Gabi goes exploring… Kenya!

Jambo! I’m Gabi. Currently a second year masters’ student of the Integrative Plant Science programme. In January I went on a three week expedition to Kenya, far from the Finnish winter, to participate in two field courses. Together with my fellow students we followed various experts around to learn about the natural world in Kenya. In my first week I went with aspiring botanists to the Taita Hills research station in South East Kenya. Where the collaboration between the University of Helsinki is most apparent when you stand in front of the small but expertly built sauna, which seems oddly out of place in the mountainous region of Kenya. In the second and third week I went traipsing through the Kenyan savannah learning about human-wildlife conflicts under the guidance of three seasoned conservationists.


Week 1 – The secret life of botanists

What do botanists do? They look at plants. And that is exactly what we did. Adorned with a hat and lathered in sunscreen, we hiked up various hills and mountains stopping every 2 to 3 metres to admire any photosynthesizers, both big and small. The forests hold a wide range of unique plants, from the small Commelina benghalensis with its blue petals to the tall Newtonia buchananii tree with its sturdy buttress roots that support an impressive trunk reaching far above our heads. 

Taita Hills is an important water catchment area. Water captured here supplies large areas of the country. Therefore, changes that occur in this area have far reaching consequences beyond the local towns. Due to the persisting drought people are forced to seek resources from the forest. Human disturbances include collecting firewood and harvesting plants for livestock fodder. On Mount Vuria, one such harvested species is Dracaena afromontana. Few individuals remain in areas that used to foster an abundance of the narrow stemmed shrub with its long and slender leaves. Besides this, the spread of introduced species such as Lantana camara presents a real nuisance. They will sprout back when they are cut down and are fire resistant.

There was a clear distinction between forests that had a high human disturbance compared to relatively intact forests. In disturbed forests we encountered more non-native plants, such as Eucalyptus spp. and Grevillea robusta, both from Australia. They are important sources of timber. Yet, in these arid regions, Eucalyptus trees are considered problematic for forest diversity. As part of its ecology, a Eucalyptus tree sheds its bark, which increases the risk of wildfires and their spread. Moreover, its leaf litter changes the soil pH to become more acidic, which favours its own propagation, but disadvantages local species. 

Aside from visiting the forests, we were invited to Darius’ farm, one of our field guides. His sloping plot of land left us in awe. He implements different intercropping strategies and combines improved and traditional crop varieties; the former for the yields and the latter to maintain a diverse gene pool. His approach is in stark contrast with the large monoculture plantations of sisal (Agave sisalana). Originally from Mexico, this fibre crop has been planted in rows as far as the eye can see. We drove past kilometres of saw-edged rosettes that have replaced native trees, shrubs and herbs.

After a week of vigorous hiking and plant inspecting, we ended the course with a feast and a bonfire. We said farewell to our field guides, the station staff and Taita Hills. With the first week behind me and the second week about to start the focus of my expedition shifted from flora to fauna.

“What I see vs. what the plant sees”


Week 2 – Putting the wild in wildlife

All facts are fun but some are more fun than others. Did you know that cheetahs have non-retractable claws? They are so fast that they need maximum grip when chasing prey. Did you know that the aardvark is closely related to the elephant? After spending two weeks with animal enthusiasts I’ve stocked up on some of these fun facts. The one I want to share most of all is the propeller tail of Africa’s most dangerous herbivore, the hippopotamus.

While defecating hippos will swing their tails energetically. In the water this results in an even distribution of nutrients, which is appreciated by fish and other aquatic organisms. By bringing nutrients from terrestrial to aquatic systems hippos fulfil an important ecological role, one that fishermen value in particular. On land, this Jackson Pollock technique is used to mark their territories and, unintentionally, to entertain the two jeeps packed with ecology students. They are very territorial and males will fight savagely to defend their patches of land and water. I don’t recommend getting caught between one of these grim neighbour disputes. Conflicts between humans and hippos arise when humans unknowingly cross paths with hippos. Hippos will not shy away from confrontation and running away won’t do you much good as they have no trouble keeping up. 

You may already know that vultures are excellent scavengers. But did you know that vultures have great vision too? While gliding in the air they will keep an eye on their peers. If one swoops down, having spotted a recently deceased or dying animal, others will follow suit. So where there is one vulture there will soon be dozens. Due to a very acidic stomach (pH ≈ 1), they are resistant to various diseases, even anthrax. Sadly, they are experiencing drastic population declines, in large part because of secondary poisoning. This happens when people poison livestock carcasses in retaliation against carnivores such as lions, leopards and cheetahs. As vultures have a slow reproduction rate, individuals that die are not readily replaced. 

Continuing with this more sombre side of these ‘fun’ facts. When giraffe calves are born they drop from a height of 2 metres. In rare cases, calves die from that impact. Last one. Spotted hyenas have a very curious social hierarchy. Mothers can raise up to two cubs which are born with their eyes open and their pointy teeth already poking out. Soon after birth they fight for the position of dominant cub. The outcome of these first contests determines their social standing and impacts many aspects of their life.


Week 3 – Caught in the middle

In addition to learning about animal ecology, we set out to shed some light on the issues that arise when animals and humans meet. We wanted to learn from the locals how certain species cause conflict and what is being done to mitigate these issues. The communities we visited live in close proximity to wildlife. While most locals appreciate the animals and understand their role as a high-profit tourist attraction, large carnivores endanger livelihoods by killing goats and cattle. In contrast to Europe, where we have food security, in these parts anything that threatens people’s livestock poses a serious risk for survival. Therefore, it is not surprising that these attacks lead to retaliatory killing of carnivores. Indubitably, as conservationists we would prefer the animals to be spared, but it is rather arrogant to tell the locals that they should not defend their livelihoods. Frequently, farmers and pastoralists lack resources and know-how. Hence, conservation efforts often focus on showing locals how to better protect their livestock by fortifying their enclosures. Efforts also include informing them on the ecological consequences of poisoning carcasses and retaliatory killings. More controversial methods include building electric fences to keep animals in or out of certain areas. 

However, conservation is not as straightforward as a conflict between farmers and animals. There are many different stakeholders with their own interests that do not always align with the preservation of wildlife. Besides local subsistence farmers or pastoralists, you have landowners that determine who has access to the land and usually cater to the tourism industry. Not to mention the governmental bodies that make land use policies and add a layer of bureaucracy. On the other side, the integral part of this web is wildlife itself. They require space, which is encroached by the growing population and changes in land use. In the middle you will find the conservationist that is trying to consider the stakeholders while safeguarding the needs of wildlife. In many cases, rather than being a human-wildlife conflict it turns out to be a human-human conflict.

“I spy with my little eye…”


All in all

It has been an invaluable experience, both culturally and academically. I’ve been enriched by the colourful welcome from the Maasai and Turkana tribes in Leikiji, the banter of the field guides in Taita Hills and the remarkable endemic flora and fauna of the African savannahs. Many thanks to both the IPS and EEB master programmes for offering these precious field courses IPS-175 and EEB-306. Thanks to the HiLIFE Trainee Conference Grant that has eased the financial burden of this three week venture. And thank you reader for reaching the end of this condensed retelling of my African adventures!

Gabriela Lemoine

The elephant in the room: Human-Wildlife Conflicts

There are things you cannot truly learn by just reading about them. You can get acquainted with the concept, but if you want an in-depth understanding of it, you need to get rid of the distance and the intermediate messengers and go observe directly with your own eyes. As a biologist, I’ve acquired most of my scientific knowledge by studying. Now I’m studying a MSc degree in Ecology and Evolutionary Biology at the University of Helsinki, where I’m doing very variated courses that allow me to learn both about the underlying ecological and evolutionary processes that shape nature as we know it, as well as the current climate and biodiversity crisis and what can we do to stop it. I’m now getting more and more interested in the branch of conservation and applied science, which involves a human and social dimension. The required degree of empathy and comprehension in this area is hard to get if you are distanced from the environment and situation.

I recently had one of the most insightful experiences of my life. With the help of the HiLIFE conference grant, I went to Kenya for two weeks to take part in a course about human-wildlife conflict (HWC) in East Africa, which is part of my MSc programme and was organized by one of my teachers, Mar Cabeza. Before leaving, I had to prepare a brief presentation about one of the most conflictive species in the area: the African elephant. I talked to my mom about this presentation, and she was honestly surprised: “How can such a kind, smart and nice grass-eating animal be the source of conflict?”. My mom loves elephants, it would be a dream for her to see one in the wild. I love them too, of course, and I know they are essential for their ecosystem, aside from being beautiful. I could observe them in Kenya and it was a magical moment that I will never forget. But what I will also never forget is what we heard when we asked local people about them. “I like all animals, but I’m terrified of elephants”, a girl said.

The views from our campsite. On the other side of the fence, we could see giraffes and elephants


As a key part of the course, we organised focus groups and interviews with local people to hear about the HWC first-hand. This girl had some scary experiences with aggressive elephants that she couldn’t just forget about. Even though we had seen electric fences targeted at elephants all over the region, they are strong and smart animals, and they keep finding ways to trespass them. The risk of having a face-to-face with an elephant is high enough to have the population concerned. And this is not even the major source of conflict with elephants. These animals cause huge losses by crop raiding and infrastructure destruction, especially water structures like dwells. Droughts like the current one in Laikipia force animals to search for water and food in human settlements, so these incidents become more frequent. In communities with a subsistence economy, this is a serious threat to the population. Situations like this one increase tensions between the people and the wildlife and are counterproductive for conservation.

Some colleagues (and me, bottom-left) and local people participating in one of the activities during the focus group


At the same time, elephants might not be very happy about some human activities, I thought. Elephants migrate long distances, so when they find an obstacle impeding this movement, it’s logical to think they will try to overcome it. They can’t just decide to stop a behaviour shaped by evolution over thousands of years just because lately humans are building and expanding more than before. In Laikipia, several landowners have built elephant fences around their huge properties, often the elephants being more of an excuse than the actual reasons. Conflicts between different stakeholders (including farmers, nomad shepherds, ranch owners and private conservancies, among others) over the uses of and rights over the territory play a big role in determining the placement and extension of the fences. Consequently, the design of this alleged solution to HWC attends very little to what is actually needed, and, predictably, it fails to prevent any conflict. This doesn’t mean that elephant fences are useless. Maybe the small village we visited would be a safer place if it was surrounded by an elephant fence. Unfortunately, effective solutions are not usually that easy to implement.

The landscape at the community we visited in Laikipia


It is very easy, from a distance, to oversimplify conflicts like this one, where we search for “good” and “bad” characters among the stakeholders. There will always be interests with which we empathize more or less and that can lead us to mistakenly think that some perspectives or opinions are less relevant or not worth taking into consideration. As biologists, we have a tendency to talk about the relevance of conservation from an ecological point of view. It is a truth that elephants are ecosystem engineers and that they play a huge ecological role. Without them, the savanna wouldn’t look like it does, and all surrounding species would be affected in an unpredictable but guaranteed chain effect. We know we need to conserve elephants, that is our position as scientists, and we see this as such a big truth that we sometimes forget to consider other needs. But conservation is an essentially human discipline: we decide to conserve, what to conserve, when, where and, maybe most importantly, how to do it. It attends to our needs, it comes from us, and ignoring how people are affected by it would be a mistake.

The elephants we saw in front of our campsite, seen through my binoculars


“The people that are less to blame for global change are the ones that are suffering the worst consequences”

This is something one of our teachers said, and in this course, it stopped being just an idea that I heard. It became a reality that I could see with my own eyes. I got to see the dry landscape, observe the wildlife, hear about the conflicts from the locals and discuss and put together all the information we were receiving. Altogether, this course has reshaped my way of seeing conservation and completely changed my perspective. And I think this new point of view will make me a better scientist and conservationist in the future.

This has been, in a nutshell, and leaving many things out, my experience in this amazing course. Thanks for reading me! And thank you to HiLIFE for helping me join this course.

Lola Fernández Multigner

Extracting knowledge from flow cytometry data

Hi there, and welcome to the HiLIFE-Trainee blog! I’m Olivia Dreilinger, a second-year Master’s student in the Genetics and Molecular Biosciences program here at UH.

This winter I participated in Physalia’s course on Flow Cytometry Analysis with R/Bioconductor. The course was held digitally to facilitate a greater geographic range of students. Throughout the course, in addition to the lectures and coding sessions, I was able to interact with researchers and PhD students from all over the world. This made for an exciting learning environment. The conversations I had with the other participants about their work and career paths were especially inspiring.

And now, let me tell you a little more about flow cytometry, how we can analyze this fascinating data, and how I will apply this new knowledge in my work at UH.

Flow Cytometry
Flow cytometry is a powerful tool that can sort a complex mixture of cells, often from blood or bone marrow or cells from solid tissue that have been separated from each other (dissociated) into populations of different cell types. This can be used to count the number of cells belonging to a certain type or for downstream investigation of the cells such as gene expression analysis or functional assays. It has applications in cancer biology, immunology, infectious disease monitoring, and numerous other areas of cell biology. Here’s how it works: one by one, cells are sent through a machine which uses multiple laser beams to “read” properties of the cell. The machine does this by measuring how light is scattered in the forward and side direction and indicates the cell’s size and complexity (granularity) respectively. Additionally, the flow cytometry machine can detect fluorescence, making even finer distinctions between cellular subpopulations possible. Cells can be made to express fluorescent markers through staining, thus allowing for this higher level of resolution.

Once the cells have been sorted, the flow cytometry instrument returns a file regarding each cell’s fluorescent intensity with respect to each marker used. This data must then be analyzed in order to extract meaning and identify different cell populations, thus allowing for downstream research and diagnosis by comparing measures such as number of cells or mean fluorescence in each subpopulation of cells.

[Flow cytometry schematic. Cells are sent through the flow cytometry instrument one by one. The machine detects their properties and sends them to a computer for analysis. The cells can be separated by type for downstream analysis. Created with]

Data Analysis
The trainee course I took focused on the step of turning the fluorescent intensity data into something meaningful about different cell populations. The first crucial step is preprocessing, which includes compensation, transformation, and cleaning—basically, the data needs to be tidied up for ease of use. Once this house-keeping task is complete, we can move on to the part we care about, namely identifying the cell populations.

The flow cytometry data can be displayed on a two dimensional plot with each axis representing the fluorescence of a given marker or how much light is scattered in a certain direction. The cells then cluster by type depending on their properties. Traditionally, these cell subpopulations were identified by eye and circled in a process called manual gating. This process can be repeated over and over again comparing different markers giving a complex gating strategy. The gating process can be automated with software packages in R such as FlowDensity and FlowSOM. This strategy looks at density of cells and uses it to determine the cell populations.

[A gating strategy for identifying cell populations. Here we can see the step-wise identification of cell populations, beginning by first identifying live cells, and then distinguishing which cells are lymphocytes from the other cells. From there, the gating strategy separates the cells that are granulocytes and continues finding subpopulations from those that are not granulocytes, and so on, using the properties of the light detected by the flow cytometry machine for each cell. Figures generated in Physalia’s Flow Cytometry Analysis with R/Bioconductor course, 2023.]

Current Research at UH
The Integrative Evolutionary Biology lab, where I am doing my thesis, uses flow cytometry to identify and investigate different types of color cells (or chromophores). We study cichlids which are tropical fish native to lakes and rivers of India, Africa, and South and Central America. There are thousands of different species of these fish with distinct and vibrant color patterns making them an exciting model system to study when it comes to the evolution of cell types and the composition of these fishes’ colorful skin. As shown below, there are a number of different chromatophores: melanophores which are dark in color, iridophores which appear iridescent and blueish, and xanthophores which are yellow. We are using flow cytometry to study the composition of cichlid skin across different species within the Cichlidae family. I’m excited to start applying what I learned in this course to our data.

[Images of the color cells (chromatophores) we are studying in cichlid skin. A) dark dendritic melanophores, B) iridescent, blue iridophores, and C) a close-up of a dendritic yellow xanthophore. Credit Alexandra Faur, Integrative Biology Lab.]

I am grateful to HiLIFE for awarding me the HiLIFE Trainee Conference Grant and to the Integrative Biology Lab for making it possible for me to participate in this excellent course, which deepened my knowledge of flow cytometry, and provided me with the tools to find meaning in this kind of data. I look forward to utilizing this technology in the future.

— Olivia Dreilinger

Reflecting on the journey so far and embarking on a research career


This is Rupesh with another blog post to provide an update on what happened during and after my traineeship. You can find my previous post here. It took me a little longer to write this post than promised, but here we are!

Let me start with a short recap: For the traineeship, I worked on my MSc thesis under the supervision of Dr. Ilona Rissanen and Prof. Juha Huiskonen at the Institute of Biotechnology in the University of Helsinki. My thesis was on a project aimed at discovering the structural basis of SARS-CoV-2 neutralization by the antigen-binding fragment of an antibody that was derived from a COVID-19 patient. We can understand how the antibody manages to neutralize the SARS-CoV-2 virus by figuring out where it binds to the spike protein. The antigen-binding fragment, as the name suggests, is the part of an antibody that recognizes and binds to the antigen. In order to find out the epitope of the antigen-binding fragment, I employed single-particle cryogenic electron microscopy (cryoEM). I was able to hypothesize the neutralization mechanism based on the location of the epitope and the subsequent analyses of it.

During the traineeship, I got to learn some cool techniques involved in studying a protein through cryoEM, right from sample preparation to processing the collected data. I would like to highlight a moment during my thesis work, when I got to see how the spike protein looked like in 2D in the early stages of processing the data. It was stunning to see the proteins I had expressed on the computer screen!

But the main takeaways, in my opinion, were the discussions I had with my supervisors and other lab members on how to troubleshoot experiments and interpret the results. That was where I got to understand how to approach science and the problems that arise in these projects. I found these discussions, both formal and informal, to be highly beneficial to my development as a researcher. Writing my thesis was another area where I found myself constantly learning and applying the knowledge to put the big picture together. It involved reading a lot of research articles, which was not an easy task but once I got into the thick of it, I was surprised to notice how fulfilling it was. Staying on top of current research in the field does feel good.

My thesis work had come to an end right after the traineeship period ended and it was time to submit my thesis before the academic year came to a close. As part of graduation requirements, the Genetics and Molecular Biosciences (GMB) master’s program provides the opportunity to present our thesis work during the annual GMB master’s thesis symposium. It was the first time I got to be a part of an in-person symposium in a very long time. In fact, it was the first time I got to see most of my fellow students in the program. All of us presented our work with great enthusiasm and held passionate discussions. It was a good experience to present my results to an audience with varied background and to also listen to talks on different lines of research that my colleagues were working on.

I graduated from the GMB master’s program a couple of months ago and I am incredibly thankful for having the opportunity to work in the research groups of Dr. Rissanen and Prof. Huiskonen. A huge thanks to HiLIFE for supporting me during my thesis. The traineeship resulted in a series of wonderful events which would go on to help me build myself as a researcher and for this, I am grateful!

As for the present, I have recently started to work as a research assistant with the same research groups where I’m hoping to enrich my skills even further before I embark on the journey towards a PhD next year. I’m cherishing this phase of my life where I get to do cool science surrounded by an awesome community, long may it continue!



Presenting your own work allows a chance to network!

What an experience!

Truly the HiLIFE traineeship period has given me so much, not only in experiences but in chances to grow and develop as a person. I have managed to collect behavioural data on reed warbler incubation (see my previous post, on to fear or not to fear) and submit my thesis for evaluation. Although in the researching world there is always something that can be polished off and rewritten, I am confident in the quality and standard of my work, thanks to the invaluable help from my supervisor and the research team. What amazed me the most was how helpful and willing others were to answer my questions, take time off their busy schedule to help me and provide me with constructive critique that helped me develop as a young researcher. These last months have left me a lot richer in skills and experiences.

Me presenting my poster at the Spring Symposium 2022.

During the last months, I had the chance to present my work in several varying setting with a changing audience and style of presentation. Although I managed to create interactive and engaging power points targeting different audiences, I must say the highlight was the poster session I got to attend. This was a part of the LUOVA Spring Symposium, organized by doctoral students, focusing on the research in ecology, evolutionary biology, and conservation. Here I presented my work to a wide audience, from fellow students to foreign researchers. The questions and constructive feedback I received helped me dive deeper into my work, and I could see new ideas taking shape through conversations I had with others. The cherry on top of the cake was that this gave me the opportunity to form new connections and network in the researching world, as well as glimpse at the current biology research that is carried out at the University of Helsinki.

Discussing scientific work with others gives a chance to hear other ideas on the same topic.

Although research is very individual based work and stems from personal interests, I learned the importance of sharing differing perspectives and ideas through conversation. As one starts to dive deeper into a topic, it may be harder to see the broader questions that arise from the work at hand. Discussing with others and brainstorming the overall impact of the topic provides a broad umbrella that allows the work to be applicable for several different research questions, as well as allows others to take the key aspects into account within their own research. This forms a web of support for the current research at hand. I am thankful to have been a part of a research group with individuals from various backgrounds, that provided diverse ideas and opinions that helped me build my research into the landscape of fear concept. As a young researcher, the help and support of experienced researchers is critical to navigate the field full of emerging questions. An extra special thank you for this to my supervisor, Rose Thorogood.

A couple of days ago an old professor told me that a few decades ago, research, particularly in birds, used to be dominated by one researcher. This meant that one researcher specialized on one species, and it was frowned upon if somebody wanted to study that species individually. I was surprised at this, and we had a very interesting discussion on why this was the case. We both agreed that research becomes richer the more people look at a similar species (or question) from their own personal angle. This provides more ideas and opportunities to form a diverse understanding of why we see what we see in nature. I really feel that my traineeship has allowed me to see this richness through working in a research group.

Having had the chance to watch experts within their fields navigate research topics, I realize there is a vast ground of knowledge to be consumed. I feel that some of these skills can be best gained in the working world, to understand what data is already existing and waiting to be analysed and pondered upon. We are very lucky to live in a society where the government supports museums and the upkeep of long-term data sets. However, these need to be actively utilized and inspected to determine what type of research is most beneficial for conserving nature and the ecosystem. I am ever so thankful for the HiLIFE traineeship that has supported me and my journey in experiencing the researching world. I hope that in my future, I can continue in the researching world and maybe even provide support to other young researcher someday, as I have been supported by the professors at the University of Helsinki and financially by HiLIFE.

A journey to understand SARS-CoV-2 neutralization through cryoEM


My name is Rupesh, and I’m a second-year master’s student studying in the Biochemistry and Structural Biology study track of the Genetics and Molecular Biosciences program at the University of Helsinki. I come from Chennai, a beautiful city in the south of India. I did my Bachelor’s in Biotechnology in Chennai and graduated with an engineering degree, B.Tech. For as long as I can remember, I have been drawn towards Molecular Biology and Biochemistry. And so, for my bachelor’s thesis, I worked in a virology lab at the CSIR – Centre for Cellular and Molecular Biology in Hyderabad, India. I thoroughly enjoyed my time there and developed an appetite for research, in viruses and molecular biology to be precise.

I started my master’s studies at the University of Helsinki in 2020, and in the very first semester, there was this one course which I really liked: GMB–105 Introduction to structural biology and biophysics. Being a part of that course felt refreshing and I still remember saying to myself, ‘When I have to search for labs to do my master’s thesis, I am going to ask the structural biology labs first’. And that is exactly what I did a few months back. I reached out to Dr. Ilona Rissanen and Prof. Juha Huiskonen who are working on structural virology and structural biology of macromolecules and interactions respectively. It was a fruitful attempt, as I got the opportunity to work on a short-term research project on the development of protein scaffolds for cryogenic electron microscopy (cryoEM) under their supervision at the Institute of Biotechnology.

Currently, I have just started working on my master’s thesis project, happily continuing under their supervision. My project is aimed at discovering the structural basis of SARS-CoV-2 neutralization by an antigen-binding fragment (Fab) from a patient-derived monoclonal antibody that targets the spike protein. I will use single-particle cryoEM to elucidate the molecular architecture of the Fab-bound spike protein trimer and identify the epitope of the Fab. The project benefits from a thriving collaboration with the iCoin consortium, funded by the Academy of Finland, which aims to isolate SARS-CoV-2 neutralizing antibodies from Finnish COVID-19 patients to further the research on virus inhibition by the humoral immune response.

I could not have asked for a better environment to guide me in carrying out this project. I got familiar with some of the techniques and protocols that will be used in my thesis during my short-term project. I hope to build on those skills and hone them even further, especially in making and handling grids for cryoEM.

I’m honored to have been chosen as a HiLIFE research trainee. The research standards are set incredibly high at the University of Helsinki, which makes this traineeship even more prestigious. With the support from HiLIFE, I believe I can do amazing science, learning from the experts. Hopefully, this is the beginning of an exciting journey in research!

I will be back later this spring to share some exciting results with you. Until then, take care!


To fear or not to fear: understanding the world of the Reed Warbler

Hi all!

My name is Sarella Arkkila and I am a second year masters student in Ecology and Evolutionary Biology at the University of Helsinki. I did my bachelor’s in Animal Behaviour at the University of Aberdeen and knew that this is what my passion lies in. Coming to the University of Helsinki, my search for a research group studying animal behaviour began. I found the amazing Information Ecology and Co-evolution research group ( ) led by Prof. Rose Thorogood and knew that this is where I wanted to continue my career within biology. I was honoured to be allowed to join the research group.

My thesis work is on the effect of the landscape of fear on the parenting behaviour of the Eurasian reed warbler. Landscape of fear (LOF) is how animals view their surroundings and the different risks associated within that surrounding. There are several factors that contribute to the LOF, such as the perception of the risk of predators and parasites. LOF in turn influences an animal’s behaviour in different areas of its habitat. For example, in an area where an animal perceives the predation risk to be higher, they may exhibit more vigilance behaviour. These changes in vigilance behaviour can influence foraging efficiency and parental provisioning, as the focus is on spotting and avoiding predation, which can ultimately affect an animal’s fitness. The study of LOF is crucial especially now that environments are changing rapidly, and where new pressures arise and the survival of species within their new or existing habitats are uncertain.

Within the concept of LOF, a few studies have been done on how changes in perceived risk of predation impact indirectly on fitness, but perceived risk of parasitism is yet to be tested. The common cuckoo is a brood parasite, laying its eggs in other species’ nests, one of which is the reed warbler. The reed warbler changes its behavioural defences when it perceives that it is at greater risk of parasitism by cuckoos. This behavioural change can either result from direct observations of seeing a cuckoo or from social information from neighbouring birds attacking a cuckoo in its nest. However it is unknown if this perception of greater risk of parasitism has indirect and long-term effects on behaviour, ultimately affecting the quality of parenting.

Looking for Reed Warbler nests within the reeds around Helsinki.

To understand the impact of the LOF from parasitism, I conducted fieldwork with the research group in the summer 2021. As part of another experiment, we manipulated the social information (SI) that the birds received about cuckoos by using model nests (previously collected nests), threats (painted 3D models), and alarm call playbacks. I then compared their ‘fear-type’ behaviour both during the presentations and afterwards to birds presented with alarm calls but an innocuous ‘threat’ (a teal), or to ambient teal calls as a control. I collected behavioural observations from video recordings at the nests, which gave me a ‘reed warbler’s perspective’ that could not be gained by observing the birds in person. To evaluate the long-term impact of the LOF, I then recorded parental behaviour 6 days later during incubation, and then again once the chicks had hatched.

A reed warbler incubating its eggs, a screenshot taken from an incubation video.

For my Master’s thesis, I have been watching a sample of these video recordings to determine how socially-provided information about parasitism risk influences behaviour. Thanks to the HiLIFE traineeship, I can now dive deeper into the videos to find out more about the longer-term effects of fear and publish a scientific article on the findings. I hope to be able to share the study results with you after this fantastic HiLIFE traineeship period. Wish me luck!

DNA, comets and shaky hands

Hi everyone!

My name is Piia Karhu and I am a first-year student in The Master’s Programme in Human Nutrition and Food-Related Behaviour at the University of Helsinki. I received a HiLIFE scholarship for the summer 2020 to work in a research project of my interest. I completed my research internship at the Viikki Molecular Nutrition group. The group studies the molecular mechanisms by which diets, foods and diet-derived compounds mediate their effects on health and prevention of non-communicable diseases. I was very happy to join this group as molecular nutrition is a very fascinating field of science. Here you can read more about Viikki Molecular Nutrition group.

During my summer, I was privileged to take part in the study that examines the impact of dietary habits on faecal water genotoxicity.  In the study, colonial epithelial cells were exposed to feacal water. Feacal water was extracted from stool samples collected during dietary intervention with healthy volunteers and the DNA damage created by the faecal water was examined. Purpose was to study whether there are differences in DNA damage of the cells when exposed to fecal water from volunteers that followed either plant protein diet, animal protein diet or diet that contains half plant protein and half animal protein. We measured the DNA damage using single-cell gel electrophoresis known as Comet assay. It is a commonly used and straightforward method for measuring DNA strand breaks in cells. The term “comet” refers to the leaked-out DNA of the cell as it often resembles a comet. The more intensive the comet tail is relative to the head of the cell, the more the cell is damaged.

microscope image of green cell comets
Here is an example picture of the comets

I had very interesting and mind opening summer job as I have never worked in this kind of project before. I acquired valuable experience working in the lab, especially in the cell lab and learned how to culture and handle cells. Working in a cell lab was a very nice experience even though it took a while before my hands stopped shaking! During my summer I gained a lot of practical experience, which will boost my confidence working as a researcher in the future.

I want to thank my supervisor Anne-Maria Pajari for this opportunity to work in her research group and Hana Slabá for excellent guidance during the summer. Also, I am deeply grateful to HiLIFE for supporting me, this was a very valuable experience!

Turtles, Herpes and Sunshine at Eastern Florida

If someone had asked me five years ago, I probably couldn’t have guessed that I would be spending my sixth year of veterinary studies thousands of miles away from home, sitting inside a lab with an air conditioning as enthusiastic as October winds in Helsinki. Yet there I was, soaked in the familiar smell of Clorox wipes, whirring tiny tissue bits through various machines in the slow spurring excitement of soon finding out something, even small, that no one else ever has before.

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