Category: General

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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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When puberty hits you

Hi all,

My name is Linda Helena Müller and I am writing to update you on my HiLIFE Research Traineeship. During the last six months, I have been working on puberty research in the Raivio group at Helsinki University. The time flew by and I am excited to have successfully finished my Master’s thesis project recently. In fact, I just submitted my thesis last month. I used the HiLIFE scholarship to explore a field of research I have not been in contact with before. In my project, I worked in the area of stem cell research and neuroscience. Specifically, I have used the CRISPR/Cas9 system to activate a gene associated with puberty initiation. The traineeship allowed me to improve my skills in the fields of genetics and cell culture. However, I have also learned a lot about other stem cell research areas by attending talks and a retreat of the Stem Cells and Metabolism Research Program at Helsinki University. I am glad to report that the HiLIFE Traineeship completely fulfilled its purpose of exploring a research curiosity of mine.

Being at the end of my Master’s degree, I am now sure that I want to keep following the academic career and enroll in a PhD program after graduation. This traineeship and the methods I have learned were a tremendous help in getting into the PhD program of my choice. I will start my PhD at the EMBL institute later this year and continue in the same research field. Therefore, I am highly thankful to have been chosen as one of the HiLIFE trainees. This research period greatly helped me to orientate on what field I would like to keep working in and allowed me to learn important methods for doing so.

Aside from the academic part, performing this traineeship also gave me the opportunity to further experience life in Helsinki. I have fallen in love with the city and was thrilled to attend this year’s Vappu celebration since it was canceled last year. I even fried Munkit with the help of a Finnish friend. I also added my favorite picture of the Helsinki city center which I took on the night of the Lux light festival – check it out below. I am sad to leave Finland, however, the last months have been an excellent ending to my Master’s studies in Helsinki.

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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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Human stem cells and puberty

Hi everyone,

I am Linda, a second-year Master’s student in the program of Genetics and Molecular Biosciences at the University of Helsinki. As one of the 2022 HiLIFE Research Trainees, I am very happy to be able to follow my scientific curiosities in the upcoming months. I applied for the HiLIFE Research Trainee scholarship to gain experience in the field of stem cell biology and cell culture, and I am excited to have found a suitable opportunity for this in the Raivio lab at Biomedicum. I have recently started working on my thesis project. Within the following months, I will learn more about the genetic and hormonal regulation of puberty initiation. The Raivio group is specialized in the differentiation of human pluripotent stem cells into GnRH-releasing neurons, which are crucial for puberty induction.

My study background is in Genetics and Genomics and during my thesis project, I will gain more practical experience in related methods such as cloning, gRNA design, and using the CRISPR/Cas9 technology. My general goal is to activate the expression of target genes associated with puberty. However, I am also thrilled to learn about new techniques and expand my skill set in the upcoming months. Especially, stem cell biology, cell culture, and neurobiology are fields I am excited to get in touch with. Also, during my first weeks working in the lab, I was able to attend the STEMM Research Program Retreat which has been a new and exciting experience for me. It helped to find out what the current hot topics in stem cell research are and to learn more about ongoing projects of different labs. Additionally, it was also a great opportunity to socialize with colleagues.

After working in bioinformatics from home during the past year, I am highly excited to be able to visit the campus and lab on a daily basis now. Despite the pandemic, I can conduct experiments and exchange ideas with other members of the team. I am very thankful for the support I was awarded with by HiLIFE, as well as for the position I received in the research lab. I am hoping to learn and develop skills for my future career, but also to enjoy my time at Biomedicum. You’ll hear from me again soon.

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Six months later. A brief reflection.

Arriving at the Baraban Epilepsy Research Laboratory typically involves either climbing eight flights of stairs or waiting an unsettlingly long time while the elevator, long overdue for repairs, shudders its way to the desired floor. My lethargy usually precludes expediency, and I regularly find myself squished in at the back of the enclosed container. On the plus side, the elevator talk is often entertaining; grumblings over the embarrassment that is the elevator, this effectively lightens the figurative load.

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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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Thinking about thoughts – my Cambridge Neuroscience experience

Text by Nejc Kejzar – HiLife trainee 2019

A sense of profound stillness settled upon me when I first set foot onto the cobbled streets of Cambridge. While gazing down Trinity Lane (pictured above), the scene momentarily took on a sephia tone as I was transported into the past. Some in animated conversation, others lost deep in their own thoughts, the scientific greats came streaming past me. There went James Clerk Maxwell, formulating the unification of electricity and magnetism in his mind. Niels Bohr arguing with Max Born over the best representation of quantum mechanics, timidly observed from the side by Paul Dirac, keeping his own to himself. Stephen Hawking playfully teasing the unphased Isaac Newton to try and reveal the gravitational secrets of black holes, followed by Alan Turing wondering just what makes their conversation distinguishable from machines. This surreal procession, stretching over hundreds of years and across disciplines, made me realize to what a special place I have arrived and that it is now my time – as Newton put it – “to see further by standing on the shoulders of Giants.”.

In Cambridge, emerald green grass is never far away from gothic architecture. This interwoven combination gives the whole town a studious feeling, which I used to my advantage on many a walk – there is nothing quite like retracing footsteps of great thinkers of the past and present to help solve a difficult problem of your own. Although fairly small in size, Cambridge contains many hidden alleys and secluded spots, creating a scholars’ paradise. What is more, the University permeates every street corner, lane and building. In fact, what makes Cambridge so special is that in a way, the town itself is the University. Departments, colleges and libraries from centuries past rub their brick shoulders with modern restaurants and bookstores. While one door might deliver to you a pint of London Stout shared with fellow intellectuals in the cosy athmosphere of one of 110 pubs, the neighbouring might open to reveal the interior of a physics’ lab – which, judging from an impressive number of novel discoveries streaming from Cambridge, is a rather harmonious relationship. It goes without saying, that the whole package has quite the Harry-Potteresque feel to it – after all, Hogwarts was inspired by dining halls, chapels and traditions of the University colleges. One of the formal dinners that I got to experience in Trinity College great dining hall (below) is a particularly fond memory – short of the floating candles and headless ghosts, I was hard-pressed to tell the difference from the Start-of-Term Feast at the School of Witchcraft and Wizardry. Regardless of whether you are a “Potterhead” or not, the subtle magical feeling is undeniable.

 

Whilst in Cambridge, I conducted my Master’s Thesis research in the Neurobiology Division of MRC Laboratory of Molecular Biology. Nestled among flowering fields (above), the imposing structure houses state-of-the-art laboratories and the highest concentration of experts in their respective fields that I have encountered to date (including 2 out of a total of 16 Nobel Laureates originating from this institute – casually saying “hi” to a passing Nobel Laureate on your way to morning coffee is quite an experience). The significance of the previous sentence with respect to the HiLIFE Trainee Scholarship cannot be overstated. Thanks to this scholarship, I not only got access to immense research resources, but could also closely interact with leading scientists. Being able to knock on a door instead of writing an email, awaiting a doubtful reply, makes a world of difference.             

My main focus here was studying the dynamics of AMPA receptors using molecular dynamics simulations. It is in part thanks to these receptors that we can learn and form memories. Therefore, in essence, I spent most of my time thinking about AMPA receptors using my AMPA receptors – quite an amusing thought. But the research I conducted in Cambridge is for me personally of greater importance still – it is through my research that I became involved in the Cambridge Neuroscience community and discovered my passion – merging the studies of artificial and biological intelligence. Prior to arriving at Cambridge I was not quite sure about where to take my career after graduating from Helsinki, but thanks to this experience, my future path is set and is looking as exciting as ever!

Alas, my 7 months in Cambridge have been gobbled up by the enigmatic Chronophage of the Corpus Christi clock. This has truly been an enriching experience and it is now up to you, my dear reader, to apply for HiLIFE Trainee Scholarships. For myself, the good-bye is only temporary, as I shall be returning to this enchating little town in October to start my PhD in Neuroscience, working on our brains’ internal GPS system!

 

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A Student Perspective on Y Science, an official side event of Slush 2019

Y Science – what’s that?

Every year, for a few days during dark Nordic winter, Slush gathers tens of thousands of changemakers and turns Helsinki into the epicenter of business and start-up stories. Y Science is one of Slush’s official side events, where the Life Sciences meet the entrepreneurial world. 

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A love letter to Oxford!

 

A city abundant with history, science and beauty. And some weird type of magic that is hard to put into words. That was my first impression of Oxford in August when I first arrived, and now after finishing my HiLIFE Traineeship here, the feeling has not changed. Except that I now know that here history is not left in the past but it’s present every day when you study in a library built in the 14th century or participate in ceremonies that have stayed intact for centuries. Also, science and learning are not hidden in big buildings away from the city but are instead scattered all across the town, with colleges and departments found behind every street corner. Here, the university is everywhere.

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