191104 VR Photo collage 1920x1080Christiane Funk top left (photo: Thomas Kieselbach), Peter Marhavy top middle (photo: Petra Marhava), Totte Niittylä top right (photo: unknown), Markus Schmid bottom left (photo: Natuschka Lee), Nathaniel Street bottom right (photo: Mattias Pettersson)

Five projects that are affiliated with UPSC were granted by the Swedish Research Council last week. The project leaders Christiane Funk, Totte Niittylä, Markus Schmid and Nathaniel Street received a project grant and Peter Marhavy, who is planning to join UPSC in spring 2020, was awarded a starting grant to establish his research group at UPSC.

Christiane Funk, professor at the Department of Chemistry at Umeå University and associated group leader at UPSC, focuses in her research on protein degrading enzymes and on microalgae and their potential use for cleaning wastewater and biomass production. The current project aims to understand and characterize the mechanisms behind programmed cell death in single cell organisms like microalgae. The focus will be on the role of a certain group of protein degrading enzymes called metacaspases and how those have developed during evolution.

Peter Marhavy, who currently works as a postdoc in Niko Geldner’s group at the University of Lausanne, will use the funding from VR to study early defence responses in plants induced by wounding. With the help of a laser he plans to artificially induce wounding and then identify and characterize the genes and proteins that are involved in the following early defence responses. A special focus will be on the intracellular organization and the cell-wall integrity that are both affected by the wounding.

The project from Totte Niittylä who is associate professor at the Department of Forest Genetics and Plant Physiology at SLU and group leader at UPSC will concentrate on the model plant Arabidopsis thaliana. His group works on plant cell walls, and on identifying essential genes indispensable for the function of a plant cell. This project follows the groups recent discovery of an evolutionary conserved gene of unknown function that is essential for processes in the nuclear envelope and mitochondria in dividing plant cells. These processes are so far uncharacterized and the purpose of the new project is to investigate their mechanism and function.

Markus Schmid, professor at the Department of Plant Physiology at Umeå University and group leader at UPSC, wants to understand the mechanisms that control flowering time in plants. The current project will focus on a specific DNA-binding protein that regulates the activation of genes, the transcription factor FD. The aim is to find proteins that guide this transcription factor to the right DNA sequence and activate the target gene and to get a better insight in how this mechanism has evolved.

The aim of Nathaniel Street’s project is to explore how the giant genome of Norway spruce is organised and changes during development. The genomes of conifer species are almost entirely made up of regions that do not encode genes, with genes existing in a vast ocean of non-coding DNA. Nathanial Street, who is associate professor at the Department of Plant Physiology at Umeå University and group leader at UPSC, wants to understand the function of these non-coding DNA regions and how genes are physically organised by analysing the three-dimensional structure of the DNA and how these changes during development. This will be done with the help of advanced sequencing methods.

The projects and contact information of the project leaders:

  • Project: Live and let die! - The involvement of metacaspase-homologues in programmed cell death of photosynthetic microorganisms

Christiane Funk
Department of Chemistry
Umeå University
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

  • Project: Electrical signal – The secret way of cell-to-cell communication

Peter Marharvy
Department of Plant Molecular Biology (DBMV)
University of Lausanne
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

  • Project: The unknown unknowns of plant cell biology

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

  • Project: Binding of Arabidopsis FD to an Unusual cis-Regulatory Element – A new Role for the Master Floral Regulator LEAFY?

Markus Schmid
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.

  • Project: Chromatin dynamics in the gigantic genome of Norway spruce

Nathaniel Street
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.

IMG 6413 1920x1080SLU's Vice-Chancellor Maria Knutson Wedel inaugurates the new phenotyping platform at UPSC

[2019-10-30] Maria Knutson Wedel, since summer vice-chancellor at SLU, inaugurated yesterday the new tree phenotyping platform at UPSC in the course of her first official visit. This new platform allows to measure automatically and in a highly standardized way tree growth and development parameters and is a very valuable new research tool. It is not just a novelty among UPSC’s research facilities but also unique in Sweden.

The inauguration of the phenotyping platform was the highlight during the first official visit of the new SLU vice-chancellor Maria Knutson Wedel to UPSC. She got first a tour to the metabolomics facility and was then introduced by Ove Nilsson, director of UPSC, to the main research topics and the most important research plants at UPSC. After this, she officially inaugurated the new phenotyping platform.

The building of the phenotyping platform started in autumn 2017. The first test experiments begun in November 2018 and since October 2019, the first official experiment with 364 trees is running on the platform. Up to 728 trees can be monitored in total at the same time. The trees are moving on a conveyer belt and are automatically watered, fertilized, weighed and photographed once a day. This allows to characterize very precisely the tree growth of e.g. genetically modified trees in comparison with unmodified trees or of different natural variants.

The funding for the phenotyping platform came from the project “UPSC Forest Biology and Biotechnology”, that was granted in 2016 with SEK 48 million by the Knut and Alice Wallenberg Foundation and is led by UPSC’s director Ove Nilsson. This large-scale project aims to identify genes that are key players in the regulation of tree growth and wood development. It is based on data that has already been collected at UPSC over the last 20 years. The long-run goal is to increase wood production while ensuring high wood quality and lowering the need of resources to help forestry to be sustainable.

After a first characterization on the phenotyping platform, trees with interesting characteristics are going to be selected and undergo closer studies including also field trials. Currently the main tree genera characterized with the help of the platform are hybrid aspen and poplar but this might be expanded in the future to eucalyptus, spruce and pine. The services from the phenotyping platform are open to all researchers working at UPSC. A steering committee will review and prioritize suggested projects.

For questions regarding the phenotyping platform, please contact:
Ove Nilsson
Director of the Umeå Plant Science Center (UPSC) and
Professor at the Department of Forest Genetics and Plant Physiology at SLU
This email address is being protected from spambots. You need JavaScript enabled to view it.

Impressions from the visit of SLU's Vice Chancellor Maria Knutson Wedel:

Inauguration IMG 6410 1920x1080Ove Nilsson (left) presents aspen as research plant Inauguration IMG 6410 1920x1080At the tree phenotyping platform

Photos: Anne Honsel

IMG 6363 1920x1080Stéphanie Robert at the Umeå Plant Science Centre (photo: Anne Honsel)

Every other year, the Sven and Ebba-Christina Hagberg foundation awards two young recognized scientists from the medical or biochemical field. This year, the prize goes to Stéphanie Robert, group leader at UPSC, and Ville Kaila from Stockholm University. They are both awarded with a personal prize and a research grant.

Stéphanie Robert, Associate Professor at the Swedish University of Agricultural Sciences, receives the prize for her studies of the regulation of plant cell growth and plant morphogenesis. Professor Ville Kaila is awarded for his theoretical studies in the bioenergetics field, especially on proton and electron transport in the respiratory chain enzymes.

Stéphanie Robert started her group at the Umeå Plant Science Centre in 2010. She combines in her research chemical biology and cell biology to dissect on the cellular level different signalling pathways involved in plant growth. “I am really honoured to receive this prize, it feels really special. This is mainly a recognition of the hard work from present and past members of my research group.”, says Stéphanie Robert.

The Sven and Ebba-Christina Hagberg foundation aims to encourage and promote scientific research within the medical and biochemical field. Every time, the prize is awarded to one female and one male young, outstanding researcher located in Sweden. In questions regarding nominations, the foundation collaborates with the Royal Swedish Academy of Sciences and Karolinska Institutet.

Sven Hagberg (1894-1961) was a civil engineer and grain chemist. He developed a new method for measuring baking properties of flour. The method, "Hagberg Falling Number", is used worldwide today. Ebba-Christina Hagberg (1900-1972) was involved in association work and shared her husband's interest in foreign cultures. The spouses had no children but bequeathed their inheritance to the foundation, which annually awards a prize to two promising researchers.

For further information regarding the Sven and Ebba-Christina Hagberg Prize, please contact:

Dr. Gunnar Hagberg, chairman of the foundation (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Prof. Gunnar von Heijne, Board Member (This email address is being protected from spambots. You need JavaScript enabled to view it.)

aphid 1920

Aphid wired to the Electrical Penetration Graph. Photo: Cecilia Ström

When a herbivore attacks a host plant, a defence response is initiated, triggered either by the herbivore or by the plant itself. Knowledge about the mechanism behind such responses are used to develop pest management strategies that align with UN-sustainability goals for crop protection. In a new article published in the journal Plant Physiology, a UPSC-team led by Karen Kloth and Benedicte Albrectsen questioned the role of a cell wall modifying enzyme for defence responses to aphid attacks.

In their experiments, the researchers investigated the feeding behaviour of an insect, the so-called green peach aphid, on plant cell walls of thale cress (Arabidopsis thaliana). The aphid manoeuvres its needle-like mouth through the cell wall matrix to reach the phloem, a transport tissue in plants transporting sugars from the leaves to the roots. It feeds on the sugar-rich phloem sap. This penetration through the cell wall damages the cell wall to a certain extent. The researchers wanted to test the hypothesis that plant defence responses are the result of certain cell wall components that break of cell wall carbohydrate pectin, in response to the aphid penetration.

Their study focused on the effect of a special pectin modifying enzyme, called Pectin Acetylesterase 9 (PAE9), which has not been studied in this context up to now. They investigated mutants of the model plant thale cress, which have been modified to shut off PAE9. Their experiments showed that PAE9 is important for general defence reactions. The mutants that did not contain the PAE9 enzyme initially produced less defence hormones and metabolites. These defence compounds seem to make the plant more resistant to aphids. In the mutants, the aphids started phloem feeding earlier than in control plants with normal levels of defence compounds. However, with time, levels of defence compounds recovered to control levels also in the mutants. The researchers concluded therefore that PAE9 act as a front door guard that delays and initially fends off intruding aphid pests. 

The article was published in Plant Physiology:
Karen J. Kloth, Ilka N Abreu, Nicolas Delhomme, Ivan Petřík, Cloé Villard, Cecilia Ström, Fariba Amini, Ondřej Novák, Thomas Moritz, Benedicte Riber Albrectsen (2019). PECTIN ACETYLESTERASE9 Affects the Transcriptome and Metabolome and Delays Aphid Feeding. Plant Physiology, Oct 2019: doi.org/10.1104/pp.19.00635 

For more information please contact:

Benedicte Albrectsen, This email address is being protected from spambots. You need JavaScript enabled to view it.
Karen J. Kloth,This email address is being protected from spambots. You need JavaScript enabled to view it.

UPSC meets ViPS - group picture with the visiting PhD students and postdocs from UPSC in front of the greenhouses at ViPSGroup picture of the PhD students and postdocs from UPSC in front of the greenhouses at ViPS; photo: Sonali Ranade

Last week, 34 PhD students and Postdocs from UPSC visited the Viikki Plant Science Centre (ViPS) in Helsinki. Within two days, they got an insight into the research that is performed at ViPS, presented their own research and visited the facilities. This was the second joint meeting between UPSC and ViPS.

Arriving on Wednesday afternoon, the programme started with a joint dinner at the Brewery of Suomenlinna in Helsinki. The next day focussed on research. After an introduction to the centre by its director Paula Elomaa, the group from UPSC got an insight into different research projects at ViPS and every one of them presented their own research in a two-minute-long flash talk.

The afternoon on Wednesday started with the ViPS Science Fair. PhD students and postdocs from ViPS research groups presented their projects in form of posters to master students. By joining the Science Fair, the visitors from UPSC got an overview about the broad range of research projects done at ViPS. The day finished with a UPSC/ViPS get-together and one-on-one meetings with ViSP group leaders. Several PhD students and postdocs used this opportunity and appreciated those personal meeting.

On Friday morning, the PhD students and postdocs from UPSC could visit different research facilities. They were interested to see how things are organised at ViSP and got tours to the greenhouse, the phenotyping facilities, the metabolomics unit, the sequencing service and some other labs. The group flew back to Umeå in the afternoon.

Two years ago, the PhD students from the Doctoral Programme in Plant Sciences that is associated with ViPS visited UPSC. The visit to Helsinki this year was a follow-up meeting that shall help to strengthen the collaboration between the two plant research centres.

raupe articledefprim 1920
Photo: Sara Westman

In case of threats plants cannot run away but they do have a defence comparable to the humane immune system. This plant immune system helps them to fight off for example microorganism attacks. By so-called defence priming the plant immune system can be trained to memorize threats and act more effective against them in future. Solid knowledge about this mechanism is still scattered. A group of UPSC researchers lead by Benedicte Albrectsen tried the first systematic approach and published a meta-analysis on defence priming in plants focusing on thale cress.

How the plant immune system memory works is not yet fully understood but it is known that different molecular mechanisms act. The whole process is triggered by external stimuli, so-called priming agents. Priming agents can be living organisms, like microorganism and arthropods or chemical compounds, like vitamins and plant hormones. These triggers can induce the priming process in all kind of plant tissues and developmental stages. During the so-called priming phase, the plant gets stimulated by a priming agent in absence of actual threats. It accumulates compounds that later play a role in the defence. The primed status is durable, does not decrease the plants fitness and can be even passed on to the next generation.

Defence priming is a known phenomenon but for applying it widely in agriculture further knowledge is needed. In the current study the researchers analysed more than 240 studies on thale cress (Arabidopsis thaliana). The group tried to find patterns in plant responses to stress and identify possible relationships between priming agents and antagonists, like pathogens or herbivores. With their analysis they clearly show that defence priming enables the plant to withstand subsequent danger better than un-primed conspecifics. It helps the plant to defend itself faster and more effective the next time the same stress occurs.

The elaborate data comparison also allowed the researchers to identify potential players in the priming challenge. “We present a list of potential priming agents that we suggest could improve plant resistance properties in the future”, explains Benedicte Albrectsen. “The list includes microorganisms and organic chemical compounds with varied effect”. They showed that several compounds, like fungi and vitamins act as strong priming agents in thale cress whereas the influence of herbivores on the priming effect seems rather week.

This publication supports the theory that defence priming has an effect. It emphasizes that on the long run it can be used to enhance thread-resilience also in crops. The current agricultural systems are facing severe challenges including increasing demands, higher costs, and a changing climate. Defence priming has the potential for raising crop productivity with little environmental risk and this could help to move towards a more sustainable agriculture.

The work was recently published in Scientific Reports:
Westman SM, Kloth KJ, Hanson J, Ohlsson AB & Albrectsen BR (2019). Defence priming in Arabidopsis – a Meta-Analysis. 9:133309 (doi.org/10.1038/s41598-019-49811-9)

For more information please contact:
Benedicte Albrectsen (
This email address is being protected from spambots. You need JavaScript enabled to view it.)

IMG 6305 1920x1080During the SPPS Congress at Elite Hotel Mimer (photo: Anne Honsel)

[2019-09-02] Last week, the SPPS (Scandinavian Plant Physiology Society) Congress took place at Elite Hotel Mimer in Umeå. During three days, members of the society discussed actual topics in plant physiology, several prizes were officially handed out and the society held its General Assembly and elected the new SPPS Council. A special highlight during the conference was the technically advanced excursion to the Field Research Site “Rosinedal” that was even mentioned in the local newspaper.

The Scandinavian Plant Physiology Society is organising every second year its main meeting, the SPPS Congress. The focus of this international meeting is on exchanging and discussing knowledge about actual topics within the field of plant physiology. Internationally renowned researchers in the field are invited to present their research in parallel to Scandinavian plant physiologists. During the general assembly of the society, the new council was elected with Christiane Funk, Professor at the Department of Chemistry at Umeå University and associated group leader at UPSC, as new president.

During the congress, SPPS handed out six different prizes to award outstanding achievements of plant scientists, located in one of the Nordic countries. Three of this year’s awardees are affiliated with the UPSC: Karin Ljung was awarded with the SPPS Prize, Åsa Strand with the Physiologia Plantarum Prize and Torgny Näsholm received the SPPS Innovation Prize together with Barbara Halkier from the DynaMo Center at the University of Copenhagen (for more information about the prizes read also here).

In the afternoon of the second day, participants of the congress were visiting the Field Research Site “Rosinedal” that is located in a forest stand east of Vindeln. At this field site, researchers are studying in a long-term experiment the effect of nitrogen on the carbon balance of the forest. During the excursion, participants got an overview about the different studies that are made at “Rosinedal”. Via an QR-code, they could access additional information about the history of the field site and the research highlights. This technically advanced tour even motivated a local newspaper to write about it.

More information about Scandinavian Plant Physiology Society (SPPS): http://spps.se/

More information about “Rosinedalen’s” Field Site: https://www.slu.se/en/departments/field-based-forest-research/experimental-forests/vindeln-experimental-forests/rosinedal/

2048px Wheat P1210892 1920x1080Copyright © 2007 David Monniaux [CC BY-SA 3.0], via Wikimedia Commons

[2019-07-25] Today, on the anniversary of the decision of the Court of Justice of the European Union (CJEU) on plant breeding with the help of gen-editing, an open letter was sent to the Swedish European parliamentarians and the Swedish government. The letter is a call to action for an expedited change of the European legislation for genetically modified organisms (GMO). It has been signed by the leaders of 14 Swedish universities/research centres, royal science academies or research financiers as representatives of the independent Swedish research community.

“The decision of the European Court of Justice has such far-reaching consequences for research and for a more sustainable and environmentally friendly agriculture that the Swedish science community found it necessary to react strongly to try to achieve a change in legislation”, says Stefan Jansson, professor at Umeå University, who coordinated the letter.

Read the open letter (English and Swedish):
pdfOpen letter concerning GMO regulations (en)
pdfOppet brev om GMO lagstiftning (sv)
pdfAttachment 1: Consequences of the EC-ruling according to Swedish companies and research groups (Swedish Board of Agriculture)
pdfAttachment 2: Follow-up from PAFF-meeting on September 11, 2018 (Swedish Board of Agriculture)

The publication of the letter coincides with other activities at the international level that pursue the same purpose (see the links below):

Open Statement from European scientists coordinated by Dirk Inze from VIB in Ghent
European citizens' initiative: 'Grow scientific progress: crops matter!

For further information, please contact:

Stefan Jansson
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Phone: +46 70 677 23 31
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

IMG 7520 1920x1080UPSC group leaders at Skeppsvik Herrgård (present at the retreat but missing on the picture: Ove Nilsson and László Bakó)

The UPSC group leaders met in Skeppsvik for a lunch-to-lunch retreat on June 13th and 14th 2019. Sixteen PIs joined the retreat and discussed subjects related to UPSC’s strategy, investments for new infrastructure and upcoming recruitments of new group leaders to cover retirements.

Carolin Grabbe from the SLU Grants Office informed about funding opportunities for research, mobility and postdoc career development. Many ideas were brought forward at the retreat, especially regarding future recruitments. The PI-retreat was a welcome and appreciated opportunity for dialog and exchange of opinions and will be repeated on a yearly basis.

Text: Judith Felten

ainhoa foto article

Photo: Sonali Ranade

Scots pine is one of the most commercially used tree species in Sweden. To be able to breed lines with improved growth, survival and properties is of great interest for tree breeders and the forest industry. Unfortunately, the tree breeding cycle of Scots pine lasts between 20 to 30 years and that causes that the evaluation of trees in breeding trials requires several years. In her PhD project Ainhoa Calleja-Rodriguez successfully evaluated new statistical methodologies that can aid to reduce the breeding cycle in the future and to improve the accuracy of the genetic parameters on growth, adaptive traits and wood quality traits of Scots pine. She successfully defended her PhD on Wednesday, 29 may at SLU Umeå.

In her study Ainhoa Calleja Rodríguez evaluated different families of Scots pine in several locations all over Sweden. Geographical variation was important as the environment has big impact on the behavior of the trees and with a new statistical method, called factor analysis, she was able to evaluate more characters simultaneously. Another new method called genomic selection was applied for the first time on Scots pine. Ainhoa showed that it may be possible to evaluate trees already at the seedling stage but also gives more accurate estimations of genetic variation of growth and wood quality traits then traditional methods.

Ainhoa was a student of the UPSC industrial graduate research school of forest genetics, biotechnology and breeding. Therefore, she was doing her PhD project not just as student at the department of forest genetics and plant physiology at SLU but also partly at the Swedish forest research institute Skogforsk, which has one main working focus on tree breeding.

Why did you choose your project?
I felt in love with tree improvement through a previous job experience as research technician and also from my master thesis in Spain, so when a colleague in Spain sent me the announce of this position in Sweden, I just did not doubt a second to send my application.

Did the fact that this PhD program you were in was located both in industry and academia influence the decision of starting on it?
Yes, it did, specially the industry part was essential for me to decide about this position. The fact that 20% of my time could be expend as internship at the host company (Skogforsk in my case), and be in direct contact with the operational breeding program and with the tree breeders, it was what made me decide for this PhD position.

What was most fascinating during your PhD?
The most fascinating was the opportunity of being Industrial PhD Student at the Second Research School of Forest Genetics, Biotechnology and Breeding, because it gave us the opportunity to attend PhD courses with the top professors in quantitative genetics and breeding, as well as to have a “field trip” to visit the most advanced breeding programs in USA and Brazil. Also, performing my internship within Skogforsk was also fascinating, especially because at the end one of the projects became part of the thesis and was key to improve my knowledge of quantitative genetics, linear mixed models and ASReml (the most common software used in plant and animal breeding).

What was the most disappointing experience you had during your PhD?
It was really hard to get good quality marker data for Scots pine. First time we tried, it took more than a year and half to get some data and finally their quality was not enough to use them, so the part of genomic prediction of my thesis was delayed. Fortunately when we tried the second time it did not take that long and we finally could use them.

What are your plans for the future?
Last month I had an interview and got a new job at Skogforsk as researcher, so I am finally going to work with the scientists there in the operational breeding program

About the defence:
The public defence took place on Wednesday, 29th of May in P-O Bäckströms sal at SLU Umeå. The faculty opponent was Heidi Dungey, Senior scientist and Science Leader of Forest Genetics, Scion (New Zealand Forest Research Institution) and her supervisor was Harry Wu.

Title of the thesis: Quantitative Genetics and Genomic Selection of Scots pine
Link to the thesis: https://pub.epsilon.slu.se/16094/

For more information, please contact:
Ainhoa Calleja-Rodriguez
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.