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PhD student Nabila El Arbi (right) successfully defended her PhD thesis that was supervised by Markus Schmid (left). The central dogma of biology states that DNA is transcribed into RNA, which is then translated into proteins, assuming that one gene contains the information for one protein. However, RNA modifications like alternative splicing can produce multiple proteins from a single gene. Not much is known about this in plants, but PhD student Nabila El Arbi dived into the unknown and started to enlighten it.
You did your PhD in Markus Schmid's research group at Umeå Plant Science Centre. What motivated you to move to Umeå and join Markus’ group?
Nabila El Arbi: Well, to be completely honest – I was not actively looking for a PhD. I was in the final weeks of wrapping up my master’s thesis project and was confronted with the simple yet scary question: “What do you want to do now?”. By chance, somebody at a festival told another person, who then told me, about a “really good plant science centre” in Northern Sweden. That is how I found UPSC and the open PhD position in Markus’ group. When I read the project description, I thought this was really tailored to me, building up on what I focussed on during my Bachelor’s and Master’s projects. I immediately had a head full of ideas. At the time, Markus had two PhD positions available and offered me and the other candidates to visit UPSC and meet people from his group. We got along well, and this gave me an additional motivation boost for the project.
During your PhD, you explored “the role of RNA metabolism in the context of plant development under temperature stress”. Why is it important to study this?
Nabila El Arbi: For me as a researcher, I want to know more about things that are not known or poorly understood. Very little is still known about how RNA metabolism is regulated in plants. When genes are activated, their DNA sequence is transcribed into RNA, which then serve as a protein template. This sounds very simple, but the process is much more complicated. Which gene is activated when and why and how is the transcript processed? We still lack a lot of information to answer these questions that are central to the regulation of RNA metabolism and plant development and adaptation in general. Just minor changes in the RNA machinery might have big effects. This can provide us with incredibly powerful tools to create more resilient plants, but it is really important that we first understand everything properly.
You focussed mainly on alternative splicing. What is that and why is it relevant for plant development under temperature stress?
Nabila El Arbi: It is not so easy to describe what alternative splicing is, but one can maybe explain it a bit by comparing it to one of these super awesome functional hiking trousers that contain a lot of zippers. You do not need several trousers but can only take one pair and by removing or adding parts you can adjust it to your needs. It is still the same pair of trousers, but it can be short or long, it can have several pockets or just a few. With alternative splicing, it is a bit similar. All information is stored in the DNA but the way how it is transcribed into RNA can vary. One gene can contain information for different protein variants depending on how the various parts of the gene are put together when transcribed into RNA. The fruit fly Drosophila has one gene that has about 38 000 different splice variants, meaning different RNA sequences that are produced based on the information of this one gene. At least 19 000 of them have a function. I think this is absolutely mind-blowing, especially when considering that Drosophila just has about 15 000 genes. This example illustrates the variety that can be produced by alternative splicing. Plants use this mechanism a lot to flexibly adjust their growth and development to their environment, especially when adjusting to cold or heat.
What do you consider as the major outcome of your thesis?
Nabila El Arbi: When I started my PhD, there were only two papers published about the splicing mutant that I focussed on. It is called porcupine because of its “spiky” look. This mutant grows completely normal under ambient temperature but develops severe defects under low temperature stress. The PORCUPINE gene contains information for a protein that is part of the splicing machinery but becomes more active under low temperature stress. We compared it with other splicing mutants that show similar behaviours and investigated how they are regulated at different temperatures. They all appear to be controlled at least partially by overlapping pathways, but they are still quite different from each other. It is very complex. The good thing is that we now have more data and knowledge about alternative splicing and temperature, and that helps us to formulate the questions more precisely. It is a very good starting point for people who will follow up on these projects. For me, this is one of the biggest outcomes.
You summarise your thesis with “It is really complicated”. Did you expect this complexity when you started your PhD?
Nabila El Arbi: No, not at all. When I started, I was very optimistic, but I was very quickly confronted with the fact that nothing worked as expected. The porcupine mutant was very interesting but also not very confined. The mutation affected everything from root growth to shoot growth, from flower development to leaf development – like the magic box where you take out a tissue that never ends. When we did an experiment to answer one question, the answer was often neither yes nor no. We even started to collaborate with a group in Germany and were sure that from these joint experiments, we would get a clear answer about how the PORCUPINE protein regulates alternative splicing, but the results are only clear in the sense that they are unclear. We know now much more about alternative splicing and temperature than when I started my PhD, but all our results opened up many more questions. It is really complicated.
What kind of challenges did you have to overcome during your PhD?
Nabila El Arbi: During my bachelor’s and master's projects, I was very protected. My supervisor was very well organised and gave me very clearly structured projects, which was great. When starting my PhD, I had to learn that the responsibility was now on me even though I was of course supported by Markus and his group. I had to plan the experiments, do the experiments and deal with troubleshooting. At one point, I was the person who knew most about the project. It is normal during the PhD; I just did not anticipate this in the beginning.
Then, I had to deal of course with the frustration that things did not work as expected. We were working with models that were based on results from humans and yeast, but in plants, the mechanisms seem to work completely differently. It was challenging not to get lost in the project and just accept that we might not get a clear answer even if I would repeat the experiment another time. I had to learn to let go of some projects even though they were interesting, choose what was safe and focus on succeeding with my PhD.
What are you planning to do now?
Nabila El Arbi: Ah, the scary question again. I do not know, honestly. Frankly, I just want to breathe for a moment. I have always put so much pressure on myself to not take a break, to keep moving and to start the next project right after another has ended – I do not feel like I want to do that anymore. I will take some time off now to see what possibilities are out there and then choose something that I really feel passionate about. I have applied for a position at the European Space Agency because I would really like to work in the space sector, maybe even go to space if possible. They were looking more for engineers and not for biologists, but I thought I just give it a try. Otherwise, I think I would like to take a break from academia and to try how it is to work in industry. But first, I will visit my family and some friends that I have not seen for a long time.
About the public defence:
Nabila El Arbi, Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, defended her PhD thesis on Tuesday, 17th of December 2024. Faculty opponent was Artur Jarmolowski from Adam Mickiewicz University in Poznań, Poland. The thesis was supervised by Markus Schmid.
Title of the thesis: Exploring the Role of RNA Metabolism in the Context of Plant Development under Temperature Stress
Link to Nabila El Arbi’s PhD thesis
For more information, please contact:
Nabila El Arbi
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email:
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For the third time in a row, UPSC is inviting Early Career Plant Scientists to visit Umeå and present their research. The goal is to motivate talented young scientists to move to Umeå and start a postdoc at UPSC. The feedback from previous participants was very positive, encouraging the organisation of a third symposium, this time in a slightly revised format. It will take place on the 26th and 27th of March 2025, with applications accepted until the 7th of January.
Many people outside of Sweden might not have heard about Umeå. Located in the North of Sweden, one might think it is at “the end of the world”, but the city offers great opportunities for research and easy access to stunning wilderness and outdoor adventures. Umeå hosts two universities, a university hospital and a growing life science and biotech scene. As part of both universities, UPSC is centrally located on the Umeå campus and offers excellent opportunities for plant scientists.
“We want to highlight the exceptional research environment here at UPSC and showcase our cutting-edge scientific projects and infrastructure”, says Stephan Wenkel, one of the three organisers of the symposium. “Our goal is to foster connections with young scientists and show them why UPSC is such a unique and inspiring place to work. We have a very supportive and collaborative environment here at UPSC, and Umeå is a great place to live.”
Great opportunity for young scientists to expand their network
One reason why UPSC focuses on early career researchers is that the Swedish system primarily allows the hiring of postdocs up to three years after their PhD. Exceptions are made for circumstances like parental leave, military service, or health-related interruptions, which extend eligibility and ensure fair opportunities for all candidates. However, the main reason is that early career researchers bring fresh perspectives, innovative ideas, and a strong drive to advance their fields.
“By connecting with young researchers early in their career, we can support their growth while benefiting from their creativity and enthusiasm, which are crucial for pushing the boundaries of plant science,” explains Laura Bacete, who has organised the previous two symposia. “For the invited candidates, this is a unique opportunity to expand their network with the scientific community, building connections that could be valuable throughout their careers - maybe not right away but in unexpected ways later on.”
Participants will receive constructive feedback on their research, helping them refine their ideas and approaches. New this time is that several UPSC group leaders will also showcase their work, encouraging participants to explore a wider range of potential research collaborations. The presentations will be followed by interactive sessions where postdocs and group leaders can engage in one-on-one meetings based on mutual interest.
More dynamic and inclusive new format
“In the past, applicants were asked to name specific group leaders they were interested in working with, which we realised could limit their exposure to the broader research environment and unintentionally favour well-established group leaders,” says Stephan Wenkel. “We think that this new approach is more dynamic and inclusive, and we hope that we can better match the research interests of the applicants and the UPSC group leaders.”
Besides stimulating scientific exchange and interaction, the programme also offers a grant-writing workshop led by Umeå University’s Research Support Office to inform about funding opportunities for postdocs. Additionally, social activities will provide the opportunity to network with researchers and staff from UPSC in a more informal environment and to hear more about postdoc life in Umeå.
“Postdoc is an incredible career stage: you’ve gained valuable knowledge and skills from your previous work, and now you have the chance to build on that foundation while learning new techniques and exploring new ideas,” adds Kelly Swarts, the third organiser of the upcoming symposium. “It is important to find a research question that one feels passionate about, but equally crucial is the relationship between the candidate and the supervisor. That is why we want to give time to get to know each other.”
The application for the symposium is still open until Tuesday, the 7th of January. Besides their CV and references, applicants are encouraged to clearly articulate in their cover letters how their expertise and interests align with the UPSC research landscape. Once the application closes, an evaluation committee will review all applications, select the most promising candidates, and invite them to the symposium in March. All applicants will be notified at the beginning of February 2025.
More information about the UPSC Symposium for Early Career Plant Scientists
For questions regarding the symposium, please contact:
Laura Bacete, Umeå Plant Science Centre, Department of Plant Physiology, Umeå University
Email:
https://www.upsc.se/laura_bacete
Kelly Swarts, Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences
Email:
https://www.upsc.se/kelly_swarts
Stephan Wenkel, Umeå Plant Science Centre, Department of Plant Physiology, Umeå University
Email:
https://www.upsc.se/stephan_wenkel
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Conifers have evolved special strategies to survive the harsh winters in the north (image: Stefan Jansson and Pushan Bag).
As the festive season approaches, evergreen conifers like spruce and pine adorn homes worldwide. But while Christmas trees bring warmth and joy into our lives, they endure some of the harshest conditions on Earth in their natural habitats. Most people take it for granted that they maintain their needles lush and green in freezing winters and blinding sunlight in the boreal forests but now scientists can unwrap the science behind conifers’ winter survival.
The photosynthetic process of most green plants is highly conserved; it functions overall the same in green algae, tulips and redwood trees. Yet, there are differences and scientists are gradually understanding more about both the differences and commonalities.
Conifers have extraordinary winter survival strategies, some of them were not understood until recently. Scientists from Umeå University have, together with colleagues from UK, Canada and Bulgaria, summarized recent breakthroughs in an article published in Trends in Plant Science.
Reorganisation within the chloroplast help conifers to stay green
One of the two main findings, both of which this group of researchers have contributed to, is that conifers change the structure of their thylakoid membranes in the chloroplast where photosynthesis takes place. This makes Photosystem I (PSI) and Photosystem II (PSII), which otherwise by large remain separated, come in winter closer to each other and work together in a special way named spill-over.
“This helps them to safely dissipate extra energy and avoid damage from too much sunlight in the cold,” says Stefan Jansson, Professor at Umeå Plant Science Centre at Umeå University.
Others have previously, without understanding the mechanism, named the process ‘Sustained Quenching’ as it could put photosynthesis into a lock down mode for days.
The second strategy, operating in parallel to spillover, is that conifers use special routes for moving the electrons in photosynthesis. These paths, known as alternative electron flow, involve flavodiiron proteins and help keep the photosynthesis process balanced. This also prevents the system from becoming overloaded when there's too much light and freezing temperatures.
Conifers have evolved intricate adaptations to extreme winter conditions
In addition, the photosynthetic apparatus of conifers differs from that of flowering plants (angiosperms) in a few other ways. They lack, for example, some so-called light-harvesting proteins found in other plants.
“All together this can explain why conifers are the dominant species in boreal forests, thriving where few others can, perhaps at the expense of advantages during less challenging conditions; few conifers, if any, grow where water, nutrients and temperature conditions are all favourable” says Pushan Bag, lead author who during his doctoral studies at Umeå Plant Science Centre studied these phenomena.
Understanding these mechanisms may also aid conservation and help predict forest responses to climate change and may in the longer perspective inform strategies for breeding crops that are resilient to extreme weather conditions.
Co-author Alexander Ivanov adds: ”This paper highlights the intricate adaptations of conifers to extreme winter conditions. By combining structural, molecular, and evolutionary insights, it advances our understanding of how these trees have come to dominate some of the harshest ecosystems on Earth.”
About the scientific article
The research, titled "Photosynthetic Advantages of Conifers in the Boreal Forest," is a collaboration among leading institutions in the UK, Canada, Sweden and Bulgaria supported by the EU research programme Horizon 2020 and the Human Frontiers Science Program and other funders. The article was published in Trends in Plant Science in December 2024.
Read the full article in Trends in Plant Science
For more information, please contact:
Dr. Pushan Bag, University of Oxford
Email:
Stefan Jansson, professor at the Department of Plant Physiology and Umeå Plant Science Centre, Umeå University
Phone: +46 70 677 23 31
Email:
https://www.upsc.se/stefan_jansson
Text: Stefan Jansson, Pushan Bag, Sara-Lena Brännström (Umeå University)
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Peter Kindgren (left) and Totte Niittylä received funding from the Novo Nordisk Foundation (photo left: Fredrik Larsson; photo right: Johan Gunséus).
The Novo Nordisk Foundation has recently approved two new research projects involving UPSC researchers. Peter Kindgren received a project grant aimed at improving crop resilience and productivity in a dynamic manner. Totte Niittylä, along with two other researchers from the University of Copenhagen and the University of Helsinki, have been awarded an interdisciplinary synergy grant. Their goal is to investigate in detail how trees direct photosynthetically assimilated carbon to wood, with the ultimate aim of enhancing the carbon capture capacity of trees.
Improving resilience and productivity in crops in a dynamic manner
Peter Kindgren received a project grant and will work on a biotechnological project to improve crops. His project focuses on a fine-tuning mechanism in plants that influences their biomass and stress resilience. Central to his project is a gene that controls several processes in plants such as activating stress response mechanisms while inhibiting biomass production.
This gene’s activity is suppressed by a long non-coding RNA which is an RNA molecule that does not contain information for a protein. This RNA is produced from a DNA segment next to the gene and prevents the production of full-length RNA from the gene. Peter Kindgren and his team plan to study the interaction between these two players to find ways to adjust them to enhance plant fitness.
“Our goal is to boost biomass production when the plants are not stressed and increase their stress resilience when adverse weather is expected,” explains Peter Kindgren. “The advantage of this system will be that it can trigger a rapid, predictable and short-term response in field-grown plants during the growing season.”
The researchers intend to test their system in the model plant thale cress before applying it to cereals like wheat and barley. Their ultimate aim is to provide farmers with an additional tool to mitigate the effects of extreme weather and enhance biomass production before harvest.
Enhancing carbon capture capacity of trees
The other project funded recently by the Novo Nordisk Foundation in which Totte Niittylä is involved is tackling a different but equally important issue: the ability of trees to assimilate and store atmospheric carbon. This project brings together the expertise of Thomas Moritz (University of Copenhagen), Totte Niittylä (UPSC and Swedish University of Agricultural Sciences) and Ari-Pekka Mähönen (University of Helsinki). Together, they aim to identify factors that limit wood formation in trees.
Their goal is to create a detailed map showing how carbon is transported, processed and metabolised within wood. The researchers will work with isolated cells from different wood tissues and analyse gene activities and metabolites within these cells. They also plan to model carbon transfer between these cells using labelled carbon atoms.
“We aim to identify the enzymes and metabolic processes that restrict wood formation in trees”, says Totte Niittylä. “Trees play a crucial role in absorbing carbon dioxide from the atmosphere, but we still do not fully understand the metabolic pathways involved in this process. This knowledge gap makes it difficult to predict how much carbon dioxide trees can capture, and it also hampers the breeding efforts to improve the production of wood in fast-growing feedstocks.”
The researchers believe their findings could lead to enhancing trees’ carbon capture capabilities through breeding and biotechnological applications. They anticipate that their results will be interesting for plant biologists and breeders working with fast-growing trees and also more widely research and development teams in private companies and public organisations working on metabolism and its regulation.
More information about the projects:
Project grant
Title: A dynamic circuit to increase biomass and stress resilience in crops
Contact: Peter Kindgren, Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences
Email:
Novo Nordisk Interdisciplinary Synergy grant
Title: CarbonTree: CO2 assimilation capacity of trees – releasing the sink limitation
Project partners: Thomas Moritz (University of Copenhagen), Totte Niittylä (UPSC, SLU), and Ari-Pekka Mähönen (University of Helsinki)
Contact: Totte Niittylä, Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences
Email:
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Thomas Dobrenel (middle) received the UPSC Agrisera prize 2024. It was presented to him by the chair of the UPSC Board Catherine Bellini (left) and by Conny Hiljanen (right) from Agrisera (photo: Anne Honsel).At today’s UPSC Christmas lunch, the UPSC Board awarded Thomas Dobrenel with this year’s UPSC Agrisera Prize. The award acknowledged his contribution to facilitating scientific discourse at UPSC and his dedication to making UPSC a good and collaborative place to work.
Thomas Dobrenel came to UPSC in 2013 as a postdoc in Johannes Hanson’s group, where he studied carbon starvation in Arabidopsis cell cultures. In 2019, he transitioned to Ove Nilsson’s group and the UPSC Spruce Transformation Facility. There, he started to work on a project to optimise methods for genetically engineering Norway spruce and propagating it via somatic embryogenesis.
The nominations for Thomas Dobrenel highlight his contributions to organising journal clubs, seminars, and PhD and Postdoc retreats, all of which stimulate scientific discussions and knowledge exchange at UPSC. He also organises social activities that strengthen the UPSC community, and nominations pointed out his approachability and willingness to assist others.
“We believe that a good and supportive work environment is essential for good research, and dedicated people like Thomas are important. With the UPSC Agrisera Prize, we show our appreciation for such commitment,” says Catherine Bellini, chairperson of the UPSC Board. She and Conny Hiljanen from Agrisera presented the prize today to Thomas Dobrenel.
About the UPSC Agrisera Prize
Each year, UPSC awards the UPSC Agrisera Prize, sponsored by Agrisera, to recognise outstanding scientific achievements and significant contributions to improving the work environment at UPSC. Everyone working at UPSC can nominate and be nominated. The recipient is chosen by the members of the UPSC Board and announced during the traditional UPSC Christmas lunch in December. The prize includes a diploma and a travel voucher.
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Stéphanie Robert (left; photo: Erik Abel) and Stephan Wenkel (right: photo Mattias Pettersson) are part of the two research consortia STARMORPH and RESYDE that are awarded an ERC Synergy Grant.
Two research consortia, including UPSC researchers Stéphanie Robert from the Swedish University of Agricultural Sciences and Stephan Wenkel from Umeå University, have been awarded prestigious ERC Synergy Grants. They aim to investigate fundamental aspects of plant development from diverse angles, paving the way for advancements in biotechnology and plant engineering.
The highly competitive ERC Synergy grants are designed to support collaborative research efforts that address complex, ambitious scientific challenges beyond the scope of individual researchers. Stéphanie Robert and Stephan Wenkel are part of the STARMORPH and RESYDE projects, which have each received €10 million in funding over six years.
STARMORPH - Creating a spatio-temporal map for auxin dynamics
The STARMORPH project, led by Stéphanie Robert from SLU, will focus on auxin - a plant hormone crucial to various aspects of plant development. For example, auxin plays a key role in promoting root and stem growth and is essential for organ formation.
Over the next six years, Stéphanie Robert will collaborate with Ondřej Novák from the Institute of Experimental Botany, Czech Academy of Sciences (Czech Republic), Jürgen Kleine-Vehn from the University of Freiburg (Germany), and Alexander Jones from the Sainsbury Laboratory, University of Cambridge (UK). Together, they aim to address the fundamental question of how auxin contributes to so many aspects of plant development.
STARMORPH introduces the innovative concept of an “auxin signature” which reflects auxin levels not only in organs, tissues, or cells but also within specific cellular compartments integrating cellular responses to developmental and external signals.
“The subcellular compartmentalization of auxin is still poorly understood,” explains Stéphanie Robert. “We believe that auxin’s specific effects are not solely determined by its overall concentration but rather by its unique subcellular distribution and how it is perceived at the different sites within the cell, creating an ‘auxin perception signature.’”
By combining their expertise in a multidisciplinary synergy, the project partners aim to map auxin dynamics with high temporal and spatial resolution. They will apply a wide range of different methods including advanced microscopy techniques, highly sensitive quantification methods of auxin and the usage of biosensors.
Their focus will be on the model plant Arabidopsis thaliana, specifically its apical hook - a structure essential for seedling survival during soil emergence. While growing in the soil, the seedling bends forming a hook to protect the delicate apex from mechanical damage. Once reaching the light, the hook is abolished, and the plant opens its leaves toward the sun.
“The hook is an excellent model for studying growth transition and plant development in general,” explains Stéphanie Robert. “Our findings could lead to a paradigm shift in understanding how auxin influences plant growth and organ formation at the cellular and subcellular levels, potentially driving advancements in plant engineering and biotechnology.”
RESYDE – Building a virtual flower
RESYDE, the project in which Stephan Wenkel is involved in, will tackle the question how multicellular organisms generate their intricate forms. The focus of the RESYDE project is on symmetry breaking during flower development – a process by which two initially identical cells adopt different cell fates – leading to diverse forms and functions. This fundamental phenomenon is crucial in all multicellular organisms and starts with an asymmetric cell division.
The research consortium comprises beside Stephan Wenkel, Kerstin Kaufmann from Humboldt-Universität zu Berlin (Germany), the coordinator of the project, Marcus Heisler from the University of Sydney (Australia) and Henrik Jönsson from Sainsbury Laboratory, University of Cambridge (UK).
Together they have an ambitious goal: they want to build a virtual flower meristem, the stem cell containing structure from which flowers originate. It will be based on data from the model plant Arabidopsis and integrate a detailed set of parameters that define how the final flower will look like.
“Flower structures are very complex and can look very different between species. We want to understand at the single cell level how such a variety of structures develops and then use this information to model and re-engineer different floral structures”, explained Stephan Wenkel.
The four project partners bring multidisciplinary expertise to the project. They plan to exploit genetic, molecular, experimental, live imaging, computational and synthetic biology techniques to better understand how floral symmetry breaking processes that occur at the single cell level have been changed during evolution to create the wealth of floral architectures.
“Our part will be to identify microProteins and other novel protein isoforms that play critical roles in flower development. Such small proteins can regulate large protein complexes and thereby affect symmetry breaking processes during flower development”, said Stephan Wenkel.
The research consortium plans among other things to apply engineered microProteins to alter floral symmetry breaking processes and change flower architecture. One of their goals is to engineer the tomato flower structure into Arabidopsis plants and vice versa.
“Flowers are not only beautiful. They must be fertilised and develop into fruits and grains. Understanding the specifics of the flower function and structure are critical for future plant breeding and agriculture”, added Stephan Wenkel.
About ERC Synergy Grants
ERC Synergy Grants are prestigious awards given by the European Research Council (ERC) to small teams of two to four Principal Investigators. The ambition is to foster collaborative research efforts aimed at addressing complex and ambitious scientific challenges that cannot be tackled by individual researchers alone. Emphasis is put on interdisciplinary collaborations that enable pushing the boundaries of scientific knowledge through innovative and synergistic approaches.
56 grants were awarded in 2024, and the research groups will share €570 million in total. The ERC Synergy Grant scheme is part of the research and innovation programme, Horizon Europe, of the European Union.
Link to the press release from the European Research Council
Short facts about the two projects:
STARMORPH - Unravelling Spatio-temporal Auxin intracellular Redistribution for Morphogenesis
The project partners:
- Stéphanie Robert (coordinator), Swedish University of Agricultural Sciences (SLU), Sweden
- Ondřej Novák (co-applicant), Institute of Experimental Botany of the Czech Academy of Sciences, Czech Republic
- Jürgen Kleine-Vehn (co-applicant), University of Freiburg, Germany
- Alexander Jones (co-applicant), Sainsbury Laboratory, University of Cambridge, United Kingdom
RESYDE - Re-engineering symmetry breaking in development and evolution
The project partners:
- Kerstin Kaufmann (coordinator), Humboldt-Universität zu Berlin, Germany
- Marcus Heisler (co-applicant), University of Sydney, Australia
- Henrik Jönsson (co-applicant), Sainsbury Laboratory, University of Cambridge, UK
- Stephan Wenkel (co-applicant), Umeå University, Sweden
For questions, please contact:
Stéphanie Robert
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
Email:
https://www.upsc.se/stephanie_robert
Stephan Wenkel
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email:
https://www.upsc.se/stephan_wenkel
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The five UPSC researchers who received a grant from the Swedish Research Council: Laura Bacete Cano (top left; photo: Mattias Pettersson), Johannes Messinger (middle top; photo: Felizitas Messinger), Ove Nilsson (top right; photo: Fredrik Larsson), Stéphanie Robert (bottom left; photo: Erik Abel) and Stephan Wenkel (bottom right; photo: Stephan Wenkel).
This year’s call from the Swedish Research Council for projects in natural and engineering sciences went very well for UPSC. Five researchers received funding. Laura Bacete Cano was awarded a starting grant, while Johannes Messinger, Ove Nilsson, Stéphanie Robert and Stephan Wenkel received a research project grant. This high number of granted projects was only reached in 2020 before.
The five researchers will receive together a total of about 22 million Swedish krona over a four-year period. They will use this funding to work on very different biological questions covering structural biology and biophysics, cell and developmental biology, plant physiology and adaptation.
Laura Bacete Cano wants to investigate how the plant cell wall maintains its functionality under stress. Cell walls provide stability to the plant and serve as first barrier against external attacks. What makes it difficult to study them is that they are not static, permanent structures but rather react dynamically to stress and can trigger plant immune responses. By using advanced microscopy techniques, Laura Bacete Cano wants to advance technologies to study the dynamic nature of the cell wall and investigate the nature and functioning of the cell wall signals.
Johannes Messinger and his team have recently published the, to date, highest-resolution structure of photosystem II, one of the two light-conversion units of photosynthesis. The photosystem II protein complex harbors metal ions that form the water-splitting cofactor and uses the released electrons during photosynthesis. In the new project, Johannes Messinger will employ photosystem II as a model system to understand how protein-water-cofactor interactions, protein dynamics and charge fields allow the activation of abundant metals for performing complex chemistry.
Ove Nilsson’s project will focus on the regulation of phenology in trees concentrating on aspen, poplar and birch. He and his group have identified genes in aspen and poplar that are similar to flowering-promoting genes of the model plant Arabidopsis but have diverse functions in trees. Now, he wants to study how these genes are involved in seasonal growth and growth adaptation at different latitudes. His long-term goal is to understand how climate change affects the regulation of these genes and thus the ability of trees to adjust to new climates.
The fundamental question that stands behind Stéphanie Robert’s research project is how cell shape contributes to multicellularity and the proper structure and function of tissues. She and her team will study the outermost cell layer of the leaf – the epidermal pavement cells - which often form very characteristic puzzle-like patterns. Her goal is to create a geometrical map of a leaf that integrates mechanical interactions between cells, cell layers and tissues to identify key molecular players that determine the shape of a cell, tissue and organ.
Stephan Wenkel investigates microProteins, small proteins that have been often ignored because of their size but that play important roles in regulating larger protein complexes. His new project will focus on a certain subgroup of microProteins that seem to be involved in DNA methylation, a process that affects the activity of genes. By using protein biochemistry, genetics and live imaging techniques, Stephan Wenkel will study how this special group of microProteins is involved in DNA methylation during development.
The five UPSC projects awarded by the Swedish Research Council:
• Project: Watchers on the Wall: Decoding the Early Stages of Plant Cell Wall Integrity
Laura Bacete Cano
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email:
https://www.upsc.se/laura_bacete
• Project: Protein-water-cofactor interactions in biological water oxidation - a paradigm for base metal activation
Johannes Messinger
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email:
https://www.umu.se/personal/johannes-messinger/
• Project: Molecular Regulation of FT-like Genes in Latitudinal Climate Adaptation in Trees
Ove Nilsson
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
Email:
https://www.upsc.se/ove_nilsson
• Project: Coordination of cell shape acquisition during plant morphogenesis
Stéphanie Robert
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
Email:
https://www.upsc.se/stephanie_robert
• Project: Decoding Tissue Patterning: The role of microProteins in epigenetic cell memory
Stephan Wenkel
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email:
https://www.upsc.se/stephan_wenkel
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Camilla Canovi showing the first aspen trees that she modified with the CRISPR-Cas9 technology to remove a putative long non-coding RNA. She successfully defended her PhD thesis last week (photo: Anne Honsel).Many things were not known when she started her PhD, but Camilla Canovi was not scared by the abyss. She developed a bioinformatics pipeline to identify and assign putative functions to long non-coding RNAs – RNA molecules that do not contain instructions for making proteins. Camilla Canovi applied this pipeline to spruce and aspen and also started to validate her predictions in aspen trees. In this interview, she explains what long non-coding RNAs are and tells more about her research.
You worked already during your master’s thesis together with Nathaniel Street on a bioinformatics project. What convinced you to continue with a PhD in his group?
Camilla Canovi: Yes, I was doing an Erasmus traineeship together with Nathaniel Street. I did my Master’s in Italy. My professor there knew Nathaniel and send me here. We worked well together and to know him and his group made it very easy for me to say yes when he offered me the PhD project. It made it also easier for me to tell him that I do not want to spend all my days in front of a computer but would like to do also things in the lab. I know myself and that I need some variety to keep my motivation up. So, we adjusted the study plan accordingly. I really appreciate that Nathaniel gave me this freedom and the possibility to take my own choices during my PhD.
You studied long non-coding RNAs in Norway spruce and aspen. What are long non-coding RNAs?
Camilla Canovi: There is a lot of DNA that is transcribed into RNA but does not contain information for a protein. All such RNA is called non-coding RNA. Some of them are more known such as microRNAs and small interfering RNAs because they have been discovered earlier. Those ones usually have a length of below 200 base pairs and some of their functions are well studied already. All non-coding RNAs that are longer than 200 base pairs are defined as long non-coding RNAs. This group is much more diverse. The sequences often differ a lot even between relatively close related species such as spruce and pine. Sometimes only the location in the genome is conserved between species but not the DNA sequence itself which made it very difficult to study them.
Why is it important to study long non-coding RNAs and what are their functions?
Camilla Canovi: Not only the structure but also the functions of long non-coding RNAs can be very different. They can regulate gene activity in many different ways, or they can influence how accessible a certain gene is by modifying the packing of the DNA double strand. They can also serve as decoys that fish out microRNAs so that those ones are not interfering with the expression of a gene anymore. In plants, they seem to be mostly activated when the plants are exposed to stress. In humans, they are a bit better studied because they can serve as marker for cancer. However, the high diversity in function and appearance makes it difficult to study long non-coding RNAs and there is not much done yet with respect to trees like spruce and aspen.
What do you consider as the major outcome of your thesis?
Camilla Canovi: To identify long non-coding RNAs with bioinformatics analyses, we need to first define parameters which is a challenge with such a diversity in appearance. I focused on a certain group of long non-coding RNAs that do not overlap with any gene but are located only in regions between genes and developed a bioinformatics pipeline to identify them in plants. I have applied this pipeline on spruce and aspen to look for this subgroup of long non-coding RNAs, but it can be also used on other plants and to search for other types of long non-coding RNAs by modifying some parameters.
In a next step, I constructed a co-expression network to see which genes are active at the same time as the identified long non-coding RNAs. Then, I checked in which biological processes those genes were involved and assumed that the long non-coding RNA is involved in the same processes as the genes, like for example photosynthesis or leaf development. And finally, I wanted to check if our predictions were correct and modified aspen trees using the CRISPR-Cas9 technology to remove a putative long non-coding RNA. This work is still in process, but I managed to get the first modified trees and some of them are really promising. That is very exciting!
Where there any results that you did not expect?
Camilla Canovi: Many things were unknown when I started, and it was not clear what to expect, especially when trying to modify long non-coding RNAs in aspen with CRISPR-Cas9. There are a few studies in Arabidopsis but not for aspen or spruce as far as I know. I focused on long non-coding RNAs that are involved in leaf development and tried to cut them out. We did not expect that this would work right away but when I tested the first modified aspen trees, it looked like our strategy worked out. There are still many more tests to do but I was very happy to see that.
Your title starts with “Tackling a genomic abyss”. Did you face any other than the “genomic abyss” during your PhD?
Camilla Canovi: When I was about to start the functional validation of some of the identified long non-coding RNAs, I discovered that we had an error in the pipeline. The programme that should make sure to choose only regions in between genes did not work properly. So, we had to fix that which costed me quite some time. However, I was very glad that I realized it before starting with modifying aspen trees which takes even more time.
And then, there was of course the Covid-19 pandemic, and I was somehow stuck here for one year and nine months which was a bit too long. I did not want to go home where my grandmothers were waiting to see me and risk that they get infected. That felt quite long but luckily, I had good friends here.
What are you planning to do now?
Camilla Canovi: My contract lasts until January which gives me time to finish the last things. But first, I will go to Namibia for vacation for ten days to see a desert. I have never seen one before and I am curious about that. Then, I would like to change air and go back to Italy and move away from academia. I would like to try working in industry and have started to look for companies in Northern Italy now. I will see how it goes.
About the public defence:
Camilla Canovi, Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, defended her PhD thesis on Thursday, 24th of October 2024. Faculty opponent was Tanja Susanna Pyhäjärvi, Department of Forest Sciences, Viikki Plant Science Centre (ViPS), Helsinki, Finland. The thesis was supervised by Nathaniel Street.
Title of the thesis: Tackling a genomic abyss: Approaches to link long non-coding RNAs to potential biological function in Norway spruce and aspen
Link to Camilla Canovi’s PhD thesis
For more information, please contact:
Camilla Canovi
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email:
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The project led by Olivier Keech from UPSC will develop sustainable methods to produce shrimp and fish in circular aquaculture systems. Photo: Sergio Zimmermann
The Swedish Agricultural Agency has granted SEK 10 million for a project on sustainable food production, led by Olivier Keech, group leader at UPSC and Associate Professor at Umeå University. The project aims to establish and optimize sustainable production of shrimp and fish in a circular aquaculture system.
“In the project we use bio-RAS, a technology where the water contains particles which are then filtered by a mixture of microorganisms such as bacteria, microalgae and zooplankton. These convert leftover nutrients into natural feed for the fish and shrimp. In addition, it acts as a probiotic for the animals. Overall, it creates a much more sustainable loop,” says Olivier Keech.
The project is interdisciplinary and involves researchers from Umeå University, the Swedish University of Agriculture in Ultuna (SLU) as well as the newly started company Cresponix AB and Brazilian partners. Together, they will apply cutting-edge research to develop and optimize the use of bio-RAS. The technology, originally developed by professor Anders Kiessling (SLU) and Sergio Zimmerman (Zimmermann Aqua Solutions) is a tropical alternative to cold water recirculating aquaculture systems (RAS) that allows for the recapture of organic resources.
The team will create an innovative, sustainable production of feed, as well as evaluate various aspects of shrimp physiology with professor Johan Dicksved and associate professor Kartik Baruah at SLU Ultuna. Furthermore, in collaboration with professor Stefan Bertilsson SLU Ultuna, a metagenomic analysis will also be carried out to assess how the microorganisms in the shrimp's gastrointestinal system develop depending on different compositions of feed and water.
Another part of the project is to develop a mathematical model that can help control and optimize energy conversion, nutrient storage, biomass production and economic viability for the pilot plant the researchers will establish.
“This is a key component for the expansion of such facilities and municipalities, industries and future investors need to know the efficiency and return on investment of such a food production platform,” explains Olivier Keech.
For this, Olivier Keech can also count on his colleagues at Umeå University, Professor Sebastian Diehl, Department of Ecology and Environmental Science, and Associate Professor Jonas Westin, Department of Mathematics and Mathematical Statistics.
The project is part of a larger project that Anders Kiessling, professor at SLU Ultuna, and Olivier Keech initiated several years ago. In a joint venture with both academics and companies, they are establishing a pilot platform for research and development at Östersjöfabriken in Västervik.
The aim is to develop a completely circular food production system that includes both fish, shrimp, vegetables, fruit, insects, mushrooms. Such platforms should ideally be placed strategically downstream of industries, such as server halls and metallurgical companies, which emit large amounts of low-grade heat, i.e. 30-60 degrees Celsius.
“Low-grade heat has no real value in itself and is currently simply cooled down to a certain threshold and released as warm air or lukewarm water into the environment. Instead, channeling the heat into greenhouses and fixing the remaining energy into biomass is a much better way to reduce the environmental impact of human activities,” says Olivier Keech.
The idea of the research is to contribute to food security and reduce dependency on imported food. Today, close to 70 percent of the fresh produce consumed in Sweden is imported.
“By producing more "tropical" products locally, you logically lower the carbon dioxide emissions related to imports from distant countries,” says Olivier Keech.
For more information, please contact:
Olivier Keech, associate professor, Department of Physiological Botany, Umeå University Phone: +46 90 786 53 88
Email:
Anders Kiessling, professor, Swedish University of Agriculture, Ultuna
Email:
Text: Anna-Lena Lindskog, Umeå University
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Thale cress in the snow. DNA previously thought to be “junk” has now been shown to help plants to cope better with cold stress (photo: Vaughan Hurry).
A vast amount of DNA contains no genetic information and was long thought to be junk. Recent research has shown that much of this “junk” DNA is in fact activated but it was not known why. Researchers from Umeå Plant Science Centre have now shown that this activation of “junk”-DNA plays a key role in promoting plant survival during stress.
The study from Peter Kindgren’s research group from Umeå Plant Science Centre and SLU was published recently in the journal The Plant Cell.
Our genetic code is stored in the DNA. When a gene is activated, the double-stranded DNA helix is unwound to make the two individual strands and the gene that is located on one of the two strands accessible. The gene, which contains the building description for a protein, is then rewritten into RNA, which is used as a template to synthesise the protein.
In humans, only one or two percent of the DNA contains genes and thus information for proteins. The rest was believed to be junk. However, new sequencing techniques have revealed that a lot of this “junk”-DNA is activated and rewritten into RNA-templates, even though it is not used for protein synthesis.
Is there a common mechanism behind the activation of so much "junk"-DNA?
“We want to understand why so much of this “junk”-DNA is activated. This is a big question among scientists. It does not only occur in plants but also in other organisms and it is quite an investment”, explains Peter Kindgren, group leader at UPSC and researcher at SLU. “We think that there must be a common reason for this activation.”
Peter Kindgren and his research team focussed on “junk”-DNA that is located on the opposite DNA strand facing a gene. Such DNA segments are called “antisense” and are complementary to the opposite “sense” DNA segment (the gene), similarly like the two different strands of a zipper. The researchers have shown earlier that this type of antisense “junk”-DNA is often activated and rewritten to RNA in the model plant thale cress, but so far only a few examples have been further characterised in plants.
By looking through the known examples, Peter Kindgren and his group tried to identify a general function of this antisense DNA activation. They hypothesised that it might play a role in the regulation of the gene on the opposite sense DNA strand. The challenge was to devise a way to test this hypothesis. They wanted to inhibit the activation of the antisense DNA without affecting the activity of the gene on the opposite DNA strand.
Great potential to make plants grow better in more stressful environments
“We used the gene scissor CRISPR-Cas9 to manipulate the region of the antisense strand where the rewriting of the DNA into RNA is initiated. Like this, the gene on the sense DNA strand could be rewritten normally into RNA and the corresponding protein could be synthesised, but less RNA was produced from the antisense strand,” says Shiv Meena, first author of the article. He was working as postdoc in Peter Kindgren’s group but has recently started to set up his independent research group in India at the National Institute of Plant Genome Research in New Delhi.
The researchers concentrated on genes that are switched on in thale cress during cold and that help the plant to adapt. When the activity of these genes was switched off, the plants were less tolerant to cold. The researchers observed a similar response in the plants that produced less antisense RNA. They concluded that the activation of the antisense DNA increases the gene activity on the opposite sense DNA strand and think that this might be a common mechanism in plants, especially important under stress.
“We are just beginning to understand why so much of this antisense “junk”-DNA is activated in plants, but we see great potential to use this knowledge to make plants grow better in more stressful environments,” says Peter Kindgren. “This story has been brewing in the lab since my postdoc. It is amazing that we finally were able to publish it. None of the people involved are actually working in my lab anymore. One moved to India, one to France, one to Spain, one to the US, and one to Uppsala. But we pulled it off!”
The article
Shiv Kumar Meena, Marti Quevedo, Sarah Muniz Nardeli, Clément Verez, Susheel Sagar Bhat, Vasiliki Zacharaki, Peter Kindgren. Antisense transcription from stress-responsive transcription factors fine-tunes the cold response in Arabidopsis. The Plant Cell, 2024; koae160, https://doi.org/10.1093/plcell/koae160
For questions, please contact:
Peter Kindgren
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
Email:
Phone: 0046 738400272
https://www.upsc.se/peter_kindgren