| 1. |
- Andelid, Kristina, 1953, et al.
(author)
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Systemic cytokine signaling via IL-17 in smokers with obstructive pulmonary disease: a link to bacterial colonization?
- 2015
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In: International Journal of Chronic Obstructive Pulmonary Disease. - : Informa UK Limited. - 1178-2005. ; 10, s. 689-702
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Journal article (peer-reviewed)abstract
- We examined whether systemic cytokine signaling via interleukin (IL)-17 and growth-related oncogene-alpha (GRO-alpha) is impaired in smokers with obstructive pulmonary disease including chronic bronchitis (OPD-CB). We also examined how this systemic cytokine signaling relates to bacterial colonization in the airways of the smokers with OPD-CB. Currently smoking OPD-CB patients (n=60, corresponding to Global initiative for chronic Obstructive Lung Disease [ GOLD] stage I-IV) underwent recurrent blood and sputum sampling over 60 weeks, during stable conditions and at exacerbations. We characterized cytokine protein concentrations in blood and bacterial growth in sputum. Asymptomatic smokers (n=10) and never-smokers (n=10) were included as control groups. During stable clinical conditions, the protein concentrations of IL-17 and GRO-alpha were markedly lower among OPD-CB patients compared with never-smoker controls, whereas the asymptomatic smoker controls displayed intermediate concentrations. Notably, among OPD-CB patients, colonization by opportunistic pathogens was associated with markedly lower IL-17 and GRO-alpha, compared with colonization by common respiratory pathogens or oropharyngeal flora. During exacerbations in the OPD-CB patients, GRO-alpha and neutrophil concentrations were increased, whereas protein concentrations and messenger RNA for IL-17 were not detectable in a reproducible manner. In smokers with OPD-CB, systemic cytokine signaling via IL-17 and GRO-alpha is impaired and this alteration may be linked to colonization by opportunistic pathogens in the airways. Given the potential pathogenic and therapeutic implications, these findings deserve to be validated in new and larger patient cohorts.
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| 2. |
- Andelid, Kristina, 1953, et al.
(author)
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Systemic signs of neutrophil mobilization during clinically stable periods and during exacerbations in smokers with obstructive pulmonary disease
- 2015
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In: International Journal of Chronic Obstructive Pulmonary Disease. - : Informa UK Limited. - 1178-2005. ; 10, s. 1253-1263
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Journal article (peer-reviewed)abstract
- Background: It is still unclear whether signs of neutrophil mobilization in the blood of patients with chronic obstructive pulmonary disease represent true systemic events and how these relate to bacterial colonization in the airways. In this study, we evaluated these issues during clinically stable periods and during exacerbations in smokers with obstructive pulmonary disease and chronic bronchitis (OPD-CB). Methods: Over a period of 60 weeks for each subject, blood samples were repeatedly collected from 60 smokers with OPD-CB during clinically stable periods, as well as during and after exacerbations. Myeloperoxidase (MPO) and neutrophil elastase (NE) protein and mRNA, growth of bacteria in sputum, and clinical parameters were analyzed. Ten asymptomatic smokers and ten never-smokers were included as controls. Results: We found that, during clinically stable periods, neutrophil and NE protein concentrations were increased in smokers with OPD-CB and in the asymptomatic smokers when compared with never-smokers. During exacerbations, neutrophil and MPO protein concentrations were further increased in smokers with OPD-CB, without a detectable increase in the corresponding mRNA during exacerbations. However, MPO and NE protein and mRNA displayed positive correlations. During exacerbations, only increased neutrophil concentrations were associated with growth of bacteria in sputum. Among patients with low transcutaneous oxygen saturation during exacerbations, PaO2 (partial oxygen pressure) correlated with concentrations of MPO and NE protein and neutrophils in a negative manner. Conclusion: There are signs of systemic neutrophil mobilization during clinically stable periods and even more so during exacerbations in chronic obstructive pulmonary disease. In this condition, MPO and NE may share a cellular origin, but its location remains uncertain. Factors other than local bacteria, including hypoxemia, may be important for driving systemic signs of neutrophil mobilization.
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| 3. |
- Chrobok, Daria, et al.
(author)
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Dissecting the Metabolic Role of Mitochondria during Developmental Leaf Senescence
- 2016
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In: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 172:4, s. 2132-2153
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Journal article (peer-reviewed)abstract
- The functions of mitochondria during leaf senescence, a type of programmed cell death aimed at the massive retrieval of nutrients from the senescing organ to the rest of the plant, remain elusive. Here, combining experimental and analytical approaches, we showed that mitochondrial integrity in Arabidopsis (Arabidopsis thaliana) is conserved until the latest stages of leaf senescence, while their number drops by 30%. Adenylate phosphorylation state assays and mitochondrial respiratory measurements indicated that the leaf energy status also is maintained during this time period. Furthermore, after establishing a curated list of genes coding for products targeted to mitochondria, we analyzed in isolation their transcript profiles, focusing on several key mitochondrial functions, such as the tricarboxylic acid cycle, mitochondrial electron transfer chain, iron-sulfur cluster biosynthesis, transporters, as well as catabolic pathways. In tandem with a metabolomic approach, our data indicated that mitochondrial metabolism was reorganized to support the selective catabolism of both amino acids and fatty acids. Such adjustments would ensure the replenishment of alpha-ketoglutarate and glutamate, which provide the carbon backbones for nitrogen remobilization. Glutamate, being the substrate of the strongly up-regulated cytosolic glutamine synthase, is likely to become a metabolically limiting factor in the latest stages of developmental leaf senescence. Finally, an evolutionary age analysis revealed that, while branched-chain amino acid and proline catabolism are very old mitochondrial functions particularly enriched at the latest stages of leaf senescence, auxin metabolism appears to be rather newly acquired. In summation, our work shows that, during developmental leaf senescence, mitochondria orchestrate catabolic processes by becoming increasingly central energy and metabolic hubs.
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| 4. |
- Law, Simon R., et al.
(author)
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Darkened leaves use different metabolic strategies for senescence and survival
- 2018
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In: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 177:1, s. 132-150
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Journal article (peer-reviewed)abstract
- In plants, an individually darkened leaf initiates senescence much more rapidly than a leaf from a whole darkened plant. Combining transcriptomic and metabolomic approaches in Arabidopsis (Arabidopsis thaliana), we present an overview of the metabolic strategies that are employed in response to different darkening treatments. Under darkened plant conditions, the perception of carbon starvation drove a profound metabolic readjustment in which branched-chain amino acids and potentially monosaccharides released from cell wall loosening became important substrates for maintaining minimal ATP production. Concomitantly, the increased accumulation of amino acids with a high nitrogen-carbon ratio may provide a safety mechanism for the storage of metabolically derived cytotoxic ammonium and a pool of nitrogen for use upon returning to typical growth conditions. Conversely, in individually darkened leaf, the metabolic profiling that followed our 13C-enrichment assays revealed a temporal and differential exchange of metabolites, including sugars and amino acids, between the darkened leaf and the rest of the plant. This active transport could be the basis for a progressive metabolic shift in the substrates fueling mitochondrial activities, which are central to the catabolic reactions facilitating the retrieval of nutrients from the senescing leaf. We propose a model illustrating the specific metabolic strategies employed by leaves in response to these two darkening treatments, which support either rapid senescence or a strong capacity for survival.
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| 5. |
- Levanen, B., et al.
(author)
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Impact of tobacco smoking on cytokine signaling via interleukin-17A in the peripheral airways
- 2016
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In: International Journal of Chronic Obstructive Pulmonary Disease. - : Informa UK Limited. - 1178-2005. ; 11, s. 2109-2116
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Journal article (peer-reviewed)abstract
- There is excessive accumulation of neutrophils in the airways in chronic obstructive pulmonary disease (COPD) but the underlying mechanisms remain poorly understood. It is known that extracellular cytokine signaling via interleukin (IL)-17A contributes to neutrophil accumulation in the airways but nothing is known about the impact of tobacco smoking on extracellular signaling via IL-17A. Here, we characterized the impact of tobacco smoking on extracellular cytokine signaling via IL-17A in the peripheral airways in long-term smokers with and without COPD and in occasional smokers before and after short-term exposure to tobacco smoke. We quantified concentrations of IL-17A protein in cell-free bronchoalveolar lavage (BAL) fluid samples (Immuno-quantitative PCR) and cytotoxic T-cells (immunoreactivity for CD8(+) and CD3(+)) in bronchial biopsies. Matrix metalloproteinase-8 and human beta defensin 2 proteins were also quantified (enzyme-linked immunosorbent assay) in the BAL samples. The concentrations of IL-17A in BAL fluid were higher in long-term smokers without COPD compared with nonsmoking healthy controls, whereas those with COPD did not differ significantly from either of the other groups. Short-term exposure to tobacco smoke did not induce sustained alterations in these concentrations in occasional smokers. Long-term smokers displayed higher concentrations of IL-17A than did occasional smokers. Moreover, these concentrations correlated with CD8(+) and CD3(+) cells in biopsies among long-term smokers with COPD. In healthy nonsmokers, BAL concentrations of matrix metalloproteinase-8 and IL-17A correlated, whereas this was not the case in the pooled group of long-term smokers with and without COPD. In contrast, BAL concentrations of human beta defensin 2 and IL-17A correlated in all study groups. This study implies that long-term but not short-term exposure to tobacco smoke increases extracellular cytokine signaling via IL-17A in the peripheral airways. In the smokers with COPD, this signaling may involve cytotoxic T-cells. Long-term exposure to tobacco smoke leads to a disturbed association of extracellular IL-17A signaling and matrix metalloproteinase-8, of potential importance for the coordination of antibacterial activity.
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| 6. |
- Liebsch, Daniela, et al.
(author)
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Metabolic adjustments required for extended leaf longevity under prolonged darkness revealed by a new loss of function allele of PIF5
- 2018
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Other publication (other academic/artistic)abstract
- Senescence is regulated by a complex interplay of factors and regulatory circuits, which may be accelerated or delayed depending on the integrated signals. Using a forward genetic screen in Arabidopsis thaliana, we identified a mutant strongly delayed in its induction of senescence in response to prolonged darkness. This mutant, which corresponds to a novel loss-of-function allele of PIF5 (PHYTOCHROME-INTERACTING FACTOR 5), exhibits even slightly more extended survival of leaves in darkness than the previously reported pif5-3 TDNA knock-out line. In the present study, we additionally aimed at deciphering the metabolic and regulatory processes conferring this enhanced capacity for survival in pif5 mutants. We combined physiological, metabolomic and transcriptomic analyses, and discovered that the extended survival of mutant leaves in darkness was associated with reduced protein degradation, slight differences in amino acid catabolism related gene expression as well as strong reduction of amino acid transporter expression, which coincided with enhanced amino acid accumulation. Our findings suggest that enhanced survival in darkness could be mediated by moderate levels of protein degradation allowing build up and slow usage of amino acids as alternative respiratory substrates, while during irreversible senescence, strong degradative processes, together with enhanced amino acid transport either to the site of their metabolization inside the leaf, or to other organs in the plant, could promote the fast progression of senescence and antagonize survival. Comparative metabolomics and gene expression analyses suggested that the senescence regulatory network downstream of PIF5 organizes these irreversible stages of leaf senescence, promoting autophagy and amino acid export, possibly by direct binding of important senescence promoting factors like ORE1 to the promoters of some of the involved genes. The failure to induce these later stages may prolong the reversible phase of darkening, thus potentially leading to drastically increased viability of individually darkened leaves under darkness for over 2 weeks.
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| 7. |
- Lindén, Malin, et al.
(author)
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FET family fusion oncoproteins target the SWI/SNF chromatin remodeling complex
- 2019
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In: EMBO Reports. - : EMBO. - 1469-221X .- 1469-3178. ; 20
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Journal article (peer-reviewed)abstract
- Members of the human FET family of RNA-binding proteins, comprising FUS, EWSR1, and TAF15, are ubiquitously expressed and engage at several levels of gene regulation. Many sarcomas and leukemias are characterized by the expression of fusion oncogenes with FET genes as 5′ partners and alternative transcription factor-coding genes as 3′ partners. Here, we report that the N terminus of normal FET proteins and their oncogenic fusion counterparts interact with the SWI/SNF chromatin remodeling complex. In contrast to normal FET proteins, increased fractions of FET oncoproteins bind SWI/SNF, indicating a deregulated and enhanced interaction in cancer. Forced expression of FET oncogenes caused changes of global H3K27 trimethylation levels, accompanied by altered gene expression patterns suggesting a shift in the antagonistic balance between SWI/SNF and repressive polycomb group complexes. Thus, deregulation of SWI/SNF activity could provide a unifying pathogenic mechanism for the large group of tumors caused by FET fusion oncoproteins. These results may help to develop common strategies for therapy. © 2019 The Authors. Published under the terms of the CC BY 4.0 license
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| 8. |
- Linden, Pernilla, et al.
(author)
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Integrated analysis of gene expression from carbon metabolism, proteome and metabolome, reveals altered primary metabolism in Eucalyptus grandis bark, in response to seasonal variation
- 2016
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In: BMC Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 16
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Journal article (peer-reviewed)abstract
- Background: Seasonal variation is presumed to play an important role in the regulation of tree growth, especially for Eucalyptus grandis, a fast-growing tree. This variation may induce changes in the whole tree at transcriptional, protein and metabolite levels. Bark represents an important group of tissues that protect trees from desiccation and pathogen attack, and it has been identified as potential feedstock for lignocellulosic derived biofuels. Despite the growing interest, little is known about the molecular mechanisms that regulates bark metabolism, particularly in tropical countries.Results: In this study we report the changes observed in the primary metabolism of E. grandis bark during two contrasting seasons in Brazil, summer (wet) and winter (dry), through the combination of transcripts (RT-qPCR), proteome (2-DE gels) and metabolome (GC-MS) analysis, in an integrated manner. Twenty-four genes, involved in carbon metabolism, were analyzed in the two seasons. Eleven were up-regulated in summer, three were up-regulated in winter and ten did not show statistical differences in the expression pattern. The proteomic analysis using 2-DE gels showed 77 proteins expressing differences in abundance, with 38 spots up-regulated in summer and 37 in winter. Different metabolites significantly accumulated during winter.Conclusions: This study revealed a metabolic reconfiguration in the primary metabolism of E. grandis bark, triggered by seasonal variation. Transcripts and protein data suggests that during winter carbohydrate formation seems to be favored by tree metabolism. Glucose, fructose and sucrose accumulated at significant levels during the winter.
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| 9. |
- Linden, Pernilla
(author)
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Monitoring primary carbon metabolism in plants using heavy isotope labelling and mass spectrometry : ¹³CO₂ labelling, detection and estimation in intact plants
- 2015
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Doctoral thesis (other academic/artistic)abstract
- This thesis covers the possibilities and limitations of studying primary metabolism in intact plants, with special focus on heavy isotope labelling and mass spectrometry methodology. In paper I, a series of Arabidopsis thaliana mutants lacking one or both genes of mitochondrial malate dehydrogenase (mMDH characterised) were characterised. We found that mMDH has a complex respiration-controlling role. In paper II, we continued to study one of the single mutants, mmdh1. We developed a method using ¹³CO₂ to label whole plants and analyse their metabolic profiles by gas and liquid chromatography coupled to mass spectrometry (GC- and LC-MS). The results show that mmdh1 had a metabolic phenotype that revealed an altered flux through photorespiration, especially under low CO₂ conditions. Combining incorporation data with metabolite pool size deepened our understanding regarding the role of mMDH in photorespiration, respiration, and cellular redox balance. The practical and theoretical aspects of ¹³C-labelling of plants learned from this study were used for designing the experimental setup of paper III, a labelling study of developing wood in hybrid aspen. The labelling strategy, time resolution, and sampling had to be adapted to suit woody plants. Two months old trees were labelled with ¹³CO₂ in a 4 h burst and then sampling of source leaves, stem phloem, and developing wood continued over 24 hours. Since sucrose is the main carbon transporter the analysis was concentrated around this metabolite. We found previously unrecognised temporal patterns in wood biosynthesis and an indication that the diurnal cycle serves as a cue in the regulation of carbon allocation in developing wood. To study systems with complex structures such as plants, it is informative to study specific cell types rather than whole plants or whole organs. In paper IV, a method was developed for analysis of metabolite profiles in cell type specific cells. Isolated protoplast from Arabidopsis roots were sorted by fluorescence-activated cell sorting (FACS) and their metabolite profiles were analysed by GC-MS. The method is fast, robust and reliable for analysis of cell type specific metabolic profiling and a beginning to meet the call for new metabolite analysis techniques with a high spatial resolution.
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| 10. |
- Linden, Pernilla, et al.
(author)
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Reduced mitochondrial malate dehydrogenase activity has a strong effect on photorespiratory metabolism as revealed by 13C labelling
- 2016
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In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 67:10, s. 3123-3135
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Journal article (peer-reviewed)abstract
- Mitochondrial malate dehydrogenase (mMDH) catalyses the interconversion of malate and oxaloacetate (OAA) in the tricarboxylic acid (TCA) cycle. Its activity is important for redox control of the mitochondrial matrix, through which it may participate in regulation of TCA cycle turnover. In Arabidopsis, there are two isoforms of mMDH. Here, we investigated to which extent the lack of the major isoform, mMDH1 accounting for about 60% of the activity, affected leaf metabolism. In air, rosettes of mmdh1 plants were only slightly smaller than wild type plants although the fresh weight was decreased by about 50%. In low CO2 the difference was much bigger, with mutant plants accumulating only 14% of fresh weight as compared to wild type. To investigate the metabolic background to the differences in growth, we developed a 13CO2 labelling method, using a custom-built chamber that enabled simultaneous treatment of sets of plants under controlled conditions. The metabolic profiles were analysed by gas- and liquid- chromatography coupled to mass spectrometry to investigate the metabolic adjustments between wild type and mmdh1. The genotypes responded similarly to high CO2 treatment both with respect to metabolite pools and 13C incorporation during a 2-h treatment. However, under low CO2 several metabolites differed between the two genotypes and, interestingly most of these were closely associated with photorespiration. We found that while the glycine/serine ratio increased, a concomitant altered glutamine/glutamate/α-ketoglutarate relation occurred. Taken together, our results indicate that adequate mMDH activity is essential to shuttle reductants out from the mitochondria to support the photorespiratory flux, and strengthen the idea that photorespiration is tightly intertwined with peripheral metabolic reactions.
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| 11. |
- Linden, Pernilla, et al.
(author)
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Seasonal Variation of Carbon Metabolism in the Cambial Zone of Eucalyptus grandis
- 2016
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In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 7
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Journal article (peer-reviewed)abstract
- Eucalyptus species are the most widely hardwood planted in the world. It is one of the successful examples of commercial forestry plantation in Brazil and other tropical and subtropical countries. The tree is valued for its rapid growth, adaptability and wood quality. Wood formation is the result of cumulative annual activity of the vascular cambium. This cambial activity is generally related to the alternation of cold and warm, and/or dry and rainy seasons. Efforts have focused on analysis of cambial zone in response to seasonal variations in trees from temperate zones. However, little is known about the molecular changes triggered by seasonal variations in trees from tropical countries. In this work we attempted to establish a global view of seasonal alterations in the cambial zone of Eucalyptus grandis Hill ex Maiden, emphasizing changes occurring in the carbon metabolism. Using transcripts, proteomics and metabolomics we analyzed the tissues harvested in summer -wet and winter -dry seasons. Based on proteomics analysis, 70 proteins that changed in abundance were successfully identified. Transcripts for some of these proteins were analyzed and similar expression patterns were observed. We identified 19 metabolites differentially abundant. Our results suggest a differential reconfiguration of carbon partioning in E. grandis cambial zone. During summer, pyruvate is primarily metabolized via ethanolic fermentation, possibly to regenerate NAD+ for glycolytic ATP production and cellular maintenance. However, in winter there seems to be a metabolic change and we found that some sugars were highly abundant. Our results revealed a dynamic change in E. grandis cambial zone due to seasonality and highlight the importance of glycolysis and ethanolic fermentation for energy generation and maintenance in Eucalyptus, a fast growing tree.
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| 12. |
- Mahboubi, Miramirhossein, et al.
(author)
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C-13 Tracking after (CO2)-C-13 Supply Revealed Diurnal Patterns of Wood Formation in Aspen
- 2015
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In: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 168, s. 478-489
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Journal article (peer-reviewed)abstract
- Wood of trees is formed from carbon assimilated in the photosynthetic tissues. Determining the temporal dynamics of carbon assimilation, subsequent transport into developing wood, and incorporation to cell walls would further our understanding of wood formation in particular and tree growth in general. To investigate these questions, we designed a (CO2)-C-13 labeling system to study carbon transport and incorporation to developing wood of hybrid aspen (Populus tremula 3 tremuloides). Tracking of C-13 incorporation to wood over a time course using nuclear magnetic resonance spectroscopy revealed diurnal patterns in wood cell wall biosynthesis. The dark period had a differential effect on C-13 incorporation to lignin and cell wall carbohydrates. No C-13 was incorporated into aromatic amino acids of cell wall proteins in the dark, suggesting that cell wall protein biosynthesis ceased during the night. The results show previously unrecognized temporal patterns in wood cell wall biosynthesis, suggest diurnal cycle as a possible cue in the regulation of carbon incorporation to wood, and establish a unique C-13 labeling method for the analysis of wood formation and secondary growth in trees.
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| 13. |
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