Jansson Stefan 5135 042409 MPN 1920x1080Jansson Stefan (Photo: Mattias Pettersson)

[2019-03-19] Stefan Jansson, Professor at the Department of Plant Physiology, talked on the radio show Morgonpasset on Radio Sweden P3. He explained how trees know that it is autumn, genetic relationships between trees, if they have feelings and why trees can be green in winter.

Please find the full interview here: https://sverigesradio.se/avsnitt/1271073

BKT 2017 1920x1080 MalinGronborgBarbara Terebieniec (Photo: Malin Grönborg)

[2019-03-14] Barbara Terebieniec, PhD student at the Department of Plant Physiology, wanted to identify the factors that determine the shape of a leaf. Using different systems biology approaches, she and her colleagues identified genes that are controlling leaf shape in European aspen. Barbara Terebieniec successfully defended her PhD thesis today at Umeå University.

Why did you choose your project?

I was interested in working with populations and phenotypic traits and leaf shape is one of the most obvious characteristics of the plant phenotype.

What was most fascinating during your PhD?

I was collecting buds throughout the summer and cross-sectioned them to prepare them for the microscope. Like this, I could follow the full development of a leaf from the start until the bud flash under the microscope. That was very fascinating to see.

What was most disappointing during your PhD?

In collaboration with SciLifeLab, we developed and optimized the Spatial Transcriptomics (ST) method for our poplar bud samples. After we successfully optimized the ST method for our bud samples, we realized that the current resolution of this technique for plant samples is too low for the tiny buds. So, we could not answer all our questions even though we achieved what we planned in this project.

What do you like about UPSC?

UPSC with all the people from different countries creates this nice multicultural bubble. I met many nice people and made lots of new friendships.

What are your plans for the future?

Two years ago, I started working on my own start-up. I was very frustrated about keeping track of my lab samples in commonly used -80°C freezers. Our idea was to develop FreezFiler, a digital, non-intrusive system using computer vision. It can be placed on the -80°C freezer to read barcode tagged samples and simplifies the inventory of the freezers. We are now on the way to register a company and launch our first product. It means a lot of work, but also a lot of excitement and I am looking forward for these new challenges.

About the PhD thesis

Barbara Terebieniec and her colleagues exploited several different bioinformatics approaches to identify genes that are controlling leaf shape. Their results show that leaf shape is controlled by a complex network of many different genes and that each of those genes contributes minorly to the final leaf shape.

They compared the genetic setup of a collection of aspen trees with different leaf shape and identified genes that are associated with leaf shape. In a next step, they showed that a number those genes also play a role during leaf development. For this, they compared the genetic setup of leaves of different age, developing on one individual tree.

In an additional approach, Barbara Terebieniec optimized successfully the method spatial transcriptomics for aspen buds together with researchers from SciLifeLab. With this technique they hoped to identify those genes that are specifically expressed in the developing leaf within the bud. Even though they successfully established the method, they could not resolve spatially which genes were active during leaf development in the very young leaf because the size of the tissue was too small for the technique.

About the defence:

Barbara Terebieniec defended her thesis entitled “Using systems genetics to explore the complexity of leaf shape variation in Populus tremula” on Thursday, 14th of March. The public defence took place at 10:00am in Lilla hörsalen (KB.E3.01) in the KBC building, Umeå University. Faculty opponent was Chung-Jui Tsai from the Department of Genetics, University of Georgia, USA. Supervisor of the PhD thesis was Nathaniel Street.

Link to the thesis: urn:nbn:se:umu:diva-156464

For more information, please contact:

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

SPPS prizes 2019 1920x1080The three SPPS awardees from UPSC (from left to right): Åsa Strand, Torgny Näsholm and Karin Ljung (Photo: Anne Honsel)

The council of the Scandinavian Plant Physiology Society (SPPS) has selected the winners of the SPPS Prizes 2019. Three of the seven awardees are affiliated with the Umeå Plant Science Centre. Karin Ljung receives the SPPS Prize, Åsa Strand the Physiologia Plantarum Prize and Torgny Näsholm receives the SPPS Innovation Prize together with Barbara Halkier from the DynaMo Center at the University of Copenhagen.

SPPS is awarding biannually six prizes to acknowledge scientists, located in one of the Nordic countries, for outstanding achievements in plant sciences. Karin Ljung, group leader at UPSC and professor at the Swedish University of Agricultural Sciences (SLU), is receiving the SPPS Prize for her extensive and significant contributions to plant science. She started her own group at UPSC in 2005 and is now for five years in a row acknowledged as one of the Highly Cited Researchers by Clarivate Analytics. Her research focusses on root growth and development and the role of plant growth substances in these processes.

The Physiologia Plantarum Prize goes to Åsa Strand for her recently published ground-breaking work. Åsa Strand, also UPSC group leader and professor at Umeå University, wants to understand how the chloroplasts and mitochondria communicate with the nucleus. Her group identified in one of her recent publications in the journal Nature Communications a new molecular link that synchronizes gene expression in the chloroplast and the nucleus during seedling development in response to light. The Physiologia Plantarum Prize is the only SPPS prize that is open to all researchers world-wide and not only to SPPS-members.

The SPPS Innovation Prize honours scientists who manage to transfer their basic plant research into practical applications. Torgny Näsholm, associated group leader at UPSC and professor at SLU, and Barbara Halkier, professor at the University of Copenhagen and head of the DynaMo Center, are sharing the prize this year. Torgny Näsholm demonstrated that trees use amino acid molecules as nitrogen source. His findings led to the development of new fertilizers. Barbara Halkier and her group are working on plant-specific substances that are serving for example as defence compounds. Based on their results, they have together with Bayer Crop Science developed a new, more resistant oilseed crop.

The other three awards go to Jens Sundström and Charles Melnyk, both from the Swedish University of Agricultural Sciences (SLU) in Uppsala, and to Moona Rahikainen from the University of Turku. She receives the SPPS Best PhD thesis prize. Jens Sundström receives the SPPS Popularisation Prize, a prize that awards public engagement for plant research. Charles Melnyk gets the SPPS Early Career Prize to honour the significant progress he made in setting up his independent research group. The awards are officially handed over in the biannual SPPS Congress that will be held this August in Umeå.

More information about the prizes on the SPPS homepage: http://spps.se/spps-prizes/

More information about the prize winners:
Karin Ljung: www.upsc.se/karin_ljung
Åsa Strand: www.upsc.se/asa_strand
Torgny Näsholm: www.upsc.se/torgny_nasholm and https://www.slu.se/en/cv/torgny-nasholm/
Barbara Halkier: https://dynamo.ku.dk/people/halkier/
Jens Sundström: https://www.slu.se/en/departments/plant-biology-forest-genetics/research/groups/jens-sundstrom/
Charles Melnyk: https://melnyklab.wordpress.com/
Moona Rahikainen: https://www.utu.fi/en/people/moona-rahikainen
Link to her PhD thesis: https://www.utupub.fi/bitstream/handle/10024/145000/AnnalesAI582Rahikainen.pdf?sequence=1&isAllowed=y

Sommarin marianne 0801 110923 EBE 1920x1080Marianne Sommarin, Professor at the Department of Plant Physiology, Umeå University (Photo: Elin Berge)

The University board of Umeå University has decided to award Marianne Sommarin with Umeå University’s Medal for Merit. The Medal is given to people that made particularly significant contribution to the University.

Marianne Sommarin started to work as guest professor at the Umeå Plant Science Centre in 2003 and became Professor at Umeå University in 2018. She was Deputy Vice-Chancellor of Umeå University in the years 2008-2016, advisor for the Vice-Chancellor and had assignments for a number of national research infrastructures. She is currently chair of the national board of the MAX IV Laboratory, the Swedish synchroton facility.

Find more information in the Swedish Press Release from Umeå University

SonaliRanade ScotsPine forest 1920x1080 2Swedish Scots Pine forest; photo: Sonali Ranade

The Knut and Alice Wallenberg Foundation approved large projects on tree research. SEK 180 million will be invested for research on tree genes, forest biotechnology and forest genetics. The projects involve a collaboration between UPSC and the Science for Life Laboratory.

The projects are coordinated by Ove Nilsson, director of UPSC, and Ulf Gyllensten from Uppsala University. The first project aims to identify new genes that control growth and wood formation in trees. Part of this project is based on a fully automated phenotyping platform that is established at UPSC. Hundreds of trees can be grown on conveyor belts at this platform and their growth and other properties are automatically measured. This platform is so far unique for dedicated tree research.

The other project has a focus on genomics and forest genetics and will follow up on the large project that led to the first mapping of a conifer tree genome, the Norway spruce genome. That previous project was also funded by the Knut and Alice Wallenberg Foundation and was as well a collaboration between UPSC and the Science for Life Laboratory. In the new project, an updated and significantly improved version of the spruce genome will be developed. In parallel, the genome of Scots pine will be sequenced.

Moreover, genetic variations in the genome of thousands of spruce and pine trees that are linked to the Swedish coniferous breeding programs will be analysed. This will provide important basic research tools to understand the trees' natural variation and allow the development of new efficient tools for tree breeding, so-called genomic selection. This part of the project takes place in close collaboration with the Forestry Research Institute of Sweden (Skogforsk).

The projects are approved together with another project on forest production and forest management at the Swedish University of Agricultural Sciences (SLU) that is coordinated by Tomas Lundmark. The latter project will ensure that the entire potential of the genetics project and the latest breakthroughs in plant nutrition research are further exploited and developed. With the support of new digital technology, forest growth will be enhanced by increasing the diversity in forestry. The idea is to combine the right plant with the right forest management action at the right place to get the best growth-enhancing effect.

Forest management programs will be developed by utilizing the latest basic research on how tree growth is affected by ecophysiological factors such as nutrition and water, how trees collaborate with fungi and microorganisms and on the effect of tree competition, not least under the ground. The aim is to at least double the growth increase that is reached today. With enlarged availability of renewable forest raw materials, the forest can further contribute to the growing bioeconomy and mitigate the effects of climate change.

For questions please contact:
Professor Ove Nilsson, SLU
email:This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone: 070-286 90 82

Professor Tomas Lundmark, SLU
email: This email address is being protected from spambots. You need JavaScript enabled to view it.
phone: 070-631 74 12

Link to the press release on the SLU homepage

Ljung Karin 3157 160210 MPN 1920x1080Photo: Mattias Pettersson

[2018-12-18] Formas, a Swedish Research Council for sustainable development, announced yesterday the members of their Scientific Council for the coming three-year period. Karin Ljung will be one of the thirteen members of the council. She was already member of Formas’ Scientific Council in 2016-2018 and her mandate was extended now for another period.

Formas is the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning. It is a government agency that belongs to the Ministry of the Environment and Energy. Formas is funding research within the areas of environment, agricultural sciences and spatial planning.

Seven of the members of Formas’ Scientific Council are researchers that are elected by an electoral community of other researchers from Swedish universities. The other six members are assigned by the government. The Scientific Council decides on the focus of the research that will be funded and how the funding will be allocated.

Link to the Swedish announcement on Formas’ homepage:
IMG 4877 Strand group Dec 2018a 1920x1080Åsa Strand (first from left in the first row) and her group in December 2018 (photo: Anne Honsel)
[2018-12-13] The Swedish Research Council announced the new members of its board and of its scientific councils. Åsa Strand, professor at UPSC, is one of the nine members of the Scientific Council for Natural and Engineering Sciences. Her mandate is for three years (2019-2021).

The Swedish Research Council is a government agency within the Ministry of Education and Research that fund research and research infrastructure in all scientific disciplines. The council also has an advisory role to the Government on research policy issues and work to increase understanding of the long-term societal benefits of research.

The new members of the Scientific Councils are elected by an election assembly that is formed by representatives from the Swedish higher education institutions. In total, 165 electors are selected to appoint the new members of the three Scientific Councils and also the members of the board of the Swedish Research Council.

IMG 4900 AgriseraPrize2018 920x1080The Agrisera prize 2018 was presented to Sacha Escamez (middle) by Joanna Porankiewicz-Asplund (right) from Agrisera and by the chair of the UPSC board, Catherine Bellini (left). Photo: Anne Honsel

[2018-12-12] Sacha Escamez receives this year’s UPSC Agrisera Prize. The award was announced today during the traditional UPSC Christmas lunch. Sacha Escamez is awarded for his scientific achievements and engagement in scientific discussions at UPSC and for his valuable contribution in upgrading the UPSC microscopy platform. The prize values that Sacha Escamez’s diverse commitments helped to improve UPSC’s work and social environment.

Sacha Escamez successfully carried out research on the regulation of lignification and cell death during xylem development first as a PhD student and now as postdoc in Hannele Tuominen’s group. He actively participates in and encourages scientific discussions at UPSC and also promoted his research in a public science talk for the Swedish television last year.

This year, he invested a lot of time in upgrading the UPSC microscopy platform by collecting the requirements and wishes from his colleagues, testing out different systems and negotiating with the companies. He is taking on a key role in setting up single molecule detection methods that can be done with the new instrumentation at the UPSC microscopy platform, and he will help to introduce users to those new methods.

The UPSC Agrisera Prize is awarded every year to a PhD student, Postdoc or technician at UPSC for excellent scientific achievement and positive contributions to improve the UPSC working environment. Four nominations were sent in by Sacha Escamez’s colleagues for the UPSC Agrisera Prize this year. Sacha Escamez’s nomination stuck out because it emphasized not only his scientific achievement and encouragement for the microscopy platform but also his social engagement (e.g. by creating the UPSC innebandy team) to make UPSC a nice place to work at.

Link to the video of Sacha Escamez public science talk "How do plants make plumbing pipes from cells?"
Haas Julia 9594 170116 MPN 1920x1080Julia Haas; photo: Mattias Pettersson

Climate change will affect Norway spruce trees and also the bacteria and fungi that are living in symbiosis with the tree. Julia Haas showed in her PhD thesis that Norway spruce uses special strategies to adjust to cold and drought stress and that the microbial community living together with the trees is more diverse when the trees are fertilized. Her findings are important to predict how future boreal forests can cope with the changing environment. Julia Haas will defend her PhD thesis on Friday, 14th of December at Umeå University.

Higher temperatures, summer droughts and changes in the seasonal cycle with increasing late frost events in spring will not only compromise the productivity of Norway spruce forests but could threaten the existence of Norway spruce in boreal forests. Breeding for higher stress tolerance will help to adapt future tree generations to those challenges. Julia Haas identified genes that are involved in the regulation of drought and frost tolerance and therefore good targets for breeders to improve the tolerance against abiotic stresses in Norway spruce.

In her experiments, Julia Haas compared drought and frost responsive genes in Norway spruce seedlings with known changes in the herbaceous model plant Arabidopsis thaliana. Her results showed that well-known transcription factors that regulate the expression of a multitude of other genes in Arabidopsis under drought or frost were not expressed or lacking corresponding gene models in the Norway spruce genome.

“Norway spruce often grows in harsh environments and in extreme climates. This, together with the evolutionary distance to flowering plants can explain the observed differences”, explains Julia Haas. “It is not possible to just transfer knowledge from evolutionary younger but better studied agricultural crops or broad-leaved trees to Norway spruce. Breeding and genetic engineering of Norway spruce requires a special tool set making it more stress tolerant. My research provides a first insight into Norway spruce-specific mechanisms.”

The fitness of a tree is also influenced by microorganisms living in symbiosis with the tree. Bacteria and fungi can have beneficial effects on the growth and improve the abiotic stress tolerance of the plant host. However, climate change and human activities that increase the nutrient input in ecosystems can have both positive and negative effects on plant-associated microorganisms.

Julia Haas and her colleagues studied the diversity and composition of microorganisms in a Norway spruce forest that was fertilised over the last 25 years. Intriguingly, they found that the effect of fertilisation on the diversity of symbiotic fungi and bacteria was positive and that microbial communities with higher nutrient preferences established.

“Responses in this forest ecosystem are highly dynamic and processes involve complex interactions between fungi, bacteria and plants. But research has focussed for long time only on mycorrhizal fungi and trees. We need to start look at functions and the role other microorganisms play to fully comprehend how future changes will affect the whole ecosystem”, says Julia Haas. “Only then can we make reliable predictions about the robustness of the ecosystem to climate change.”

To identify beneficial plant microbiota is also interesting for the forest industry. The microorganisms can be applied in tree nurseries to improve the growth of the seedlings and this may help to secure tree production and growth in challenging climatic conditions in the future.

Julia Haas performed her graduate studies at the Umeå Plant Science Centre, Department of Plant Physiology, Umeå University. Her projects were in close collaboration with the Swedish forest company Holmen Skog AB.

Link to the thesis: http://umu.diva-portal.org/ 

About the thesis defence:

On Friday, the 14th of December, Julia Haas, Department of Plant Physiology, Umeå University, will defend her thesis, entitled ’ Abiotic stress and plant microbe interaction in Norway spruce’. The public defence will take place at 10:00am in Carl Kempe salen (KB.E3.03) in the KBC building, Umeå University. The faculty opponent will be Jennifer Baltzer, Associate Professor and Canada Research Chair in Forest and Global Change Department of Biology, Wilfrid Laurier University, Waterloo, Canada. Supervisor of the PhD thesis was Vaughan Hurry.

For more information, please contact:
Julia Haas
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

Text: Julia Haas, Anne Honsel

KarinLjung T1A8799 ElisabethOhlsonWallin 1920x1080Photo: Elisabeth Ohlson Wallin

Clarivate Analytics published recently their list of world-class researchers in social sciences and sciences. Karin Ljung is again one of those. Her papers are highly cited and rank in the top one percent in the field Plant & Animal Science in the years 2006-2016 in Web of Science.

Since 2014, Clarivate Analytics is publishing its Highly Cited Researchers list once a year based on citation analysis in Web of Science. In all five years, Karin Ljung was named in the list. This year, Clarivate Analytics extended their 21 field categories to a new category that considers researchers that publish across fields. About 6000 researchers are identified in the list as top researcher, 4000 in specific fields like Karin Ljung and 2000 in the new category “Cross-Field”.

The Clarivate Analytics list of Highly Cited Researchers 2018:

Read more about the methodology how Clarivate Analytics selects Highly Cited Researchers:

Here you can find more about Karin Ljung's research and a publication list