Year in review – 2022

Leave a reply

This is Lauren writing our second annual progress report for the blog! Some ups and downs this year, but lots of progress as well. Heli and I attended the 14th Carbohydrate Bioengineering Meeting in Norway, and I presented our work both there and at a Treesearch Progress workshop in Sweden. Ioanna gave several presentations of her work, touring the lignin conference circuit as she prepares to settle in for the last year of her PhD. In some ways, getting people together was a main theme for the year, as we also managed to have our first proper lab Christmas party and Division Day since before the pandemic – lots of fun memories and photos!

A montage of photos taken at the KTH Glycoscience Division Day 2022. Also showing Ioanna and Lauren giving conference presentations.

Research

A big goal for this year was to publish data from the projects we have been working on for a while. So we worked hard to finalise the last few experiments for several projects, then to write up those papers, getting feedback from collaborators/co-authors, etc. There were several projects ready to be wrapped up simultaneously and the team has done a great job pushing multiple lines of research to completion! I am especially grateful to postdoc extraordinaire Heli for this, and to Alma, our former research engineer. As always though, these things took longer to finalise than hoped, so our papers aren’t out yet. But as I write this on December 30th, we have one paper accepted, two in review, and two ready to submit in the new year. I plan for a blog post discussing each paper as they are published.

Students

In the spring, two exchange students (Kasane from Tokyo Institute of Technology and Beatriz from Instituto Superior Técnico in Lisbon) submitted theses based on work they did with us in 2021-22. And in January we were joined by three KTH students on the Biotechnology Master’s programme who performed their final thesis projects with us: Emelie, Lova, and Vicky all defended successfully in early June! Emelie had been working with Ioanna on a green extraction procedure for lignin, contributing to our fundamental understanding of that important biopolymer. Meanwhile, Vicky and Lova were working with Heli on an enzyme discovery project, trying to figure out the impact of carbohydrate-binding modules on some enzymes from environmental bacteria. They stayed on as paid research interns through the summer, and generated a lot of excellent data in the process.

Theresa Schaufler from BOKU, Vienna, joined us in October with support from the Erasmus programme, to perform her Master’s thesis project in our group. She is performing the first life cycle analysis of our hydrogel biomaterial and will help us to optimise the sustainable process! I also supervised a group of five students for a project course on Biopolymers, and they helped us to understand the interactions happening in our protein-carbohydrate hydrogel system. Now we know a lot more about the properties the polysaccharide needs to have in order to work correctly in our cross-linking system.

A PhD student I was co-supervising, Salla Koskela, successfully defended her thesis in June, and it was wonderful that her supervisor Prof Qi Zhou, the examiner, and the whole defence committee were there in person. Salla’s work had focussed on enzymes called lytic polysaccharide monooxygenases and how they can be used to make nanocellulose, and you can read it at this link. Congratulations Salla! And thank you again for your important contributions to our polysaccharide hydrogel project.

This year I also really enjoyed taking part in several PhD defences, as I sat on two committees in Sweden, and was the examiner for Dr Hannah Gibson at Newcastle University, UK. Topics ranged from bacterial polysaccharide characterisation to the intricacies of CAZyme mechanisms, and all of the students were very impressive.

Photo taken by Dr Shennan Wang after the successful PhD defence of Dr Salla Koskela, third from left.

Recruitment

Our brilliant research engineer Alma Kvammen left us in July to work for an exciting company in Tromsø, Norway. Lova and Vicky were hired as laboratory assistants for three months over the summer, after finishing their respective thesis projects in the spring. I am happy to say that we are in the process of recruiting a PhD student thanks to financial support from the Wallenberg Wood Science Centre (WWSC). The application deadline for this position was a couple of weeks ago, and I plan to conduct the first interviews in January. In addition, I will be recruiting a post-doc for our hydrogel project in spring or summer 2023, so stay tuned.

Funding

This was a big year for proposal writing and we have had some notable successes, as well as a few disappointments. In early July, Heli was awarded 500 kSEK from the ÅForsk foundation for a new project on transglycosylating enzymes! We are using these funds to invest in some equipment that will speed up our enzyme discovery work. Around the same time, Ioanna was awarded two foundation grants to support her plant cell transcriptomics experiments. The awards totalled almost 200 kSEK, letting us cover the full costs of the project and related publications! As mentioned above, I was awarded financial support for a PhD project by the WWSC, and I’m excited to start this new line of investigation in 2023. New funds from the Carl Trygger foundation will be used to recruit a post-doc for the hydrogel project later in the year! As always, you can read details about all of our financing at this link.

Innovation

This was again a major focus area for me this year, and I have learned so much about the challenging journey of translating academic research into a commercial venture.

Working with my colleague Amparo, I completed the KTH Innovation Pre-Incubator Programme with our concept MycOligo. In a 12-month programme of seminars and workshops, we learned how to found a spin-off start-up company. We were awarded funds from KTH Innovation to conduct a market research survey of customer interest in our idea, and I’m looking forwards to seeing how far we can push MycOligo in the months and years to come. The photo montage below shows some highlights from our innovation journey, including Demo Day and presenting our idea to King Carl XVI Gustaf and Prince Daniel of Sweden!

My own early-stage start-up company Glycolink, of which I am the CEO, made some great progress this year. The biomaterial we are developing was recognised by the IVA as an important sustainable innovation, and in the autumn we received funding from the Vinnova research council in their Innovative Impact Startups programme! This is an important step for our young company, and will help us with product validation, up-scaling, safety testing, and sustainability assessment. I made my first commercial pitch of Glycolink to an investor group in December, and hope I can share some details in the new year! Lots to look forward to here 🙂

A montage of photos of Lauren and Amparo taken at KTH Innovation during two special events: a visit from th King of Sweden, and Demo Day for the pre-incubator programme.

Looking ahead

All in all, this year was a heavy one, with lots of pressure, but with successes to celebrate as well. A lot of special events bringing people together, several new projects to get excited about, and a completion to some long-term initiatives. We have much to be proud of this year and I hope we can keep up the momentum for 2023. I look forward to welcoming four new Master’s thesis students in the spring and can’t wait to see what you can do, Rasmus, Felise, Ida, and Piltan!

A special event in the coming year will be the PhD defence of Ioanna Sapouna – stay tuned for details! Now that she has several good publications on the way, she will be working on her thesis throughout the spring.

I want to say an extra special thank you to Alma Kvammen, our talented former research engineer who is now working in Norway, but whose incredible work ethic and scientific rigour pushed multiple projects to completion and kick-started several others. We miss you but wish you the very best of luck!

PhD position available: Sustainable biotechnology to circularise forestry waste sludge

Leave a reply

Note: the application process for this position closed in October 2022.

In brief: We have a PhD position available in our group, ideally to start in the spring of 2023. Email Lauren with questions. Full details below. You must apply at this link: apply here.

Scientific goals: Thousands of tonnes of sludge waste are produced each year at pulp and paper mills, and we aim to find new ways to recover components from this waste. The sludge contains valuable organic materials like starch, cellulose, and lignin, but it is heavily contaminated by metals and minerals that inhibit recycling. Most sludge is therefore sent to landfill. In this 4-year PhD project, we will use isolation techniques and DNA sequencing to identify the microbial species that thrive in this harsh industrial ecosystem, and use advanced “omics” methods to reveal the enzymes used in sludge breakdown. We will characterise these enzymes to create new precision tools for the forestry biorefinery, and to clean up the sludge by removing organic matter (leaving large amounts of recoverable metals, particularly aluminium). This project will advance fundamental knowledge and reduce industrial waste, helping to move the industry towards a more sustainable and circular model. You will be based at the KTH Division of Glycoscience, and your main supervisor will be Lauren McKee. You will collaborate closely with researchers at Chalmers University of Technology in the department of Industrial Biotechnology, as you will be co-supervised by Johan Larsbrink.

Where we work: KTH Royal Institute of Technology in Stockholm is one of Europe’s leading technical and engineering universities, as well as a key centre of intellectual talent and innovation. We are Sweden’s largest technical research and learning institution and home to students, researchers, and faculty from around the world. Our research and education covers a wide area including natural sciences and all branches of engineering, as well as architecture, industrial management, urban planning, history and philosophy. The Division of Glycoscience is a multi-disciplinary department focussed on solving environmental and industrial challenges relating to sustainable production and usage of renewable natural resources, as well as advancing fundamental knowledge of complex carbohydrates.

The broader context: This project is funded by the Wallenberg Wood Science Centre. The WWSC is a research centre striving for scientific excellence, with a focus on new materials from trees. The centre creates knowledge and builds competence for an innovative and sustainable future value creation from forest raw materials. WWSC is a multidisciplinary collaboration between KTH, Chalmers, and Linköping University. The funding base is a donation from Knut and Alice Wallenberg Foundation, and the Swedish forest industry is supporting the WWSC via the national platform Treesearch. As members of the WWSC, you and your supervisors will be expected to attend the workshops that take place in the Stockholm and Gothenburg areas twice per year, where you will present updates on your research and network with colleagues. You will be invited to regular Treesearch events, giving you further chances to present about your work and get access to the national Treesearch infrastructure platform.

Education and skills development: You will perform your PhD within the scope of the WWSC Academy. As a WWSC PhD student, you will attend two week-long graduate schools per year. This programme gives you a broad and deep insight into diverse forest-related topics, and helps you build a community of students aiming towards similar goals on the same timeline as you. You will also get to visit industrial sites and areas of natural beauty around Sweden, helping you get to know the country and its landscape as well. To complement your academy training, you will take doctoral courses at KTH, including online learning, lectures, and short lab projects. In addition, you will receive formal training in scientific writing and data visualisation. As part of your research, we will help you to write funding proposals to access additional financial support for travel and experimentation, giving you an even broader range of experience in science communication. I will also encourage you to write semi-regular pieces for this blog and to use other online channels to communicate with the public about your research.

Responsibilities as a PhD student: Your primary responsibility will of course be to advance the research project and to complete sufficient doctoral-level courses to earn the 60 credits you need to graduate. Your supervisors will help you to make sure you achieve these goals on time. In addition, you will spend up to 10 % of your time on Division/Departmental duties such as being responsible for a piece of equipment in the lab. Finally, you will take part in teaching younger students. The details of teaching are decided once the PhD has begun and the amount of teaching you do will be balanced against your other roles, but typically you will do some combination of lab teaching in a course for 1 or 2 years, supervising 1 or 2 MSc thesis students, and supervising 1 or 2 groups of BSc thesis students.

Eligibility for the position: To be eligible for this position, you should have a Master of Science or Engineering degree or equivalent qualification in a relevant subject area such as biotechnology. You should have completed a practical research-based (wet lab) thesis project. Documented proof of experience in areas such as molecular biology, biochemistry, and enzyme characterisation is appreciated but not necessarily required. Please email Lauren (find my email address at my KTH profile page) if you have queries about your eligibility for the role.

How to apply: You can find further specific details about this positon on the official advert, available at this link: apply here. Please note: applications can only be considered if they are made through the KTH application portal, linked at the bottom of the advert. Informal applications made by email cannot be considered. However, you are welcome to email Lauren if you have questions or are curious about this position.

Introducing Glycolink, a new start-up company

2 Replies

One of the projects ongoing in our group at KTH aims to develop the use of carbohydrate-binding proteins as polysaccharide cross-linkers in hydrogels and viscous formulations. We see this technology as a sustainable, fossil-free, and catalyst-free alternative to hydrogels made from petrochemicals and chemically modifed biopolymers. In 2021, the Royal Swedish Academy of Engineering Sciences (IVA) supported this view by listing us as one of the Top 100 sustainable projects of the year.

Group leader Lauren McKee and postdoc Mengshu Hao co-founded the start-up company Glycolink AB in the autumn of 2021, with the goal of exploring commercialisation of this hydrogel technology. Our third and final co-founder is Mohamad Takwa, a serial biotech entrepeneur who has supported a number of successful start-ups. We are ably assisted by business developer Isak Edvardsson, who has worked alongside Mohamad for several years.

We filed our first patent application in November 2021 and are now pursuing several lines of basic research both at KTH and with partners. In the coming months we will be measuring the sustainability of our hydrogel-making innovation, testing the scaleability of our manufacturing processes, and screening the safety of our material for on-skin applications such as cosmetics and wound dressings.

In the earliest days of this project, I received an award from KTH Innovation that supported market research to verify the commercial viability of the material. Since 2019 our research in this area at KTH has been funded by the Swedish research council Formas. And most recently we secured a small business loan from Almi for hypothesis testing and MVP (minimal viable product) validation.

I’m sure we have a long journey ahead of us, but you can follow our progress on our LinkedIn page or company website.

Our hydrogel project is recognised on this year’s “Top 100 List” by the Royal Swedish Academy of Engineering Sciences

3 Replies

Post updated 14/11/2022. We have now founded a company to explore commericalisation of the Glycolink project described here. See this blog post to read about the company founding, check out our company webpage, and follow us on LinkedIn!

On May 10th, the Royal Swedish Academy of Engineering Sciences (IVA) published their selection of projects “deemed to have great potential to benefit through commercialisation, business and method development, or societal impact.” The list has a different theme each year, and for 2022 the theme was “technology in the service of humanity.”

In February this year, we submitted our biomaterials-focussed project GlycoLink for consideration for inclusion on the list, and we are delighted to be one of the 70 projects the IVA has chosen to highlight. This is a project I have been working on for a long time, since I first observed an unusual binding interaction while testing protein activity on microbial polysaccharides. In late 2019, I was awarded funding by Formas, the Swedish national research council for sustainable development, and at the time of that award I was interviewed by the popular science magazine Extrakt (article in Swedish is at this link, my approximate translation into English is at this link).

In 2020, I used the Formas award to recruit Mengshu Hao as a post-doctoral fellow, and she has been working on this project full-time since the autumn of that year. Mengshu is, like me, a biochemist by training, and it has been a learning curve for both of us to pursue this line of biomaterials research, but Mengshu has made a tremendous effort to advance our understanding of the hydrogels we can produce. We have benefitted from collaboration with Qi Zhou and Salla Koskela of KTH, who have helped us to start a detailed rheological study of our gels, and who are co-applicants on our first patent application (submitted November 2021). We have also been working closely with Johan Larsbrink and Scott Mazurkewich of Chalmers University, Gothenburg to investigate the three-dimensional structures of our binding proteins.

We are currently working on two manuscripts that we plan to publish as soon as possible, describing the binding proteins we have discovered, and their exploitable polysaccharide interactions. We also plan for further collaborations with scientists at KTH and Stockholm University to respectively explore the polymer chemistry and biochemistry of our system. I look forward to being able to share the data from this project with you, both in publications and at conferences. I was happy to be able to share some information on the project at the recent Treesearch Progress 2022 event held in Kolmården, Sweden, which was also the first conference that our group could attend together post-Covid.

Photograph taken by Ioanna Sapouna at the 2022 Treesearch Progress event. Image shows Lauren McKee presenting a slide entitled “New protein cross-linkers for polysaccharide hydrogel formation.”

Year in review – 2021

2 Replies

Hi! This is Lauren, writing our group’s first (hopefully) annual review blog! Despite *everything* I feel quite positive looking back at 2021. There have certainly been some hurdles, delays, and setbacks, due to the *everything* going on in the world. And we have all faced problems now and then, or been distracted by concerns back home. But I feel strongly that this was the year that a research group really coalesced – I love being part of this team, I am immensely proud of what we have achieved this year, and I can’t wait to capitalise on all the work we’ve done and share it with the world in 2022. I started this website in the summer when I began to feel a group identity coming to life. I want this site to be a place that brings visibility to everyone in the group, and I have been pleased that several members have taken the chance to write updates and reflective pieces for this blog! The blog is also something you can browse through to catch up on what we and our students have been doing, if you’re interested in that kind of thing. Don’t forget that if you ever have questions about us or our work, you can get in touch with me via this website, or you can find my contact details at my KTH profile page.

Research

We made solid progress in all of our major lines of experimentation this year. Mengshu’s hydrogel research is especially well advanced: we now understand how the material forms, and are beginning to assess its basic properties so we can hopefully design some applications for it. Already, Heli has established new methods for protein analysis in our lab, and her work on thermostable enzymes has some interesting results that we will build on in the spring. And Ioanna’s lignin-focussed projects have continued to become more and more interdisciplinary, as she steps outside of her chemistry comfort zone and starts to learn more about plant biology and molecular biology techniques. We are now working on manuscripts relating to all of these projects, while research continues into the new year.

Students

Supervising Master’s students for their final thesis projects is a major part of working in this lab, and 2021 was no exception. In fact, because the pandemic meant a shortage of available jobs, there were more students looking for thesis projects in the university than I ever remember! As a group, we took on four KTH students who worked January-June, and another who worked from March-September. We also had two guest students from other Swedish universities who completed 12-month thesis projects in 2021: Zijia and Amrutha both worked on some aspect of biocontrol, investigating different bacterial species to see if they might be valuable tools to suppress plant diseases.

Busy times! The KTH students worked on diverse aspects of biomaterials, bioremediation, biocontrol, and biorefinery, and I admit I found it tough to keep up with everyone’s work, so I was happy to have effective co-supervisors for all students. We also had two student interns work with Mengshu and Heli for about seven weeks. Most of our student projects were very fruitful, although some were frustrating – Amrutha learned some lessons about coping with “negative data” while still producing a fantastic thesis on plant protection.

This year I was most happy to welcome two students whose time in our lab had been long-planned and delayed by Covid restrictions! Kasane from Tokyo Institute of Technology and Beatriz from Instituto Superior Técnico in Lisbon finally joined us to perform thesis projects as exchange students at KTH. Beatriz is working with Mengshu on a hydrogels project, and Kasane is working with Heli and Amparo Jimenez Quero on a biorefinery project. I’m so happy to have them both here! They will be with us until early 2022.

Recruitment

Our group has expanded quite a lot in 2021. We had several master’s thesis students in the spring-summer, but we were also joined by three longer-term members through the year. Ioanna joined our group in April, and I will be her main supervisor for the rest of her PhD. Heli also joined us in April, for a postdoc expected to last at least two years. And in October, Alma started her position as a research engineer with our team, and I hope she will stay for at least a year, as she is already making very valuable contributions to all of our projects. Right now, we have no plans for new recruitments any time soon, although the funding landscape can change, and I am happy to discuss with anyone who can bring their own funding.

Funding

Heli wrote and submitted her first major grant application this year, a daunting but important step for any early career researcher. Fingers crossed for good news in 2022! Ioanna and Mengshu also each wrote a small proposal for an internal funding call at KTH, which was a first experience for them. I was happy in late 2021 to be awarded funds from the Carl Trygger Foundation to support the purchase of some much needed equipment for analysing hydrogels. And I was very pleased that my good friend Johan Larsbrink at Chalmers University, Gothenburg received project funding from Novo Nordisk Fonden – Ioanna and I will contribute to that exciting project in a small way, and I am always happy to have a chance to work with Johan.

Innovation

I learned a lot this year about “innovation” and the commercialisation of research: specifically, about how academic research can be translated into real industrial output, either through partnerships or via the founding of new companies. At the beginning of the year, I was one of the first cohort of KTH researchers to take part in a mentorship programme, where I was matched with a mentor who had founded his own company after doing a postdoc in Sweden, and has since gone on to start several successful biotech firms. He gave me a great practical education in how to determine whether a ‘research project’ can become a ‘business idea’, and I learned a lot from this scheme about how to talk about innovation, and about all of the non-scientific skills I would be able to transfer from my life in academia into the start-up ecosystem.

Then, later in the year, together with my friend and colleague Amparo, I joined a pre-incubator programme at KTH, where we are exploring the commercial potential of one of our joint research lines. Our ‘batch’ of start-up concepts meets on Thursday lunchtime every week, and we discuss everything from financing, business management, and branding, to project planning, building a strong team, and giving effective feedback. It has been extremely cool to hang out with a large group of innovators from fields ranging from AI and games/app development to biotech and space exploration, and it is especially rewarding to hear that these diverse teams are facing such similar challenges to our own. It has been a crash course in “business speak“, for sure, but by now we’re comfortable in the group, and are able to think and communicate coherently about our hopes and plans for the next few years. Amparo also recently joined the mentor programme to get an additional perspective on what we are doing, and you can read about both of our experiences in this interview.

In related news, Mengshu and I also have an exciting initiative in the works, but that announcement will come later…!

Looking ahead

As a group, we have mostly been initiating major new projects this year, and so we didn’t publish a lot of papers in 2021, although some Covid-delayed collaborations with other groups did see papers coming out, which was very nice. I also published an invited review in Environmental Microbiology Reports, co-written with colleagues in Gothenburg and Norway. All of our research projects are in full swing now so a big priority for early 2022 is to start publishing our work! We have two near-complete manuscripts that I want to submit in January, and advanced plans for at least two more we’ll be working on in the spring, so I hope you’ll get to read those in the not-too distant future. Working on these papers feels like an important step for the group, as they will represent our first joint accomplishments. As Ioanna has just passed her half-time evaluation, we also need to focus on guiding her towards PhD completion, wrapping up the projects that she has been advancing this year, and starting to work on the publications needed for a defence at KTH.

January-March is always a very busy time. I will have a heavy teaching load and at least three significant research grants to write, so I am happy to know that our experimental work is in the best of hands. Both Heli and Ioanna will be joined in their projects by Master’s thesis students, and I will supervise a group of students through a smaller project for a biopolymers-related course. I’m looking forward to meeting them, and giving them their first hands-on lab experience since pre-pandemic! I also hope that the world will open up enough that we can travel safely, so that we can attend at least one conference as a group. Maybe see you there 🙂

Microbe vs. Microbe: My experience at CAZyme lab

1 Reply

It was the spring semester of my Masters programme at Stockholm University when I first contacted Lauren McKee to ask about a potential Masters thesis. From the very beginning, she was welcoming and talked with me at length about the possible projects that I could do for my thesis. Following our meeting, I had a lecture on “Microbial interactions in the rhizosphere“ from Lauren. A particularly interesting concept to me was manipulating the behaviour of a biocontrol agent (BCA) to perform better in terms of increased growth or increased production of anti-pathogenic enzymes. This manipulation can be achieved by providing carbon sources specific to both the BCA and the plant pathogen. And that is where most commercial biocontrol formulations go wrong. Failing to understand how and what a BCA responds to leads to inefficiency. One of the important research themes at the CAZyme lab is to elucidate the molecular mechanism of nutrient-microbiota interactions: this will help us to create more effective and science-based solutions for sustainable agriculture. In this photo you can see me setting up one of the dozens of six-well agar plates I used during my thesis project!

I decided to work on a 3-week course project to familiarise myself with the ongoing work within Lauren’s group. In this project, I looked at the biocontrol properties of a gram-positive bacterium Bacillus subtilis natto against plant pathogenic oomycetes – Aphanomyces euteiches and Aphanomyces cochlioides – based on a previous thesis and publication from Anna Schönbichler, a former student in the group. During this period, I got to interact with CAZyme group members and other research groups within the Division. The best part is that it was a multicultural environment in the lab and it has been amazing getting to know people from many different backgrounds.

Working with plant pathogens, in terms of plant protection, has always interested me and I believed that this would be a great opportunity for me. I started my year-long thesis in September 2020 and I worked on the topic “Assessment of Bacillus subtilis natto as a potential biocontrol agent against Aphanomyces euteiches,” which was a continuation of my earlier short project. For my thesis, I grew the bacterium in a variety of carbon sources that were representative of the cell-wall of the oomycete pathogen. This was done in order to gain an understanding of how the bacterium will respond when faced with the “real” pathogen. Following this, the enzymes and proteins produced by the bacterium in response to these carbon sources were analysed for cell wall-degrading activities and their ability to inhibit pathogen growth on an agar plate. This was really a fundamental investigation into bacterial biochemistry. Being a plant biologist, I wanted to understand the dynamics of the relationship between the host plant, pathogen, and biocontrol agent. For this, experiments using pea plants were conducted in growth chambers in a collaborator’s lab in Uppsala. It was found that there was some inhibition when a certain carbon source was used to manipulate B. subtilis natto. But, sufficient data was not produced to conclusively say that this bacterium could potentially be used as a BCA against this particular pathogen. Due to the natural variability in how plants grow, and how they respond to a pathogen, more replicates than I could study in my thesis would likely be required in order to generate statistically meaningful data. However, I believe that this project will serve as a blueprint for further experiments using B. subtilis in combination with other plant pathogens.

The research in Lauren’s group on biocontrol using soil bacteria is absolutely relevant for both the present and future world scenarios. I have to mention that the entire time I spent in the Division of Glycoscience with Lauren and other members was a fantastic learning phase. As a newbie researcher, I made mistakes (quite a few!), but I learnt from them and I couldn’t have asked for a better learning experience. I was able to work very independently within the group, so I figured out how to think ahead and manage my own time. Lauren was very encouraging and seldom lost her patience with me. Throughout my project, I learned better ways to communicate, plan, and truly understand the impact of science in everyday life. Scientific research is infinite, like human stupidity (sic). I have talked to other people working on biocontrol research and they tell me a similar story: there is always one small detail that is left to be discovered. I hope that future group members will continue with this project, avoid making the mistakes I made, optimise, and discover more and more.

My first big conference in real life – a travel blog

1 Reply

A few weeks ago, I travelled to France to present our research at an international conference. This whole sentence seems surreal now that I see it written! Due to the Covid-19 pandemic, most meetings, workshops, courses, and conferences have been online for almost two years, basically since the start of my PhD. Going to a real-life event after a long time of working from home as much as possible felt awkwardly real. I want to write about my experience as a record of my first international meeting as a PhD student. I will start from the beginning of the trip since conveniently enough for the timeline of this post, my presentation was one of the very last of the whole conference!

The 7th International Congress of the European Polysaccharide Network of Excellence (EPNOE) took place in Nantes, France. Apart from the interesting sessions and the networking opportunities, a trip to France was a golden opportunity for me to practice my long-forgotten French…and reminded me that it is indeed long-forgotten. The trip started on a Sunday morning with a ride to the airport in Stockholm, and we arrived to our final destination late on Sunday evening. I was excited to spend a week with warm and sunny weather to contrast the often cold and gloomy autumn in Stockholm. Due to the pandemic, we had to have our vaccination certificates scanned before we were allowed to enter shops and restaurants, and of course the same applied to the conference venue, reminding us that we are not exactly “back to normal”, not just yet.

Château des ducs de Bretagne in Nantes, France.

The regulations regarding face masks requirements indoors changed the week before the conference and it was no longer mandatory to wear a face mask in the conference venue, which made it a lot easier to meet and discuss with people. This was a great relief, since I already find it difficult enough trying to remember new faces and match them with names! I hope “practice makes perfect” applies here too.

The first day of the conference started after lunch, with a plenary lecture by Prof. Ingo Burgert from ETH Zürich, who talked about using wood as a renewable resource for sustainable materials. The lecture underlined the necessity of replacing mineral-based construction materials as society moves towards greater sustainability. According to the United Nations Environment Programme, energy consumption in building/construction represents about 36% of the global demand, and the related emissions reach approximately 40%. Wood is a common building material in Sweden, as it has compelling properties that make it useful for many types of construction. Of course, wood has always been used as a construction material, but more advanced techniques are now available to enhance certain properties of wood. For example, partial delignification allows larger deformation of wood which in turn can enhance its inherent piezoelectric properties for applications in smart building technologies.

The Urbach Tower in Germany. A great example of the utilization of the inherent properties of wood in construction. Photograph by ICD/ITKE University of Stuttgart, accessed through the website of University of Stuttgart.

The Urbach Tower in Germany is a great example of how interdisciplinary collaborations in basic research can shape a sustainable future. Mechanical methods for wood deformation for architectural and building purposes have been known for many years. With these methods, wood is mechanically forced to take a desired shape. This is usually done while carefully controlling the relative humidity of the environment during the process, since changes in the moisture content of timber cause natural deformations and shrinking. However, by understanding the science behind this effect, it is possible to model and predict these deformations and allow a “self-shaping” process to take place. Another extraordinary example of what can be achieved with wood is the production of Janus membranes. Their ability to transport water in only one direction, while blocking movement in the other direction, is fascinating to me, and could have an incredible impact if used in smart building technologies, such as for collecting water from fog.

The closing talk for the first day was especially interesting to me, as I begin to look ahead to life post-PhD. Three professors shared their experiences of moving from the academy to industry and back, and urged us to explore every diverse opportunity we come across, since we can never know what the future holds for us. This was a fascinating session, although it would have been inspiring to also hear about some similar experiences from women who have moved from the academy into entrepeneurship.

The welcome reception was the perfect ending to this first busy day. A variety of French cheese, cold cuts, and oysters were served in the foyer where most of the posters were already placed, inviting interesting conversations to begin.

Over the next few days, I had the opportunity to attend talks and lectures that made me reflect on sustainability even more. It is a well-known fact that food and agricultural waste is a big problem and fast action is required to minimize waste production as we move to a “greener” future. However, since national-scale overhaul of entire industrial sectors is a rather slow process, we might as well find ways to utilize waste as an intermediate step. Several talks focused on the extraction of hemicelluloses from different starting materials, using combinations of enzymes, optimized chemical extractions, and mechanical pre-treatments. Just to summarize the societal impact of this research with an example, mushroom “waste” biomass accounts for approximately 200 kg per capita per year of food waste. At the same time, fungal biomass is an important raw material that can be used for the extraction of polysaccharides via green methods. The extracts can then be utilized in the food industry as food additives or as raw materials for other high-value applications. The EU-funded FungusChain project is just one research initiative focussed on this hot topic.

Analytical methods for polysaccharide characterization was another important topic of the conference: if you want to design technologies for extracting polysaccharides from biomass, or for using them in high-value applications, you first need information on what they look like, since this impacts the properties they will have! Since my research does not focus solely on polysaccharides but on wood biomass as a whole, I found this section especially helpful. I was happy to hear that Nuclear Magnetic Resonance (NMR) spectroscopy is considered a powerful technique, although it is not as popular in carbohydrate chemistry compared to in lignin analysis, due to difficulties posed by the nature of the raw materials. Inspiring talks by Dr Alistair King (University of Helsinki) and Dr Marion Gaborieau (Western Sydney University) showcased the spectrum of NMR applications in the polysaccharide field.

One of the last sections of the conference explored end-of-life assessment of bio-based materials. Do we really know the difference between bio-based and biodegradable materials, or do we put them both under the same umbrella? If it says “bio-“, it must be good for the environment, right? Well, not exactly. Bio-based materials are built from renewable biological resources, but by design they have the exact same properties as their fossil-based homologues. This is not by accident: bio-plastic must have all the same properties as conventional plastic, or it will not be an effective substitute. The difference between PET and bio-based PET lies solely in the raw material used for production; the production method used does not change the fact that we need to come up with solutions for the recycling and reduced use of plastics.

On the same note, the bio-degradability of any material depends on the precise way in which we dispose of a product, and is not an inherent property of any material. If we are using a compostable plastic, but it ends up in the ocean because of bad disposal, we really defeat the purpose of using it in the first place, as composting cannot occur in an aquatic environment. Industry has been collaborating with research on biodegradability assessments of materials, on finding new, more efficient methods of degrading plastic. But these efforts could be undermined if we, as consumers, are not well informed about how exactly we should dispose of our waste.

My presentation was the last one in the conference, alongside two other parallel sessions.

My contribution to this conference was about the effect of the presence of hemicelluloses on the structure of extracellular lignin and as a result the final structure of the cell wall in Spruce cell cultures. This was my first conference presentation in real life and although I was excited, I was also becoming increasingly nervous throughout the whole week, until Friday afternoon. Right up until I saw my title slide set up on the big screen, I could feel my heart beating so loudly that I thought the people around me must be able to hear it as well. Until the moment I stood up and faced the audience. In those seconds before I started talking, I realized that these people are actually interested in my research, they are here to learn about what we are doing, and I am here to present our data. My stress disappeared! Excitement kicked in and I felt confident as I was going through my slides: seeing people in the audience nodding in understanding was definitely motivating, and is so welcome after a long period of Zoom seminars. This amazing opportunity to share knowledge with scientists from around the world was so much better IRL than just talking at my laptop screen. I cannot find the words to describe the energy in the room during my almost 20-minute presentation. Saying that the experience was “amazing”, “rewarding”, and “exciting” are truly understatements.

To conclude my trip and this travel blog, I want to acknowlegde that this experience will stay with me for a long time. Being immersed in conference life for a whole week, I had the time to reflect on sustainability and my role as a scientist and as a consumer. I got to admire again the tremendous potential of wood and other plant biomass as a raw material, I networked with interesting scientists from all over the world, and I had a lot of fun! It was a week full of new experiences and I cannot wait to see what comes up next! I hope that every PhD student has such a positive experience with their first big conference.

My Top Five List For Your First Conference

1. Be prepared. Book all the tickets you will need before you start your journey and plan your trip in as much detail as possible. This is especially useful if the conference takes place in another country and will let you focus your mind on the conference itself.

2. Socialize. One of the main reasons you attend a conference is to meet new people and network! Take the chance and talk to as many people as possible.

3. Explore the city. Yes, the main event is the conference and yes, it takes up most of the day (if not all of it). However, if you are in a new city, take the opportunity to explore it with your colleagues!

4. Know your stuff! If you are there to present your own research, remember that you are the expert, and you are more than capable to discuss it with other researchers. But it never hurts to do some extra reading to clear up any “foggy” aspects before you arrive.

5. Have fun! You are in a venue full of people ready to engage in scientific discussions, socialize, and create an inspiring network. Enjoy the experience!!

Networking and having fun at the gala organized by the conference. A cherished memory of the conference, now pinned up at my desk in Stockholm.

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

1 Reply

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

1 Reply

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.

When your business is protein production and purification, not every day is a great day… 😉

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🌟

Leave a reply

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!

Leave a reply

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.