The Swedish Foundation for Strategic Research (SFF) approved last week four SSF Agenda 2030 Research (ARC) Centers on Future Advanced Technology for Sustainability. The project “Re-designing photosynthesis for future food security” with Åsa Strand from UPSC as main applicant was granted. Åsa Strand and her three co-applicants want to improve photosynthesis and apply CRISPR/Cas9 and other genetic modification techniques to increase crop productivity.

The world-wide crop production is stagnating while the population is growing which threatens food security. “Zero hunger” is defined as one of 17 Sustainable Development Goals that are addressed by the Agenda 2030. Åsa Strand and her co-applicants plan to target this goal by improving crop productivity through optimising the efficiency of photosynthesis. Because plants are only using a fraction of the light energy that they perceive, the researchers want to optimise the harvest of the light energy by plants and identify limiting steps during carbon fixation.

Åsa Strand’s co-applicants are Alexey Amunts from Stockholm University, Paul Hudson from the Royal Institute of Technology (KTH) and Alizée Malnoë who is like Åsa Strand working at the Department of Plant Physiology at Umeå University. All of them are internationally recognized and bring in different competences to the project. They will closely collaborate with the biotechnology company SweTree Technologies which will help them to test their engineering strategies in transformable crop species that are relevant to the Swedish agriculture.

The researchers will use cyanobacteria and Arabidopsis as two model systems in parallel. Cyanobacteria use the light energy much more efficiently compared to plants and also their carbon fixation rates are higher. The plant chloroplasts, the place where photosynthesis takes place, share the same ancestor as todays cyanobacteria. During evolution, photosynthesis in the chloroplast was adjusted to coordinate it with the more complex development and growth of plants – on the expense of the photosynthetic efficiency. The researchers hope that they can transfer knowledge from cyanobacteria to the chloroplasts of plants and maybe even re-introduce genes that were lost or modified in plants during evolution.

Their assumption is that photosynthesis in Cyanobacteria is adapted first and foremost to biomass formation. They think that the comparison between Cyanobacteria and plants will allow them to define the bottlenecks that restrict the light harvesting efficiency and limits the carbon fixation rate. Using multiple research lines and genetic engineering, they hope to break the bottlenecks and improve the efficiency of photosynthesis in plants and like this increase their productivity. Several initiatives are working internationally on improving biological photosynthetic efficiency using different approaches and the researchers hope to complement these efforts with their novel approach.

Four strategic areas have been identified by the Swedish Foundation for Strategic Research in the frame of their call for SSF-ARC Centers. These were “Future Nuclear Power”, “Plant Biotechnology including GMO and CRISPR/Cas9” which is the area that Åsa Strand applied for, “Hydrogen/Fuel Cells and Next Generation of Antibiotics and/or Actions to prevent pandemics”. In every strategic area, one application was granted. The four centers will share 200 million SEK.

The researchers plan to compare cyanobacteria and plant chloroplasts. Both have common ancestors, but their evolution separated about 1 billion years ago (1bya). The researchers want to transfer knowledge from the photosynthetic more efficient cyanobacteria to the plant chloroplast and like this improve crop productivity. Figure: Daria Chrobok, DC SciArtThe researchers plan to compare cyanobacteria and plant chloroplasts. Both have common ancestors, but their evolution separated about 1 billion years ago (1bya). The researchers want to transfer knowledge from the photosynthetic more efficient cyanobacteria to the plant chloroplast and like this improve crop productivity (Figure: Daria Chrobok, DC SciArt).

Link to the Swedish press release from SSF:

Information about the applicants:

Alexey Amunts
Associate Professor
Department of Biochemistry and Biophysics
Stockholm University
E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: +46(0)8161003

Paul Hudson
Associate Professor
Division of Systems Biology
KTH Royal Institute of Technology
E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: +46 (0)70 783 95 07

Alizée Malnoë
Assistant Professor
Department of Plant Physiology
Umeå Plant Science Centre
Umeå University
E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: +46(0)907869314

Åsa Strand
Department of Plant Physiology
Umeå Plant Science Centre
Umeå University
E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: +46 (0)90 786 9314

Photo of Chanaka MannapperumaPhD student Chanaka Mannapperuma (photo: Lena Maria)

[2020-06-04] Chanaka Mannapperuma, PhD student in Nathaniel Street’s group at the Department of Plant Physiology and co-supervised by John Waterworth from the Department of Informatics, has developed bioinformatics tools that help biologists to analyse their complex genomics data. His aim was to create intuitive, easy to use tools that do not require specialized bioinformatics knowledge. He improved the design of the tools based on user experiences and general principals of the field of Human-computer interaction. Chanaka Mannapperuma will defend his PhD thesis at Umeå University on Thursday, 11th of June.

The topic of your PhD thesis is unusual for UPSC. What aroused your interest in this topic?

When I started at UPSC, there were not so many analysis tools available for Biologists to do their analysis easily. I have a computer science and interaction design education background, so this was a good opportunity to apply previous knowledge to make a database system and tools for Plant Biologists. Since most Biologists are not familiar with programming, they needed tools to analyse their data without learning to program themselves. I thought that this type of work is useful for UPSC and Stefan Jansson, Nathaniel Street, Andreas Sjödin and Simon Birve made me more interested and motivated to continue this work at the beginning.

How was it for you to do this type of work at UPSC?

I had a great companionship and pleasurable friendly working atmosphere at UPSC during my work. Most of my colleagues are plant biologists and they wanted to have a database system to store, filter and analyse their data. Thanks to my supervisor and his team, we managed to establish a web resource specialised for Biologists to make their research easier. I want to express my gratitude towards my colleagues and fellows at UPSC who offered constant support, availability and productive suggestions which were a determining factor for the success of my thesis.

Did it help that John Waterworth from the Department of Informatics, who is an expert in Human-computer interaction (HCI), was your second supervisor?

Yes, it was a great experience to work with John – already since I was a student in Human-computer interaction. He is an expert in this field as he has many years of experience as a psychologist. Being a psychologist, John has a good understanding and exceptional knowledge of human perception and cognitive behaviour. He was a great help to accomplish this work and thanks to John for this. Many more people from the Department of Informatics also contributed to this work. Anna Croon Fors, Karin Danielsson, Mikael Wiberg and Patrik Bjornfot are among others.

What is meant with Human-computer interaction?

The aim is to study how users interact with computer interfaces and how to use design principles, and visualization techniques to improve user interaction and make usable systems. HCI is a multidisciplinary field combining design, computer science, psychology, anthropology, sociology, ergonomics and others. This will help us to understand how we perceive different signals, process and interpret them using our cognitive abilities and evaluate the outcome. These are some of the main questions in HCI, and the entire design process helps us to make user-friendly tools.

Your thesis contains different aspects: programming, design and I guess a lot of communication with users. Which aspect did you like most?

Design, programming and user interaction are well connected. I am enjoying all three aspects and the entire design process, especially making useful tools for biologists that they can explore to gain biological insights. The design process starts with the prototype or the production tool of the previous version. To be specific, starting with the prototype, then apply design principles and visualisation techniques to reshape the tool and use heuristic evaluation methods to make usable tools with the help of user feedback. Users expect an interactively engaging and appealing experience in addition to the usable tool. Mere iteration of the design process will make better user-friendly and usable tools.

Was it difficult to get usable feedback from the users of your tools?

We used online surveys as our initial usability methods. However, we realised that although we have 1000 users that are using the PlantGenIE platform, very few of them were willing to answer the survey questions. But thanks to the technology, we had alternative usability methods such as web analytics to gain implicit user feedback. So, we could easily capture the user feedback.

I guess many biologists are very grateful for your work. Do you plan to continue working in this direction?

It was a pleasant experience, and I am enjoying work in this direction. I can also see the need for designing user centred tools that will help biologist to do their analysis much more easy. In addition to that, I have an excellent supervisor with a nice team. I am planning to continue working at UPSC and improving the resource for a while.

Chanaka Mannapperuma started to work at UPSC in 2010 as programmer with the task to develop an online tool to do a simple BLAST (Basic Local Alignment Search Tool) search for gene analyses as part of the PopGenIE website. This tool allows to compare a gene or protein sequences with a library of sequences and to identify similarities between the sequence of interest and library sequences. After four years working as programmer, he started his PhD and developed the primary tool further into an extended web resource with different functionalities for gene and genome analyses. The web resource can be found here:

Screenshot from the PlantGenIE sites Screenshot from the PlantGenIE sites

About the public defence:

The public defence will take place on Thursday, 11th of June at Umeå University. Faculty opponent will be Marek Mutwil from The School of Biological Sciences, Nanyang Technological University, Singapore. Chanaka Mannapperuma's supervisors are Nathaniel Street from the Department of Plant Physiology (UPSC) and John Waterworth from the Department of Informatics. The dissertation will be live broadcasted via Zoom.

Title of the thesis: Human-computer interaction principles for developing web-based genomics resources

Link to the thesis:

Link to the Zoom live broadcast:
Meeting ID: 623 6678 9113
Password: 878277

For more information, please contact:

Chanaka Mannapperuma
Department of Plant Physiology
Umeå Plant Science Centre
Umeå University
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

Nathanial Street and Judith Lundberg-Felten in a shared Zoom meetingNathaniel Street (left) and Judith Lundberg-Felten (right) in an online Zoom meeting

Judith Lundberg-Felten and Nathaniel Street were recently appointed as docents at SLU and Umeå University, respectively. Both are working already for several years at UPSC, first as postdocs and now as group leaders. The appointment as docent is the next career step within the Swedish academic system. Here they are talking about their career, what is driving them and their future goals.

Did you always want to make an academic career?

Judith: I have enjoyed doing research in plant biology since my Master’s project. I love the analytical, scientific approach. This and my curiosity for science has motivated me to continue on the academic path.

Nathaniel: No, for me, that came late. I didn’t think properly about it until during my PhD. By then, I knew that I loved research enough to always want to do that.

What is your driving force?

Nathaniel: The world around me. I have always been fascinated by the fact that the largescale emerges from processes at the small scale and trees are an ultimate example of that for me. I love the ordered chaos of biology and the challenge of trying to understand that system. So, my biology interest is the major force but I also want to pass on that passion to others and to create an environment where people can explore and develop their own ideas, interests and skills.

Judith: As a group leader, I also want to empower young scientists on their road to discover the molecular processes happening inside plants and to understand how these fascinating and highly diverse organisms develop and function. I believe that one day, the knowledge that I create through my research team will foster creating innovative solutions for a future sustainable society.

Why did you come to UPSC?

Nathaniel: Trees. I love working on trees and Sweden loves trees. I visited UPSC during my PhD and loved working there. People at UPSC were passionate about tree genomics and that was inspiring. They were using the latest techniques and technologies – at the time cDNA microarrays – and that also appealed to the side of me that loves new technology. Microarrays really fuelled my love of working with largescale datasets and applying that also at larger scales out in the field.

Judith: I had worked on poplar trees during my PhD project in France and when I heard about UPSC, it seemed like a dream place for me to work at, both because of its scientific excellence and extraordinary infrastructure and, because of its ‘exotic’ Northern geographical location. Moving to Sweden and receiving a (rather unexpected) postdoc-opportunity at UPSC – this was like a dream come true for me as a young scientist.

What do you like about teaching?

Judith: I love to interact with students, to hear what they are curious about and to see them learn and grow in their reflections with every new piece of knowledge and skills they acquire. Also, I find teaching a very rewarding activity as the feedback that I receive from the students makes me reflect about myself and develop new skills. I see teaching as a continuous dialogue and opportunity for development for both students and teacher.

Nathaniel: Initially, I liked simply trying to pass on my own passion for the subject. Now, I also enjoy challenging and encouraging students to develop their own learning skills to become independent learners and thinkers.

What are your goals for the future?

Nathaniel: More of the same but better – both in the research and teaching or career development aspects of the job. I enjoy approaching research from a system-wide perspective, but this does not always provide concrete end results. Learning how to do this better is my major aim at the moment. In teaching, I want to continue exploring which teaching techniques provide the best learning and development opportunities for students and to evolve my courses accordingly. For my group, I want to create an environment that supports each person in identifying, developing and exploring their interest in biology. I want to make sure that their time in the group is providing them with the skills, output and opportunities they need to advance in their careers. I don’t want my own limitations to limit others.

Judith: I have used flipped classroom techniques in the past for my own lectures and want to develop that throughout my courses even more. I have students with varying background knowledge, and I see an advantage in having them learn the basics at their own pace through recorded lectures that integrate interactive moments such as quizzes. As teacher, I can focus then on interactive activities in the physical classroom such as case scenarios, problem-based learning, group exercises, discussions and so on. The students do not only learn to remember new material, but also to apply, compare, analyse and evaluate information. It is surprising not only for me but also for the students how much they learned through such discussions and interactive lectures and I would like to develop my teaching skills further to stimulate this type of learning.

Do you have some tips for young researchers?

Nathaniel: Be sure you know what inspires you about research and always remind yourself of that to let it drive you forward. There’s lots of important, practical advice about publishing papers and thinking strategically about the next move in your career. However, if you forget why you’re doing it then none of that practical advice really matters as you need that drive to provide the energy for those practical concerns. It’s good to remember that also other routes can lead you forward. If an opportunity arises that interests you but diverges from the model career path, don’t be blind by focusing only on strategic career advices.

Judith: Yes, I agree on that. I think it is very important to find out early during your career what you are passionate about, what you are good at and what makes you get out of bed in the morning with a smile on your face. Set yourself a goal and pave your unique path with patience and kindness for yourself. And remember: Doubt will kill more dreams than failure ever will. Believe in your dreams!

Irena Fundová successfully defended her PhD thesis at SLUIrena Fundová successfully defended her PhD thesis at SLU (photo: Sonali Ranade)

[2020-04-29] It is easy to measure the height or the stem diameter of a tree. But how can you get a clue about the quality of the wood without cutting down the tree? Irena Fundová, PhD student in Harry Wu’s group at UPSC, tested in her PhD thesis different methods to estimate the wood quality of Scots pine without harming the tree. Based on her results, she gives advices on the applicability of the tested methods and suggests a breeding strategy to improve growth, fibre and wood quality of Scots pine at the same time. Irena Fundová has successfully defended her PhD thesis on Friday, the 24th of April in P-O Bäckströms sal at SLU in Umeå.

What aroused your interest in your PhD project?

I wanted to continue with research on wood quality in forest trees that I started already at the University of British Columbia in Canada. I was particularly interested in applied research that would be as practical as possible for forestry and wood processing industries.

Did the fact that the PhD project was part of the industrial graduate school, that is a collaboration project between the UPSC Centre for Forest Biotechnology and its industrial partners, influence your decision?

Yes, it was important for me. I viewed it as a bridge between university science and industrial application. I hope that my thesis will be useful for my host company (Skogforsk).

What was most fascinating during your PhD?

I really enjoyed fieldwork. I travelled all over Sweden and visited many remote places. Sometimes we had to stay in a tent as there was no accommodation nearby. We met a lot of wildlife including a bear. I also had the opportunity to visit USA, Brazil and China and see their forest tree improvement programs. It was a great experience for me.

What was the most disappointing experience you had during your PhD?

The first year of my PhD was very difficult because I had no data. But then we shifted the direction a little bit, got enough funding through several research grants and my work started to progress.

What is the major outcome from your thesis? Can you provide practical information or tips for forestry and wood processing industries?

I tested the suitability of various methods for rapid and non destructive assessment of wood quality traits that are important for construction, pulp & paper and bioenergy industries. I concluded that 1- the resistograph, a tool based on drilling resistance, is suitable for non-destructive wood density assessment, 2- standing-tree acoustic velocity provides a good estimate of sawn-board stiffness and strength, 3- grain angle measured under bark of standing trees well predicts sawn-board twisting and crooking, and 4- Fourier transform infrared spectroscopy is suitable for non-destructive assessment of the chemical composition of wood in Scots pine. Furthermore, I evaluated the potential of growth and wood quality traits for simultaneous genetic improvement through recurrent selective breeding.

What are your plans for the future?

I have got several job offers (although none of them is from Sweden) but it is hard to make any plans during the current coronavirus pandemic. Before the situation clears off, I would like to process the tons of data I have generated during my studies that I could not include in my thesis.

Irena Fundová was student of the industrial graduate student Research School of Forest Genetics, Biotechnology and Breeding at UPSC. She performed her PhD studies in close collaboration with Skogforsk, the Forestry Research Institute of Sweden.

About the public defence:

The public defence took place on Friday, 24th of April at SLU Umeå. Faculty opponent was Philippe Rozenberg from the French National Research Institute for Agriculture, Food, and Environment (INRAE), Val de Loire, France. Irena Fundová's supervisor is Prof. Harry Xiaming Wu. The dissertation was live broadcasted on

Title of the thesis: Quantitative Genetics of Wood Quality Traits in Scots Pine

Link to the thesis:

For more information, please contact:

Irena Fundová
Department of Forest Genetics and Plant Physiology
Umeå Plant Science Centre
Swedish University of Agricultural Sciences
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

One of Irena Fundová's trial plots - a Scots pine progeny test that is used for breeding (photo: Irena Fundová)One of Irena Fundová's trial plots - a Scots pine progeny test that is used for breeding (photo: Irena Fundová)Irena Fundová measuring acoustic velocity on a standing Scots pine tree (photo: xxx)Irena Fundová measuring acoustic velocity on a standing Scots pine tree (photo: Tomáš Funda)
Scots pine logs in a sawmill - Irena Fundová used logs as reference to assess wood quality in standing trees (photo: Irena Fundová)Scots pine logs in a sawmill (photo: Irena Fundová)The final product - sawn boards from Scots pine (photo: Irena Fundová)The final product - sawn boards from Scots pine (photo: Irena Fundová)
Thesis defence of Shashank Sane (left); his supervisor was Ove Nilsson (right); photo: Sonali RanadeShashank Sane (left) and his supervisor Ove Nilsson (right) after the dissertation; photo: Sonali Ranade

[2020-04-07] The genetic machinery controlling aging and seasonal growth in hybrid aspen is using at least partly the same molecular components. Shashank Sane, PhD student in Ove Nilsson’s group at UPSC, modified some of these components and characterised their function during those developmental processes. By comparing his results from hybrid aspen with findings in the annual plant thale cress, he demonstrated that the genetic components are similar but the way how the components work together differs. He successfully defended his PhD thesis today in P-O Bäckströms sal at SLU in Umeå.

Shashank Sane has focussed in his PhD thesis on two aspects of vegetative growth in hybrid aspen: the transition from a young to an adult stage and the adaptation to seasonal growth. The underlying regulation networks are very complex but uses similar components that are also involved in the regulation of flowering in thale cress. By genetically modifying three of these components in hybrid aspen, Shashank Sane demonstrated that they can interact in different ways with the other regulatory components of this network than was previously described for thale cress.

In his experiments, Shashank Sane used modified hybrid aspen that were overexpressing microRNA miR156 and others in which microRNA miR172 was inactivated. MicroRNAs are small molecular regulators of gene expression that are found in all plants and animals. MiR156 is in thale cress active in seeds and young plants and inhibits genes that induce flowering. In contrast, miR172 becomes activated with increasing age and blocks genes that repress flowering. The two microRNAs counteract each other in its action and their regulation is closely adjusted to each other.

The two differently modified hybrid aspen trees showed similar characteristics. In the second growing season when the leaves are normally getting a shorter and rounded form and become darker green, the leaves of the modified trees were still longer and lighter green, typical characteristics of young leaves. Shashank and his colleagues concluded that the modified trees need longer to pass from the young state into the adult state than the non-modified trees. They also simulated autumn conditions through shortening of the day length. The modified trees needed one week more than non-modified trees until they stopped their growth.

“We expected that these two gene modifications have similar effects on the growth of the trees as miR156 is once overactive and in the other trees, its antagonist miR172 is blocked,” says Shashank Sane. “But it was really astonishing for us to see that some of the genes that are regulated by those two microRNAs were regulated in the opposite way in hybrid aspen than in thale cress. Our suggestion is that the function of these genes has evolved differently in hybrid aspen than in thale cress, probably to adjust to the perennial growth.”

The researchers made a similar observation when studying the hybrid aspen genes that correspond to the thale cress gene GIGANTEA. In thale cress, this gene is part of a regulation network that senses the day length and regulates flowering. Shashank Sane and his colleagues focussed on the role of the poplar GIGANTEA genes for growth cessation and bud formation. Also here, they demonstrated that the network components interact in different ways to regulate the growth stop and bud set in hybrid aspen than they do during induction of flowering in thale cress.

About the public defence:

The public defence took place on Tuesday, 7th of April at SLU Umeå. The faculty opponent was Professor Miguel Blazquez from the Institute for Plant Molecular and Cellular Biology, Valencia, Spain who participated in the defence remotely. Shashank Sane's supervisor was Prof. Ove Nilsson. The defence was live broadcasted.

Title of the thesis: Molecular Regulation of Bud Phenology and Vegetative Phase Change in Populus Trees

Link to the thesis:

For more information, please contact:

Shashank Sane
Department of Forest Genetics and Plant Physiology
Umeå Plant Science Centre
Swedish University of Agricultural Sciences
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

Female scientists working at UPSCSeveral of the female scientists currently working at UPSC (photo: Anne Honsel)

[2020-02-11] Today is the International Day for Women and Girls in Science. Time to reflect on UPSC’s achievements in terms of gender equality. Since 2007, UPSC is working on improving its gender balance among its scientists and has reached now its goal of having 40-60 percent of women throughout the different career stages – from PhD students to full professors.

It all started on initiative of Vinnova and VR who funded a large project, the Berzelii Centre for Forest Biotechnology that continues now as a Vinnova Competence Centre. The funding agencies asked to analyse the gender equality within the centre and which actions were planned to improve the situation. This was when the UPSC management started to think about ways to address a gender imbalance among group leaders. Since then, the percentage of female group leaders at UPSC has increased continuously and is now at 45 percent.

“When we started to analyse the gender balance in 2007, we were pretty much balanced for PhD students, slightly imbalanced for postdocs but at the group leader positions there was a clear bias towards men that got progressively worse as you moved from assistant to associate professors and with just one full professor that was female”, says Ove Nilsson, director of UPSC. “We realized that if we could maintain the balance that we have at the PhD and postdoc level when these people move further on in their career, the imbalance would start to even out.”

That is why the UPSC management started to implement a programme to support specifically newly started group leaders. This was possible due to the funding from Vinnova and VR and the matching funding from the universities. All new group leaders received extra resources to hire e.g. PhD students and postdocs and it ensured that they had six instead of four years of funding for their own positions. The aim was to give them the good conditions to merit themselves and to allow them to establish their group.

“We did not do anything that was specifically targeted towards women”, explains Ove Nilsson. “Just by giving young researchers good starting conditions we managed to level out the gender imbalance among group leaders. The challenge now is to maintain this balance. We continue to support new group leaders with good starting packages but we also hope that now when our environment is more balanced, it becomes more attractive for all genders and like this maintains its balance.”

Special caution is set on the recruitment process. The goal is to prevent any bias but focus on recruiting the best qualified person for the respective position. The UPSC management tries to enforce this all the way from PhD students, to postdocs and group leaders. Of special help for recruiting excellent scientists and especially female scientists is of course Sweden’s family friendliness. “Many foreign scientists are not aware of the support that is offered to families with kids when they come to Sweden but after a while, they appreciate it a lot”, emphasizes Ove Nilsson.

The purpose of the International Day for Women and Girls in Science is to empower women and girls in science to achieve equality. It was established in 2005 by the United Nations General Assembly and implemented by UNESCO and UN-Women. According to UN-Women, 30 percent of researchers world-wide are women and they are still disadvantaged in their career.

Hannele Tuominen and Sacha Escamez in the UPSC greenhouse, watching Arabidopsis seedlings on plateHannele Tuominen (left) and Sacha Escamez (right) in the UPSC greenhouse (photo: Anne Honsel)

[2020-01-16] For long, it was assumed that cell death occurs mainly during animal organ growth but not in plant organs. A research group led by Hannele Tuominen from UPSC demonstrated now that the death of certain cells in the root facilitated the growth of lateral roots. These new findings hint at organ growth of plants and animals might not be so different as thought. The study was published today in the journal Current Biology.

In contrast to animals, plants are forming new organs like lateral roots continuously. These roots grow out from the main root and help to explore the soil for nutrients and give additional stability to anchor the plant in the soil. Elimination of cells plays an important role in animal development, e.g. for the formation of fingers or toes. The cells between the digits die during development to allow the establishment of the individual digits. Also in plants, developmental cell death occurs but so far it was not clear that it is needed to facilitate the emergence of lateral roots like it is shown now in the recent publication.

The researchers around Hannele Tuominen, until 2019 associate professor at Umeå University and now professor at SLU, and her postdoc Sacha Escamez used different methods to demonstrate that cell death is occurring and enables lateral roots to emerge from the main root in the plant thale cress. “We first found that genes, indicating developmental cell death, were activated in cells that are laying over those cells that form the future lateral roots”, says Hannele Tuominen. “That made us curious and we wanted to analyse this in more detail.”

The researchers used different microscopic techniques to show that those cells were actually dying. Among others, they applied dyes that stain either living cells or dead cells and fluorescent markers that are only visible at certain pH values. Important parts of the plant cells become acidic when the cell dies causing the signal from the marker to disappear.

To make the story even more thorough, the researchers used an additional approach. They analysed a thale cress mutant which is lacking a cell death regulating protein. The growth of lateral roots in this mutant was delayed. The researchers could restore the normal development genetically and also physically by using optical tweezers.

In the genetic approach, they introduced a mammalian gene, known to induce cell death, into the mutant and targeted it to only affect those cell types that they observed to die in the non-mutated plants. The lateral roots of the resulting double mutant grew normal without any delay.

In parallel, the researchers applied optical tweezers to wound cells and like this induce the death of the cell. Optical tweezers use a highly focused laser beam to manipulate microscopically small objects. “This is a very precise optical tool. We can target individual cells and wound them. Three hours after we wounded the cells, they died”, explained Sacha Escamez. “When we applied this method to the mutant whose lateral roots normally grow slower, their lateral roots grew significantly faster.”

Researchers from UPSC, from Umeå University, Israel, Germany and the United Kingdom contributed to the publication. “We started this project several years ago and are very pleased that we could now round it up with help of the expertise of all contributing authors”, pointed Hannele Tuominen out. “However, as it is often in science, this will not be the end of the story but it opens up many new questions for further studies.”

About the article:

Sacha Escamez, Domenique André, Bernadette Sztojka, Benjamin Bollhöner, Hardy Hall, Béatrice Berthet, Ute Voß, Amnon Lers, Alexis Maizel, Magnus Andersson, Malcolm Bennett and Hannele Tuominen (2020). Cell death in cells overlying lateral root primordia facilitates organ growth in Arabidopsis. Current Biology.

For more information, please contact:

Hannele Tuominen
Department of Plant Physiology
Umeå Plant Science Centre
Umeå University
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: +46 90 786 9693
Twitter: @hanneletuominen

Sacha Escamez
Department of Plant Physiology
Umeå Plant Science Centre
Umeå University
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Twitter: @SachaEscamez

Research on trees is one of our main focus at UPSC. We often use genetically modified trees as tool to understand tree growth and development. Take a look on how we make and work with genetically modified trees!

OveNilsson 1920x1080

Ove Nilsson (Photo: Anne Honsel)

On their meeting on the 12th of December 2019, the Royal Swedish Academy of Agriculture and Forestry (KSLA) elected 30 new fellows. Ove Nilsson, director of UPSC and professor at the Swedish University of Agricultural Science, will be one of eight new fellows that will join the Forestry section of the academy. The fellows are chosen because of their outstanding knowledge and experience in their respective field of work. They are expected to actively participate in the activities of the Academy.

The Forestry section of the Academy works with questions regarding forest management and usage of the forest as natural resource including industrial and market aspects. It takes up specific education and counselling questions and questions related to hunting as well as environmental issues that are associated with the liability of the industry sector. Among the eight new Forestry sector fellows are six Swedish citizens and two foreign fellows. 

The Royal Swedish Academy of Agriculture and Forestry (KSLA) was founded in 1811. Apart from the Forestry section, it comprises two other sections, a General section and an Agricultural section. The Academy is a free and independent network organization working with issues related to agriculture, food, forestry, fishing and hunting. Its independent position shall create a unique opportunity for meetings and constructive discussions, which can be used as starting point for taking initiatives on measures or activities that stimulate development in the respective focus areas. 

Link to the announcement of the Royal Swedish Academy of Agriculture and Forestry (in Swedish) 

1920 special issue
The newly printed version of the special issue.  (Photo: Carolin Rebernig)

The Scandinavian Journal of Forest Research recently published a special issue on the usage of vegetatively propagated Norway spruce clones in Swedish forestry. The UPSC Centre for Forest Biotechnology, a Vinnova Competence Centre, initiated this publication to disseminate research findings widely within the forest sector. Lately, the large-scale usage of genomically selected, vegetatively propagated plants became technically possible and the researchers want to launch a discussion about the pros and cons of the usage of clones. During 2020, the results of the issue will also be presented and discussed in an open seminar. 

The need of an educated discussion about gains and possible risks advanced the idea of publishing a special issue about the usage of clones in Swedish forestry. “We initiated an extensive literature search on the current knowledge related to the use of clones in forestry and its implications for Swedish forestry. This involves knowledge about the effects from a breeding, silviculture, population genetics and ecology standpoint” explains Ove Nilsson, the Director of the Vinnova Competence Centre and guest editor of the special issue. 

All together the reviews show that not only from an economical viewpoint considerable gains can be made by the use of clonal mixtures, but also that the effect on the genetic diversity in Swedish forests will be very minor during the foreseeable future. Ove Nilsson emphasizes that due to the rapidly changing climate quick selection methods to deploy better adapted plants are needed. “We show that these techniques can be key to be able to meet future rapid changes reacting on for example pathogens and droughts caused by the climate change. This adaptation process is currently very slow.” He also pointed out that it is important for UPSC to discuss this topic. “We have knowledge in this area and we have a goal to make sure that our basic research findings can be used to breed for future generations of tree seedlings with better properties and better adaptation to new climate.”

Norway spruce is one of the economically most important forest trees in Sweden. Efforts to optimize productivity, resistance to diseases and to get more resilient plants adapted to a changing climate are constantly made. One way to get rapid access to the very best material from the operational tree breeding programs is vegetative propagation – especially when this method is used in combination with applications of genomic information through a process called genomic selection. The discussion about gains and possible risks of such applications, especially about the effects of a reduced genetic diversity when using clones, is ongoing. 

Full reference of the publication and link to the online edition:
Special Issue: Using Norway Spruce Clones in Swedish Forestry. Scandinavian Journal of Forest Research, vol. 34, 2019, Issue 5.

For more information please contact:
Ove Nilsson
Umeå Plant Science Centre 
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Science
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