Category: Research Trainee Scholarships 2023

 

I’m Pinja Perkkiö, an aspiring microbiologist and a HiLIFE scholarship trainee in Reetta Satokari’s lab (University of Helsinki, Faculty of Medicine)! I’ve just finished my bachelor’s degree and I will start my studies in the master’s programme of Microbiology and Microbial biotechnology next autumn. This summer, I will be diving deep into the world of gut microbiota as I research the microbiota restoring potential of NGPs in intestinal inflammation and dysbiosis. 

 

How antibiotics disturb our gut microbiota 

The gut microbiota is defined as a community of microbes, e.g. bacteria, fungi, viruses and archaea residing within the gut. The microbiota is responsible for many important functions, such as breaking down complex carbohydrates and protecting the gut from infections. When a person takes antibiotics, it not only kills the bacteria causing the disease, but also the beneficial ones as antibiotics aren’t strain-specific. This allows potentially pathogenic bacteria to grow in larger numbers – the situation is called dysbiosis, meaning that the microbial community composition has been altered in a harmful way. 

Luckily, we have a tight layer of cells – the epithelium – that lines the walls of the gut and is covered by two layers of mucus. The mucus combined with the epithelium acts as a barrier between our intestines and the rest of our body, preventing intestinal pathogens from causing too much harm. Normally, it is very difficult for microbes to cross the mucus layer as it traps microbes and is loaded with antibacterial substances. In addition, the cells of the epithelium are tightly attached to each other, preventing any further movement of microbes. There are also lots of immune cells embedded in gut tissues that are ready for action, should a pathogen try to cause an infection. 

However, as dysbiosis leads to the growth of pathogenic bacteria, our immune cells (neutrophils, NK cells and macrophages, for example) activate inflammatory reactions. While these reactions are necessary for the elimination of pathogens, they also damage gut tissue. Pathogenic bacteria also activate the secretion of inflammatory molecules, cytokines, in a type of gut epithelial cell called enterocyte, which leads to the epithelium getting “leaky” – this means that microbes can cross the epithelium more easily and cause further inflammation in gut tissue. These bacteria can not only cause nasty infections, but they may also travel deeper in gut tissue or even to other sites in the body, increasing the risk of certain cancers (Bastos et al., 2023; Kouzu et al., 2022)! 

 

Next-generation probiotics against dysbiosis 

To fight antibiotic-induced dysbiosis and reduce the inflammation and leaky gut syndrome caused by it, researchers have turned their attention to potential new bacterial strains that could function as next-generation probiotics. They are defined as “live microorganisms identified on the basis of comparative microbiota analyses that, when administered in adequate amounts, confer a health benefit on the host” (Martín R, Langella P., 2019) – in simpler terms, microbes that can potentially help boost our health. Traditional probiotics, such as Bifidobacteria and Lactobacilli, have shown great potential in restoring a healthy microbial community in the gut after taking antibiotics, thus preventing dysbiosis and infections. They have also been shown to inhibit the production of inflammatory molecules in both immune cells and epithelium and boost the production of anti-inflammatory molecules.  

 

Probiotics exert anti-inflammatory effects on several cell types. Created with Biorender.com. 

 

There’s still lots of research to be done to bring next-generation probiotics into wide use. More information is needed on the different strains of potential probiotic bacteria and their specific effects on both the immune system and the gut epithelium. This is where my research project comes in! 

The project I’m collaborating on focuses on a mix of 14 different anaerobic bacterial strains that have the potential to restore the gut microbiota after antibiotic use and prevent or reduce inflammation. The next-generation probiotic mix was originally tested in an in vitro mucosal-simulator of the human gastrointestinal tract (M-SHIME(R)) model. A natural gut microbiota was obtained from the stool sample of a healthy human donor, after which it could grow. Then, the “gut” was exposed to antibiotics to induce dysbiosis. After the antibiotic treatment, one system was treated with the probiotic mixture and the other one with a negative control. Finally, samples from probiotic- and control-treated microbiotas were taken. Bacteria present on these will be studied to check the impact of the antibiotic intake in the microbiota and compare its possible recovery after the probiotic treatment. The production of short-chained and branched fatty acids, lactate and ammonia at different time points will also be measured since their levels indicate how much beneficial bacteria there are compared to harmful ones. 

To study how the anaerobic isolates might affect intestinal inflammation, I will culture two different intestinal epithelial cell lines: Caco-2 and HT-29. These cell lines were chosen because they are well-characterized and resemble enterocytes on the gut epithelium. Then, I will expose the HT-29 cell line to either the anaerobic bacterial blend or a placebo. After incubation, pro-inflammatory IL-8 production in the HT-29 cell line will be measured using ELISA assay. Later, the capability of a single freeze-dried strain in attenuating the IL-8 levels produced by HT-29 cell line will be assessed.  

Caco-2 cell line will be used to measure the effect of the microbiota samples collected from M-SHIME(R) on the barrier integrity of the Caco-2 (enterocyte) monolayer. The integrity will be assessed by measuring the TEER (transepithelial/transendothelial electrical resistance) of the cell monolayer, and the results will tell us if our strains can alleviate leakiness in the epithelial cell layer caused by dysbiosis. 

 

HT-29 cells under a microscope. 

 

Starting my research 

So far, I’ve read lots of literature related to the gut microbiota and treating inflammation with probiotics and next-generation probiotics. This has given me a good foundation on which to build my knowledge. The steps using M-SHIME(R) human gut simulator have been completed previously, so I’ve mainly been growing the intestinal cell lines required for our experiments. Luckily, I already have some experience with cell culture, so the start hasn’t been too difficult. My group has also been supportive and helpful, so I’m optimistic about the upcoming months! 

 

Seeding HT-29 cells for our experiments. 

 

The next step will be starting the IL-8 induction experiments, and once the initial results are ready, we can proceed to plan further. If you’re interested in our results, stay tuned for my next blog post! 

 

Sources: 

Bastos AR, Pereira-Marques J, Ferreira RM, Figueiredo C. Harnessing the Microbiome to Reduce Pancreatic Cancer Burden. Cancers (Basel). 2023 May 5;15(9):2629. doi: 10.3390/cancers15092629. PMID: 37174095; PMCID: PMC10177253. 

Kouzu K, Tsujimoto H, Kishi Y, Ueno H, Shinomiya N. Bacterial Translocation in Gastrointestinal Cancers and Cancer Treatment. Biomedicines. 2022 Feb 4;10(2):380. doi: 10.3390/biomedicines10020380. PMID: 35203589; PMCID: PMC8962358. 

Martín R, Langella P. Emerging Health Concepts in the Probiotics Field: Streamlining the Definitions. Front Microbiol. 2019 May 21;10:1047. doi: 10.3389/fmicb.2019.01047. PMID: 31164874; PMCID: PMC6536656. 

 

Some literature: 

Berta Bosch, Saliha Moutaharrik, Andrea Gazzaniga, Kaisa Hiippala, Hélder A. Santos, Alessandra Maroni, Reetta Satokari. Development of a time-dependent oral colon delivery system of anaerobic Odoribacter splanchnicus for bacteriotherapy. European Journal of Pharmaceutics and Biopharmaceutics. 2023; 190. 73-80. https://doi.org/10.1016/j.ejpb.2023.07.010. 

Cristofori F, Dargenio VN, Dargenio C, Miniello VL, Barone M, Francavilla R. Anti-Inflammatory and Immunomodulatory Effects of Probiotics in Gut Inflammation: A Door to the Body. Front Immunol. 2021; 26(12):578386. doi: 10.3389/fimmu.2021.578386.  

Marzorati M, Van den Abbeele P, Bubeck SS, Bayne T, Krishnan K, Young A, Mehta D, DeSouza A. Bacillus subtilis HU58 and Bacillus coagulans SC208 Probiotics Reduced the Effects of Antibiotic-Induced Gut Microbiome Dysbiosis in an M-SHIME® Model. Microorganisms. 2020; 8(7):1028. https://doi.org/10.3390/microorganisms8071028 

 

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.

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.

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.

References:

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.

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.

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: https://blogs.helsinki.fi/hilife-trainees/2023/06/26/my-battle-against-rnases/

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.

 

References

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. https://doi.org/10.1093/nar/gkz011

Delaunay, S., Helm, M., & Frye, M. (2024). RNA modifications in physiology and disease: towards clinical applications. Nature reviews. Genetics, 25(2), 104–122. https://doi.org/10.1038/s41576-023-00645-2

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. https://doi.org/10.1074/jbc.REV118.002982

Lauman, R., & Garcia, B. A. (2020). Unraveling the RNA modification code with mass spectrometry. Molecular omics, 16(4), 305–315. https://doi.org/10.1039/c8mo00247a

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. https://doi.org/10.3390/biology3040670

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. https://doi.org/10.1016/j.molcel.2021.12.007

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.

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.

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.

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.

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.

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.

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. https://doi.org/10.1039/D0FO02324H

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. https://doi.org/10.1111/nph.16394

Robinson, J. M. (1990). Lignin, land plants, and fungi: Biological evolution affecting Phanerozoic oxygen balance. Geology, 18(7), 607–610. https://doi.org/10.1130/0091-7613(1990)018<0607:LLPAFB>2.3.CO;2

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.

Conclusion

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.

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.

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

Reflections

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: https://helda.helsinki.fi/items/c29c4de9-f1b7-4ecc-89de-041820cac57b

                   

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!

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).