
Research

The research in my group focuses on developing bioelectronic technologies for real time monitoring and dynamic modulation of plant physiology. Bioelectronics devices are very promising for interfacing with biology. Bioelectronic sensors can translate complex biological inputs to electronic readout signals while bioelectronic actuators can modulate biological networks via electronic addressing. Our aim is to develop bioelectronic technologies that overcome limitations of conventional methods and establish bioelectronics in plant biology. Focus is given on understanding and enhancing plant responses to environmental stress.
Recently we developed sensors based on the organic electrochemical transistor for monitoring sugar concentration in in-vitro and in-vivo plant systems. OECTs can operate in complex biological environment and directly detect analytes upon functionalization with biological recognition elements such as enzymes. OECTs also offer signal amplification and fast response times. In a first example we developed OECT glucose sensors and measured quantitively and in real-time the export of glucose from isolated chloroplasts1. Glucose was detected only from chloroplasts isolated in night-time in agreement with our understanding of starch degradation in plants. With the OECT sensors we achieved a temporal resolution of 1min that surpass conventional methods. In another work we developed implantable OECT sugar sensors for in-vivo, real time monitoring of sugar transport in trees2. Glucose and Sucrose sensors were implanted into the stem of Populus tremula x tremuloides (Hybrid Aspen tree) and could monitor sugar variations for 48h in the mature xylem tissue. The sensors revealed diurnal fluctuation in sucrose concentration while glucose concentration remained constant, something that was not observed before.

Furthermore, we developed a capillary based organic electronic ion pump (c-OEIP) for electronically controlled delivery of phytohormones. The OEIP is an electrophoretic delivery device that converts the electronic addressing signal into ionic fluxes allowing precise and dynamic delivery of ions and charged biomolecules with high spatiotemporal resolution. With the c-OEIP we could efficiently deliver the phytohormone Abscisic Acid, in the leaf apoplast of intact Nicotiana tabacum plants and induced stomata closure3. Our work revealed kinetics of ABA signal propagation in the leaf that were unknown.

Our proof-of-concept studies so far have shown that with bioelectronic devices, both sensors and actuators, we revealed biological processes that were not observed previously with conventional methods, highlighting the potential of bioelectronics for plant science.
Read more about Eleni Stavrinidou's research
References
- “Real-Time Monitoring of Glucose Export from Isolated Chloroplasts Using an Organic Electrochemical Transistor” C. Diacci, J. W. Lee, P. Janson, G. Dufil, G. Méhes, M. Berggren*, D. T. Simon, E. Stavrinidou* Advanced Materials Technologies, 1900262 (2019)
- "Diurnal in vivo xylem sap glucose and sucrose monitoring using implantable organic electrochemical transistor sensors” C. Diacci, T. Abedi, J. W. Lee, E. O. Gabrielsson, M. Berggren, D.T. Simon, T. Niittylä,* and E. Stavrinidou* iScience, 24, 101966 (2021)
- “Implantable Organic Electronic Ion Pump Enables ABA Hormone Delivery for Control of Stomata in an Intact Tobacco Plant” I. Bernacka-Wojcik, M. Huerta, K. Tybrandt, M. Karady, Y. Mulla, D. J. Poxson, E. O. Gabrielsson, K. Ljung, D. T. Simon, M. Berggren, and E. Stavrinidou* Small, 1902189 (2019)
Contact

Eleni Stavrinidou
Associate Professor and Head of Unit at the Laboratory of Organic Electronics (LOE)
Department of Science and Technology (ITN)
Linköping University
Email:
Main homepage: https://liu.se/en/research/electronic-plants
CV E. Stavrinidou
- Since 2020: Associate Professor, Dept. of Science and Technology, Linköping University
- 2020: Docent in Applied Physics, Institute of Technology, Linköping University
- 2017-2020: Assistant Professor, Dept. of Science and Technology, Linköping University.
- 2016-2018: Marie Curie Fellow, Dept. of Science and Technology, Linköping University.
- 2014-2016: Postdoctoral Scholar, Dept. of Science and Technology, Linköping University.
- 2014: PhD in Microelectronics, Ecole Nationale Supérieure des Mines de St.-Étienne, France
- 2010: M.Sc. in Nanotechnology, Aristotle University of Thessaloniki, Greece
- 2008: BSc in Physics, Aristotle University of Thessaloniki, Greece
Publications

Research

My group’s research revolves around understanding the mechanisms governing plant nitrogen availability at the root-soil interface. A key tool in our research is the sampling technique microdialysis.
Our main aim is to develop microdialysis as a tool for root simulation, investigating key aspects of root physiology and plant-microbial interactions and how that influence plant nitrogen availability at the root surface, in a root growing in undisturbed soil.
In many ecosystems, nitrogen availability is limiting plant growth. Nitrogen is therefore applied to increase yields. Further insight into the plant perspective of nitrogen availability could lead to identifying ways to increase nitrogen use efficiency and decrease nitrogen pollution in managed environments. Critical in this seems to be the sampling methods used. Microdialysis is an approach for seeing nitrogen availability from a roots perspective.
We use microdialysis for measuring induced diffusive fluxes of foremost nitrogen, simulating what a plant root would experience in the field. An important factor in mirroring plant nitrogen availability at the root surface, particularly for the organic forms, in soil, is that this tool enables sampling with very little disturbance of the soil and that it allows continuous sampling. Due these sampling benefits, this technique has unveiled that in unfertilized soil, plant roots has access to a larger proportion of organic nitrogen than previously detected.
In a recent study, we used microdialysis to simulate root exudation by retrodialysis and its effect on nitrogen availability. Our study revealed that in a short-term perspective, nitrogen availability decreased, rather than increased most likely due to microbial immobilization.
Microdialysis allows repeated sampling, in situ in a small scale. This has led us to develop the application of this technique in additional directions. This includes sampling low molecular weight organic carbon compounds, enzymes and signalling molecules involved in plant-mycorrhiza interactions.
Our close collaboration with the Swedish Metabolomics Centre (SMC) enables our work on organic nitrogen in analysis of amino acids LC-MS (QQQ) and dipeptides and LC-MS (qTOF) quantification of isotopically labelled amino acids and metabolomic screening with GC-MS. This collaboration led to a recent study highlighting how critical the analysis is for evaluating the importance of plant uptake of organic nitrogen.

Read more about Sandra Jämtgård's research
Key publications
- Buckley S, Brackin R, Näsholm T, Schmidt S, Jämtgård S. 2022. The influence of sucrose on soil nitrogen availability–A root exudate simulation using microdialysis. Geoderma 409, 115645. https://doi.org/10.1016/j.geoderma.2021.115645
- Svennerstam H, Jämtgård S. 2022. Timing is everything–obtaining accurate measures of plant uptake of amino acids. New Phytologist 234: 311-318. https://doi.org/10.1111/nph.17964
- Plett K, Buckley S, Plett J, Anderson I, Lundberg-Felten J, Jämtgård S. 2021. Novel microdialysis technique reveals a dramatic shift in metabolite secretion during the early stages of the interaction between the ectomycorrhizal fungus Pisolithus microcarpus and its host Eucalyptus grandis. Microorganisms 9: 1817. https://doi.org/10.3390/microorganisms9091817
- Buckley S, Brackin R, Jämtgård S, Näsholm T, Schmidt S, 2020. Microdialysis in soil environments: Current practice and future perspectives. Soil Biology & Biochemistry 143: 107743. https://doi.org/10.1016/j.soilbio.2020.107743
- Buckley S, Brackin R, Näsholm T, Schmidt S, Jämtgård S. 2017. Improving in situ recovery of soil nitrogen using the microdialysis technique. Soil Biology & Biochemistry 114:93-103. https://doi.org/10.1016/j.soilbio.2017.07.009
- Ganeteg U, Ahmad I, Jämtgård S, Aguetoni Cambui C, Inselsbacher E, Svennerstam H, Schmidt S and Näsholm T. 2017. Amino acid transporter mutants of Arabidopsis provides evidence that a non-mycorrhizal plant acquires organic nitrogen from agricultural soil. Plant Cell and Environment 40: 413-423. https://doi.org/10.1111/pce.12881
- Jämtgård S, Näsholm T and Huss-Danell K. 2010. Nitrogen compounds in soil solutions of agricultural land. Soil Biology & Biochemistry 42: 2325-2330. https://doi.org/10.1016/j.soilbio.2010.09.011
Publications
Contact

Sandra Jämtgård
Researcher at the Department of Forest Ecology and Management
Swedish University of Agricultural Sciences
Email:
Main homepage: https://www.slu.se/en/ew-cv/sandra-jamtgard/

Research

The ability of a species to sustain environmental change is primarily determined by its genetic reservoir, which is shaped over the course of history through demography and selection. We apply ecological and genomics tools to understand the origin and distribution of genetic diversity across landscapes in Eurasian conifer species. We use seed orchards as a study system to evaluate the impact of abiotic and biotic factors and management practices on genetic diversity and breeding gain in seed crops, and the adaptability of the regenerated production forests to future climate.
Ecological genomics
Local adaptation in which local genotypes have a fitness advantage than foreign genotypes is well known among long-lived tree species. Rapid climate change can break this genetic-environmental association much faster than trees’ ability to evolve in situ or migrate, thus creating a mismatch between genetic adaptation to altered environmental conditions. Inferences of genotype-environment associations due to polygenic nature of adaptive traits and the complexity of adaptive and dispersal-demographic factors that contribute to genetic differentiation across species range. Using landscape genomics approaches, we interrogate genome-wide variation across landscapes for understanding the extent to which evolutionary forces, e.g. demographic events, gene flow, introgression and selection, shape past and contemporary populations’ genetic structure, and identify those populations that may be most at risk under climate change. This research is conducted for major conifer species in Eurasia, e.g. Pinus sylvestris, Pinus tabuliformis, Pinus yunnanensis, Pinus densata and Picea abies.
A) Pinus densata on the Tibetan Plateau; B) Spatial structure of genomic diversity in P. densata; C) Hardiness variation in Scots pine; D) Controlled mating experiment in a Scots pine seed orchard
Seed orchards and adaptability of production forests
Efficient use of breeding resources requires a good understanding of the genetic composition of the founder materials for predicting the gain and diversity in future generations. For conifer trees, seed orchard is the link between tree breeding and the production forest. Well-functioning seed orchard is the most cost efficient and realistic way to increase timber production from forestland during the coming century. Our research in this area focuses on: 1) the assessment of diversity and coancestry in breeding populations of Scots pine (Pinus sylvestris) and Norway spruce (Picea abies); 2) the mating system in seed orchards of the two species, and pedigree structure and diversity in seed crops; and 3) the adaptation of orchard crops to different climate zones and thus formulating site-specific seedlot selection system for reforestation. These activities are in close collaboration with Skogforsk.
Read more about Xiao-Ru Wang's research on the homepage of Umeå University
Key publications
- Hall, D., Olsson, J., Zhao, W., Kroon, J., Wennström, U., Wang, X-R. 2021. Divergent patterns between phenotypic and genetic variation in Scots pine. Plant Communications,2:100139.
- Zhao, W., Sun, Y-Q., Pan, J., Sullivan, A., Arnold, M.L., Mao, J-F., Wang, X-R. 2020. Effects of landscapes and range expansion on population structure and local adaptation. New Phytologist. 228: 330-343.
- Sullivan, A.R., Schiffthaler, B., Thompson, S.L., Street, N.R., Wang, X-R. 2017. Interspecific plastome recombination reflects ancient reticulate evolution in Picea (Pinaceae). Molecular Biology and Evolution 34:1689-1701.
- Funda, T., Wennström, U., Almqvist, C., Andersson Gull, B., Wang, X-R. 2016. Mating dynamics of Scots pine in isolation tents. Tree Genetics & Genomes 12:112.
- Wang, B., Mao, J-F., Gao, J. Zhao, W., Wang, X-R. 2011. Colonization of the Tibetan Plateau by the homoploid hybrid pine Pinus densata. Molecular Ecology 20: 3796-3811.
Contact

Xiao-Ru Wang
Professor at Department of Ecology and Environmental Sciences
Umeå University
E-mail:
More information: https://www.umu.se/en/staff/xiao-ru-wang/
CV X.-R. Wang
- 2014: Professor, Department of Ecology and Environmental Science, Umeå University
- 2000: Adjunct professor, Inst. Botany, Chinese Academy of Sciences
- 2000: Senior scientist, PI, National Institute for Working Life, Sweden
- 1997: Docent, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences
- 1997 – 1999, STA Fellow, Forestry and Forest Product Research Institute, Japan
- 1993: Assistant Professor, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences
- 1992: PhD, Swedish University of Agricultural Sciences
- 1987: MSc, Beijing Forestry University
- 1984: BSc, Beijing Forestry University
Publications
Svenska

Arters förmåga att klara av miljöförändringar bestäms framförallt av deras genetiska reserv, vilken formats av demografi och naturligt urval över tid. Vi använder ekologiska och genetiska verktyg för att bättre förstå ursprunget och utbredningen av den genetiska diversiteten hos barrträd från Eurasien. Vi använder fröplantager som vårt studiesystem för att utvärdera hur biologiska faktorer och skötsel påverkar den genetisk diversiteten och förädlingsvinsten hos fröskördar, och vilken effekt det i sin tur har på produktionsskogens anpassning till framtida klimat.

Research
Plants commonly have strategies for both sexual and asexual reproduction. These reproductive functions do not evolve independently, but asexual reproduction e.g. through clonality, has consequences for sexual reproduction, typically by relaxing selection for sexual traits and allowing mutational degeneration in genes related to sexual functions. In my research, I am interested in both sexual and asexual reproduction of plants.
Related to sexual reproduction, I study genetics of speciation – i.e. genes involved in development of reproductive isolation. I have been using hybrids within and between outcrossing Arabidopsis species (A. lyrata, A. halleri and A. arenosa) to investigate reproductive barriers. Species barriers commonly manifest themselves as reduced hybrid viability and/or fertility. In these Arabidopsis species, reduction of hybrid pollen fertility is one of the first barriers to emerge between incipient species. Therefore, my main focus is on pollen related traits.

Regarding asexual reproduction, my main interest is in clonality and its relation to sexual reproduction. Vegetative reproduction is typically associated with longevity and perenniality, and it can also be seen as a survival strategy, in conditions where sexual recruitment is low. Clonality has consequences for sexual reproduction, typically by relaxing selection for sexual traits and allowing mutational degeneration in genes related to sexual functions. The genetic basis of clonality has remained unknown, as the model plants of genetics are typically annuals. I use European aspen (Populus tremula) and Arabidopsis lyrata, as model species to study clonality and its genetic basis. In addition, I aim to identify whether clonality has affected sexual functions, specifically pollen quality and flowering frequency in these species.

Contact

Johanna Leppälä
Senior Scientist
Production of field crops
Natural Resources Institute Finland (LUKE)
Rovaniemi, Finland
E-mail:
More information: https://www.luke.fi/en/experts/johanna-leppala
CV J. Leppälä
- 2018: Assistant professor, Umeå University
- 2011-2017: Postdoc, University of Helsinki, Finland
- 2010-2011: Researcher/postdoc, Umeå University
- 2011: PhD genetics, University of Oulu, Finland
- 2003: MSc genetics, University of Oulu, Finland
Publications

Research

Plant nitrogen (N) nutrition is a topic that challenges the researcher with a number of problems not encountered in other areas of plant mineral nutrition research. The diversity of N forms present in the soil, their interconversions, their different chemical and physical characteristics and not the least the multitude of adaptations and acclimatisations that plants display to optimize acquisition of various N forms all contribute to the complexity of plant N nutrition.
Thus, plants can use a wide array of chemical N forms, ranging from the simple inorganic N compounds such as NH4+ and NO3- as well as polymeric N forms such as proteins. My research deals with plant N physiology, particularly N acquisition and metabolism of forest plants. This research spans from detailed studies of uptake processes to forest fertilization and environmental effects of N.

We have studied uptake of various N forms and demonstrated how field-grown plants acquire different organic N compounds. These studies have stimulated us to characterize the molecular mechanisms underpinning plant organic N nutrition, specifically the specific transporters mediating uptake of various amino acids as well as metabolism of absorbed organic compounds.
We have discovered that plants have a well-developed capacity for using the common L-enantiomers of amino acids but a very restricted capacity to metabolise their D-counterparts. We have also shown how transgenic plants expressing genes encoding D-amino acid metabolising enzymes can detoxify and grow on D-amino acids. This finding has formed the basis for the development of a new selectable marker in plant biotechnology, now commercialized under the tradename SELDA. Basic L-amino acids, and in particular L-arginine, are absorbed at high rates by many plants and we have shown that such N forms have specific advantages for cultivation of woody plants such as conifer seedlings.
This finding forms the basis for the development of a new fertilizer – arGrow®, which is now commercialized by the company SweTree Technologies.
Read more about Torgny Näsholm's research here
Key Publications
- Näsholm, T., Kielland, K. & Ganeteg, U. (2009). Uptake of organic nitrogen by plants. Tansley Review New Phytologist, 182: 31- 48.
- Svennerstam, H., Ganeteg, U., Bellini, C. & Näsholm, T. (2007). Comprehensive screening of Arabidopsis mutants suggests the Lysine Histidine Tranporter 1 to be involved in root uptake of amino acids. Plant Physiology 143: 1-8
- Erikson, O., Hertzberg, M. & Näsholm, T. (2004). A conditional marker gene allowing both positive and negative selection in plants. Nature Biotechnology, 22: 455-458.
- Lipson, D. and Näsholm, T. (2001). The unexpected versatility of plants: Organic Nitrogen Use and Availability in Terrestrial Ecosystems. Commissioned review. Oecologia 128: 305-316
- Näsholm, T., Ekblad, A., Nordin, A., Giesler, R., Högberg, M. and Högberg, P. (1998). Boreal forest plants take up organic nitrogen. Nature 392, 914-916, 1998.
Contact

Torgny Näsholm
Professor at the Department of Forest Ecology and Management
Swedish University of Agricultural Sciences
e-mail:
More information: https://www.slu.se/en/ew-cv/torgny-nasholm/
CV T. Näsholm
- 2007: Professor in Tree Ecophysiology, Swedish University of Agricultural Sciences
- 2000: Professor in Plant Physiology, Swedish University of Agricultural Sciences
- 1998: Senior researcher; Plant Physiology (Formas)
- 1995: Docent in Plant Physiology, Swedish University of Agricultural Sciences
- 1992: Assistant Professor in Plant Physiology, Swedish University of Agricultural Sciences
- 1991: PhD, Swedish University of Agricultural Sciences
- 1985: BSc, Umeå University
Svenska

Min forskning rör växters kvävefysiologi. I många ekosystem förekommer kväve i marken företrädesvis i form av olika organiska kväveformer och jag studerar växters förmåga att ta upp och växa på sådana kväveföreningar. Vår forskning har visat att växter har en mycket god förmåga att nyttja basiska aminosyror och denna upptäckt har lett fram till utvecklandet av ett nytt gödselmedel – arGrow.
Vi har också visat att vissa sorters aminosyror – D-enantiomererna – inte kan användas av växter. Genom att flytta en gen från en jästsvamp till en växt har vi framställt en transgen växt med den unika förmågan att kunna växa på D-aminosyror. Denna upptäckt har visats vara mycket värdefull inom växtbiotekniken.

Research

My research within the subject photosynthesis currently has developed into two different projects: 1. Investigating the potential of Nordic microalgae for wastewater reclamation and biomass generation and 2. Finding the function of plant proteases. Research objects in my group range from cyanobacteria, via green microalgae and cryptomonad algae to higher plants.
Wastewater reclamation and biomass generation by Nordic microalgae
With the expanding human population, we will need more food, more fuel and more water. At the same time, we have to reduce CO2 emissions by over 80%. One approach to address this problem is to recycle CO2 for fuel- or chemical-production using photosynthesis. Photosynthetic organisms use solar energy to incorporate atmospheric CO2 into organic molecules. We let microalgae perform photosynthesis and at the same time clean municipal and industrial wastewater. The algal biomass then can be used for biofuel, biogas, biofertilizer or even bioplastic. Our challenge is the sub-arctic climate we have in Northern Sweden with low temperatures and short-day lengths. Therefore, we investigate the potential of local, natural algal strains. We test their performance in cleaning wastewater, analyze their biomass and investigate, how to prolong their growth phase.
Plant proteases
Proteases are proteins that break down other proteins. They are involved in many different biological functions, e.g. the digestion of our food, cleaning the cell from malfunctioning proteins or cell signaling. Even though hundreds of proteases are encoded in the genomes of various plants, their biological roles are mostly unknown. Using molecular biological and biochemical methods, we try to find identify the function of some of them. Metacaspases, for example, are proteases thought to be involved in programmed cell death (PCD), the genetically encoded process leading to suicide of specific cells or tissues. In single-cell algae and cyanobacteria the necessity for PCD is less obvious, still these microorganisms contain metacaspases. The aim of our research is to investigate the broad network of PCD in photosynthetic single-cell organisms and at the same time to perform detailed functional, structural and evolutionary studies of the metacaspase homologues.
A) Various green microalgae found in municipal wastewater; B) Scanning electron microscope (SEM) image of the green microalga C. vulgaris 13-1 and its symbiotic bacterium Rhizobium sp. at 50 K magnification (Photos: Lorenza Ferro); C) Electron microscopy image of the cyanobacterium Synechocystis sp. 6803 (Photo: Tania Tibiletti); D) Chlorophyll fluorescence emitted from Arabidopsis thaliana leaves (Photo: Laxmi Mishra)
Read more about Christiane Funk's research on the homepage of Umeå University
Key publications
- Mehariya S, Plöhn M, Leon-Vaz A, Patel A, Funk C (2022) Improving the content of high value compounds in Nordic Desmodesmus microalgal strains. Bioresource Technology 359, 127445.
- Spain O, Funk C (2022) Detailed characterisation of the cell wall structure and composition of Nordic green microalgae. J Agricultural and Food Chemistry 70, 9711-9721.
- Martínez JM, Gojkovic Z, Ferro L, Maza M, Álvarez I, Raso J, Funk C. (2019) Use of Pulsed Electric Field permeabilization to extract astaxanthin from the Nordic microalga Haematococcus pluvialis. Bioresource Technology 289, 121694.
- Mishra, L.S., Mielke, K., Wagner, R., Funk, C. (2019) Reduced expression of the presumably proteolytic inactive FtsHi members has impact on the Darwinian Figness of Arabidopsis thaliana. J. Exp. Botany 70, 2173-2184.
- Karan, H.*, Funk, C.*, Grabert, M., Oey, M., Hankamer, B. (2019) Green bioplastics as part of a circular bioeconomy, Trends in Plant Science 24, 237-249.
- Klemencic, M., Funk, C. (2018) Type III Metacaspases: calcium-dependent activity proposes new function for the p10 domain, New Phytologist 218, 1179-1191.
Contact

Christiane Funk
Professor at the Department of Chemistry
Umeå University
Email:
More information: https://www.umu.se/en/staff/christiane-funk/
CV C. Funk
Education and academic degrees
- 2008 Professor in Biochemistry, Umeå University, Sweden.
- 2001 Docent. Biochemistry, Stockholm University, Sweden.
- 1995 PhD. Chemistry, Technical University Berlin, Germany
- 1991 MSc Georg-August University Göttingen, Germany
Employments
- Since 2008: Professor in Biochemistry, Dept of Chemistry, Umeå University
- 2006 – 2011 Research fellow position of the Royal Swedish Academy of Sciences (KVA)
- 2002-2008 Associate Prof., Dept. of Biochemistry, Umeå University, Sweden
- 1998-2001 Assistant Prof., Arrhenius. Lab., Dept. of Biochemistry and Biophysics, Stockholm University, Sweden
- 1997 Postdoctoral Research Associate, Research School of Biological Sciences, Australian National University, Canberra, Australia
- 1995/1996 Postdoctoral Scientist, Dept. of Botany and Center for the Early Events in Photosynthesis, Tempe, Arizona, USA
Special Awards and Honours
- 2008 Young researcher award, Umeå University
- 2007-2011 Research fellow position of Royal Swedish Academy of Sciences (KVA)
- 1989-94 Scholar of the Studienstiftung des Deutschen Volkes
Publications
Svenska

Utifrån min tidigare forskning om fotosyntes fokussera mitt arbete för närvarande på två nya inriktningar: Växtproteasernas funktion och Nordiska mikroalgernas potential för återvinning av avloppsvatten och produktion av biomassa.
Återvinning av avloppsvatten och produktion av biomassa med hjälp av nordiska mikroalger
Fotosyntes är en process där koldioxid från luften tas upp och omvandlas till kemisk lagrad energi med hjälp av solljus. Vi låter mikroalger utföra sin fotosyntes i avloppsvatten som renas, och samtidigt bildas biomassa. Algbiomassan kan sedan användas för biobränsle, biogas, biogödsel eller till och med för produktion av bioplaster. Vår utmaning är det subarktiska klimatet vi har här i norra Sverige med låga temperaturer och korta dagslängder vintertid. Därför undersöker vi möjligheten att använd lokala, naturligt förkommande alg-stammar. Vi undersöker deras förmåga att rena avloppsvatten, analyserar deras biomassa och undersöker hur man kan förlänga deras tillväxtfas.
Växtproteaser
Proteaser är proteiner som bryter ner andra proteiner. De är involverade i många olika biologiska funktioner, t.ex. matsmältningen, nedbrytning av proteiner som inte fungerar eller cell signalering. Även om hundratals gener som kodar för proteaser i olika växter har identifierats, är deras biologiska funktion mestadels okända. Med hjälp av molekylär-biologiska och biokemiska metoder försöker vi identifiera funktionen av olika växtproteaser. Våra modellorganismer sträcker sig från cyanobakterier över alger till högre växter.

Research

Plants need to integrate an array of signals to regulate complex patterns of gene expression. This is important since plants have specialized needs to respond to changes in the environment. Regulation of gene expression in plants is important for integration of external signals such as temperature, day length, concentration of different metabolites and light quality in the series of events that ultimately lead to owering. Finally, the regulation of gene expression during specific stages of seed development is an interesting example of tissue and developmental control which is of considerable agricultural importance.
In all eukaryotes, protein-encoding genes are transcribed by RNA polymerase II (pol II). To perform its most basal functions; promoter recognition, melting of the DNA template at the transcription start, formation of the first phosphodiester bonds and promoter escape, pol II requires five so called general transcription factors (GTFs). These GTFs, TBP, TFIIB, E, F, and H are conserved in all eukaryotes and together with pol II they form a preinitiation complex comprising nearly 30 polypeptides. Mediator is a multisubunit complex which functions as a connector between the promoter-bound transcriptional regulators and pol II.

Surprisingly, Mediator had not been identified in plants until we recently succeeded to purify Mediator from A. thaliana through conventional biochemical purification combined with reversed-phase LC-ESI-MS/MS. This was the first description of Mediator in a plant, and it was evident that it required a biochemical approach since most of the A. thaliana Mediator subunits show very low sequence homology to the corresponding proteins in yeast and metazoans. Plant Mediator is probably structurally conserved, but the amino acid sequences of individual subunits differ considerably when compared to other eukaryotes. Plants also contain a set of unique Mediator subunits, which are likely to be involved in regulation of plant-specific gene expression.
Link to Stefan Björklund's main research page
Key publications
- Blomberg J, Aguilar X, Brännström K, Rautio L, Olofsson A, Wittung-Stafshede P, and Björklund S. (2012). Interactions between DNA, transcriptional regulator Dreb2a and the Med25 mediator subunit from Arabidopsis thaliana involve conformational changes Nucleic Acids Res. 40:5938-5950
- Elfving, N., Davoine, C., Benlloch, R., Blomberg, J., Brännström, K., Müller, D., Nilsson, A., Ulfstedt, M., Ronne, H., Wingsle, G., Nilsson, O., and Björklund, S. (2011). The Arabidopsis thaliana Med25 mediator subunit integrates environmental cues to control plant development. Proc. Natl. Acad. Sci. USA. 108(20):8245-8250
- Shaikhibrahim, Z., Rahaman, H., Wittung-Stafshede, P., and Björklund, S. (2009). Med8, Med18, and Med20 subunits of the Mediator head domain are interdependent upon each other for folding and complex formation. Proc. Natl. Acad. Sci. USA. 106:20728-20733
- Bäckström, S., Elfving, N., Nilsson, R., Wingsle, G., and Björklund, S. (2007). Purification of a Plant Mediator from Arabidopsis thaliana identifies PFT1 as the Med25 subunit. Molecular Cell 5: 717-729.
- Hallberg, M., Hu, G-Z., Balciunas, D., Sheikhibrahim, Z., Björklund, S., and Ronne, H. (2006). Functional and physical interactions of the Mediator subunit Med21/Srb7. Mol. Genet Genomics 276:197-210
Contact

Stefan Björklund
Professor at Department of Medical Biochemistry and Biophysics
Umeå University
e-mail:
Main homepage: https://www.umu.se/en/research/groups/stefan-bjorklund/
CV S. Björklund
- 2008: Chairman for the Medical Faculty Board of Research
- 2007: Chairman, Department of Medical Biochemistry and Biophysics
- 2005: Professor, Umeå University
- 1999: Docent, Umeå University
- 1995: Assistant professor, Umeå University
- 1993-1995: Postdoc, Stanford University School of Medicine
- 1993: PhD, Umeå University
- 1988: Bachelor of Medicine, Umeå University
Publications
Svenska

Mediatorn är ett stort proteinkomplex som är konserverat i alla eukaryoter från jästsvampar till mänskliga celler. Mediatorn fungerar som en transkriptionell koregulator genom att överföra signaler från promotorbundna transkriptionella reglerproteiner, till det generella RNA polymeras II transkriptionskomplexet.
Vi har identifierat Mediatorkomplexet i Arabidopsis thaliana och visat att det består av 21 konserverade proteinsubenheter och 6 st subenheter som är specifika för växter. Vi har funnit att vissa proteiner i växtmediatorkomplexet är viktiga för att samordna olika signaler från omgivningen (ljuskvalité, temperatur, tillgång på vatten, saltkoncentration etc) för att styra blomning. Vårt mål är att klargöra hur dessa signaler samordnas på molekylär nivå.

Research

The aim of my research is to understand the mechanisms of metabolic control of shoot elongation and wood formation in the model plant Populus. We want to understand how plant hormones and other metabolites are involved in the control of plant development, and how different environmental cues, such as photoperiod, affect the metabolic control of growth and development. The metabolic control of growth and development are studied by using both targeted and untargeted metabolomics approaches.
Gibberellins (GAs) are a group of tetracyclic diterpenes, some of which are essential endogenous regulators that influence growth and development events throughout the life cycle of a plant, e.g. shoot elongation, expansion and shape of leaves, flowering and seed germination. Our project is concerned with the role of GAs in plant development, and daylength responses, focusing on the tree hybrid aspen (Populus tremula x P. tremuloides) as a model system. Our approach for studying the role of GAs in trees is to study endogenous expression of GA biosynthetic and signalling genes and to transform Populus with genes encoding those genes.
Populus transformed with the AtGA20ox1 under the control of the 35S promoter shows elongated internodes, longer petioles and larger leaves, reduced root formation and increased shoot biomass.We have also char- acterized the GA receptor, GID1 in Populus. Four orthologs of GID1 have been identified in Populus tremula x P. tremuloides (PttGID1.1 to 1.4). When PttGID1.1 and PttGID1.3 were overexpressed in Populus with a 35S promoter, overexpressors shared several similar phenotypic traits with previously described 35S:AtGA20ox1 overexpressors, including rapid growth and increased elongation.

We are also studying the role of GAs and other signaling compounds in wood formation. The role of GAs is done by both using transgenic Populus with increased levels of GAs and signalling and by predicting where GAs are formed and perceived during wood formation. For example, we have quantified GAs and analyzed the expression of GA biosynthesis genes and genes with predicted roles in GA signalling in tangential sections across the cambial region of aspen trees (Populus tremula). The results show, for example inter alia, that the bioactive GA and GA 14 predominantly occur in the zone of expansion of xylem cells.
Studies with transgenic Populus overexpressing AtGA20ox1 or PttGID1 with 35S or a xylem-specific promoter, suggest that GAs are required for two distinct processes in wood formation with tissue-specific signalling pathways: xylogenesis, mediated by GA signalling in the cambium, and fibre elongation in developing xylem.
By using a metabolomics approach we are also studying how specific patterns of metabolites, including signalling compounds, are vary in different regions of the wood-forming zone in Populus. From the data we can conclude that cambial activity, cell expansion and secondary cell wall thickening are tightly coupled processes, Many of these patterns can be explained on the basis of the developmental processes taking place within these regions, e.g. in the cambium.
Many woody species with indeterminate growth show complete cessation of elongation growth after only a few weeks in short photoperiods. In hybrid aspen transformed with the oat PHYA gene, the dwarf phenotype is correlated with a reduction in GA levels, but in short photoperiods there is no further reduction in GA contents, in marked contrast to the pattern in wild-type plants. These observations imply that GAs have an important role as signals in the photoperiodic regulation of shoot elongation. We have also been studying transgenic GA plants to elucidate how changes in GA levels and signalling affect photoperiodic growth. Studies in PHYA and GA biosynthesis/signalling overexpressors are used with transcriptomic and metabolomic approaches to elucidate the early signalling pathways in short-day induced growth cessation, including identification of new putative signalling compounds.
Key Publications
- Davoine, C., Abreu, I. N. Khajeh, K., Blomberg, J., Kidd, B. N., Kazan, K., Schenk, P. M., Gerber, L., Nilsson, O., Moritz, T. , Bjorklund, S. 2017. Functional metabolomics as a tool to analyze mediator function and structure in plants. Plos One 12(6).
- Lindén, P., Keech, O., Stenlund, H., Gardeström, P., Moritz, T. 2016 Reduced mitochondrial malate dehydrogenase activity has a strong effect on photorespiratory metabolism as revealed by 13C-labelling. J. Exp. Bot., 67: 3123-3135
- Eriksson, M.E., Hoffman, D., Kaduk, M., Mauriat, M., Moritz, T. 2015 Transgenic hybrid aspen trees with increased gibberellin (GA) concentrations suggest that GA acts in parallel with FLOWERING LOCUS T2 to control shoot elongation. New Phytologist, 205, 1288-1295.
- Mauriat M., Sandberg L., Moritz T. 2011 Proper gibberellin localization in vascular tissue is required to control auxin dependent leaf development and bud outgrowth in hybrid aspen. Plant J. 67: 805-816.
- Mauriat M., Moritz T. 2009 Analyses of GA20ox- and GID1-overexpressing Populus suggest gibberellins play two distinct roles in wood formation. Plant J. 58: 989-1003.
- Israelsson M., Sundberg B., Moritz T. 2005 Tissue-specific localisation of gibberellins in wood-forming tissues in aspen. Plant J. 44: 494-504.
- Jonsson P., Johansson A., Gullberg J., Trygg J., A J., Grung B., Marklund S., Sjöström M., Antti H., Moritz T. 2005 High through-put data analysis for detecting and identifying differences between samples in GC/MS-based metabolomic analyses Anal. Chem. 77: 5635-5642.
- Eriksson M., Israelsson M., Olsson O., Moritz T. 2000. Increased gibberellin biosynthesis in transgenic trees promotes growth, biomass production and xylem fibre length. Nature Biotech. 784-788.
Team
- Since 2019: Professor, University of Copenhagen (80%); Swedish University of Agricultural Sciences (20%)
- 2013-2019: Director Swedish Metabolomics Centre
- 2007-2015: Head of Department (Dept. Forest Genetics and Plant Physiology)
- 2002: Professor, Swedish University of Agricultural Sciences
- 1997: Docent, Swedish University of Agricultural Sciences
- 1992: Assistant Professor, Swedish University of Agricultural Sciences
- 1991: Postdoc, Long Ashton Research Station, Bristol, UK
- 1990: PhD, Swedish University of Agricultural Sciences
- 1985: BSc, Umeå University
- Bru P, Steen CJ, Park S, Amstutz CL, Sylak-Glassman EJ, Leuenberger M, Lam L, Longoni F, Fleming GR, Niyogi KK and Malnoë A* (2021) Isolation of quenched light-harvesting complex II trimers from Arabidopsis leaves with sustained photoprotection (qH). bioRxiv: 2021.2007.2009.450705.
- Yu, G, Pan, X, Hao, J, Shi, L, Zhang, Y, Wang, J, Xiao, Y, Yang, F, Lou, J, Chang, W, Malnoë, A* and Li, M* (2021) Structure of SOQ1 lumenal domains identifies potential disulfide exchange for negative regulation of photoprotection, qH. bioRxiv: 2021.2003.2016.435614
https://www.biorxiv.org/content/10.1101/2021.03.16.435614v1 - Amstutz, C, Fristedt, R, Schultink, A, Merchant, S, Niyogi, KK, & Malnoë, A* (2020) An atypical short-chain dehydrogenase-reductase functions in the relaxation of photoprotective qH in Arabidopsis. Nat Plants 6:154–166
https://doi.org/10.1038/s41477-020-0591-9 - Malnoë A (2018). Photoinhibition or photoprotection of photosynthesis? Update on the (newly termed) sustained quenching component qH. Environmental and Experimental Botany 154: 123-133
https://doi.org/10.1016/j.envexpbot.2018.05.005 - Malnoë, A*, Schultink, A, Shahrasbi, S, Rumeau, D, Havaux, M, and Niyogi, KK* (2018). The Plastid Lipocalin LCNP is Required for Sustained Photoprotective Energy Dissipation in Arabidopsis. Plant Cell 30: 196-208
https://doi.org/10.1105/tpc.17.00536 - 2023 - present: Associate Professor
- 2018 - 2022: Assistant/Associate Professor
- 2012 - 2017: Postdoctoral Researcher
- 2011 (6 months): Postdoctoral Researcher
- 2007 - 2011: Ph.D., Biology (with Honors)
- 2007 (6 months): Visiting Research Associate
- 2006 (3 months): Undergraduate Researcher
- 2006 - 2007: M.Sc., Plant Genetic and Molecular Physiology (with Honors)
- 2004 - 2007: Engineer in Agronomical Sciences
- Chowdhury J, Kemppainen M, Delhomme N, Shutava I, Zhou J, Takahashi J, Pardo AG and J Lundberg-Felten Laccaria bicolor pectin methylesterases are involved in ectomycorrhiza development with Populus tremula × Populus tremuloides. New Phytologist 2022, 236(2):639-655
- Kemppainen M, Chowdhury J, Lundberg-Felten J and A Pardo Fluorescent protein expression in the ectomycorrhizal fungus Laccaria bicolor: a plasmid toolkit for easy use of fluorescent markers in basidiomycetes. Current Genetics 2020 66(4):791-811.
- Felten J, Hall H, Jaumot J, Tauler R, de Juan A and A Gorzsás. Vibrational spectroscopic image analysis of biological material using multivariate curve resolution-alternating least squares (MCR-ALS). Nature protocols 2015, 10 (2) 217-240
- Vayssieres A, Pencik A, Felten J, Kohler A, Ljung K, Martin F and V Legué. Development of the poplar-Laccaria ectomycorrhiza modifies root auxin metabolism, signalling and response. Plant Physiology 2015, 169 (1), 890
- Ditengou FA, Müller A, Rosenkranz M, Felten J, Lasok H, Miloradovid van Doorn M, Legue V, Palme K and JP Schnitzler. Volatile signalling by sesquiterpenes from ectomycorrhizal fungi reprograms root architecture. Nature Communications 2015, 6: 6279-6279
- Felten J, Martin F and V Legué. Signaling in ectomycorrhizal symbiosis. in S. Perotto and F. Baluska (eds.), Signaling and Communication in Plant Symbiosis, Signaling and Communication in Plants 11, Volume 10, 2012, pp 123-142, Springer-Verlag Berlin Heidelberg
- Felten J, Legué V and F Ditengou. Lateral root stimulation in the early interaction between Arabidopsis thaliana and the ectomycorrhizal fungus Laccaria bicolor: Is fungal auxin the trigger? Plant Signaling & Behavior 2010, 5(7) pp 864-867
- Felten J, Kohler A, Morin E, Bhalerao RP, Palme K, Martin Ditengou, FA and V Legue. The ectomycorrhizal fungus Laccaria bicolor stimulates lateral root formation in poplar and Arabidopsis through auxin transport and signaling. Plant Physiology 2009, 151 (4) pp 1991-2005
- since 2020 Senior lecturer and docent in plant biology, Swedish University of Agricultural Sciences, Umeå Plant Science Centre
- 2016-2020 Assistant senior lecturer, Swedish University of Agricultural Sciences, Umeå Plant Science Centre
- 2014-2016 Researcher, Swedish University of Agricultural Sciences, Umeå Plant Science Centre
- 2010-2013 Postdoc, Swedish University of Agricultural Sciences, Umeå Plant Science Centre
- 2009 German-French PhD in Plant Biology, Université Henri Poincaré Nancy, France and Albert Ludwigs Universität Freiburg, Germany
- 2006 MSc Molecular and Cell Biology, Ecole Normale Supérieure de Lyon, France
- 2004 BSc Biochemistry, Ruhr-Universität Bochum, Germany
CV T. Moritz
Publications
Svenska

Min grupp studerar hur växthormoner och andra metaboliter reglerar tillväxt och utveckling i träd. Vi studerar framförallt hormonet gibberellin och dess roll i skottsträckning och vedbildning.
Vi har visat att genom att öka mängden gibberelliner i hybridasp så får man träd som i växthus uppvisar ökad höjd- och diametertillväxt. En upptäckt som kan få betydelse även ur ett prakiskt perspektiv.
I ett flertal projekt använder vi även metodik som kallas metabolomik för att kunna identifiera ämnen som är kopplade till trädets olika utvecklingsfaser. Fokus är framförallt mot hur olika metaboliter varierar i vedbildningszonen och deras function under vedbildningens olika faser.

Research

Light in excess of photosynthetic capacity can be damaging to cells constituents. Thus ways to protect against damage have evolved in photosynthetic organisms, including ways to minimize light absorption, detoxify reactive oxygen species generated by excess light, and dissipate excess absorbed light. Together, these processes are known as photoprotection.
For more information see also our lab website at https://malnoelab.com.
Despite the physiological importance of photoprotection, the molecular mechanisms that protect against light stress, especially those protecting against sustained light stress, remain largely unknown. In my group, we combine genetics, biochemistry, biophysics and physiology to elucidate the molecular mechanisms of photoprotection under sustained abiotic stress. Our research will provide insights into fundamental mechanisms of light energy capture, utilization and dissipation in plants.

Key Publications
CV A. Malnoë
Department of Biology, Indiana University Bloomington
Department of Plant Physiology, Umeå University, Sweden.
Molecular mechanisms of sustained photoprotection. VR, MSCA IF-RI, Kempe, KAW, SSF ARC2030
University of California Berkeley, USA. Advisor: Krishna K. Niyogi
Photoprotection mechanisms in Arabidopsis thaliana. US DOE FWP449B
University of California Berkeley, USA. Advisor: Krishna K. Niyogi
Photoprotection mechanisms in Arabidopsis thaliana. US DOE FWP449B
CNRS UMR7141 IBPC Paris, France. Advisor: Francis-André Wollman
Role of the FtsH protease in Chlamydomonas reinhardtii. EU FP7 SUNBIOPATH
CNRS UMR7141 IBPC Paris, France. Advisor: Catherine de Vitry.
Graduate School Plant Sciences, University of Paris-Sud XI, Orsay, France.
Cytochrome b6f heme ci function in Chlamydomonas reinhardtii. ANR BLANC
University of Queensland, Brisbane, Australia. Advisor: Ben Hankamer
Biochemical and structural characterization of the photosynthetic apparatus during sulfur deprivation in Chlamydomonas reinhardtii.
LB3M, CEA Cadarache, France. Advisor: Laurent Cournac
Identification and characterization of NADH dehydrogenases type II in the microalga Chlamydomonas reinhardtii.
Graduate School Biology, Health & Biotechnologies
University of Paul-Sabatier, Toulouse, France
Ecole Nationale Supérieure Agronomique de Toulouse, France
French National School of Agricultural Sciences and Engineering
Publications
Contact
Photo: Queena Xu Alizée Malnoë
Associate Professor, Biology
Department of Biology
Indiana University Bloomington
USA
Email:
Main homepage: https://malnoelab.com/

Research
Photo: Johan Gunséus We are studying the development of ectomycorrhizal symbioses. This type of symbiosis forms naturally between the majority of temperate and boreal forest trees and soil fungi. Ectomycorrhizal fungi exploit the soil very efficiently to absorb nutrients (N, P) through their extensive hyphal networks. A part of these nutrients can be exchanged with tree partners for photosynthetic sugars. The nutrient exchange can benefit ree and fungus. Despite the importance of ectomycorrhizal symbiosis for the health of the forest (soil) ecosystem, the molecular mechanisms that trigger ectomycorrhiza establishment remain largely unknown.
Ectomycorrhizal roots (ECM) (Figure 1) are characterized by three tissues: a fungal mantle surrounding the root from which extramatrical hyphae reach out into the soil to gather nutrients (N, P). These nutrients are exchanged with the plant for photosynthetic derived sugars in the Hartig Net, where a number of specific plant and fungal transport proteins are expressed (Martin and Nehls, Current Opinion in Plant Biology 2009). The structure of the Hartig Net is characterized by fungal hyphae that invade the apoplastic space between root epidermis/cortex cells (Figure 1C).

Hartig Net development requires loosening of the radial wall between adjacent epidermis cells. This process involves degradation of the middle lamella between these cells. It has been proposed that fungus- and plant-derived enzymes from the Carbohydrate Active Enzyme (CAzyme) family, which have the potential to modify cell wall polymers, could mediate the cell wall release. Fungal genes coding for CAzymes have been identified in Laccaria bicolor and Tuber melanosporum ECM (Balestrini et al., Current Genetics 2012; Veneault-Fourrey et al., Fungal Genetics and Biology 2014; Sillo et al., Planta 2016, Chowdhury et al. 2022) and some of these are induced within the Hartig Net (Hacquard et al., Environmental Microbiology 2013).
Ectomycorrhizal fungi secrete effectors such as Mycorrhiza induced Small Secreted Protein 7 (MiSSP7), which can be taken up into the plant and trigger plant responses that may contribute to cell wall release (Plett et al., Current Biology 2011). MiSSP7 is required for Hartig Net formation and fungal strains of L. bicolor that lack this peptide form only a very shallow Hartig Net, suggesting that even plant-triggered processes are required for Hartig Net formation. Fungal auxin is yet another fungal factor that is likely to contribute to cell wall remodelling and Hartig Net formation (Gay et al., New Phytologist 1994), but again functional studies are needed to prove this assumption and how auxin may interact with effectors and CAzymes remains to be investigated. The different categories of actors potentially contributing to cell wall remodelling and Hartig Net formation are depicted in Figure 2.

The aim of my research is to uncover the nature of cell wall remodelling during Hartig Net establishment and to reveal the crucial molecular factors behind this process and their interplay. In my group we are using an elegant combination of state of the art cell wall analysis techniques together with microscopy, hormone metabolomics, transcriptomics and cell biology on material from ectomycorrhiza from gymnosperm and angiosperm trees with fungi having different mycorrhization capacity, to reveal the nature of cell wall remodelling required for Hartig Net establishment.
In 2022 we demonstrated that a pectin methylesterase from the fungus L. bicolor is involved in Hartig Net formation with hybrid aspen trees (Chowdhury et al. 2022). L. bicolor harbours two types of pectin modifying enzyme families. Our work together with the one by Zhang et al. (2022) is showing that at least one member of each of these families is required for normal Hartig Net formation and that therefore L. bicolor actively contributes to the separation of adjacent cells for Hartig Net formation with Populus trees roots.
Key Publications
Team
Former group members:
Postdocs
Caroline Seyfferth, Yohann Daguerre, Jamil Chowdhury, Sabine Kunz, Jingjing Zhou, Raghuram Badmi
PhD students
Bernard Wessles (co-supervisor)
Master students
Alexandra Goetsch, Archana Kumari
Bachelor students
Imko van Dijk, Carina Lubrecht
Assistants and project students
Alexander Karlsson, Lina Nilsson, Johanna Urzua, Silvia Pruna