Publications 2003

@article{jenny_absence_2003,
	title = {Absence of the {Lhcb1} and {Lhcb2} proteins of the light-harvesting complex of photosystem {II} – effects on photosynthesis, grana stacking and fitness},
	volume = {35},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-313X.2003.01811.x},
	doi = {10.1046/j.1365-313X.2003.01811.x},
	abstract = {We have constructed Arabidopsis thaliana plants that are virtually devoid of the major light-harvesting complex, LHC II. This was accomplished by introducing the Lhcb2.1 coding region in the antisense orientation into the genome by Agrobacterium-mediated transformation. Lhcb1 and Lhcb2 were absent, while Lhcb3, a protein present in LHC II associated with photosystem (PS) II, was retained. Plants had a pale green appearance and showed reduced chlorophyll content and an elevated chlorophyll a/b ratio. The content of PS II reaction centres was unchanged on a leaf area basis, but there was evidence for increases in the relative levels of other light harvesting proteins, notably CP26, associated with PS II, and Lhca4, associated with PS I. Electron microscopy showed the presence of grana. Photosynthetic rates at saturating irradiance were the same in wild-type and antisense plants, but there was a 10–15\% reduction in quantum yield that reflected the decrease in light absorption by the leaf. The antisense plants were not able to perform state transitions, and their capacity for non-photochemical quenching was reduced. There was no difference in growth between wild-type and antisense plants under controlled climate conditions, but the antisense plants performed worse compared to the wild type in the field, with decreases in seed production of up to 70\%.},
	language = {en},
	number = {3},
	urldate = {2024-06-28},
	journal = {The Plant Journal},
	author = {Jenny, Andersson and Mark, Wentworth and Robin G., Walters and Caroline A., Howard and Alexander V., Ruban and Peter, Horton and Stefan, Jansson},
	year = {2003},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313X.2003.01811.x},
	keywords = {Arabidopsis, LHC II, antisense, fitness, photosynthesis, state transitions},
	pages = {350--361},
}

We have constructed Arabidopsis thaliana plants that are virtually devoid of the major light-harvesting complex, LHC II. This was accomplished by introducing the Lhcb2.1 coding region in the antisense orientation into the genome by Agrobacterium-mediated transformation. Lhcb1 and Lhcb2 were absent, while Lhcb3, a protein present in LHC II associated with photosystem (PS) II, was retained. Plants had a pale green appearance and showed reduced chlorophyll content and an elevated chlorophyll a/b ratio. The content of PS II reaction centres was unchanged on a leaf area basis, but there was evidence for increases in the relative levels of other light harvesting proteins, notably CP26, associated with PS II, and Lhca4, associated with PS I. Electron microscopy showed the presence of grana. Photosynthetic rates at saturating irradiance were the same in wild-type and antisense plants, but there was a 10–15% reduction in quantum yield that reflected the decrease in light absorption by the leaf. The antisense plants were not able to perform state transitions, and their capacity for non-photochemical quenching was reduced. There was no difference in growth between wild-type and antisense plants under controlled climate conditions, but the antisense plants performed worse compared to the wild type in the field, with decreases in seed production of up to 70%.

@article{wissel_what_2003,
	title = {What {Affects} {mRNA} {Levels} in {Leaves} of {Field}-{Grown} {Aspen}? {A} {Study} of {Developmental} and {Environmental} {Influences}},
	volume = {133},
	issn = {0032-0889},
	shorttitle = {What {Affects} {mRNA} {Levels} in {Leaves} of {Field}-{Grown} {Aspen}?},
	url = {https://doi.org/10.1104/pp.103.028191},
	doi = {10.1104/pp.103.028191},
	abstract = {We have analyzed the abundance of mRNAs expressed from 11 nuclear genes in leaves of a free-growing aspen (Populus tremula) tree throughout the growing season. We used multivariate statistics to determine the influence of environmental factors (i.e. the weather before sampling) and developmental responses to seasonal changes at the mRNA level for each of these genes. The gene encoding a germin-like protein was only expressed early in the season, whereas the other tested genes were expressed throughout the season and showed mRNA variations on a day-to-day basis. For six of the genes, reliable models were found that described the mRNA level as a function of weather, but the leaf age was also important for all genes except one encoding an early light-inducible protein (which appeared to be regulated purely by environmental factors under these conditions). The results confirmed the importance of several environmental factors previously shown to regulate the genes, but we also detected a number of less obvious factors (such as the variation in weather parameters and the weather of the previous day) that correlated with the mRNA levels of individual genes. The study shows the power of multivariate statistical methods in analyzing gene regulation under field conditions.},
	number = {3},
	urldate = {2024-06-28},
	journal = {Plant Physiology},
	author = {Wissel, Kirsten and Pettersson, Fredrik and Berglund, Anders and Jansson, Stefan},
	month = nov,
	year = {2003},
	pages = {1190--1197},
}

We have analyzed the abundance of mRNAs expressed from 11 nuclear genes in leaves of a free-growing aspen (Populus tremula) tree throughout the growing season. We used multivariate statistics to determine the influence of environmental factors (i.e. the weather before sampling) and developmental responses to seasonal changes at the mRNA level for each of these genes. The gene encoding a germin-like protein was only expressed early in the season, whereas the other tested genes were expressed throughout the season and showed mRNA variations on a day-to-day basis. For six of the genes, reliable models were found that described the mRNA level as a function of weather, but the leaf age was also important for all genes except one encoding an early light-inducible protein (which appeared to be regulated purely by environmental factors under these conditions). The results confirmed the importance of several environmental factors previously shown to regulate the genes, but we also detected a number of less obvious factors (such as the variation in weather parameters and the weather of the previous day) that correlated with the mRNA levels of individual genes. The study shows the power of multivariate statistical methods in analyzing gene regulation under field conditions.

@article{bhalerao_gene_2003,
	title = {Gene {Expression} in {Autumn} {Leaves}},
	volume = {131},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.012732},
	doi = {10.1104/pp.012732},
	abstract = {Two cDNA libraries were prepared, one from leaves of a field-grown aspen (Populus tremula) tree, harvested just before any visible sign of leaf senescence in the autumn, and one from young but fully expanded leaves of greenhouse-grown aspen (Populus tremula × tremuloides). Expressed sequence tags (ESTs; 5,128 and 4,841, respectively) were obtained from the two libraries. A semiautomatic method of annotation and functional classification of the ESTs, according to a modified Munich Institute of Protein Sequences classification scheme, was developed, utilizing information from three different databases. The patterns of gene expression in the two libraries were strikingly different. In the autumn leaf library, ESTs encoding metallothionein, early light-inducible proteins, and cysteine proteases were most abundant. Clones encoding other proteases and proteins involved in respiration and breakdown of lipids and pigments, as well as stress-related genes, were also well represented. We identified homologs to many known senescence-associated genes, as well as seven different genes encoding cysteine proteases, two encoding aspartic proteases, five encoding metallothioneins, and 35 additional genes that were up-regulated in autumn leaves. We also indirectly estimated the rate of plastid protein synthesis in the autumn leaves to be less that 10\% of that in young leaves.},
	number = {2},
	urldate = {2024-06-28},
	journal = {Plant Physiology},
	author = {Bhalerao, Rupali and Keskitalo, Johanna and Sterky, Fredrik and Erlandsson, Rikard and Björkbacka, Harry and Birve, Simon Jonsson and Karlsson, Jan and Gardeström, Per and Gustafsson, Petter and Lundeberg, Joakim and Jansson, Stefan},
	month = feb,
	year = {2003},
	pages = {430--442},
}

Two cDNA libraries were prepared, one from leaves of a field-grown aspen (Populus tremula) tree, harvested just before any visible sign of leaf senescence in the autumn, and one from young but fully expanded leaves of greenhouse-grown aspen (Populus tremula × tremuloides). Expressed sequence tags (ESTs; 5,128 and 4,841, respectively) were obtained from the two libraries. A semiautomatic method of annotation and functional classification of the ESTs, according to a modified Munich Institute of Protein Sequences classification scheme, was developed, utilizing information from three different databases. The patterns of gene expression in the two libraries were strikingly different. In the autumn leaf library, ESTs encoding metallothionein, early light-inducible proteins, and cysteine proteases were most abundant. Clones encoding other proteases and proteins involved in respiration and breakdown of lipids and pigments, as well as stress-related genes, were also well represented. We identified homologs to many known senescence-associated genes, as well as seven different genes encoding cysteine proteases, two encoding aspartic proteases, five encoding metallothioneins, and 35 additional genes that were up-regulated in autumn leaves. We also indirectly estimated the rate of plastid protein synthesis in the autumn leaves to be less that 10% of that in young leaves.

@article{ruban_plants_2003,
	title = {Plants lacking the main light-harvesting complex retain photosystem {II} macro-organization},
	volume = {421},
	copyright = {2003 Macmillan Magazines Ltd.},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/nature01344},
	doi = {10.1038/nature01344},
	abstract = {Photosystem II (PSII) is a key component of photosynthesis, the process of converting sunlight into the chemical energy of life. In plant cells, it forms a unique oligomeric macrostructure in membranes of the chloroplasts1. Several light-harvesting antenna complexes are organized precisely in the PSII macrostructure—the major trimeric complexes (LHCII)2 that bind 70\% of PSII chlorophyll and three minor monomeric complexes3—which together form PSII supercomplexes4,5,6. The antenna complexes are essential for collecting sunlight and regulating photosynthesis7,8,9, but the relationship between these functions and their molecular architecture is unresolved. Here we report that antisense Arabidopsis plants lacking the proteins that form LHCII trimers10 have PSII supercomplexes with almost identical abundance and structure to those found in wild-type plants. The place of LHCII is taken by a normally minor and monomeric complex, CP26, which is synthesized in large amounts and organized into trimers. Trimerization is clearly not a specific attribute of LHCII. Our results highlight the importance of the PSII macrostructure: in the absence of one of its main components, another protein is recruited to allow it to assemble and function.},
	language = {en},
	number = {6923},
	urldate = {2024-06-28},
	journal = {Nature},
	author = {Ruban, A. V. and Wentworth, M. and Yakushevska, A. E. and Andersson, J. and Lee, P. J. and Keegstra, W. and Dekker, J. P. and Boekema, E. J. and Jansson, S. and Horton, P.},
	month = feb,
	year = {2003},
	note = {Publisher: Nature Publishing Group},
	keywords = {Humanities and Social Sciences, Science, multidisciplinary},
	pages = {648--652},
}

Photosystem II (PSII) is a key component of photosynthesis, the process of converting sunlight into the chemical energy of life. In plant cells, it forms a unique oligomeric macrostructure in membranes of the chloroplasts1. Several light-harvesting antenna complexes are organized precisely in the PSII macrostructure—the major trimeric complexes (LHCII)2 that bind 70% of PSII chlorophyll and three minor monomeric complexes3—which together form PSII supercomplexes4,5,6. The antenna complexes are essential for collecting sunlight and regulating photosynthesis7,8,9, but the relationship between these functions and their molecular architecture is unresolved. Here we report that antisense Arabidopsis plants lacking the proteins that form LHCII trimers10 have PSII supercomplexes with almost identical abundance and structure to those found in wild-type plants. The place of LHCII is taken by a normally minor and monomeric complex, CP26, which is synthesized in large amounts and organized into trimers. Trimerization is clearly not a specific attribute of LHCII. Our results highlight the importance of the PSII macrostructure: in the absence of one of its main components, another protein is recruited to allow it to assemble and function.

@article{ogura_chromosome_2003,
	title = {Chromosome constitution of seven wild {Allium} species in the {Tianshan} {Mountains} ({Abstracts} of the oral and poster presentations, {Abstracts} of the 54th {Annual} {Meeting} of the {Society} of {Chromosome} {Research})},
	volume = {7},
	shorttitle = {Chromosome constitution of seven wild {Allium} species in the {Tianshan} {Mountains}({Abstracts} of the oral and poster presentations, {Abstracts} of the 54th {Annual} {Meeting} of the {Society} of {Chromosome} {Research})},
	url = {https://cir.nii.ac.jp/crid/1540854195286041984},
	language = {en},
	number = {4},
	urldate = {2023-04-27},
	journal = {Chromosome science},
	author = {Ogura, Hisakazu and Kondo, Katsuhiko and Mao, Jian-Feng and Funamoto, Tsuneo and Tan, Dun-yan and Ge, Song and Hong, De-yuan},
	year = {2003},
	note = {Publisher: Society of Chromosome Research},
	keywords = {⛔ No DOI found},
	pages = {128},
}

@article{funamoto_comparative_2003,
	title = {A comparative chromosomal study of three {Rhodiola} species ({Crassulaceae}) collected in central {Tianshan} {Mountains}, {Xinjiang}, {China}},
	volume = {7},
	shorttitle = {A comparative chromosomal study of three {Rhodiola} species ({Crassulaceae}) collected in central {Tianshan} {Mountains}, {Xinjiang}, {China}},
	url = {https://cir.nii.ac.jp/crid/1521417755499686144},
	abstract = {Chromosomal characters of three Rhodiola species (R. gelida, R. quadrifida and R. aff. litwinowii) collected in central Tianshan Mountains in Xinjiang, China, had commonly the simple chromocenter type in the resting chromosomes and the proximal type in the mitotic prophase chromosomes. Rhodiola gelida and R. quadrifida showed the chromosome number of 2n=20 and R. aff. litwinowii showed the chromosome number of 2n=16. The chromosome numbers of R. gelida and R. aff. litwinowii were reported here for the first time, and the chromosome number of R. quadrifida verified the previous report. Rhodiola gelida and R. quadrifida had monomodal (gradual) decrease in chromosome length from the largest to the smallest chromosomes in alighment and R. aff. litwinowii had bimodal decrease in chromosome length.},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {Chromosome Science},
	author = {Funamoto, Tsuneo and Kondo, Katsuhiko and Hong, De-yuan and Mao, Jian-Feng and Ogura, Hisakazu},
	year = {2003},
	note = {Publisher: The Society of Chromosome Research},
	keywords = {⛔ No DOI found},
	pages = {55--60},
}

Chromosomal characters of three Rhodiola species (R. gelida, R. quadrifida and R. aff. litwinowii) collected in central Tianshan Mountains in Xinjiang, China, had commonly the simple chromocenter type in the resting chromosomes and the proximal type in the mitotic prophase chromosomes. Rhodiola gelida and R. quadrifida showed the chromosome number of 2n=20 and R. aff. litwinowii showed the chromosome number of 2n=16. The chromosome numbers of R. gelida and R. aff. litwinowii were reported here for the first time, and the chromosome number of R. quadrifida verified the previous report. Rhodiola gelida and R. quadrifida had monomodal (gradual) decrease in chromosome length from the largest to the smallest chromosomes in alighment and R. aff. litwinowii had bimodal decrease in chromosome length.

@article{becker_regulation_2003,
	title = {Regulation of the {ABA}-sensitive {Arabidopsis} potassium channel gene {GORK} in response to water stress},
	volume = {554},
	copyright = {FEBS Letters 554 (2003) 1873-3468 © 2015 Federation of European Biochemical Societies},
	issn = {1873-3468},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1016/S0014-5793%2803%2901118-9},
	doi = {10.1016/S0014-5793(03)01118-9},
	abstract = {The phytohormone abscisic acid (ABA) regulates many stress-related processes in plants. In this context ABA mediates the responsiveness of plants to environmental stresses such as drought, cold or salt. In response to water stress, ABA induces stomatal closure by activating Ca2+, K+ and anion channels in guard cells. To understand the signalling pathways that regulate these turgor control elements, we studied the transcriptional control of the K+ release channel gene GORK that is expressed in guard cells, roots and vascular tissue. GORK transcription was up-regulated upon onset of drought, salt stress and cold. The wilting hormone ABA that integrates responses to these stimuli induced GORK expression in seedlings in a time- and concentration-dependent manner and this induction was dependent on extracellular Ca2+. ABA-responsive expression of GORK was impaired in the ABA-insensitive mutants abi1-1 and abi2-1, indicating that these protein phosphatases are regulators of GORK expression. Application of ABA to suspension-cultured cells for 2 min followed by a 4 h chase was sufficient to manifest transcriptional activation of the K+ channel gene. As predicted for a process involved in drought adaptation, only 12–24 h after the release of the stress hormone, GORK mRNA slowly decreased. In contrast to other tissues, GORK expression as well as K+ out channel activity in guard cells is ABA insensitive, allowing the plant to adjust stomatal movement and water status control separately.},
	language = {en},
	number = {1-2},
	urldate = {2022-11-30},
	journal = {FEBS Letters},
	author = {Becker, D. and Hoth, S. and Ache, P. and Wenkel, S. and Roelfsema, M.r.g. and Meyerhoff, O. and Hartung, W. and Hedrich, R.},
	year = {2003},
	keywords = {Abscisic acid, GORK, Guard cell, K+ channel, Water stress},
	pages = {119--126},
}

The phytohormone abscisic acid (ABA) regulates many stress-related processes in plants. In this context ABA mediates the responsiveness of plants to environmental stresses such as drought, cold or salt. In response to water stress, ABA induces stomatal closure by activating Ca2+, K+ and anion channels in guard cells. To understand the signalling pathways that regulate these turgor control elements, we studied the transcriptional control of the K+ release channel gene GORK that is expressed in guard cells, roots and vascular tissue. GORK transcription was up-regulated upon onset of drought, salt stress and cold. The wilting hormone ABA that integrates responses to these stimuli induced GORK expression in seedlings in a time- and concentration-dependent manner and this induction was dependent on extracellular Ca2+. ABA-responsive expression of GORK was impaired in the ABA-insensitive mutants abi1-1 and abi2-1, indicating that these protein phosphatases are regulators of GORK expression. Application of ABA to suspension-cultured cells for 2 min followed by a 4 h chase was sufficient to manifest transcriptional activation of the K+ channel gene. As predicted for a process involved in drought adaptation, only 12–24 h after the release of the stress hormone, GORK mRNA slowly decreased. In contrast to other tissues, GORK expression as well as K+ out channel activity in guard cells is ABA insensitive, allowing the plant to adjust stomatal movement and water status control separately.

@article{israelsson_changes_2003,
	title = {Changes in gene expression in the wood-forming tissue of transgenic hybrid aspen with increased secondary growth},
	volume = {52},
	issn = {1573-5028},
	url = {https://doi.org/10.1023/A:1025097410445},
	doi = {10/b7zwj2},
	abstract = {Transgenic lines of hybrid aspen with elevated levels of gibberellin (GA) show greatly increased numbers of xylem fibres and increases in xylem fibre length. These plants therefore provide excellent models for studying secondary growth. We have used cDNA microarry analysis to investigate how gene transcription in the developing xylem is affected by GA-induced growth. A recent investigation has shown that genes encoding lignin and cellulose biosynthetic enzymes, as well as a number of transcription factors and other potential regulators of xylogenesis, are under developmental-stage-specific transcriptional control. The present study shows that the highest transcript changes in our transgenic trees occurs in genes generally restricted to the early stages of xylogenesis, including cell division, early expansion and late expansion. The results reveal genes among those arrayed that are up-regulated with an increased xylem production, thus indicating key components in the production of wood.},
	language = {en},
	number = {4},
	urldate = {2022-03-11},
	journal = {Plant Molecular Biology},
	author = {Israelsson, Maria and Eriksson, Maria E. and Hertzberg, Magnus and Aspeborg, Henrik and Nilsson, Peter and Moritz, Thomas},
	month = jul,
	year = {2003},
	pages = {893--903},
}

Transgenic lines of hybrid aspen with elevated levels of gibberellin (GA) show greatly increased numbers of xylem fibres and increases in xylem fibre length. These plants therefore provide excellent models for studying secondary growth. We have used cDNA microarry analysis to investigate how gene transcription in the developing xylem is affected by GA-induced growth. A recent investigation has shown that genes encoding lignin and cellulose biosynthetic enzymes, as well as a number of transcription factors and other potential regulators of xylogenesis, are under developmental-stage-specific transcriptional control. The present study shows that the highest transcript changes in our transgenic trees occurs in genes generally restricted to the early stages of xylogenesis, including cell division, early expansion and late expansion. The results reveal genes among those arrayed that are up-regulated with an increased xylem production, thus indicating key components in the production of wood.

@article{siedlecka_small_2003,
	title = {The small subunit {ADP}-glucose pyrophosphorylase ({ApS}) promoter mediates okadaic acid-sensitive {uidA} expression in starch-synthesizing tissues and cells in {Arabidopsis}},
	volume = {217},
	issn = {1432-2048},
	url = {https://doi.org/10.1007/s00425-003-0982-y},
	doi = {10.1007/s00425-003-0982-y},
	abstract = {Transgenic plants of Arabidopsis thaliana Heynh., transformed with a bacterial β-glucuronidase (GUS) gene under the control of the promoter of the small subunit (ApS) of ADP-glucose pyrophosphorylase (AGPase), exhibited GUS staining in leaves (including stomata), stems, roots and flowers. Cross-sections of stems revealed GUS staining in protoxylem parenchyma, primary phloem and cortex. In young roots, the staining was found in the root tips, including the root cap, and in vascular tissue, while the older root–hypocotyl axis showed prominent staining in the secondary phloem and paratracheary parenchyma of secondary xylem. The GUS staining co-localized with ApS protein, as found by tissue printing using antibodies against ApS. Starch was found only in cell and tissue types exhibiting GUS staining and ApS labelling, but not in all of them. For example, starch was lacking in the xylem parenchyma and secondary phloem of the root–hypocotyl axis. Sucrose potently activated ApS gene expression in leaves of wild-type (wt) plants, and in transgenic seedlings grown on sucrose medium where GUS activity was quantified with 4-methylumbelliferyl-β-glucuronide as substrate. Okadaic acid, an inhibitor of protein phosphatases 1 and 2A, completely blocked expression of ApS in mature leaves of wt plants and prevented GUS staining in root tips and flowers of the transgenic plants, suggesting a similar signal transduction mechanism for ApS expression in various tissues. The data support the key role of AGPase in starch synthesis, but they also underlie the ubiquitous importance of the ApS gene for AGPase function in all organs/tissues of Arabidopsis.},
	language = {en},
	number = {2},
	urldate = {2021-10-21},
	journal = {Planta},
	author = {Siedlecka, Anna and Ciereszko, Iwona and Mellerowicz, Ewa and Martz, Françoise and Chen, Jychian and Kleczkowski, Leszek A.},
	month = jun,
	year = {2003},
	pages = {184--192},
}

Transgenic plants of Arabidopsis thaliana Heynh., transformed with a bacterial β-glucuronidase (GUS) gene under the control of the promoter of the small subunit (ApS) of ADP-glucose pyrophosphorylase (AGPase), exhibited GUS staining in leaves (including stomata), stems, roots and flowers. Cross-sections of stems revealed GUS staining in protoxylem parenchyma, primary phloem and cortex. In young roots, the staining was found in the root tips, including the root cap, and in vascular tissue, while the older root–hypocotyl axis showed prominent staining in the secondary phloem and paratracheary parenchyma of secondary xylem. The GUS staining co-localized with ApS protein, as found by tissue printing using antibodies against ApS. Starch was found only in cell and tissue types exhibiting GUS staining and ApS labelling, but not in all of them. For example, starch was lacking in the xylem parenchyma and secondary phloem of the root–hypocotyl axis. Sucrose potently activated ApS gene expression in leaves of wild-type (wt) plants, and in transgenic seedlings grown on sucrose medium where GUS activity was quantified with 4-methylumbelliferyl-β-glucuronide as substrate. Okadaic acid, an inhibitor of protein phosphatases 1 and 2A, completely blocked expression of ApS in mature leaves of wt plants and prevented GUS staining in root tips and flowers of the transgenic plants, suggesting a similar signal transduction mechanism for ApS expression in various tissues. The data support the key role of AGPase in starch synthesis, but they also underlie the ubiquitous importance of the ApS gene for AGPase function in all organs/tissues of Arabidopsis.

@article{corander_bayesian_2003,
	title = {Bayesian {Analysis} of {Genetic} {Differentiation} {Between} {Populations}},
	volume = {163},
	issn = {1943-2631},
	url = {https://doi.org/10.1093/genetics/163.1.367},
	doi = {10.1093/genetics/163.1.367},
	abstract = {We introduce a Bayesian method for estimating hidden population substructure using multilocus molecular markers and geographical information provided by the sampling design. The joint posterior distribution of the substructure and allele frequencies of the respective populations is available in an analytical form when the number of populations is small, whereas an approximation based on a Markov chain Monte Carlo simulation approach can be obtained for a moderate or large number of populations. Using the joint posterior distribution, posteriors can also be derived for any evolutionary population parameters, such as the traditional fixation indices. A major advantage compared to most earlier methods is that the number of populations is treated here as an unknown parameter. What is traditionally considered as two genetically distinct populations, either recently founded or connected by considerable gene flow, is here considered as one panmictic population with a certain probability based on marker data and prior information. Analyses of previously published data on the Moroccan argan tree (Argania spinosa) and of simulated data sets suggest that our method is capable of estimating a population substructure, while not artificially enforcing a substructure when it does not exist. The software (BAPS) used for the computations is freely available from http://www.rni.helsinki.fi/{\textasciitilde}mjs.},
	number = {1},
	urldate = {2021-10-14},
	journal = {Genetics},
	author = {Corander, Jukka and Waldmann, Patrik and Sillanpää, Mikko J},
	month = jan,
	year = {2003},
	pages = {367--374},
}

We introduce a Bayesian method for estimating hidden population substructure using multilocus molecular markers and geographical information provided by the sampling design. The joint posterior distribution of the substructure and allele frequencies of the respective populations is available in an analytical form when the number of populations is small, whereas an approximation based on a Markov chain Monte Carlo simulation approach can be obtained for a moderate or large number of populations. Using the joint posterior distribution, posteriors can also be derived for any evolutionary population parameters, such as the traditional fixation indices. A major advantage compared to most earlier methods is that the number of populations is treated here as an unknown parameter. What is traditionally considered as two genetically distinct populations, either recently founded or connected by considerable gene flow, is here considered as one panmictic population with a certain probability based on marker data and prior information. Analyses of previously published data on the Moroccan argan tree (Argania spinosa) and of simulated data sets suggest that our method is capable of estimating a population substructure, while not artificially enforcing a substructure when it does not exist. The software (BAPS) used for the computations is freely available from http://www.rni.helsinki.fi/~mjs.

@article{keun_improved_2003,
	title = {Improved analysis of multivariate data by variable stability scaling: application to {NMR}-based metabolic profiling},
	volume = {490},
	issn = {0003-2670},
	shorttitle = {Improved analysis of multivariate data by variable stability scaling},
	doi = {10/cv3sj3},
	abstract = {Variable scaling alters the covariance structure of data, affecting the outcome of multivariate analysis and calibration. Here we present a new method, variable stability (VAST) scaling, which weights each variable according to a metric of its stability. The beneficial effect of VAST scaling is demonstrated for a data set of H-1 NMR spectra of urine acquired as part of a metabonomic study into the effects of unilateral nephrectomy in an animal model. The application of VAST scaling improved the class distinction and predictive power of partial least squares discriminant analysis (PLS-DA) models. The effects of other data scaling and pre-processing methods, such as orthogonal signal correction (OSC), were also tested. VAST scaling produced the most robust models in terms of class prediction, outperforming OSC in this aspect. As a result the subtle, but consistent, metabolic perturbation caused by unilateral nephrectomy could be accurately characterised despite the presence of much greater biological differences caused by normal physiological variation. VAST scaling presents itself as an interpretable, robust and easily implemented data treatment for the enhancement of multivariate data analysis. (C) 2003 Elsevier Science B.V. All rights reserved.},
	language = {English},
	number = {1-2},
	journal = {Analytica Chimica Acta},
	author = {Keun, H. C. and Ebbels, T. M. D. and Antti, H. and Bollard, M. E. and Beckonert, O. and Holmes, E. and Lindon, J. C. and Nicholson, J. K.},
	month = aug,
	year = {2003},
	note = {Place: Amsterdam
Publisher: Elsevier
WOS:000185047900022},
	keywords = {biofluid   NMR, coefficient of   variations, data pre-processing, metabolomics, metabonomics, orthogonal signal correction, partial least squares   discriminant analysis, spectra, toxicity, variable scaling, variable stability},
	pages = {265--276},
}

Variable scaling alters the covariance structure of data, affecting the outcome of multivariate analysis and calibration. Here we present a new method, variable stability (VAST) scaling, which weights each variable according to a metric of its stability. The beneficial effect of VAST scaling is demonstrated for a data set of H-1 NMR spectra of urine acquired as part of a metabonomic study into the effects of unilateral nephrectomy in an animal model. The application of VAST scaling improved the class distinction and predictive power of partial least squares discriminant analysis (PLS-DA) models. The effects of other data scaling and pre-processing methods, such as orthogonal signal correction (OSC), were also tested. VAST scaling produced the most robust models in terms of class prediction, outperforming OSC in this aspect. As a result the subtle, but consistent, metabolic perturbation caused by unilateral nephrectomy could be accurately characterised despite the presence of much greater biological differences caused by normal physiological variation. VAST scaling presents itself as an interpretable, robust and easily implemented data treatment for the enhancement of multivariate data analysis. (C) 2003 Elsevier Science B.V. All rights reserved.

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

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

@article{stasolla_transcript_2003,
	title = {Transcript profiles of stress-related genes in developing white spruce ({Picea} glauca) somatic embryos cultured with polyethylene glycol},
	volume = {165},
	issn = {0168-9452},
	url = {https://www.sciencedirect.com/science/article/pii/S0168945203002280},
	doi = {10/fk3m4b},
	abstract = {The effect of polyethylene glycol (PEG) on the transcript level of 512 stress-related genes was analyzed by cDNA microarray. Major changes in gene expression between control and PEG-treated embryos were observed during the initial stages of development, upon transfer of the embryogenic tissue on maturation medium, and during the late phases of development, culminating with the generation of cotyledonary embryos. Only small changes in gene expression were observed during the intermediate phases of embryo development. The transcript levels of several genes involved in cell aging and detoxification mechanisms, including peroxidases and chitinases, were developmentally regulated during the embryogenic process. Major differences in the expression of these genes were observed between control and PEG-treated embryos. Based on their expression profiles, four different clusters of genes involved in stress response mechanisms were identified. The first group of genes, which included several heat shock proteins, was up-regulated in PEG-treated immature embryos. An opposite tendency was observed for a second cluster of genes, which included a glutathione-S-transferase, and a cysteine protease. The third class included genes repressed by PEG in fully developed embryos, whereas a fourth group of genes, which included several heat shock proteins and ubiquitin, was induced in PEG-treated embryos at the end of the culture period. Difference in transcript levels and profiles of several genes involved in cell wall and lignin biosynthesis were also observed between control and PEG-treated embryos.},
	language = {en},
	number = {4},
	urldate = {2021-07-05},
	journal = {Plant Science},
	author = {Stasolla, Claudio and van Zyl, Leonel and Egertsdotter, Ulrika and Craig, Deborah and Liu, Wenbin and Sederoff, Ronald R.},
	month = oct,
	year = {2003},
	keywords = {Microarray, Polyethylene glycol, Transcript levels, White spruce},
	pages = {719--729},
}

The effect of polyethylene glycol (PEG) on the transcript level of 512 stress-related genes was analyzed by cDNA microarray. Major changes in gene expression between control and PEG-treated embryos were observed during the initial stages of development, upon transfer of the embryogenic tissue on maturation medium, and during the late phases of development, culminating with the generation of cotyledonary embryos. Only small changes in gene expression were observed during the intermediate phases of embryo development. The transcript levels of several genes involved in cell aging and detoxification mechanisms, including peroxidases and chitinases, were developmentally regulated during the embryogenic process. Major differences in the expression of these genes were observed between control and PEG-treated embryos. Based on their expression profiles, four different clusters of genes involved in stress response mechanisms were identified. The first group of genes, which included several heat shock proteins, was up-regulated in PEG-treated immature embryos. An opposite tendency was observed for a second cluster of genes, which included a glutathione-S-transferase, and a cysteine protease. The third class included genes repressed by PEG in fully developed embryos, whereas a fourth group of genes, which included several heat shock proteins and ubiquitin, was induced in PEG-treated embryos at the end of the culture period. Difference in transcript levels and profiles of several genes involved in cell wall and lignin biosynthesis were also observed between control and PEG-treated embryos.

@article{tournier_new_2003,
	title = {New members of the tomato {ERF} family show specific expression pattern and diverse {DNA}-binding capacity to the {GCC} box element},
	volume = {550},
	issn = {1873-3468},
	url = {https://febs.onlinelibrary.wiley.com/doi/abs/10.1016/S0014-5793%2803%2900757-9},
	doi = {10/dws9jc},
	abstract = {Four new members of the ERF (ethylene-response factor) family of plant-specific DNA-binding (GCC box) factors were isolated from tomato fruit (LeERF1–4). Phylogenetic analysis indicated that LeERF2 belongs to a new ERF class, characterized by a conserved N-terminal signature sequence. Expression patterns and cis/trans binding affinities differed between the LeERFs. Combining experimental data and modeled three-dimensional analysis, it was shown that binding affinity of the LeERFs was affected by both the variation of nucleotides surrounding the DNA cis-element sequence and the nature of critical amino acid residues within the ERF domain.},
	language = {en},
	number = {1-3},
	urldate = {2021-07-05},
	journal = {FEBS Letters},
	author = {Tournier, Barthélémy and Sanchez-Ballesta, Maria Theresa and Jones, Brian and Pesquet, Edouard and Regad, Farid and Latché, Alain and Pech, Jean-Claude and Bouzayen, Mondher},
	year = {2003},
	note = {\_eprint: https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/S0014-5793\%2803\%2900757-9},
	keywords = {3D modeling, Ethylene response factor, Lycopersicon esculentum},
	pages = {149--154},
}

Four new members of the ERF (ethylene-response factor) family of plant-specific DNA-binding (GCC box) factors were isolated from tomato fruit (LeERF1–4). Phylogenetic analysis indicated that LeERF2 belongs to a new ERF class, characterized by a conserved N-terminal signature sequence. Expression patterns and cis/trans binding affinities differed between the LeERFs. Combining experimental data and modeled three-dimensional analysis, it was shown that binding affinity of the LeERFs was affected by both the variation of nucleotides surrounding the DNA cis-element sequence and the nature of critical amino acid residues within the ERF domain.

@article{glaubitz_impacts_2003,
	title = {Impacts of silviculture on genetic diversity in the native forest species {Eucalyptus} sieberi},
	volume = {4},
	issn = {1572-9737},
	url = {https://doi.org/10.1023/A:1024025331750},
	doi = {10/ddfq62},
	abstract = {Potential impacts of regeneration practices ongenetic diversity in the Australian nativeforest species Eucalyptus sieberi L.A.S.Johnson. (silvertop ash) were assessed usingDNA markers. Three different silviculturaltreatments were examined: clear-felling withaerial re-sowing, and the seed tree system withsite preparation by either burning ormechanical disturbance. In addition, twounharvested stands were chosen as controls. Atotal sample of 825 trees were genotyped at 35Mendelian markers: 26 single-copy nuclear RFLPsand 9 microsatellites. No significantdifferences were found among the treatments inany of four population genetic statistics:allelic richness, effective number of alleles,expected heterozygosity and the panmictic index(f). Rare alleles were prevalent, and a MonteCarlo simulation showed that the apparent lossof four rare alleles from the saplingregenerants was highly statisticallysignificant. There was no evidence for recentbottlenecks from analyses of either the levelsof expected heterozygosity relative to thatexpected under mutation drift equilibrium, orthe allele frequency profiles. A dendrogram ofthe relationships between the sampledpopulations suggested that the seed tree systemmay result in the promotion of genetic drift(slight expansion of the dendrogram) whileaerial re-sowing of clear falls with the sameseedlot will lead to genetic homogenisation(contraction of the dendrogram). The apparentgenetic robustness of E. sieberi tonative forest regeneration practices isattributed to its local abundance combined withthe favourable properties of its reproductivebiology, as well as to the limitation that onlya single rotation was examined.},
	language = {en},
	number = {3},
	urldate = {2021-07-05},
	journal = {Conservation Genetics},
	author = {Glaubitz, Jeffrey C. and Wu, Harry X. and Moran, Gavin F.},
	month = may,
	year = {2003},
	pages = {275--287},
}

Potential impacts of regeneration practices ongenetic diversity in the Australian nativeforest species Eucalyptus sieberi L.A.S.Johnson. (silvertop ash) were assessed usingDNA markers. Three different silviculturaltreatments were examined: clear-felling withaerial re-sowing, and the seed tree system withsite preparation by either burning ormechanical disturbance. In addition, twounharvested stands were chosen as controls. Atotal sample of 825 trees were genotyped at 35Mendelian markers: 26 single-copy nuclear RFLPsand 9 microsatellites. No significantdifferences were found among the treatments inany of four population genetic statistics:allelic richness, effective number of alleles,expected heterozygosity and the panmictic index(f). Rare alleles were prevalent, and a MonteCarlo simulation showed that the apparent lossof four rare alleles from the saplingregenerants was highly statisticallysignificant. There was no evidence for recentbottlenecks from analyses of either the levelsof expected heterozygosity relative to thatexpected under mutation drift equilibrium, orthe allele frequency profiles. A dendrogram ofthe relationships between the sampledpopulations suggested that the seed tree systemmay result in the promotion of genetic drift(slight expansion of the dendrogram) whileaerial re-sowing of clear falls with the sameseedlot will lead to genetic homogenisation(contraction of the dendrogram). The apparentgenetic robustness of E. sieberi tonative forest regeneration practices isattributed to its local abundance combined withthe favourable properties of its reproductivebiology, as well as to the limitation that onlya single rotation was examined.

@article{alonso_genome-wide_2003,
	title = {Genome-wide insertional mutagenesis of {Arabidopsis} thaliana},
	volume = {301},
	issn = {1095-9203},
	doi = {10/fqhtnq},
	abstract = {Over 225,000 independent Agrobacterium transferred DNA (T-DNA) insertion events in the genome of the reference plant Arabidopsis thaliana have been created that represent near saturation of the gene space. The precise locations were determined for more than 88,000 T-DNA insertions, which resulted in the identification of mutations in more than 21,700 of the approximately 29,454 predicted Arabidopsis genes. Genome-wide analysis of the distribution of integration events revealed the existence of a large integration site bias at both the chromosome and gene levels. Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene.},
	language = {eng},
	number = {5633},
	journal = {Science (New York, N.Y.)},
	author = {Alonso, José M. and Stepanova, Anna N. and Leisse, Thomas J. and Kim, Christopher J. and Chen, Huaming and Shinn, Paul and Stevenson, Denise K. and Zimmerman, Justin and Barajas, Pascual and Cheuk, Rosa and Gadrinab, Carmelita and Heller, Collen and Jeske, Albert and Koesema, Eric and Meyers, Cristina C. and Parker, Holly and Prednis, Lance and Ansari, Yasser and Choy, Nathan and Deen, Hashim and Geralt, Michael and Hazari, Nisha and Hom, Emily and Karnes, Meagan and Mulholland, Celene and Ndubaku, Ral and Schmidt, Ian and Guzman, Plinio and Aguilar-Henonin, Laura and Schmid, Markus and Weigel, Detlef and Carter, David E. and Marchand, Trudy and Risseeuw, Eddy and Brogden, Debra and Zeko, Albana and Crosby, William L. and Berry, Charles C. and Ecker, Joseph R.},
	month = aug,
	year = {2003},
	pmid = {12893945},
	keywords = {3' Untranslated Regions, 5' Untranslated Regions, Alleles, Arabidopsis, Arabidopsis Proteins, Base Composition, Chromosomes, Plant, DNA, Bacterial, DNA, Plant, Ethylenes, Exons, Expressed Sequence Tags, Gene Expression, Gene Expression Profiling, Gene Expression Regulation, Plant, Genes, Plant, Genome, Plant, Introns, Mutagenesis, Insertional, Mutation, Oligonucleotide Array Sequence Analysis, Promoter Regions, Genetic, Recombination, Genetic, Rhizobium},
	pages = {653--657},
}

Over 225,000 independent Agrobacterium transferred DNA (T-DNA) insertion events in the genome of the reference plant Arabidopsis thaliana have been created that represent near saturation of the gene space. The precise locations were determined for more than 88,000 T-DNA insertions, which resulted in the identification of mutations in more than 21,700 of the approximately 29,454 predicted Arabidopsis genes. Genome-wide analysis of the distribution of integration events revealed the existence of a large integration site bias at both the chromosome and gene levels. Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene.

@article{stasolla_analysis_2003,
	title = {Analysis of lignin produced by cinnamyl alcohol dehydrogenase-deficient {Pinus} taeda cultured cells},
	volume = {41},
	issn = {0981-9428},
	url = {https://www.sciencedirect.com/science/article/pii/S0981942803000512},
	doi = {10/bkcwgq},
	abstract = {Comparative studies were conducted on composition of lignin produced both in vivo and in vitro by cinnamyl alcohol dehydrogenase (CAD)-deficient mutant loblolly pine (Pinus taeda L.). In vivo studies were performed using differentiating xylem obtained from two genotypes of heterozygous (CAD/cad) and two genotypes of homozygous (cad/cad) CAD-deficient mutant trees. In vitro studies were performed using a culture system in which cells, generated from the same genotypes, were induced to produce lignin in culture. Steady state RNA levels and enzyme activity of CAD were dramatically reduced in both xylem and cultured cells obtained from homozygous mutant trees, compared to their heterozygous counterparts. Light microscopic studies showed pronounced differences during the lignin formation between homozygous and heterozygous cells. Phenolic compounds in the heterozygous (CAD/cad) cells were deposited around the cell wall, accumulated preferentially in vacuoles of the homozygous (cad/cad) cells. Differences in lignin composition as revealed by thioacidolysis were also observed. Lignin of both xylem tissue and cultured cells obtained from CAD-deficient homozygotes showed lower levels of coniferyl alcohols and significant enrichments in dihydroconiferyl alcohol (DHCA) and coniferyl aldehyde, compared to their heterozygous counterparts. The striking similarities in lignin composition observed both in vivo and in vitro, open new possibilities for the use of culture systems aimed at revealing the mechanisms controlling lignin biosynthesis, and the formation of DHCA subunits.},
	language = {en},
	number = {5},
	urldate = {2021-07-05},
	journal = {Plant Physiology and Biochemistry},
	author = {Stasolla, Claudio and Scott, Jay and Egertsdotter, Ulrika and Kadla, John and O’ Malley, David and Sederoff, Ronald and van Zyl, Leonel},
	month = may,
	year = {2003},
	keywords = {Cinnamyl alcohol dehydrogenase, Cultured cells, Dihydroconiferyl alcohol, Lignin, Xylem},
	pages = {439--445},
}

Comparative studies were conducted on composition of lignin produced both in vivo and in vitro by cinnamyl alcohol dehydrogenase (CAD)-deficient mutant loblolly pine (Pinus taeda L.). In vivo studies were performed using differentiating xylem obtained from two genotypes of heterozygous (CAD/cad) and two genotypes of homozygous (cad/cad) CAD-deficient mutant trees. In vitro studies were performed using a culture system in which cells, generated from the same genotypes, were induced to produce lignin in culture. Steady state RNA levels and enzyme activity of CAD were dramatically reduced in both xylem and cultured cells obtained from homozygous mutant trees, compared to their heterozygous counterparts. Light microscopic studies showed pronounced differences during the lignin formation between homozygous and heterozygous cells. Phenolic compounds in the heterozygous (CAD/cad) cells were deposited around the cell wall, accumulated preferentially in vacuoles of the homozygous (cad/cad) cells. Differences in lignin composition as revealed by thioacidolysis were also observed. Lignin of both xylem tissue and cultured cells obtained from CAD-deficient homozygotes showed lower levels of coniferyl alcohols and significant enrichments in dihydroconiferyl alcohol (DHCA) and coniferyl aldehyde, compared to their heterozygous counterparts. The striking similarities in lignin composition observed both in vivo and in vitro, open new possibilities for the use of culture systems aimed at revealing the mechanisms controlling lignin biosynthesis, and the formation of DHCA subunits.

@article{komulainen_comparing_2003,
	title = {Comparing {EST}-based genetic maps between {Pinus} sylvestris and {Pinus} taeda},
	volume = {107},
	issn = {1432-2242},
	url = {https://doi.org/10.1007/s00122-003-1312-2},
	doi = {10/fvc7mz},
	abstract = {A genetic map of Pinus sylvestris was constructed using ESTP (expressed sequence tag polymorphism) markers and other gene-based markers, AFLP markers and microsatellites. Part of the ESTP markers (40) were developed and mapped earlier in Pinus taeda, and additional markers were generated based on P. sylvestris sequences or sequences from other pine species. The mapping in P. sylvestris was based on 94 F1 progeny from a cross between plus-tree parents E635C and E1101. AFLP framework maps for the parent trees were first constructed. The ESTP and other gene sequence-based markers were added to the framework maps, as well as five published microsatellite loci. The separate maps were then integrated with the aid of AFLPs segregating in both trees (dominant segregation ratios 3:1) as well as gene markers and microsatellites segregating in both parent trees (segregation ratios 1:1:1:1 or 1:2:1). The integrated map consisted of 12 groups corresponding to the P. taeda linkage groups, and additionally three and six smaller groups for E1101 and E635C, respectively. The number of framework AFLP markers in the integrated map is altogether 194 and the number of gene markers 61. The total length of the integrated map was 1,314 cM. The set of markers developed for P. sylvestris was also added to existing maps of two P. taeda pedigrees. Starting with a mapped marker from one pedigree in the source species resulted in a mapped marker in a pedigree of the other species in more than 40\% of the cases, with about equal success in both directions. The maps of the two species are largely colinear, even if the species have diverged more than 70 MYA. Most cases of different locations were probably due to problems in identifying the orthologous members of gene families. These data provide a first ESTP-containing map of P. sylvestris, which can also be used for comparing this species to additional species mapped with the same markers.},
	language = {en},
	number = {4},
	urldate = {2021-07-05},
	journal = {Theoretical and Applied Genetics},
	author = {Komulainen, P. and Brown, G. R. and Mikkonen, M. and Karhu, A. and García-Gil, M. R. and O'Malley, D. and Lee, B. and Neale, D. B. and Savolainen, O.},
	month = aug,
	year = {2003},
	pages = {667--678},
}

A genetic map of Pinus sylvestris was constructed using ESTP (expressed sequence tag polymorphism) markers and other gene-based markers, AFLP markers and microsatellites. Part of the ESTP markers (40) were developed and mapped earlier in Pinus taeda, and additional markers were generated based on P. sylvestris sequences or sequences from other pine species. The mapping in P. sylvestris was based on 94 F1 progeny from a cross between plus-tree parents E635C and E1101. AFLP framework maps for the parent trees were first constructed. The ESTP and other gene sequence-based markers were added to the framework maps, as well as five published microsatellite loci. The separate maps were then integrated with the aid of AFLPs segregating in both trees (dominant segregation ratios 3:1) as well as gene markers and microsatellites segregating in both parent trees (segregation ratios 1:1:1:1 or 1:2:1). The integrated map consisted of 12 groups corresponding to the P. taeda linkage groups, and additionally three and six smaller groups for E1101 and E635C, respectively. The number of framework AFLP markers in the integrated map is altogether 194 and the number of gene markers 61. The total length of the integrated map was 1,314 cM. The set of markers developed for P. sylvestris was also added to existing maps of two P. taeda pedigrees. Starting with a mapped marker from one pedigree in the source species resulted in a mapped marker in a pedigree of the other species in more than 40% of the cases, with about equal success in both directions. The maps of the two species are largely colinear, even if the species have diverged more than 70 MYA. Most cases of different locations were probably due to problems in identifying the orthologous members of gene families. These data provide a first ESTP-containing map of P. sylvestris, which can also be used for comparing this species to additional species mapped with the same markers.

@article{pesquet_zinnia_2003,
	title = {Zinnia elegans: the missing link from in vitro tracheary elements to xylem},
	volume = {119},
	issn = {1399-3054},
	shorttitle = {Zinnia elegans},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1399-3054.2003.00226.x},
	doi = {10/bwgf2c},
	abstract = {For the last 20 years, in vitro xylogenic cultures of Zinnia elegans have been routinely used to study tracheary element (TE) formation. That said, the precise anatomical relationship between in vitro and in planta xylogenesis in Zinnia has been completely ignored. In order to make this comparison, we provide herein a much needed description of xylem tissue of the Zinnia plant. Based on the proportions of secondary wall thickenings, the in vitro TE system most closely resembles hypocotyl vasculature. Moreover, we have shown by confocal microscopy that vessel-like structures of up to five individual TEs are produced in vitro, suggesting that the formation of multicellular structures and cell–cell communication during in vitro TE formation are far more extensive than previously suspected. Finally, as more and more genes become available through genomic approaches of Zinnia TEs, it will be necessary to precisely localize them in planta as a first step in elucidating gene function. Our results provide the histological groundwork for this very purpose.},
	language = {en},
	number = {4},
	urldate = {2021-07-05},
	journal = {Physiologia Plantarum},
	author = {Pesquet, Edouard and Jauneau, Alain and Digonnet, Catherine and Boudet, Alain M. and Pichon, Magalie and Goffner, Deborah},
	year = {2003},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1399-3054.2003.00226.x},
	pages = {463--468},
}

For the last 20 years, in vitro xylogenic cultures of Zinnia elegans have been routinely used to study tracheary element (TE) formation. That said, the precise anatomical relationship between in vitro and in planta xylogenesis in Zinnia has been completely ignored. In order to make this comparison, we provide herein a much needed description of xylem tissue of the Zinnia plant. Based on the proportions of secondary wall thickenings, the in vitro TE system most closely resembles hypocotyl vasculature. Moreover, we have shown by confocal microscopy that vessel-like structures of up to five individual TEs are produced in vitro, suggesting that the formation of multicellular structures and cell–cell communication during in vitro TE formation are far more extensive than previously suspected. Finally, as more and more genes become available through genomic approaches of Zinnia TEs, it will be necessary to precisely localize them in planta as a first step in elucidating gene function. Our results provide the histological groundwork for this very purpose.

@article{ebbels_toxicity_2003,
	title = {Toxicity classification from metabonomic data using a density superposition approach: '{CLOUDS}'},
	volume = {490},
	issn = {0003-2670},
	shorttitle = {Toxicity classification from metabonomic data using a density superposition approach},
	doi = {10/bqxp45},
	abstract = {Predicting and avoiding the potential toxicity of candidate drugs is of fundamental importance to the pharmaceutical industry. The consortium for metabonomic toxicology (COMET) project aims to construct databases and metabolic models of drug toxicity using ca. 100,000 600 MHz H-1 NMR spectra of biofluids from laboratory rats and mice treated with model toxic compounds. Chemometric methods are being used to characterise the time-related and dose-specific effects of toxins on the endogenous metabolite profiles. Here we present a probabilistic approach to the classification of a large data set of COMET samples using Classification Of Unknowns by Density Superposition (CLOUDS), a novel non-neural implementation of a classification technique developed from probabilistic neural networks. NMR spectra of urine from rats from 19 different treatment groups, collected over 8 days, were processed to produce a data matrix with 2844 samples and 205 spectral variables. The spectra were normalised to account for gross concentration differences in the urine and regions corresponding to non-endogenous metabolites (0.4\% of the data) were treated as missing values. Modeling the data according to organ of effect (control, liver, kidney or other organ), with a 50/50 train/test set split, over 90\% of the test samples were classified as belonging to the correct group. In particular, samples from liver and kidney treatments were classified with 77 and 90\% success, respectively, with only a 2\% misclassification rate between these classes. Further analysis of the data, counting each of the 19 treatment groups as separate classes, resulted in a mean success rate across groups of 74\%. Finally, as a severe test, the data were split into 88 classes, each representing a particular toxin at a particular time point. Fifty-four percent of the spectra from non-control samples were classified correctly, particularly successful when compared to the null success rate of similar to1\% expected from random class assignment. The CLOUDS technique has advantages when modelling complex multi-dimensional distributions, giving a probabilistic rather than absolute class description of the data and is particularly amenable to inclusion of prior knowledge such as uncertainties in the data descriptors. This work shows that it is possible to construct viable and informative models of metabonomic data using the CLOUDS methodology, delineating the whole time course of toxicity. These models will be useful in building hybrid expert systems for predicting toxicology, which are the ultimate goal of the COMET project. (C) 2003 Elsevier Science B.V. All rights reserved.},
	language = {English},
	number = {1-2},
	journal = {Analytica Chimica Acta},
	author = {Ebbels, T. and Keun, H. and Beckonert, O. and Antti, H. and Bollard, M. and Holmes, E. and Lindon, J. and Nicholson, J.},
	month = aug,
	year = {2003},
	note = {Place: Amsterdam
Publisher: Elsevier
WOS:000185047900010},
	keywords = {clouds, h-1-nmr spectroscopy, metabolic-responses, metabonomics, model, nmr, pattern-recognition, probabilistic classification, probabilistic neural networks, profile, toxicity prediction, urine},
	pages = {109--122},
}

Predicting and avoiding the potential toxicity of candidate drugs is of fundamental importance to the pharmaceutical industry. The consortium for metabonomic toxicology (COMET) project aims to construct databases and metabolic models of drug toxicity using ca. 100,000 600 MHz H-1 NMR spectra of biofluids from laboratory rats and mice treated with model toxic compounds. Chemometric methods are being used to characterise the time-related and dose-specific effects of toxins on the endogenous metabolite profiles. Here we present a probabilistic approach to the classification of a large data set of COMET samples using Classification Of Unknowns by Density Superposition (CLOUDS), a novel non-neural implementation of a classification technique developed from probabilistic neural networks. NMR spectra of urine from rats from 19 different treatment groups, collected over 8 days, were processed to produce a data matrix with 2844 samples and 205 spectral variables. The spectra were normalised to account for gross concentration differences in the urine and regions corresponding to non-endogenous metabolites (0.4% of the data) were treated as missing values. Modeling the data according to organ of effect (control, liver, kidney or other organ), with a 50/50 train/test set split, over 90% of the test samples were classified as belonging to the correct group. In particular, samples from liver and kidney treatments were classified with 77 and 90% success, respectively, with only a 2% misclassification rate between these classes. Further analysis of the data, counting each of the 19 treatment groups as separate classes, resulted in a mean success rate across groups of 74%. Finally, as a severe test, the data were split into 88 classes, each representing a particular toxin at a particular time point. Fifty-four percent of the spectra from non-control samples were classified correctly, particularly successful when compared to the null success rate of similar to1% expected from random class assignment. The CLOUDS technique has advantages when modelling complex multi-dimensional distributions, giving a probabilistic rather than absolute class description of the data and is particularly amenable to inclusion of prior knowledge such as uncertainties in the data descriptors. This work shows that it is possible to construct viable and informative models of metabonomic data using the CLOUDS methodology, delineating the whole time course of toxicity. These models will be useful in building hybrid expert systems for predicting toxicology, which are the ultimate goal of the COMET project. (C) 2003 Elsevier Science B.V. All rights reserved.

@article{strengbom_regional_2003,
	title = {Regional differences in the occurrence of understorey species reflect nitrogen deposition in {Swedish} forests},
	volume = {32},
	issn = {0044-7447},
	doi = {10/dq35fc},
	abstract = {Possible links between the occurrence of Vaccinium myrtillus, V. vitis-idaea and Deschampsia flexuosa and rates of nitrogen deposition were investigated in 557 coniferous forest stands. In areas with high N-deposition, V. myrtillus was less frequent, less abundant and more susceptible to the leaf pathogen Valdensia heterodoxa than in areas with lower levels of N-deposition. The occurrence of V. vitis-idaea was also strongly negatively correlated with increasing N-deposition, but no such trend was found for D. flexuosa. In regions with high N-deposition, V. myrtillus was more common in stands dominated by Scots pine than in stands dominated by Norway spruce. This was not the case in regions with lower levels of N-deposition. The patterns observed accord with results from N-addition experiments that demonstrate significant effects on vegetation, caused by N-deposition. The data suggest that even low rates of N-deposition may decrease the abundance of the most dominant species in coniferous forest ground flora.},
	language = {English},
	number = {2},
	journal = {Ambio},
	author = {Strengbom, J. and Walheim, M. and Nasholm, T. and Ericson, L.},
	month = mar,
	year = {2003},
	note = {Place: Dordrecht
Publisher: Springer
WOS:000182798700004},
	keywords = {beech, boreal coniferous forest, dynamics, growth, heathland, model, oak forests, pollutants, soil, vegetation},
	pages = {91--97},
}

Possible links between the occurrence of Vaccinium myrtillus, V. vitis-idaea and Deschampsia flexuosa and rates of nitrogen deposition were investigated in 557 coniferous forest stands. In areas with high N-deposition, V. myrtillus was less frequent, less abundant and more susceptible to the leaf pathogen Valdensia heterodoxa than in areas with lower levels of N-deposition. The occurrence of V. vitis-idaea was also strongly negatively correlated with increasing N-deposition, but no such trend was found for D. flexuosa. In regions with high N-deposition, V. myrtillus was more common in stands dominated by Scots pine than in stands dominated by Norway spruce. This was not the case in regions with lower levels of N-deposition. The patterns observed accord with results from N-addition experiments that demonstrate significant effects on vegetation, caused by N-deposition. The data suggest that even low rates of N-deposition may decrease the abundance of the most dominant species in coniferous forest ground flora.

@article{stasolla_effects_2003,
	title = {The {Effects} of {Polyethylene} {Glycol} on {Gene} {Expression} of {Developing} {White} {Spruce} {Somatic} {Embryos}},
	volume = {131},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.015214},
	doi = {10/b6z454},
	abstract = {Somatic embryogenic cultures of white spruce (Picea glauca) represent a valuable system to study molecular mechanisms regulating embryo development because many embryos of defined developmental stages can be generated. The inclusion of polyethylene glycol (PEG) in the maturation medium can improve the number and quality of embryos produced. To learn more about the mechanism of action of PEG, we analyzed transcript profiles of stage-specific embryos matured without (control) or with (PEG treated) PEG. RNA extracted from maturing spruce embryos was analyzed on DNA microarrays containing 2,178 cDNAs from loblolly pine (Pinus taeda). The efficiency of heterologous hybridization between spruce and pine species on microarrays has been documented previously (L. van Zyl, S. von Arnold, P. Bozhkov, Y. Chen, U. Egertsdotter, J. MacKay, R. Sederoff, J. Shen, L. Zelena, D. Clapham [2002] Comp Funct Genomics 3: 306–318). Several pine genes, including the apparent homologs to the Arabidopsis genes ZWILLE, FIDDLEHEAD, FUSCA, and SCARECROW, increased in expression after PEG treatments. These genes are known to be involved in the formation of the embryo body plan and in the control of the shoot and root apical meristems. The increased transcript levels of these genes in immature PEG-treated embryos suggest that PEG may improve the quality of spruce somatic embryos by promoting normal differentiation of the embryonic shoot and root. Changes in the transcript levels of many genes involved in sucrose catabolism and nitrogen assimilation and utilization were also observed between control and PEG-treated embryos.},
	number = {1},
	urldate = {2021-07-05},
	journal = {Plant Physiology},
	author = {Stasolla, Claudio and van Zyl, Leonel and Egertsdotter, Ulrika and Craig, Deborah and Liu, Wenbin and Sederoff, Ron R.},
	month = jan,
	year = {2003},
	pages = {49--60},
}

Somatic embryogenic cultures of white spruce (Picea glauca) represent a valuable system to study molecular mechanisms regulating embryo development because many embryos of defined developmental stages can be generated. The inclusion of polyethylene glycol (PEG) in the maturation medium can improve the number and quality of embryos produced. To learn more about the mechanism of action of PEG, we analyzed transcript profiles of stage-specific embryos matured without (control) or with (PEG treated) PEG. RNA extracted from maturing spruce embryos was analyzed on DNA microarrays containing 2,178 cDNAs from loblolly pine (Pinus taeda). The efficiency of heterologous hybridization between spruce and pine species on microarrays has been documented previously (L. van Zyl, S. von Arnold, P. Bozhkov, Y. Chen, U. Egertsdotter, J. MacKay, R. Sederoff, J. Shen, L. Zelena, D. Clapham [2002] Comp Funct Genomics 3: 306–318). Several pine genes, including the apparent homologs to the Arabidopsis genes ZWILLE, FIDDLEHEAD, FUSCA, and SCARECROW, increased in expression after PEG treatments. These genes are known to be involved in the formation of the embryo body plan and in the control of the shoot and root apical meristems. The increased transcript levels of these genes in immature PEG-treated embryos suggest that PEG may improve the quality of spruce somatic embryos by promoting normal differentiation of the embryonic shoot and root. Changes in the transcript levels of many genes involved in sucrose catabolism and nitrogen assimilation and utilization were also observed between control and PEG-treated embryos.

@article{schmid_dissection_2003,
	title = {Dissection of floral induction pathways using global expression analysis},
	volume = {130},
	issn = {0950-1991},
	doi = {10/c56qz2},
	abstract = {Flowering of the reference plant Arabidopsis thaliana is controlled by several signaling pathways, which converge on a small set of genes that function as pathway integrators. We have analyzed the genomic response to one type of floral inductive signal, photoperiod, to dissect the function of several genes transducing this stimulus, including CONSTANS, thought to be the major output of the photoperiod pathway. Comparing the effects of CONSTANS with those of FLOWERING LOCUS T, which integrates inputs from CONSTANS and other floral inductive pathways, we find that expression profiles of shoot apices from plants with mutations in either gene are very similar. In contrast, a mutation in LEAFY, which also acts downstream of CONSTANS, has much more limited effects. Another pathway integrator, SUPPRESSOR OF OVEREXPRESSION OF CO 1, is responsive to acute induction by photoperiod even in the presence of the floral repressor encoded by FLOWERING LOCUS C. We have discovered a large group of potential floral repressors that are down-regulated upon photoperiodic induction. These include two AP2 domain-encoding genes that can repress flowering. The two paralogous genes, SCHLAFMUTZE and SCHNARCHZAPFEN, share a signature with partial complementarity to the miR172 microRNA, whose precursor we show to be induced upon flowering. These and related findings on SPL genes suggest that microRNAs play an important role in the regulation of flowering.},
	language = {eng},
	number = {24},
	journal = {Development (Cambridge, England)},
	author = {Schmid, Markus and Uhlenhaut, N. Henriette and Godard, François and Demar, Monika and Bressan, Ray and Weigel, Detlef and Lohmann, Jan U.},
	month = dec,
	year = {2003},
	pmid = {14573523},
	keywords = {Animals, Arabidopsis, Arabidopsis Proteins, DNA-Binding Proteins, Flowers, Gene Expression Profiling, Gene Expression Regulation, Plant, MicroRNAs, Photoperiod, Polymorphism, Genetic, Signal Transduction, Statistics as Topic, Transcription Factors},
	pages = {6001--6012},
}

Flowering of the reference plant Arabidopsis thaliana is controlled by several signaling pathways, which converge on a small set of genes that function as pathway integrators. We have analyzed the genomic response to one type of floral inductive signal, photoperiod, to dissect the function of several genes transducing this stimulus, including CONSTANS, thought to be the major output of the photoperiod pathway. Comparing the effects of CONSTANS with those of FLOWERING LOCUS T, which integrates inputs from CONSTANS and other floral inductive pathways, we find that expression profiles of shoot apices from plants with mutations in either gene are very similar. In contrast, a mutation in LEAFY, which also acts downstream of CONSTANS, has much more limited effects. Another pathway integrator, SUPPRESSOR OF OVEREXPRESSION OF CO 1, is responsive to acute induction by photoperiod even in the presence of the floral repressor encoded by FLOWERING LOCUS C. We have discovered a large group of potential floral repressors that are down-regulated upon photoperiodic induction. These include two AP2 domain-encoding genes that can repress flowering. The two paralogous genes, SCHLAFMUTZE and SCHNARCHZAPFEN, share a signature with partial complementarity to the miR172 microRNA, whose precursor we show to be induced upon flowering. These and related findings on SPL genes suggest that microRNAs play an important role in the regulation of flowering.

@article{wang_spectral_2003,
	title = {Spectral editing and pattern recognition methods applied to high-resolution magic-angle spinning {H}-1 nuclear magnetic resonance spectroscopy of liver tissues},
	volume = {323},
	issn = {0003-2697},
	doi = {10/bbj5hx},
	abstract = {Principal component analysis (PCA) has been applied to three nuclear magnetic resonance (NMR) spectral editing methods, namely, the Carr-Purcell-Meiboom-Gill spin-echo, diffusion editing, and skyline projection of a two-dimensional J-resolved spectrum, obtained from high-resolution magic-angle spinning NMR spectroscopy of liver tissues, to distinguish between control and hydrazine-treated rats. The effects of the toxin on rat liver biochemistry were directly observed and characterized by depleted levels of liver glycogen, choline, taurine, trimethylamine N-oxide, and glucose and by elevated levels of lipids and alanine. The highly unsaturated omega-3-type fatty acid was observed for the first time in hydrazine-treated rat liver. The contributions of the metabolites to the separation of control from dosed liver tissues varied depending on the type of spectral editing method used. We have shown that subtle changes in the metabolic profiles can be selectively amplified using a metabonomics approach based on the different NMR spectral editing techniques in conjunction with PCA. (C) 2003 Elsevier Inc. All rights reserved.},
	language = {English},
	number = {1},
	journal = {Analytical Biochemistry},
	author = {Wang, Y. L. and Bollard, M. E. and Keun, H. and Antti, H. and Beckonert, O. and Ebbels, T. M. and Lindon, J. C. and Holmes, E. and Tang, H. R. and Nicholson, J. K.},
	month = dec,
	year = {2003},
	note = {Place: San Diego
Publisher: Academic Press Inc Elsevier Science
WOS:000186822700005},
	keywords = {HRMAS H-1 NMR spectroscopy, NMR spectral editing, h-1-nmr spectroscopy, hydrazine, liver tissue, metabonomics, nmr-spectroscopy, principal components analysis, urine},
	pages = {26--32},
}

Principal component analysis (PCA) has been applied to three nuclear magnetic resonance (NMR) spectral editing methods, namely, the Carr-Purcell-Meiboom-Gill spin-echo, diffusion editing, and skyline projection of a two-dimensional J-resolved spectrum, obtained from high-resolution magic-angle spinning NMR spectroscopy of liver tissues, to distinguish between control and hydrazine-treated rats. The effects of the toxin on rat liver biochemistry were directly observed and characterized by depleted levels of liver glycogen, choline, taurine, trimethylamine N-oxide, and glucose and by elevated levels of lipids and alanine. The highly unsaturated omega-3-type fatty acid was observed for the first time in hydrazine-treated rat liver. The contributions of the metabolites to the separation of control from dosed liver tissues varied depending on the type of spectral editing method used. We have shown that subtle changes in the metabolic profiles can be selectively amplified using a metabonomics approach based on the different NMR spectral editing techniques in conjunction with PCA. (C) 2003 Elsevier Inc. All rights reserved.

@article{novak_quantitative_2003,
	title = {Quantitative analysis of cytokinins in plants by liquid chromatography-single-quadrupole mass spectrometry},
	volume = {480},
	issn = {0003-2670},
	doi = {10/fmp3ss},
	abstract = {A sensitive method for the quantitative analysis of all natural isoprenoid cytokinins in plant material by electrospray single-quadrupole mass spectrometry is presented. A baseline chromatographic separation of 20 non-derivatised naturally occurring cytokinins has been developed. Precise analyses of O-glucoside and ribonucleotide fractions were also performed by the high-performance liquid chromatography-mass spectrometry (HPLC-MS) but run separately from the basic cytokinin metabolites. Using post-column splitting, the flux from narrow-bore (2.1 mm, i.d.) reversed-phase liquid chromatography column was simultaneously introduced into the diode array and mass detector. Optimal conditions, including final flow rate, desolvation temperature, desolvation gas flow, capillary and cone voltage for effective ionisation in the electrospray ion source were found. When low cone voltage (20 V) was applied, all studied cytokinins were determined in aqueous methanol as dominant quasi-molecular ions of [M + H](+) with limits of detection ranging between 10 and 50 fmol. For routine analysis a linearity range between 25 (75) fmol and 100 pmol was obtained. Developed liquid chromatography-mass spectrometry (LC-MS) method in selective ion monitoring mode was employed to quantify cytokinin species in tobacco BY-2 suspension culture and poplar leaves (Populus x canadensis Moench, cv Robusta). Purified plant cell (BY-2) and plant tissue (poplar leaves) extracts were obtained by using two different ion-exchange chromatography steps, in combination with immunoaffinity purification using a broad-spectrum monoclonal anti-cytokinin antibody. The antibody strongly recognises the presence of N-6-substituent on purine skeleton and thus does not bind adenine and related compounds. The presence of authentic cytokinins in the extracts quantified by LC-MS was further verified by enzyme-linked immunosorbent assays (ELISAs) with priorLC preparation. The combination of liquid chromatography-single-quadrupole mass spectrometry with immumoaffinity chromatography offers an efficient and elegant method for detection and quantification of cytokinin metabolites. (C) 2003 Elsevier Science B.V. All rights reserved.},
	language = {English},
	number = {2},
	journal = {Analytica Chimica Acta},
	author = {Novak, O. and Tarkowski, P. and Tarkowska, D. and Dolezal, K. and Lenobel, R. and Strnad, M.},
	month = mar,
	year = {2003},
	note = {Place: Amsterdam
Publisher: Elsevier
WOS:000181491200003},
	keywords = {cytokinins, derivatives, derivatization, elisa, gas-chromatography, liquid chromatography-mass spectrometry, metabolism, poplar, quantification, tobacco},
	pages = {207--218},
}

A sensitive method for the quantitative analysis of all natural isoprenoid cytokinins in plant material by electrospray single-quadrupole mass spectrometry is presented. A baseline chromatographic separation of 20 non-derivatised naturally occurring cytokinins has been developed. Precise analyses of O-glucoside and ribonucleotide fractions were also performed by the high-performance liquid chromatography-mass spectrometry (HPLC-MS) but run separately from the basic cytokinin metabolites. Using post-column splitting, the flux from narrow-bore (2.1 mm, i.d.) reversed-phase liquid chromatography column was simultaneously introduced into the diode array and mass detector. Optimal conditions, including final flow rate, desolvation temperature, desolvation gas flow, capillary and cone voltage for effective ionisation in the electrospray ion source were found. When low cone voltage (20 V) was applied, all studied cytokinins were determined in aqueous methanol as dominant quasi-molecular ions of [M + H](+) with limits of detection ranging between 10 and 50 fmol. For routine analysis a linearity range between 25 (75) fmol and 100 pmol was obtained. Developed liquid chromatography-mass spectrometry (LC-MS) method in selective ion monitoring mode was employed to quantify cytokinin species in tobacco BY-2 suspension culture and poplar leaves (Populus x canadensis Moench, cv Robusta). Purified plant cell (BY-2) and plant tissue (poplar leaves) extracts were obtained by using two different ion-exchange chromatography steps, in combination with immunoaffinity purification using a broad-spectrum monoclonal anti-cytokinin antibody. The antibody strongly recognises the presence of N-6-substituent on purine skeleton and thus does not bind adenine and related compounds. The presence of authentic cytokinins in the extracts quantified by LC-MS was further verified by enzyme-linked immunosorbent assays (ELISAs) with priorLC preparation. The combination of liquid chromatography-single-quadrupole mass spectrometry with immumoaffinity chromatography offers an efficient and elegant method for detection and quantification of cytokinin metabolites. (C) 2003 Elsevier Science B.V. All rights reserved.

@article{beckonert_nmr-based_2003,
	title = {{NMR}-based metabonomic toxicity classification: hierarchical cluster analysis and k-nearest-neighbour approaches},
	volume = {490},
	issn = {0003-2670},
	shorttitle = {{NMR}-based metabonomic toxicity classification},
	doi = {10/bq63jx},
	abstract = {The COnsortium for MEtabonomic Toxicology (COMET) project is constructing databases and metabolic models of drug toxicity using ca. 100,000 H-1 NMR spectra of biofluids from animals treated with model toxins. Mathematical models characterising the effects of toxins on endogenous metabolite profiles will enable rapid toxicological screening of potential drug candidates and discovery of novel mechanisms and biomarkers of specific types of toxicity. The metabolic effects and toxicity of 19 model compounds administered to rats in separate studies at toxic (high) and sub-toxic (low) doses were investigated. Urine samples were collected from control and dosed rats at 10 time points over 8 days and were subsequently analysed by 600 MHz H-1 NMR spectroscopy. In order to classify toxicity and to reveal similarities in the response of animals to different toxins, principal component analysis (PCA), hierarchical cluster analysis (HCA) and k-nearest-neighbour (kNN) classification were applied to the data from the high-dose studies to reveal dose and time-related effects. Both PCA and HCA provided valuable overviews of the data, highlighting characteristic metabolic perturbations in the urine spectra between the four groups: controls (C), liver (L) toxins, kidney (K) toxins and other (O) treatments, and revealed further differences between subgroups of liver toxins. kNN analysis of the multivariate data using both leave-one-out (LOO) cross-validation and training and test-set (50:50) classification successfully predicted all the different toxin classes. The four treatment groups (control, liver, kidney and other) were predicted with 86, 85, 91 and 88\% success rate (training/test). In a study-by-study comparison, 81\% of the samples were predicted into the correct toxin study (training/test). This work illustrates the high power and reliability of metabonomic data analysis using H-1 NMR spectroscopy together with chemometric techniques for the exploration and prediction of toxic effects in the rat. (C) 2003 Elsevier Science B.V. All rights reserved.},
	language = {English},
	number = {1-2},
	journal = {Analytica Chimica Acta},
	author = {Beckonert, O. and Bollard, M. E. and Ebbels, T. M. D. and Keun, H. C. and Antti, H. and Holmes, E. and Lindon, J. C. and Nicholson, J. K.},
	month = aug,
	year = {2003},
	note = {Place: Amsterdam
Publisher: Elsevier Science Bv
WOS:000185047900002},
	keywords = {biofluid, h-1-nmr spectroscopy, hierarchical cluster analysis, k-nearest-neighbour, kidney, metabonomics, mouse, nmr, partial-least, pattern-recognition, principal component analysis, squares discriminant   analysis, toxicity prediction, urine},
	pages = {3--15},
}

The COnsortium for MEtabonomic Toxicology (COMET) project is constructing databases and metabolic models of drug toxicity using ca. 100,000 H-1 NMR spectra of biofluids from animals treated with model toxins. Mathematical models characterising the effects of toxins on endogenous metabolite profiles will enable rapid toxicological screening of potential drug candidates and discovery of novel mechanisms and biomarkers of specific types of toxicity. The metabolic effects and toxicity of 19 model compounds administered to rats in separate studies at toxic (high) and sub-toxic (low) doses were investigated. Urine samples were collected from control and dosed rats at 10 time points over 8 days and were subsequently analysed by 600 MHz H-1 NMR spectroscopy. In order to classify toxicity and to reveal similarities in the response of animals to different toxins, principal component analysis (PCA), hierarchical cluster analysis (HCA) and k-nearest-neighbour (kNN) classification were applied to the data from the high-dose studies to reveal dose and time-related effects. Both PCA and HCA provided valuable overviews of the data, highlighting characteristic metabolic perturbations in the urine spectra between the four groups: controls (C), liver (L) toxins, kidney (K) toxins and other (O) treatments, and revealed further differences between subgroups of liver toxins. kNN analysis of the multivariate data using both leave-one-out (LOO) cross-validation and training and test-set (50:50) classification successfully predicted all the different toxin classes. The four treatment groups (control, liver, kidney and other) were predicted with 86, 85, 91 and 88% success rate (training/test). In a study-by-study comparison, 81% of the samples were predicted into the correct toxin study (training/test). This work illustrates the high power and reliability of metabonomic data analysis using H-1 NMR spectroscopy together with chemometric techniques for the exploration and prediction of toxic effects in the rat. (C) 2003 Elsevier Science B.V. All rights reserved.

@article{gowda_spines_2003,
	title = {Spines as a mechanical defence: the effects of fertiliser treatment on juvenile {Acacia} tortilis plants},
	volume = {24},
	issn = {1146-609X},
	shorttitle = {Spines as a mechanical defence},
	doi = {10/c5c6n4},
	abstract = {Using growth of different tissues in Acacia tortilis as a model, we tested current hypotheses on how nutrients affect mechanical plant defence. In a greenhouse experiment we applied a balanced commercial fertiliser (NPK) at three treatment levels to juvenile potted Acacias. As expected, plants increased in size with nutrient addition. More importantly, however, the relative mass of long spines increased significantly more than other structural components (leaves and twigs). This effect is not predicted by current nutrient availability hypotheses; which suggest either equal or proportionally lower investment in mechanical defence with increasing nutrient availability. Our results suggest that investment in spine size is nutrient limited in Acacia tortilis. It is commonly observed that the risk of damage by herbivores is highest on plants growing in nutrient-rich soils. If spines act as an effective form of anti-herbivore protection, then these plants might be expected to increase their production of physical defences (long spines) under such circumstances. Plants growing under higher nutrient conditions might therefore invest more in constitutive defences. These changes in allocation pattern are consistent with the increase in production of long spines, which are also induced by browsing. (C) 2003 Editions scientifiques et medicales Elsevier SAS. All rights reserved.},
	language = {English},
	number = {1},
	journal = {Acta Oecologica-International Journal of Ecology},
	author = {Gowda, J. H. and Albrectsen, B. R. and Ball, J. P. and Sjoberg, M. and Palo, R. T.},
	month = mar,
	year = {2003},
	note = {Place: Paris
Publisher: Gauthier-Villars/Editions Elsevier
WOS:000182473100001},
	keywords = {balance, carbon-nutrient balance, growth pattern, herbivory, mammalian herbivores, nitrogen fertilisation, nutrient addition, plant-herbivore interactions, resistance, resource availability, thorns, trees},
	pages = {1--4},
}

Using growth of different tissues in Acacia tortilis as a model, we tested current hypotheses on how nutrients affect mechanical plant defence. In a greenhouse experiment we applied a balanced commercial fertiliser (NPK) at three treatment levels to juvenile potted Acacias. As expected, plants increased in size with nutrient addition. More importantly, however, the relative mass of long spines increased significantly more than other structural components (leaves and twigs). This effect is not predicted by current nutrient availability hypotheses; which suggest either equal or proportionally lower investment in mechanical defence with increasing nutrient availability. Our results suggest that investment in spine size is nutrient limited in Acacia tortilis. It is commonly observed that the risk of damage by herbivores is highest on plants growing in nutrient-rich soils. If spines act as an effective form of anti-herbivore protection, then these plants might be expected to increase their production of physical defences (long spines) under such circumstances. Plants growing under higher nutrient conditions might therefore invest more in constitutive defences. These changes in allocation pattern are consistent with the increase in production of long spines, which are also induced by browsing. (C) 2003 Editions scientifiques et medicales Elsevier SAS. All rights reserved.

@article{schumann_athpex10_2003,
	title = {{AthPEX10}, a nuclear gene essential for peroxisome and storage organelle formation during {Arabidopsis} embryogenesis},
	volume = {100},
	issn = {0027-8424},
	doi = {10/dzx29q},
	abstract = {In yeasts and mammals, PEX10 encodes an integral membrane protein with a C3HC4 RING finger motif in its C-terminal domain and is required for peroxisome biogenesis and matrix protein import. In humans, its dysfunction in peroxisome biogenesis leads to severe Zellweger Syndrome and infantile Refsum disease. Here we show that dysfunction of a homologous gene in Arabidopsis leads to lethality at the heart stage of embryogenesis, impairing the biogenesis of peroxisomes, lipid bodies, and protein bodies. In a T-DNA insertion mutant disrupting the fourth exon of the AthPEX10 gene, ultrastructural analyses fail to detect peroxisomes characteristic for wild-type embryogenesis. Storage triacyl glycerides are not assembled into lipid bodies (oil bodies; oleosomes) surrounded by the phospholipid-protein monolayer membrane. Instead, the dysfunctional monolayer membranes, which derive from the bilayer membrane of the endoplasmic reticulum, accumulate in the cytosol. Concomitantly the transfer of the storage proteins from their site of synthesis at the endoplasmic reticulum to the vacuoles is disturbed. The mutant can be rescued by transformation with wild-type AthPEX10 cDNA. Transformants of wild-type Hansenula polymorpha cells with the AthPEX10 cDNA did produce the encoded protein without targeting it to peroxisomes. Additionally, the cDNA could not complement a Hansenula pex10 mutant unable to form peroxisomes. The ultrastructural knockout phenotype of AthPEX10p suggests that this protein in Arabidopsis is essential for peroxisome, oleosome, and protein transport vesicle formation.},
	language = {eng},
	number = {16},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Schumann, Uwe and Wanner, Gerhard and Veenhuis, Marten and Schmid, Markus and Gietl, Christine},
	month = aug,
	year = {2003},
	pmid = {12883010},
	pmcid = {PMC170968},
	keywords = {Amino Acid Sequence, Arabidopsis, Arabidopsis Proteins, Carrier Proteins, Cell Membrane, Cell Nucleus, Cytosol, DNA, Complementary, Endoplasmic Reticulum, Exons, Lipid Bilayers, Lipid Metabolism, Membrane Transport Proteins, Microscopy, Electron, Molecular Sequence Data, Mutation, Organelles, Peroxins, Peroxisomes, Phospholipids, Plants, Genetically Modified, Protein Structure, Tertiary, Receptors, Cytoplasmic and Nuclear},
	pages = {9626--9631},
}

In yeasts and mammals, PEX10 encodes an integral membrane protein with a C3HC4 RING finger motif in its C-terminal domain and is required for peroxisome biogenesis and matrix protein import. In humans, its dysfunction in peroxisome biogenesis leads to severe Zellweger Syndrome and infantile Refsum disease. Here we show that dysfunction of a homologous gene in Arabidopsis leads to lethality at the heart stage of embryogenesis, impairing the biogenesis of peroxisomes, lipid bodies, and protein bodies. In a T-DNA insertion mutant disrupting the fourth exon of the AthPEX10 gene, ultrastructural analyses fail to detect peroxisomes characteristic for wild-type embryogenesis. Storage triacyl glycerides are not assembled into lipid bodies (oil bodies; oleosomes) surrounded by the phospholipid-protein monolayer membrane. Instead, the dysfunctional monolayer membranes, which derive from the bilayer membrane of the endoplasmic reticulum, accumulate in the cytosol. Concomitantly the transfer of the storage proteins from their site of synthesis at the endoplasmic reticulum to the vacuoles is disturbed. The mutant can be rescued by transformation with wild-type AthPEX10 cDNA. Transformants of wild-type Hansenula polymorpha cells with the AthPEX10 cDNA did produce the encoded protein without targeting it to peroxisomes. Additionally, the cDNA could not complement a Hansenula pex10 mutant unable to form peroxisomes. The ultrastructural knockout phenotype of AthPEX10p suggests that this protein in Arabidopsis is essential for peroxisome, oleosome, and protein transport vesicle formation.

@article{oquist_photosynthesis_2003,
	title = {Photosynthesis of {Overwintering} {Evergreen} {Plants}},
	volume = {54},
	issn = {1543-5008},
	url = {https://www.annualreviews.org/doi/10.1146/annurev.arplant.54.072402.115741},
	doi = {10/fpw6m5},
	abstract = {In this review we focus on photosynthetic behavior of overwintering evergreens with an emphasis on both the acclimative responses of photosynthesis to cold and the winter behavior of photosynthesis in conifers. Photosynthetic acclimation is discussed in terms of the requirement for a balance between the energy absorbed through largely temperature-insensitive photochemical processes and the energy used for temperature-sensitive biochemical processes and growth. Cold acclimation transforms the xanthophyll-mediated nonphotochemical antenna quenching of absorbed light from a short-term dynamic response to a long-term sustained quenching for the whole winter period. This acclimative response helps protect the evergreen foliage from photooxidative damage during the winter when photosynthesis is restricted or prevented by low temperatures. Although the molecular mechanisms behind the sustained winter excitation quenching are largely unknown, it does involve major alterations in the organization and composition of the photosystem II antenna. In addition, photosystem I may play an important role in overwintering evergreens not only by quenching absorbed light photochemically via its support of cyclic electron transport at low temperatures, but also by nonphotochemical quenching of absorbed light irrespective of temperature. The possible role of photosystem II reaction centers in nonphotochemical quenching of absorbed energy in overwintering evergreens is also discussed. Processes like chlororespiration and cyclic electron transport may also be important for maintaining the functional integrity of the photosynthetic apparatus of overwintering evergreens both during periods of thawing in winter and during recovery from winter stress in spring. We suggest that the photosynthetic acclimation responses of overwintering evergreens represent specific evolutionary adaptations for plant species that invest in the long-term maintenance of leaf structure in cold climatic zones as exemplified by the boreal forests of the Northern Hemisphere.},
	number = {1},
	urldate = {2021-07-05},
	journal = {Annual Review of Plant Biology},
	author = {Öquist, Gunnar and Huner, Norman P.A.},
	month = jun,
	year = {2003},
	note = {Publisher: Annual Reviews},
	pages = {329--355},
}

In this review we focus on photosynthetic behavior of overwintering evergreens with an emphasis on both the acclimative responses of photosynthesis to cold and the winter behavior of photosynthesis in conifers. Photosynthetic acclimation is discussed in terms of the requirement for a balance between the energy absorbed through largely temperature-insensitive photochemical processes and the energy used for temperature-sensitive biochemical processes and growth. Cold acclimation transforms the xanthophyll-mediated nonphotochemical antenna quenching of absorbed light from a short-term dynamic response to a long-term sustained quenching for the whole winter period. This acclimative response helps protect the evergreen foliage from photooxidative damage during the winter when photosynthesis is restricted or prevented by low temperatures. Although the molecular mechanisms behind the sustained winter excitation quenching are largely unknown, it does involve major alterations in the organization and composition of the photosystem II antenna. In addition, photosystem I may play an important role in overwintering evergreens not only by quenching absorbed light photochemically via its support of cyclic electron transport at low temperatures, but also by nonphotochemical quenching of absorbed light irrespective of temperature. The possible role of photosystem II reaction centers in nonphotochemical quenching of absorbed energy in overwintering evergreens is also discussed. Processes like chlororespiration and cyclic electron transport may also be important for maintaining the functional integrity of the photosynthetic apparatus of overwintering evergreens both during periods of thawing in winter and during recovery from winter stress in spring. We suggest that the photosynthetic acclimation responses of overwintering evergreens represent specific evolutionary adaptations for plant species that invest in the long-term maintenance of leaf structure in cold climatic zones as exemplified by the boreal forests of the Northern Hemisphere.

@article{bhalerao_out_2003,
	title = {Out of the woods: forest biotechnology enters the genomic era},
	volume = {14},
	issn = {0958-1669},
	shorttitle = {Out of the woods},
	url = {https://www.sciencedirect.com/science/article/pii/S0958166903000296},
	doi = {10/fp8hj9},
	abstract = {Trees represent a unique life form of upmost importance for mankind, as these organisms have developed a perennial lifestyle that produces the majority of terrestrial biomass. The difference between trees and annual plants is one of the main arguments behind the effort to sequence the entire genome of the poplar tree. This initiative is being backed up with a full-scale functional genomics effort on trees that will set a completely new agenda for forest research.},
	language = {en},
	number = {2},
	urldate = {2021-07-05},
	journal = {Current Opinion in Biotechnology},
	author = {Bhalerao, Rishikesh and Nilsson, Ove and Sandberg, Goran},
	month = apr,
	year = {2003},
	pages = {206--213},
}

Trees represent a unique life form of upmost importance for mankind, as these organisms have developed a perennial lifestyle that produces the majority of terrestrial biomass. The difference between trees and annual plants is one of the main arguments behind the effort to sequence the entire genome of the poplar tree. This initiative is being backed up with a full-scale functional genomics effort on trees that will set a completely new agenda for forest research.

@article{igamberdiev_regulation_2003,
	title = {Regulation of {NAD}- and {NADP}-dependent isocitrate dehydrogenases by reduction levels of pyridine nucleotides in mitochondria and cytosol of pea leaves},
	volume = {1606},
	issn = {0005-2728},
	doi = {10/frnr6s},
	abstract = {Regulation of NAD- and NADP-dependent isocitrate dehydrogenases (NAD-ICDH, EC 1.1.1.41, and NADP-ICDH, EC 1.1.1.42) by the level of reduced and oxidized pyridine nucleotides has been investigated in pea (Pisum sativum L.) leaves. The affinities of mitochondrial and cytosolic ICDH enzymes to substrates and inhibitors were determined on partially purified preparations in forward and reverse directions. From the kinetic data, it follows that NADP(+)- and NAD+-dependent isocitrate dehydrogenases in mitochondria represent a system strongly responding to the intramitochondrial NADPH and NADH levels. The NADPH, NADP(+), NADH and NAD(+) concentrations were determined by subcellular fractionation of pea leaf protoplasts using membrane filtration in mitochondria and cytosol in darkness and in the light under saturating and limiting CO2 Conditions. The cytosolic NADPH/NADP ratio was about I and almost constant both in darkness and in the light. In mitochondria, the NADPH/NADP ratio was low in darkness (0.2) and increased in the light, reaching 3 in limiting CO2 conditions compared to I in saturating CO2. At high reduction levels of NADP and NAD observed at limiting CO2 in the light, i.e. when photorespiratory glycine is the main mitochondrial substrate, isocitrate oxidation in mitochondria will be suppressed and citrate will be transported to the cytosol ('citrate valve'), where the cytosolic NADP-ICDH supplies 2-oxoglutarate for the photorespiratory ammonia refixation. (C) 2003 Elsevier B.V. All rights reserved.},
	language = {English},
	number = {1-3},
	journal = {Biochimica Et Biophysica Acta-Bioenergetics},
	author = {Igamberdiev, A. U. and Gardestrom, P.},
	month = sep,
	year = {2003},
	note = {Place: Amsterdam
Publisher: Elsevier Science Bv
WOS:000185593100009},
	keywords = {NAD(P)H/NAD(P) ratio, alternative oxidase, ammonia refixation, barley leaf protoplasts, citrate valve, glycine decarboxylase, isocitrate dehydrogenase, metabolite concentrations, photorespiration, plant mitochondria, plant-mitochondria, purification, rapid   fractionation, redox transfer, subcellular volumes, transhydrogenase},
	pages = {117--125},
}

Regulation of NAD- and NADP-dependent isocitrate dehydrogenases (NAD-ICDH, EC 1.1.1.41, and NADP-ICDH, EC 1.1.1.42) by the level of reduced and oxidized pyridine nucleotides has been investigated in pea (Pisum sativum L.) leaves. The affinities of mitochondrial and cytosolic ICDH enzymes to substrates and inhibitors were determined on partially purified preparations in forward and reverse directions. From the kinetic data, it follows that NADP(+)- and NAD+-dependent isocitrate dehydrogenases in mitochondria represent a system strongly responding to the intramitochondrial NADPH and NADH levels. The NADPH, NADP(+), NADH and NAD(+) concentrations were determined by subcellular fractionation of pea leaf protoplasts using membrane filtration in mitochondria and cytosol in darkness and in the light under saturating and limiting CO2 Conditions. The cytosolic NADPH/NADP ratio was about I and almost constant both in darkness and in the light. In mitochondria, the NADPH/NADP ratio was low in darkness (0.2) and increased in the light, reaching 3 in limiting CO2 conditions compared to I in saturating CO2. At high reduction levels of NADP and NAD observed at limiting CO2 in the light, i.e. when photorespiratory glycine is the main mitochondrial substrate, isocitrate oxidation in mitochondria will be suppressed and citrate will be transported to the cytosol ('citrate valve'), where the cytosolic NADP-ICDH supplies 2-oxoglutarate for the photorespiratory ammonia refixation. (C) 2003 Elsevier B.V. All rights reserved.

@article{borodich_segregation_2003,
	title = {Segregation of the photosystems in thylakoids depends on their size},
	volume = {1606},
	issn = {0005-2728},
	doi = {10/bd6ctt},
	abstract = {Lateral segregation of two types of photosystems in thylakoid membranes of green plants is one of the key factors that provide the stability and fine-tuning of the light quanta supply by pigment proteins and non-cyclic electron transport. Due to this specific feature of the membrane structural organization, the photosynthetic units function in the green plants with optimal performance. In this report a mesoscopic theory is outlined to address the physical aspects of segregation phenomenon. Results of theoretical studies and computer simulations suggest that charge mismatch and the size difference between two photosystems in grana are most responsible for their lateral segregation, which is driven by the screened electrostatic and lipid-induced interactions. Comparative simulations of photosystems of different sizes show the crucial dependence of their ordering on a geometrical parameter. It seems that the size effect alone may prevent photosystems from segregated arrangement in cyanobacterial thylakoids. (C) 2003 Elsevier B.V. All rights reserved.},
	language = {English},
	number = {1-3},
	journal = {Biochimica Et Biophysica Acta-Bioenergetics},
	author = {Borodich, A. and Rojdestvenski, I. and Cottam, M. and Oquist, G.},
	month = sep,
	year = {2003},
	note = {Place: Amsterdam
Publisher: Elsevier Science Bv
WOS:000185593100005},
	keywords = {Brownian dynamics, angstrom   resolution, cation-induced phenomenon, chlorophyll   fluorescence, colloidal dispersions, depletion interactions, grana stacking, green   plants, integral membrane-protein, light-harvesting complex, lipid-membranes, protein-protein interaction, segregation of photosystem, size-dependent lipid-induced potential, surface-charges, thylakoid},
	pages = {73--82},
}

Lateral segregation of two types of photosystems in thylakoid membranes of green plants is one of the key factors that provide the stability and fine-tuning of the light quanta supply by pigment proteins and non-cyclic electron transport. Due to this specific feature of the membrane structural organization, the photosynthetic units function in the green plants with optimal performance. In this report a mesoscopic theory is outlined to address the physical aspects of segregation phenomenon. Results of theoretical studies and computer simulations suggest that charge mismatch and the size difference between two photosystems in grana are most responsible for their lateral segregation, which is driven by the screened electrostatic and lipid-induced interactions. Comparative simulations of photosystems of different sizes show the crucial dependence of their ordering on a geometrical parameter. It seems that the size effect alone may prevent photosystems from segregated arrangement in cyanobacterial thylakoids. (C) 2003 Elsevier B.V. All rights reserved.

@article{yakushevska_structure_2003,
	title = {The {Structure} of {Photosystem} {II} in {Arabidopsis}: {Localization} of the {CP26} and {CP29} {Antenna} {Complexes}},
	volume = {42},
	issn = {0006-2960},
	shorttitle = {The {Structure} of {Photosystem} {II} in {Arabidopsis}},
	url = {https://doi.org/10.1021/bi027109z},
	doi = {10/c63zsj},
	abstract = {A genetic approach has been adopted to investigate the organization of the light-harvesting proteins in the photosystem II (PSII) complex in plants. PSII membrane fragments were prepared from wild-type Arabidopis thaliana and plants expressing antisense constructs to Lhcb4 and Lhcb5 genes, lacking CP29 and CP26, respectively (Andersson et al. (2001) Plant Cell 13, 1193−1204). Ordered PS II arrays and PS II supercomplexes were isolated from the membranes of plants lacking CP26 but could not be prepared from those lacking CP29. Membranes and supercomplexes lacking CP26 were less stable than those prepared from the wild type. Transmission electron microscopy aided by single-particle image analysis was applied to the ordered arrays and the isolated PSII complexes. The difference between the images obtained from wild type and antisense plants showed the location of CP26 to be near CP43 and one of the light-harvesting complex trimers. Therefore, the location of the CP26 within PSII was directly established for the first time, and the location of the CP29 complex was determined by elimination. Alterations in the packing of the PSII complexes in the thylakoid membrane also resulted from the absence of CP26. The minor light-harvesting complexes each have a unique location and important roles in the stabilization of the oligomeric PSII structure.},
	number = {3},
	urldate = {2021-07-05},
	journal = {Biochemistry},
	author = {Yakushevska, Alevtyna E. and Keegstra, Wilko and Boekema, Egbert J. and Dekker, Jan P. and Andersson, Jenny and Jansson, Stefan and Ruban, Alexander V. and Horton, Peter},
	month = jan,
	year = {2003},
	note = {Publisher: American Chemical Society},
	pages = {608--613},
}

A genetic approach has been adopted to investigate the organization of the light-harvesting proteins in the photosystem II (PSII) complex in plants. PSII membrane fragments were prepared from wild-type Arabidopis thaliana and plants expressing antisense constructs to Lhcb4 and Lhcb5 genes, lacking CP29 and CP26, respectively (Andersson et al. (2001) Plant Cell 13, 1193−1204). Ordered PS II arrays and PS II supercomplexes were isolated from the membranes of plants lacking CP26 but could not be prepared from those lacking CP29. Membranes and supercomplexes lacking CP26 were less stable than those prepared from the wild type. Transmission electron microscopy aided by single-particle image analysis was applied to the ordered arrays and the isolated PSII complexes. The difference between the images obtained from wild type and antisense plants showed the location of CP26 to be near CP43 and one of the light-harvesting complex trimers. Therefore, the location of the CP26 within PSII was directly established for the first time, and the location of the CP29 complex was determined by elimination. Alterations in the packing of the PSII complexes in the thylakoid membrane also resulted from the absence of CP26. The minor light-harvesting complexes each have a unique location and important roles in the stabilization of the oligomeric PSII structure.

@article{miszalski_cam_2003,
	title = {{CAM} induction and oxidative stress in common ice plant},
	volume = {37},
	issn = {1071-5762},
	language = {English},
	journal = {Free Radical Research},
	author = {Miszalski, Z. and Slesak, I. and Libik, M. and Surowka, E. and Pater, B. and Haag-Kerwer, A. and Gawronska, K. and Karpinski, S. and Niewiadomska, E.},
	year = {2003},
	note = {Place: Abingdon
Publisher: Taylor \& Francis Ltd
WOS:000185828100067},
	keywords = {⛔ No DOI found},
	pages = {28--29},
}

@article{ahlfors_hormonal_2003,
	title = {Hormonal interactions and {ROS}-dependent cell death},
	volume = {37},
	issn = {1071-5762},
	language = {English},
	journal = {Free Radical Research},
	author = {Ahlfors, R. and Keinanen, M. and Kollist, H. and Kuusela, T. and Lang, S. and Overmyer, K. and Pulkkinen, P. and Tuominen, H. and Kangasjarvi, J.},
	year = {2003},
	note = {Place: Abingdon
Publisher: Taylor \& Francis Ltd
WOS:000185828100016},
	keywords = {⛔ No DOI found},
	pages = {6--7},
}

@article{witzell_plant-part_2003,
	title = {Plant-part specific and temporal variation in phenolic compounds of boreal bilberry ({Vaccinium} myrtillus) plants},
	volume = {31},
	issn = {0305-1978},
	doi = {10/cfpzvc},
	abstract = {Leaves and stems of bilberry were analysed for phenolic metabolites using a simple method of extraction and HPLC analysis. Hydroxycinnamic acid derivatives (HCAs) and flavonoids were identified on the basis of their UV-spectra. Temporal fluctuations in the levels of selected phenolic compounds were followed during the growth season of 2000. Qualitative and quantitative differences were detected in phenolic profiles between leaf and stem tissues. The most abundant peak in. leaf samples was tentatively identified as chlorogenic acid (5-O-caffeoylquinic acid). In stems, this compound was found at much lower levels than in leaves and an unidentified p-coumaric acid derivative dominated the phenolic profile. The most abundant flavonols in leaves and stems were quercetin derivatives. The total sum of methanol-soluble phenolics was generally higher in leaves than in stems. The concentrations of some alkaline hydrolysis products were higher in stems than in leaves, indicating that a larger part of the phenolic pool was incorporated into lignified cell walls in the stems. Individual phenolic compounds differed in their seasonal fluctuation patterns. It is suggested that the observed plant-part specific and within-seasonal variation may influence the ecological interactions between bilberry and its natural enemies. (C) 2002 Elsevier Science Ltd. All rights reserved.},
	language = {English},
	number = {2},
	journal = {Biochemical Systematics and Ecology},
	author = {Witzell, J. and Gref, R. and Nasholm, T.},
	month = feb,
	year = {2003},
	note = {Place: Oxford
Publisher: Pergamon-Elsevier Science Ltd
WOS:000180726900001},
	keywords = {Vaccinium myrtillus, acids, berries, chemical defence, disease resistance, extracts, flavonoids, glycosides, hplc, identification, metabolism, mycorrhizal fungi, phenolic. acids, vegetation},
	pages = {115--127},
}

Leaves and stems of bilberry were analysed for phenolic metabolites using a simple method of extraction and HPLC analysis. Hydroxycinnamic acid derivatives (HCAs) and flavonoids were identified on the basis of their UV-spectra. Temporal fluctuations in the levels of selected phenolic compounds were followed during the growth season of 2000. Qualitative and quantitative differences were detected in phenolic profiles between leaf and stem tissues. The most abundant peak in. leaf samples was tentatively identified as chlorogenic acid (5-O-caffeoylquinic acid). In stems, this compound was found at much lower levels than in leaves and an unidentified p-coumaric acid derivative dominated the phenolic profile. The most abundant flavonols in leaves and stems were quercetin derivatives. The total sum of methanol-soluble phenolics was generally higher in leaves than in stems. The concentrations of some alkaline hydrolysis products were higher in stems than in leaves, indicating that a larger part of the phenolic pool was incorporated into lignified cell walls in the stems. Individual phenolic compounds differed in their seasonal fluctuation patterns. It is suggested that the observed plant-part specific and within-seasonal variation may influence the ecological interactions between bilberry and its natural enemies. (C) 2002 Elsevier Science Ltd. All rights reserved.

@article{shutova_comparative_2003,
	title = {Comparative studies on the properties of the extrinsic manganese-stabilizing protein from higher plants and of a synthetic peptide of its {C}-terminus},
	volume = {1604},
	issn = {0005-2728},
	doi = {10/cx7k4m},
	abstract = {The present study describes a comparative analysis on the fluorescence properties of the manganese-stabilizing protein (MSP), a synthetic peptide corresponding to its C terminus and a 7:1 (molar ratio) mixture of N-acetyl-tyrosine and N-acetyl-tryptophan, respectively, together with reconstitution experiments of oxygen evolution in MSP-depleted photosystem II (PS II) membrane fragments. It is found: (i) at neutral pH, the fluorescence from Trp(241) is strongly diminished in MSP solutions, whereas it highly dominates the overall emission from the C-terminus peptide; (ii) at alkaline pH, the emission of Tyr and Trp is quenched in both, MSP and C-terminus peptide, with increasing pH but the decline curve is shifted by about two pH units towards the alkaline region in MSP; (iii) a drastically different pattern emerges in the 7:1 mixture where the Trp emission even slightly increases at high pH; (iv) the anisotropy of the fluorescence emission is wavelength-independent (310-395 nm) and indicative of one emitter type (Trp) in the C-terminus peptide and of two emitter types (Tyr, Trp) in MSP; and (v) in MSP-depleted PS H membrane fragments the oxygen evolution is restored (up to 85\% of untreated control) by rebinding of MSP but not by the C-terminus peptide, however, the presence of the latter diminishes the restoration effect of MSP. A quenching mechanism of Trp fluorescence by a next neighbored tyrosinate in the peptide chain is proposed and the relevance of the C terminus of MSP briefly discussed. (C) 2003 Elsevier Science B.V. All rights reserved.},
	language = {English},
	number = {2},
	journal = {Biochimica Et Biophysica Acta-Bioenergetics},
	author = {Shutova, T. and Villarejo, A. and Zietz, B. and Klimov, V. and Gillbro, T. and Samuelsson, G. and Renger, G.},
	month = jun,
	year = {2003},
	note = {Place: Amsterdam
Publisher: Elsevier Science Bv
WOS:000183222900005},
	keywords = {33 kda, 33-kda protein, C-terminus synthetic peptide, chlamydomonas-reinhardtii, molten globule, msp, oxygen-evolving complex, photosystem II, proton-transfer, ps-ii, reconstitution of   oxygen evolution, spinach photosystem-ii, synechococcus-elongatus, tryptophan fluorescence, tyrosine and tryptophan fluorescence},
	pages = {95--104},
}

The present study describes a comparative analysis on the fluorescence properties of the manganese-stabilizing protein (MSP), a synthetic peptide corresponding to its C terminus and a 7:1 (molar ratio) mixture of N-acetyl-tyrosine and N-acetyl-tryptophan, respectively, together with reconstitution experiments of oxygen evolution in MSP-depleted photosystem II (PS II) membrane fragments. It is found: (i) at neutral pH, the fluorescence from Trp(241) is strongly diminished in MSP solutions, whereas it highly dominates the overall emission from the C-terminus peptide; (ii) at alkaline pH, the emission of Tyr and Trp is quenched in both, MSP and C-terminus peptide, with increasing pH but the decline curve is shifted by about two pH units towards the alkaline region in MSP; (iii) a drastically different pattern emerges in the 7:1 mixture where the Trp emission even slightly increases at high pH; (iv) the anisotropy of the fluorescence emission is wavelength-independent (310-395 nm) and indicative of one emitter type (Trp) in the C-terminus peptide and of two emitter types (Tyr, Trp) in MSP; and (v) in MSP-depleted PS H membrane fragments the oxygen evolution is restored (up to 85% of untreated control) by rebinding of MSP but not by the C-terminus peptide, however, the presence of the latter diminishes the restoration effect of MSP. A quenching mechanism of Trp fluorescence by a next neighbored tyrosinate in the peptide chain is proposed and the relevance of the C terminus of MSP briefly discussed. (C) 2003 Elsevier Science B.V. All rights reserved.

@article{igamberdiev_membrane_2003,
	title = {Membrane potential, adenylate levels and {Mg2}+ are interconnected via adenylate kinase equilibrium in plant cells},
	volume = {1607},
	issn = {0005-2728},
	doi = {10/b97n7t},
	abstract = {Concentrations of adenylate species and free magnesium (Mg2+) within cells are mediated by the equilibrium governed by adenylate kinase (AK), the enzyme abundant in plants in chloroplast stroma and intermembrane spaces of chloroplasts and mitochondria. Ratios of free and Mg-bound adenylates (linked to the values of [Mg2+] established under AK equilibrium) can be rationalized in terms of the overall dependence of concentrations of Mg2+ and free and Mg-bound adenylates, as well as electric potential values across the inner membranes of mitochondria and chloroplasts. The potential across the inner mitochondrial membrane, by driving adenylate translocators, equilibrates free adenylates across the inner membrane according to the Nernst equation and contributes to the ATP(total)/ADP(total) ratio in the cytosol. The ratio affects the exchange of free adenylates with chloroplasts and this, in turn, influences the value of potential across the inner chloroplast membrane. From measurements of subcellular ATP(total)/ADP(total) ratios, we suggest a method of estimating the values of potential across inner membranes of mitochondria and chloroplasts in vivo, which allows a comparison of the operation of these organelles under different physiological conditions. We discuss also how the equilibration of adenylates by AK drives adenylate transport across membranes, and establishes [Mg2+] in the cytosol and chloroplast stroma, maintaining the rates of photosynthesis and respiration. This provides a tool for metabolomic research, by which the determined concentrations of adenylate species could be used for computation of essential metabolic parameters in the cell and in subcellular compartments. (C) 2003 Elsevier B.V. All rights reserved.},
	language = {English},
	number = {2-3},
	journal = {Biochimica Et Biophysica Acta-Bioenergetics},
	author = {Igamberdiev, A. U. and Kleczkowski, L. A.},
	month = dec,
	year = {2003},
	note = {Place: Amsterdam
Publisher: Elsevier Science Bv
WOS:000187241500005},
	keywords = {adenylate kinase, adp, atp/adp ratios, barley, chloroplast, cytosol, free magnesium, hordeum-vulgare protoplasts, intermembrane space, leaf   protoplasts, membrane potential, metabolomics, mitochondrial electron-transport, mitochondrion, photosynthesis, spinach-chloroplasts},
	pages = {111--119},
}

Concentrations of adenylate species and free magnesium (Mg2+) within cells are mediated by the equilibrium governed by adenylate kinase (AK), the enzyme abundant in plants in chloroplast stroma and intermembrane spaces of chloroplasts and mitochondria. Ratios of free and Mg-bound adenylates (linked to the values of [Mg2+] established under AK equilibrium) can be rationalized in terms of the overall dependence of concentrations of Mg2+ and free and Mg-bound adenylates, as well as electric potential values across the inner membranes of mitochondria and chloroplasts. The potential across the inner mitochondrial membrane, by driving adenylate translocators, equilibrates free adenylates across the inner membrane according to the Nernst equation and contributes to the ATP(total)/ADP(total) ratio in the cytosol. The ratio affects the exchange of free adenylates with chloroplasts and this, in turn, influences the value of potential across the inner chloroplast membrane. From measurements of subcellular ATP(total)/ADP(total) ratios, we suggest a method of estimating the values of potential across inner membranes of mitochondria and chloroplasts in vivo, which allows a comparison of the operation of these organelles under different physiological conditions. We discuss also how the equilibration of adenylates by AK drives adenylate transport across membranes, and establishes [Mg2+] in the cytosol and chloroplast stroma, maintaining the rates of photosynthesis and respiration. This provides a tool for metabolomic research, by which the determined concentrations of adenylate species could be used for computation of essential metabolic parameters in the cell and in subcellular compartments. (C) 2003 Elsevier B.V. All rights reserved.

@article{kang_estimation_2003,
	title = {Estimation of fertility variation in forest tree populations},
	volume = {76},
	issn = {0015-752X},
	doi = {10/fpp6vs},
	abstract = {Forecasts of the effects of tree breeding and conservation operations require information on fertility variation. In most cases, however, the information does not exist or is highly unreliable. In this paper, published studies on flowering abundance, fruit and seed production were used to estimate and review fertility variation in 99 stands and 36 seed orchards. Fertility variations were described by the coefficient of variation (CV) and the sibling coefficient (Psi). Both measures express how parents differ in fertility; the former focuses on the variance of fertility among individuals while the later focuses on probabilistic aspects. As expected, fertility varied considerably within and among populations. Only similar to15 per cent in both stands and seed orchards indicated small variations in fertility. Fertility variation was higher in stands than in seed orchards. Differences in fertility were usually higher during poor flowering years and in young populations. In seed orchards, fertility differences were slightly larger on the male side than on the female side. For fertility predictions concerning objects that are neither juvenile nor characterized by poor flowering, we suggest, for seed orchards, a CV equal to 100 per cent with Psi equal to 2 and, for stands, a CV equal to 140 per cent with Psi equal to 3.},
	language = {English},
	number = {3},
	journal = {Forestry},
	author = {Kang, K. S. and Bila, A. D. and Harju, A. M. and Lindgren, D.},
	month = jun,
	year = {2003},
	note = {Place: Oxford
Publisher: Oxford Univ Press
WOS:000183835100005},
	keywords = {clonal seed orchard, cone, genetic diversity, management, number, picea-abies, pinus-sylvestris, plantation},
	pages = {329--344},
}

Forecasts of the effects of tree breeding and conservation operations require information on fertility variation. In most cases, however, the information does not exist or is highly unreliable. In this paper, published studies on flowering abundance, fruit and seed production were used to estimate and review fertility variation in 99 stands and 36 seed orchards. Fertility variations were described by the coefficient of variation (CV) and the sibling coefficient (Psi). Both measures express how parents differ in fertility; the former focuses on the variance of fertility among individuals while the later focuses on probabilistic aspects. As expected, fertility varied considerably within and among populations. Only similar to15 per cent in both stands and seed orchards indicated small variations in fertility. Fertility variation was higher in stands than in seed orchards. Differences in fertility were usually higher during poor flowering years and in young populations. In seed orchards, fertility differences were slightly larger on the male side than on the female side. For fertility predictions concerning objects that are neither juvenile nor characterized by poor flowering, we suggest, for seed orchards, a CV equal to 100 per cent with Psi equal to 2 and, for stands, a CV equal to 140 per cent with Psi equal to 3.

@article{shockcor_lc-msms_2003,
	title = {{LC}-{MS}/{MS} approach to 'metabonomics' - {What} can it do for drug discovery/development?},
	volume = {35},
	issn = {0360-2532},
	language = {English},
	journal = {Drug Metabolism Reviews},
	author = {Shockcor, J. P. and Nichols, A. and Antti, H. and Plumb, R. S. and Castro-Perez, J. M. and Major, H. and Preece, S.},
	year = {2003},
	note = {Place: New York
Publisher: Marcel Dekker Inc
WOS:000182128400003},
	keywords = {⛔ No DOI found},
	pages = {1--1},
}

@article{waldmann_bayesian_2003,
	title = {Bayesian inference of inbreeding depression in controlled crosses},
	volume = {57},
	issn = {0014-3820},
	doi = {10/cmwff3},
	abstract = {This study shows how a Gibbs sampling approach can be used for Bayesian inference of inbreeding depression. The method presented is mainly concerned with organisms that can be both selfed and outcrossed. Tests performed on simulated data with unequal variances and missing observations show that the method works well. Real data from the plant Scabiosa canescens is also analyzed.},
	language = {eng},
	number = {8},
	journal = {Evolution; International Journal of Organic Evolution},
	author = {Waldmann, Patrik},
	month = aug,
	year = {2003},
	pmid = {14503634},
	keywords = {Analysis of Variance, Bayes Theorem, Crosses, Genetic, Inbreeding, Magnoliopsida, Models, Genetic},
	pages = {1947--1951},
}

This study shows how a Gibbs sampling approach can be used for Bayesian inference of inbreeding depression. The method presented is mainly concerned with organisms that can be both selfed and outcrossed. Tests performed on simulated data with unequal variances and missing observations show that the method works well. Real data from the plant Scabiosa canescens is also analyzed.

@article{schubert_proteome_2003,
	title = {Proteome map of the chloroplast lumen of {Arabidopsis} thaliana (vol 277, pg 8354, 2002)},
	volume = {278},
	issn = {0021-9258},
	doi = {10/gmhq7m},
	language = {English},
	number = {15},
	journal = {Journal of Biological Chemistry},
	author = {Schubert, M. and Petersson, U. A. and Haas, B. J. and Funk, C. and Schroder, W. P. and Kieselbach, T.},
	month = apr,
	year = {2003},
	note = {Place: Bethesda
Publisher: Amer Soc Biochemistry Molecular Biology Inc
WOS:000182189500125},
	pages = {13590--13590},
}

@article{karpinski_light_2003,
	title = {Light perception in plant disease defence signalling},
	volume = {6},
	issn = {1369-5266},
	url = {https://www.sciencedirect.com/science/article/pii/S136952660300061X},
	doi = {10/cc95fs},
	abstract = {Light is a predominant factor in the control of plant growth, development and stress responses. Many biotic stress responses in plants are therefore specifically adjusted by the prevailing light conditions. The plant cell is equipped with sophisticated light-sensing mechanisms that are localised inside and outside of the chloroplast and the nucleus. Recent progress has provided models of how the signalling pathways that are involved in light perception and in defence could operate and interact to form a plant defence network. Such a signalling network includes systems to sense light and regulate gene expression. Photo-produced H2O2 and other reactive oxygen species in the cell also play an essential role in this regulatory network, controlling biotic and abiotic stress responses.},
	language = {en},
	number = {4},
	urldate = {2021-07-05},
	journal = {Current Opinion in Plant Biology},
	author = {Karpinski, Stanislaw and Gabrys, Halina and Mateo, Alfonso and Karpinska, Barbara and Mullineaux, Philip M},
	month = aug,
	year = {2003},
	pages = {390--396},
}

Light is a predominant factor in the control of plant growth, development and stress responses. Many biotic stress responses in plants are therefore specifically adjusted by the prevailing light conditions. The plant cell is equipped with sophisticated light-sensing mechanisms that are localised inside and outside of the chloroplast and the nucleus. Recent progress has provided models of how the signalling pathways that are involved in light perception and in defence could operate and interact to form a plant defence network. Such a signalling network includes systems to sense light and regulate gene expression. Photo-produced H2O2 and other reactive oxygen species in the cell also play an essential role in this regulatory network, controlling biotic and abiotic stress responses.

@article{parker_isolation_2003,
	title = {Isolation of {COV1}, a gene involved in the regulation of vascular patterning in the stem of {Arabidopsis}},
	volume = {130},
	issn = {0950-1991},
	url = {https://doi.org/10.1242/dev.00441},
	doi = {10/cmn59q},
	abstract = {The molecular mechanisms that control the ordered patterning of vascular tissue development in plants are not well understood. Several models propose a two-component system for vascular differentiation. These components include an inducer of vascular tissue development and an inhibitor that prevents the formation of vascular bundles near pre-existing bundles. We have identified two recessive allelic mutants in Arabidopsis, designated continuous vascular ring (cov1), that display a dramatic increase in vascular tissue development in the stem in place of the interfascicular region that normally separates the vascular bundles. The mutant plants exhibited relatively normal vascular patterning in leaves and cotyledons. Analysis of the interaction of cov1 with a known auxin signalling mutant and direct analysis of auxin concentrations suggests that cov1 affects vascular pattering by some mechanism that is independent of auxin. The COV1 protein is predicted to be an integral membrane protein of unknown function, highly conserved between plants and bacteria. In plants, COV1 is likely to be involved in a mechanism that negatively regulates the differentiation of vascular tissue in the stem.},
	number = {10},
	urldate = {2021-07-05},
	journal = {Development},
	author = {Parker, Garry and Schofield, Rebecca and Sundberg, Björn and Turner, Simon},
	month = may,
	year = {2003},
	pages = {2139--2148},
}

The molecular mechanisms that control the ordered patterning of vascular tissue development in plants are not well understood. Several models propose a two-component system for vascular differentiation. These components include an inducer of vascular tissue development and an inhibitor that prevents the formation of vascular bundles near pre-existing bundles. We have identified two recessive allelic mutants in Arabidopsis, designated continuous vascular ring (cov1), that display a dramatic increase in vascular tissue development in the stem in place of the interfascicular region that normally separates the vascular bundles. The mutant plants exhibited relatively normal vascular patterning in leaves and cotyledons. Analysis of the interaction of cov1 with a known auxin signalling mutant and direct analysis of auxin concentrations suggests that cov1 affects vascular pattering by some mechanism that is independent of auxin. The COV1 protein is predicted to be an integral membrane protein of unknown function, highly conserved between plants and bacteria. In plants, COV1 is likely to be involved in a mechanism that negatively regulates the differentiation of vascular tissue in the stem.

@article{gentili_local_2003,
	title = {Local and systemic effects of phosphorus and nitrogen on nodulation and nodule function in {Alnus} incana},
	volume = {54},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erg311},
	doi = {10/fvn9fd},
	abstract = {Phosphorus (P) and nitrogen (N) effects on nodulation, nitrogenase activity and plant growth were studied in the root‐hair‐infected actinorhizal plant Alnus incana (L.) Moench. A split‐root experiment, as well as a short‐term experiment with entire root systems and a broader range of P concentrations, showed that P effects were specific on nodulation and not a general stimulation via a plant growth effect. These results indicate that nodule initiation and nodule growth have a high P demand. The split‐root assay, comprising seven combinations of two N and two P levels, showed that P could counteract systemic N inhibition of nodulation, but did not counteract N inhibition of nitrogenase activity.},
	number = {393},
	urldate = {2021-07-05},
	journal = {Journal of Experimental Botany},
	author = {Gentili, Francesco and Huss‐Danell, Kerstin},
	month = dec,
	year = {2003},
	pages = {2757--2767},
}

Phosphorus (P) and nitrogen (N) effects on nodulation, nitrogenase activity and plant growth were studied in the root‐hair‐infected actinorhizal plant Alnus incana (L.) Moench. A split‐root experiment, as well as a short‐term experiment with entire root systems and a broader range of P concentrations, showed that P effects were specific on nodulation and not a general stimulation via a plant growth effect. These results indicate that nodule initiation and nodule growth have a high P demand. The split‐root assay, comprising seven combinations of two N and two P levels, showed that P could counteract systemic N inhibition of nodulation, but did not counteract N inhibition of nitrogenase activity.

@article{morling_method_2003,
	title = {A method to estimate fibre length distribution in conifers based on wood samples from increment cores},
	volume = {57},
	issn = {0018-3830},
	doi = {10/ddfg4c},
	abstract = {We propose a method to estimate fibre length distribution in conifers based on wood samples from increment cores processed by automatic optical fibre-analysers. Automatic fibre-analysers are unable to distinguish: a) fibres from other tissues, "fines", and b) cut from uncut fibres. However, our proposed method can handle these problems if the type of distributions that fibre lengths and fines, follow is known. In our study the length distributions of fines and fibres were assumed to follow truncated normal distributions, characterised by means and standard deviations of the two distributions. Parameter estimates were obtained by the maximum likelihood method. Wood samples from two 22-year-old Scots pine trees at breast height were used to evaluate the performance of the method. From stem discs at 1.5 m, adjacent samples of 5 mm increment cores and wood pieces were taken. The cores were trimmed I mm at each side and samples were, after maceration, analysed in a Kajaani FiberLab 3.0. The results showed that the method works well and gives a possibility to distinguish fine and fibre length distribution.},
	language = {English},
	number = {3},
	journal = {Holzforschung},
	author = {Morling, T. and Sjostedt-de Luna, S. and Svensson, I. and Fries, A. and Ericsson, T.},
	year = {2003},
	note = {Place: Berlin
Publisher: Walter De Gruyter \& Co
WOS:000183030100004},
	keywords = {Pinus sylvestris, density, fibre length distribution, fines, increment core, softwood},
	pages = {248--254},
}

We propose a method to estimate fibre length distribution in conifers based on wood samples from increment cores processed by automatic optical fibre-analysers. Automatic fibre-analysers are unable to distinguish: a) fibres from other tissues, "fines", and b) cut from uncut fibres. However, our proposed method can handle these problems if the type of distributions that fibre lengths and fines, follow is known. In our study the length distributions of fines and fibres were assumed to follow truncated normal distributions, characterised by means and standard deviations of the two distributions. Parameter estimates were obtained by the maximum likelihood method. Wood samples from two 22-year-old Scots pine trees at breast height were used to evaluate the performance of the method. From stem discs at 1.5 m, adjacent samples of 5 mm increment cores and wood pieces were taken. The cores were trimmed I mm at each side and samples were, after maceration, analysed in a Kajaani FiberLab 3.0. The results showed that the method works well and gives a possibility to distinguish fine and fibre length distribution.

@article{fries_measuring_2003,
	title = {Measuring relative fibre length in {Scots} pine by non-destructive wood sampling},
	volume = {57},
	issn = {0018-3830},
	doi = {10/cqbnzg},
	abstract = {Wood fibre length of Scots pine (Pinus sylvestris L.) was measured in wood sticks and 5-mm increment cores. The aim was to evaluate whether fibre length estimates from such small-diameter cores could be used to calculate genetic parameters, in spite of the increased amount of cut fibres produced at boring. The correlation between mean fibre lengths obtained from cores and sticks, with substantially fewer cut fibres, was high (r = 0.87, n = 53) and of the same magnitude as the correlation between samples from varied positions in the same tree (r = 0.87, n = 46). As regards evaluation of genetic tests and ranking for selection purposes, values from non-destructively sampled 5-mm cores from 0.5 m tree height appear to serve well. Fibre length development along annual ring classes started to differentiate between trees at annual rings 13-15, and after ring 16 there was a slight tendency towards stabilisation which may be interpreted as a reasonably advanced transition from juvenile wood to mature wood.},
	language = {English},
	number = {4},
	journal = {Holzforschung},
	author = {Fries, A. and Ericsson, T. and Morling, T.},
	year = {2003},
	note = {Place: Berlin
Publisher: Walter De Gruyter \& Co
WOS:000184291100009},
	keywords = {Pinus sylvestris, correlation, density, fibre length, fines, genetic parameters, genetic-variation, heartwood, heritability, increment core, increment cores, juvenile, maceration, mature wood, sapwood, taeda, tracheid length, transition},
	pages = {400--406},
}

Wood fibre length of Scots pine (Pinus sylvestris L.) was measured in wood sticks and 5-mm increment cores. The aim was to evaluate whether fibre length estimates from such small-diameter cores could be used to calculate genetic parameters, in spite of the increased amount of cut fibres produced at boring. The correlation between mean fibre lengths obtained from cores and sticks, with substantially fewer cut fibres, was high (r = 0.87, n = 53) and of the same magnitude as the correlation between samples from varied positions in the same tree (r = 0.87, n = 46). As regards evaluation of genetic tests and ranking for selection purposes, values from non-destructively sampled 5-mm cores from 0.5 m tree height appear to serve well. Fibre length development along annual ring classes started to differentiate between trees at annual rings 13-15, and after ring 16 there was a slight tendency towards stabilisation which may be interpreted as a reasonably advanced transition from juvenile wood to mature wood.

@article{leitz_laser-based_2003,
	title = {Laser-based micromanipulation for separation and identification of individual {Frankia} vesicles},
	volume = {224},
	issn = {0378-1097},
	doi = {10/bf78w8},
	abstract = {In studies of symbiotic efficiency it is of great importance to identify and separate individual Frankia strains from a nodule. Therefore, a new laser-based micromanipulation technique has been developed in which individual vesicles from root nodules of two Frankia-Alnus symbioses have been successfully cut loose and separated from clusters of vesicles in sterile conditions under light microscopy using a laser scalpel and optical tweezers. Vesicles from the Alnus incana-Frankia AvCIl symbiosis were successfully isolated and grown in culture using this technique. The DNA from both Frankia sources was amplified by polymerase chain reaction (PCR). The work shows that a combination of laser-based manipulation techniques and PCR can be used for the separation and study of individual vesicles. This novel laser-based micromanipulation technique opens up various new possibilities, for instance, to study whether several Frankia strains can grow simultaneously in the same root nodule. (C) 2003 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.},
	language = {English},
	number = {1},
	journal = {Fems Microbiology Letters},
	author = {Leitz, G. and Lundberg, C. and Fallman, E. and Axner, O. and Sellstedt, A.},
	month = jul,
	year = {2003},
	note = {Place: Amsterdam
Publisher: Elsevier Science Bv
WOS:000184248400014},
	keywords = {Frankia, bacteria, casuarina, dna, hydrogen metabolism, laser scalpel, manipulation, nitrogen-fixation, optical tweezers, pcr, polymerase chain-reaction, rflp, root-nodules, strains},
	pages = {97--100},
}

In studies of symbiotic efficiency it is of great importance to identify and separate individual Frankia strains from a nodule. Therefore, a new laser-based micromanipulation technique has been developed in which individual vesicles from root nodules of two Frankia-Alnus symbioses have been successfully cut loose and separated from clusters of vesicles in sterile conditions under light microscopy using a laser scalpel and optical tweezers. Vesicles from the Alnus incana-Frankia AvCIl symbiosis were successfully isolated and grown in culture using this technique. The DNA from both Frankia sources was amplified by polymerase chain reaction (PCR). The work shows that a combination of laser-based manipulation techniques and PCR can be used for the separation and study of individual vesicles. This novel laser-based micromanipulation technique opens up various new possibilities, for instance, to study whether several Frankia strains can grow simultaneously in the same root nodule. (C) 2003 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.

@article{borodich_segregation_2003,
	title = {Segregation of the photosystems in higher plant thylakoids and short- and long-term regulation by a mesoscopic approach},
	volume = {225},
	issn = {0022-5193},
	url = {https://www.sciencedirect.com/science/article/pii/S0022519303002765},
	doi = {10/dz35mn},
	abstract = {In this paper we consider the relationship between the lateral segregation of photosystems I and II in the grana and characteristics of the short- and long-term regulation in thylakoids following the mesoscopic approach. Our study is thermodynamic; it is based on the Flory–Huggins theory for binary mixtures and the McMillan–Mayer theory of heterogeneous solutions. We demonstrate that state transitions promote rearrangement of photosystems by either favoring their mixing after LHCII phosphorylation or enhancing their segregation after LHCII dephosphorylation. This regulation influences the entire system properties locally. We also demonstrate that the variations of the photosystem ratio promote rearrangement of the photosystems preserving their segregation. This regulation influences the entire system properties globally. The studies presented are another indication of the importance of the segregation of the photosystems in the grana thylakoids of higher plants. Segregation of PSIs and PSIIs is a signature of the spinodal decomposition, which is a fine regulatory mechanism, related to both the short- and long-term adaptations of the photosynthetic apparatus in higher plant thylakoids.},
	language = {en},
	number = {4},
	urldate = {2021-07-05},
	journal = {Journal of Theoretical Biology},
	author = {Borodich, Andrei and Rojdestvenski, Igor and Cottam, Michael and Anderson, Jan and Öquist, Gunnar},
	month = dec,
	year = {2003},
	keywords = {Grana, Phase separation, Photosystem stoichiometric ratio, Segregation of photosystems, Short- and long-term regulations, Spinodal decomposition, State transitions, Thylakoid},
	pages = {431--441},
}

In this paper we consider the relationship between the lateral segregation of photosystems I and II in the grana and characteristics of the short- and long-term regulation in thylakoids following the mesoscopic approach. Our study is thermodynamic; it is based on the Flory–Huggins theory for binary mixtures and the McMillan–Mayer theory of heterogeneous solutions. We demonstrate that state transitions promote rearrangement of photosystems by either favoring their mixing after LHCII phosphorylation or enhancing their segregation after LHCII dephosphorylation. This regulation influences the entire system properties locally. We also demonstrate that the variations of the photosystem ratio promote rearrangement of the photosystems preserving their segregation. This regulation influences the entire system properties globally. The studies presented are another indication of the importance of the segregation of the photosystems in the grana thylakoids of higher plants. Segregation of PSIs and PSIIs is a signature of the spinodal decomposition, which is a fine regulatory mechanism, related to both the short- and long-term adaptations of the photosynthetic apparatus in higher plant thylakoids.

@article{kumar_reciprocal_2003,
	title = {Reciprocal and {Maternal} {Effects} on {Growth} and {Form} {Traits} in {Radiata} {Pine} in {New} {Zealand}},
	abstract = {The information from two experiments was used to study reciprocal and maternal effects on several growth and form traits in Pinus radiata. In Experiment 1, 10 families and their reciprocals obtained from a 5 x 5 diallel experiment were planted across three sites. In Experiment 2, 17 parents were used in a partial diallel design and all available crosses were planted at a single site. All three sites for Experiment 1 were assessed at 9 years of age. The site for Experiment 2 was assessed at the age of 6-years. Four growth and form traits, namely diameter at breast height (DBH), straightness (STR), branching (BR) and malformation (MAL) were measured in both experiments while needle retention (NRA) was assessed only in Experiment 1.},
	language = {en},
	number = {52},
	author = {Kumar, S and Wu, H X},
	year = {2003},
	pages = {2},
}

The information from two experiments was used to study reciprocal and maternal effects on several growth and form traits in Pinus radiata. In Experiment 1, 10 families and their reciprocals obtained from a 5 x 5 diallel experiment were planted across three sites. In Experiment 2, 17 parents were used in a partial diallel design and all available crosses were planted at a single site. All three sites for Experiment 1 were assessed at 9 years of age. The site for Experiment 2 was assessed at the age of 6-years. Four growth and form traits, namely diameter at breast height (DBH), straightness (STR), branching (BR) and malformation (MAL) were measured in both experiments while needle retention (NRA) was assessed only in Experiment 1.

@article{taylor_common_2003,
	title = {Common features of segregation distortion in plants and animals},
	volume = {117},
	issn = {0016-6707},
	doi = {10.1023/a:1022308414864},
	abstract = {Segregation distortion is increasingly recognized as a potentially powerful evolutionary force. This runs counter to the perception that non-Mendelian genes are rare genetic curiosities, a view that seems to be supported by the near ubiquity of the Mendelian system of inheritance. There are several reasons why segregation distortion may be more important than is evidenced by known empirical examples. One possibility is that the types of segregation distorters we have found are only a subset of a broader range of non-Mendelian systems, many of which go undetected. In this paper, we review what is known about the sex-linked meiotic drive system in the plant, Silene latifolia, and present some data on the mechanism of segregation distortion. We outline the general features that segregation distorters in plants and animals have in common. In some cases, such as the paucity of systems that directly alter meiotic segregation, there are likely to be inherent constraints on the range of systems that can possibly occur. Other generalities, however, support the notion that many forms of meiotic drive are possible, and that the known examples of segregation distortion are likely to be only subset of those that can possibly occur. Non-Mendelian genes may therefore have greater evolutionary importance than their current abundance in nature would suggest.},
	language = {eng},
	number = {1},
	journal = {Genetica},
	author = {Taylor, Douglas R. and Ingvarsson, Pär K.},
	month = jan,
	year = {2003},
	pmid = {12656570},
	keywords = {Animals, Chromosome Segregation, Drosophila, Evolution, Molecular, Gametogenesis, Meiosis, Pollen, Polymorphism, Genetic, Sex Ratio, Silene, X Chromosome},
	pages = {27--35},
}

Segregation distortion is increasingly recognized as a potentially powerful evolutionary force. This runs counter to the perception that non-Mendelian genes are rare genetic curiosities, a view that seems to be supported by the near ubiquity of the Mendelian system of inheritance. There are several reasons why segregation distortion may be more important than is evidenced by known empirical examples. One possibility is that the types of segregation distorters we have found are only a subset of a broader range of non-Mendelian systems, many of which go undetected. In this paper, we review what is known about the sex-linked meiotic drive system in the plant, Silene latifolia, and present some data on the mechanism of segregation distortion. We outline the general features that segregation distorters in plants and animals have in common. In some cases, such as the paucity of systems that directly alter meiotic segregation, there are likely to be inherent constraints on the range of systems that can possibly occur. Other generalities, however, support the notion that many forms of meiotic drive are possible, and that the known examples of segregation distortion are likely to be only subset of those that can possibly occur. Non-Mendelian genes may therefore have greater evolutionary importance than their current abundance in nature would suggest.

@article{niewiadomska_catalase_2003,
	title = {Catalase in common ice plant leaves},
	volume = {37},
	issn = {1071-5762},
	language = {English},
	journal = {Free Radical Research},
	author = {Niewiadomska, E. and Miszalski, Z. and Karpinski, S. and Karpinska, B. and Haag-Kerwer, A.},
	year = {2003},
	note = {Place: Abingdon
Publisher: Taylor \& Francis Ltd
WOS:000185828100068},
	pages = {29--29},
}

@article{mullineaux_foliar_2003,
	title = {Foliar responses to excess light stress in {Arabidopsis} mediated by the antioxidant glutathione.},
	volume = {37},
	issn = {1071-5762},
	language = {English},
	journal = {Free Radical Research},
	author = {Mullineaux, P. and Ball, L. and Karpinski, B. and Fryer, M. and Leyland, N. and Baker, N. and Karpinski, S.},
	year = {2003},
	note = {Place: Abingdon
Publisher: Taylor \& Francis Ltd
WOS:000184458700037},
	pages = {31--31},
}

@article{mullineaux_foliar_2003,
	title = {Foliar responses to excess light stress and pathogens in {Arabidopsis} mediated by the antioxidant glutathione},
	volume = {37},
	issn = {1071-5762},
	language = {English},
	journal = {Free Radical Research},
	author = {Mullineaux, P. and Ball, L. and Karpinski, B. and Fryer, M. and Leyland, N. and Baker, N. and Karpinski, S.},
	year = {2003},
	note = {Place: Abingdon
Publisher: Taylor \& Francis Ltd
WOS:000185828100007},
	pages = {3--3},
}

@article{grebe_arabidopsis_2003,
	title = {Arabidopsis sterol endocytosis involves actin-mediated trafficking via {ARA6}-positive early endosomes},
	volume = {13},
	issn = {0960-9822},
	doi = {10.1016/s0960-9822(03)00538-4},
	abstract = {BACKGROUND: In contrast to the intense attention devoted to research on intracellular sterol trafficking in animal cells, knowledge about sterol transport in plant cells remains limited, and virtually nothing is known about plant endocytic sterol trafficking. Similar to animals, biosynthetic sterol transport occurs from the endoplasmic reticulum (ER) via the Golgi apparatus to the plasma membrane. The vesicle trafficking inhibitor brefeldin A (BFA) has been suggested to disrupt biosynthetic sterol transport at the Golgi level.
RESULTS: Here, we report on early endocytic sterol trafficking in Arabidopsis root epidermal cells by introducing filipin as a tool for fluorescent sterol detection. Sterols can be internalized from the plasma membrane and localize to endosomes positive for the early endosomal Rab5 GTPase homolog ARA6 fused to green fluorescent protein (GFP) (ARA6-GFP). Early endocytic sterol transport is actin dependent and highly BFA sensitive. BFA causes coaccumulation of sterols, endocytic markers like ARA6-GFP, and PIN2, a polarly localized presumptive auxin transport protein, in early endosome agglomerations that can be distinguished from ER and Golgi. Sterol accumulation in such aggregates is enhanced in actin2 mutants, and the actin-depolymerizing drug cytochalasin D inhibits sterol redistribution from endosome aggregations.
CONCLUSIONS: Early endocytic sterol trafficking involves transport via ARA6-positive early endosomes that, in contrast to animal cells, is actin dependent. Our results reveal sterol-enriched early endosomes as targets for BFA interference in plants. Early endocytic sterol trafficking and recycling of polar PIN2 protein share a common pathway, suggesting a connection between plant endocytic sterol transport and polar sorting events.},
	language = {eng},
	number = {16},
	journal = {Current biology: CB},
	author = {Grebe, Markus and Xu, Jian and Möbius, Wiebke and Ueda, Takashi and Nakano, Akihiko and Geuze, Hans J. and Rook, Martin B. and Scheres, Ben},
	month = aug,
	year = {2003},
	pmid = {12932321},
	keywords = {Actins, Arabidopsis, Arabidopsis Proteins, Base Sequence, Biological Transport, Active, Brefeldin A, DNA, Plant, Endocytosis, Endosomes, GTP Phosphohydrolases, Green Fluorescent Proteins, Luminescent Proteins, Microscopy, Electron, Models, Biological, Recombinant Fusion Proteins, Sterols, Subcellular Fractions, rab GTP-Binding Proteins},
	pages = {1378--1387},
}

BACKGROUND: In contrast to the intense attention devoted to research on intracellular sterol trafficking in animal cells, knowledge about sterol transport in plant cells remains limited, and virtually nothing is known about plant endocytic sterol trafficking. Similar to animals, biosynthetic sterol transport occurs from the endoplasmic reticulum (ER) via the Golgi apparatus to the plasma membrane. The vesicle trafficking inhibitor brefeldin A (BFA) has been suggested to disrupt biosynthetic sterol transport at the Golgi level. RESULTS: Here, we report on early endocytic sterol trafficking in Arabidopsis root epidermal cells by introducing filipin as a tool for fluorescent sterol detection. Sterols can be internalized from the plasma membrane and localize to endosomes positive for the early endosomal Rab5 GTPase homolog ARA6 fused to green fluorescent protein (GFP) (ARA6-GFP). Early endocytic sterol transport is actin dependent and highly BFA sensitive. BFA causes coaccumulation of sterols, endocytic markers like ARA6-GFP, and PIN2, a polarly localized presumptive auxin transport protein, in early endosome agglomerations that can be distinguished from ER and Golgi. Sterol accumulation in such aggregates is enhanced in actin2 mutants, and the actin-depolymerizing drug cytochalasin D inhibits sterol redistribution from endosome aggregations. CONCLUSIONS: Early endocytic sterol trafficking involves transport via ARA6-positive early endosomes that, in contrast to animal cells, is actin dependent. Our results reveal sterol-enriched early endosomes as targets for BFA interference in plants. Early endocytic sterol trafficking and recycling of polar PIN2 protein share a common pathway, suggesting a connection between plant endocytic sterol transport and polar sorting events.

@article{tarkowska_electrochemical_2003,
	title = {Electrochemical reduction of 6-benzylaminopurine at mercury electrodes and its analytical application},
	volume = {68},
	issn = {0010-0765},
	doi = {10.1135/cccc20031076},
	abstract = {The commercial exploitation of modern, in vitro plant micropropagation methods, featuring synthetic cytokinins as essential components of the cultivation media, is rapidly increasing. Thus, development of rapid, inexpensive and less labour-intensive methods for monitoring cytokinin levels could help to optimise media consumption and reduce costs. Therefore, we studied the electrochemical behaviour of the highly active and widely used cytokinin, 6-benzylaminopurine (BAP), in aqueous solutions by DC polarography, cyclic and differential pulse voltammetry and constant potential coulometry. The BAP molecule undergoes a six-electron irreversible reduction process that starts with four-electron reduction of the protonated pyrimidine skeleton. As a result of elimination of the amine from the side chain, the N1=C6 electrochemically active bond is re-established and the last two-electron step follows. The intermediates of constant potential electrolysis were identified using mass spectrometric analysis. The dissociation constant (pK(a)) of BAP was found, spectrophotometrically, to be 4.16. BAP concentrations were measured using two voltammetric techniques, fast-scan differential pulse (FSDPV) and adsorptive stripping voltammetry (AdSV). The relative standard deviations for these two methods were lower than 4.5\% (c {\textless} 28.7 ng ml(-1)) and 1.2\% (c {\textless}20 ng ml(-1)), while the detection limits were 7.88 and 0.80 ng ml(-1), respectively. Using these techniques, BAP was determined in two types of nutrition media used for the micropropagation of plants in vitro (Gerbera and banana media). In the case of media samples containing the interfering agent adenine (i.e. Gerbera plant medium), the analyte was preconcentrated by ion-exchange chromatography and immunoaffinity chromatography. This preconcentration process gives 92\% recovery. In contrast, it was possible to determine BAP levels in simple banana cultivation medium directly, without any pre-purification process. Both methods, reported here (FSDPV and AdSV), were found to be useful for rapidly monitoring BAP consumption by plants during their growth under in vitro conditions.},
	language = {English},
	number = {6},
	journal = {Collection of Czechoslovak Chemical Communications},
	author = {Tarkowska, D. and Kotoucek, M. and Dolezal, K.},
	year = {2003},
	note = {Place: Prague 6
Publisher: Inst Organic Chem and Biochem
WOS:000182886300005},
	keywords = {6-benzylaminopurine, carbon-fiber microelectrode, coulometry, cytokinins, dependent kinase inhibitor, dihydrozeatin   riboside, electrochemistry, extracts, magnetic-resonance, mass spectrometry, olomoucine, phytohormones, polarography, purines, stripping voltammetry, voltammetry, zeatin},
	pages = {1076--1093},
}

The commercial exploitation of modern, in vitro plant micropropagation methods, featuring synthetic cytokinins as essential components of the cultivation media, is rapidly increasing. Thus, development of rapid, inexpensive and less labour-intensive methods for monitoring cytokinin levels could help to optimise media consumption and reduce costs. Therefore, we studied the electrochemical behaviour of the highly active and widely used cytokinin, 6-benzylaminopurine (BAP), in aqueous solutions by DC polarography, cyclic and differential pulse voltammetry and constant potential coulometry. The BAP molecule undergoes a six-electron irreversible reduction process that starts with four-electron reduction of the protonated pyrimidine skeleton. As a result of elimination of the amine from the side chain, the N1=C6 electrochemically active bond is re-established and the last two-electron step follows. The intermediates of constant potential electrolysis were identified using mass spectrometric analysis. The dissociation constant (pK(a)) of BAP was found, spectrophotometrically, to be 4.16. BAP concentrations were measured using two voltammetric techniques, fast-scan differential pulse (FSDPV) and adsorptive stripping voltammetry (AdSV). The relative standard deviations for these two methods were lower than 4.5% (c \textless 28.7 ng ml(-1)) and 1.2% (c \textless20 ng ml(-1)), while the detection limits were 7.88 and 0.80 ng ml(-1), respectively. Using these techniques, BAP was determined in two types of nutrition media used for the micropropagation of plants in vitro (Gerbera and banana media). In the case of media samples containing the interfering agent adenine (i.e. Gerbera plant medium), the analyte was preconcentrated by ion-exchange chromatography and immunoaffinity chromatography. This preconcentration process gives 92% recovery. In contrast, it was possible to determine BAP levels in simple banana cultivation medium directly, without any pre-purification process. Both methods, reported here (FSDPV and AdSV), were found to be useful for rapidly monitoring BAP consumption by plants during their growth under in vitro conditions.

@article{borodich_lateral_2003,
	title = {Lateral {Heterogeneity} of {Photosystems} in {Thylakoid} {Membranes} {Studied} by {Brownian} {Dynamics} {Simulations}},
	volume = {85},
	issn = {0006-3495},
	url = {https://www.sciencedirect.com/science/article/pii/S0006349503745196},
	doi = {10.1016/S0006-3495(03)74519-6},
	abstract = {The aggregation and segregation of photosystems in higher plant thylakoid membranes as stromal cation-induced phenomena are studied by the Brownian dynamics method. A theoretical model of photosystems lateral movement within the membrane plane is developed, assuming their pairwise effective potential interaction in aqueous and lipid media and their diffusion. Along with the screened electrostatic repulsive interaction the model accounts for the van der Waals-type, elastic, and lipid-induced attractive forces between photosystems of different sizes and charges. Simulations with a priori estimated parameters demonstrate that all three studied repulsion-attraction alternatives might favor the local segregation of photosystems under physiologically reasonable conditions. However, only the lipid-induced potential combined with the size-corrected screened Coulomb interaction provides the segregated configurations with photosystems II localized in the central part of the grana-size simulation cell and photosystems I occupying its margins, as observed experimentally. Mapping of thermodynamic states reveals that the coexistence curves between isotropic and aggregated phases are the sigmoidlike functions regardless of the effective potential type. It correlates with measurements of the chlorophyll content of thylakoid fragments. Also the universality of the phase curves characterizes the aggregation and segregation of photosystems as order-disorder phase transitions with the Debye radius as a governing parameter.},
	language = {en},
	number = {2},
	urldate = {2021-07-05},
	journal = {Biophysical Journal},
	author = {Borodich, Andrei and Rojdestvenski, Igor and Cottam, Michael},
	month = aug,
	year = {2003},
	pages = {774--789},
}

The aggregation and segregation of photosystems in higher plant thylakoid membranes as stromal cation-induced phenomena are studied by the Brownian dynamics method. A theoretical model of photosystems lateral movement within the membrane plane is developed, assuming their pairwise effective potential interaction in aqueous and lipid media and their diffusion. Along with the screened electrostatic repulsive interaction the model accounts for the van der Waals-type, elastic, and lipid-induced attractive forces between photosystems of different sizes and charges. Simulations with a priori estimated parameters demonstrate that all three studied repulsion-attraction alternatives might favor the local segregation of photosystems under physiologically reasonable conditions. However, only the lipid-induced potential combined with the size-corrected screened Coulomb interaction provides the segregated configurations with photosystems II localized in the central part of the grana-size simulation cell and photosystems I occupying its margins, as observed experimentally. Mapping of thermodynamic states reveals that the coexistence curves between isotropic and aggregated phases are the sigmoidlike functions regardless of the effective potential type. It correlates with measurements of the chlorophyll content of thylakoid fragments. Also the universality of the phase curves characterizes the aggregation and segregation of photosystems as order-disorder phase transitions with the Debye radius as a governing parameter.

@article{johansson_multivariate_2003,
	title = {A multivariate approach applied to microarray data for identification of genes with cell cycle-coupled transcription},
	volume = {19},
	issn = {1367-4803},
	doi = {10.1093/bioinformatics/btg017},
	abstract = {We have analyzed microarray data using a modeling approach based on the multivariate statistical method partial least squares (PLS) regression to identify genes with periodic fluctuations in expression levels coupled to the cell cycle in the budding yeast, Saccharomyces cerevisiae. PLS has major advantages for analyzing microarray data since it can model data sets with large numbers of variables and with few observations. A response model was derived describing the expression profile over time expected for periodically transcribed genes, and was used to identify budding yeast transcripts with similar profiles. PLS was then used to interpret the importance of the variables (genes) for the model, yielding a ranking list of how well the genes fitted the generated model. Application of an appropriate cutoff value, calculated from randomized data, allows the identification of genes whose expression appears to be synchronized with cell cycling. Our approach also provides information about the stage in the cell cycle where their transcription peaks. Three synchronized yeast cell microarray data sets were analyzed, both separately and combined. Cell cycle-coupled periodicity was suggested for 455 of the 6,178 transcripts monitored in the combined data set, at a significance level of 0.5\%. Among the candidates, 85\% of the known periodic transcripts were included. Analysis of the three data sets separately yielded similar ranking lists, showing that the method is robust.},
	language = {eng},
	number = {4},
	journal = {Bioinformatics (Oxford, England)},
	author = {Johansson, Daniel and Lindgren, Petter and Berglund, Anders},
	month = mar,
	year = {2003},
	pmid = {12611801},
	keywords = {Algorithms, Cell Cycle, Gene Expression Profiling, Gene Expression Regulation, Least-Squares Analysis, Models, Genetic, Models, Statistical, Multivariate Analysis, Oligonucleotide Array Sequence Analysis, Periodicity, Regression Analysis, Reproducibility of Results, Sensitivity and Specificity, Sequence Alignment, Sequence Analysis, DNA, Transcription, Genetic, Yeasts},
	pages = {467--473},
}

We have analyzed microarray data using a modeling approach based on the multivariate statistical method partial least squares (PLS) regression to identify genes with periodic fluctuations in expression levels coupled to the cell cycle in the budding yeast, Saccharomyces cerevisiae. PLS has major advantages for analyzing microarray data since it can model data sets with large numbers of variables and with few observations. A response model was derived describing the expression profile over time expected for periodically transcribed genes, and was used to identify budding yeast transcripts with similar profiles. PLS was then used to interpret the importance of the variables (genes) for the model, yielding a ranking list of how well the genes fitted the generated model. Application of an appropriate cutoff value, calculated from randomized data, allows the identification of genes whose expression appears to be synchronized with cell cycling. Our approach also provides information about the stage in the cell cycle where their transcription peaks. Three synchronized yeast cell microarray data sets were analyzed, both separately and combined. Cell cycle-coupled periodicity was suggested for 455 of the 6,178 transcripts monitored in the combined data set, at a significance level of 0.5%. Among the candidates, 85% of the known periodic transcripts were included. Analysis of the three data sets separately yielded similar ranking lists, showing that the method is robust.

@article{koch_interaction_2003,
	title = {Interaction between weak low frequency magnetic fields and cell membranes},
	volume = {24},
	issn = {1521-186X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/bem.10136},
	doi = {10.1002/bem.10136},
	abstract = {The question of whether very weak low frequency magnetic fields can affect biological systems, has attracted attention by many research groups for quite some time. Still, today, the theoretical possibility of such an interaction is often questioned and the site of interaction in the cell is unknown. In the present study, the influence of extremely low frequency (ELF) magnetic fields on the transport of Ca2+ was studied in a biological system consisting of highly purified plasma membrane vesicles. We tested two quantum mechanical theoretical models that assume that biologically active ions can be bound to a channel protein and influence the opening state of the channel. Vesicles were exposed for 30 min at 32 °C and the calcium efflux was studied using radioactive 45Ca as a tracer. Static magnetic fields ranging from 27 to 37 μT and time varying magnetic fields with frequencies between 7 and 72 Hz and amplitudes between 13 and 114 μT (peak) were used. We show that suitable combinations of static and time varying magnetic fields directly interact with the Ca2+ channel protein in the cell membrane, and we could quantitatively confirm the model proposed by Blanchard. Bioelectromagnetics 24:395–402, 2003. © 2003 Wiley-Liss, Inc.},
	language = {en},
	number = {6},
	urldate = {2021-07-05},
	journal = {Bioelectromagnetics},
	author = {Koch, C. L. M. Bauréus and Sommarin, M. and Persson, B. R. R. and Salford, L. G. and Eberhardt, J. L.},
	year = {2003},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/bem.10136},
	keywords = {AC/DC magnetic fields, calcium channel, ion magnetic resonance, paramagnetic resonance, plasma membrane},
	pages = {395--402},
}

The question of whether very weak low frequency magnetic fields can affect biological systems, has attracted attention by many research groups for quite some time. Still, today, the theoretical possibility of such an interaction is often questioned and the site of interaction in the cell is unknown. In the present study, the influence of extremely low frequency (ELF) magnetic fields on the transport of Ca2+ was studied in a biological system consisting of highly purified plasma membrane vesicles. We tested two quantum mechanical theoretical models that assume that biologically active ions can be bound to a channel protein and influence the opening state of the channel. Vesicles were exposed for 30 min at 32 °C and the calcium efflux was studied using radioactive 45Ca as a tracer. Static magnetic fields ranging from 27 to 37 μT and time varying magnetic fields with frequencies between 7 and 72 Hz and amplitudes between 13 and 114 μT (peak) were used. We show that suitable combinations of static and time varying magnetic fields directly interact with the Ca2+ channel protein in the cell membrane, and we could quantitatively confirm the model proposed by Blanchard. Bioelectromagnetics 24:395–402, 2003. © 2003 Wiley-Liss, Inc.

@article{watkinson_photosynthetic_2003,
	title = {Photosynthetic {Acclimation} {Is} {Reflected} in {Specific} {Patterns} of {Gene} {Expression} in {Drought}-{Stressed} {Loblolly} {Pine}},
	volume = {133},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.103.026914},
	doi = {10.1104/pp.103.026914},
	abstract = {Because the product of a single gene can influence many aspects of plant growth and development, it is necessary to understand how gene products act in concert and upon each other to effect adaptive changes to stressful conditions. We conducted experiments to improve our understanding of the responses of loblolly pine (Pinus taeda) to drought stress. Water was withheld from rooted plantlets of to a measured water potential of -1 MPa for mild stress and -1.5 MPa for severe stress. Net photosynthesis was measured for each level of stress. RNA was isolated from needles and used in hybridizations against a microarray consisting of 2,173 cDNA clones from five pine expressed sequence tag libraries. Gene expression was estimated using a two-stage mixed linear model. Subsequently, data mining via inductive logic programming identified rules (relationships) among gene expression, treatments, and functional categories. Changes in RNA transcript profiles of loblolly pine due to drought stress were correlated with physiological data reflecting photosynthetic acclimation to mild stress or photosynthetic failure during severe stress. Analysis of transcript profiles indicated that there are distinct patterns of expression related to the two levels of stress. Genes encoding heat shock proteins, late embryogenic-abundant proteins, enzymes from the aromatic acid and flavonoid biosynthetic pathways, and from carbon metabolism showed distinctive responses associated with acclimation. Five genes shown to have different transcript levels in response to either mild or severe stress were chosen for further analysis using real-time polymerase chain reaction. The real-time polymerase chain reaction results were in good agreement with those obtained on microarrays.},
	number = {4},
	urldate = {2021-07-05},
	journal = {Plant Physiology},
	author = {Watkinson, Jonathan I. and Sioson, Allan A. and Vasquez-Robinet, Cecilia and Shukla, Maulik and Kumar, Deept and Ellis, Margaret and Heath, Lenwood S. and Ramakrishnan, Naren and Chevone, Boris and Watson, Layne T. and van Zyl, Leonel and Egertsdotter, Ulrika and Sederoff, Ronald R. and Grene, Ruth},
	month = dec,
	year = {2003},
	pages = {1702--1716},
}

Because the product of a single gene can influence many aspects of plant growth and development, it is necessary to understand how gene products act in concert and upon each other to effect adaptive changes to stressful conditions. We conducted experiments to improve our understanding of the responses of loblolly pine (Pinus taeda) to drought stress. Water was withheld from rooted plantlets of to a measured water potential of -1 MPa for mild stress and -1.5 MPa for severe stress. Net photosynthesis was measured for each level of stress. RNA was isolated from needles and used in hybridizations against a microarray consisting of 2,173 cDNA clones from five pine expressed sequence tag libraries. Gene expression was estimated using a two-stage mixed linear model. Subsequently, data mining via inductive logic programming identified rules (relationships) among gene expression, treatments, and functional categories. Changes in RNA transcript profiles of loblolly pine due to drought stress were correlated with physiological data reflecting photosynthetic acclimation to mild stress or photosynthetic failure during severe stress. Analysis of transcript profiles indicated that there are distinct patterns of expression related to the two levels of stress. Genes encoding heat shock proteins, late embryogenic-abundant proteins, enzymes from the aromatic acid and flavonoid biosynthetic pathways, and from carbon metabolism showed distinctive responses associated with acclimation. Five genes shown to have different transcript levels in response to either mild or severe stress were chosen for further analysis using real-time polymerase chain reaction. The real-time polymerase chain reaction results were in good agreement with those obtained on microarrays.

@article{johannesson_arabidopsis_2003,
	title = {The {Arabidopsis} thaliana homeobox gene {ATHB5} is a potential regulator of abscisic acid responsiveness in developing seedlings},
	volume = {51},
	issn = {0167-4412},
	doi = {10.1023/a:1022567625228},
	abstract = {ATHB5 is a member of the homeodomain-leucine zipper (HDZip) transcription factor gene family of Arabidopsis thaliana. In this report we show that increased expression levels of ATHB5 in transgenic Arabidopsis plants cause an enhanced sensitivity to the inhibitory effect of abscisic acid (ABA) on seed germination and seedling growth. Consistent with this finding we demonstrate in northern blot experiments that the ABA-responsive gene RAB18 is hyperinduced by ABA in transgenic overexpressor lines as compared to the wild type. Northern blot and promoter-GUS fusion analyses show that ATHB5 gene transcription is initiated rapidly after the onset of germination and localized primarily to the hypocotyl of germinating seedlings. Moreover, analysis of ATHB5 gene expression during post-germinative growth in different ABA response mutants shows that ATHB5 gene activity is down-regulated in the abil-1, abi3-1 and abi5-1 mutant lines, but not in abi2-1 or abi4-1. The identification of a T-DNA insertion mutant line of ATHB5 is described and no phenotypic alterations could be discerned, suggesting that ATHB5 may act redundantly with other HDZip genes. Taken together, these data suggest that ATHB5 is a positive regulator of ABA-responsiveness, mediating the inhibitory effect of ABA on growth during seedling establishment.},
	language = {eng},
	number = {5},
	journal = {Plant Molecular Biology},
	author = {Johannesson, Henrik and Wang, Yan and Hanson, Johannes and Engström, Peter},
	month = mar,
	year = {2003},
	pmid = {12678559},
	keywords = {Abscisic Acid, Arabidopsis, Arabidopsis Proteins, Blotting, Northern, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Germination, Glucuronidase, Homeodomain Proteins, Plants, Genetically Modified, Recombinant Fusion Proteins, Seeds, Signal Transduction, Transcription Factors},
	pages = {719--729},
}

ATHB5 is a member of the homeodomain-leucine zipper (HDZip) transcription factor gene family of Arabidopsis thaliana. In this report we show that increased expression levels of ATHB5 in transgenic Arabidopsis plants cause an enhanced sensitivity to the inhibitory effect of abscisic acid (ABA) on seed germination and seedling growth. Consistent with this finding we demonstrate in northern blot experiments that the ABA-responsive gene RAB18 is hyperinduced by ABA in transgenic overexpressor lines as compared to the wild type. Northern blot and promoter-GUS fusion analyses show that ATHB5 gene transcription is initiated rapidly after the onset of germination and localized primarily to the hypocotyl of germinating seedlings. Moreover, analysis of ATHB5 gene expression during post-germinative growth in different ABA response mutants shows that ATHB5 gene activity is down-regulated in the abil-1, abi3-1 and abi5-1 mutant lines, but not in abi2-1 or abi4-1. The identification of a T-DNA insertion mutant line of ATHB5 is described and no phenotypic alterations could be discerned, suggesting that ATHB5 may act redundantly with other HDZip genes. Taken together, these data suggest that ATHB5 is a positive regulator of ABA-responsiveness, mediating the inhibitory effect of ABA on growth during seedling establishment.