Category: biology

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

Hello!

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!

Cheers,

Rupesh

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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.

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

Hello!

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!

Rupesh

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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 ( https://www2.helsinki.fi/en/researchgroups/evolution-sociality-behaviour/information-ecology-co-evolution ) 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!

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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!

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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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