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  • 1. Abbasi, Arshad Mehmood
    et al.
    Khan, Mir Ajab
    Khan, Nadeem
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Shah, Munir H
    Ethnobotanical survey of medicinally important wild edible fruits species used by tribal communities of Lesser Himalayas-Pakistan2013In: Journal of Ethnopharmacology, ISSN 0378-8741, E-ISSN 1872-7573, Vol. 148, no 2, 528-536 p.Article in journal (Refereed)
    Abstract [en]

    Ethnopharmacological relevance: Present survey was conducted to explore ethnomedicinal uses and cultural importance of wild edible fruits species by the inhabitants of Lesser Himalayas-Pakistan. Materials and methods: Information was obtained through informed consent semi-structured interviews, questionnaires, market survey, focus group conversation, unceremonious dialogue and village walks with key informants. Cultural significance of each species was calculated based on use report by participants at each study site. Results: A total of 35 wild edible fruits belonging to 21 genera and 17 families were used for the treatment of various ailments and consumed. Rosaceae was found dominating family with (8 spp.), followed by Moraceae (6 spp.), Rhamnaceae (5 spp.), Palmae and Vitaceae (2 spp. each) and remaining families were represented by one species each. Fruits (48%) were found highly utilized plant parts, followed by leaves (34%), bark, flowers and seeds (4% each), branches, latex and roots (2% each). Water was used as a medium for preparation while milk, ghee, oil, egg and butter are used for application. Modes of preparation were fall into seven categories like fresh parts eaten raw (38%), powder (24%), decoction (20%), extract (12 %), paste (4%), juice and latex (2% each). Based on cultural important index (CI) Morus nigra was found most significant species within top ten fruit plants followed by Morus alba, Olea ferruginea, Berberis lycium, Pyrus pashia, Ficus carica, Ficus palmata, Ziziphus mauritiana, Diospyros lotus and Ziziphus nummularia. Conclusions: Traditional uses of wild edible plant depend mainly on socio-economic factors rather than climatic conditions or wealth of flora. Use reports and citation demonstrated that there is a common cultural heritage regarding the gathered food plants. Further investigation is required for Antioxidant study, essential and toxic components, pharmacological applications; dietary requirements and biotechnological techniques to improve yields.

    (C) 2013 Elsevier Ireland Ltd. All rights reserved.

  • 2. Aksmann, Anna
    et al.
    Shutova, Tatiana
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Samuelsson, Göran
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Tukaj, Zbigniew
    The mechanism of anthracene interaction with photosynthetic apparatus: A study using intact cells, thylakoid membranes and PS II complexes isolated from Chlamydomonas reinhardtii2011In: Aquatic Toxicology, ISSN 0166-445X, E-ISSN 1879-1514, Vol. 104, no 3-4, 205-210 p.Article in journal (Refereed)
    Abstract [en]

    Intact cells of Chlamydomonas reinhardtii as well as isolated thylakoid membranes and photosystem II complexes were used to examine a possible mechanism of anthracene (ANT) interaction with the photosynthetic apparatus. Since ANT concentrations above 1 mM were required to significantly inhibit the rate of oxygen evolution in PS II membrane fragments it may indicate that the toxicant did not directly interact with this photosystem. On the other hand, stimulation of oxygen uptake by ANT-treated thylakoids suggested that ANT could either act as an artificial electron acceptor in the photosynthetic electron transport chain or function as an uncoupler. Electron transfer from excited chlorophyll to ANT is impossible due to the very low reduction potential of ANT and therefore we propose that toxic concentrations of ANT increase the thylakoid membrane permeability and thereby function as an uncoupler, enhancing electron transport in vitro. Hence, its unspecific interference with photosynthetic membranes in vitro suggests that the inhibitory effect observed on intact cell photosynthesis is caused by uncoupling of phosphorylation. 

  • 3. Ali, Qasim
    et al.
    Haider, Muhammad Zulqurnain
    Iftikhar, Wasif
    Jamil, Sidra
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Department of Botany, Faculty of Science and Technology, Government College University, Faisalabad, Pakistan.
    Javed, M. Tariq
    Noman, Ali
    Iqbal, Muhammad
    Perveen, Rashida
    Drought tolerance potential of Vigna mungo L. lines as deciphered by modulated growth, antioxidant defense, and nutrient acquisition patterns2016In: Revista Brasileira de Botânica, ISSN 0100-8404, E-ISSN 1806-9959, Vol. 39, no 3, 801-812 p.Article in journal (Refereed)
    Abstract [en]

    Water shortage is one of the major environmental constraints that hamper the crop productivity worldwide. The present study was aimed to examine the drought tolerance potential of seven cultivars/lines of Vigna mungo L. depending upon their germination behavior, seedling growth, antioxidative defense mechanism, and nutrient acquisition. An experiment was conducted in the growth chamber using petri-plates and laid out in a completely randomized design (CRD). Hoagland's nutrient solution supplemented with 12 % PEG-8000 (drought treatment) or without PEG-800 (control) was used. Drought stress significantly altered the germination attributes as well as biomass production of all the studied cultivars/lines. Least adversative effects of drought stress were recorded in lines M-01001-1 and M-6036-21, respectively. The studied cultivars/lines exhibited differential response for various biochemical attributes under drought stress. The maximum increase in MDA and SOD activities and protein content was recorded in line M-603621, while the maximum AsA was recorded in line M-01001-1. Drought stress resulted in a significant reduction of plant N, P, K, Ca, and Mg contents, while the plant iron (Fe) contents remained unaffected. Results revealed that cultivars/lines M-01001-1 and M-6036-21 exhibited enhanced performance in terms of nutrient acquisition when stressed by drought. Based upon seed germination behavior, plant biomass production, biochemical attributes and mineral elements, the cultivars/lines M-01001-1 and M-6036-21 were identified as drought tolerant, while M-97 and Arroj-II were identified as drought sensitive.

  • 4.
    Andersson, Jenny
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Dissecting the photosystem II light-harvesting antenna2003Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In photosynthesis, sunlight is converted into chemical energy that is stored mainly as carbohydrates and supplies basically all life on Earth with energy.

    In order to efficiently absorb the light energy, plants have developed the outer light harvesting antenna, which is composed of ten different protein subunits (LHC) that bind chlorophyll a and b as well as different carotenoids. In addition to the light harvesting function, the antenna has the capacity to dissipate excess energy as heat (feedback de-excitation or qE), which is crucial to avoid oxidative damage under conditions of high excitation pressure. Another regulatory function in the antenna is the state transitions in which the distribution of the trimeric LHC II between photosystem I (PS I) and II is controlled. The same ten antenna proteins are conserved in all higher plants and based on evolutionary arguments this has led to the suggestion that each protein has a specific function.

    I have investigated the functions of individual antenna proteins of PS II (Lhcb proteins) by antisense inhibition in the model plant Arabidopsis thaliana. Four antisense lines were obtained, in which the target proteins were reduced, in some cases beyond detection level, in other cases small amounts remained.

    The results show that CP29 has a unique function as organising the antenna. CP26 can form trimers that substitute for Lhcb1 and Lhcb2 in the antenna structure, but the trimers that accumulate as a response to the lack of Lhcb1 and Lhcb2 cannot take over the LHC II function in state transitions. It has been argued that LHC II is essential for grana stacking, but antisense plants without Lhcb1 and Lhcb2 do form grana. Furthermore, LHC II is necessary to maintain growth rates in very low light.

    Numerous biochemical evidences have suggested that CP29 and/or CP26 were crucial for feedback de-excitation. Analysis of two antisense lines each lacking one of these proteins clearly shows that there is no direct involvement of either CP29 or CP26 in this process. Investigation of the other antisense lines shows that no Lhcb protein is indispensable for qE. A model for feedback de-excitation is presented in which PsbS plays a major role.

    The positions of the minor antenna proteins in the PS II supercomplex were established by comparisons of transmission electron micrographs of supercomplexes from the wild type and antisense plants.

    A fitness experiment was conducted where the antisense plants were grown in the field and seed production was used to estimate the fitness of the different genotypes. Based on the results from this experiment it is concluded that each Lhcb protein is important, because all antisense lines show reduced fitness in the field.

  • 5.
    Andersson-Gunnerås, Sara
    et al.
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå.
    Hellgren, Jenny M
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå.
    Björklund, Simon
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå.
    Regan, Sharon
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå.
    Moritz, Thomas
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå.
    Sundberg, Björn
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå.
    Asymmetric expression of a poplar ACC oxidase controls ethylene production during gravitational induction of tension wood2003In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 34, no 3, 339-349 p.Article in journal (Refereed)
    Abstract [en]

    Ethylene is produced in wood-forming tissues, and when applied exogenously, it has been shown to cause profound effects on the pattern and rate of wood development. However, the molecular regulation of ethylene biosynthesis during wood formation is poorly understood. We have characterised an abundant 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase gene (PttACO1) in the wood-forming tissues of Populus tremula (L.) × P. tremuloides (Michx). PttACO1 is primarily expressed in developing secondary xylem, and is specifically upregulated during secondary wall formation. Nevertheless, according to GC–MS analysis combined with tangential cryosectioning, the distribution of ACC was found to be fairly uniform across the cambial-region tissues. Gravitational stimulation, which causes tension wood to form on the upper side of the stem, resulted in a strong induction of PttACO1 expression and ACC oxidase activity in the tension wood-forming tissues. The ACC levels increased in parallel to the PttACO1 expression. However, the increase on the upper (tension wood) side was only minor, whereas large amounts of both ACC and its hydrolysable conjugates accumulated on the lower (opposite) side of the stem. This suggests that the relatively low level of ACC on the tension wood side is a result of its conversion to ethylene by the highly upregulated PttACO1, and the concurrent accumulation of ACC on the opposite side of the wood is because of the low PttACO1 levels. We conclude that PttACO1 and ACC oxidase activity, but not ACC availability, are important in the control of the asymmetric ethylene production within the poplar stem when tension wood is induced by gravitational stimulation.

  • 6.
    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, 545-555 p.Article 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.

  • 7. Aronsson, Mora
    et al.
    Black-Samuelsson, Sanna
    Edqvist, Margareta
    Persson, Erik
    Nordiskt Genresurscenter (NordGen) och SLU.
    Ståhlberg, David
    Weibull, Jens
    Kulturväxtsläktingar: något att bry sig om2012In: Svensk Botanisk Tidskrift, ISSN 0039-646X, Vol. 106, 309-318 p.Article in journal (Refereed)
  • 8.
    Ashelford, Kevin
    et al.
    School of Biological Sciences, University of Liverpool, Liverpool, UK.
    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).
    Allen, Christopher M
    Applied Biosystems, part of Life Technologies, Warrington, UK.
    D’Amore, Linda
    School of Biological Sciences, University of Liverpool, Liverpool, UK.
    Johansson, Mikael
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Gould, Peter
    School of Biological Sciences, University of Liverpool, Liverpool, UK.
    Kay, Susanne
    School of Biological Sciences, University of Liverpool, Liverpool, UK.
    Millar, Andrew J.
    Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
    Hall, Neil
    School of Biological Sciences, University of Liverpool, Liverpool, UK.
    Hall, Anthony
    School of Biological Sciences, University of Liverpool, Liverpool, UK.
    Full genome re-sequencing reveals a novel circadian clock mutationin Arabidopsis2011In: Genome Biology, ISSN 1465-6906, E-ISSN 1465-6914, Vol. 12, R28- p.Article in journal (Refereed)
    Abstract [en]

    Background: Map based cloning in Arabidopsis thaliana can be a difficult and time-consuming process,specifically if the phenotype is subtle and scoring labour intensive. An alternative to map basedcloning would be to directly sequence the whole genome of a mutant to uncover the mutationresponsible for the phenotype.

    Results: Here, we have re-sequenced the 120 Mb genome of a novel Arabidopsis clock mutant earlybird (ebi-1), using massively parallel sequencing by ligation. This process was further complicated by the fact that ebi-1 is in Wassilewskija (Ws-2), not the reference accession ofArabidopsis. The approach reveals evidence of DNA strand bias in the ethyl methanesulfonate(EMS) mutation process. We have demonstrated the utility of sequencing a backcrossed line andusing gene expression data to limit the number of SNP considered. Using new SNP informationwe have excluded a previously identified clock gene, PRR7. Finally, we have identified a SNPin the gene AtNFXL-2 as the likely cause of the ebi-1 phenotype and validated this bycharacterising a further allele.

    Conclusion: In Arabidopsis, as in other organisms, the (EMS) mutation load can be high. Here wedescribe how sequencing a backcrossed line, using functional genomics and analysing new SNPinformation can be used to reduce the number EMS mutations for consideration. Moreover, theapproach we describe here does not require out-crossing and scoring F2 mapping populations, anapproach which can be compromised by background effects. The strategy has broad utility andwill be an extremely useful tool to identify causative SNP in other organisms.

  • 9.
    Augusti, Angela
    Umeå University, Faculty of Science and Technology, Plant Physiology.
    Monitoring climate and plant physiology using deuterium isotopomers of carbohydrates2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Climate is changing and it is certain that this change is due to human activities. Atmospheric greenhouse gases have been rising in an unprecedented way during the last two centuries, although the land biosphere has dampened their increase by absorbing CO2 emitted by anthropogenic activities. However, it is unclear if this will continue in the future. This uncertainty makes it difficult to predict future climate changes and to determine how much greenhouse gas emissions must be reduced to protect climate.

    To understand the future role of plants in limiting the atmospheric CO2 level, the effect of increasing CO2 on plant photosynthesis and productivity has been studied. However, studies on trees showed contradictory results, which depended on the duration of the experiment. This revealed that an initial strong CO2 fertilization may be a transient response that disappears after a few years. Because climate changes over centuries, we must explore the response of vegetation to increasing CO2 on this time scale. Studying tree rings is a good alternative to impractical decade-long experiments, because trees have experienced the CO2 increase during the last 200 years and may already have responded to it.

    This thesis shows that the intramolecular distribution of the stable hydrogen isotope deuterium (deuterium isotopomer distribution, DID) of tree rings is a reliable tool to study long-term plant-climate adaptations. The premise for this is that the deuterium abundance in tree rings depends on environmental as well as physiological factors. Using newly developed methodology for DID measurements, the influences of both factors can be separated. Applied to tree rings, separating both factors opens a strategy for simultaneous reconstruction of climate and of physiological responses.

    The results presented show that DIDs are influenced by kinetic isotope effects of enzymes, allowing studies of metabolic regulation. We show that the abundances of specific D isotopomers in tree-ring cellulose indeed allow identifying environmental and physiological factors. For example, the D2 isotopomer is mostly influenced by environment, its abundance should allow better reconstruction of past temperature. On the other hand, the abundance ratio of two isotopomers (D6R and D6S) depends on atmospheric CO2, and might serve as a measure of the efficiency of photosynthesis (ratio of photorespiration to assimilation). The presence of this dependence in all species tested and in tree-ring cellulose allows studying adaptations of plants to increasing CO2 on long time scales, using tree-ring series or other remnant plant material.

  • 10. Baena-González, Elena
    et al.
    Hanson, Johannes
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Shaping plant development through the SnRK1–TOR metabolic regulators2017In: Current opinion in plant biology, ISSN 1369-5266, E-ISSN 1879-0356, Vol. 35, 152-157 p.Article in journal (Refereed)
    Abstract [en]

    SnRK1 (Snf1-related protein kinase 1) and TOR (target of rapamycin) are evolutionarily conserved protein kinases that lie at the heart of energy sensing, playing central and antagonistic roles in the regulation of metabolism and gene expression. Increasing evidence links these metabolic regulators to numerous aspects of plant development, from germination to flowering and senescence. This prompts the hypothesis that SnRK1 and TOR modify developmental programs according to the metabolic status to adjust plant growth to a specific environment. The aim of this review is to provide support to this hypothesis and to incentivize further studies on this topic by summarizing the work that establishes a genetic connection between SnRK1-TOR and plant development.

  • 11.
    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, 233-244 p.Article 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.

  • 12.
    Bandau, Franziska
    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.
    Decker, Vicki Huizu Guo
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Gundale, Michael J.
    Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, SE 90183 Umeå, Sweden.
    Albrectsen, Benedicte Riber
    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 Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK 1871 Frederiksberg C, Denmark.
    Genotypic tannin levels in Populus tremula impact the way nitrogen enrichment affects growth and allocation responses for some traits and not for others2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 10, e0140971Article in journal (Refereed)
    Abstract [en]

    Plant intraspecific variability has been proposed as a key mechanism by which plants adapt to environmental change. In boreal forests where nitrogen availability is strongly limited, nitrogen addition happens indirectly through atmospheric N deposition and directly through industrial forest fertilization. These anthropogenic inputs of N have numerous environmental consequences, including shifts in plant species composition and reductions in plant species diversity. However, we know less about how genetic differences within plant populations determine how species respond to eutrophication in boreal forests. According to plant defense theories, nitrogen addition will cause plants to shift carbon allocation more towards growth and less to chemical defense, potentially enhancing vulnerability to antagonists. Aspens are keystone species in boreal forests that produce condensed tannins to serve as chemical defense. We conducted an experiment using ten Populus tremula genotypes from the Swedish Aspen Collection that express extreme levels of baseline investment into foliar condensed tannins. We investigated whether investment into growth and phenolic defense compounds in young plants varied in response to two nitrogen addition levels, corresponding to atmospheric N deposition and industrial forest fertilization. Nitrogen addition generally caused growth to increase, and tannin levels to decrease; however, individualistic responses among genotypes were found for height growth, biomass of specific tissues, root: shoot ratios, and tissue lignin and N concentrations. A genotype's baseline ability to produce and store condensed tannins also influenced plant responses to N, although this effect was relatively minor. High-tannin genotypes tended to grow less biomass under low nitrogen levels and more at the highest fertilization level. Thus, the ability in aspen to produce foliar tannins is likely associated with a steeper reaction norm of growth responses, which suggests a higher plasticity to nitrogen addition, and potentially an advantage when adapting to higher concentrations of soil nitrogen.

  • 13.
    Barros, Jaime
    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).
    Serk, Henrik
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Granlund, Irene
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Pesquet, Edouard
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The cell biology of lignification in higher plants2015In: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 115, no 7, 1053-1074 p.Article, review/survey (Refereed)
    Abstract [en]

    Background Lignin is a polyphenolic polymer that strengthens and waterproofs the cell wall of specialized plant cell types. Lignification is part of the normal differentiation programme and functioning of specific cell types, but can also be triggered as a response to various biotic and abiotic stresses in cells that would not otherwise be lignifying.

    Scope Cell wall lignification exhibits specific characteristics depending on the cell type being considered. These characteristics include the timing of lignification during cell differentiation, the palette of associated enzymes and substrates, the sub-cellular deposition sites, the monomeric composition and the cellular autonomy for lignin monomer production. This review provides an overview of the current understanding of lignin biosynthesis and polymerization at the cell biology level.

    Conclusions The lignification process ranges from full autonomy to complete co-operation depending on the cell type. The different roles of lignin for the function of each specific plant cell type are clearly illustrated by the multiple phenotypic defects exhibited by knock-out mutants in lignin synthesis, which may explain why no general mechanism for lignification has yet been defined. The range of phenotypic effects observed include altered xylem sap transport, loss of mechanical support, reduced seed protection and dispersion, and/or increased pest and disease susceptibility.

  • 14.
    Benedict, Catherine
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Cold Acclimation: Dissecting the plant low temperature signaling pathway using functional genomics2006Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The physiological process of cold acclimation protects plants native to the temperate regions of the world from the deleterious effects of low and freezing temperatures. This is achieved by a series of transcriptional, regulatory, and metabolic changes that enable continued growth and survival. Within minutes of exposure to temperatures below ca. 10°C, a complex cascade of transcriptional events is initiated to accomplish these changes. The initial alarm phase favors the rapid induction of a library of stress proteins with protective functions (e.g. COR proteins). This is followed by a cold hardened phase, characterized by maximal freezing tolerance, which continues until either the stress is removed, or the plant's metabolic and/or developmental state can no longer support maximal resistance.

    We have studied some of the important transcription factors and transcriptional changes associated with the initial alarm and later hardened phases of cold acclimation in the herbaceous annual Arabidopsis thaliana and the woody perennial Populus spp. We confirmed the functionality of the CBF-mediated signaling cascade in Poplar overexpressing AtCBF1, but noted that regulon composition and endogenous poplar CBF ortholog induction appeared to be tissue-specific. The lack of statistically significant DRE enrichment in the Poplar AtCBF1 regulons led us to investige cis-element abundance in the cold-associated transcription factor regulons of publicly available microarray data from Arabidopsis, leading to the development of a gene voting method of microarray analysis that we used to test for regulatory associations between transcription factors and their downstream cis-elements and gene targets. This analysis resulted in a new transcriptional model of the ICE1-mediated signaling cascade and implicated a role for phytochrome A. Application of this same method to microarray data from arabidopsis leaves developed at low temperature allowed us to identify a new cis-element, called DDT, which possessed enhancer-blocking function during the alarm stage of cold stress, but was enriched in the promoters of genes upregulated during the later cold hardened stages. As leaf growth and development at low temperature correlated with the enhancement freeze tolerance in Arabidopsis, we compared the transcriptomes of rapidly growing and fully grown poplar leaves at night (when both low temperatures and PhyA status might play important roles in nature), in the hopes of comparing this data with that of cold-treated leaves in the future. We identified the nocturnal mode of leaf growth in Populus deltoides as predominantly proliferative as opposed to expansive, and potentially linked to cellular carbohydrate status.

  • 15.
    Benedict, Catherine
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Skinner, J. S.
    Meng, R.
    Chang, Y.
    Bhalerao, R.
    Finn, C.
    Chen, T. H. H.
    Umeå University, Faculty of Science and Technology.
    Hurry, Vaughan
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    The Role of the CBF-dependent Signalling Pathway in Woody Perennials2006In: Cold Hardiness in Plants: Molecular Genetics, Cell Biology and Physiology / [ed] T Chen, M Uemura, S Fujikawa, Wallingford: CABI Publishing, 2006, 167-180 p.Chapter in book (Other academic)
  • 16.
    Benlloch, Reyes
    et al.
    Department of Forest Genetics and Plant Physiology, SLU.
    Shevela, Dmitriy
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hainzl, Tobias
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Grundström, Christin
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Shutova, Tatyana
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Messinger, Johannes
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    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).
    Sauer-Eriksson, Elisabeth
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Crystal structure and functional characterization of Photosystem II-associated carbonic anhydrase CAH3 in Chlamydomonas reinhardtii2015In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 167, no 3, 950-962 p.Article in journal (Refereed)
    Abstract [en]

    In oxygenic photosynthesis, light energy is stored in the form of chemical energy by converting CO2 and water into carbohydrates.The light-driven oxidation of water that provides the electrons and protons for the subsequent CO2 fixation takes place inphotosystem II (PSII). Recent studies show that in higher plants, HCO3– increases PSII activity by acting as a mobile acceptor ofthe protons produced by PSII. In the green alga Chlamydomonas reinhardtii, a luminal carbonic anhydrase, CrCAH3, was suggested toimprove proton removal from PSII, possibly by rapid reformation of HCO3– from CO2. In this study, we investigated the interplaybetween PSII and CrCAH3 by membrane inlet mass spectrometry and x-ray crystallography. Membrane inlet mass spectrometrymeasurements showed that CrCAH3 was most active at the slightly acidic pH values prevalent in the thylakoid lumen underillumination. Two crystal structures of CrCAH3 in complex with either acetazolamide or phosphate ions were determined at 2.6- and2.7-Å resolution, respectively. CrCAH3 is a dimer at pH 4.1 that is stabilized by swapping of the N-terminal arms, a feature notpreviously observed in a-type carbonic anhydrases. The structure contains a disulfide bond, and redox titration of CrCAH3 functionwith dithiothreitol suggested a possible redox regulation of the enzyme. The stimulating effect of CrCAH3 and CO2/HCO3– on PSIIactivity was demonstrated by comparing the flash-induced oxygen evolution pattern of wild-type and CrCAH3-less PSIIpreparations. We showed that CrCAH3 has unique structural features that allow this enzyme to maximize PSII activity at lowpH and CO2 concentration.

  • 17. Benson, Samuel L
    et al.
    Maheswaran, Pratheesh
    Ware, Maxwell A
    Hunter, C Neil
    Horton, Peter
    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).
    Ruban, Alexander V
    Johnson, Matthew P
    An intact light harvesting complex I antenna system is required for complete state transitions in Arabidopsis2015In: Nature plants, ISSN 2055-026X, Vol. 1, no 12, 15176Article in journal (Refereed)
    Abstract [en]

    Efficient photosynthesis depends on maintaining balance between the rate of light-driven electron transport occurring in photosystem I (PSI) and photosystem II (PSII), located in the chloroplast thylakoid membranes. Balance is achieved through a process of 'state transitions' that increases energy transfer towards PSI when PSII is overexcited (state II), and towards PSII when PSI is overexcited (state I). This is achieved through redox control of the phosphorylation state of light-harvesting antenna complex II (LHCII). PSI is served by both LHCII and four light-harvesting antenna complex I (LHCI) subunits, Lhca1, 2, 3 and 4. Here we demonstrate that despite unchanged levels of LHCII phosphorylation, absence of specific Lhca subunits reduces state transitions in Arabidopsis. The severest phenotype-observed in a mutant lacking Lhca4 (Delta Lhca4)-displayed a 69% reduction compared with the wild type. Yet, surprisingly, the amounts of the PSI-LHCI-LHCII supercomplex isolated by blue native polyacrylamide gel electrophoresis (BN-PAGE) from digitonin-solubilized thylakoids were similar in the wild type and Delta Lhca mutants. Fluorescence excitation spectroscopy revealed that in the wild type this PSI-LHCI-LHCII supercomplex is supplemented by energy transfer from additional LHCII trimers in state II, whose binding is sensitive to digitonin, and which are absent in Delta Lhca4. The grana margins of the thylakoid membrane were found to be the primary site of interaction between this 'extra' LHCII and the PSI-LHCI-LHCII supercomplex in state II. The results suggest that the LHCI complexes mediate energetic interactions between LHCII and PSI in the intact membrane.

  • 18. Bergman, Anders
    et al.
    Gardeström, Per
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ericson, Ingemar
    Method to Obtain a Chlorophyll-free Preparation of Intact Mitochondria from Spinach Leaves.1980In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 66, no 3, 442-445 p.Article in journal (Refereed)
    Abstract [en]

    Mitochondria from green leaves of spinach have been prepared using a three-step procedure involving differential centrifugation, partition in an aqueous dextran polyethylene glycol two-phase system and Percoll gradient centrifugation. The mitochondrial fractions after the different steps of purification were compared. The final mitochondrial preparation was totally free from chloroplast material measured as chlorophyll content. The enrichment of mitochondria in relation to peroxisomes and microsomes was approximately 12 and 33 times, respectively, based on NAD:isocitrate dehydrogenase activity, glycolate oxidase activity, and NADPH:cytochrome c oxidoreductase activity. The apparent intactness of the inner and the outer mitochondrial membranes was higher than 90% as measured by latency of enzyme activities. The mitochondria showed high respiratory rates with respiratory control and the ADP/O ratios approached the theoretical limits.

  • 19. Bergman, Birgitta
    et al.
    Huss-Danell, Kerstin
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    ULTRASTRUCTURE OF STIGONEMA IN THE CEPHALODIA OF STEREOCAULON-PASCHALE1983In: The Lichenologist, ISSN 0024-2829, E-ISSN 1096-1135, Vol. 15, 181-190 p.Article in journal (Refereed)
  • 20.
    Besya, Azim-Berdy
    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.
    Grönlund, Andreas
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Intrinsic phenotypic stability of a bi-stable auto regulatory gene2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 22951Article in journal (Refereed)
    Abstract [en]

    Even under homogenous conditions clonal cells can assume different distinct states for generations to follow, also known as epigenetic inheritance. Such long periods of different phenotypic states can be formed due to the existence of more than one stable state in the molecule concentration, where the different states are explored through molecular fluctuations. By formulating a single reaction variable representing the birth and death of molecules, including transcription, translation and decay, we calculate the escape time from the phenotypic states attained from autocatalytic synthesis through a Fokker-Planck formulation and integration of an effective pseudo-potential. We calculate the stability of the phenotypic states both for cooperative binding feedback and dimer binding feedback, resulting in non-linear decay.

  • 21. Betti, Marco
    et al.
    Bauwe, Hermann
    Busch, Florian A.
    Fernie, Alisdair R.
    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).
    Levey, Myles
    Ort, Donald R.
    Parry, Martin A. J.
    Sage, Rowan
    Timm, Stefan
    Walker, Berkley
    Weber, Andreas P. M.
    Manipulating photorespiration to increase plant productivity: recent advances and perspectives for crop improvement2016In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 67, no 10, 2977-2988 p.Article, review/survey (Refereed)
    Abstract [en]

    Recycling of the 2-phosphoglycolate generated by the oxygenase reaction of Rubisco requires a complex and energy-consuming set of reactions collectively known as the photorespiratory cycle. Several approaches aimed at reducing the rates of photorespiratory energy or carbon loss have been proposed, based either on screening for natural variation or by means of genetic engineering. Recent work indicates that plant yield can be substantially improved by the alteration of photorespiratory fluxes or by engineering artificial bypasses to photorespiration. However, there is also evidence indicating that, under certain environmental and/or nutritional conditions, reduced photorespiratory capacity may be detrimental to plant performance. Here we summarize recent advances obtained in photorespiratory engineering and discuss prospects for these advances to be transferred to major crops to help address the globally increasing demand for food and biomass production.

  • 22. Bishop, NI
    et al.
    Öquist, Gunnar
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    CORRELATION OF THE PHOTOSYSTEM-I AND PHOTOSYSTEM-II REACTION CENTER CHLOROPHYLL-PROTEIN COMPLEXES, CP-AI AND CP-AII, WITH PHOTOSYSTEM ACTIVITY AND LOW-TEMPERATURE FLUORESCENCE EMISSION PROPERTIES IN MUTANTS OF SCENEDESMUS1980In: Physiologia Plantarum: An International Journal for Plant Biology, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 49, no 4, 477-486 p.Article in journal (Refereed)
  • 23.
    Blanco, Nicolas 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).
    Guinea-Diaz, Manuel
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Whelan, James
    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).
    Interaction between plastid and mitochondrial retrograde signalling pathways during changes to plastid redox status2014In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 369, no 1640, 20130231Article in journal (Refereed)
    Abstract [en]

    Mitochondria and chloroplasts depend upon each other; photosynthesis provides substrates for mitochondrial respiration and mitochondrial metabolism is essential for sustaining photosynthetic carbon assimilation. In addition, mitochondrial respiration protects photosynthesis against photoinhibition by dissipating excess redox equivalents from the chloroplasts. Genetic defects in mitochondrial function result in an excessive reduction and energization of the chloroplast. Thus, it is clear that the activities of mitochondria and plastids need to be coordinated, but the manner by which the organelles communicate to coordinate their activities is unknown. The regulator of alternative oxidase (rao1) mutant was isolated as a mutant unable to induce AOX1a expression in response to the inhibitor of the mitochondrial cytochrome c reductase (complex III), antimycin A. RAO1 encodes the nuclear localized cyclin-dependent kinase E1 (CDKE1). Interestingly, the rao1 mutant demonstrates a genome uncoupled phenotype also in response to redox changes in the photosynthetic electron transport chain. Thus, CDKE1 was shown to regulate both LIGHT HARVESTING COMPLEX B (LHCB) and ALTERNATIVE OXIDASE 1 (AOX1a) expression in response to retrograde signals. Our results suggest that CDKE1 is a central nuclear component integrating mitochondrial and plastid retrograde signals and plays a role in regulating energy metabolism during the response to stress.

  • 24.
    Blumenstein, Kathrin
    et al.
    Swedish University of Agricultural Sciences, Alnarp, Sweden.
    Macaya-Sanz, David
    Madrid, Spain.
    Martin, Juana A.
    Madrid, Spain.
    Albrectsen, Benedicte R.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark.
    Witzell, Johanna
    Joensuu, Finland.
    Phenotype MicroArrays as a complementary tool to next generation sequencing for characterization of tree endophytes2015In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 6, 1033Article in journal (Refereed)
    Abstract [en]

    There is an increasing need to calibrate microbial community profiles obtained through next generation sequencing (NGS) with relevant taxonomic identities of the microbes, and to further associate these identities with phenotypic attributes. Phenotype MicroArray (PM) techniques provide a semi-high throughput assay for characterization and monitoring the microbial cellular phenotypes. Here, we present detailed descriptions of two different PM protocols used in our recent studies on fungal endophytes of forest trees, and highlight the benefits and limitations of this technique. We found that the PM approach enables effective screening of substrate utilization by endophytes. However, the technical limitations are multifaceted and the interpretation of the PM data challenging. For the best result, we recommend that the growth conditions for the fungi are carefully standardized. In addition, rigorous replication and control strategies should be employed whether using pre-configured, commercial microwell-plates or in-house designed PM plates for targeted substrate analyses. With these precautions, the PM technique is a valuable tool to characterize the metabolic capabilities of individual endophyte isolates, or successional endophyte communities identified by NGS, allowing a functional interpretation of the taxonomic data. Thus, PM approaches can provide valuable complementary information for NGS studies of fungal endophytes in forest trees.

  • 25.
    Blume-Werry, Gesche
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Jansson, Roland
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Milbau, Ann
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Department of Biodiversity and Natural Environment, Research Institute for Nature and Forest INBO, Kliniekstraat 25,1070 Brussels, Belgium.
    Root phenology unresponsive to earlier snowmelt despite advanced above-ground phenology in two subarctic plant communities2017In: Functional Ecology, ISSN 0269-8463, E-ISSN 1365-2435, Vol. 31, no 7, 1493-1502 p.Article in journal (Refereed)
    Abstract [en]

    1. Earlier snowmelt at high latitudes advances above-ground plant phenology, thereby affecting water, nutrient and carbon cycles. Despite the key role of fine roots in these ecosystem processes, phenological responses to earlier snowmelt have never been assessed below-ground. 2. We experimentally advanced snowmelt in two contrasting plant community types (heath and meadow) in northern Sweden and measured above- and below-ground phenology (leaf-out, flowering and fine root growth). We expected earlier snowmelt to advance both above- and below-ground phenology, and shrub-dominated heath to be more responsive than meadow. 3. Snow melted on average 9 days earlier in the manipulated plots than in controls, and soil temperatures were on average 0.9 degrees C higher during the snowmelt period of 3 weeks. This resulted in small advances in above-ground phenology, but contrary to our expectations, root phenology was unresponsive, with root growth generally starting before leaf-out. These responses to the snowmelt treatment were similar in both plant community types, despite strong differences in dominating plant functional types and root properties, such as root length and turnover. 4. The lack of a response in root phenology, despite warmer soil temperatures and above-ground phenological advances, adds evidence that above-ground plant responses might not be directly translated to below-ground plant responses, and that our understanding of factors driving below-ground phenology is still limited, although of major importance for water, nutrient and carbon cycling.

  • 26.
    Bollhöner, Benjamin
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Significance of hydrolytic enzymes expressed during xylem cell death2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Xylem is an inherent feature of all vascular plants and functions in water transport and mechanical support. In order to efficiently transport water, xylem cells are reinforced by secondary walls before they undergo programmed cell death and their cell contents are removed by autolysis to create a hollow tube. During their differentiation, xylem cells express various hydrolytic enzymes, such as proteases, nucleases and lipases, but only in a few examples has their role in xylem cell death been characterized. This thesis focuses on the regulatory aspects of xylem cell death and the autolytic cell clearance in vessel elements and fibers of hybrid aspen (Populus tremula L. x tremuloides Michx.) and in vessel elements of Arabidopsis thaliana. Using comparative transcriptomic analysis, candidate genes for fiber-specific cell death processes were identified. Further, a hypothesis is presented on the regulation of thermospermine levels in the vasculature by a negative feedback-loop involving auxin and the class III Homeodomain-Leucine Zipper (HD-ZIP III) transcription factor HOMEOBOX8 (PtHB8). The role of the Arabidopsis METACASPASE9 (AtMC9) in xylem cell death was characterized using molecular tools, such as reporter lines and fluorescent fusion proteins, and electron microscopy (TEM). This showed that cell death initiation is not controlled by AtMC9. Instead, evidence is presented for the involvement of AtMC9 in the post mortem autolysis of vessel elements that follows tonoplast rupture and leads to the formation of the hollow conduit. Cell death-associated genes were further observed to be expressed during the emergence of lateral roots in Arabidopsis thaliana. This led to the discovery that cells overlying a lateral root primordium undergo cell death, which was demonstrated by detection of DNA degradation and TEM analysis. It is concluded that cell death facilitates emergence of lateral roots through the overlying tissues in a concerted manner with cell wall remodelling. Together, these findings show that although individual hydrolytic enzymes may be dispensable for plant growth and development, their common regulators are the tool for understanding their function and importance.

  • 27.
    Bollhöner, Benjamin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Voss, Ute
    Prestele, Jakob
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Wilson, Michael
    Kenobi, Kim
    Viotti, Corrado
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    André, Domenique
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Lers, Amnon
    Bennett, Malcolm
    Tuominen, Hannele
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Programmed cell death in overlying tissues facilitates lateral root emergenceManuscript (preprint) (Other academic)
  • 28.
    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, 498-510 p.Article 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.

  • 29. Boone, Celia K
    et al.
    Keefover-Ring, Ken
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Mapes, Abigail C
    Adams, Aaron S
    Bohlmann, Jörg
    Raffa, Kenneth F
    Bacteria associated with a tree-killing insect reduce concentrations of plant defense compounds2013In: Journal of Chemical Ecology, ISSN 0098-0331, E-ISSN 1573-1561, Vol. 39, no 7, 1003-1006 p.Article in journal (Refereed)
  • 30.
    Boutté, Yohann
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Men, Shuzhen
    Grebe, Markus
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Fluorescent in situ visualization of sterols in Arabidopsis roots2011In: Nature Protocols, ISSN 1754-2189, Vol. 6, no 4, 446-456 p.Article in journal (Refereed)
    Abstract [en]

    Sterols are eukaryotic membrane components with crucial roles in diverse cellular processes. Elucidation of sterol function relies on development of tools for in situ sterol visualization. Here we describe protocols for in situ sterol localization in Arabidopsis thaliana root cells, using filipin as a specific probe for detection of fluorescent filipin-sterol complexes. Currently, filipin is the only established tool for sterol visualization in plants. Filipin labeling can be performed on aldehyde-fixed samples, largely preserving fluorescent proteins and being compatible with immunocytochemistry. Filipin can also be applied for probing live cells, taking into account the fact that it inhibits sterol-dependent endocytosis. The experimental procedures described are designed for fluorescence detection by confocal laser-scanning microscopy with excitation of filipin-sterol complexes at 364 nm. The protocols require 1 d for sterol covisualization with fluorescent proteins in fixed or live roots and 2 d for immunocytochemistry on whole-mount roots.

  • 31.
    Brackmann, Klaus
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Contribution of endocytic trafficking and epidermal morphology genes to planar polarity formation in the Arabidopsis root epidermis2010Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 32.
    Brouwer, Bastiaan
    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.
    Gardeström, Per
    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, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    In response to partial plant shading, the lack of phytochrome A does not directly induce leaf senescence but alters the fine-tuning of chlorophyll biosynthesis2014In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 65, no 14, 4037-4049 p.Article in journal (Refereed)
    Abstract [en]

    Phytochrome is thought to control the induction of leaf senescence directly, however, the signalling and molecular mechanisms remain unclear. In the present study, an ecophysiological approach was used to establish a functional connection between phytochrome signalling and the physiological processes underlying the induction of leaf senescence in response to shade. With shade it is important to distinguish between complete and partial shading, during which either the whole or only a part of the plant is shaded, respectively. It is first shown here that, while PHYB is required to maintain chlorophyll content in a completely shaded plant, only PHYA is involved in maintaining the leaf chlorophyll content in response to partial plant shading. Second, it is shown that leaf yellowing associated with strong partial shading in phyA-mutant plants actually correlates to a decreased biosynthesis of chlorophyll rather than to an increase of its degradation. Third, it is shown that the physiological impact of this decreased biosynthesis of chlorophyll in strongly shaded phyA-mutant leaves is accompanied by a decreased capacity to adjust the Light Compensation Point. However, the increased leaf yellowing in phyA-mutant plants is not accompanied by an increase of senescence-specific molecular markers, which argues against a direct role of PHYA in inducing leaf senescence in response to partial shade. In conclusion, it is proposed that PHYA, but not PHYB, is essential for fine-tuning the chlorophyll biosynthetic pathway in response to partial shading. In turn, this mechanism allows the shaded leaf to adjust its photosynthetic machinery to very low irradiances, thus maintaining a positive carbon balance and repressing the induction of leaf senescence, which can occur under prolonged periods of shade.

  • 33. BRUNES, L
    et al.
    Öquist, Gunnar
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    ELIASSON, L
    ON THE REASON FOR THE DIFFERENT PHOTOSYNTHETIC RATES OF SEEDLINGS OF PINUS-SILVESTRIS AND BETULA-VERRUCOSA1980In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 66, no 5, 940-944 p.Article in journal (Refereed)
  • 34.
    Buckland, Philip I.
    Umeå University, Faculty of Arts, Department of historical, philosophical and religious studies, Environmental Archaeology Lab. Umeå University, Faculty of Arts, Humlab.
    SEAD - The Strategic Environmental Archaeology Database. Inter-linking multiproxy environmental data with archaeological investigations and ecology.2013In: CAA2012, Proceedings of the 40th Annual Conference of Computer Applications and Quantitative Methods in Archaeology (CAA), Southampton, England. / [ed] Graeme Earl, Tim Sly, Angeliki Chrysanthi, Patricia Murrieta-Flores, Constantinos Papadopoulos, Iza Romanowska & David Wheatley, Amsterdam, 2013, 320-331 p.Conference paper (Refereed)
    Abstract [en]

    The volume of data on past environmental and climate changes, as well as human interactions with these, has long since passed the level where it is manageable outside of large scale database systems. The Strategic Environmental Archaeology Database project aims to not only store and disseminate such data, but also provide tools for querying and analysing them, whilst maintaining a close connection with the archaeological and ecological data that are essential for their comprehensive interpretation. Large scale, geographically and chronologically unrestricted databases provide us with essentially unlimited scope for putting individual sites into a broader context and applying locally collated data to the investigation of earth system level changes. By providing integrated access to data from a variety of proxies, including plant macrofossils, pollen, insects and geochemistry, along with dating evidence, more complex questions can be answered where any single proxy would not be able to provide comprehensive answers.

  • 35.
    Buckland, Philip I.
    et al.
    Umeå University, Faculty of Arts, Department of historical, philosophical and religious studies, Environmental Archaeology Lab.
    Eriksson, Erik J.
    Umeå University, Faculty of Arts, Department of historical, philosophical and religious studies, Environmental Archaeology Lab.
    Palm, Fredrik
    Umeå University, Faculty of Arts, Humlab.
    SEAD - The Strategic Environmental Archaeology Database: Progress Report Spring 20142014Report (Other academic)
    Abstract [en]

    This report provides an overview of the progress and results of the VR:KFI infrastructure projects 2007-7494 and (825-)2010-5976. It should be considered as a status report in an on-going long-term research infrastructure development project.

  • 36.
    Burdon, Jeremy J.
    et al.
    CSIRO-Plant Industry, Canberra, Australia.
    Thrall, Peter H.
    CSIRO-Plant Industry, Canberra, Australia.
    Ericson, Lars
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    The current and future dynamics of disease in plant communities2006In: Annual Review of Phytopathology, ISSN 0066-4286, E-ISSN 1545-2107, Vol. 44, 19-39 p.Article in journal (Refereed)
    Abstract [en]

    Pathogens are powerful evolutionary forces shaping the structure and dynamics of both individual species and of the communities of which they are part, at a broad range of genetic, ecological, spatial, and temporal scales. At all these levels their impact varies from the subtle and little recognized through to the most obvious destruction. Today the direct role of pathogens in natural plant communities is better recognized than at previous times, although the nuances of their interactions and the cascade of ramifications that can flow through changing biotic and abiotic effects are only now gaining recognition. However, as human influence on pathogens increases either directly through enhanced if accidental dispersal, or through anthropogenic impacts on climate-we may expect to see increasing evidence of pathogens affecting plant species, community structure, and ecosystem function.

  • 37.
    Bygdell, Joakim
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Srivastava, Vaibhav
    Obudulu, Ogonna
    Srivastava, Manoj K.
    Nilsson, Robert
    Sundberg, Björn
    Trygg, Johan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mellerowicz, Ewa J.
    Wingsle, Gunnar
    Protein expression in tension wood formation monitored at high tissue resolution in Populus2017In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 68, no 13, 3405-3417 p.Article in journal (Refereed)
    Abstract [en]

    Tension wood (TW) is a specialized tissue with contractile properties that is formed by the vascular cambium in response to gravitational stimuli. We quantitatively analysed the proteomes of Populus tremula cambium and its xylem cell derivatives in stems forming normal wood (NW) and TW to reveal the mechanisms underlying TW formation. Phloem-, cambium-, and wood-forming tissues were sampled by tangential cryosectioning and pooled into nine independent samples. The proteomes of TW and NW samples were similar in the phloem and cambium samples, but diverged early during xylogenesis, demonstrating that reprogramming is an integral part of TW formation. For example, 14-3-3, reactive oxygen species, ribosomal and ATPase complex proteins were found to be up-regulated at early stages of xylem differentiation during TW formation. At later stages of xylem differentiation, proteins involved in the biosynthesis of cellulose and enzymes involved in the biosynthesis of rhamnogalacturonan-I, rhamnogalacturonan-II, arabinogalactan-II and fasciclin-like arabinogalactan proteins were up-regulated in TW. Surprisingly, two isoforms of exostosin family proteins with putative xylan xylosyl transferase function and several lignin biosynthesis proteins were also up-regulated, even though xylan and lignin are known to be less abundant in TW than in NW. These data provided new insight into the processes behind TW formation.

  • 38.
    Båmstedt, Ulf
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Marine Sciences Centre (UMF).
    Wikner, Johan
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Marine Sciences Centre (UMF).
    Mixing depth and allochthonous dissolved organic carbon: controlling factors of coastal trophic balance2016In: Marine Ecology Progress Series, ISSN 0171-8630, E-ISSN 1616-1599, Vol. 561, 17-29 p.Article in journal (Refereed)
    Abstract [en]

    ABSTRACT: The interacting effects of different mixing depths and increased allochthonous dissolved organic carbon (DOC) on the ratio of heterotrophic to autotrophic production (i.e. trophic balance) was evaluated in a mesocosm study with a stratified water column. An autumn plankton community from the northern Bothnian Sea showed significantly decreased phytoplankton production and somewhat increased bacterial production with added DOC. In addition, increased mixing depth further reduced phytoplankton production. With a deep pycnocline and added DOC, the system became net-heterotrophic, with an average bacteria-to-phytoplankton production ratio of 1.24. With a deep pycnocline without added DOC, the trophic balance was changed to 0.44 (i.e. autotrophic). With a shallow pycnocline, the system remained net-autotrophic irrespective of DOC addition. We propose that increased precipitation in northern Europe due to climate change may result in changed density stratification and increased allochthonous DOC transport to the sea, leading to more heterotrophic coastal aquatic ecosystems. Such a scenario may entail reduced biological production at higher trophic levels and enhanced CO2 emission to the atmosphere.

  • 39. Capovilla, Giovanna
    et al.
    Pajoro, Alice
    Immink, Richard GH
    Schmid, Markus
    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 Molecular Biology, Max Planck Institute for Developmental Biology, 72074 Tübingen, Germany.
    Role of alternative pre-mRNA splicing in temperature signaling2015In: Current opinion in plant biology, ISSN 1369-5266, E-ISSN 1879-0356, Vol. 27, 97-103 p.Article, review/survey (Refereed)
    Abstract [en]

    Developmental plasticity enables plants to respond rapidly to changing environmental conditions, such as temperature fluctuations. Understanding how plants measure temperature and integrate this information into developmental programs at the molecular level will be essential to breed thermo-tolerant crop varieties. Recent studies identified alternative splicing (AS) as a possible 'molecular thermometer', allowing plants to quickly adjust the abundance of functional transcripts to environmental perturbations. In this review, recent advances regarding the effects of temperature-responsive AS on plant development will be discussed, with emphasis on the circadian clock and flowering time control. The challenge for the near future will be to understand the molecular mechanisms by which temperature can influence AS regulation.

  • 40. Capovilla, Giovanna
    et al.
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tübingen, Germany.
    Posé, David
    Control of flowering by ambient temperature2015In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 66, no 1, 59-69 p.Article in journal (Refereed)
    Abstract [en]

    The timing of flowering is a crucial decision in the life cycle of plants since favourable conditions are needed to maximize reproductive success and, hence, the survival of the species. It is therefore not surprising that plants constantly monitor endogenous and environmental signals, such as day length (photoperiod) and temperature, to adjust the timing of the floral transition. Temperature in particular has been shown to have a tremendous effect on the timing of flowering: the effect of prolonged periods of cold, called the vernalization response, has been extensively studied and the underlying epigenetic mechanisms are reasonably well understood in Arabidopsis thaliana. In contrast, the effect of moderate changes in ambient growth temperature on the progression of flowering, the thermosensory pathway, is only starting to be understood on the molecular level. Several genes and molecular mechanisms underlying the thermosensory pathway have already been identified and characterized in detail. At a time when global temperature is rising due to climate change, this knowledge will be pivotal to ensure crop production in the future.

  • 41. Carlsson, Johanna
    et al.
    Svennerstam, Henrik
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Moritz, Thomas
    Egertsdotter, Ulrika
    Ganeteg, Ulrika
    Nitrogen uptake and assimilation in proliferating embryogenic cultures of Norway spruce-Investigating the specific role of glutamine2017In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 8, e0181785Article in journal (Refereed)
    Abstract [en]

    Somatic embryogenesis is an in vitro system employed for plant propagation and the study of embryo development. Nitrogen is essential for plant growth and development and, hence, the production of healthy embryos during somatic embryogenesis. Glutamine has been shown to increase plant biomass in many in vitro applications, including somatic embryogenesis. However, several aspects of nitrogen nutrition during somatic embryogenesis remain unclear. Therefore, we investigated the uptake and assimilation of nitrogen in Norway spruce pro-embryogenic masses to elucidate some of these aspects. In our study, addition of glutamine had a more positive effect on growth than inorganic nitrogen. The nitrogen uptake appeared to be regulated, with a strong preference for glutamine; 67% of the assimilated nitrogen in the free amino acid pool originated from glutamine-nitrogen. Glutamine addition also relieved the apparently limited metabolism (as evidenced by the low concentration of free amino acids) of pro-embryogenic masses grown on inorganic nitrogen only. The unusually high alanine concentration in the presence of glutamine, suggests that alanine biosynthesis was involved in alleviating these constraints. These findings inspire further studies of nitrogen nutrition during the somatic embryogenesis process; identifying the mechanism(s) that govern glutamine enhancement of pro-embryogenic masses growth is especially important in this regard.

  • 42. Chardon, Fabien
    et al.
    Bedu, Magali
    Calenge, Fanny
    Klemens, Patrick A. W.
    Spinner, Lara
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Clement, Gilles
    Chietera, Giorgiana
    Leran, Sophie
    Ferrand, Marina
    Lacombe, Benoit
    Loudet, Olivier
    Dinant, Sylvie
    Bellini, Catherine
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Neuhaus, H. Ekkehard
    Daniel-Vedele, Francoise
    Krapp, Anne
    Leaf Fructose Content Is Controlled by the Vacuolar Transporter SWEET17 in Arabidopsis2013In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 23, no 8, 697-702 p.Article in journal (Refereed)
    Abstract [en]

    In higher plants, soluble sugars are mainly present as sucrose, glucose, and fructose [1]. Sugar allocation is based on both source-to-sink transport and intracellular transport between the different organelles [2,3] and depends on actual plant requirements [4]. Under abiotic stress conditions, such as nitrogen limitation, carbohydrates accumulate in plant cells [5]. Despite an increasing number of genetic studies [6, 7], the genetic architecture determining carbohydrate composition is poorly known. Using a quantitative genetics approach, we determined that the carrier protein SWEET17 is a major factor controlling fructose content in Arabidopsis leaves. We observed that when SWEET17 expression is reduced, either by induced or natural variation, fructose accumulates in leaves, suggesting an enhanced storage capacity. Subcellular localization of SWEET17-GFP to the tonoplast and functional expression in Xenopus oocytes showed that SWEET17 is the first vacuolar fructose transporter to be characterized in plants. Physiological studies in planta provide evidence that SWEET17 acts to export fructose out of the vacuole. Overall, our results suggest that natural variation in leaf fructose levels is controlled by the vacuolar fructose transporter SWEET17. SWEET17 is highly conserved across the plant kingdom; thus, these findings offer future possibilities to modify carbohydrate partitioning in crops.

  • 43. Chow, Wah Soon
    et al.
    Fan, Da-Yong
    Oguchi, Riichi
    Jia, Husen
    Losciale, Pasquale
    Park, Youn-Il
    He, Jie
    Öquist, Gunnar
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Shen, Yun-Gang
    Anderson, Jan M.
    Quantifying and monitoring functional photosystem II and the stoichiometry of the two photosystems in leaf segments: approaches and approximations2012In: Photosynthesis Research, ISSN 0166-8595, E-ISSN 1573-5079, Vol. 113, no 1-3, 63-74 p.Article, review/survey (Refereed)
    Abstract [en]

    Given its unique function in light-induced water oxidation and its susceptibility to photoinactivation during photosynthesis, photosystem II (PS II) is often the focus of studies of photosynthetic structure and function, particularly in environmental stress conditions. Here we review four approaches for quantifying or monitoring PS II functionality or the stoichiometry of the two photosystems in leaf segments, scrutinizing the approximations in each approach. (1) Chlorophyll fluorescence parameters are convenient to derive, but the information-rich signal suffers from the localized nature of its detection in leaf tissue. (2) The gross O-2 yield per single-turnover flash in CO2-enriched air is a more direct measurement of the functional content, assuming that each functional PS II evolves one O-2 molecule after four flashes. However, the gross O-2 yield per single-turnover flash (multiplied by four) could over-estimate the content of functional PS II if mitochondrial respiration is lower in flash illumination than in darkness. (3) The cumulative delivery of electrons from PS II to P700(+) (oxidized primary donor in PS I) after a flash is added to steady background far-red light is a whole-tissue measurement, such that a single linear correlation with functional PS II applies to leaves of all plant species investigated so far. However, the magnitude obtained in a simple analysis (with the signal normalized to the maximum photo-oxidizable P700 signal), which should equal the ratio of PS II to PS I centers, was too small to match the independently-obtained photosystem stoichiometry. Further, an under-estimation of functional PS II content could occur if some electrons were intercepted before reaching PS I. (4) The electrochromic signal from leaf segments appears to reliably quantify the photosystem stoichiometry, either by progressively photoinactivating PS II or suppressing PS I via photo-oxidation of a known fraction of the P700 with steady far-red light. Together, these approaches have the potential for quantitatively probing PS II in vivo in leaf segments, with prospects for application of the latter two approaches in the field.

  • 44.
    Chrobok, Daria
    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).
    Law, Simon R.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Brouwer, Bastiaan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Linden, Pernilla
    Ziolkowska, Agnieszka
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Liebsch, Daniela
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Narsai, Reena
    Szal, Bozena
    Moritz, Thomas
    Rouhier, Nicolas
    Whelan, James
    Gardeström, Per
    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).
    Dissecting the Metabolic Role of Mitochondria during Developmental Leaf Senescence2016In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 172, no 4, 2132-2153 p.Article in journal (Refereed)
    Abstract [en]

    The functions of mitochondria during leaf senescence, a type of programmed cell death aimed at the massive retrieval of nutrients from the senescing organ to the rest of the plant, remain elusive. Here, combining experimental and analytical approaches, we showed that mitochondrial integrity in Arabidopsis (Arabidopsis thaliana) is conserved until the latest stages of leaf senescence, while their number drops by 30%. Adenylate phosphorylation state assays and mitochondrial respiratory measurements indicated that the leaf energy status also is maintained during this time period. Furthermore, after establishing a curated list of genes coding for products targeted to mitochondria, we analyzed in isolation their transcript profiles, focusing on several key mitochondrial functions, such as the tricarboxylic acid cycle, mitochondrial electron transfer chain, iron-sulfur cluster biosynthesis, transporters, as well as catabolic pathways. In tandem with a metabolomic approach, our data indicated that mitochondrial metabolism was reorganized to support the selective catabolism of both amino acids and fatty acids. Such adjustments would ensure the replenishment of alpha-ketoglutarate and glutamate, which provide the carbon backbones for nitrogen remobilization. Glutamate, being the substrate of the strongly up-regulated cytosolic glutamine synthase, is likely to become a metabolically limiting factor in the latest stages of developmental leaf senescence. Finally, an evolutionary age analysis revealed that, while branched-chain amino acid and proline catabolism are very old mitochondrial functions particularly enriched at the latest stages of leaf senescence, auxin metabolism appears to be rather newly acquired. In summation, our work shows that, during developmental leaf senescence, mitochondria orchestrate catabolic processes by becoming increasingly central energy and metabolic hubs.

  • 45.
    Claes, Andrea
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Characterization of mutants in the ACTIN-INTERACTING PROTEIN 1-2 (AIP1-2) gene of Arabidopsis thaliana and of AIP1-1 and AIP1-2 protein interactions2010Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 46.
    Damkjaer, Jakob
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Phosphorylation in State Transition: Less cause more effect2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Study of the Arabidopsis thaliana knockout mutant lacking Lhcb3 (koLhcb3) have revealed a close similarity to the wild type plants. Growth rate, NPQ, qP, Φ(PSII), circular dichroism spectra, pigment composition and content of LCHII trimers have been found to be unaffected by this mutation. The proteomic analysis shows only some minor increases in the amount of Lhcb1 and Lhcb2. PAM fluorometry revealed a significant increase in the rate of the state 1 to state 2 state transition in the koLhcb3. None the less, the extent of state transition is identical to wild type. Alterations in the PSII-LHCII supercomplex structure have been demonstrated as well. The M-trimer was found to be rotated ~21° CCW. This altered binding of the LHCII M-trimer is likely the cause of the altered affinity resulting in the increased rate of state transition. Proteomic analysis of the phosphorylation of LHCII revealed a significant increase in state 1 and 2 LHCII phosphorylation relative to wild type. Investigation whether phosphorylation or the altered LHCII binding is the cause of the accelerated rate of state transition have not been conclusive so far. A Lhcb6 depleted mutant (koLhcb6) showed a significant alteration of the PSII-LHCII supercomplex structure and photosynthetic acclimation processes. The LHCII M-trimer is depleted in the PSII-LHCII supercomplexes causing the state transition process to be “stuck” in state 2 and the mutants ability to preform NPQ is inhibited as well. The Lhcb6 protein was concluded to be essential for the binding of the LHCII M-trimer to the PSII core as well as energy transfer. The depletion of LHCII M-trimer was linked to the reduced ability to photoacclimate using NPQ as well.

  • 47. De Frenne, Pieter
    et al.
    Graae, Bente J
    Department of Biology, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.
    Brunet, Joerg
    Shevtsova, Anna
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    De Schrijver, An
    Chabrerie, Olivier
    Cousins, Sara AO
    Decocq, Guillaume
    Diekmann, Martin
    Hermy, Martin
    Heinken, Thilo
    Kolb, Annette
    Nilsson, Christer
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Stanton, Sharon
    Verheyen, Kris
    The response of forest plant regeneration to temperature variation along a latitudinal gradient2012In: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 109, no 5, 1037-1046 p.Article in journal (Refereed)
    Abstract [en]

    The response of forest herb regeneration from seed to temperature variations across latitudes was experimentally assessed in order to forecast the likely response of understorey community dynamics to climate warming. Seeds of two characteristic forest plants (Anemone nemorosa and Milium effusum) were collected in natural populations along a latitudinal gradient from northern France to northern Sweden and exposed to three temperature regimes in growth chambers (first experiment). To test the importance of local adaptation, reciprocal transplants were also made of adult individuals that originated from the same populations in three common gardens located in southern, central and northern sites along the same gradient, and the resulting seeds were germinated (second experiment). Seedling establishment was quantified by measuring the timing and percentage of seedling emergence, and seedling biomass in both experiments. Spring warming increased emergence rates and seedling growth in the early-flowering forb A. nemorosa. Seedlings of the summer-flowering grass M. effusum originating from northern populations responded more strongly in terms of biomass growth to temperature than southern populations. The above-ground biomass of the seedlings of both species decreased with increasing latitude of origin, irrespective of whether seeds were collected from natural populations or from the common gardens. The emergence percentage decreased with increasing home-away distance in seeds from the transplant experiment, suggesting that the maternal plants were locally adapted. Decreasing seedling emergence and growth were found from the centre to the northern edge of the distribution range for both species. Stronger responses to temperature variation in seedling growth of the grass M. effusum in the north may offer a way to cope with environmental change. The results further suggest that climate warming might differentially affect seedling establishment of understorey plants across their distribution range and thus alter future understorey plant dynamics.

  • 48. De Long, Jonathan R.
    et al.
    Sundqvist, Maja K.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Center for Macroecology, Evolution and Climate, The Natural History Museum of Denmark, University of Copenhagen, 2100 Copenhagen, Denmark.
    Gundale, Michael J.
    Giesler, Reiner
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Climate Impacts Research Centre, Department of Ecology and Environmental Sciences, Umeå University, SE-981 07 Abisko, Sweden.
    Wardle, David A.
    Effects of elevation and nitrogen and phosphorus fertilization on plant defence compounds in subarctic tundra heath vegetation2016In: Functional Ecology, ISSN 0269-8463, E-ISSN 1365-2435, Vol. 30, no 2, 314-325 p.Article in journal (Refereed)
    Abstract [en]

    Plant chemical and structural defence compounds are well known to impact upon herbivory of fresh leaves and influence decomposition rates after leaf senescence. A number of theories predict that alleviating nutrient limitation and reducing other environmental stressors will result in decreased production of plant chemical defences. In this study, we measured plant defence properties [total polyphenols (TP), condensed tannins (CT) and lignin concentrations, and protein complexation capacity (PCC)] in both fresh and senesced plant leaves in a fully factorial N and P fertilization experiment set-up at each of three elevations along an elevational gradient in Swedish subarctic tundra heath vegetation. Further, we performed a decomposition of variance analysis on community-weighted averages (CWAs) of plant defence properties to determine the relative contributions of interspecific and intraspecific variation to the total variation observed in response to elevation and nutrient addition. We hypothesized that N fertilization would reduce plant defence properties and that this reduction would be greater at higher elevations, while the effects of P fertilization would have no effect at any elevation. At the community level, N addition reduced CT and PCC in both fresh and senesced leaves and TP in senesced leaves, while P addition had few effects, broadly in line with our hypothesis. The effects of N addition frequently varied with elevation, but in contrast to our hypothesis, the said effects were strongest at the lowest elevations. The effects of N addition and the interactive effect of N with elevation were primarily driven by intraspecific, rather than interspecific, variation. Our findings suggest that as temperatures warm and N availability increases due to global climate change, secondary metabolites in subarctic heath vegetation will decline particularly within species. Our results highlight the need to consider the effects of both nutrient availability and temperature, and their interaction, in driving subarctic plant defence.

  • 49.
    Decker, Daniel
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Phenotype study of Leucine rich repeat receptor like kinase in mutants Arabidopsis thaliana2010Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Meristem regulation has previously been shown to be essential to maintain continuous growth. The mechanism controlling the primary meristems is fairly well known compared to the secondary meristem. This report is focused on studying phenotypic effects of leucine rich repeat receptor like kinases (LRR RLK) in the model organism Arabidopsis thaliana. Expression was also examined in plants transformed with LRR RLK promoters connected to the uidA gene. The effect on secondary growth that was observed is discussed below.

  • 50.
    Decker, Daniel
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Kleczkowski, Leszek
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Substrate Specificity and Inhibitor Sensitivity of Plant UDP-Sugar Producing Pyrophosphorylases2017In: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 8, 1610Article in journal (Refereed)
    Abstract [en]

    UDP-sugars are essential precursors for glycosylation reactions producing cell wall polysaccharides, sucrose, glycoproteins, glycolipids, etc. Primary mechanisms of UDP sugar formation involve the action of at least three distinct pyrophosphorylases using UTP and sugar-1-P as substrates. Here, substrate specificities of barley and Arabidopsis (two isozymes) UDP-glucose pyrophosphorylases (UGPase), Arabidopsis UDP-sugar pyrophosphorylase (USPase) and Arabidopsis UDP-N-acetyl glucosamine pyrophosphorylase2 (UAGPase2) were investigated using a range of sugar-1-phosphates and nucleoside-triphosphates as substrates. Whereas all the enzymes preferentially used UTP as nucleotide donor, they differed in their specificity for sugar-1-P. UGPases had high activity with D-Glc-1-P, but could also react with Fru-1-P and Fru-2-P (Km values over 10 mM). Contrary to an earlier report, their activity with Gal-1-P was extremely low. USPase reacted with a range of sugar-1-phosphates, including D-Glc-1-P, D-Gal-1-P, D-GalA-1-P (K-m of 1.3 mM), beta-L-Ara-1-P and alpha-D-Fuc-1-P (K-m of 3.4 mM), but not beta-L-Fuc-1-P. In contrast, UAGPase2 reacted only with D-GlcNAc-1-P, D-GalNAc-1-P (K-m of 1 mM) and, to some extent, D-Glc-1-P (Km of 3.2 mM). Generally, different conformations/substituents at C2, C4, and C5 of the pyranose ring of a sugar were crucial determinants of substrate specificity of a given pyrophosphorylase. Homology models of UDP-sugar binding to UGPase, USPase and UAGPase2 revealed more common amino acids for UDP binding than for sugar binding, reflecting differences in substrate specificity of these proteins. UAGPase2 was inhibited by a salicylate derivative that was earlier shown to affect UGPase and USPase activities, consistent with a common structural architecture of the three pyrophosphorylases. The results are discussed with respect to the role of the pyrophosphorylases in sugar activation for glycosylated end-products.

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