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  • 1.
    Angelcheva, Liudmila
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mishra, Yogesh
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Antti, Henrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kjellsen, Trygve D.
    Department of Biology, Norwegian University of Science and Technology.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Strimbeck, Richard G.
    Department of Biology, Norwegian University of Science and Technology.
    Schröder, Wolfgang P.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Metabolomic analysis of extreme freezing tolerance in Siberian spruce (Picea obovata)2014In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 204, no 3, p. 545-555Article in journal (Refereed)
    Abstract [en]

    Siberian spruce (Picea obovata) is one of several boreal conifer species that can survive at extremely low temperatures (ELTs). When fully acclimated, its tissues can survive immersion in liquid nitrogen. Relatively little is known about the biochemical and biophysical strategies of ELT survival. We profiled needle metabolites using gas chromatography coupled with mass spectrometry (GC-MS) to explore the metabolic changes that occur during cold acclimation caused by natural temperature fluctuations. In total, 223 metabolites accumulated and 52 were depleted in fully acclimated needles compared with pre-acclimation needles. The metabolite profiles were found to develop in four distinct phases, which are referred to as pre-acclimation, early acclimation, late acclimation and fully acclimated. Metabolite changes associated with carbohydrate and lipid metabolism were observed, including changes associated with increased raffinose family oligosaccharide synthesis and accumulation, accumulation of sugar acids and sugar alcohols, desaturation of fatty acids, and accumulation of digalactosylglycerol. We also observed the accumulation of protein and nonprotein amino acids and polyamines that may act as compatible solutes or cryoprotectants. These results provide new insight into the mechanisms of freezing tolerance development at the metabolite level and highlight their importance in rapid acclimation to ELT in P.obovata.

  • 2.
    Atkin, Owen K
    et al.
    Department of Biology, The University of York, PO Box 373, York YO10 5YW, UK.
    Sherlock, David
    Department of Biology, The University of York, PO Box 373, York YO10 5YW, UK.
    Fitter, Alastair H
    Department of Biology, The University of York, PO Box 373, York YO10 5YW, UK.
    Jarvis, Susan
    Department of Biology, The University of York, PO Box 373, York YO10 5YW, UK.
    Hughes, John K
    Department of Biology, The University of York, PO Box 373, York YO10 5YW, UK.
    Campbell, Catherine
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Hurry, Vaughan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Hodge, Angela
    Department of Biology, The University of York, PO Box 373, York YO10 5YW, UK.
    Temperature dependence of respiration in roots colonized by arbuscular mycorrhizal fungi2009In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 182, no 1, p. 188-199Article in journal (Refereed)
    Abstract [en]

    * The arbuscular mycorrhizal (AM) symbiosis is ubiquitous, and the fungus represents a major pathway for carbon movement in the soil-plant system. Here, we investigated the impacts of AM colonization of Plantago lanceolata and temperature on the regulation of root respiration (R). * Warm-grown AM plants exhibited higher rates of R than did nonAM plants, irrespective of root mass. AM plants exhibited higher maximal rates of R (R(max)-R measured in the presence of an uncoupler and exogenous substrate) and greater proportional use of R(max) as a result of increased energy demand and/or substrate supply. The higher R values exhibited by AM plants were not associated with higher maximal rates of cytochrome c oxidase (COX) or protein abundance of either the COX or the alternative oxidase. * Arbuscular mycorrhizal colonization had no effect on the short-term temperature dependence (Q(10)) of R. Cold-acclimated nonAM plants exhibited higher rates of R than their warm-grown nonAM counterparts. By contrast, chilling had a negligible effect on R of AM-plants. Thus, AM plants exhibited less cold acclimation than their nonAM counterparts. * Overall, these results highlight the way in which AM colonization alters the underlying components of respiratory metabolism and the response of root R to sustained changes in growth temperature.

  • 3.
    Augusti, Angela
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Betson, Tatiana R
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Schleucher, Jürgen
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Hydrogen exchange during cellulose synthesis distinguishes climatic and biochemical isotope fractionations in tree rings.2006In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 172, no 3, p. 490-499Article in journal (Refereed)
    Abstract [en]

    • The abundance of the hydrogen isotope deuterium (D) in tree rings is an attractive record of climate; however, use of this record has proved difficult so far, presumably because climatic and physiological influences on D abundance are difficult to distinguish.

    • Using D labelling, we created a D gradient in trees. Leaf soluble sugars of relatively low D abundance entered cellulose synthesis in stems containing strongly D-labelled water. We used nuclear magnetic resonance (NMR) spectroscopy to quantify D in the C-H groups of leaf glucose and of tree-ring cellulose.

    • Ratios of D abundances of individual C-H groups of leaf glucose depended only weakly on leaf D labelling, indicating that the D abundance pattern was determined by physiological influences. The D abundance pattern of tree-ring cellulose revealed C-H groups that exchanged strongly (C(2)-H) or weakly (C(6)-H2) with water during cellulose synthesis.

    • We propose that strongly exchanging C-H groups of tree-ring cellulose adopt a climate signal stemming from the D abundance of source water. C-H groups that exchange weakly retain their D abundance established in leaf glucose, which reflects physiological influences. Combining both types of groups may allow simultaneous reconstruction of climate and physiology from tree rings.

  • 4. Augusti, Angela
    et al.
    Schleucher, Jürgen
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    The ins and outs of stable isotopes in plants.2007In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 174, no 3, p. 473-475Article in journal (Refereed)
  • 5. Bai, Bing
    et al.
    Novák, Ondrej
    Ljung, Karin
    Hanson, Johannes
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, the Netherlands.
    Bentsink, Leonie
    Combined transcriptome and translatome analyses reveal a role for tryptophan-dependent auxin biosynthesis in the control of DOG1-dependent seed dormancy2018In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 217, no 3, p. 1077-1085Article in journal (Refereed)
    Abstract [en]

    The importance of translational regulation during Arabidopsis seed germination has been shown previously. Here the role of transcriptional and translational regulation during seed imbibition of the very dormant DELAY OF GERMINATION 1 (DOG1) near-isogenic line was investigated. Polysome profiling was performed on dormant and after-ripened seeds imbibed for 6 and 24 h in water and in the transcription inhibitor cordycepin. Transcriptome and translatome changes were investigated. Ribosomal profiles of after-ripened seeds imbibed in cordycepin mimic those of dormant seeds. The polysome occupancy of mRNA species is not affected by germination inhibition, either as a result of seed dormancy or as a result of cordycepin treatment, indicating the importance of the regulation of transcript abundance. The expression of auxin metabolism genes is discriminative during the imbibition of after-ripened and dormant seeds, which is confirmed by altered concentrations of indole-3-acetic acid conjugates and precursors.

  • 6.
    Bai, Bing
    et al.
    Department of Molecular Plant Physiology, Utrecht University, 3584 CH Utrecht, the Netherlands; Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, the Netherlands.
    Peviani, Alessia
    van der Horst, Sjors
    Gamm, Magdalena
    Snel, Berend
    Bentsink, Leónie
    Hanson, Johannes
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Department of Molecular Plant Physiology, Utrecht University, 3584 CH Utrecht, the Netherlands.
    Extensive translational regulation during seed germination revealed by polysomal profiling2017In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 214, no 1, p. 233-244Article in journal (Refereed)
    Abstract [en]

    This work investigates the extent of translational regulation during seed germination. The polysome occupancy of each gene is determined by genome-wide profiling of total mRNA and polysome-associated mRNA. This reveals extensive translational regulation during Arabidopsis thaliana seed germination. The polysome occupancy of thousands of individual mRNAs changes to a large extent during the germination process. Intriguingly, these changes are restricted to two temporal phases (shifts) during germination, seed hydration and germination. Sequence features, such as upstream open reading frame number, transcript length, mRNA stability, secondary structures, and the presence and location of specific motifs correlated with this translational regulation. These features differed significantly between the two shifts, indicating that independent mechanisms regulate translation during seed germination. This study reveals substantial translational dynamics during seed germination and identifies development-dependent sequence features and cis elements that correlate with the translation control, uncovering a novel and important layer of gene regulation during seed germination.

  • 7.
    Blume-Werry, Gesche
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Wilson, Scott D.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Department of Biology, University of Regina, Regina, Saskatchewan S4S 0A2 Canada.
    Kreyling, Juergen
    Milbau, Ann
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Research Institute for Nature and Forest INBO, Kliniekstraat 25, 1070 Brussels, Belgium.
    The hidden season: growing season is 50% longer below than above ground along an arctic elevation gradient2016In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 209, no 3, p. 978-986Article in journal (Refereed)
    Abstract [en]

    There is compelling evidence from experiments and observations that climate warming prolongs the growing season in arctic regions. Until now, the start, peak, and end of the growing season, which are used to model influences of vegetation on biogeochemical cycles, were commonly quantified using above-ground phenological data. Yet, over 80% of the plant biomass in arctic regions can be below ground, and the timing of root growth affects biogeochemical processes by influencing plant water and nutrient uptake, soil carbon input and microbial activity. We measured timing of above- and below-ground production in three plant communities along an arctic elevation gradient over two growing seasons. Below-ground production peaked later in the season and was more temporally uniform than above-ground production. Most importantly, the growing season continued c. 50% longer below than above ground. Our results strongly suggest that traditional above-ground estimates of phenology in arctic regions, including remotely sensed information, are not as complete a representation of whole-plant production intensity or duration, as studies that include root phenology. We therefore argue for explicit consideration of root phenology in studies of carbon and nutrient cycling, in terrestrial biosphere models, and scenarios of how arctic ecosystems will respond to climate warming.

  • 8.
    Bollhöner, Benjamin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jokipii-Lukkari, Soile
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Bygdell, Joakim
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Stael, Simon
    Adriasola, Mathilda
    Muñiz, Luis
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Van Breusegem, Frank
    Ezcurra, Inés
    Wingsle, Gunnar
    Tuominen, Hannele
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The function of two type II metacaspases in woody tissues of Populus trees2018In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 217, no 4, p. 1551-1565Article in journal (Refereed)
    Abstract [en]

    Metacaspases (MCs) are cysteine proteases that are implicated in programmed cell death of plants. AtMC9 (Arabidopsis thaliana Metacaspase9) is a member of the Arabidopsis MC family that controls the rapid autolysis of the xylem vessel elements, but its downstream targets in xylem remain uncharacterized. PttMC13 and PttMC14 were identified as AtMC9 homologs in hybrid aspen (Populustremulaxtremuloides). A proteomic analysis was conducted in xylem tissues of transgenic hybrid aspen trees which carried either an overexpression or an RNA interference construct for PttMC13 and PttMC14. The proteomic analysis revealed modulation of levels of both previously known targets of metacaspases, such as Tudor staphylococcal nuclease, heat shock proteins and 14-3-3 proteins, as well as novel proteins, such as homologs of the PUTATIVE ASPARTIC PROTEASE3 (PASPA3) and the cysteine protease RD21 by PttMC13 and PttMC14. We identified here the pathways and processes that are modulated by PttMC13 and PttMC14 in xylem tissues. In particular, the results indicate involvement of PttMC13 and/or PttMC14 in downstream proteolytic processes and cell death of xylem elements. This work provides a valuable reference dataset on xylem-specific metacaspase functions for future functional and biochemical analyses.

  • 9.
    Bollhöner, Benjamin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Zhang, Bo
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Stael, Simon
    Denancé, Nicolas
    Overmyer, Kirk
    Goffner, Deborah
    Van Breusegem, Frank
    Tuominen, Hannele
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Post mortem function of AtMC9 in xylem vessel elements2013In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 200, no 2, p. 498-510Article in journal (Refereed)
    Abstract [en]

    Cell death of xylem elements is manifested by rupture of the tonoplast and subsequent autolysis of the cellular contents. Metacaspases have been implicated in various forms of plant cell death but regulation and execution of xylem cell death by metacaspases remains unknown. Analysis of the type II metacaspase gene family in Arabidopsis thaliana supported the function of METACASPASE 9 (AtMC9) in xylem cell death. Progression of xylem cell death was analysed in protoxylem vessel elements of 3-d-old atmc9 mutant roots using reporter gene analysis and electron microscopy. Protoxylem cell death was normally initiated in atmc9 mutant lines, but detailed electron microscopic analyses revealed a role for AtMC9 in clearance of the cell contents post mortem, that is after tonoplast rupture. Subcellular localization of fluorescent AtMC9 reporter fusions supported a post mortem role for AtMC9. Further, probe-based activity profiling suggested a function of AtMC9 on activities of papain-like cysteine proteases. Our data demonstrate that the function of AtMC9 in xylem cell death is to degrade vessel cell contents after vacuolar rupture. We further provide evidence on a proteolytic cascade in post mortem autolysis of xylem vessel elements and suggest that AtMC9 is part of this cascade.

  • 10. Catford, Jane A.
    et al.
    Jansson, Roland
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Drowned, buried and carried away: effects of plant traits on the distribution of native and alien species in riparian ecosystems2014In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 204, no 1, p. 19-36Article, review/survey (Refereed)
    Abstract [en]

    Riparian vegetation is exposed to stress from inundation and hydraulic disturbance, and is often rich in native and alien plant species. We describe 35 traits that enable plants to cope with riparian conditions. These include traits for tolerating or avoiding anoxia and enabling underwater photosynthesis, traits that confer resistance and resilience to hydraulic disturbance, and attributes that facilitate dispersal, such as floating propagules. This diversity of life-history strategies illustrates that there are many ways of sustaining life in riparian zones, which helps to explain high riparian biodiversity. Using community assembly theory, we examine how adaptations to inundation, disturbance and dispersal shape plant community composition along key environmental gradients, and how human actions have modified communities. Dispersal-related processes seem to explain many patterns, highlighting the influence of regional processes on local species assemblages. Using alien plant invasions like an (uncontrolled) experiment in community assembly, we use an Australian and a global dataset to examine possible causes of high degrees of riparian invasion. We found that high proportions of alien species in the regional species pools have invaded riparian zones, despite not being riparian specialists, and that riparian invaders disperse in more ways, including by water and humans, than species invading other ecosystems.

  • 11. Chahtane, Hicham
    et al.
    Zhang, Bo
    Norberg, Mikael
    LeMasson, Marie
    Thevenon, Emmanuel
    Bakó, László
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Benlloch, Reyes
    Holmlund, Mattias
    Parcy, Francois
    Nilsson, Ove
    Vachon, Gilles
    LEAFY activity is post-transcriptionally regulated by BLADE ON PETIOLE2 and CULLIN3 in Arabidopsis2018In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 220, no 2, p. 579-592Article in journal (Refereed)
    Abstract [en]

    The Arabidopsis LEAFY (LFY) transcription factor is a key regulator of floral meristem emergence and identity. LFY interacts genetically and physically with UNUSUAL FLORAL ORGANS, a substrate adaptor of CULLIN1-RING ubiquitin ligase complexes (CRL1). The functionally redundant genes BLADE ON PETIOLE1 (BOP1) and -2 (BOP2) are potential candidates to regulate LFY activity and have recently been shown to be substrate adaptors of CULLIN3 (CUL3)-RING ubiquitin ligases (CRL3). We tested the hypothesis that LFY activity is controlled by BOPs and CUL3s in plants and that LFY is a substrate for ubiquitination by BOP-containing CRL3 complexes. When constitutively expressed, LFY activity is fully dependent on BOP2 as well as on CUL3A and B to regulate target genes such as APETALA1 and to induce ectopic flower formation. We also show that LFY and BOP2 proteins interact physically and that LFY-dependent ubiquitinated species are produced invitro in a reconstituted cell-free CRL3 system in the presence of LFY, BOP2 and CUL3. This new post-translational regulation of LFY activity by CRL3 complexes makes it a unique transcription factor subjected to a positive dual regulation by both CRL1 and CRL3 complexes and suggests a novel mechanism for promoting flower development.

  • 12. Cormier, Marc-André
    et al.
    Werner, Roland A.
    Sauer, Peter E.
    Gröcke, Darren R.
    Leuenberger, Markus C.
    Wieloch, Thomas
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Schleucher, Jürgen
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Kahmen, Ansgar
    2H-fractionations during the biosynthesis of carbohydrates and lipids imprint a metabolic signal on the δ2H values of plant organic compounds2018In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 218, no 2, p. 479-491Article in journal (Refereed)
    Abstract [en]

    Hydrogen (H) isotope ratio (δ2H) analyses of plant organic compounds have been applied to assess ecohydrological processes in the environment despite a large part of the δ2H variability observed in plant compounds not being fully elucidated.

    We present a conceptual biochemical model based on empirical H isotope data that we generated in two complementary experiments that clarifies a large part of the unexplained variability in the δ2H values of plant organic compounds.

    The experiments demonstrate that information recorded in the δ2H values of plant organic compounds goes beyond hydrological signals and can also contain important information on the carbon and energy metabolism of plants. Our model explains where 2H‐fractionations occur in the biosynthesis of plant organic compounds and how these 2H‐fractionations are tightly coupled to a plant's carbon and energy metabolism. Our model also provides a mechanistic basis to introduce H isotopes in plant organic compounds as a new metabolic proxy for the carbon and energy metabolism of plants and ecosystems.

    Such a new metabolic proxy has the potential to be applied in a broad range of disciplines, including plant and ecosystem physiology, biogeochemistry and palaeoecology.

  • 13.
    De La Torre, Amanda R.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Wang, Tongli
    Jaquish, Barry
    Aitken, Sally N.
    Adaptation and exogenous selection in a Picea glauca x Picea engelmannii hybrid zone: implications for forest management under climate change2014In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 201, no 2, p. 687-699Article in journal (Refereed)
    Abstract [en]

    The nature of selection responsible for the maintenance of the economically and ecologically important Picea glaucaxPicea engelmannii hybrid zone was investigated. Genomic, phenotypic and climatic data were used to test assumptions of hybrid zone maintenance and to model future scenarios under climate change. Genome-wide estimates of admixture based on a panel of 86 candidate gene single nucleotide polymorphisms were combined with long-term quantitative data on growth and survival (over 20yr), as well as one-time assessments of bud burst and bud set phenology, and cold hardiness traits. A total of 15498 individuals were phenotyped for growth and survival. Our results suggest that the P.glaucaxP.engelmannii hybrid zone is maintained by local adaptation to growing season length and snowpack (exogenous selection). Hybrids appeared to be fitter than pure species in intermediate environments, which fits expectations of the bounded hybrid superiority model of hybrid zone maintenance. Adaptive introgression from parental species has probably contributed to increased hybrid fitness in intermediate habitats. While P.engelmannii ancestry is higher than P.glauca ancestry in hybrid populations, on average, selective breeding in managed hybrid populations is shifting genomic composition towards P.glauca, potentially pre-adapting managed populations to warmer climates.

  • 14. Ding, Jihua
    et al.
    Böhlenius, Henrik
    Rühl, Mark Georg
    Chen, Peng
    Sane, Shashank
    Zambrano, Jose A.
    Zheng, Bo
    Nilsson, Ove
    Eriksson, Maria E.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    GIGANTEA-like genes control seasonal growth cessation in Populus2018In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 218, no 4, p. 1491-1503Article in journal (Refereed)
    Abstract [en]

    Survival of trees growing in temperate zones requires cycling between active growth and dormancy. This involves growth cessation in the autumn triggered by a photoperiod shorter than the critical day length. Variations in GIGANTEA (GI)-like genes have been associated with phenology in a range of different tree species, but characterization of the functions of these genes in the process is still lacking. We describe the identification of the Populus orthologs of GI and their critical role in short-day-induced growth cessation. Using ectopic expression and silencing, gene expression analysis, protein interaction and chromatin immunoprecipitation experiments, we show that PttGIs are likely to act in a complex with PttFKF1s (FLAVIN-BINDING, KELCH REPEAT, F-BOX 1) and PttCDFs (CYCLING DOF FACTOR) to control the expression of PttFT2, the key gene regulating short-day-induced growth cessation in Populus. In contrast to Arabidopsis, in which the GI-CONSTANS (CO)-FLOWERING LOCUS T (FT) regulon is a crucial day-length sensor for flowering time, our study suggests that, in Populus, PttCO-independent regulation of PttFT2 by PttGI is more important in the photoperiodic control of growth cessation and bud set.

  • 15.
    Eriksson, Maria E.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Hoffman, Daniel
    Kaduk, Mateusz
    Mauriat, Melanie
    Moritz, Thomas
    Transgenic hybrid aspen trees with increased gibberellin (GA) concentrations suggest that GA acts in parallel with FLOWERING LOCUS T2 to control shoot elongation2015In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 205, no 3, p. 1288-1295Article in journal (Refereed)
    Abstract [en]

    Bioactive gibberellins (GAs) have been implicated in short day (SD)-induced growth cessation in Populus, because exogenous applications of bioactive GAs to hybrid aspens (Populus tremulaxtremuloides) under SD conditions delay growth cessation. However, this effect diminishes with time, suggesting that plants may cease growth following exposure to SDs due to a reduction in sensitivity to GAs.

    In order to validate and further explore the role of GAs in growth cessation, we perturbed GA biosynthesis or signalling in hybrid aspen plants by overexpressing AtGA20ox1, AtGA2ox2 and PttGID1.3 (encoding GA biosynthesis enzymes and a GA receptor).

    We found trees with elevated concentrations of bioactive GA, due to overexpression of AtGA20ox1, continued to grow in SD conditions and were insensitive to the level of FLOWERING LOCUS T2 (FT2) expression. As transgenic plants overexpressing the PttGID1.3 GA receptor responded in a wild-type (WT) manner to SD conditions, this insensitivity did not result from limited receptor availability.

    As high concentrations of bioactive GA during SD conditions were sufficient to sustain shoot elongation growth in hybrid aspen trees, independent of FT2 expression levels, we conclude elongation growth in trees is regulated by both GA- and long day-responsive pathways, similar to the regulation of flowering in Arabidopsis thaliana.

  • 16. Felten, Judith
    et al.
    Vahala, Jorma
    Love, Jonathan
    Gorzsás, András
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Ruggeberg, Markus
    Delhomme, Nicolas
    Lesniewska, Joanna
    Kangasjarvi, Jaakko
    Hvidsten, Torgeir R.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences,Ås, Norway.
    Mellerowicz, Ewa J.
    Sundberg, Bjorn
    Ethylene signaling induces gelatinous layers with typical features of tension wood in hybrid aspen2018In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 218, no 3, p. 999-1014Article in journal (Refereed)
    Abstract [en]

    The phytohormone ethylene impacts secondary stem growth in plants by stimulating cambial activity, xylem development and fiber over vessel formation. We report the effect of ethylene on secondary cell wall formation and the molecular connection between ethylene signaling and wood formation. We applied exogenous ethylene or its precursor 1-aminocyclopropane-1-carboxylic acid (ACC) to wild-type and ethylene-insensitive hybrid aspen trees (Populus tremulaxtremuloides) and studied secondary cell wall anatomy, chemistry and ultrastructure. We furthermore analyzed the transcriptome (RNA Seq) after ACC application to wild-type and ethylene-insensitive trees. We demonstrate that ACC and ethylene induce gelatinous layers (G-layers) and alter the fiber cell wall cellulose microfibril angle. G-layers are tertiary wall layers rich in cellulose, typically found in tension wood of aspen trees. A vast majority of transcripts affected by ACC are downstream of ethylene perception and include a large number of transcription factors (TFs). Motif-analyses reveal potential connections between ethylene TFs (Ethylene Response Factors (ERFs), ETHYLENE INSENSITIVE 3/ETHYLENE INSENSITIVE3-LIKE1 (EIN3/EIL1)) and wood formation. G-layer formation upon ethylene application suggests that the increase in ethylene biosynthesis observed during tension wood formation is important for its formation. Ethylene-regulated TFs of the ERF and EIN3/EIL1 type could transmit the ethylene signal.

  • 17.
    Frenkel, Martin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Johansson Jänkänpää, Hanna
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Moen, Jon
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    An illustrated gardener's guide to transgenic Arabidopsis field experiments2008In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 180, no 2, p. 545-555Article in journal (Refereed)
    Abstract [en]

    Field studies with transgenic Arabidopsislines have been performed over 8 yr, to better understand the influence that certain genes have on plant performance. Many (if not most) plant phenotypes cannot be observed under the near constant, low-stress conditions in growth chambers, making field experiments necessary. However, there are challenges in performing such experiments: permission must be obtained and regulations obeyed, the profound influence of uncontrollable biotic and abiotic factors has to be considered, and experimental design has to be strictly controlled.

    The aim here is to provide inspiration and guidelines for researchers who are not used to setting up such experiments, allowing others to learn from our mistakes. This is believed to be the first example of a ‘manual’ for field experiments with transgenic Arabidopsisplants. Many of the challenges encountered are common for all field experiments, and many researchers from ecological backgrounds are skilled in such methods. There is huge potential in combining the detailed mechanistic understanding of molecular biologists with ecologists’ expertise in examining plant performance under field conditions, and it is suggested that more interdisciplinary collaborations will open up new scientific avenues to aid analyses of the roles of genetic and physiological variation in natural systems.

  • 18. Gauslaa, Yngvar
    et al.
    Palmqvist, Kristin
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Solhaug, Knut Asbjørn
    Hilmo, Olga
    Holien, Håkon
    Nybakken, Line
    Ohlson, Mikael
    Size-dependent growth of two old-growth associated macrolichen species2009In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 181, no 3, p. 683-692Article in journal (Refereed)
    Abstract [en]

    Relationships between thallus size and growth variables were analysed for the foliose Lobaria pulmonaria and the pendulous Usnea longissima with the aim of elucidating their morphogenesis and the factors determining thallus area (A) versus biomass (dry weight (DW) gain. Size and growth data originated from a factorial transplantation experiment that included three boreal climate zones (Atlantic, suboceanic and continental), each with three successional forest stands (clear-cut, young and old). When A was replaced by the estimated photobiont layer area in an area-DW scatterplot including all thalli (n = 1080), the two separate species clusters merged into one, suggesting similar allocation patterns between photobionts and mycobionts across growth forms. During transplantation, stand-specific water availability boosted area gain in foliose transplants, consistent with a positive role of water in fungal expansion. In pendulous lichens, A gain greatly exceeded DW gain, particularly in small transplants. The A gain in U. longissima increased with increasing DW:A ratio, consistent with a reallocation of carbon, presumably mobilized from the dense central chord. Pendulous lichens with cylindrical photobiont layers harvest light from all sides. Rapid and flexible three-dimensional A gain allows the colonization of spaces between canopy branches to utilize temporary windows of light in a growing canopy. Foliose lichens with a two-dimensional photobiont layer have more coupled A and DW gains.

  • 19. Grimberg, Åsa
    et al.
    Lager, Ida
    Street, Nathaniel
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Robinson, Kathryn M
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Marttila, Salla
    Mähler, Niklas
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Ingvarsson, Pär K.
    Bhalerao, Rishikesh P.
    Storage lipid accumulation is controlled by photoperiodic signal acting via regulators of growth cessation and dormancy in hybrid aspen2018In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 219, no 2, p. 619-630Article in journal (Refereed)
    Abstract [en]

    The signalling pathways that control seasonal modulation of carbon metabolism in perennial plants are poorly understood. Using genetic, metabolic and natural variation approaches, we identify factors mediating photoperiodic control of storage lipid accumulation in the model tree hybrid aspen (Populus tremula x tremuloides). We characterized lipid accumulation in transgenic hybrid aspen with impaired photoperiodic and hormonal responses. Genome-wide association mapping was performed in Swedish aspen (P.tremula) genotypes to determine genetic loci associated with genotype variation in lipid content. Our data show that the storage lipid triacylglycerol (TAG) accumulates in cambial meristem and pith rays of aspen in response to photoperiodic signal controlling growth cessation and dormancy induction. We show that photoperiodic control of TAG accumulation is mediated by the FLOWERING LOCUS T/CONSTANS module, which also controls the induction of growth cessation. Hormonal and chromatin remodelling pathways also contribute to TAG accumulation by photoperiodic signal. Natural variation exists in lipid accumulation that is controlled by input from multiple loci. Our data shed light on how the control of storage metabolism is temporally coordinated with growth cessation and dormancy by photoperiodic signal, and reveals that storage lipid accumulation between seeds and perennating organs of trees may involve distinct regulatory circuits.

  • 20.
    Grönlund, Andreas
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Bhalerao, Rishikesh P
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Karlsson, Jan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Modular gene expression in Poplar: a multilayer network approach2009In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 181, no 2, p. 315-322Article in journal (Refereed)
    Abstract [en]

    * By applying a multilayer network approach to an extensive set of Poplar microarray data, a genome-wide coexpression network has been detected and explored.

    * Multilayer networks were generated from minimum spanning trees (MSTs) using Kruskal's algorithm from random jack-knife resamplings of half of the full data set. The final network is obtained from the union of all the generated MSTs.

    * The gene expression correlations display a highly clustered topology, which is more pronounced when introducing links appearing in relatively few of the generated MSTs. The network also reveals a modular architecture, reflecting functional groups with relatively frequent gene-to-gene communication. Furthermore, the observed modular structure overlaps with different gene activities in different tissues, and closely related tissues show similar over- and/or under-expression patterns at the modular scale.

    * It is shown that including links that appear in a few of the generated MSTs increases the information quality of the network. In other words, a link may be 'weak' because it reflects rare signaling events rather than merely a signal weakened by noise. The method allows, from comparisons of random 'null networks', tuning to maximize the information obtainable.

  • 21. Hogberg, Mona N.
    et al.
    Briones, Maria J. I.
    Keel, Sonja G.
    Metcalfe, Daniel B.
    Campbell, Catherine
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Midwood, Andrew J.
    Thornton, Barry
    Hurry, Vaughan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Linder, Sune
    Nasholm, Torgny
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Hogberg, Peter
    Quantification of effects of season and nitrogen supply on tree below-ground carbon transfer to ectomycorrhizal fungi and other soil organisms in a boreal pine forest2010In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 187, no 2, p. 485-493Article in journal (Refereed)
    Abstract [en]

    P>The flux of carbon from tree photosynthesis through roots to ectomycorrhizal (ECM) fungi and other soil organisms is assumed to vary with season and with edaphic factors such as nitrogen availability, but these effects have not been quantified directly in the field. To address this deficiency, we conducted high temporal-resolution tracing of 13C from canopy photosynthesis to different groups of soil organisms in a young boreal Pinus sylvestris forest. There was a 500% higher below-ground allocation of plant C in the late (August) season compared with the early season (June). Labelled C was primarily found in fungal fatty acid biomarkers (and rarely in bacterial biomarkers), and in Collembola, but not in Acari and Enchytraeidae. The production of sporocarps of ECM fungi was totally dependent on allocation of recent photosynthate in the late season. There was no short-term (2 wk) effect of additions of N to the soil, but after 1 yr, there was a 60% reduction of below-ground C allocation to soil biota. Thus, organisms in forest soils, and their roles in ecosystem functions, appear highly sensitive to plant physiological responses to two major aspects of global change: changes in seasonal weather patterns and N eutrophication.

  • 22.
    HUSSDANELL, K
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    NITROGEN-FIXATION AND BIOMASS PRODUCTION IN CLONES OF ALNUS-INCANA1980In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 85, no 4, p. 503-511Article in journal (Refereed)
  • 23.
    Ingvarsson, Pär K.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Hvidsten, Torgeir R.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432,As, Norway.
    Street, Nathaniel R.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Towards integration of population and comparative genomics in forest trees2016In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 212, no 2, p. 338-344Article, review/survey (Refereed)
    Abstract [en]

    The past decade saw the initiation of an ongoing revolution in sequencing technologies that is transforming all fields of biology. This has been driven by the advent and widespread availability of high-throughput, massively parallel short-read sequencing (MPS) platforms. These technologies have enabled previously unimaginable studies, including draft assemblies of the massive genomes of coniferous species and population-scale resequencing. Transcriptomics studies have likewise been transformed, with RNA-sequencing enabling studies in nonmodel organisms, the discovery of previously unannotated genes (novel transcripts), entirely new classes of RNAs and previously unknown regulatory mechanisms. Here we touch upon current developments in the areas of genome assembly, comparative regulomics and population genetics as they relate to studies of forest tree species.

  • 24.
    Ingvarsson, Pär K
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Street, Nathaniel R
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Association genetics of complex traits in plants2011In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 189, no 4, p. 909-922Article in journal (Refereed)
    Abstract [en]

    Association mapping is rapidly becoming the main method for dissecting the genetic architecture of complex traits in plants. Currently most association mapping studies in plants are preformed using sets of genes selected to be putative candidates for the trait of interest, but rapid developments in genomics will allow for genome-wide mapping in virtually any plant species in the near future. As the costs for genotyping are decreasing, the focus has shifted towards phenotyping. In plants, clonal replication and/or inbred lines allows for replicated phenotyping under many different environmental conditions. Reduced sequencing costs will increase the number of studies that use RNA sequencing data to perform expression quantitative trait locus (eQTL) mapping, which will increase our knowledge of how gene expression variation contributes to phenotypic variation. Current population sizes used in association mapping studies are modest in size and need to be greatly increased if mutations explaining less than a few per cent of the phenotypic variation are to be detected. Association mapping has started to yield insights into the genetic architecture of complex traits in plants, and future studies with greater genome coverage will help to elucidate how plants have managed to adapt to a wide variety of environmental conditions.

  • 25.
    Johansson, Otilia
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Nordin, Annika
    Olofsson, Johan
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Palmqvist, Kristin
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Responses of epiphytic lichens to an experimental whole-tree nitrogen-deposition gradient2010In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 188, no 4, p. 1075-1084Article in journal (Refereed)
    Abstract [en]

    • Here, we examined the responses of the epiphytic lichens Alectoria sarmentosa and Platismatia glauca to increased atmospheric nitrogen (N) deposition in an old-growth boreal spruce forest, to assess the sensitivity of these species to N and define their critical N load. • Nitrogen deposition was simulated by irrigating 15 trees over a 3 yr period with water and isotopically labeled NH(4) NO(3) , providing N loads ranging from ambient to 50 kg N ha(-1)  yr(-1) . • Thallus N concentration increased in both species with increasing N load, and uptake rates of both NH(4) (+) and NO(3) (-) were similar. Photobiont concentration increased linearly with increased N in both species, saturating in A. sarmentosa in the third year at the highest N loads (25 and 50 kg ha(-1 ) yr(-1) ). The simulated N deposition decreased the phosphorus (P) concentration in A. sarmentosa, and increased the N : P ratio in both species. • Significant responses in lichen chemistry were detected to inputs of 12.5 kg N ha(-1)  yr(-1) or higher, suggesting that resources other than N limit lichens at higher N loads. However, the data also suggest that N saturation may be cumulative over time, even at low N.

  • 26.
    Johansson, Otilia
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Olofsson, Johan
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Giesler, Reiner
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Palmqvist, Kristin
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Lichen responses to nitrogen and phosphorus additions can be explained by the different symbiont responses2011In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 191, no 3, p. 795-805Article in journal (Refereed)
    Abstract [en]

    Responses to simulated nitrogen (N) deposition with or without added phosphorus (P) were investigated for three contrasting lichen species – the N-sensitive Alectoria sarmentosa, the more N-tolerant Platismatia glauca and the N2-fixing Lobaria pulmonaria– in a field experiment.

    To examine whether nutrient limitation differed between the photobiont and the mycobiont within the lichen, the biomass responses of the respective bionts were estimated.

    The lichenized algal cells were generally N-limited, because N-stimulated algal growth in all three species. The mycobiont was P-limited in one species (A. sarmentosa), but the growth response of the mycobionts was complex, as fungal growth is also dependent on a reliable carbon export from the photobiont, which may have been the reason for the decrease of the mycobiont with N addition in P. glauca.

    Our findings showed that P availability was an important factor when studying effects of N deposition, as P supply can both mitigate and intensify the negative effects of N on epiphytic lichens.

  • 27.
    Jokipii-Lukkari, Soile
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology,Swedish University of Agricultural Sciences, SE-901 84 Umeå, Sweden.
    Sundell, David
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Nilsson, Ove
    Hvidsten, Torgeir R.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway.
    Street, Nathaniel R.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Tuominen, Hannele
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    NorWood: a gene expression resource for evo-devo studies of conifer wood development2017In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 216, no 2, p. 482-494Article in journal (Refereed)
    Abstract [en]

    The secondary xylem of conifers is composed mainly of tracheids that differ anatomically and chemically from angiosperm xylem cells. There is currently no high-spatial-resolution data available profiling gene expression during wood formation for any coniferous species, which limits insight into tracheid development.

    RNA-sequencing data from replicated, high-spatial-resolution section series throughout the cambial and woody tissues of Picea abies were used to generate the NorWood.conGenIE.org web resource, which facilitates exploration of the associated gene expression profiles and co-expression networks.

    Integration within PlantGenIE.org enabled a comparative regulomics analysis, revealing divergent co-expression networks between P. abies and the two angiosperm species Arabidopsis thaliana and Populus tremula for the secondary cell wall (SCW) master regulator NAC Class IIB transcription factors. The SCW cellulose synthase genes (CesAs) were located in the neighbourhoods of the NAC factors in Athaliana and P. tremula, but not in Pabies. The NorWood co-expression network enabled identification of potential SCW CesA regulators in P. abies.

    The NorWood web resource represents a powerful community tool for generating evo-devo insights into the divergence of wood formation between angiosperms and gymnosperms and for advancing understanding of the regulation of wood development in P. abies.

  • 28. Kardol, Paul
    et al.
    De Long, Jonathan R
    Sundqvist, Maja K.
    Crossing the threshold: the power of multi-level experiments in identifying global change responses.2012In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 196, no 2, p. 323-6Article in journal (Refereed)
  • 29. Keel, Sonja G.
    et al.
    Campbell, Catherine D.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Hogberg, Mona N.
    Richter, Andreas
    Wild, Birgit
    Zhou, Xuhui
    Hurry, Vaughan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Linder, Sune
    Nasholm, Torgny
    Hogberg, Peter
    Allocation of carbon to fine root compounds and their residence times in a boreal forest depend on root size class and season2012In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 194, no 4, p. 972-981Article in journal (Refereed)
    Abstract [en]

    Fine roots play a key role in the forest carbon balance, but their carbon dynamics remain largely unknown. We pulse labelled 50 m2 patches of young boreal forest by exposure to 13CO2 in early and late summer. Labelled photosynthates were traced into carbon compounds of < 1 and 13 mm diameter roots (fine roots), and into bulk tissue of these and first-order roots (root tips). Root tips were the most strongly labelled size class. Carbon allocation to all size classes was higher in late than in early summer; mean residence times (MRTs) in starch increased from 4 to 11 months. In structural compounds, MRTs were 0.8 yr in tips and 1.8 yr in fine roots. The MRT of carbon in sugars was in the range of days. Functional differences within the fine root population were indicated by carbon allocation patterns and residence times. Pronounced allocation of recent carbon and higher turnover rates in tips are associated with their role in nutrient and water acquisition. In fine roots, longer MRTs but high allocation to sugars and starch reflect their role in structural support and storage. Accounting for heterogeneity in carbon residence times will improve and most probably reduce the estimates of fine root production.

  • 30.
    Kindgren, Peter
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Strand, Åsa
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Chloroplast transcription, untangling the Gordian Knot2015In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 206, no 3, p. 889-891Article in journal (Other academic)
  • 31.
    Klemenčič, Marina
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, SI-1000 Ljubljana, Slovenia.
    Type III metacaspases: calcium-dependent activity proposes new function for the p10 domain2018In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 218, no 3 Special issue, p. 1179-1191Article in journal (Refereed)
    Abstract [en]

    Metacaspases are a subgroup of caspase homologues represented in bacteria, algae and plants. Although type I and type II metacaspases are present in plants, recently discovered and uncharacterized type III metacaspases can only be found in algae which have undergone secondary endosymbiosis. We analysed the expression levels of all 13 caspase homologues in the cryptophyte Guillardia theta in vivo and biochemically characterized its only type III metacaspase, GtMC2, in vitro. Type III metacaspase GtMC2 was shown to be an endopeptidase with a preference for basic amino acids in the P1 position, which exhibited specific N-terminal proteolytic cleavage for full catalytic efficiency. Autolytic processing, as well as the activity of the mature enzyme, required the presence of calcium ions in low millimolar concentrations. In GtMC2, two calcium-binding sites were identified, one with a dissociation constant at low and the other at high micromolar concentrations. We show high functional relatedness of type III metacaspases to type I metacaspases. Moreover, our data suggest that the low-affinity calcium-binding site is located in the p10 domain, which contains a well-conserved N-terminal region. This region can only be found in type I/II/III metacaspases, but is absent in calcium-independent caspase homologues.

  • 32. Klintenas, Maria
    et al.
    Pin, Pierre A.
    Benlloch, Reyes
    Ingvarsson, Pär K.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Nilsson, Ove
    Analysis of conifer FLOWERING LOCUS T/TERMINAL FLOWER1-like genes provides evidence for dramatic biochemical evolution in the angiosperm FT lineage2012In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 196, no 4, p. 1260-1273Article in journal (Refereed)
    Abstract [en]

    In flowering plants, homologs of the Arabidopsis phosphatidylethanolamine-binding protein (PEBP) FLOWERING LOCUS T (FT) are key components in controlling flowering time. We show here that, although FT homologs are found in all angiosperms with completed genome sequences, there is no evidence to date that FT-like genes exist in other groups of plants. Through phylogeny reconstructions and heterologous expression, we examined the biochemical function of the Picea (spruces) and Pinus (pines) PEBP families two gymnosperm taxa phylogenetically distant from the angiosperms. We have defined a lineage of gymnosperm PEBP genes, termed the FT/TERMINAL FLOWER1 (TFL1)-like genes, that share sequence characteristics with both the angiosperm FT- and TFL1-like clades. When expressed in Arabidopsis, FT/TFL1-like genes repressed flowering, indicating that the proteins are biochemically more similar to the angiosperm TFL1-like proteins than to the FT-like proteins. This suggests that the regulation of the vegetative-to-reproductive switch might differ in gymnosperms compared with angiosperms. Molecular evolution studies suggest that plasticity at exon 4 contributes to the divergence of FT-like function in floral promotion. In addition, the presence of FT-like genes in basal angiosperms indicates that the FT-like function emerged at an early stage during the evolution of flowering plants as a means to regulate flowering time.

  • 33. Lafon-Placette, Clément
    et al.
    Faivre-Rampant, Patricia
    Delaunay, Alain
    Street, Nathaniel
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Brignolas, Franck
    Maury, Stéphane
    Methylome of DNase I sensitive chromatin in Populus trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene-body DNA methylation in open chromatin state2013In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 197, no 2, p. 416-430Article in journal (Refereed)
    Abstract [en]

    DNA methylation is involved in the control of plant development and adaptation to the environment through modifications of chromatin compaction and gene expression. In poplar (Populus trichocarpa), a perennial plant, variations in DNA methylation have been reported between genotypes and tissues or in response to drought. Nevertheless, the relationships between gene-body DNA methylation, gene expression and chromatin compaction still need clarification.

    Here, DNA methylation was mapped in the noncondensed chromatin fraction from P. trichocarpa shoot apical meristematic cells, the center of plant morphogenesis, where DNA methylation variations could influence the developmental trajectory. DNase I was used to isolate the noncondensed chromatin fraction. Methylated sequences were immunoprecipitated, sequenced using Illumina/Solexa technology and mapped on the v2.0 poplar genome. Bisulfite sequencing of candidate sequences was used to confirm mapping data and to assess cytosine contexts and methylation levels.

    While the methylated DNase I hypersensitive site fraction covered 1.9% of the poplar genome, it contained sequences corresponding to 74% of poplar gene models, mostly exons. The level and cytosine context of gene-body DNA methylation varied with the structural characteristics of the genes.

    Taken together, our data show that DNA methylation is widespread and variable among genes in open chromatin of meristematic cells, in agreement with a role in their developmental trajectory.

  • 34.
    Liebsch, Daniela
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Keech, Olivier
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Dark-induced leaf senescence: new insights into a complex light-dependent regulatory pathway2016In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 212, no 3, p. 563-570Article, review/survey (Refereed)
    Abstract [en]

    Leaf senescence - the coordinated, active process leading to the organized dismantling of cellular components to remobilize resources - is a fundamental aspect of plant life. Its tight regulation is essential for plant fitness and has crucial implications for the optimization of plant productivity and storage properties. Various investigations have shown light deprivation and light perception via phytochromes as key elements modulating senescence. However, the signalling pathways linking light deprivation and actual senescence processes have long remained obscure. Recent analyses have demonstrated that PHYTOCHROME-INTERACTING FACTORS (PIFs) are major transcription factors orchestrating dark-induced senescence (DIS) by targeting chloroplast maintenance, chlorophyll metabolism, hormone signalling and production, and the expression of senescence master regulators, uncovering potential molecular links to the energy deprivation signalling pathway. PIF-dependent feed-forward regulatory modules might be of critical importance for the highly complex and initially light-reversible DIS induction.

  • 35.
    Lindh, Magnus
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Johansson, Jacob
    Lund University.
    Bolmgren, Kjell
    SLU.
    Lundström, Niklas
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Brännström, Åke
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics. Evolution and Ecology Program International Institute for Applied Systems Analysis, Laxenburg, Austria.
    Jonzén, Niclas
    Lund University.
    Constrained growth flips the direction of optimal phenological responses among annual plants2016In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 209, no 4, p. 1591-1599Article in journal (Refereed)
    Abstract [en]

    Phenological changes among plants due to climate change are well documented, but often hard to interpret. In order to assess the adaptive value of observed changes, we study how annual plants with and without growth constraints should optimize their flowering time when productivity and season length changes. We consider growth constraints that depend on the plant's vegetative mass: self-shading, costs for nonphotosynthetic structural tissue and sibling competition. We derive the optimal flowering time from a dynamic energy allocation model using optimal control theory. We prove that an immediate switch (bang-bang control) from vegetative to reproductive growth is optimal with constrained growth and constant mortality. Increasing mean productivity, while keeping season length constant and growth unconstrained, delayed the optimal flowering time. When growth was constrained and productivity was relatively high, the optimal flowering time advanced instead. When the growth season was extended equally at both ends, the optimal flowering time was advanced under constrained growth and delayed under unconstrained growth. Our results suggests that growth constraints are key factors to consider when interpreting phenological flowering responses. It can help to explain phenological patterns along productivity gradients, and links empirical observations made on calendar scales with life-history theory.

  • 36. Ma, Jingkun
    et al.
    Hanssen, Micha
    Lundgren, Krister
    Hernández, Lázaro
    Delatte, Thierry
    Ehlert, Andrea
    Liu, Chun-Ming
    Schluepmann, Henriette
    Dröge-Laser, Wolfgang
    Moritz, Thomas
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Smeekens, Sjef
    Hanson, Johannes
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The sucrose-regulated Arabidopsis transcription factor bZIP11 reprograms metabolism and regulates trehalose metabolism2011In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 191, no 3, p. 733-745Article in journal (Refereed)
    Abstract [en]

    • The Arabidopsis basic region-leucine zipper transcription factor 11 (bZIP11) is known to be repressed by sucrose through a translational inhibition mechanism that requires the conserved sucrose control peptide encoded by the mRNA leader. The function of bZIP11 has been investigated in over-expression studies, and bZIP11 has been found to inhibit plant growth. The addition of sugar does not rescue the growth inhibition phenotype. Here, the function of the bZIP11 transcription factor was investigated. • The mechanism by which bZIP11 regulates growth was studied using large-scale and dedicated metabolic analysis, biochemical assays and molecular studies. • bZIP11 induction results in a reprogramming of metabolism and activation of genes involved in the metabolism of trehalose and other minor carbohydrates such as myo-inositol and raffinose. bZIP11 induction leads to reduced contents of the prominent growth regulatory molecule trehalose 6-phosphate (T6P). • The metabolic changes detected mimic in part those observed in carbon-starved plants. It is proposed that bZIP11 is a powerful regulator of carbohydrate metabolism that functions in a growth regulatory network that includes T6P and the sucrose non-fermenting-1 related protein kinase 1 (SnRK1).

  • 37.
    Milbau, Ann
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Shevtsova, Anna
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Osler, Nora
    Mooshammer, Maria
    Graae, Bente J
    Plant community type and small-scale disturbances, but not altitude, influence the invasibility in subarctic ecosystems2013In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 197, no 3, p. 1002-1011Article in journal (Refereed)
    Abstract [en]

    Little of our knowledge about invasibility comes from arctic and alpine ecosystems, despite increasing plant migration and invasion in those regions. Here, we examine how community type, altitude, and small-scale disturbances affect invasibility in a subarctic ecosystem. Over a period of 4 yr, we studied seedling emergence and establishment in 17 species sown in gaps or undisturbed vegetation in four subarctic community types (Salix scrub, meadow, rich heath, poor heath) along an elevation gradient. Invasibility was lowest in rich heath and highest in Salix scrub. Small disturbances significantly increased the invasibility in most communities, thereby showing the importance of biotic resistance to invasion in subarctic regions. Unexpectedly, invasibility did not decrease with increasing elevation, and it was also not related to summer temperature. Our data suggest that biotic resistance might be more important than abiotic stress for invasibility in subarctic tundra and that low temperatures do not necessarily limit seedling establishment at high altitudes. High elevations are therefore potentially more vulnerable to invasion than was originally thought. Changes in community composition as a result of species migration or invasion are most likely to occur in Salix scrub and meadow, whereas Empetrum-dominated rich heath will largely remain unchanged.

  • 38. Moles, Angela T
    et al.
    Peco, Begoña
    Wallis, Ian R
    Foley, William J
    Poore, Alistair G B
    Seabloom, Eric W
    Vesk, Peter A
    Bisigato, Alejandro J
    Cella-Pizarro, Lucrecia
    Clark, Connie J
    Cohen, Philippe S
    Cornwell, William K
    Edwards, Will
    Ejrnæs, Rasmus
    Gonzales-Ojeda, Therany
    Graae, Bente J
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Department of Biology, NTNU, Trondheim, Norway.
    Hay, Gregory
    Lumbwe, Fainess C
    Magaña-Rodríguez, Benjamín
    Moore, Ben D
    Peri, Pablo L
    Poulsen, John R
    Stegen, James C
    Veldtman, Ruan
    Zeipel, Hugovon
    Andrew, Nigel R
    Boulter, Sarah L
    Borer, Elizabeth T
    Cornelissen, Johannes H C
    Farji-Brener, Alejandro G
    DeGabriel, Jane L
    Jurado, Enrique
    Kyhn, Line A
    Low, Bill
    Mulder, Christa P H
    Reardon-Smith, Kathryn
    Rodríguez-Velázquez, Jorge
    De Fortier, An
    Zheng, Zheng
    Blendinger, Pedro G
    Enquist, Brian J
    Facelli, Jose M
    Knight, Tiffany
    Majer, Jonathan D
    Martínez-Ramos, Miguel
    McQuillan, Peter
    Hui, Francis K C
    Correlations between physical and chemical defences in plants: tradeoffs, syndromes, or just many different ways to skin a herbivorous cat?2013In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 198, no 1, p. 252-263Article in journal (Refereed)
    Abstract [en]

    Most plant species have a range of traits that deter herbivores. However, understanding of how different defences are related to one another is surprisingly weak. Many authors argue that defence traits trade off against one another, while others argue that they form coordinated defence syndromes. We collected a dataset of unprecedented taxonomic and geographic scope (261 species spanning 80 families, from 75 sites across the globe) to investigate relationships among four chemical and six physical defences. Five of the 45 pairwise correlations between defence traits were significant and three of these were tradeoffs. The relationship between species' overall chemical and physical defence levels was marginally nonsignificant (P=0.08), and remained nonsignificant after accounting for phylogeny, growth form and abundance. Neither categorical principal component analysis (PCA) nor hierarchical cluster analysis supported the idea that species displayed defence syndromes. Our results do not support arguments for tradeoffs or for coordinated defence syndromes. Rather, plants display a range of combinations of defence traits. We suggest this lack of consistent defence syndromes may be adaptive, resulting from selective pressure to deploy a different combination of defences to coexisting species.

  • 39. Moles, Angela T
    et al.
    Wallis, Ian R
    Foley, William J
    Warton, David I
    Stegen, James C
    Bisigato, Alejandro J
    Cella-Pizarro, Lucrecia
    Clark, Connie J
    Cohen, Philippe S
    Cornwell, William K
    Edwards, Will
    Ejrnæs, Rasmus
    Gonzales-Ojeda, Therany
    Graae, Bente J
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Hay, Gregory
    Lumbwe, Fainess C
    Magaña-Rodríguez, Benjamín
    Moore, Ben D
    Peri, Pablo L
    Poulsen, John R
    Veldtman, Ruan
    von Zeipel, Hugo
    Andrew, Nigel R
    Boulter, Sarah L
    Borer, Elizabeth T
    Fernández Campón, Florencia
    Coll, Moshe
    Farji-Brener, Alejandro G
    De Gabriel, Jane
    Jurado, Enrique
    Kyhn, Line A
    Low, Bill
    Mulder, Christa P H
    Reardon-Smith, Kathryn
    Rodríguez-Velázquez, Jorge
    Seabloom, Eric W
    Vesk, Peter A
    van Cauter, An
    Waldram, Matthew S
    Zheng, Zheng
    Blendinger, Pedro G
    Enquist, Brian J
    Facelli, Jose M
    Knight, Tiffany
    Majer, Jonathan D
    Martínez-Ramos, Miguel
    McQuillan, Peter
    Prior, Lynda D
    Putting plant resistance traits on the map: a test of the idea that plants are better defended at lower latitudes2011In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 191, no 3, p. 777-788Article in journal (Refereed)
    Abstract [en]

    It has long been believed that plant species from the tropics have higher levels of traits associated with resistance to herbivores than do species from higher latitudes. A meta-analysis recently showed that the published literature does not support this theory. However, the idea has never been tested using data gathered with consistent methods from a wide range of latitudes. We quantified the relationship between latitude and a broad range of chemical and physical traits across 301 species from 75 sites world-wide. Six putative resistance traits, including tannins, the concentration of lipids (an indicator of oils, waxes and resins), and leaf toughness were greater in high-latitude species. Six traits, including cyanide production and the presence of spines, were unrelated to latitude. Only ash content (an indicator of inorganic substances such as calcium oxalates and phytoliths) and the properties of species with delayed greening were higher in the tropics. Our results do not support the hypothesis that tropical plants have higher levels of resistance traits than do plants from higher latitudes. If anything, plants have higher resistance toward the poles. The greater resistance traits of high-latitude species might be explained by the greater cost of losing a given amount of leaf tissue in low-productivity environments.

  • 40.
    Näsholm, Torgny
    et al.
    Swedish Univ Agr Sci SLU, Dept Forest Ecol & Management, SE-90183 Umea, Sweden.
    Högberg, Peter
    Swedish Univ Agr Sci SLU, Dept Forest Ecol & Management, SE-90183 Umeå, Sweden.
    Franklin, Oskar
    Int Inst Appl Syst Anal, A-2361 Laxenburg, Austria.
    Metcalfe, Daniel
    Swedish Univ Agr Sci SLU, Dept Forest Ecol & Management, SE-90183 Umeå, Sweden.
    Keel, Sonja G.
    Swedish Univ Agr Sci SLU, Dept Forest Ecol & Management, SE-90183 Umeå, Sweden.
    Campbell, Catherine
    SLU, Umeå Plant Sci Ctr, Dept Forest Genet & Plant Physiol, SE-90185 Umeå, Sweden.
    Hurry, Vaughan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Linder, Sune
    SLU, Southern Swedish Forest Res Ctr, SE-23053 Alnarp, Sweden.
    Högberg, Mona N.
    Swedish Univ Agr Sci SLU, Dept Forest Ecol & Management, SE-90183 Umeå, Sweden.
    Are ectomycorrhizal fungi alleviating or aggravating nitrogen limitation of tree growth in boreal forests?2013In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 198, no 1, p. 214-221Article in journal (Refereed)
    Abstract [en]

    Symbioses between plant roots and mycorrhizal fungi are thought to enhance plant uptake of nutrients through a favourable exchange for photosynthates. Ectomycorrhizal fungi are considered to play this vital role for trees in nitrogen (N)-limited boreal forests. We followed symbiotic carbon (C)N exchange in a large-scale boreal pine forest experiment by tracing 13CO2 absorbed through tree photosynthesis and 15N injected into a soil layer in which ectomycorrhizal fungi dominate the microbial community. We detected little 15N in tree canopies, but high levels in soil microbes and in mycorrhizal root tips, illustrating effective soil N immobilization, especially in late summer, when tree belowground C allocation was high. Additions of N fertilizer to the soil before labelling shifted the incorporation of 15N from soil microbes and root tips to tree foliage. These results were tested in a model for CN exchange between trees and mycorrhizal fungi, suggesting that ectomycorrhizal fungi transfer small fractions of absorbed N to trees under N-limited conditions, but larger fractions if more N is available. We suggest that greater allocation of C from trees to ectomycorrhizal fungi increases N retention in soil mycelium, driving boreal forests towards more severe N limitation at low N supply.

  • 41. Pawar, Prashant Mohan-Anupama
    et al.
    Ratke, Christine
    Balasubramanian, Vimal K.
    Chong, Sun-Li
    Gandla, Madhavi Latha
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Adriasola, Mathilda
    Sparrman, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hedenstrom, Mattias
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Szwaj, Klaudia
    Derba-Maceluch, Marta
    Gaertner, Cyril
    Mouille, Gregory
    Ezcurra, Ines
    Tenkanen, Maija
    Jonsson, Leif J.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mellerowicz, Ewa J.
    Downregulation of RWA genes in hybrid aspen affects xylan acetylation and wood saccharification2017In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 214, p. 1491-1505Article in journal (Refereed)
    Abstract [en]

    High acetylation of angiosperm wood hinders its conversion to sugars by glycoside hydrolases, subsequent ethanol fermentation and (hence) its use for biofuel production. We studied the REDUCED WALL ACETYLATION (RWA) gene family of the hardwood model Populus to evaluate its potential for improving saccharification. The family has two clades, AB and CD, containing two genes each. All four genes are expressed in developing wood but only RWA-A and -B are activated by master switches of the secondary cell wall PtNST1 and PtMYB21. Histochemical analysis of promoter:: GUS lines in hybrid aspen (Populus tremula x tremuloides) showed activation of RWA-A and -B promoters in the secondary wall formation zone, while RWA-C and -D promoter activity was diffuse. Ectopic downregulation of either clade reduced wood xylan and xyloglucan acetylation. Suppressing both clades simultaneously using the wood-specific promoter reduced wood acetylation by 25% and decreased acetylation at position 2 of Xylp in the dimethyl sulfoxide-extracted xylan. This did not affect plant growth but decreased xylose and increased glucose contents in the noncellulosic monosaccharide fraction, and increased glucose and xylose yields of wood enzymatic hydrolysis without pretreatment. Both RWA clades regulate wood xylan acetylation in aspen and are promising targets to improve wood saccharification.

  • 42.
    Pesquet, Edouard
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Tuominen, Hannele
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ethylene stimulates tracheary element differentiation in Zinnia elegans cell cultures2011In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 190, no 1, p. 138-149Article in journal (Refereed)
    Abstract [en]

    • The exact role of ethylene in xylogenesis remains unclear, but the Zinnia elegans cell culture system provides an excellent model with which to study its role during the differentiation of tracheary elements (TEs) in vitro. • Here, we analysed ethylene homeostasis and function during Z. elegans TE differentiation using biochemical, molecular and pharmacological methods. • Ethylene evolution was confined to specific stages of TE differentiation. It was found to peak at the time of TE maturation and to correlate with the activity of the ethylene biosynthetic 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase. The ethylene precursor ACC was exported and accumulated to high concentrations in the extracellular medium, which also displayed a high capacity to convert ACC into ethylene. The effects of adding inhibitors of the ethylene biosynthetic ACC synthase and ACC oxidase enzymes to the TE cultures demonstrated for the first time strict dependence of TE differentiation on ethylene biosynthesis and a stimulatory effect of ethylene on the rate of TE differentiation. • In a whole-plant context, our results suggest that ethylene synthesis occurs in the apoplast of the xylem elements and that ethylene participates, in a paracrine manner, in the control of the cambial stem cell pool size during secondary xylem formation.

  • 43. RAVEN, JA
    et al.
    HANDLEY, LL
    MACFARLANE, JJ
    MCINROY, S
    MCKENZIE, L
    RICHARDS, JH
    Samuelsson, Göran
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    THE ROLE OF CO2 UPTAKE BY ROOTS AND CAM IN ACQUISITION OF INORGANIC C BY PLANTS OF THE ISOETID LIFE-FORM - A REVIEW, WITH NEW DATA ON ERIOCAULON-DECANGULARE L1988In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 108, no 2, p. 125-148Article in journal (Refereed)
  • 44. RAVEN, JA
    et al.
    Samuelsson, Göran
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    REPAIR OF PHOTOINHIBITORY DAMAGE IN ANACYSTIS-NIDULANS-625 (SYNECHOCOCCUS-6301) - RELATION TO CATALYTIC CAPACITY FOR, AND ENERGY SUPPLY TO, PROTEIN-SYNTHESIS, AND IMPLICATIONS FOR MU-MAX AND THE EFFICIENCY OF LIGHT-LIMITED GROWTH1986In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 103, no 4, p. 625-643Article in journal (Refereed)
  • 45. Rende, Umut
    et al.
    Wang, Wei
    Gandla, Madhavi Latha
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Jönsson, Leif J.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Niittylä, Totte
    Cytosolic invertase contributes to the supply of substrate for cellulose biosynthesis in developing wood2017In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 214, no 2, p. 796-807Article in journal (Refereed)
    Abstract [en]

    Carbon for cellulose biosynthesis is derived from sucrose. Cellulose is synthesized from uridine 5'-diphosphoglucose (UDP-glucose), but the enzyme(s) responsible for the initial sucrose cleavage and the source of UDP-glucose for cellulose biosynthesis in developing wood have not been defined. We investigated the role of CYTOSOLIC INVERTASEs (CINs) during wood formation in hybrid aspen (Populus tremula × tremuloides) and characterized transgenic lines with reduced CIN activity during secondary cell wall biosynthesis. Suppression of CIN activity by 38–55% led to a 9–13% reduction in crystalline cellulose. The changes in cellulose were reflected in reduced diameter of acid-insoluble cellulose microfibrils and increased glucose release from wood upon enzymatic digestion of cellulose. Reduced CIN activity decreased the amount of the cellulose biosynthesis precursor UDP-glucose in developing wood, pointing to the likely cause of the cellulose phenotype. The findings suggest that CIN activity has an important role in the cellulose biosynthesis of trees, and indicate that cellulose biosynthesis in wood relies on a quantifiable UDP-glucose pool. The results also introduce a concept of altering cellulose microfibril properties by modifying substrate supply to cellulose biosynthesis.

  • 46. Riba, Miquel
    et al.
    Mayol, Maria
    Giles, Barbara E.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Ronce, Ophélie
    Imbert, Eric
    van der Velde, Marco
    Chauvet, Stéphanie
    Lars Ericson, Lars
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. lars.ericson@emg.umu.se.
    Bijlsma, R
    Vosman, Ben
    Smulders, MJM
    Olivieri, Isabelle
    Darwin's wind hypothesis: does it work for plant dispersal in fragmented habitats?2009In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 183, no 3, p. 667-677Article in journal (Refereed)
    Abstract [en]

    Using the wind-dispersed plant Mycelis muralis, we examined how landscape fragmentation affects variation in seed traits contributing to dispersal. Inverse terminal velocity () of field-collected achenes was used as a proxy for individual seed dispersal ability. We related this measure to different metrics of landscape connectivity, at two spatial scales: in a detailed analysis of eight landscapes in Spain and along a latitudinal gradient using 29 landscapes across three European regions. In the highly patchy Spanish landscapes, seed increased significantly with increasing connectivity. A common garden experiment suggested that differences in may be in part genetically based. The was also found to increase with landscape occupancy, a coarser measure of connectivity, on a much broader (European) scale. Finally, was found to increase along a south2013north latitudinal gradient. Our results for M. muralis are consistent with 'Darwin's wind dispersal hypothesis' that high cost of dispersal may select for lower dispersal ability in fragmented landscapes, as well as with the 'leading edge hypothesis' that most recently colonized populations harbour more dispersive phenotypes.

  • 47. Scott, Alison Dawn
    et al.
    Stenz, Noah W. M.
    Ingvarsson, Pär K.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Baum, David A.
    Whole genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers2016In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 211, no 1, p. 186-193Article in journal (Refereed)
    Abstract [en]

    Polyploidy is common and an important evolutionary factor in most land plant lineages, but it is rare in gymnosperms. Coast redwood (Sequoia sempervirens) is one of just two polyploid conifer species and the only hexaploid. Evidence from fossil guard cell size suggests that polyploidy in Sequoia dates to the Eocene. Numerous hypotheses about the mechanism of polyploidy and parental genome donors have been proposed, based primarily on morphological and cytological data, but it remains unclear how Sequoia became polyploid and why this lineage overcame an apparent gymnosperm barrier to whole-genome duplication (WGD). We sequenced transcriptomes and used phylogenetic inference, Bayesian concordance analysis and paralog age distributions to resolve relationships among gene copies in hexaploid coast redwood and close relatives. Our data show that hexaploidy in coast redwood is best explained by autopolyploidy or, if there was allopolyploidy, it happened within the Californian redwood clade. We found that duplicate genes have more similar sequences than expected, given the age of the inferred polyploidization. Conflict between molecular and fossil estimates of WGD can be explained if diploidization occurred very slowly following polyploidization. We extrapolate from this to suggest that the rarity of polyploidy in gymnosperms may be due to slow diploidization in this clade.

  • 48. Searle, Stephanie Y
    et al.
    Thomas, Samuel
    Griffin, Kevin L
    Horton, Travis
    Kornfeld, Ari
    Yakir, Dan
    Hurry, Vaughan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Turnbull, Matthew H
    Leaf respiration and alternative oxidase in field-grown alpine grasses respond to natural changes in temperature and light2011In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 189, no 4, p. 1027-1039Article in journal (Refereed)
    Abstract [en]

    • We report the first investigation of changes in electron partitioning via the alternative respiratory pathway (AP) and alternative oxidase (AOX) protein abundance in field-grown plants and their role in seasonal acclimation of respiration. • We sampled two alpine grasses native to New Zealand, Chionochloa rubra and Chionochloa pallens, from field sites of different altitudes, over 1 yr and also intensively over a 2-wk period. • In both species, respiration acclimated to seasonal changes in temperature through changes in basal capacity (R₁₀) but not temperature sensitivity (E₀). In C. pallens, acclimation of respiration may be associated with a higher AOX : cytochrome c oxidase (COX) protein abundance ratio. Oxygen isotope discrimination (D), which reflects relative changes in AP electron partitioning, correlated positively with daily integrated photosynthetically active radiation (PAR) in both species over seasonal timescales. Respiratory parameters, the AOX : COX protein ratio and D were stable over a 2-wk period, during which significant temperature changes were experienced in the field. • We conclude that respiration in Chionochloa spp. acclimates strongly to seasonal, but not to short-term, temperature variation. Alternative oxidase appears to be involved in the plant response to both seasonal changes in temperature and daily changes in light, highlighting the complexity of the function of AOX in the field.

  • 49.
    Sjödin, Andreas
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Street, Nathaniel R
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Sandberg, Göran
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Gustafsson, Petter
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The populus genome integrative explorer (PopGenIE): a new resource for exploring the populus genome2009In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 182, no 4, p. 1013-1025Article in journal (Refereed)
    Abstract [en]

    * Populus has become an important model plant system. However, utilization of the increasingly extensive collection of genetics and genomics data created by the community is currently hindered by the lack of a central resource, such as a model organism database (MOD). Such MODs offer a single entry point to the collection of resources available within a model system, typically including tools for exploring and querying those resources. * As a starting point to overcoming the lack of such an MOD for Populus, we present the Populus Genome Integrative Explorer (PopGenIE), an integrated set of tools for exploring the Populus genome and transcriptome. The resource includes genome, synteny and quantitative trait locus (QTL) browsers for exploring genetic data. * Expression tools include an electronic fluorescent pictograph (eFP) browser, expression profile plots, co-regulation within collated transcriptomics data sets, and identification of over-represented functional categories and genomic hotspot locations. A number of collated transcriptomics data sets are made available in the eFP browser to facilitate functional exploration of gene function. Additional homology and data extraction tools are provided. * PopGenIE significantly increases accessibility to Populus genomics resources and allows exploration of transcriptomics data without the need to learn or understand complex statistical analysis methods. PopGenIE is available at http://www.popgenie.org or via http://www.populusgenome.info.

  • 50. Soler, Marçal
    et al.
    Plasencia, Anna
    Larbat, Romain
    Pouzet, Cécile
    Jauneau, Alain
    Rivas, Susana
    Pesquet, Edouard
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Lapierre, Catherine
    Truchet, Isabelle
    Grima-Pettenati, Jacqueline
    The Eucalyptus linker histone variant EgH1.3 cooperates with the transcription factor EgMYB1 to control lignin biosynthesis during wood formation2017In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 213, no 1, p. 287-299Article in journal (Refereed)
    Abstract [en]

    Wood, also called secondary xylem, is a specialized vascular tissue constituted by different cell types that undergo a differentiation process involving deposition of thick, lignified secondary cell walls. The mechanisms needed to control the extent of lignin deposition depending on the cell type and the differentiation stage are far from being fully understood. We found that the Eucalyptus transcription factor EgMYB1, which is known to repress lignin biosynthesis, interacts specifically with a linker histone variant, EgH1.3. This interaction enhances the repression of EgMYB1' s target genes, strongly limiting the amount of lignin deposited in xylem cell walls. The expression profiles of EgMYB1 and EgH1.3 overlap in xylem cells at early stages of their differentiation as well as in mature parenchymatous xylem cells, which have no or only thin lignified secondary cell walls. This suggests that a complex between EgMYB1 and EgH1.3 integrates developmental signals to prevent premature or inappropriate lignification of secondary cell walls, providing a mechanism to fine-tune the differentiation of xylem cells in time and space. We also demonstrate a role for a linker histone variant in the regulation of a specific developmental process through interaction with a transcription factor, illustrating that plant linker histones have other functions beyond chromatin organization.

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