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Nanda, S., Shutova, T., Cainzos, M., Bag, P., Jansson, S. & Holzwarth, A. R. (2024). ChloroSpec: A new in vivo chlorophyll fluorescence spectrometer for simultaneous wavelength- and time-resolved detection. Physiologia Plantarum, 176(2), Article ID e14306.
Open this publication in new window or tab >>ChloroSpec: A new in vivo chlorophyll fluorescence spectrometer for simultaneous wavelength- and time-resolved detection
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2024 (English)In: Physiologia Plantarum, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 176, no 2, article id e14306Article in journal (Refereed) Published
Abstract [en]

Chlorophyll fluorescence is a ubiquitous tool in basic and applied plant science research. Various standard commercial instruments are available for characterization of photosynthetic material like leaves or microalgae, most of which integrate the overall fluorescence signals above a certain cut-off wavelength. However, wavelength-resolved (fluorescence signals appearing at different wavelengths having different time dependent decay) signals contain vast information required to decompose complex signals and processes into their underlying components that can untangle the photo-physiological process of photosynthesis. Hence, to address this we describe an advanced chlorophyll fluorescence spectrometer - ChloroSpec - allowing three-dimensional simultaneous detection of fluorescence intensities at different wavelengths in a time-resolved manner. We demonstrate for a variety of typical examples that most of the generally used fluorescence parameters are strongly wavelength dependent. This indicates a pronounced heterogeneity and a highly dynamic nature of the thylakoid and the photosynthetic apparatus under actinic illumination. Furthermore, we provide examples of advanced global analysis procedures integrating this three-dimensional signal and relevant information extracted from them that relate to the physiological properties of the organism. This conveniently obtained broad range of data can make ChloroSpec a new standard tool in photosynthesis research.

Place, publisher, year, edition, pages
John Wiley & Sons, 2024
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-223953 (URN)10.1111/ppl.14306 (DOI)001207485500001 ()38659135 (PubMedID)2-s2.0-85191196422 (Scopus ID)
Funder
The Kempe FoundationsSwedish Research CouncilKnut and Alice Wallenberg FoundationSwedish Foundation for Strategic Research
Available from: 2024-05-03 Created: 2024-05-03 Last updated: 2024-05-03Bibliographically approved
Bag, P., Shutova, T., Shevela, D., Lihavainen, J., Nanda, S., Ivanov, A. G., . . . Jansson, S. (2023). Flavodiiron-mediated O2 photoreduction at photosystem I acceptor-side provides photoprotection to conifer thylakoids in early spring. Nature Communications, 14(1), Article ID 3210.
Open this publication in new window or tab >>Flavodiiron-mediated O2 photoreduction at photosystem I acceptor-side provides photoprotection to conifer thylakoids in early spring
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2023 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 3210Article in journal (Refereed) Published
Abstract [en]

Green organisms evolve oxygen (O2) via photosynthesis and consume it by respiration. Generally, net O2 consumption only becomes dominant when photosynthesis is suppressed at night. Here, we show that green thylakoid membranes of Scots pine (Pinus sylvestris L) and Norway spruce (Picea abies) needles display strong O2 consumption even in the presence of light when extremely low temperatures coincide with high solar irradiation during early spring (ES). By employing different electron transport chain inhibitors, we show that this unusual light-induced O2 consumption occurs around photosystem (PS) I and correlates with higher abundance of flavodiiron (Flv) A protein in ES thylakoids. With P700 absorption changes, we demonstrate that electron scavenging from the acceptor-side of PSI via O2 photoreduction is a major alternative pathway in ES. This photoprotection mechanism in vascular plants indicates that conifers have developed an adaptative evolution trajectory for growing in harsh environments.

Place, publisher, year, edition, pages
Springer Nature, 2023
National Category
Biochemistry and Molecular Biology Botany
Identifiers
urn:nbn:se:umu:diva-209538 (URN)10.1038/s41467-023-38938-z (DOI)001002562700001 ()37270605 (PubMedID)2-s2.0-85160880215 (Scopus ID)
Funder
EU, Horizon 2020, 675006Swedish Research Council, (2016-04894 aSwedish Research Council, 2021-05062Swedish Research Council, 2020-03809The Kempe Foundations, 2014Swedish Research Council Formas, 2015-00907Swedish Research Council Formas, 2021-01474Swedish Foundation for Strategic Research, FFF20- 0008Vinnova, 2016-00504Knut and Alice Wallenberg Foundation, 2016-0352Knut and Alice Wallenberg Foundation, 2020.0240Göran Gustafsson Foundation for Research in Natural Sciences and Medicine, BS2022-0021
Available from: 2023-06-13 Created: 2023-06-13 Last updated: 2023-09-05Bibliographically approved
Escamez, S., Robinson, K. M., Luomaranta, M., Gandla, M. L., Mähler, N., Yassin, Z., . . . Tuominen, H. (2023). Genetic markers and tree properties predicting wood biorefining potential in aspen (Populus tremula) bioenergy feedstock. Biotechnology for Biofuels and Bioproducts, 16(1), Article ID 65.
Open this publication in new window or tab >>Genetic markers and tree properties predicting wood biorefining potential in aspen (Populus tremula) bioenergy feedstock
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2023 (English)In: Biotechnology for Biofuels and Bioproducts, E-ISSN 2731-3654, Vol. 16, no 1, article id 65Article in journal (Refereed) Published
Abstract [en]

Background: Wood represents the majority of the biomass on land and constitutes a renewable source of biofuels and other bioproducts. However, wood is recalcitrant to bioconversion, raising a need for feedstock improvement in production of, for instance, biofuels. We investigated the properties of wood that affect bioconversion, as well as the underlying genetics, to help identify superior tree feedstocks for biorefining.

Results: We recorded 65 wood-related and growth traits in a population of 113 natural aspen genotypes from Sweden (https://doi.org/10.5061/dryad.gtht76hrd). These traits included three growth and field performance traits, 20 traits for wood chemical composition, 17 traits for wood anatomy and structure, and 25 wood saccharification traits as indicators of bioconversion potential. Glucose release after saccharification with acidic pretreatment correlated positively with tree stem height and diameter and the carbohydrate content of the wood, and negatively with the content of lignin and the hemicellulose sugar units. Most of these traits displayed extensive natural variation within the aspen population and high broad-sense heritability, supporting their potential in genetic improvement of feedstocks towards improved bioconversion. Finally, a genome-wide association study (GWAS) revealed 13 genetic loci for saccharification yield (on a whole-tree-biomass basis), with six of them intersecting with associations for either height or stem diameter of the trees.

Conclusions: The simple growth traits of stem height and diameter were identified as good predictors of wood saccharification yield in aspen trees. GWAS elucidated the underlying genetics, revealing putative genetic markers for bioconversion of bioenergy tree feedstocks.

Place, publisher, year, edition, pages
BioMed Central (BMC), 2023
Keywords
Bioenergy, Biomass, Biorefining, Feedstock recalcitrance, Forest feedstocks, Saccharification
National Category
Forest Science
Identifiers
urn:nbn:se:umu:diva-206938 (URN)10.1186/s13068-023-02315-1 (DOI)000967835900001 ()2-s2.0-85152632077 (Scopus ID)
Funder
Swedish Research Council Formas, 942-2015-84Swedish Research Council Formas, 2018-01381Knut and Alice Wallenberg Foundation, 2016.0341Knut and Alice Wallenberg Foundation, 2016.0352Vinnova, 2016-00504Bio4Energy
Available from: 2023-04-27 Created: 2023-04-27 Last updated: 2023-11-06Bibliographically approved
Lihavainen, J., Šimura, J., Bag, P., Fataftah, N., Robinson, K. M., Delhomme, N., . . . Jansson, S. (2023). Salicylic acid metabolism and signalling coordinate senescence initiation in aspen in nature. Nature Communications, 14(1), Article ID 4288.
Open this publication in new window or tab >>Salicylic acid metabolism and signalling coordinate senescence initiation in aspen in nature
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2023 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 4288Article in journal (Refereed) Published
Abstract [en]

Deciduous trees exhibit a spectacular phenomenon of autumn senescence driven by the seasonality of their growth environment, yet there is no consensus which external or internal cues trigger it. Senescence starts at different times in European aspen (Populus tremula L.) genotypes grown in same location. By integrating omics studies, we demonstrate that aspen genotypes utilize similar transcriptional cascades and metabolic cues to initiate senescence, but at different times during autumn. The timing of autumn senescence initiation appeared to be controlled by two consecutive “switches”; 1) first the environmental variation induced the rewiring of the transcriptional network, stress signalling pathways and metabolic perturbations and 2) the start of senescence process was defined by the ability of the genotype to activate and sustain stress tolerance mechanisms mediated by salicylic acid. We propose that salicylic acid represses the onset of leaf senescence in stressful natural conditions, rather than promoting it as often observed in annual plants.

Place, publisher, year, edition, pages
Springer Nature, 2023
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-212477 (URN)10.1038/s41467-023-39564-5 (DOI)37463905 (PubMedID)2-s2.0-85165262787 (Scopus ID)
Funder
Swedish Research CouncilSwedish Research Council FormasThe Kempe FoundationsSwedish Foundation for Strategic ResearchKnut and Alice Wallenberg FoundationVinnova
Available from: 2023-08-03 Created: 2023-08-03 Last updated: 2023-08-03Bibliographically approved
Arshad, R., Saccon, F., Bag, P., Biswas, A., Calvaruso, C., Bhatti, A. F., . . . Büchel, C. (2022). A kaleidoscope of photosynthetic antenna proteins and their emerging roles. Plant Physiology, 189(3), 1204-1219
Open this publication in new window or tab >>A kaleidoscope of photosynthetic antenna proteins and their emerging roles
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2022 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 189, no 3, p. 1204-1219Article in journal (Refereed) Published
Abstract [en]

Photosynthetic light-harvesting antennae are pigment-binding proteins that perform one of the most fundamental tasks on Earth, capturing light and transferring energy that enables life in our biosphere. Adaptation to different light environments led to the evolution of an astonishing diversity of light-harvesting systems. At the same time, several strategies have been developed to optimize the light energy input into photosynthetic membranes in response to fluctuating conditions. The basic feature of these prompt responses is the dynamic nature of antenna complexes, whose function readily adapts to the light available. High-resolution microscopy and spectroscopic studies on membrane dynamics demonstrate the crosstalk between antennae and other thylakoid membrane components. With the increased understanding of light-harvesting mechanisms and their regulation, efforts are focusing on the development of sustainable processes for effective conversion of sunlight into functional bio-products. The major challenge in this approach lies in the application of fundamental discoveries in light-harvesting systems for the improvement of plant or algal photosynthesis. Here, we underline some of the latest fundamental discoveries on the molecular mechanisms and regulation of light harvesting that can potentially be exploited for the optimization of photosynthesis.

Place, publisher, year, edition, pages
Oxford University Press, 2022
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-194031 (URN)10.1093/plphys/kiac175 (DOI)000790909500001 ()35512089 (PubMedID)2-s2.0-85133103283 (Scopus ID)
Funder
EU, Horizon 2020, 675006
Available from: 2022-04-22 Created: 2022-04-22 Last updated: 2023-03-23Bibliographically approved
Fataftah, N., Edlund, E., Lihavainen, J., Bag, P., Björkén, L., Näsholm, T. & Jansson, S. (2022). Nitrate fertilization may delay autumn leaf senescence, while amino acid treatments do not. Physiologia Plantarum, 174(3), Article ID e13690.
Open this publication in new window or tab >>Nitrate fertilization may delay autumn leaf senescence, while amino acid treatments do not
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2022 (English)In: Physiologia Plantarum, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 174, no 3, article id e13690Article in journal (Refereed) Published
Abstract [en]

Fertilization with nitrogen (N)-rich compounds leads to increased growth but may compromise phenology and winter survival of trees in boreal regions. During autumn, N is remobilized from senescing leaves and stored in other parts of the tree to be used in the next growing season. However, the mechanism behind the N fertilization effect on winter survival is not well understood, and it is unclear how N levels or forms modulate autumn senescence. We performed fertilization experiments and showed that treating Populus saplings with inorganic nitrogen resulted in a delay in senescence. In addition, by using precise delivery of solutes into the xylem stream of Populus trees in their natural environment, we found that delay of autumn senescence was dependent on the form of N administered: inorganic N ((Formula presented.)) delayed senescence, but amino acids (Arg, Glu, Gln, and Leu) did not. Metabolite profiling of leaves showed that the levels of tricarboxylic acids, arginine catabolites (ammonium, ornithine), glycine, glycine-serine ratio and overall carbon-to-nitrogen (C/N) ratio were affected differently by the way of applying NO3− and Arg treatments. In addition, the onset of senescence did not coincide with soluble sugar accumulation in control trees or in any of the treatments. We propose that different regulation of C and N status through direct molecular signaling of NO3− and/or different allocation of N between tree parts depending on N forms could account for the contrasting effects of NO3− and tested here amino acids (Arg, Glu, Gln, and Leu) on autumn senescence.

Place, publisher, year, edition, pages
John Wiley & Sons, 2022
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-203158 (URN)10.1111/ppl.13690 (DOI)000798701400001 ()35460591 (PubMedID)2-s2.0-85132885123 (Scopus ID)
Funder
Swedish Research CouncilSwedish Research Council FormasKnut and Alice Wallenberg FoundationVinnova
Available from: 2023-01-16 Created: 2023-01-16 Last updated: 2023-01-16Bibliographically approved
Boussardon, C., Bag, P., Juvany, M., Šimura, J., Ljung, K., Jansson, S. & Keech, O. (2022). The RPN12a proteasome subunit is essential for the multiple hormonal homeostasis controlling the progression of leaf senescence. Communications Biology, 5(1), Article ID 1043.
Open this publication in new window or tab >>The RPN12a proteasome subunit is essential for the multiple hormonal homeostasis controlling the progression of leaf senescence
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2022 (English)In: Communications Biology, E-ISSN 2399-3642, Vol. 5, no 1, article id 1043Article in journal (Refereed) Published
Abstract [en]

The 26S proteasome is a conserved multi-subunit machinery in eukaryotes. It selectively degrades ubiquitinated proteins, which in turn provides an efficient molecular mechanism to regulate numerous cellular functions and developmental processes. Here, we studied a new loss-of-function allele of RPN12a, a plant ortholog of the yeast and human structural component of the 19S proteasome RPN12. Combining a set of biochemical and molecular approaches, we confirmed that a rpn12a knock-out had exacerbated 20S and impaired 26S activities. The altered proteasomal activity led to a pleiotropic phenotype affecting both the vegetative growth and reproductive phase of the plant, including a striking repression of leaf senescence associate cell-death. Further investigation demonstrated that RPN12a is involved in the regulation of several conjugates associated with the auxin, cytokinin, ethylene and jasmonic acid homeostasis. Such enhanced aptitude of plant cells for survival in rpn12a contrasts with reports on animals, where 26S proteasome mutants generally show an accelerated cell death phenotype.

Place, publisher, year, edition, pages
Nature Publishing Group, 2022
National Category
Botany Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-200406 (URN)10.1038/s42003-022-03998-2 (DOI)000862402500001 ()36180574 (PubMedID)2-s2.0-85139221413 (Scopus ID)
Funder
The Kempe FoundationsCarl Tryggers foundation , CTS2018-193Swedish Foundation for Strategic Research, FFF20-0008Knut and Alice Wallenberg FoundationVinnova
Available from: 2022-10-21 Created: 2022-10-21 Last updated: 2024-04-09Bibliographically approved
Rendón-Anaya, M., Wilson, J., Sveinsson, S., Fedorkov, A., Cottrell, J., Bailey, M. E. S., . . . Ingvarsson, P. K. (2021). Adaptive Introgression Facilitates Adaptation to High Latitudes in European Aspen (Populus tremula L.). Molecular biology and evolution, 38(11), 5034-5050
Open this publication in new window or tab >>Adaptive Introgression Facilitates Adaptation to High Latitudes in European Aspen (Populus tremula L.)
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2021 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 38, no 11, p. 5034-5050Article in journal (Refereed) Published
Abstract [en]

Understanding local adaptation has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems, and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole-genome resequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum, we detected an adaptive introgression event in a genome region of ∼500 kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of Northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin—probably Russian—of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results, therefore, emphasize the importance of migration–selection balance underlying the genetic architecture of key adaptive quantitative traits.

Place, publisher, year, edition, pages
Oxford University Press, 2021
Keywords
adaptation, balancing selection, introgression, postglacial colonization, selective sweep
National Category
Genetics Evolutionary Biology
Identifiers
urn:nbn:se:umu:diva-189999 (URN)10.1093/molbev/msab229 (DOI)000715560700028 ()34329481 (PubMedID)2-s2.0-85119599061 (Scopus ID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilSwedish National Infrastructure for Computing (SNIC), 2017/7-219Swedish National Infrastructure for Computing (SNIC), 2018/3-552Swedish National Infrastructure for Computing (SNIC), 2019/3-597Swedish National Infrastructure for Computing (SNIC), 2020/5-621
Available from: 2021-12-07 Created: 2021-12-07 Last updated: 2021-12-07Bibliographically approved
Bag, P., Lihavainen, J., Delhomme, N., Riquelme, T., Robinson, K. M. & Jansson, S. (2021). An atlas of the Norway spruce needle seasonal transcriptome. The Plant Journal, 108(6), 1815-1829
Open this publication in new window or tab >>An atlas of the Norway spruce needle seasonal transcriptome
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2021 (English)In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 108, no 6, p. 1815-1829Article in journal (Refereed) Published
Abstract [en]

Boreal conifers possess a tremendous ability to survive and remain evergreen during harsh winter conditions and resume growth during summer. This is enabled by coordinated regulation of major cellular functions at the level of gene expression, metabolism, and physiology. Here we present a comprehensive characterization of the annual changes in the global transcriptome of Norway spruce (Picea abies) needles as a resource to understand needle development and acclimation processes throughout the year. In young, growing needles (May 15 until June 30), cell walls, organelles, etc., were formed, and this developmental program heavily influenced the transcriptome, explained by over-represented Gene Ontology (GO) categories. Later changes in gene expression were smaller but four phases were recognized: summer (July–August), autumn (September–October), winter (November–February), and spring (March–April), where over-represented GO categories demonstrated how the needles acclimated to the various seasons. Changes in the seasonal global transcriptome profile were accompanied by differential expression of members of the major transcription factor families. We present a tentative model of how cellular activities are regulated over the year in needles of Norway spruce, which demonstrates the value of mining this dataset, accessible in ConGenIE together with advanced visualization tools.

Place, publisher, year, edition, pages
John Wiley & Sons, 2021
Keywords
conifers, Norway spruce, resource, seasonal adaptation, transcriptomics
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-188962 (URN)10.1111/tpj.15530 (DOI)000709512700001 ()34624161 (PubMedID)2-s2.0-85117463119 (Scopus ID)
Funder
EU, Horizon 2020, 675006VinnovaSwedish Research Council FormasKnut and Alice Wallenberg FoundationSwedish Research Council, 2018‐05973The Kempe Foundations
Available from: 2021-10-28 Created: 2021-10-28 Last updated: 2023-03-24Bibliographically approved
Fataftah, N., Bag, P., André, D., Lihavainen, J., Zhang, B., Ingvarsson, P. K., . . . Jansson, S. (2021). GIGANTEA influences leaf senescence in trees in two different ways. Plant Physiology, 187(4), 2435-2450
Open this publication in new window or tab >>GIGANTEA influences leaf senescence in trees in two different ways
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2021 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 187, no 4, p. 2435-2450Article in journal (Refereed) Published
Abstract [en]

GIGANTEA (GI) genes have a central role in plant development and influence several processes. Hybrid aspen T89 (Populus tremula x tremuloides) trees with low GI expression engineered through RNAi show severely compromised growth. To study the effect of reduced GI expression on leaf traits with special emphasis on leaf senescence, we grafted GI-RNAi scions onto wild-type rootstocks and successfully restored growth of the scions. The RNAi line had a distorted leaf shape and reduced photosynthesis, probably caused by modulation of phloem or stomatal function, increased starch accumulation, a higher carbon-to-nitrogen ratio, and reduced capacity to withstand moderate light stress. GI-RNAi also induced senescence under long day (LD) and moderate light conditions. Furthermore, the GI-RNAi lines were affected in their capacity to respond to “autumn environmental cues” inducing senescence, a type of leaf senescence that has physiological and biochemical characteristics that differ from those of senescence induced directly by stress under LD conditions. Overexpression of GI delayed senescence under simulated autumn conditions. The two different effects on leaf senescence under LD or simulated autumn conditions were not affected by the expression of FLOWERING LOCUS T. GI expression regulated leaf senescence locally-the phenotype followed the genotype of the branch, independent of its position on the tree-and trees with modified gene expression were affected in a similar way when grown in the field as under controlled conditions. Taken together, GI plays a central role in sensing environmental changes during autumn and determining the appropriate timing for leaf senescence in Populus.

Place, publisher, year, edition, pages
Oxford University Press, 2021
National Category
Botany Plant Biotechnology
Identifiers
urn:nbn:se:umu:diva-190823 (URN)10.1093/plphys/kiab439 (DOI)000733403700044 ()2-s2.0-85121117394 (Scopus ID)
Funder
VinnovaSwedish Research Council FormasKnut and Alice Wallenberg FoundationSwedish Research CouncilEU, Horizon 2020, 675006
Available from: 2021-12-29 Created: 2021-12-29 Last updated: 2023-09-05Bibliographically approved
Projects
How do trees know it is autumn? [2009-05669_VR]; Umeå UniversityINFORMATIVE GENETICS MARKERS FOR TREES [2010-1450_Formas]; Umeå UniversityStructure and function of the proteins of the LHC family [2012-04755_VR]; Umeå UniversityHOW DO TREES KNOW IT IS AUTUMN? [2015-907_Formas]; Umeå UniversityHow do trees survive the winter? [2016-04894_VR]; Umeå University
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-7906-6891

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