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  • 1. Abbasi, Arshad Mehmood
    et al.
    Khan, Mir Ajab
    Khan, Nadeem
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Shah, Munir H
    Ethnobotanical survey of medicinally important wild edible fruits species used by tribal communities of Lesser Himalayas-Pakistan2013Ingår i: Journal of Ethnopharmacology, ISSN 0378-8741, E-ISSN 1872-7573, Vol. 148, nr 2, s. 528-536Artikel i tidskrift (Refereegranskat)
    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. Agostinelli, Marta
    et al.
    Cleary, Michelle
    Martin, Juan A.
    Albrectsen, Benedicte R.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Witzell, Johanna
    Pedunculate Oaks (Quercus robur L.) Differing in Vitality as Reservoirs for Fungal Biodiversity2018Ingår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, artikel-id 1758Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Ecological significance of trees growing in urban and peri-urban settings is likely to increase in future land-use regimes, calling for better understanding of their role as potential reservoirs or stepping stones for associated biodiversity. We studied the diversity of fungal endophytes in woody tissues of asymptomatic even aged pedunculate oak trees, growing as amenity trees in a peri-urban setting. The trees were classified into three groups according to their phenotypic vitality (high, medium, and low). Endophytes were cultured on potato dextrose media from surface sterilized twigs and DNA sequencing was performed to reveal the taxonomic identity of the morphotypes. In xylem tissues, the frequency and diversity of endophytes was highest in oak trees showing reduced vitality. This difference was not found for bark samples, in which the endophyte infections were more frequent and communities more diverse than in xylem. In general, most taxa were shared across the samples with few morphotypes being recovered in unique samples. Leaf phenolic profiles were found to accurately classify the trees according to their phenotypic vitality. Our results confirm that xylem is more selective substrate for endophytes than bark and that endophyte assemblages in xylem are correlated to the degree of host vitality. Thus, high vitality of trees may be associated with reduced habitat quality to wood-associated endophytes.

  • 3. Aksmann, Anna
    et al.
    Shutova, Tatiana
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Samuelsson, Göran
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Tukaj, Zbigniew
    The mechanism of anthracene interaction with photosynthetic apparatus: A study using intact cells, thylakoid membranes and PS II complexes isolated from Chlamydomonas reinhardtii2011Ingår i: Aquatic Toxicology, ISSN 0166-445X, E-ISSN 1879-1514, Vol. 104, nr 3-4, s. 205-210Artikel i tidskrift (Refereegranskat)
    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. 

  • 4.
    Albrectsen, Benedicte Riber
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Siddique, Abu Bakar
    Decker, Vicki Huizu Guo
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Unterseher, Martin
    Robinson, Kathryn M
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Both plant genotype and herbivory shape aspen endophyte communities2018Ingår i: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 187, nr 2, s. 535-545Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Salicinoid phenolic glycosides are common defence substances in salicaceous trees and specialist leaf beetles use these compounds for their own defence against predators. Salicinoids vary qualitatively and qualitatively in aspen (Populus tremula) and this variation has a genetic basis. The foliar endophyte mycobiome is plentiful and we hypothesised that it is related to plant genotype, potentially mediated by salicinoid composition, and that interactions with the leaf beetle Chrysomela tremula may alter this relationship. We studied these three-way interactions in controlled greenhouse experiments. Endophytic fungi were isolated from sterilised leaf tissues with and without beetle damage, and from beetles. We confirmed that endophyte composition was influenced by host genotype. Beetle activity added generalist morphs to the mycobiome that overrode the initial host association. Yeast-like genera (Cryptococcus and Rhodotorula) were isolated only from beetle-damaged tissues and from beetles, whereas fast-growing filamentous fungi dominated beetle-free control plants. Competition experiments between filamentous fungi of plant origin and beetle-related yeasts suggested interaction of both stimulating and inhibiting modes of action amongst the fungi. As a result, we detected examples of amensalism, commensalism, parasitism and competition between the morphs tested, but we found no evidence of mutualism, and consequently no co-evolutionary relationship could be demonstrated, between yeasts carried by beetles, host genotype and associated filamentous morphs. Endophyte studies are method-dependent and high-throughput sequencing technology best define the fungal mycobiome, culturing however continues to be a cheap way to provide fundamental ecological insights and it is also required for experimental studies.

  • 5. Ali, Qasim
    et al.
    Haider, Muhammad Zulqurnain
    Iftikhar, Wasif
    Jamil, Sidra
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, 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 patterns2016Ingår i: Revista Brasileira de Botânica, ISSN 0100-8404, E-ISSN 1806-9959, Vol. 39, nr 3, s. 801-812Artikel i tidskrift (Refereegranskat)
    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.

  • 6. Allakhverdiev, Suleyman I.
    et al.
    Zharmukhamedov, Sergey K.
    Rodionova, Margarita V.
    Shuvalov, Vladimir A.
    Dismukes, Charles
    Shen, Jian-Ren
    Barber, James
    Samuelsson, Göran
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Govindjee,
    Vyacheslav (Slava) Klimov (1945-2017): A scientist par excellence, a great human being, a friend, and a Renaissance man2018Ingår i: Photosynthesis Research, ISSN 0166-8595, E-ISSN 1573-5079, Vol. 136, nr 1, s. 1-16Artikel i tidskrift (Övrigt vetenskapligt)
    Abstract [en]

    Vyacheslav Vasilevich (V.V.) Klimov (or Slava, as most of us called him) was born on January 12, 1945 and passed away on May 9, 2017. He began his scientific career at the Bach Institute of Biochemistry of the USSR Academy of Sciences (Akademy Nauk (AN) SSSR), Moscow, Russia, and then, he was associated with the Institute of Photosynthesis, Pushchino, Moscow Region, for about 50 years. He worked in the field of biochemistry and biophysics of photosynthesis. He is known for his studies on the molecular organization of photosystem II (PSII). He was an eminent scientist in the field of photobiology, a well-respected professor, and, above all, an outstanding researcher. Further, he was one of the founding members of the Institute of Photosynthesis in Pushchino, Russia. To most, Slava Klimov was a great human being. He was one of the pioneers of research on the understanding of the mechanism of light energy conversion and of water oxidation in photosynthesis. Slava had many collaborations all over the world, and he is (and will be) very much missed by the scientific community and friends in Russia as well as around the World. We present here a brief biography and some comments on his research in photosynthesis. We remember him as a friendly and enthusiastic person who had an unflagging curiosity and energy to conduct outstanding research in many aspects of photosynthesis, especially that related to PSII.

  • 7.
    Andersson, Jenny
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Dissecting the photosystem II light-harvesting antenna2003Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    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.

  • 8.
    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 wood2003Ingår i: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 34, nr 3, s. 339-349Artikel i tidskrift (Refereegranskat)
    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.

  • 9.
    Angelcheva, Liudmila
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Mishra, Yogesh
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Antti, Henrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Kjellsen, Trygve D.
    Department of Biology, Norwegian University of Science and Technology.
    Funk, Christiane
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Strimbeck, Richard G.
    Department of Biology, Norwegian University of Science and Technology.
    Schröder, Wolfgang P.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Metabolomic analysis of extreme freezing tolerance in Siberian spruce (Picea obovata)2014Ingår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 204, nr 3, s. 545-555Artikel i tidskrift (Refereegranskat)
    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.

  • 10. Anoman, Armand D.
    et al.
    Flores-Tornero, Maria
    Benstein, Ruben M.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Biocenter–Botanical Institute II, University of Cologne, Cologne, Germany.
    Blau, Samira
    Rosa-Tellez, Sara
    Braeutigam, Andrea
    Fernie, Alisdair R.
    Munoz-Bertomeu, Jesus
    Schilasky, Soeren
    Meyer, Andreas J.
    Kopriva, Stanislav
    Segura, Juan
    Krueger, Stephan
    Ros, Roc
    Deficiency in the Phosphorylated Pathway of Serine Biosynthesis Perturbs Sulfur Assimilation2019Ingår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 180, nr 1, s. 153-170Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Although the plant Phosphorylated Pathway of L-Ser Biosynthesis (PPSB) is essential for embryo and pollen development, and for root growth, its metabolic implications have not been fully investigated. A transcriptomics analysis of Arabidopsis (Arabidopsis thaliana) PPSB-deficient mutants at night, when PPSB activity is thought to be more important, suggested interaction with the sulfate assimilation process. Because sulfate assimilation occurs mainly in the light, we also investigated it in PPSB-deficient lines in the day. Key genes in the sulfate starvation response, such as the adenosine 5'phosphosulfate reductase genes, along with sulfate transporters, especially those involved in sulfate translocation in the plant, were induced in the PPSB-deficient lines. However, sulfate content was not reduced in these lines as compared with wild-type plants; besides the glutathione (GSH) steady-state levels in roots of PPSB-deficient lines were even higher than in wild type. This suggested that PPSB deficiency perturbs the sulfate assimilation process between tissues/organs. Alteration of thiol distribution in leaves from different developmental stages, and between aerial parts and roots in plants with reduced PPSB activity, provided evidence supporting this idea. Diminished PPSB activity caused an enhanced flux of S-35 into thiol biosynthesis, especially in roots. GSH turnover also accelerated in the PPSB-deficient lines, supporting the notion that not only biosynthesis, but also transport and allocation, of thiols were perturbed in the PPSB mutants. Our results suggest that PPSB is required for sulfide assimilation in specific heterotrophic tissues and that a lack of PPSB activity perturbs sulfur homeostasis between photosynthetic and nonphotosynthetic tissues.

  • 11. 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 om2012Ingår i: Svensk Botanisk Tidskrift, ISSN 0039-646X, Vol. 106, s. 309-318Artikel i tidskrift (Refereegranskat)
  • 12.
    Ashelford, Kevin
    et al.
    School of Biological Sciences, University of Liverpool, Liverpool, UK.
    Eriksson, Maria E
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, 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 universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, 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 Arabidopsis2011Ingår i: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 12, s. R28-Artikel i tidskrift (Refereegranskat)
    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.

  • 13. Aubry, Emilie
    et al.
    Dinant, Sylvie
    Vilaine, Francoise
    Bellini, C
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Le Hir, Rozenn
    Lateral Transport of Organic and Inorganic Solutes2019Ingår i: PLANTS, E-ISSN 2223-7747, Vol. 8, nr 1, artikel-id 20Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Organic (e.g., sugars and amino acids) and inorganic (e.g., K+, Na+, PO42−, and SO42−) solutes are transported long-distance throughout plants. Lateral movement of these compounds between the xylem and the phloem, and vice versa, has also been reported in several plant species since the 1930s, and is believed to be important in the overall resource allocation. Studies of Arabidopsis thaliana have provided us with a better knowledge of the anatomical framework in which the lateral transport takes place, and have highlighted the role of specialized vascular and perivascular cells as an interface for solute exchanges. Important breakthroughs have also been made, mainly in Arabidopsis, in identifying some of the proteins involved in the cell-to-cell translocation of solutes, most notably a range of plasma membrane transporters that act in different cell types. Finally, in the future, state-of-art imaging techniques should help to better characterize the lateral transport of these compounds on a cellular level. This review brings the lateral transport of sugars and inorganic solutes back into focus and highlights its importance in terms of our overall understanding of plant resource allocation.

  • 14.
    Augusti, Angela
    Umeå universitet, Teknisk-naturvetenskaplig fakultet, Fysiologisk botanik.
    Monitoring climate and plant physiology using deuterium isotopomers of carbohydrates2007Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [sv]

    Klimatet förändras och det är numera allmänt vedertaget att detta beror på människans aktiviteter. Halten av växthusgaser har stigit onormalt mycket under de senaste två århundradena och detta beror i största del på människans användning av fossila bränslen. Landbiosfären har hittills haft en buffrande effekt på klimatförändringen eftersom den tar upp och lagrar mycket av växthusgasen CO2. Det är dock osäkert om, och i så fall hur länge, denna effekt kvarstår. Detta gör det mycket svårt att förutsäga framtida klimatförändringar, och därmed hur mycket utsläppen av växthusgaser måste reduceras för att skydda klimatet.

    För att förstå växternas framtida förmåga att begränsa halten atmosfäriskt CO2 har man studerat effekten av förhöjda halter av CO2 på växters fotosyntes och produktivitet. Resultaten av dessa försök varierar i stor omfattning. Studier på träd odlade under höga halter CO2 indikerar att den initiala ökningen av en trädets produktivitet kan vara en temporär effekt som försvinner redan efter några år. Eftersom klimatförändringen sker under århundraden, måste även växternas anpassningar på förhöjd CO2 halt utforskas på denna tidsskala, men experiment som skulle ta tiotals år är opraktiska att utföra. Trädringar är ett bra sätt att studera sådana anpassningar, eftersom träd redan har upplevt de senaste två hundra årens ökning av koldioxid och dess trädringar därför kan innehålla information om en respons som redan skett.

    Denna avhandling visar att den intramolekylära fördelningen av den stabila väteisotopen deuterium i trädringar är en tillförlitlig metod för att studera växters anpassningsförmåga till långsiktiga klimatförändringar. Antagandet bakom denna strategi är att isotopfördelningen i trädringar beror på faktorer både från miljön och växtens fysiologi. Om båda faktorerna skulle kunna utvinnas från trädringar, skulle detta öppna en helt ny väg för parallell rekonstruktion av klimatet och växters anpassning till det. Avhandlingen presenterar den första tekniken för att mäta isotopfördelningen av deuterium i växtglukos. Resultaten visar att deuteriumfördelningen hos växtglukos påverkas av enzymers isotopeffekter, vilket möjliggör att regleringen av växternas metabolism kan kartläggas. I avhandlingen bevisas att halten deuterium i skilda intramolekylära positioner (isotopomerer) av glukos från trädringcellulosa bestäms av miljöfaktorer respektive trädets fysiologi. T.ex. påverkas deuteriumhalten i position 2 (D2 isotopomer) av glukosmolekylen huvudsakligen av miljön, vilket kan användas för att förbättra temperaturrekonstruktioner från trädringar. Å andra sidan är kvoten deuterium mellan två andra positioner (D6R och D6S) relaterat till halten atmosfäriskt koldioxid, och kvoten skulle kunna användas som mått för fotosyntesens effektivitet, dvs. förhållandet mellan fotorespiration och fotosyntes. Närvaron av denna relation i trädringar och annat växtmaterial i alla de växter vi hittills studerat, öppnar en helt ny möjlighet att studera växters anpassning till den ökande mängden CO2 i atmosfären under århundraden.

  • 15. Baena-González, Elena
    et al.
    Hanson, Johannes
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Shaping plant development through the SnRK1–TOR metabolic regulators2017Ingår i: Current opinion in plant biology, ISSN 1369-5266, E-ISSN 1879-0356, Vol. 35, s. 152-157Artikel i tidskrift (Refereegranskat)
    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.

  • 16. Bai, Bing
    et al.
    Novák, Ondrej
    Ljung, Karin
    Hanson, Johannes
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, the Netherlands.
    Bentsink, Leonie
    Combined transcriptome and translatome analyses reveal a role for tryptophan-dependent auxin biosynthesis in the control of DOG1-dependent seed dormancy2018Ingår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 217, nr 3, s. 1077-1085Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 17.
    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 universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Department of Molecular Plant Physiology, Utrecht University, 3584 CH Utrecht, the Netherlands.
    Extensive translational regulation during seed germination revealed by polysomal profiling2017Ingår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 214, nr 1, s. 233-244Artikel i tidskrift (Refereegranskat)
    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.

  • 18.
    Bandau, Franziska
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Decker, Vicki Huizu Guo
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Gundale, Michael J.
    Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, SE 90183 Umeå, Sweden.
    Albrectsen, Benedicte Riber
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. 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 others2015Ingår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, nr 10, artikel-id e0140971Artikel i tidskrift (Refereegranskat)
    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.

  • 19.
    Barros, Jaime
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Serk, Henrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Granlund, Irene
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Pesquet, Edouard
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    The cell biology of lignification in higher plants2015Ingår i: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 115, nr 7, s. 1053-1074Artikel, forskningsöversikt (Refereegranskat)
    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.

  • 20.
    Barthelemy, Hélène
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Stark, Sari
    Michelsen, Anders
    Olofsson, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Urine is an important nitrogen source for plants irrespective of vegetation composition in an Arctic tundra: Insights from a N-15-enriched urea tracer experiment2018Ingår i: Journal of Ecology, ISSN 0022-0477, E-ISSN 1365-2745, Vol. 106, nr 1, s. 367-378Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    1. Mammalian herbivores can strongly influence nitrogen (N) cycling and herbivore urine could be a central component of the N cycle in grazed ecosystems. Despite its potential role for ecosystem productivity and functioning, the fate of N derived from urine has rarely been investigated in grazed ecosystems. 2. This study explored the fate of N-15-enriched urea in tundra sites that have been either lightly or intensively grazed by reindeer for more than 50years. We followed the fate of the N-15 applied to the plant canopy, at 2weeks and 1year after tracer addition, in the different ecosystem N pools. 3. N-15-urea was rapidly incorporated in cryptogams and in above-ground parts of vascular plants, while the soil microbial pool and plant roots sequestered only a marginal proportion. Furthermore, the litter layer constituted a large sink for the N-15-urea, at least in the short term, indicating a high biological activity in the litter layer and high immobilization in the first phases of organic matter decomposition. 4. Mosses and lichens still constituted the largest sink for the N-15-urea 1year after tracer addition at both levels of grazing intensity demonstrating their large ability to capture and retain N from urine. Despite large fundamental differences in their traits, deciduous and evergreen shrubs were just as efficient as graminoids in taking up the N-15-urea. The total recovery of N-15-urea was lower in the intensively grazed sites, suggesting that reindeer reduce ecosystem N retention. 5. Synthesis. The rapid incorporation of the applied N-15-urea indicates that arctic plants can take advantage of a pulse of incoming N from urine. In addition, N-15 values of all taxa in the heavily grazed sites converged towards the N-15 values for urine, bringing further evidence that urine is an important N source for plants in grazed tundra ecosystems.

  • 21.
    Benedict, Catherine
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Cold Acclimation: Dissecting the plant low temperature signaling pathway using functional genomics2006Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    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.

  • 22.
    Benedict, Catherine
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Skinner, J. S.
    Meng, R.
    Chang, Y.
    Bhalerao, R.
    Finn, C.
    Chen, T. H. H.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten.
    Hurry, Vaughan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    The Role of the CBF-dependent Signalling Pathway in Woody Perennials2006Ingår i: Cold Hardiness in Plants: Molecular Genetics, Cell Biology and Physiology / [ed] T Chen, M Uemura, S Fujikawa, Wallingford: CABI Publishing, 2006, s. 167-180Kapitel i bok, del av antologi (Övrigt vetenskapligt)
  • 23.
    Benlloch, Reyes
    et al.
    Department of Forest Genetics and Plant Physiology, SLU.
    Shevela, Dmitriy
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Hainzl, Tobias
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Grundström, Christin
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Shutova, Tatyana
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Messinger, Johannes
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Samuelsson, Göran
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Sauer-Eriksson, Elisabeth
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Crystal structure and functional characterization of Photosystem II-associated carbonic anhydrase CAH3 in Chlamydomonas reinhardtii2015Ingår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 167, nr 3, s. 950-962Artikel i tidskrift (Refereegranskat)
    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.

  • 24. Benson, Samuel L
    et al.
    Maheswaran, Pratheesh
    Ware, Maxwell A
    Hunter, C Neil
    Horton, Peter
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, 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 Arabidopsis2015Ingår i: Nature plants, ISSN 2055-026X, Vol. 1, nr 12, artikel-id 15176Artikel i tidskrift (Refereegranskat)
    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.

  • 25. Bergman, Anders
    et al.
    Gardeström, Per
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Ericson, Ingemar
    Method to Obtain a Chlorophyll-free Preparation of Intact Mitochondria from Spinach Leaves.1980Ingår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 66, nr 3, s. 442-445Artikel i tidskrift (Refereegranskat)
    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.

  • 26. Bergman, Birgitta
    et al.
    Huss-Danell, Kerstin
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    ULTRASTRUCTURE OF STIGONEMA IN THE CEPHALODIA OF STEREOCAULON-PASCHALE1983Ingår i: The Lichenologist, ISSN 0024-2829, E-ISSN 1096-1135, Vol. 15, s. 181-190Artikel i tidskrift (Refereegranskat)
  • 27.
    Besya, Azim-Berdy
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Grönlund, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Intrinsic phenotypic stability of a bi-stable auto regulatory gene2016Ingår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, artikel-id 22951Artikel i tidskrift (Refereegranskat)
    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.

  • 28. Betti, Marco
    et al.
    Bauwe, Hermann
    Busch, Florian A.
    Fernie, Alisdair R.
    Keech, Olivier
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, 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 improvement2016Ingår i: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 67, nr 10, s. 2977-2988Artikel, forskningsöversikt (Refereegranskat)
    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.

  • 29. Bishop, NI
    et al.
    Öquist, Gunnar
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    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 SCENEDESMUS1980Ingår i: Physiologia Plantarum: An International Journal for Plant Biology, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 49, nr 4, s. 477-486Artikel i tidskrift (Refereegranskat)
  • 30.
    Blanco, Nicolas E.
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Guinea-Diaz, Manuel
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Whelan, James
    Strand, Åsa
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Interaction between plastid and mitochondrial retrograde signalling pathways during changes to plastid redox status2014Ingår i: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 369, nr 1640, artikel-id 20130231Artikel i tidskrift (Refereegranskat)
    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.

  • 31.
    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 universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. 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 endophytes2015Ingår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 6, artikel-id 1033Artikel i tidskrift (Refereegranskat)
    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.

  • 32.
    Blume-Werry, Gesche
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Jansson, Roland
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Milbau, Ann
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. 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 communities2017Ingår i: Functional Ecology, ISSN 0269-8463, E-ISSN 1365-2435, Vol. 31, nr 7, s. 1493-1502Artikel i tidskrift (Refereegranskat)
    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.

  • 33.
    Blume-Werry, Gesche
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Experimental Plant Ecology, Institute of Botany and Landscape Ecology, Greifswald University, Greifswald, Germany.
    Lindén, Elin
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Andresen, Lisa
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Classen, Aimée T.
    Sanders, Nathan J.
    von Oppen, Jonathan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Sundqvist, Maja K.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Center for Macroecology, Evolution and Climate, The Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark.
    Proportion of fine roots, but not plant biomass allocation below ground, increases with elevation in arctic tundra2018Ingår i: Journal of Vegetation Science, ISSN 1100-9233, E-ISSN 1654-1103, Vol. 29, nr 2, s. 226-235Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Questions: Roots represent a considerable proportion of biomass, primary production and litter input in arctic tundra, and plant allocation of biomass to above- or below-ground tissue in response to climate change is a key factor in the future C balance of these ecosystems. According to optimality theory plants allocate C to the above- or below-ground structure that captures the most limiting resource. We used an elevational gradient to test this theory and as a space-for-time substitution to inform on tundra carbon allocation patterns under a shifting climate, by exploring if increasing elevation was positively related to the root:shoot ratio, as well as a larger plant allocation to adsorptive over storage roots.

    Location: Arctic tundra heath dominated by Empetrum hermaphroditum close to Abisko, Sweden.

    Methods: We measured root:shoot and fine:coarse root ratios of the plant communities along an elevational gradient by sampling above- and below-ground biomass, further separating root biomass into fine (<1 mm) and coarse roots.

    Results: Plant biomass was higher at the lower elevations, but the root:shoot ratio did not vary with elevation. Resource allocation to fine relative to coarse roots increased with elevation, resulting in a fine:coarse root ratio that more than doubled with increasing elevation.

    Conclusions: Contrary to previous works, the root:shoot ratio along this elevational gradient remained stable. However, communities along our study system were dominated by the same species at each elevation, which suggests that when changes in the root:shoot ratio occur with elevation these changes may be driven by differences in allocation patterns among species and thus turnover in plant community structure. Our results further reveal that the allocation of biomass to fine relative to coarse roots can differ between locations along an elevational gradient, even when overall above- vs below-ground biomass allocation does not. Given the functionally different roles of fine vs coarse roots this could have large implications for below-ground C cycling. Our results highlight the importance of direct effects vs indirect effects (such as changes in plant community composition and nutrient availability) of climate change for future C allocation above and below ground.

  • 34.
    Bollhöner, Benjamin
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Significance of hydrolytic enzymes expressed during xylem cell death2013Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [sv]

    Xylem är en karakteristisk vävnad i alla kärlväxter som leder vatten och mineraler samt har mekanisk stödfunktion. För att effektivt kunna transportera vatten förstärks xylemceller med sekundära cellväggar innan de dör genom programmerad celldöd. Deras cellinnehåll bryts ner genom autolys för att skapa ett ihåligt rör. Xylemceller uttrycker under sin differentiering olika hydrolytiska enzymer, såsom proteaser, lipaser och nukleaser, men bara för ett fåtal av dessa har funktionen under xylemcelldöd kartlagts. Denna avhandling fokuserar på reglering av xylemcelldöden och den autolytiska nedbrytningen av cellen, i såväl kärlelement och fibrer av hybridasp (Populus tremula L. x tremuloides Michx.) som i kärlelement av backtrav (Arabidopsis thaliana). Med hjälp av jämförande transkriptomanalys identifierades kandidatgener för fiber-specifika celldödsprocesser i hybridasp. Vidare utvecklades en hypotes om reglering av termosperminnivåer i vaskulaturen genom en negativ feedback-loop, som omfattar auxin reglering och klass III homeodomän-leucinzipper (HD-ZIP III) transkriptionsfaktorn HOMEOBOX8 (PtHB8). Funktionen av Arabidopsis METACASPASE9 (AtMC9) under xylemcelldöd karakteriserades med molekylära verktyg, såsom reporterlinjer och fluorescerande fusionsproteiner och elektronmikroskopi (TEM). Dessa analyser visade att celldödens initiering inte styrs av AtMC9. Istället presenteras bevis för en roll av AtMC9 i autolysen av kärlelement som sker post mortem efter att vakuolen har gått sönder och som slutför bildandet av det tomma kärlet. Genuttryck som associeras med celldöd observerades också under utvecklingen av laterala rötter i Arabidopsis thaliana. Detta ledde till upptäckten att celler som ligger ovanför ett lateralrotprimordium dör en programmerad celldöd och visar tecken på DNA-nedbrytning och autolys i TEM-analyser. Slutsatsen av denna studie är att celldöd i samspel med cellväggsmodifiering underlättar utväxten av laterala rötter genom de överliggande cellagren. Sammantaget tyder dessa upptäckter på att även om enstaka hydrolyserande enzymer inte är nödvändiga för växternas tillväxt och utveckling, så kan deras gemensamma reglering nyttjas för att förstå deras funktion och betydelse.

  • 35.
    Bollhöner, Benjamin
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Voss, Ute
    Prestele, Jakob
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Wilson, Michael
    Kenobi, Kim
    Viotti, Corrado
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    André, Domenique
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Lers, Amnon
    Bennett, Malcolm
    Tuominen, Hannele
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Programmed cell death in overlying tissues facilitates lateral root emergenceManuskript (preprint) (Övrigt vetenskapligt)
  • 36.
    Bollhöner, Benjamin
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Zhang, Bo
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Stael, Simon
    Denancé, Nicolas
    Overmyer, Kirk
    Goffner, Deborah
    Van Breusegem, Frank
    Tuominen, Hannele
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Post mortem function of AtMC9 in xylem vessel elements2013Ingår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 200, nr 2, s. 498-510Artikel i tidskrift (Refereegranskat)
    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.

  • 37. Boone, Celia K
    et al.
    Keefover-Ring, Ken
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Mapes, Abigail C
    Adams, Aaron S
    Bohlmann, Jörg
    Raffa, Kenneth F
    Bacteria associated with a tree-killing insect reduce concentrations of plant defense compounds2013Ingår i: Journal of Chemical Ecology, ISSN 0098-0331, E-ISSN 1573-1561, Vol. 39, nr 7, s. 1003-1006Artikel i tidskrift (Refereegranskat)
  • 38.
    Boussardon, Clément
    et al.
    Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France.
    Martin-Magniette, Marie-Laure
    Godin, Béatrice
    Benamar, Abdelilah
    Vittrant, Benjamin
    Citerne, Sylvie
    Mary-Huard, Tristan
    Macherel, David
    Rajjou, Loïc
    Budar, Françoise
    Novel Cytonuclear Combinations Modify Arabidopsis thaliana Seed Physiology and Vigor2019Ingår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 10, artikel-id 32Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Dormancy and germination vigor are complex traits of primary importance for adaptation and agriculture. Intraspecific variation in cytoplasmic genomes and cytonuclear interactions were previously reported to affect germination in Arabidopsis using novel cytonuclear combinations that disrupt co-adaptation between natural variants of nuclear and cytoplasmic genomes. However, specific aspects of dormancy and germination vigor were not thoroughly explored, nor the parental contributions to the genetic effects. Here, we specifically assessed dormancy, germination performance and longevity of seeds from Arabidopsis plants with natural and new genomic compositions. All three traits were modified by cytonuclear reshuffling. Both depth and release rate of dormancy could be modified by a changing of cytoplasm. Significant changes on dormancy and germination performance due to specific cytonuclear interacting combinations mainly occurred in opposite directions, consistent with the idea that a single physiological consequence of the new genetic combination affected both traits oppositely. However, this was not always the case. Interestingly, the ability of parental accessions to contribute to significant cytonuclear interactions modifying the germination phenotype was different depending on whether they provided the nuclear or cytoplasmic genetic compartment. The observed deleterious effects of novel cytonuclear combinations (in comparison with the nuclear parent) were consistent with a contribution of cytonuclear interactions to germination adaptive phenotypes. More surprisingly, we also observed favorable effects of novel cytonuclear combinations, suggesting suboptimal genetic combinations exist in natural populations for these traits. Reduced sensitivity to exogenous ABA and faster endogenous ABA decay during germination were observed in a novel cytonuclear combination that also exhibited enhanced longevity and better germination performance, compared to its natural nuclear parent. Taken together, our results strongly support that cytoplasmic genomes represent an additional resource of natural variation for breeding seed vigor traits.

  • 39.
    Boutté, Yohann
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Men, Shuzhen
    Grebe, Markus
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Fluorescent in situ visualization of sterols in Arabidopsis roots2011Ingår i: Nature Protocols, ISSN 1754-2189, E-ISSN 1750-2799, Vol. 6, nr 4, s. 446-456Artikel i tidskrift (Refereegranskat)
    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.

  • 40.
    Brackmann, Klaus
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Contribution of endocytic trafficking and epidermal morphology genes to planar polarity formation in the Arabidopsis root epidermis2010Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
  • 41.
    Brouwer, Bastiaan
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Gardeström, Per
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Keech, Olivier
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    In response to partial plant shading, the lack of phytochrome A does not directly induce leaf senescence but alters the fine-tuning of chlorophyll biosynthesis2014Ingår i: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 65, nr 14, s. 4037-4049Artikel i tidskrift (Refereegranskat)
    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.

  • 42. BRUNES, L
    et al.
    Öquist, Gunnar
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    ELIASSON, L
    ON THE REASON FOR THE DIFFERENT PHOTOSYNTHETIC RATES OF SEEDLINGS OF PINUS-SILVESTRIS AND BETULA-VERRUCOSA1980Ingår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 66, nr 5, s. 940-944Artikel i tidskrift (Refereegranskat)
  • 43.
    Brunoni, Federica
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Ljung, Karin
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Bellini, Catherine
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Control of root meristem establishment in conifers2019Ingår i: Physiologia Plantarum: An International Journal for Plant Biology, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 165, nr 1, s. 81-89Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The evolution of terrestrial plant life was made possible by the establishment of a root system, which enabled plants to migrate from aquatic to terrestrial habitats. During evolution, root organization has gradually progressed from a very simple to a highly hierarchical architecture. Roots are initiated during embryogenesis and branch afterward through lateral root formation. Additionally, adventitious roots can be formed post-embryonically from aerial organs. Induction of adventitious roots (ARs) forms the basis of the vegetative propagation via cuttings in horticulture, agriculture and forestry. This method, together with somatic embryogenesis, is routinely used to clonally multiply conifers. In addition to being utilized as propagation techniques, adventitious rooting and somatic embryogenesis have emerged as versatile models to study cellular and molecular mechanisms of embryo formation and organogenesis of coniferous species. Both formation of the embryonic root and the AR primordia require the establishment of auxin gradients within cells that coordinate the developmental response. These processes also share key elements of the genetic regulatory networks that, e.g. are triggering cell fate. This minireview gives an overview of the molecular control mechanisms associated with root development in conifers, from initiation in the embryo to post-embryonic formation in cuttings.

  • 44.
    Buckland, Philip I.
    Umeå universitet, Humanistiska fakulteten, Institutionen för idé- och samhällsstudier, Miljöarkeologiska laboratoriet. Umeå universitet, Humanistiska fakulteten, Humlab.
    SEAD - The Strategic Environmental Archaeology Database Inter-linking Multiproxy Environmental Data with Archaeological Investigations and Ecology2013Ingår i: Archaeology in the Digital Era: Papers from the 40th Annual Conference of Computer Applications and Quantitative Methods in Archaeology (CAA), Southampton, 26-29 March 2012 / [ed] Graeme Earl, Tim Sly, Angeliki Chrysanthi, Patricia Murrieta-Flores, Constantinos Papadopoulos, Iza Romanowska & David Wheatley, Amsterdam University Press, 2013, Vol. 1, s. 320-331Konferensbidrag (Refereegranskat)
    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.

  • 45.
    Buckland, Philip I.
    et al.
    Umeå universitet, Humanistiska fakulteten, Institutionen för idé- och samhällsstudier, Miljöarkeologiska laboratoriet.
    Eriksson, Erik J.
    Umeå universitet, Humanistiska fakulteten, Institutionen för idé- och samhällsstudier, Miljöarkeologiska laboratoriet.
    Palm, Fredrik
    Umeå universitet, Humanistiska fakulteten, Humlab.
    SEAD - The Strategic Environmental Archaeology Database: Progress Report Spring 20142014Rapport (Övrigt vetenskapligt)
    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.

  • 46.
    Burdon, Jeremy J.
    et al.
    CSIRO-Plant Industry, Canberra, Australia.
    Thrall, Peter H.
    CSIRO-Plant Industry, Canberra, Australia.
    Ericson, Lars
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    The current and future dynamics of disease in plant communities2006Ingår i: Annual Review of Phytopathology, ISSN 0066-4286, E-ISSN 1545-2107, Vol. 44, s. 19-39Artikel i tidskrift (Refereegranskat)
    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.

  • 47.
    Bygdell, Joakim
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Srivastava, Vaibhav
    Obudulu, Ogonna
    Srivastava, Manoj K.
    Nilsson, Robert
    Sundberg, Björn
    Trygg, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Mellerowicz, Ewa J.
    Wingsle, Gunnar
    Protein expression in tension wood formation monitored at high tissue resolution in Populus2017Ingår i: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 68, nr 13, s. 3405-3417Artikel i tidskrift (Refereegranskat)
    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.

  • 48.
    Båmstedt, Ulf
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå marina forskningscentrum (UMF).
    Wikner, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå marina forskningscentrum (UMF).
    Mixing depth and allochthonous dissolved organic carbon: controlling factors of coastal trophic balance2016Ingår i: Marine Ecology Progress Series, ISSN 0171-8630, E-ISSN 1616-1599, Vol. 561, s. 17-29Artikel i tidskrift (Refereegranskat)
    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.

  • 49. Capovilla, Giovanna
    et al.
    Delhomme, Nicolas
    Collani, Silvio
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tübingen, Germany.
    Shutava, Iryna
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Bezrukov, Ilja
    Symeonidi, Efthymia
    Amorim, Marcella de Francisco
    Laubinger, Sascha
    Schmid, Markus
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tübingen, Germany.
    PORCUPINE regulates development in response to temperature through alternative splicing2018Ingår i: Nature plants, ISSN 2055-026X, Vol. 4, nr 8, s. 534-539Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Recent findings suggest that alternative splicing has a critical role in controlling the responses of plants to temperature variations. However, alternative splicing factors in plants are largely uncharacterized. Here we establish the putative splice regulator, PORCUPINE (PCP), as temperature-specific regulator of development in Arabidopsis thaliana. Our findings point to the misregulation of WUSCHEL and CLAVATA3 as the possible cause for the meristem defects affecting the pcp-1 loss-of-function mutants at low temperatures.

  • 50. Capovilla, Giovanna
    et al.
    Pajoro, Alice
    Immink, Richard GH
    Schmid, Markus
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, 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 signaling2015Ingår i: Current opinion in plant biology, ISSN 1369-5266, E-ISSN 1879-0356, Vol. 27, s. 97-103Artikel, forskningsöversikt (Refereegranskat)
    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.

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