they do with their eggs. Then, males release sperm and fecundation takes place. Evolution is amazing.

In a nutshell, and if you are wondering, my short internship project didn’t come up with significant differences of mate preference under light and dark conditions. I did not find out how colorful fish fall in love in the dark. Instead, I found out how usual — and important — it is to not have results in science. It is crucial to get a glimpse on what questions are relevant to answer, and what research lines are worth following and investing on. There is just so much to find out, trial-and-error is necessary to keep going.

I learned new limits of the beauty of commitment. For my experiments, controlling fish schedules involved feeding them, and I decided to take care of it. I found myself showing up in the fish room every single day, sometimes in breaks between classes, sometimes during lazy Sundays, sometimes under absolutely crazy weather… And I loved it. Working March to June, I got to experience the Finnish weather every day at least for a bit. It was not too special at the moment, and anyone could do it if living in Helsinki. But now I am really glad I got to see how the seasons change. Very often, I stopped by the fish room only to go walking in the forest or birdwatching later, and experiencing nature changing with the seasons before my very eyes. Days became longer, snow melt, flowers sprung, everything sprung. And this experience is just so different to what I grew into, coming from the other side of the continent.

Dramatic winter panorama after a blizzard at the end of March in Viikki Campus, back from visiting the fish room.

I also found myself becoming part of a community, formed by all the members of IntEvoBio lab. Over my working weeks, it was easy to be motivated to plan and act thanks to the great support and hospitality of all the members of the lab. I always felt encouraged to keep up and be up to date on meetings, presentations, and the deadlines I kept setting myself to meet ends — something vital in such a small project. Indeed, perfecting the art of managing time has been one of the most valuable assets I got out of the internship. But in this case, considering the inspiring time planning the whole lab follows, being organized myself was a piece of cake.

Another thing I learned and cherish is the value of kindness and humanity. During my internship, I always found a smile and willingness to help of the members of the lab I treated with, including people of all levels, from PI to Master’s students. Without this help, my project wouldn’t have developed after the very first stage. I received life-changing lessons on how to build my research career without falling into mistakes others fell into in the past. I learned how important it is to build and take care of relationships, as we got to welcome incoming researchers from distant countries and prepared the departure of some of IntEvoBio staff to other universities abroad. This is the spirit of the science of today: learning by sharing.

Although almost no one in the lab was a Finn during my stay, the spirit of properly balancing work and life was a rule throughout my internship, and I feel this is also part of the kindness and humanity I experienced. I felt welcome not only by having a cozy desk with plenty of lovely pictures and catchy fish jokes hung on the wall. I also loved lab outings. To wrap up the work of months, give farewell to a visiting researcher and say hello to summer, we went all together kayaking the Vanhankaupunginlahti in a hot day of June, right before the end of my internship, and then stayed for dinner. We really had a blast. And although few of this has to do with how fishes mate in the dark, it proved vital for the development of this project which tried to answer that question.

Laughs and fun on a lab outing, kayaking around Kulosaari on a warm, sunny day of June, with IntEvoBio lab. A great memory of a great experience overall.

As the proverb says, ‘Give a man a fish and you’ll feed him for a day; teach a man to fish and you’ll feed him for a lifetime’. Thanks IntEvoBio and thanks HiLIFE for helping me so much on my journey to learn how to fish.

Lignin in leatherwood: the key to replacing petroleum based plastic?

For the past several decades, forestry has been interested in developing transgenics to improve wood production. This is because in the majority of vascular plants, lignin biomass averages 20-30%, which means there is a large energetic and monetary cost to remove this unwanted lignin, a hydrophobic molecule with strong covalent bonds, during processing (Robinson, 1990). But despite its cost to paper and pulp mills, lignin has exciting potential applications as an organic molecule in the pharmaceutical, construction, and packaging fields, among others (Albuquerque et al., 2021). With proper bioengineering, lignin could even be used as a biomaterial capable of replacing fossil fuels in plastic production. However, current research and knowledge of lignification, the process wherein lignin is deposited in the plant, is lacking when it comes to our ability to produce widely-commercially viable plants with manipulated lignin properties. This is where the small, bendy shrub, Eastern leatherwood, enters the picture.

Eastern leatherwood. Image by Tom Potterfield

During the course of my four months with the Fagerstedt lab, I had the opportunity to work with leatherwood, a species that was recently discovered to have unique lignin patterning, in a completely novel way (Mottiar et al., 2020). While I knew that I would likely use antibody staining to identify the locations of molecules, such as pectin, I didn’t know that I would have the opportunity to use a transmission electron microscope, or to turn this research into a thesis project.

One of the best things about science, and this traineeship with HiLIFE, is that I was able to try things that I, nor anyone else, had ever done before. With Yaseen’s expertise, the post-doc supervising me, I went from researching how to use a transmission electron microscope, which sends a particle beam through your ultra thin sample, allowing you to see where electrons are able to pass through, and where they are blocked, to actually embedding samples in small, pill-shaped resin capsules and eventually imaging those samples on a machine that looks like a spaceship (the transmission electron microscope). This type of microscopy allowed us to see, in extremely fine detail, the cell wall of leatherwood tissue. While the image below has some sample flaws (the dark line is a wrinkle in the wood section, and a few of the cell walls have torn), I think it’s a really cool way to see the cambium (with inner cellular contents that have been destroyed) and the empty xylem cells that, in a living tree, would transport water. Below is a sample of leatherwood, and if you look at the area between the cell walls, or middle lamella, you can see that it’s lighter in color, indicating that there is not staining present, and therefore there is not enough lignin present to darken the area.

TEM image of leatherwood sample stained with potassium permanganate.

I’m so grateful for the opportunity to spend four months of full-time work trying out different wet lab techniques and learning about what it is like to be a full time researcher. Additionally, this research has provided a step further in the quest to generate transgenic trees with modified lignin content and distribution. Hopefully in the future, scientists will be able to modify commercial species with lignin in ways that allow lignin to be used to replace plastics, among other things.


Works cited

Albuquerque, B. R., Heleno, S. A., Oliveira, M. B. P. P., Barros, L., & Ferreira, I. C. F. R. (2021). Phenolic compounds: Current industrial applications, limitations and future challenges. Food & Function, 12(1), 14–29.

Mottiar, Y., Gierlinger, N., Jeremic, D., Master, E. R., & Mansfield, S. D. (2020). Atypical lignification in eastern leatherwood (Dirca palustris). New Phytologist, 226(3), 704–713.

Robinson, J. M. (1990). Lignin, land plants, and fungi: Biological evolution affecting Phanerozoic oxygen balance. Geology, 18(7), 607–610.<0607:LLPAFB>2.3.CO;2

Exploring Cancer drug treatment through the lens of The Powerhouse of the Cell: My Journey with the HiLIFE Research Trainee Scholarship

From the very early days of my scientific curiosity, mitochondria have always held a special place in my heart. Not just labeling it as the powerhouse of the cell, but as a key to understanding our very essence, our homeostasis, and heritage. The  Helsinki Institute of Life Science (HiLIFE) Research Trainee Scholarship allowed me to delve deeper into this fascination, offering me a unique traineeship across two distinguished labs at the University of Helsinki.

What is HiLIFE:

The  Helsinki Institute of Life Science (HiLIFE) is an international institute where outstanding researchers across the University’s campuses solve today’s grand challenges in health and environment together.

The Battersby Lab Experience

My initial month at the Battersby Lab at the Institute of Biotechnology was an enriching experience of learning and exploration. Here, I was introduced to the intricate world of RNA-seq data analysis, specifically focusing on the cellular response to mitochondrial protein synthesis quality control defects. The cells of interest were cultured mouse fibroblasts (MEF), and the conditions involved knock-in mutations in AFG3L2 with matching wild-type control. The aim was clear: identify differentially expressed genes in MEF AFG3L2 KI/KI. The entire process, from data analysis to pathway analysis, was a revelation, and it provided me with a foundational understanding of the techniques and tools used in RNA-seq data analysis.

The Kallioniemi Group Experience

Transitioning to the Kallioniemi and Paavolainen’s group for the subsequent three months, I got exposure to a high-throughput lab environment. Here, I embarked on a research project under the guidance of Dr. Isabel Mogollon Figueroa at the Institute for Molecular Medicine Finland (FIMM). The project spanned from basic cell culture techniques to advanced analysis using data collected with the Opera Phenix microscope and GSEA analysis.

The Kallioniemi Group, specializes in precision systems medicine. In collaboration with Dr. Lassi Paavolainen’s group, they have made significant strides in bioimage profiling using AI tools. One of the recent publications of their collaborator, the Carpenter group of the Broad Institute, published in Nature Methods presented a dataset correlating gene expression data with Cell Painting imaging data. This dataset became the foundation of my project, aiming to characterize novel compounds/genes affecting mitochondrial morphology and function in cancer cells.

The project had specific aims, both in silico and in vitro. The in-silico analysis focused on data mining and big data analysis, identifying relevant genes affecting mitochondrial morphology based imaging features as potential drug targets. The in vitro work involved culturing the renal cancer cell line 786-O, optimizing it for the Cell Painting assay, and performing drug testing using custom-designed drug plates.

The learning curve from the project:

I learned some very important techniques, like cell culture, Cell Painting and western blotting. One of the key aspects was that I learned to approach a scientific question of my topic of interest through completely different perspectives. In the case of Battersby lab, the approach was more towards understanding biology, whereas in the case of Kallioniemi group, it was more centered towards drug testing.


My journey with the HiLIFE Research Trainee Scholarship was not just about learning techniques and conducting experiments. It was about understanding the profound impact of mitochondria on our health and exploring the potential of modern biotechnological tools to unravel its mysteries. As I reflect on my experiences at the Battersby Lab and the Kallioniemi Group, I am filled with gratitude for the opportunities I’ve had and excitement for the future of mitochondrial research.

From the Hub of Thousand Lakes to the World’s Leading Biotech Hub

“Everything is bigger there, one needs a car to get anywhere, the baseball and football they play are something else, and it is supposedly the college town and biotechnology hub.” This was the rather stereotypical view of Boston I had seen and heard from multiple sources (such as many American movies) before crossing the Atlantic for the first time and landing to one of the oldest cities in the United States. For the next six months, I was going to work as a HiLIFE Visiting Graduate Researcher at the Wyss Institute for Biologically Inspired Engineering at Harvard University.

The Wyss Institute has a strong emphasis on translating bioinspired innovations and research findings into clinical use. The number of patents, licenses and start-ups deriving from the Wyss is astonishing: during the 14 years of the institute’s existence, over 4000 patents have been filed and 56 start-ups founded. To enable this technology translation, Wyss operates through extensive collaboration with industry, government, foundations, and philanthropists. The Wyss teams have experts from different fields ranging from engineering to veterinary medicine, from general medicine to bioinformatics, and from molecular biology to bioethics.

The original six months got extended and therefore, during the past eight months, I got the opportunity to work in Donald Ingber’s (M.D., Ph.D.) lab in the Brain Targeting Program at the Wyss. Of these months, six I was present in Boston and the final two contributing to the program remotely from Finland. The Brain Targeting Program aims at discovering and developing new brain transport shuttles and brain-targeted therapies to more efficiently treat diseases in the central nervous system, such as neurodegenerative diseases and brain tumors. For reading more about the research topic, please have a look at my first blog post. The internship was certainly the most remarkable experience during my Translational Medicine Master’s studies at the University of Helsinki, and I could have not imagined a better way to complete my studies.

Laboratory setting
My dear lab bench at the Wyss Institute

What comes to my presumptions about Boston, at least one of them proved very accurate. According to the EPM Scientific (2023), this year, Massachusetts has earned the title of “the largest and leading Biotech hub in the world”. The life science and biopharmaceutical sector has grown massively in the Boston metropolitan area, this growth corresponding to increase in venture capital, employment rate, and governmental funding received. In fact, there are almost 1000 biotech companies, and over 60 colleges and universities in the area! Combine this with specialized medical centers and university teaching hospitals such as Dana-Farber Cancer Institute, Boston Children’s Hospital, Beth Israel Deaconess Medical Center, or Massachusetts General Hospital, and you have the foundation for boundless opportunities.

During my daily bike commute along the Charles River, not only could I enjoy the views of prestigious red brick buildings from the 18th century, but also appreciate the modern glass office buildings with biopharma company names like Biogen, Takeda, Pfizer, or Eli Lilly written on top of them. The different universities, non-profit organizations, venture capital firms and other groups were organizing various incubator and accelerator programs with pitching events open to attend for anyone interested. In addition, there were free of charge conferences, seminars, and lectures given by top scholars of the field, by people you had previously only seen in Ted Talks or had read their state-of-the-art work from Nature, Cell, and Science. You would see advertisements of novel RNA technology in the subway and randomly hear discussion of a given research topic in almost any bar or restaurant in the city. Even if you would go on a walk in a national park hundreds of miles outside Massachusetts, you would encounter other hikers with their company or institute swag, portraying very clearly the amount of biotech and medicine professionals in Boston and Massachusetts area.

Building with pillars and a yard surrounded by trees
The Quad at Harvard Medical School

For the work of our Brain Targeting Program and my internship this meant that I would be immersed into science, innovation, and biotechnology. Truly feeling like a child in a candy store. It was deeply inspirational and improved my thinking to be more creative yet critical. I could meet like-minded people and create networks with scientists working on topics of my interest. We could also work with clinicians and hospitals from around the corner and foster collaborations with other research groups somewhat effortlessly.

To conclude, I wanted to summarize three main learnings from my internship experience that are not only applicable to Boston but can be utilized in other contexts as well.

1. Keep an open mind

The amount of biotech companies and research initiatives makes it possible for anyone to find their research niche from Boston. There are hundreds and hundreds of job posts on LinkedIn, in positions rarely – if at all – seen back home in Finland. The challenge is not how to find what you would like to do, but how to choose from all the possibilities. That is why especially if you are in your early career, keep your mind, eyes, and options open.

Participate in different events, listen to talks from various specialties from academia and industry, talk to undergrads, PhDs, professors, R&D scientists, COOs, patient representatives… and you never know if you happen to sit next to a company CEO ready to hire a talent. Reflect on what you already know and have experience on, what would you like to learn, what is your aspiration, and get inspired. If you cannot travel to a big biotech center at this moment, see possibilities online or gather information and plan possibilities for a research visit, for example via funded traineeships or short training courses.

2. Networking is key

Sorry, I know you have heard this a million times, but it just is so important… All the opportunities and events you attend will also gather important and interesting people for you to meet. These people can provide you with valuable insights into your research and career or introduce you to other connections. So even if you would not necessarily consider yourself the most outgoing person and have always felt that networking is anxiety provoking and definitely not for you, dare to get in contact with and meet people.

In addition to introducing yourself and engaging into conversations spontaneously in events, you can send emails and meet people in person after you have had some time to think what you would discuss with them. It is not a bad idea either to review the speakers of an event beforehand and formulate questions you would like to ask them. In this way you will feel more confident and importantly, not waste anyone’s time. Even though the art of small talk is very much mastered in the United States, and it is a big part of the culture, people are busy and appreciate using their time well. Yet, avoid thinking of what you have to say is not of importance and because of it cause you not to talk to people. Despite their overbooked schedules, it was amazing to see how top scholars with over 100 000 citations would stop and truly listen to what you had to say, no matter in which career stage you were.

But in all, you will get the most out of these situations when you are clear and concise. Thus, tell honestly who you are, what you would like to do and learn, and ask for advice or even collaboration if you have a potential idea. You can also create a short pitch for yourself, it will help you to focus. And remember to be gentle with yourself, practice makes perfect.

People in an auditorium
Brain Targeting Program Consortium Meeting. Picture courtesy of the Wyss Institute at Harvard University

3. Have fun and explore outside the hub

Even though Boston, or any place you work and study, is such an exciting place considering your career, do not just biotech and network 24/7 – even if conversations with your friends would every now and then slip to the lab experiments and recently approved therapeutics. It is good to take some distance from constantly thinking about career and go explore the city and its surroundings. Go to the nature, delve deep into the history, visit art museums, join block parties, and enjoy the culinary scene. This will give you a full internship experience which should not be just fun science but fun experiences overall!

The HiLIFE Research Trainee Scholarship gives you a unique possibility to work and contribute to science nearly anywhere in the world and with a vast amount of life science topics. The opportunities for you to go after your dreams are out there. What will be your path?



EPM Scientific. (2023). Boston is Now the Largest Biotech Hub in the World.

Elephants, people and fences: conflict or coexistence?

Dream come true

It has been my dream since I was a kid to visit Africa one day and witness all the incredible wildlife there. And in December 2022, I actually had the chance to do this, all thanks to the HiLIFE traineeship!

My name is Mihika Sen, and I am part of the Ecology and Evolutionary Biology Master’s Programme at the University of Helsinki. Growing up in Assam, Northeast India, I was exposed at a very early age to the many fascinating yet threatened species of my region, and consequently the importance of wildlife conservation. Particularly in my hometown, Guwahati, I became increasingly aware of how Asian elephant habitats were constantly shrinking, bringing them closer and closer to people. It soon became evident to me that the future survival of elephants (and other wildlife) in human-dominated spaces largely hinges on the interactions they have with the people around them.

5 year old me in Kaziranga National Park, Assam (where my love for wildlife began!)

The research journey begins

Given my interests, my research has largely been focused on the mitigation of negative human-elephant interactions, also termed as human-elephant conflict. As I took part in several projects across India, I soon understood that the support of local communities living close to wildlife is essential to truly achieve coexistence. And with an eagerness to learn more about human-elephant conflict in the African context, I ended up packing my bags and travelling more than 6000 km from India to Finland (where there are no elephants), finally knocking on the door of the Global Change and Conservation Group at the University of Helsinki. To explain why I made this decision, this very interdisciplinary group, led by Dr. Mar Cabeza, has done years of fascinating research on human-wildlife interactions in Kenya, and I knew this was my place to be! Mar was thankfully equally eager to have me join her team, and then the discussions for a Master’s thesis topic began.

After considering several ideas, I finally decided to focus on the use of electric fences as a human-elephant conflict mitigation tool, particularly in Laikipia county, Kenya. Laikipia is a region in Kenya where human-elephant conflict has historically been a widespread problem, mainly arising from intense land-use zoning there since the 1970s. The conflict there mainly takes the form of elephants raiding crops in community farmlands adjoining conservation areas. Electric fencing is the primary conflict management tool used there to prevent elephants from entering croplands. While the ecological effects of electric fencing have been looked at in various studies, the social perceptions of local communities towards them is largely neglected. These perceptions can play a crucial role in long-term fence effectiveness, and this is precisely what I delved into in my research.


An African elephant near the West Laikipia Fence in Mutara Conservancy; A regular day in Laikipia with people, livestock and elephants coexisting in the same landscape.

Preparing for the field

Next up was the most challenging part: how do I actually get to Kenya and conduct the research? Despite the fact that my research group has worked in Kenya before, they had not worked specifically in my study region. This meant I would have to develop my own set of contacts there to plan the project. So I wrote multiple emails to multiple people across the globe who have worked in Laikipia before, and I was lucky enough to receive a very kind response from Marcia Van Eden from the US, who had conducted interviews with local communities there in 2016. Through her, I was able to get a set of contacts for Kenya and I finally managed to arrange my accommodation, travel, research equipments, as well as a local research assistant. There was also the issue of funding. Finland unfortunately has very few grants that fund research abroad during the Master’s degree, and the HiLife traineeship was the only grant I could actually apply to. So it really was a blessing to be able to receive this grant, and I would urge anyone reading this to apply for it too!

Jambo Kenya!

After months of planning, I finally made it to Kenya! The wildlife and the landscapes were exactly as stunning as I had imagined, and the people extremely kind and welcoming. As I had only around two months to finish interviewing three communities, I immediately set off to my study site to begin my research. For the first time in my life I saw zebras, giraffes and of course, African elephants! It was hard not to feel emotional during these moments. My assistant, Lucy, and I were lucky enough to be offered a place to stay at the ADC Mutara Ranch in Laikipia. From here, we travelled on motorbike every day to interview the communities, conducting a total of 188 interviews with farmers (and occasionally pastoralists) over the course of three weeks.


My first African elephant sighting; Lucy and me on our loyal motorbike that survived some of the worst terrains.

For me personally the best part of conducting this research was meeting the local people! Despite the fact that I was a stranger to them, each family opened their doors and welcomed me into their homes, many times even offering me warm tea and delicious food. And even though I was so far away, I still felt like I was at home.


Happy faces; After a successful focused group discussion with the Mutara community.


My study ultimately revealed that human-elephant conflict continues to be a persistent problem in Laikipia, with farmers often facing crop raids by elephants. Maize was the most frequently raided crop, and elephants mostly raided crops at night to minimise interactions with people. Community perceptions showed considerable changes over the years, revealing important insights for long-term fence effectiveness as well as elephant movement patterns in the region. One of the most significant results of my study was that higher involvement of local communities in electric fence management can lead to more positive community perceptions towards electric fences. I was also able to identify crop raiding hotspots in the target communities, and I found that the higher the diversity of crops grown in a given farm, the higher the chances of an elephant raiding it. My next step now is to submit a detailed report on all my findings to the various stakeholders involved in the establishment of the electric fences in my study region. For more details about my research, you can read my thesis at the following link:


Damages by elephants to crops and electric fences.

Overall this project was an unforgettable learning experience for me both personally and professionally, and I’m very grateful to HiLIFE for helping me turn my dreams into reality. Signing off with a picture of a beautiful moment between a mother and her calf!

Unveiling the World of Ovarian Oncology: My HiLIFE Traineeship Journey


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.

  1. Surgery for Recurrent Ovarian Cancer May Help Selected Patients – NCI. (2022).

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.