Publications 2007

@article{hall_adaptive_2007,
	title = {Adaptive {Population} {Differentiation} in {Phenology} across a {Latitudinal} {Gradient} in {European} {Aspen} ({Populus} tremula, {L}.): {A} {Comparison} of {Neutral} {Markers}, {Candidate} {Genes} and {Phenotypic} {Traits}},
	volume = {61},
	issn = {0014-3820, 1558-5646},
	shorttitle = {Adaptive {Population} {Differentiation} in {Phenology} across a {Latitudinal} {Gradient} in {European} {Aspen} ({Populus} tremula, {L}.)},
	url = {http://doi.wiley.com/10.1111/j.1558-5646.2007.00230.x},
	doi = {10/bv9gz6},
	language = {en},
	number = {12},
	urldate = {2021-06-10},
	journal = {Evolution},
	author = {Hall, David and Luquez, Virginia and Garcia, Victoria M. and St Onge, Kate R. and Jansson, Stefan and Ingvarsson, Pär K.},
	month = dec,
	year = {2007},
	pages = {2849--2860},
}

@article{frenkel_hierarchy_2007,
	title = {Hierarchy amongst photosynthetic acclimation responses for plant fitness},
	volume = {129},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1399-3054.2006.00831.x},
	doi = {10.1111/j.1399-3054.2006.00831.x},
	abstract = {We have compared the seed production of Arabidopsis wild-type and mutant plants impaired in the regulation of the photosynthetic light reactions grown under natural conditions in the field. Mutant plants (npq4) lacking feedback de-excitation were, as previously demonstrated, severely affected in seed production. Seed sets of plants deficient in state transitions (stn7) were 19\% smaller than those of wild-type plants, whereas plants missing the STN8 kinase required for the phosphorylation of the core photosystem II reaction centre polypeptides (stn8) had a normal seed production. Plants lacking both STN7 and STN8 kinases were strongly affected, indicating that these mutations act synergistically. In contrast, npq4×stn7 double mutants had the same seed set as npq4 mutants.},
	language = {en},
	number = {2},
	urldate = {2024-06-28},
	journal = {Physiologia Plantarum},
	author = {Frenkel, Martin and Bellafiore, Stephane and Rochaix, Jean-David and Jansson, Stefan},
	year = {2007},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1399-3054.2006.00831.x},
	pages = {455--459},
}

We have compared the seed production of Arabidopsis wild-type and mutant plants impaired in the regulation of the photosynthetic light reactions grown under natural conditions in the field. Mutant plants (npq4) lacking feedback de-excitation were, as previously demonstrated, severely affected in seed production. Seed sets of plants deficient in state transitions (stn7) were 19% smaller than those of wild-type plants, whereas plants missing the STN8 kinase required for the phosphorylation of the core photosystem II reaction centre polypeptides (stn8) had a normal seed production. Plants lacking both STN7 and STN8 kinases were strongly affected, indicating that these mutations act synergistically. In contrast, npq4×stn7 double mutants had the same seed set as npq4 mutants.

@article{mao_cone_2007,
	title = {Cone and seed characteristics of {Pinus} {Densata} and their adaptive fitness implications},
	volume = {31},
	issn = {1005-264X},
	url = {https://www.plant-ecology.com/EN/10.17521/cjpe.2007.0033},
	doi = {10.17521/cjpe.2007.0033},
	abstract = {Aims Pinus densata is an important forest species in the high mountain...},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {Chinese Journal of Plant Ecology},
	author = {Mao, Jian-Feng and Li, Yue and Liu, Yu-Jun and Liu, Hao and Wang, Xiao-Ru},
	month = oct,
	year = {2007},
	pages = {291},
}

Aims Pinus densata is an important forest species in the high mountain...

@article{wenkel_feedback_2007,
	title = {A {Feedback} {Regulatory} {Module} {Formed} by {LITTLE} {ZIPPER} and {HD}-{ZIPIII} {Genes}},
	volume = {19},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.107.055772},
	doi = {10.1105/tpc.107.055772},
	abstract = {The Arabidopsis thaliana REVOLUTA (REV) protein is a member of the class III homeodomain-leucine zipper (HD-ZIPIII) proteins. REV is a potent regulator of leaf polarity and vascular development. Here, we report the identification of a gene family that encodes small leucine zipper–containing proteins (LITTLE ZIPPER [ZPR] proteins) where the leucine zipper is similar to that found in REV, PHABULOSA, and PHAVOLUTA proteins. The transcript levels of the ZPR genes increase in response to activation of a steroid-inducible REV protein. We show that the ZPR proteins interact with REV in vitro and that ZPR3 prevents DNA binding by REV in vitro. Overexpression of ZPR proteins in Arabidopsis results in phenotypes similar to those seen when HD-ZIPIII function is reduced. We propose a negative feedback model in which REV promotes transcription of the ZPR genes. The ZPR proteins in turn form heterodimers with the REV protein, preventing it from binding DNA. The HD-ZIPIII/ZPR regulatory module would serve not only to dampen the effect of fluctuations in HD-ZIPIII protein levels but more importantly would provide a potential point of regulation (control over the ratio of inactive heterodimers to active homodimers) that could be influenced by other components of the pathway governing leaf polarity.},
	number = {11},
	urldate = {2022-11-30},
	journal = {The Plant Cell},
	author = {Wenkel, Stephan and Emery, John and Hou, Bi-Huei and Evans, Matthew M.S. and Barton, M.K.},
	month = nov,
	year = {2007},
	pages = {3379--3390},
}

The Arabidopsis thaliana REVOLUTA (REV) protein is a member of the class III homeodomain-leucine zipper (HD-ZIPIII) proteins. REV is a potent regulator of leaf polarity and vascular development. Here, we report the identification of a gene family that encodes small leucine zipper–containing proteins (LITTLE ZIPPER [ZPR] proteins) where the leucine zipper is similar to that found in REV, PHABULOSA, and PHAVOLUTA proteins. The transcript levels of the ZPR genes increase in response to activation of a steroid-inducible REV protein. We show that the ZPR proteins interact with REV in vitro and that ZPR3 prevents DNA binding by REV in vitro. Overexpression of ZPR proteins in Arabidopsis results in phenotypes similar to those seen when HD-ZIPIII function is reduced. We propose a negative feedback model in which REV promotes transcription of the ZPR genes. The ZPR proteins in turn form heterodimers with the REV protein, preventing it from binding DNA. The HD-ZIPIII/ZPR regulatory module would serve not only to dampen the effect of fluctuations in HD-ZIPIII protein levels but more importantly would provide a potential point of regulation (control over the ratio of inactive heterodimers to active homodimers) that could be influenced by other components of the pathway governing leaf polarity.

@article{baltunis_inheritance_2007,
	title = {Inheritance of density, microfibril angle, and modulus of elasticity in juvenile wood of {Pinus} radiata at two locations in {Australia}},
	copyright = {2007},
	url = {https://cdnsciencepub.com/doi/abs/10.1139/X07-061},
	doi = {10/b2z5mv},
	abstract = {A total of 1640 increment cores from 343 radiata pine (Pinus radiata D. Don) families were sampled at two second-generation progeny trials, aged 6 and 7 years, for a detailed genetic study of juven...},
	language = {en},
	urldate = {2021-06-10},
	journal = {Canadian Journal of Forest Research},
	author = {Baltunis, Brian S. BaltunisB S. and Wu, H. X. and Powell, Mike B. PowellM B.},
	month = nov,
	year = {2007},
}

A total of 1640 increment cores from 343 radiata pine (Pinus radiata D. Don) families were sampled at two second-generation progeny trials, aged 6 and 7 years, for a detailed genetic study of juven...

@article{ankele_vivo_2007,
	title = {In {Vivo} {Visualization} of {Mg}-{ProtoporphyrinIX}, a {Coordinator} of {Photosynthetic} {Gene} {Expression} in the {Nucleus} and the {Chloroplast}},
	volume = {19},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.106.048744},
	doi = {10/cttnp7},
	abstract = {The photosynthetic apparatus is composed of proteins encoded by genes from both the nucleus and the chloroplast. To ensure that the photosynthetic complexes are assembled stoichiometrically and to enable their rapid reorganization in response to a changing environment, the plastids emit signals that regulate nuclear gene expression to match the status of the plastids. One of the plastid signals, the chlorophyll intermediate Mg-ProtoporphyrinIX (Mg-ProtoIX) accumulates under stress conditions and acts as a negative regulator of photosynthetic gene expression. By taking advantage of the photoreactive property of tetrapyrroles, Mg-ProtoIX could be visualized in the cells using confocal laser scanning spectroscopy. Our results demonstrate that Mg-ProtoIX accumulated both in the chloroplast and in the cytosol during stress conditions. Thus, the signaling metabolite is exported from the chloroplast, transmitting the plastid signal to the cytosol. Our results from the Mg-ProtoIX over- and underaccumulating mutants copper response defect and genome uncoupled5, respectively, demonstrate that the expression of both nuclear- and plastid-encoded photosynthesis genes is regulated by the accumulation of Mg-ProtoIX. Thus, stress-induced accumulation of the signaling metabolite Mg-ProtoIX coordinates nuclear and plastidic photosynthetic gene expression.},
	number = {6},
	urldate = {2021-09-02},
	journal = {The Plant Cell},
	author = {Ankele, Elisabeth and Kindgren, Peter and Pesquet, Edouard and Strand, Åsa},
	month = jun,
	year = {2007},
	pages = {1964--1979},
}

The photosynthetic apparatus is composed of proteins encoded by genes from both the nucleus and the chloroplast. To ensure that the photosynthetic complexes are assembled stoichiometrically and to enable their rapid reorganization in response to a changing environment, the plastids emit signals that regulate nuclear gene expression to match the status of the plastids. One of the plastid signals, the chlorophyll intermediate Mg-ProtoporphyrinIX (Mg-ProtoIX) accumulates under stress conditions and acts as a negative regulator of photosynthetic gene expression. By taking advantage of the photoreactive property of tetrapyrroles, Mg-ProtoIX could be visualized in the cells using confocal laser scanning spectroscopy. Our results demonstrate that Mg-ProtoIX accumulated both in the chloroplast and in the cytosol during stress conditions. Thus, the signaling metabolite is exported from the chloroplast, transmitting the plastid signal to the cytosol. Our results from the Mg-ProtoIX over- and underaccumulating mutants copper response defect and genome uncoupled5, respectively, demonstrate that the expression of both nuclear- and plastid-encoded photosynthesis genes is regulated by the accumulation of Mg-ProtoIX. Thus, stress-induced accumulation of the signaling metabolite Mg-ProtoIX coordinates nuclear and plastidic photosynthetic gene expression.

@article{kleine_genome-wide_2007,
	title = {Genome-{Wide} {Gene} {Expression} {Analysis} {Reveals} a {Critical} {Role} for {CRYPTOCHROME1} in the {Response} of {Arabidopsis} to {High} {Irradiance}},
	volume = {144},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.107.098293},
	doi = {10/fh8w86},
	abstract = {Exposure to high irradiance results in dramatic changes in nuclear gene expression in plants. However, little is known about the mechanisms by which changes in irradiance are sensed and how the information is transduced to the nucleus to initiate the genetic response. To investigate whether the photoreceptors are involved in the response to high irradiance, we analyzed expression of EARLY  LIGHT-INDUCIBLE PROTEIN1 (ELIP1), ELIP2, ASCORBATE PEROXIDASE2 (APX2), and LIGHT-HARVESTING CHLOROPHYLL A/B-BINDING PROTEIN2.4 (LHCB2.4) in the phytochrome A (phyA), phyB, cryptochrome1 (cry1), and cry2 photoreceptor mutants and long hypocotyl5 (hy5) and HY5 homolog (hyh) transcription factor mutants. Following exposure to high intensity white light for 3 h (1,000 μmol quanta m−2 s−1) expression of ELIP1/2 and APX2 was strongly induced and LHCB2.4 expression repressed in wild type. The cry1 and hy5 mutants showed specific misregulation of ELIP1/2, and we show that the induction of ELIP1/2 expression is mediated via CRY1 in a blue light intensity-dependent manner. Furthermore, using the Affymetrix Arabidopsis (Arabidopsis thaliana) 24 K Gene-Chip, we showed that 77 of the high light-responsive genes are regulated via CRY1, and 26 of those genes were also HY5 dependent. As a consequence of the misregulation of these genes, the cry1 mutant displayed a high irradiance-sensitive phenotype with significant photoinactivation of photosystem II, indicated by reduced maximal fluorescence ratio. Thus, we describe a novel function of CRY1 in mediating plant responses to high irradiances that is essential to the induction of photoprotective mechanisms. This indicates that high irradiance can be sensed in a chloroplast-independent manner by a cytosolic/nucleic component.},
	number = {3},
	urldate = {2021-09-02},
	journal = {Plant Physiology},
	author = {Kleine, Tatjana and Kindgren, Peter and Benedict, Catherine and Hendrickson, Luke and Strand, Åsa},
	month = jul,
	year = {2007},
	pages = {1391--1406},
}

Exposure to high irradiance results in dramatic changes in nuclear gene expression in plants. However, little is known about the mechanisms by which changes in irradiance are sensed and how the information is transduced to the nucleus to initiate the genetic response. To investigate whether the photoreceptors are involved in the response to high irradiance, we analyzed expression of EARLY  LIGHT-INDUCIBLE PROTEIN1 (ELIP1), ELIP2, ASCORBATE PEROXIDASE2 (APX2), and LIGHT-HARVESTING CHLOROPHYLL A/B-BINDING PROTEIN2.4 (LHCB2.4) in the phytochrome A (phyA), phyB, cryptochrome1 (cry1), and cry2 photoreceptor mutants and long hypocotyl5 (hy5) and HY5 homolog (hyh) transcription factor mutants. Following exposure to high intensity white light for 3 h (1,000 μmol quanta m−2 s−1) expression of ELIP1/2 and APX2 was strongly induced and LHCB2.4 expression repressed in wild type. The cry1 and hy5 mutants showed specific misregulation of ELIP1/2, and we show that the induction of ELIP1/2 expression is mediated via CRY1 in a blue light intensity-dependent manner. Furthermore, using the Affymetrix Arabidopsis (Arabidopsis thaliana) 24 K Gene-Chip, we showed that 77 of the high light-responsive genes are regulated via CRY1, and 26 of those genes were also HY5 dependent. As a consequence of the misregulation of these genes, the cry1 mutant displayed a high irradiance-sensitive phenotype with significant photoinactivation of photosystem II, indicated by reduced maximal fluorescence ratio. Thus, we describe a novel function of CRY1 in mediating plant responses to high irradiances that is essential to the induction of photoprotective mechanisms. This indicates that high irradiance can be sensed in a chloroplast-independent manner by a cytosolic/nucleic component.

@article{swarup_ethylene_2007,
	title = {Ethylene {Upregulates} {Auxin} {Biosynthesis} in \textit{{Arabidopsis}} {Seedlings} to {Enhance} {Inhibition} of {Root} {Cell} {Elongation}},
	volume = {19},
	issn = {1532-298X},
	url = {https://academic.oup.com/plcell/article/19/7/2186/6092109},
	doi = {10/cd3mq3},
	abstract = {Abstract
            Ethylene represents an important regulatory signal for root development. Genetic studies in Arabidopsis thaliana have demonstrated that ethylene inhibition of root growth involves another hormone signal, auxin. This study investigated why auxin was required by ethylene to regulate root growth. We initially observed that ethylene positively controls auxin biosynthesis in the root apex. We subsequently demonstrated that ethylene-regulated root growth is dependent on (1) the transport of auxin from the root apex via the lateral root cap and (2) auxin responses occurring in multiple elongation zone tissues. Detailed growth studies revealed that the ability of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid to inhibit root cell elongation was significantly enhanced in the presence of auxin. We conclude that by upregulating auxin biosynthesis, ethylene facilitates its ability to inhibit root cell expansion.},
	language = {en},
	number = {7},
	urldate = {2021-06-10},
	journal = {The Plant Cell},
	author = {Swarup, Ranjan and Perry, Paula and Hagenbeek, Dik and Van Der Straeten, Dominique and Beemster, Gerrit T.S. and Sandberg, Göran and Bhalerao, Rishikesh P. and Ljung, Karin and Bennett, Malcolm J.},
	month = aug,
	year = {2007},
	pages = {2186--2196},
}

Abstract Ethylene represents an important regulatory signal for root development. Genetic studies in Arabidopsis thaliana have demonstrated that ethylene inhibition of root growth involves another hormone signal, auxin. This study investigated why auxin was required by ethylene to regulate root growth. We initially observed that ethylene positively controls auxin biosynthesis in the root apex. We subsequently demonstrated that ethylene-regulated root growth is dependent on (1) the transport of auxin from the root apex via the lateral root cap and (2) auxin responses occurring in multiple elongation zone tissues. Detailed growth studies revealed that the ability of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid to inhibit root cell elongation was significantly enhanced in the presence of auxin. We conclude that by upregulating auxin biosynthesis, ethylene facilitates its ability to inhibit root cell expansion.

@article{jansson_populus_2007,
	title = {Populus: {A} {Model} {System} for {Plant} {Biology}},
	volume = {58},
	issn = {1543-5008},
	shorttitle = {Populus},
	url = {https://www.annualreviews.org/doi/10.1146/annurev.arplant.58.032806.103956},
	doi = {10/d42zfw},
	abstract = {With the completion of the Populus trichocarpa genome sequence and the development of various genetic, genomic, and biochemical tools, Populus now offers many possibilities to study questions that cannot be as easily addressed in Arabidopsis and rice, the two prime model systems of plant biology and genomics. Tree-specific traits such as wood formation, long-term perennial growth, and seasonality are obvious areas of research, but research in other areas such as control of flowering, biotic interactions, and evolution of adaptive traits is enriched by adding a tree to the suite of model systems. Furthermore, the reproductive biology of Populus (a dioeceous wind-pollinated long-lived tree) offers both new possibilities and challenges in the study and analysis of natural genetic and phenotypic variation. The relatively close phylogenetic relationship of Populus to Arabidopsis in the Eurosid clade of Eudicotyledonous plants aids in comparative functional studies and comparative genomics, and has the potential to greatly facilitate studies on genome and gene family evolution in eudicots.},
	number = {1},
	urldate = {2021-06-21},
	journal = {Annual Review of Plant Biology},
	author = {Jansson, Stefan and Douglas, Carl J.},
	month = jun,
	year = {2007},
	note = {Publisher: Annual Reviews},
	pages = {435--458},
}

With the completion of the Populus trichocarpa genome sequence and the development of various genetic, genomic, and biochemical tools, Populus now offers many possibilities to study questions that cannot be as easily addressed in Arabidopsis and rice, the two prime model systems of plant biology and genomics. Tree-specific traits such as wood formation, long-term perennial growth, and seasonality are obvious areas of research, but research in other areas such as control of flowering, biotic interactions, and evolution of adaptive traits is enriched by adding a tree to the suite of model systems. Furthermore, the reproductive biology of Populus (a dioeceous wind-pollinated long-lived tree) offers both new possibilities and challenges in the study and analysis of natural genetic and phenotypic variation. The relatively close phylogenetic relationship of Populus to Arabidopsis in the Eurosid clade of Eudicotyledonous plants aids in comparative functional studies and comparative genomics, and has the potential to greatly facilitate studies on genome and gene family evolution in eudicots.

@article{muhlenbock_lysigenous_2007,
	title = {Lysigenous {Aerenchyma} {Formation} in \textit{{Arabidopsis}} {Is} {Controlled} by \textit{{LESION} {SIMULATING} {DISEASE1}}},
	volume = {19},
	issn = {1532-298X},
	url = {https://academic.oup.com/plcell/article/19/11/3819/6100043},
	doi = {10/bxqzzq},
	abstract = {Abstract
            Aerenchyma tissues form gas-conducting tubes that provide roots with oxygen under hypoxic conditions. Although aerenchyma have received considerable attention in Zea mays, the signaling events and genes controlling aerenchyma induction remain elusive. Here, we show that Arabidopsis thaliana hypocotyls form lysigenous aerenchyma in response to hypoxia and that this process involves H2O2 and ethylene signaling. By studying Arabidopsis mutants that are deregulated for excess light acclimation, cell death, and defense responses, we find that the formation of lysigenous aerenchyma depends on the plant defense regulators LESION SIMULATING DISEASE1 (LSD1), ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1), and PHYTOALEXIN DEFICIENT4 (PAD4) that operate upstream of ethylene and reactive oxygen species production. The obtained results indicate that programmed cell death of lysigenous aerenchyma in hypocotyls occurs in a similar but independent manner from the foliar programmed cell death. Thus, the induction of aerenchyma is subject to a genetic and tissue-specific program. The data lead us to conclude that the balanced activities of LSD1, EDS1, and PAD4 regulate lysigenous aerenchyma formation in response to hypoxia.},
	language = {en},
	number = {11},
	urldate = {2021-06-10},
	journal = {The Plant Cell},
	author = {Mühlenbock, Per and Plaszczyca, Malgorzata and Plaszczyca, Marian and Mellerowicz, Ewa and Karpinski, Stanislaw},
	month = dec,
	year = {2007},
	pages = {3819--3830},
}

Abstract Aerenchyma tissues form gas-conducting tubes that provide roots with oxygen under hypoxic conditions. Although aerenchyma have received considerable attention in Zea mays, the signaling events and genes controlling aerenchyma induction remain elusive. Here, we show that Arabidopsis thaliana hypocotyls form lysigenous aerenchyma in response to hypoxia and that this process involves H2O2 and ethylene signaling. By studying Arabidopsis mutants that are deregulated for excess light acclimation, cell death, and defense responses, we find that the formation of lysigenous aerenchyma depends on the plant defense regulators LESION SIMULATING DISEASE1 (LSD1), ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1), and PHYTOALEXIN DEFICIENT4 (PAD4) that operate upstream of ethylene and reactive oxygen species production. The obtained results indicate that programmed cell death of lysigenous aerenchyma in hypocotyls occurs in a similar but independent manner from the foliar programmed cell death. Thus, the induction of aerenchyma is subject to a genetic and tissue-specific program. The data lead us to conclude that the balanced activities of LSD1, EDS1, and PAD4 regulate lysigenous aerenchyma formation in response to hypoxia.

@article{kusano_unbiased_2007,
	title = {Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in {Arabidopsis} thaliana},
	volume = {1},
	issn = {1752-0509},
	url = {http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-1-53},
	doi = {10/djdc4c},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {BMC Systems Biology},
	author = {Kusano, Miyako and Fukushima, Atsushi and Arita, Masanori and Jonsson, Pär and Moritz, Thomas and Kobayashi, Makoto and Hayashi, Naomi and Tohge, Takayuki and Saito, Kazuki},
	year = {2007},
	pages = {53},
}

@article{leple_downregulation_2007,
	title = {Downregulation of {Cinnamoyl}-{Coenzyme} {A} {Reductase} in {Poplar}: {Multiple}-{Level} {Phenotyping} {Reveals} {Effects} on {Cell} {Wall} {Polymer} {Metabolism} and {Structure}},
	volume = {19},
	issn = {1532-298X},
	shorttitle = {Downregulation of {Cinnamoyl}-{Coenzyme} {A} {Reductase} in {Poplar}},
	url = {https://academic.oup.com/plcell/article/19/11/3669/6100060},
	doi = {10/b4rvsq},
	abstract = {Abstract
            Cinnamoyl-CoA reductase (CCR) catalyzes the penultimate step in monolignol biosynthesis. We show that downregulation of CCR in transgenic poplar (Populus tremula × Populus alba) was associated with up to 50\% reduced lignin content and an orange-brown, often patchy, coloration of the outer xylem. Thioacidolysis, nuclear magnetic resonance (NMR), immunocytochemistry of lignin epitopes, and oligolignol profiling indicated that lignin was relatively more reduced in syringyl than in guaiacyl units. The cohesion of the walls was affected, particularly at sites that are generally richer in syringyl units in wild-type poplar. Ferulic acid was incorporated into the lignin via ether bonds, as evidenced independently by thioacidolysis and by NMR. A synthetic lignin incorporating ferulic acid had a red-brown coloration, suggesting that the xylem coloration was due to the presence of ferulic acid during lignification. Elevated ferulic acid levels were also observed in the form of esters. Transcript and metabolite profiling were used as comprehensive phenotyping tools to investigate how CCR downregulation impacted metabolism and the biosynthesis of other cell wall polymers. Both methods suggested reduced biosynthesis and increased breakdown or remodeling of noncellulosic cell wall polymers, which was further supported by Fourier transform infrared spectroscopy and wet chemistry analysis. The reduced levels of lignin and hemicellulose were associated with an increased proportion of cellulose. Furthermore, the transcript and metabolite profiling data pointed toward a stress response induced by the altered cell wall structure. Finally, chemical pulping of wood derived from 5-year-old, field-grown transgenic lines revealed improved pulping characteristics, but growth was affected in all transgenic lines tested.},
	language = {en},
	number = {11},
	urldate = {2021-06-10},
	journal = {The Plant Cell},
	author = {Leplé, Jean-Charles and Dauwe, Rebecca and Morreel, Kris and Storme, Véronique and Lapierre, Catherine and Pollet, Brigitte and Naumann, Annette and Kang, Kyu-Young and Kim, Hoon and Ruel, Katia and Lefèbvre, Andrée and Joseleau, Jean-Paul and Grima-Pettenati, Jacqueline and De Rycke, Riet and Andersson-Gunnerås, Sara and Erban, Alexander and Fehrle, Ines and Petit-Conil, Michel and Kopka, Joachim and Polle, Andrea and Messens, Eric and Sundberg, Björn and Mansfield, Shawn D. and Ralph, John and Pilate, Gilles and Boerjan, Wout},
	month = dec,
	year = {2007},
	pages = {3669--3691},
}

Abstract Cinnamoyl-CoA reductase (CCR) catalyzes the penultimate step in monolignol biosynthesis. We show that downregulation of CCR in transgenic poplar (Populus tremula × Populus alba) was associated with up to 50% reduced lignin content and an orange-brown, often patchy, coloration of the outer xylem. Thioacidolysis, nuclear magnetic resonance (NMR), immunocytochemistry of lignin epitopes, and oligolignol profiling indicated that lignin was relatively more reduced in syringyl than in guaiacyl units. The cohesion of the walls was affected, particularly at sites that are generally richer in syringyl units in wild-type poplar. Ferulic acid was incorporated into the lignin via ether bonds, as evidenced independently by thioacidolysis and by NMR. A synthetic lignin incorporating ferulic acid had a red-brown coloration, suggesting that the xylem coloration was due to the presence of ferulic acid during lignification. Elevated ferulic acid levels were also observed in the form of esters. Transcript and metabolite profiling were used as comprehensive phenotyping tools to investigate how CCR downregulation impacted metabolism and the biosynthesis of other cell wall polymers. Both methods suggested reduced biosynthesis and increased breakdown or remodeling of noncellulosic cell wall polymers, which was further supported by Fourier transform infrared spectroscopy and wet chemistry analysis. The reduced levels of lignin and hemicellulose were associated with an increased proportion of cellulose. Furthermore, the transcript and metabolite profiling data pointed toward a stress response induced by the altered cell wall structure. Finally, chemical pulping of wood derived from 5-year-old, field-grown transgenic lines revealed improved pulping characteristics, but growth was affected in all transgenic lines tested.

@article{vandenbussche_ethylene-induced_2007,
	title = {Ethylene-induced {Arabidopsis} hypocotyl elongation is dependent on but not mediated by gibberellins},
	volume = {58},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/erm288},
	doi = {10/c9kqxg},
	language = {en},
	number = {15-16},
	urldate = {2021-06-10},
	journal = {Journal of Experimental Botany},
	author = {Vandenbussche, F. and Vancompernolle, B. and Rieu, I. and Ahmad, M. and Phillips, A. and Moritz, T. and Hedden, P. and Van Der Straeten, D.},
	month = nov,
	year = {2007},
	pages = {4269--4281},
}

@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{sveshnikov_psbp-like_2007,
	title = {The {PsbP}-like protein (sll1418) of {Synechocystis} sp. {PCC} 6803 stabilises the donor side of {Photosystem} {II}},
	volume = {93},
	issn = {0166-8595, 1573-5079},
	url = {http://link.springer.com/10.1007/s11120-007-9171-3},
	doi = {10/bmkkvh},
	language = {en},
	number = {1-3},
	urldate = {2021-06-10},
	journal = {Photosynthesis Research},
	author = {Sveshnikov, Dmitry and Funk, Christiane and Schröder, Wolfgang P.},
	month = aug,
	year = {2007},
	pages = {101--109},
}

@article{kupriyanova_extracellular_2007,
	title = {Extracellular carbonic anhydrases of the stromatolite-forming cyanobacterium {Microcoleus} chthonoplastes},
	volume = {153},
	issn = {1350-0872, 1465-2080},
	url = {https://www.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.2006/003905-0},
	doi = {10/bn9bg2},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {Microbiology},
	author = {Kupriyanova, Elena and Villarejo, Arsenio and Markelova, Alexandra and Gerasimenko, Lyudmila and Zavarzin, Georgy and Samuelsson, Göran and Los, Dmitry A and Pronina, Natalia},
	month = apr,
	year = {2007},
	pages = {1149--1156},
}

@article{pyhajarvi_demographic_2007,
	title = {Demographic {History} {Has} {Influenced} {Nucleotide} {Diversity} in {European} \textit{{Pinus} sylvestris} {Populations}},
	volume = {177},
	issn = {1943-2631},
	url = {https://academic.oup.com/genetics/article/177/3/1713/6064487},
	doi = {10/cmrqmt},
	abstract = {Abstract
            To infer the role of natural selection in shaping standing genetic diversity, it is necessary to assess the genomewide impact of demographic history on nucleotide diversity. In this study we analyzed sequence diversity of 16 nuclear loci in eight Pinus sylvestris populations. Populations were divided into four geographical groups on the basis of their current location and the geographical history of the region: northern Europe, central Europe, Spain, and Turkey. There were no among-group differences in the level of silent nucleotide diversity, which was ∼0.005/bp in all groups. There was some evidence that linkage disequilibrium extended further in northern Europe than in central Europe: the estimates of the population recombination rate parameter, ρ, were 0.0064 and 0.0294, respectively. The summary statistics of nucleotide diversity in central and northern European populations were compatible with an ancient bottleneck rather than the standard neutral model.},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Genetics},
	author = {Pyhäjärvi, Tanja and García-Gil, M Rosario and Knürr, Timo and Mikkonen, Merja and Wachowiak, Witold and Savolainen, Outi},
	month = nov,
	year = {2007},
	pages = {1713--1724},
}

Abstract To infer the role of natural selection in shaping standing genetic diversity, it is necessary to assess the genomewide impact of demographic history on nucleotide diversity. In this study we analyzed sequence diversity of 16 nuclear loci in eight Pinus sylvestris populations. Populations were divided into four geographical groups on the basis of their current location and the geographical history of the region: northern Europe, central Europe, Spain, and Turkey. There were no among-group differences in the level of silent nucleotide diversity, which was ∼0.005/bp in all groups. There was some evidence that linkage disequilibrium extended further in northern Europe than in central Europe: the estimates of the population recombination rate parameter, ρ, were 0.0064 and 0.0294, respectively. The summary statistics of nucleotide diversity in central and northern European populations were compatible with an ancient bottleneck rather than the standard neutral model.

@article{notivol_genetic_2007,
	title = {Genetic variation of growth rhythm traits in the limits of a latitudinal cline in {Scots} pine},
	volume = {37},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/X06-243},
	doi = {10/bjtx48},
	abstract = {Scots pine ( Pinus sylvestris L.) has the widest distribution of pine species and the populations are locally adapted to very different environmental conditions. Adaptive traits such as those related to growth are optimal for understanding adaptation of populations to local conditions in widely distributed forest species. A study of the timing of growth during the first growing period of families in four populations from the latitudinal limits of the distribution range was conducted. Individual growth curves were fitted, and a set of variables related to growth rhythm and timing of budset was obtained for genetic analyses. Pooled heritabilities across populations were very high for most of the traits (0.43–1.09), and population differentiation for growth variables showed high values as well (Q
              ST
              = 0.19–0.71). Phenotypic correlations were higher than genetic ones, and most of them were positives. Even no general patterns of additive variances were found, the high additive genetic variance obtained (14\% ± 8\%, mean ± SE) suggests that additive genetic variance is not the limiting factor for adaptation to a new optimum within much of the range for these traits. Changes in means, additive genetic variances, and additive genetic coefficient of variation by population are also discussed.},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Canadian Journal of Forest Research},
	author = {Notivol, E. and García-Gil, M. R. and Alía, R. and Savolainen, O.},
	month = mar,
	year = {2007},
	pages = {540--551},
}

Scots pine ( Pinus sylvestris L.) has the widest distribution of pine species and the populations are locally adapted to very different environmental conditions. Adaptive traits such as those related to growth are optimal for understanding adaptation of populations to local conditions in widely distributed forest species. A study of the timing of growth during the first growing period of families in four populations from the latitudinal limits of the distribution range was conducted. Individual growth curves were fitted, and a set of variables related to growth rhythm and timing of budset was obtained for genetic analyses. Pooled heritabilities across populations were very high for most of the traits (0.43–1.09), and population differentiation for growth variables showed high values as well (Q ST = 0.19–0.71). Phenotypic correlations were higher than genetic ones, and most of them were positives. Even no general patterns of additive variances were found, the high additive genetic variance obtained (14% ± 8%, mean ± SE) suggests that additive genetic variance is not the limiting factor for adaptation to a new optimum within much of the range for these traits. Changes in means, additive genetic variances, and additive genetic coefficient of variation by population are also discussed.

@article{robert_isolation_2007,
	title = {Isolation of intact vacuoles from {Arabidopsis} rosette leaf–derived protoplasts},
	volume = {2},
	copyright = {2007 Nature Publishing Group},
	issn = {1750-2799},
	url = {https://www.nature.com/articles/nprot.2007.26},
	doi = {10/c58qb9},
	abstract = {Vacuoles are very prominent compartments within plant cells, and understanding of their function relies on knowledge of their content. Here, we present a simple vacuole purification protocol that was successfully used for large-scale isolation of vacuoles, free of significant contamination from other endomembrane compartments. This method is based on osmotic and thermal disruption of mesophyl-derived Arabidopsis protoplasts, followed by a density gradient fractionation of the cellular content. The whole procedure, including protoplast isolation, takes approximately 6 h.},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Nature Protocols},
	author = {Robert, Stéphanie and Zouhar, Jan and Carter, Clay and Raikhel, Natasha},
	month = feb,
	year = {2007},
	note = {Number: 2
Publisher: Nature Publishing Group},
	pages = {259--262},
}

Vacuoles are very prominent compartments within plant cells, and understanding of their function relies on knowledge of their content. Here, we present a simple vacuole purification protocol that was successfully used for large-scale isolation of vacuoles, free of significant contamination from other endomembrane compartments. This method is based on osmotic and thermal disruption of mesophyl-derived Arabidopsis protoplasts, followed by a density gradient fractionation of the cellular content. The whole procedure, including protoplast isolation, takes approximately 6 h.

@article{sanmartin_divergent_2007,
	title = {Divergent functions of {VTI12} and {VTI11} in trafficking to storage and lytic vacuoles in {Arabidopsis}},
	volume = {104},
	issn = {0027-8424},
	doi = {10/bt2khm},
	abstract = {The protein storage vacuole (PSV) is a plant-specific organelle that accumulates reserve proteins, one of the main agricultural products obtained from crops. Despite the importance of this process, the cellular machinery required for transport and accumulation of storage proteins remains largely unknown. Interfering with transport to PSVs has been shown to result in secretion of cargo. Therefore, secretion of a suitable marker could be used as an assay to identify mutants in this pathway. CLV3, a negative regulator of shoot stem cell proliferation, is an extracellular ligand that is rendered inactive when targeted to vacuoles. We devised an assay where trafficking mutants secrete engineered vacuolar CLV3 and show reduced meristems, a phenotype easily detected by visual inspection of plants. We tested this scheme in plants expressing VAC2, a fusion of CLV3 to the vacuolar sorting signal from the storage protein barley lectin. In this way, we determined that trafficking of VAC2 requires the SNARE VTI12 but not its close homologue, the conditionally redundant VTI11 protein. Furthermore, a vti12 mutant is specifically altered in transport of storage proteins, whereas a vti11 mutant is affected in transport of a lytic vacuole marker. These results demonstrate the specialization of VTI12 and VTI11 in mediating trafficking to storage and lytic vacuoles, respectively. Moreover, they validate the VAC2 secretion assay as a simple method to isolate genes that mediate trafficking to the PSV.},
	language = {eng},
	number = {9},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Sanmartín, Maite and Ordóñez, Angel and Sohn, Eun Ju and Robert, Stephanie and Sánchez-Serrano, José Juán and Surpin, Marci A. and Raikhel, Natasha V. and Rojo, Enrique},
	month = feb,
	year = {2007},
	pmid = {17360696},
	pmcid = {PMC1805581},
	keywords = {Arabidopsis, Arabidopsis Proteins, Microscopy, Fluorescence, Plant Lectins, Protein Transport, Qb-SNARE Proteins, Vacuoles},
	pages = {3645--3650},
}

The protein storage vacuole (PSV) is a plant-specific organelle that accumulates reserve proteins, one of the main agricultural products obtained from crops. Despite the importance of this process, the cellular machinery required for transport and accumulation of storage proteins remains largely unknown. Interfering with transport to PSVs has been shown to result in secretion of cargo. Therefore, secretion of a suitable marker could be used as an assay to identify mutants in this pathway. CLV3, a negative regulator of shoot stem cell proliferation, is an extracellular ligand that is rendered inactive when targeted to vacuoles. We devised an assay where trafficking mutants secrete engineered vacuolar CLV3 and show reduced meristems, a phenotype easily detected by visual inspection of plants. We tested this scheme in plants expressing VAC2, a fusion of CLV3 to the vacuolar sorting signal from the storage protein barley lectin. In this way, we determined that trafficking of VAC2 requires the SNARE VTI12 but not its close homologue, the conditionally redundant VTI11 protein. Furthermore, a vti12 mutant is specifically altered in transport of storage proteins, whereas a vti11 mutant is affected in transport of a lytic vacuole marker. These results demonstrate the specialization of VTI12 and VTI11 in mediating trafficking to storage and lytic vacuoles, respectively. Moreover, they validate the VAC2 secretion assay as a simple method to isolate genes that mediate trafficking to the PSV.

@article{gough_new_2007,
	title = {A new method for isolating physiologically active {Mg}-protoporphyrin monomethyl ester, the substrate of the cyclase enzyme of the chlorophyll biosynthetic pathway},
	volume = {45},
	issn = {09819428},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0981942807001775},
	doi = {10/fsxp89},
	language = {en},
	number = {12},
	urldate = {2021-06-10},
	journal = {Plant Physiology and Biochemistry},
	author = {Gough, Simon P. and Rzeznicka, Kamila and Peterson Wulff, Ragna and Francisco, Jose da Cruz and Hansson, Andreas and Jensen, Poul Erik and Hansson, Mats},
	month = dec,
	year = {2007},
	pages = {932--936},
}

@article{deng_two_2007,
	title = {Two {Iron}-{Responsive} {Promoter} {Elements} {Control} {Expression} of \textit{{FOX1}} in \textit{{Chlamydomonas} reinhardtii}},
	volume = {6},
	issn = {1535-9778, 1535-9786},
	url = {https://journals.asm.org/doi/10.1128/EC.00324-07},
	doi = {10/bbxdkg},
	abstract = {ABSTRACT
            
              FOX1
              encodes an iron deficiency-induced ferroxidase involved in a high-affinity iron uptake system. Mutagenesis analysis of the
              FOX1
              promoter identified two separate iron-responsive elements, FeRE1 (CACACG) and FeRE2 (CACGCG), between positions −87 and −82 and between positions −65 and −60, respectively, and both are needed for induced
              FOX1
              expression under conditions of iron deficiency.},
	language = {en},
	number = {11},
	urldate = {2021-06-10},
	journal = {Eukaryotic Cell},
	author = {Deng, Xiaodong and Eriksson, Mats},
	month = nov,
	year = {2007},
	pages = {2163--2167},
}

ABSTRACT FOX1 encodes an iron deficiency-induced ferroxidase involved in a high-affinity iron uptake system. Mutagenesis analysis of the FOX1 promoter identified two separate iron-responsive elements, FeRE1 (CACACG) and FeRE2 (CACGCG), between positions −87 and −82 and between positions −65 and −60, respectively, and both are needed for induced FOX1 expression under conditions of iron deficiency.

@article{bylesjo_data_2007,
	title = {Data integration in plant biology: the {O2PLS} method for combined modeling of transcript and metabolite data},
	volume = {52},
	issn = {09607412, 1365313X},
	shorttitle = {Data integration in plant biology},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2007.03293.x},
	doi = {10/dq2z2k},
	language = {en},
	number = {6},
	urldate = {2021-06-10},
	journal = {The Plant Journal},
	author = {Bylesjö, Max and Eriksson, Daniel and Kusano, Miyako and Moritz, Thomas and Trygg, Johan},
	month = dec,
	year = {2007},
	pages = {1181--1191},
}

@article{el-kassaby_advanced_2007,
	title = {Advanced generation seed orchards’ turnover as affected by breeding advance, time to sexual maturity and costs, with special reference to \textit{{Pinus} sylvestris} in {Sweden}},
	volume = {22},
	issn = {0282-7581, 1651-1891},
	url = {https://www.tandfonline.com/doi/full/10.1080/02827580701217752},
	doi = {10/b86kpf},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Scandinavian Journal of Forest Research},
	author = {El-Kassaby, Yousry A. and Prescher, Finnvid and Lindgren, Dag},
	month = apr,
	year = {2007},
	pages = {88--98},
}

@article{boutte_mechanisms_2007,
	title = {Mechanisms of auxin-dependent cell and tissue polarity},
	volume = {10},
	issn = {13695266},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S136952660700101X},
	doi = {10/bfztfs},
	language = {en},
	number = {6},
	urldate = {2021-06-10},
	journal = {Current Opinion in Plant Biology},
	author = {Boutté, Yohann and Ikeda, Yoshihisa and Grebe, Markus},
	month = dec,
	year = {2007},
	pages = {616--623},
}

@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{lee_growth-phase-dependent_2007,
	title = {Growth-phase-dependent gene expression profiling of poplar ({Populus} alba × {Populus} tremula var. glandulosa) suspension cells},
	volume = {131},
	issn = {0031-9317, 1399-3054},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2007.00987.x},
	doi = {10/b8dzcg},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {Physiologia Plantarum},
	author = {Lee, Hyoshin and Bae, Eun-Kyung and Park, So-Young and Sjödin, Andreas and Lee, Jae-Soon and Noh, Eun-Woon and Jansson, Stefan},
	month = dec,
	year = {2007},
	pages = {599--613},
}

@article{ivkovic_modelling_2007,
	title = {Modelling the effects of stem sweep, branch size and wood stiffness of radiata pine on structural timber production},
	volume = {70},
	issn = {0004-9158},
	url = {https://doi.org/10.1080/00049158.2007.10675018},
	doi = {10/gkhqbc},
	abstract = {The effects of changing three important biological traits — stem sweep (SWE), branch size (BRS) and modulus of elasticity (MoE) — on the radiata pine production system were examined using data obtained from the Australian radiata pine industry and from scientific experiments. Significant improvements in sawlog grade, structural timber grade recovery and the proportion of higher-grade timber can be obtained by reducing SWE and BRS and by increasing MoE. A 10\% reduction in sweep reduced sawlog degrade by 17.1\% and increased green timber recovery by about 0.5\%. A 10\% reduction in BRS decreased the volume of degraded sawlog by 68\% and increased structural timber recovery by 0.6–1.6\%. An increase of 10\% in MoE increased structural timber recovery by 12.3–13.1\%. The main advantage of modelling the effects of biological traits using data from industry is greater reliability relative to models based on assumptions. The modelling provides quantitative information that the timber industry can use to increase its productivity and profitability.},
	number = {3},
	urldate = {2021-06-10},
	journal = {Australian Forestry},
	author = {Ivković, M. and Wu, H. X. and Spencer, D. J. and McRae, T. A.},
	month = jan,
	year = {2007},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/00049158.2007.10675018},
	keywords = {Pinus radiala, models, production, profitability, structural timbers, traits, wood properties},
	pages = {173--184},
}

The effects of changing three important biological traits — stem sweep (SWE), branch size (BRS) and modulus of elasticity (MoE) — on the radiata pine production system were examined using data obtained from the Australian radiata pine industry and from scientific experiments. Significant improvements in sawlog grade, structural timber grade recovery and the proportion of higher-grade timber can be obtained by reducing SWE and BRS and by increasing MoE. A 10% reduction in sweep reduced sawlog degrade by 17.1% and increased green timber recovery by about 0.5%. A 10% reduction in BRS decreased the volume of degraded sawlog by 68% and increased structural timber recovery by 0.6–1.6%. An increase of 10% in MoE increased structural timber recovery by 12.3–13.1%. The main advantage of modelling the effects of biological traits using data from industry is greater reliability relative to models based on assumptions. The modelling provides quantitative information that the timber industry can use to increase its productivity and profitability.

@article{wu_efficiency_2007,
	title = {Efficiency of early selection for rotation-aged wood quality traits in radiata pine},
	volume = {64},
	copyright = {INRA, EDP Sciences},
	issn = {1286-4560, 1297-966X},
	url = {http://dx.doi.org/10.1051/forest:2006082},
	doi = {10/dsj2r9},
	abstract = {Annals of Forest Science, is a source of information about current developments and trends in forest research and forestry},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Annals of Forest Science},
	author = {Wu, Harry X. and Powell, Mike B. and Yang, Junli L. and Ivković, Milo and McRae, Tony A.},
	month = jan,
	year = {2007},
	note = {Publisher: EDP Sciences},
	pages = {1--9},
}

Annals of Forest Science, is a source of information about current developments and trends in forest research and forestry

@article{wu_achievements_2007,
	title = {Achievements in forest tree improvement in {Australia} and {New} {Zealand} 8. {Successful} introduction and breeding of radiata pine in {Australia}},
	volume = {70},
	issn = {0004-9158},
	url = {https://doi.org/10.1080/00049158.2007.10675023},
	doi = {10/gkhp99},
	abstract = {Radiata pine (Pinus radiata) was originally known as Pinus insignis or ‘remarkable pine’, an apt name for a tree which has had such a dramatic impact on the world timber scene. It is a native conifer of California, USA, and was first introduced into Australia around 1857 for ornamental plantings. There were two major sources of original importation, one through Ferdinand von Mueller to Victoria and South Australia in the 1860s, and the second through New Zealand seed merchants. Forty-year-old trees were clearfelled for sawing in 1908 in Victoria. The fast early growth of radiata pine in Mount Gambier and north of Adelaide in the 1870s and 80s prompted the state forest services of South Australia, Victoria and New South Wales to advocate planting of the remarkable pine as an exotic conifer to compensate for the relative paucity of indigenous softwood in Australia. There was some plantation development in the 1920s and 1930s, but planting almost stopped during World War II. Large-scale planting of radiata pine started again only in the late 1950s. Up to the late 1960s, unimproved seeds used to establish plantations in Australia were at first from early ornamental plantings, then from small plantations and later, in part, imported from New Zealand. Initial research and breeding were undertaken by the Forestry and Timber Bureau (at Canberra and Mt Gambier) and the Queensland Forestry Department — both studied reproductive biology, selected superior trees and established progeny tests in the early 1950s. Following the Seventh British Commonwealth Forestry Conference in Australia and New Zealand in 1957, the other five state forest services and two private companies initiated genetic improvement work in the late 1950s. After establishment of the first grafted seed orchard in 1957, a total of 145 ha of seed orchard was established by 1968. Large-scale plantings using improved seeds started in the early 1970s. Many clones were received from NZ before the 1970s, and a range-wide seed collection was made in the five native stands in California in 1978. In 1983, the Southern Tree Breeding Association (STBA) was formed to coordinate the national breeding program of radiata pine, and it now serves about half of Australia's radiata pine estate. The other half is controlled by Forests New South Wales (FNSW) and the Western Australian Forest Products Commission (FPC). Radiata pine has been bred for three generations since the 1950s, with realised genetic gain up to 33\% for volume from the first generation and more than 10\% gain predicted from the second generation. The focus of the third-generation breeding in STBA has shifted to wood quality traits with: • integration of quantitative genetics, molecular genetics and wood science • development of economic breeding objectives • application of best linear unbiased prediction (BLUP) and a Web-based interactive database for customised delivery of breeding values. During 50 years of breeding radiata pine in southern Australia, several changes in strategic directions have been developed and implemented. Options for such flexibility must be maintained. To further increase genetic gain, infusion of new genetic material from the range-wide collections, increased recombination rate and selection intensity, purging of inbreeding depression, deployment by clonal forestry, and development of strategies dealing with adverse genetic correlation between wood volume and quality traits will be critical.},
	number = {4},
	urldate = {2021-06-10},
	journal = {Australian Forestry},
	author = {Wu, Harry X. and Eldridge, Ken G. and Matheson, A. Colin and Powell, Mike B. and McRae, Tony A. and Butcher, Trevor B. and Johnson, Ian G.},
	month = jan,
	year = {2007},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/00049158.2007.10675023},
	keywords = {breeding programs, economics, genetic improvement, genetic resources, growth rate, history, information systems, provenance, radiata pine, traits, wood properties},
	pages = {215--225},
}

Radiata pine (Pinus radiata) was originally known as Pinus insignis or ‘remarkable pine’, an apt name for a tree which has had such a dramatic impact on the world timber scene. It is a native conifer of California, USA, and was first introduced into Australia around 1857 for ornamental plantings. There were two major sources of original importation, one through Ferdinand von Mueller to Victoria and South Australia in the 1860s, and the second through New Zealand seed merchants. Forty-year-old trees were clearfelled for sawing in 1908 in Victoria. The fast early growth of radiata pine in Mount Gambier and north of Adelaide in the 1870s and 80s prompted the state forest services of South Australia, Victoria and New South Wales to advocate planting of the remarkable pine as an exotic conifer to compensate for the relative paucity of indigenous softwood in Australia. There was some plantation development in the 1920s and 1930s, but planting almost stopped during World War II. Large-scale planting of radiata pine started again only in the late 1950s. Up to the late 1960s, unimproved seeds used to establish plantations in Australia were at first from early ornamental plantings, then from small plantations and later, in part, imported from New Zealand. Initial research and breeding were undertaken by the Forestry and Timber Bureau (at Canberra and Mt Gambier) and the Queensland Forestry Department — both studied reproductive biology, selected superior trees and established progeny tests in the early 1950s. Following the Seventh British Commonwealth Forestry Conference in Australia and New Zealand in 1957, the other five state forest services and two private companies initiated genetic improvement work in the late 1950s. After establishment of the first grafted seed orchard in 1957, a total of 145 ha of seed orchard was established by 1968. Large-scale plantings using improved seeds started in the early 1970s. Many clones were received from NZ before the 1970s, and a range-wide seed collection was made in the five native stands in California in 1978. In 1983, the Southern Tree Breeding Association (STBA) was formed to coordinate the national breeding program of radiata pine, and it now serves about half of Australia's radiata pine estate. The other half is controlled by Forests New South Wales (FNSW) and the Western Australian Forest Products Commission (FPC). Radiata pine has been bred for three generations since the 1950s, with realised genetic gain up to 33% for volume from the first generation and more than 10% gain predicted from the second generation. The focus of the third-generation breeding in STBA has shifted to wood quality traits with: • integration of quantitative genetics, molecular genetics and wood science • development of economic breeding objectives • application of best linear unbiased prediction (BLUP) and a Web-based interactive database for customised delivery of breeding values. During 50 years of breeding radiata pine in southern Australia, several changes in strategic directions have been developed and implemented. Options for such flexibility must be maintained. To further increase genetic gain, infusion of new genetic material from the range-wide collections, increased recombination rate and selection intensity, purging of inbreeding depression, deployment by clonal forestry, and development of strategies dealing with adverse genetic correlation between wood volume and quality traits will be critical.

@article{ruzicka_ethylene_2007,
	title = {Ethylene {Regulates} {Root} {Growth} through {Effects} on {Auxin} {Biosynthesis} and {Transport}-{Dependent} {Auxin} {Distribution}},
	volume = {19},
	issn = {1532-298X},
	url = {https://academic.oup.com/plcell/article/19/7/2197/6092111},
	doi = {10/c2w5xb},
	abstract = {Abstract
            In plants, each developmental process integrates a network of signaling events that are regulated by different phytohormones, and interactions among hormonal pathways are essential to modulate their effect. Continuous growth of roots results from the postembryonic activity of cells within the root meristem that is controlled by the coordinated action of several phytohormones, including auxin and ethylene. Although their interaction has been studied intensively, the molecular and cellular mechanisms underlying this interplay are unknown. We show that the effect of ethylene on root growth is largely mediated by the regulation of the auxin biosynthesis and transport-dependent local auxin distribution. Ethylene stimulates auxin biosynthesis and basipetal auxin transport toward the elongation zone, where it activates a local auxin response leading to inhibition of cell elongation. Consistently, in mutants affected in auxin perception or basipetal auxin transport, ethylene cannot activate the auxin response nor regulate the root growth. In addition, ethylene modulates the transcription of several components of the auxin transport machinery. Thus, ethylene achieves a local activation of the auxin signaling pathway and regulates root growth by both stimulating the auxin biosynthesis and by modulating the auxin transport machinery.},
	language = {en},
	number = {7},
	urldate = {2021-06-10},
	journal = {The Plant Cell},
	author = {Růžička, Kamil and Ljung, Karin and Vanneste, Steffen and Podhorská, Radka and Beeckman, Tom and Friml, Jiří and Benková, Eva},
	month = aug,
	year = {2007},
	pages = {2197--2212},
}

Abstract In plants, each developmental process integrates a network of signaling events that are regulated by different phytohormones, and interactions among hormonal pathways are essential to modulate their effect. Continuous growth of roots results from the postembryonic activity of cells within the root meristem that is controlled by the coordinated action of several phytohormones, including auxin and ethylene. Although their interaction has been studied intensively, the molecular and cellular mechanisms underlying this interplay are unknown. We show that the effect of ethylene on root growth is largely mediated by the regulation of the auxin biosynthesis and transport-dependent local auxin distribution. Ethylene stimulates auxin biosynthesis and basipetal auxin transport toward the elongation zone, where it activates a local auxin response leading to inhibition of cell elongation. Consistently, in mutants affected in auxin perception or basipetal auxin transport, ethylene cannot activate the auxin response nor regulate the root growth. In addition, ethylene modulates the transcription of several components of the auxin transport machinery. Thus, ethylene achieves a local activation of the auxin signaling pathway and regulates root growth by both stimulating the auxin biosynthesis and by modulating the auxin transport machinery.

@article{yin_ubiquitin_2007,
	title = {Ubiquitin {Lysine} 63 {Chain}–{Forming} {Ligases} {Regulate} {Apical} {Dominance} in \textit{{Arabidopsis}}},
	volume = {19},
	issn = {1532-298X},
	url = {https://academic.oup.com/plcell/article/19/6/1898/6092124},
	doi = {10/cwwcnr},
	abstract = {Abstract
            Lys-63–linked multiubiquitin chains play important roles in signal transduction in yeast and in mammals, but the functions for this type of chain in plants remain to be defined. The RING domain protein RGLG2 (for RING domain Ligase2) from Arabidopsis thaliana can be N-terminally myristoylated and localizes to the plasma membrane. It can form Lys-63–linked multiubiquitin chains in an in vitro reaction. RGLG2 has overlapping functions with its closest sequelog, RGLG1, and single mutants in either gene are inconspicuous. rglg1 rglg2 double mutant plants exhibit loss of apical dominance and altered phyllotaxy, two traits critically influenced by the plant hormone auxin. Auxin and cytokinin levels are changed, and the plants show a decreased response to exogenously added auxin. Changes in the abundance of PIN family auxin transport proteins and synthetic lethality with a mutation in the auxin transport regulator BIG suggest that the directional flow of auxin is modulated by RGLG activity. Modification of proteins by Lys-63–linked multiubiquitin chains is thus important for hormone-regulated, basic plant architecture.},
	language = {en},
	number = {6},
	urldate = {2021-06-10},
	journal = {The Plant Cell},
	author = {Yin, Xiao-Jun and Volk, Sara and Ljung, Karin and Mehlmer, Norbert and Dolezal, Karel and Ditengou, Franck and Hanano, Shigeru and Davis, Seth J. and Schmelzer, Elmon and Sandberg, Göran and Teige, Markus and Palme, Klaus and Pickart, Cecile and Bachmair, Andreas},
	month = jul,
	year = {2007},
	pages = {1898--1911},
}

Abstract Lys-63–linked multiubiquitin chains play important roles in signal transduction in yeast and in mammals, but the functions for this type of chain in plants remain to be defined. The RING domain protein RGLG2 (for RING domain Ligase2) from Arabidopsis thaliana can be N-terminally myristoylated and localizes to the plasma membrane. It can form Lys-63–linked multiubiquitin chains in an in vitro reaction. RGLG2 has overlapping functions with its closest sequelog, RGLG1, and single mutants in either gene are inconspicuous. rglg1 rglg2 double mutant plants exhibit loss of apical dominance and altered phyllotaxy, two traits critically influenced by the plant hormone auxin. Auxin and cytokinin levels are changed, and the plants show a decreased response to exogenously added auxin. Changes in the abundance of PIN family auxin transport proteins and synthetic lethality with a mutation in the auxin transport regulator BIG suggest that the directional flow of auxin is modulated by RGLG activity. Modification of proteins by Lys-63–linked multiubiquitin chains is thus important for hormone-regulated, basic plant architecture.

@article{leul_organization_2007,
	title = {The organization, regulation and phylogeny of uptake hydrogenase genes in {Frankia}},
	volume = {130},
	issn = {0031-9317, 1399-3054},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2007.00861.x},
	doi = {10/fm8kd2},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Physiologia Plantarum},
	author = {Leul, Melakeselam and Normand, Philippe and Sellstedt, Anita},
	month = jul,
	year = {2007},
	pages = {464--470},
}

@article{edvardsson_immunophilin_2007,
	title = {Immunophilin {AtFKBP13} {Sustains} {All} {Peptidyl}−{Prolyl} {Isomerase} {Activity} in the {Thylakoid} {Lumen} from {Arabidopsis} thaliana {Deficient} in {AtCYP20}-2},
	volume = {46},
	issn = {0006-2960},
	url = {https://doi.org/10.1021/bi700426q},
	doi = {10/c2bw2c},
	abstract = {The physiological roles of immunophilins are unclear, but many possess peptidyl−prolyl isomerase (PPIase) activity, and they have been found in all organisms examined to date, implying that they are involved in fundamental, protein-folding processes. The chloroplast thylakoid lumen of the higher plant Arabidopsis thaliana contains up to 16 immunophilins (five cyclophilins and 11 FKBPs), but only two of them, AtCYP20-2 and AtFKBP13, have been found to be active PPIases, indicating that the other immunophilins in this cellular compartment may have lost their putative PPIase activities. To assess this possibility, we characterized two independent Arabidopsis knockout lines lacking AtCYP20-2 in enzymological and quantitative proteomic analyses. The PPIase activity in thylakoid lumen preparations of both mutants was equal to that of corresponding wild-type preparations, and comparative two-dimensional difference gel electrophoresis analyses of the lumenal proteins of the mutants and wild type showed that none of the potential PPIases was more abundant in the AtCYP20-2 deficient plants. Enzymatic analyses established that all PPIase activity in the mutant thylakoid lumen was attributable to AtFKBP13, and oxidative activation of this enzyme compensated for the lack of AtCYP20-2. Accordingly, sequence analyses of the potential catalytic domains of lumenal cyclophilins and FKBPs demonstrated that only AtCYP20-2 and AtFKBP13 possess all of the amino acid residues found to be essential for PPIase activity in earlier studies of human cyclophilin A and FKBP12. Thus, none of the immunophilins in the chloroplast thylakoid lumen of Arabidopsis except AtCYP20-2 and AtFKBP13 appear to possess prolyl isomerase activity toward peptide substrates.},
	number = {33},
	urldate = {2021-06-10},
	journal = {Biochemistry},
	author = {Edvardsson, Anna and Shapiguzov, Alexey and Petersson, Ulrika A. and Schröder, Wolfgang P. and Vener, Alexander V.},
	month = aug,
	year = {2007},
	note = {Publisher: American Chemical Society},
	pages = {9432--9442},
}

The physiological roles of immunophilins are unclear, but many possess peptidyl−prolyl isomerase (PPIase) activity, and they have been found in all organisms examined to date, implying that they are involved in fundamental, protein-folding processes. The chloroplast thylakoid lumen of the higher plant Arabidopsis thaliana contains up to 16 immunophilins (five cyclophilins and 11 FKBPs), but only two of them, AtCYP20-2 and AtFKBP13, have been found to be active PPIases, indicating that the other immunophilins in this cellular compartment may have lost their putative PPIase activities. To assess this possibility, we characterized two independent Arabidopsis knockout lines lacking AtCYP20-2 in enzymological and quantitative proteomic analyses. The PPIase activity in thylakoid lumen preparations of both mutants was equal to that of corresponding wild-type preparations, and comparative two-dimensional difference gel electrophoresis analyses of the lumenal proteins of the mutants and wild type showed that none of the potential PPIases was more abundant in the AtCYP20-2 deficient plants. Enzymatic analyses established that all PPIase activity in the mutant thylakoid lumen was attributable to AtFKBP13, and oxidative activation of this enzyme compensated for the lack of AtCYP20-2. Accordingly, sequence analyses of the potential catalytic domains of lumenal cyclophilins and FKBPs demonstrated that only AtCYP20-2 and AtFKBP13 possess all of the amino acid residues found to be essential for PPIase activity in earlier studies of human cyclophilin A and FKBP12. Thus, none of the immunophilins in the chloroplast thylakoid lumen of Arabidopsis except AtCYP20-2 and AtFKBP13 appear to possess prolyl isomerase activity toward peptide substrates.

@article{nishikubo_xyloglucan_2007,
	title = {Xyloglucan {Endo}-transglycosylase ({XET}) {Functions} in {Gelatinous} {Layers} of {Tension} {Wood} {Fibers} in {Poplar}—{A} {Glimpse} into the {Mechanism} of the {Balancing} {Act} of {Trees}},
	volume = {48},
	issn = {1471-9053, 0032-0781},
	url = {https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/pcm055},
	doi = {10/dm4c3z},
	language = {en},
	number = {6},
	urldate = {2021-06-10},
	journal = {Plant and Cell Physiology},
	author = {Nishikubo, Nobuyuki and Awano, Tatsuya and Banasiak, Alicja and Bourquin, Veronica and Ibatullin, Farid and Funada, Ryo and Brumer, Harry and Teeri, Tuula T. and Hayashi, Takahisa and Sundberg, Björn and Mellerowicz, Ewa J.},
	month = jun,
	year = {2007},
	pages = {843--855},
}

@article{thysell_reliable_2007,
	title = {Reliable {Profile} {Detection} in {Comparative} {Metabolomics}},
	volume = {11},
	issn = {1536-2310, 1557-8100},
	url = {http://www.liebertpub.com/doi/10.1089/omi.2007.0006},
	doi = {10/cvvjjh},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {OMICS: A Journal of Integrative Biology},
	author = {Thysell, Elin and Pohjanen, Elin and Lindberg, Johan and Schuppe-Koistinen, Ina and Moritz, Thomas and Jonsson, Pär and Antti, Henrik},
	month = jun,
	year = {2007},
	pages = {209--224},
}

@article{santos_modulation_2007,
	title = {Modulation of {Frankia} alni {ACN14a} oxidative stress response: activity, expression and phylogeny of catalases},
	volume = {130},
	issn = {0031-9317, 1399-3054},
	shorttitle = {Modulation of {Frankia} alni {ACN14a} oxidative stress response},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2007.00868.x},
	doi = {10/cvrx56},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Physiologia Plantarum},
	author = {Santos, Catarina L. and Vieira, João and Sellstedt, Anita and Normand, Philippe and Moradas-Ferreira, Pedro and Tavares, Fernando},
	month = jul,
	year = {2007},
	pages = {454--463},
}

@article{tavares_reactive_2007,
	title = {Reactive oxygen species in legume and actinorhizal nitrogen-fixing symbioses: the microsymbiont?s responses to an unfriendly reception},
	volume = {130},
	issn = {0031-9317, 1399-3054},
	shorttitle = {Reactive oxygen species in legume and actinorhizal nitrogen-fixing symbioses},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2007.00933.x},
	doi = {10/bfbmkh},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Physiologia Plantarum},
	author = {Tavares, Fernando and Santos, Catarina L. and Sellstedt, Anita},
	month = jul,
	year = {2007},
	pages = {344--356},
}

@article{sellstedt_frankia_2007,
	title = {Frankia ? the friendly bacteria ? infecting actinorhizal plants},
	volume = {130},
	issn = {0031-9317, 1399-3054},
	shorttitle = {Frankia ?},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2007.00932.x},
	doi = {10/cv28q8},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Physiologia Plantarum},
	author = {Sellstedt, Anita and Normand, Philippe and Dawson, Jeff},
	month = jul,
	year = {2007},
	pages = {315--317},
}

@article{bjorklund_cross-talk_2007,
	title = {Cross-talk between gibberellin and auxin in development of {Populus} wood: gibberellin stimulates polar auxin transport and has a common transcriptome with auxin: {Cross}-talk between {GA} and auxin in wood development},
	volume = {52},
	issn = {09607412},
	shorttitle = {Cross-talk between gibberellin and auxin in development of {Populus} wood},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2007.03250.x},
	doi = {10/chbxht},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {The Plant Journal},
	author = {Björklund, Simon and Antti, Henrik and Uddestrand, Ida and Moritz, Thomas and Sundberg, Björn},
	month = sep,
	year = {2007},
	pages = {499--511},
}

@article{ruttink_molecular_2007,
	title = {A {Molecular} {Timetable} for {Apical} {Bud} {Formation} and {Dormancy} {Induction} in {Poplar}},
	volume = {19},
	issn = {1532-298X},
	url = {https://academic.oup.com/plcell/article/19/8/2370/6088927},
	doi = {10/bcfnqh},
	abstract = {Abstract
            The growth of perennial plants in the temperate zone alternates with periods of dormancy that are typically initiated during bud development in autumn. In a systems biology approach to unravel the underlying molecular program of apical bud development in poplar (Populus tremula × Populus alba), combined transcript and metabolite profiling were applied to a high-resolution time course from short-day induction to complete dormancy. Metabolite and gene expression dynamics were used to reconstruct the temporal sequence of events during bud development. Importantly, bud development could be dissected into bud formation, acclimation to dehydration and cold, and dormancy. To each of these processes, specific sets of regulatory and marker genes and metabolites are associated and provide a reference frame for future functional studies. Light, ethylene, and abscisic acid signal transduction pathways consecutively control bud development by setting, modifying, or terminating these processes. Ethylene signal transduction is positioned temporally between light and abscisic acid signals and is putatively activated by transiently low hexose pools. The timing and place of cell proliferation arrest (related to dormancy) and of the accumulation of storage compounds (related to acclimation processes) were established within the bud by electron microscopy. Finally, the identification of a large set of genes commonly expressed during the growth-to-dormancy transitions in poplar apical buds, cambium, or Arabidopsis thaliana seeds suggests parallels in the underlying molecular mechanisms in different plant organs.},
	language = {en},
	number = {8},
	urldate = {2021-06-10},
	journal = {The Plant Cell},
	author = {Ruttink, Tom and Arend, Matthias and Morreel, Kris and Storme, Véronique and Rombauts, Stephane and Fromm, Jörg and Bhalerao, Rishikesh P. and Boerjan, Wout and Rohde, Antje},
	month = oct,
	year = {2007},
	pages = {2370--2390},
}

Abstract The growth of perennial plants in the temperate zone alternates with periods of dormancy that are typically initiated during bud development in autumn. In a systems biology approach to unravel the underlying molecular program of apical bud development in poplar (Populus tremula × Populus alba), combined transcript and metabolite profiling were applied to a high-resolution time course from short-day induction to complete dormancy. Metabolite and gene expression dynamics were used to reconstruct the temporal sequence of events during bud development. Importantly, bud development could be dissected into bud formation, acclimation to dehydration and cold, and dormancy. To each of these processes, specific sets of regulatory and marker genes and metabolites are associated and provide a reference frame for future functional studies. Light, ethylene, and abscisic acid signal transduction pathways consecutively control bud development by setting, modifying, or terminating these processes. Ethylene signal transduction is positioned temporally between light and abscisic acid signals and is putatively activated by transiently low hexose pools. The timing and place of cell proliferation arrest (related to dormancy) and of the accumulation of storage compounds (related to acclimation processes) were established within the bud by electron microscopy. Finally, the identification of a large set of genes commonly expressed during the growth-to-dormancy transitions in poplar apical buds, cambium, or Arabidopsis thaliana seeds suggests parallels in the underlying molecular mechanisms in different plant organs.

@article{kusano_application_2007,
	title = {Application of a metabolomic method combining one-dimensional and two-dimensional gas chromatography-time-of-flight/mass spectrometry to metabolic phenotyping of natural variants in rice},
	volume = {855},
	issn = {15700232},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1570023207003479},
	doi = {10/ds6j34},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Journal of Chromatography B},
	author = {Kusano, Miyako and Fukushima, Atsushi and Kobayashi, Makoto and Hayashi, Naomi and Jonsson, Pär and Moritz, Thomas and Ebana, Kaworu and Saito, Kazuki},
	month = aug,
	year = {2007},
	pages = {71--79},
}

@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{selstam_structural_2007,
	title = {Structural organisation of prolamellar bodies ({PLB}) isolated from {Zea} mays. {Parallel} {TEM}, {SAXS} and absorption spectra measurements on samples subjected to freeze–thaw, reduced {pH} and high-salt perturbation},
	volume = {1768},
	issn = {00052736},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0005273607001678},
	doi = {10/d2ztr9},
	language = {en},
	number = {9},
	urldate = {2021-06-10},
	journal = {Biochimica et Biophysica Acta (BBA) - Biomembranes},
	author = {Selstam, Eva and Schelin, Jenny and Williams, W. Patrick and Brain, Anthony P.R.},
	month = sep,
	year = {2007},
	pages = {2235--2245},
}

@article{gutierrez_combined_2007,
	title = {Combined networks regulating seed maturation},
	volume = {12},
	issn = {13601385},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1360138507001343},
	doi = {10/d2p7pf},
	language = {en},
	number = {7},
	urldate = {2021-06-10},
	journal = {Trends in Plant Science},
	author = {Gutierrez, Laurent and Van Wuytswinkel, Olivier and Castelain, Mathieu and Bellini, Catherine},
	month = jul,
	year = {2007},
	pages = {294--300},
}

@article{prescher_female_2007,
	title = {Female fertility variation in mature \textit{{Pinus} sylvestris} clonal seed orchards},
	volume = {22},
	issn = {0282-7581, 1651-1891},
	url = {https://www.tandfonline.com/doi/full/10.1080/02827580701419259},
	doi = {10/dmqpmz},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {Scandinavian Journal of Forest Research},
	author = {Prescher, Finnvid and Lindgren, Dag and Almqvist, Curt and Kroon, Johan and Lestander, Torbjörn A. and Mullin, Tim J.},
	month = aug,
	year = {2007},
	pages = {280--289},
}

@article{bjorn_tribute_2007,
	title = {A tribute to {Per} {Halldal} (1922–1986), a {Norwegian} photobiologist in {Sweden}},
	volume = {92},
	issn = {0166-8595, 1573-5079},
	url = {http://link.springer.com/10.1007/s11120-006-9072-x},
	doi = {10/fkspwm},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Photosynthesis Research},
	author = {Björn, Lars Olof and Sundqvist, Christer and Öquist, Gunnar},
	month = jul,
	year = {2007},
	pages = {7--11},
}

@article{pelloux_new_2007,
	title = {New insights into pectin methylesterase structure and function},
	volume = {12},
	issn = {13601385},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1360138507000969},
	doi = {10/fj8zv4},
	language = {en},
	number = {6},
	urldate = {2021-06-10},
	journal = {Trends in Plant Science},
	author = {Pelloux, J and Rusterucci, C and Mellerowicz, E},
	month = jun,
	year = {2007},
	pages = {267--277},
}

@article{ivanov_induction_2007,
	title = {The induction of {CP43}′ by iron-stress in {Synechococcus} sp. {PCC} 7942 is associated with carotenoid accumulation and enhanced fatty acid unsaturation},
	volume = {1767},
	issn = {00052728},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0005272807000345},
	doi = {10/cn52mr},
	language = {en},
	number = {6},
	urldate = {2021-06-10},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {Ivanov, Alexander G. and Krol, Marianna and Selstam, Eva and Sane, Prafullachandra Vishnu and Sveshnikov, Dmitry and Park, Youn-Il and Öquist, Gunnar and Huner, Norman P.A.},
	month = jun,
	year = {2007},
	pages = {807--813},
}

@article{moller_plant_2007,
	title = {Plant mitochondria?more active than ever!},
	volume = {129},
	issn = {0031-9317, 1399-3054},
	shorttitle = {Plant mitochondria?},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2006.00847.x},
	doi = {10/c2247w},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Physiologia Plantarum},
	author = {Møller, Ian M. and Gardeström, Per},
	month = jan,
	year = {2007},
	pages = {1--5},
}

@article{augusti_ins_2007,
	title = {The ins and outs of stable isotopes in plants},
	volume = {174},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2007.02075.x},
	doi = {10/dj9jt2},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {New Phytologist},
	author = {Augusti, Angela and Schleucher, Jürgen},
	month = may,
	year = {2007},
	pages = {473--475},
}

@article{wikberg_variation_2007,
	title = {Variation in drought resistance, drought acclimation and water conservation in four willow cultivars used for biomass production},
	volume = {27},
	issn = {0829-318X},
	doi = {10/dwsvcj},
	abstract = {Growth and water-use parameters of four willow (Salix spp.) clones grown in a moderate drought regime or with ample water supply were determined to characterize their water-use efficiency, drought resistance and capacity for drought acclimation. At the end of the 10-week, outdoor pot experiment, clonal differences were observed in: (1) water-use efficiency of aboveground biomass production (WUE); (2) resistance to xylem cavitation; and (3) stomatal conductance to leaf-specific, whole-plant hydraulic conductance ratio (g(st)/K(P); an indicator of water balance). Across clones and regimes, WUE was positively correlated with the assimilation rate to stomatal conductance ratio (A/g(st)), a measure of instantaneous water-use efficiency. Both of these water-use efficiency indicators were generally higher in drought-treated trees compared with well-watered trees. However, the between-treatment differences in (shoot-based) WUE were smaller than expected, considering the differences in A/g(st) for two of the clones, possibly because plants reallocated dry mass from shoots to roots when subject to drought. Higher root hydraulic conductance to shoot hydraulic conductance ratios (K(R)/K(S)) during drought supports this hypothesis. The same clones were also the most sensitive to xylem cavitation and, accordingly, showed the strongest reduction in g(st)/K(P) in response to drought. Drought acclimation was manifested in decreased g(st), g(st)/K(P), osmotic potential and leaf area to vessel internal cross-sectional area ratio, and increased K(R), K(P) and WUE. Increased resistance to stem xylem cavitation in response to drought was observed in only one clone. It is concluded that WUE and drought resistance traits are inter-linked and that both may be enhanced by selection and breeding.},
	language = {eng},
	number = {9},
	journal = {Tree Physiology},
	author = {Wikberg, Jenny and Ogren, Erling},
	month = sep,
	year = {2007},
	pmid = {17545133},
	keywords = {Acclimatization, Biomass, Plant Leaves, Salix, Water, Xylem},
	pages = {1339--1346},
}

Growth and water-use parameters of four willow (Salix spp.) clones grown in a moderate drought regime or with ample water supply were determined to characterize their water-use efficiency, drought resistance and capacity for drought acclimation. At the end of the 10-week, outdoor pot experiment, clonal differences were observed in: (1) water-use efficiency of aboveground biomass production (WUE); (2) resistance to xylem cavitation; and (3) stomatal conductance to leaf-specific, whole-plant hydraulic conductance ratio (g(st)/K(P); an indicator of water balance). Across clones and regimes, WUE was positively correlated with the assimilation rate to stomatal conductance ratio (A/g(st)), a measure of instantaneous water-use efficiency. Both of these water-use efficiency indicators were generally higher in drought-treated trees compared with well-watered trees. However, the between-treatment differences in (shoot-based) WUE were smaller than expected, considering the differences in A/g(st) for two of the clones, possibly because plants reallocated dry mass from shoots to roots when subject to drought. Higher root hydraulic conductance to shoot hydraulic conductance ratios (K(R)/K(S)) during drought supports this hypothesis. The same clones were also the most sensitive to xylem cavitation and, accordingly, showed the strongest reduction in g(st)/K(P) in response to drought. Drought acclimation was manifested in decreased g(st), g(st)/K(P), osmotic potential and leaf area to vessel internal cross-sectional area ratio, and increased K(R), K(P) and WUE. Increased resistance to stem xylem cavitation in response to drought was observed in only one clone. It is concluded that WUE and drought resistance traits are inter-linked and that both may be enhanced by selection and breeding.

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

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

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

@article{bylesjo_orthogonal_2007,
	title = {Orthogonal projections to latent structures as a strategy for microarray data normalization},
	volume = {8},
	issn = {1471-2105},
	url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-207},
	doi = {10/dfs78z},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {BMC Bioinformatics},
	author = {Bylesjö, Max and Eriksson, Daniel and Sjödin, Andreas and Jansson, Stefan and Moritz, Thomas and Trygg, Johan},
	month = dec,
	year = {2007},
	pages = {207},
}

@article{barkefors_effect_2007,
	title = {Effect of {Fluid} {Shear} {Stress} on {Endocytosis} of {Heparan} {Sulfate} and {Low}-density {Lipoproteins}},
	volume = {2007},
	issn = {1110-7243, 1110-7251},
	url = {http://www.hindawi.com/journals/bmri/2007/065136/abs/},
	doi = {10/fvr8sr},
	abstract = {Hemodynamic stress is a critical factor in the onset of atherosclerosis such that reduced rates of shear stress occurring at regions of high curvature are more prone to disease. The level of shear stress has direct influence on the thickness and integrity of the glycocalyx layer. Here we show that heparan sulfate, the main component of the glycocalyx layer, forms an intact layer only on cell surfaces subjected to shear, and not under static conditions. Furthermore, receptor-mediated endocytosis of heparan sulfate and low-density liporoteins is not detectable in cells exposed to shear stress. The internalized heparan sulfate and low-density lipoproteins are colocalized as shown by confocal imaging.},
	language = {en},
	urldate = {2021-06-10},
	journal = {Journal of Biomedicine and Biotechnology},
	author = {Barkefors, Irmeli and Aidun, Cyrus K. and Ulrika Egertsdotter, E. M.},
	year = {2007},
	pages = {1--8},
}

Hemodynamic stress is a critical factor in the onset of atherosclerosis such that reduced rates of shear stress occurring at regions of high curvature are more prone to disease. The level of shear stress has direct influence on the thickness and integrity of the glycocalyx layer. Here we show that heparan sulfate, the main component of the glycocalyx layer, forms an intact layer only on cell surfaces subjected to shear, and not under static conditions. Furthermore, receptor-mediated endocytosis of heparan sulfate and low-density liporoteins is not detectable in cells exposed to shear stress. The internalized heparan sulfate and low-density lipoproteins are colocalized as shown by confocal imaging.

@article{wiedermann_global_2007,
	title = {{GLOBAL} {CHANGE} {SHIFTS} {VEGETATION} {AND} {PLANT}–{PARASITE} {INTERACTIONS} {IN} {A} {BOREAL} {MIRE}},
	volume = {88},
	issn = {0012-9658},
	url = {http://doi.wiley.com/10.1890/05-1823},
	doi = {10/d9c3bc},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Ecology},
	author = {Wiedermann, Magdalena M. and Nordin, Annika and Gunnarsson, Urban and Nilsson, Mats B. and Ericson, Lars},
	month = feb,
	year = {2007},
	pages = {454--464},
}

@article{achard_plant_2007,
	title = {The plant stress hormone ethylene controls floral transition via {DELLA}-dependent regulation of floral meristem-identity genes},
	volume = {104},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0610717104},
	doi = {10/d92wbd},
	language = {en},
	number = {15},
	urldate = {2021-06-10},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Achard, P. and Baghour, M. and Chapple, A. and Hedden, P. and Van Der Straeten, D. and Genschik, P. and Moritz, T. and Harberd, N. P.},
	month = apr,
	year = {2007},
	pages = {6484--6489},
}

@article{backstrom_purification_2007,
	title = {Purification of a {Plant} {Mediator} from {Arabidopsis} thaliana {Identifies} {PFT1} as the {Med25} {Subunit}},
	volume = {26},
	issn = {10972765},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1097276507002882},
	doi = {10/ctkcp5},
	language = {en},
	number = {5},
	urldate = {2021-06-10},
	journal = {Molecular Cell},
	author = {Bäckström, Stefan and Elfving, Nils and Nilsson, Robert and Wingsle, Gunnar and Björklund, Stefan},
	month = jun,
	year = {2007},
	pages = {717--729},
}

@article{garcia_excess_2007,
	title = {An excess of nonsynonymous polymorphism and extensive haplotype structure at the {PtABI1B} locus in {European} aspen ({Populus} tremula): a case of balancing selection in an obligately outcrossing plant?},
	volume = {99},
	issn = {0018-067X, 1365-2540},
	shorttitle = {An excess of nonsynonymous polymorphism and extensive haplotype structure at the {PtABI1B} locus in {European} aspen ({Populus} tremula)},
	url = {http://www.nature.com/articles/6801012},
	doi = {10/b5fgpn},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {Heredity},
	author = {García, M V and Ingvarsson, P K},
	month = oct,
	year = {2007},
	pages = {381--388},
}

@article{lundin_subsequent_2007,
	title = {Subsequent events to {GTP} binding by the plant {PsbO} protein: {Structural} changes, {GTP} hydrolysis and dissociation from the photosystem {II} complex},
	volume = {1767},
	issn = {00052728},
	shorttitle = {Subsequent events to {GTP} binding by the plant {PsbO} protein},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0005272806003252},
	doi = {10/cr7hch},
	language = {en},
	number = {6},
	urldate = {2021-06-10},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {Lundin, Björn and Thuswaldner, Sophie and Shutova, Tatiana and Eshaghi, Said and Samuelsson, Göran and Barber, James and Andersson, Bertil and Spetea, Cornelia},
	month = jun,
	year = {2007},
	pages = {500--508},
}

@article{shutova_cluster_2007,
	title = {A cluster of carboxylic groups in {PsbO} protein is involved in proton transfer from the water oxidizing complex of {Photosystem} {II}},
	volume = {1767},
	issn = {00052728},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0005272807000230},
	doi = {10/dqpz9x},
	language = {en},
	number = {6},
	urldate = {2021-06-10},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {Shutova, Tatiana and Klimov, Vyacheslav V. and Andersson, Bertil and Samuelsson, Göran},
	month = jun,
	year = {2007},
	pages = {434--440},
}

@article{druart_environmental_2007,
	title = {Environmental and hormonal regulation of the activity-dormancy cycle in the cambial meristem involves stage-specific modulation of transcriptional and metabolic networks: {Molecular} analysis of cambial activity-dormancy cycle},
	volume = {50},
	issn = {09607412, 1365313X},
	shorttitle = {Environmental and hormonal regulation of the activity-dormancy cycle in the cambial meristem involves stage-specific modulation of transcriptional and metabolic networks},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2007.03077.x},
	doi = {10/cgt589},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {The Plant Journal},
	author = {Druart, Nathalie and Johansson, Annika and Baba, Kyoko and Schrader, Jarmo and Sjödin, Andreas and Bhalerao, Rupali R. and Resman, Lars and Trygg, Johan and Moritz, Thomas and Bhalerao, Rishikesh P.},
	month = apr,
	year = {2007},
	pages = {557--573},
}

@article{barr_variation_2007,
	title = {Variation in {Mutation} {Rate} and {Polymorphism} {Among} {Mitochondrial} {Genes} of {Silene} vulgaris},
	volume = {24},
	issn = {0737-4038, 1537-1719},
	url = {https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msm106},
	doi = {10/bbvgk8},
	language = {en},
	number = {8},
	urldate = {2021-06-10},
	journal = {Molecular Biology and Evolution},
	author = {Barr, C. M. and Keller, S. R. and Ingvarsson, P. K. and Sloan, D. B. and Taylor, D. R.},
	month = apr,
	year = {2007},
	pages = {1783--1791},
}

@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{jensen_structure_2007,
	title = {Structure, function and regulation of plant photosystem {I}},
	volume = {1767},
	issn = {00052728},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0005272807000722},
	doi = {10/fdc7p3},
	language = {en},
	number = {5},
	urldate = {2021-06-10},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {Jensen, Poul Erik and Bassi, Roberto and Boekema, Egbert J. and Dekker, Jan P. and Jansson, Stefan and Leister, Dario and Robinson, Colin and Scheller, Henrik Vibe},
	month = may,
	year = {2007},
	pages = {335--352},
}

@article{svennerstam_comprehensive_2007,
	title = {Comprehensive {Screening} of {Arabidopsis} {Mutants} {Suggests} the {Lysine} {Histidine} {Transporter} 1 to {Be} {Involved} in {Plant} {Uptake} of {Amino} {Acids}},
	volume = {143},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/143/4/1853/6106923},
	doi = {10/cgtd2h},
	abstract = {Abstract
            Plant nitrogen (N) uptake is a key process in the global N cycle and is usually considered a “bottleneck” for biomass production in land ecosystems. Earlier, mineral N was considered the only form available to plants. Recent studies have questioned this dogma and shown that plants may access organic N sources such as amino acids. The actual mechanism enabling plants to access amino acid N is still unknown. However, a recent study suggested the Lysine Histidine Transporter 1 (LHT1) to be involved in root amino acid uptake. In this study, we isolated mutants defective in root amino acid uptake by screening Arabidopsis (Arabidopsis thaliana) seeds from ethyl methanesulfonate-treated plants and seeds from amino acid transporter T-DNA knockout mutants for resistance against the toxic d-enantiomer of alanine (Ala). Both ethyl methanesulfonate and T-DNA knockout plants identified as d-Ala resistant were found to be mutated in the LHT1 gene. LHT1 mutants displayed impaired capacity for uptake of a range of amino acids from solutions, displayed impaired growth when N was supplied in organic forms, and acquired substantially lower amounts of amino acids than wild-type plants from solid growth media. LHT1 mutants grown on mineral N did not display a phenotype until at the stage of flowering, when premature senescence of old leaf pairs occurred, suggesting that LHT1 may fulfill an important function at this developmental stage. Based on the broad and unbiased screening of mutants resistant to d-Ala, we suggest that LHT1 is an important mediator of root uptake of amino acids. This provides a molecular background for plant acquisition of organic N from the soil.},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {Plant Physiology},
	author = {Svennerstam, Henrik and Ganeteg, Ulrika and Bellini, Catherine and Näsholm, Torgny},
	month = apr,
	year = {2007},
	pages = {1853--1860},
}

Abstract Plant nitrogen (N) uptake is a key process in the global N cycle and is usually considered a “bottleneck” for biomass production in land ecosystems. Earlier, mineral N was considered the only form available to plants. Recent studies have questioned this dogma and shown that plants may access organic N sources such as amino acids. The actual mechanism enabling plants to access amino acid N is still unknown. However, a recent study suggested the Lysine Histidine Transporter 1 (LHT1) to be involved in root amino acid uptake. In this study, we isolated mutants defective in root amino acid uptake by screening Arabidopsis (Arabidopsis thaliana) seeds from ethyl methanesulfonate-treated plants and seeds from amino acid transporter T-DNA knockout mutants for resistance against the toxic d-enantiomer of alanine (Ala). Both ethyl methanesulfonate and T-DNA knockout plants identified as d-Ala resistant were found to be mutated in the LHT1 gene. LHT1 mutants displayed impaired capacity for uptake of a range of amino acids from solutions, displayed impaired growth when N was supplied in organic forms, and acquired substantially lower amounts of amino acids than wild-type plants from solid growth media. LHT1 mutants grown on mineral N did not display a phenotype until at the stage of flowering, when premature senescence of old leaf pairs occurred, suggesting that LHT1 may fulfill an important function at this developmental stage. Based on the broad and unbiased screening of mutants resistant to d-Ala, we suggest that LHT1 is an important mediator of root uptake of amino acids. This provides a molecular background for plant acquisition of organic N from the soil.

@article{martz_effects_2007,
	title = {Effects of ultraviolet ({UV}) exclusion on the seasonal concentration of photosynthetic and {UV}-screening pigments in {Scots} pine needles},
	volume = {13},
	issn = {1354-1013, 1365-2486},
	url = {http://doi.wiley.com/10.1111/j.1365-2486.2006.01275.x},
	doi = {10/fp26ss},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Global Change Biology},
	author = {Martz, Françoise and Sutinen, Marja-Liisa and Derome, Kirsti and Wingsle, Gunnar and Julkunen-Tiitto, Riitta and Turunen, Minna},
	month = jan,
	year = {2007},
	pages = {252--265},
}

@article{gama_mitochondrial_2007,
	title = {The mitochondrial type {II} peroxiredoxin from poplar},
	volume = {129},
	issn = {0031-9317, 1399-3054},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2006.00785.x},
	doi = {10/d9wwkk},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Physiologia Plantarum},
	author = {Gama, Filipe and Keech, Olivier and Eymery, Françoise and Finkemeier, Iris and Gelhaye, Eric and Gardeström, Per and Dietz, Karl Josef and Rey, Pascal and Jacquot, Jean-Pierre and Rouhier, Nicolas},
	month = jan,
	year = {2007},
	pages = {196--206},
}

@article{covey-crump_temperature-dependent_2007,
	title = {Temperature-dependent changes in respiration rates and redox poise of the ubiquinone pool in protoplasts and isolated mitochondria of potato leaves},
	volume = {129},
	issn = {0031-9317, 1399-3054},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2006.00823.x},
	doi = {10/c32v64},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Physiologia Plantarum},
	author = {Covey-Crump, Elizabeth M. and Bykova, Natalia V. and Affourtit, Charles and Hoefnagel, Marcel H. N. and Gardeström, Per and Atkin, Owen K.},
	month = jan,
	year = {2007},
	pages = {175--184},
}

@article{henz_distinct_2007,
	title = {Distinct expression patterns of natural antisense transcripts in {Arabidopsis}},
	volume = {144},
	issn = {0032-0889},
	doi = {10/d6krth},
	abstract = {It has been shown that overlapping cis-natural antisense transcripts (cis-NATs) can form a regulatory circuit in which small RNAs derived from one transcript regulate stability of the other transcript, which manifests itself as anticorrelated expression. However, little is known about how widespread antagonistic expression of cis-NATs is. We have determined how frequently cis-NAT pairs, which make up 7.4\% of annotated transcription units in the Arabidopsis (Arabidopsis thaliana) genome, show anticorrelated expression patterns. Indeed, global expression profiles of pairs of cis-NATs on average have significantly lower pairwise Pearson correlation coefficients than other pairs of neighboring genes whose transcripts do not overlap. However, anticorrelated expression that is greater than expected by chance is found in only a small number of cis-NAT pairs. The degree of anticorrelation does not depend on the length of the overlap or on the distance of the 5' ends of the transcripts. Consistent with earlier findings, cis-NATs do not exhibit an increased likelihood to give rise to small RNAs, as determined from available small RNA sequences and massively parallel signature sequencing tags. However, the overlapping regions of cis-NATs appeared to be enriched for small RNA loci compared to nonoverlapping regions. Furthermore, expression of cis-NATs was not disproportionately affected in various RNA-silencing mutants. Our results demonstrate that there is a trend toward anticorrelated expression of cis-NAT pairs in Arabidopsis, but currently available data do not produce a strong signature of small RNA-mediated silencing for this process.},
	language = {eng},
	number = {3},
	journal = {Plant Physiology},
	author = {Henz, Stefan R. and Cumbie, Jason S. and Kasschau, Kristin D. and Lohmann, Jan U. and Carrington, James C. and Weigel, Detlef and Schmid, Markus},
	month = jul,
	year = {2007},
	pmid = {17496106},
	pmcid = {PMC1914114},
	keywords = {Arabidopsis, Gene Expression Regulation, Plant, Genome, Plant, Oligonucleotide Array Sequence Analysis, Promoter Regions, Genetic, RNA Interference, RNA, Antisense},
	pages = {1247--1255},
}

It has been shown that overlapping cis-natural antisense transcripts (cis-NATs) can form a regulatory circuit in which small RNAs derived from one transcript regulate stability of the other transcript, which manifests itself as anticorrelated expression. However, little is known about how widespread antagonistic expression of cis-NATs is. We have determined how frequently cis-NAT pairs, which make up 7.4% of annotated transcription units in the Arabidopsis (Arabidopsis thaliana) genome, show anticorrelated expression patterns. Indeed, global expression profiles of pairs of cis-NATs on average have significantly lower pairwise Pearson correlation coefficients than other pairs of neighboring genes whose transcripts do not overlap. However, anticorrelated expression that is greater than expected by chance is found in only a small number of cis-NAT pairs. The degree of anticorrelation does not depend on the length of the overlap or on the distance of the 5' ends of the transcripts. Consistent with earlier findings, cis-NATs do not exhibit an increased likelihood to give rise to small RNAs, as determined from available small RNA sequences and massively parallel signature sequencing tags. However, the overlapping regions of cis-NATs appeared to be enriched for small RNA loci compared to nonoverlapping regions. Furthermore, expression of cis-NATs was not disproportionately affected in various RNA-silencing mutants. Our results demonstrate that there is a trend toward anticorrelated expression of cis-NAT pairs in Arabidopsis, but currently available data do not produce a strong signature of small RNA-mediated silencing for this process.

@article{mathieu_export_2007,
	title = {Export of {FT} protein from phloem companion cells is sufficient for floral induction in {Arabidopsis}},
	volume = {17},
	issn = {0960-9822},
	doi = {10/bts4m3},
	abstract = {Several endogenous and environmental factors need to be integrated to time the onset of flowering. Genetic and molecular analyses, primarily in Arabidopsis thaliana and rice, have shown that CONSTANS (CO) and FLOWERING LOCUS T (FT) play central roles in photoperiod-dependent flowering. The overall picture is that CO acts in the phloem companion cells of leaves and that its main effect is to induce FT mRNA in these cells. Surprisingly, FT, a small globular protein of 20 kDa, interacts at the shoot apex with the bZIP transcription factor FLOWERING LOCUS D (FD) to induce downstream targets. Given that green fluorescent protein (GFP), which as a monomer is 27 kDa, can be easily exported to sink tissue including flowers when expressed in phloem companion cells, the latter finding strongly implied that FT protein is the mobile floral-inductive signal. In agreement with this hypothesis, an FT-GFP fusion, just like GFP, can be exported from the phloem of both rice and Arabidopsis. It has been unknown, however, whether mobile FT protein is sufficient for transmitting the flowering signal. Here we show that FT mRNA is required in phloem companion cells where it acts partially redundant with its paralog TWIN SISTER OF FT (TSF) to induce flowering. Furthermore, we have devised a method that uncouples FT mRNA and protein effects in vivo. We demonstrate that export of FT protein from phloem companion cells is sufficient to induce flowering.},
	language = {eng},
	number = {12},
	journal = {Current biology: CB},
	author = {Mathieu, Johannes and Warthmann, Norman and Küttner, Frank and Schmid, Markus},
	month = jun,
	year = {2007},
	pmid = {17540570},
	keywords = {Arabidopsis, Arabidopsis Proteins, Flowers, Gene Expression Regulation, Plant, Phloem, Phosphatidylethanolamine Binding Protein, RNA, Messenger, Signal Transduction},
	pages = {1055--1060},
}

Several endogenous and environmental factors need to be integrated to time the onset of flowering. Genetic and molecular analyses, primarily in Arabidopsis thaliana and rice, have shown that CONSTANS (CO) and FLOWERING LOCUS T (FT) play central roles in photoperiod-dependent flowering. The overall picture is that CO acts in the phloem companion cells of leaves and that its main effect is to induce FT mRNA in these cells. Surprisingly, FT, a small globular protein of 20 kDa, interacts at the shoot apex with the bZIP transcription factor FLOWERING LOCUS D (FD) to induce downstream targets. Given that green fluorescent protein (GFP), which as a monomer is 27 kDa, can be easily exported to sink tissue including flowers when expressed in phloem companion cells, the latter finding strongly implied that FT protein is the mobile floral-inductive signal. In agreement with this hypothesis, an FT-GFP fusion, just like GFP, can be exported from the phloem of both rice and Arabidopsis. It has been unknown, however, whether mobile FT protein is sufficient for transmitting the flowering signal. Here we show that FT mRNA is required in phloem companion cells where it acts partially redundant with its paralog TWIN SISTER OF FT (TSF) to induce flowering. Furthermore, we have devised a method that uncouples FT mRNA and protein effects in vivo. We demonstrate that export of FT protein from phloem companion cells is sufficient to induce flowering.

@incollection{mcwatters_plant_2007,
	title = {Plant {Circadian} {Rhythms}},
	copyright = {Copyright © 2007 John Wiley \& Sons, Ltd. All rights reserved.},
	isbn = {978-0-470-01590-2},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9780470015902.a0020113},
	abstract = {Circadian clocks are found in most eukaryotic organisms. By allowing anticipation of daily and seasonal changes they enable coordination of metabolism and life cycle with the natural rhythms of the environment. Plant circadian rhythms are generated by a series of interlocking feedback loops of ribonucleic acid (RNA) and protein expression that respond to environmental cycles of light and temperature. They control essential processes in the plant's development, such as the transition to flowering or growth cessation.},
	language = {en},
	urldate = {2021-06-10},
	booktitle = {{eLS}},
	publisher = {American Cancer Society},
	author = {McWatters, Harriet G. and Eriksson, Maria E.},
	year = {2007},
	doi = {10.1002/9780470015902.a0020113},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9780470015902.a0020113},
	keywords = {Arabidopsis thaliana, Populus, bud set, circadian clock, entrainment, photoperiodism},
}

Circadian clocks are found in most eukaryotic organisms. By allowing anticipation of daily and seasonal changes they enable coordination of metabolism and life cycle with the natural rhythms of the environment. Plant circadian rhythms are generated by a series of interlocking feedback loops of ribonucleic acid (RNA) and protein expression that respond to environmental cycles of light and temperature. They control essential processes in the plant's development, such as the transition to flowering or growth cessation.

@article{helariutta_cell_2007,
	title = {Cell signalling during vascular morphogenesis},
	volume = {35},
	issn = {0300-5127},
	url = {https://doi.org/10.1042/BST0350152},
	doi = {10/fqh268},
	abstract = {Vascular tissue in plants is unique due to its diverse and dynamic cellular patterns. Through research in several organisms, such as Arabidopsis, Populus and Zinnia, using biochemical, genetic and genomic approaches, significant progress has recently been made in revealing the molecular nature of several signals underlying the patterning of vascular tissue. These signals include ligands, receptors and transcriptional regulators. The future challenge is to understand how the identified signals work together to control vascular morphogenesis.},
	number = {1},
	urldate = {2021-06-10},
	journal = {Biochemical Society Transactions},
	author = {Helariutta, Y.},
	month = jan,
	year = {2007},
	pages = {152--155},
}

Vascular tissue in plants is unique due to its diverse and dynamic cellular patterns. Through research in several organisms, such as Arabidopsis, Populus and Zinnia, using biochemical, genetic and genomic approaches, significant progress has recently been made in revealing the molecular nature of several signals underlying the patterning of vascular tissue. These signals include ligands, receptors and transcriptional regulators. The future challenge is to understand how the identified signals work together to control vascular morphogenesis.

@article{jansson_genome_2007,
	title = {Genome studies and molecular {geneticsGenomics} — deeper and wider in order to understanding plant diversity},
	volume = {10},
	issn = {13695266},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526607000210},
	doi = {10/dbfgdx},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Current Opinion in Plant Biology},
	author = {Jansson, S and Buckler, E},
	month = apr,
	year = {2007},
	pages = {107--108},
}

@article{hallander_effect_2007,
	title = {The effect of non-additive genetic interactions on selection in multi-locus genetic models},
	volume = {98},
	issn = {0018-067X, 1365-2540},
	url = {http://www.nature.com/articles/6800946},
	doi = {10/bdgvbh},
	language = {en},
	number = {6},
	urldate = {2021-06-10},
	journal = {Heredity},
	author = {Hallander, J and Waldmann, P},
	month = jun,
	year = {2007},
	pages = {349--359},
}

@article{svensson_adjusting_2007,
	title = {Adjusting for fibre length-biased sampling probability using increment cores from standing trees},
	volume = {61},
	issn = {0018-3830, 1437-434X},
	url = {https://www.degruyter.com/document/doi/10.1515/HF.2007.016/html},
	doi = {10/d4k92c},
	number = {1},
	urldate = {2021-06-10},
	journal = {Holzforschung},
	author = {Svensson, Ingrid and Sjöstedt-de Luna, Sara and Mörling, Tommy and Fries, Anders and Ericsson, Tore},
	month = jan,
	year = {2007},
	pages = {101--103},
}

@article{fischer_planar_2007,
	title = {Planar polarity of root hair positioning in {Arabidopsis}},
	volume = {35},
	issn = {0300-5127, 1470-8752},
	url = {https://portlandpress.com/biochemsoctrans/article/35/1/149/64058/Planar-polarity-of-root-hair-positioning-in},
	doi = {10/b7wr53},
	abstract = {The co-ordinated polarity of cells within the plane of a single tissue layer (planar polarity) is intensively studied in animal epithelia but has only recently been systematically analysed in plants. The polar positioning of hairs in the root epidermis of Arabidopsis thaliana provides an easily accessible system for the functional dissection of a plant-specific planar polarity. Recently, mutants originally isolated in genetic screens for defects in root hair morphogenesis and changes in the sensitivity to or the production of the plant hormones auxin and ethylene have identified players that contribute to polar root hair placement. Here, we summarize and discuss recent progress in research on polar root hair positioning from studies in Arabidopsis.},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Biochemical Society Transactions},
	author = {Fischer, U. and Ikeda, Y. and Grebe, M.},
	month = feb,
	year = {2007},
	pages = {149--151},
}

The co-ordinated polarity of cells within the plane of a single tissue layer (planar polarity) is intensively studied in animal epithelia but has only recently been systematically analysed in plants. The polar positioning of hairs in the root epidermis of Arabidopsis thaliana provides an easily accessible system for the functional dissection of a plant-specific planar polarity. Recently, mutants originally isolated in genetic screens for defects in root hair morphogenesis and changes in the sensitivity to or the production of the plant hormones auxin and ethylene have identified players that contribute to polar root hair placement. Here, we summarize and discuss recent progress in research on polar root hair positioning from studies in Arabidopsis.

@article{meng_differential_2007,
	title = {Differential tissue/organ-dependent expression of two sucrose- and cold-responsive genes for {UDP}-glucose pyrophosphorylase in {Populus}},
	volume = {389},
	issn = {03781119},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378111906007062},
	doi = {10/fn8z4c},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Gene},
	author = {Meng, Meng and Geisler, Matt and Johansson, Henrik and Mellerowicz, Ewa J. and Karpinski, Stanislaw and Kleczkowski, Leszek A.},
	month = mar,
	year = {2007},
	pages = {186--195},
}

@article{albrectsen_does_2007,
	title = {Does the differential seedling mortality caused by slugs alter the foliar traits and subsequent susceptibility of hybrid willows to a generalist herbivore?},
	volume = {0},
	issn = {0307-6946, 1365-2311},
	url = {http://doi.wiley.com/10.1111/j.1365-2311.2006.00860.x},
	doi = {10/bzhmrr},
	language = {en},
	number = {0},
	urldate = {2021-06-10},
	journal = {Ecological Entomology},
	author = {Albrectsen, Benedicte R. and Guiterrez, Laura and Fritz, Robert S. and Fritz, Robert D. and Orians, Colin M.},
	month = jan,
	year = {2007},
	pages = {070130195410003--???},
}

@article{yao_localization_2007,
	title = {Localization of the {Small} {CAB}-like {Proteins} in {Photosystem} {II}},
	volume = {282},
	issn = {00219258},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0021925820798157},
	doi = {10/cj6mmb},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Journal of Biological Chemistry},
	author = {Yao, Danny and Kieselbach, Thomas and Komenda, Josef and Promnares, Kamoltip and Prieto, Miguel A. Hernández and Tichy, Martin and Vermaas, Wim and Funk, Christiane},
	month = jan,
	year = {2007},
	pages = {267--276},
}

@article{segerman_characterization_2007,
	title = {Characterization of genes with tissue-specific differential expression patterns in {Populus}},
	volume = {3},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-006-0077-6},
	doi = {10/ct8snb},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {Tree Genetics \& Genomes},
	author = {Segerman, Bo and Jansson, Stefan and Karlsson, Jan},
	month = aug,
	year = {2007},
	pages = {351--362},
}

@article{deluca_ecosystem_2007,
	title = {Ecosystem controls on nitrogen fixation in boreal feather moss communities},
	volume = {152},
	issn = {0029-8549, 1432-1939},
	url = {http://link.springer.com/10.1007/s00442-006-0626-6},
	doi = {10/c2tmkt},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Oecologia},
	author = {DeLuca, Thomas H. and Zackrisson, Olle and Gentili, Francesco and Sellstedt, Anita and Nilsson, Marie-Charlotte},
	month = apr,
	year = {2007},
	pages = {121--130},
}

@article{guy_plant_2007,
	title = {Plant metabolomics coming of age},
	volume = {132},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2007.01020.x},
	doi = {10/dt585v},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Physiologia Plantarum},
	author = {Guy, Charles and Kopka, Joachim and Moritz, Thomas},
	month = dec,
	year = {2007},
	pages = {113--116},
}

@article{rieu_gibberellin_2007,
	title = {The gibberellin biosynthetic genes {AtGA20ox1} and {AtGA20ox2} act, partially redundantly, to promote growth and development throughout the {Arabidopsis} life cycle: {GA20ox} function in {Arabidopsis}},
	volume = {53},
	issn = {09607412},
	shorttitle = {The gibberellin biosynthetic genes {AtGA20ox1} and {AtGA20ox2} act, partially redundantly, to promote growth and development throughout the {Arabidopsis} life cycle},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2007.03356.x},
	doi = {10/cqvbmx},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {The Plant Journal},
	author = {Rieu, Ivo and Ruiz-Rivero, Omar and Fernandez-Garcia, Nieves and Griffiths, Jayne and Powers, Stephen J. and Gong, Fan and Linhartova, Terezie and Eriksson, Sven and Nilsson, Ove and Thomas, Stephen G. and Phillips, Andrew L. and Hedden, Peter},
	month = oct,
	year = {2007},
	pages = {488--504},
}

@article{gray-mitsumune_ectopic_2007,
	title = {Ectopic expression of a wood-abundant expansin {PttEXPA1} promotes cell expansion in primary and secondary tissues in aspen},
	volume = {0},
	issn = {1467-7644, 1467-7652},
	url = {http://doi.wiley.com/10.1111/j.1467-7652.2007.00295.x},
	doi = {10/cz7ht2},
	language = {en},
	number = {0},
	urldate = {2021-06-10},
	journal = {Plant Biotechnology Journal},
	author = {Gray-Mitsumune, Madoka and Blomquist, Kristina and McQueen-Mason, Simon and Teeri, Tuula T. and Sundberg, Björn and Mellerowicz, Ewa J.},
	month = oct,
	year = {2007},
	pages = {071003005211001--???},
}