Half-time review seminar – thoughts on native lignin and personal development

In the beginning of a PhD student employment, an introductory meeting takes place where the student is introduced to the director of studies, the PhD administrator, and the HR team. During this meeting, I felt overwhelmed by all the information I was receiving but also excited about my new start. The concept of the “half-time review seminar” was explained to me back then and it seemed to be so far in the future. Two quick years later, the moment to have my seminar has come and it feels that my introductory meeting was only a few days ago.

The half-time review seminar is a requirement for doctoral students employed at KTH. The student presents an overview of the research so far, participation at conferences, courses completed, workshops attended, and so on. An important part of the seminar is the plan for future work. The evaluators and director of studies need to see that the student not only has been making progress in the first years but also that the progress will continue in the following years of the doctoral studies. Furthermore, the seminar is a great opportunity to evaluate if the workload of the student is bearable and if adaptations to the plan are required.

And just like that I realized that I am now half-way through my doctoral studies. That realization shocked me, as it means that two years from now I will give up the title “student”. This title followed me for about 22 years and soon I will no longer be associated with it. No more ECTS will be required of me, and my continuous learning will be driven solely by my own curiosity. Until now I always had a plan and knew what lay ahead. At least I had a pretty good idea. However, this next chapter of my life comes closer every day, as the defence of my PhD will signify the end of my current path of being a student. In front of me there is a sea of endless possibilities. Should I continue with a career in the academy? This work environment is very demanding but somehow also familiar. A researcher’s position in industry sounds intriguing too. Or should I start something of my own? After all I live in Sweden, an ideal country to found a start-up. The fact that I have so many options is proof of the great teachers and mentors I had all these years and especially during the past six months since I joined the CAZyme group. The support and bonding in this group is the perfect ground to grow, be creative, and dare to develop as a researcher.

A couple of weeks ago I faced my first public evaluation, during my half-time review seminar. I started my presentation nervously, with an introduction to the subject of my doctoral studies: native (i.e. natural, unmodified) lignin. Native lignin is an intriguing material, absolutely ideal to fuel my curiosity as a soon-to-be independent researcher. I initially decided to apply for this particular PhD project mainly because I was fascinated by the fact that gaps in fundamental knowledge still exist for the second most abundant biopolymer on Earth! Lignin is a major component of plants and yet so far, we have failed to quite grasp its native structure and many aspects of its biosynthesis. There are several factors that affect the structure of lignin, summarised in the image below. The plant species, cell type, and plant age are only a few. From my point of view, the complexity of the biomolecule’s nature is linked to one of its biological roles as a response to stress. By definition, trying to perform reproducible research on a molecule that can be provoked as the defence mechanism of a living organism cannot be an easy task! Sometimes I like to think of native lignin like a property in quantum mechanics; when we take a measurement the wavefunction collapses at the resulting value. The measurement method we choose to use has a specific influence on what is observed, and the two are inextricably linked. Similarly, as an example, an extraction protocol that is optimized to obtain high amounts of a specific bond within the lignin polymer might fail to give high overall lignin yields, meaning that only a fraction of total lignin is studied. This irony is inherent in classical methods of lignin analysis. We cannot avoid affecting the structure and chemical properties of a molecule that forms via radical polymerization, especially one that can rearrange its bond structure to defend the plant. The different extraction methods one can use have different yields and show variations in relative amounts of the lignin interunit linkages. The classical methods that are typically used to produce standard lignins are simply no longer good enough to answer the remaining fundamental biological questions about lignin. This is what motivates me in my doctoral work.

Lots of different factors can affect the structure and properties of lignin, including all of the natural phenomena mentioned here as well as the method we use to extract it for analysis. This last factor is the focus of much of my current research – I want to understand how we change lignin when we decide to study it! Figure made by Ioanna Sapouna using stock image photos.

After my presentation at the half-time meeting, the evaluators asked questions about my studies in general and about my research in specifics. My two evaluators were not from the same field, which gave me the opportunity to discuss lignin from different perspectives. The first one was an expert in extraction and valorisation of technical lignins. The discussion with her was focused on the experimental part of our previous work on extracting lignin, details like the yields and standards used for comparing our results to previous work. I was relieved to be able to easily answer these questions, and felt secure and confident because I performed the experimental work myself. The second evaluator was an expert in biotechnology. Being a chemist myself, I was nervous about being challenged on the biotech implications of lignin. However, during the discussion with him I had the opportunity and pleasure to express my thoughts about the versatility of lignin in the cell wall and the effect that has on its extractability. I couldn’t help but notice my personal development during these past two years. Before I started my studies I only had some basic knowledge about this molecule and here I am, two years later, developing my own ideas and hypotheses on its native aspects.

To be able to defend these thoughts and ideas is really a privilege gained by working with Lauren. It takes a Teacher to build a student’s confidence and help her move towards being an independent researcher, and Lauren surely is. Unfortunately, women in academia are still underrepresented and the importance of having strong female role models is greater than ever. I consider myself lucky to work in such an environment and to be inspired by strong women who thrive in science. After my half-time seminar I feel a stronger connection to my work and its significance to society. I aspire to complete my studies and be of service to the scientific community as a researcher and as a person.

A Summer at the Stockholm CAZyme Lab – Insights and Experiences

As students, there are definitely times when it is hard to see how all of the knowledge that you are gathering during your study period can be applied in reality. When you are getting towards the end of your studies, you can definitely start to feel confused about what you actually want to work with after graduating. It is difficult to choose a certain career path when it is not clear what the roads are that lie in front of you. As we are currently still master’s students, we are still eager to learn and get new experience. Therefore, this was a perfect time and opportunity for a full-time summer internship at KTH. We are Elin and Srijani, and here we will share our experience of summer work at the Division of Glycoscience.

We undertook a seven-week internship in Lauren McKee’s group at the laboratory, where both of us were working on different projects under different supervisors; He Li and Mengshu Hao. Elin was helping He Li with her post doctoral project on biomass hydrolysis, and Srijani was working with Mengshu on a project on sustainable polysaccharide hydrogel formation. Both of us mainly focused our work on protein production and purification, and further testing these proteins in necessary assays. Srijani was performing an assay named Pull Down Assay, which basically checked the potential for ligand-binding and hydrogel formation at room temperature. Elin was working on optimizing the production and purification of a few proteins, and also tried some temperature optimization in assays of the purified enzymes.

What could a work week look like? The week usually started with preparation for protein purification, which meant that we had to cultivate the over-expressing bacteria and everything that comes along with that. For instance, these preparations could be making litres of growth media, autoclaving culture flasks and as many pipette tips as you can fit in the autoclave, booking instruments/machines that are needed, etc. The proteins are produced by overnight bacterial cultivation, before the more fun (and stressful) experimental work could begin. On the first day of protein production, the bacterial cultivation was started, followed by induction by IPTG. On the third day we could finally start the purification. This included many steps, like sonication, a bunch of centrifugation, and affinity chromatography as purification method. We used SDS-PAGE to check the success of the protein production and purification. The purification and analysis done afterwards usually took a whole day, with addition of a couple more hours if we started concentrating the protein.

Hopefully after this we would have a good amount of protein on which the assays could be performed during the rest of the week. How did it go then? Well, at first things did go according to this schedule, but as with many things in life, they do not always go exactly as planned. It is common when testing the production yield and stability of new enzymes that several of the production steps need to be repeated or optimized to get them perfect. In some cases, if it got really late to be in the lab, we could postpone one task until later the same day or the next day, but in other cases (like when you mix the proteins up or have contaminated growth media) we had to start again from the beginning. 

When we started as research interns, we didn’t imagine that the greatest thing that the internship would teach us would not be laboratory skills but self-confidence and patience. There were many moments when we asked ourselves “What else could possibly go wrong!?” We definitely sometimes felt disappointed and disheartened maybe due to some failed experiment. What we learned from this was to own our mistakes, learn from them, and move forward without dwelling on the failures too much. In these times it was very helpful to have our supervisors there to guide us with their knowledge. These frustrating and unexpected experiences really shaped us and helped us learn from them and grow personally.

Our final message: it’s okay to shed some exasperated tears. In the lab, we know we can expect to face many moments where everything seems to be going wrong, and that we’ll feel every emotion that comes along with that. But then, we lean on our colleagues, we learn from our experiences, and we do everything possible to overcome the challenges before us. Everything may not go as planned, but we do everything in our power to make the outcome golden. Lastly, we would like to thank Lauren, Mengshu, Heli, and the CAZyme team for giving us this great opportunity and experience that will last a lifetime.

Reflections – Project work in the CAZyme group🌟

August 2021 has been my eighth month working with Lauren and the CAZyme group. It would be a lie if I say there has not been one time that I felt exhausted – what other kind of mood should one have when a just-autoclaved waste bag that is full of agar plates is leaking!? However, I genuinely enjoy every day, and every bit of progress that we have reached here in the biocontrol project.

At the very beginning of my time with the group, I was a master thesis student. From several interesting lectures Lauren gave in my program, Industrial and Environmental Biotechnology (starting Autumn ’19) at KTH, I was hugely intrigued by environmental biotechnology and its applications incorporating sustainability, such as agri-biotech, green food-tech, etc. The importance of microbiology in dealing with environmental contamination is another big aspect that cannot be overlooked. Among the various kinds of microbial application in environmental science and engineering, I have an interest in green agriculture, where the well-known downfall of large-scale commercialized production of crops has endangered the environment more and more drastically via over-fertilization, mono-species cultivation, over-irrigation, etc. Many of these issues have causal links to disproportionate chemical usage, and the abuse of pesticides as well as fungicides is another prime culprit.

Everyday our crop plants are fighting against pathogenic attack. For us to help them survive and grow, the most commonly used measure in this fight is for farmers and growers to apply chemicals to repel the invasion of pathogens. While this might lead to powerful short-term positive results, the tragic side effect lies within the soil, where the supposedly healthy microbial community is destroyed along with the pathogens, if the chemicals aren’t selective. The unbalanced soil consortium is then slowly losing its resilience to recover from the damage caused either by pathogens or chemicals. This is of course ironic, because the chemicals were supposed to be helping the plants!

The theme in green agriculture that I have investigated throughout my project is about “Biocontrol”. I work with a particular soil-inhabiting bacterium, C. pinensis, which is likely to interfere in the ability of pathogens to attack plants, thanks to its own pathogen cell wall-degrading potential. I try to amplify the growth of the bacterium and further mediate its secretion of pathogen-degrading enzymes. The enzymes secreted might be the key to unlocking an alternative to commercial fungicides.

Thanks to other master students and preliminary studies done in the CAZyme lab, I continued the C. pinensis project: I was in charge of testing for in vitro inhibition performance of the bacteria-derived enzymes against pathogenic oomycetes. The oomycetes chosen are ones that can attack plants and bring about severe crop diseases, for instance, root rot, blight, etc. I hope that in the near future you’ll be able to read a publication showcasing my data, but in short, I managed to boost bacterial enzyme secretion through supplementing different kinds of carbon sources in bacterial cultures. Up to now, combined with results from other team members, our hypothesis leads to quite a positive vindication – the carbon source provided and the enzymes henceforth secreted are certainly affecting the bacterium’s inhibition ability in a better than expected way. I won’t give you too much more detail for now 😉

To be able to play a part in this agriculture-related biotechnological research is a great pleasure of mine, for I am concerned with food justice, and to solve major agricultural issues with more sustainable methods is definitely an ultimate goal in the long-term food production scheme: A more recovered soil status means a more fertile/healthy growth condition for crops, which will eventually lead to a better yield in the hope of easing hunger problems. Of course, the issue of hunger is complex to deal with, and only one step forwards towards sustainable production is not enough. But why not see this as a positive step, showing we are heading somewhere, somewhere food justice is to be fulfilled little by little?

Though having had project experience back in my bachelor years, to conduct a research thesis project was an entirely new experience for me, let alone to have the opportunity to extend the project into a paid summer internship, significantly advancing my work through the summer following my graduation. I feel grateful for this chance, and for the advice I have gained from Lauren and all who have helped me in this journey.

Life in the lab feels a bit like working around the train schedule; there exist peak hours and off-peak hours. In the peak hours where several people are waiting to use the same equipment, we learn how to plan ahead better and how to find common benefits via efficient communication; during the off-peak hours, like when the precious summer sun comes out and says “Hi!”, we have the chance to calmly spend time in whatever our work is, listening to ourselves and appreciating the privilege of having access to knowledge. This is what higher education and a scientific career is for, I suppose, to repay what we have received from our teachers, by heading elsewhere to make new efforts in research. The train never stops.

The project is currently still going onwards with many endeavors. Thanks sincerely to Lauren and the CAZyme Group for welcoming and guiding me when executing the project. Even when I was sometimes unsure of which direction to follow in the project, the strong communication and positive working dynamics have never failed to give firm hands, gently assisting step after step. I am glad that I have contributed to some of the results. Let’s finger-cross for cheerful updates on the biocontrol project in the near future!

Welcome to our website!

Hello! We are the Stockholm CAZyme group, based at the Division of Glycoscience at KTH Royal Institute of Technology! We will be using this website to collate information about our group members and to share announcements about new events, publications, and updates on our work. If you want to learn about opportunities to join the group or collaborate with us, please see the Get In Touch page.

We are all passionate about complex carbohydrates like those found in plant and fungal cell walls: what do they look like, what are their properties, how are they made, and how can we use them? Feel free to browse around this site to learn more!

This site will be mostly maintained by me, Lauren – my biggest job is to make sure that everyone else on the team has what they need to do their work in an effective way. But other members of the team will be writing news updates as we progress, so stay tuned! If you wish, you can subscribe to this blog or sign up to get email alerts when we post something new.