@article{jeong_phenotyping_2026,
	title = {Phenotyping seasonal photosynthetic energy-partitioning states in temperate evergreen conifers using hyperspectral imaging},
	volume = {8},
	issn = {2643-6515},
	url = {https://www.sciencedirect.com/science/article/pii/S2643651526000786},
	doi = {10.1016/j.plaphe.2026.100241},
	abstract = {Evergreen conifers retain needles and photosynthetic capacity during winter despite prolonged exposure to freezing temperatures and high irradiance, yet it remains unclear which aspects of this seasonal photosynthetic regulation can be reliably detected using passive optical sensing. Here, we phenotype seasonal photosynthetic energy-partitioning states in two temperate evergreen conifers, Pinus densiflora and Pinus koraiensis, by integrating chlorophyll (Chl) fluorescence imaging, pigment analyses, photosynthetic oxygen evolution, and hyperspectral reflectance imaging. Across three years, Chl fluorescence parameters (e.g., Fv/Fm, YPSII, YNPQ, and YNR) indicated reduced PSII photochemical efficiency and increased energy dissipation during winter, accompanied by changes in carotenoid-to-chlorophyll (Car/Chl) ratio, xanthophyll cycle de-epoxidation (DEPS), and photosynthetic oxygen evolution. Despite reduced PSII photochemical efficiency, photosynthetic oxygen evolution and pigment pools remained comparatively stable, indicating that reductions in PSII photochemistry were not accompanied by proportional declines in whole-leaf photosynthetic capacity. These seasonal physiological states were consistently reflected in hyperspectral vegetation indices. Photochemical Reflectance Index (PRI) showed correlations with both regulated (r = 0.57) and non-regulated light energy dissipation (r = −0.67), consistent with its sensitivity to Car/Chl ratio (r = −0.87) and DEPS (r = −0.85). Indices including Fluorescence Curvature Index (FCI) and Ratio Analysis of Reflectance Spectra chlorophyll b (RARSb) showed consistent seasonal correlations with photosynthetic oxygen evolution (r = −0.68 and −0.68), while also reflecting variation in pigment composition (e.g., Chl content; r = 0.73 and 0.78). Drone-based hyperspectral imaging further indicated that these needle-level physiological patterns were detected at the canopy level under the conditions examined. Indices such as FCI exhibited clear seasonal profiles, with separation between summer and winter values. By framing seasonal photosynthetic regulation as a phenotyping problem rather than a mechanistic one, this study provides a data-supported proof-of-concept framework for non-invasive, scalable monitoring of evergreen forests using hyperspectral sensing.},
	number = {3},
	urldate = {2026-06-26},
	journal = {Plant Phenomics},
	author = {Jeong, Seok-Won and Choi, Myoung-Goo and Kim, Young-Won and Kim, Jaewook and Hurry, Vaughan and Ivanov, Alexander G. and Chow, Wah Soon and Park, Youn-Il},
	month = sep,
	year = {2026},
	keywords = {Chlorophyll fluorescence, Cold acclimation, Hyperspectral vegetation indices, PSII energy partitioning, Temperate conifers},
	pages = {100241},
}

Evergreen conifers retain needles and photosynthetic capacity during winter despite prolonged exposure to freezing temperatures and high irradiance, yet it remains unclear which aspects of this seasonal photosynthetic regulation can be reliably detected using passive optical sensing. Here, we phenotype seasonal photosynthetic energy-partitioning states in two temperate evergreen conifers, Pinus densiflora and Pinus koraiensis, by integrating chlorophyll (Chl) fluorescence imaging, pigment analyses, photosynthetic oxygen evolution, and hyperspectral reflectance imaging. Across three years, Chl fluorescence parameters (e.g., Fv/Fm, YPSII, YNPQ, and YNR) indicated reduced PSII photochemical efficiency and increased energy dissipation during winter, accompanied by changes in carotenoid-to-chlorophyll (Car/Chl) ratio, xanthophyll cycle de-epoxidation (DEPS), and photosynthetic oxygen evolution. Despite reduced PSII photochemical efficiency, photosynthetic oxygen evolution and pigment pools remained comparatively stable, indicating that reductions in PSII photochemistry were not accompanied by proportional declines in whole-leaf photosynthetic capacity. These seasonal physiological states were consistently reflected in hyperspectral vegetation indices. Photochemical Reflectance Index (PRI) showed correlations with both regulated (r = 0.57) and non-regulated light energy dissipation (r = −0.67), consistent with its sensitivity to Car/Chl ratio (r = −0.87) and DEPS (r = −0.85). Indices including Fluorescence Curvature Index (FCI) and Ratio Analysis of Reflectance Spectra chlorophyll b (RARSb) showed consistent seasonal correlations with photosynthetic oxygen evolution (r = −0.68 and −0.68), while also reflecting variation in pigment composition (e.g., Chl content; r = 0.73 and 0.78). Drone-based hyperspectral imaging further indicated that these needle-level physiological patterns were detected at the canopy level under the conditions examined. Indices such as FCI exhibited clear seasonal profiles, with separation between summer and winter values. By framing seasonal photosynthetic regulation as a phenotyping problem rather than a mechanistic one, this study provides a data-supported proof-of-concept framework for non-invasive, scalable monitoring of evergreen forests using hyperspectral sensing.

@article{hogberg_improved_2025,
	title = {Improved methodology for tracing a pulse of {13C}-labelled tree photosynthate carbon to ectomycorrhizal roots, other soil biota and soil processes in the field},
	volume = {45},
	issn = {1758-4469},
	url = {https://doi.org/10.1093/treephys/tpae169},
	doi = {10.1093/treephys/tpae169},
	abstract = {Isotopic pulse-labelling of photosynthate allows tracing of carbon (C) from tree canopies to below-ground biota and calculations of its turnover in roots and recipient soil microorganisms. A high concentration of label is desirable but is difficult to achieve in field studies of intact ecosystem patches with trees. Moreover, root systems of trees overlap considerably in most forests, which requires a large labelled area to minimize the impact of C allocated below-ground by un-labelled trees. We describe a method which combines a high level of labelling at ambient concentrations of CO2, [CO2], with undisturbed root systems and a model to account for root C and root-derived C from un-labelled trees. We raised 5-m-tall chambers, each covering 50 m2 of ground (volume 250 m3) in a young boreal Pinus sylvestris L. forest with up to 5 m tall trees. Rather than a conventional single release of 13CO2, we used five consecutive releases, each followed by a draw-down period, thus avoiding high [CO2]. Hence, we elevated successively the 13CO2 from 1.1 to 23 atom\% after the first release to 61 atom\% after the fifth, while maintaining [CO2] below 500 p.p.m. during 4–4.5 h of labelling. The average abundance of 13CO2 was as high as 42 atom\%. We used the central 10 m2 of the 50 m2 area for sampling of roots and other soil biota. We modelled the dilution of labelled C across the plots by un-labelled C from roots of trees outside the area. In the central 10 m2 area, {\textasciitilde}85\% of roots and root-associated biota received C from labelled trees. In summary, we elevated the labelling of roots and associated soil biota four-fold compared with previous studies and described the commonly overlooked impact of roots from un-labelled trees outside the labelled area.},
	number = {1},
	urldate = {2025-02-21},
	journal = {Tree Physiology},
	author = {Högberg, Peter and Klatt, Christian and Franklin, Oskar and Henriksson, Nils and Lim, Hyungwoo and Inselsbacher, Erich and Hurry, Vaughan and Näsholm, Torgny and Högberg, Mona N},
	month = jan,
	year = {2025},
	pages = {tpae169},
}

Isotopic pulse-labelling of photosynthate allows tracing of carbon (C) from tree canopies to below-ground biota and calculations of its turnover in roots and recipient soil microorganisms. A high concentration of label is desirable but is difficult to achieve in field studies of intact ecosystem patches with trees. Moreover, root systems of trees overlap considerably in most forests, which requires a large labelled area to minimize the impact of C allocated below-ground by un-labelled trees. We describe a method which combines a high level of labelling at ambient concentrations of CO2, [CO2], with undisturbed root systems and a model to account for root C and root-derived C from un-labelled trees. We raised 5-m-tall chambers, each covering 50 m2 of ground (volume 250 m3) in a young boreal Pinus sylvestris L. forest with up to 5 m tall trees. Rather than a conventional single release of 13CO2, we used five consecutive releases, each followed by a draw-down period, thus avoiding high [CO2]. Hence, we elevated successively the 13CO2 from 1.1 to 23 atom% after the first release to 61 atom% after the fifth, while maintaining [CO2] below 500 p.p.m. during 4–4.5 h of labelling. The average abundance of 13CO2 was as high as 42 atom%. We used the central 10 m2 of the 50 m2 area for sampling of roots and other soil biota. We modelled the dilution of labelled C across the plots by un-labelled C from roots of trees outside the area. In the central 10 m2 area, ~85% of roots and root-associated biota received C from labelled trees. In summary, we elevated the labelling of roots and associated soil biota four-fold compared with previous studies and described the commonly overlooked impact of roots from un-labelled trees outside the labelled area.

@article{asao_leaf_2025,
	title = {Leaf nonstructural carbohydrate residence time, not concentration, correlates with leaf functional traits following the leaf economic spectrum in woody plants},
	volume = {246},
	copyright = {© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.20315},
	doi = {10.1111/nph.20315},
	abstract = {Nonstructural carbohydrate (NSC) concentrations might reflect the strategies described in the leaf economic spectrum (LES) due to their dependence on photosynthesis and respiration. We examined if NSC concentrations correlate with leaf structure, chemistry, and physiology traits for 114 species from 19 sites and 5 biomes around the globe. Total leaf NSC concentrations varied greatly from 16 to 199 mg g−1 dry mass and were mostly independent of leaf gas exchange and the LES traits. By contrast, leaf NSC residence time was shorter in species with higher rates of photosynthesis, following the fast-slow strategies in the LES. An average leaf held an amount of NSCs that could sustain one night of leaf respiration and could be replenished in just a few hours of photosynthesis under saturating light, indicating that most daily carbon gain is exported. Our results suggest that NSC export is clearly linked to the economics of return on resource investment.},
	language = {en},
	number = {4},
	urldate = {2025-05-09},
	journal = {New Phytologist},
	author = {Asao, Shinichi and Way, Danielle A. and Turnbull, Matthew H. and Stitt, Mark and McDowell, Nate G. and Reich, Peter B. and Bloomfield, Keith J. and Zaragoza-Castells, Joana and Creek, Danielle and O'Sullivan, Odhran and Crous, Kristine Y. and Egerton, John J.G. and Mirotchnick, Nicholas and Weerasinghe, Lasantha K. and Griffin, Kevin L. and Hurry, Vaughan and Meir, Patrick and Sitch, Stephen and Atkin, Owen K.},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.20315},
	keywords = {export, leaf economic spectrum, leaf functional traits, nonstructural carbohydrate, residence time},
	pages = {1505--1519},
}

Nonstructural carbohydrate (NSC) concentrations might reflect the strategies described in the leaf economic spectrum (LES) due to their dependence on photosynthesis and respiration. We examined if NSC concentrations correlate with leaf structure, chemistry, and physiology traits for 114 species from 19 sites and 5 biomes around the globe. Total leaf NSC concentrations varied greatly from 16 to 199 mg g−1 dry mass and were mostly independent of leaf gas exchange and the LES traits. By contrast, leaf NSC residence time was shorter in species with higher rates of photosynthesis, following the fast-slow strategies in the LES. An average leaf held an amount of NSCs that could sustain one night of leaf respiration and could be replenished in just a few hours of photosynthesis under saturating light, indicating that most daily carbon gain is exported. Our results suggest that NSC export is clearly linked to the economics of return on resource investment.

@article{aro_multivariate_2025,
	title = {Multivariate models improve accuracy of genomic prediction for spring frost tolerance in {Norway} spruce},
	volume = {18},
	copyright = {© 2025 The Author(s). The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.},
	issn = {1940-3372},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/tpg2.70151},
	doi = {10.1002/tpg2.70151},
	abstract = {Warming spring temperatures increase the risk of frost damage to emerging Norway spruce (Picea abies) buds by advancing their spring phenology and increasing the frost event frequency. We present a field-based electrolyte leakage assay to assess basal frost tolerance in newly emerging buds. Using this assay, we estimated genetic parameters and tested the effectiveness of multivariate genomic selection (GS) models integrating frost tolerance, bud burst phenology, and height growth. Multivariate models significantly improved frost tolerance prediction accuracy, particularly when incorporating bud burst data, due to a strong genetic correlation between traits (r ≈ –0.63) and high heritability of bud burst (h2 ≈ 0.60). The observed genetic correlations suggest that early-flushing genotypes exhibit higher tolerance to spring frost. Our findings underscore the importance of basal frost tolerance as a complementary trait to traditional phenological frost-avoidance strategies. Additionally, we emphasize that early-stage bud burst assessments in controlled environments can accelerate genomic predictions, overcoming the limitations imposed by long growth cycles. Integrating multi-trait genomic prediction models optimized with bud burst as an assisting trait and optimized model parameters enhances prediction accuracy of spring frost tolerance and supports the development of climate-resilient breeding strategies in Norway spruce.},
	language = {en},
	number = {4},
	urldate = {2025-11-28},
	journal = {The Plant Genome},
	author = {Aro, Tuuli and Tan, Biyue and Chen, Zhi-Qiang and Hallingbäck, Henrik and Suontama, Mari and Westin, Johan and Wu, Harry and Hurry, Vaughan},
	year = {2025},
	note = {\_eprint: https://acsess.onlinelibrary.wiley.com/doi/pdf/10.1002/tpg2.70151},
	pages = {e70151},
}

Warming spring temperatures increase the risk of frost damage to emerging Norway spruce (Picea abies) buds by advancing their spring phenology and increasing the frost event frequency. We present a field-based electrolyte leakage assay to assess basal frost tolerance in newly emerging buds. Using this assay, we estimated genetic parameters and tested the effectiveness of multivariate genomic selection (GS) models integrating frost tolerance, bud burst phenology, and height growth. Multivariate models significantly improved frost tolerance prediction accuracy, particularly when incorporating bud burst data, due to a strong genetic correlation between traits (r ≈ –0.63) and high heritability of bud burst (h2 ≈ 0.60). The observed genetic correlations suggest that early-flushing genotypes exhibit higher tolerance to spring frost. Our findings underscore the importance of basal frost tolerance as a complementary trait to traditional phenological frost-avoidance strategies. Additionally, we emphasize that early-stage bud burst assessments in controlled environments can accelerate genomic predictions, overcoming the limitations imposed by long growth cycles. Integrating multi-trait genomic prediction models optimized with bud burst as an assisting trait and optimized model parameters enhances prediction accuracy of spring frost tolerance and supports the development of climate-resilient breeding strategies in Norway spruce.

@article{jeong_spectral_2025,
	title = {Spectral unmixing of hyperspectral images revealed pine wilt disease sensitive endmembers},
	volume = {177},
	copyright = {© 2025 Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70090},
	doi = {10.1111/ppl.70090},
	abstract = {Throughout the entire cycle of leaf phenological events, leaf colour undergoes changes that are influenced by either abiotic stress or biotic infection. These changes in colouration are closely linked to the quantity and quality of photosynthetic pigments, which directly impact the primary productivity of plants. Therefore, monitoring and quantifying leaf colouration changes are crucial for distinguishing damage caused by pine wilt nematodes from natural tree senescence. In this study, a hyperspectral camera sensor was employed for the non-invasive and non-destructive evaluation of needle colour changes in coniferous trees grown in field tests. Three distinct needle colour variations of six coniferous tree species were selected and monitored using a hyperspectral sensor: those displaying seasonal autumn colours, undergoing nematode-infected necrosis processes, and experiencing natural death. To mitigate the inherently mixed spectral properties of hyperspectral data, endmembers were extracted from individual images using the Purity Pixel Index algorithm under the assumption of linear mixing of endmembers. From a total of 1,321 endmembers extracted from 378 hyperspectral images of six pine species, eight endmembers were ultimately chosen to reconstruct hyperspectral images and generate abundance maps. Among these eight endmembers, four represent varying levels of photosynthetic pigment contents—ranging from very low to high. Consequently, these coniferous endmembers hold promise for assessing seasonal leaf phenology and the extent of damage in pine trees infected by pine wilt nematodes. This comprehensive approach underscores the effectiveness of spectral unmixing of hyperspectral images in advancing precision forestry through meticulous coniferous needle trait analysis.},
	language = {en},
	number = {1},
	urldate = {2025-02-07},
	journal = {Physiologia Plantarum},
	author = {Jeong, Seok Won and Lee, Il Hwan and Kim, Yang-Gil and Kang, Kyu-Suk and Shim, Donghwan and Hurry, Vaughan and Ivanov, Alexander G. and Park, Youn-Il},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70090},
	pages = {e70090},
}

Throughout the entire cycle of leaf phenological events, leaf colour undergoes changes that are influenced by either abiotic stress or biotic infection. These changes in colouration are closely linked to the quantity and quality of photosynthetic pigments, which directly impact the primary productivity of plants. Therefore, monitoring and quantifying leaf colouration changes are crucial for distinguishing damage caused by pine wilt nematodes from natural tree senescence. In this study, a hyperspectral camera sensor was employed for the non-invasive and non-destructive evaluation of needle colour changes in coniferous trees grown in field tests. Three distinct needle colour variations of six coniferous tree species were selected and monitored using a hyperspectral sensor: those displaying seasonal autumn colours, undergoing nematode-infected necrosis processes, and experiencing natural death. To mitigate the inherently mixed spectral properties of hyperspectral data, endmembers were extracted from individual images using the Purity Pixel Index algorithm under the assumption of linear mixing of endmembers. From a total of 1,321 endmembers extracted from 378 hyperspectral images of six pine species, eight endmembers were ultimately chosen to reconstruct hyperspectral images and generate abundance maps. Among these eight endmembers, four represent varying levels of photosynthetic pigment contents—ranging from very low to high. Consequently, these coniferous endmembers hold promise for assessing seasonal leaf phenology and the extent of damage in pine trees infected by pine wilt nematodes. This comprehensive approach underscores the effectiveness of spectral unmixing of hyperspectral images in advancing precision forestry through meticulous coniferous needle trait analysis.

@article{schneider_effects_2024,
	title = {Effects of small-scale outplanting fertilization on conifer seedling growth and fungal community establishment},
	volume = {16},
	issn = {2666-7193},
	url = {https://www.sciencedirect.com/science/article/pii/S266671932400075X},
	doi = {10.1016/j.tfp.2024.100568},
	abstract = {Forestry in Sweden largely relies on planting genetically improved seedlings after clear-cutting, and high survival and early growth of planted seedlings is vital for stand establishment, economic viability, and carbon sequestration. Norway spruce (Picea abies) and Scots pine (Pinus sylvestris) are the two most important tree species in Swedish forest stands and both are associated with a variety of ectomycorrhizal fungi. While seedlings are generally not fertilized at outplanting, previous results have shown that fertilization with arginine phosphate can increase root growth and seedling survival. However, it is not clear how this affects fungal community composition on the roots of growing seedlings. In a planting experiment sampled after one and two growing seasons, we found that planting position had the largest effects both on seedling performance and on fungal community composition and provide insight into the early stages of fungal community succession on planted Norway spruce and Scots pine seedlings. Fungal taxa present on seedlings before planting persisted on seedling roots, while some degree of novel colonization by site indigenous taxa was observed. Fertilization modified the relative abundance of some fungal taxa but did not lead to significant changes in overall community composition. In terms of seedling performance, ammonium nitrate led to increased mortality while arginine phosphate improved root growth.},
	urldate = {2024-06-10},
	journal = {Trees, Forests and People},
	author = {Schneider, Andreas N. and Castro, David and Holmlund, Mattias and Näsholm, Torgny and Hurry, Vaughan and Street, Nathaniel R.},
	month = jun,
	year = {2024},
	keywords = {Ectomycorrhiza, Fertilization, Norway spruce, Rotation forestry, Scots pine, Seedling establishment},
	pages = {100568},
}

Forestry in Sweden largely relies on planting genetically improved seedlings after clear-cutting, and high survival and early growth of planted seedlings is vital for stand establishment, economic viability, and carbon sequestration. Norway spruce (Picea abies) and Scots pine (Pinus sylvestris) are the two most important tree species in Swedish forest stands and both are associated with a variety of ectomycorrhizal fungi. While seedlings are generally not fertilized at outplanting, previous results have shown that fertilization with arginine phosphate can increase root growth and seedling survival. However, it is not clear how this affects fungal community composition on the roots of growing seedlings. In a planting experiment sampled after one and two growing seasons, we found that planting position had the largest effects both on seedling performance and on fungal community composition and provide insight into the early stages of fungal community succession on planted Norway spruce and Scots pine seedlings. Fungal taxa present on seedlings before planting persisted on seedling roots, while some degree of novel colonization by site indigenous taxa was observed. Fertilization modified the relative abundance of some fungal taxa but did not lead to significant changes in overall community composition. In terms of seedling performance, ammonium nitrate led to increased mortality while arginine phosphate improved root growth.

@article{law_metatranscriptomics_2022,
	title = {Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests},
	volume = {119},
	url = {https://www.pnas.org/doi/full/10.1073/pnas.2118852119},
	doi = {10.1073/pnas.2118852119},
	abstract = {Carbon storage and cycling in boreal forests—the largest terrestrial carbon store—is moderated by complex interactions between trees and soil microorganisms. However, existing methods limit our ability to predict how changes in environmental conditions will alter these associations and the essential ecosystem services they provide. To address this, we developed a metatranscriptomic approach to analyze the impact of nutrient enrichment on Norway spruce fine roots and the community structure, function, and tree–microbe coordination of over 350 root-associated fungal species. In response to altered nutrient status, host trees redefined their relationship with the fungal community by reducing sugar efflux carriers and enhancing defense processes. This resulted in a profound restructuring of the fungal community and a collapse in functional coordination between the tree and the dominant Basidiomycete species, and an increase in functional coordination with versatile Ascomycete species. As such, there was a functional shift in community dominance from Basidiomycetes species, with important roles in enzymatically cycling recalcitrant carbon, to Ascomycete species that have melanized cell walls that are highly resistant to degradation. These changes were accompanied by prominent shifts in transcriptional coordination between over 60 predicted fungal effectors, with more than 5,000 Norway spruce transcripts, providing mechanistic insight into the complex molecular dialogue coordinating host trees and their fungal partners. The host–microbe dynamics captured by this study functionally inform how these complex and sensitive biological relationships may mediate the carbon storage potential of boreal soils under changing nutrient conditions.},
	number = {26},
	urldate = {2022-06-22},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Law, Simon R. and Serrano, Alonso R. and Daguerre, Yohann and Sundh, John and Schneider, Andreas N. and Stangl, Zsofia R. and Castro, David and Grabherr, Manfred and Näsholm, Torgny and Street, Nathaniel R. and Hurry, Vaughan},
	month = jun,
	year = {2022},
	pages = {e2118852119},
}

Carbon storage and cycling in boreal forests—the largest terrestrial carbon store—is moderated by complex interactions between trees and soil microorganisms. However, existing methods limit our ability to predict how changes in environmental conditions will alter these associations and the essential ecosystem services they provide. To address this, we developed a metatranscriptomic approach to analyze the impact of nutrient enrichment on Norway spruce fine roots and the community structure, function, and tree–microbe coordination of over 350 root-associated fungal species. In response to altered nutrient status, host trees redefined their relationship with the fungal community by reducing sugar efflux carriers and enhancing defense processes. This resulted in a profound restructuring of the fungal community and a collapse in functional coordination between the tree and the dominant Basidiomycete species, and an increase in functional coordination with versatile Ascomycete species. As such, there was a functional shift in community dominance from Basidiomycetes species, with important roles in enzymatically cycling recalcitrant carbon, to Ascomycete species that have melanized cell walls that are highly resistant to degradation. These changes were accompanied by prominent shifts in transcriptional coordination between over 60 predicted fungal effectors, with more than 5,000 Norway spruce transcripts, providing mechanistic insight into the complex molecular dialogue coordinating host trees and their fungal partners. The host–microbe dynamics captured by this study functionally inform how these complex and sensitive biological relationships may mediate the carbon storage potential of boreal soils under changing nutrient conditions.

@article{vergara_norway_2022,
	title = {Norway spruce deploys tissue-specific responses during acclimation to cold},
	volume = {45},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.14241},
	doi = {10.1111/pce.14241},
	abstract = {Climate change in the conifer-dominated boreal forest is expected to lead to warmer but more dynamic winter air temperatures, reducing the depth and duration of snow cover, which in turn results in colder winter soils. To gain insight into the mechanisms that have enabled conifers to dominate when exposed to extremes of long exposure to freezing temperatures, we performed genome-wide RNA-Seq analysis from needles and roots of non-dormant two-year Norway spruce (Picea abies (L.) H. Karst), and contrasted these response to herbaceous model Arabidopsis We show that, relative to Arabidopsis leaves, the main transcriptional response of Norway spruce (Picea abies (L.) H. Karst) needles exposed to cold was delayed, and this delay was associated with slower development of freezing tolerance. However, despite this difference in timing, our results indicate that Norway spruce principally utilizes early response transcription factors (TFs) belonging to the same gene families as used by Arabidopsis, indicating broad evolutionary conservation of cold response networks. However, needles and root of Norway spruce showed contrasting results, in keeping with their different metabolic and developmental states. Regulatory network analysis identified conserved TFs, including a root-specific bHLH101 homolog, and other members of the same TF family with a pervasive role in cold regulation, such as homologs of ICE1 and AKS3, and also homologs of the NAC (anac47 and anac28) and AP2/ERF superfamilies (DREB2 and ERF3), providing new functional insights into cold stress response strategies in Norway spruce. This article is protected by copyright. All rights reserved.},
	language = {en},
	number = {2},
	urldate = {2021-12-09},
	journal = {Plant, Cell \& Environment},
	author = {Vergara, Alexander and Haas, Julia Christa and Aro, Tuuli and Stachula, Paulina and Street, Nathaniel Robert and Hurry, Vaughan},
	month = feb,
	year = {2022},
	keywords = {Norway spruce, cold, transcriptome},
}

Climate change in the conifer-dominated boreal forest is expected to lead to warmer but more dynamic winter air temperatures, reducing the depth and duration of snow cover, which in turn results in colder winter soils. To gain insight into the mechanisms that have enabled conifers to dominate when exposed to extremes of long exposure to freezing temperatures, we performed genome-wide RNA-Seq analysis from needles and roots of non-dormant two-year Norway spruce (Picea abies (L.) H. Karst), and contrasted these response to herbaceous model Arabidopsis We show that, relative to Arabidopsis leaves, the main transcriptional response of Norway spruce (Picea abies (L.) H. Karst) needles exposed to cold was delayed, and this delay was associated with slower development of freezing tolerance. However, despite this difference in timing, our results indicate that Norway spruce principally utilizes early response transcription factors (TFs) belonging to the same gene families as used by Arabidopsis, indicating broad evolutionary conservation of cold response networks. However, needles and root of Norway spruce showed contrasting results, in keeping with their different metabolic and developmental states. Regulatory network analysis identified conserved TFs, including a root-specific bHLH101 homolog, and other members of the same TF family with a pervasive role in cold regulation, such as homologs of ICE1 and AKS3, and also homologs of the NAC (anac47 and anac28) and AP2/ERF superfamilies (DREB2 and ERF3), providing new functional insights into cold stress response strategies in Norway spruce. This article is protected by copyright. All rights reserved.

@article{castro_soil_2022,
	title = {Soil {Microbiome} {Influences} on {Seedling} {Establishment} and {Growth} of {Prosopis} chilensis and {Prosopis} tamarugo from {Northern} {Chile}},
	volume = {11},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2223-7747},
	url = {https://www.mdpi.com/2223-7747/11/20/2717},
	doi = {10.3390/plants11202717},
	abstract = {Prosopis chilensis and Prosopis tamarugo, two woody legumes adapted to the arid regions of Chile, have a declining distribution due to the lack of new seedling establishment. This study investigated the potential of both species to establish in soil collected from four locations in Chile, within and outside the species distribution, and to assess the role of the root-colonizing microbiome in seedling establishment and growth. Seedling survival, height, and water potential were measured to assess establishment success and growth. 16S and ITS2 amplicon sequencing was used to characterize the composition of microbial communities from the different soils and to assess the ability of both Prosopis species to recruit bacteria and fungi from the different soils. Both species were established on three of the four soils. P. tamarugo seedlings showed significantly higher survival in foreign soils and maintained significantly higher water potential in Mediterranean soils. Amplicon sequencing showed that the four soils harbored distinct microbial communities. Root-associated microbial composition indicated that P. chilensis preferentially recruited mycorrhizal fungal partners while P. tamarugo recruited abundant bacteria with known salt-protective functions. Our results suggest that a combination of edaphic properties and microbial soil legacy are potential factors mediating the Prosopis establishment success in different soils.},
	language = {en},
	number = {20},
	urldate = {2022-10-18},
	journal = {Plants},
	author = {Castro, David and Concha, Christopher and Jamett, Fabiola and Ibáñez, Cristian and Hurry, Vaughan},
	month = oct,
	year = {2022},
	keywords = {\textit{Prosopis chilensis}, \textit{Prosopis tamarugo}, Atacama desert, northern Chile, plant–microbe interactions, soil microbiome},
	pages = {2717},
}

Prosopis chilensis and Prosopis tamarugo, two woody legumes adapted to the arid regions of Chile, have a declining distribution due to the lack of new seedling establishment. This study investigated the potential of both species to establish in soil collected from four locations in Chile, within and outside the species distribution, and to assess the role of the root-colonizing microbiome in seedling establishment and growth. Seedling survival, height, and water potential were measured to assess establishment success and growth. 16S and ITS2 amplicon sequencing was used to characterize the composition of microbial communities from the different soils and to assess the ability of both Prosopis species to recruit bacteria and fungi from the different soils. Both species were established on three of the four soils. P. tamarugo seedlings showed significantly higher survival in foreign soils and maintained significantly higher water potential in Mediterranean soils. Amplicon sequencing showed that the four soils harbored distinct microbial communities. Root-associated microbial composition indicated that P. chilensis preferentially recruited mycorrhizal fungal partners while P. tamarugo recruited abundant bacteria with known salt-protective functions. Our results suggest that a combination of edaphic properties and microbial soil legacy are potential factors mediating the Prosopis establishment success in different soils.

@article{ivanov_decreased_2022,
	title = {The decreased {PG} content of pgp1 inhibits {PSI} photochemistry and limits reaction center and light-harvesting polypeptide accumulation in response to cold acclimation},
	volume = {255},
	issn = {1432-2048},
	url = {https://doi.org/10.1007/s00425-022-03819-0},
	doi = {10/gn64qq},
	abstract = {Decreased PG constrains PSI activity due to inhibition of transcript and polypeptide abundance of light-harvesting and reaction center polypeptides generating a reversible, yellow phenotype during cold acclimation of pgp1.},
	language = {en},
	number = {2},
	urldate = {2022-01-17},
	journal = {Planta},
	author = {Ivanov, Alexander G. and Krol, Marianna and Savitch, Leonid V. and Szyszka-Mroz, Beth and Roche, Jessica and Sprott, D. P. and Selstam, Eva and Wilson, Kenneth W. and Gardiner, Richard and Öquist, Gunnar and Hurry, Vaughan M. and Hüner, Norman P. A.},
	month = jan,
	year = {2022},
	pages = {36},
}

Decreased PG constrains PSI activity due to inhibition of transcript and polypeptide abundance of light-harvesting and reaction center polypeptides generating a reversible, yellow phenotype during cold acclimation of pgp1.

@article{zhu_acclimation_2021,
	title = {Acclimation of leaf respiration temperature responses across thermally contrasting biomes},
	volume = {229},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.16929},
	doi = {10.1111/nph.16929},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Zhu, Lingling and Bloomfield, Keith J. and Asao, Shinichi and Tjoelker, Mark G. and Egerton, John J.G. and Hayes, Lucy and Weerasinghe, Lasantha K. and Creek, Danielle and Griffin, Kevin L. and Hurry, Vaughan and Liddell, Michael and Meir, Patrick and Turnbull, Matthew H. and Atkin, Owen K.},
	month = feb,
	year = {2021},
	pages = {1312--1325},
}

@article{haas_candidate_2021,
	title = {Candidate regulators and target genes of drought stress in needles and roots of {Norway} spruce},
	volume = {41},
	issn = {1758-4469},
	url = {https://doi.org/10.1093/treephys/tpaa178},
	doi = {10.1093/treephys/tpaa178},
	abstract = {Drought stress impacts seedling establishment, survival and whole-plant productivity. Molecular responses to drought stress have been most extensively studied in herbaceous species, mostly considering only aboveground tissues. Coniferous tree species dominate boreal forests, which are predicted to be exposed to more frequent and acute drought as a result of ongoing climate change. The associated impact at all stages of the forest tree life cycle is expected to have large-scale ecological and economic impacts. However, the molecular response to drought has not been comprehensively profiled for coniferous species. We assayed the physiological and transcriptional response of Picea abies (L.) H. Karst seedling needles and roots after exposure to mild and severe drought. Shoots and needles showed an extensive reversible plasticity for physiological measures indicative of drought-response mechanisms, including changes in stomatal conductance (gs), shoot water potential and abscisic acid (ABA). In both tissues, the most commonly observed expression profiles in response to drought were highly correlated with the ABA levels. Still, root and needle transcriptional responses contrasted, with extensive root-specific down-regulation of growth. Comparison between previously characterized Arabidopsis thaliana L. drought-response genes and P. abies revealed both conservation and divergence of transcriptional response to drought. In P. abies, transcription factors belonging to the ABA responsive element(ABRE) binding/ABRE binding factors ABA-dependent pathway had a more limited role. These results highlight the importance of profiling both above- and belowground tissues, and provide a comprehensive framework to advance the understanding of the drought response of P. abies. The results demonstrate that a short-term, severe drought induces severe physiological responses coupled to extensive transcriptome modulation and highlight the susceptibility of Norway spruce seedlings to such drought events.},
	number = {7},
	urldate = {2021-11-04},
	journal = {Tree Physiology},
	author = {Haas, Julia C and Vergara, Alexander and Serrano, Alonso R and Mishra, Sanatkumar and Hurry, Vaughan and Street, Nathaniel R},
	month = jul,
	year = {2021},
	pages = {1230--1246},
}

Drought stress impacts seedling establishment, survival and whole-plant productivity. Molecular responses to drought stress have been most extensively studied in herbaceous species, mostly considering only aboveground tissues. Coniferous tree species dominate boreal forests, which are predicted to be exposed to more frequent and acute drought as a result of ongoing climate change. The associated impact at all stages of the forest tree life cycle is expected to have large-scale ecological and economic impacts. However, the molecular response to drought has not been comprehensively profiled for coniferous species. We assayed the physiological and transcriptional response of Picea abies (L.) H. Karst seedling needles and roots after exposure to mild and severe drought. Shoots and needles showed an extensive reversible plasticity for physiological measures indicative of drought-response mechanisms, including changes in stomatal conductance (gs), shoot water potential and abscisic acid (ABA). In both tissues, the most commonly observed expression profiles in response to drought were highly correlated with the ABA levels. Still, root and needle transcriptional responses contrasted, with extensive root-specific down-regulation of growth. Comparison between previously characterized Arabidopsis thaliana L. drought-response genes and P. abies revealed both conservation and divergence of transcriptional response to drought. In P. abies, transcription factors belonging to the ABA responsive element(ABRE) binding/ABRE binding factors ABA-dependent pathway had a more limited role. These results highlight the importance of profiling both above- and belowground tissues, and provide a comprehensive framework to advance the understanding of the drought response of P. abies. The results demonstrate that a short-term, severe drought induces severe physiological responses coupled to extensive transcriptome modulation and highlight the susceptibility of Norway spruce seedlings to such drought events.

@article{schneider_comparative_2021,
	title = {Comparative {Fungal} {Community} {Analyses} {Using} {Metatranscriptomics} and {Internal} {Transcribed} {Spacer} {Amplicon} {Sequencing} from {Norway} {Spruce}},
	volume = {6},
	issn = {2379-5077},
	url = {https://journals.asm.org/doi/10.1128/mSystems.00884-20},
	doi = {10/gjnmqq},
	abstract = {A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present.
          , 
            ABSTRACT
            
              The health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples. In contrast, phylogenetic marker gene amplicon sequencing data are used to assess taxonomic composition and community structure of the microbiome. Few studies have considered how much of this structural and taxonomic information is included in transcriptomic data from matched samples. Here, we described fungal communities using both host-derived RNA-Seq and fungal ITS1 DNA amplicon sequencing to compare the outcomes between the methods. We used a panel of root and needle samples from the coniferous tree species
              Picea abies
              (Norway spruce) growing in untreated (nutrient-deficient) and nutrient-enriched plots at the Flakaliden forest research site in boreal northern Sweden. We show that the relationship between samples and alpha and beta diversity indicated by the fungal transcriptome is in agreement with that generated by the ITS data, while also identifying a lack of taxonomic overlap due to limitations imposed by current database coverage. Furthermore, we demonstrate how metatranscriptomics data additionally provide biologically informative functional insights. At the community level, there were changes in starch and sucrose metabolism, biosynthesis of amino acids, and pentose and glucuronate interconversions, while processing of organic macromolecules, including aromatic and heterocyclic compounds, was enriched in transcripts assigned to the genus
              Cortinarius
              .
            
            
              IMPORTANCE
              A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. Typically, gene expression studies focus on the plant component or, in a limited number of studies, expression in one or more associated organisms. However, metatranscriptomic data are rarely used for taxonomic profiling, which is currently performed using amplicon approaches. We created an assembly-based, reproducible, and hardware-agnostic workflow to taxonomically and functionally annotate fungal RNA-Seq data obtained from Norway spruce roots, which we compared to matching ITS amplicon sequencing data. While we identified some limitations and caveats, we show that functional, taxonomic, and compositional insights can all be obtained from RNA-Seq data. These findings highlight the potential of metatranscriptomics to advance our understanding of interaction, response, and effect between host plants and their associated microbial communities.},
	language = {en},
	number = {1},
	urldate = {2021-06-03},
	journal = {mSystems},
	author = {Schneider, Andreas N. and Sundh, John and Sundström, Görel and Richau, Kerstin and Delhomme, Nicolas and Grabherr, Manfred and Hurry, Vaughan and Street, Nathaniel R.},
	editor = {McClure, Ryan},
	month = feb,
	year = {2021},
}

A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. , ABSTRACT The health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples. In contrast, phylogenetic marker gene amplicon sequencing data are used to assess taxonomic composition and community structure of the microbiome. Few studies have considered how much of this structural and taxonomic information is included in transcriptomic data from matched samples. Here, we described fungal communities using both host-derived RNA-Seq and fungal ITS1 DNA amplicon sequencing to compare the outcomes between the methods. We used a panel of root and needle samples from the coniferous tree species Picea abies (Norway spruce) growing in untreated (nutrient-deficient) and nutrient-enriched plots at the Flakaliden forest research site in boreal northern Sweden. We show that the relationship between samples and alpha and beta diversity indicated by the fungal transcriptome is in agreement with that generated by the ITS data, while also identifying a lack of taxonomic overlap due to limitations imposed by current database coverage. Furthermore, we demonstrate how metatranscriptomics data additionally provide biologically informative functional insights. At the community level, there were changes in starch and sucrose metabolism, biosynthesis of amino acids, and pentose and glucuronate interconversions, while processing of organic macromolecules, including aromatic and heterocyclic compounds, was enriched in transcripts assigned to the genus Cortinarius . IMPORTANCE A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. Typically, gene expression studies focus on the plant component or, in a limited number of studies, expression in one or more associated organisms. However, metatranscriptomic data are rarely used for taxonomic profiling, which is currently performed using amplicon approaches. We created an assembly-based, reproducible, and hardware-agnostic workflow to taxonomically and functionally annotate fungal RNA-Seq data obtained from Norway spruce roots, which we compared to matching ITS amplicon sequencing data. While we identified some limitations and caveats, we show that functional, taxonomic, and compositional insights can all be obtained from RNA-Seq data. These findings highlight the potential of metatranscriptomics to advance our understanding of interaction, response, and effect between host plants and their associated microbial communities.

@article{castro_effects_2021,
	title = {Effects of {Early}, {Small}-{Scale} {Nitrogen} {Addition} on {Germination} and {Early} {Growth} of {Scots} {Pine} ({Pinus} sylvestris) {Seedlings} and on the {Recruitment} of the {Root}-{Associated} {Fungal} {Community}},
	volume = {12},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	url = {https://www.mdpi.com/1999-4907/12/11/1589},
	doi = {10/gnr3sf},
	abstract = {Scots pine (Pinus sylvestris L.) is one of the most economically important species to the Swedish forest industry, and cost-efficient planting methods are needed to ensure successful reestablishment after harvesting forest stands. While the majority of clear-cuts are replanted with pre-grown seedlings, direct seeding can be a viable option on poorer sites. Organic fertilizer has been shown to improve planted seedling establishment, but the effect on direct seeding is less well known. Therefore, at a scarified (disc trencher harrowed) clear-cut site in northern Sweden, we evaluated the effect of early, small-scale nitrogen addition on establishment and early recruitment of fungi from the disturbed soil community by site-planted Scots pine seeds. Individual seeds were planted using a moisture retaining germination matrix containing 10 mg nitrogen in the form of either arginine phosphate or ammonium nitrate. After one growing season, we collected seedlings and assessed the fungal community of seedling roots and the surrounding soil. Our results demonstrate that early, small-scale N addition increases seedling survival and needle carbon content, that there is rapid recruitment of ectomycorrhizal fungi to the roots and rhizosphere of the young seedlings and that this rapid recruitment was modified but not prevented by N addition.},
	language = {en},
	number = {11},
	urldate = {2021-12-16},
	journal = {Forests},
	author = {Castro, David and Schneider, Andreas N. and Holmlund, Mattias and Näsholm, Torgny and Street, Nathaniel R. and Hurry, Vaughan},
	month = nov,
	year = {2021},
	keywords = {Scots pine, boreal forest, clear-cut, ectomycorrhiza, fungal community composition, mycobiome, nitrogen addition},
	pages = {1589},
}

Scots pine (Pinus sylvestris L.) is one of the most economically important species to the Swedish forest industry, and cost-efficient planting methods are needed to ensure successful reestablishment after harvesting forest stands. While the majority of clear-cuts are replanted with pre-grown seedlings, direct seeding can be a viable option on poorer sites. Organic fertilizer has been shown to improve planted seedling establishment, but the effect on direct seeding is less well known. Therefore, at a scarified (disc trencher harrowed) clear-cut site in northern Sweden, we evaluated the effect of early, small-scale nitrogen addition on establishment and early recruitment of fungi from the disturbed soil community by site-planted Scots pine seeds. Individual seeds were planted using a moisture retaining germination matrix containing 10 mg nitrogen in the form of either arginine phosphate or ammonium nitrate. After one growing season, we collected seedlings and assessed the fungal community of seedling roots and the surrounding soil. Our results demonstrate that early, small-scale N addition increases seedling survival and needle carbon content, that there is rapid recruitment of ectomycorrhizal fungi to the roots and rhizosphere of the young seedlings and that this rapid recruitment was modified but not prevented by N addition.

@article{colesie_differences_2020,
	title = {Differences in growth-economics of fast vs. slow growing grass species in response to temperature and nitrogen limitation individually, and in combination},
	volume = {20},
	issn = {1472-6785},
	url = {https://bmcecol.biomedcentral.com/articles/10.1186/s12898-020-00333-3},
	doi = {10.1186/s12898-020-00333-3},
	abstract = {Abstract
            
              Background
              
                Fast growing invasive alien species are highly efficient with little investment in their tissues. They often outcompete slower growing species with severe consequences for diversity and community composition. The plant economics trait-based approach provides a theoretical framework, allowing the classification of plants with different performance characteristics. However, in multifaceted background, this approach needs testing. The evaluation and prediction of plant performance outcomes in ecologically relevant settings is among the most pressing topics to understand and predict ecosystem functioning, especially in a quickly changing environment. Temperature and nutrient availability are major components of the global environmental change and this study examines the response of growth economic traits, photosynthesis and respiration to such changes for an invasive fast-growing (
                Bromus hordaceus
                ) and a slow-growing perennial (
                Bromus erectus
                ) grass species.
              
            
            
              Results
              
                The fully controlled growth chamber experiment simulated temperature—and changes in nitrogen availability individually and in combination. We therefore provide maximum control and monitoring of growth responses allowing general growth trait response patterns to be tested. Under optimal nitrogen availability the slow growing
                B. erectus
                was better able to handle the lower temperatures (7 °C) whilst both species had problems at higher temperatures (30 °C). Stresses produced by a combination of heat and nutrient availability were identified to be less limiting for the slow growing species but the combination of chilling with low nutrient availability was most detrimental to both species.
              
            
            
              Conclusions
              
                For the fast-growing invader
                B. hordeaceus
                a reduction of nitrogen availability in combination with a temperature increase, leads to limited growth performance in comparison to the slow-growing perennial species
                B.erectus
                and this may explain why nutrient-rich habitats often experience more invasion than resource-poor habitats.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Ecology},
	author = {Colesie, Claudia and Stangl, Zsofia Reka and Hurry, Vaughan},
	month = dec,
	year = {2020},
	pages = {63},
}

Abstract Background Fast growing invasive alien species are highly efficient with little investment in their tissues. They often outcompete slower growing species with severe consequences for diversity and community composition. The plant economics trait-based approach provides a theoretical framework, allowing the classification of plants with different performance characteristics. However, in multifaceted background, this approach needs testing. The evaluation and prediction of plant performance outcomes in ecologically relevant settings is among the most pressing topics to understand and predict ecosystem functioning, especially in a quickly changing environment. Temperature and nutrient availability are major components of the global environmental change and this study examines the response of growth economic traits, photosynthesis and respiration to such changes for an invasive fast-growing ( Bromus hordaceus ) and a slow-growing perennial ( Bromus erectus ) grass species. Results The fully controlled growth chamber experiment simulated temperature—and changes in nitrogen availability individually and in combination. We therefore provide maximum control and monitoring of growth responses allowing general growth trait response patterns to be tested. Under optimal nitrogen availability the slow growing B. erectus was better able to handle the lower temperatures (7 °C) whilst both species had problems at higher temperatures (30 °C). Stresses produced by a combination of heat and nutrient availability were identified to be less limiting for the slow growing species but the combination of chilling with low nutrient availability was most detrimental to both species. Conclusions For the fast-growing invader B. hordeaceus a reduction of nitrogen availability in combination with a temperature increase, leads to limited growth performance in comparison to the slow-growing perennial species B.erectus and this may explain why nutrient-rich habitats often experience more invasion than resource-poor habitats.

@article{yang_two_2020,
	title = {Two dominant boreal conifers use contrasting mechanisms to reactivate photosynthesis in the spring},
	volume = {11},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-019-13954-0},
	doi = {10.1038/s41467-019-13954-0},
	abstract = {Abstract
            
              Boreal forests are dominated by evergreen conifers that show strongly regulated seasonal photosynthetic activity. Understanding the mechanisms behind seasonal modulation of photosynthesis is crucial for predicting how these forests will respond to changes in seasonal patterns and how this will affect their role in the terrestrial carbon cycle. We demonstrate that the two co-occurring dominant boreal conifers, Scots pine (
              Pinus sylvestris L
              .) and Norway spruce
              (Picea abies
              ), use contrasting mechanisms to reactivate photosynthesis in the spring. Scots pine downregulates its capacity for CO
              2
              assimilation during winter and activates alternative electron sinks through accumulation of PGR5 and PGRL1 during early spring until the capacity for CO
              2
              assimilation is recovered. In contrast, Norway spruce lacks this ability to actively switch between different electron sinks over the year and as a consequence suffers severe photooxidative damage during the critical spring period.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Yang, Qi and Blanco, Nicolás E. and Hermida-Carrera, Carmen and Lehotai, Nóra and Hurry, Vaughan and Strand, Åsa},
	month = dec,
	year = {2020},
	pages = {128},
}

Abstract Boreal forests are dominated by evergreen conifers that show strongly regulated seasonal photosynthetic activity. Understanding the mechanisms behind seasonal modulation of photosynthesis is crucial for predicting how these forests will respond to changes in seasonal patterns and how this will affect their role in the terrestrial carbon cycle. We demonstrate that the two co-occurring dominant boreal conifers, Scots pine ( Pinus sylvestris L .) and Norway spruce (Picea abies ), use contrasting mechanisms to reactivate photosynthesis in the spring. Scots pine downregulates its capacity for CO 2 assimilation during winter and activates alternative electron sinks through accumulation of PGR5 and PGRL1 during early spring until the capacity for CO 2 assimilation is recovered. In contrast, Norway spruce lacks this ability to actively switch between different electron sinks over the year and as a consequence suffers severe photooxidative damage during the critical spring period.

@article{vico_can_2019,
	title = {Can leaf net photosynthesis acclimate to rising and more variable temperatures?},
	volume = {42},
	issn = {0140-7791, 1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.13525},
	doi = {10/gjcr7x},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Vico, Giulia and Way, Danielle A. and Hurry, Vaughan and Manzoni, Stefano},
	month = jun,
	year = {2019},
	pages = {1913--1928},
}

@article{bonner_why_2019,
	title = {Why does nitrogen addition to forest soils inhibit decomposition?},
	volume = {137},
	issn = {00380717},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0038071719302342},
	doi = {10.1016/j.soilbio.2019.107570},
	language = {en},
	urldate = {2021-06-07},
	journal = {Soil Biology and Biochemistry},
	author = {Bonner, Mark TL. and Castro, David and Schneider, Andreas N. and Sundström, Görel and Hurry, Vaughan and Street, Nathaniel R. and Näsholm, Torgny},
	month = oct,
	year = {2019},
	pages = {107570},
}

@article{colesie_can_2018,
	title = {Can {Antarctic} lichens acclimatize to changes in temperature?},
	volume = {24},
	issn = {1354-1013, 1365-2486},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.13984},
	doi = {10.1111/gcb.13984},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Global Change Biology},
	author = {Colesie, Claudia and Büdel, Burkhard and Hurry, Vaughan and Green, Thomas George Allan},
	month = mar,
	year = {2018},
	pages = {1123--1135},
}

@article{kurepin_contrasting_2018,
	title = {Contrasting acclimation abilities of two dominant boreal conifers to elevated {CO} $_{\textrm{2}}$ and temperature: {CO} $_{\textrm{2}}$ and warming effects on spruce and pine},
	volume = {41},
	issn = {01407791},
	shorttitle = {Contrasting acclimation abilities of two dominant boreal conifers to elevated {CO} $_{\textrm{2}}$ and temperature},
	url = {http://doi.wiley.com/10.1111/pce.13158},
	doi = {10.1111/pce.13158},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Kurepin, Leonid V. and Stangl, Zsofia R. and Ivanov, Alexander G. and Bui, Vi and Mema, Marin and Hüner, Norman P.A. and Öquist, Gunnar and Way, Danielle and Hurry, Vaughan},
	month = jun,
	year = {2018},
	pages = {1331--1345},
}

@article{haas_microbial_2018,
	title = {Microbial community response to growing season and plant nutrient optimisation in a boreal {Norway} spruce forest},
	volume = {125},
	issn = {00380717},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0038071718302335},
	doi = {10.1016/j.soilbio.2018.07.005},
	language = {en},
	urldate = {2021-06-07},
	journal = {Soil Biology and Biochemistry},
	author = {Haas, Julia C. and Street, Nathaniel R. and Sjödin, Andreas and Lee, Natuschka M. and Högberg, Mona N. and Näsholm, Torgny and Hurry, Vaughan},
	month = oct,
	year = {2018},
	pages = {197--209},
}

@article{metcalfe_informing_2017,
	title = {Informing climate models with rapid chamber measurements of forest carbon uptake},
	volume = {23},
	issn = {13541013},
	url = {http://doi.wiley.com/10.1111/gcb.13451},
	doi = {10/f3vbr8},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Global Change Biology},
	author = {Metcalfe, Daniel B. and Ricciuto, Daniel and Palmroth, Sari and Campbell, Catherine and Hurry, Vaughan and Mao, Jiafu and Keel, Sonja G. and Linder, Sune and Shi, Xiaoying and Näsholm, Torgny and Ohlsson, Klas E. A. and Blackburn, M. and Thornton, Peter E. and Oren, Ram},
	month = may,
	year = {2017},
	pages = {2130--2139},
}

@article{hurry_metabolic_2017,
	title = {Metabolic reprogramming in response to cold stress is like real estate, it's all about location},
	volume = {40},
	copyright = {© 2017 John Wiley \& Sons Ltd},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.12923},
	doi = {https://doi.org/10.1111/pce.12923},
	abstract = {This article comments on: Subcellular reprogramming of metabolism during cold acclimation in Arabidopsis thaliana},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Hurry, Vaughan},
	year = {2017},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.12923},
	pages = {599--601},
}

This article comments on: Subcellular reprogramming of metabolism during cold acclimation in Arabidopsis thaliana

@article{osullivan_thermal_2017,
	title = {Thermal limits of leaf metabolism across biomes},
	volume = {23},
	issn = {13541013},
	url = {http://doi.wiley.com/10.1111/gcb.13477},
	doi = {10/f9hd2s},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Global Change Biology},
	author = {O'sullivan, Odhran S. and Heskel, Mary A. and Reich, Peter B. and Tjoelker, Mark G. and Weerasinghe, Lasantha K. and Penillard, Aurore and Zhu, Lingling and Egerton, John J. G. and Bloomfield, Keith J. and Creek, Danielle and Bahar, Nur H. A. and Griffin, Kevin L. and Hurry, Vaughan and Meir, Patrick and Turnbull, Matthew H. and Atkin, Owen K.},
	month = jan,
	year = {2017},
	pages = {209--223},
}

@article{noren_circadian_2016,
	title = {Circadian and {Plastid} {Signaling} {Pathways} {Are} {Integrated} to {Ensure} {Correct} {Expression} of the {CBF} and {COR} {Genes} during {Photoperiodic} {Growth}},
	volume = {171},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.16.00374},
	doi = {10/f3rvjv},
	abstract = {The circadian clock synchronizes a wide range of biological processes with the day/night cycle, and correct circadian regulation is essential for photosynthetic activity and plant growth. We describe here a mechanism where a plastid signal converges with the circadian clock to fine-tune the regulation of nuclear gene expression in Arabidopsis (Arabidopsis thaliana). Diurnal oscillations of tetrapyrrole levels in the chloroplasts contribute to the regulation of the nucleus-encoded transcription factors C-REPEAT BINDING FACTORS (CBFs). The plastid signal triggered by tetrapyrrole accumulation inhibits the activity of cytosolic HEAT SHOCK PROTEIN90 and, as a consequence, the maturation and stability of the clock component ZEITLUPE (ZTL). ZTL negatively regulates the transcription factor LONG HYPOCOTYL5 (HY5) and PSEUDO-RESPONSE REGULATOR5 (PRR5). Thus, low levels of ZTL result in a HY5- and PRR5-mediated repression of CBF3 and PRR5-mediated repression of CBF1 and CBF2 expression. The plastid signal thereby contributes to the rhythm of CBF expression and the downstream COLD RESPONSIVE expression during day/night cycles. These findings provide insight into how plastid signals converge with, and impact upon, the activity of well-defined clock components involved in circadian regulation.},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Norén, Louise and Kindgren, Peter and Stachula, Paulina and Rühl, Mark and Eriksson, Maria E. and Hurry, Vaughan and Strand, Åsa},
	month = jun,
	year = {2016},
	pages = {1392--1406},
}

The circadian clock synchronizes a wide range of biological processes with the day/night cycle, and correct circadian regulation is essential for photosynthetic activity and plant growth. We describe here a mechanism where a plastid signal converges with the circadian clock to fine-tune the regulation of nuclear gene expression in Arabidopsis (Arabidopsis thaliana). Diurnal oscillations of tetrapyrrole levels in the chloroplasts contribute to the regulation of the nucleus-encoded transcription factors C-REPEAT BINDING FACTORS (CBFs). The plastid signal triggered by tetrapyrrole accumulation inhibits the activity of cytosolic HEAT SHOCK PROTEIN90 and, as a consequence, the maturation and stability of the clock component ZEITLUPE (ZTL). ZTL negatively regulates the transcription factor LONG HYPOCOTYL5 (HY5) and PSEUDO-RESPONSE REGULATOR5 (PRR5). Thus, low levels of ZTL result in a HY5- and PRR5-mediated repression of CBF3 and PRR5-mediated repression of CBF1 and CBF2 expression. The plastid signal thereby contributes to the rhythm of CBF expression and the downstream COLD RESPONSIVE expression during day/night cycles. These findings provide insight into how plastid signals converge with, and impact upon, the activity of well-defined clock components involved in circadian regulation.

@article{heskel_convergence_2016,
	title = {Convergence in the temperature response of leaf respiration across biomes and plant functional types},
	volume = {113},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1520282113},
	doi = {10.1073/pnas.1520282113},
	abstract = {Plant respiration constitutes a massive carbon flux to the atmosphere, and a major control on the evolution of the global carbon cycle. It therefore has the potential to modulate levels of climate change due to the human burning of fossil fuels. Neither current physiological nor terrestrial biosphere models adequately describe its short-term temperature response, and even minor differences in the shape of the response curve can significantly impact estimates of ecosystem carbon release and/or storage. Given this, it is critical to establish whether there are predictable patterns in the shape of the respiration–temperature response curve, and thus in the intrinsic temperature sensitivity of respiration across the globe. Analyzing measurements in a comprehensive database for 231 species spanning 7 biomes, we demonstrate that temperature-dependent increases in leaf respiration do not follow a commonly used exponential function. Instead, we find a decelerating function as leaves warm, reflecting a declining sensitivity to higher temperatures that is remarkably uniform across all biomes and plant functional types. Such convergence in the temperature sensitivity of leaf respiration suggests that there are universally applicable controls on the temperature response of plant energy metabolism, such that a single new function can predict the temperature dependence of leaf respiration for global vegetation. This simple function enables straightforward description of plant respiration in the land-surface components of coupled earth system models. Our cross-biome analyses shows significant implications for such fluxes in cold climates, generally projecting lower values compared with previous estimates.},
	language = {en},
	number = {14},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Heskel, Mary A. and O’Sullivan, Odhran S. and Reich, Peter B. and Tjoelker, Mark G. and Weerasinghe, Lasantha K. and Penillard, Aurore and Egerton, John J. G. and Creek, Danielle and Bloomfield, Keith J. and Xiang, Jen and Sinca, Felipe and Stangl, Zsofia R. and Martinez-de la Torre, Alberto and Griffin, Kevin L. and Huntingford, Chris and Hurry, Vaughan and Meir, Patrick and Turnbull, Matthew H. and Atkin, Owen K.},
	month = apr,
	year = {2016},
	pages = {3832--3837},
}

Plant respiration constitutes a massive carbon flux to the atmosphere, and a major control on the evolution of the global carbon cycle. It therefore has the potential to modulate levels of climate change due to the human burning of fossil fuels. Neither current physiological nor terrestrial biosphere models adequately describe its short-term temperature response, and even minor differences in the shape of the response curve can significantly impact estimates of ecosystem carbon release and/or storage. Given this, it is critical to establish whether there are predictable patterns in the shape of the respiration–temperature response curve, and thus in the intrinsic temperature sensitivity of respiration across the globe. Analyzing measurements in a comprehensive database for 231 species spanning 7 biomes, we demonstrate that temperature-dependent increases in leaf respiration do not follow a commonly used exponential function. Instead, we find a decelerating function as leaves warm, reflecting a declining sensitivity to higher temperatures that is remarkably uniform across all biomes and plant functional types. Such convergence in the temperature sensitivity of leaf respiration suggests that there are universally applicable controls on the temperature response of plant energy metabolism, such that a single new function can predict the temperature dependence of leaf respiration for global vegetation. This simple function enables straightforward description of plant respiration in the land-surface components of coupled earth system models. Our cross-biome analyses shows significant implications for such fluxes in cold climates, generally projecting lower values compared with previous estimates.

@article{kurepin_stress-related_2015,
	title = {Stress-related hormones and glycinebetaine interplay in protection of photosynthesis under abiotic stress conditions},
	volume = {126},
	issn = {1573-5079 (Electronic) 0166-8595 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25823797},
	doi = {10.1007/s11120-015-0125-x},
	abstract = {Plants subjected to abiotic stresses such as extreme high and low temperatures, drought or salinity, often exhibit decreased vegetative growth and reduced reproductive capabilities. This is often associated with decreased photosynthesis via an increase in photoinhibition, and accompanied by rapid changes in endogenous levels of stress-related hormones such as abscisic acid (ABA), salicylic acid (SA) and ethylene. However, certain plant species and/or genotypes exhibit greater tolerance to abiotic stress because they are capable of accumulating endogenous levels of the zwitterionic osmolyte-glycinebetaine (GB). The accumulation of GB via natural production, exogenous application or genetic engineering, enhances plant osmoregulation and thus increases abiotic stress tolerance. The final steps of GB biosynthesis occur in chloroplasts where GB has been shown to play a key role in increasing the protection of soluble stromal and lumenal enzymes, lipids and proteins, of the photosynthetic apparatus. In addition, we suggest that the stress-induced GB biosynthesis pathway may well serve as an additional or alternative biochemical sink, one which consumes excess photosynthesis-generated electrons, thus protecting photosynthetic apparatus from overreduction. Glycinebetaine biosynthesis in chloroplasts is up-regulated by increases in endogenous ABA or SA levels. In this review, we propose and discuss a model describing the close interaction and synergistic physiological effects of GB and ABA in the process of cold acclimation of higher plants.},
	language = {en},
	number = {2-3},
	urldate = {2021-06-07},
	journal = {Photosynth Res},
	author = {Kurepin, L. V. and Ivanov, A. G. and Zaman, M. and Pharis, R. P. and Allakhverdiev, S. I. and Hurry, V. and Huner, N. P.},
	month = dec,
	year = {2015},
	note = {Edition: 2015/04/01},
	keywords = {*Acclimatization, *Stress, Physiological, Abscisic Acid/*metabolism, Abscisic acid, Betaine/*metabolism, Cold Temperature, Cold acclimation, Droughts, Environmental stress, Glycinebetaine, Photosynthesis/*drug effects/physiology, Photosynthetic apparatus, Plant Growth Regulators/*metabolism, Plant hormones, Salinity},
	pages = {221--35},
}

Plants subjected to abiotic stresses such as extreme high and low temperatures, drought or salinity, often exhibit decreased vegetative growth and reduced reproductive capabilities. This is often associated with decreased photosynthesis via an increase in photoinhibition, and accompanied by rapid changes in endogenous levels of stress-related hormones such as abscisic acid (ABA), salicylic acid (SA) and ethylene. However, certain plant species and/or genotypes exhibit greater tolerance to abiotic stress because they are capable of accumulating endogenous levels of the zwitterionic osmolyte-glycinebetaine (GB). The accumulation of GB via natural production, exogenous application or genetic engineering, enhances plant osmoregulation and thus increases abiotic stress tolerance. The final steps of GB biosynthesis occur in chloroplasts where GB has been shown to play a key role in increasing the protection of soluble stromal and lumenal enzymes, lipids and proteins, of the photosynthetic apparatus. In addition, we suggest that the stress-induced GB biosynthesis pathway may well serve as an additional or alternative biochemical sink, one which consumes excess photosynthesis-generated electrons, thus protecting photosynthetic apparatus from overreduction. Glycinebetaine biosynthesis in chloroplasts is up-regulated by increases in endogenous ABA or SA levels. In this review, we propose and discuss a model describing the close interaction and synergistic physiological effects of GB and ABA in the process of cold acclimation of higher plants.

@article{nasholm_genetics_2014,
	title = {Genetics of superior growth traits in trees are being mapped but will the faster-growing risk-takers make it in the wild?},
	volume = {34},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article-lookup/doi/10.1093/treephys/tpu112},
	doi = {10/f3p5bh},
	language = {en},
	number = {11},
	urldate = {2021-06-08},
	journal = {Tree Physiology},
	author = {Nasholm, T. and Palmroth, S. and Ganeteg, U. and Moshelion, M. and Hurry, V. and Franklin, O.},
	month = nov,
	year = {2014},
	pages = {1141--1148},
}

@article{vico_snowed_2014,
	title = {Snowed in for survival: {Quantifying} the risk of winter damage to overwintering field crops in northern temperate latitudes},
	volume = {197},
	issn = {01681923},
	shorttitle = {Snowed in for survival},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0168192314001452},
	doi = {10/f25c8w},
	language = {en},
	urldate = {2021-06-08},
	journal = {Agricultural and Forest Meteorology},
	author = {Vico, Giulia and Hurry, Vaughan and Weih, Martin},
	month = oct,
	year = {2014},
	pages = {65--75},
}

@article{nasholm_are_2013,
	title = {Are ectomycorrhizal fungi alleviating or aggravating nitrogen limitation of tree growth in boreal forests?},
	volume = {198},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.12139},
	doi = {10/f2zz5x},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Näsholm, Torgny and Högberg, Peter and Franklin, Oskar and Metcalfe, Daniel and Keel, Sonja G. and Campbell, Catherine and Hurry, Vaughan and Linder, Sune and Högberg, Mona N.},
	month = apr,
	year = {2013},
	pages = {214--221},
}

@article{kurepin_role_2013,
	title = {Role of {CBFs} as {Integrators} of {Chloroplast} {Redox}, {Phytochrome} and {Plant} {Hormone} {Signaling} during {Cold} {Acclimation}},
	volume = {14},
	issn = {1422-0067},
	url = {http://www.mdpi.com/1422-0067/14/6/12729},
	doi = {10/f23sbq},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {International Journal of Molecular Sciences},
	author = {Kurepin, Leonid and Dahal, Keshav and Savitch, Leonid and Singh, Jas and Bode, Rainer and Ivanov, Alexander and Hurry, Vaughan and Hüner, Norman},
	month = jun,
	year = {2013},
	pages = {12729--12763},
}

@article{keel_allocation_2012,
	title = {Allocation of carbon to fine root compounds and their residence times in a boreal forest depend on root size class and season},
	volume = {194},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2012.04120.x},
	doi = {10/f24b8q},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Keel, Sonja G. and Campbell, Catherine D. and Högberg, Mona N. and Richter, Andreas and Wild, Birgit and Zhou, Xuhui and Hurry, Vaughan and Linder, Sune and Näsholm, Torgny and Högberg, Peter},
	month = jun,
	year = {2012},
	pages = {972--981},
}

@article{ivanov_implications_2012,
	title = {Implications of alternative electron sinks in increased resistance of {PSII} and {PSI} photochemistry to high light stress in cold-acclimated {Arabidopsis} thaliana},
	volume = {113},
	issn = {0166-8595, 1573-5079},
	url = {http://link.springer.com/10.1007/s11120-012-9769-y},
	doi = {10/f23h5g},
	language = {en},
	number = {1-3},
	urldate = {2021-06-08},
	journal = {Photosynthesis Research},
	author = {Ivanov, A. G. and Rosso, D. and Savitch, L. V. and Stachula, P. and Rosembert, M. and Oquist, G. and Hurry, V. and Hüner, N. P. A.},
	month = sep,
	year = {2012},
	pages = {191--206},
}

@article{searle_leaf_2011,
	title = {Leaf respiration and alternative oxidase in field‐grown alpine grasses respond to natural changes in temperature and light},
	volume = {189},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2010.03557.x},
	doi = {10/bjq25k},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Searle, Stephanie Y. and Thomas, Samuel and Griffin, Kevin L. and Horton, Travis and Kornfeld, Ari and Yakir, Dan and Hurry, Vaughan and Turnbull, Matthew H.},
	month = mar,
	year = {2011},
	pages = {1027--1039},
}

@article{atkinson_impact_2010,
	title = {Impact of growth temperature on scaling relationships linking photosynthetic metabolism to leaf functional traits: {Impacts} of growth temperature on scaling relationships},
	volume = {24},
	issn = {02698463},
	shorttitle = {Impact of growth temperature on scaling relationships linking photosynthetic metabolism to leaf functional traits},
	url = {http://doi.wiley.com/10.1111/j.1365-2435.2010.01758.x},
	doi = {10/dmdkm7},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Functional Ecology},
	author = {Atkinson, Lindsey J. and Campbell, Catherine D. and Zaragoza-Castells, Joana and Hurry, Vaughan and Atkin, Owen K.},
	month = dec,
	year = {2010},
	pages = {1181--1191},
}

@article{metcalfe_impacts_2010,
	title = {Impacts of experimentally imposed drought on leaf respiration and morphology in an {Amazon} rain forest: {Drought} affects rain forest leaf respiration},
	volume = {24},
	issn = {02698463},
	shorttitle = {Impacts of experimentally imposed drought on leaf respiration and morphology in an {Amazon} rain forest},
	url = {http://doi.wiley.com/10.1111/j.1365-2435.2009.01683.x},
	doi = {10/cpr644},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Functional Ecology},
	author = {Metcalfe, Daniel B. and Lobo-do-Vale, Raquel and Chaves, Manuela M. and Maroco, Joao P. and C Aragão, Luiz E. O. and Malhi, Yadvinder and Da Costa, Antonio L. and Braga, Alan P. and Gonçalves, Paulo L. and De Athaydes, Joao and Da Costa, Mauricio and Almeida, Samuel S. and Campbell, Catherine and Hurry, Vaughan and Williams, Mathew and Meir, Patrick},
	month = jun,
	year = {2010},
	pages = {524--533},
}

@article{hogberg_quantification_2010,
	title = {Quantification of effects of season and nitrogen supply on tree below‐ground carbon transfer to ectomycorrhizal fungi and other soil organisms in a boreal pine forest},
	volume = {187},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2010.03274.x},
	doi = {10/b9nhbk},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Högberg, Mona N. and Briones, Maria J. I. and Keel, Sonja G. and Metcalfe, Daniel B. and Campbell, Catherine and Midwood, Andrew J. and Thornton, Barry and Hurry, Vaughan and Linder, Sune and Näsholm, Torgny and Högberg, Peter},
	month = jul,
	year = {2010},
	pages = {485--493},
}

@incollection{ruelland_chapter_2009,
	title = {Chapter 2 {Cold} {Signalling} and {Cold} {Acclimation} in {Plants}},
	volume = {49},
	isbn = {978-0-12-374735-8},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0065229608006022},
	doi = {10.1016/S0065-2296(08)00602-2},
	language = {en},
	urldate = {2021-06-08},
	booktitle = {Advances in {Botanical} {Research}},
	publisher = {Elsevier},
	author = {Ruelland, Eric and Vaultier, Marie-Noelle and Zachowski, Alain and Hurry, Vaughan},
	year = {2009},
	pages = {35--150},
}

@article{lundmark_low_2009,
	title = {Low temperature maximizes growth of {Crocus} vernus ({L}.) {Hill} via changes in carbon partitioning and corm development},
	volume = {60},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/erp103},
	doi = {10/c9zwbh},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Lundmark, M. and Hurry, V. and Lapointe, L.},
	month = may,
	year = {2009},
	pages = {2203--2213},
}

@article{atkin_temperature_2009,
	title = {Temperature dependence of respiration in roots colonized by arbuscular mycorrhizal fungi},
	volume = {182},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2008.02727.x},
	doi = {10/djs8g3},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Atkin, Owen K. and Sherlock, David and Fitter, Alastair H. and Jarvis, Susan and Hughes, John K. and Campbell, Catherine and Hurry, Vaughan and Hodge, Angela},
	month = apr,
	year = {2009},
	pages = {188--199},
}

@article{hogberg_high_2008,
	title = {High temporal resolution tracing of photosynthate carbon from the tree canopy to forest soil microorganisms},
	volume = {177},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2007.02238.x},
	doi = {10/d2q3v2},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {New Phytologist},
	author = {Högberg, P. and Högberg, M. N. and Göttlicher, S. G. and Betson, N. R. and Keel, S. G. and Metcalfe, D. B. and Campbell, C. and Schindlbacher, A. and Hurry, V. and Lundmark, T. and Linder, S. and Näsholm, T.},
	month = jan,
	year = {2008},
	pages = {220--228},
}

@article{ivanov_photosystem_2008,
	title = {Photosystem {II} reaction centre quenching: mechanisms and physiological role},
	volume = {98},
	issn = {0166-8595, 1573-5079},
	shorttitle = {Photosystem {II} reaction centre quenching},
	url = {http://link.springer.com/10.1007/s11120-008-9365-3},
	doi = {10/b9ssbn},
	language = {en},
	number = {1-3},
	urldate = {2021-06-10},
	journal = {Photosynthesis Research},
	author = {Ivanov, Alexander G. and Sane, Prafullachandra V. and Hurry, Vaughan and Öquist, Gunnar and Huner, Norman P. A.},
	month = oct,
	year = {2008},
	pages = {565--574},
}

@article{ivanov_reaction_2008,
	title = {Reaction centre quenching of excess light energy and photoprotection of photosystem {II}},
	volume = {51},
	issn = {1867-0725},
	url = {https://doi.org/10.1007/BF03030716},
	doi = {10/frvq84},
	abstract = {In addition to the energy dissipation of excess light occurring in PSII antenna via the xanthophyll cycle, there is mounting evidence of a zeaxanthin-independent pathway for non-photochemical quenching based within the PSII reaction centre (reaction centre quenching) that may also play a significant role in photoprotection. It has been demonstrated that acclimation of higher plants, green algae and cyanobacteria to low temperature or high light conditions which potentially induce an imbalance between energy supply and energy utilization is accompanied by the development of higher reduction state of QA and higher resistance to photoinhibition (Huner et al., 1998). Although this is a fundamental feature of all photoautotrophs, and the acquisition of increased tolerance to photoinhibition has been ascribed to growth and development under high PSII excitation pressure, the precise mechanism controlling the redox state of QA and its physiological significance in developing higher resistance to photoinhibition has not been fully elucidated. In this review we summarize recent data indicating that the increased resistance to high light in a broad spectrum of photosynthetic organisms acclimated to high excitation pressure conditions is associated with an increase probability for alternative non-radiative P680+QA- radical pair recombination pathway for energy dissipation within the reaction centre of PSII. The various molecular mechanisms that could account for non-photochemical quenching through PSII reaction centre are also discussed.},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Journal of Plant Biology},
	author = {Ivanov, Alexander G. and Hurry, Vaughan and Sane, Prafullachandra V. and Öquist, Gunnar and Huner, Norman P. A.},
	month = mar,
	year = {2008},
	pages = {85},
}

In addition to the energy dissipation of excess light occurring in PSII antenna via the xanthophyll cycle, there is mounting evidence of a zeaxanthin-independent pathway for non-photochemical quenching based within the PSII reaction centre (reaction centre quenching) that may also play a significant role in photoprotection. It has been demonstrated that acclimation of higher plants, green algae and cyanobacteria to low temperature or high light conditions which potentially induce an imbalance between energy supply and energy utilization is accompanied by the development of higher reduction state of QA and higher resistance to photoinhibition (Huner et al., 1998). Although this is a fundamental feature of all photoautotrophs, and the acquisition of increased tolerance to photoinhibition has been ascribed to growth and development under high PSII excitation pressure, the precise mechanism controlling the redox state of QA and its physiological significance in developing higher resistance to photoinhibition has not been fully elucidated. In this review we summarize recent data indicating that the increased resistance to high light in a broad spectrum of photosynthetic organisms acclimated to high excitation pressure conditions is associated with an increase probability for alternative non-radiative P680+QA- radical pair recombination pathway for energy dissipation within the reaction centre of PSII. The various molecular mechanisms that could account for non-photochemical quenching through PSII reaction centre are also discussed.

@article{atkin_using_2008,
	title = {Using temperature-dependent changes in leaf scaling relationships to quantitatively account for thermal acclimation of respiration in a coupled global climate-vegetation model: {THERMAL} {HISTORY} {AND} {RESPIRATORY} {ACCLIMATION}},
	volume = {14},
	issn = {13541013},
	shorttitle = {Using temperature-dependent changes in leaf scaling relationships to quantitatively account for thermal acclimation of respiration in a coupled global climate-vegetation model},
	url = {http://doi.wiley.com/10.1111/j.1365-2486.2008.01664.x},
	doi = {10/fk2hwr},
	language = {en},
	number = {11},
	urldate = {2021-06-10},
	journal = {Global Change Biology},
	author = {Atkin, Owen K. and Atkinson, Lindsey J. and Fisher, Rosie A. and Campbell, Catherine D. and Zaragoza-Castells, Joana and Pitchford, Jon W. and Woodward, F. Ian and Hurry, Vaughan},
	month = nov,
	year = {2008},
	pages = {2709--2726},
}

@article{campbell_acclimation_2007,
	title = {Acclimation of photosynthesis and respiration is asynchronous in response to changes in temperature regardless of plant functional group},
	volume = {176},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2007.02183.x},
	doi = {10/b82dn5},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {New Phytologist},
	author = {Campbell, Catherine and Atkinson, Lindsey and Zaragoza‐Castells, Joana and Lundmark, Maria and Atkin, Owen and Hurry, Vaughan},
	month = oct,
	year = {2007},
	pages = {375--389},
}

@article{zaragoza-castells_does_2007,
	title = {Does growth irradiance affect temperature dependence and thermal acclimation of leaf respiration? {Insights} from a {Mediterranean} tree with long-lived leaves},
	volume = {30},
	issn = {0140-7791, 1365-3040},
	shorttitle = {Does growth irradiance affect temperature dependence and thermal acclimation of leaf respiration?},
	url = {http://doi.wiley.com/10.1111/j.1365-3040.2007.01672.x},
	doi = {10/dm64zx},
	language = {en},
	number = {7},
	urldate = {2021-06-10},
	journal = {Plant, Cell \& Environment},
	author = {Zaragoza-Castells, Joana and Sánchez-Gómez, David and Valladares, Fernando and Hurry, Vaughan and Atkin, Owen K.},
	month = jul,
	year = {2007},
	pages = {820--833},
}

@article{keech_different_2007,
	title = {The different fates of mitochondria and chloroplasts during dark-induced senescence in {Arabidopsis} leaves},
	volume = {30},
	issn = {0140-7791, 1365-3040},
	url = {http://doi.wiley.com/10.1111/j.1365-3040.2007.01724.x},
	doi = {10/bpfzq8},
	language = {en},
	number = {12},
	urldate = {2021-06-10},
	journal = {Plant, Cell \& Environment},
	author = {Keech, Olivier and Pesquet, Edouard and Ahad, Abdul and Askne, Anna and Nordvall, Dag and Vodnala, Sharvani Munender and Tuominen, Hannele and Hurry, Vaughan and Dizengremel, Pierre and Gardeström, Per},
	month = dec,
	year = {2007},
	pages = {1523--1534},
}

@article{hjalten_unintentional_2007,
	title = {Unintentional changes of defence traits in {GM} trees can influence plant–herbivore interactions},
	volume = {8},
	issn = {14391791},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1439179106000855},
	doi = {10/drg7p8},
	language = {en},
	number = {5},
	urldate = {2021-06-10},
	journal = {Basic and Applied Ecology},
	author = {Hjältén, Joakim and Lindau, Anna and Wennström, Anders and Blomberg, Patrik and Witzell, Johanna and Hurry, Vaughan and Ericson, Lars},
	month = sep,
	year = {2007},
	pages = {434--443},
}

@article{zheng_nuclear-encoded_2006,
	title = {A nuclear-encoded {ClpP} subunit of the chloroplast {ATP}-dependent {Clp} protease is essential for early development in {Arabidopsis} thaliana},
	volume = {224},
	issn = {1432-2048},
	url = {https://doi.org/10.1007/s00425-006-0292-2},
	doi = {10/bw57xc},
	abstract = {ClpP4 is a nuclear-encoded plastid protein that functions as a proteolytic subunit of the ATP-dependent Clp protease of higher plants. Given the lack of viable clpP4 knockout mutants, antisense clpP4 repression lines were prepared to study the functional importance of ClpP4 in Arabidopsis thaliana. Screening of transformants revealed viable lines with up to 90\% loss of wild type levels of ClpP4 protein, while those with {\textgreater} 90\% were severely bleached and strongly retarded in vegetative growth, failing to reach reproductive maturity. Of the viable antisense plants, repression of clpP4 expression produced a pleiotropic phenotype, of which slow growth and leaf variegation were most prominent. Chlorosis was most severe in younger leaves, with the affected regions localized around the mid-vein and exhibiting impaired chloroplast development and mesophyll cell differentiation. Chlorosis lessened during leaf expansion until all had regained the wild type appearance upon maturity. This change in phenotype correlated with the developmental expression of ClpP4 in the wild type, in which ClpP4 was less abundant in mature leaves due to post-transcriptional/translational regulation. Repression of ClpP4 caused a concomitant down-regulation of other nuclear-encoded ClpP paralogs in the antisense lines, but no change in other chloroplast-localized Clp proteins. Greening of the young chlorotic antisense plants upon maturation was accelerated by increased light, either by longer photoperiod or by higher growth irradiance; conditions that both raised levels of ClpP4 in wild type leaves. In contrast, shift to low growth irradiance decreased the relative amount of ClpP4 in wild type leaves, and caused newly developed leaves of fully greened antisense lines to regain the chlorotic phenotype.},
	language = {en},
	number = {5},
	urldate = {2021-06-11},
	journal = {Planta},
	author = {Zheng, Bo and MacDonald, Tara M. and Sutinen, Sirkka and Hurry, Vaughan and Clarke, Adrian K.},
	month = oct,
	year = {2006},
	keywords = {Arabidopsis, Clp proteins, chloroplast, complexes, escherichia-coli, ftsh, gene, identification, leaf development, leaf variegation, mitochondria, norway spruce, protease, proteins, translocation},
	pages = {1103--1115},
}

ClpP4 is a nuclear-encoded plastid protein that functions as a proteolytic subunit of the ATP-dependent Clp protease of higher plants. Given the lack of viable clpP4 knockout mutants, antisense clpP4 repression lines were prepared to study the functional importance of ClpP4 in Arabidopsis thaliana. Screening of transformants revealed viable lines with up to 90% loss of wild type levels of ClpP4 protein, while those with \textgreater 90% were severely bleached and strongly retarded in vegetative growth, failing to reach reproductive maturity. Of the viable antisense plants, repression of clpP4 expression produced a pleiotropic phenotype, of which slow growth and leaf variegation were most prominent. Chlorosis was most severe in younger leaves, with the affected regions localized around the mid-vein and exhibiting impaired chloroplast development and mesophyll cell differentiation. Chlorosis lessened during leaf expansion until all had regained the wild type appearance upon maturity. This change in phenotype correlated with the developmental expression of ClpP4 in the wild type, in which ClpP4 was less abundant in mature leaves due to post-transcriptional/translational regulation. Repression of ClpP4 caused a concomitant down-regulation of other nuclear-encoded ClpP paralogs in the antisense lines, but no change in other chloroplast-localized Clp proteins. Greening of the young chlorotic antisense plants upon maturation was accelerated by increased light, either by longer photoperiod or by higher growth irradiance; conditions that both raised levels of ClpP4 in wild type leaves. In contrast, shift to low growth irradiance decreased the relative amount of ClpP4 in wild type leaves, and caused newly developed leaves of fully greened antisense lines to regain the chlorotic phenotype.

@article{ivanov_characterization_2006,
	title = {Characterization of the photosynthetic apparatus in cortical bark chlorenchyma of {Scots} pine},
	volume = {223},
	issn = {0032-0935},
	doi = {10/dpb2b4},
	abstract = {Winter-induced inhibition of photosynthesis in Scots pine (Pinus sylvestris L.) needles is accompanied by a 65\% reduction of the maximum photochemical efficiency of photosystem II (PSII), measured as F (v)/F (m), but relatively stable photosystem I (PSI) activity. In contrast, the photochemical efficiency of PSII in bark chlorenchyma of Scots pine twigs was shown to be well preserved, while PSI capacity was severely decreased. Low-temperature (77 K) chlorophyll fluorescence measurements also revealed lower relative fluorescence intensity emitted from PSI in bark chlorenchyma compared to needles regardless of the growing season. Nondenaturating SDS-PAGE analysis of the chlorophyll-protein complexes also revealed much lower abundance of LHCI and the CPI band related to light harvesting and the core complex of PSI, respectively, in bark chlorenchyma. These changes were associated with a 38\% reduction in the total amount of chlorophyll in the bark chlorenchyma relative to winter needles, but the Chl a/b ratio and carotenoid composition were similar in the two tissues. As distinct from winter pine needles exhibiting ATP/ADP ratio of 11.3, the total adenylate content in winter bark chlorenchyma was 2.5-fold higher and the estimated ATP/ADP ratio was 20.7. The photochemical efficiency of PSII in needles attached to the twig recovered significantly faster (28-30 h) then in detached needles. Fluorescence quenching analysis revealed a high reduction state of Q (A) and the PQ-pool in the green bark tissue. The role of bark chlorenchyma and its photochemical performance during the recovery of photosynthesis from winter stress in Scots pine is discussed.},
	language = {English},
	number = {6},
	journal = {Planta},
	publisher = {Springer},
	author = {Ivanov, A. G. and Krol, M. and Sveshnikov, D. and Malmberg, G. and Gardestrom, P. and Hurry, V. and Oquist, G. and Huner, N. P. A.},
	month = may,
	year = {2006},
	note = {Place: New York
WOS:000237335300006},
	keywords = {Pinus needles, absorbency changes, bark chlorenchyma, c-4   photosynthesis, chlorophyll fluorescence, co2 fixation, electron-transport, energy partitioning P700, fagus-sylvatica, nad-malic enzyme, photosystem-ii, recovery of photosynthesis, seasonal-changes, stem tissues},
	pages = {1165--1177},
}

Winter-induced inhibition of photosynthesis in Scots pine (Pinus sylvestris L.) needles is accompanied by a 65% reduction of the maximum photochemical efficiency of photosystem II (PSII), measured as F (v)/F (m), but relatively stable photosystem I (PSI) activity. In contrast, the photochemical efficiency of PSII in bark chlorenchyma of Scots pine twigs was shown to be well preserved, while PSI capacity was severely decreased. Low-temperature (77 K) chlorophyll fluorescence measurements also revealed lower relative fluorescence intensity emitted from PSI in bark chlorenchyma compared to needles regardless of the growing season. Nondenaturating SDS-PAGE analysis of the chlorophyll-protein complexes also revealed much lower abundance of LHCI and the CPI band related to light harvesting and the core complex of PSI, respectively, in bark chlorenchyma. These changes were associated with a 38% reduction in the total amount of chlorophyll in the bark chlorenchyma relative to winter needles, but the Chl a/b ratio and carotenoid composition were similar in the two tissues. As distinct from winter pine needles exhibiting ATP/ADP ratio of 11.3, the total adenylate content in winter bark chlorenchyma was 2.5-fold higher and the estimated ATP/ADP ratio was 20.7. The photochemical efficiency of PSII in needles attached to the twig recovered significantly faster (28-30 h) then in detached needles. Fluorescence quenching analysis revealed a high reduction state of Q (A) and the PQ-pool in the green bark tissue. The role of bark chlorenchyma and its photochemical performance during the recovery of photosynthesis from winter stress in Scots pine is discussed.

@article{hendrickson_cold_2006,
	title = {Cold acclimation of the {Arabidopsis} dgd1 mutant results in recovery from photosystem {I}-limited photosynthesis},
	volume = {580},
	issn = {0014-5793},
	url = {https://www.sciencedirect.com/science/article/pii/S0014579306009495},
	doi = {10.1016/j.febslet.2006.07.081},
	abstract = {We compared the thylakoid membrane composition and photosynthetic properties of non- and cold-acclimated leaves from the dgd1 mutant (lacking {\textgreater}90\% of digalactosyl–diacylglycerol; DGDG) and wild type (WT) Arabidopsis thaliana. In contrast to warm grown plants, cold-acclimated dgd1 leaves recovered pigment-protein pools and photosynthetic function equivalent to WT. Surprisingly, this recovery was not correlated with an increase in DGDG. When returned to warm temperatures the severe dgd1 mutant phenotype reappeared. We conclude that the relative recovery of photosynthetic activity at 5°C resulted from a temperature/lipid interaction enabling the stable assembly of PSI complexes in the thylakoid.},
	language = {en},
	number = {20},
	urldate = {2021-06-11},
	journal = {FEBS Letters},
	author = {Hendrickson, Luke and Vlčková, Alexandra and Selstam, Eva and Huner, Norman and Öquist, Gunnar and Hurry, Vaughan},
	month = sep,
	year = {2006},
	keywords = {Cold acclimation, Digalactosyl–diacylglycerol, Lipid, Monogalactosyl–diacylglycerol, P700, Phosphatidylglycerol, Photosynthesis, Photosystem I, Photosystem II, chloroplast thylakoids, cold acclimation, deficient, digalactosyl-diacylglycerol, galactolipids, leaves, lipid, membrane-proteins, monogalactosyl-diacylglycerol, nonbilayer lipids, p700, phosphatidylglycerol, photoinhibition, photosynthesis, photosystem I, photosystem II, plants, temperature, unsaturation},
	pages = {4959--4968},
}

We compared the thylakoid membrane composition and photosynthetic properties of non- and cold-acclimated leaves from the dgd1 mutant (lacking \textgreater90% of digalactosyl–diacylglycerol; DGDG) and wild type (WT) Arabidopsis thaliana. In contrast to warm grown plants, cold-acclimated dgd1 leaves recovered pigment-protein pools and photosynthetic function equivalent to WT. Surprisingly, this recovery was not correlated with an increase in DGDG. When returned to warm temperatures the severe dgd1 mutant phenotype reappeared. We conclude that the relative recovery of photosynthetic activity at 5°C resulted from a temperature/lipid interaction enabling the stable assembly of PSI complexes in the thylakoid.

@article{benedict_consensus_2006,
	title = {Consensus by democracy. {Using} meta-analyses of microarray and genomic data to model the cold acclimation signaling pathway in {Arabidopsis}},
	volume = {141},
	issn = {0032-0889},
	doi = {10/fhmj9k},
	abstract = {The whole-genome response of Arabidopsis ( Arabidopsis thaliana) exposed to different types and durations of abiotic stress has now been described by a wealth of publicly available microarray data. When combined with studies of how gene expression is affected in mutant and transgenic Arabidopsis with altered ability to transduce the low temperature signal, these data can be used to test the interactions between various low temperature-associated transcription factors and their regulons. We quantized a collection of Affymetrix microarray data so that each gene in a particular regulon could vote on whether a cis-element found in its promoter conferred induction ( 11), repression (21), or no transcriptional change (0) during cold stress. By statistically comparing these election results with the voting behavior of all genes on the same gene chip, we verified the bioactivity of novel cis-elements and defined whether they were inductive or repressive. Using in silico mutagenesis we identified functional binding consensus variants for the transcription factors studied. Our results suggest that the previously identified ICEr1 ( induction of CBF expression region 1) consensus does not correlate with cold gene induction, while the ICEr3/ICEr4 consensuses identified using our algorithms are present in regulons of genes that were induced coordinate with observed ICE1 transcript accumulation and temporally preceding genes containing the dehydration response element. Statistical analysis of overlap and cis-element enrichment in the ICE1, CBF2, ZAT12, HOS9, and PHYA regulons enabled us to construct a regulatory network supported by multiple lines of evidence that can be used for future hypothesis testing.},
	language = {English},
	number = {4},
	journal = {Plant Physiology},
	publisher = {Amer Soc Plant Biologists},
	author = {Benedict, Catherine and Geisler, Matt and Trygg, Johan and Huner, Norman and Hurry, Vaughan},
	month = aug,
	year = {2006},
	note = {Place: Rockville
WOS:000239636800007},
	keywords = {element, freezing tolerance, identification, low-temperature induction, osmotic-stress, promoter, regulated gene-expression, sequence, thaliana, transcription   factors},
	pages = {1219--1232},
}

The whole-genome response of Arabidopsis ( Arabidopsis thaliana) exposed to different types and durations of abiotic stress has now been described by a wealth of publicly available microarray data. When combined with studies of how gene expression is affected in mutant and transgenic Arabidopsis with altered ability to transduce the low temperature signal, these data can be used to test the interactions between various low temperature-associated transcription factors and their regulons. We quantized a collection of Affymetrix microarray data so that each gene in a particular regulon could vote on whether a cis-element found in its promoter conferred induction ( 11), repression (21), or no transcriptional change (0) during cold stress. By statistically comparing these election results with the voting behavior of all genes on the same gene chip, we verified the bioactivity of novel cis-elements and defined whether they were inductive or repressive. Using in silico mutagenesis we identified functional binding consensus variants for the transcription factors studied. Our results suggest that the previously identified ICEr1 ( induction of CBF expression region 1) consensus does not correlate with cold gene induction, while the ICEr3/ICEr4 consensuses identified using our algorithms are present in regulons of genes that were induced coordinate with observed ICE1 transcript accumulation and temporally preceding genes containing the dehydration response element. Statistical analysis of overlap and cis-element enrichment in the ICE1, CBF2, ZAT12, HOS9, and PHYA regulons enabled us to construct a regulatory network supported by multiple lines of evidence that can be used for future hypothesis testing.

@article{ivanov_digalactosyl-diacylglycerol_2006,
	title = {Digalactosyl-diacylglycerol deficiency impairs the capacity for photosynthetic intersystem electron transport and state transitions in {Arabidopsis} thaliana due to photosystem {I} acceptor-side limitations},
	volume = {47},
	issn = {0032-0781},
	doi = {10.1093/pcp/pcj089},
	abstract = {Compared with wild type, the dgd1 mutant of Arabidopsis thaliana exhibited a lower amount of PSI-related Chl-protein complexes and lower abundance of the PSI-associated polypeptides, PsaA, PsaB, PsaC, PsaL and PsaH, with no changes in the levels of Lhca1-4. Functionally, the dgd1 mutant exhibited a significantly lower light-dependent, steady-state oxidation level of P700 (P700(+)) in vivo, a higher intersystem electron pool size, restricted linear electron transport and a higher rate of reduction of P700(+) in the dark, indicating an increased capacity for PSI cyclic electron transfer compared with the wild type. Concomitantly, the dgd1 mutant exhibited a higher sensitivity to and incomplete recovery of photoinhibition of PSI. Furthermore, dgd1 exhibited a lower capacity to undergo state transitions compared with the wild type, which was associated with a higher reduction state of the plastoquinone (PQ) pool. We conclude that digalactosyl-diacylglycerol (DGDG) deficiency results in PSI acceptor-side limitations that alter the flux of electrons through the photosynthetic electron chain and impair the regulation of distribution of excitation energy between the photosystems. These results are discussed in terms of thylakoid membrane domain reorganization in response to DGDG deficiency in A. thaliana.},
	language = {eng},
	number = {8},
	journal = {Plant \& Cell Physiology},
	author = {Ivanov, Alexander G. and Hendrickson, Luke and Krol, Marianna and Selstam, Eva and Oquist, Gunnar and Hurry, Vaughan and Huner, Norman P. A.},
	month = aug,
	year = {2006},
	keywords = {Arabidopsis, Arabidopsis dgd1 mutant, Electron Transport, Galactolipids, Photosynthesis, Photosystem I Protein Complex, Thylakoids, chlorophyll fluorescence, dgd1 mutant, digalactosyl-diacylglycerol, excitation-energy, leaves, light-harvesting complex, lipid-content, membranes, p700, photoinhibition, plants, protein, redox state, state transitions},
	pages = {1146--1157},
}

Compared with wild type, the dgd1 mutant of Arabidopsis thaliana exhibited a lower amount of PSI-related Chl-protein complexes and lower abundance of the PSI-associated polypeptides, PsaA, PsaB, PsaC, PsaL and PsaH, with no changes in the levels of Lhca1-4. Functionally, the dgd1 mutant exhibited a significantly lower light-dependent, steady-state oxidation level of P700 (P700(+)) in vivo, a higher intersystem electron pool size, restricted linear electron transport and a higher rate of reduction of P700(+) in the dark, indicating an increased capacity for PSI cyclic electron transfer compared with the wild type. Concomitantly, the dgd1 mutant exhibited a higher sensitivity to and incomplete recovery of photoinhibition of PSI. Furthermore, dgd1 exhibited a lower capacity to undergo state transitions compared with the wild type, which was associated with a higher reduction state of the plastoquinone (PQ) pool. We conclude that digalactosyl-diacylglycerol (DGDG) deficiency results in PSI acceptor-side limitations that alter the flux of electrons through the photosynthetic electron chain and impair the regulation of distribution of excitation energy between the photosystems. These results are discussed in terms of thylakoid membrane domain reorganization in response to DGDG deficiency in A. thaliana.

@article{rosso_immutans_2006,
	title = {{IMMUTANS} does not act as a stress-induced safety valve in the protection of the photosynthetic apparatus of {Arabidopsis} during steady-state photosynthesis},
	volume = {142},
	issn = {0032-0889},
	doi = {10.1104/pp.106.085886},
	abstract = {IMMUTANS (IM) encodes a thylakoid membrane protein that has been hypothesized to act as a terminal oxidase that couples the reduction of O(2) to the oxidation of the plastoquinone (PQ) pool of the photosynthetic electron transport chain. Because IM shares sequence similarity to the stress-induced mitochondrial alternative oxidase (AOX), it has been suggested that the protein encoded by IM acts as a safety valve during the generation of excess photosynthetically generated electrons. We combined in vivo chlorophyll fluorescence quenching analyses with measurements of the redox state of P(700) to assess the capacity of IM to compete with photosystem I for intersystem electrons during steady-state photosynthesis in Arabidopsis (Arabidopsis thaliana). Comparisons were made between wild-type plants, im mutant plants, as well as transgenics in which IM protein levels had been overexpressed six (OE-6 x) and 16 (OE-16 x) times. Immunoblots indicated that IM abundance was the only major variant that we could detect between these genotypes. Overexpression of IM did not result in increased capacity to keep the PQ pool oxidized compared to either the wild type or im grown under control conditions (25 degrees C and photosynthetic photon flux density of 150 micromol photons m(-2) s(-1)). Similar results were observed either after 3-d cold stress at 5 degrees C or after full-leaf expansion at 5 degrees C and photosynthetic photon flux density of 150 micromol photons m(-2) s(-1). Furthermore, IM abundance did not enhance protection of either photosystem II or photosystem I from photoinhibition at either 25 degrees C or 5 degrees C. Our in vivo data indicate that modulation of IM expression and polypeptide accumulation does not alter the flux of intersystem electrons to P(700)(+) during steady-state photosynthesis and does not provide any significant photoprotection. In contrast to AOX1a, meta-analyses of published Arabidopsis microarray data indicated that IM expression exhibited minimal modulation in response to myriad abiotic stresses, which is consistent with our functional data. However, IM exhibited significant modulation in response to development in concert with changes in AOX1a expression. Thus, neither our functional analyses of the IM knockout and overexpression lines nor meta-analyses of gene expression support the model that IM acts as a safety valve to regulate the redox state of the PQ pool during stress and acclimation. Rather, IM appears to be strongly regulated by developmental stage of Arabidopsis.},
	language = {eng},
	number = {2},
	journal = {Plant Physiology},
	author = {Rosso, Dominic and Ivanov, Alexander G. and Fu, Aigen and Geisler-Lee, Jane and Hendrickson, Luke and Geisler, Matt and Stewart, Gregory and Krol, Marianna and Hurry, Vaughan and Rodermel, Steven R. and Maxwell, Denis P. and Hüner, Norman P. A.},
	month = oct,
	year = {2006},
	keywords = {Acclimatization, Arabidopsis, Arabidopsis Proteins, Cold Temperature, Gene Expression Profiling, Gene Expression Regulation, Plant, Genotype, Mitochondrial Proteins, Molecular Sequence Data, Oxidoreductases, Photosynthesis, Photosystem I Protein Complex, Photosystem II Protein Complex, Plant Proteins, alternative oxidase, chlorophyll-a, electron-transport, gene, in-vitro, intersystem chain, oxidative stress, photosystem-ii, plastid terminal oxidase, redox state},
	pages = {574--585},
}

IMMUTANS (IM) encodes a thylakoid membrane protein that has been hypothesized to act as a terminal oxidase that couples the reduction of O(2) to the oxidation of the plastoquinone (PQ) pool of the photosynthetic electron transport chain. Because IM shares sequence similarity to the stress-induced mitochondrial alternative oxidase (AOX), it has been suggested that the protein encoded by IM acts as a safety valve during the generation of excess photosynthetically generated electrons. We combined in vivo chlorophyll fluorescence quenching analyses with measurements of the redox state of P(700) to assess the capacity of IM to compete with photosystem I for intersystem electrons during steady-state photosynthesis in Arabidopsis (Arabidopsis thaliana). Comparisons were made between wild-type plants, im mutant plants, as well as transgenics in which IM protein levels had been overexpressed six (OE-6 x) and 16 (OE-16 x) times. Immunoblots indicated that IM abundance was the only major variant that we could detect between these genotypes. Overexpression of IM did not result in increased capacity to keep the PQ pool oxidized compared to either the wild type or im grown under control conditions (25 degrees C and photosynthetic photon flux density of 150 micromol photons m(-2) s(-1)). Similar results were observed either after 3-d cold stress at 5 degrees C or after full-leaf expansion at 5 degrees C and photosynthetic photon flux density of 150 micromol photons m(-2) s(-1). Furthermore, IM abundance did not enhance protection of either photosystem II or photosystem I from photoinhibition at either 25 degrees C or 5 degrees C. Our in vivo data indicate that modulation of IM expression and polypeptide accumulation does not alter the flux of intersystem electrons to P(700)(+) during steady-state photosynthesis and does not provide any significant photoprotection. In contrast to AOX1a, meta-analyses of published Arabidopsis microarray data indicated that IM expression exhibited minimal modulation in response to myriad abiotic stresses, which is consistent with our functional data. However, IM exhibited significant modulation in response to development in concert with changes in AOX1a expression. Thus, neither our functional analyses of the IM knockout and overexpression lines nor meta-analyses of gene expression support the model that IM acts as a safety valve to regulate the redox state of the PQ pool during stress and acclimation. Rather, IM appears to be strongly regulated by developmental stage of Arabidopsis.

@article{druart_molecular_2006,
	title = {Molecular targets of elevated [{CO2}] in leaves and stems of {Populus} deltoides: implications for future tree growth and carbon sequestration},
	volume = {33},
	issn = {1445-4408},
	shorttitle = {Molecular targets of elevated [{CO2}] in leaves and stems of {Populus} deltoides},
	doi = {10.1071/FP05139},
	abstract = {We report the first comprehensive analysis of the effects of elevated [CO2] on gene expression in source leaf and stem sink tissues in woody plants. We have taken advantage of coppiced Populus deltoides (Bartr.) stands grown for 3 years under three different and constant elevated [CO2] in the agriforest mesocosms of Biosphere 2. Leaf area per tree was doubled by elevated [CO2] but although growth at 800 v. 400 mu mol mol(-1) CO2 resulted in a significant increase in stem biomass, growth was not stimulated at 1200 mu mol mol(-1) CO2. Growth under elevated [CO2] also resulted in significant increases in stem wood density. Analysis of expression data for the 13 490 clones present on POP1 microarrays revealed 95 and 277 [CO2]-responsive clones in leaves and stems respectively, with the response being stronger at 1200 mu mol mol(-1). When these [CO2]-responsive genes were assigned to functional categories, metabolism- related genes were the most responsive to elevated [CO2]. However within this category, expression of genes relating to bioenergetic processes was unchanged in leaves whereas the expression of genes for storage proteins and of those involved in control of wall expansion was enhanced. In contrast to leaves, the genes up-regulated in stems under elevated [CO2] were primarily enzymes responsible for lignin formation and polymerisation or ethylene response factors, also known to induce lignin biosynthesis. Concomitant with this enhancement of lignin biosynthesis in stems, there was a pronounced repression of genes related to cell wall formation and cell growth. These changes in gene expression have clear consequences for long-term carbon sequestration, reducing the carbon-fertilisation effect, and the potential for increased lignification may negatively impact on future wood quality for timber and paper production.},
	language = {English},
	number = {2},
	journal = {Functional Plant Biology},
	publisher = {Csiro Publishing},
	author = {Druart, N. and Rodriguez-Buey, M. and Barron-Gafford, G. and Sjodin, A. and Bhalerao, Rishikesh P. and Hurry, V.},
	year = {2006},
	note = {Place: Clayton
WOS:000235065100002},
	keywords = {Populus, atmospheric co2, betula-pendula roth, cdna microarray, cell-wall protein, cottonwood, deciduous   forest, elevated CO2, enrichment popface, global change, leaf growth, microarray, pinus-sylvestris, plant-growth, wood   properties},
	pages = {121--131},
}

We report the first comprehensive analysis of the effects of elevated [CO2] on gene expression in source leaf and stem sink tissues in woody plants. We have taken advantage of coppiced Populus deltoides (Bartr.) stands grown for 3 years under three different and constant elevated [CO2] in the agriforest mesocosms of Biosphere 2. Leaf area per tree was doubled by elevated [CO2] but although growth at 800 v. 400 mu mol mol(-1) CO2 resulted in a significant increase in stem biomass, growth was not stimulated at 1200 mu mol mol(-1) CO2. Growth under elevated [CO2] also resulted in significant increases in stem wood density. Analysis of expression data for the 13 490 clones present on POP1 microarrays revealed 95 and 277 [CO2]-responsive clones in leaves and stems respectively, with the response being stronger at 1200 mu mol mol(-1). When these [CO2]-responsive genes were assigned to functional categories, metabolism- related genes were the most responsive to elevated [CO2]. However within this category, expression of genes relating to bioenergetic processes was unchanged in leaves whereas the expression of genes for storage proteins and of those involved in control of wall expansion was enhanced. In contrast to leaves, the genes up-regulated in stems under elevated [CO2] were primarily enzymes responsible for lignin formation and polymerisation or ethylene response factors, also known to induce lignin biosynthesis. Concomitant with this enhancement of lignin biosynthesis in stems, there was a pronounced repression of genes related to cell wall formation and cell growth. These changes in gene expression have clear consequences for long-term carbon sequestration, reducing the carbon-fertilisation effect, and the potential for increased lignification may negatively impact on future wood quality for timber and paper production.

@article{matsubara_nocturnal_2006,
	title = {Nocturnal changes in leaf growth of {Populus} deltoides are controlled by cytoplasmic growth},
	volume = {223},
	issn = {0032-0935},
	doi = {10/dvrkzw},
	abstract = {Growing leaves do not expand at a constant rate but exhibit pronounced diel growth rhythms. However, the mechanisms giving rise to distinct diel growth dynamics in different species are still largely unknown. As a first step towards identifying genes controlling rate and timing of leaf growth, we analysed the transcriptomes of rapidly expanding and fully expanded leaves of Populus deltoides Bartr. ex. Marsh at points of high and low expansion at night. Tissues with well defined temporal growth rates were harvested using an online growth-monitoring system based on a digital image sequence processing method developed for quantitative mapping of dicot leaf growth. Unlike plants studied previously, leaf growth in P. deltoides was characterised by lack of a base-tip gradient across the lamina, and by maximal and minimal growth at dusk and dawn, respectively. Microarray analysis revealed that the nocturnal decline in growth coincided with a concerted down-regulation of ribosomal protein genes, indicating deceleration of cytoplasmic growth. In a subsequent time-course experiment, Northern blotting and real-time RT-PCR confirmed that the ribosomal protein gene RPL12 and a cell-cycle gene H2B were down-regulated after midnight following a decrease in cellular carbohydrate concentrations. Thus, we propose that the spatio-temporal growth pattern in leaves of P. deltoides primarily arises from cytoplasmic growth whose activity increases from afternoon to midnight and thereafter decreases in this species.},
	language = {English},
	number = {6},
	journal = {Planta},
	publisher = {Springer},
	author = {Matsubara, S. and Hurry, V. and Druart, N. and Benedict, C. and Janzik, I. and Chavarria-Krauser, A. and Walter, A. and Schurr, U.},
	month = may,
	year = {2006},
	note = {Place: New York
WOS:000237335300020},
	keywords = {Populus, arabidopsis, cell cycle, cell-cycle, chlamydomonas-reinhardtii, circadian clock, cytoplasmic growth, functional genomics, gene-expression, leaf growth, leaves, microarray, photoperiodic control, plant, ribosomal protein, ultraviolet-radiation},
	pages = {1315--1328},
}

Growing leaves do not expand at a constant rate but exhibit pronounced diel growth rhythms. However, the mechanisms giving rise to distinct diel growth dynamics in different species are still largely unknown. As a first step towards identifying genes controlling rate and timing of leaf growth, we analysed the transcriptomes of rapidly expanding and fully expanded leaves of Populus deltoides Bartr. ex. Marsh at points of high and low expansion at night. Tissues with well defined temporal growth rates were harvested using an online growth-monitoring system based on a digital image sequence processing method developed for quantitative mapping of dicot leaf growth. Unlike plants studied previously, leaf growth in P. deltoides was characterised by lack of a base-tip gradient across the lamina, and by maximal and minimal growth at dusk and dawn, respectively. Microarray analysis revealed that the nocturnal decline in growth coincided with a concerted down-regulation of ribosomal protein genes, indicating deceleration of cytoplasmic growth. In a subsequent time-course experiment, Northern blotting and real-time RT-PCR confirmed that the ribosomal protein gene RPL12 and a cell-cycle gene H2B were down-regulated after midnight following a decrease in cellular carbohydrate concentrations. Thus, we propose that the spatio-temporal growth pattern in leaves of P. deltoides primarily arises from cytoplasmic growth whose activity increases from afternoon to midnight and thereafter decreases in this species.

@incollection{huner_photoprotection_2006,
	address = {Dordrecht},
	series = {Advances in {Photosynthesis} and {Respiration}},
	title = {Photoprotection of {Photosystem} {II}: {Reaction} {Center} {Quenching} {Versus} {Antenna} {Quenching}},
	isbn = {978-1-4020-3579-1},
	shorttitle = {Photoprotection of {Photosystem} {II}},
	url = {https://doi.org/10.1007/1-4020-3579-9_11},
	doi = {10.1007/1-4020-3579-9_11},
	abstract = {SummaryUnderstanding the role of the xanthophyll cycle and elucidating the mechanisms of antenna quenching through the non-photochemical dissipation of excess absorbed energy in the photoprotection of the photochemical apparatus continues to be a major focus of photosynthetic research. In addition to antenna quenching, there is evidence for the non-photochemical dissipation of excess energy through the PS II reaction center. Hence, this photoprotective mechanism is called reaction center quenching. One technique to assess reaction center quenching is photosynthetic thermoluminescence. This technique represents a simple but powerful probe of PS II photochemistry that measures the light emitted due to the reversal of PS II charge separation through the thermally-dependent recombination of the negative charges stabilized on Q− A and Q− B on the acceptor side of PS II with the positive charges accumulated in the S2- and S3-states of the oxygen evolving complex. Changes in the temperature maxima for photosynthetic thermoluminescence may reflect changes in redox potentials of recombining species within PS II reaction centers. Exposure of Synechococcussp. PCC 7942, Pinus sylvestrisL., Arabidopsis thaliana, and Chlamydomonas reinhardtii to either lowtemperatures or to high light induces a significant downshift in the temperature maxima for S2Q− B and S3Q− B recombinations relative to S2Q− A and S3Q− A recombinations. These shifts in recombination temperatures are indicative of lower activation energy for the S2Q− B redox pair recombination and a narrowing of the free energy gap betweenQAandQB electron acceptors. This, in turn, is associated with a decrease in the overall thermoluminescence emission. We propose that environmental factors such as high light and low temperature result in an increased population of reduced QA (Q− A), that is, increased excitation pressure, facilitating non-radiative P680+Q− A radical pair recombination within the PS II reaction center. The underlying molecular mechanisms regulating reaction center quenching appear to be species dependent. We conclude that reaction center quenching and antenna quenching are complementary mechanisms that may function to photoprotect PS II to different extents in vivo depending on the species as well as the environmental conditions to which the organism is exposed.},
	language = {en},
	urldate = {2021-06-11},
	booktitle = {Photoprotection, {Photoinhibition}, {Gene} {Regulation}, and {Environment}},
	publisher = {Springer Netherlands},
	author = {Huner, Norman P.A. and Ivanov, Alexander G. and Sane, Prafullachandra V. and Pocock, Tessa and Król, Marianna and Balseris, Andrius and Rosso, Dominic and Savitch, Leonid V. and Hurry, Vaughan M. and Öquist, Gunnar},
	editor = {Demmig-Adams, Barbara and Adams, William W. and Mattoo, Autar K.},
	year = {2006},
	keywords = {Glow Curve, Photosynthetic Light Harvesting, PsbS Protein, Reaction Center Polypeptide, Xanthophyll Cycle},
	pages = {155--173},
}

SummaryUnderstanding the role of the xanthophyll cycle and elucidating the mechanisms of antenna quenching through the non-photochemical dissipation of excess absorbed energy in the photoprotection of the photochemical apparatus continues to be a major focus of photosynthetic research. In addition to antenna quenching, there is evidence for the non-photochemical dissipation of excess energy through the PS II reaction center. Hence, this photoprotective mechanism is called reaction center quenching. One technique to assess reaction center quenching is photosynthetic thermoluminescence. This technique represents a simple but powerful probe of PS II photochemistry that measures the light emitted due to the reversal of PS II charge separation through the thermally-dependent recombination of the negative charges stabilized on Q− A and Q− B on the acceptor side of PS II with the positive charges accumulated in the S2- and S3-states of the oxygen evolving complex. Changes in the temperature maxima for photosynthetic thermoluminescence may reflect changes in redox potentials of recombining species within PS II reaction centers. Exposure of Synechococcussp. PCC 7942, Pinus sylvestrisL., Arabidopsis thaliana, and Chlamydomonas reinhardtii to either lowtemperatures or to high light induces a significant downshift in the temperature maxima for S2Q− B and S3Q− B recombinations relative to S2Q− A and S3Q− A recombinations. These shifts in recombination temperatures are indicative of lower activation energy for the S2Q− B redox pair recombination and a narrowing of the free energy gap betweenQAandQB electron acceptors. This, in turn, is associated with a decrease in the overall thermoluminescence emission. We propose that environmental factors such as high light and low temperature result in an increased population of reduced QA (Q− A), that is, increased excitation pressure, facilitating non-radiative P680+Q− A radical pair recombination within the PS II reaction center. The underlying molecular mechanisms regulating reaction center quenching appear to be species dependent. We conclude that reaction center quenching and antenna quenching are complementary mechanisms that may function to photoprotect PS II to different extents in vivo depending on the species as well as the environmental conditions to which the organism is exposed.

@article{guy_plant_2006,
	title = {Plant cold and abiotic stress gets hot},
	volume = {126},
	issn = {0031-9317},
	doi = {10.1111/j.1399-3054.2006.00628.x},
	language = {English},
	number = {1},
	journal = {Physiologia Plantarum},
	publisher = {Wiley-Blackwell},
	author = {Guy, C. and Porat, R. and Hurry, V.},
	month = jan,
	year = {2006},
	note = {Place: Malden
WOS:000234672300001},
	pages = {1--4},
}

@article{benedict_cbf1-dependent_2006,
	title = {The {CBF1}-dependent low temperature signalling pathway, regulon and increase in freeze tolerance are conserved in {Populus} spp.},
	volume = {29},
	issn = {0140-7791},
	doi = {10.1111/j.1365-3040.2006.01505.x},
	abstract = {The meristematic tissues of temperate woody perennials must acclimate to freezing temperatures to survive the winter and resume growth the following year. To determine whether the C-repeat binding factor (CBF) family of transcription factors contributing to this process in annual herbaceous species also functions in woody perennials, we investigated the changes in phenotype and transcript profile of transgenic Populus constitutively expressing CBF1 from Arabidopsis (AtCBF1). Ectopic expression of AtCBF1 was sufficient to significantly increase the freezing tolerance of non-acclimated leaves and stems relative to wild-type plants. cDNA microarray experiments identified genes up-regulated by ectopic AtCBF1 expression in Populus, demonstrated a strong conservation of the CBF regulon between Populus and Arabidopsis and identified differences between leaf and stem regulons. We studied the induction kinetics and tissue specificity of four CBF paralogues identified from the Populus balsamifera subsp. trichocarpa genome sequence (PtCBFs). All four PtCBFs are cold-inducible in leaves, but only PtCBF1 and PtCBF3 show significant induction in stems. Our results suggest that the central role played by the CBF family of transcriptional activators in cold acclimation of Arabidopsis has been maintained in Populus. However, the differential expression of the PtCBFs and differing clusters of CBF-responsive genes in annual (leaf) and perennial (stem) tissues suggest that the perennial-driven evolution of winter dormancy may have given rise to specific roles for these 'master-switches' in the different annual and perennial tissues of woody species.},
	language = {English},
	number = {7},
	journal = {Plant Cell and Environment},
	publisher = {Wiley},
	author = {Benedict, Catherine and Skinner, Jeffrey S. and Meng, Rengong and Chang, Yongjian and Bhalerao, Rishikesh P. and Huner, Norman P. A. and Finn, Chad E. and Chen, Tony H. H. and Hurry, Vaughan},
	month = jul,
	year = {2006},
	note = {Place: Hoboken
WOS:000238064400006},
	keywords = {abscisic-acid, arabidopsis-thaliana, birch betula-pendula, cold tolerance, cold-response pathway, induced gene-expression, microarray, peach prunus-persica, seasonal-changes, short photoperiod, silver birch, transcription factors},
	pages = {1259--1272},
}

The meristematic tissues of temperate woody perennials must acclimate to freezing temperatures to survive the winter and resume growth the following year. To determine whether the C-repeat binding factor (CBF) family of transcription factors contributing to this process in annual herbaceous species also functions in woody perennials, we investigated the changes in phenotype and transcript profile of transgenic Populus constitutively expressing CBF1 from Arabidopsis (AtCBF1). Ectopic expression of AtCBF1 was sufficient to significantly increase the freezing tolerance of non-acclimated leaves and stems relative to wild-type plants. cDNA microarray experiments identified genes up-regulated by ectopic AtCBF1 expression in Populus, demonstrated a strong conservation of the CBF regulon between Populus and Arabidopsis and identified differences between leaf and stem regulons. We studied the induction kinetics and tissue specificity of four CBF paralogues identified from the Populus balsamifera subsp. trichocarpa genome sequence (PtCBFs). All four PtCBFs are cold-inducible in leaves, but only PtCBF1 and PtCBF3 show significant induction in stems. Our results suggest that the central role played by the CBF family of transcriptional activators in cold acclimation of Arabidopsis has been maintained in Populus. However, the differential expression of the PtCBFs and differing clusters of CBF-responsive genes in annual (leaf) and perennial (stem) tissues suggest that the perennial-driven evolution of winter dormancy may have given rise to specific roles for these 'master-switches' in the different annual and perennial tissues of woody species.

@article{goulas_chloroplast_2006,
	title = {The chloroplast lumen and stromal proteomes of \textit{{Arabidopsis} thaliana} show differential sensitivity to short- and long-term exposure to low temperature: \textit{{Response} of the soluble chloroplast proteomes to cold acclimation}},
	volume = {47},
	issn = {09607412},
	shorttitle = {The chloroplast lumen and stromal proteomes of \textit{{Arabidopsis} thaliana} show differential sensitivity to short- and long-term exposure to low temperature},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2006.02821.x},
	doi = {10/ftpwqm},
	language = {en},
	number = {5},
	urldate = {2021-06-11},
	journal = {The Plant Journal},
	author = {Goulas, Estelle and Schubert, Maria and Kieselbach, Thomas and Kleczkowski, Leszek A. and Gardeström, Per and Schröder, Wolfgang and Hurry, Vaughan},
	month = sep,
	year = {2006},
	pages = {720--734},
}

@article{gardestrom_new_2005,
	title = {New in {Physiologia} {Plantarum}},
	volume = {124},
	issn = {0031-9317},
	doi = {10/cfjjkc},
	language = {English},
	number = {1},
	journal = {Physiologia Plantarum},
	publisher = {Wiley},
	author = {Gardestrom, P. and Hurry, V.},
	month = may,
	year = {2005},
	note = {Place: Hoboken
WOS:000228975000001},
	keywords = {chloroplasts, gene-expression, photosynthesis, redox regulation, responses, stress, tolerance},
	pages = {1--3},
}

@incollection{hurry_respiration_2005,
	address = {Dordrecht},
	series = {Advances in {Photosynthesis} and {Respiration}},
	title = {Respiration in {Photosynthetic} {Cells}: {Gas} {Exchange} {Components}, {Interactions} with {Photorespiration} and the {Operation} of {Mitochondria} in the {Light}},
	isbn = {978-1-4020-3589-0},
	shorttitle = {Respiration in {Photosynthetic} {Cells}},
	url = {https://doi.org/10.1007/1-4020-3589-6_4},
	doi = {10.1007/1-4020-3589-6_4},
	abstract = {SummaryAccording to gas exchange measurements, mitochondrial oxygen consumption in the light is always fast, while respiratory CO2 evolution is markedly decreased (compared with rates in darkness). We analyze the metabolic events that lead to such contrasting responses. In the light, the generation of NADH in mitochondria, both in the glycine decarboxylase reaction and in the tricarboxylic acid cycle, leads to increased NAD(P)H levels, which may increase the activity of the rotenone-insensitive NAD(P)H dehydrogenases. The resulting increase of the reduction level of ubiquinone activates the alternative oxidase. Stabilization of (photo)respiratory flux during the transition from darkness to light takes place at higher NADH/NAD+ and ATP/ADP ratios. Maintenance of fast rates of mitochondrial electron transport in the light is facilitated by the import of oxaloacetate (OAA) from the cytosol to remove NADH, and by the export of citrate to the cytosol. This reduces the flow of metabolites in the tricarboxylic acid cycle, decreasing decarboxylation rates, while the rate of oxygen consumption reactions remain fast.},
	language = {en},
	urldate = {2021-06-11},
	booktitle = {Plant {Respiration}: {From} {Cell} to {Ecosystem}},
	publisher = {Springer Netherlands},
	author = {Hurry, Vaughan and Igamberdiev, Abir U. and Keerberg, Olav and Pärnik, Tiit and Atkin, Owen K. and Zaragoza-Castells, Joana and Gardeström, Per},
	editor = {Lambers, Hans and Ribas-Carbo, Miquel},
	year = {2005},
	keywords = {Alternative Oxidase, Comp LETE, Glycine Decarboxylase, Leaf Respiration, PHOTORESPIRATORY Condition},
	pages = {43--61},
}

SummaryAccording to gas exchange measurements, mitochondrial oxygen consumption in the light is always fast, while respiratory CO2 evolution is markedly decreased (compared with rates in darkness). We analyze the metabolic events that lead to such contrasting responses. In the light, the generation of NADH in mitochondria, both in the glycine decarboxylase reaction and in the tricarboxylic acid cycle, leads to increased NAD(P)H levels, which may increase the activity of the rotenone-insensitive NAD(P)H dehydrogenases. The resulting increase of the reduction level of ubiquinone activates the alternative oxidase. Stabilization of (photo)respiratory flux during the transition from darkness to light takes place at higher NADH/NAD+ and ATP/ADP ratios. Maintenance of fast rates of mitochondrial electron transport in the light is facilitated by the import of oxaloacetate (OAA) from the cytosol to remove NADH, and by the export of citrate to the cytosol. This reduces the flow of metabolites in the tricarboxylic acid cycle, decreasing decarboxylation rates, while the rate of oxygen consumption reactions remain fast.

@article{atkin_hot_2005,
	title = {The hot and the cold: unravelling the variable response of plant respiration to temperature},
	volume = {32},
	issn = {1445-4408},
	shorttitle = {The hot and the cold},
	doi = {10.1071/FP03176},
	abstract = {When predicting the effects of climate change, global carbon circulation models that include a positive feedback effect of climate warming on the carbon cycle often assume that ( 1) plant respiration increases exponentially with temperature ( with a constant Q(10)) and ( 2) that there is no acclimation of respiration to long-term changes in temperature. In this review, we show that these two assumptions are incorrect. While Q(10) does not respond systematically to elevated atmospheric CO2 concentrations, other factors such as temperature, light, and water availability all have the potential to influence the temperature sensitivity of respiratory CO2 efflux. Roots and leaves can also differ in their Q(10) values, as can upper and lower canopy leaves. The consequences of such variable Q(10) values need to be fully explored in carbon modelling. Here, we consider the extent of variability in the degree of thermal acclimation of respiration, and discuss in detail the biochemical mechanisms underpinning this variability; the response of respiration to long-term changes in temperature is highly dependent on the effect of temperature on plant development, and on interactive effects of temperature and other abiotic factors ( e. g. irradiance, drought and nutrient availability). Rather than acclimating to the daily mean temperature, recent studies suggest that other components of the daily temperature regime can be important ( e. g. daily minimum and / or night temperature). In some cases, acclimation may simply reflect a passive response to changes in respiratory substrate availability, whereas in others acclimation may be critical in helping plants grow and survive at contrasting temperatures. We also consider the impact of acclimation on the balance between respiration and photosynthesis; although environmental factors such as water availability can alter the balance between these two processes, the available data suggests that temperature-mediated differences in dark leaf respiration are closely linked to concomitant differences in leaf photosynthesis. We conclude by highlighting the need for a greater process-based understanding of thermal acclimation of respiration if we are to successfully predict future ecosystem CO2 fluxes and potential feedbacks on atmospheric CO2 concentrations.},
	language = {English},
	number = {2},
	journal = {Functional Plant Biology},
	publisher = {Csiro Publishing},
	author = {Atkin, O. K. and Bruhn, D. and Hurry, Vaughan and Tjoelker, M. G.},
	year = {2005},
	note = {Place: Clayton
WOS:000227247600001},
	keywords = {alternative oxidase, arabidopsis-thaliana leaves, atmospheric co2 concentration, carbon fluxes, carbon-dioxide concentration, climate change, leaf dark respiration, long-term, relative growth-rate, respiration, ribulose-1,5-bisphosphate carboxylase oxygenase, root respiration, secale-cereale l, temperature},
	pages = {87--105},
}

When predicting the effects of climate change, global carbon circulation models that include a positive feedback effect of climate warming on the carbon cycle often assume that ( 1) plant respiration increases exponentially with temperature ( with a constant Q(10)) and ( 2) that there is no acclimation of respiration to long-term changes in temperature. In this review, we show that these two assumptions are incorrect. While Q(10) does not respond systematically to elevated atmospheric CO2 concentrations, other factors such as temperature, light, and water availability all have the potential to influence the temperature sensitivity of respiratory CO2 efflux. Roots and leaves can also differ in their Q(10) values, as can upper and lower canopy leaves. The consequences of such variable Q(10) values need to be fully explored in carbon modelling. Here, we consider the extent of variability in the degree of thermal acclimation of respiration, and discuss in detail the biochemical mechanisms underpinning this variability; the response of respiration to long-term changes in temperature is highly dependent on the effect of temperature on plant development, and on interactive effects of temperature and other abiotic factors ( e. g. irradiance, drought and nutrient availability). Rather than acclimating to the daily mean temperature, recent studies suggest that other components of the daily temperature regime can be important ( e. g. daily minimum and / or night temperature). In some cases, acclimation may simply reflect a passive response to changes in respiratory substrate availability, whereas in others acclimation may be critical in helping plants grow and survive at contrasting temperatures. We also consider the impact of acclimation on the balance between respiration and photosynthesis; although environmental factors such as water availability can alter the balance between these two processes, the available data suggests that temperature-mediated differences in dark leaf respiration are closely linked to concomitant differences in leaf photosynthesis. We conclude by highlighting the need for a greater process-based understanding of thermal acclimation of respiration if we are to successfully predict future ecosystem CO2 fluxes and potential feedbacks on atmospheric CO2 concentrations.

@article{stitt_plant_2002,
	title = {A plant for all seasons: alterations in photosynthetic carbon metabolism during cold acclimation in {Arabidopsis}},
	volume = {5},
	issn = {1369-5266},
	shorttitle = {A plant for all seasons},
	url = {https://www.sciencedirect.com/science/article/pii/S1369526602002583},
	doi = {10.1016/S1369-5266(02)00258-3},
	abstract = {Low temperatures lead to the inhibition of sucrose synthesis and photosynthesis. The biochemical and physiological adaptations of plants to low temperatures include the post-translational activation and increased expression of enzymes of the sucrose synthesis pathway, the changed expression of Calvin cycle enzymes, and changes in the leaf protein content. Recent progress has been made in understanding both the signals that trigger these processes and how the regulation of photosynthetic carbon metabolism interacts with other processes during cold acclimation.},
	language = {en},
	number = {3},
	urldate = {2021-10-19},
	journal = {Current Opinion in Plant Biology},
	author = {Stitt, Mark and Hurry, Vaughan},
	month = jun,
	year = {2002},
	keywords = {cold acclimation, phosphate, photosynthesis, sucrose synthesis},
	pages = {199--206},
}

Low temperatures lead to the inhibition of sucrose synthesis and photosynthesis. The biochemical and physiological adaptations of plants to low temperatures include the post-translational activation and increased expression of enzymes of the sucrose synthesis pathway, the changed expression of Calvin cycle enzymes, and changes in the leaf protein content. Recent progress has been made in understanding both the signals that trigger these processes and how the regulation of photosynthetic carbon metabolism interacts with other processes during cold acclimation.

@article{krol_low_2002,
	title = {Low growth temperature inhibition of photosynthesis in cotyledons of jack pine seedlings ({Pinus} banksiana) is due to impaired chloroplast development},
	volume = {80},
	issn = {0008-4026},
	url = {https://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=DOISource&SrcApp=WOS&KeyAID=10.1139%2Fb02-093&DestApp=DOI&SrcAppSID=E6OBdVIk3N3sJssnJl2&SrcJTitle=CANADIAN+JOURNAL+OF+BOTANY-REVUE+CANADIENNE+DE+BOTANIQUE&DestDOIRegistrantName=Canadian+Science+Publishing},
	doi = {10.1139/B02-093},
	abstract = {Cotyledons of jack pine seedlings (Pinus banksiana Lamb.) grown from seeds were expanded at low temperature (5degreesC), and total Chl content per unit area of cotyledons in these seedlings was only 57\% of that observed for cotyledons on 20degreesC-grown controls. Chl a/b ratio of 5degreesC-grown jack pine was about 20\% lower (2.3 +/- 0.1) than 20degreesC controls (2.8 +/- 0.3). Separation of Chl-protein complexes and SDS-PAGE indicated a significant reduction in the major Chl a containing complex of PSI (CP1) and PSII (CPa) relative to LHCII1 in 5degreesC compared to 20degreesC-grown seedlings. In addition, LHCII1/LHCII3 ratio increased from 3.8 in control (20degreesC) to 5.5 in 5degreesC-grown cotyledons. Ultrastructurally, 5degreesC-grown cotyledons had chloroplasts with swollen thylakoids as well as etiochloroplasts with distinct prolamellar bodies. Based on CO2-saturated O-2 evolution and in vivo Chl a fluorescence, cotyledons of 5degreesC jack pine exhibited an apparent photosynthetic efficiency that was 40\% lower than 20degreesC controls. Seedlings grown at 5degreesC were photoinhibited more rapidly at 5degreesC and 1200 mumol.m(-2).s(-1) than controls grown at 20degreesC, although the final extent of photoinhibition was similar. Exposure to high light at 5degreesC stimulated the xanthophyll cycle in cotyledons of both controls and 5degreesC-grown seedlings. In contrast to winter cereals, we conclude that growth of jack pine at 5degreesC impairs normal chloroplast biogenesis, which leads to an inhibition of photosynthetic efficiency.},
	language = {English},
	number = {10},
	urldate = {2021-10-19},
	journal = {Canadian Journal of Botany-Revue Canadienne De Botanique},
	publisher = {Canadian Science Publishing},
	author = {Krol, M. and Hurry, V. and Maxwell, D. P. and Malek, L. and Ivanov, A. G. and Huner, N. P. A.},
	month = oct,
	year = {2002},
	note = {Place: Ottawa
WOS:000179039600003},
	keywords = {Pinus   banksiana Lamb., chlorophyll fluorescence, chloroplast, cold-hardening temperatures, electron-transport, freezing tolerance, frost damage, growth, harvesting complex-ii, light, photoinhibition, photosynthesis, scots pine, spinach leaves, temperature, ultrastructure, winter stress},
	pages = {1042--1051},
}

Cotyledons of jack pine seedlings (Pinus banksiana Lamb.) grown from seeds were expanded at low temperature (5degreesC), and total Chl content per unit area of cotyledons in these seedlings was only 57% of that observed for cotyledons on 20degreesC-grown controls. Chl a/b ratio of 5degreesC-grown jack pine was about 20% lower (2.3 +/- 0.1) than 20degreesC controls (2.8 +/- 0.3). Separation of Chl-protein complexes and SDS-PAGE indicated a significant reduction in the major Chl a containing complex of PSI (CP1) and PSII (CPa) relative to LHCII1 in 5degreesC compared to 20degreesC-grown seedlings. In addition, LHCII1/LHCII3 ratio increased from 3.8 in control (20degreesC) to 5.5 in 5degreesC-grown cotyledons. Ultrastructurally, 5degreesC-grown cotyledons had chloroplasts with swollen thylakoids as well as etiochloroplasts with distinct prolamellar bodies. Based on CO2-saturated O-2 evolution and in vivo Chl a fluorescence, cotyledons of 5degreesC jack pine exhibited an apparent photosynthetic efficiency that was 40% lower than 20degreesC controls. Seedlings grown at 5degreesC were photoinhibited more rapidly at 5degreesC and 1200 mumol.m(-2).s(-1) than controls grown at 20degreesC, although the final extent of photoinhibition was similar. Exposure to high light at 5degreesC stimulated the xanthophyll cycle in cotyledons of both controls and 5degreesC-grown seedlings. In contrast to winter cereals, we conclude that growth of jack pine at 5degreesC impairs normal chloroplast biogenesis, which leads to an inhibition of photosynthetic efficiency.

@incollection{hurry_photosynthesis_2002,
	address = {Boston, MA},
	title = {Photosynthesis at {Low} {Temperatures}},
	isbn = {978-1-4615-0711-6},
	url = {https://doi.org/10.1007/978-1-4615-0711-6_12},
	doi = {10.1007/978-1-4615-0711-6_12},
	abstract = {One of the most variable conditions in the field is temperature and relatively severe frost, caused by temperatures below -20°C, can be expected to occur over 42\% of the earth’s surface (Larcher 1995). Low temperature is therefore a major determinant of the geographical distribution and productivity of plant species. Exacerbating this problem, plants from high latitudes and high altitudes are faced with short growing seasons and the need to grow at low temperatures for prolonged periods to extend the growing season. Thus, the capacity for active photosynthesis during prolonged exposure to low growth temperatures is essential in determining their successful site occupancy and subsequent productivity. Despite the importance of low temperatures in determining agricultural productivity and ecological diversity at higher latitudes and altitudes, relatively little is known about either the short-term or long-term effects of cold on the underlying biochemical responses of plant energy metabolism, processes that contribute to plant growth.},
	language = {en},
	urldate = {2021-10-19},
	booktitle = {Plant {Cold} {Hardiness}: {Gene} {Regulation} and {Genetic} {Engineering}},
	publisher = {Springer US},
	author = {Hurry, Vaughan and Druart, Nathalie and Cavaco, Ana and Gardeström, Per and Strand, Åsa},
	editor = {Li, Paul H. and Palva, E. Tapio},
	year = {2002},
	keywords = {Antisense Line, Calvin Cycle, Cold Acclimation, Freezing Tolerance, Sucrose Synthesis},
	pages = {161--179},
}

One of the most variable conditions in the field is temperature and relatively severe frost, caused by temperatures below -20°C, can be expected to occur over 42% of the earth’s surface (Larcher 1995). Low temperature is therefore a major determinant of the geographical distribution and productivity of plant species. Exacerbating this problem, plants from high latitudes and high altitudes are faced with short growing seasons and the need to grow at low temperatures for prolonged periods to extend the growing season. Thus, the capacity for active photosynthesis during prolonged exposure to low growth temperatures is essential in determining their successful site occupancy and subsequent productivity. Despite the importance of low temperatures in determining agricultural productivity and ecological diversity at higher latitudes and altitudes, relatively little is known about either the short-term or long-term effects of cold on the underlying biochemical responses of plant energy metabolism, processes that contribute to plant growth.

@article{stitt_plant_2002,
	title = {Plant odyssey - {Adaptation} of plants to cold},
	issn = {0294-3506},
	url = {https://www.webofscience.com/wos/woscc/full-record/WOS:000177435900003?SID=E6OBdVIk3N3sJssnJl2},
	abstract = {Low temperatures lead to the inhibition of sucrose synthesis and photosynthesis. The biochemical and physiological adaptations of plants to low temperatures include the post-translational activation and increased expression of enzymes of the sucrose synthesis pathway, the changed expression of Calvin cycle enzymes, and changes in the leaf protein content. Recent progress has been made in understanding both the signals that trigger these processes and how the regulation of photosynthetic carbon metabolism interacts with other processes during cold acclimation.},
	language = {French},
	number = {224},
	urldate = {2021-10-19},
	journal = {Biofutur},
	publisher = {Editions Scientifiques Medicales Elsevier},
	author = {Stitt, M. and Hurry, V.},
	month = aug,
	year = {2002},
	note = {Place: Paris Cedex 15
WOS:000177435900003},
	keywords = {acclimation, expression, temperature},
	pages = {18--21},
}

Low temperatures lead to the inhibition of sucrose synthesis and photosynthesis. The biochemical and physiological adaptations of plants to low temperatures include the post-translational activation and increased expression of enzymes of the sucrose synthesis pathway, the changed expression of Calvin cycle enzymes, and changes in the leaf protein content. Recent progress has been made in understanding both the signals that trigger these processes and how the regulation of photosynthetic carbon metabolism interacts with other processes during cold acclimation.

@article{savitch_cold_2001,
	title = {Cold acclimation of {Arabidopsis} thaliana results in incomplete recovery of photosynthetic capacity, associated with an increased reduction of the chloroplast stroma},
	volume = {214},
	issn = {1432-2048},
	url = {https://doi.org/10.1007/s004250100622},
	doi = {10/bsfvpb},
	abstract = {The effects of short-term cold stress and long-term cold acclimation on the light reactions of photosynthesis were examined in vivo to assess their contributions to photosynthetic acclimation to low temperature in Arabidopsis thaliana (L.) Heynh.. All photosynthetic measurements were made at the temperature of exposure: 23 °C for non-acclimated plants and 5 °C for cold-stressed and cold-acclimated plants. Three-day cold-stress treatments at 5 °C inhibited light-saturated rates of CO2 assimilation and O2 evolution by approximately 75\%. The 3-day exposure to 5 °C also increased the proportion of reduced QA by 50\%, decreased the yield of PSII electron transport by 65\% and decreased PSI activity by 31\%. In contrast, long-term cold acclimation resulted in a strong but incomplete recovery of light-saturated photosynthesis at 5 °C. The rates of light-saturated CO2 and O2 gas exchange and the in vivo yield of PSII activity under light-saturating conditions were only 35–40\% lower, and the relative redox state of QA only 20\% lower, at 5 °C after cold acclimation than in controls at 23 °C. PSI activity showed full recovery during long-term cold acclimation. Neither short-term cold stress nor long-term cold acclimation of Arabidopsis was associated with a limitation in ATP, and both treatments resulted in an increase in the ATP/NADPH ratio. This increase in ATP/NADPH was associated with an inhibition of PSI cyclic electron transport but there was no apparent change in the Mehler reaction activity in either cold-stressed or cold-acclimated leaves. Cold acclimation also resulted in an increase in the reduction state of the stroma, as indicated by an increased total activity and activation state of NADP-dependent malate dehydrogenase, and increased light-dependent activities of the major regulatory enzymes of the oxidative pentose-phosphate pathway. We suggest that the photosynthetic capacity during cold stress as well as cold acclimation is altered by limitations at the level of consumption of reducing power in carbon metabolism.},
	language = {en},
	number = {2},
	urldate = {2021-11-02},
	journal = {Planta},
	author = {Savitch, Leonid V. and Barker-Åstrom, Johan and Ivanov, Alexander G. and Hurry, Vaughan and Öquist, Gunnar and Huner, Norman P. and Gardeström, Per},
	month = dec,
	year = {2001},
	pages = {295--303},
}

The effects of short-term cold stress and long-term cold acclimation on the light reactions of photosynthesis were examined in vivo to assess their contributions to photosynthetic acclimation to low temperature in Arabidopsis thaliana (L.) Heynh.. All photosynthetic measurements were made at the temperature of exposure: 23 °C for non-acclimated plants and 5 °C for cold-stressed and cold-acclimated plants. Three-day cold-stress treatments at 5 °C inhibited light-saturated rates of CO2 assimilation and O2 evolution by approximately 75%. The 3-day exposure to 5 °C also increased the proportion of reduced QA by 50%, decreased the yield of PSII electron transport by 65% and decreased PSI activity by 31%. In contrast, long-term cold acclimation resulted in a strong but incomplete recovery of light-saturated photosynthesis at 5 °C. The rates of light-saturated CO2 and O2 gas exchange and the in vivo yield of PSII activity under light-saturating conditions were only 35–40% lower, and the relative redox state of QA only 20% lower, at 5 °C after cold acclimation than in controls at 23 °C. PSI activity showed full recovery during long-term cold acclimation. Neither short-term cold stress nor long-term cold acclimation of Arabidopsis was associated with a limitation in ATP, and both treatments resulted in an increase in the ATP/NADPH ratio. This increase in ATP/NADPH was associated with an inhibition of PSI cyclic electron transport but there was no apparent change in the Mehler reaction activity in either cold-stressed or cold-acclimated leaves. Cold acclimation also resulted in an increase in the reduction state of the stroma, as indicated by an increased total activity and activation state of NADP-dependent malate dehydrogenase, and increased light-dependent activities of the major regulatory enzymes of the oxidative pentose-phosphate pathway. We suggest that the photosynthetic capacity during cold stress as well as cold acclimation is altered by limitations at the level of consumption of reducing power in carbon metabolism.

@article{ciereszko_phosphate_2001,
	title = {Phosphate status affects the gene expression, protein content and enzymatic activity of {UDP}-glucose pyrophosphorylase in wild-type and pho mutants of {Arabidopsis}},
	volume = {212},
	issn = {1432-2048},
	url = {https://doi.org/10.1007/s004250000424},
	doi = {10/ct6jfd},
	abstract = {The effects of inorganic phosphate (Pi) deficiency on the expression of the UDP-glucose pyrophosphorylase (UGPase) gene (Ugp), involved in sucrose synthesis/metabolism, and on carbohydrate status were investigated in different tissues of Arabidopsis thaliana (L.) Heynh. For leaves, a decrease in internal Pi status caused by growth of plants on a medium lacking Pi (−P conditions) led to an increase in the overall content of glucose and starch, but had little effect on sucrose content. The Pi deficiency also led to an increased carbohydrate content in stems/flowers, but not in roots. The expression of Ugp was upregulated in both leaves and roots, but not in stems/flowers. The effects of Pi status on Ugp expression were confirmed using leaves of both pho1-2 and pho2-1 mutants of Arabidopsis (Pi-deficient and Pi-accumulating, respectively) and by feeding the leaves with d-mannose, which acts as a sink for Pi. The Pi-status-dependent changes in Ugp expression followed the same patterns as those of ApS, a gene encoding the small subunit of ADP-glucose pyrophosphorylase, a key enzyme of starch synthesis. The changes in Ugp mRNA levels, depending on internal Pi status, were generally correlated with changes in UGPase protein content and enzymatic activity. This was demonstrated both for wild-type plants grown under Pi-deficiency and for Pi mutants. The data suggest that, under Pi-deficiency, UGPase represents a transcriptionally regulated step in sucrose synthesis/metabolism, involved in homeostatic mechanisms readjusting the nutritional status of a plant under Pi-stress conditions.},
	language = {en},
	number = {4},
	urldate = {2021-11-02},
	journal = {Planta},
	author = {Ciereszko, Iwona and Johansson, Henrik and Hurry, Vaughan and Kleczkowski, Leszek A.},
	month = mar,
	year = {2001},
	pages = {598--605},
}

The effects of inorganic phosphate (Pi) deficiency on the expression of the UDP-glucose pyrophosphorylase (UGPase) gene (Ugp), involved in sucrose synthesis/metabolism, and on carbohydrate status were investigated in different tissues of Arabidopsis thaliana (L.) Heynh. For leaves, a decrease in internal Pi status caused by growth of plants on a medium lacking Pi (−P conditions) led to an increase in the overall content of glucose and starch, but had little effect on sucrose content. The Pi deficiency also led to an increased carbohydrate content in stems/flowers, but not in roots. The expression of Ugp was upregulated in both leaves and roots, but not in stems/flowers. The effects of Pi status on Ugp expression were confirmed using leaves of both pho1-2 and pho2-1 mutants of Arabidopsis (Pi-deficient and Pi-accumulating, respectively) and by feeding the leaves with d-mannose, which acts as a sink for Pi. The Pi-status-dependent changes in Ugp expression followed the same patterns as those of ApS, a gene encoding the small subunit of ADP-glucose pyrophosphorylase, a key enzyme of starch synthesis. The changes in Ugp mRNA levels, depending on internal Pi status, were generally correlated with changes in UGPase protein content and enzymatic activity. This was demonstrated both for wild-type plants grown under Pi-deficiency and for Pi mutants. The data suggest that, under Pi-deficiency, UGPase represents a transcriptionally regulated step in sucrose synthesis/metabolism, involved in homeostatic mechanisms readjusting the nutritional status of a plant under Pi-stress conditions.

@article{pocock_susceptibility_2001,
	title = {Susceptibility to low-temperature photoinhibition and the acquisition of freezing tolerance in winter and spring wheat: {The} role of growth temperature and irradiance},
	volume = {113},
	issn = {1399-3054},
	shorttitle = {Susceptibility to low-temperature photoinhibition and the acquisition of freezing tolerance in winter and spring wheat},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1034/j.1399-3054.2001.1130408.x},
	doi = {10.1034/j.1399-3054.2001.1130408.x},
	abstract = {Five winter and five spring wheat (Triticum aestivum L.) cultivars were grown under either control conditions (20°C/250 photosynthetic photon flux density (PPFD) [μmol m−2 s−1]), high irradiance (20°C/800 PPFD) or at low temperature (either 5°C/250 PPFD or 5°C/50 PPFD). To eliminate any potential bias, the wheat cultivars were arbitrarily chosen without any previous knowledge of their freezing tolerance or photosynthetic competence. We show that the differential susceptibilities to photoinhibition exhibited between spring and winter wheat cultivars, as assessed by chlorophyll fluorescence cannot be explained on the basis of either growth irradiance or low growth temperature per se. The role of excitation pressure is discussed. We assessed the correlation between susceptibility to low-temperature photoinhibition, maximum ribulose 1,5-bisphosphate carboxylase-oxygenase (EC 4.1.1.39) and NADP-dependent malate dehydrogenase (EC 1.1.1.82) activities, chlorophyll and protein concentrations and freezing tolerance determined by electrolyte leakage. Susceptibility to photoinhibition is the only parameter examined that is strongly and negatively correlated with freezing tolerance. We suggest that the assessment of susceptibility to photoinhibition may be a useful predictor of freezing tolerance and field survival of cereals.},
	language = {en},
	number = {4},
	urldate = {2021-11-02},
	journal = {Physiologia Plantarum},
	author = {Pocock, Tessa H. and Hurry, Vaughan and Savitch, Leonid V. and Huner, Norman P. A.},
	year = {2001},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1034/j.1399-3054.2001.1130408.x},
	pages = {499--506},
}

Five winter and five spring wheat (Triticum aestivum L.) cultivars were grown under either control conditions (20°C/250 photosynthetic photon flux density (PPFD) [μmol m−2 s−1]), high irradiance (20°C/800 PPFD) or at low temperature (either 5°C/250 PPFD or 5°C/50 PPFD). To eliminate any potential bias, the wheat cultivars were arbitrarily chosen without any previous knowledge of their freezing tolerance or photosynthetic competence. We show that the differential susceptibilities to photoinhibition exhibited between spring and winter wheat cultivars, as assessed by chlorophyll fluorescence cannot be explained on the basis of either growth irradiance or low growth temperature per se. The role of excitation pressure is discussed. We assessed the correlation between susceptibility to low-temperature photoinhibition, maximum ribulose 1,5-bisphosphate carboxylase-oxygenase (EC 4.1.1.39) and NADP-dependent malate dehydrogenase (EC 1.1.1.82) activities, chlorophyll and protein concentrations and freezing tolerance determined by electrolyte leakage. Susceptibility to photoinhibition is the only parameter examined that is strongly and negatively correlated with freezing tolerance. We suggest that the assessment of susceptibility to photoinhibition may be a useful predictor of freezing tolerance and field survival of cereals.

@article{hurry_role_2000,
	title = {The role of inorganic phosphate in the development of freezing tolerance and the acclimatization of photosynthesis to low temperature is revealed by the pho mutants of {Arabidopsis} thaliana},
	volume = {24},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-313x.2000.00888.x},
	doi = {10/c6xzqg},
	abstract = {Low temperature inhibits sucrose synthesis, leading to a phosphate-limitation of photosynthesis. We have used the Arabidopsis pho1-2 and pho2-1 mutants with decreased and increased shoot phosphate, respectively, to investigate whether low phosphate triggers cold acclimatization of photosynthetic carbon metabolism. Wild-type Arabidopsis, pho1-2 and pho2-1 were grown at 23°C and transferred to 5°C to investigate acclimatization in pre-existing leaves and in new leaves developing at 5°C. The development of frost tolerance and the accumulation of proline and sugars was unaltered or improved in pho1-2, and impaired in pho2-1. Sucrose phosphate synthase and cytoplasmic fructose-1,6-bisphosphatase activity and protein increase after transfer to 5°C. This increase was accentuated in pho1-2 and attenuated in pho2-1. RBCS and LHCB2 transcript levels decrease in pre-formed wild-type leaves after transfer to 5°C and recover in new leaves that develop at 5°C. The initial decrease was attenuated in pho1-2, and accentuated in pho2-1, where the recovery in new leaves was also suppressed. Rubisco activity increased in wild-type leaves that developed at 5°C. This increase was accentuated in pho1-2 and absent in pho2-1. NADP-glyceraldehyde-3-phosphate dehydrogenase, plastidic fructose-1,6-bisphosphatase and aldolase activity increase relative to phosphoglycerate kinase, transketolase and phosphoribulokinase in wild-type leaves at 5°C. This shift was accentuated in pho1-2 and reversed in pho2-1. Transcript levels for COR genes increase transiently 1 day after transfer to 5°C but were very low in leaves that developed at 5°C in wild-type Arabidopsis, pho1-2 and pho2-1. We conclude that low phosphate plays an important role in triggering cold acclimatization of leaves, leading in particular to an increase of Rubisco expression, changes in other Calvin cycle enzymes to minimize sequestration of phosphate in metabolites, and increased expression of sucrose biosynthesis enzymes.},
	language = {en},
	number = {3},
	urldate = {2021-11-08},
	journal = {The Plant Journal},
	author = {Hurry, Vaughan and Strand, Åsa and Furbank, Robert and Stitt, Mark},
	year = {2000},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313x.2000.00888.x},
	keywords = {Arabidopsis, cold acclimatization, low temperature, phosphate, photosynthesis, sucrose synthesis},
	pages = {383--396},
}

Low temperature inhibits sucrose synthesis, leading to a phosphate-limitation of photosynthesis. We have used the Arabidopsis pho1-2 and pho2-1 mutants with decreased and increased shoot phosphate, respectively, to investigate whether low phosphate triggers cold acclimatization of photosynthetic carbon metabolism. Wild-type Arabidopsis, pho1-2 and pho2-1 were grown at 23°C and transferred to 5°C to investigate acclimatization in pre-existing leaves and in new leaves developing at 5°C. The development of frost tolerance and the accumulation of proline and sugars was unaltered or improved in pho1-2, and impaired in pho2-1. Sucrose phosphate synthase and cytoplasmic fructose-1,6-bisphosphatase activity and protein increase after transfer to 5°C. This increase was accentuated in pho1-2 and attenuated in pho2-1. RBCS and LHCB2 transcript levels decrease in pre-formed wild-type leaves after transfer to 5°C and recover in new leaves that develop at 5°C. The initial decrease was attenuated in pho1-2, and accentuated in pho2-1, where the recovery in new leaves was also suppressed. Rubisco activity increased in wild-type leaves that developed at 5°C. This increase was accentuated in pho1-2 and absent in pho2-1. NADP-glyceraldehyde-3-phosphate dehydrogenase, plastidic fructose-1,6-bisphosphatase and aldolase activity increase relative to phosphoglycerate kinase, transketolase and phosphoribulokinase in wild-type leaves at 5°C. This shift was accentuated in pho1-2 and reversed in pho2-1. Transcript levels for COR genes increase transiently 1 day after transfer to 5°C but were very low in leaves that developed at 5°C in wild-type Arabidopsis, pho1-2 and pho2-1. We conclude that low phosphate plays an important role in triggering cold acclimatization of leaves, leading in particular to an increase of Rubisco expression, changes in other Calvin cycle enzymes to minimize sequestration of phosphate in metabolites, and increased expression of sucrose biosynthesis enzymes.

@article{strand_acclimation_1999,
	title = {Acclimation of {Arabidopsis} {Leaves} {Developing} at {Low} {Temperatures}. {Increasing} {Cytoplasmic} {Volume} {Accompanies} {Increased} {Activities} of {Enzymes} in the {Calvin} {Cycle} and in the {Sucrose}-{Biosynthesis} {Pathway1}},
	volume = {119},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.119.4.1387},
	doi = {10/fgpkmw},
	abstract = {Photosynthetic and metabolic acclimation to low growth temperatures were studied in Arabidopsis (Heynh.). Plants were grown at 23°C and then shifted to 5°C. We compared the leaves shifted to 5°C for 10 d and the new leaves developed at 5°C with the control leaves on plants that had been left at 23°C. Leaf development at 5°C resulted in the recovery of photosynthesis to rates comparable with those achieved by control leaves at 23°C. There was a shift in the partitioning of carbon from starch and toward sucrose (Suc) in leaves that developed at 5°C. The recovery of photosynthetic capacity and the redirection of carbon to Suc in these leaves were associated with coordinated increases in the activity of several Calvin-cycle enzymes, even larger increases in the activity of key enzymes for Suc biosynthesis, and an increase in the phosphate available for metabolism. Development of leaves at 5°C also led to an increase in cytoplasmic volume and a decrease in vacuolar volume, which may provide an important mechanism for increasing the enzymes and metabolites in cold-acclimated leaves. Understanding the mechanisms underlying such structural changes during leaf development in the cold could result in novel approaches to increasing plant yield.},
	number = {4},
	urldate = {2021-11-08},
	journal = {Plant Physiology},
	author = {Strand, Åsa and Hurry, Vaughan and Henkes, Stefan and Huner, Norman and Gustafsson, Petter and Gardeström, Per and Stitt, Mark},
	month = apr,
	year = {1999},
	pages = {1387--1398},
}

Photosynthetic and metabolic acclimation to low growth temperatures were studied in Arabidopsis (Heynh.). Plants were grown at 23°C and then shifted to 5°C. We compared the leaves shifted to 5°C for 10 d and the new leaves developed at 5°C with the control leaves on plants that had been left at 23°C. Leaf development at 5°C resulted in the recovery of photosynthesis to rates comparable with those achieved by control leaves at 23°C. There was a shift in the partitioning of carbon from starch and toward sucrose (Suc) in leaves that developed at 5°C. The recovery of photosynthetic capacity and the redirection of carbon to Suc in these leaves were associated with coordinated increases in the activity of several Calvin-cycle enzymes, even larger increases in the activity of key enzymes for Suc biosynthesis, and an increase in the phosphate available for metabolism. Development of leaves at 5°C also led to an increase in cytoplasmic volume and a decrease in vacuolar volume, which may provide an important mechanism for increasing the enzymes and metabolites in cold-acclimated leaves. Understanding the mechanisms underlying such structural changes during leaf development in the cold could result in novel approaches to increasing plant yield.