Niittylä, Totte - Carbon Allocation and Metabolism

@article{bas_influence_2025,
	title = {Influence of {TEMPO} on preparation of softwood nanofibrils and their hydrogel network properties},
	volume = {348},
	issn = {0144-8617},
	url = {https://www.sciencedirect.com/science/article/pii/S0144861724010385},
	doi = {10.1016/j.carbpol.2024.122812},
	abstract = {From an economic and environmental perspective, the use of less chemicals in the production of cellulose nanofibrils (CNFs) is advantageous. In this study, we investigated the oxidation (TEMPO/NaClO2/NaClO, pH 6.8) of softwood (SW) particles with varying amounts of TEMPO (16, 8 or 0 mg g−1 of wood). Following, TEMPO-oxidized SW nanofibrils (TO-SWNFs) were obtained by nanofibrillation and their size, morphology, and crystallite size were assessed. Hydrogel networks of TO-SWNFs were prepared and mechanical properties were measured in dH2O and phosphate buffered saline (PBS) to compare their performance for possible biomedical applications such as wound dressings. The results reveal that the presence of TEMPO is of importance for TO-SWNF network properties, presenting higher eq. H2O absorption (≈2500 \%) and elongation at break (≈10 \%) with good wet strength (≈180 kPa). In addition, a decrease in use of TEMPO catalyst from 16 to 8 mg g−1 of wood is possible, without detrimental effects on hydrogel network properties (dH2O absorption ≈ 2000 \%, elongation at break ≈ 13 \%, wet strength ≈ 190 kPa) related to applications as wound dressings.},
	urldate = {2024-10-18},
	journal = {Carbohydrate Polymers},
	author = {Baş, Yağmur and Berglund, Linn and Stevanic, Jasna S. and Scheepers, Gerhard and Niittylä, Totte and Oksman, Kristiina},
	month = jan,
	year = {2025},
	keywords = {Absorption, Cellulose nanofibrils, Hydrogel network, TEMPO-oxidation, Wood},
	pages = {122812},
}

From an economic and environmental perspective, the use of less chemicals in the production of cellulose nanofibrils (CNFs) is advantageous. In this study, we investigated the oxidation (TEMPO/NaClO2/NaClO, pH 6.8) of softwood (SW) particles with varying amounts of TEMPO (16, 8 or 0 mg g−1 of wood). Following, TEMPO-oxidized SW nanofibrils (TO-SWNFs) were obtained by nanofibrillation and their size, morphology, and crystallite size were assessed. Hydrogel networks of TO-SWNFs were prepared and mechanical properties were measured in dH2O and phosphate buffered saline (PBS) to compare their performance for possible biomedical applications such as wound dressings. The results reveal that the presence of TEMPO is of importance for TO-SWNF network properties, presenting higher eq. H2O absorption (≈2500 %) and elongation at break (≈10 %) with good wet strength (≈180 kPa). In addition, a decrease in use of TEMPO catalyst from 16 to 8 mg g−1 of wood is possible, without detrimental effects on hydrogel network properties (dH2O absorption ≈ 2000 %, elongation at break ≈ 13 %, wet strength ≈ 190 kPa) related to applications as wound dressings.

@article{bernacka-wojcik_flexible_2023,
	title = {Flexible {Organic} {Electronic} {Ion} {Pump} for {Flow}-{Free} {Phytohormone} {Delivery} into {Vasculature} of {Intact} {Plants}},
	volume = {10},
	issn = {2198-3844},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/advs.202206409},
	doi = {10.1002/advs.202206409},
	abstract = {Plant vasculature transports molecules that play a crucial role in plant signaling including systemic responses and acclimation to diverse environmental conditions. Targeted controlled delivery of molecules to the vascular tissue can be a biomimetic way to induce long distance responses, providing a new tool for the fundamental studies and engineering of stress-tolerant plants. Here, a flexible organic electronic ion pump, an electrophoretic delivery device, for controlled delivery of phytohormones directly in plant vascular tissue is developed. The c-OEIP is based on polyimide-coated glass capillaries that significantly enhance the mechanical robustness of these microscale devices while being minimally disruptive for the plant. The polyelectrolyte channel is based on low-cost and commercially available precursors that can be photocured with blue light, establishing much cheaper and safer system than the state-of-the-art. To trigger OEIP-induced plant response, the phytohormone abscisic acid (ABA) in the petiole of intact Arabidopsis plants is delivered. ABA is one of the main phytohormones involved in plant stress responses and induces stomata closure under drought conditions to reduce water loss and prevent wilting. The OEIP-mediated ABA delivery triggered fast and long-lasting stomata closure far away from the delivery point demonstrating systemic vascular transport of the delivered ABA, verified delivering deuterium-labeled ABA.},
	language = {en},
	number = {14},
	urldate = {2023-05-26},
	journal = {Advanced Science},
	author = {Bernacka-Wojcik, Iwona and Talide, Loïc and Abdel Aziz, Ilaria and Simura, Jan and Oikonomou, Vasileios K. and Rossi, Stefano and Mohammadi, Mohsen and Dar, Abdul Manan and Seitanidou, Maria and Berggren, Magnus and Simon, Daniel T. and Tybrandt, Klas and Jonsson, Magnus P. and Ljung, Karin and Niittylä, Totte and Stavrinidou, Eleni},
	month = may,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/advs.202206409},
	keywords = {bioelectronic devices, drug delivery, photo-crosslinking, plants vasculature, polyelectrolytes},
	pages = {2206409},
}

Plant vasculature transports molecules that play a crucial role in plant signaling including systemic responses and acclimation to diverse environmental conditions. Targeted controlled delivery of molecules to the vascular tissue can be a biomimetic way to induce long distance responses, providing a new tool for the fundamental studies and engineering of stress-tolerant plants. Here, a flexible organic electronic ion pump, an electrophoretic delivery device, for controlled delivery of phytohormones directly in plant vascular tissue is developed. The c-OEIP is based on polyimide-coated glass capillaries that significantly enhance the mechanical robustness of these microscale devices while being minimally disruptive for the plant. The polyelectrolyte channel is based on low-cost and commercially available precursors that can be photocured with blue light, establishing much cheaper and safer system than the state-of-the-art. To trigger OEIP-induced plant response, the phytohormone abscisic acid (ABA) in the petiole of intact Arabidopsis plants is delivered. ABA is one of the main phytohormones involved in plant stress responses and induces stomata closure under drought conditions to reduce water loss and prevent wilting. The OEIP-mediated ABA delivery triggered fast and long-lasting stomata closure far away from the delivery point demonstrating systemic vascular transport of the delivered ABA, verified delivering deuterium-labeled ABA.

@article{bas_preparation_2023,
	title = {Preparation and {Characterization} of {Softwood} and {Hardwood} {Nanofibril} {Hydrogels}: {Toward} {Wound} {Dressing} {Applications}},
	volume = {24},
	issn = {1525-7797},
	shorttitle = {Preparation and {Characterization} of {Softwood} and {Hardwood} {Nanofibril} {Hydrogels}},
	url = {https://doi.org/10.1021/acs.biomac.3c00596},
	doi = {10.1021/acs.biomac.3c00596},
	abstract = {Hydrogels of cellulose nanofibrils (CNFs) are promising wound dressing candidates due to their biocompatibility, high water absorption, and transparency. Herein, two different commercially available wood species, softwood and hardwood, were subjected to TEMPO-mediated oxidation to proceed with delignification and oxidation in a one-pot process, and thereafter, nanofibrils were isolated using a high-pressure microfluidizer. Furthermore, transparent nanofibril hydrogel networks were prepared by vacuum filtration. Nanofibril properties and network performance correlated with oxidation were investigated and compared with commercially available TEMPO-oxidized pulp nanofibrils and their networks. Softwood nanofibril hydrogel networks exhibited the best mechanical properties, and in vitro toxicological risk assessment showed no detrimental effect for any of the studied hydrogels on human fibroblast or keratinocyte cells. This study demonstrates a straightforward processing route for direct oxidation of different wood species to obtain nanofibril hydrogels for potential use as wound dressings, with softwood having the most potential.},
	number = {12},
	urldate = {2023-12-22},
	journal = {Biomacromolecules},
	author = {Baş, Yağmur and Berglund, Linn and Niittylä, Totte and Zattarin, Elisa and Aili, Daniel and Sotra, Zeljana and Rinklake, Ivana and Junker, Johan and Rakar, Jonathan and Oksman, Kristiina},
	month = dec,
	year = {2023},
	note = {Publisher: American Chemical Society},
	pages = {5605--5619},
}

Hydrogels of cellulose nanofibrils (CNFs) are promising wound dressing candidates due to their biocompatibility, high water absorption, and transparency. Herein, two different commercially available wood species, softwood and hardwood, were subjected to TEMPO-mediated oxidation to proceed with delignification and oxidation in a one-pot process, and thereafter, nanofibrils were isolated using a high-pressure microfluidizer. Furthermore, transparent nanofibril hydrogel networks were prepared by vacuum filtration. Nanofibril properties and network performance correlated with oxidation were investigated and compared with commercially available TEMPO-oxidized pulp nanofibrils and their networks. Softwood nanofibril hydrogel networks exhibited the best mechanical properties, and in vitro toxicological risk assessment showed no detrimental effect for any of the studied hydrogels on human fibroblast or keratinocyte cells. This study demonstrates a straightforward processing route for direct oxidation of different wood species to obtain nanofibril hydrogels for potential use as wound dressings, with softwood having the most potential.

@article{wang_aspen_2022,
	title = {Aspen growth is not limited by starch reserves},
	volume = {32},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982222010181},
	doi = {10.1016/j.cub.2022.06.056},
	abstract = {All photosynthetic organisms balance CO2 assimilation with growth and carbon storage. Stored carbon is used for growth at night and when demand exceeds assimilation. Gaining a mechanistic understanding of carbon partitioning between storage and growth in trees is important for biological studies and for estimating the potential of terrestrial photosynthesis to sequester anthropogenic CO2 emissions.1,2 Starch represents the main carbon storage in plants.3,4 To examine the carbon storage mechanism and role of starch during tree growth, we generated and characterized low-starch hybrid aspen (Populus tremula × tremuloides) trees using CRISPR-Cas9-mediated gene editing of two PHOSPHOGLUCOMUTASE (PGM) genes coding for plastidial PGM isoforms essential for starch biosynthesis. We demonstrate that starch deficiency does not reduce tree growth even in short days, showing that starch is not a critical carbon reserve during diel growth of aspen. The low-starch trees assimilated up to ∼30\% less CO2 compared to the wild type under a range of irradiance levels, but this did not reduce growth or wood density. This implies that aspen growth is not limited by carbon assimilation under benign growth conditions. Moreover, the timing of bud set and bud flush in the low-starch trees was not altered, implying that starch reserves are not critical for the seasonal growth-dormancy cycle. The findings are consistent with a passive starch storage mechanism that contrasts with the annual Arabidopsis and indicate that the capacity of the aspen to absorb CO2 is limited by the rate of sink tissue growth.},
	language = {en},
	number = {16},
	urldate = {2022-10-10},
	journal = {Current Biology},
	author = {Wang, Wei and Talide, Loic and Viljamaa, Sonja and Niittylä, Totte},
	month = aug,
	year = {2022},
	keywords = {Populus, carbon partitioning, phosphoglucomutase, starch},
	pages = {3619--3627.e4},
}

All photosynthetic organisms balance CO2 assimilation with growth and carbon storage. Stored carbon is used for growth at night and when demand exceeds assimilation. Gaining a mechanistic understanding of carbon partitioning between storage and growth in trees is important for biological studies and for estimating the potential of terrestrial photosynthesis to sequester anthropogenic CO2 emissions.1,2 Starch represents the main carbon storage in plants.3,4 To examine the carbon storage mechanism and role of starch during tree growth, we generated and characterized low-starch hybrid aspen (Populus tremula × tremuloides) trees using CRISPR-Cas9-mediated gene editing of two PHOSPHOGLUCOMUTASE (PGM) genes coding for plastidial PGM isoforms essential for starch biosynthesis. We demonstrate that starch deficiency does not reduce tree growth even in short days, showing that starch is not a critical carbon reserve during diel growth of aspen. The low-starch trees assimilated up to ∼30% less CO2 compared to the wild type under a range of irradiance levels, but this did not reduce growth or wood density. This implies that aspen growth is not limited by carbon assimilation under benign growth conditions. Moreover, the timing of bud set and bud flush in the low-starch trees was not altered, implying that starch reserves are not critical for the seasonal growth-dormancy cycle. The findings are consistent with a passive starch storage mechanism that contrasts with the annual Arabidopsis and indicate that the capacity of the aspen to absorb CO2 is limited by the rate of sink tissue growth.

@article{nibbering_cages_2022,
	title = {{CAGEs} are {Golgi}-localized {GT31} enzymes involved in cellulose biosynthesis in {Arabidopsis}},
	volume = {110},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.15734},
	doi = {10.1111/tpj.15734},
	abstract = {Cellulose is the main structural component in the plant cell walls. We show that two glycosyltransferase family 31 (GT31) enzymes of Arabidopsis thaliana, here named cellulose synthesis associated glycosyltransferases 1 and 2 (CAGE1 and 2), influence both primary and secondary cell wall cellulose biosynthesis. cage1cage2 mutants show primary cell wall defects manifesting as impaired growth and cell expansion in seedlings and etiolated hypocotyls, along with secondary cell wall defects, apparent as collapsed xylem vessels and reduced xylem wall thickness in the inflorescence stem. Single and double cage mutants also show increased sensitivity to the cellulose biosynthesis inhibitor isoxaben. The cage1cage2 phenotypes were associated with an approximately 30\% reduction in cellulose content, an approximately 50\% reduction in secondary cell wall CELLULOSE SYNTHASE (CESA) protein levels in stems and reduced cellulose biosynthesis rate in seedlings. CESA transcript levels were not significantly altered in cage1cage2 mutants, suggesting that the reduction in CESA levels was caused by a post-transcriptional mechanism. Both CAGE1 and 2 localize to the Golgi apparatus and are predicted to synthesize β-1,3-galactans on arabinogalactan proteins. In line with this, the cage1cage2 mutants exhibit reduced levels of β-Yariv binding to arabinogalactan protein linked β-1,3-galactan. This leads us to hypothesize that defects in arabinogalactan biosynthesis underlie the cellulose deficiency of the mutants.},
	language = {en},
	number = {5},
	urldate = {2022-06-09},
	journal = {The Plant Journal},
	author = {Nibbering, Pieter and Castilleux, Romain and Wingsle, Gunnar and Niittylä, Totte},
	year = {2022},
	keywords = {Arabidopsis, Golgi, arabinogalactan protein, cell wall, cellulose, glycosyltransferase family 31},
	pages = {1271--1285},
}

Cellulose is the main structural component in the plant cell walls. We show that two glycosyltransferase family 31 (GT31) enzymes of Arabidopsis thaliana, here named cellulose synthesis associated glycosyltransferases 1 and 2 (CAGE1 and 2), influence both primary and secondary cell wall cellulose biosynthesis. cage1cage2 mutants show primary cell wall defects manifesting as impaired growth and cell expansion in seedlings and etiolated hypocotyls, along with secondary cell wall defects, apparent as collapsed xylem vessels and reduced xylem wall thickness in the inflorescence stem. Single and double cage mutants also show increased sensitivity to the cellulose biosynthesis inhibitor isoxaben. The cage1cage2 phenotypes were associated with an approximately 30% reduction in cellulose content, an approximately 50% reduction in secondary cell wall CELLULOSE SYNTHASE (CESA) protein levels in stems and reduced cellulose biosynthesis rate in seedlings. CESA transcript levels were not significantly altered in cage1cage2 mutants, suggesting that the reduction in CESA levels was caused by a post-transcriptional mechanism. Both CAGE1 and 2 localize to the Golgi apparatus and are predicted to synthesize β-1,3-galactans on arabinogalactan proteins. In line with this, the cage1cage2 mutants exhibit reduced levels of β-Yariv binding to arabinogalactan protein linked β-1,3-galactan. This leads us to hypothesize that defects in arabinogalactan biosynthesis underlie the cellulose deficiency of the mutants.

@article{jonasson_characteristics_2022,
	title = {Characteristics of {Cellulose} {Nanofibrils} from {Transgenic} {Trees} with {Reduced} {Expression} of {Cellulose} {Synthase} {Interacting} 1},
	volume = {12},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2079-4991},
	url = {https://www.mdpi.com/2079-4991/12/19/3448},
	doi = {10.3390/nano12193448},
	abstract = {Cellulose nanofibrils can be derived from the native load-bearing cellulose microfibrils in wood. These microfibrils are synthesized by a cellulose synthase enzyme complex that resides in the plasma membrane of developing wood cells. It was previously shown that transgenic hybrid aspen trees with reduced expression of CSI1 have different wood mechanics and cellulose microfibril properties. We hypothesized that these changes in the native cellulose may affect the quality of the corresponding nanofibrils. To test this hypothesis, wood from wild-type and transgenic trees with reduced expression of CSI1 was subjected to oxidative nanofibril isolation. The transgenic wood-extracted nanofibrils exhibited a significantly lower suspension viscosity and estimated surface area than the wild-type nanofibrils. Furthermore, the nanofibril networks manufactured from the transgenics exhibited high stiffness, as well as reduced water uptake, tensile strength, strain-to-break, and degree of polymerization. Presumably, the difference in wood properties caused by the decreased expression of CSI1 resulted in nanofibrils with distinctive qualities. The observed changes in the physicochemical properties suggest that the differences were caused by changes in the apparent nanofibril aspect ratio and surface accessibility. This study demonstrates the possibility of influencing wood-derived nanofibril quality through the genetic engineering of trees.},
	language = {en},
	number = {19},
	urldate = {2022-10-04},
	journal = {Nanomaterials},
	author = {Jonasson, Simon and Bünder, Anne and Berglund, Linn and Niittylä, Totte and Oksman, Kristiina},
	month = oct,
	year = {2022},
	keywords = {cellulose nanofibrils, fibrillation, network properties, transgenic wood},
	pages = {3448},
}

Cellulose nanofibrils can be derived from the native load-bearing cellulose microfibrils in wood. These microfibrils are synthesized by a cellulose synthase enzyme complex that resides in the plasma membrane of developing wood cells. It was previously shown that transgenic hybrid aspen trees with reduced expression of CSI1 have different wood mechanics and cellulose microfibril properties. We hypothesized that these changes in the native cellulose may affect the quality of the corresponding nanofibrils. To test this hypothesis, wood from wild-type and transgenic trees with reduced expression of CSI1 was subjected to oxidative nanofibril isolation. The transgenic wood-extracted nanofibrils exhibited a significantly lower suspension viscosity and estimated surface area than the wild-type nanofibrils. Furthermore, the nanofibril networks manufactured from the transgenics exhibited high stiffness, as well as reduced water uptake, tensile strength, strain-to-break, and degree of polymerization. Presumably, the difference in wood properties caused by the decreased expression of CSI1 resulted in nanofibrils with distinctive qualities. The observed changes in the physicochemical properties suggest that the differences were caused by changes in the apparent nanofibril aspect ratio and surface accessibility. This study demonstrates the possibility of influencing wood-derived nanofibril quality through the genetic engineering of trees.

@article{dominguez_mobile_2022,
	title = {Mobile forms of carbon in trees: metabolism and transport},
	volume = {42},
	issn = {1758-4469},
	shorttitle = {Mobile forms of carbon in trees},
	url = {https://doi.org/10.1093/treephys/tpab123},
	doi = {10.1093/treephys/tpab123},
	abstract = {Plants constitute 80\% of the biomass on earth, and almost two thirds of this biomass is found in wood. Wood formation is a carbon demanding process and relies on carbon transport from photosynthetic tissues. Thus, understanding the transport process is of major interest for understanding terrestrial biomass formation. Here we review the molecules and mechanisms used to transport and allocate carbon in trees. Sucrose is the major form in which carbon is transported, found in the phloem sap of all so far investigated tree species. However, in several tree species sucrose is accompanied by other molecules, notably polyols and the raffinose family of oligosaccharides. We describe the molecules that constitute each of these transport groups, and their distribution across different tree species. Further, we detail the metabolic reactions for their synthesis, the mechanisms by which trees load and unload these compounds in and out of the vascular system, and how they are radially transported in the trunk and finally catabolized during wood formation. We also address a particular carbon recirculation process between phloem and xylem that occurs in trees during the annual cycle of growth and dormancy. A search of possible evolutionary drivers behind the diversity of C carrying molecules in trees reveals no consistent differences in carbon transport mechanisms between angiosperm and gymnosperm trees. Furthermore, the distribution of C forms across species suggests that climate related environmental factors will not either explain the diversity of carbon transport forms. However, the consideration of C transport mechanisms in relation to tree—rhizosphere coevolution deserves further attention. To conclude the review, we identify possible future lines of research in this field.},
	number = {3},
	urldate = {2021-09-21},
	journal = {Tree Physiology},
	author = {Dominguez, Pia Guadalupe and Niittylä, Totte},
	month = mar,
	year = {2022},
	pages = {458--487},
}

Plants constitute 80% of the biomass on earth, and almost two thirds of this biomass is found in wood. Wood formation is a carbon demanding process and relies on carbon transport from photosynthetic tissues. Thus, understanding the transport process is of major interest for understanding terrestrial biomass formation. Here we review the molecules and mechanisms used to transport and allocate carbon in trees. Sucrose is the major form in which carbon is transported, found in the phloem sap of all so far investigated tree species. However, in several tree species sucrose is accompanied by other molecules, notably polyols and the raffinose family of oligosaccharides. We describe the molecules that constitute each of these transport groups, and their distribution across different tree species. Further, we detail the metabolic reactions for their synthesis, the mechanisms by which trees load and unload these compounds in and out of the vascular system, and how they are radially transported in the trunk and finally catabolized during wood formation. We also address a particular carbon recirculation process between phloem and xylem that occurs in trees during the annual cycle of growth and dormancy. A search of possible evolutionary drivers behind the diversity of C carrying molecules in trees reveals no consistent differences in carbon transport mechanisms between angiosperm and gymnosperm trees. Furthermore, the distribution of C forms across species suggests that climate related environmental factors will not either explain the diversity of carbon transport forms. However, the consideration of C transport mechanisms in relation to tree—rhizosphere coevolution deserves further attention. To conclude the review, we identify possible future lines of research in this field.

@article{wang_sucrose_2022,
	title = {Sucrose synthase activity is not required for cellulose biosynthesis in {Arabidopsis}},
	volume = {110},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.15752},
	doi = {10.1111/tpj.15752},
	abstract = {Biosynthesis of plant cell walls requires UDP-glucose as the substrate for cellulose biosynthesis, and as an intermediate for the synthesis of other matrix polysaccharides. The sucrose cleaving enzyme sucrose synthase (SUS) is thought to have a central role in UDP-glucose biosynthesis, and a long-held and much debated hypothesis postulates that SUS is required to supply UDP-glucose to cellulose biosynthesis. To investigate the role of SUS in cellulose biosynthesis of Arabidopsis thaliana we characterized mutants in which four or all six Arabidopsis SUS genes were disrupted. These sus mutants showed no growth phenotypes, vascular tissue cell wall defects, or changes in cellulose content. Moreover, the UDP-glucose content of rosette leaves of the sextuple sus mutants was increased by approximately 20\% compared with wild type. It can thus be concluded that cellulose biosynthesis is able to employ alternative UDP-glucose biosynthesis pathway(s), and thereby the model of SUS requirements for cellulose biosynthesis in Arabidopsis can be refuted.},
	language = {en},
	number = {5},
	urldate = {2022-06-09},
	journal = {The Plant Journal},
	author = {Wang, Wei and Viljamaa, Sonja and Hodek, Ondrej and Moritz, Thomas and Niittylä, Totte},
	year = {2022},
	keywords = {Arabidopsis thaliana, UDP-glucose, cellulose, sucrose synthase},
	pages = {1493--1497},
}

Biosynthesis of plant cell walls requires UDP-glucose as the substrate for cellulose biosynthesis, and as an intermediate for the synthesis of other matrix polysaccharides. The sucrose cleaving enzyme sucrose synthase (SUS) is thought to have a central role in UDP-glucose biosynthesis, and a long-held and much debated hypothesis postulates that SUS is required to supply UDP-glucose to cellulose biosynthesis. To investigate the role of SUS in cellulose biosynthesis of Arabidopsis thaliana we characterized mutants in which four or all six Arabidopsis SUS genes were disrupted. These sus mutants showed no growth phenotypes, vascular tissue cell wall defects, or changes in cellulose content. Moreover, the UDP-glucose content of rosette leaves of the sextuple sus mutants was increased by approximately 20% compared with wild type. It can thus be concluded that cellulose biosynthesis is able to employ alternative UDP-glucose biosynthesis pathway(s), and thereby the model of SUS requirements for cellulose biosynthesis in Arabidopsis can be refuted.

@article{funfgeld_sucrose_2022,
	title = {Sucrose synthases are not involved in starch synthesis in {Arabidopsis} leaves},
	volume = {8},
	copyright = {2022 The Author(s)},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-022-01140-y},
	doi = {10.1038/s41477-022-01140-y},
	abstract = {Many plants accumulate transitory starch reserves in their leaves during the day to buffer their carbohydrate supply against fluctuating light conditions, and to provide carbon and energy for survival at night. It is universally accepted that transitory starch is synthesized from ADP-glucose (ADPG) in the chloroplasts. However, the consensus that ADPG is made in the chloroplasts by ADPG pyrophosphorylase has been challenged by a controversial proposal that ADPG is made primarily in the cytosol, probably by sucrose synthase (SUS), and then imported into the chloroplasts. To resolve this long-standing controversy, we critically re-examined the experimental evidence that appears to conflict with the consensus pathway. We show that when precautions are taken to avoid artefactual changes during leaf sampling, Arabidopsis thaliana mutants that lack SUS activity in mesophyll cells (quadruple sus1234) or have no SUS activity (sextuple sus123456) have wild-type levels of ADPG and starch, while ADPG is 20 times lower in the pgm and adg1 mutants that are blocked in the consensus chloroplastic pathway of starch synthesis. We conclude that the ADPG needed for starch synthesis in leaves is synthesized primarily by ADPG pyrophosphorylase in the chloroplasts.},
	language = {en},
	number = {5},
	urldate = {2022-05-30},
	journal = {Nature Plants},
	author = {Fünfgeld, Maximilian M. F. F. and Wang, Wei and Ishihara, Hirofumi and Arrivault, Stéphanie and Feil, Regina and Smith, Alison M. and Stitt, Mark and Lunn, John E. and Niittylä, Totte},
	month = may,
	year = {2022},
	keywords = {Plant molecular biology, Plant physiology},
	pages = {574--582},
}

Many plants accumulate transitory starch reserves in their leaves during the day to buffer their carbohydrate supply against fluctuating light conditions, and to provide carbon and energy for survival at night. It is universally accepted that transitory starch is synthesized from ADP-glucose (ADPG) in the chloroplasts. However, the consensus that ADPG is made in the chloroplasts by ADPG pyrophosphorylase has been challenged by a controversial proposal that ADPG is made primarily in the cytosol, probably by sucrose synthase (SUS), and then imported into the chloroplasts. To resolve this long-standing controversy, we critically re-examined the experimental evidence that appears to conflict with the consensus pathway. We show that when precautions are taken to avoid artefactual changes during leaf sampling, Arabidopsis thaliana mutants that lack SUS activity in mesophyll cells (quadruple sus1234) or have no SUS activity (sextuple sus123456) have wild-type levels of ADPG and starch, while ADPG is 20 times lower in the pgm and adg1 mutants that are blocked in the consensus chloroplastic pathway of starch synthesis. We conclude that the ADPG needed for starch synthesis in leaves is synthesized primarily by ADPG pyrophosphorylase in the chloroplasts.

@article{jonasson_comparison_2021,
	title = {Comparison of tension wood and normal wood for oxidative nanofibrillation and network characteristics},
	volume = {28},
	issn = {0969-0239, 1572-882X},
	url = {http://link.springer.com/10.1007/s10570-020-03556-1},
	doi = {10.1007/s10570-020-03556-1},
	abstract = {Abstract
            
              Cellulose nanofibrils (CNFs) are top-down nanomaterials obtainable from abundant lignocelluloses. Despite recent advances in processing technologies, the effects of variations in the lignocellulose structure and composition on CNF isolation and properties are poorly understood. In this study, we compared the isolation of CNFs from tension wood (TW) and normal wood (NW) from
              Populus tremula
              (aspen). The TW has a higher cellulose content, native cellulose fibrils with a larger crystalline diameter, and less lignin than the NW, making it an interesting material for CNF isolation. The wood powders were oxidized directly by 2,2,6,6-tetramethylpiperidin-1-oxyl, and the morphology and mechanical behaviors of the nanofibril suspensions and networks were characterized. The TW was more difficult to fibrillate by both chemical and mechanical means. Larger nanofibrils (5–10 nm) composed of 1.2 nm structures were present in the TW CNFs, whereas the NW samples contained more of thin (1.6 nm) structures, which also comprised 77\% of the solid yield compared to the 33\% for TW. This difference was reflected in the TW CNF networks as decreased transmittance (15\% vs. 50\%), higher degree of crystallinity (85.9\% vs. 78.0\%), doubled toughness (11 MJ/m
              3
              ) and higher elongation at break (12\%) compared to NW. The difference was ascribed to greater preservation of the hierarchical, more crystalline microfibril structure, combined with a more cellulose-rich network (84\% vs. 70\%). This knowledge of the processing, structure, and properties of CNFs can facilitate the breeding and design of wood feedstocks to meet the increasing demand for nanoscale renewable materials.
            
            
              Graphic abstract},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Cellulose},
	author = {Jonasson, Simon and Bünder, Anne and Das, Oisik and Niittylä, Totte and Oksman, Kristiina},
	month = jan,
	year = {2021},
	pages = {1085--1104},
}

Abstract Cellulose nanofibrils (CNFs) are top-down nanomaterials obtainable from abundant lignocelluloses. Despite recent advances in processing technologies, the effects of variations in the lignocellulose structure and composition on CNF isolation and properties are poorly understood. In this study, we compared the isolation of CNFs from tension wood (TW) and normal wood (NW) from Populus tremula (aspen). The TW has a higher cellulose content, native cellulose fibrils with a larger crystalline diameter, and less lignin than the NW, making it an interesting material for CNF isolation. The wood powders were oxidized directly by 2,2,6,6-tetramethylpiperidin-1-oxyl, and the morphology and mechanical behaviors of the nanofibril suspensions and networks were characterized. The TW was more difficult to fibrillate by both chemical and mechanical means. Larger nanofibrils (5–10 nm) composed of 1.2 nm structures were present in the TW CNFs, whereas the NW samples contained more of thin (1.6 nm) structures, which also comprised 77% of the solid yield compared to the 33% for TW. This difference was reflected in the TW CNF networks as decreased transmittance (15% vs. 50%), higher degree of crystallinity (85.9% vs. 78.0%), doubled toughness (11 MJ/m 3 ) and higher elongation at break (12%) compared to NW. The difference was ascribed to greater preservation of the hierarchical, more crystalline microfibril structure, combined with a more cellulose-rich network (84% vs. 70%). This knowledge of the processing, structure, and properties of CNFs can facilitate the breeding and design of wood feedstocks to meet the increasing demand for nanoscale renewable materials. Graphic abstract

@article{diacci_diurnal_2021,
	title = {Diurnal in vivo xylem sap glucose and sucrose monitoring using implantable organic electrochemical transistor sensors},
	volume = {24},
	issn = {25890042},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2589004220311639},
	doi = {10/gjgsjg},
	language = {en},
	number = {1},
	urldate = {2021-06-03},
	journal = {iScience},
	author = {Diacci, Chiara and Abedi, Tayebeh and Lee, Jee Woong and Gabrielsson, Erik O. and Berggren, Magnus and Simon, Daniel T. and Niittylä, Totte and Stavrinidou, Eleni},
	month = jan,
	year = {2021},
	pages = {101966},
}

@article{escamez_fluorescence_2021,
	title = {Fluorescence {Lifetime} {Imaging} as an {In} {Situ} and {Label}-{Free} {Readout} for the {Chemical} {Composition} of {Lignin}},
	volume = {9},
	url = {https://doi.org/10.1021/acssuschemeng.1c06780},
	doi = {10/gnr3sb},
	abstract = {Naturally fluorescent polymeric molecules such as collagen, resilin, cutin, suberin, or lignin can serve as renewable sources of bioproducts. Theoretical physics predicts that the fluorescence lifetime of these polymers is related to their chemical composition. We verified this prediction for lignin, a major structural element in plant cell walls that form woody biomass. Lignin is composed of different phenylpropanoid units, and its composition affects its properties, biological functions, and the utilization of wood biomass. We carried out fluorescence lifetime imaging microscopy (FLIM) measurements of wood cell wall lignin in a population of 90 hybrid aspen trees genetically engineered to display differences in cell wall chemistry and structure. We also measured the wood cell wall composition by classical analytical methods in these trees. Using statistical modeling and machine learning algorithms, we identified parameters of fluorescence lifetime that predict the content of S-type and G-type lignin units, the two main types of units in the lignin of angiosperm (flowering) plants. In a first step toward tailoring lignin biosynthesis toward improvement of woody biomass feedstocks, we show how FLIM can reveal the dynamics of lignin biosynthesis in two different biological contexts, including in vivo while lignin is being synthesized in the walls of living cells.},
	number = {51},
	urldate = {2021-12-14},
	journal = {ACS Sustainable Chemistry \& Engineering},
	author = {Escamez, Sacha and Terryn, Christine and Gandla, Madhavi Latha and Yassin, Zakiya and Scheepers, Gerhard and Näsholm, Torgny and Sundman, Ola and Jönsson, Leif J. and Lundberg-Felten, Judith and Tuominen, Hannele and Niittylä, Totte and Paës, Gabriel},
	month = dec,
	year = {2021},
	pages = {17381--17392},
}

Naturally fluorescent polymeric molecules such as collagen, resilin, cutin, suberin, or lignin can serve as renewable sources of bioproducts. Theoretical physics predicts that the fluorescence lifetime of these polymers is related to their chemical composition. We verified this prediction for lignin, a major structural element in plant cell walls that form woody biomass. Lignin is composed of different phenylpropanoid units, and its composition affects its properties, biological functions, and the utilization of wood biomass. We carried out fluorescence lifetime imaging microscopy (FLIM) measurements of wood cell wall lignin in a population of 90 hybrid aspen trees genetically engineered to display differences in cell wall chemistry and structure. We also measured the wood cell wall composition by classical analytical methods in these trees. Using statistical modeling and machine learning algorithms, we identified parameters of fluorescence lifetime that predict the content of S-type and G-type lignin units, the two main types of units in the lignin of angiosperm (flowering) plants. In a first step toward tailoring lignin biosynthesis toward improvement of woody biomass feedstocks, we show how FLIM can reveal the dynamics of lignin biosynthesis in two different biological contexts, including in vivo while lignin is being synthesized in the walls of living cells.

@article{dominguez_sucrose_2021,
	title = {Sucrose synthase determines carbon allocation in developing wood and alters carbon flow at the whole tree level in aspen},
	volume = {229},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.16721},
	doi = {10.1111/nph.16721},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Dominguez, Pia Guadalupe and Donev, Evgeniy and Derba‐Maceluch, Marta and Bünder, Anne and Hedenström, Mattias and Tomášková, Ivana and Mellerowicz, Ewa J. and Niittylä, Totte},
	month = jan,
	year = {2021},
	pages = {186--198},
}

@article{jonasson_effect_2021,
	title = {The {Effect} of {High} {Lignin} {Content} on {Oxidative} {Nanofibrillation} of {Wood} {Cell} {Wall}},
	volume = {11},
	issn = {2079-4991},
	url = {https://www.mdpi.com/2079-4991/11/5/1179},
	doi = {10/gjznf2},
	abstract = {Wood from field-grown poplars with different genotypes and varying lignin content (17.4 wt \% to 30.0 wt \%) were subjected to one-pot 2,2,6,6-Tetramethylpiperidin-1-yl)oxyl catalyzed oxidation and high-pressure homogenization in order to investigate nanofibrillation following simultaneous delignification and cellulose oxidation. When comparing low and high lignin wood it was found that the high lignin wood was more easily fibrillated as indicated by a higher nanofibril yield (68\% and 45\%) and suspension viscosity (27 and 15 mPa·s). The nanofibrils were monodisperse with diameter ranging between 1.2 and 2.0 nm as measured using atomic force microscopy. Slightly less cellulose oxidation (0.44 and 0.68 mmol·g−1) together with a reduced process yield (36\% and 44\%) was also found which showed that the removal of a larger amount of lignin increased the efficiency of the homogenization step despite slightly reduced oxidation of the nanofibril surfaces. The surface area of oxidized high lignin wood was also higher than low lignin wood (114 m2·g−1 and 76 m2·g−1) which implicates porosity as a factor that can influence cellulose nanofibril isolation from wood in a beneficial manner.},
	language = {en},
	number = {5},
	urldate = {2021-06-03},
	journal = {Nanomaterials},
	author = {Jonasson, Simon and Bünder, Anne and Berglund, Linn and Hertzberg, Magnus and Niittylä, Totte and Oksman, Kristiina},
	month = apr,
	year = {2021},
	pages = {1179},
}

Wood from field-grown poplars with different genotypes and varying lignin content (17.4 wt % to 30.0 wt %) were subjected to one-pot 2,2,6,6-Tetramethylpiperidin-1-yl)oxyl catalyzed oxidation and high-pressure homogenization in order to investigate nanofibrillation following simultaneous delignification and cellulose oxidation. When comparing low and high lignin wood it was found that the high lignin wood was more easily fibrillated as indicated by a higher nanofibril yield (68% and 45%) and suspension viscosity (27 and 15 mPa·s). The nanofibrils were monodisperse with diameter ranging between 1.2 and 2.0 nm as measured using atomic force microscopy. Slightly less cellulose oxidation (0.44 and 0.68 mmol·g−1) together with a reduced process yield (36% and 44%) was also found which showed that the removal of a larger amount of lignin increased the efficiency of the homogenization step despite slightly reduced oxidation of the nanofibril surfaces. The surface area of oxidized high lignin wood was also higher than low lignin wood (114 m2·g−1 and 76 m2·g−1) which implicates porosity as a factor that can influence cellulose nanofibril isolation from wood in a beneficial manner.

@article{abreu_metabolite_2020,
	title = {A metabolite roadmap of the wood‐forming tissue in {Populus} tremula},
	volume = {228},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.16799},
	doi = {10.1111/nph.16799},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Abreu, Ilka N. and Johansson, Annika I. and Sokołowska, Katarzyna and Niittylä, Totte and Sundberg, Björn and Hvidsten, Torgeir R. and Street, Nathaniel R. and Moritz, Thomas},
	month = dec,
	year = {2020},
	pages = {1559--1572},
}

@article{bunder_cellulose_2020,
	title = {{CELLULOSE} {SYNTHASE} {INTERACTING} 1 is required for wood mechanics and leaf morphology in aspen},
	volume = {103},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14873},
	doi = {10.1111/tpj.14873},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Bünder, Anne and Sundman, Ola and Mahboubi, Amir and Persson, Staffan and Mansfield, Shawn D. and Rüggeberg, Markus and Niittylä, Totte},
	month = aug,
	year = {2020},
	pages = {1858--1868},
}

@article{nibbering_golgi-localized_2020,
	title = {Golgi-localized exo-β1,3-galactosidases involved in cell expansion and root growth in {Arabidopsis}},
	volume = {295},
	issn = {00219258},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S002192581750099X},
	doi = {10.1074/jbc.RA120.013878},
	language = {en},
	number = {31},
	urldate = {2021-06-07},
	journal = {Journal of Biological Chemistry},
	author = {Nibbering, Pieter and Petersen, Bent L. and Motawia, Mohammed Saddik and Jørgensen, Bodil and Ulvskov, Peter and Niittylä, Totte},
	month = jul,
	year = {2020},
	pages = {10581--10592},
}

@article{jonasson_isolation_2020,
	title = {Isolation and characterization of cellulose nanofibers from aspen wood using derivatizing and non-derivatizing pretreatments},
	volume = {27},
	issn = {0969-0239, 1572-882X},
	url = {http://link.springer.com/10.1007/s10570-019-02754-w},
	doi = {10.1007/s10570-019-02754-w},
	abstract = {Abstract
              The link between wood and corresponding cellulose nanofiber (CNF) behavior is complex owing the multiple chemical pretreatments required for successful preparation. In this study we apply a few pretreatments on aspen wood and compare the final CNF behavior in order to rationalize quantitative studies of CNFs derived from aspen wood with variable properties. This is relevant for efforts to improve the properties of woody biomass through tree breeding. Three different types of pretreatments were applied prior to disintegration (microfluidizer) after a mild pulping step; derivatizing TEMPO-oxidation, carboxymethylation and non-derivatizing soaking in deep-eutectic solvents. TEMPO-oxidation was also performed directly on the plain wood powder without pulping. Obtained CNFs (44–55\% yield) had hemicellulose content between 8 and 26 wt\% and were characterized primarily by fine (height ≈ 2 nm) and coarser (2 nm {\textless} height {\textless} 100 nm) grade CNFs from the derivatizing and non-derivatizing treatments, respectively. Nanopapers from non-derivatized CNFs had higher thermal stability (280 °C) compared to carboxymethylated (260 °C) and TEMPO-oxidized (220 °C). Stiffness of nanopapers made from non-derivatized treatments was higher whilst having less tensile strength and elongation-at-break than those made from derivatized CNFs. The direct TEMPO-oxidized CNFs and nanopapers were furthermore morphologically and mechanically indistinguishable from those that also underwent a pulping step. The results show that utilizing both derivatizing and non-derivatizing pretreatments can facilitate studies of the relationship between wood properties and final CNF behavior. This can be valuable when studying engineered trees for the purpose of decreasing resource consumption when isolation cellulose nanomaterials.
            
            
              Graphic abstract},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Cellulose},
	author = {Jonasson, Simon and Bünder, Anne and Niittylä, Totte and Oksman, Kristiina},
	month = jan,
	year = {2020},
	pages = {185--203},
}

Abstract The link between wood and corresponding cellulose nanofiber (CNF) behavior is complex owing the multiple chemical pretreatments required for successful preparation. In this study we apply a few pretreatments on aspen wood and compare the final CNF behavior in order to rationalize quantitative studies of CNFs derived from aspen wood with variable properties. This is relevant for efforts to improve the properties of woody biomass through tree breeding. Three different types of pretreatments were applied prior to disintegration (microfluidizer) after a mild pulping step; derivatizing TEMPO-oxidation, carboxymethylation and non-derivatizing soaking in deep-eutectic solvents. TEMPO-oxidation was also performed directly on the plain wood powder without pulping. Obtained CNFs (44–55% yield) had hemicellulose content between 8 and 26 wt% and were characterized primarily by fine (height ≈ 2 nm) and coarser (2 nm \textless height \textless 100 nm) grade CNFs from the derivatizing and non-derivatizing treatments, respectively. Nanopapers from non-derivatized CNFs had higher thermal stability (280 °C) compared to carboxymethylated (260 °C) and TEMPO-oxidized (220 °C). Stiffness of nanopapers made from non-derivatized treatments was higher whilst having less tensile strength and elongation-at-break than those made from derivatized CNFs. The direct TEMPO-oxidized CNFs and nanopapers were furthermore morphologically and mechanically indistinguishable from those that also underwent a pulping step. The results show that utilizing both derivatizing and non-derivatizing pretreatments can facilitate studies of the relationship between wood properties and final CNF behavior. This can be valuable when studying engineered trees for the purpose of decreasing resource consumption when isolation cellulose nanomaterials. Graphic abstract

@article{abedi_spatio-temporal_2020,
	title = {The {Spatio}-{Temporal} {Distribution} of {Cell} {Wall}-{Associated} {Glycoproteins} {During} {Wood} {Formation} in {Populus}},
	volume = {11},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2020.611607/full},
	doi = {10/gjcxhp},
	abstract = {Plant cell wall associated hydroxyproline-rich glycoproteins (HRGPs) are involved in several aspects of plant growth and development, including wood formation in trees. HRGPs such as arabinogalactan-proteins (AGPs), extensins (EXTs), and proline rich proteins (PRPs) are important for the development and architecture of plant cell walls. Analysis of publicly available gene expression data revealed that many
              HRGP
              encoding genes show tight spatio-temporal expression patterns in the developing wood of
              Populus
              that are indicative of specific functions during wood formation. Similar results were obtained for the expression of glycosyl transferases putatively involved in HRGP glycosylation.
              In situ
              immunolabelling of transverse wood sections using AGP and EXT antibodies revealed the cell type specificity of different epitopes. In mature wood AGP epitopes were located in xylem ray cell walls, whereas EXT epitopes were specifically observed between neighboring xylem vessels, and on the ray cell side of the vessel walls, likely in association with pits. Molecular mass and glycan analysis of AGPs and EXTs in phloem/cambium, developing xylem, and mature xylem revealed clear differences in glycan structures and size between the tissues. Separation of AGPs by agarose gel electrophoresis and staining with β-D-glucosyl Yariv confirmed the presence of different AGP populations in phloem/cambium and xylem. These results reveal the diverse changes in HRGP-related processes that occur during wood formation at the gene expression and HRGP glycan biosynthesis levels, and relate HRGPs and glycosylation processes to the developmental processes of wood formation.},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Abedi, Tayebeh and Castilleux, Romain and Nibbering, Pieter and Niittylä, Totte},
	month = dec,
	year = {2020},
	pages = {611607},
}

Plant cell wall associated hydroxyproline-rich glycoproteins (HRGPs) are involved in several aspects of plant growth and development, including wood formation in trees. HRGPs such as arabinogalactan-proteins (AGPs), extensins (EXTs), and proline rich proteins (PRPs) are important for the development and architecture of plant cell walls. Analysis of publicly available gene expression data revealed that many HRGP encoding genes show tight spatio-temporal expression patterns in the developing wood of Populus that are indicative of specific functions during wood formation. Similar results were obtained for the expression of glycosyl transferases putatively involved in HRGP glycosylation. In situ immunolabelling of transverse wood sections using AGP and EXT antibodies revealed the cell type specificity of different epitopes. In mature wood AGP epitopes were located in xylem ray cell walls, whereas EXT epitopes were specifically observed between neighboring xylem vessels, and on the ray cell side of the vessel walls, likely in association with pits. Molecular mass and glycan analysis of AGPs and EXTs in phloem/cambium, developing xylem, and mature xylem revealed clear differences in glycan structures and size between the tissues. Separation of AGPs by agarose gel electrophoresis and staining with β-D-glucosyl Yariv confirmed the presence of different AGP populations in phloem/cambium and xylem. These results reveal the diverse changes in HRGP-related processes that occur during wood formation at the gene expression and HRGP glycan biosynthesis levels, and relate HRGPs and glycosylation processes to the developmental processes of wood formation.

@article{baison_genomewide_2019,
	title = {Genome‐wide association study identified novel candidate loci affecting wood formation in {Norway} spruce},
	volume = {100},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14429},
	doi = {10/gjcj3d},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Baison, John and Vidalis, Amaryllis and Zhou, Linghua and Chen, Zhi‐Qiang and Li, Zitong and Sillanpää, Mikko J. and Bernhardsson, Carolina and Scofield, Douglas and Forsberg, Nils and Grahn, Thomas and Olsson, Lars and Karlsson, Bo and Wu, Harry and Ingvarsson, Pär K. and Lundqvist, Sven‐Olof and Niittylä, Totte and García‐Gil, M Rosario},
	month = oct,
	year = {2019},
	pages = {83--100},
}

@incollection{giacomello_high_2019,
	title = {High {Spatial} {Resolution} {Profiling} in {Tree} {Species}},
	isbn = {978-1-119-31299-4},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9781119312994.apr0688},
	abstract = {Until recently, the majority of genomics assays have been performed on bulk tissue samples containing multiple cell types. Tissues such as the wood formation zone in trees contain a complex mix of cell types organised in three-dimensional space. Moreover, cells within the wood formation zone represent a continual developmental progression from meristematic cambial initials through to cell death. This spatiotemporal developmental gradient and cell type information are not assayed by bulk samples. New and improved sampling methods coupled to next-generation sequencing assays are enabling the generation of high spatial resolution and single-cell transcriptomics data, offering unprecedented insight into the biology of unique cell types and cell developmental programs. We overview the application of these approaches to the study of wood development, in particular, and highlight challenges associated with the analysis of such data.},
	language = {en},
	urldate = {2021-10-20},
	booktitle = {Annual {Plant} {Reviews} online},
	publisher = {American Cancer Society},
	author = {Giacomello, Stefania and Delhomme, Nicolas and Niittylä, Totte and Tuominen, Hannele and Street, Nathaniel R.},
	year = {2019},
	doi = {10.1002/9781119312994.apr0688},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781119312994.apr0688},
	keywords = {RNA sequencing, cell type, single cell, spatial resolution, transcriptome, wood formation, xylem},
	pages = {329--360},
}

Until recently, the majority of genomics assays have been performed on bulk tissue samples containing multiple cell types. Tissues such as the wood formation zone in trees contain a complex mix of cell types organised in three-dimensional space. Moreover, cells within the wood formation zone represent a continual developmental progression from meristematic cambial initials through to cell death. This spatiotemporal developmental gradient and cell type information are not assayed by bulk samples. New and improved sampling methods coupled to next-generation sequencing assays are enabling the generation of high spatial resolution and single-cell transcriptomics data, offering unprecedented insight into the biology of unique cell types and cell developmental programs. We overview the application of these approaches to the study of wood development, in particular, and highlight challenges associated with the analysis of such data.

@article{wang_opener_2019,
	title = {{OPENER} {Is} a {Nuclear} {Envelope} and {Mitochondria} {Localized} {Protein} {Required} for {Cell} {Cycle} {Progression} in {Arabidopsis}},
	volume = {31},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/31/7/1446-1465/5985717},
	doi = {10/gjcsgx},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {Wang, Wei and Zhang, Xueyang and Niittylä, Totte},
	month = jul,
	year = {2019},
	pages = {1446--1465},
}

@article{rende_two-step_2019,
	title = {Two-step derivatization for determination of sugar phosphates in plants by combined reversed phase chromatography/tandem mass spectrometry},
	volume = {15},
	issn = {1746-4811},
	url = {https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0514-9},
	doi = {10.1186/s13007-019-0514-9},
	abstract = {Abstract
            
              Background
              Sugar phosphates are important intermediates of central carbon metabolism in biological systems, with roles in glycolysis, the pentose–phosphate pathway, tricarboxylic acid (TCA) cycle, and many other biosynthesis pathways. Understanding central carbon metabolism requires a simple, robust and comprehensive analytical method. However, sugar phosphates are notoriously difficult to analyze by traditional reversed phase liquid chromatography.
            
            
              Results
              
                Here, we show a two-step derivatization of sugar phosphates by methoxylamine and propionic acid anhydride after chloroform/methanol (3:7) extraction from
                Populus
                leaf and developing wood that improves separation, identification and quantification of sugar phosphates by ultra high performance liquid chromatography–electrospray ionization–mass spectrometry (UHPLC–ESI–MS). Standard curves of authentic sugar phosphates were generated for concentrations from pg to ng/μl with a correlation coefficient
                R
                2
                 {\textgreater} 0.99. The method showed high sensitivity and repeatability with relative standard deviation (RSD) {\textless} 20\% based on repeated extraction, derivatization and detection. The analytical accuracy for
                Populus
                leaf extracts, determined by a two-level spiking approach of selected metabolites, was 79–107\%.
              
            
            
              Conclusion
              
                The results show the reliability of combined reversed phase liquid chromatography–tandem mass spectrometry for sugar phosphate analysis and demonstrate the presence of two unknown sugar phosphates in
                Populus
                extracts.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Methods},
	author = {Rende, Umut and Niittylä, Totte and Moritz, Thomas},
	month = dec,
	year = {2019},
	pages = {127},
}

Abstract Background Sugar phosphates are important intermediates of central carbon metabolism in biological systems, with roles in glycolysis, the pentose–phosphate pathway, tricarboxylic acid (TCA) cycle, and many other biosynthesis pathways. Understanding central carbon metabolism requires a simple, robust and comprehensive analytical method. However, sugar phosphates are notoriously difficult to analyze by traditional reversed phase liquid chromatography. Results Here, we show a two-step derivatization of sugar phosphates by methoxylamine and propionic acid anhydride after chloroform/methanol (3:7) extraction from Populus leaf and developing wood that improves separation, identification and quantification of sugar phosphates by ultra high performance liquid chromatography–electrospray ionization–mass spectrometry (UHPLC–ESI–MS). Standard curves of authentic sugar phosphates were generated for concentrations from pg to ng/μl with a correlation coefficient R 2  \textgreater 0.99. The method showed high sensitivity and repeatability with relative standard deviation (RSD) \textless 20% based on repeated extraction, derivatization and detection. The analytical accuracy for Populus leaf extracts, determined by a two-level spiking approach of selected metabolites, was 79–107%. Conclusion The results show the reliability of combined reversed phase liquid chromatography–tandem mass spectrometry for sugar phosphate analysis and demonstrate the presence of two unknown sugar phosphates in Populus extracts.

@article{zhang_cellulose_2018,
	title = {Cellulose {Synthase} {Stoichiometry} in {Aspen} {Differs} from {Arabidopsis} and {Norway} {Spruce}},
	volume = {177},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/177/3/1096-1107/6117105},
	doi = {10.1104/pp.18.00394},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Zhang, Xueyang and Dominguez, Pia Guadalupe and Kumar, Manoj and Bygdell, Joakim and Miroshnichenko, Sergey and Sundberg, Björn and Wingsle, Gunnar and Niittylä, Totte},
	month = jul,
	year = {2018},
	pages = {1096--1107},
}

@article{mahboubi_sucrose_2018,
	title = {Sucrose transport and carbon fluxes during wood formation},
	volume = {164},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12729},
	doi = {10.1111/ppl.12729},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Mahboubi, Amir and Niittylä, Totte},
	month = sep,
	year = {2018},
	pages = {67--81},
}

@article{sundell_aspwood_2017,
	title = {{AspWood}: {High}-{Spatial}-{Resolution} {Transcriptome} {Profiles} {Reveal} {Uncharacterized} {Modularity} of {Wood} {Formation} in {Populus} tremula},
	volume = {29},
	issn = {1040-4651, 1532-298X},
	shorttitle = {{AspWood}},
	url = {https://academic.oup.com/plcell/article/29/7/1585-1604/6099151},
	doi = {10/gbshnb},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {Sundell, David and Street, Nathaniel R. and Kumar, Manoj and Mellerowicz, Ewa J. and Kucukoglu, Melis and Johnsson, Christoffer and Kumar, Vikash and Mannapperuma, Chanaka and Delhomme, Nicolas and Nilsson, Ove and Tuominen, Hannele and Pesquet, Edouard and Fischer, Urs and Niittylä, Totte and Sundberg, Björn and Hvidsten, Torgeir R.},
	month = jul,
	year = {2017},
	pages = {1585--1604},
}

@article{rende_cytosolic_2017,
	title = {Cytosolic invertase contributes to the supply of substrate for cellulose biosynthesis in developing wood},
	volume = {214},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.14392},
	doi = {10.1111/nph.14392},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Rende, Umut and Wang, Wei and Gandla, Madhavi Latha and Jönsson, Leif J. and Niittylä, Totte},
	month = apr,
	year = {2017},
	pages = {796--807},
}

@article{blokhina_laser_2017,
	title = {Laser {Capture} {Microdissection} {Protocol} for {Xylem} {Tissues} of {Woody} {Plants}},
	volume = {07},
	issn = {1664-462X},
	url = {http://journal.frontiersin.org/article/10.3389/fpls.2016.01965/full},
	doi = {10.3389/fpls.2016.01965},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Blokhina, Olga and Valerio, Concetta and Sokołowska, Katarzyna and Zhao, Lei and Kärkönen, Anna and Niittylä, Totte and Fagerstedt, Kurt},
	month = jan,
	year = {2017},
}

@article{roach_spatially_2017,
	title = {Spatially resolved metabolic analysis reveals a central role for transcriptional control in carbon allocation to wood},
	volume = {68},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article/68/13/3529/3883921},
	doi = {10/gbs95x},
	language = {en},
	number = {13},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Roach, Melissa and Arrivault, Stéphanie and Mahboubi, Amir and Krohn, Nicole and Sulpice, Ronan and Stitt, Mark and Niittylä, Totte},
	month = jun,
	year = {2017},
	pages = {3529--3539},
}

@article{schneider_two_2017,
	title = {Two {Complementary} {Mechanisms} {Underpin} {Cell} {Wall} {Patterning} during {Xylem} {Vessel} {Development}},
	volume = {29},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/29/10/2433-2449/6100385},
	doi = {10/cf9j},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {Schneider, Rene and Tang, Lu and Lampugnani, Edwin R. and Barkwill, Sarah and Lathe, Rahul and Zhang, Yi and McFarlane, Heather E. and Pesquet, Edouard and Niittylä, Totte and Mansfield, Shawn D. and Zhou, Yihua and Persson, Staffan},
	month = oct,
	year = {2017},
	pages = {2433--2449},
}

@article{mahboubi_13c_2015,
	title = {{13C} {Tracking} after {13CO2} {Supply} {Revealed} {Diurnal} {Patterns} of {Wood} {Formation} in {Aspen}},
	volume = {168},
	issn = {1532-2548 (Electronic) 0032-0889 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25931520},
	doi = {10.1104/pp.15.00292},
	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 (13)CO2 labeling system to study carbon transport and incorporation to developing wood of hybrid aspen (Populus tremula x tremuloides). Tracking of (13)C 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 (13)C incorporation to lignin and cell wall carbohydrates. No (13)C 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 (13)C labeling method for the analysis of wood formation and secondary growth in trees.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Physiol},
	author = {Mahboubi, A. and Linden, P. and Hedenstrom, M. and Moritz, T. and Niittylä, T.},
	month = jun,
	year = {2015},
	keywords = {*Circadian Rhythm, Analysis of Variance, Carbon Dioxide/*metabolism, Carbon Isotopes, Cell Wall/metabolism, Cellulose/metabolism, Magnetic Resonance Spectroscopy, Metabolic Networks and Pathways, Metabolome, Models, Biological, Phloem/metabolism, Plant Leaves/metabolism, Populus/*physiology, Principal Component Analysis, Sucrose/metabolism, Wood/*growth \& development},
	pages = {478--89},
}

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 (13)CO2 labeling system to study carbon transport and incorporation to developing wood of hybrid aspen (Populus tremula x tremuloides). Tracking of (13)C 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 (13)C incorporation to lignin and cell wall carbohydrates. No (13)C 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 (13)C labeling method for the analysis of wood formation and secondary growth in trees.

@article{gerber_deficient_2014,
	title = {Deficient sucrose synthase activity in developing wood does not specifically affect cellulose biosynthesis, but causes an overall decrease in cell wall polymers},
	volume = {203},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.12888},
	doi = {10/f3p3rs},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Gerber, Lorenz and Zhang, Bo and Roach, Melissa and Rende, Umut and Gorzsás, András and Kumar, Manoj and Burgert, Ingo and Niittylä, Totte and Sundberg, Björn},
	month = sep,
	year = {2014},
	pages = {1220--1230},
}

@article{mahboubi_aspen_2013,
	title = {Aspen {SUCROSE} {TRANSPORTER3} {Allocates} {Carbon} into {Wood} {Fibers}},
	volume = {163},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/163/4/1729-1740/6111119},
	doi = {10/f24j68},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {PLANT PHYSIOLOGY},
	author = {Mahboubi, A. and Ratke, C. and Gorzsas, A. and Kumar, M. and Mellerowicz, E. J. and Niittylä, T.},
	month = dec,
	year = {2013},
	pages = {1729--1740},
}

@article{nystedt_norway_2013,
	title = {The {Norway} spruce genome sequence and conifer genome evolution},
	volume = {497},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/articles/nature12211},
	doi = {10/f2zsx6},
	language = {en},
	number = {7451},
	urldate = {2021-06-08},
	journal = {Nature},
	author = {Nystedt, Björn and Street, Nathaniel R. and Wetterbom, Anna and Zuccolo, Andrea and Lin, Yao-Cheng and Scofield, Douglas G. and Vezzi, Francesco and Delhomme, Nicolas and Giacomello, Stefania and Alexeyenko, Andrey and Vicedomini, Riccardo and Sahlin, Kristoffer and Sherwood, Ellen and Elfstrand, Malin and Gramzow, Lydia and Holmberg, Kristina and Hällman, Jimmie and Keech, Olivier and Klasson, Lisa and Koriabine, Maxim and Kucukoglu, Melis and Käller, Max and Luthman, Johannes and Lysholm, Fredrik and Niittylä, Totte and Olson, Åke and Rilakovic, Nemanja and Ritland, Carol and Rosselló, Josep A. and Sena, Juliana and Svensson, Thomas and Talavera-López, Carlos and Theißen, Günter and Tuominen, Hannele and Vanneste, Kevin and Wu, Zhi-Qiang and Zhang, Bo and Zerbe, Philipp and Arvestad, Lars and Bhalerao, Rishikesh P. and Bohlmann, Joerg and Bousquet, Jean and Garcia Gil, Rosario and Hvidsten, Torgeir R. and de Jong, Pieter and MacKay, John and Morgante, Michele and Ritland, Kermit and Sundberg, Björn and Lee Thompson, Stacey and Van de Peer, Yves and Andersson, Björn and Nilsson, Ove and Ingvarsson, Pär K. and Lundeberg, Joakim and Jansson, Stefan},
	month = may,
	year = {2013},
	pages = {579--584},
}

@article{roach_fructokinase_2012,
	title = {Fructokinase is required for carbon partitioning to cellulose in aspen wood: {Fructokinase} in aspen wood formation},
	volume = {70},
	issn = {09607412},
	shorttitle = {Fructokinase is required for carbon partitioning to cellulose in aspen wood},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2012.04929.x},
	doi = {10/fzm62x},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Roach, Melissa and Gerber, Lorenz and Sandquist, David and Gorzsás, András and Hedenström, Mattias and Kumar, Manoj and Steinhauser, Marie Caroline and Feil, Regina and Daniel, Geoffrey and Stitt, Mark and Sundberg, Björn and Niittylä, Totte},
	month = jun,
	year = {2012},
	pages = {967--977},
}

@article{xue_paramutation-like_2012,
	title = {Paramutation-{Like} {Interaction} of {T}-{DNA} {Loci} in {Arabidopsis}},
	volume = {7},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0051651},
	doi = {10/f22djh},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Xue, Weiya and Ruprecht, Colin and Street, Nathaniel and Hematy, Kian and Chang, Christine and Frommer, Wolf B. and Persson, Staffan and Niittylä, Totte},
	editor = {Schiefelbein, John},
	month = dec,
	year = {2012},
	pages = {e51651},
}

@incollection{belostotsky_comparison_2009,
	address = {Totowa, NJ},
	title = {Comparison of {Quantitative} {Metabolite} {Imaging} {Tools} and {Carbon}-13 {Techniques} for {Fluxomics}},
	volume = {553},
	isbn = {978-1-60327-562-0 978-1-60327-563-7},
	url = {http://link.springer.com/10.1007/978-1-60327-563-7_19},
	urldate = {2021-06-08},
	booktitle = {Plant {Systems} {Biology}},
	publisher = {Humana Press},
	author = {Niittylae, Totte and Chaudhuri, Bhavna and Sauer, Uwe and Frommer, Wolf B.},
	editor = {Belostotsky, Dmitry A.},
	year = {2009},
	doi = {10.1007/978-1-60327-563-7_19},
	note = {Series Title: Methods in Molecular Biology™},
	pages = {355--372},
}

@article{chaudhuri_fluxomics_2007,
	title = {Fluxomics with {Ratiometric} {Metabolite} {Dyes}},
	volume = {2},
	issn = {1559-2324},
	url = {http://www.tandfonline.com/doi/abs/10.4161/psb.2.2.3643},
	doi = {10/bwhxwc},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Plant Signaling \& Behavior},
	author = {Chaudhuri, Bhavna and Niittylä, Totte and Hörmann, Friederike and Frommer, Wolf B.},
	month = mar,
	year = {2007},
	pages = {120--122},
}

@article{niittyla_temporal_2007,
	title = {Temporal {Analysis} of {Sucrose}-induced {Phosphorylation} {Changes} in {Plasma} {Membrane} {Proteins} of {Arabidopsis}*},
	volume = {6},
	issn = {1535-9476},
	url = {https://www.sciencedirect.com/science/article/pii/S1535947620319435},
	doi = {10/cggvjv},
	abstract = {Sucrose is the main product of photosynthesis and the most common transport form of carbon in plants. In addition, sucrose is a compound that serves as a signal affecting metabolic flux and development. Here we provide first results of externally induced phosphorylation changes of plasma membrane proteins in Arabidopsis. In an unbiased approach, seedlings were grown in liquid medium with sucrose and then depleted of carbon before sucrose was resupplied. Plasma membranes were purified, and phosphopeptides were enriched and subsequently analyzed quantitatively by mass spectrometry. In total, 67 phosphopeptides were identified, most of which were quantified over five time points of sucrose resupply. Among the identified phosphorylation sites, the well described phosphorylation site at the C terminus of plasma membrane H+-ATPases showed a relative increase in phosphorylation level in response to sucrose. This corresponded to a significant increase of proton pumping activity of plasma membrane vesicles from sucrose-supplied seedlings. A new phosphorylation site was identified in the plasma membrane H+-ATPase AHA1 and/or AHA2. This phosphorylation site was shown to be crucial for ATPase activity and overrode regulation via the well known C-terminal phosphorylation site. Novel phosphorylation sites were identified for both receptor kinases and cytosolic kinases that showed rapid increases in relative intensities after short times of sucrose treatment. Seven response classes were identified including non-responsive, rapid increase (within 3 min), slow increase, and rapid decrease. Relative quantification of phosphorylation changes by phosphoproteomics provides a means for identification of fast responses to external stimuli in plants as a basis for further functional characterization.},
	language = {en},
	number = {10},
	urldate = {2021-06-10},
	journal = {Molecular \& Cellular Proteomics},
	author = {Niittylä, Totte and Fuglsang, Anja T. and Palmgren, Michael G. and Frommer, Wolf B. and Schulze, Waltraud X.},
	month = oct,
	year = {2007},
	pages = {1711--1726},
}

Sucrose is the main product of photosynthesis and the most common transport form of carbon in plants. In addition, sucrose is a compound that serves as a signal affecting metabolic flux and development. Here we provide first results of externally induced phosphorylation changes of plasma membrane proteins in Arabidopsis. In an unbiased approach, seedlings were grown in liquid medium with sucrose and then depleted of carbon before sucrose was resupplied. Plasma membranes were purified, and phosphopeptides were enriched and subsequently analyzed quantitatively by mass spectrometry. In total, 67 phosphopeptides were identified, most of which were quantified over five time points of sucrose resupply. Among the identified phosphorylation sites, the well described phosphorylation site at the C terminus of plasma membrane H+-ATPases showed a relative increase in phosphorylation level in response to sucrose. This corresponded to a significant increase of proton pumping activity of plasma membrane vesicles from sucrose-supplied seedlings. A new phosphorylation site was identified in the plasma membrane H+-ATPase AHA1 and/or AHA2. This phosphorylation site was shown to be crucial for ATPase activity and overrode regulation via the well known C-terminal phosphorylation site. Novel phosphorylation sites were identified for both receptor kinases and cytosolic kinases that showed rapid increases in relative intensities after short times of sucrose treatment. Seven response classes were identified including non-responsive, rapid increase (within 3 min), slow increase, and rapid decrease. Relative quantification of phosphorylation changes by phosphoproteomics provides a means for identification of fast responses to external stimuli in plants as a basis for further functional characterization.

@article{niittyla_similar_2006,
	title = {Similar {Protein} {Phosphatases} {Control} {Starch} {Metabolism} in {Plants} and {Glycogen} {Metabolism} in {Mammals}*},
	volume = {281},
	issn = {0021-9258},
	url = {https://www.sciencedirect.com/science/article/pii/S0021925819466878},
	doi = {10/fvpqmw},
	abstract = {We report that protein phosphorylation is involved in the control of starch metabolism in Arabidopsis leaves at night. sex4 (starch excess 4) mutants, which have strongly reduced rates of starch metabolism, lack a protein predicted to be a dual specificity protein phosphatase. We have shown that this protein is chloroplastic and can bind to glucans and have presented evidence that it acts to regulate the initial steps of starch degradation at the granule surface. Remarkably, the most closely related protein to SEX4 outside the plant kingdom is laforin, a glucan-binding protein phosphatase required for the metabolism of the mammalian storage carbohydrate glycogen and implicated in a severe form of epilepsy (Lafora disease) in humans.},
	language = {en},
	number = {17},
	urldate = {2021-06-10},
	journal = {Journal of Biological Chemistry},
	author = {Niittylä, Totte and Comparot-Moss, Sylviane and Lue, Wei-Ling and Messerli, Gaëlle and Trevisan, Martine and Seymour, Michael D. J. and Gatehouse, John A. and Villadsen, Dorthe and Smith, Steven M. and Chen, Jychian and Zeeman, Samuel C. and Smith, Alison M.},
	month = apr,
	year = {2006},
	pages = {11815--11818},
}

We report that protein phosphorylation is involved in the control of starch metabolism in Arabidopsis leaves at night. sex4 (starch excess 4) mutants, which have strongly reduced rates of starch metabolism, lack a protein predicted to be a dual specificity protein phosphatase. We have shown that this protein is chloroplastic and can bind to glucans and have presented evidence that it acts to regulate the initial steps of starch degradation at the granule surface. Remarkably, the most closely related protein to SEX4 outside the plant kingdom is laforin, a glucan-binding protein phosphatase required for the metabolism of the mammalian storage carbohydrate glycogen and implicated in a severe form of epilepsy (Lafora disease) in humans.

@article{niittyla_previously_2004,
	title = {A {Previously} {Unknown} {Maltose} {Transporter} {Essential} for {Starch} {Degradation} in {Leaves}},
	volume = {303},
	copyright = {American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	url = {https://science.sciencemag.org/content/303/5654/87},
	doi = {10/dpgjgv},
	abstract = {A previously unknown maltose transporter is essential for the conversion of starch to sucrose in Arabidopsis leaves at night. The transporter was identified by isolating two allelic mutants with high starch levels and very high maltose, an intermediate of starch breakdown. The mutations affect a gene of previously unknown function, MEX1. We show that MEX1is a maltose transporter that is unrelated to other sugar transporters. The severe mex1 phenotype demonstrates that MEX1is the predominant route of carbohydrate export from chloroplasts at night. Homologous genes in plants including rice and potato indicate that maltose export is of widespread significance.},
	language = {en},
	number = {5654},
	urldate = {2021-06-15},
	journal = {Science},
	author = {Niittylä, Totte and Messerli, Gaëlle and Trevisan, Martine and Chen, Jychian and Smith, Alison M. and Zeeman, Samuel C.},
	month = jan,
	year = {2004},
	pmid = {14704427},
	note = {Publisher: American Association for the Advancement of Science
Section: Report},
	pages = {87--89},
}

A previously unknown maltose transporter is essential for the conversion of starch to sucrose in Arabidopsis leaves at night. The transporter was identified by isolating two allelic mutants with high starch levels and very high maltose, an intermediate of starch breakdown. The mutations affect a gene of previously unknown function, MEX1. We show that MEX1is a maltose transporter that is unrelated to other sugar transporters. The severe mex1 phenotype demonstrates that MEX1is the predominant route of carbohydrate export from chloroplasts at night. Homologous genes in plants including rice and potato indicate that maltose export is of widespread significance.

@article{smith_starch_2003,
	title = {Starch {Degradation} in {Leaves}},
	volume = {50},
	doi = {10/gmhq7n},
	abstract = {Study of mutants of the model plant Arabidopsis is providing new information about the nature and regulation of starch degradation in leaves. The onlyoc-amylase currently predicted to be in the chloroplast is not necessary for the initial attack on the starch granule, and the enzyme(s) responsible for this attack remain unknown. A starch-water dikinase that phosphorylates glucose residues in amylopectin is necessary for starch degradation, and it seems likely that the enzyme(s) responsible for the initial attack require either the dikinase itself or phosphorylated regions of amylopectin for their activity. At least four chloroplastic enzymes could potentially debranch glucans released by the initial attack on the granule: the relative importance of these enzymes is not yet known. The degradation of linear glucans to monomers is catalysed by β-amylasesrather than starch phosphorylase. Plants lacking chloroplastic starch phosphorylase have normal rates of starch degradation. The fate of the maltose produced by β-amylolysis of linear glucans is being investigated through study of maltose-accumulating mutants. Other malto-oligosaccharides too short to be attacked by β-amylase are metabolised by disproportionating enzyme to produce longer chains susceptible to further attack. The process of starch degradation is subject to strong diurnal regulation. The nature of this regulation is not understood, but new approaches to the problem are suggested.},
	number = {2},
	journal = {Journal of Applied Glycoscience},
	author = {Smith, Alison M. and Zeeman, Samuel and Niittylä, Totte and Kofler, Heike and Thorneycroft, David and Smith, Steven M.},
	year = {2003},
	keywords = {Arabidopsis, Rl protein, amylase, starch debranching enzyme, starch degradation},
	pages = {173--176},
}

Study of mutants of the model plant Arabidopsis is providing new information about the nature and regulation of starch degradation in leaves. The onlyoc-amylase currently predicted to be in the chloroplast is not necessary for the initial attack on the starch granule, and the enzyme(s) responsible for this attack remain unknown. A starch-water dikinase that phosphorylates glucose residues in amylopectin is necessary for starch degradation, and it seems likely that the enzyme(s) responsible for the initial attack require either the dikinase itself or phosphorylated regions of amylopectin for their activity. At least four chloroplastic enzymes could potentially debranch glucans released by the initial attack on the granule: the relative importance of these enzymes is not yet known. The degradation of linear glucans to monomers is catalysed by β-amylasesrather than starch phosphorylase. Plants lacking chloroplastic starch phosphorylase have normal rates of starch degradation. The fate of the maltose produced by β-amylolysis of linear glucans is being investigated through study of maltose-accumulating mutants. Other malto-oligosaccharides too short to be attacked by β-amylase are metabolised by disproportionating enzyme to produce longer chains susceptible to further attack. The process of starch degradation is subject to strong diurnal regulation. The nature of this regulation is not understood, but new approaches to the problem are suggested.

@article{de_torres_zabela_differential_2002,
	title = {Differential {Expression} of {Genes} {Encoding} {Arabidopsis} {Phospholipases} {After} {Challenge} with {Virulent} or {Avirulent} {Pseudomonas} {Isolates}},
	volume = {15},
	issn = {0894-0282},
	url = {https://apsjournals.apsnet.org/doi/10.1094/MPMI.2002.15.8.808},
	doi = {10.1094/MPMI.2002.15.8.808},
	abstract = {Phospholipase D (PLD; EC 3.1.4.4) has been linked to a number of cellular processes, including Tran membrane signaling and membrane degradation. Four PLD genes (α, β, γ1, and γ2) have been cloned from Arabidopsis thalami. They encode isoforms with distinct regulatory and catalytic properties but little is known about their physiological roles. Using cDNA amplified fragment length polymorphism display and RNA blot analysis, we identified Arabidopsis PLDγ1 and a gene encoding a lysophospholipase (EC 3.1.1.5), lysoPL1, to be differentially expressed during host response to virulent and avirulent pathogen challenge. Examination of the expression pattern of phospholipase genes induced in response to pathogen challenge was undertaken using the lysoPL1 and gene-specific probes corresponding to the PLD isoforms α, β, and γ1. Each mRNA class exhibited different temporal patterns of expression after infiltration of leaves with Pseudomonas syringae pv. tomato with or without avrRpm1. PLDα was rapidly induced and remained constitutively elevated regardless of treatment. PLDβ was transiently induced upon pathogen challenge. However, mRNA for the lysoPL1 and PLDγ1 genes showed enhanced and sustained elevation during an incompatible interaction, in both ndr1 and overexpressing NahG genetic backgrounds. Further evidence for differential engagement of these PLD mRNA during defense responses, other than gene-for-gene interactions, was demonstrated by their response to salicylic acid treatment or wounding. Our results indicate that genes encoding lysoPL1, PLDγ1, and PLDβ are induced during early responses to pathogen challenge and, additionally, PLDγ1 and lysoPL1 are specifically upregulated during gene-for-gene interactions, leading to the hypersensitive response. We discuss the possible role of these genes in plant-pathogen interactions.},
	number = {8},
	urldate = {2021-10-19},
	journal = {Molecular Plant-Microbe Interactions®},
	author = {de Torres Zabela, Marta and Fernandez-Delmond, Isabelle and Niittylä, Totte and Sanchez, Pedro and Grant, Murray},
	month = aug,
	year = {2002},
	note = {Publisher: Scientific Societies},
	keywords = {RPM1},
	pages = {808--816},
}

Phospholipase D (PLD; EC 3.1.4.4) has been linked to a number of cellular processes, including Tran membrane signaling and membrane degradation. Four PLD genes (α, β, γ1, and γ2) have been cloned from Arabidopsis thalami. They encode isoforms with distinct regulatory and catalytic properties but little is known about their physiological roles. Using cDNA amplified fragment length polymorphism display and RNA blot analysis, we identified Arabidopsis PLDγ1 and a gene encoding a lysophospholipase (EC 3.1.1.5), lysoPL1, to be differentially expressed during host response to virulent and avirulent pathogen challenge. Examination of the expression pattern of phospholipase genes induced in response to pathogen challenge was undertaken using the lysoPL1 and gene-specific probes corresponding to the PLD isoforms α, β, and γ1. Each mRNA class exhibited different temporal patterns of expression after infiltration of leaves with Pseudomonas syringae pv. tomato with or without avrRpm1. PLDα was rapidly induced and remained constitutively elevated regardless of treatment. PLDβ was transiently induced upon pathogen challenge. However, mRNA for the lysoPL1 and PLDγ1 genes showed enhanced and sustained elevation during an incompatible interaction, in both ndr1 and overexpressing NahG genetic backgrounds. Further evidence for differential engagement of these PLD mRNA during defense responses, other than gene-for-gene interactions, was demonstrated by their response to salicylic acid treatment or wounding. Our results indicate that genes encoding lysoPL1, PLDγ1, and PLDβ are induced during early responses to pathogen challenge and, additionally, PLDγ1 and lysoPL1 are specifically upregulated during gene-for-gene interactions, leading to the hypersensitive response. We discuss the possible role of these genes in plant-pathogen interactions.

@article{wieloch_new_nodate,
	title = {New insights into the mechanisms of plant isotope fractionation from combined analysis of intramolecular {13C} and deuterium abundances in {Pinus} nigra tree-ring glucose},
	volume = {n/a},
	copyright = {© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.20113},
	doi = {10.1111/nph.20113},
	abstract = {Understanding isotope fractionation mechanisms is fundamental for analyses of plant ecophysiology and paleoclimate based on tree-ring isotope data. To gain new insights into isotope fractionation, we analysed intramolecular 13C discrimination in tree-ring glucose (Δi′, i = C-1 to C-6) and metabolic deuterium fractionation at H1 and H2 (εmet) combinedly. This dual-isotope approach was used for isotope-signal deconvolution. We found evidence for metabolic processes affecting Δ1′ and Δ3′, which respond to air vapour pressure deficit (VPD), and processes affecting Δ1′, Δ2′, and εmet, which respond to precipitation but not VPD. These relationships exhibit change points dividing a period of homeostasis (1961–1980) from a period of metabolic adjustment (1983–1995). Homeostasis may result from sufficient groundwater availability. Additionally, we found Δ5′ and Δ6′ relationships with radiation and temperature, which are temporally stable and consistent with previously proposed isotope fractionation mechanisms. Based on the multitude of climate covariables, intramolecular carbon isotope analysis has a remarkable potential for climate reconstruction. While isotope fractionation beyond leaves is currently considered to be constant, we propose significant parts of the carbon and hydrogen isotope variation in tree-ring glucose originate in stems (precipitation-dependent signals). As basis for follow-up studies, we propose mechanisms introducing Δ1′, Δ2′, Δ3′, and εmet variability.},
	language = {en},
	number = {n/a},
	urldate = {2024-09-27},
	journal = {New Phytologist},
	author = {Wieloch, Thomas and Holloway-Phillips, Meisha and Yu, Jun and Niittylä, Totte},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.20113},
	keywords = {carbon stable isotopes, hydrogen stable isotopes, intramolecular isotope analysis, isotope fractionation mechanisms, leaf water status, plant–environment interactions, stem water status, tree rings},
}

Understanding isotope fractionation mechanisms is fundamental for analyses of plant ecophysiology and paleoclimate based on tree-ring isotope data. To gain new insights into isotope fractionation, we analysed intramolecular 13C discrimination in tree-ring glucose (Δi′, i = C-1 to C-6) and metabolic deuterium fractionation at H1 and H2 (εmet) combinedly. This dual-isotope approach was used for isotope-signal deconvolution. We found evidence for metabolic processes affecting Δ1′ and Δ3′, which respond to air vapour pressure deficit (VPD), and processes affecting Δ1′, Δ2′, and εmet, which respond to precipitation but not VPD. These relationships exhibit change points dividing a period of homeostasis (1961–1980) from a period of metabolic adjustment (1983–1995). Homeostasis may result from sufficient groundwater availability. Additionally, we found Δ5′ and Δ6′ relationships with radiation and temperature, which are temporally stable and consistent with previously proposed isotope fractionation mechanisms. Based on the multitude of climate covariables, intramolecular carbon isotope analysis has a remarkable potential for climate reconstruction. While isotope fractionation beyond leaves is currently considered to be constant, we propose significant parts of the carbon and hydrogen isotope variation in tree-ring glucose originate in stems (precipitation-dependent signals). As basis for follow-up studies, we propose mechanisms introducing Δ1′, Δ2′, Δ3′, and εmet variability.