Publications 2004

@article{ohlund_regulation_2004,
	title = {Regulation of organic and inorganic nitrogen uptake in {Scots} pine ( {Pinus} sylvestris ) seedlings},
	volume = {24},
	issn = {0829-318X},
	url = {https://doi.org/10.1093/treephys/24.12.1397},
	doi = {10.1093/treephys/24.12.1397},
	abstract = {Plants possess regulatory mechanisms that enhance nitrogen (N) uptake under conditions of spatial and temporal variation in N availabilily. Study of regulatory mechanisms has focused almost exclusively on the uptake of inorganic N sources (i.e., ammonium (NH 4+ ), nitrate (NO 3− )). Several lines of evidence, however, suggest that amino acids may constitute a potential source of N for a number of plant species, including conifers. In the present study, we investigated the uptake of amino acids and inorganic N in Scots pine ( Pinus sylvestris L.) seedlings grown at different N concentrations. We compared the uptake rate of the individual N sources using U-[ 13 C 2 ], [ 15 N]-glycine, U-[ 13 C 6 ], [ 15 N 4 ]-arginine, 15 NH 4 , or 15 NO 3 , and tested the short-term effect of N supply on the uptake rate of glycine, arginine and in field-grown Scots pine seedlings. Our data indicate that Scots pine seedlings can absorb substantial amounts of N in the form of intact arginine and glycine molecules. The data also suggest that Scots pine seedlings down-regulate their uptake of NH 4+ -N and arginine-N, but not of glycine-N in response to increased endogenous N concentrations.},
	number = {12},
	urldate = {2021-10-14},
	journal = {Tree Physiology},
	author = {Öhlund, Jonas and Näsholm, Torgny},
	month = dec,
	year = {2004},
	pages = {1397--1402},
}

Plants possess regulatory mechanisms that enhance nitrogen (N) uptake under conditions of spatial and temporal variation in N availabilily. Study of regulatory mechanisms has focused almost exclusively on the uptake of inorganic N sources (i.e., ammonium (NH 4+ ), nitrate (NO 3− )). Several lines of evidence, however, suggest that amino acids may constitute a potential source of N for a number of plant species, including conifers. In the present study, we investigated the uptake of amino acids and inorganic N in Scots pine ( Pinus sylvestris L.) seedlings grown at different N concentrations. We compared the uptake rate of the individual N sources using U-[ 13 C 2 ], [ 15 N]-glycine, U-[ 13 C 6 ], [ 15 N 4 ]-arginine, 15 NH 4 , or 15 NO 3 , and tested the short-term effect of N supply on the uptake rate of glycine, arginine and in field-grown Scots pine seedlings. Our data indicate that Scots pine seedlings can absorb substantial amounts of N in the form of intact arginine and glycine molecules. The data also suggest that Scots pine seedlings down-regulate their uptake of NH 4+ -N and arginine-N, but not of glycine-N in response to increased endogenous N concentrations.

@article{antti_chemometric_2004,
	title = {Chemometric and bioinformatic methodologies in modeling and interpretation of metabolic and genomic data},
	volume = {228},
	issn = {0065-7727},
	language = {English},
	journal = {Abstracts of Papers of the American Chemical Society},
	author = {Antti, H.},
	month = aug,
	year = {2004},
	note = {Patent Number: 1
Place: Washington
Publisher: Amer Chemical Soc
WOS:000223712800499},
	keywords = {⛔ No DOI found},
	pages = {U112--U113},
}

@article{friml_pinoid-dependent_2004,
	title = {A {PINOID}-{Dependent} {Binary} {Switch} in {Apical}-{Basal} {PIN} {Polar} {Targeting} {Directs} {Auxin} {Efflux}},
	volume = {306},
	url = {https://www.science.org/doi/10.1126/science.1100618},
	doi = {10.1126/science.1100618},
	number = {5697},
	urldate = {2021-10-14},
	journal = {Science},
	author = {Friml, Jiří and Yang, Xiong and Michniewicz, Marta and Weijers, Dolf and Quint, Ab and Tietz, Olaf and Benjamins, René and Ouwerkerk, Pieter B. F. and Ljung, Karin and Sandberg, Göran and Hooykaas, Paul J. J. and Palme, Klaus and Offringa, Remko},
	month = oct,
	year = {2004},
	pages = {862--865},
}

@article{rae_morphological_2004,
	title = {Morphological and physiological traits influencing biomass productivity in short-rotation coppice poplar},
	volume = {34},
	issn = {0045-5067},
	url = {https://cdnsciencepub.com/doi/10.1139/x04-033},
	doi = {10/d4fjbn},
	number = {7},
	urldate = {2021-08-23},
	journal = {Canadian Journal of Forest Research},
	author = {Rae, A M and Robinson, K M and Street, N R and Taylor, G},
	month = jul,
	year = {2004},
	note = {Publisher: NRC Research Press},
	pages = {1488--1498},
}

@article{robinson_defining_2004,
	title = {Defining leaf traits linked to yield in short-rotation coppice {Salix}},
	volume = {26},
	issn = {0961-9534},
	url = {https://www.sciencedirect.com/science/article/pii/S0961953403001600},
	doi = {10/ctstfz},
	abstract = {Short-rotation coppice Salix genotypes of differing biomass yields were studied over two growing seasons with the long-term aim of identifying traits definitive of high yield for the breeding of elite energy crops. In the first season, basic leaf and stem traits were measured in six Salix genotypes, to identify morphological characteristics associated with high biomass yields. Thereafter, S. viminalis L. ‘L78183’ (low yield) and the hybrid genotype S. schwerinii E. Wolf× S. viminalis L. ‘Tora’ (high yield) were compared. Maximum stem heights and stem diameters increased with biomass yield. ‘Tora’ produced more sylleptic branches on the leading stems than ‘L78183’. Leaf traits differed significantly between the two genotypes: individual leaf area and cell number per leaf was greater in ‘Tora’, whereas cell area was greater in ‘L78183’, suggesting that final leaf areas were attained in ‘Tora’ through the production of many, small cells, and in ‘L78183’ through fewer, large cells. Leaf extension rates were higher in ‘Tora’ than ‘L78183’. This result was mirrored for leaf production rate. Leaf area index, examined at two coppice stages, was higher in ‘L78183’ (values of 2.06 and 1.67) than in ‘Tora’ (maximum value 1.43) which had a very open canopy. Furthermore, A/Ci analysis revealed the low-yielding genotype as the most photosynthetically efficient at the individual leaf level whereas light response curves suggest that ‘Tora’ utilised light more efficiently. The results presented in this study suggest that leaf extension rate, final leaf size and cell number per leaf may be indicative of yield, and may be useful as selection criteria for potentially high-yielding hybrids for biomass use.},
	language = {en},
	number = {5},
	urldate = {2021-08-23},
	journal = {Biomass and Bioenergy},
	author = {Robinson, K. M and Karp, A and Taylor, Gail},
	month = may,
	year = {2004},
	keywords = {Cell area, Leaf area, Leaf extension rate, Short-rotation coppice, Yield physiology},
	pages = {417--431},
}

Short-rotation coppice Salix genotypes of differing biomass yields were studied over two growing seasons with the long-term aim of identifying traits definitive of high yield for the breeding of elite energy crops. In the first season, basic leaf and stem traits were measured in six Salix genotypes, to identify morphological characteristics associated with high biomass yields. Thereafter, S. viminalis L. ‘L78183’ (low yield) and the hybrid genotype S. schwerinii E. Wolf× S. viminalis L. ‘Tora’ (high yield) were compared. Maximum stem heights and stem diameters increased with biomass yield. ‘Tora’ produced more sylleptic branches on the leading stems than ‘L78183’. Leaf traits differed significantly between the two genotypes: individual leaf area and cell number per leaf was greater in ‘Tora’, whereas cell area was greater in ‘L78183’, suggesting that final leaf areas were attained in ‘Tora’ through the production of many, small cells, and in ‘L78183’ through fewer, large cells. Leaf extension rates were higher in ‘Tora’ than ‘L78183’. This result was mirrored for leaf production rate. Leaf area index, examined at two coppice stages, was higher in ‘L78183’ (values of 2.06 and 1.67) than in ‘Tora’ (maximum value 1.43) which had a very open canopy. Furthermore, A/Ci analysis revealed the low-yielding genotype as the most photosynthetically efficient at the individual leaf level whereas light response curves suggest that ‘Tora’ utilised light more efficiently. The results presented in this study suggest that leaf extension rate, final leaf size and cell number per leaf may be indicative of yield, and may be useful as selection criteria for potentially high-yielding hybrids for biomass use.

@article{wu_inbreeding_2004,
	title = {Inbreeding in {Pinus} radiata - {V}. {The} effects of inbreeding on fecundity},
	volume = {53},
	issn = {00375349},
	url = {https://www.mendeley.com/catalogue/15b5790a-f00c-327c-805e-9fd9b8b7ed12/},
	doi = {10/gkm3fw},
	abstract = {(2004) Wu et al. Silvae Genetica. A successful inbreeding and hybrid breeding strategy in tree improvement requires that 1) inbreeding (selfing) can produce superior inbred lines (effective purging...},
	language = {en-GB},
	number = {2},
	urldate = {2021-08-26},
	journal = {Silvae Genetica},
	author = {Wu, H. X. and Owen, J. V. and Abarquez, A. and Matheson, A. C.},
	year = {2004},
	note = {Number: 2},
	pages = {80--87},
}

(2004) Wu et al. Silvae Genetica. A successful inbreeding and hybrid breeding strategy in tree improvement requires that 1) inbreeding (selfing) can produce superior inbred lines (effective purging...

@article{andersson_transcriptional_2004,
	title = {A transcriptional timetable of autumn senescence},
	volume = {5},
	issn = {1474-760X},
	doi = {10/dw5fcc},
	abstract = {Background: We have developed genomic tools to allow the genus Populus ( aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag ( EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence. Results: On the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92\%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree ( Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates. Conclusions: We observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components.},
	language = {English},
	number = {4},
	journal = {Genome Biology},
	author = {Andersson, A. and Keskitalo, J. and Sjodin, A. and Bhalerao, Rishikesh P. and Sterky, F. and Wissel, K. and Tandre, K. and Aspeborg, H. and Moyle, R. and Ohmiya, Y. and Bhalerao, R. and Brunner, A. and Gustafsson, P. and Karlsson, J. and Lundeberg, J. and Nilsson, O. and Sandberg, G. and Strauss, S. and Sundberg, B. and Uhlen, M. and Jansson, S. and Nilsson, P.},
	year = {2004},
	note = {Place: London
Publisher: Bmc
WOS:000220584700010},
	keywords = {aspen, biology, cytosolic glutamine-synthetase, gene-expression, genomics, leaf senescence, leaves, plants, programmed cell-death, proteins},
	pages = {R24},
}

Background: We have developed genomic tools to allow the genus Populus ( aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag ( EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence. Results: On the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree ( Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates. Conclusions: We observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components.

@article{karpinska_myb_2004,
	title = {{MYB} transcription factors are differentially expressed and regulated during secondary vascular tissue development in hybrid aspen},
	volume = {56},
	issn = {1573-5028},
	url = {https://doi.org/10.1007/s11103-004-3354-5},
	doi = {10/bg9dms},
	abstract = {More than 120,000 poplar ESTs have been sequenced from 20 different cDNA libraries by the Swedish Centre for Tree Functional Genomics. We screened this EST collection for MYB transcription factors involved in secondary vascular tissue formation, and genes assigned as PttMYB3Ra, PttMYB4a and PttMYB21a were selected for further characterisation. Three MYB genes showed different expression patterns in various organs, tissues and stem sub-sections representing different developmental stages of vascular tissue formation. Furthermore, the analysis showed that PttMYB21a expression was much higher in secondary cell wall formation zone of xylem and phloem fibers than in other developmental zones. Transgenic hybrid aspen plants, expressing the 3′-part of the PttMYB21a gene in antisense orientation were generated to assess the function of PttMYB21a gene in vascular tissue formation and lignification. All transgenic lines showed reduced growth and had fewer internodes compared to the wild-type. The analysis of selected lines showed that acid soluble lignin present in the bark was higher in transgenic lines as compared to wild-type plants. Moreover a higher transcript level of caffeoyl-CoA 3-O-methyltransferase [CCoAOMT]; EC 2.1.1.104) was found in the phloem of the transgenic plants, suggesting that PttMYB21a might function as a transcriptional repressor.},
	language = {en},
	number = {2},
	urldate = {2021-06-15},
	journal = {Plant Molecular Biology},
	author = {Karpinska, Barbara and Karlsson, Marlene and Srivastava, Manoj and Stenberg, Anneli and Schrader, Jarmo and Sterky, Fredrik and Bhalerao, Rishikesh P. and Wingsle, Gunnar},
	month = sep,
	year = {2004},
	pages = {255--270},
}

More than 120,000 poplar ESTs have been sequenced from 20 different cDNA libraries by the Swedish Centre for Tree Functional Genomics. We screened this EST collection for MYB transcription factors involved in secondary vascular tissue formation, and genes assigned as PttMYB3Ra, PttMYB4a and PttMYB21a were selected for further characterisation. Three MYB genes showed different expression patterns in various organs, tissues and stem sub-sections representing different developmental stages of vascular tissue formation. Furthermore, the analysis showed that PttMYB21a expression was much higher in secondary cell wall formation zone of xylem and phloem fibers than in other developmental zones. Transgenic hybrid aspen plants, expressing the 3′-part of the PttMYB21a gene in antisense orientation were generated to assess the function of PttMYB21a gene in vascular tissue formation and lignification. All transgenic lines showed reduced growth and had fewer internodes compared to the wild-type. The analysis of selected lines showed that acid soluble lignin present in the bark was higher in transgenic lines as compared to wild-type plants. Moreover a higher transcript level of caffeoyl-CoA 3-O-methyltransferase [CCoAOMT]; EC 2.1.1.104) was found in the phloem of the transgenic plants, suggesting that PttMYB21a might function as a transcriptional repressor.

@article{lescot_annotation_2004,
	title = {Annotation of a 95-kb {Populus} deltoides genomic sequence reveals a disease resistance gene cluster and novel class {I} and class {II} transposable elements},
	volume = {109},
	issn = {1432-2242},
	url = {https://doi.org/10.1007/s00122-004-1621-0},
	doi = {10/d4g3m9},
	abstract = {Poplar has become a model system for functional genomics in woody plants. Here, we report the sequencing and annotation of the first large contiguous stretch of genomic sequence (95 kb) of poplar, corresponding to a bacterial artificial chromosome clone mapped 0.6 centiMorgan from the Melampsora larici-populina resistance locus. The annotation revealed 15 putative genetic objects, of which five were classified as hypothetical genes that were similar only with expressed sequence tags from poplar. Ten putative objects showed similarity with known genes, of which one was similar to a kinase. Three other objects corresponded to the toll/interleukin-1 receptor/nucleotide-binding site/leucine-rich repeat class of plant disease resistance genes, of which two were predicted to encode an amino terminal nuclear localization signal. Four objects were homologous to the Ty1/copia family of class I transposable elements, one of which was designated Retropop and interrupted one of the disease resistance genes. Two other objects constituted a novel Spm-like class II transposable element, which we designated Magali.},
	language = {en},
	number = {1},
	urldate = {2021-06-30},
	journal = {Theoretical and Applied Genetics},
	author = {Lescot, M. and Rombauts, S. and Zhang, J. and Aubourg, S. and Mathé, C. and Jansson, S. and Rouzé, P. and Boerjan, W.},
	month = jun,
	year = {2004},
	pages = {10--22},
}

Poplar has become a model system for functional genomics in woody plants. Here, we report the sequencing and annotation of the first large contiguous stretch of genomic sequence (95 kb) of poplar, corresponding to a bacterial artificial chromosome clone mapped 0.6 centiMorgan from the Melampsora larici-populina resistance locus. The annotation revealed 15 putative genetic objects, of which five were classified as hypothetical genes that were similar only with expressed sequence tags from poplar. Ten putative objects showed similarity with known genes, of which one was similar to a kinase. Three other objects corresponded to the toll/interleukin-1 receptor/nucleotide-binding site/leucine-rich repeat class of plant disease resistance genes, of which two were predicted to encode an amino terminal nuclear localization signal. Four objects were homologous to the Ty1/copia family of class I transposable elements, one of which was designated Retropop and interrupted one of the disease resistance genes. Two other objects constituted a novel Spm-like class II transposable element, which we designated Magali.

@article{varghese_fertility_2004,
	title = {Fertility and effective population size in seedling seed orchards of {Casuarina} equisetifolia and {C}-junghuhniana},
	volume = {53},
	issn = {0037-5349},
	doi = {10/gkzpmq},
	abstract = {Two seedling seed orchards each of C. equisetifolia and C. junghuhniana established by thinning provenance trials in coastal and inland locations in South India were evaluated for sex expression and fertility variation at four years. More than 80\% of the trees in C. equisetifolia orchards were fertile in both sites with a similar pattern of more (almost 2 times) female trees and equal proportion of monoecious and non-flowering trees. In C. junghuhniana, the coastal orchard had twice the proportion of fertile trees as that of the inland. Orchards established in coastal environment had less fertility variation and hence maintained lower coancestry values in both species. Coastal site has more trees contributing effectively to seed production than inland locations and the orchards maintain higher (almost two times) effective population sizes. Genetic drift is also 3 times higher in inland locations in both species. Male and female trees in inland orchards of both species however had greater reproductive output than coastal trees. Monoecious Casuarina equisetifolia trees showed a different trend of greater male fertility in coastal site, but seed output was the same in both locations. Gene diversity values of all orchards are high though it is marginally higher in coastal sites. Measures like constrained seed collection from large number of trees and promoting representation of superior provenances with low fertility would be useful in checking diversity loss during domestication.},
	language = {English},
	number = {4},
	journal = {Silvae Genetica},
	author = {Varghese, M. and Lindgren, D. and Nicodemus, A.},
	year = {2004},
	note = {Place: Warsaw
Publisher: Sciendo
WOS:000228214100005},
	keywords = {breeding population, coancestry, gene diversity, number, provenance trial, relatedness, relative status number, seed orchard},
	pages = {164--168},
}

Two seedling seed orchards each of C. equisetifolia and C. junghuhniana established by thinning provenance trials in coastal and inland locations in South India were evaluated for sex expression and fertility variation at four years. More than 80% of the trees in C. equisetifolia orchards were fertile in both sites with a similar pattern of more (almost 2 times) female trees and equal proportion of monoecious and non-flowering trees. In C. junghuhniana, the coastal orchard had twice the proportion of fertile trees as that of the inland. Orchards established in coastal environment had less fertility variation and hence maintained lower coancestry values in both species. Coastal site has more trees contributing effectively to seed production than inland locations and the orchards maintain higher (almost two times) effective population sizes. Genetic drift is also 3 times higher in inland locations in both species. Male and female trees in inland orchards of both species however had greater reproductive output than coastal trees. Monoecious Casuarina equisetifolia trees showed a different trend of greater male fertility in coastal site, but seed output was the same in both locations. Gene diversity values of all orchards are high though it is marginally higher in coastal sites. Measures like constrained seed collection from large number of trees and promoting representation of superior provenances with low fertility would be useful in checking diversity loss during domestication.

@article{danusevicius_progeny_2004,
	title = {Progeny testing preceded by phenotypic pre-selection - {Timing} considerations},
	volume = {53},
	issn = {0037-5349},
	doi = {10/gkzpms},
	abstract = {Progeny-testing is a common element in tree breeding. It takes long time until trees reach the sexual maturity. That time could be used for field testing followed by progeny-test of the selected phenotypes (two-stage strategy), or the time until mating could be reduced by forcing early flowering (single-stage strategy). Benefit of phenotypic pre-selection followed by progeny testing in long-term breeding was assessed as a function of the age at the pre-selection by the aid of a deterministic tree breeding simulator. As a criterion of goodness of a breeding program, annual progress in group merit (GM/Y-refers to the rate of change in the average of genetic gain and gene diversity) at a total budget constraint was used. For simplicity, a long-term program with balanced selection was studied. Scenarios with different genetic parameters, cost and time components were evaluated and optimised for resource allocation. At the optimum age of mating for progeny test, two-stage Phenotype/Progeny strategy generated higher GM/Y than single-stage Progeny strategy at the age of mating for progeny test equal to three years, except for a typical scenario with weak J-M correlation, low heritability and long rotation time. High heritability, short rotation and strong J-M genetic correlation favoured phenotypic pre-selection. Optimum age for phenotypic pre-selection varied from 6 to 17 years and the percentage of GM/Y lost in comparison to the maximum due to delay of mating for the progeny test until age 15 and 25 years ranged from 0 to 14\% and from 1 to 29\%, respectively. In the case of low heritability, long rotation, low J-M correlation, high cost for cycling and low budget, early mating age would bring little benefit if compared to mating at the optimum age. We suggest that, in long-term breeding based on progeny testing, investment in phenotypic pre-selection is more beneficial than investment to achieve early flowering to initiate the progeny test early.},
	language = {English},
	number = {1},
	journal = {Silvae Genetica},
	author = {Danusevicius, D. and Lindgren, D.},
	year = {2004},
	note = {Place: Warsaw
Publisher: De Gruyter Poland Sp Zoo
WOS:000223916000004},
	keywords = {age, annual gain, early selection, efficiencies, flowering   induction, gene diversity, genetic-control, group merit, growth, intensity, juvenile-mature correlation, loblolly-pine, optimisation, relatedness, stage-wise selection, two-stage selection},
	pages = {20--26},
}

Progeny-testing is a common element in tree breeding. It takes long time until trees reach the sexual maturity. That time could be used for field testing followed by progeny-test of the selected phenotypes (two-stage strategy), or the time until mating could be reduced by forcing early flowering (single-stage strategy). Benefit of phenotypic pre-selection followed by progeny testing in long-term breeding was assessed as a function of the age at the pre-selection by the aid of a deterministic tree breeding simulator. As a criterion of goodness of a breeding program, annual progress in group merit (GM/Y-refers to the rate of change in the average of genetic gain and gene diversity) at a total budget constraint was used. For simplicity, a long-term program with balanced selection was studied. Scenarios with different genetic parameters, cost and time components were evaluated and optimised for resource allocation. At the optimum age of mating for progeny test, two-stage Phenotype/Progeny strategy generated higher GM/Y than single-stage Progeny strategy at the age of mating for progeny test equal to three years, except for a typical scenario with weak J-M correlation, low heritability and long rotation time. High heritability, short rotation and strong J-M genetic correlation favoured phenotypic pre-selection. Optimum age for phenotypic pre-selection varied from 6 to 17 years and the percentage of GM/Y lost in comparison to the maximum due to delay of mating for the progeny test until age 15 and 25 years ranged from 0 to 14% and from 1 to 29%, respectively. In the case of low heritability, long rotation, low J-M correlation, high cost for cycling and low budget, early mating age would bring little benefit if compared to mating at the optimum age. We suggest that, in long-term breeding based on progeny testing, investment in phenotypic pre-selection is more beneficial than investment to achieve early flowering to initiate the progeny test early.

@article{tarkowski_analytical_2004,
	title = {Analytical methods in cytokinin research},
	volume = {98},
	issn = {0009-2770},
	abstract = {Cytokinins, a group of N-6-substituted adenine derivatives, are phytohormones that play an important role in plant growth and development. Plant tissue extracts are complex mixtures containing cytokinins in minute quantities. Therefore, sensitive and sufficiently selective analytical tools are required for determination and/or identification of cytokinins in plants. Main techniques (GC/MS, HPLC/MS) currently employed for qualitative and quantitative analyses of cytokinins as well as widely utilised extraction and purification procedures are discussed.},
	language = {Czech},
	number = {9},
	journal = {Chemicke Listy},
	author = {Tarkowski, P. and Dolezal, K. and Strnad, M.},
	year = {2004},
	note = {Place: Prague 6
Publisher: Chemicke Listy
WOS:000224366000004},
	keywords = {arabidopsis-thaliana, bombardment mass-spectrometry, capillary liquid   chromatography/frit, crown-gall tissue, dihydrozeatin riboside, electrochemical reduction, gas-chromatography, monoclonal-antibodies, stripping voltammetry, zeatin-riboside, ⛔ No DOI found},
	pages = {834--841},
}

Cytokinins, a group of N-6-substituted adenine derivatives, are phytohormones that play an important role in plant growth and development. Plant tissue extracts are complex mixtures containing cytokinins in minute quantities. Therefore, sensitive and sufficiently selective analytical tools are required for determination and/or identification of cytokinins in plants. Main techniques (GC/MS, HPLC/MS) currently employed for qualitative and quantitative analyses of cytokinins as well as widely utilised extraction and purification procedures are discussed.

@article{gullberg_design_2004,
	title = {Design of experiments: an efficient strategy to identify factors influencing extraction and derivatization of {Arabidopsis} thaliana samples in metabolomic studies with gas chromatography/mass spectrometry},
	volume = {331},
	issn = {0003-2697},
	shorttitle = {Design of experiments},
	url = {https://www.sciencedirect.com/science/article/pii/S0003269704003811},
	doi = {10/ftg6fz},
	abstract = {The usual aim in metabolomic studies is to quantify the entire metabolome of each of a series of biological samples. To do this for complex biological matrices, e.g., plant tissues, efficient and reproducible extraction protocols must be developed. However, derivatization protocols must also be developed if GC/MS (one of the mostly widely used analytical methods for metabolomics) is involved. The aim of this study was to investigate how different chemical and physical factors (extraction solvent, derivatization reagents, and temperature) affect the extraction and derivatization of the metabolome from leaves of the plant Arabidopsis thaliana. Using design of experiment procedures, variation was systematically introduced, and the effects of this variation were analyzed using regression models. The results show that this approach allows a reliable protocol for metabolomic analysis of Arabidopsis to be determined with a relatively limited number of experiments. Following two different investigations an extraction and derivatization protocol was chosen. Further, the reproducibility of the analysis of 66 endogenous compounds was investigated, and it was shown that both hydrophilic and lipophilic compounds were detected with high reproducibility.},
	language = {en},
	number = {2},
	urldate = {2021-06-30},
	journal = {Analytical Biochemistry},
	author = {Gullberg, Jonas and Jonsson, Pär and Nordström, Anders and Sjöström, Michael and Moritz, Thomas},
	month = aug,
	year = {2004},
	keywords = {Derivatization, Design of experiments, Extraction, Mass spectrometry, Metabolomics},
	pages = {283--295},
}

The usual aim in metabolomic studies is to quantify the entire metabolome of each of a series of biological samples. To do this for complex biological matrices, e.g., plant tissues, efficient and reproducible extraction protocols must be developed. However, derivatization protocols must also be developed if GC/MS (one of the mostly widely used analytical methods for metabolomics) is involved. The aim of this study was to investigate how different chemical and physical factors (extraction solvent, derivatization reagents, and temperature) affect the extraction and derivatization of the metabolome from leaves of the plant Arabidopsis thaliana. Using design of experiment procedures, variation was systematically introduced, and the effects of this variation were analyzed using regression models. The results show that this approach allows a reliable protocol for metabolomic analysis of Arabidopsis to be determined with a relatively limited number of experiments. Following two different investigations an extraction and derivatization protocol was chosen. Further, the reproducibility of the analysis of 66 endogenous compounds was investigated, and it was shown that both hydrophilic and lipophilic compounds were detected with high reproducibility.

@article{eriksson_using_2004,
	title = {Using chemometrics for navigating in the large data sets of genomics, proteomics, and metabonomics (gpm)},
	volume = {380},
	issn = {1618-2650},
	url = {https://doi.org/10.1007/s00216-004-2783-y},
	doi = {10/ct97hh},
	abstract = {This article describes the applicability of multivariate projection techniques, such as principal-component analysis (PCA) and partial least-squares (PLS) projections to latent structures, to the large-volume high-density data structures obtained within genomics, proteomics, and metabonomics. PCA and PLS, and their extensions, derive their usefulness from their ability to analyze data with many, noisy, collinear, and even incomplete variables in both X and Y. Three examples are used as illustrations: the first example is a genomics data set and involves modeling of microarray data of cell cycle-regulated genes in the microorganism Saccharomyces cerevisiae. The second example contains NMR-metabonomics data, measured on urine samples of male rats treated with either of the drugs chloroquine or amiodarone. The third and last data set describes sequence-function classification studies in a set of G-protein-coupled receptors using hierarchical PCA.},
	language = {en},
	number = {3},
	urldate = {2021-06-30},
	journal = {Analytical and Bioanalytical Chemistry},
	author = {Eriksson, Lennart and Antti, Henrik and Gottfries, Johan and Holmes, Elaine and Johansson, Erik and Lindgren, Fredrik and Long, Ingrid and Lundstedt, Torbjörn and Trygg, Johan and Wold, Svante},
	month = oct,
	year = {2004},
	pages = {419--429},
}

This article describes the applicability of multivariate projection techniques, such as principal-component analysis (PCA) and partial least-squares (PLS) projections to latent structures, to the large-volume high-density data structures obtained within genomics, proteomics, and metabonomics. PCA and PLS, and their extensions, derive their usefulness from their ability to analyze data with many, noisy, collinear, and even incomplete variables in both X and Y. Three examples are used as illustrations: the first example is a genomics data set and involves modeling of microarray data of cell cycle-regulated genes in the microorganism Saccharomyces cerevisiae. The second example contains NMR-metabonomics data, measured on urine samples of male rats treated with either of the drugs chloroquine or amiodarone. The third and last data set describes sequence-function classification studies in a set of G-protein-coupled receptors using hierarchical PCA.

@article{nordstrom_derivatization_2004,
	title = {Derivatization for {LC}-{Electrospray} {Ionization}-{MS}:  {A} {Tool} for {Improving} {Reversed}-{Phase} {Separation} and {ESI} {Responses} of {Bases}, {Ribosides}, and {Intact} {Nucleotides}},
	volume = {76},
	issn = {0003-2700},
	shorttitle = {Derivatization for {LC}-{Electrospray} {Ionization}-{MS}},
	url = {https://doi.org/10.1021/ac0499017},
	doi = {10/b9ckbc},
	abstract = {We have developed a method for analyzing polar compounds by reversed-phase LC-ESI-MS following esterification of the analytes' free hydroxyl groups with propionyl or benzoyl acid anhydride. The method was applied to members of the plant hormone group cytokinins, which includes adenine bases, ribosides/glycosides, and nucleotides substituted at N-6 with an isoprenoid side chain, spanning a wide range of polarity. It was also used to analyze other compounds of biological importance, e.g., the nucleotides AMP, ADP, and ATP. The formation of more hydrophobic derivatives had a significant impact on two aspects of the analysis. The retention on a reversed-phase material was greatly increased without the use of any acetate/formate buffer or ion pairing reagent, and the ESI response was enhanced, due to the higher surface activities of the derivatives. Detection limits of propionylated cytokinins were in the high-attomole to low-femtomole range, an improvement by factors of 10−100 compared to previously reported figures. Using an automated SPE-based purification method, 12 endogenous cytokinins were quantified in extracts from 20- to 100-mg samples of leaves (from the plant Arabidopsis thaliana) with high accuracy and precision. Furthermore, the chromatographic properties of the benzoylated AMP, ADP, and ATP in the reversed-phase LC−MS system were much better in terms of retention, separation, and sensitivity than those of their underivatized counterparts, even without the use of any ion pairing reagent. Our data show that derivatization followed by LC-ESI-MS is an effective strategy for analyzing low molecular weight compounds, enabling compounds with a wide range of polarity to be determined in a single-injection LC−MS analysis.},
	number = {10},
	urldate = {2021-06-30},
	journal = {Analytical Chemistry},
	author = {Nordström, Anders and Tarkowski, Petr and Tarkowska, Danuse and Dolezal, Karel and Åstot, Crister and Sandberg, Göran and Moritz, Thomas},
	month = may,
	year = {2004},
	note = {Publisher: American Chemical Society},
	pages = {2869--2877},
}

We have developed a method for analyzing polar compounds by reversed-phase LC-ESI-MS following esterification of the analytes' free hydroxyl groups with propionyl or benzoyl acid anhydride. The method was applied to members of the plant hormone group cytokinins, which includes adenine bases, ribosides/glycosides, and nucleotides substituted at N-6 with an isoprenoid side chain, spanning a wide range of polarity. It was also used to analyze other compounds of biological importance, e.g., the nucleotides AMP, ADP, and ATP. The formation of more hydrophobic derivatives had a significant impact on two aspects of the analysis. The retention on a reversed-phase material was greatly increased without the use of any acetate/formate buffer or ion pairing reagent, and the ESI response was enhanced, due to the higher surface activities of the derivatives. Detection limits of propionylated cytokinins were in the high-attomole to low-femtomole range, an improvement by factors of 10−100 compared to previously reported figures. Using an automated SPE-based purification method, 12 endogenous cytokinins were quantified in extracts from 20- to 100-mg samples of leaves (from the plant Arabidopsis thaliana) with high accuracy and precision. Furthermore, the chromatographic properties of the benzoylated AMP, ADP, and ATP in the reversed-phase LC−MS system were much better in terms of retention, separation, and sensitivity than those of their underivatized counterparts, even without the use of any ion pairing reagent. Our data show that derivatization followed by LC-ESI-MS is an effective strategy for analyzing low molecular weight compounds, enabling compounds with a wide range of polarity to be determined in a single-injection LC−MS analysis.

@article{jonsson_strategy_2004,
	title = {A {Strategy} for {Identifying} {Differences} in {Large} {Series} of {Metabolomic} {Samples} {Analyzed} by {GC}/{MS}},
	volume = {76},
	issn = {0003-2700},
	url = {https://doi.org/10.1021/ac0352427},
	doi = {10/dm24rr},
	abstract = {In metabolomics, the purpose is to identify and quantify all the metabolites in a biological system. Combined gas chromatography and mass spectrometry (GC/MS) is one of the most commonly used techniques in metabolomics together with 1H NMR, and it has been shown that more than 300 compounds can be distinguished with GC/MS after deconvolution of overlapping peaks. To avoid having to deconvolute all analyzed samples prior to multivariate analysis of the data, we have developed a strategy for rapid comparison of nonprocessed MS data files. The method includes baseline correction, alignment, time window determinations, alternating regression, PLS-DA, and identification of retention time windows in the chromatograms that explain the differences between the samples. Use of alternating regression also gives interpretable loadings, which retain the information provided by m/z values that vary between the samples in each retention time window. The method has been applied to plant extracts derived from leaves of different developmental stages and plants subjected to small changes in day length. The data show that the new method can detect differences between the samples and that it gives results comparable to those obtained when deconvolution is applied prior to the multivariate analysis. We suggest that this method can be used for rapid comparison of large sets of GC/MS data, thereby applying time-consuming deconvolution only to parts of the chromatograms that contribute to explain the differences between the samples.},
	number = {6},
	urldate = {2021-06-30},
	journal = {Analytical Chemistry},
	author = {Jonsson, Pär and Gullberg, Jonas and Nordström, Anders and Kusano, Miyako and Kowalczyk, Mariusz and Sjöström, Michael and Moritz, Thomas},
	month = mar,
	year = {2004},
	note = {Publisher: American Chemical Society},
	pages = {1738--1745},
}

In metabolomics, the purpose is to identify and quantify all the metabolites in a biological system. Combined gas chromatography and mass spectrometry (GC/MS) is one of the most commonly used techniques in metabolomics together with 1H NMR, and it has been shown that more than 300 compounds can be distinguished with GC/MS after deconvolution of overlapping peaks. To avoid having to deconvolute all analyzed samples prior to multivariate analysis of the data, we have developed a strategy for rapid comparison of nonprocessed MS data files. The method includes baseline correction, alignment, time window determinations, alternating regression, PLS-DA, and identification of retention time windows in the chromatograms that explain the differences between the samples. Use of alternating regression also gives interpretable loadings, which retain the information provided by m/z values that vary between the samples in each retention time window. The method has been applied to plant extracts derived from leaves of different developmental stages and plants subjected to small changes in day length. The data show that the new method can detect differences between the samples and that it gives results comparable to those obtained when deconvolution is applied prior to the multivariate analysis. We suggest that this method can be used for rapid comparison of large sets of GC/MS data, thereby applying time-consuming deconvolution only to parts of the chromatograms that contribute to explain the differences between the samples.

@article{fischer_lipid_2004,
	title = {Lipid function in plant cell polarity},
	volume = {7},
	issn = {1369-5266},
	url = {https://www.sciencedirect.com/science/article/pii/S1369526604001281},
	doi = {10/dt4txx},
	abstract = {The establishment and maintenance of cell polarity play pivotal roles during plant development. During the past five years, proteins that are required for different aspects of plant cell polarity have been identified. However, the functions of lipids and their interactions with proteins that mediate polarity remained largely unaddressed. Recent genetic studies have discovered cell and tissue polarity mutants that have defects in sterol composition, glycosylphosphatidylinositol-anchored proteins, glycosylphosphatidylinositol biosynthesis and phospholipid signalling. Analyses of the affected gene products have provided a first glance at the roles of lipids in cell polarity signalling, as well as in the trafficking and anchoring of polar proteins.},
	language = {en},
	number = {6},
	urldate = {2021-06-30},
	journal = {Current Opinion in Plant Biology},
	author = {Fischer, Urs and Men, Shuzhen and Grebe, Markus},
	month = dec,
	year = {2004},
	pages = {670--676},
}

The establishment and maintenance of cell polarity play pivotal roles during plant development. During the past five years, proteins that are required for different aspects of plant cell polarity have been identified. However, the functions of lipids and their interactions with proteins that mediate polarity remained largely unaddressed. Recent genetic studies have discovered cell and tissue polarity mutants that have defects in sterol composition, glycosylphosphatidylinositol-anchored proteins, glycosylphosphatidylinositol biosynthesis and phospholipid signalling. Analyses of the affected gene products have provided a first glance at the roles of lipids in cell polarity signalling, as well as in the trafficking and anchoring of polar proteins.

@article{keun_geometric_2004,
	title = {Geometric {Trajectory} {Analysis} of {Metabolic} {Responses} {To} {Toxicity} {Can} {Define} {Treatment} {Specific} {Profiles}},
	volume = {17},
	issn = {0893-228X},
	url = {https://doi.org/10.1021/tx034212w},
	doi = {10/cm5x4j},
	abstract = {Metabonomics can be viewed as the process of defining multivariate metabolic trajectories that describe the systemic response of organisms to physiological perturbations through time. We have explored the hypothesis that the homothetic geometry of a metabolic trajectory, i.e., the metabolic response irrespective of baseline values and overall magnitude, defines the mode of response of the organism to treatment and is hence the key property when considering the similarity between two sets of measurements. A modeling strategy to test for homothetic geometry, called scaled-to-maximum, aligned, and reduced trajectories (SMART) analysis, is presented that together with principal components analysis (PCA) facilitates the visualization of multivariate response similarity and hence the interpretation of metabonomic data. Several examples of the utility of this approach from toxicological studies are presented as follows:  interlaboratory variation in hydrazine response, CCl4 dose−response relationships, and interspecies comparison of bromobenzene toxicity. In each case, the homothetic trajectories hypothesis is shown to be an important concept for the successful multivariate modeling and interpretation of systemic metabolic change. Overall, geometric trajectory analysis based on a homothetic modeling strategy like SMART facilitates the amalgamation and comparison of metabonomic data sets and can improve the accuracy and precision of classification models based on metabolic profile data. Because interlaboratory variation, normal physiological variation, dose−response relationships, and interspecies differences are also key areas of concern in genomic and proteomic as well as metabonomic studies, the methods presented here may also have an impact on many other multilaboratory efforts to produce screenable “-omics” databases useful for gauging toxicity in safety assessment and drug discovery.},
	number = {5},
	urldate = {2021-06-30},
	journal = {Chemical Research in Toxicology},
	author = {Keun, Hector C. and Ebbels, Timothy M. D. and Bollard, Mary E. and Beckonert, Olaf and Antti, Henrik and Holmes, Elaine and Lindon, John C. and Nicholson, Jeremy K.},
	month = may,
	year = {2004},
	note = {Publisher: American Chemical Society},
	pages = {579--587},
}

Metabonomics can be viewed as the process of defining multivariate metabolic trajectories that describe the systemic response of organisms to physiological perturbations through time. We have explored the hypothesis that the homothetic geometry of a metabolic trajectory, i.e., the metabolic response irrespective of baseline values and overall magnitude, defines the mode of response of the organism to treatment and is hence the key property when considering the similarity between two sets of measurements. A modeling strategy to test for homothetic geometry, called scaled-to-maximum, aligned, and reduced trajectories (SMART) analysis, is presented that together with principal components analysis (PCA) facilitates the visualization of multivariate response similarity and hence the interpretation of metabonomic data. Several examples of the utility of this approach from toxicological studies are presented as follows:  interlaboratory variation in hydrazine response, CCl4 dose−response relationships, and interspecies comparison of bromobenzene toxicity. In each case, the homothetic trajectories hypothesis is shown to be an important concept for the successful multivariate modeling and interpretation of systemic metabolic change. Overall, geometric trajectory analysis based on a homothetic modeling strategy like SMART facilitates the amalgamation and comparison of metabonomic data sets and can improve the accuracy and precision of classification models based on metabolic profile data. Because interlaboratory variation, normal physiological variation, dose−response relationships, and interspecies differences are also key areas of concern in genomic and proteomic as well as metabonomic studies, the methods presented here may also have an impact on many other multilaboratory efforts to produce screenable “-omics” databases useful for gauging toxicity in safety assessment and drug discovery.

@article{djerbi_identification_2004,
	title = {Identification and expression analysis of genes encoding putative cellulose synthases ({CesA}) in the hybrid aspen, {Populus} tremula ({L}.) x {P}-tremuloides ({Michx}.)},
	volume = {11},
	issn = {0969-0239},
	doi = {10/bc795m},
	abstract = {Cellulose is synthesized in plant cell walls by large membrane-bound protein complexes proposed to contain several copies of the catalytic subunit of the cellulose synthase, CesA. Here we report identification of 10 distinct CesA genes within a database of 100,000 ESTs of the hybrid aspen, Populus tremula (L.) x P. tremuloides (Michx.). Expression analyses in normal wood undergoing xylogenesis and in tension wood indicate xylem specific expression of four putative CesA isoenzymes, PttCesA1, PttCesA3-1, PttCesA3-2 and PttCesA9. Both the protein sequences and the expression profiles of PttCesA3-1 and PttCesA3-2 are very similar, and they may thus represent redundant copies of an enzyme with essentially the same function. Further, one of the generally more constitutively expressed CesA genes, PttCesA2, seems to be activated on the opposite side of a tension wood induced stem, while PttCesA6 appears to be more specific for leaf tissues. The rest of the hybrid aspen CesA genes were found to be relatively evenly expressed over the poplar tissues hereby studied.},
	language = {English},
	number = {3-4},
	journal = {Cellulose},
	author = {Djerbi, S. and Aspeborg, H. and Nilsson, P. and Sundberg, B. and Mellerowicz, E. and Blomqvist, K. and Teeri, T. T.},
	month = dec,
	year = {2004},
	note = {Place: Dordrecht
Publisher: Springer
WOS:000225573000004},
	keywords = {arabidopsis, biosynthesis, catalytic subunits, cellulose synthesis, expression profiling, glycosyltransferases, higher-plants, hybrid aspen, isoxaben, plant cell   wall, resistance, sequence-analysis, tension, tension wood, xylem},
	pages = {301--312},
}

Cellulose is synthesized in plant cell walls by large membrane-bound protein complexes proposed to contain several copies of the catalytic subunit of the cellulose synthase, CesA. Here we report identification of 10 distinct CesA genes within a database of 100,000 ESTs of the hybrid aspen, Populus tremula (L.) x P. tremuloides (Michx.). Expression analyses in normal wood undergoing xylogenesis and in tension wood indicate xylem specific expression of four putative CesA isoenzymes, PttCesA1, PttCesA3-1, PttCesA3-2 and PttCesA9. Both the protein sequences and the expression profiles of PttCesA3-1 and PttCesA3-2 are very similar, and they may thus represent redundant copies of an enzyme with essentially the same function. Further, one of the generally more constitutively expressed CesA genes, PttCesA2, seems to be activated on the opposite side of a tension wood induced stem, while PttCesA6 appears to be more specific for leaf tissues. The rest of the hybrid aspen CesA genes were found to be relatively evenly expressed over the poplar tissues hereby studied.

@article{antti_statistical_2004,
	title = {Statistical experimental design and partial least squares regression analysis of biofluid metabonomic {NMR} and clinical chemistry data for screening of adverse drug effects},
	volume = {73},
	issn = {0169-7439},
	doi = {10/cndrbv},
	abstract = {Metabonomic analysis is increasingly recognised as a powerful approach for delineating the integrated metabolic changes in biofluids and tissues due to toxicity, disease processes or genetic modification in whole animal systems. When dealing with complex biological data sets, as generated within metabonomics, as well as related fields such as genomics and proteomics, reliability and significance of identified biomarkers associated with specific states related to toxicity or disease are crucial in order to gain detailed and relevant interpretations of the metabolic fluxes in the studied systems. Since various physiological factors, such as diet, state of health, age, diurnal cycles, stress, genetic drift, and strain differences, affect the metabolic composition of biological matrices, it is of great importance to create statistically reliable decision tools for distinguishing between physiological and pathological responses in animal models. In the screening for new biomarkers or patterns of pathological dysfunction, methods providing statistically valid measures of effect-related changes will become increasingly important as the data within areas such as genomics, proteomics and metabonomics continues to grow in size and complexity. H-1 NMR spectroscopy and mass spectrometry are the principal analytical platforms used to derive the data and, because extensively large data sets are required, as much consideration has to be given to optimum design of experiments (DoE) as for subsequent data analysis. Thus, statistical experimental design combined with partial least squares (PLS) regression is proposed as an efficient approach for undertaking metabonomic studies and for analysis of the results. The method was applied to data from a liver toxicology study in the rat using hydrazine as a model toxin. 1D projections of 2D J-resolved (J-RES) H-1 NMR spectra and the corresponding clinical chemistry parameters of blood serum samples from control and dosed rats (30 and 90 mg/ kg) collected at 48 and 168 h post dose were analysed. Confidence intervals for the PLS regression coefficients were used to create a statistical means for screening of biomarkers in the two combined data blocks (NMR and clinical chemistry data). PLS analysis was also used to reveal the correlation pattern between the two blocks of data as well as the within the two blocks according to dose, time and the interaction dose x time. (C) 2004 Elsevier B.V. All rights reserved.},
	language = {English},
	number = {1},
	journal = {Chemometrics and Intelligent Laboratory Systems},
	author = {Antti, H. and Ebbels, T. M. D. and Keun, H. C. and Bollard, M. E. and Beckonert, O. and Lindon, J. C. and Nicholson, J. K. and Holmes, E.},
	month = sep,
	year = {2004},
	note = {Place: Amsterdam
Publisher: Elsevier
WOS:000223990900016},
	keywords = {PLS analysis, classification, clinical chemistry, design of experiments, h-1, h-1-nmr   spectroscopy, lesions, magnetic-resonance spectroscopy, metabonomics, model, nmr, pattern-recognition methods, spectra, urine},
	pages = {139--149},
}

Metabonomic analysis is increasingly recognised as a powerful approach for delineating the integrated metabolic changes in biofluids and tissues due to toxicity, disease processes or genetic modification in whole animal systems. When dealing with complex biological data sets, as generated within metabonomics, as well as related fields such as genomics and proteomics, reliability and significance of identified biomarkers associated with specific states related to toxicity or disease are crucial in order to gain detailed and relevant interpretations of the metabolic fluxes in the studied systems. Since various physiological factors, such as diet, state of health, age, diurnal cycles, stress, genetic drift, and strain differences, affect the metabolic composition of biological matrices, it is of great importance to create statistically reliable decision tools for distinguishing between physiological and pathological responses in animal models. In the screening for new biomarkers or patterns of pathological dysfunction, methods providing statistically valid measures of effect-related changes will become increasingly important as the data within areas such as genomics, proteomics and metabonomics continues to grow in size and complexity. H-1 NMR spectroscopy and mass spectrometry are the principal analytical platforms used to derive the data and, because extensively large data sets are required, as much consideration has to be given to optimum design of experiments (DoE) as for subsequent data analysis. Thus, statistical experimental design combined with partial least squares (PLS) regression is proposed as an efficient approach for undertaking metabonomic studies and for analysis of the results. The method was applied to data from a liver toxicology study in the rat using hydrazine as a model toxin. 1D projections of 2D J-resolved (J-RES) H-1 NMR spectra and the corresponding clinical chemistry parameters of blood serum samples from control and dosed rats (30 and 90 mg/ kg) collected at 48 and 168 h post dose were analysed. Confidence intervals for the PLS regression coefficients were used to create a statistical means for screening of biomarkers in the two combined data blocks (NMR and clinical chemistry data). PLS analysis was also used to reveal the correlation pattern between the two blocks of data as well as the within the two blocks according to dose, time and the interaction dose x time. (C) 2004 Elsevier B.V. All rights reserved.

@article{savolainen_genetic_2004,
	title = {Genetic variation in cessation of growth and frost hardiness and consequences for adaptation of {Pinus} sylvestris to climatic changes},
	volume = {197},
	issn = {0378-1127},
	doi = {10/dvn6cp},
	abstract = {Responses to climate change will include changes in species composition, but adaptation through genetic change may also be possible. The response to selection depends on the availability of additive genetic variation and the strength of selection. We found that Finnish populations of Scots pine have much genetic variation within the populations with respect to two traits related to climatic adaptation. Heritabilities (standard deviations) were 0.67 (0.16) and 0.33 (0.17) for the timing of bud set of 1-year-old seedlings and for frost hardiness 0.36 (0.14) and 0.20 (0.13) (not significantly different from zero) in the northern and southern populations, respectively. The additive genetic correlation between the traits was 0.57 (0.07). The proportion of additive genetic variation between the populations (Q(ST)) was 0.86 (0.11). Assuming that the new phenotypic optimum can be deduced based on the current match of temperature sums and phenotypic means, we test whether Scots pine in northern Finland can change to the new predicted optimum through migration and local selection during the next 100 years. The simulation model was based on monitoring 10 populations of 100 individuals. Five independent loci with two alleles were used to model the phenotypic trait of growth period. The results showed that genetic change will be slow and lag behind the moving optimum. Part of the slowness was due to the survival of current trees, which makes establishment of new trees with more suitable genotypes slower. Adaptation in species with fragmented populations and little migration could be even slower. Artificial regeneration with suitable seed sources can increase the proportion of adapted genotypes in cultivated species. (C) 2004 Published by Elsevier B.V.},
	language = {English},
	number = {1-3},
	journal = {Forest Ecology and Management},
	author = {Savolainen, O. and Bokma, F. and Garcia-Gil, R. and Komulainen, P. and Repo, T.},
	month = aug,
	year = {2004},
	note = {Place: Amsterdam
Publisher: Elsevier Science Bv
WOS:000223382700007},
	keywords = {abies l karst, adaptation, boreal forests, climate change, cold-hardiness, contorta, f-st, frost hardiness, nucleotide diversity, pollen migration, populations, responses, scots pine, timing of growth, traits},
	pages = {79--89},
}

Responses to climate change will include changes in species composition, but adaptation through genetic change may also be possible. The response to selection depends on the availability of additive genetic variation and the strength of selection. We found that Finnish populations of Scots pine have much genetic variation within the populations with respect to two traits related to climatic adaptation. Heritabilities (standard deviations) were 0.67 (0.16) and 0.33 (0.17) for the timing of bud set of 1-year-old seedlings and for frost hardiness 0.36 (0.14) and 0.20 (0.13) (not significantly different from zero) in the northern and southern populations, respectively. The additive genetic correlation between the traits was 0.57 (0.07). The proportion of additive genetic variation between the populations (Q(ST)) was 0.86 (0.11). Assuming that the new phenotypic optimum can be deduced based on the current match of temperature sums and phenotypic means, we test whether Scots pine in northern Finland can change to the new predicted optimum through migration and local selection during the next 100 years. The simulation model was based on monitoring 10 populations of 100 individuals. Five independent loci with two alleles were used to model the phenotypic trait of growth period. The results showed that genetic change will be slow and lag behind the moving optimum. Part of the slowness was due to the survival of current trees, which makes establishment of new trees with more suitable genotypes slower. Adaptation in species with fragmented populations and little migration could be even slower. Artificial regeneration with suitable seed sources can increase the proportion of adapted genotypes in cultivated species. (C) 2004 Published by Elsevier B.V.

@article{eriksson_genetic_2004,
	title = {Genetic {Dissection} of {Nutritional} {Copper} {Signaling} in {Chlamydomonas} {Distinguishes} {Regulatory} and {Target} {Genes}},
	volume = {168},
	issn = {1943-2631},
	url = {https://doi.org/10.1534/genetics.104.030460},
	doi = {10/c6z9cj},
	abstract = {A genetic screen for Chlamydomonas reinhardtii mutants with copper-dependent growth or nonphotosynthetic phenotypes revealed three loci, COPPER RESPONSE REGULATOR 1 (CRR1), COPPER RESPONSE DEFECT 1 (CRD1), and COPPER RESPONSE DEFECT 2 (CRD2), distinguished as regulatory or target genes on the basis of phenotype. CRR1 was shown previously to be required for transcriptional activation of target genes like CYC6, CPX1, and CRD1, encoding, respectively, cytochrome c6 (which is a heme-containing substitute for copper-containing plastocyanin), coproporphyrinogen III oxidase, and Mg-protoporphyrin IX monomethylester cyclase. We show here that CRR1 is required also for normal accumulation of copper proteins like plastocyanin and ferroxidase in copper-replete medium and for apoplastocyanin degradation in copper-deficient medium, indicating that a single pathway controls nutritional copper homeostasis at multiple levels. CRR1 is linked to the SUPPRESSOR OF PCY1-AC208 13 (SOP13) locus, which corresponds to a gain-of-function mutation resulting in copper-independent expression of CYC6. CRR1 is required also for hypoxic growth, pointing to a physiologically meaningful regulatory connection between copper deficiency and hypoxia. The growth phenotype of crr1 strains results primarily from secondary iron deficiency owing to reduced ferroxidase abundance, suggesting a role for CRR1 in copper distribution to a multicopper ferroxidase involved in iron assimilation. Mutations at the CRD2 locus also result in copper-conditional iron deficiency, which is consistent with a function for CRD2 in a pathway for copper delivery to the ferroxidase. Taken together, the observations argue for a specialized copper-deficiency adaptation for iron uptake in Chlamydomonas.},
	number = {2},
	urldate = {2021-06-30},
	journal = {Genetics},
	author = {Eriksson, Mats and Moseley, Jeffrey L and Tottey, Stephen and del Campo, Jose A and Quinn, Jeanette and Kim, Youngbae and Merchant, Sabeeha},
	month = oct,
	year = {2004},
	pages = {795--807},
}

A genetic screen for Chlamydomonas reinhardtii mutants with copper-dependent growth or nonphotosynthetic phenotypes revealed three loci, COPPER RESPONSE REGULATOR 1 (CRR1), COPPER RESPONSE DEFECT 1 (CRD1), and COPPER RESPONSE DEFECT 2 (CRD2), distinguished as regulatory or target genes on the basis of phenotype. CRR1 was shown previously to be required for transcriptional activation of target genes like CYC6, CPX1, and CRD1, encoding, respectively, cytochrome c6 (which is a heme-containing substitute for copper-containing plastocyanin), coproporphyrinogen III oxidase, and Mg-protoporphyrin IX monomethylester cyclase. We show here that CRR1 is required also for normal accumulation of copper proteins like plastocyanin and ferroxidase in copper-replete medium and for apoplastocyanin degradation in copper-deficient medium, indicating that a single pathway controls nutritional copper homeostasis at multiple levels. CRR1 is linked to the SUPPRESSOR OF PCY1-AC208 13 (SOP13) locus, which corresponds to a gain-of-function mutation resulting in copper-independent expression of CYC6. CRR1 is required also for hypoxic growth, pointing to a physiologically meaningful regulatory connection between copper deficiency and hypoxia. The growth phenotype of crr1 strains results primarily from secondary iron deficiency owing to reduced ferroxidase abundance, suggesting a role for CRR1 in copper distribution to a multicopper ferroxidase involved in iron assimilation. Mutations at the CRD2 locus also result in copper-conditional iron deficiency, which is consistent with a function for CRD2 in a pathway for copper delivery to the ferroxidase. Taken together, the observations argue for a specialized copper-deficiency adaptation for iron uptake in Chlamydomonas.

@article{hilson_versatile_2004,
	title = {Versatile {Gene}-{Specific} {Sequence} {Tags} for {Arabidopsis} {Functional} {Genomics}: {Transcript} {Profiling} and {Reverse} {Genetics} {Applications}},
	volume = {14},
	issn = {1088-9051, 1549-5469},
	shorttitle = {Versatile {Gene}-{Specific} {Sequence} {Tags} for {Arabidopsis} {Functional} {Genomics}},
	url = {https://genome.cshlp.org/content/14/10b/2176},
	doi = {10/brkpzf},
	abstract = {Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization between complementary nucleic acid strands, inciting us to create a collection of gene-specific sequence tags (GSTs) representing at least 21,500 Arabidopsis genes and which are compatible with both approaches. The GSTs were carefully selected to ensure that each of them shared no significant similarity with any other region in the Arabidopsis genome. They were synthesized by PCR amplification from genomic DNA. Spotted microarrays fabricated from the GSTs show good dynamic range, specificity, and sensitivity in transcript profiling experiments. The GSTs have also been transferred to bacterial plasmid vectors via recombinational cloning protocols. These cloned GSTs constitute the ideal starting point for a variety of functional approaches, including reverse genetics. We have subcloned GSTs on a large scale into vectors designed for gene silencing in plant cells. We show that in planta expression of GST hairpin RNA results in the expected phenotypes in silenced Arabidopsis lines. These versatile GST resources provide novel and powerful tools for functional genomics.},
	language = {en},
	number = {10b},
	urldate = {2021-06-30},
	journal = {Genome Research},
	author = {Hilson, Pierre and Allemeersch, Joke and Altmann, Thomas and Aubourg, Sébastien and Avon, Alexandra and Beynon, Jim and Bhalerao, Rishikesh P. and Bitton, Frédérique and Caboche, Michel and Cannoot, Bernard and Chardakov, Vasil and Cognet-Holliger, Cécile and Colot, Vincent and Crowe, Mark and Darimont, Caroline and Durinck, Steffen and Eickhoff, Holger and Longevialle, Andéol Falcon de and Farmer, Edward E. and Grant, Murray and Kuiper, Martin T. R. and Lehrach, Hans and Léon, Céline and Leyva, Antonio and Lundeberg, Joakim and Lurin, Claire and Moreau, Yves and Nietfeld, Wilfried and Paz-Ares, Javier and Reymond, Philippe and Rouzé, Pierre and Sandberg, Goran and Segura, Maria Dolores and Serizet, Carine and Tabrett, Alexandra and Taconnat, Ludivine and Thareau, Vincent and Hummelen, Paul Van and Vercruysse, Steven and Vuylsteke, Marnik and Weingartner, Magdalena and Weisbeek, Peter J. and Wirta, Valtteri and Wittink, Floyd R. A. and Zabeau, Marc and Small, Ian},
	month = oct,
	year = {2004},
	pmid = {15489341},
	note = {Company: Cold Spring Harbor Laboratory Press
Distributor: Cold Spring Harbor Laboratory Press
Institution: Cold Spring Harbor Laboratory Press
Label: Cold Spring Harbor Laboratory Press
Publisher: Cold Spring Harbor Lab},
	pages = {2176--2189},
}

Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization between complementary nucleic acid strands, inciting us to create a collection of gene-specific sequence tags (GSTs) representing at least 21,500 Arabidopsis genes and which are compatible with both approaches. The GSTs were carefully selected to ensure that each of them shared no significant similarity with any other region in the Arabidopsis genome. They were synthesized by PCR amplification from genomic DNA. Spotted microarrays fabricated from the GSTs show good dynamic range, specificity, and sensitivity in transcript profiling experiments. The GSTs have also been transferred to bacterial plasmid vectors via recombinational cloning protocols. These cloned GSTs constitute the ideal starting point for a variety of functional approaches, including reverse genetics. We have subcloned GSTs on a large scale into vectors designed for gene silencing in plant cells. We show that in planta expression of GST hairpin RNA results in the expected phenotypes in silenced Arabidopsis lines. These versatile GST resources provide novel and powerful tools for functional genomics.

@article{ingvarsson_population_2004,
	title = {Population subdivision and the {Hudson}–{Kreitman}–{Aguade} test: testing for deviations from the neutral model in organelle genomes},
	volume = {83},
	issn = {1469-5073, 0016-6723},
	shorttitle = {Population subdivision and the {Hudson}–{Kreitman}–{Aguade} test},
	url = {https://www.cambridge.org/core/journals/genetics-research/article/population-subdivision-and-the-hudsonkreitmanaguade-test-testing-for-deviations-from-the-neutral-model-in-organelle-genomes/93CED9CE02E5299CC8BD9FE65201B707},
	doi = {10/cpkvwm},
	abstract = {The Hudson–Kreitman–Aguade (HKA) test is based on the prediction from the neutral theory that levels of polymorphism within a species and the divergence between two closely related species should be correlated. Population subdivision has been shown to alter both the amounts of polymorphism segregating within species and the rate of divergence between species, meaning that genomic regions with different population structures also differ in their divergence to polymorphism ratios. Population subdivision may hence hamper the utility of the HKA test for detecting deviations from the standard neutral model, especially for organelle genomes that often have different patterns of population structure compared with nuclear genes. In this paper, I show that population subdivision inflates the number of instances where the HKA test detects deviations from the neutral model. Using coalescent simulations I show that this bias is most apparent when population subdivision is strong and differs substantially between the loci included. However, if divergence time is large and population structure substantial even changes in the levels of polymorphism and divergence associated with differences in the effective population size between two loci is enough to substantially alter the number of significant outcomes of the HKA test. A dataset on cytoplasmic diversity in Silene vulgaris and S. latifolia (Ingvarsson \& Taylor, 2002) is also reanalysed. The previous study had shown a marked excess of intraspecific polymorphism in both species. However, when effects of population subdivision were removed, ad hoc, levels of intraspecific polymorphism were no longer significantly different from neutral expectations, suggesting that population subdivision contributed to the observed excess of intraspecific polymorphism seen in both species of Silene.},
	language = {en},
	number = {1},
	urldate = {2021-06-30},
	journal = {Genetics Research},
	author = {Ingvarsson, Pär K.},
	month = feb,
	year = {2004},
	note = {Publisher: Cambridge University Press},
	pages = {31--39},
}

The Hudson–Kreitman–Aguade (HKA) test is based on the prediction from the neutral theory that levels of polymorphism within a species and the divergence between two closely related species should be correlated. Population subdivision has been shown to alter both the amounts of polymorphism segregating within species and the rate of divergence between species, meaning that genomic regions with different population structures also differ in their divergence to polymorphism ratios. Population subdivision may hence hamper the utility of the HKA test for detecting deviations from the standard neutral model, especially for organelle genomes that often have different patterns of population structure compared with nuclear genes. In this paper, I show that population subdivision inflates the number of instances where the HKA test detects deviations from the neutral model. Using coalescent simulations I show that this bias is most apparent when population subdivision is strong and differs substantially between the loci included. However, if divergence time is large and population structure substantial even changes in the levels of polymorphism and divergence associated with differences in the effective population size between two loci is enough to substantially alter the number of significant outcomes of the HKA test. A dataset on cytoplasmic diversity in Silene vulgaris and S. latifolia (Ingvarsson & Taylor, 2002) is also reanalysed. The previous study had shown a marked excess of intraspecific polymorphism in both species. However, when effects of population subdivision were removed, ad hoc, levels of intraspecific polymorphism were no longer significantly different from neutral expectations, suggesting that population subdivision contributed to the observed excess of intraspecific polymorphism seen in both species of Silene.

@article{ensminger_intermittent_2004,
	title = {Intermittent low temperatures constrain spring recovery of photosynthesis in boreal {Scots} pine forests},
	volume = {10},
	issn = {1354-1013},
	doi = {10/bg8q75},
	abstract = {During winter and early spring, evergreen boreal conifers are severely stressed because light energy cannot be used when photosynthesis is pre-empted by low ambient temperatures. To study photosynthetic performance dynamics in a severe boreal climate, seasonal changes in photosynthetic pigments, chloroplast proteins and photochemical efficiency were studied in a Scots pine forest near Zotino, Central Siberia. In winter, downregulation of photosynthesis involved loss of chlorophylls, a twofold increase in xanthophyll cycle pigments and sustained high levels of the light stress-induced zeaxanthin pigment. The highest levels of xanthophylls and zeaxanthin did not occur during the coldest winter period, but rather in April when light was increasing, indicating an increased capacity for thermal dissipation of excitation energy at that time. Concomitantly, in early spring the D1 protein of the photosystem II (PSII) reaction centre and the light-harvesting complex of PSII dropped to their lowest annual levels. In April and May, recovery of PSII activity, chloroplast protein synthesis and rearrangements of pigments were observed as air temperatures increased above 0degreesC. Nevertheless, severe intermittent low-temperature episodes during this period not only halted but actually reversed the physiological recovery. During these spring low-temperature episodes, protective processes involved a complementary function of the PsbS and early light-induced protein thylakoid proteins. Full recovery of photosynthesis did not occur until the end of May. Our results show that even after winter cold hardening, photosynthetic activity in evergreens responds opportunistically to environmental change throughout the cold season. Therefore, climate change effects potentially improve the sink capacity of boreal forests for atmospheric carbon. However, earlier photosynthesis in spring in response to warmer temperatures is strongly constrained by environmental variation, counteracting the positive effects of an early recovery process.},
	language = {English},
	number = {6},
	journal = {Global Change Biology},
	author = {Ensminger, I. and Sveshnikov, D. and Campbell, D. A. and Funk, C. and Jansson, S. and Lloyd, J. and Shibistova, O. and Oquist, G.},
	month = jun,
	year = {2004},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000221741800006},
	keywords = {Pinus sylvestris, carbon balance, chlorophyll   fluorescence, cold stress, light-use efficiency, northern forests, photoinhibition, photosystem-ii, pigment composition, psbs protein, seasonal variations, seasonal-changes, snow cover, stress, xanthophyll cycle},
	pages = {995--1008},
}

During winter and early spring, evergreen boreal conifers are severely stressed because light energy cannot be used when photosynthesis is pre-empted by low ambient temperatures. To study photosynthetic performance dynamics in a severe boreal climate, seasonal changes in photosynthetic pigments, chloroplast proteins and photochemical efficiency were studied in a Scots pine forest near Zotino, Central Siberia. In winter, downregulation of photosynthesis involved loss of chlorophylls, a twofold increase in xanthophyll cycle pigments and sustained high levels of the light stress-induced zeaxanthin pigment. The highest levels of xanthophylls and zeaxanthin did not occur during the coldest winter period, but rather in April when light was increasing, indicating an increased capacity for thermal dissipation of excitation energy at that time. Concomitantly, in early spring the D1 protein of the photosystem II (PSII) reaction centre and the light-harvesting complex of PSII dropped to their lowest annual levels. In April and May, recovery of PSII activity, chloroplast protein synthesis and rearrangements of pigments were observed as air temperatures increased above 0degreesC. Nevertheless, severe intermittent low-temperature episodes during this period not only halted but actually reversed the physiological recovery. During these spring low-temperature episodes, protective processes involved a complementary function of the PsbS and early light-induced protein thylakoid proteins. Full recovery of photosynthesis did not occur until the end of May. Our results show that even after winter cold hardening, photosynthetic activity in evergreens responds opportunistically to environmental change throughout the cold season. Therefore, climate change effects potentially improve the sink capacity of boreal forests for atmospheric carbon. However, earlier photosynthesis in spring in response to warmer temperatures is strongly constrained by environmental variation, counteracting the positive effects of an early recovery process.

@article{trygg_prediction_2004,
	title = {Prediction and spectral profile estimation in multivariate calibration},
	volume = {18},
	issn = {0886-9383},
	doi = {10/b8vgz6},
	abstract = {Direct and indirect calibration have been compared with respect to both prediction and model interpretation. This included their ability to estimate the pure spectral profile of each known constituent in a mixture of different metal-ion complexes. In the examples, the predictions by indirect calibration, represented by the PLS and O-PLS methods, were consistently better than those of direct calibration, exemplified by the CLS method. It was further demonstrated that indirect calibration is equally capable to direct calibration in estimating the pure spectral profiles, as long as the unknown systematic variation is properly handled. A linear transformation of the regression coefficient matrix, given by K = B((BB)-B-T)(-1), is all that is needed. Note that this does not only apply to spectral data, but any situation where the Y-variables can be assumed to additively contribute to the variation in the X matrix. Throughout the examples, the O-PLS method was able to maintain good spectral profile estimates and predictions. This indicates that O-PLS may be the approach for simultaneous good prediction and interpretation of complex multivariate systems. Copyright (C) 2004 John Wiley Sons, Ltd.},
	language = {English},
	number = {3-4},
	journal = {Journal of Chemometrics},
	author = {Trygg, J.},
	month = apr,
	year = {2004},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000223467300007},
	keywords = {cls, direct calibration, indirect calibration, o-pls, o2-pls, pls, pure profile   estimation, regression},
	pages = {166--172},
}

Direct and indirect calibration have been compared with respect to both prediction and model interpretation. This included their ability to estimate the pure spectral profile of each known constituent in a mixture of different metal-ion complexes. In the examples, the predictions by indirect calibration, represented by the PLS and O-PLS methods, were consistently better than those of direct calibration, exemplified by the CLS method. It was further demonstrated that indirect calibration is equally capable to direct calibration in estimating the pure spectral profiles, as long as the unknown systematic variation is properly handled. A linear transformation of the regression coefficient matrix, given by K = B((BB)-B-T)(-1), is all that is needed. Note that this does not only apply to spectral data, but any situation where the Y-variables can be assumed to additively contribute to the variation in the X matrix. Throughout the examples, the O-PLS method was able to maintain good spectral profile estimates and predictions. This indicates that O-PLS may be the approach for simultaneous good prediction and interpretation of complex multivariate systems. Copyright (C) 2004 John Wiley Sons, Ltd.

@article{jonsson_strategies_2004,
	title = {Strategies for implementation and validation of on-line models for multivariate monitoring and control of wood chip properties},
	volume = {18},
	issn = {0886-9383},
	doi = {10/dkmxzw},
	abstract = {Here we present an approach for on-line control and monitoring of pulpwood chip properties based on near infrared (NIR) spectroscopy and multivariate data analysis. In addition, this paper suggests how to deal with large multivariate data sets in order to extract information which can be used as a basis for changes in raw material or process conditions in the drive towards more optimal intermediate or end product properties within the pulp and paper industry. The pulpwood chips used as raw material in a pulp and paper making process were characterized at- and on-line using NIR spectroscopic measurements. Collected NIR spectra were used in mulitivariate calibration models for prediction of the moisture content as well as the between- and within-species variation in the studied raw material. Statistical experimental design was used to form a calibration data set including most of the variation occurring in a 'real' on-line situation. NIR spectra for all designed samples were measured at-line and the estimated calibration models were used for carrying out predictions on-line. Predictions of the moisture content (\% dry weight) as well as the percentage contents of pine and sawmill chips in the raw material were carried out using partial least squares projections to latent structures (PLS) methodology. NIR spectra were collected subsequently on-line once every minute, and, to reduce the problem with noise in the time series predictions, the measured signals were filtered using a moving average of 100 predicted values. This provided smoother predictions more suitable for process monitoring and control. To validate the quality of the predictions, wood chips from the studied process were sampled and analysed in the laboratory before being subjected to predictions in the on-line model. Comparison of the filtered on-line predictions with the results obtained from the laboratory measurements indicated that moisture and pine chip contents could be well predicted by the on-line model, while predictions of sawmill chip content showed less promising results. Copyright (C) 2004 John Wiley Sons, Ltd.},
	language = {English},
	number = {3-4},
	journal = {Journal of Chemometrics},
	author = {Jonsson, P. and Sjostrom, M. and Wallbacks, L. and Antti, H.},
	month = apr,
	year = {2004},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000223467300011},
	keywords = {design of experiments (DoE), mspc, nir, on-line, performance monitoring, pls, process control, process monitoring, pulp, spectroscopy, statistical experimental design},
	pages = {203--207},
}

Here we present an approach for on-line control and monitoring of pulpwood chip properties based on near infrared (NIR) spectroscopy and multivariate data analysis. In addition, this paper suggests how to deal with large multivariate data sets in order to extract information which can be used as a basis for changes in raw material or process conditions in the drive towards more optimal intermediate or end product properties within the pulp and paper industry. The pulpwood chips used as raw material in a pulp and paper making process were characterized at- and on-line using NIR spectroscopic measurements. Collected NIR spectra were used in mulitivariate calibration models for prediction of the moisture content as well as the between- and within-species variation in the studied raw material. Statistical experimental design was used to form a calibration data set including most of the variation occurring in a 'real' on-line situation. NIR spectra for all designed samples were measured at-line and the estimated calibration models were used for carrying out predictions on-line. Predictions of the moisture content (% dry weight) as well as the percentage contents of pine and sawmill chips in the raw material were carried out using partial least squares projections to latent structures (PLS) methodology. NIR spectra were collected subsequently on-line once every minute, and, to reduce the problem with noise in the time series predictions, the measured signals were filtered using a moving average of 100 predicted values. This provided smoother predictions more suitable for process monitoring and control. To validate the quality of the predictions, wood chips from the studied process were sampled and analysed in the laboratory before being subjected to predictions in the on-line model. Comparison of the filtered on-line predictions with the results obtained from the laboratory measurements indicated that moisture and pine chip contents could be well predicted by the on-line model, while predictions of sawmill chip content showed less promising results. Copyright (C) 2004 John Wiley Sons, Ltd.

@article{witzell_nitrogen-induced_2004,
	title = {Nitrogen-induced changes in phenolics of {Vaccinium} myrtillus - {Implications} for interaction with a parasitic fungus},
	volume = {30},
	issn = {0098-0331},
	doi = {10/fbxkw8},
	abstract = {The effects of nitrogen (N) fertilization on the phenolic status of Vaccinium myrtillus leaves were studied to assess whether N amendment affects the potentially defensive phenolic metabolites in a way that could have consequences for the interaction with a parasitic fungus (Valdensia heterodoxa). Healthy (symptomless) and V. heterodoxa-infected leaves were collected from plants grown in the understorey of a boreal coniferous forest, where they received no additional N or either a moderate or a high dose of N fertilizer. Leaf samples were taken during a single growth season and analyzed for individual phenolics using HPLC. The effect of a moderate N dose on the concentration and content of phenolics was in most cases nonsignificant. In contrast, the high N dose resulted in pronounced effects. In healthy leaves, N fertilization reduced concentration of three of five individual phenolics. Moreover, fertilization with high dose of N accompanied by infection by V. heterodoxa often increased the concentration and content of phenolics as compared to unfertilized plants. Addition of N had no significant effect on the growth of the analyzed V. myrtillus leaves, and the N-induced variation in phenolic levels seemed to be due to changed rate of their production. The concentration and content of phenolic metabolites in healthy leaves collected from unfertilized plots fluctuated compound-specifically during the growth season, and the phenolic responses to N and infection showed temporal and compound-specific variations.},
	language = {English},
	number = {10},
	journal = {Journal of Chemical Ecology},
	author = {Witzell, J. and Shevtsova, A.},
	month = oct,
	year = {2004},
	note = {Place: Dordrecht
Publisher: Springer
WOS:000224670400004},
	keywords = {Boreal forest, Valdensia heterodoxa, arabidopsis, availability, balsam poplar, bilberry, carbon-nutrient balance, chemical defense, deposition, disease resistance, elevated co2, hypothesis, interpreting phenotypic variation, nitrogen   fertilization, plant defense, secondary   metabolism},
	pages = {1937--1956},
}

The effects of nitrogen (N) fertilization on the phenolic status of Vaccinium myrtillus leaves were studied to assess whether N amendment affects the potentially defensive phenolic metabolites in a way that could have consequences for the interaction with a parasitic fungus (Valdensia heterodoxa). Healthy (symptomless) and V. heterodoxa-infected leaves were collected from plants grown in the understorey of a boreal coniferous forest, where they received no additional N or either a moderate or a high dose of N fertilizer. Leaf samples were taken during a single growth season and analyzed for individual phenolics using HPLC. The effect of a moderate N dose on the concentration and content of phenolics was in most cases nonsignificant. In contrast, the high N dose resulted in pronounced effects. In healthy leaves, N fertilization reduced concentration of three of five individual phenolics. Moreover, fertilization with high dose of N accompanied by infection by V. heterodoxa often increased the concentration and content of phenolics as compared to unfertilized plants. Addition of N had no significant effect on the growth of the analyzed V. myrtillus leaves, and the N-induced variation in phenolic levels seemed to be due to changed rate of their production. The concentration and content of phenolic metabolites in healthy leaves collected from unfertilized plots fluctuated compound-specifically during the growth season, and the phenolic responses to N and infection showed temporal and compound-specific variations.

@article{xu_multiple_2004,
	title = {Multiple {Deletions} of {Small} {Cab}-like {Proteins} in the {Cyanobacterium} {Synechocystis} sp. {PCC} 6803: {CONSEQUENCES} {FOR} {PIGMENT} {BIOSYNTHESIS} {AND} {ACCUMULATION}*},
	volume = {279},
	issn = {0021-9258},
	shorttitle = {Multiple {Deletions} of {Small} {Cab}-like {Proteins} in the {Cyanobacterium} {Synechocystis} sp. {PCC} 6803},
	url = {https://www.sciencedirect.com/science/article/pii/S002192582073228X},
	doi = {10/cf4k6b},
	abstract = {Deletion of the genes for four or five small Cab-like proteins (SCPs) in photosystem (PS) I-less and PS I-less/PS II-less strains of Synechocystis sp. PCC 6803 caused a large decrease in the chlorophyll and carotenoid content of the cells without accumulation of early intermediates in the chlorophyll biosynthesis pathway, suggesting limited chlorophyll availability. The PS II/PS I ratio increased upon deletion of multiple SCPs in a wild type background, similar to what is observed in the presence of subsaturating concentrations of gabaculin, an inhibitor of an early step in the tetrapyrrole biosynthesis pathway. Upon deletion of multiple SCPs, neither 77 K fluorescence emission properties of phycobilisomeless thylakoids from the PS I-less/PS II-less strain nor the energy trapping efficiency of PS II were affected, indicating that under steady-state conditions SCPs do not bind much chlorophyll and do not serve as PS II antenna. Under conditions where protochlorophyllide reduction and thus chlorophyll synthesis were inhibited, chlorophyll disappeared quickly in a mutant lacking all five SCPs. This implies a role of SCPs in stabilization of chlorophyll-binding proteins and/or in reuse of chlorophylls. Under these conditions of inhibited reduction of protochlorophyllide, the accumulation kinetics of this intermediate were greatly altered in the absence of the five SCPs. This indicates an alteration of tetrapyrrole biosynthesis kinetics by SCPs. Based on this and other evidence, we propose that SCPs bind carotenoids and transiently bind chlorophyll, aiding in the supply of chlorophyll to nascent or reassembling photosynthetic complexes, and regulate the tetrapyrrole biosynthesis pathway as a function of the demand for chlorophyll.},
	language = {en},
	number = {27},
	urldate = {2021-06-30},
	journal = {Journal of Biological Chemistry},
	author = {Xu, Hong and Vavilin, Dmitrii and Funk, Christiane and Vermaas, Wim},
	month = jul,
	year = {2004},
	pages = {27971--27979},
}

Deletion of the genes for four or five small Cab-like proteins (SCPs) in photosystem (PS) I-less and PS I-less/PS II-less strains of Synechocystis sp. PCC 6803 caused a large decrease in the chlorophyll and carotenoid content of the cells without accumulation of early intermediates in the chlorophyll biosynthesis pathway, suggesting limited chlorophyll availability. The PS II/PS I ratio increased upon deletion of multiple SCPs in a wild type background, similar to what is observed in the presence of subsaturating concentrations of gabaculin, an inhibitor of an early step in the tetrapyrrole biosynthesis pathway. Upon deletion of multiple SCPs, neither 77 K fluorescence emission properties of phycobilisomeless thylakoids from the PS I-less/PS II-less strain nor the energy trapping efficiency of PS II were affected, indicating that under steady-state conditions SCPs do not bind much chlorophyll and do not serve as PS II antenna. Under conditions where protochlorophyllide reduction and thus chlorophyll synthesis were inhibited, chlorophyll disappeared quickly in a mutant lacking all five SCPs. This implies a role of SCPs in stabilization of chlorophyll-binding proteins and/or in reuse of chlorophylls. Under these conditions of inhibited reduction of protochlorophyllide, the accumulation kinetics of this intermediate were greatly altered in the absence of the five SCPs. This indicates an alteration of tetrapyrrole biosynthesis kinetics by SCPs. Based on this and other evidence, we propose that SCPs bind carotenoids and transiently bind chlorophyll, aiding in the supply of chlorophyll to nascent or reassembling photosynthetic complexes, and regulate the tetrapyrrole biosynthesis pathway as a function of the demand for chlorophyll.

@article{lindgren_balancing_2004,
	title = {Balancing seed yield and breeding value in clonal seed orchards},
	volume = {28},
	issn = {0169-4286},
	doi = {10/db6qps},
	abstract = {Seed orchards should produce seeds that are both abundant and of high genetic value. This study suggests methods to achieve such a compromise and study their efficiency. The methods were applied on data obtained from 41 seed orchard clones of Scots pine from mid-Sweden. The value of the seed orchard crop was set as a function of its breeding value, the amount of seeds produced and their gene diversity, measured as the effective number of clones. The proportion of ramets of different clones that maximized this value was regarded as the optimum for deployment of the clones in a seed orchard. The results were compared with truncation selection for breeding value, truncation selection for clone benefit ( the product of seed production and breeding value) and linear deployment ( where ramets are deployed linearly in relation to breeding value). The influence of two parameters was studied: the relative importance of breeding value for seed value and the size of the penalty for reducing the value of the seed crop with respect to lost gene diversity. The conventional wisdom is to select the clones with the highest breeding values, but that turned out to be the most inferior alternative studied. Clone benefit truncation provided a good approximation to optimal benefit for cases, where the effective number was low and dependence of breeding value limited.},
	language = {English},
	number = {1},
	journal = {New Forests},
	author = {Lindgren, D. and Cui, J. G. and Son, S. G. and Sonesson, J.},
	month = jul,
	year = {2004},
	note = {Place: Dordrecht
Publisher: Kluwer Academic Publ
WOS:000221938600002},
	keywords = {Scots pine, effective number, gene diversity, number, relatedness, seed productivity, status   number, truncation selection},
	pages = {11--22},
}

Seed orchards should produce seeds that are both abundant and of high genetic value. This study suggests methods to achieve such a compromise and study their efficiency. The methods were applied on data obtained from 41 seed orchard clones of Scots pine from mid-Sweden. The value of the seed orchard crop was set as a function of its breeding value, the amount of seeds produced and their gene diversity, measured as the effective number of clones. The proportion of ramets of different clones that maximized this value was regarded as the optimum for deployment of the clones in a seed orchard. The results were compared with truncation selection for breeding value, truncation selection for clone benefit ( the product of seed production and breeding value) and linear deployment ( where ramets are deployed linearly in relation to breeding value). The influence of two parameters was studied: the relative importance of breeding value for seed value and the size of the penalty for reducing the value of the seed crop with respect to lost gene diversity. The conventional wisdom is to select the clones with the highest breeding values, but that turned out to be the most inferior alternative studied. Clone benefit truncation provided a good approximation to optimal benefit for cases, where the effective number was low and dependence of breeding value limited.

@article{huang_isolation_2004,
	title = {Isolation of outer membrane of {Synechocystis} sp {PCC} 6803 and its proteomic characterization},
	volume = {3},
	issn = {1535-9476},
	doi = {10/dxr94c},
	abstract = {In this report, we describe a newly developed method for isolating outer membranes from Synechocystis sp. PCC 6803 cells. The purity of the outer membrane fraction was verified by immunoblot analysis using antibodies against membrane-specific marker proteins. We investigated the protein composition of the outer membrane using two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry followed by database identification. Forty-nine proteins were identified corresponding to 29 different gene products. All of the identified proteins have a putative N-terminal signal peptide. About 40\% of the proteins identified represent hypothetical proteins with unknown function. Among the proteins identified are a Toc75 homologue, a protein that was initially found in the outer envelope of chloroplasts in pea, as well as TolC, putative porins, and a pilus protein. Other proteins identified include ABC transporters and GumB, which has a suggested function in carbohydrate export. A number of proteases such as HtrA were also found in the outer membrane of Synechocystis sp. PCC 6803.},
	language = {English},
	number = {6},
	journal = {Molecular \& Cellular Proteomics},
	author = {Huang, F. and Hedman, E. and Funk, C. and Kieselbach, T. and Schroder, W. P. and Norling, B.},
	month = jun,
	year = {2004},
	note = {Place: Rockville
Publisher: Amer Soc Biochemistry Molecular Biology Inc
WOS:000222029100007},
	keywords = {crystal-structure, escherichia-coli, genetic-analysis, htra family, multidrug efflux, photosystem-ii, plasma-membranes, protein, pseudomonas-aeruginosa, thylakoid membranes},
	pages = {586--595},
}

In this report, we describe a newly developed method for isolating outer membranes from Synechocystis sp. PCC 6803 cells. The purity of the outer membrane fraction was verified by immunoblot analysis using antibodies against membrane-specific marker proteins. We investigated the protein composition of the outer membrane using two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry followed by database identification. Forty-nine proteins were identified corresponding to 29 different gene products. All of the identified proteins have a putative N-terminal signal peptide. About 40% of the proteins identified represent hypothetical proteins with unknown function. Among the proteins identified are a Toc75 homologue, a protein that was initially found in the outer envelope of chloroplasts in pea, as well as TolC, putative porins, and a pilus protein. Other proteins identified include ABC transporters and GumB, which has a suggested function in carbohydrate export. A number of proteases such as HtrA were also found in the outer membrane of Synechocystis sp. PCC 6803.

@article{erikson_conditional_2004,
	title = {A conditional marker gene allowing both positive and negative selection in plants},
	volume = {22},
	issn = {1087-0156},
	doi = {10/fpj7wk},
	abstract = {Selectable markers enable transgenic plants or cells to be identified after transformation. They can be divided into positive and negative markers conferring a selective advantage or disadvantage, respectively. We present a marker gene, dao1, encoding D-amino acid oxidase (DAAO, EC 1.4.3.3) that can be used for either positive or negative selection, depending on the substrate. DAAO catalyzes the oxidative deamination of a range of D-amino acids(1). Selection is based on differences in the toxicity of different D-amino acids and their metabolites to plants. Thus, D-alanine and D-serine are toxic to plants, but are metabolized by DAAO into nontoxic products, whereas D-isoleucine and D-valine have low toxicity, but are metabolized by DAAO into the toxic keto acids 3-methyl-2-oxopentanoate and 3-methyl-2-oxobutanoate, respectively. Hence, both positive and negative selection is possible with the same marker gene. The marker has been successfully established in Arabidopsis thaliana, and proven to be versatile, rapidly yielding unambiguous results, and allowing selection immediately after germination.},
	language = {English},
	number = {4},
	journal = {Nature Biotechnology},
	author = {Erikson, O. and Hertzberg, M. and Nasholm, T.},
	month = apr,
	year = {2004},
	note = {Place: New York
Publisher: Nature Publishing Group
WOS:000220610100036},
	keywords = {amino-acid oxidase, expression, mechanism, metabolism, transformation, transporter},
	pages = {455--458},
}

Selectable markers enable transgenic plants or cells to be identified after transformation. They can be divided into positive and negative markers conferring a selective advantage or disadvantage, respectively. We present a marker gene, dao1, encoding D-amino acid oxidase (DAAO, EC 1.4.3.3) that can be used for either positive or negative selection, depending on the substrate. DAAO catalyzes the oxidative deamination of a range of D-amino acids(1). Selection is based on differences in the toxicity of different D-amino acids and their metabolites to plants. Thus, D-alanine and D-serine are toxic to plants, but are metabolized by DAAO into nontoxic products, whereas D-isoleucine and D-valine have low toxicity, but are metabolized by DAAO into the toxic keto acids 3-methyl-2-oxopentanoate and 3-methyl-2-oxobutanoate, respectively. Hence, both positive and negative selection is possible with the same marker gene. The marker has been successfully established in Arabidopsis thaliana, and proven to be versatile, rapidly yielding unambiguous results, and allowing selection immediately after germination.

@article{talts_respiratory_2004,
	title = {Respiratory acclimation in {Arabidopsis} thaliana leaves at low temperature},
	volume = {161},
	issn = {0176-1617},
	doi = {10/ddt8s8},
	abstract = {Acclimation of 25 degreesC-grown Arabidopsis thaliana at 5 degreesC resulted in a marked increase of leaf respiration in darkness (R-d) measured at 5 degreesC. R-d was particularly high in leaves developed at 5 degreesC. Leaf respiration (non-photorespiratory intracellular decarboxylation) in the light (R-l) also increased during cold acclimation, but less so than did R-d. The ratio R-d/P-t (P-t - true photosynthesis) was higher in more acclimated or cold-developed leaves, while the ratio R-l/P-t remained unchanged. In cold-acclimated leaves, R-l did not correlate with 3-phosphoglycerate and pyruvate nor with hexose phosphate pools in the cytosol. R-l in A. thaliana leaves was probably not limited by the substrate during cold acclimation. Under the conditions tested, R-d was more sensitive to low temperature stress than R-l.},
	language = {English},
	number = {5},
	journal = {Journal of Plant Physiology},
	author = {Talts, P. and Parnik, T. and Gardestrom, P. and Keerberg, O.},
	month = may,
	year = {2004},
	note = {Place: Munich
Publisher: Elsevier Gmbh
WOS:000221613300009},
	keywords = {Arabidopsis thaliana, acclimation, capacity, chloroplasts, cytosolic metabolites, decarboxylation, leaf respiration, light, low   temperature, metabolism, mitochondria, photosynthesis, snow gum, winter rye},
	pages = {573--579},
}

Acclimation of 25 degreesC-grown Arabidopsis thaliana at 5 degreesC resulted in a marked increase of leaf respiration in darkness (R-d) measured at 5 degreesC. R-d was particularly high in leaves developed at 5 degreesC. Leaf respiration (non-photorespiratory intracellular decarboxylation) in the light (R-l) also increased during cold acclimation, but less so than did R-d. The ratio R-d/P-t (P-t - true photosynthesis) was higher in more acclimated or cold-developed leaves, while the ratio R-l/P-t remained unchanged. In cold-acclimated leaves, R-l did not correlate with 3-phosphoglycerate and pyruvate nor with hexose phosphate pools in the cytosol. R-l in A. thaliana leaves was probably not limited by the substrate during cold acclimation. Under the conditions tested, R-d was more sensitive to low temperature stress than R-l.

@article{dedic_hole_2004,
	title = {Hole burning study of cyanobacterial {Photosystem} {II} complexes differing in the content of small putative chlorophyll-binding proteins},
	volume = {107},
	issn = {0022-2313},
	doi = {10/bvfqd3},
	abstract = {This contribution presents low-temperature absorption, both broad-band and site-selective excited fluorescence, and persistent hole burning spectra of Photosystem II complexes from the Photosystem I-lacking strains of the cyanobacterium Synechocystis sp. PCC 6803 differing in the content of small putative chlorophyll-binding proteins (Scps). These proteins are homologous to light-harvesting complex of higher plants and may bind pigments. The excited state lifetimes of the complexes were determined from zero-phonon hole widths extrapolated to zero-burning dose. The area and spectral position of a phonon side-band with respect to the zero-phonon hole provided additional information concerning chlorophyll-protein coupling and the Stokes shift. Decrease of three absorption subbands at (670.0, 672.9, and 675.7 nm) in the Photosystem II isolated from the strain lacking ScpC and ScpD is in agreement with a hypothesis about the role of Scps in the chlorophyll binding. In addition, narrowing of the zero-phonon hole in Photosystem II without both Scps indicates slowering of the excitation energy transfer which may be explained by the absence of a protective excitation energy quenching related to the presence of Scps. (C) 2003 Elsevier B.V. All rights reserved.},
	language = {English},
	number = {1-4},
	journal = {Journal of Luminescence},
	author = {Dedic, R. and Promnares, K. and Psencik, J. and Svoboda, A. and Korinek, M. and Tichy, M. and Komenda, J. and Funk, C. and Hala, J.},
	month = may,
	year = {2004},
	note = {Place: Amsterdam
Publisher: Elsevier
WOS:000220706100031},
	keywords = {antenna complex, chlorophyll-protein interaction, cp 34, cyanobacteria, energy-transfer, hole burning, low-temperature, mutant, small cab like proteins},
	pages = {230--235},
}

This contribution presents low-temperature absorption, both broad-band and site-selective excited fluorescence, and persistent hole burning spectra of Photosystem II complexes from the Photosystem I-lacking strains of the cyanobacterium Synechocystis sp. PCC 6803 differing in the content of small putative chlorophyll-binding proteins (Scps). These proteins are homologous to light-harvesting complex of higher plants and may bind pigments. The excited state lifetimes of the complexes were determined from zero-phonon hole widths extrapolated to zero-burning dose. The area and spectral position of a phonon side-band with respect to the zero-phonon hole provided additional information concerning chlorophyll-protein coupling and the Stokes shift. Decrease of three absorption subbands at (670.0, 672.9, and 675.7 nm) in the Photosystem II isolated from the strain lacking ScpC and ScpD is in agreement with a hypothesis about the role of Scps in the chlorophyll binding. In addition, narrowing of the zero-phonon hole in Photosystem II without both Scps indicates slowering of the excitation energy transfer which may be explained by the absence of a protective excitation energy quenching related to the presence of Scps. (C) 2003 Elsevier B.V. All rights reserved.

@article{galindo_changes_2004,
	title = {Changes in the carrot ({Daucus} carota {L}. cv. {Nerac}) cell wall during storage},
	volume = {37},
	issn = {0963-9969},
	doi = {10.1016/j.foodres.2003.11.006},
	abstract = {The aim of this study was to examine biochemical changes in cell wall carbohydrates and extensin proteins during long-term storage of carrots (Daucus carota L. cv. Nerac). During the storage period of 6 months, cell wall fractions were isolated from the carrot at various times for carbohydrate and protein analysis. Signs of extensin cross-linking and its concomitant insolubilisation in the cell wall were found after 7 and 12 weeks of storage. During the same period the concentration of galactose and arabinose decreased, while other carbohydrate components as well as the degree of methylesterification remained virtually unchanged. After the 12th week of storage no changes in the extensin or carbohydrates were detected. Oxidative cross-linking between extensin molecules in the cell wall has been implicated in cell wall strengthening and may be part of the mechanism behind the storage-induced firmness of carrots. (C) 2003 Elsevier Ltd. All rights reserved.},
	language = {English},
	number = {3},
	journal = {Food Research International},
	author = {Galindo, F. G. and Brathen, E. and Knutsen, S. H. and Sommarin, M. and Gekas, V. and Sjoholm, I.},
	year = {2004},
	note = {Place: Amsterdam
Publisher: Elsevier
WOS:000220123100004},
	keywords = {acclimation, carbohydrate, carbohydrates, carrot, cell walls, extensin, glycoproteins, localization, nonstarch polysaccharides, oxidative   cross-linking, oxidative cross-linking, plants, proteins, rich, storage},
	pages = {225--232},
}

The aim of this study was to examine biochemical changes in cell wall carbohydrates and extensin proteins during long-term storage of carrots (Daucus carota L. cv. Nerac). During the storage period of 6 months, cell wall fractions were isolated from the carrot at various times for carbohydrate and protein analysis. Signs of extensin cross-linking and its concomitant insolubilisation in the cell wall were found after 7 and 12 weeks of storage. During the same period the concentration of galactose and arabinose decreased, while other carbohydrate components as well as the degree of methylesterification remained virtually unchanged. After the 12th week of storage no changes in the extensin or carbohydrates were detected. Oxidative cross-linking between extensin molecules in the cell wall has been implicated in cell wall strengthening and may be part of the mechanism behind the storage-induced firmness of carrots. (C) 2003 Elsevier Ltd. All rights reserved.

@article{mohapatra_hydrogen-evolving_2004,
	title = {A hydrogen-evolving enzyme is present in {Frankia} sp. {R43}},
	volume = {236},
	issn = {0378-1097},
	url = {https://doi.org/10.1111/j.1574-6968.2004.tb09652.x},
	doi = {10.1111/j.1574-6968.2004.tb09652.x},
	abstract = {The ability to evolve hydrogen using methyl viologen as an electron donor was assayed in the nitrogen-fixing actinomycetes Frankia sp. R43 and Frankia sp. KB5. To further examine the nature of hydrogen-evolving enzymes that may be present in these organisms immunological studies were performed. Under anaerobic conditions (both nitrogen-limiting and nitrogen-containing) Frankia sp. R43 but not Frankia sp. KB5 evolved hydrogen, which was not linked to NAD-reducing activity. Immunological analysis of total protein from Frankia sp. R43 and Frankia sp. KB5 using an antiserum raised against Ralstonia eutropha HoxF, recognized an antigen in Frankia sp. R43 but not in Frankia sp. KB5. Immunogold labeling using antibodies raised against the R. eutropha HoxH recognized sites in both hyphae and vesicles of Frankia sp. R43, but not in Frankia sp. KB5. Based on these physiological and immunological findings, we conclude that Frankia sp. R43 has a hydrogen-evolving hydrogenase.},
	number = {2},
	urldate = {2021-06-30},
	journal = {FEMS Microbiology Letters},
	author = {Mohapatra, Anasuya and Leul, Melakeselam and Mattsson, Ulrika and Sellstedt, Anita},
	month = jul,
	year = {2004},
	pages = {235--240},
}

The ability to evolve hydrogen using methyl viologen as an electron donor was assayed in the nitrogen-fixing actinomycetes Frankia sp. R43 and Frankia sp. KB5. To further examine the nature of hydrogen-evolving enzymes that may be present in these organisms immunological studies were performed. Under anaerobic conditions (both nitrogen-limiting and nitrogen-containing) Frankia sp. R43 but not Frankia sp. KB5 evolved hydrogen, which was not linked to NAD-reducing activity. Immunological analysis of total protein from Frankia sp. R43 and Frankia sp. KB5 using an antiserum raised against Ralstonia eutropha HoxF, recognized an antigen in Frankia sp. R43 but not in Frankia sp. KB5. Immunogold labeling using antibodies raised against the R. eutropha HoxH recognized sites in both hyphae and vesicles of Frankia sp. R43, but not in Frankia sp. KB5. Based on these physiological and immunological findings, we conclude that Frankia sp. R43 has a hydrogen-evolving hydrogenase.

@article{turkina_transit_2004,
	title = {The transit peptide of {CP29} thylakoid protein in {Chlamydomonas} reinhardtii is not removed but undergoes acetylation and phosphorylation},
	volume = {564},
	issn = {1873-3468},
	url = {https://febs.onlinelibrary.wiley.com/doi/abs/10.1016/S0014-5793%2804%2900323-0},
	doi = {10.1016/S0014-5793(04)00323-0},
	abstract = {The surface-exposed peptides were cleaved by trypsin from the photosynthetic thylakoid membranes isolated from the green alga Chlamydomonas reinhardtii. Two phosphorylated peptides, enriched from the peptide mixture and sequenced by nanospray quadrupole time-of-flight mass spectrometry, revealed overlapping sequences corresponding to the N-terminus of a nuclear-encoded chlorophyll a/b-binding protein CP29. In contrast to all known nuclear-encoded thylakoid proteins, the transit peptide in the mature algal CP29 was not removed but processed by methionine excision, N-terminal acetylation and phosphorylation on threonine 6. The importance of this phosphorylation site is proposed as the reason of the unique transit peptide retention.},
	language = {en},
	number = {1-2},
	urldate = {2021-06-30},
	journal = {FEBS Letters},
	author = {Turkina, Maria V. and Villarejo, Arsenio and Vener, Alexander V.},
	year = {2004},
	note = {\_eprint: https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/S0014-5793\%2804\%2900323-0},
	keywords = {CID, CP29, Chlamydomonas reinhardtii, IMAC, LHCP, Mass spectrometry, Protein phosphorylation, Thylakoid membrane, Transit peptide, collision-induced dissociation, immobilized metal affinity chromatography, light-harvesting chlorophyll a/b-binding protein, minor chlorophyll a/b-binding protein of photosystem II},
	pages = {104--108},
}

The surface-exposed peptides were cleaved by trypsin from the photosynthetic thylakoid membranes isolated from the green alga Chlamydomonas reinhardtii. Two phosphorylated peptides, enriched from the peptide mixture and sequenced by nanospray quadrupole time-of-flight mass spectrometry, revealed overlapping sequences corresponding to the N-terminus of a nuclear-encoded chlorophyll a/b-binding protein CP29. In contrast to all known nuclear-encoded thylakoid proteins, the transit peptide in the mature algal CP29 was not removed but processed by methionine excision, N-terminal acetylation and phosphorylation on threonine 6. The importance of this phosphorylation site is proposed as the reason of the unique transit peptide retention.

@article{waldmann_quantitative_2004,
	title = {A quantitative genetic method for estimating developmental instability},
	volume = {58},
	issn = {0014-3820},
	abstract = {The concept of developmental instability (DI) is frequently used in evolutionary biology, and a range of definitions has been proposed. Moreover, numerous different statistical methods have been used for estimation of DI. The common basis for all methods is that measures need to be obtained from repeated structures within organisms. In the case of fluctuating asymmetry, mirror images could be interpreted as the repeats of each other. All repeats of a trait on one organism should, from a quantitative perspective, have the same genetic foundation. Most previous methods have not accounted for the genetics of the underlying trait. It is here shown how a statistical method from quantitative genetics (the repeated records animal model) can be used for assessment of DI, based on estimation of the variance due to the permanent environment. Moreover, Gibbs sampling is used for inference of the parameters, which provides a Bayesian framework where posterior distributions easily can be calculated from any functions of the variance components. The method is applied to a real dataset from two populations of the plant Scabiosa canescens, and results shows that it works well under realistic situations.},
	language = {eng},
	number = {2},
	journal = {Evolution; International Journal of Organic Evolution},
	author = {Waldmann, Patrik},
	month = feb,
	year = {2004},
	pmid = {15068342},
	keywords = {Analysis of Variance, Bayes Theorem, Biological Evolution, Body Patterning, Environment, Growth, Magnoliopsida, Models, Genetic},
	pages = {238--244},
}

The concept of developmental instability (DI) is frequently used in evolutionary biology, and a range of definitions has been proposed. Moreover, numerous different statistical methods have been used for estimation of DI. The common basis for all methods is that measures need to be obtained from repeated structures within organisms. In the case of fluctuating asymmetry, mirror images could be interpreted as the repeats of each other. All repeats of a trait on one organism should, from a quantitative perspective, have the same genetic foundation. Most previous methods have not accounted for the genetics of the underlying trait. It is here shown how a statistical method from quantitative genetics (the repeated records animal model) can be used for assessment of DI, based on estimation of the variance due to the permanent environment. Moreover, Gibbs sampling is used for inference of the parameters, which provides a Bayesian framework where posterior distributions easily can be calculated from any functions of the variance components. The method is applied to a real dataset from two populations of the plant Scabiosa canescens, and results shows that it works well under realistic situations.

@article{galindo_influence_2004,
	title = {Influence of cold acclimation on the mechanical strength of carrot ({Daucus} carota {L}.) tissue},
	volume = {69},
	issn = {1611-4426},
	abstract = {We have investigated the influence of cold acclimation on the mechanical strength of carrot (Daucus carota L.) taproots. Changes in the mechanical strength were monitored when cold acclimation was induced in carrot plants cultivated in a growth chamber under strict climate control and in taproots harvested from field cultivation, where the plants had been exposed to the natural variations in climate. The appearance and accumulation of an antifreeze protein in the cell wall isolated from cold-stored taproots showed that a cold acclimation process is in progress in the harvested taproot derived from carrot plants grown in the field. The force needed to slice the taproots significantly increased during the first 12 weeks of storage, where the higher concentration of the antifreeze protein indicated the highest development of cold acclimation during that period of time. The increase in tissue rigidity during cold acclimation was also shown by the increase of the Young's modulus in taproot tissue from carrot plants acclimated 11 weeks under controlled temperature conditions. After 24 weeks of storage there was a significant increase in slicing force that was accompanied by signs of cell membrane deterioration, as measured by relative electrolyte leakage. Thus, the later increase in tissue strength might be related with a senescence process.},
	language = {English},
	number = {6},
	journal = {European Journal of Horticultural Science},
	author = {Galindo, F. G. and Vaughan, D. and Herppich, W. and Smallwood, M. and Sommarin, M. and Gekas, V. and Sjoholm, I.},
	month = dec,
	year = {2004},
	note = {Place: Leuven
Publisher: Int Soc Horticultural Science-Ishs
WOS:000226796000002},
	keywords = {antifreeze protein, cell tension, protein, relative electrolyte leakage, temperature, tissue strength},
	pages = {229--234},
}

We have investigated the influence of cold acclimation on the mechanical strength of carrot (Daucus carota L.) taproots. Changes in the mechanical strength were monitored when cold acclimation was induced in carrot plants cultivated in a growth chamber under strict climate control and in taproots harvested from field cultivation, where the plants had been exposed to the natural variations in climate. The appearance and accumulation of an antifreeze protein in the cell wall isolated from cold-stored taproots showed that a cold acclimation process is in progress in the harvested taproot derived from carrot plants grown in the field. The force needed to slice the taproots significantly increased during the first 12 weeks of storage, where the higher concentration of the antifreeze protein indicated the highest development of cold acclimation during that period of time. The increase in tissue rigidity during cold acclimation was also shown by the increase of the Young's modulus in taproot tissue from carrot plants acclimated 11 weeks under controlled temperature conditions. After 24 weeks of storage there was a significant increase in slicing force that was accompanied by signs of cell membrane deterioration, as measured by relative electrolyte leakage. Thus, the later increase in tissue strength might be related with a senescence process.

@article{baud_gurke_2004,
	title = {gurke and pasticcino3 mutants affected in embryo development are impaired in acetyl-{CoA} carboxylase},
	volume = {5},
	issn = {1469-221X},
	url = {https://www.embopress.org/doi/full/10.1038/sj.embor.7400124},
	doi = {10.1038/sj.embor.7400124},
	abstract = {Normal embryo development is required for correct seedling formation. The Arabidopsis gurke and pasticcino3 mutants were isolated from different developmental screens and the corresponding embryos exhibit severe defects in their apical region, affecting bilateral symmetry. We have recently identified lethal acc1 mutants affected in acetyl-CoA carboxylase 1 (ACCase 1) that display a similar embryo phenotype. A series of crosses showed that gk and pas3 are allelic to acc1 mutants, and direct sequencing of the ACC1 gene revealed point mutations in these new alleles. The isolation of leaky acc1 alleles demonstrated that ACCase 1 is essential for correct plant development and that mutations in ACCase affect cellular division in plants, as is the case in yeast. Interestingly, significant metabolic complementation of the mutant phenotype was obtained by exogenous supply of malonate, suggesting that the lack of cytosolic malonyl-CoA is likely to be the initial factor leading to abnormal development in the acc1 mutants.},
	number = {5},
	urldate = {2021-06-30},
	journal = {EMBO reports},
	author = {Baud, Sébastien and Bellec, Yannick and Miquel, Martine and Bellini, Catherine and Caboche, Michel and Lepiniec, Loïc and Faure, Jean-Denis and Rochat, Christine},
	month = may,
	year = {2004},
	note = {Publisher: John Wiley \& Sons, Ltd},
	keywords = {cell division, embryo development, plant development, very-long-chain fatty acids},
	pages = {515--520},
}

Normal embryo development is required for correct seedling formation. The Arabidopsis gurke and pasticcino3 mutants were isolated from different developmental screens and the corresponding embryos exhibit severe defects in their apical region, affecting bilateral symmetry. We have recently identified lethal acc1 mutants affected in acetyl-CoA carboxylase 1 (ACCase 1) that display a similar embryo phenotype. A series of crosses showed that gk and pas3 are allelic to acc1 mutants, and direct sequencing of the ACC1 gene revealed point mutations in these new alleles. The isolation of leaky acc1 alleles demonstrated that ACCase 1 is essential for correct plant development and that mutations in ACCase affect cellular division in plants, as is the case in yeast. Interestingly, significant metabolic complementation of the mutant phenotype was obtained by exogenous supply of malonate, suggesting that the lack of cytosolic malonyl-CoA is likely to be the initial factor leading to abnormal development in the acc1 mutants.

@article{zackrisson_nitrogen_2004,
	title = {Nitrogen fixation increases with successional age in boreal forests},
	volume = {85},
	issn = {0012-9658},
	doi = {10.1890/04-0461},
	abstract = {There is little understanding of successional dynamics of N fixation in northern boreal forests. Recent evidence suggests that N fixation by cyanobacteria in association with the common feather moss Pleurozium schreberi contributes to a significant proportion of the total N economy. The Purpose Of the work herein was to determine how time since last fire influences N fixation rates in boreal forests. We evaluated seasonal N fixation rates oil a total of 12 natural forest preserves varying in time since last fire (35-355 years). Each site was monitored for N fixation activity using a calibrated acetylene reduction assay. Nitrogen fixation rates were found to increase linearly with time since fire. This increase in N fixation with succession is likely a function of degree of colonization by cyanobacteria and site factors Such as presence of available N. Surface applications of 4.5 kg N(.)ha (1.)yr(-1) as NH4NO3 Were found to eliminate N fixation while applications of P resulted in only a slight and temporary increase of N fixation rates. In contrast to common observation our findings suggest that N fixation in boreal forests becomes more important in late Succession. Limited N availability in late Succession is clearly one of the primary drivers of N fixation rates in boreal forest ecosystems. These findings may help to explain the origin of high rates of net N accumulation in Soil unaccounted for at northern boreal sites.},
	language = {English},
	number = {12},
	journal = {Ecology},
	author = {Zackrisson, O. and DeLuca, T. H. and Nilsson, M. C. and Sellstedt, A. and Berglund, L. M.},
	month = dec,
	year = {2004},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000226297500014},
	keywords = {Pleurozium schreberi, Sweden, abiotic factors, accumulation, acetylene, acetylene reduction, boreal forest, cyanobacteria, ecosystem properties, feather mosses, fire, gradient, hawaii, island area, nitrogen   fixation, photosynthesis, plants, succession},
	pages = {3327--3334},
}

There is little understanding of successional dynamics of N fixation in northern boreal forests. Recent evidence suggests that N fixation by cyanobacteria in association with the common feather moss Pleurozium schreberi contributes to a significant proportion of the total N economy. The Purpose Of the work herein was to determine how time since last fire influences N fixation rates in boreal forests. We evaluated seasonal N fixation rates oil a total of 12 natural forest preserves varying in time since last fire (35-355 years). Each site was monitored for N fixation activity using a calibrated acetylene reduction assay. Nitrogen fixation rates were found to increase linearly with time since fire. This increase in N fixation with succession is likely a function of degree of colonization by cyanobacteria and site factors Such as presence of available N. Surface applications of 4.5 kg N(.)ha (1.)yr(-1) as NH4NO3 Were found to eliminate N fixation while applications of P resulted in only a slight and temporary increase of N fixation rates. In contrast to common observation our findings suggest that N fixation in boreal forests becomes more important in late Succession. Limited N availability in late Succession is clearly one of the primary drivers of N fixation rates in boreal forest ecosystems. These findings may help to explain the origin of high rates of net N accumulation in Soil unaccounted for at northern boreal sites.

@article{nordin_nitrogen_2004,
	title = {Nitrogen uptake by arctic soil microbes and plants in relation to soil nitrogen supply},
	volume = {85},
	issn = {0012-9658},
	doi = {10.1890/03-0084},
	abstract = {In Alaska, evergreen and deciduous shrubs dominate the vegetation of moist acidic arctic tundra (soil pH {\textless} 5.5) while graminoids and forbs are important at the more species-rich moist nonacidic arctic tundra (soil pH {\textgreater} 5.5). In this study we compare soil concentrations and microbial and plant uptake of amino acids, ammonium (NH4+), and nitrate (NO3-) in acidic and nonacidic tundra. The objective was to determine any differences between the tundra sites that may relate to the differences in vegetation. We sampled the water-extractable soil N pool over one growing season and found that it at all times was higher at the nonacidic than at the acidic site, while at both sites it was dominated by NH4+ followed in order by amino acid N and NO3-. In addition, we designed an experiment in which a mixture of aspartic acid, glycine, NH4+, and NO3- were injected into the soil in the middle of the growth period. In the mixture, one N form at a time was labeled with N-15 and in the case of amino acids also with C-13. Soil and plant samples were collected 4 h following the injection of labeled N. A large portion of the experimental N was recovered in the soil microbial biomass (on average 49\% at the acidic site and 40\% at the nonacidic site), while less than 1\% was recovered in plants. Soil microbes and plants at both acidic and nonacidic tundra were able to take up all isotopically labeled N forms in the presence of added unlabeled N, demonstrating adequate potential to use any N form available. In addition, gas chromatography-mass spectrometry (GC-MS) analysis of plant roots revealed plant uptake of intact glycine, while isotopically labeled aspartic acid was not recovered inside plants.},
	language = {English},
	number = {4},
	journal = {Ecology},
	author = {Nordin, A. and Schmidt, I. K. and Shaver, G. R.},
	month = apr,
	year = {2004},
	note = {Place: Washington
Publisher: Ecological Soc Amer
WOS:000220766600007},
	keywords = {(nh4+)-n-15, (no3-)-n-15, C-13-N-15-amino acids, amino-acid, arctic vegetation, biomass, biosynthesis, boreal forest, calibration, fumigation-extraction method, growth, inorganic nitrogen, metabolism, nitrogen uptake, organic-nitrogen, soil PH, tundra},
	pages = {955--962},
}

In Alaska, evergreen and deciduous shrubs dominate the vegetation of moist acidic arctic tundra (soil pH \textless 5.5) while graminoids and forbs are important at the more species-rich moist nonacidic arctic tundra (soil pH \textgreater 5.5). In this study we compare soil concentrations and microbial and plant uptake of amino acids, ammonium (NH4+), and nitrate (NO3-) in acidic and nonacidic tundra. The objective was to determine any differences between the tundra sites that may relate to the differences in vegetation. We sampled the water-extractable soil N pool over one growing season and found that it at all times was higher at the nonacidic than at the acidic site, while at both sites it was dominated by NH4+ followed in order by amino acid N and NO3-. In addition, we designed an experiment in which a mixture of aspartic acid, glycine, NH4+, and NO3- were injected into the soil in the middle of the growth period. In the mixture, one N form at a time was labeled with N-15 and in the case of amino acids also with C-13. Soil and plant samples were collected 4 h following the injection of labeled N. A large portion of the experimental N was recovered in the soil microbial biomass (on average 49% at the acidic site and 40% at the nonacidic site), while less than 1% was recovered in plants. Soil microbes and plants at both acidic and nonacidic tundra were able to take up all isotopically labeled N forms in the presence of added unlabeled N, demonstrating adequate potential to use any N form available. In addition, gas chromatography-mass spectrometry (GC-MS) analysis of plant roots revealed plant uptake of intact glycine, while isotopically labeled aspartic acid was not recovered inside plants.

@article{jiye_global_2004,
	title = {Global analysis of low-molecular-weight compounds in human plasma using {GC}/{TOF}-{MS}},
	volume = {36},
	issn = {0360-2532},
	language = {English},
	journal = {Drug Metabolism Reviews},
	author = {Jiye, A. and Trygg, J. and Gullberg, J. and Moritz, T. and Marklund, S.},
	month = aug,
	year = {2004},
	note = {Place: Philadelphia
Publisher: Taylor \& Francis Inc
WOS:000224023200489},
	pages = {246--246},
}

@article{strand_plastid--nucleus_2004,
	title = {Plastid-to-nucleus signalling},
	volume = {7},
	issn = {1369-5266},
	url = {https://www.sciencedirect.com/science/article/pii/S1369526604001256},
	doi = {10.1016/j.pbi.2004.09.004},
	abstract = {The function of the eukaryotic cell depends on the reciprocal interaction between its different compartments. Plastids emit signals that regulate nuclear gene expression to ensure the stoichiometric assembly of plastid protein complexes and to initiate macromolecular reorganisation in response to environmental cues. It is now clear that several different plastid processes produce signals that influence the expression of photosynthetic genes in the nucleus. The genome uncoupled (gun) mutants recently revealed one of the plastid signals, the chlorophyll intermediate Mg-protoporphyrinIX.},
	language = {en},
	number = {6},
	urldate = {2021-06-30},
	journal = {Current Opinion in Plant Biology},
	author = {Strand, Åsa},
	month = dec,
	year = {2004},
	pages = {621--625},
}

The function of the eukaryotic cell depends on the reciprocal interaction between its different compartments. Plastids emit signals that regulate nuclear gene expression to ensure the stoichiometric assembly of plastid protein complexes and to initiate macromolecular reorganisation in response to environmental cues. It is now clear that several different plastid processes produce signals that influence the expression of photosynthetic genes in the nucleus. The genome uncoupled (gun) mutants recently revealed one of the plastid signals, the chlorophyll intermediate Mg-protoporphyrinIX.

@article{strengbom_light_2004,
	title = {Light, not nitrogen, limits growth of the grass {Deschampsia} flexuosa in boreal forests},
	volume = {82},
	issn = {0008-4026},
	doi = {10.1139/B04-017},
	abstract = {Increased nitrogen (N) input in boreal forests has previously been shown to induce a shift from Vaccinium myrtillus L. to Deschampsia flexuosa (L.) Trin. as the dominant understory species. We investigated the relative importance of increased light and N for this shift, in a field experiment. We increased light availability, that is, we reduced aboveground competition from V myrtillus, and increased N by adding 50 kg N.ha(-1). Increased light availability had a positive effect on both the growth rate and final biomass of D. flexuosa. Although N addition increased the uptake of fertilizer N by both species, it had no effect on the growth or biomass of either species. Thus, aboveground competition from V myrtillus prevented expansion of D. flexuosa, regardless of N treatment. The results suggest that aboveground competition may be more important than belowground competition for structuring understory boreal forest communities. As light availability is important, both the structure and total amount of standing crop will be important for the outcome of species interactions.},
	language = {English},
	number = {4},
	journal = {Canadian Journal of Botany-Revue Canadienne De Botanique},
	author = {Strengbom, J. and Nasholm, T. and Ericson, L.},
	month = apr,
	year = {2004},
	note = {Place: Ottawa
Publisher: Canadian Science Publishing
WOS:000222035300002},
	keywords = {aboveground competition, below-ground competition, belowground competition, deposition, diversity, experimental gradient, fertilization, heathland, mineral-nutrition, natural   enemies, nitrogen deposition, plants, productivity, vegetation, vegetation change},
	pages = {430--435},
}

Increased nitrogen (N) input in boreal forests has previously been shown to induce a shift from Vaccinium myrtillus L. to Deschampsia flexuosa (L.) Trin. as the dominant understory species. We investigated the relative importance of increased light and N for this shift, in a field experiment. We increased light availability, that is, we reduced aboveground competition from V myrtillus, and increased N by adding 50 kg N.ha(-1). Increased light availability had a positive effect on both the growth rate and final biomass of D. flexuosa. Although N addition increased the uptake of fertilizer N by both species, it had no effect on the growth or biomass of either species. Thus, aboveground competition from V myrtillus prevented expansion of D. flexuosa, regardless of N treatment. The results suggest that aboveground competition may be more important than belowground competition for structuring understory boreal forest communities. As light availability is important, both the structure and total amount of standing crop will be important for the outcome of species interactions.

@article{corander_baps_2004,
	title = {{BAPS} 2: enhanced possibilities for the analysis of genetic population structure},
	volume = {20},
	issn = {1367-4803},
	shorttitle = {{BAPS} 2},
	url = {https://doi.org/10.1093/bioinformatics/bth250},
	doi = {10.1093/bioinformatics/bth250},
	abstract = {Summary: Bayesian statistical methods based on simulation techniques have recently been shown to provide powerful tools for the analysis of genetic population structure. We have previously developed a Markov chain Monte Carlo (MCMC) algorithm for characterizing genetically divergent groups based on molecular markers and geographical sampling design of the dataset. However, for large-scale datasets such algorithms may get stuck to local maxima in the parameter space. Therefore, we have modified our earlier algorithm to support multiple parallel MCMC chains, with enhanced features that enable considerably faster and more reliable estimation compared to the earlier version of the algorithm. We consider also a hierarchical tree representation, from which a Bayesian model-averaged structure estimate can be extracted. The algorithm is implemented in a computer program that features a user-friendly interface and built-in graphics. The enhanced features are illustrated by analyses of simulated data and an extensive human molecular dataset.Availability: Freely available at http://www.rni.helsinki.fi/{\textasciitilde}jic/bapspage.html},
	number = {15},
	urldate = {2021-06-30},
	journal = {Bioinformatics},
	author = {Corander, Jukka and Waldmann, Patrik and Marttinen, Pekka and Sillanpää, Mikko J.},
	month = oct,
	year = {2004},
	pages = {2363--2369},
}

Summary: Bayesian statistical methods based on simulation techniques have recently been shown to provide powerful tools for the analysis of genetic population structure. We have previously developed a Markov chain Monte Carlo (MCMC) algorithm for characterizing genetically divergent groups based on molecular markers and geographical sampling design of the dataset. However, for large-scale datasets such algorithms may get stuck to local maxima in the parameter space. Therefore, we have modified our earlier algorithm to support multiple parallel MCMC chains, with enhanced features that enable considerably faster and more reliable estimation compared to the earlier version of the algorithm. We consider also a hierarchical tree representation, from which a Bayesian model-averaged structure estimate can be extracted. The algorithm is implemented in a computer program that features a user-friendly interface and built-in graphics. The enhanced features are illustrated by analyses of simulated data and an extensive human molecular dataset.Availability: Freely available at http://www.rni.helsinki.fi/~jic/bapspage.html

@article{grebe_ups_2004,
	title = {Ups and downs of tissue and planar polarity in plants},
	volume = {26},
	issn = {1521-1878},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.20065},
	doi = {10.1002/bies.20065},
	abstract = {The polar orientation of cells within a tissue is an intensively studied research area in animal cells. The term planar polarity refers to the common polar arrangement of cells within the plane of an epithelium. In plants, the subcellular analysis of tissue polarity has been limited by the lack of appropriate markers. Recently, research on plant tissue polarity has come of age. Advances are based on studies of Arabidopsis patterning, cell polarity and auxin transport mutants employing the coordinated, polar localization of auxin transporters and the planar polarity of root epidermal hairs as markers. These approaches have revealed auxin transport and response, vesicular trafficking, membrane sterol and cytoskeletal requirements of tissue polarity. This review summarizes recent progress in research on vascular tissue and planar epidermal polarity in the Arabidopsis root and compares it to findings on planar polarity in animals and cell polarity in yeast. BioEssays 26:719–729, 2004. © 2004 Wiley Periodicals, Inc.},
	language = {en},
	number = {7},
	urldate = {2021-06-30},
	journal = {BioEssays},
	author = {Grebe, Markus},
	year = {2004},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/bies.20065},
	pages = {719--729},
}

The polar orientation of cells within a tissue is an intensively studied research area in animal cells. The term planar polarity refers to the common polar arrangement of cells within the plane of an epithelium. In plants, the subcellular analysis of tissue polarity has been limited by the lack of appropriate markers. Recently, research on plant tissue polarity has come of age. Advances are based on studies of Arabidopsis patterning, cell polarity and auxin transport mutants employing the coordinated, polar localization of auxin transporters and the planar polarity of root epidermal hairs as markers. These approaches have revealed auxin transport and response, vesicular trafficking, membrane sterol and cytoskeletal requirements of tissue polarity. This review summarizes recent progress in research on vascular tissue and planar epidermal polarity in the Arabidopsis root and compares it to findings on planar polarity in animals and cell polarity in yeast. BioEssays 26:719–729, 2004. © 2004 Wiley Periodicals, Inc.

@article{shi_low_2004,
	title = {The low molecular mass subunits of the photosynthetic supracomplex, photosystem {II}},
	volume = {1608},
	issn = {0005-2728},
	doi = {10.1016/j.bbabio.2003.12.004},
	abstract = {The photosystem II (PSII) complex is located in the thylakoid membrane of higher plants, algae and cyanobacteria and drives the water oxidation process of photosynthesis, which splits water into reducing equivalents and molecular oxygen by solar energy. Electron and X-ray crystallography analyses have revealed that the PSII core complex contains between 34 and 36 transmembrane CL-helices, depending on the organism. Of these helices at least 12-14 are attributed to low molecular mass proteins. However, to date, at least 18 low molecular mass ({\textless} 10 kDa) subunits are putatively associated with the PSII complex. Most of them contain a single transmembrane span and their protein sequences are conserved among photosynthetic organisms. In addition, these proteins do not have any similarity to any known functional proteins in any type of organism, and only two of them bind a cofactor. These findings raise intriguing questions about why there are so many small protein subunits with single-transmembrane spans in the PSII complex, and their possible functions. This article reviews our current knowledge of this group of proteins. Deletion mutations of the low molecular mass subunits from both prokaryotic and eukaryotic model systems are compared in an attempt to understand the function of these proteins. From these comparisons it seems that the majority of them are involved in stabilization, assembly or dimerization of the PSII complex. The small proteins may facilitate fast dynamic conformational changes that the PSII complex needs to perform an optimal photosynthetic activity. (C) 2004 Elsevier B.V. All rights reserved.},
	language = {English},
	number = {2-3},
	journal = {Biochimica Et Biophysica Acta-Bioenergetics},
	author = {Shi, L. X. and Schroder, W. P.},
	month = feb,
	year = {2004},
	note = {Place: Amsterdam
Publisher: Elsevier Science Bv
WOS:000220012300001},
	keywords = {Arabidopsis, Synechocystis, arabidopsis-thaliana, center core   complex, cyanobacterium synechococcus-elongatus, function, light-harvesting antenna, open reading frames, ps2, psii-h subunit, reaction-center complex, sec-independent insertion, small protein, synechocystis sp pcc-6803, thylakoid   membrane-proteins},
	pages = {75--96},
}

The photosystem II (PSII) complex is located in the thylakoid membrane of higher plants, algae and cyanobacteria and drives the water oxidation process of photosynthesis, which splits water into reducing equivalents and molecular oxygen by solar energy. Electron and X-ray crystallography analyses have revealed that the PSII core complex contains between 34 and 36 transmembrane CL-helices, depending on the organism. Of these helices at least 12-14 are attributed to low molecular mass proteins. However, to date, at least 18 low molecular mass (\textless 10 kDa) subunits are putatively associated with the PSII complex. Most of them contain a single transmembrane span and their protein sequences are conserved among photosynthetic organisms. In addition, these proteins do not have any similarity to any known functional proteins in any type of organism, and only two of them bind a cofactor. These findings raise intriguing questions about why there are so many small protein subunits with single-transmembrane spans in the PSII complex, and their possible functions. This article reviews our current knowledge of this group of proteins. Deletion mutations of the low molecular mass subunits from both prokaryotic and eukaryotic model systems are compared in an attempt to understand the function of these proteins. From these comparisons it seems that the majority of them are involved in stabilization, assembly or dimerization of the PSII complex. The small proteins may facilitate fast dynamic conformational changes that the PSII complex needs to perform an optimal photosynthetic activity. (C) 2004 Elsevier B.V. All rights reserved.

@article{lennartsson_screening_2004,
	title = {Screening for efficient cold hardening in a breeding population of {Salix} using near infrared reflectance spectroscopy},
	volume = {61},
	issn = {1286-4560},
	doi = {10.1051/forest:2004038},
	abstract = {The inheritance of cold hardening components-the timing of onset and the inherent rate-was studied in Salix spp. This was achieved by characterising the F-2 population of a cross between an early-and-rapidly hardening clone and a late-and-slowly hardening clone. The cold hardiness of stems was estimated using the infrared reflectance spectra of dried and homogenised samples. This method was first calibrated against the freeze test method. The timing of growth cessation was used to determine the onset of cold hardening. In the F-2 progeny, traits were partly recombined as indicated by the occurrence of clones with early-and-slowly hardening characteristics. The frequency distributions of clones also indicated that the timing of onset and the inherent rate of hardening were independently inherited traits. None of the clones exhibited the desirable late-and-rapidly hardening characteristics, combining a long growing period with effective cold hardening. This is not surprising since few F-2 clones exhibited late hardening.},
	language = {English},
	number = {5},
	journal = {Annals of Forest Science},
	author = {Lennartsson, M. and Ogren, E.},
	month = aug,
	year = {2004},
	note = {Place: Paris
Publisher: Springer France
WOS:000225059100007},
	keywords = {Salix, acclimation, biomass production, coastal douglas-fir, cold hardiness, dormancy, fall frost-resistance, growth, growth cessation, hardiness, near infrared spectroscopy, seedlings, temperature, tolerance, tree breeding},
	pages = {449--454},
}

The inheritance of cold hardening components-the timing of onset and the inherent rate-was studied in Salix spp. This was achieved by characterising the F-2 population of a cross between an early-and-rapidly hardening clone and a late-and-slowly hardening clone. The cold hardiness of stems was estimated using the infrared reflectance spectra of dried and homogenised samples. This method was first calibrated against the freeze test method. The timing of growth cessation was used to determine the onset of cold hardening. In the F-2 progeny, traits were partly recombined as indicated by the occurrence of clones with early-and-slowly hardening characteristics. The frequency distributions of clones also indicated that the timing of onset and the inherent rate of hardening were independently inherited traits. None of the clones exhibited the desirable late-and-rapidly hardening characteristics, combining a long growing period with effective cold hardening. This is not surprising since few F-2 clones exhibited late hardening.

@article{wikberg_interrelationships_2004,
	title = {Interrelationships between water use and growth traits in biomass-producing willows},
	volume = {18},
	issn = {0931-1890},
	doi = {10.1007/s00468-003-0282-y},
	abstract = {Water use, drought response and growth were examined under controlled conditions in four interbreeding willow species from different geographical origins (two clones of Salix viminalis L., one clone of S. viminalis x S. schwerenii E. Wolf and one clone of S. purpurea L.). The levels of soil water depletion that plants could sustain without wilting varied markedly between the clones. The level of drought resistance expressed this way was positively related to resistance to xylem cavitation, negatively related to the maximum stomatal conductance, and positively related to early stomatal closure. The rate of stomatal closure, however, was negatively related to the resistance to xylem cavitation. Prior to drought, there were no significant differences between leaf-specific hydraulic conductances of the clones when whole plants were considered. However, there were differences if the roots and shoots were considered separately. Drought resistance was negatively related to maximum growth yields. This is probably because resources were diverted away from leaf production to the production of denser wood (wood density was positively related to cavitation resistance), and, for one clone, to the growth of a larger root system. In addition, because the level of drought resistance was negatively related to the maximum stomatal conductance, growth may have been adversely affected as a result of reduced photosynthesis. Given its high water extraction ability, one of the clones started to wilt sooner than expected, although only lateral shoots were affected. This appeared to indicate a strategy of sacrificing expendable shoots.},
	language = {English},
	number = {1},
	journal = {Trees-Structure and Function},
	author = {Wikberg, J. and Ogren, E.},
	month = jan,
	year = {2004},
	note = {Place: New York
Publisher: Springer-Verlag
WOS:000187549100009},
	keywords = {cavitation, drought, embolism, hydraulic conductance, plant, resistance, riparian cottonwoods, salix-viminalis, shoot hydraulic conductance, stomatal conductance, stomatal control, vulnerability, water   potential, xylem cavitation},
	pages = {70--76},
}

Water use, drought response and growth were examined under controlled conditions in four interbreeding willow species from different geographical origins (two clones of Salix viminalis L., one clone of S. viminalis x S. schwerenii E. Wolf and one clone of S. purpurea L.). The levels of soil water depletion that plants could sustain without wilting varied markedly between the clones. The level of drought resistance expressed this way was positively related to resistance to xylem cavitation, negatively related to the maximum stomatal conductance, and positively related to early stomatal closure. The rate of stomatal closure, however, was negatively related to the resistance to xylem cavitation. Prior to drought, there were no significant differences between leaf-specific hydraulic conductances of the clones when whole plants were considered. However, there were differences if the roots and shoots were considered separately. Drought resistance was negatively related to maximum growth yields. This is probably because resources were diverted away from leaf production to the production of denser wood (wood density was positively related to cavitation resistance), and, for one clone, to the growth of a larger root system. In addition, because the level of drought resistance was negatively related to the maximum stomatal conductance, growth may have been adversely affected as a result of reduced photosynthesis. Given its high water extraction ability, one of the clones started to wilt sooner than expected, although only lateral shoots were affected. This appeared to indicate a strategy of sacrificing expendable shoots.

@article{hjelm_photosynthetic_2004,
	title = {Photosynthetic responses to short-term and long-term light variation in {Pinus} sylvestris and {Salix} dasyclados},
	volume = {18},
	issn = {0931-1890},
	doi = {10.1007/s00468-004-0329-8},
	abstract = {Pinus sylvestris and Salix dasyclados, which differ in leaf longevity, were compared with respect to four aspects of photosynthetic light use and response: high light acclimation, photoinhibition resistance and recovery, lightfleck exposure and use and chloroplast acclimation across leaves. The first two aspects were examined using seedlings under controlled conditions and the other two were tested using trees in the field. When exposed to high light, shade leaves of Pinus acclimated completely, achieving the same photosynthetic capacities as sun leaves, whereas shade leaves of Salix did not reach sun leaf capacities although the absolute magnitude of their acclimation was larger. Shade leaves of Pinus were also more resistant to photoinhibition than those of Salix. Much of the direct light supplied within the canopy was in the form of rapid fluctuations, lightflecks, for Pinus and Salix alike. They exploited short lightflecks with similar efficiency. The greater proportion of diffuse light in the canopy for Pinus than Salix seems to lead to a lesser degree of differential intra-leaf acclimation of chloroplasts, in turn leading to lower efficiency of photosynthesis under unilateral light as reflected by a lower convexity, rate of bending, of the light-response curve. The differences in light use and responses are discussed in relation to possible differences in characteristics of the long and short-lived leaf.},
	language = {English},
	number = {6},
	journal = {Trees-Structure and Function},
	author = {Hjelm, U. and Ogren, E.},
	month = nov,
	year = {2004},
	note = {Place: New York
Publisher: Springer
WOS:000224755300002},
	keywords = {chlorophyll fluorescence, field conditions, growth-rate, leaf life-span, leaf longevity, light-response, lightfleck, lived leaves, nitrogen   concentration, norway spruce, photoinhibition, photosynthetic acclimation, picea-abies, rain-forest},
	pages = {622--629},
}

Pinus sylvestris and Salix dasyclados, which differ in leaf longevity, were compared with respect to four aspects of photosynthetic light use and response: high light acclimation, photoinhibition resistance and recovery, lightfleck exposure and use and chloroplast acclimation across leaves. The first two aspects were examined using seedlings under controlled conditions and the other two were tested using trees in the field. When exposed to high light, shade leaves of Pinus acclimated completely, achieving the same photosynthetic capacities as sun leaves, whereas shade leaves of Salix did not reach sun leaf capacities although the absolute magnitude of their acclimation was larger. Shade leaves of Pinus were also more resistant to photoinhibition than those of Salix. Much of the direct light supplied within the canopy was in the form of rapid fluctuations, lightflecks, for Pinus and Salix alike. They exploited short lightflecks with similar efficiency. The greater proportion of diffuse light in the canopy for Pinus than Salix seems to lead to a lesser degree of differential intra-leaf acclimation of chloroplasts, in turn leading to lower efficiency of photosynthesis under unilateral light as reflected by a lower convexity, rate of bending, of the light-response curve. The differences in light use and responses are discussed in relation to possible differences in characteristics of the long and short-lived leaf.

@article{lstiburek_open-nucleus_2004,
	title = {Open-nucleus breeding strategies compared with population-wide positive assortative mating},
	volume = {109},
	issn = {1432-2242},
	url = {https://doi.org/10.1007/s00122-004-1737-2},
	doi = {10.1007/s00122-004-1737-2},
	abstract = {This study compares population-wide positive assortative mating (PAM) with open-nucleus breeding with an elite and main population when more effort is allocated to parents of the elite. A companion study showed that PAM is advantageous when testing effort is independent of parental value. In the present study, unbalanced testing was imposed by varying the number of crosses or the number of genotypes per cross. These unbalanced alternatives are compared with PAM, where the testing effort was varied so that better parents were mated more frequently. More effort allocated to parents of higher rank increased the additive effect and the additive variance and only slightly altered the group coancestry and inbreeding in the breeding population (BP) compared with completely balanced scenarios. Of particular interest to the breeder, large enhancement of the additive variance in the BP contributed to higher gains in the production population (PP). These simulations demonstrate that population-wide PAM leads to higher genetic gains compared with open-nucleus alternatives at any desired target level of diversity in the PP. This is true for both balanced (part I) and unbalanced distribution of testing effort (part II).},
	language = {en},
	number = {6},
	urldate = {2021-06-30},
	journal = {Theoretical and Applied Genetics},
	author = {Lstibůrek, M. and Mullin, T. J. and Lindgren, D. and Rosvall, O.},
	month = oct,
	year = {2004},
	pages = {1169--1177},
}

This study compares population-wide positive assortative mating (PAM) with open-nucleus breeding with an elite and main population when more effort is allocated to parents of the elite. A companion study showed that PAM is advantageous when testing effort is independent of parental value. In the present study, unbalanced testing was imposed by varying the number of crosses or the number of genotypes per cross. These unbalanced alternatives are compared with PAM, where the testing effort was varied so that better parents were mated more frequently. More effort allocated to parents of higher rank increased the additive effect and the additive variance and only slightly altered the group coancestry and inbreeding in the breeding population (BP) compared with completely balanced scenarios. Of particular interest to the breeder, large enhancement of the additive variance in the BP contributed to higher gains in the production population (PP). These simulations demonstrate that population-wide PAM leads to higher genetic gains compared with open-nucleus alternatives at any desired target level of diversity in the PP. This is true for both balanced (part I) and unbalanced distribution of testing effort (part II).

@article{lstiburek_open-nucleus_2004,
	title = {Open-nucleus breeding strategies compared with population-wide positive assortative mating},
	volume = {109},
	issn = {1432-2242},
	url = {https://doi.org/10.1007/s00122-004-1746-1},
	doi = {10.1007/s00122-004-1746-1},
	abstract = {Positive assortative mating (PAM) can enhance the additive genetic variance in a breeding population (BP). This increases the potential for gains in the production population (PP, selected subset of the BP) for recurrent selection programs in forest trees. The assortment of mates can be either: (1) by individual tree rank across the whole BP (PAM), or (2) trees of similar rank can be merged into larger hierarchical groups and then mated randomly within group (“open”-nucleus breeding, NB). The objective of this study was to compare PAM and NB in quantitative terms. The NB simulation model assumed two tiers (nucleus, main) with unrestricted migration between the tiers. Clonal tests were used to predict breeding values and test resources per mate were kept constant for all mates. Both gain and diversity were combined into a single selection criterion, “group-merit selection.” Alternatives were compared over five breeding cycles by considering genetic gain and diversity in a selected PP established in a seed orchard. The assortment of mates in both alternatives enhanced additive variance and increased the additive effect in the BP, leading to additional gain in the PP. Gains generated under PAM always exceeded gains under NB. Thus, the main message from this study is that PAM in both the short- and long-term results in more gain at any target level of diversity in the PP (the breeder’s target) than is achieved by the NB alternative. The optimum size of the nucleus varies with the desired level of seed orchard diversity. At lower target diversity, smaller nucleus sizes are favorable, while larger sizes result in more gain when seed orchard diversity is considered more important.},
	language = {en},
	number = {6},
	urldate = {2021-06-30},
	journal = {Theoretical and Applied Genetics},
	author = {Lstibůrek, M. and Mullin, T. J. and Lindgren, D. and Rosvall, O.},
	month = oct,
	year = {2004},
	pages = {1196--1203},
}

Positive assortative mating (PAM) can enhance the additive genetic variance in a breeding population (BP). This increases the potential for gains in the production population (PP, selected subset of the BP) for recurrent selection programs in forest trees. The assortment of mates can be either: (1) by individual tree rank across the whole BP (PAM), or (2) trees of similar rank can be merged into larger hierarchical groups and then mated randomly within group (“open”-nucleus breeding, NB). The objective of this study was to compare PAM and NB in quantitative terms. The NB simulation model assumed two tiers (nucleus, main) with unrestricted migration between the tiers. Clonal tests were used to predict breeding values and test resources per mate were kept constant for all mates. Both gain and diversity were combined into a single selection criterion, “group-merit selection.” Alternatives were compared over five breeding cycles by considering genetic gain and diversity in a selected PP established in a seed orchard. The assortment of mates in both alternatives enhanced additive variance and increased the additive effect in the BP, leading to additional gain in the PP. Gains generated under PAM always exceeded gains under NB. Thus, the main message from this study is that PAM in both the short- and long-term results in more gain at any target level of diversity in the PP (the breeder’s target) than is achieved by the NB alternative. The optimum size of the nucleus varies with the desired level of seed orchard diversity. At lower target diversity, smaller nucleus sizes are favorable, while larger sizes result in more gain when seed orchard diversity is considered more important.

@article{lennartsson_clonal_2004,
	title = {Clonal {Variation} in {Temperature} {Requirements} for {Budburst} and {Dehardening} in {Salix} {Species} {Used} for {Biomass} {Production}},
	volume = {19},
	issn = {0282-7581},
	url = {https://doi.org/10.1080/02827580410030145},
	doi = {10.1080/02827580410030145},
	abstract = {Differences in temperature requirements for budburst were investigated among Salix clones used for biomass production spanning a wide range of geographical origins. When assessed under controlled conditions, the threshold temperature for the accumulation of the temperature sum for budburst was not significantly different among clones, with six out of the seven clones having a value of 1.0–1.2°C. However, there were significant clonal differences in the temperature sum required for budburst, with values ranging from 110 to 191 d °C. This variation was only weakly linked to the geographical origin of the clones. The decline during the spring in levels of cold hardiness and sugars was also investigated in field-grown plants. All clones could tolerate temperatures ≤−15°C, according to freeze tests, until at least a couple of weeks before budburst. This finding, together with the fact that buds become frost sensitive when they burst, suggests that the clonal variation in susceptibility to spring frosts, as observed in field trials, is related to the clonal variation in the timing of budburst, largely determined by the temperature sum requirement. Stem contents of cryoprotective sugars (sucrose, raffinose and stachyose) declined in spring in parallel with dehardening at first, but reached summer levels before dehardening was completed.},
	number = {4},
	urldate = {2021-06-30},
	journal = {Scandinavian Journal of Forest Research},
	author = {Lennartsson, Mattias and Ögren, Erling},
	month = jul,
	year = {2004},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/02827580410030145},
	keywords = {Basket willow, cold hardiness, sugars, temperature sum, thermal time},
	pages = {295--302},
}

Differences in temperature requirements for budburst were investigated among Salix clones used for biomass production spanning a wide range of geographical origins. When assessed under controlled conditions, the threshold temperature for the accumulation of the temperature sum for budburst was not significantly different among clones, with six out of the seven clones having a value of 1.0–1.2°C. However, there were significant clonal differences in the temperature sum required for budburst, with values ranging from 110 to 191 d °C. This variation was only weakly linked to the geographical origin of the clones. The decline during the spring in levels of cold hardiness and sugars was also investigated in field-grown plants. All clones could tolerate temperatures ≤−15°C, according to freeze tests, until at least a couple of weeks before budburst. This finding, together with the fact that buds become frost sensitive when they burst, suggests that the clonal variation in susceptibility to spring frosts, as observed in field trials, is related to the clonal variation in the timing of budburst, largely determined by the temperature sum requirement. Stem contents of cryoprotective sugars (sucrose, raffinose and stachyose) declined in spring in parallel with dehardening at first, but reached summer levels before dehardening was completed.

@article{ericsson_genetic_2004,
	title = {Genetic analysis of fibre size in a full-sib {Pinus} sylvestris {L}. progeny test},
	volume = {19},
	issn = {0282-7581},
	url = {https://doi.org/10.1080/02827580310019031},
	doi = {10.1080/02827580310019031},
	abstract = {Fibre length, fibre width, tree height and stem diameter in 25-yr-old Scots pine (Pinus sylvestris L.) were investigated by genetic analysis. The analysis was carried out on nearly 400 trees for all traits simultaneously using multiple-trait, individual tree equations with simultaneous variance estimation. Narrow-sense heritabilities were estimated at about 0.3 for all traits except for stem diameter, which was lower (0.17). Low genetic coefficients of variation for fibre length may be partially explained by the sampling method, which was 5 mm increment boring resulting in fibre fragmentation, but the method served well for heritability and correlation analysis. The additive genetic correlation was strongly negative between fibre length and stem diameter, and strongly positive between fibre width and growth traits. The pair of fibre traits showed mutually strong negative additive-genetic but weak positive environmental correlation. The pair of growth traits showed no genetic but strong positive environmental correlation. Other correlation estimates were minor and uncertain, with the exception of a weak negative environmental correlation between fibre length and stem diameter. An additional approach, where stem diameter was regarded as a covariate, revealed positive environmental correlation between fibre length and tree height and negative environmental correlation between fibre width and tree height.},
	number = {1},
	urldate = {2021-06-30},
	journal = {Scandinavian Journal of Forest Research},
	author = {Ericsson, Tore and Fries, Anders},
	month = feb,
	year = {2004},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/02827580310019031},
	keywords = {Fibre length, Scots pine, fibre width, full-sib, genetic correlation, growth trait, heritability, multiple-trait individual tree model, tracheids},
	pages = {7--13},
}

Fibre length, fibre width, tree height and stem diameter in 25-yr-old Scots pine (Pinus sylvestris L.) were investigated by genetic analysis. The analysis was carried out on nearly 400 trees for all traits simultaneously using multiple-trait, individual tree equations with simultaneous variance estimation. Narrow-sense heritabilities were estimated at about 0.3 for all traits except for stem diameter, which was lower (0.17). Low genetic coefficients of variation for fibre length may be partially explained by the sampling method, which was 5 mm increment boring resulting in fibre fragmentation, but the method served well for heritability and correlation analysis. The additive genetic correlation was strongly negative between fibre length and stem diameter, and strongly positive between fibre width and growth traits. The pair of fibre traits showed mutually strong negative additive-genetic but weak positive environmental correlation. The pair of growth traits showed no genetic but strong positive environmental correlation. Other correlation estimates were minor and uncertain, with the exception of a weak negative environmental correlation between fibre length and stem diameter. An additional approach, where stem diameter was regarded as a covariate, revealed positive environmental correlation between fibre length and tree height and negative environmental correlation between fibre width and tree height.

@article{eriksson_three-block_2004,
	title = {Three-block bi-focal {PLS} ({3BIF}-{PLS}) and its application in {QSAR}},
	volume = {15},
	issn = {1062-936X},
	url = {https://doi.org/10.1080/10629360412331297452},
	doi = {10.1080/10629360412331297452},
	abstract = {When X and Y are multivariate, the two-block partial least squares (PLS) method is often used. In this paper, we outline an extension addressing a special case of the three-block (X/Y/Z) problem, where Z sits "under" Y. We have called this approach three-block bi-focal PLS (3BIF-PLS). It views the X/Y relationship as the dominant problem, and seeks to use the additional information in Z in order to improve the interpretation of the Y-part of the X/Y association. Two data sets are used to illustrate 3BIF-PLS. Example I relates to single point mutants of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 and their ability to transform halogenated hydrocarbons, some of which are found as organic pollutants in soil. Example II deals with soil remediation capability of bacteria. Whole bacterial communities are monitored over time using "DNA-fingerprinting" technology to see how pollution affects population composition. Since the data sets are large, hierarchical multivariate modelling is invoked to compress data prior to 3BIF-PLS analysis. It is concluded that the 3BIF-PLS approach works well. The paper contains a discussion of pros and cons of the method, and hints at further developmental opportunities.},
	number = {5-6},
	urldate = {2021-06-30},
	journal = {SAR and QSAR in Environmental Research},
	author = {Eriksson, L. and Damborsky, J. and Earll, M. and Johansson, E. and Trygg, J. and Wold, S.},
	month = oct,
	year = {2004},
	pmid = {15669704},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/10629360412331297452},
	keywords = {Hierarchical modelling, PLS, QSAR, Three-block PLS, Two-block PLS},
	pages = {481--499},
}

When X and Y are multivariate, the two-block partial least squares (PLS) method is often used. In this paper, we outline an extension addressing a special case of the three-block (X/Y/Z) problem, where Z sits "under" Y. We have called this approach three-block bi-focal PLS (3BIF-PLS). It views the X/Y relationship as the dominant problem, and seeks to use the additional information in Z in order to improve the interpretation of the Y-part of the X/Y association. Two data sets are used to illustrate 3BIF-PLS. Example I relates to single point mutants of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 and their ability to transform halogenated hydrocarbons, some of which are found as organic pollutants in soil. Example II deals with soil remediation capability of bacteria. Whole bacterial communities are monitored over time using "DNA-fingerprinting" technology to see how pollution affects population composition. Since the data sets are large, hierarchical multivariate modelling is invoked to compress data prior to 3BIF-PLS analysis. It is concluded that the 3BIF-PLS approach works well. The paper contains a discussion of pros and cons of the method, and hints at further developmental opportunities.

@article{lovgren_prc-barrel_2004,
	title = {The {PRC}-barrel domain of the ribosome maturation protein {RimM} mediates binding to ribosomal protein {S19} in the {30S} ribosomal subunits},
	volume = {10},
	issn = {1355-8382},
	doi = {10.1261/rna.7720204},
	abstract = {The RimM protein in Escherichia coli is associated with free 30S ribosomal subunits but not with 70S ribosomes. A DeltarimM mutant is defective in 30S maturation and accumulates 17S rRNA. To study the interaction of RimM with the 30S and its involvement in 30S maturation, RimM amino acid substitution mutants were constructed. A mutant RimM (RimM-YY--{\textgreater}AA), containing alanine substitutions for two adjacent tyrosines within the PRC beta-barrel domain, showed a reduced binding to 30S and an accumulation of 17S rRNA compared to wild-type RimM. The (RimM-YY--{\textgreater}AA) and DeltarimM mutants had significantly lower amounts of polysomes and also reduced levels of 30S relative to 50S compared to a wild-type strain. A mutation in rpsS, which encodes r-protein S19, suppressed the polysome- and 16S rRNA processing deficiencies of the RimM-YY--{\textgreater}AA but not that of the DeltarimM mutant. A mutation in rpsM, which encodes r-protein S13, suppressed the polysome deficiency of both rimM mutants. Suppressor mutations, found in either helices 31 or 33b of 16S rRNA, improved growth of both the RimM-YY--{\textgreater}AA and DeltarimM mutants. However, they suppressed the 16S rRNA processing deficiency of the RimM-YY--{\textgreater}AA mutant more efficiently than that of the DeltarimM mutant. Helices 31 and 33b are known to interact with S13 and S19, respectively, and S13 is known to interact with S19. A GST-RimM but not a GST-RimM(YY--{\textgreater}AA) protein bound strongly to S19 in 30S. Thus, RimM likely facilitates maturation of the region of the head of 30S that contains S13 and S19 as well as helices 31 and 33b.},
	language = {English},
	number = {11},
	journal = {Rna},
	author = {Lovgren, J. M. and Bylund, G. O. and Srivastava, M. K. and Lundberg, L. a. C. and Persson, O. P. and Wingsle, G. and Wikstrom, P. M.},
	month = nov,
	year = {2004},
	note = {Place: Cold Spring Harbor
Publisher: Cold Spring Harbor Lab Press, Publications Dept
WOS:000224746300015},
	keywords = {16S rRNA processing, 30S maturation, RimM, dead, dnak, escherichia-coli, gene, helices 31 and 33b, mutant, mutations, rbfa, rna helicase, s13, s19, site-specific mutagenesis, temperature},
	pages = {1798--1812},
}

The RimM protein in Escherichia coli is associated with free 30S ribosomal subunits but not with 70S ribosomes. A DeltarimM mutant is defective in 30S maturation and accumulates 17S rRNA. To study the interaction of RimM with the 30S and its involvement in 30S maturation, RimM amino acid substitution mutants were constructed. A mutant RimM (RimM-YY–\textgreaterAA), containing alanine substitutions for two adjacent tyrosines within the PRC beta-barrel domain, showed a reduced binding to 30S and an accumulation of 17S rRNA compared to wild-type RimM. The (RimM-YY–\textgreaterAA) and DeltarimM mutants had significantly lower amounts of polysomes and also reduced levels of 30S relative to 50S compared to a wild-type strain. A mutation in rpsS, which encodes r-protein S19, suppressed the polysome- and 16S rRNA processing deficiencies of the RimM-YY–\textgreaterAA but not that of the DeltarimM mutant. A mutation in rpsM, which encodes r-protein S13, suppressed the polysome deficiency of both rimM mutants. Suppressor mutations, found in either helices 31 or 33b of 16S rRNA, improved growth of both the RimM-YY–\textgreaterAA and DeltarimM mutants. However, they suppressed the 16S rRNA processing deficiency of the RimM-YY–\textgreaterAA mutant more efficiently than that of the DeltarimM mutant. Helices 31 and 33b are known to interact with S13 and S19, respectively, and S13 is known to interact with S19. A GST-RimM but not a GST-RimM(YY–\textgreaterAA) protein bound strongly to S19 in 30S. Thus, RimM likely facilitates maturation of the region of the head of 30S that contains S13 and S19 as well as helices 31 and 33b.

@article{mateo_lesion_2004,
	title = {Lesion simulating disease 1 - {Is} required for acclimation to conditions that promote excess excitation energy},
	volume = {136},
	issn = {0032-0889},
	doi = {10/cpzzj3},
	abstract = {The lsd1 mutant of Arabidopsis fails to limit the boundaries of hypersensitive cell death response during avirulent pathogen infection and initiates unchecked lesions in long day photoperiod. giving rise to the runaway cell death (rcd) phenotype. We link here the initiation and propagation of rcd to the activity of photosystem II, stomatal conductance and ultimately to photorespiratory H2O2. A cross of lsd1 with the chlorophyll a/b binding harvesting-organelle specific (designated cao) mutant, which has a reduced photosystem II antenna, led to reduced lesion formation in the lsd1/cao double mutant. This lsd1 mutant also had reduced stomatal conductance and catalase activity in short-day permissive conditions and induced H2O2 accumulation followed by rcd when stomatal gas exchange was further impeded. All of these traits depended on the defense regulators EDS1 and PAD4. Furthermore, nonphotorespiratory conditions retarded propagation of lesions in lsd1. These data suggest that lsd1 failed to acclimate to light conditions that promote excess excitation energy (EEE) and that LSD1 function was required for optimal catalase activity. Through this regulation LSD1 can influence the effectiveness of photorespiration in dissipating EEE and consequently may be a key determinant of acclimatory processes. Salicylic acid, which induces stomatal closure, inhibits catalase activity and triggers the rcd phenotype in lsd1, also impaired acclimation of wild-type plants to conditions that promote EEE. We propose that the roles of LSD1 in light acclimation and in restricting pathogen-induced cell death are functionally linked.},
	language = {English},
	number = {1},
	journal = {Plant Physiology},
	author = {Mateo, A. and Muhlenbock, P. and Rusterucci, C. and Chang, C. C. C. and Miszalski, Z. and Karpinska, B. and Parker, J. E. and Mullineaux, P. M. and Karpinski, S.},
	month = sep,
	year = {2004},
	note = {Place: Rockville
Publisher: Amer Soc Plant Biologists
WOS:000223962100034},
	keywords = {arabidopsis-thaliana, catalase activity, cell-death, defense responses, hydrogen-peroxide, induced stomatal closure, oxidative burst, phaseolus-vulgaris   l., salicylic-acid, transgenic tobacco plants},
	pages = {2818--2830},
}

The lsd1 mutant of Arabidopsis fails to limit the boundaries of hypersensitive cell death response during avirulent pathogen infection and initiates unchecked lesions in long day photoperiod. giving rise to the runaway cell death (rcd) phenotype. We link here the initiation and propagation of rcd to the activity of photosystem II, stomatal conductance and ultimately to photorespiratory H2O2. A cross of lsd1 with the chlorophyll a/b binding harvesting-organelle specific (designated cao) mutant, which has a reduced photosystem II antenna, led to reduced lesion formation in the lsd1/cao double mutant. This lsd1 mutant also had reduced stomatal conductance and catalase activity in short-day permissive conditions and induced H2O2 accumulation followed by rcd when stomatal gas exchange was further impeded. All of these traits depended on the defense regulators EDS1 and PAD4. Furthermore, nonphotorespiratory conditions retarded propagation of lesions in lsd1. These data suggest that lsd1 failed to acclimate to light conditions that promote excess excitation energy (EEE) and that LSD1 function was required for optimal catalase activity. Through this regulation LSD1 can influence the effectiveness of photorespiration in dissipating EEE and consequently may be a key determinant of acclimatory processes. Salicylic acid, which induces stomatal closure, inhibits catalase activity and triggers the rcd phenotype in lsd1, also impaired acclimation of wild-type plants to conditions that promote EEE. We propose that the roles of LSD1 in light acclimation and in restricting pathogen-induced cell death are functionally linked.

@article{sterky_populus_2004,
	title = {A {Populus} {EST} resource for plant functional genomics},
	volume = {101},
	copyright = {Copyright © 2004, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/101/38/13951},
	doi = {10/brt6bx},
	abstract = {Trees present a life form of paramount importance for terrestrial ecosystems and human societies because of their ecological structure and physiological function and provision of energy and industrial materials. The genus Populus is the internationally accepted model for molecular tree biology. We have analyzed 102,019 Populus ESTs that clustered into 11,885 clusters and 12,759 singletons. We also provide {\textgreater}4,000 assembled full clone sequences to serve as a basis for the upcoming annotation of the Populus genome sequence. A public web-based EST database (populusdb) provides digital expression profiles for 18 tissues that comprise the majority of differentiated organs. The coding content of Populus and Arabidopsis genomes shows very high similarity, indicating that differences between these annual and perennial angiosperm life forms result primarily from differences in gene regulation. The high similarity between Populus and Arabidopsis will allow studies of Populus to directly benefit from the detailed functional genomic information generated for Arabidopsis, enabling detailed insights into tree development and adaptation. These data will also valuable for functional genomic efforts in Arabidopsis.},
	language = {en},
	number = {38},
	urldate = {2021-06-15},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Sterky, Fredrik and Bhalerao, Rupali R. and Unneberg, Per and Segerman, Bo and Nilsson, Peter and Brunner, Amy M. and Charbonnel-Campaa, Laurence and Lindvall, Jenny Jonsson and Tandre, Karolina and Strauss, Steven H. and Sundberg, Björn and Gustafsson, Petter and Uhlén, Mathias and Bhalerao, Rishikesh P. and Nilsson, Ove and Sandberg, Göran and Karlsson, Jan and Lundeberg, Joakim and Jansson, Stefan},
	month = sep,
	year = {2004},
	pmid = {15353603},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	pages = {13951--13956},
}

Trees present a life form of paramount importance for terrestrial ecosystems and human societies because of their ecological structure and physiological function and provision of energy and industrial materials. The genus Populus is the internationally accepted model for molecular tree biology. We have analyzed 102,019 Populus ESTs that clustered into 11,885 clusters and 12,759 singletons. We also provide \textgreater4,000 assembled full clone sequences to serve as a basis for the upcoming annotation of the Populus genome sequence. A public web-based EST database (populusdb) provides digital expression profiles for 18 tissues that comprise the majority of differentiated organs. The coding content of Populus and Arabidopsis genomes shows very high similarity, indicating that differences between these annual and perennial angiosperm life forms result primarily from differences in gene regulation. The high similarity between Populus and Arabidopsis will allow studies of Populus to directly benefit from the detailed functional genomic information generated for Arabidopsis, enabling detailed insights into tree development and adaptation. These data will also valuable for functional genomic efforts in Arabidopsis.

@article{nordstrom_auxin_2004,
	title = {Auxin regulation of cytokinin biosynthesis in {Arabidopsis} thaliana: {A} factor of potential importance for auxin–cytokinin-regulated development},
	volume = {101},
	copyright = {Copyright © 2004, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	shorttitle = {Auxin regulation of cytokinin biosynthesis in {Arabidopsis} thaliana},
	url = {https://www.pnas.org/content/101/21/8039},
	doi = {10/c2tzk7},
	abstract = {One of the most long-lived models in plant science is the belief that the long-distance transport and ratio of two plant hormones, auxin and cytokinin, at the site of action control major developmental events such as apical dominance. We have used in vivo deuterium labeling and mass spectrometry to investigate the dynamics of homeostatic cross talk between the two plant hormones. Interestingly, auxin mediates a very rapid negative control of the cytokinin pool by mainly suppressing the biosynthesis via the isopentenyladenosine-5′-monophosphate-independent pathway. In contrast, the effect of cytokinin overproduction on the entire auxin pool in the plant was slower, indicating that this most likely is mediated through altered development. In addition, we were able to confirm that the lateral root meristems are likely to be the main sites of isopentenyladenosine-5′-monophosphate-dependent cytokinin synthesis, and that the aerial tissue of the plant surprisingly also was a significant source of cytokinin biosynthesis. Our demonstration of shoot-localized synthesis, together with data demonstrating that auxin imposes a very rapid regulation of cytokinin biosynthesis, illustrates that the two hormones can interact also on the metabolic level in controlling plant development, and that the aerial part of the plant has the capacity to synthesize its own cytokinin independent of long-range transport from the root system.},
	language = {en},
	number = {21},
	urldate = {2021-06-15},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Nordström, Anders and Tarkowski, Petr and Tarkowska, Danuse and Norbaek, Rikke and Åstot, Crister and Dolezal, Karel and Sandberg, Göran},
	month = may,
	year = {2004},
	pmid = {15146070},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	pages = {8039--8044},
}

One of the most long-lived models in plant science is the belief that the long-distance transport and ratio of two plant hormones, auxin and cytokinin, at the site of action control major developmental events such as apical dominance. We have used in vivo deuterium labeling and mass spectrometry to investigate the dynamics of homeostatic cross talk between the two plant hormones. Interestingly, auxin mediates a very rapid negative control of the cytokinin pool by mainly suppressing the biosynthesis via the isopentenyladenosine-5′-monophosphate-independent pathway. In contrast, the effect of cytokinin overproduction on the entire auxin pool in the plant was slower, indicating that this most likely is mediated through altered development. In addition, we were able to confirm that the lateral root meristems are likely to be the main sites of isopentenyladenosine-5′-monophosphate-dependent cytokinin synthesis, and that the aerial tissue of the plant surprisingly also was a significant source of cytokinin biosynthesis. Our demonstration of shoot-localized synthesis, together with data demonstrating that auxin imposes a very rapid regulation of cytokinin biosynthesis, illustrates that the two hormones can interact also on the metabolic level in controlling plant development, and that the aerial part of the plant has the capacity to synthesize its own cytokinin independent of long-range transport from the root system.

@article{higuchi_planta_2004,
	title = {In planta functions of the {Arabidopsis} cytokinin receptor family},
	volume = {101},
	copyright = {Copyright © 2004, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/101/23/8821},
	doi = {10/fs2hnt},
	abstract = {Since their discovery as cell-division factors in plant tissue culture about five decades ago, cytokinins have been hypothesized to play a central role in the regulation of cell division and differentiation in plants. To test this hypothesis in planta, we isolated Arabidopsis plants lacking one, two, or three of the genes encoding a subfamily of histidine kinases (CRE1, AHK2, and AHK3) that function as cytokinin receptors. Seeds were obtained for homozygous plants containing mutations in all seven genotypes, namely single, double, and triple mutants, and the responses of germinated seedlings in various cytokinin assays were compared. Both redundant and specific functions for the three different cytokinin receptors were observed. Plants carrying mutations in all three genes did not show cytokinin responses, including inhibition of root elongation, inhibition of root formation, cell proliferation in and greening of calli, and induction of cytokinin primary-response genes. The triple mutants were small and infertile, with a reduction in meristem size and activity, yet they possessed basic organs: roots, stems, and leaves. These results confirm that cytokinins are a pivotal class of plant growth regulators but provide no evidence that cytokinins are required for the processes of gametogenesis and embryogenesis.},
	language = {en},
	number = {23},
	urldate = {2021-06-15},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Higuchi, Masayuki and Pischke, Melissa S. and Mähönen, Ari Pekka and Miyawaki, Kaori and Hashimoto, Yukari and Seki, Motoaki and Kobayashi, Masatomo and Shinozaki, Kazuo and Kato, Tomohiko and Tabata, Satoshi and Helariutta, Ykä and Sussman, Michael R. and Kakimoto, Tatsuo},
	month = jun,
	year = {2004},
	pmid = {15166290},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	pages = {8821--8826},
}

Since their discovery as cell-division factors in plant tissue culture about five decades ago, cytokinins have been hypothesized to play a central role in the regulation of cell division and differentiation in plants. To test this hypothesis in planta, we isolated Arabidopsis plants lacking one, two, or three of the genes encoding a subfamily of histidine kinases (CRE1, AHK2, and AHK3) that function as cytokinin receptors. Seeds were obtained for homozygous plants containing mutations in all seven genotypes, namely single, double, and triple mutants, and the responses of germinated seedlings in various cytokinin assays were compared. Both redundant and specific functions for the three different cytokinin receptors were observed. Plants carrying mutations in all three genes did not show cytokinin responses, including inhibition of root elongation, inhibition of root formation, cell proliferation in and greening of calli, and induction of cytokinin primary-response genes. The triple mutants were small and infertile, with a reduction in meristem size and activity, yet they possessed basic organs: roots, stems, and leaves. These results confirm that cytokinins are a pivotal class of plant growth regulators but provide no evidence that cytokinins are required for the processes of gametogenesis and embryogenesis.

@article{gelhaye_specific_2004,
	title = {A specific form of thioredoxin h occurs in plant mitochondria and regulates the alternative oxidase},
	volume = {101},
	copyright = {Copyright © 2004, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/101/40/14545},
	doi = {10/bhgv8p},
	abstract = {The plant mitochondrial thioredoxin (Trx) system has been described as containing an NADPH-dependent Trx reductase and Trx o. In addition to the mitochondrial isoform, Trx o, plants are known to contain several chloroplastic Trx isoforms and the cytosolic Trx h isoforms. We report here the presence in plant mitochondria of a Trx isoform (PtTrxh2) belonging to the Trx h group. Western blot analyses with mitochondrial proteins isolated from both poplar and GFP fusion constructs indicate that PtTrxh2 is targeted to plant mitochondria. The recombinant protein, PtTrxh2, has been shown to be reduced efficiently by the mitochondrial Trx reductase AtNTRA. PtTrxh2 is also able to reduce alternative oxidase homodimers and to allow its activation by pyruvate. In contrast, neither PtTrxh2 nor AtTrxo1 exhibits activity with several poplar glutathione peroxidases and especially a putative mitochondrial isoform. Incubation of PtTrxh2 with glutathione disulfide led to the formation of glutathionylated Trx, identified by mass spectrometry. The formation of a glutathione adduct increases the redox potential of PtTrxh2 from -290 to -225 mV. In addition to Trx o, this study shows that Trx h could also be present in mitochondria. This previously unrecognized complexity is not unexpected, considering the multiple redox-regulated processes found in plant mitochondria.},
	language = {en},
	number = {40},
	urldate = {2021-06-15},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Gelhaye, Eric and Rouhier, Nicolas and Gérard, Joelle and Jolivet, Yves and Gualberto, José and Navrot, Nicolas and Ohlsson, Per-Ingvard and Wingsle, Gunnar and Hirasawa, Masakazu and Knaff, David B. and Wang, Hongmei and Dizengremel, Pierre and Meyer, Yves and Jacquot, Jean-Pierre},
	month = oct,
	year = {2004},
	pmid = {15385674},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	keywords = {glutathione peroxidase, glutathionylation, poplar, redox potential},
	pages = {14545--14550},
}

The plant mitochondrial thioredoxin (Trx) system has been described as containing an NADPH-dependent Trx reductase and Trx o. In addition to the mitochondrial isoform, Trx o, plants are known to contain several chloroplastic Trx isoforms and the cytosolic Trx h isoforms. We report here the presence in plant mitochondria of a Trx isoform (PtTrxh2) belonging to the Trx h group. Western blot analyses with mitochondrial proteins isolated from both poplar and GFP fusion constructs indicate that PtTrxh2 is targeted to plant mitochondria. The recombinant protein, PtTrxh2, has been shown to be reduced efficiently by the mitochondrial Trx reductase AtNTRA. PtTrxh2 is also able to reduce alternative oxidase homodimers and to allow its activation by pyruvate. In contrast, neither PtTrxh2 nor AtTrxo1 exhibits activity with several poplar glutathione peroxidases and especially a putative mitochondrial isoform. Incubation of PtTrxh2 with glutathione disulfide led to the formation of glutathionylated Trx, identified by mass spectrometry. The formation of a glutathione adduct increases the redox potential of PtTrxh2 from -290 to -225 mV. In addition to Trx o, this study shows that Trx h could also be present in mitochondria. This previously unrecognized complexity is not unexpected, considering the multiple redox-regulated processes found in plant mitochondria.

@article{dahlman_organic_2004,
	title = {Organic and inorganic nitrogen uptake in lichens},
	volume = {219},
	issn = {1432-2048},
	url = {https://doi.org/10.1007/s00425-004-1247-0},
	doi = {10/d579ss},
	abstract = {In order to learn more about nitrogen (N) acquisition in lichens, and to see whether different lichens differ in their affinity to various N sources, N uptake was measured in 14 various lichen associations (“species”). These species represented various morphologies (fruticose or foliose), contrasting microhabitat preferences (epiphytic or terricolous), and had green algal, cyanobacterial or both forms of photobionts. N was supplied under non-limiting conditions as an amino acid mixture, ammonium, or nitrate, using 15N to quantify uptake. Carbonyl cyanide m-chlorophenylhydrazone (CCCP) was used to separate active and passive uptake. Thallus N, amino acids, soluble polyol concentrations, and the biont-specific markers chlorophyll a and ergosterol were quantified, aiming to test if these metabolites or markers were correlated with N uptake capacity. Ammonium uptake was significantly greater and to a higher extent passive, relative to the other two N sources. Nitrate uptake differed among lichen photobiont groups, cyanobacterial lichens having a lower uptake rate. All lichens had the capacity to assimilate amino acids, in many species at rates equal to nitrate uptake or even higher, suggesting that organic N compounds could potentially have an important role in the N nutrition of these organisms. There were no clear correlations between N uptake rates and any of the measured metabolites or markers. The relative uptake rates of ammonium, nitrate and amino acids were not related to morphology or microhabitat.},
	language = {en},
	number = {3},
	urldate = {2021-06-15},
	journal = {Planta},
	author = {Dahlman, Lena and Persson, Jörgen and Palmqvist, Kristin and Näsholm, Torgny},
	month = jul,
	year = {2004},
	pages = {459--467},
}

In order to learn more about nitrogen (N) acquisition in lichens, and to see whether different lichens differ in their affinity to various N sources, N uptake was measured in 14 various lichen associations (“species”). These species represented various morphologies (fruticose or foliose), contrasting microhabitat preferences (epiphytic or terricolous), and had green algal, cyanobacterial or both forms of photobionts. N was supplied under non-limiting conditions as an amino acid mixture, ammonium, or nitrate, using 15N to quantify uptake. Carbonyl cyanide m-chlorophenylhydrazone (CCCP) was used to separate active and passive uptake. Thallus N, amino acids, soluble polyol concentrations, and the biont-specific markers chlorophyll a and ergosterol were quantified, aiming to test if these metabolites or markers were correlated with N uptake capacity. Ammonium uptake was significantly greater and to a higher extent passive, relative to the other two N sources. Nitrate uptake differed among lichen photobiont groups, cyanobacterial lichens having a lower uptake rate. All lichens had the capacity to assimilate amino acids, in many species at rates equal to nitrate uptake or even higher, suggesting that organic N compounds could potentially have an important role in the N nutrition of these organisms. There were no clear correlations between N uptake rates and any of the measured metabolites or markers. The relative uptake rates of ammonium, nitrate and amino acids were not related to morphology or microhabitat.

@article{olsson_expression_2004,
	title = {Expression of bovine calmodulin in tobacco plants confers faster germination on saline media},
	volume = {166},
	issn = {0168-9452},
	doi = {10/cwh744},
	abstract = {Calmodulin is a Ca2+-dependent regulatory protein in eukaryotic cells involved in a variety of intracellular activities. Many responses to abiotic stresses involve signaling by Ca2+ and Ca2+/calmodulin regulation, including water and salinity stress. To investigate how calmodulin affects germination on media with high concentrations of NaCl, transgenic tobacco plants expressing heterologous calmodulin were generated and characterized. Transgenic tobacco seeds showed significantly shortened germination times on media containing varying salt (120-160 mM) and calcium (3 and 13 mM) concentrations, compared to control seeds. Using media containing 140 mM NaCl and 13 mM CaCl2, the average germination time was shortened by 2-3 days compared to control (P {\textless} 0.05). In addition, the germinating transgenic seeds contained higher transient levels of gamma-aminobutyric acid compared to control seeds (P {\textless} 0.05). The tobacco Ca2+/calmodulin-regulated glutamate decarboxylase, synthesizing gamma-aminobutyric acid may therefore be stimulated by the heterologous calmodulin. (C) 2004 Elsevier Ireland Ltd. All rights reserved.},
	language = {English},
	number = {6},
	journal = {Plant Science},
	author = {Olsson, P. and Yilmaz, J. L. and Sommarin, M. and Persson, S. and Bulow, L.},
	month = jun,
	year = {2004},
	note = {Place: Clare
Publisher: Elsevier Ireland Ltd
WOS:000221136600023},
	keywords = {NaCl, Nicotiana tabacum, calcium, differential expression, gamma-amino butyric acid, genes, glutamate decarboxylase, growth, messenger-rna, metabolism, nacl stress, protein-levels, responses, salt, stress tolerance},
	pages = {1595--1604},
}

Calmodulin is a Ca2+-dependent regulatory protein in eukaryotic cells involved in a variety of intracellular activities. Many responses to abiotic stresses involve signaling by Ca2+ and Ca2+/calmodulin regulation, including water and salinity stress. To investigate how calmodulin affects germination on media with high concentrations of NaCl, transgenic tobacco plants expressing heterologous calmodulin were generated and characterized. Transgenic tobacco seeds showed significantly shortened germination times on media containing varying salt (120-160 mM) and calcium (3 and 13 mM) concentrations, compared to control seeds. Using media containing 140 mM NaCl and 13 mM CaCl2, the average germination time was shortened by 2-3 days compared to control (P \textless 0.05). In addition, the germinating transgenic seeds contained higher transient levels of gamma-aminobutyric acid compared to control seeds (P \textless 0.05). The tobacco Ca2+/calmodulin-regulated glutamate decarboxylase, synthesizing gamma-aminobutyric acid may therefore be stimulated by the heterologous calmodulin. (C) 2004 Elsevier Ireland Ltd. All rights reserved.

@article{rampey_family_2004,
	title = {A {Family} of {Auxin}-{Conjugate} {Hydrolases} {That} {Contributes} to {Free} {Indole}-3-{Acetic} {Acid} {Levels} during {Arabidopsis} {Germination}},
	volume = {135},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.104.039677},
	doi = {10/cxw94f},
	abstract = {Auxins are hormones important for numerous processes throughout plant growth and development. Plants use several mechanisms to regulate levels of the auxin indole-3-acetic acid (IAA), including the formation and hydrolysis of amide-linked conjugates that act as storage or inactivation forms of the hormone. Certain members of an Arabidopsis amidohydrolase family hydrolyze these conjugates to free IAA in vitro. We examined amidohydrolase gene expression using northern and promoter-β-glucuronidase analyses and found overlapping but distinct patterns of expression. To examine the in vivo importance of auxin-conjugate hydrolysis, we generated a triple hydrolase mutant, ilr1 iar3 ill2, which is deficient in three of these hydrolases. We compared root and hypocotyl growth of the single, double, and triple hydrolase mutants on IAA-Ala, IAA-Leu, and IAA-Phe. The hydrolase mutant phenotypic profiles on different conjugates reveal the in vivo activities and relative importance of ILR1, IAR3, and ILL2 in IAA-conjugate hydrolysis. In addition to defective responses to exogenous conjugates, ilr1 iar3 ill2 roots are slightly less responsive to exogenous IAA. The triple mutant also has a shorter hypocotyl and fewer lateral roots than wild type on unsupplemented medium. As suggested by the mutant phenotypes, ilr1 iar3 ill2 imbibed seeds and seedlings have lower IAA levels than wild type and accumulate IAA-Ala and IAA-Leu, conjugates that are substrates of the absent hydrolases. These results indicate that amidohydrolases contribute free IAA to the auxin pool during germination in Arabidopsis.},
	number = {2},
	urldate = {2021-06-15},
	journal = {Plant Physiology},
	author = {Rampey, Rebekah A. and LeClere, Sherry and Kowalczyk, Mariusz and Ljung, Karin and Sandberg, Göran and Bartel, Bonnie},
	month = jun,
	year = {2004},
	pages = {978--988},
}

Auxins are hormones important for numerous processes throughout plant growth and development. Plants use several mechanisms to regulate levels of the auxin indole-3-acetic acid (IAA), including the formation and hydrolysis of amide-linked conjugates that act as storage or inactivation forms of the hormone. Certain members of an Arabidopsis amidohydrolase family hydrolyze these conjugates to free IAA in vitro. We examined amidohydrolase gene expression using northern and promoter-β-glucuronidase analyses and found overlapping but distinct patterns of expression. To examine the in vivo importance of auxin-conjugate hydrolysis, we generated a triple hydrolase mutant, ilr1 iar3 ill2, which is deficient in three of these hydrolases. We compared root and hypocotyl growth of the single, double, and triple hydrolase mutants on IAA-Ala, IAA-Leu, and IAA-Phe. The hydrolase mutant phenotypic profiles on different conjugates reveal the in vivo activities and relative importance of ILR1, IAR3, and ILL2 in IAA-conjugate hydrolysis. In addition to defective responses to exogenous conjugates, ilr1 iar3 ill2 roots are slightly less responsive to exogenous IAA. The triple mutant also has a shorter hypocotyl and fewer lateral roots than wild type on unsupplemented medium. As suggested by the mutant phenotypes, ilr1 iar3 ill2 imbibed seeds and seedlings have lower IAA levels than wild type and accumulate IAA-Ala and IAA-Leu, conjugates that are substrates of the absent hydrolases. These results indicate that amidohydrolases contribute free IAA to the auxin pool during germination in Arabidopsis.

@article{nieminen_weed_2004,
	title = {A {Weed} for {Wood}? {Arabidopsis} as a {Genetic} {Model} for {Xylem} {Development}},
	volume = {135},
	issn = {0032-0889},
	shorttitle = {A {Weed} for {Wood}?},
	url = {https://doi.org/10.1104/pp.104.040212},
	doi = {10/bbhrgx},
	abstract = {Wood, or secondary xylem, is a water-conductive and supportive vascular tissue highly characteristic of trees. In addition to parenchymatous cells adapted for storage and transport functions, wood is mainly composed of various vertically elongated cell types. These are classified either as tracheary elements or fibers, both of which are characterized with extensive secondary cell wall thickenings. The cell wall characteristics contribute to the properties of wood as a significant raw material for various human applications.Wood formation occurs during the secondary phase of plant development (Fig. 1  Figure 1.Organization of the primary and secondary vascular tissues in Arabidopsis schematically. Whole plant, longitudinal view (A). Shoot apex, cross section (B). Leaf, cross section (C). Root tip, cross section. D, Organization of vascular tissues in the basal region of the inflorescence stem during the secondary phase of vascular development (E). Inside the secondary xylem, the position of layers associated with cell expansion, cell wall deposition and cell death has been indicated.). This results from the activity of the vascular cambium, a lateral meristem that is established and functional during the secondary phase. On the other hand, already the primary phase of vascular development, associated with the procambial development of apical meristems, involves xylem production. The formation of both primary and secondary xylem involves a cascade of interesting processes including specification of primary vascular tissue as bundles, cell proliferation within the primary bundles or in the secondary vascular cambium, initiation of xylem differentiation, regulation of cell expansion, deposition of a secondary cell wall, and programmed cell death (Fig. 1). Even as these processes have been extensively documented at the structural level, relatively little is known of the genetic mechanisms behind them.},
	number = {2},
	urldate = {2021-06-15},
	journal = {Plant Physiology},
	author = {Nieminen, Kaisa M. and Kauppinen, Leila and Helariutta, Ykä},
	month = jun,
	year = {2004},
	pages = {653--659},
}

Wood, or secondary xylem, is a water-conductive and supportive vascular tissue highly characteristic of trees. In addition to parenchymatous cells adapted for storage and transport functions, wood is mainly composed of various vertically elongated cell types. These are classified either as tracheary elements or fibers, both of which are characterized with extensive secondary cell wall thickenings. The cell wall characteristics contribute to the properties of wood as a significant raw material for various human applications.Wood formation occurs during the secondary phase of plant development (Fig. 1  Figure 1.Organization of the primary and secondary vascular tissues in Arabidopsis schematically. Whole plant, longitudinal view (A). Shoot apex, cross section (B). Leaf, cross section (C). Root tip, cross section. D, Organization of vascular tissues in the basal region of the inflorescence stem during the secondary phase of vascular development (E). Inside the secondary xylem, the position of layers associated with cell expansion, cell wall deposition and cell death has been indicated.). This results from the activity of the vascular cambium, a lateral meristem that is established and functional during the secondary phase. On the other hand, already the primary phase of vascular development, associated with the procambial development of apical meristems, involves xylem production. The formation of both primary and secondary xylem involves a cascade of interesting processes including specification of primary vascular tissue as bundles, cell proliferation within the primary bundles or in the secondary vascular cambium, initiation of xylem differentiation, regulation of cell expansion, deposition of a secondary cell wall, and programmed cell death (Fig. 1). Even as these processes have been extensively documented at the structural level, relatively little is known of the genetic mechanisms behind them.

@article{gray-mitsumune_expansins_2004,
	title = {Expansins {Abundant} in {Secondary} {Xylem} {Belong} to {Subgroup} {A} of the α-{Expansin} {Gene} {Family}},
	volume = {135},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.104.039321},
	doi = {10/dd876s},
	abstract = {Differentiation of xylem cells in dicotyledonous plants involves expansion of the radial primary cell walls and intrusive tip growth of cambial derivative cells prior to the deposition of a thick secondary wall essential for xylem function. Expansins are cell wall-residing proteins that have an ability to plasticize the cellulose-hemicellulose network of primary walls. We found expansin activity in proteins extracted from the cambial region of mature stems in a model tree species hybrid aspen (Populus tremula × Populus tremuloides Michx). We identified three α-expansin genes (PttEXP1, PttEXP2, and PttEXP8) and one β-expansin gene (PttEXPB1) in a cambial region expressed sequence tag library, among which PttEXP1 was most abundantly represented. Northern-blot analyses in aspen vegetative organs and tissues showed that PttEXP1 was specifically expressed in mature stems exhibiting secondary growth, where it was present in the cambium and in the radial expansion zone. By contrast, PttEXP2 was mostly expressed in developing leaves. In situ reverse transcription-PCR provided evidence for accumulation of mRNA of PttEXP1 along with ribosomal rRNA at the tips of intrusively growing xylem fibers, suggesting that PttEXP1 protein has a role in intrusive tip growth. An examination of tension wood and leaf cDNA libraries identified another expansin, PttEXP5, very similar to PttEXP1, as the major expansin in developing tension wood, while PttEXP3 was the major expansin expressed in developing leaves. Comparative analysis of expansins expressed in woody stems in aspen, Arabidopsis, and pine showed that the most abundantly expressed expansins share sequence similarities, belonging to the subfamily A of α-expansins and having two conserved motifs at the beginning and end of the mature protein, RIPVG and KNFRV, respectively. This conservation suggests that these genes may share a specialized, not yet identified function.},
	number = {3},
	urldate = {2021-06-15},
	journal = {Plant Physiology},
	author = {Gray-Mitsumune, Madoka and Mellerowicz, Ewa J. and Abe, Hisashi and Schrader, Jarmo and Winzéll, Anders and Sterky, Fredrik and Blomqvist, Kristina and McQueen-Mason, Simon and Teeri, Tuula T. and Sundberg, Björn},
	month = jul,
	year = {2004},
	pages = {1552--1564},
}

Differentiation of xylem cells in dicotyledonous plants involves expansion of the radial primary cell walls and intrusive tip growth of cambial derivative cells prior to the deposition of a thick secondary wall essential for xylem function. Expansins are cell wall-residing proteins that have an ability to plasticize the cellulose-hemicellulose network of primary walls. We found expansin activity in proteins extracted from the cambial region of mature stems in a model tree species hybrid aspen (Populus tremula × Populus tremuloides Michx). We identified three α-expansin genes (PttEXP1, PttEXP2, and PttEXP8) and one β-expansin gene (PttEXPB1) in a cambial region expressed sequence tag library, among which PttEXP1 was most abundantly represented. Northern-blot analyses in aspen vegetative organs and tissues showed that PttEXP1 was specifically expressed in mature stems exhibiting secondary growth, where it was present in the cambium and in the radial expansion zone. By contrast, PttEXP2 was mostly expressed in developing leaves. In situ reverse transcription-PCR provided evidence for accumulation of mRNA of PttEXP1 along with ribosomal rRNA at the tips of intrusively growing xylem fibers, suggesting that PttEXP1 protein has a role in intrusive tip growth. An examination of tension wood and leaf cDNA libraries identified another expansin, PttEXP5, very similar to PttEXP1, as the major expansin in developing tension wood, while PttEXP3 was the major expansin expressed in developing leaves. Comparative analysis of expansins expressed in woody stems in aspen, Arabidopsis, and pine showed that the most abundantly expressed expansins share sequence similarities, belonging to the subfamily A of α-expansins and having two conserved motifs at the beginning and end of the mature protein, RIPVG and KNFRV, respectively. This conservation suggests that these genes may share a specialized, not yet identified function.

@article{kleczkowski_udp-glucose_2004,
	title = {{UDP}-{Glucose} {Pyrophosphorylase}. {An} {Old} {Protein} with {New} {Tricks}},
	volume = {134},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.103.036053},
	doi = {10/dwmw23},
	number = {3},
	urldate = {2021-06-15},
	journal = {Plant Physiology},
	author = {Kleczkowski, Leszek A. and Geisler, Matt and Ciereszko, Iwona and Johansson, Henrik},
	month = mar,
	year = {2004},
	pages = {912--918},
}

@article{israelsson_cloning_2004,
	title = {Cloning and {Overproduction} of {Gibberellin} 3-{Oxidase} in {Hybrid} {Aspen} {Trees}. {Effects} on {Gibberellin} {Homeostasis} and {Development}},
	volume = {135},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.104.038935},
	doi = {10/bpzz6v},
	abstract = {To broaden our understanding of gibberellin (GA) biosynthesis and the mechanism whereby GA homeostasis is maintained in plants, we have investigated the degree to which the enzyme GA 3-oxidase (GA3ox) limits the formation of bioactive GAs in elongating shoots of hybrid aspen (Populus tremula × Populus tremuloides). We describe the cloning of a hybrid aspen GA3ox and its functional characterization, which confirmed that it has 3β-hydroxylation activity and more efficiently converts GA9 to GA4 than GA20 to GA1. To complement previous studies, in which transgenic GA 20-oxidase (GA20ox) overexpressers were found to produce 20-fold higher bioactive GA levels and subsequently grew faster than wild-type plants, we overexpressed an Arabidopsis GA3ox in hybrid aspen. The generated GA3ox overexpresser lines had increased 3β-hydroxylation activity but exhibited no major changes in morphology. The nearly unaltered growth pattern was associated with relatively small changes in GA1 and GA4 levels, although tissue-dependent differences were observed. The absence of increases in bioactive GA levels did not appear to be due to feedback or feed-forward regulation of dioxygenase transcripts, according to semiquantitative reverse transcription polymerase chain reaction analysis of PttGA20ox1, PttGA3ox1, and two putative PttGA2ox genes. We conclude that 20-oxidation is the limiting step, rather than 3β-hydroxylation, in the formation of GA1 and GA4 in elongating shoots of hybrid aspen, and that ectopic GA3ox expression alone cannot increase the flux toward bioactive GAs. Finally, several lines of evidence now suggest that GA4 has a more pivotal role in the tree hybrid aspen than previously believed.},
	number = {1},
	urldate = {2021-06-15},
	journal = {Plant Physiology},
	author = {Israelsson, Maria and Mellerowicz, Ewa and Chono, Makiko and Gullberg, Jonas and Moritz, Thomas},
	month = may,
	year = {2004},
	pages = {221--230},
}

To broaden our understanding of gibberellin (GA) biosynthesis and the mechanism whereby GA homeostasis is maintained in plants, we have investigated the degree to which the enzyme GA 3-oxidase (GA3ox) limits the formation of bioactive GAs in elongating shoots of hybrid aspen (Populus tremula × Populus tremuloides). We describe the cloning of a hybrid aspen GA3ox and its functional characterization, which confirmed that it has 3β-hydroxylation activity and more efficiently converts GA9 to GA4 than GA20 to GA1. To complement previous studies, in which transgenic GA 20-oxidase (GA20ox) overexpressers were found to produce 20-fold higher bioactive GA levels and subsequently grew faster than wild-type plants, we overexpressed an Arabidopsis GA3ox in hybrid aspen. The generated GA3ox overexpresser lines had increased 3β-hydroxylation activity but exhibited no major changes in morphology. The nearly unaltered growth pattern was associated with relatively small changes in GA1 and GA4 levels, although tissue-dependent differences were observed. The absence of increases in bioactive GA levels did not appear to be due to feedback or feed-forward regulation of dioxygenase transcripts, according to semiquantitative reverse transcription polymerase chain reaction analysis of PttGA20ox1, PttGA3ox1, and two putative PttGA2ox genes. We conclude that 20-oxidation is the limiting step, rather than 3β-hydroxylation, in the formation of GA1 and GA4 in elongating shoots of hybrid aspen, and that ectopic GA3ox expression alone cannot increase the flux toward bioactive GAs. Finally, several lines of evidence now suggest that GA4 has a more pivotal role in the tree hybrid aspen than previously believed.

@article{hellgren_patterns_2004,
	title = {Patterns of {Auxin} {Distribution} during {Gravitational} {Induction} of {Reaction} {Wood} in {Poplar} and {Pine}},
	volume = {135},
	issn = {0032-0889},
	url = {https://academic.oup.com/plphys/article/135/1/212/6111952},
	doi = {10/dbz7hq},
	abstract = {Abstract. Gravistimulation of tree stems affects wood development by unilaterally inducing wood with modified properties, called reaction wood. Commonly, it als},
	language = {en},
	number = {1},
	urldate = {2021-06-15},
	journal = {Plant Physiology},
	author = {Hellgren, Jenny M. and Olofsson, Kjell and Sundberg, Björn},
	month = may,
	year = {2004},
	note = {Publisher: Oxford Academic},
	pages = {212--220},
}

Abstract. Gravistimulation of tree stems affects wood development by unilaterally inducing wood with modified properties, called reaction wood. Commonly, it als

@article{ganeteg_is_2004,
	title = {Is {Each} {Light}-{Harvesting} {Complex} {Protein} {Important} for {Plant} {Fitness}?},
	volume = {134},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.103.033324},
	doi = {10/bmspz3},
	abstract = {Many of the photosynthetic genes are conserved among all higher plants, indicating that there is strong selective pressure to maintain the genes of each protein. However, mutants of these genes often lack visible growth phenotypes, suggesting that they are important only under certain conditions or have overlapping functions. To assess the importance of specific genes encoding the light-harvesting complex (LHC) proteins for the survival of the plant in the natural environment, we have combined two different scientific traditions by using an ecological fitness assay on a set of genetically modified Arabidopsis plants with differing LHC protein contents. The fitness of all of the LHC-deficient plants was reduced in some of the growth environments, supporting the hypothesis that each of the genes has been conserved because they provide ecological flexibility, which is of great adaptive value given the highly variable conditions encountered in nature.},
	number = {1},
	urldate = {2021-06-15},
	journal = {Plant Physiology},
	author = {Ganeteg, Ulrika and Külheim, Carsten and Andersson, Jenny and Jansson, Stefan},
	month = jan,
	year = {2004},
	pages = {502--509},
}

Many of the photosynthetic genes are conserved among all higher plants, indicating that there is strong selective pressure to maintain the genes of each protein. However, mutants of these genes often lack visible growth phenotypes, suggesting that they are important only under certain conditions or have overlapping functions. To assess the importance of specific genes encoding the light-harvesting complex (LHC) proteins for the survival of the plant in the natural environment, we have combined two different scientific traditions by using an ecological fitness assay on a set of genetically modified Arabidopsis plants with differing LHC protein contents. The fitness of all of the LHC-deficient plants was reduced in some of the growth environments, supporting the hypothesis that each of the genes has been conserved because they provide ecological flexibility, which is of great adaptive value given the highly variable conditions encountered in nature.

@article{curaba_atga3ox2_2004,
	title = {{AtGA3ox2}, a {Key} {Gene} {Responsible} for {Bioactive} {Gibberellin} {Biosynthesis}, {Is} {Regulated} during {Embryogenesis} by {LEAFY} {COTYLEDON2} and {FUSCA3} in {Arabidopsis}},
	volume = {136},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.104.047266},
	doi = {10/d4dh37},
	abstract = {Embryonic regulators LEC2 (LEAFY COTYLEDON2) and FUS3 (FUSCA3) are involved in multiple aspects of Arabidopsis (Arabidopsis thaliana) seed development, including repression of leaf traits and premature germination and activation of seed storage protein genes. In this study, we show that gibberellin (GA) hormone biosynthesis is regulated by LEC2 and FUS3 pathways. The level of bioactive GAs is increased in immature seeds of lec2 and fus3 mutants relative to wild-type level. In addition, we show that the formation of ectopic trichome cells on lec2 and fus3 embryos is a GA-dependent process as in true leaves, suggesting that the GA pathway is misactivated in embryonic mutants. We next demonstrate that the GA-biosynthesis gene AtGA3ox2, which encodes the key enzyme AtGA3ox2 that catalyzes the conversion of inactive to bioactive GAs, is ectopically activated in embryos of the two mutants. Interestingly, both β-glucuronidase reporter gene expression and in situ hybridization indicate that FUS3 represses AtGA3ox2 expression mainly in epidermal cells of embryo axis, which is distinct from AtGA3ox2 pattern at germination. Finally, we show that the FUS3 protein physically interacts with two RY elements (CATGCATG) present in the AtGA3ox2 promoter. This work suggests that GA biosynthesis is directly controlled by embryonic regulators during Arabidopsis embryonic development.},
	number = {3},
	urldate = {2021-06-15},
	journal = {Plant Physiology},
	author = {Curaba, Julien and Moritz, Thomas and Blervaque, Renaud and Parcy, François and Raz, Vered and Herzog, Michel and Vachon, Gilles},
	month = nov,
	year = {2004},
	pages = {3660--3669},
}

Embryonic regulators LEC2 (LEAFY COTYLEDON2) and FUS3 (FUSCA3) are involved in multiple aspects of Arabidopsis (Arabidopsis thaliana) seed development, including repression of leaf traits and premature germination and activation of seed storage protein genes. In this study, we show that gibberellin (GA) hormone biosynthesis is regulated by LEC2 and FUS3 pathways. The level of bioactive GAs is increased in immature seeds of lec2 and fus3 mutants relative to wild-type level. In addition, we show that the formation of ectopic trichome cells on lec2 and fus3 embryos is a GA-dependent process as in true leaves, suggesting that the GA pathway is misactivated in embryonic mutants. We next demonstrate that the GA-biosynthesis gene AtGA3ox2, which encodes the key enzyme AtGA3ox2 that catalyzes the conversion of inactive to bioactive GAs, is ectopically activated in embryos of the two mutants. Interestingly, both β-glucuronidase reporter gene expression and in situ hybridization indicate that FUS3 represses AtGA3ox2 expression mainly in epidermal cells of embryo axis, which is distinct from AtGA3ox2 pattern at germination. Finally, we show that the FUS3 protein physically interacts with two RY elements (CATGCATG) present in the AtGA3ox2 promoter. This work suggests that GA biosynthesis is directly controlled by embryonic regulators during Arabidopsis embryonic development.

@article{cox_roles_2004,
	title = {The {Roles} of {Ethylene}, {Auxin}, {Abscisic} {Acid}, and {Gibberellin} in the {Hyponastic} {Growth} of {Submerged} {Rumex} palustris {Petioles}},
	volume = {136},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.104.049197},
	doi = {10/bkt5tx},
	abstract = {Rumex palustris responds to complete submergence with upward movement of the younger petioles. This so-called hyponastic response, in combination with stimulated petiole elongation, brings the leaf blade above the water surface and restores contact with the atmosphere. We made a detailed study of this differential growth process, encompassing the complete range of the known signal transduction pathway: from the cellular localization of differential growth, to the hormonal regulation, and the possible involvement of a cell wall loosening protein (expansin) as a downstream target. We show that hyponastic growth is caused by differential cell elongation across the petiole base, with cells on the abaxial (lower) surface elongating faster than cells on the adaxial (upper) surface. Pharmacological studies and endogenous hormone measurements revealed that ethylene, auxin, abscisic acid (ABA), and gibberellin regulate different and sometimes overlapping stages of hyponastic growth. Initiation of hyponastic growth and (maintenance of) the maximum petiole angle are regulated by ethylene, ABA, and auxin, whereas the speed of the response is influenced by ethylene, ABA, and gibberellin. We found that a submergence-induced differential redistribution of endogenous indole-3-acetic acid in the petiole base could play a role in maintenance of the response, but not in the onset of hyponastic growth. Since submergence does not induce a differential expression of expansins across the petiole base, it is unlikely that this cell wall loosening protein is the downstream target for the hormones that regulate the differential cell elongation leading to submergence-induced hyponastic growth in R. palustris.},
	number = {2},
	urldate = {2021-06-15},
	journal = {Plant Physiology},
	author = {Cox, Marjolein C.H. and Benschop, Joris J. and Vreeburg, Robert A.M. and Wagemaker, Cornelis A.M. and Moritz, Thomas and Peeters, Anton J.M. and Voesenek, Laurentius A.C.J.},
	month = oct,
	year = {2004},
	pages = {2948--2960},
}

Rumex palustris responds to complete submergence with upward movement of the younger petioles. This so-called hyponastic response, in combination with stimulated petiole elongation, brings the leaf blade above the water surface and restores contact with the atmosphere. We made a detailed study of this differential growth process, encompassing the complete range of the known signal transduction pathway: from the cellular localization of differential growth, to the hormonal regulation, and the possible involvement of a cell wall loosening protein (expansin) as a downstream target. We show that hyponastic growth is caused by differential cell elongation across the petiole base, with cells on the abaxial (lower) surface elongating faster than cells on the adaxial (upper) surface. Pharmacological studies and endogenous hormone measurements revealed that ethylene, auxin, abscisic acid (ABA), and gibberellin regulate different and sometimes overlapping stages of hyponastic growth. Initiation of hyponastic growth and (maintenance of) the maximum petiole angle are regulated by ethylene, ABA, and auxin, whereas the speed of the response is influenced by ethylene, ABA, and gibberellin. We found that a submergence-induced differential redistribution of endogenous indole-3-acetic acid in the petiole base could play a role in maintenance of the response, but not in the onset of hyponastic growth. Since submergence does not induce a differential expression of expansins across the petiole base, it is unlikely that this cell wall loosening protein is the downstream target for the hormones that regulate the differential cell elongation leading to submergence-induced hyponastic growth in R. palustris.

@article{geisler_toward_2004,
	title = {Toward a blueprint for {UDP}-glucose pyrophosphorylase structure/function properties: homology-modeling analyses},
	volume = {56},
	issn = {1573-5028},
	shorttitle = {Toward a blueprint for {UDP}-glucose pyrophosphorylase structure/function properties},
	url = {https://doi.org/10.1007/s11103-004-4953-x},
	doi = {10/dtvfpb},
	abstract = {UDP-glucose pyrophosphorylase (UGPase) is an important enzyme of synthesis of sucrose, cellulose, and several other polysaccharides in all plants. The protein is evolutionarily conserved among eukaryotes, but has little relation, aside from its catalytic reaction, to UGPases of prokaryotic origin. Using protein homology modeling strategy, 3D structures for barley, poplar, and Arabidopsis UGPases have been derived, based on recently published crystal structure of human UDP-N-acetylglucosamine pyrophosphorylase. The derived 3D structures correspond to a bowl-shaped protein with the active site at a central groove, and a C-terminal domain that includes a loop (I-loop) possibly involved in dimerization. Data on a plethora of earlier described UGPase mutants from a variety of eukaryotic organisms have been revisited, and we have, in most cases, verified the role of each mutation in enzyme catalysis/regulation/structural integrity. We have also found that one of two alternatively spliced forms of poplar UGPase has a very short I-loop, suggesting differences in oligomerization ability of the two isozymes. The derivation of the structural model for plant UGPase should serve as a useful blueprint for further function/structure studies on this protein.},
	language = {en},
	number = {5},
	urldate = {2021-06-15},
	journal = {Plant Molecular Biology},
	author = {Geisler, Matt and Wilczynska, Malgorzata and Karpinski, Stanislaw and Kleczkowski, Leszek A.},
	month = nov,
	year = {2004},
	pages = {783--794},
}

UDP-glucose pyrophosphorylase (UGPase) is an important enzyme of synthesis of sucrose, cellulose, and several other polysaccharides in all plants. The protein is evolutionarily conserved among eukaryotes, but has little relation, aside from its catalytic reaction, to UGPases of prokaryotic origin. Using protein homology modeling strategy, 3D structures for barley, poplar, and Arabidopsis UGPases have been derived, based on recently published crystal structure of human UDP-N-acetylglucosamine pyrophosphorylase. The derived 3D structures correspond to a bowl-shaped protein with the active site at a central groove, and a C-terminal domain that includes a loop (I-loop) possibly involved in dimerization. Data on a plethora of earlier described UGPase mutants from a variety of eukaryotic organisms have been revisited, and we have, in most cases, verified the role of each mutation in enzyme catalysis/regulation/structural integrity. We have also found that one of two alternatively spliced forms of poplar UGPase has a very short I-loop, suggesting differences in oligomerization ability of the two isozymes. The derivation of the structural model for plant UGPase should serve as a useful blueprint for further function/structure studies on this protein.

@article{ganeteg_lhca5_2004,
	title = {Lhca5 – an {LHC}-{Type} {Protein} {Associated} with {Photosystem} {I}},
	volume = {54},
	issn = {1573-5028},
	url = {https://doi.org/10.1023/B:PLAN.0000040813.05224.94},
	doi = {10/bkhvhq},
	abstract = {The light-harvesting antenna of higher plant photosystem (PS) I is known to be composed of four different types of light-harvesting complex (LHC) proteins (Lhca1–4). However, the genomic sequence of Arabidopsis thaliana contains open reading frames coding for two additional LHC type proteins (Lhca5–6) that are presumably associated with PSI. While Lhca6 might not be expressed at all, ESTs have been detected for the Lhca5 gene in Arabidopsis and a number of other plant species. Here we demonstrate the presence of the Lhca5 gene product in the thylakoid membrane of Arabidopsis as an additional type of Lhca-protein associated with PSI. Lhca5 seems to be regulated differently from the other LHC proteins since Lhca5 mRNA levels increase under high light conditions. Analyses reported here of Lhca5 in plants lacking individual Lhca1–4 proteins show that it is more abundant in plants lacking Lhca1/4, and suggest that it interacts in a direct physical fashion with Lhca2 or Lhca3. We propose that Lhca5 binds chlorophylls in a similar fashion to the other Lhca proteins and is associated with PSI only in sub-stoichiometric amounts.},
	language = {en},
	number = {5},
	urldate = {2021-06-15},
	journal = {Plant Molecular Biology},
	author = {Ganeteg, Ulrika and Klimmek, Frank and Jansson, Stefan},
	month = mar,
	year = {2004},
	pages = {641--651},
}

The light-harvesting antenna of higher plant photosystem (PS) I is known to be composed of four different types of light-harvesting complex (LHC) proteins (Lhca1–4). However, the genomic sequence of Arabidopsis thaliana contains open reading frames coding for two additional LHC type proteins (Lhca5–6) that are presumably associated with PSI. While Lhca6 might not be expressed at all, ESTs have been detected for the Lhca5 gene in Arabidopsis and a number of other plant species. Here we demonstrate the presence of the Lhca5 gene product in the thylakoid membrane of Arabidopsis as an additional type of Lhca-protein associated with PSI. Lhca5 seems to be regulated differently from the other LHC proteins since Lhca5 mRNA levels increase under high light conditions. Analyses reported here of Lhca5 in plants lacking individual Lhca1–4 proteins show that it is more abundant in plants lacking Lhca1/4, and suggest that it interacts in a direct physical fashion with Lhca2 or Lhca3. We propose that Lhca5 binds chlorophylls in a similar fashion to the other Lhca proteins and is associated with PSI only in sub-stoichiometric amounts.

@article{tuominen_mutual_2004,
	title = {Mutual antagonism of ethylene and jasmonic acid regulates ozone-induced spreading cell death in {Arabidopsis}},
	volume = {39},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2004.02107.x},
	doi = {10/ft54t9},
	abstract = {Ethylene (ET) and jasmonic acid (JA) have opposite effects on ozone (O3)-induced spreading cell death; ET stimulates, and is required for the spreading cell death, whereas JA protects tissues. We studied the underlying molecular mechanisms with the O3-sensitive, JA-insensitive jasmonate resistant 1 (jar1), and the O3-tolerant, ET-insensitive ethylene insensitive 2 (ein2) mutants. Blocking ET perception pharmacologically with norbornadiene (NBD) in jar1, or ET signaling genetically in the jar1 ein2 double mutant prevented the spread of cell death. This suggests that EIN2 function is epistatic to JAR1, and that the JAR1-dependent JA pathway halts oxidative cell death by directly inhibiting ET signaling. JAR1-dependent suppression of the ET pathway was apparent also as increased EIN2-dependent gene expression and ET hypersensitivity of jar1. Physiological experiments suggested that the target of JA is upstream of Constitutive Triple Response 1 (CTR1), but downstream of ET biosynthesis. Gene expression analysis of 1-aminocyclopropane-1-carboxylic acid (ACC)-treated and O3-exposed ein2 and jar1 revealed reciprocal antagonism: the EIN2-mediated suppression of the JA pathway. The results imply that the O3-induced spreading cell death is stimulated by early, rapid accumulation of ET, which can suppress the protecting function of JA thereby allowing cell death to proceed. Extended spreading cell death induces late accumulation of JA, which inhibits the propagation of cell death through inhibition of the ET pathway.},
	language = {en},
	number = {1},
	urldate = {2021-06-15},
	journal = {The Plant Journal},
	author = {Tuominen, Hannele and Overmyer, Kirk and Keinänen, Markku and Kollist, Hannes and Kangasjärvi, Jaakko},
	year = {2004},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2004.02107.x},
	keywords = {antagonism, ethylene, hormonal interactions, jasmonic acid, oxidative stress, ozone},
	pages = {59--69},
}

Ethylene (ET) and jasmonic acid (JA) have opposite effects on ozone (O3)-induced spreading cell death; ET stimulates, and is required for the spreading cell death, whereas JA protects tissues. We studied the underlying molecular mechanisms with the O3-sensitive, JA-insensitive jasmonate resistant 1 (jar1), and the O3-tolerant, ET-insensitive ethylene insensitive 2 (ein2) mutants. Blocking ET perception pharmacologically with norbornadiene (NBD) in jar1, or ET signaling genetically in the jar1 ein2 double mutant prevented the spread of cell death. This suggests that EIN2 function is epistatic to JAR1, and that the JAR1-dependent JA pathway halts oxidative cell death by directly inhibiting ET signaling. JAR1-dependent suppression of the ET pathway was apparent also as increased EIN2-dependent gene expression and ET hypersensitivity of jar1. Physiological experiments suggested that the target of JA is upstream of Constitutive Triple Response 1 (CTR1), but downstream of ET biosynthesis. Gene expression analysis of 1-aminocyclopropane-1-carboxylic acid (ACC)-treated and O3-exposed ein2 and jar1 revealed reciprocal antagonism: the EIN2-mediated suppression of the JA pathway. The results imply that the O3-induced spreading cell death is stimulated by early, rapid accumulation of ET, which can suppress the protecting function of JA thereby allowing cell death to proceed. Extended spreading cell death induces late accumulation of JA, which inhibits the propagation of cell death through inhibition of the ET pathway.

@article{schrader_cambial_2004,
	title = {Cambial meristem dormancy in trees involves extensive remodelling of the transcriptome},
	volume = {40},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2004.02199.x},
	doi = {10/bfwz2r},
	abstract = {The establishment of the dormant state in meristems involves considerable physiological and metabolic alterations necessary for surviving unfavourable growth conditions. However, a global molecular analysis of dormancy in meristems has been hampered by the difficulty in isolating meristem cells. We used cryosectioning to isolate purified cambial meristem cells from the woody plant Populus tremula during active growth and dormancy. These samples were used to generate meristem-specific cDNA libraries and for cDNA microarray experiments to define the global transcriptional changes underlying cambial dormancy. The results indicate a significant reduction in the complexity of the cambial transcriptome in the dormant state. Although cell division is terminated in the dormant cambium, the cell cycle machinery appears to be maintained in a skeletal state as suggested by the continued presence of transcripts for several cell cycle regulators. The downregulation of PttPIN1 and PttPIN2 transcripts explains the reduced basipetal polar auxin transport during dormancy. The induction of a member of the SINA family of ubiquitin ligases implicated in auxin signalling indicates a potential mechanism for modulation of auxin sensitivity during cambial dormancy. The metabolic alterations during dormancy are mirrored in the induction of genes involved in starch breakdown and the glyoxysomal cycle. Interestingly, the induction of RGA1 like gene suggests modification of gibberellin signalling in cambial dormancy. The induction of genes such as poplar orthologues of FIE and HAP2 indicates a potential role for these global regulators of transcription in orchestrating extensive changes in gene expression during dormancy.},
	language = {en},
	number = {2},
	urldate = {2021-06-15},
	journal = {The Plant Journal},
	author = {Schrader, Jarmo and Moyle, Richard and Bhalerao, Rupali and Hertzberg, Magnus and Lundeberg, Joakim and Nilsson, Peter and Bhalerao, Rishikesh P.},
	year = {2004},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2004.02199.x},
	keywords = {Populus tremula, cambium, dormancy, meristem, microarray, wood formation},
	pages = {173--187},
}

The establishment of the dormant state in meristems involves considerable physiological and metabolic alterations necessary for surviving unfavourable growth conditions. However, a global molecular analysis of dormancy in meristems has been hampered by the difficulty in isolating meristem cells. We used cryosectioning to isolate purified cambial meristem cells from the woody plant Populus tremula during active growth and dormancy. These samples were used to generate meristem-specific cDNA libraries and for cDNA microarray experiments to define the global transcriptional changes underlying cambial dormancy. The results indicate a significant reduction in the complexity of the cambial transcriptome in the dormant state. Although cell division is terminated in the dormant cambium, the cell cycle machinery appears to be maintained in a skeletal state as suggested by the continued presence of transcripts for several cell cycle regulators. The downregulation of PttPIN1 and PttPIN2 transcripts explains the reduced basipetal polar auxin transport during dormancy. The induction of a member of the SINA family of ubiquitin ligases implicated in auxin signalling indicates a potential mechanism for modulation of auxin sensitivity during cambial dormancy. The metabolic alterations during dormancy are mirrored in the induction of genes involved in starch breakdown and the glyoxysomal cycle. Interestingly, the induction of RGA1 like gene suggests modification of gibberellin signalling in cambial dormancy. The induction of genes such as poplar orthologues of FIE and HAP2 indicates a potential role for these global regulators of transcription in orchestrating extensive changes in gene expression during dormancy.

@article{espinosa-ruiz_differential_2004,
	title = {Differential stage-specific regulation of cyclin-dependent kinases during cambial dormancy in hybrid aspen},
	volume = {38},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2004.02070.x},
	doi = {10/d4fk2f},
	abstract = {The cambium of woody plants cycles between active and dormant states. Dormancy can be subdivided into eco- and endodormant stages. Ecodormant trees resume growth upon exposure to growth-promotive signals, while the establishment of endodormant state results in loss of the ability to respond to these signals. In this paper, we analysed the regulation of cyclin-dependent kinases (CDKs) to understand the differential response of cell division machinery to growth-promotive signals during the distinct stages of dormancy in hybrid aspen. We show that 4 weeks of short-day (SD) treatment causes termination of the cambial cell division and establishment of the ecodormant state. This coincides with a steady decline in the histone H1 kinase activity of the PSTAIRE-type poplar CDKA (PttCDKA) and the PPTTLRE-type PttCDKB kinase complexes. However, neither the transcript nor the polypeptide levels of PttCDKA and PttCDKB are reduced during ecodormancy. In contrast, 6 weeks of SD treatment establishes endodormancy, which is marked by the reduction and disappearance of the PttCDKA and PttCDKB protein levels and the PttCDKB transcript levels. The transition to endodormancy is preceded by an elevated E2F (adenosine E2 promoter binding factor) phosphorylation activity of the PttCDKA kinase that reduces the DNA-binding activity of E2F in vitro. The transition to endodormancy is followed by a reduction of retinoblastoma (Rb) phosphorylation activity of PttCDKA protein complexes. Both phosphorylation events could contribute to block the G1 to S phase transition upon the establishment of endodormancy. Our results indicate that eco- and endodormant stages of cambial dormancy involve a stage-specific regulation of the cell cycle effectors at multiple levels.},
	language = {en},
	number = {4},
	urldate = {2021-06-15},
	journal = {The Plant Journal},
	author = {Espinosa-Ruiz, Ana and Saxena, Sangeeta and Schmidt, Julien and Mellerowicz, Ewa and Miskolczi, Pál and Bakó, László and Bhalerao, Rishikesh P.},
	year = {2004},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2004.02070.x},
	keywords = {CDK regulation, cambial dormancy, cell cycle, ecodormancy, endodormancy, hybrid aspen},
	pages = {603--615},
}

The cambium of woody plants cycles between active and dormant states. Dormancy can be subdivided into eco- and endodormant stages. Ecodormant trees resume growth upon exposure to growth-promotive signals, while the establishment of endodormant state results in loss of the ability to respond to these signals. In this paper, we analysed the regulation of cyclin-dependent kinases (CDKs) to understand the differential response of cell division machinery to growth-promotive signals during the distinct stages of dormancy in hybrid aspen. We show that 4 weeks of short-day (SD) treatment causes termination of the cambial cell division and establishment of the ecodormant state. This coincides with a steady decline in the histone H1 kinase activity of the PSTAIRE-type poplar CDKA (PttCDKA) and the PPTTLRE-type PttCDKB kinase complexes. However, neither the transcript nor the polypeptide levels of PttCDKA and PttCDKB are reduced during ecodormancy. In contrast, 6 weeks of SD treatment establishes endodormancy, which is marked by the reduction and disappearance of the PttCDKA and PttCDKB protein levels and the PttCDKB transcript levels. The transition to endodormancy is preceded by an elevated E2F (adenosine E2 promoter binding factor) phosphorylation activity of the PttCDKA kinase that reduces the DNA-binding activity of E2F in vitro. The transition to endodormancy is followed by a reduction of retinoblastoma (Rb) phosphorylation activity of PttCDKA protein complexes. Both phosphorylation events could contribute to block the G1 to S phase transition upon the establishment of endodormancy. Our results indicate that eco- and endodormant stages of cambial dormancy involve a stage-specific regulation of the cell cycle effectors at multiple levels.

@article{chang_induction_2004,
	title = {Induction of {ASCORBATE} {PEROXIDASE} 2 expression in wounded {Arabidopsis} leaves does not involve known wound-signalling pathways but is associated with changes in photosynthesis},
	volume = {38},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2004.02066.x},
	doi = {10/dkbvj8},
	abstract = {ASCORBATE PEROXIDASE 2 (APX2) encodes a key enzyme of the antioxidant network. In excess light-stressed Arabidopsis leaves, photosynthetic electron transport (PET), hydrogen peroxide (H2O2) and abscisic acid (ABA) regulate APX2 expression. Wounded leaves showed low induction of APX2 expression, and when exposed to excess light, APX2 expression was increased synergistically. Signalling pathways dependent upon jasmonic acid (JA), chitosan and ABA were not involved in the wound-induced expression of APX2, but were shown to require PET and were preceded by a depressed rate of CO2 fixation. This led to an accumulation of H2O2 in veinal tissue. Diphenyl iodonium (DPI), which has been shown previously to be a potent inhibitor of H2O2 accumulation in the veins of wounded leaves, prevented induction of APX2 expression probably by inhibition of PET. Thus, the weak induction of APX2 expression in wounded leaves may require H2O2 and PET only. As in other environmental stresses, wounding of leaves resulted in decreased photosynthesis leading to increased reactive oxygen species (ROS) production. This may signal the induction of many ‘wound-responsive’ genes not regulated by JA-dependent or other known JA-independent pathways.},
	language = {en},
	number = {3},
	urldate = {2021-06-15},
	journal = {The Plant Journal},
	author = {Chang, Christine Chi-Chen and Ball, Louise and Fryer, Michael J. and Baker, Neil R. and Karpinski, Stanislaw and Mullineaux, Philip M.},
	year = {2004},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2004.02066.x},
	keywords = {ASCORBATE PEROXIDASE 2, chitosan, jasmonic acid, photosynthesis, reactive oxygen species, wounding},
	pages = {499--511},
}

ASCORBATE PEROXIDASE 2 (APX2) encodes a key enzyme of the antioxidant network. In excess light-stressed Arabidopsis leaves, photosynthetic electron transport (PET), hydrogen peroxide (H2O2) and abscisic acid (ABA) regulate APX2 expression. Wounded leaves showed low induction of APX2 expression, and when exposed to excess light, APX2 expression was increased synergistically. Signalling pathways dependent upon jasmonic acid (JA), chitosan and ABA were not involved in the wound-induced expression of APX2, but were shown to require PET and were preceded by a depressed rate of CO2 fixation. This led to an accumulation of H2O2 in veinal tissue. Diphenyl iodonium (DPI), which has been shown previously to be a potent inhibitor of H2O2 accumulation in the veins of wounded leaves, prevented induction of APX2 expression probably by inhibition of PET. Thus, the weak induction of APX2 expression in wounded leaves may require H2O2 and PET only. As in other environmental stresses, wounding of leaves resulted in decreased photosynthesis leading to increased reactive oxygen species (ROS) production. This may signal the induction of many ‘wound-responsive’ genes not regulated by JA-dependent or other known JA-independent pathways.

@article{baba_organellar_2004,
	title = {Organellar gene transcription and early seedling development are affected in the {rpoT};2 mutant of {Arabidopsis}},
	volume = {38},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2004.02022.x},
	doi = {10/dtrc6f},
	abstract = {An Arabidopsis mutant that exhibited reduced root length was isolated from a population of activation-tagged T-DNA insertion lines in a screen for aberrant root growth. This mutant also exhibited reduced hypocotyl length as well as a delay in greening and altered leaf shape. Molecular genetic analysis of the mutant indicated a single T-DNA insertion in the gene RpoT;2 encoding a homolog of the phage-type RNA polymerase (RNAP), that is targeted to both mitochondria and plastids. A second T-DNA-tagged allele also showed a similar phenotype. The mutation in RpoT;2 affected the light-induced accumulation of several plastid mRNAs and proteins and resulted in a lower photosynthetic efficiency. In contrast to the alterations in the plastid gene expression, no major effect of the rpoT;2 mutation on the accumulation of examined mitochondrial gene transcripts and proteins was observed. The rpoT;2 mutant exhibited tissue-specific alterations in the transcript levels of two other organelle-directed nuclear-encoded RNAPs, RpoT;1 and RpoT;3. This suggests the existence of cross-talk between the regulatory pathways of the three RNAPs through organelle to nucleus communication. These data provide an important information on a role of RpoT;2 in plastid gene expression and early plant development.},
	language = {en},
	number = {1},
	urldate = {2021-06-15},
	journal = {The Plant Journal},
	author = {Baba, Kyoko and Schmidt, Julien and Espinosa-Ruiz, Ana and Villarejo, Arsenio and Shiina, Takashi and Gardeström, Per and Sane, Aniruddha P. and Bhalerao, Rishikesh P.},
	year = {2004},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2004.02022.x},
	keywords = {NEP, PEP, mitochondria, organelle-nucleus signaling, plastid, transcription},
	pages = {38--48},
}

An Arabidopsis mutant that exhibited reduced root length was isolated from a population of activation-tagged T-DNA insertion lines in a screen for aberrant root growth. This mutant also exhibited reduced hypocotyl length as well as a delay in greening and altered leaf shape. Molecular genetic analysis of the mutant indicated a single T-DNA insertion in the gene RpoT;2 encoding a homolog of the phage-type RNA polymerase (RNAP), that is targeted to both mitochondria and plastids. A second T-DNA-tagged allele also showed a similar phenotype. The mutation in RpoT;2 affected the light-induced accumulation of several plastid mRNAs and proteins and resulted in a lower photosynthetic efficiency. In contrast to the alterations in the plastid gene expression, no major effect of the rpoT;2 mutation on the accumulation of examined mitochondrial gene transcripts and proteins was observed. The rpoT;2 mutant exhibited tissue-specific alterations in the transcript levels of two other organelle-directed nuclear-encoded RNAPs, RpoT;1 and RpoT;3. This suggests the existence of cross-talk between the regulatory pathways of the three RNAPs through organelle to nucleus communication. These data provide an important information on a role of RpoT;2 in plastid gene expression and early plant development.

@article{niewiadomska_salinity-induced_2004,
	title = {A {Salinity}-{Induced} {C3}-{CAM} {Transition} {Increases} {Energy} {Conservation} in the {Halophyte} {Mesembryanthemum} crystallinum {L}.},
	volume = {45},
	issn = {0032-0781},
	url = {https://doi.org/10.1093/pcp/pch079},
	doi = {10/bwvbrh},
	abstract = {A strongly increased ATP/ADP ratio was found during the nocturnal phase I in crassulacean acid metabolism (CAM)-induced Mesembryanthemum crystallinum plants. Conversely, during the daytime phase III in CAM-performing plants the ATP/ADP ratio dropped to a similar level to that of C3 plants, cytochrome c oxidase activity was stimulated and mitochondrial Mn-superoxide dismutase activity was strongly increased. The findings suggest that a salinity-induced C3-CAM transition might be an efficient energy-conserving strategy for M. crystallinum plants, in which the strong nocturnal ATP production seems to be, at least partially, independent from the coupled mitochondrial electron transport.},
	number = {6},
	urldate = {2021-06-15},
	journal = {Plant and Cell Physiology},
	author = {Niewiadomska, Ewa and Karpinska, Barbara and Romanowska, Elzbieta and Slesak, Ireneusz and Karpinski, Stanislaw},
	month = jun,
	year = {2004},
	pages = {789--794},
}

A strongly increased ATP/ADP ratio was found during the nocturnal phase I in crassulacean acid metabolism (CAM)-induced Mesembryanthemum crystallinum plants. Conversely, during the daytime phase III in CAM-performing plants the ATP/ADP ratio dropped to a similar level to that of C3 plants, cytochrome c oxidase activity was stimulated and mitochondrial Mn-superoxide dismutase activity was strongly increased. The findings suggest that a salinity-induced C3-CAM transition might be an efficient energy-conserving strategy for M. crystallinum plants, in which the strong nocturnal ATP production seems to be, at least partially, independent from the coupled mitochondrial electron transport.

@article{alsterfjord_plasma_2004,
	title = {Plasma {Membrane} {H}+-{ATPase} and 14-3-3 {Isoforms} of {Arabidopsis} {Leaves}: {Evidence} for {Isoform} {Specificity} in the 14-3-3/{H}+-{ATPase} {Interaction}},
	volume = {45},
	issn = {0032-0781},
	shorttitle = {Plasma {Membrane} {H}+-{ATPase} and 14-3-3 {Isoforms} of {Arabidopsis} {Leaves}},
	url = {https://doi.org/10.1093/pcp/pch136},
	doi = {10/cbp4j9},
	abstract = {The plasma membrane H+-ATPase is activated by binding of 14-3-3 protein to the phosphorylated C terminus. Considering the large number of 14-3-3 and H+-ATPase isoforms in Arabidopsis (13 and 11 expressed genes, respectively), specificity in binding may exist between 14-3-3 and H+-ATPase isoforms. We now show that the H+-ATPase is the main target for 14-3-3 binding at the plasma membrane, and that all twelve 14-3-3 isoforms tested bind to the H+-ATPase in vitro. Using specific antibodies for nine of the 14-3-3 isoforms, we show that GF14epsilon, mu, lambda, omega, chi, phi, nu, and upsilon are present in leaves, but that isolated plasma membranes lack GF14chi, phi and upsilon. Northern blots using isoform-specific probes for all 14-3-3 and H+-ATPase isoforms showed that transcripts were present for most of the isoforms. Based on mRNA levels, GF14epsilon, mu, lambda and chi are highly expressed 14-3-3 isoforms, and AHA1, 3, and 11 highly expressed H+-ATPase isoforms in leaves. However, mass peptide fingerprinting identified AHA1 and 2 with the highest score, and their presence could be confirmed by MS/MS. It may be calculated that under ‘unstressed’ conditions less than one percent of total 14-3-3 is attached to the H+-ATPase. However, during a condition requiring full activation of H+ pumping, as induced here by the presence of the fungal toxin fusicoccin, several percent of total 14-3-3 may be engaged in activation of the H+-ATPase.},
	number = {9},
	urldate = {2021-06-15},
	journal = {Plant and Cell Physiology},
	author = {Alsterfjord, Magnus and Sehnke, Paul C. and Arkell, Annika and Larsson, Håkan and Svennelid, Fredrik and Rosenquist, Magnus and Ferl, Robert J. and Sommarin, Marianne and Larsson, Christer},
	month = sep,
	year = {2004},
	pages = {1202--1210},
}

The plasma membrane H+-ATPase is activated by binding of 14-3-3 protein to the phosphorylated C terminus. Considering the large number of 14-3-3 and H+-ATPase isoforms in Arabidopsis (13 and 11 expressed genes, respectively), specificity in binding may exist between 14-3-3 and H+-ATPase isoforms. We now show that the H+-ATPase is the main target for 14-3-3 binding at the plasma membrane, and that all twelve 14-3-3 isoforms tested bind to the H+-ATPase in vitro. Using specific antibodies for nine of the 14-3-3 isoforms, we show that GF14epsilon, mu, lambda, omega, chi, phi, nu, and upsilon are present in leaves, but that isolated plasma membranes lack GF14chi, phi and upsilon. Northern blots using isoform-specific probes for all 14-3-3 and H+-ATPase isoforms showed that transcripts were present for most of the isoforms. Based on mRNA levels, GF14epsilon, mu, lambda and chi are highly expressed 14-3-3 isoforms, and AHA1, 3, and 11 highly expressed H+-ATPase isoforms in leaves. However, mass peptide fingerprinting identified AHA1 and 2 with the highest score, and their presence could be confirmed by MS/MS. It may be calculated that under ‘unstressed’ conditions less than one percent of total 14-3-3 is attached to the H+-ATPase. However, during a condition requiring full activation of H+ pumping, as induced here by the presence of the fungal toxin fusicoccin, several percent of total 14-3-3 may be engaged in activation of the H+-ATPase.

@article{swarup_structure-function_2004,
	title = {Structure-{Function} {Analysis} of the {Presumptive} {Arabidopsis} {Auxin} {Permease} {AUX1}[{W}]},
	volume = {16},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.104.024737},
	doi = {10/dfj7nb},
	abstract = {We have investigated the subcellular localization, the domain topology, and the amino acid residues that are critical for the function of the presumptive Arabidopsis thaliana auxin influx carrier AUX1. Biochemical fractionation experiments and confocal studies using an N-terminal yellow fluorescent protein (YFP) fusion observed that AUX1 colocalized with plasma membrane (PM) markers. Because of its PM localization, we were able to take advantage of the steep pH gradient that exists across the plant cell PM to investigate AUX1 topology using YFP as a pH-sensitive probe. The YFP-coding sequence was inserted in selected AUX1 hydrophilic loops to orient surface domains on either apoplastic or cytoplasmic faces of the PM based on the absence or presence of YFP fluorescence, respectively. We were able to demonstrate in conjunction with helix prediction programs that AUX1 represents a polytopic membrane protein composed of 11 transmembrane spanning domains. In parallel, a large aux1 allelic series containing null, partial-loss-of-function, and conditional mutations was characterized to identify the functionally important domains and amino acid residues within the AUX1 polypeptide. Whereas almost all partial-loss-of-function and null alleles cluster in the core permease region, the sole conditional allele aux1-7 modifies the function of the external C-terminal domain.},
	number = {11},
	urldate = {2021-06-15},
	journal = {The Plant Cell},
	author = {Swarup, Ranjan and Kargul, Joanna and Marchant, Alan and Zadik, Daniel and Rahman, Abidur and Mills, Rebecca and Yemm, Anthony and May, Sean and Williams, Lorraine and Millner, Paul and Tsurumi, Seiji and Moore, Ian and Napier, Richard and Kerr, Ian D. and Bennett, Malcolm J.},
	month = nov,
	year = {2004},
	pages = {3069--3083},
}

We have investigated the subcellular localization, the domain topology, and the amino acid residues that are critical for the function of the presumptive Arabidopsis thaliana auxin influx carrier AUX1. Biochemical fractionation experiments and confocal studies using an N-terminal yellow fluorescent protein (YFP) fusion observed that AUX1 colocalized with plasma membrane (PM) markers. Because of its PM localization, we were able to take advantage of the steep pH gradient that exists across the plant cell PM to investigate AUX1 topology using YFP as a pH-sensitive probe. The YFP-coding sequence was inserted in selected AUX1 hydrophilic loops to orient surface domains on either apoplastic or cytoplasmic faces of the PM based on the absence or presence of YFP fluorescence, respectively. We were able to demonstrate in conjunction with helix prediction programs that AUX1 represents a polytopic membrane protein composed of 11 transmembrane spanning domains. In parallel, a large aux1 allelic series containing null, partial-loss-of-function, and conditional mutations was characterized to identify the functionally important domains and amino acid residues within the AUX1 polypeptide. Whereas almost all partial-loss-of-function and null alleles cluster in the core permease region, the sole conditional allele aux1-7 modifies the function of the external C-terminal domain.

@article{schrader_high-resolution_2004,
	title = {A {High}-{Resolution} {Transcript} {Profile} across the {Wood}-{Forming} {Meristem} of {Poplar} {Identifies} {Potential} {Regulators} of {Cambial} {Stem} {Cell} {Identity}[{W}]},
	volume = {16},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.104.024190},
	doi = {10/d94rmq},
	abstract = {Plant growth is the result of cell proliferation in meristems, which requires a careful balance between the formation of new tissue and the maintenance of a set of undifferentiated stem cells. Recent studies have provided important information on several genetic networks responsible for stem cell maintenance and regulation of cell differentiation in the apical meristems of shoots and roots. Nothing, however, is known about the regulatory networks in secondary meristems like the vascular cambium of trees. We have made use of the large size and highly regular layered organization of the cambial meristem to create a high-resolution transcriptional map covering 220 μm of the cambial region of aspen (Populus tremula). Clusters of differentially expressed genes revealed substantial differences in the transcriptomes of the six anatomically homogenous cell layers in the meristem zone. Based on transcriptional and anatomical data, we present a model for the position of the stem cells and the proliferating mother cells in the cambial zone. We also provide sets of marker genes for different stages of xylem and phloem differentiation and identify potential regulators of cambial meristem activity. Interestingly, analysis of known regulators of apical meristem development indicates substantial similarity in regulatory networks between primary and secondary meristems.},
	number = {9},
	urldate = {2021-06-15},
	journal = {The Plant Cell},
	author = {Schrader, Jarmo and Nilsson, Jeanette and Mellerowicz, Ewa and Berglund, Anders and Nilsson, Peter and Hertzberg, Magnus and Sandberg, Göran},
	month = sep,
	year = {2004},
	pages = {2278--2292},
}

Plant growth is the result of cell proliferation in meristems, which requires a careful balance between the formation of new tissue and the maintenance of a set of undifferentiated stem cells. Recent studies have provided important information on several genetic networks responsible for stem cell maintenance and regulation of cell differentiation in the apical meristems of shoots and roots. Nothing, however, is known about the regulatory networks in secondary meristems like the vascular cambium of trees. We have made use of the large size and highly regular layered organization of the cambial meristem to create a high-resolution transcriptional map covering 220 μm of the cambial region of aspen (Populus tremula). Clusters of differentially expressed genes revealed substantial differences in the transcriptomes of the six anatomically homogenous cell layers in the meristem zone. Based on transcriptional and anatomical data, we present a model for the position of the stem cells and the proliferating mother cells in the cambial zone. We also provide sets of marker genes for different stages of xylem and phloem differentiation and identify potential regulators of cambial meristem activity. Interestingly, analysis of known regulators of apical meristem development indicates substantial similarity in regulatory networks between primary and secondary meristems.

@article{ball_evidence_2004,
	title = {Evidence for a {Direct} {Link} between {Glutathione} {Biosynthesis} and {Stress} {Defense} {Gene} {Expression} in {Arabidopsis}[{W}]},
	volume = {16},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.104.022608},
	doi = {10/dnj446},
	abstract = {The mutant regulator of APX2 1-1 (rax1-1) was identified in Arabidopsis thaliana that constitutively expressed normally photooxidative stress-inducible ASCORBATE PEROXIDASE2 (APX2) and had ≥50\% lowered foliar glutathione levels. Mapping revealed that rax1-1 is an allele of γ-GLUTAMYLCYSTEINE SYNTHETASE 1 (GSH1), which encodes chloroplastic γ-glutamylcysteine synthetase, the controlling step of glutathione biosynthesis. By comparison of rax1-1 with the GSH1 mutant cadmium hypersensitive 2, the expression of 32 stress-responsive genes was shown to be responsive to changed glutathione metabolism. Under photo-oxidative stress conditions, the expression of a wider set of defense-related genes was altered in the mutants. In wild-type plants, glutathione metabolism may play a key role in determining the degree of expression of defense genes controlled by several signaling pathways both before and during stress. This control may reflect the physiological state of the plant at the time of the onset of an environmental challenge and suggests that changes in glutathione metabolism may be one means of integrating the function of several signaling pathways.},
	number = {9},
	urldate = {2021-06-15},
	journal = {The Plant Cell},
	author = {Ball, Louise and Accotto, Gian-Paolo and Bechtold, Ulrike and Creissen, Gary and Funck, Dietmar and Jimenez, Ana and Kular, Baldeep and Leyland, Nicola and Mejia-Carranza, Jaime and Reynolds, Helen and Karpinski, Stanislaw and Mullineaux, Philip M.},
	month = sep,
	year = {2004},
	pages = {2448--2462},
}

The mutant regulator of APX2 1-1 (rax1-1) was identified in Arabidopsis thaliana that constitutively expressed normally photooxidative stress-inducible ASCORBATE PEROXIDASE2 (APX2) and had ≥50% lowered foliar glutathione levels. Mapping revealed that rax1-1 is an allele of γ-GLUTAMYLCYSTEINE SYNTHETASE 1 (GSH1), which encodes chloroplastic γ-glutamylcysteine synthetase, the controlling step of glutathione biosynthesis. By comparison of rax1-1 with the GSH1 mutant cadmium hypersensitive 2, the expression of 32 stress-responsive genes was shown to be responsive to changed glutathione metabolism. Under photo-oxidative stress conditions, the expression of a wider set of defense-related genes was altered in the mutants. In wild-type plants, glutathione metabolism may play a key role in determining the degree of expression of defense genes controlled by several signaling pathways both before and during stress. This control may reflect the physiological state of the plant at the time of the onset of an environmental challenge and suggests that changes in glutathione metabolism may be one means of integrating the function of several signaling pathways.

@article{ahlfors_arabidopsis_2004,
	title = {Arabidopsis {RADICAL}-{INDUCED} {CELL} {DEATH1} {Belongs} to the {WWE} {Protein}–{Protein} {Interaction} {Domain} {Protein} {Family} and {Modulates} {Abscisic} {Acid}, {Ethylene}, and {Methyl} {Jasmonate} {Responses}},
	volume = {16},
	issn = {1040-4651},
	url = {https://academic.oup.com/plcell/article/16/7/1925/6010421},
	doi = {10/c8t7cs},
	abstract = {Abstract. Experiments with several Arabidopsis thaliana mutants have revealed a web of interactions between hormonal signaling. Here, we show that the Arabidops},
	language = {en},
	number = {7},
	urldate = {2021-06-15},
	journal = {The Plant Cell},
	author = {Ahlfors, Reetta and Lång, Saara and Overmyer, Kirk and Jaspers, Pinja and Broscheé, Mikael and Tauriainen, Airi and Kollist, Hannes and Tuominen, Hannele and Belles-Boix, Enric and Piippo, Mirva and Inzeé, Dirk and Palva, E. Tapio and Kangasjärvi, Jaakko},
	month = jul,
	year = {2004},
	note = {Publisher: Oxford Academic},
	pages = {1925--1937},
}

Abstract. Experiments with several Arabidopsis thaliana mutants have revealed a web of interactions between hormonal signaling. Here, we show that the Arabidops

@article{gray-mitsumune_liquid_2004,
	title = {Liquid {Phase} {Fluorescence} in situ {RT}-{PCR} {Analysis} for {Gene} {Expression} {Analysis} in {Woody} {Stems}},
	volume = {6},
	issn = {1438-8677},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1055/s-2003-44747},
	doi = {10/bf7fs7},
	abstract = {Abstract: We explore a rapid in situ RT-PCR protocol for gene expression studies in woody stem tissues. In situ RT-PCR was performed using fluorescent dye-conjugated nucleic acid and the fluorescence signals derived from target RNAs were detected using confocal laser scanning microscopy. The signal to background ratio was greatly enhanced by performing two rounds of PCR reactions, first without the fluorescent dye and second with the dye. Using this protocol, we obtained strong gene-specific signals in secondary stem tissues. The signals were PCR-dependent, as shown by the lack of cytoplasmic signals in the tissue sections in which either DNA polymerase or primers were omitted from PCR reactions, and were RNA-dependent, as shown by great reduction of cytoplasmic signals when sections were treated with RNase before RT reactions. To verify our protocol, transcript localization of the rbcS gene was examined in secondary stems of hybrid aspen (Populus tremula L. ×tremuloides Michx.) and compared to the chlorophyll autofluorescence signal. The in situ RT-PCR signals form the rbcS gene and chlorophyll autofluorescence co-localized in the same cell types. The signal was also confirmed by Northern blot analysis of isolated RNA from the cambium and developing xylem, thus confirming the validity of the protocol. Some difficulties of in situ transcript localization and the interpretation of the signal distribution in the secondary tissues are discussed.},
	language = {en},
	number = {1},
	urldate = {2021-06-15},
	journal = {Plant Biology},
	author = {Gray-Mitsumune, M. and Abe, H. and Takahashi, J. and Sundberg, B. and Mellerowicz, E. J.},
	year = {2004},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1055/s-2003-44747},
	keywords = {Confocal laser scanning microscopy, Populus, in situ RT-PCR, vascular cambium, wood, xylem},
	pages = {47--54},
}

Abstract: We explore a rapid in situ RT-PCR protocol for gene expression studies in woody stem tissues. In situ RT-PCR was performed using fluorescent dye-conjugated nucleic acid and the fluorescence signals derived from target RNAs were detected using confocal laser scanning microscopy. The signal to background ratio was greatly enhanced by performing two rounds of PCR reactions, first without the fluorescent dye and second with the dye. Using this protocol, we obtained strong gene-specific signals in secondary stem tissues. The signals were PCR-dependent, as shown by the lack of cytoplasmic signals in the tissue sections in which either DNA polymerase or primers were omitted from PCR reactions, and were RNA-dependent, as shown by great reduction of cytoplasmic signals when sections were treated with RNase before RT reactions. To verify our protocol, transcript localization of the rbcS gene was examined in secondary stems of hybrid aspen (Populus tremula L. ×tremuloides Michx.) and compared to the chlorophyll autofluorescence signal. The in situ RT-PCR signals form the rbcS gene and chlorophyll autofluorescence co-localized in the same cell types. The signal was also confirmed by Northern blot analysis of isolated RNA from the cambium and developing xylem, thus confirming the validity of the protocol. Some difficulties of in situ transcript localization and the interpretation of the signal distribution in the secondary tissues are discussed.

@article{lundquist_nitrogenase_2004,
	title = {Nitrogenase activity and root nodule metabolism in response to {O}-2 and short-term {N}-2 deprivation in dark-treated {Frankia}-{Alnus} incana plants (vol 119, pg 244, 2003)},
	volume = {120},
	issn = {0031-9317},
	language = {English},
	number = {1},
	journal = {Physiologia Plantarum},
	author = {Lundquist, P. O. and Nasholm, T. and Huss-Danell, K.},
	month = jan,
	year = {2004},
	note = {Place: Copenhagen
Publisher: Blackwell Munksgaard
WOS:000187890700020},
	keywords = {⛔ No DOI found},
	pages = {171--171},
}

@article{corbesier_gibberellins_2004,
	title = {Gibberellins and the floral transition in {Sinapis} alba},
	volume = {122},
	issn = {0031-9317},
	doi = {10/fqn2j7},
	abstract = {The putative role of gibberellins in the transition to flowering was investigated in Sinapis alba, a caulescent long-day (LD) plant. It was observed that: (1) physiological doses of exogenous gibberellins (GA(1), GA(3), GA(9)) do not cause the floral shift of the meristem when applied to plants grown in short days but have some positive effect on the flowering response to a suboptimal LD; no inhibition was observed in any case; (2) GA-biosynthesis inhibitors (prohexadione-Ca and paclobutrazol) considerably inhibit stem growth but have some negative effect on flowering only when a suboptimal LD is given; and (3) the floral transition induced by one 22-h LD does not correlate with any detectable change in GA content of the apical bud, of the leaves, and of the phloem exudate reaching the apex. Taken together, these results suggest that GAs do not act as a major signal for photoperiodic flower induction in Sinapis.},
	language = {English},
	number = {1},
	journal = {Physiologia Plantarum},
	author = {Corbesier, L. and Kustermans, G. and Perilleux, C. and Melzer, S. and Moritz, T. and Havelange, A. and Bernier, G.},
	month = sep,
	year = {2004},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000223589000018},
	keywords = {arabidopsis-thaliana, biosynthesis, cytokinins, endogenous gibberellins, induction, localization, phloem, photoperiod, shoot, stem growth},
	pages = {152--158},
}

The putative role of gibberellins in the transition to flowering was investigated in Sinapis alba, a caulescent long-day (LD) plant. It was observed that: (1) physiological doses of exogenous gibberellins (GA(1), GA(3), GA(9)) do not cause the floral shift of the meristem when applied to plants grown in short days but have some positive effect on the flowering response to a suboptimal LD; no inhibition was observed in any case; (2) GA-biosynthesis inhibitors (prohexadione-Ca and paclobutrazol) considerably inhibit stem growth but have some negative effect on flowering only when a suboptimal LD is given; and (3) the floral transition induced by one 22-h LD does not correlate with any detectable change in GA content of the apical bud, of the leaves, and of the phloem exudate reaching the apex. Taken together, these results suggest that GAs do not act as a major signal for photoperiodic flower induction in Sinapis.

@article{igamberdiev_photorespiration_2004,
	title = {Photorespiration contributes to stomatal regulation and carbon isotope fractionation: a study with barley, potato and {Arabidopsis} plants deficient in glycine decarboxylase},
	volume = {81},
	issn = {0166-8595},
	shorttitle = {Photorespiration contributes to stomatal regulation and carbon isotope fractionation},
	doi = {10/bshffc},
	abstract = {The rates of respiration in light and darkness, C-i/C-a and carbon isotope fractionation were investigated in glycine decarboxylase-deficient plants of barley, potato and Arabidopsis thaliana grown in climate chambers with controlled light intensity, temperature, humidity, irradiation and different CO2 concentrations (360, 700 and 1400 mul l(-1)) and compared to the wild-type plants. All photorespiration-impaired plants exhibited higher C-i/C-a and corresponding lower apparent water-use efficiencies, which were more expressed under high irradiance and elevated temperature. The mutants were depleted in C-13 as compared to the wild-type plants, with a difference of up to 6parts per thousand following growth in 360 mul l(-1) CO2. We determined the carbon isotope content at different CO2 concentrations to calculate the contribution of both C-i/C-a and photorespiration for C-13/C-12 fractionation. The direct effect of photorespiration was in the range of 0.7 - 1.0parts per thousand, from which we calculated the value of fractionation at the site of glycine decarboxylation as being 10 - 13parts per thousand, which is in agreement with the previously reported carbon isotope discrimination exerted by the glycine decarboxylase. Respiratory rates, particularly in the light, were increased in the glycine decarboxylase mutants. The necessity of the maintenance of a high CO2 concentration near the site of carboxylation in chloroplasts in plants deficient in photorespiratory enzymes, requires an increased opening of the stomata with a corresponding decrease in water-use efficiency. It is concluded that photorespiration participates in the regulation of C-i/C-a and contributes to carbon isotope fractionation, both via effects on stomata and via discrimination of C-13 in the glycine decarboxylase reaction.},
	language = {English},
	number = {2},
	journal = {Photosynthesis Research},
	author = {Igamberdiev, A. U. and Mikkelsen, T. N. and Ambus, P. and Bauwe, H. and Lea, P. J. and Gardestrom, P.},
	year = {2004},
	note = {Place: Dordrecht
Publisher: Springer
WOS:000222680700004},
	keywords = {carbon isotope fractionation, co2 concentration, dark   respiration, dioxide, discrimination, elevated co2, glycine decarboxylase, leaf respiration, leaves, nicotiana-sylvestris, photorespiration, photorespiratory mutants, photosynthesis, reduced activities, stomata},
	pages = {139--152},
}

The rates of respiration in light and darkness, C-i/C-a and carbon isotope fractionation were investigated in glycine decarboxylase-deficient plants of barley, potato and Arabidopsis thaliana grown in climate chambers with controlled light intensity, temperature, humidity, irradiation and different CO2 concentrations (360, 700 and 1400 mul l(-1)) and compared to the wild-type plants. All photorespiration-impaired plants exhibited higher C-i/C-a and corresponding lower apparent water-use efficiencies, which were more expressed under high irradiance and elevated temperature. The mutants were depleted in C-13 as compared to the wild-type plants, with a difference of up to 6parts per thousand following growth in 360 mul l(-1) CO2. We determined the carbon isotope content at different CO2 concentrations to calculate the contribution of both C-i/C-a and photorespiration for C-13/C-12 fractionation. The direct effect of photorespiration was in the range of 0.7 - 1.0parts per thousand, from which we calculated the value of fractionation at the site of glycine decarboxylation as being 10 - 13parts per thousand, which is in agreement with the previously reported carbon isotope discrimination exerted by the glycine decarboxylase. Respiratory rates, particularly in the light, were increased in the glycine decarboxylase mutants. The necessity of the maintenance of a high CO2 concentration near the site of carboxylation in chloroplasts in plants deficient in photorespiratory enzymes, requires an increased opening of the stomata with a corresponding decrease in water-use efficiency. It is concluded that photorespiration participates in the regulation of C-i/C-a and contributes to carbon isotope fractionation, both via effects on stomata and via discrimination of C-13 in the glycine decarboxylase reaction.

@article{moskvin_carbonic_2004,
	title = {Carbonic {Anhydrase} {Activities} in {Pea} {Thylakoids}},
	volume = {79},
	issn = {1573-5079},
	url = {https://doi.org/10.1023/B:PRES.0000011925.93313.db},
	doi = {10/fqdpjw},
	abstract = {Pea thylakoids with high carbonic anhydrase (CA) activity (average rates of 5000 µmol H+ (mg Chl)−1 h−1 at pH 7.0) were prepared. Western blot analysis using antibodies raised against the soluble stromal β-CA from spinach clearly showed that this activity is not a result of contamination of the thylakoids with the stromal CA but is derived from a thylakoid membrane-associated CA. Increase of the CA activity after partial membrane disintegration by detergent treatment, freezing or sonication implies the location of the CA in the thylakoid interior. Salt treatment of thylakoids demonstrated that while one part of the initial enzyme activity is easily soluble, the rest of it appears to be tightly associated with the membrane. CA activity being measured as HCO3− dehydration (dehydrase activity) in Photosystem II particles (BBY) was variable and usually low. The highest and most reproducible activities (approximately 2000 µmol H+ (mg Chl)−1 h−1) were observed in the presence of detergents (Triton X-100 or n-octyl-β-D-glucopyranoside) in low concentrations. The dehydrase CA activity of BBY particles was more sensitive to the lipophilic CA inhibitor, ethoxyzolamide, than to the hydrophilic CA inhibitor, acetazolamide. CA activity was detected in PS II core complexes with average rate of 13,000 µmol H+ (mg Chl)−1 h−1 which was comparable to CA activity in BBY particles normalized on a PS II reaction center basis.},
	language = {en},
	number = {1},
	urldate = {2021-06-15},
	journal = {Photosynthesis Research},
	author = {Moskvin, O.V. and Shutova, T.V. and Khristin, M.S. and Ignatova, L.K. and Villarejo, A. and Samuelsson, G. and Klimov, V.V. and Ivanov, B.N.},
	month = jan,
	year = {2004},
	pages = {93--100},
}

Pea thylakoids with high carbonic anhydrase (CA) activity (average rates of 5000 µmol H+ (mg Chl)−1 h−1 at pH 7.0) were prepared. Western blot analysis using antibodies raised against the soluble stromal β-CA from spinach clearly showed that this activity is not a result of contamination of the thylakoids with the stromal CA but is derived from a thylakoid membrane-associated CA. Increase of the CA activity after partial membrane disintegration by detergent treatment, freezing or sonication implies the location of the CA in the thylakoid interior. Salt treatment of thylakoids demonstrated that while one part of the initial enzyme activity is easily soluble, the rest of it appears to be tightly associated with the membrane. CA activity being measured as HCO3− dehydration (dehydrase activity) in Photosystem II particles (BBY) was variable and usually low. The highest and most reproducible activities (approximately 2000 µmol H+ (mg Chl)−1 h−1) were observed in the presence of detergents (Triton X-100 or n-octyl-β-D-glucopyranoside) in low concentrations. The dehydrase CA activity of BBY particles was more sensitive to the lipophilic CA inhibitor, ethoxyzolamide, than to the hydrophilic CA inhibitor, acetazolamide. CA activity was detected in PS II core complexes with average rate of 13,000 µmol H+ (mg Chl)−1 h−1 which was comparable to CA activity in BBY particles normalized on a PS II reaction center basis.

@article{albrectsen_slugs_2004,
	title = {Slugs, willow seedlings and nutrient fertilization: intrinsic vigor inversely affects palatability},
	volume = {105},
	issn = {0030-1299},
	shorttitle = {Slugs, willow seedlings and nutrient fertilization},
	doi = {10/fccj89},
	abstract = {This study evaluates how preference by a generalist slug herbivore Arion subfuscus changes inversely with seedling size across three levels of fertilization for three full-sib families of willow seedlings. We analyzed seedlings for condensed tannin and protein concentration, and related these data to changes in palatability. In preference tests over time, leaf discs from more fertilized seedlings experienced an extended window of vulnerability compared to discs from less fertilized seedlings, which were also more tannin-rich. In a whole seedling selection study, slugs readily attacked smaller seedlings ({\textless}5 cm) but rarely attacked taller seedlings ({\textgreater}10 cm). However, a general difference in risk of damage close to 50\% existed when comparing shorter and taller individuals within each family and level of fertilizer. The decrease in palatability with height of the seedlings was positively correlated with an increase in condensed tannin concentration. We found no effect of seedling size on protein concentration. Akaiki index criterion model comparisons suggested that only main effects were important for explaining seedling choice by slugs as well as the ratio between proteins and condensed tannins. Seedling size, had the largest effect, followed by fertilizer level and family. Surprisingly, seedling size and fertilizer treatment had opposite effects on palatability to slugs. Size decreased probability of damage, whereas fertilization extended the window of susceptibility. Because the seedlings were even-aged, differences in size are interpreted as differences in growth rate or vigor. The positive phenotypic correlation found between size and tannin production in the less preferred willow seedlings confirms that several plant defense traits may be selected for simultaneously, because fast growth may allow an early development of plant defenses. We discuss these results in the light of plant-defense theories that predict a negative correlation between the allocation to growth and the production of secondary defense compounds.},
	language = {English},
	number = {2},
	journal = {Oikos},
	author = {Albrectsen, B. R. and Gardfjell, H. and Orians, C. M. and Murray, B. and Fritz, R. S.},
	month = may,
	year = {2004},
	note = {Place: Hoboken
Publisher: Wiley-Blackwell
WOS:000220383100007},
	keywords = {chemical defense, deroceras-reticulatum, grassland, herbivory, hybrid, hypothesis, performance, plants, resource availability, tannin},
	pages = {268--278},
}

This study evaluates how preference by a generalist slug herbivore Arion subfuscus changes inversely with seedling size across three levels of fertilization for three full-sib families of willow seedlings. We analyzed seedlings for condensed tannin and protein concentration, and related these data to changes in palatability. In preference tests over time, leaf discs from more fertilized seedlings experienced an extended window of vulnerability compared to discs from less fertilized seedlings, which were also more tannin-rich. In a whole seedling selection study, slugs readily attacked smaller seedlings (\textless5 cm) but rarely attacked taller seedlings (\textgreater10 cm). However, a general difference in risk of damage close to 50% existed when comparing shorter and taller individuals within each family and level of fertilizer. The decrease in palatability with height of the seedlings was positively correlated with an increase in condensed tannin concentration. We found no effect of seedling size on protein concentration. Akaiki index criterion model comparisons suggested that only main effects were important for explaining seedling choice by slugs as well as the ratio between proteins and condensed tannins. Seedling size, had the largest effect, followed by fertilizer level and family. Surprisingly, seedling size and fertilizer treatment had opposite effects on palatability to slugs. Size decreased probability of damage, whereas fertilization extended the window of susceptibility. Because the seedlings were even-aged, differences in size are interpreted as differences in growth rate or vigor. The positive phenotypic correlation found between size and tannin production in the less preferred willow seedlings confirms that several plant defense traits may be selected for simultaneously, because fast growth may allow an early development of plant defenses. We discuss these results in the light of plant-defense theories that predict a negative correlation between the allocation to growth and the production of secondary defense compounds.

@article{smith_response_2004,
	title = {The response of the poplar transcriptome to wounding and subsequent infection by a viral pathogen},
	volume = {164},
	issn = {0028-646X},
	doi = {10/cg756g},
	abstract = {The Populus-Poplar Mosaic Virus (PopMV) pathosystem is the best characterized of all forest tree-virus interactions. The details of the host response to this virus are completely unknown. The transcript abundance for approximately 10 000 Populus genes was simultaneously interrogated using spotted cDNA microarrays. Relative transcript abundance was compared for RNA extracted from Populus leaves that were untreated, mock-inoculated leaves that were wounded by leaf abrasion and inoculated leaves that were abraded and then infected by virus. Statistical analysis of the microarray data identified suites of genes that exhibited increased or decreased transcript abundance in response to wounding, systemic PopMV infection or both together. Genes implicated in programmed cell death, and cell wall reinforcement were a major feature of the wound response, whereas genes encoding metallothionein-like proteins, and proteins implicated in cell wall remodelling were a major feature of the PopMV response. The identification of wound- and PopMV-regulated genes opens the door for future studies aimed at testing specific hypotheses related to the mechanisms used by forest trees to contend with stress.},
	language = {English},
	number = {1},
	journal = {New Phytologist},
	author = {Smith, C. M. and Rodriguez-Buey, M. and Karlsson, J. and Campbell, M. M.},
	month = oct,
	year = {2004},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000223662000013},
	keywords = {Poplar Mosaic Virus, Populus, arabidopsis-thaliana, cell-wall, disease resistance, jasmonic acid, melampsora-larici-populina, metallothionein-like gene, microarray, molecular-genetics, mosaic-virus   movement, pectin methylesterase, systemic movement, transcription, transcriptome, wounding},
	pages = {123--136},
}

The Populus-Poplar Mosaic Virus (PopMV) pathosystem is the best characterized of all forest tree-virus interactions. The details of the host response to this virus are completely unknown. The transcript abundance for approximately 10 000 Populus genes was simultaneously interrogated using spotted cDNA microarrays. Relative transcript abundance was compared for RNA extracted from Populus leaves that were untreated, mock-inoculated leaves that were wounded by leaf abrasion and inoculated leaves that were abraded and then infected by virus. Statistical analysis of the microarray data identified suites of genes that exhibited increased or decreased transcript abundance in response to wounding, systemic PopMV infection or both together. Genes implicated in programmed cell death, and cell wall reinforcement were a major feature of the wound response, whereas genes encoding metallothionein-like proteins, and proteins implicated in cell wall remodelling were a major feature of the PopMV response. The identification of wound- and PopMV-regulated genes opens the door for future studies aimed at testing specific hypotheses related to the mechanisms used by forest trees to contend with stress.

@article{hunt_gene-specific_2004,
	title = {Gene-specific expression and calcium activation of {Arabidopsis} thaliana phospholipase {C} isoforms},
	volume = {162},
	issn = {0028-646X},
	doi = {10/bps2mq},
	abstract = {PI-PLCs synthesise the calcium releasing second messenger IP(3). We investigated the expression patterns of the Arabidopsis PI-PLC gene family and measured in vitro activity of encoded enzymes. Gene specific RT-PCR and promoter-GUS fusions were used to analyse AtPLC gene expression patterns. The five available AtPLC cDNAs were expressed as fusion proteins in Escherichia coli. All members of the AtPLC gene family were expressed in multiple organs of the plant. AtPLC1, and AtPLC5 expression was localized to the vascular cells of roots and leaves with AtPLC5::GUS also detected in the guard cells. AtPLC4::GUS was detected in pollen and cells of the stigma surface. In seedlings, AtPLC2 and AtPLC3 were constitutively expressed, while AtPLCs 1, 4 and 5 were induced by abiotic stresses. AtPLC1-5 were all shown to have phospholipase C activity in the presence of calcium ions. AtPLCs showed limited tissue specific expression and expression of at least three genes was increased by abiotic stress. The differing calcium sensitivities of recombinant AtPLC protein activities may provide a mechanism for generating calcium signatures.},
	language = {English},
	number = {3},
	journal = {New Phytologist},
	author = {Hunt, L. and Otterhag, L. and Lee, J. C. and Lasheen, T. and Hunt, J. and Seki, M. and Shinozaki, K. and Sornmarin, M. and Gilmour, D. J. and Pical, C. and Gray, J. E.},
	month = jun,
	year = {2004},
	note = {Place: Malden
Publisher: Wiley-Blackwell
WOS:000221913500007},
	keywords = {Arabidopsis, abscisic-acid, calcium, cyclic   adp-ribose, cytosolic-free calcium, diacylglycerol   pyrophosphate, gene expression, guard cell, guard-cells, inositol 1,4,5-trisphosphate, papaver-rhoeas, phosphatidylinositol 4,5-bisphosphate, phosphoinositide turnover, phospholipase C, pi-plc, pollen, self-incompatibility response, stress},
	pages = {643--654},
}

PI-PLCs synthesise the calcium releasing second messenger IP(3). We investigated the expression patterns of the Arabidopsis PI-PLC gene family and measured in vitro activity of encoded enzymes. Gene specific RT-PCR and promoter-GUS fusions were used to analyse AtPLC gene expression patterns. The five available AtPLC cDNAs were expressed as fusion proteins in Escherichia coli. All members of the AtPLC gene family were expressed in multiple organs of the plant. AtPLC1, and AtPLC5 expression was localized to the vascular cells of roots and leaves with AtPLC5::GUS also detected in the guard cells. AtPLC4::GUS was detected in pollen and cells of the stigma surface. In seedlings, AtPLC2 and AtPLC3 were constitutively expressed, while AtPLCs 1, 4 and 5 were induced by abiotic stresses. AtPLC1-5 were all shown to have phospholipase C activity in the presence of calcium ions. AtPLCs showed limited tissue specific expression and expression of at least three genes was increased by abiotic stress. The differing calcium sensitivities of recombinant AtPLC protein activities may provide a mechanism for generating calcium signatures.

@article{brunner_revisiting_2004,
	title = {Revisiting tree maturation and floral initiation in the poplar functional genomics era},
	volume = {164},
	issn = {0028-646X},
	doi = {10/bhcb7q},
	abstract = {The recent release of the Populus trichocarpa genome sequence will dramatically enhance the efficiency of functional and comparative genomics research in trees. This provides researchers studying various developmental processes related to the perennial and tree life strategies with a completely new set of tools. Intimately associated with the life strategy of trees are their abilities to maintain juvenile or nonflowering phases for years to decades, and once reproductively competent, to alternate between the production of vegetative and reproductive shoots. Most of what we know about the regulation of the floral transition comes from research on Arabidopsis thaliana, a small, herbaceous, rapid-cycling, annual plant. In this review, we discuss the similarities and differences between Arabidopsis and tree flowering, and how recent findings in Arabidopsis, coupled to comparative and functional genomics in poplars, will help answer the question of how tree maturation and floral initiation is regulated.},
	language = {English},
	number = {1},
	journal = {New Phytologist},
	author = {Brunner, A. M. and Nilsson, O.},
	month = oct,
	year = {2004},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000223662000006},
	keywords = {Populus, activation, arabidopsis, expression, floral initiation, flowering time, gene, genomics, gibberellin, induction, juvenile phase, pathways, phase-change, populus, tree maturation},
	pages = {43--51},
}

The recent release of the Populus trichocarpa genome sequence will dramatically enhance the efficiency of functional and comparative genomics research in trees. This provides researchers studying various developmental processes related to the perennial and tree life strategies with a completely new set of tools. Intimately associated with the life strategy of trees are their abilities to maintain juvenile or nonflowering phases for years to decades, and once reproductively competent, to alternate between the production of vegetative and reproductive shoots. Most of what we know about the regulation of the floral transition comes from research on Arabidopsis thaliana, a small, herbaceous, rapid-cycling, annual plant. In this review, we discuss the similarities and differences between Arabidopsis and tree flowering, and how recent findings in Arabidopsis, coupled to comparative and functional genomics in poplars, will help answer the question of how tree maturation and floral initiation is regulated.

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

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

@article{stasolla_variation_2004,
	title = {Variation in transcript abundance during somatic embryogenesis in gymnosperms},
	volume = {24},
	issn = {0829-318X},
	url = {https://academic.oup.com/treephys/article/24/10/1073/1646975},
	doi = {10/fxjbcn},
	abstract = {Abstract. Somatic embryogenesis of Norway spruce (Picea abies L.) is a versatile model system to study molecular mechanisms regulating embryo development becaus},
	language = {en},
	number = {10},
	urldate = {2021-06-15},
	journal = {Tree Physiology},
	author = {Stasolla, Claudio and Bozhkov, Peter V. and Chu, Tzu-Ming and van Zyl, Leonel and Egertsdotter, Ulrika and Suarez, Maria F. and Craig, Deborah and Wolfinger, Russ D. and Von Arnold, Sara and Sederoff, Ronald R.},
	month = oct,
	year = {2004},
	note = {Publisher: Oxford Academic},
	pages = {1073--1085},
}

Abstract. Somatic embryogenesis of Norway spruce (Picea abies L.) is a versatile model system to study molecular mechanisms regulating embryo development becaus

@article{pesquet_multiple_2004,
	title = {Multiple gene detection by in situ {RT}-{PCR} in isolated plant cells and tissues},
	volume = {39},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2004.02170.x},
	doi = {10/dqq84x},
	abstract = {With the number of functional genomic approaches in plant biology increasing daily, the demand for rapid and reliable RNA localization techniques for gene characterization is being felt. We present herein a novel, liquid phase in situ RT-PCR (IS-RT-PCR) protocol using a combination of gene-specific fluorescent primers and spectral confocal microscopy to localize target RNA in epicotyl sections and xylogenic suspension cultures of Zinnia elegans. Potential sources of artefacts from fixation to gene detection were systematically eliminated using both fluorescent primers and nucleotides for 18S rRNA gene detection, resulting in a set of optimal parameters for IS-RT-PCR that may be readily adapted to any target gene. By judiciously choosing fluorescent primers with non-overlapping fluorochromes, we have shown that our technique is readily adapted to multiplex IS-RT-PCR, enabling the simultaneous localization of more than one gene within a complex tissue or heterogeneous cell population. A 6-carboxy-2′,4,4′,5′,7,7′-hexachlorofluorescein (6-HEX)-labelled primer and a tetrachloro-6-carboxy-fluorescein (TET)-labelled primer were designed for two marker genes associated with programmed cell death in tracheary elements (TEs): an endonuclease (Zen1) and a cysteine protease (ZcP4), respectively. An additional Cyan5 (Cy5)-labelled primer was used to monitor 18SrRNA expression. As expected, the 18S signal was constitutively expressed throughout epicotyls sections and living cells in xylogenic in vitro cultures, whereas Zen1 and ZcP4 were co-localized in forming TEs both in planta and in vitro. Analogous to clustering analysis of gene expression using microarrays to elucidate common metabolic pathways and developmental processes, this novel technique is perfectly adapted to gaining a better understanding of gene function via the coordinated expression of genes in specific cell types of complex tissues and cell populations.},
	language = {en},
	number = {6},
	urldate = {2021-06-15},
	journal = {The Plant Journal},
	author = {Pesquet, Edouard and Barbier, Odile and Ranocha, Philippe and Jauneau, Alain and Goffner, Deborah},
	year = {2004},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2004.02170.x},
	keywords = {Zinnia elegans, fluorescent spectral confocal microscopy, in situ RT-PCR, tracheary elements, xylogenesis},
	pages = {947--959},
}

With the number of functional genomic approaches in plant biology increasing daily, the demand for rapid and reliable RNA localization techniques for gene characterization is being felt. We present herein a novel, liquid phase in situ RT-PCR (IS-RT-PCR) protocol using a combination of gene-specific fluorescent primers and spectral confocal microscopy to localize target RNA in epicotyl sections and xylogenic suspension cultures of Zinnia elegans. Potential sources of artefacts from fixation to gene detection were systematically eliminated using both fluorescent primers and nucleotides for 18S rRNA gene detection, resulting in a set of optimal parameters for IS-RT-PCR that may be readily adapted to any target gene. By judiciously choosing fluorescent primers with non-overlapping fluorochromes, we have shown that our technique is readily adapted to multiplex IS-RT-PCR, enabling the simultaneous localization of more than one gene within a complex tissue or heterogeneous cell population. A 6-carboxy-2′,4,4′,5′,7,7′-hexachlorofluorescein (6-HEX)-labelled primer and a tetrachloro-6-carboxy-fluorescein (TET)-labelled primer were designed for two marker genes associated with programmed cell death in tracheary elements (TEs): an endonuclease (Zen1) and a cysteine protease (ZcP4), respectively. An additional Cyan5 (Cy5)-labelled primer was used to monitor 18SrRNA expression. As expected, the 18S signal was constitutively expressed throughout epicotyls sections and living cells in xylogenic in vitro cultures, whereas Zen1 and ZcP4 were co-localized in forming TEs both in planta and in vitro. Analogous to clustering analysis of gene expression using microarrays to elucidate common metabolic pathways and developmental processes, this novel technique is perfectly adapted to gaining a better understanding of gene function via the coordinated expression of genes in specific cell types of complex tissues and cell populations.

@article{egertsdotter_gene_2004,
	title = {Gene {Expression} during {Formation} of {Earlywood} and {Latewood} in {Loblolly} {Pine}: {Expression} {Profiles} of 350 {Genes}},
	volume = {6},
	issn = {1438-8677},
	shorttitle = {Gene {Expression} during {Formation} of {Earlywood} and {Latewood} in {Loblolly} {Pine}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1055/s-2004-830383},
	doi = {10/cndbxc},
	abstract = {Abstract: The natural variability of wood formation in trees affords opportunities to correlate transcript profiles with the resulting wood properties. We have used cDNA microarrays to study transcript abundance in developing secondary xylem of loblolly pine (Pinus taeda) over a growing season. The cDNAs were selected from a collection of 75 000 ESTs that have been sequenced and annotated (http:web.ahc.umn.edubiodatansfpine). Cell wall thickness and climatic data were related to earlywood and latewood formation at different time points during the growing season. Seventy-one ESTs showed preferential expression in earlywood or latewood, including 23 genes with no significant similarity to genes in GenBank. Seven genes involved in lignin synthesis were preferentially expressed in latewood. The studies have provided initial insights into the variation of expression patterns of some of the genes related to the wood formation process.},
	language = {en},
	number = {6},
	urldate = {2021-06-15},
	journal = {Plant Biology},
	author = {Egertsdotter, U. and Zyl, L. M. van and MacKay, J. and Peter, G. and Kirst, M. and Clark, C. and Whetten, R. and Sederoff, R.},
	year = {2004},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1055/s-2004-830383},
	keywords = {Microarray analysis, Pinus taeda, earlywood, latewood, transcript abundance},
	pages = {654--663},
}

Abstract: The natural variability of wood formation in trees affords opportunities to correlate transcript profiles with the resulting wood properties. We have used cDNA microarrays to study transcript abundance in developing secondary xylem of loblolly pine (Pinus taeda) over a growing season. The cDNAs were selected from a collection of 75 000 ESTs that have been sequenced and annotated (http:web.ahc.umn.edubiodatansfpine). Cell wall thickness and climatic data were related to earlywood and latewood formation at different time points during the growing season. Seventy-one ESTs showed preferential expression in earlywood or latewood, including 23 genes with no significant similarity to genes in GenBank. Seven genes involved in lignin synthesis were preferentially expressed in latewood. The studies have provided initial insights into the variation of expression patterns of some of the genes related to the wood formation process.

@article{wu_geographic_2004,
	title = {Geographic pattern of local optimality in natural populations of lodgepole pine},
	volume = {194},
	issn = {0378-1127},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112704001380},
	doi = {10/dt45ng},
	abstract = {Adaptive optimality of local populations is central to evolutionary biology. It also provides a genetic framework for planning gene conservation. We examined local optimality using 20-year height growth as an indicator of population fitness. The height growth data were obtained from a network of 57 long-term field trials in interior British Columbia involving a range-wide samples of 142 lodgepole pine (Pinus contorta Doug) populations. Local optimality was defined statistically and tested, and its geographic patterns were examined in both multi-dimensional mode and component dimensions along latitude, longitude and elevation. Fitness values of local and optimal populations were derived by fitting population variation to response functions for individual sites. Local optimality was an interval estimate, i.e. within the 95\% confidence limit of the projected fitness value of the optimal populations. Both biological and physical distances between local and optimal population were used to examine geographic pattern of local optimality. Study leads to following key results: (1) local optimality prevails at majority of sites; (2) populations at northeast bordering the northern Rocky Mountain Trench are most local optimal, whereas non-local optimality most evident along the eastern foothills of the Coastal Mountains in the coast-interior transition climate zone and the high mountains in the southern interior; (3) there is a geographic cline oriented from southwest to northeast, but with a steep west-east incline; and (4) along component dimensions, a steep longitudinal cline, i.e. the farther the west, the lesser the local optimality, and an elevational cline, i.e. the higher the elevation, the lesser the local optimality. Based on the ecological and life-history characteristics of the species and the climate in interior British Columbia, we propose that a selection gradient coupled with directional gene flow was the process influencing the formation of the observed geographic pattern. The selection gradient parallels the general climate pattern from continental northeast to sub-continental southwest. The gene flow brought the migration of undesirable genes from the coastal subspecies contorta to interior populations of the subspecies latifolia, which further diminished the effectiveness of natural selection. Practical applications through seed transfer in reforestation and genetic resources management are discussed.},
	language = {en},
	number = {1},
	urldate = {2021-06-15},
	journal = {Forest Ecology and Management},
	author = {Wu, Harry X. and Ying, Cheng C.},
	month = jun,
	year = {2004},
	keywords = {Adaptation, Gene flow, Local optimality, Lodgepole pine, Natural selection},
	pages = {177--198},
}

Adaptive optimality of local populations is central to evolutionary biology. It also provides a genetic framework for planning gene conservation. We examined local optimality using 20-year height growth as an indicator of population fitness. The height growth data were obtained from a network of 57 long-term field trials in interior British Columbia involving a range-wide samples of 142 lodgepole pine (Pinus contorta Doug) populations. Local optimality was defined statistically and tested, and its geographic patterns were examined in both multi-dimensional mode and component dimensions along latitude, longitude and elevation. Fitness values of local and optimal populations were derived by fitting population variation to response functions for individual sites. Local optimality was an interval estimate, i.e. within the 95% confidence limit of the projected fitness value of the optimal populations. Both biological and physical distances between local and optimal population were used to examine geographic pattern of local optimality. Study leads to following key results: (1) local optimality prevails at majority of sites; (2) populations at northeast bordering the northern Rocky Mountain Trench are most local optimal, whereas non-local optimality most evident along the eastern foothills of the Coastal Mountains in the coast-interior transition climate zone and the high mountains in the southern interior; (3) there is a geographic cline oriented from southwest to northeast, but with a steep west-east incline; and (4) along component dimensions, a steep longitudinal cline, i.e. the farther the west, the lesser the local optimality, and an elevational cline, i.e. the higher the elevation, the lesser the local optimality. Based on the ecological and life-history characteristics of the species and the climate in interior British Columbia, we propose that a selection gradient coupled with directional gene flow was the process influencing the formation of the observed geographic pattern. The selection gradient parallels the general climate pattern from continental northeast to sub-continental southwest. The gene flow brought the migration of undesirable genes from the coastal subspecies contorta to interior populations of the subspecies latifolia, which further diminished the effectiveness of natural selection. Practical applications through seed transfer in reforestation and genetic resources management are discussed.

@article{wu_general_2004,
	title = {General and specific combining ability from partial diallels of radiata pine: implications for utility of {SCA} in breeding and deployment populations},
	volume = {108},
	issn = {1432-2242},
	shorttitle = {General and specific combining ability from partial diallels of radiata pine},
	url = {https://doi.org/10.1007/s00122-004-1598-8},
	doi = {10/d84w8d},
	abstract = {Variances for general combining ability (GCA) and specific combining ability (SCA) and the relationship between mid-parental GCA and SCA effects were estimated for tree diameter (DBH) from a series of 20 sets of 6×6 half-diallel mating experiments in radiata pine, planted at ten sites across Australia. Significant SCA variance for DBH was almost equal to GCA variance for the combined analysis of all ten sites. The importance of SCA variance varied among sites, from non-significant to SCA variance accounting for all genetic variation among full-sib families. Significant SCA × site interaction was detected among the ten sites. A significant and positive correlation between mid-parental breeding values and best linear unbiased predictions of the SCA effects was observed. About a quarter of extra genetic gain is achievable through use of SCA variance if selection is based on the best breeding values. To fully exploit genetic gain from SCA variance in a deployment population, positive assortative matings are required for the best parents. It is estimated that the additional deployment gain of 46.0\% for ten sites combined, or 52.9\% for four sites combined that had significant GCA as well as SCA effects, were achievable relative to gain from GCA only, if all SCA variance within this breeding population was exploited. For a breeding population, selection for breeding values may be sufficient due to positive correlations between breeding values and SCA values. For a deployment population to capture more SCA genetic gain, it is preferable to make more pair-wise mating for parents with higher breeding values.},
	language = {en},
	number = {8},
	urldate = {2021-06-15},
	journal = {Theoretical and Applied Genetics},
	author = {Wu, Harry X. and Matheson, A. Colin},
	month = may,
	year = {2004},
	pages = {1503--1512},
}

Variances for general combining ability (GCA) and specific combining ability (SCA) and the relationship between mid-parental GCA and SCA effects were estimated for tree diameter (DBH) from a series of 20 sets of 6×6 half-diallel mating experiments in radiata pine, planted at ten sites across Australia. Significant SCA variance for DBH was almost equal to GCA variance for the combined analysis of all ten sites. The importance of SCA variance varied among sites, from non-significant to SCA variance accounting for all genetic variation among full-sib families. Significant SCA × site interaction was detected among the ten sites. A significant and positive correlation between mid-parental breeding values and best linear unbiased predictions of the SCA effects was observed. About a quarter of extra genetic gain is achievable through use of SCA variance if selection is based on the best breeding values. To fully exploit genetic gain from SCA variance in a deployment population, positive assortative matings are required for the best parents. It is estimated that the additional deployment gain of 46.0% for ten sites combined, or 52.9% for four sites combined that had significant GCA as well as SCA effects, were achievable relative to gain from GCA only, if all SCA variance within this breeding population was exploited. For a breeding population, selection for breeding values may be sufficient due to positive correlations between breeding values and SCA values. For a deployment population to capture more SCA genetic gain, it is preferable to make more pair-wise mating for parents with higher breeding values.

@article{robert_mechanism_2004,
	title = {The mechanism and regulation of cellulose synthesis in primary walls: lessons from cellulose-deficient {Arabidopsis} mutants},
	volume = {11},
	issn = {1572-882X},
	shorttitle = {The mechanism and regulation of cellulose synthesis in primary walls},
	url = {https://doi.org/10.1023/B:CELL.0000046415.45774.80},
	doi = {10/ftnsm7},
	abstract = {Cellulose-deficient Arabidopsis mutants were identified using FT-IR microspectroscopy. The study of these mutants not only led to the identification of actors in cellulose synthesis, but also provided insights in the organization of the hexameric terminal complex from CESA mutants and identified unsuspected accessory proteins with so far unknown roles in the synthesis and/or assembly of cellulose microfibrils. Finally, mutant analysis established a role for protein glycosylation in cellulose synthesis and provided new perspectives on the developmental regulation of cell wall synthesis and the role that cellulose synthesis plays in the control of cell elongation.},
	language = {en},
	number = {3},
	urldate = {2021-06-15},
	journal = {Cellulose},
	author = {Robert, Stéphanie and Mouille, Grégory and Höfte, Herman},
	month = sep,
	year = {2004},
	pages = {351--364},
}

Cellulose-deficient Arabidopsis mutants were identified using FT-IR microspectroscopy. The study of these mutants not only led to the identification of actors in cellulose synthesis, but also provided insights in the organization of the hexameric terminal complex from CESA mutants and identified unsuspected accessory proteins with so far unknown roles in the synthesis and/or assembly of cellulose microfibrils. Finally, mutant analysis established a role for protein glycosylation in cellulose synthesis and provided new perspectives on the developmental regulation of cell wall synthesis and the role that cellulose synthesis plays in the control of cell elongation.