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Barbara 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:
https://www.kleinlabs.eu/
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The 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
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Marianne 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
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Swedish 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:
Phone: 070-286 90 82
Professor Tomas Lundmark, SLU
email:
phone: 070-631 74 12
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Photo: Mattias Petterssonhttp://www.formas.se/sv/Press-Nyheter/Nyheter/Nya-ledamoter-i-Formas-forskarrad/
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Åsa Strand (first from left in the first row) and her group in December 2018 (photo: Anne Honsel) 
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The 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.
Link to the video of Sacha Escamez public science talk "How do plants make plumbing pipes from cells?"
Climate change challenges not only Norway spruce growth but also its set of symbiotic microorganisms
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Julia Haas; photo: Mattias PetterssonClimate 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.
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:
Text: Julia Haas, Anne Honsel
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Photo: Elisabeth Ohlson WallinClarivate 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.
https://hcr.clarivate.com/methodology/
Here you can find more about Karin Ljung's research and a publication list
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The HyPhOE project – Hybrid Electronics based on Photosynthetic Organisms – has held its start-up meeting. It provided an opportunity for the participating groups to share knowledge and plan common strategies.
The HyPhOE project is part of Horizon 2020, and is looking for ways to use plants, algae and bacteria to manufacture electronic materials and devices. The project is led by the Laboratory of Organic Electronics (LOE) at LiU, Campus Norrköping, and its Electronic Plants research group, with Eleni Stavrinidou as principal investigator.
In addition to researchers from LOE, the project has participants from the Umeå Plant Science Center in Sweden, the University of Bari in Italy, and two universities in France: Institut Polytechnique de Bordeaux and Université Paris Diderot. The involved researchers from UPSC are Totte Niittylä and Torgny Näsholm.
More information about the project can be found here:
News article about the project on the homepage of Linköping University:
https://liu.se/en/news-item/3-3-miljoner-euro-till-elektroniska-vaxter
Project information on the homepage from the European Commission:
https://cordis.europa.eu/project/rcn/216306_en.html
Information about electronic plants and the responsible group on the homepage of Linköping University:
Electronic Plants: https://liu.se/en/research/electronic-plants
Laboratory of Organic Electronics (LOE): https://liu.se/en/research/laboratory-of-organic-electronics