Publications 2002

@article{robblee_mn_2002,
	title = {The {Mn} {Cluster} in the {S0} {State} of the {Oxygen}-{Evolving} {Complex} of {Photosystem} {II} {Studied} by {EXAFS} {Spectroscopy}:  {Are} {There} {Three} {Di}-μ-oxo-bridged {Mn2} {Moieties} in the {Tetranuclear} {Mn} {Complex}?},
	volume = {124},
	issn = {0002-7863},
	shorttitle = {The {Mn} {Cluster} in the {S0} {State} of the {Oxygen}-{Evolving} {Complex} of {Photosystem} {II} {Studied} by {EXAFS} {Spectroscopy}},
	url = {https://doi.org/10.1021/ja011621a},
	doi = {10.1021/ja011621a},
	abstract = {A key component required for an understanding of the mechanism of the evolution of molecular oxygen by the photosynthetic oxygen-evolving complex (OEC) in photosystem II (PS II) is the knowledge of the structures of the Mn cluster in the OEC in each of its intermediate redox states, or S-states. In this paper, we report the first detailed structural characterization using Mn extended X-ray absorption fine structure (EXAFS) spectroscopy of the Mn cluster of the OEC in the S0 state, which exists immediately after the release of molecular oxygen. On the basis of the EXAFS spectroscopic results, the most likely interpretation is that one of the di-μ-oxo-bridged Mn−Mn moieties in the OEC has increased in distance from 2.7 Å in the dark-stable S1 state to 2.85 Å in the S0 state. Furthermore, curve fitting of the distance heterogeneity present in the EXAFS data from the S0 state leads to the intriguing possibility that three di-μ-oxo-bridged Mn−Mn moieties may exist in the OEC instead of the two di-μ-oxo-bridged Mn−Mn moieties that are widely used in proposed structural models for the OEC. This possibility is developed using novel structural models for the Mn cluster in the OEC which are consistent with the structural information available from EXAFS and the recent X-ray crystallographic structure of PS II at 3.8 Å resolution.},
	number = {25},
	urldate = {2024-11-29},
	journal = {Journal of the American Chemical Society},
	author = {Robblee, John H. and Messinger, Johannes and Cinco, Roehl M. and McFarlane, Karen L. and Fernandez, Carmen and Pizarro, Shelly A. and Sauer, Kenneth and Yachandra, Vittal K.},
	month = jun,
	year = {2002},
	note = {Publisher: American Chemical Society},
	pages = {7459--7471},
}

A key component required for an understanding of the mechanism of the evolution of molecular oxygen by the photosynthetic oxygen-evolving complex (OEC) in photosystem II (PS II) is the knowledge of the structures of the Mn cluster in the OEC in each of its intermediate redox states, or S-states. In this paper, we report the first detailed structural characterization using Mn extended X-ray absorption fine structure (EXAFS) spectroscopy of the Mn cluster of the OEC in the S0 state, which exists immediately after the release of molecular oxygen. On the basis of the EXAFS spectroscopic results, the most likely interpretation is that one of the di-μ-oxo-bridged Mn−Mn moieties in the OEC has increased in distance from 2.7 Å in the dark-stable S1 state to 2.85 Å in the S0 state. Furthermore, curve fitting of the distance heterogeneity present in the EXAFS data from the S0 state leads to the intriguing possibility that three di-μ-oxo-bridged Mn−Mn moieties may exist in the OEC instead of the two di-μ-oxo-bridged Mn−Mn moieties that are widely used in proposed structural models for the OEC. This possibility is developed using novel structural models for the Mn cluster in the OEC which are consistent with the structural information available from EXAFS and the recent X-ray crystallographic structure of PS II at 3.8 Å resolution.

@incollection{asins_molecular_2002,
	address = {Dordrecht},
	title = {Molecular {Markers} for the {Genetic} {Analysis} of {Apomixis}},
	isbn = {978-94-017-2356-5},
	url = {https://doi.org/10.1007/978-94-017-2356-5_9},
	abstract = {Most flowering plants reproduce sexually through seeds. A zygote is formed by fusion of reduced female and male gametes (amphimixis) and develops into an embryo. However, some angiosperms commonly reproduce through seeds having an embryo, which is formed without reduction of the chromosome number nor fertilisation, by a process called apomixis (Nogler, 1984).},
	language = {en},
	urldate = {2024-10-16},
	booktitle = {Molecular {Techniques} in {Crop} {Improvement}},
	publisher = {Springer Netherlands},
	author = {Asins, M. J. and Garcia, M. R. and Ruiz, C. and Carbonell, E. A.},
	editor = {Jain, S. Mohan and Brar, D. S. and Ahloowalia, B. S.},
	year = {2002},
	doi = {10.1007/978-94-017-2356-5_9},
	pages = {265--281},
}

Most flowering plants reproduce sexually through seeds. A zygote is formed by fusion of reduced female and male gametes (amphimixis) and develops into an embryo. However, some angiosperms commonly reproduce through seeds having an embryo, which is formed without reduction of the chromosome number nor fertilisation, by a process called apomixis (Nogler, 1984).

@article{funamoto_somatic_2002,
	title = {Somatic chromosomes of three {Parnassia} species({Saxifragaceae}) in {Xinjiang}, {China}},
	volume = {6},
	url = {https://cir.nii.ac.jp/crid/1520573331025517696},
	abstract = {Somatic chromosomes of three Parnassia species collected in Xinjiang, China were observed. They had commonly the simple chromocenter type of resting chromosomes and the proximal type of mitotic prophase chromosomes. The chromosome numbers of 2n=36 and 2n=36+1～8 supernumerary chromosomes for P. bifolia were reported here for the first time. The chromosome number of 2n=18 for P. laxmannii and P. palustris var. palustris was verified the previous reports. Three Parnassia species had similar small size chromosomes and the basic chromosome number of x=9. The karyotype of Parnassia laxmannii consisted of 18 mediancentromeric chromosomes, while that of the other two species consisted commonly of median- and submedian-centromeric chromosomes.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Chromosome Science},
	author = {Funamoto, Tsuneo and Kondo, Katsuhiko and Hong, De-yuan and Ge, Song and Mao, Jian-Feng and Ogura, Hisakazu},
	year = {2002},
	note = {Publisher: The Society of Chromosome Research},
	pages = {27--34},
}

Somatic chromosomes of three Parnassia species collected in Xinjiang, China were observed. They had commonly the simple chromocenter type of resting chromosomes and the proximal type of mitotic prophase chromosomes. The chromosome numbers of 2n=36 and 2n=36+1～8 supernumerary chromosomes for P. bifolia were reported here for the first time. The chromosome number of 2n=18 for P. laxmannii and P. palustris var. palustris was verified the previous reports. Three Parnassia species had similar small size chromosomes and the basic chromosome number of x=9. The karyotype of Parnassia laxmannii consisted of 18 mediancentromeric chromosomes, while that of the other two species consisted commonly of median- and submedian-centromeric chromosomes.

@article{villarejo_photosystem_2002,
	title = {A photosystem {II}-associated carbonic anhydrase regulates the efficiency of photosynthetic oxygen evolution},
	volume = {21},
	issn = {0261-4189},
	url = {https://www.embopress.org/doi/full/10.1093/emboj/21.8.1930},
	doi = {10/c58pd8},
	abstract = {We show for the first time that Cah3, a carbonic anhydrase associated with the photosystem II (PSII) donor side in Chlamydomonas reinhardtii, regulates the water oxidation reaction. The mutant cia3, lacking Cah3 activity, has an impaired water splitting capacity, as shown for intact cells, thylakoids and PSII particles. To compensate this impairment, the mutant overproduces PSII reaction centres (1.6 times more than wild type). We present compelling evidence that the mutant has an average of two manganese atoms per PSII reaction centre. When bicarbonate is added to mutant thylakoids or PSII particles, the O2 evolution rates exceed those of the wild type by up to 50\%. The donor side of PSII in the mutant also exhibits a much higher sensitivity to overexcitation than that of the wild type. We therefore conclude that Cah3 activity is necessary to stabilize the manganese cluster and maintain the water-oxidizing complex in a functionally active state. The possibility that two manganese atoms are enough for water oxidation if bicarbonate ions are available is discussed.},
	number = {8},
	urldate = {2021-10-19},
	journal = {The EMBO Journal},
	author = {Villarejo, Arsenio and Shutova, Tatiana and Moskvin, Oleg and Forssén, Magnus and Klimov, Vyacheslav V. and Samuelsson, Göran},
	month = apr,
	year = {2002},
	note = {Publisher: John Wiley \& Sons, Ltd},
	keywords = {Chlamydomonas, carbonic anhydrase, manganese cluster, photosystem II, water oxidation complex},
	pages = {1930--1938},
}

We show for the first time that Cah3, a carbonic anhydrase associated with the photosystem II (PSII) donor side in Chlamydomonas reinhardtii, regulates the water oxidation reaction. The mutant cia3, lacking Cah3 activity, has an impaired water splitting capacity, as shown for intact cells, thylakoids and PSII particles. To compensate this impairment, the mutant overproduces PSII reaction centres (1.6 times more than wild type). We present compelling evidence that the mutant has an average of two manganese atoms per PSII reaction centre. When bicarbonate is added to mutant thylakoids or PSII particles, the O2 evolution rates exceed those of the wild type by up to 50%. The donor side of PSII in the mutant also exhibits a much higher sensitivity to overexcitation than that of the wild type. We therefore conclude that Cah3 activity is necessary to stabilize the manganese cluster and maintain the water-oxidizing complex in a functionally active state. The possibility that two manganese atoms are enough for water oxidation if bicarbonate ions are available is discussed.

@article{persson_identification_2002,
	title = {Identification of a novel calreticulin isoform ({Crt2}) in human and mouse},
	volume = {297},
	issn = {0378-1119},
	url = {https://www.sciencedirect.com/science/article/pii/S0378111902008806},
	doi = {10/dzp6kq},
	abstract = {Calreticulin is a Ca2+-binding chaperone localized mainly in the endoplasmic/sarcoplasmic reticulum in all higher organisms. To date, only one calreticulin isoform has been identified in human and mouse. Here we report a novel calreticulin isoform (Crt2) in human and mouse, with 53 (human) and 49\% (mouse) identity to the previously identified calreticulin in respective species. The gene encoding the novel human calreticulin isoform spans 17 kb of genomic DNA and is expressed in testis, showing a similar expression as the chaperone calmegin. Phylogenetic analysis shows that two or more calreticulin (crt) genes are present both in plants and in mammals. The duplication of the crt gene in human and mouse suggests functional diversity, and variations in expression patterns among calreticulins. Two novel calreticulin (Crt2) isoforms, with high homology to the human and mouse calreticulin isoform (Crt2), were also identified in pig and rat via expressed sequence tags.},
	language = {en},
	number = {1},
	urldate = {2021-10-19},
	journal = {Gene},
	author = {Persson, Staffan and Rosenquist, Magnus and Sommarin, Marianne},
	month = sep,
	year = {2002},
	keywords = {Calcium, Calmegin, Calnexin, Chaperone, Endoplasmic reticulum},
	pages = {151--158},
}

Calreticulin is a Ca2+-binding chaperone localized mainly in the endoplasmic/sarcoplasmic reticulum in all higher organisms. To date, only one calreticulin isoform has been identified in human and mouse. Here we report a novel calreticulin isoform (Crt2) in human and mouse, with 53 (human) and 49% (mouse) identity to the previously identified calreticulin in respective species. The gene encoding the novel human calreticulin isoform spans 17 kb of genomic DNA and is expressed in testis, showing a similar expression as the chaperone calmegin. Phylogenetic analysis shows that two or more calreticulin (crt) genes are present both in plants and in mammals. The duplication of the crt gene in human and mouse suggests functional diversity, and variations in expression patterns among calreticulins. Two novel calreticulin (Crt2) isoforms, with high homology to the human and mouse calreticulin isoform (Crt2), were also identified in pig and rat via expressed sequence tags.

@article{witzell_anisogramma_2002,
	title = {Anisogramma virgultorum on saplings of {Betula} pendula and {Betula} pubescens in a district of northern {Sweden}},
	volume = {32},
	issn = {1439-0329},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1439-0329.2002.00284.x},
	doi = {10/cwkspv},
	abstract = {During the autumn of 1999, the occurrence of the ascomycete Anisogramma virgultorum on saplings of Betula pubescens and Betula pendula was studied in two stands of B. pubescens, two stands of B. pendula and two mixed (B. pubescens and Pinus sylvestris) stands (age approximately 10 years, mean height 2–4 m, d.b.h. 10–20 mm) in a district in the vicinity of Umeå, northern Sweden. Stem and branch cankers associated with A. virgultorum were found on 54.8\% of the investigated saplings, without significant difference between B. pendula and B. pubescens. Cankers were observed on 16.0\% of stems and on branches of 54.2\% of the saplings. Stem cankers appeared on the current year's shoot, as well as at the base of the trees. The mean diameter of the damaged saplings was significantly greater than the mean diameter of undamaged saplings. All samples of cankers with stromata examined in the laboratory showed perithecia with asci.},
	language = {en},
	number = {4-5},
	urldate = {2021-10-19},
	journal = {Forest Pathology},
	author = {Witzell, J. and Karlsson, A.},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1439-0329.2002.00284.x},
	pages = {207--212},
}

During the autumn of 1999, the occurrence of the ascomycete Anisogramma virgultorum on saplings of Betula pubescens and Betula pendula was studied in two stands of B. pubescens, two stands of B. pendula and two mixed (B. pubescens and Pinus sylvestris) stands (age approximately 10 years, mean height 2–4 m, d.b.h. 10–20 mm) in a district in the vicinity of Umeå, northern Sweden. Stem and branch cankers associated with A. virgultorum were found on 54.8% of the investigated saplings, without significant difference between B. pendula and B. pubescens. Cankers were observed on 16.0% of stems and on branches of 54.2% of the saplings. Stem cankers appeared on the current year's shoot, as well as at the base of the trees. The mean diameter of the damaged saplings was significantly greater than the mean diameter of undamaged saplings. All samples of cankers with stromata examined in the laboratory showed perithecia with asci.

@article{thidholm_novel_2002,
	title = {Novel approach reveals localisation and assembly pathway of the {PsbS} and {PsbW} proteins into the photosystem {II} dimer},
	volume = {513},
	copyright = {FEBS Letters 513 (2002) 1873-3468 © 2015 Federation of European Biochemical Societies},
	issn = {1873-3468},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1016/S0014-5793%2802%2902314-1},
	doi = {10/c8cg4v},
	abstract = {A blue-native gel electrophoresis system was combined with an in organello import assay to specifically analyse the location and assembly of two nuclear-encoded photosystem II (PSII) subunits. With this method we were able to show that initially the low molecular mass PsbW protein is not associated with the monomeric form of PSII. Instead a proportion of newly imported PsbW is directly assembled in dimeric PSII supercomplexes with very fast kinetics; its negatively charged N-terminal domain is essential for this process. The chlorophyll-binding PsbS protein, which is involved in energy dissipation, is first detected in the monomeric PSII subcomplexes, and only at later time points in the dimeric form of PSII. It seems to be bound tighter to the PSII core complex than to light harvesting complex II. These data point to radically different assembly pathways for different PSII subunits.},
	language = {en},
	number = {2-3},
	urldate = {2021-10-19},
	journal = {FEBS Letters},
	author = {Thidholm, Ellinor and Lindström, Viktoria and Tissier, Christophe and Robinson, Colin and P. Schröder, Wolfgang and Funk, Christiane},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1016/S0014-5793\%2802\%2902314-1},
	keywords = {5-bisphosphate carboxylase/oxygenase, Assembly, BN-PAGE, Blue-native polyacrylamide gel electrophoresis, Import, LHCII, PSI, PSII, PVDF, Photosystem II dimer, PsbS, PsbW, Rubisco, SDS, blue-native polyacrylamide gel electrophoresis, light harvesting complex II, n-dodecyl-β-D-maltoside, pPsbS, pPsbW, photosystem I and photosystem II, polyvinylidene difluoride, precursors of PsbW and PsbS, respectively, ribulose-1, sodium dodecyl sulphate, β-DM},
	pages = {217--222},
}

A blue-native gel electrophoresis system was combined with an in organello import assay to specifically analyse the location and assembly of two nuclear-encoded photosystem II (PSII) subunits. With this method we were able to show that initially the low molecular mass PsbW protein is not associated with the monomeric form of PSII. Instead a proportion of newly imported PsbW is directly assembled in dimeric PSII supercomplexes with very fast kinetics; its negatively charged N-terminal domain is essential for this process. The chlorophyll-binding PsbS protein, which is involved in energy dissipation, is first detected in the monomeric PSII subcomplexes, and only at later time points in the dimeric form of PSII. It seems to be bound tighter to the PSII core complex than to light harvesting complex II. These data point to radically different assembly pathways for different PSII subunits.

@article{ingvarsson_metapopulation_2002,
	title = {A {Metapopulation} {Perspective} on {Genetic} {Diversity} and {Differentiation} in {Partially} {Self}-{Fertilizing} {Plants}},
	volume = {56},
	issn = {1558-5646},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.0014-3820.2002.tb00162.x},
	doi = {10/ftnfgf},
	abstract = {Abstract.— Partial self-fertilization is common in higher plants. Mating system variation is known to have important consequences for how genetic variation is distributed within and among populations. Selfing is known to reduce effective population size, and inbreeding species are therefore expected to have lower levels of genetic variation than comparable out crossing taxa. However, several recent empirical studies have shown that reductions in genetic diversity within populations of inbreeding species are far greater than the expected reductions based on the reduced effective population size. Two different processes have been argued to cause these patterns, selective sweeps (or hitchhiking) and background selection. Both are expected to be most effective in reducing genetic variation in regions of low recombination rates. Selfing is known to reduce the effective recombination rate, and inbreeding taxa are thus thought to be particularly vulnerable to the effects of hitchhiking or background selection. Here I propose a third explanation for the lower-than-expected levels of genetic diversity within populations of selfing species; recurrent extinctions and recolonizations of local populations, also known as metapopulation dynamics. I show that selfing in a metapopulation setting can result in large reductions in genetic diversity within populations, far greater than expected based the lower effective population size inbreeding species is expected to have. The reason for this depends on an interaction between selfing and pollen migration.},
	language = {en},
	number = {12},
	urldate = {2021-10-19},
	journal = {Evolution},
	author = {Ingvarsson, Pärk.},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.0014-3820.2002.tb00162.x},
	keywords = {Colonization, extinction, genetic diversity, metapopulation, selfing},
	pages = {2368--2373},
}

Abstract.— Partial self-fertilization is common in higher plants. Mating system variation is known to have important consequences for how genetic variation is distributed within and among populations. Selfing is known to reduce effective population size, and inbreeding species are therefore expected to have lower levels of genetic variation than comparable out crossing taxa. However, several recent empirical studies have shown that reductions in genetic diversity within populations of inbreeding species are far greater than the expected reductions based on the reduced effective population size. Two different processes have been argued to cause these patterns, selective sweeps (or hitchhiking) and background selection. Both are expected to be most effective in reducing genetic variation in regions of low recombination rates. Selfing is known to reduce the effective recombination rate, and inbreeding taxa are thus thought to be particularly vulnerable to the effects of hitchhiking or background selection. Here I propose a third explanation for the lower-than-expected levels of genetic diversity within populations of selfing species; recurrent extinctions and recolonizations of local populations, also known as metapopulation dynamics. I show that selfing in a metapopulation setting can result in large reductions in genetic diversity within populations, far greater than expected based the lower effective population size inbreeding species is expected to have. The reason for this depends on an interaction between selfing and pollen migration.

@article{selstam_effects_2002,
	title = {The effects of low {pH} on the properties of protochlorophyllide oxidoreductase and the organization of prolamellar bodies of maize ({Zea} mays)},
	volume = {269},
	issn = {1432-1033},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1432-1033.2002.02897.x},
	doi = {10/c4kmx9},
	abstract = {Prolamellar bodies (PLB) contain two photochemically active forms of the enzyme protochlorophyllide oxidoreductase POR-PChlide640 and POR-PChlide650 (the spectral forms of POR-Chlide complexes with absorption maxima at the indicated wavelengths). Resuspension of maize PLB in media with a pH below 6.8 leads to a rapid conversion of POR-PChlide650 to POR-PChlide640 and a dramatic re-organization of the PLB membrane system. In the absence of excess NADPH, the absorption maximum of the POR complex undergoes a further shift to about 635 nm. This latter shift is reversible on the re-addition of NADPH with a half-saturation value of about 0.25 mm NADPH for POR-PChlide640 reformation. The disappearance of POR-PChlide650 and the reorganization of the PLB, however, are irreversible. Restoration of low-pH treated PLB to pH 7.5 leads to a further breakdown down of the PLB membrane and no reformation of POR-PChlide650. Related spectral changes are seen in PLB aged at room temperature at pH 7.5 in NADPH-free assay medium. The reformation of POR-PChlide650 in this system is readily reversible on re-addition of NADPH with a half-saturation value about 1.0 µm. Comparison of the two sets of changes suggest a close link between the stability of the POR-PChlide650, membrane organization and NADPH binding. The low-pH driven spectral changes seen in maize PLB are shown to be accelerated by adenosine AMP, ADP and ATP. The significance of this is discussed in terms of current suggestions of the possible involvement of phosphorylation (or adenylation) in changes in the aggregational state of the POR complex.},
	language = {en},
	number = {9},
	urldate = {2021-10-19},
	journal = {European Journal of Biochemistry},
	author = {Selstam, Eva and Schelin, Jenny and Brain, Tony and Williams, W. Patrick},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1432-1033.2002.02897.x},
	keywords = {chlorophyllide, oxidoreductase, prolamellar body, protochlorophyllide, protochlorophyllide oxidoreductase},
	pages = {2336--2346},
}

Prolamellar bodies (PLB) contain two photochemically active forms of the enzyme protochlorophyllide oxidoreductase POR-PChlide640 and POR-PChlide650 (the spectral forms of POR-Chlide complexes with absorption maxima at the indicated wavelengths). Resuspension of maize PLB in media with a pH below 6.8 leads to a rapid conversion of POR-PChlide650 to POR-PChlide640 and a dramatic re-organization of the PLB membrane system. In the absence of excess NADPH, the absorption maximum of the POR complex undergoes a further shift to about 635 nm. This latter shift is reversible on the re-addition of NADPH with a half-saturation value of about 0.25 mm NADPH for POR-PChlide640 reformation. The disappearance of POR-PChlide650 and the reorganization of the PLB, however, are irreversible. Restoration of low-pH treated PLB to pH 7.5 leads to a further breakdown down of the PLB membrane and no reformation of POR-PChlide650. Related spectral changes are seen in PLB aged at room temperature at pH 7.5 in NADPH-free assay medium. The reformation of POR-PChlide650 in this system is readily reversible on re-addition of NADPH with a half-saturation value about 1.0 µm. Comparison of the two sets of changes suggest a close link between the stability of the POR-PChlide650, membrane organization and NADPH binding. The low-pH driven spectral changes seen in maize PLB are shown to be accelerated by adenosine AMP, ADP and ATP. The significance of this is discussed in terms of current suggestions of the possible involvement of phosphorylation (or adenylation) in changes in the aggregational state of the POR complex.

@article{ohlund_low_2002,
	title = {Low {Nitrogen} {Losses} with a {New} {Source} of {Nitrogen} for {Cultivation} of {Conifer} {Seedlings}},
	volume = {36},
	issn = {0013-936X},
	url = {https://doi.org/10.1021/es025629b},
	doi = {10/c23fx2},
	abstract = {Losses of nitrogen (N) when cultivating plants may cause a number of adverse environmental effects. N losses from conifer nurseries, for instance, may have a considerable impact on the local environment, and studies indicate that the bulk of added N is not recovered in the cultivated plants. This study was conducted to obtain insight into the causes of the low recovery and to test an alternative N fertilizer. Hence, growth of the economically important Scots pine (Pinus sylvestris (L).) seedlings and the recovery of different forms of added nitrogen (N) were investigated in a greenhouse experiment. Containerized seedlings were grown in peat for one summer, with two different N fertilizers, one organic (arginine) and one inorganic (a commercial fertilizer (CF) containing a mixture of ammonium and nitrate) each at an N concentration of 3 mM. At the end of the growth period, some seedlings were labeled with solutions containing either U-[13C6], [15N4]-arginine, (15NH4)2SO4, or K15NO3 supplied to the growth substrate. Labeled seedlings were harvested 1 h, 5 days, and 19 days after tracer addition, and the recovery of each added nitrogen source in both the seedlings and the growth substrate was measured. The retention of the three N forms during discharge of solutions from the growth substrate, peat, was tested in a separate experiment. Arginine-fed seedlings grew better and had higher needle N concentrations than the CF-fed seedlings. Isotopic data showed that the arginine treatment gave significantly higher N recoveries (80\%) compared to the CF treatment (50\%). The low recovery of N in the CF treatment was largely due to very low recovery (30\%) of NO3- -N. The retention of the different N forms during discharge of solutions from the growth substrate was highest for arginine, somewhat lower for NH4+, and very low for NO3-. The high rate of seedling growth and the small nitrogen losses observed when using arginine suggest that this amino acid may be an efficient and environmentally favorable N source for cultivating conifer seedlings.},
	number = {22},
	urldate = {2021-10-19},
	journal = {Environmental Science \& Technology},
	author = {Öhlund, Jonas and Näsholm, Torgny},
	month = nov,
	year = {2002},
	note = {Publisher: American Chemical Society},
	pages = {4854--4859},
}

Losses of nitrogen (N) when cultivating plants may cause a number of adverse environmental effects. N losses from conifer nurseries, for instance, may have a considerable impact on the local environment, and studies indicate that the bulk of added N is not recovered in the cultivated plants. This study was conducted to obtain insight into the causes of the low recovery and to test an alternative N fertilizer. Hence, growth of the economically important Scots pine (Pinus sylvestris (L).) seedlings and the recovery of different forms of added nitrogen (N) were investigated in a greenhouse experiment. Containerized seedlings were grown in peat for one summer, with two different N fertilizers, one organic (arginine) and one inorganic (a commercial fertilizer (CF) containing a mixture of ammonium and nitrate) each at an N concentration of 3 mM. At the end of the growth period, some seedlings were labeled with solutions containing either U-[13C6], [15N4]-arginine, (15NH4)2SO4, or K15NO3 supplied to the growth substrate. Labeled seedlings were harvested 1 h, 5 days, and 19 days after tracer addition, and the recovery of each added nitrogen source in both the seedlings and the growth substrate was measured. The retention of the three N forms during discharge of solutions from the growth substrate, peat, was tested in a separate experiment. Arginine-fed seedlings grew better and had higher needle N concentrations than the CF-fed seedlings. Isotopic data showed that the arginine treatment gave significantly higher N recoveries (80%) compared to the CF treatment (50%). The low recovery of N in the CF treatment was largely due to very low recovery (30%) of NO3- -N. The retention of the different N forms during discharge of solutions from the growth substrate was highest for arginine, somewhat lower for NH4+, and very low for NO3-. The high rate of seedling growth and the small nitrogen losses observed when using arginine suggest that this amino acid may be an efficient and environmentally favorable N source for cultivating conifer seedlings.

@article{strengbom_parasitic_2002,
	title = {Parasitic fungus mediates change in nitrogen-exposed boreal forest vegetation},
	volume = {90},
	issn = {1365-2745},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.0022-0477.2001.00629.x},
	doi = {10/bgscwh},
	abstract = {1 Experimental additions of N to an old-growth boreal forest resulted in elevated levels of free amino acids in leaves of the dominant dwarf-shrub Vaccinium myrtillus and increased attack from a parasitic fungus, Valdensia heterodoxa. 2 Glutamine additions to the leaf surface of V. myrtillus increased disease incidence by an average of almost three times compared to controls and suggested a causal connection between amino acid availability and fungal infection. 3 Increased abundance of the grass Deschampsia flexuosa followed N addition but infection by the parasitic fungus, which causes premature leaf loss of its primary host V. myrtillus, explained four times as much of the variation in grass abundance as N did. 4 Nitrogen deposition can have marked effects on vegetation by affecting the interaction between dominant hosts and their natural enemies. A shift in abundance of dominating species occurred within 3 years of treatment, with nitrogen loads similar to those deposited over large areas in Europe and North America, suggesting that such effects may by important for the vegetation of large areas subjected to low levels of nitrogen input.},
	language = {en},
	number = {1},
	urldate = {2021-10-19},
	journal = {Journal of Ecology},
	author = {Strengbom, Joachim and Nordin, Annika and Näsholm, Torgny and Ericson, Lars},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.0022-0477.2001.00629.x},
	keywords = {Deschampsia flexuosa, Vaccinium myrtillus, Valdensia heterodoxa, free amino acids, natural enemies, nitrogen deposition},
	pages = {61--67},
}

1 Experimental additions of N to an old-growth boreal forest resulted in elevated levels of free amino acids in leaves of the dominant dwarf-shrub Vaccinium myrtillus and increased attack from a parasitic fungus, Valdensia heterodoxa. 2 Glutamine additions to the leaf surface of V. myrtillus increased disease incidence by an average of almost three times compared to controls and suggested a causal connection between amino acid availability and fungal infection. 3 Increased abundance of the grass Deschampsia flexuosa followed N addition but infection by the parasitic fungus, which causes premature leaf loss of its primary host V. myrtillus, explained four times as much of the variation in grass abundance as N did. 4 Nitrogen deposition can have marked effects on vegetation by affecting the interaction between dominant hosts and their natural enemies. A shift in abundance of dominating species occurred within 3 years of treatment, with nitrogen loads similar to those deposited over large areas in Europe and North America, suggesting that such effects may by important for the vegetation of large areas subjected to low levels of nitrogen input.

@article{tobena-santamaria_floozy_2002,
	title = {{FLOOZY} of petunia is a flavin mono-oxygenase-like protein required for the specification of leaf and flower architecture},
	volume = {16},
	issn = {0890-9369, 1549-5477},
	url = {http://genesdev.cshlp.org/content/16/6/753},
	doi = {10/d6fq3h},
	abstract = {The mechanisms that determine the relative positions of floral organs, and thereby their numbers, is a poorly understood aspect of flower development. We isolated a petunia mutant, floozy(fzy), in which the formation of floral organ primordia in the outermost three floral whorls and one of the two bracts at the base of the flower is blocked at an early stage. In addition, fzymutants fail to generate secondary veins in leaves and bracts and display a decreased apical dominance in the inflorescence. FZYencodes an enzyme with homology to flavin mono-oxygenases and appears to be the ortholog of YUCCA genes of Arabidopsis. FZY is expressed in young leafs and bracts and in developing flowers. In young floral meristems FZY is expressed in the center of the meristem dome and, later, expression becomes localized on the flanks of the initiating petal and stamen primordia and at several sites in maturing anthers and carpels. These findings indicate that FZY is involved in synthesizing a signaling compound that is required for floral organ initiation and specification of the vascularization pattern in leaves. Although fzy mutants contain normal auxin levels, ectopic expression of FZY results in excessive auxin accumulation, suggesting that the signaling compound is auxin.},
	language = {en},
	number = {6},
	urldate = {2021-10-19},
	journal = {Genes \& Development},
	author = {Tobeña-Santamaria, Rafael and Bliek, Mattijs and Ljung, Karin and Sandberg, Göran and Mol, Joseph N. M. and Souer, Erik and Koes, Ronald},
	month = mar,
	year = {2002},
	pmid = {11914280},
	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},
	keywords = {Flavin mono-oxygenase, flower development, leaf development, meristem initiation, transposon tagging, vascularization},
	pages = {753--763},
}

The mechanisms that determine the relative positions of floral organs, and thereby their numbers, is a poorly understood aspect of flower development. We isolated a petunia mutant, floozy(fzy), in which the formation of floral organ primordia in the outermost three floral whorls and one of the two bracts at the base of the flower is blocked at an early stage. In addition, fzymutants fail to generate secondary veins in leaves and bracts and display a decreased apical dominance in the inflorescence. FZYencodes an enzyme with homology to flavin mono-oxygenases and appears to be the ortholog of YUCCA genes of Arabidopsis. FZY is expressed in young leafs and bracts and in developing flowers. In young floral meristems FZY is expressed in the center of the meristem dome and, later, expression becomes localized on the flanks of the initiating petal and stamen primordia and at several sites in maturing anthers and carpels. These findings indicate that FZY is involved in synthesizing a signaling compound that is required for floral organ initiation and specification of the vascularization pattern in leaves. Although fzy mutants contain normal auxin levels, ectopic expression of FZY results in excessive auxin accumulation, suggesting that the signaling compound is auxin.

@article{trygg_orthogonal_2002,
	title = {Orthogonal projections to latent structures ({O}-{PLS})},
	volume = {16},
	issn = {1099-128X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cem.695},
	doi = {10/c3vf9q},
	abstract = {A generic preprocessing method for multivariate data, called orthogonal projections to latent structures (O-PLS), is described. O-PLS removes variation from X (descriptor variables) that is not correlated to Y (property variables, e.g. yield, cost or toxicity). In mathematical terms this is equivalent to removing systematic variation in X that is orthogonal to Y. In an earlier paper, Wold et al. (Chemometrics Intell. Lab. Syst. 1998; 44: 175–185) described orthogonal signal correction (OSC). In this paper a method with the same objective but with different means is described. The proposed O-PLS method analyzes the variation explained in each PLS component. The non-correlated systematic variation in X is removed, making interpretation of the resulting PLS model easier and with the additional benefit that the non-correlated variation itself can be analyzed further. As an example, near-infrared (NIR) reflectance spectra of wood chips were analyzed. Applying O-PLS resulted in reduced model complexity with preserved prediction ability, effective removal of non-correlated variation in X and, not least, improved interpretational ability of both correlated and non-correlated variation in the NIR spectra. Copyright © 2002 John Wiley \& Sons, Ltd.},
	language = {fr},
	number = {3},
	urldate = {2021-10-19},
	journal = {Journal of Chemometrics},
	author = {Trygg, Johan and Wold, Svante},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/cem.695},
	keywords = {NIPALS PLS, calibration, multivariate data analysis, orthogonal projections to latent structures (O-PLS), orthogonal signal correction (OSC), preprocessing},
	pages = {119--128},
}

A generic preprocessing method for multivariate data, called orthogonal projections to latent structures (O-PLS), is described. O-PLS removes variation from X (descriptor variables) that is not correlated to Y (property variables, e.g. yield, cost or toxicity). In mathematical terms this is equivalent to removing systematic variation in X that is orthogonal to Y. In an earlier paper, Wold et al. (Chemometrics Intell. Lab. Syst. 1998; 44: 175–185) described orthogonal signal correction (OSC). In this paper a method with the same objective but with different means is described. The proposed O-PLS method analyzes the variation explained in each PLS component. The non-correlated systematic variation in X is removed, making interpretation of the resulting PLS model easier and with the additional benefit that the non-correlated variation itself can be analyzed further. As an example, near-infrared (NIR) reflectance spectra of wood chips were analyzed. Applying O-PLS resulted in reduced model complexity with preserved prediction ability, effective removal of non-correlated variation in X and, not least, improved interpretational ability of both correlated and non-correlated variation in the NIR spectra. Copyright © 2002 John Wiley & Sons, Ltd.

@article{antti_batch_2002,
	title = {Batch statistical processing of {1H} {NMR}-derived urinary spectral data},
	volume = {16},
	issn = {1099-128X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cem.733},
	doi = {10/bn57ft},
	abstract = {Multivariate statistical batch processing (BP) analysis of 1H nuclear magnetic resonance (NMR) urine spectra was employed to establish time-dependent metabolic variations in animals treated with the model hepatotoxin hydrazine. Hydrazine was administered orally to rats (at 90 mg kg−1), and urine samples were collected from dosed rats and matched control animals (n = 5 per group) at time points up to 168 h post-dose. Urine samples were analysed via 1H NMR spectroscopy and partial least squares-based batch processing analysis, treating each rat as an individual batch comprising a series of timed urine samples. A model defining the mean urine profile was established for the control group, and samples obtained from hydrazine-treated animals were assessed using this model. Time-dependent deviations from the control model were evident in all hydrazine-treated animals, and hepatotoxicity was manifested by increased urinary excretion of taurine, creatine, 2-aminoadipate, citrulline and β-alanine together with depletion of urinary levels of citrate, succinate and hippurate. The experiment was repeated at six different pharmaceutical centres in order to assess the robustness of the technology and to establish the natural variability in the data. Results were consistent across the data for all centres. BP plots showed a characteristic pattern for each toxin, allowing the time points at which there were maximum metabolic differences to be determined and providing a means of visualizing the net toxin-induced metabolic movement of urinary metabolism. BP may prove to be a powerful metabonomic tool in defining time-dependent metabolic consequences of toxicity and is an efficient means of visualizing inter-animal variations in response as well as defining multivariate statistical limits of normality in terms of biofluid composition. Copyright © 2002 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {8-10},
	urldate = {2021-10-19},
	journal = {Journal of Chemometrics},
	author = {Antti, H. and Bollard, M. E. and Ebbels, T. and Keun, H. and Lindon, J. C. and Nicholson, J. K. and Holmes, E.},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/cem.733},
	keywords = {batch processing, hepatotoxicity, hydrazine, metabonomics, nuclear magnetic resonance spectroscopy, rat},
	pages = {461--468},
}

Multivariate statistical batch processing (BP) analysis of 1H nuclear magnetic resonance (NMR) urine spectra was employed to establish time-dependent metabolic variations in animals treated with the model hepatotoxin hydrazine. Hydrazine was administered orally to rats (at 90 mg kg−1), and urine samples were collected from dosed rats and matched control animals (n = 5 per group) at time points up to 168 h post-dose. Urine samples were analysed via 1H NMR spectroscopy and partial least squares-based batch processing analysis, treating each rat as an individual batch comprising a series of timed urine samples. A model defining the mean urine profile was established for the control group, and samples obtained from hydrazine-treated animals were assessed using this model. Time-dependent deviations from the control model were evident in all hydrazine-treated animals, and hepatotoxicity was manifested by increased urinary excretion of taurine, creatine, 2-aminoadipate, citrulline and β-alanine together with depletion of urinary levels of citrate, succinate and hippurate. The experiment was repeated at six different pharmaceutical centres in order to assess the robustness of the technology and to establish the natural variability in the data. Results were consistent across the data for all centres. BP plots showed a characteristic pattern for each toxin, allowing the time points at which there were maximum metabolic differences to be determined and providing a means of visualizing the net toxin-induced metabolic movement of urinary metabolism. BP may prove to be a powerful metabonomic tool in defining time-dependent metabolic consequences of toxicity and is an efficient means of visualizing inter-animal variations in response as well as defining multivariate statistical limits of normality in terms of biofluid composition. Copyright © 2002 John Wiley & Sons, Ltd.

@article{sane_transient_2002,
	title = {A {Transient} {Exchange} of the {Photosystem} {II} {Reaction} {Center} {Protein} {D1}:1 with {D1}:2 during {Low} {Temperature} {Stress} {ofSynechococcus} sp. {PCC} 7942 in the {Light} {Lowers} the {Redox} {Potential} of {QB}*},
	volume = {277},
	issn = {0021-9258},
	shorttitle = {A {Transient} {Exchange} of the {Photosystem} {II} {Reaction} {Center} {Protein} {D1}},
	url = {https://www.sciencedirect.com/science/article/pii/S0021925820744169},
	doi = {10/cxhmsg},
	abstract = {Upon exposure to low temperature under constant light conditions, the cyanobacterium Synechococcus sp. PCC 7942 exchanges the photosystem II reaction center D1 protein form 1 (D1:1) with D1 protein form 2 (D1:2). This exchange is only transient, and after acclimation to low temperature the cells revert back to D1:1, which is the preferred form in acclimated cells (Campbell, D., Zhou, G., Gustafsson, P., O¨quist, G., and Clarke, A. K. (1995) EMBO J. 14, 5457–5466). In the present work we use thermoluminescence to study charge recombination events between the acceptor and donor sides of photosystem II in relation to D1 replacement. The data indicate that in cold-stressed cells exhibiting D1:2, the redox potential of QB becomes lower approaching that of QA. This was confirmed by examining theSynechococcus sp. PCC 7942 inactivation mutants R2S2C3 and R2K1, which possess only D1:1 or D1:2, respectively. In contrast, the recombination of Q A− with the S2 and S3 states did not show any change in their redox characteristics upon the shift from D1:1 to D1:2. We suggest that the change in redox properties of QB results in altered charge equilibrium in favor of QA. This would significantly increase the probability of Q A−and P680+ recombination. The resulting non-radiative energy dissipation within the reaction center of PSII may serve as a highly effective protective mechanism against photodamage upon excessive excitation. The proposed reaction center quenching is an important protective mechanism because antenna and zeaxanthin cycle-dependent quenching are not present in cyanobacteria. We suggest that lowering the redox potential of QB by exchanging D1:1 for D1:2 imparts the increased resistance to high excitation pressure induced by exposure to either low temperature or high light.},
	language = {en},
	number = {36},
	urldate = {2021-10-19},
	journal = {Journal of Biological Chemistry},
	author = {Sane, P. V. and Ivanov, Alexander G. and Sveshnikov, Dmitry and Huner, Norman P. A. and O¨quist, Gunnar},
	month = sep,
	year = {2002},
	pages = {32739--32745},
}

Upon exposure to low temperature under constant light conditions, the cyanobacterium Synechococcus sp. PCC 7942 exchanges the photosystem II reaction center D1 protein form 1 (D1:1) with D1 protein form 2 (D1:2). This exchange is only transient, and after acclimation to low temperature the cells revert back to D1:1, which is the preferred form in acclimated cells (Campbell, D., Zhou, G., Gustafsson, P., O¨quist, G., and Clarke, A. K. (1995) EMBO J. 14, 5457–5466). In the present work we use thermoluminescence to study charge recombination events between the acceptor and donor sides of photosystem II in relation to D1 replacement. The data indicate that in cold-stressed cells exhibiting D1:2, the redox potential of QB becomes lower approaching that of QA. This was confirmed by examining theSynechococcus sp. PCC 7942 inactivation mutants R2S2C3 and R2K1, which possess only D1:1 or D1:2, respectively. In contrast, the recombination of Q A− with the S2 and S3 states did not show any change in their redox characteristics upon the shift from D1:1 to D1:2. We suggest that the change in redox properties of QB results in altered charge equilibrium in favor of QA. This would significantly increase the probability of Q A−and P680+ recombination. The resulting non-radiative energy dissipation within the reaction center of PSII may serve as a highly effective protective mechanism against photodamage upon excessive excitation. The proposed reaction center quenching is an important protective mechanism because antenna and zeaxanthin cycle-dependent quenching are not present in cyanobacteria. We suggest that lowering the redox potential of QB by exchanging D1:1 for D1:2 imparts the increased resistance to high excitation pressure induced by exposure to either low temperature or high light.

@article{andersson_inbreeding_2002,
	title = {Inbreeding depression in a rare plant, {Scabiosa} canescens ({Dipsacaceae})},
	volume = {136},
	issn = {1601-5223},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1034/j.1601-5223.2002.1360305.x},
	doi = {10/d2nkvs},
	abstract = {Plants from a population of Scabiosa canescens, a locally rare species with a narrow ecological amplitude, were raised under uniform growth conditions to examine the phenotypic effects of one generation selfing and outcrossing. Particular attention was given to direct components of fitness (seedling biomass, rosette leaf number, head number, flower number per head), but two morphological characters (plant height, flower size) were also considered. Estimates of inbreeding depression (δ), adjusted for maternal effects and lack of balance, were compared and tested for significance using randomization and bootstrap procedures. Inbreeding significantly depressed several characters during both early and late stages of the life cycle, with δ ranging from 0.14 (flower size) to 0.37 (seedling biomass). Based on these and other results, we propose that S. canescens is susceptible to inbreeding and that the genetic basis of inbreeding depression varies across life stages.},
	language = {en},
	number = {3},
	urldate = {2021-10-19},
	journal = {Hereditas},
	author = {Andersson, Stefan and Waldmann, Patrik},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1034/j.1601-5223.2002.1360305.x},
	pages = {207--211},
}

Plants from a population of Scabiosa canescens, a locally rare species with a narrow ecological amplitude, were raised under uniform growth conditions to examine the phenotypic effects of one generation selfing and outcrossing. Particular attention was given to direct components of fitness (seedling biomass, rosette leaf number, head number, flower number per head), but two morphological characters (plant height, flower size) were also considered. Estimates of inbreeding depression (δ), adjusted for maternal effects and lack of balance, were compared and tested for significance using randomization and bootstrap procedures. Inbreeding significantly depressed several characters during both early and late stages of the life cycle, with δ ranging from 0.14 (flower size) to 0.37 (seedling biomass). Based on these and other results, we propose that S. canescens is susceptible to inbreeding and that the genetic basis of inbreeding depression varies across life stages.

@article{wold_new_2002,
	title = {New and old trends in chemometrics. {How} to deal with the increasing data volumes in {R}\&{D}\&{P} (research, development and production)—with examples from pharmaceutical research and process modeling},
	volume = {16},
	issn = {1099-128X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cem.746},
	doi = {10/b2hpvs},
	abstract = {Chemometrics was started around 30 years ago to cope with and utilize the rapidly increasing volumes of data produced in chemical laboratories. The methods of early chemometrics were mainly focused on the analysis of data, but slowly we came to realize that it is equally important to make the data contain reliable information, and methods for design of experiments (DOE) were added to the chemometrics toolbox. This toolbox is now fairly adequate for solving most R\&D problems of today in both academia and industry, as will be illustrated with a few examples. However, with the further increase in the size of our data sets, we start to see inadequacies in our multivariate methods, both in their efficiency and interpretability. Drift and non-linearities occur with time or in other directions in data space, and models with masses of coefficients become increasingly difficult to interpret and use. Starting from a few examples of some very complicated problems confronting chemical researchers today, possible extensions and generalizations of the existing chemometrics methods, as well as more appropriate preprocessing of the data before the analysis, will be discussed. Criteria such as scalability of methods to increasing size of problems and data, increasing sophistication in the handling of noise and non-linearities, interpretability of results, and relative simplicity of use will be held as important. The discussion will be made from a perspective of the evolution of the scientific methodology as driven by new technology, e.g. computers, and constrained by the limitations of the human brain, i.e. our ability to understand and interpret scientific and data analytical results. Quilt-PCA and Quilt-PLS presented here address and offer a possible solution to these problems. Copyright © 2002 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {8-10},
	urldate = {2021-10-19},
	journal = {Journal of Chemometrics},
	author = {Wold, Svante and Berglund, Anders and Kettaneh, Nouna},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/cem.746},
	keywords = {PLS, chemometrics, interpretability of results, large data sets, non-linearities},
	pages = {377--386},
}

Chemometrics was started around 30 years ago to cope with and utilize the rapidly increasing volumes of data produced in chemical laboratories. The methods of early chemometrics were mainly focused on the analysis of data, but slowly we came to realize that it is equally important to make the data contain reliable information, and methods for design of experiments (DOE) were added to the chemometrics toolbox. This toolbox is now fairly adequate for solving most R&D problems of today in both academia and industry, as will be illustrated with a few examples. However, with the further increase in the size of our data sets, we start to see inadequacies in our multivariate methods, both in their efficiency and interpretability. Drift and non-linearities occur with time or in other directions in data space, and models with masses of coefficients become increasingly difficult to interpret and use. Starting from a few examples of some very complicated problems confronting chemical researchers today, possible extensions and generalizations of the existing chemometrics methods, as well as more appropriate preprocessing of the data before the analysis, will be discussed. Criteria such as scalability of methods to increasing size of problems and data, increasing sophistication in the handling of noise and non-linearities, interpretability of results, and relative simplicity of use will be held as important. The discussion will be made from a perspective of the evolution of the scientific methodology as driven by new technology, e.g. computers, and constrained by the limitations of the human brain, i.e. our ability to understand and interpret scientific and data analytical results. Quilt-PCA and Quilt-PLS presented here address and offer a possible solution to these problems. Copyright © 2002 John Wiley & Sons, Ltd.

@article{trygg_o2-pls_2002,
	title = {O2-{PLS} for qualitative and quantitative analysis in multivariate calibration},
	volume = {16},
	issn = {1099-128X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cem.724},
	doi = {10/fwbqdw},
	abstract = {In this paper the O-PLS method [1] has been modified to further improve its interpretational functionality to give (a) estimates of the pure constituent profiles in X as well as model (b) the Y-orthogonal variation in X, (c) the X-orthogonal variation in Y and (d) the joint X–Y covariation. It is also predictive in both ways, X ↔ Y. We call this the O2-PLS approach. In earlier papers we discussed the improved interpretation using O-PLS compared to the partial least squares projections to latent structures (PLS) when systematic Y-orthogonal variation in X exists, i.e. when a PLS model has more components than the number of Y variables. In this paper we show how the parameters in the PLS model are affected and to what degree the interpretational ability of the PLS components changes with the amount of Y-orthogonal variation. In both real and synthetic examples, the O2-PLS method provided improved interpretation of the model and gave a good estimate of the pure constituent profiles, and the prediction ability was similar to the standard PLS model. The method is discussed from geometric and algebraic points of view, and a detailed description of this modified O2-PLS method is given and reviewed. Copyright © 2002 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {6},
	urldate = {2021-10-19},
	journal = {Journal of Chemometrics},
	author = {Trygg, Johan},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/cem.724},
	keywords = {O-PLS, O2-PLS, PLS, multivariate calibration, preprocessing, pure profile estimation},
	pages = {283--293},
}

In this paper the O-PLS method [1] has been modified to further improve its interpretational functionality to give (a) estimates of the pure constituent profiles in X as well as model (b) the Y-orthogonal variation in X, (c) the X-orthogonal variation in Y and (d) the joint X–Y covariation. It is also predictive in both ways, X ↔ Y. We call this the O2-PLS approach. In earlier papers we discussed the improved interpretation using O-PLS compared to the partial least squares projections to latent structures (PLS) when systematic Y-orthogonal variation in X exists, i.e. when a PLS model has more components than the number of Y variables. In this paper we show how the parameters in the PLS model are affected and to what degree the interpretational ability of the PLS components changes with the amount of Y-orthogonal variation. In both real and synthetic examples, the O2-PLS method provided improved interpretation of the model and gave a good estimate of the pure constituent profiles, and the prediction ability was similar to the standard PLS model. The method is discussed from geometric and algebraic points of view, and a detailed description of this modified O2-PLS method is given and reviewed. Copyright © 2002 John Wiley & Sons, Ltd.

@article{schubert_proteome_2002,
	title = {Proteome {Map} of the {Chloroplast} {Lumen} of {Arabidopsis} thaliana *},
	volume = {277},
	issn = {0021-9258},
	url = {https://www.sciencedirect.com/science/article/pii/S0021925819364397},
	doi = {10/b54qvm},
	abstract = {The thylakoid membrane of the chloroplast is the center of oxygenic photosynthesis. To better understand the function of the luminal compartment within the thylakoid network, we have carried out a systematic characterization of the luminal thylakoid proteins from the model organism Arabidopsis thaliana. Our data show that the thylakoid lumen has its own specific proteome, of which 36 proteins were identified. Besides a large group of peptidyl-prolyl cis-trans isomerases and proteases, a family of novel PsbP domain proteins was found. An analysis of the luminal signal peptides showed that 19 of 36 luminal precursors were marked by a twin-arginine motif for import via the Tat pathway. To compare the model organismArabidopsis with another typical higher plant, we investigated the proteome from the thylakoid lumen of spinach and found that the luminal proteins from both plants corresponded well. As a complement to our experimental investigation, we made a theoretical prediction of the luminal proteins from the whole Arabidopsisgenome and estimated that the thylakoid lumen of the chloroplast contains ∼80 proteins.},
	language = {en},
	number = {10},
	urldate = {2021-10-19},
	journal = {Journal of Biological Chemistry},
	author = {Schubert, Maria and Petersson, Ulrika A. and Haas, Brian J. and Funk, Christiane and Schröder, Wolfgang P. and Kieselbach, Thomas},
	month = mar,
	year = {2002},
	pages = {8354--8365},
}

The thylakoid membrane of the chloroplast is the center of oxygenic photosynthesis. To better understand the function of the luminal compartment within the thylakoid network, we have carried out a systematic characterization of the luminal thylakoid proteins from the model organism Arabidopsis thaliana. Our data show that the thylakoid lumen has its own specific proteome, of which 36 proteins were identified. Besides a large group of peptidyl-prolyl cis-trans isomerases and proteases, a family of novel PsbP domain proteins was found. An analysis of the luminal signal peptides showed that 19 of 36 luminal precursors were marked by a twin-arginine motif for import via the Tat pathway. To compare the model organismArabidopsis with another typical higher plant, we investigated the proteome from the thylakoid lumen of spinach and found that the luminal proteins from both plants corresponded well. As a complement to our experimental investigation, we made a theoretical prediction of the luminal proteins from the whole Arabidopsisgenome and estimated that the thylakoid lumen of the chloroplast contains ∼80 proteins.

@article{waldmann_fluctuating_2002,
	title = {Fluctuating {Asymmetry} in {Scabiosa} canescens and {Scabiosa} columbaria: {Association} with {Genetic} {Variation} and {Population} {Size}},
	volume = {163},
	issn = {1058-5893},
	shorttitle = {Fluctuating {Asymmetry} in {Scabiosa} canescens and {Scabiosa} columbaria},
	url = {https://www.journals.uchicago.edu/doi/10.1086/338394},
	doi = {10/cf6nwc},
	abstract = {Developmental instability and fluctuating asymmetry (FA) have become important topics in evolutionary biology. For example, it has been suggested that FA could be a useful tool for identification of genetic and environmental stress factors. This study used plants from each of six populations of Scabiosa canescens and Scabiosa columbaria grown under greenhouse conditions. I tested whether there was a relationship between petal FA and allozyme heterozygosity, the heritabilities of eight traits, and population size. Flowers displayed no directional asymmetry or antisymmetry. The rare species S. canescens had significantly higher FA values than S. columbaria, but only the latter demonstrated interpopulation differentiation for the expression of FA levels. There was no evidence for an association between population‐level FA and genetic variation when compared with the allozyme heterozygosity or with the heritabilities of the quantitative traits. A tendency for a negative association between FA and population size was found for both species, but it was not significant when adjusted for multiple comparison. Hence, flower FA should not be considered a reliable indicator of the amount of genetic variation in populations of S. canescens and S. columbaria.},
	number = {2},
	urldate = {2021-10-19},
	journal = {International Journal of Plant Sciences},
	author = {Waldmann, Patrik},
	month = mar,
	year = {2002},
	note = {Publisher: The University of Chicago Press},
	keywords = {Scabiosa, allozyme heterozygosity, fluctuating asymmetry, heritability, population size},
	pages = {329--334},
}

Developmental instability and fluctuating asymmetry (FA) have become important topics in evolutionary biology. For example, it has been suggested that FA could be a useful tool for identification of genetic and environmental stress factors. This study used plants from each of six populations of Scabiosa canescens and Scabiosa columbaria grown under greenhouse conditions. I tested whether there was a relationship between petal FA and allozyme heterozygosity, the heritabilities of eight traits, and population size. Flowers displayed no directional asymmetry or antisymmetry. The rare species S. canescens had significantly higher FA values than S. columbaria, but only the latter demonstrated interpopulation differentiation for the expression of FA levels. There was no evidence for an association between population‐level FA and genetic variation when compared with the allozyme heterozygosity or with the heritabilities of the quantitative traits. A tendency for a negative association between FA and population size was found for both species, but it was not significant when adjusted for multiple comparison. Hence, flower FA should not be considered a reliable indicator of the amount of genetic variation in populations of S. canescens and S. columbaria.

@article{gustavsson_characterisation_2002,
	title = {Characterisation of a plasma membrane-associated phospholipase {A2} activity increased in response to cold acclimation},
	volume = {159},
	issn = {0176-1617},
	url = {https://www.sciencedirect.com/science/article/pii/S0176161704703466},
	doi = {10/b6t267},
	abstract = {We here demonstrate the presence of a plasma membrane-associated phospholipase A2 (EC 3.1.1.4; PLA2) activity in spinach (Spinacia oleracea) leaves. The pH profile of the spinach plasma membrane PLA2 activity revealed two peaks, one at pH 4.4 and one at pH 5.5. The activity at pH 5.5 had an absolute requirement of Ca2+, with full enzyme activity at 10 μmol/L Ca2+. The Ca2+-dependent PLA2 activity was both heat sensitive and stimulated by diacylglycerol, whereas ATP completely inhibited the activity. Thus, the spinach plasma membrane contains a Ca2+-dependent PLA2 activity, which has not previously been characterised in plants. Cold acclimation of spinach resulted in a 2.2-fold higher plasma membrane PLA2 activity whereas the plasma membrane phospholipase D activity remained unaffected. Taken together, our data suggest a role of PLA2 in cold acclimation in plants.},
	language = {en},
	number = {11},
	urldate = {2021-10-19},
	journal = {Journal of Plant Physiology},
	author = {Gustavsson, Maria H. and Sommarin, Marianne},
	month = jan,
	year = {2002},
	keywords = {Ca dependency, cold acclimation, phospholipase A, plasma membrane},
	pages = {1219--1227},
}

We here demonstrate the presence of a plasma membrane-associated phospholipase A2 (EC 3.1.1.4; PLA2) activity in spinach (Spinacia oleracea) leaves. The pH profile of the spinach plasma membrane PLA2 activity revealed two peaks, one at pH 4.4 and one at pH 5.5. The activity at pH 5.5 had an absolute requirement of Ca2+, with full enzyme activity at 10 μmol/L Ca2+. The Ca2+-dependent PLA2 activity was both heat sensitive and stimulated by diacylglycerol, whereas ATP completely inhibited the activity. Thus, the spinach plasma membrane contains a Ca2+-dependent PLA2 activity, which has not previously been characterised in plants. Cold acclimation of spinach resulted in a 2.2-fold higher plasma membrane PLA2 activity whereas the plasma membrane phospholipase D activity remained unaffected. Taken together, our data suggest a role of PLA2 in cold acclimation in plants.

@article{deluca_quantifying_2002,
	title = {Quantifying nitrogen-fixation in feather moss carpets of boreal forests},
	volume = {419},
	copyright = {2002 Macmillan Magazines Ltd.},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/nature01051},
	doi = {10/bp7gfx},
	abstract = {Biological nitrogen (N) fixation is the primary source of N within natural ecosystems1, yet the origin of boreal forest N has remained elusive. The boreal forests of Eurasia and North America lack any significant, widespread symbiotic N-fixing plants1,2,3,4,5,6. With the exception of scattered stands of alder in early primary successional forests7, N-fixation in boreal forests is considered to be extremely limited. Nitrogen-fixation in northern European boreal forests has been estimated2 at only 0.5 kg N ha-1 yr-1; however, organic N is accumulated in these ecosystems at a rate of 3 kg N ha-1 yr-1 (ref. 8). Our limited understanding of the origin of boreal N is unacceptable given the extent of the boreal forest region, but predictable given our imperfect knowledge of N-fixation1,9. Herein we report on a N-fixing symbiosis between a cyanobacterium (Nostoc sp.) and the ubiquitous feather moss, Pleurozium schreberi (Bird) Mitt. that alone fixes between 1.5 and 2.0 kg N ha-1 yr-1 in mid- to late-successional forests of northern Scandinavia and Finland. Previous efforts have probably underestimated N-fixation potential in boreal forests.},
	language = {en},
	number = {6910},
	urldate = {2021-10-19},
	journal = {Nature},
	author = {DeLuca, Thomas H. and Zackrisson, Olle and Nilsson, Marie-Charlotte and Sellstedt, Anita},
	month = oct,
	year = {2002},
	note = {Bandiera\_abtest: a
Cg\_type: Nature Research Journals
Number: 6910
Primary\_atype: Research
Publisher: Nature Publishing Group},
	pages = {917--920},
}

Biological nitrogen (N) fixation is the primary source of N within natural ecosystems1, yet the origin of boreal forest N has remained elusive. The boreal forests of Eurasia and North America lack any significant, widespread symbiotic N-fixing plants1,2,3,4,5,6. With the exception of scattered stands of alder in early primary successional forests7, N-fixation in boreal forests is considered to be extremely limited. Nitrogen-fixation in northern European boreal forests has been estimated2 at only 0.5 kg N ha-1 yr-1; however, organic N is accumulated in these ecosystems at a rate of 3 kg N ha-1 yr-1 (ref. 8). Our limited understanding of the origin of boreal N is unacceptable given the extent of the boreal forest region, but predictable given our imperfect knowledge of N-fixation1,9. Herein we report on a N-fixing symbiosis between a cyanobacterium (Nostoc sp.) and the ubiquitous feather moss, Pleurozium schreberi (Bird) Mitt. that alone fixes between 1.5 and 2.0 kg N ha-1 yr-1 in mid- to late-successional forests of northern Scandinavia and Finland. Previous efforts have probably underestimated N-fixation potential in boreal forests.

@article{schmidt_mineralization_2002,
	title = {Mineralization and distribution of nutrients in plants and microbes in four arctic ecosystems: responses to warming},
	volume = {242},
	issn = {1573-5036},
	shorttitle = {Mineralization and distribution of nutrients in plants and microbes in four arctic ecosystems},
	url = {https://doi.org/10.1023/A:1019642007929},
	doi = {10/bh8mzs},
	abstract = {Mineralization and nutrient distribution in plants and microbes were studied in four arctic ecosystems at Abisko, Northern Sweden and Toolik Lake, Alaska, which have been subjected to long-term warming with plastic greenhouses. Net mineralization and microbial immobilization were studied by the buried bag method and ecosystem pool sizes of C, N and P were determined by harvest methods. The highest amounts of organic N and P were bound in the soil organic matter. Microbial N and P constituted the largest labile pools often equal to (N) or exceeding (P) the amounts stored in the vegetation. Despite large pools of N and P in the soil, net mineralization of N and P was generally low during the growing season, except in the wet sedge tundra, and in most cases lower than the plant uptake requirement. In contrast, the microorganisms immobilized high amounts of nutrients in the buried bags during incubation. The same high immobilization was not observed in the surrounding soil, where the microbial nutrient content in most cases remained constant or decreased over the growing season. This suggests that the low mineralization measured in many arctic ecosystems over the growing season is due to increased immobilization by soil microbes when competition from plant roots is prevented. Furthermore, it suggests that plants compete well with microbes for nutrients in these four ecosystems. Warming increased net mineralization in several cases, which led to increased assimilation of nutrients by plants but not by the microbes.},
	language = {en},
	number = {1},
	urldate = {2021-10-19},
	journal = {Plant and Soil},
	author = {Schmidt, I.K. and Jonasson, S. and Shaver, G. R. and Michelsen, A. and Nordin, A.},
	month = may,
	year = {2002},
	pages = {93--106},
}

Mineralization and nutrient distribution in plants and microbes were studied in four arctic ecosystems at Abisko, Northern Sweden and Toolik Lake, Alaska, which have been subjected to long-term warming with plastic greenhouses. Net mineralization and microbial immobilization were studied by the buried bag method and ecosystem pool sizes of C, N and P were determined by harvest methods. The highest amounts of organic N and P were bound in the soil organic matter. Microbial N and P constituted the largest labile pools often equal to (N) or exceeding (P) the amounts stored in the vegetation. Despite large pools of N and P in the soil, net mineralization of N and P was generally low during the growing season, except in the wet sedge tundra, and in most cases lower than the plant uptake requirement. In contrast, the microorganisms immobilized high amounts of nutrients in the buried bags during incubation. The same high immobilization was not observed in the surrounding soil, where the microbial nutrient content in most cases remained constant or decreased over the growing season. This suggests that the low mineralization measured in many arctic ecosystems over the growing season is due to increased immobilization by soil microbes when competition from plant roots is prevented. Furthermore, it suggests that plants compete well with microbes for nutrients in these four ecosystems. Warming increased net mineralization in several cases, which led to increased assimilation of nutrients by plants but not by the microbes.

@article{bourquin_xyloglucan_2002,
	title = {Xyloglucan {Endotransglycosylases} {Have} a {Function} during the {Formation} of {Secondary} {Cell} {Walls} of {Vascular} {Tissues}},
	volume = {14},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.007773},
	doi = {10/cfv573},
	abstract = {Xyloglucan transglycosylases (XETs) have been implicated in many aspects of cell wall biosynthesis, but their function in vascular tissues, in general, and in the formation of secondary walls, in particular, is less well understood. Using an in situ XET activity assay in poplar stems, we have demonstrated XET activity in xylem and phloem fibers at the stage of secondary wall formation. Immunolocalization of fucosylated xylogucan with CCRC-M1 antibodies showed that levels of this species increased at the border between the primary and secondary wall layers at the time of secondary wall deposition. Furthermore, one of the most abundant XET isoforms in secondary vascular tissues (PttXET16A) was cloned and immunolocalized to fibers at the stage of secondary wall formation. Together, these data strongly suggest that XET has a previously unreported role in restructuring primary walls at the time when secondary wall layers are deposited, probably creating and reinforcing the connections between the primary and secondary wall layers. We also observed that xylogucan is incorporated at a high level in the inner layer of nacreous walls of mature sieve tube elements.},
	number = {12},
	urldate = {2021-10-19},
	journal = {The Plant Cell},
	author = {Bourquin, Veronica and Nishikubo, Nobuyuki and Abe, Hisashi and Brumer, Harry and Denman, Stuart and Eklund, Marlin and Christiernin, Maria and Teeri, Tunla T. and Sundberg, Björn and Mellerowicz, Ewa J.},
	month = dec,
	year = {2002},
	pages = {3073--3088},
}

Xyloglucan transglycosylases (XETs) have been implicated in many aspects of cell wall biosynthesis, but their function in vascular tissues, in general, and in the formation of secondary walls, in particular, is less well understood. Using an in situ XET activity assay in poplar stems, we have demonstrated XET activity in xylem and phloem fibers at the stage of secondary wall formation. Immunolocalization of fucosylated xylogucan with CCRC-M1 antibodies showed that levels of this species increased at the border between the primary and secondary wall layers at the time of secondary wall deposition. Furthermore, one of the most abundant XET isoforms in secondary vascular tissues (PttXET16A) was cloned and immunolocalized to fibers at the stage of secondary wall formation. Together, these data strongly suggest that XET has a previously unreported role in restructuring primary walls at the time when secondary wall layers are deposited, probably creating and reinforcing the connections between the primary and secondary wall layers. We also observed that xylogucan is incorporated at a high level in the inner layer of nacreous walls of mature sieve tube elements.

@article{marchant_aux1_2002,
	title = {{AUX1} {Promotes} {Lateral} {Root} {Formation} by {Facilitating} {Indole}-3-{Acetic} {Acid} {Distribution} between {Sink} and {Source} {Tissues} in the {Arabidopsis} {Seedling}},
	volume = {14},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.010354},
	doi = {10/btp7mv},
	abstract = {Arabidopsis root architecture is regulated by shoot-derived signals such as nitrate and auxin. We report that mutations in the putative auxin influx carrier AUX1 modify root architecture as a result of the disruption in hormone transport between indole-3-acetic acid (IAA) source and sink tissues. Gas chromatography–selected reaction monitoring–mass spectrometry measurements revealed that the aux1 mutant exhibited altered IAA distribution in young leaf and root tissues, the major IAA source and sink organs, respectively, in the developing seedling. Expression studies using the auxin-inducible reporter IAA2::uidA revealed that AUX1 facilitates IAA loading into the leaf vascular transport system. AUX1 also facilitates IAA unloading in the primary root apex and developing lateral root primordium. Exogenous application of the synthetic auxin 1-naphthylacetic acid is able to rescue the aux1 lateral root phenotype, implying that root auxin levels are suboptimal for lateral root primordium initiation in the mutant.},
	number = {3},
	urldate = {2021-10-19},
	journal = {The Plant Cell},
	author = {Marchant, Alan and Bhalerao, Rishikesh and Casimiro, Ilda and Eklöf, Jan and Casero, Pedro J. and Bennett, Malcolm and Sandberg, Goran},
	month = mar,
	year = {2002},
	pages = {589--597},
}

Arabidopsis root architecture is regulated by shoot-derived signals such as nitrate and auxin. We report that mutations in the putative auxin influx carrier AUX1 modify root architecture as a result of the disruption in hormone transport between indole-3-acetic acid (IAA) source and sink tissues. Gas chromatography–selected reaction monitoring–mass spectrometry measurements revealed that the aux1 mutant exhibited altered IAA distribution in young leaf and root tissues, the major IAA source and sink organs, respectively, in the developing seedling. Expression studies using the auxin-inducible reporter IAA2::uidA revealed that AUX1 facilitates IAA loading into the leaf vascular transport system. AUX1 also facilitates IAA unloading in the primary root apex and developing lateral root primordium. Exogenous application of the synthetic auxin 1-naphthylacetic acid is able to rescue the aux1 lateral root phenotype, implying that root auxin levels are suboptimal for lateral root primordium initiation in the mutant.

@article{camilleri_arabidopsis_2002,
	title = {The {Arabidopsis} {TONNEAU2} {Gene} {Encodes} a {Putative} {Novel} {Protein} {Phosphatase} {2A} {Regulatory} {Subunit} {Essential} for the {Control} of the {Cortical} {Cytoskeleton}},
	volume = {14},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.010402},
	doi = {10/d79s3z},
	abstract = {In Arabidopsis ton2 mutants, abnormalities of the cortical microtubular cytoskeleton, such as disorganization of the interphase microtubule array and lack of the preprophase band before mitosis, markedly affect cell shape and arrangement as well as overall plant morphology. We present the molecular isolation of the TON2 gene, which is highly conserved in higher plants and has a vertebrate homolog of unknown function. It encodes a protein similar in its C-terminal part to B″ regulatory subunits of type 2A protein phosphatases (PP2As). We show that the TON2 protein interacts with an Arabidopsis type A subunit of PP2A in the yeast two-hybrid system and thus likely defines a novel subclass of PP2A subunits that are possibly involved in the control of cytoskeletal structures in plants.},
	number = {4},
	urldate = {2021-10-19},
	journal = {The Plant Cell},
	author = {Camilleri, Christine and Azimzadeh, Juliette and Pastuglia, Martine and Bellini, Catherine and Grandjean, Olivier and Bouchez, David},
	month = apr,
	year = {2002},
	pages = {833--845},
}

In Arabidopsis ton2 mutants, abnormalities of the cortical microtubular cytoskeleton, such as disorganization of the interphase microtubule array and lack of the preprophase band before mitosis, markedly affect cell shape and arrangement as well as overall plant morphology. We present the molecular isolation of the TON2 gene, which is highly conserved in higher plants and has a vertebrate homolog of unknown function. It encodes a protein similar in its C-terminal part to B″ regulatory subunits of type 2A protein phosphatases (PP2As). We show that the TON2 protein interacts with an Arabidopsis type A subunit of PP2A in the yeast two-hybrid system and thus likely defines a novel subclass of PP2A subunits that are possibly involved in the control of cytoskeletal structures in plants.

@article{zheng_characterization_2002,
	title = {Characterization of {Chloroplast} {Clp} proteins in {Arabidopsis}: {Localization}, tissue specificity and stress responses},
	volume = {114},
	issn = {1399-3054},
	shorttitle = {Characterization of {Chloroplast} {Clp} proteins in {Arabidopsis}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1034/j.1399-3054.2002.1140113.x},
	doi = {10/ct26b4},
	abstract = {The ATP-dependent Clp protease is one of the newly identified proteolytic systems in plant organelles that incorporate the activity of molecular chaperones to target specific polypeptide substrates and avoid inadvertent degradation of others. We describe new nuclear-encoded ClpC (ClpC1) and ClpP (ClpP3–5) isomers in Arabidopsis thaliana that raise the total number of identified Clp proteins to 19. The extra Clp proteins are localized within the stroma of chloroplasts along with the ClpD, –P1 and –P6 proteins. Potential differential regulation among these Clp proteins was analysed at both the mRNA and protein level. A comparison between different tissues showed increasing amounts of all plastid Clp proteins from roots to stems to leaves suggested the greatest abundance of proteins was in chloroplasts. The increases in protein were mirrored at the mRNA level for most ClpP isomers (ClpP1, −3, −4 and −6) but not for the three Hsp100 proteins (ClpC1, –C2 and –D) and ClpP5, which exhibited little change in transcript levels, suggesting post-transcriptional/translational regulation. Potential stress induction was also tested for all chloroplast Clp proteins by a series of brief and prolonged stress conditions. Short-term moderate and severe stresses (desiccation, high salt, cold, heat, oxidation, wounding and high light) all failed to elicit significant or rapid increases in any chloroplast Clp protein. However, increases in mRNA and protein content for ClpD and several ClpP isomers did occur during long-term high light and cold acclimation of Arabidopsis plants. These results reveal the great complexity of Clp proteins within the stroma of plant chloroplasts, and that these proteins, rather than being rapidly induced stress proteins, are primarily constitutive proteins that may also be involved in plant acclimation to different physiological conditions.},
	language = {en},
	number = {1},
	urldate = {2021-10-19},
	journal = {Physiologia Plantarum},
	author = {Zheng, Bo and Halperin, Tami and Hruskova-Heidingsfeldova, Olga and Adam, Zach and Clarke, Adrian K.},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1034/j.1399-3054.2002.1140113.x},
	pages = {92--101},
}

The ATP-dependent Clp protease is one of the newly identified proteolytic systems in plant organelles that incorporate the activity of molecular chaperones to target specific polypeptide substrates and avoid inadvertent degradation of others. We describe new nuclear-encoded ClpC (ClpC1) and ClpP (ClpP3–5) isomers in Arabidopsis thaliana that raise the total number of identified Clp proteins to 19. The extra Clp proteins are localized within the stroma of chloroplasts along with the ClpD, –P1 and –P6 proteins. Potential differential regulation among these Clp proteins was analysed at both the mRNA and protein level. A comparison between different tissues showed increasing amounts of all plastid Clp proteins from roots to stems to leaves suggested the greatest abundance of proteins was in chloroplasts. The increases in protein were mirrored at the mRNA level for most ClpP isomers (ClpP1, −3, −4 and −6) but not for the three Hsp100 proteins (ClpC1, –C2 and –D) and ClpP5, which exhibited little change in transcript levels, suggesting post-transcriptional/translational regulation. Potential stress induction was also tested for all chloroplast Clp proteins by a series of brief and prolonged stress conditions. Short-term moderate and severe stresses (desiccation, high salt, cold, heat, oxidation, wounding and high light) all failed to elicit significant or rapid increases in any chloroplast Clp protein. However, increases in mRNA and protein content for ClpD and several ClpP isomers did occur during long-term high light and cold acclimation of Arabidopsis plants. These results reveal the great complexity of Clp proteins within the stroma of plant chloroplasts, and that these proteins, rather than being rapidly induced stress proteins, are primarily constitutive proteins that may also be involved in plant acclimation to different physiological conditions.

@article{romanowska_stimulation_2002,
	title = {Stimulation of respiration by {Pb2}+ in detached leaves and mitochondria of {C3} and {C4} plants},
	volume = {116},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1034/j.1399-3054.2002.1160203.x},
	doi = {10/b54t5q},
	abstract = {The exposure of detached leaves of C3 plants (pea, barley) and C4 plant (maize) to 5 mM Pb (NO3)2 for 24 h caused a reduction of their photosynthetic activity by 40–60\%, whereas the respiratory rate was stimulated by 20–50\%. Mitochondria isolated from Pb2+-treated pea leaves oxidized substrates (glycine, succinate, malate) at higher rates than mitochondria from control leaves. The respiratory control (RCR) and the ADP/O ratio were not affected. Pb2+ caused an increase in ATP content and the ATP/ADP ratio in pea and maize leaves. Rapid fractionation of barley protoplasts incubated at low and high CO2 conditions, indicated that the increased ATP/ADP ratio in Pb2+-treated leaves resulted mainly from the production of mitochondrial ATP. The measurements of membrane potential of mitochondria with a TPP+-sensitive electrode further showed that mitochondria isolated from Pb2+-treated leaves had at least as high membrane potential as mitochondria from control leaves. The activity of NAD-malate dehydrogenase in the protoplasts from barley leaves treated with Pb2+ was 3-fold higher than in protoplasts from control leaves. The activities of photorespiratory enzymes NADH-hydroxypyruvate reductase and glycolate oxidase as well as of NAD-malic enzyme were not affected. The presented data indicate that stimulation of respiration in leaves treated by lead is in a close relationship with activation of malate dehydrogenase and stimulation of the mitochondrial ATP production. Thus, respiration might fulfil a protective role during heavy metal exposure.},
	language = {en},
	number = {2},
	urldate = {2021-10-19},
	journal = {Physiologia Plantarum},
	author = {Romanowska, Elżbieta and Igamberdiev, Abir U. and Parys, Eugeniusz and Gardeström, Per},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1034/j.1399-3054.2002.1160203.x},
	pages = {148--154},
}

The exposure of detached leaves of C3 plants (pea, barley) and C4 plant (maize) to 5 mM Pb (NO3)2 for 24 h caused a reduction of their photosynthetic activity by 40–60%, whereas the respiratory rate was stimulated by 20–50%. Mitochondria isolated from Pb2+-treated pea leaves oxidized substrates (glycine, succinate, malate) at higher rates than mitochondria from control leaves. The respiratory control (RCR) and the ADP/O ratio were not affected. Pb2+ caused an increase in ATP content and the ATP/ADP ratio in pea and maize leaves. Rapid fractionation of barley protoplasts incubated at low and high CO2 conditions, indicated that the increased ATP/ADP ratio in Pb2+-treated leaves resulted mainly from the production of mitochondrial ATP. The measurements of membrane potential of mitochondria with a TPP+-sensitive electrode further showed that mitochondria isolated from Pb2+-treated leaves had at least as high membrane potential as mitochondria from control leaves. The activity of NAD-malate dehydrogenase in the protoplasts from barley leaves treated with Pb2+ was 3-fold higher than in protoplasts from control leaves. The activities of photorespiratory enzymes NADH-hydroxypyruvate reductase and glycolate oxidase as well as of NAD-malic enzyme were not affected. The presented data indicate that stimulation of respiration in leaves treated by lead is in a close relationship with activation of malate dehydrogenase and stimulation of the mitochondrial ATP production. Thus, respiration might fulfil a protective role during heavy metal exposure.

@article{brindle_rapid_2002,
	title = {Rapid and noninvasive diagnosis of the presence and severity of coronary heart disease using {1H}-{NMR}-based metabonomics},
	volume = {8},
	copyright = {2002 Nature Publishing Group},
	issn = {1546-170X},
	url = {https://www.nature.com/articles/nm802},
	doi = {10/bdjd29},
	abstract = {Although a wide range of risk factors for coronary heart disease have been identified from population studies, these measures, singly or in combination, are insufficiently powerful to provide a reliable, noninvasive diagnosis of the presence of coronary heart disease. Here we show that pattern-recognition techniques applied to proton nuclear magnetic resonance (1H-NMR) spectra of human serum can correctly diagnose not only the presence, but also the severity, of coronary heart disease. Application of supervised partial least squares-discriminant analysis to orthogonal signal-corrected data sets allows {\textgreater}90\% of subjects with stenosis of all three major coronary vessels to be distinguished from subjects with angiographically normal coronary arteries, with a specificity of {\textgreater}90\%. Our studies show for the first time a technique capable of providing an accurate, noninvasive and rapid diagnosis of coronary heart disease that can be used clinically, either in population screening or to allow effective targeting of treatments such as statins.},
	language = {en},
	number = {12},
	urldate = {2021-10-19},
	journal = {Nature Medicine},
	author = {Brindle, Joanne T. and Antti, Henrik and Holmes, Elaine and Tranter, George and Nicholson, Jeremy K. and Bethell, Hugh W. L. and Clarke, Sarah and Schofield, Peter M. and McKilligin, Elaine and Mosedale, David E. and Grainger, David J.},
	month = dec,
	year = {2002},
	note = {Bandiera\_abtest: a
Cg\_type: Nature Research Journals
Number: 12
Primary\_atype: Advertorial
Publisher: Nature Publishing Group},
	pages = {1439--1445},
}

Although a wide range of risk factors for coronary heart disease have been identified from population studies, these measures, singly or in combination, are insufficiently powerful to provide a reliable, noninvasive diagnosis of the presence of coronary heart disease. Here we show that pattern-recognition techniques applied to proton nuclear magnetic resonance (1H-NMR) spectra of human serum can correctly diagnose not only the presence, but also the severity, of coronary heart disease. Application of supervised partial least squares-discriminant analysis to orthogonal signal-corrected data sets allows \textgreater90% of subjects with stenosis of all three major coronary vessels to be distinguished from subjects with angiographically normal coronary arteries, with a specificity of \textgreater90%. Our studies show for the first time a technique capable of providing an accurate, noninvasive and rapid diagnosis of coronary heart disease that can be used clinically, either in population screening or to allow effective targeting of treatments such as statins.

@article{sandstrom_iron_2002,
	title = {Iron stress responses in the cyanobacterium {Synechococcus} sp. {PCC7942}},
	volume = {116},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1034/j.1399-3054.2002.1160216.x},
	doi = {10/ftvtg7},
	abstract = {In the present study, we describe the sequential events by which the cyanobacterium Synechococcus sp. PCC 7942 adapts to iron deficiency. In doing so, we have tried to elucidate both short and long-term acclimation to low iron stress in order to understand how the photosynthetic apparatus adjusts to low iron conditions. Our results show that after an initial step, where CP43′ is induced and where ferredoxin is partly replaced by flavodoxin, the photosynthetic unit starts to undergo major rearrangements. All measured components of Photosystem I (PSI), PSII and cytochrome (Cyt) ƒ decrease relative to chlorophyll (Chl) a. The photochemical efficiencies of the two photosystems also decline during this phase of acclimation. The well-known drop in phycobilisome content measured as phycocyanin (PC)/Chl was not due to an increased degradation, but rather to a decreased rate of synthesis. The largest effects of iron deficiency were observed on PSI, the most iron-rich structure of the photosynthetic apparatus. In the light of the recent discovery of an iron deficiency induced CP43′ ring around PSI a possible dual function of this protein as both an antenna and a quencher is discussed. We also describe the time course of a blue shift in the low temperature Chl emission peak around 715 nm, which originates in PSI. The shift might reflect the disassembly and/or degradation of PSI during iron deficiency and, as a consequence, PSI might under these conditions be found predominantly in a monomeric form. We suggest that the observed functional and compositional alterations represent cellular acclimation enabling growth and development under iron deficiency, and that growth ceases when the acclimation capacity is exhausted. However, the cells remain viable even after growth has ceased, since they resumed growth once iron was added back to the culture.},
	language = {en},
	number = {2},
	urldate = {2021-10-19},
	journal = {Physiologia Plantarum},
	author = {Sandström, Stefan and Ivanov, Alexander G and Park, Youn-Il and Öquist, Gunnar and Gustafsson, Petter},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1034/j.1399-3054.2002.1160216.x},
	pages = {255--263},
}

In the present study, we describe the sequential events by which the cyanobacterium Synechococcus sp. PCC 7942 adapts to iron deficiency. In doing so, we have tried to elucidate both short and long-term acclimation to low iron stress in order to understand how the photosynthetic apparatus adjusts to low iron conditions. Our results show that after an initial step, where CP43′ is induced and where ferredoxin is partly replaced by flavodoxin, the photosynthetic unit starts to undergo major rearrangements. All measured components of Photosystem I (PSI), PSII and cytochrome (Cyt) ƒ decrease relative to chlorophyll (Chl) a. The photochemical efficiencies of the two photosystems also decline during this phase of acclimation. The well-known drop in phycobilisome content measured as phycocyanin (PC)/Chl was not due to an increased degradation, but rather to a decreased rate of synthesis. The largest effects of iron deficiency were observed on PSI, the most iron-rich structure of the photosynthetic apparatus. In the light of the recent discovery of an iron deficiency induced CP43′ ring around PSI a possible dual function of this protein as both an antenna and a quencher is discussed. We also describe the time course of a blue shift in the low temperature Chl emission peak around 715 nm, which originates in PSI. The shift might reflect the disassembly and/or degradation of PSI during iron deficiency and, as a consequence, PSI might under these conditions be found predominantly in a monomeric form. We suggest that the observed functional and compositional alterations represent cellular acclimation enabling growth and development under iron deficiency, and that growth ceases when the acclimation capacity is exhausted. However, the cells remain viable even after growth has ceased, since they resumed growth once iron was added back to the culture.

@article{chaffey_secondary_2002,
	title = {Secondary xylem development in {Arabidopsis}: a model for wood formation},
	volume = {114},
	issn = {1399-3054},
	shorttitle = {Secondary xylem development in {Arabidopsis}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1034/j.1399-3054.2002.1140413.x},
	doi = {10/b76b5r},
	abstract = {Our understanding of the molecular controls regulating the identity of the vascular cambium and the development of secondary xylem and phloem have not yet benefited much from the use of Arabidopsis as a genetic system. Under appropriate growth conditions Arabidopsis undergoes extensive secondary growth in the hypocotyl, with the development of both a vascular and a cork cambium. The secondary xylem of the hypocotyl develops in two phases, an early phase in which only vessel elements mature and a later stage in which both vessel elements and fibres are found. During this second phase the secondary xylem of Arabidopsis closely resembles the anatomy of the wood of an angiosperm tree, and can be used to address basic questions about wood formation. The development of the vascular cambium and secondary growth in Arabidopsis hypocotyl is described and its utility as a model for wood formation in trees is considered.},
	language = {en},
	number = {4},
	urldate = {2021-10-19},
	journal = {Physiologia Plantarum},
	author = {Chaffey, Nigel and Cholewa, Ewa and Regan, Sharon and Sundberg, Björn},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1034/j.1399-3054.2002.1140413.x},
	pages = {594--600},
}

Our understanding of the molecular controls regulating the identity of the vascular cambium and the development of secondary xylem and phloem have not yet benefited much from the use of Arabidopsis as a genetic system. Under appropriate growth conditions Arabidopsis undergoes extensive secondary growth in the hypocotyl, with the development of both a vascular and a cork cambium. The secondary xylem of the hypocotyl develops in two phases, an early phase in which only vessel elements mature and a later stage in which both vessel elements and fibres are found. During this second phase the secondary xylem of Arabidopsis closely resembles the anatomy of the wood of an angiosperm tree, and can be used to address basic questions about wood formation. The development of the vascular cambium and secondary growth in Arabidopsis hypocotyl is described and its utility as a model for wood formation in trees is considered.

@article{dahlman_growth_2002,
	title = {Growth, nitrogen uptake, and resource allocation in the two tripartite lichens {Nephroma} arcticum and {Peltigera} aphthosa during nitrogen stress},
	volume = {153},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.0028-646X.2001.00321.x},
	doi = {10/d2q5rz},
	abstract = {• Lichen responses towards nitrogen stress, both increased exposure and deprivation of N, were investigated by measuring N uptake, growth, ergosterol, chitin and Chla in two tripartite nitrogen-fixing species, Nephroma arctium and Peltigera aphthosa. • The lichens were irrigated with different N forms, enriched in 15N to assess N uptake, during 3 months in the field, with a total N dosage of 500 mg m−2. Nitrogen deprivation was induced by removing the nitrogen-fixing cephalodia. • The lichens took up 11–134 mg N m−2 of the added N, corresponding to 1–4\% of their total thallus N. Uptake was 4 times higher for NH4+ than for NO3−, and the highest 15N concentrations were found in newly synthesized tissue. Both forms of N stress affected thallus expansion rates in both species. • It is concluded that the two lichens were able to maintain a balanced tissue N concentration despite large variations in N supply, and that assimilated N might be transported to growing apices. Alternatively, N assimilation from external sources might be greater in the margins than in the mature thallus. Thallus expansion was sensitive to N stress, apparently being tightly coupled to N assimilation.},
	language = {en},
	number = {2},
	urldate = {2021-10-19},
	journal = {New Phytologist},
	author = {Dahlman, Lena and Näsholm, Torgny and Palmqvist, Kristin},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.0028-646X.2001.00321.x},
	keywords = {15N, chitin, chlorophyll, ergosterol, lichen growth, nitrogen stress, nitrogen uptake, resource allocation},
	pages = {307--315},
}

• Lichen responses towards nitrogen stress, both increased exposure and deprivation of N, were investigated by measuring N uptake, growth, ergosterol, chitin and Chla in two tripartite nitrogen-fixing species, Nephroma arctium and Peltigera aphthosa. • The lichens were irrigated with different N forms, enriched in 15N to assess N uptake, during 3 months in the field, with a total N dosage of 500 mg m−2. Nitrogen deprivation was induced by removing the nitrogen-fixing cephalodia. • The lichens took up 11–134 mg N m−2 of the added N, corresponding to 1–4% of their total thallus N. Uptake was 4 times higher for NH4+ than for NO3−, and the highest 15N concentrations were found in newly synthesized tissue. Both forms of N stress affected thallus expansion rates in both species. • It is concluded that the two lichens were able to maintain a balanced tissue N concentration despite large variations in N supply, and that assimilated N might be transported to growing apices. Alternatively, N assimilation from external sources might be greater in the margins than in the mature thallus. Thallus expansion was sensitive to N stress, apparently being tightly coupled to N assimilation.

@article{ingvarsson_lone_2002,
	title = {Lone wolf to the rescue},
	volume = {420},
	copyright = {2002 Nature Publishing Group},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/420472a},
	doi = {10/cnb2xt},
	abstract = {Genetic analysis has revealed how a small and isolated population of grey wolves found salvation in the form of the genetic variation offered by a single, immigrant male.},
	language = {en},
	number = {6915},
	urldate = {2021-10-19},
	journal = {Nature},
	author = {Ingvarsson, Pär K.},
	month = dec,
	year = {2002},
	note = {Bandiera\_abtest: a
Cg\_type: Nature Research Journals
Number: 6915
Primary\_atype: News \& Views
Publisher: Nature Publishing Group},
	pages = {472--472},
}

Genetic analysis has revealed how a small and isolated population of grey wolves found salvation in the form of the genetic variation offered by a single, immigrant male.

@article{savitch_two_2002,
	title = {Two different strategies for light utilization in photosynthesis in relation to growth and cold acclimation},
	volume = {25},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-3040.2002.00861.x},
	doi = {10/fdjtd5},
	abstract = {Seedlings of Lodgepole pine (Pinus contorta L.) and winter wheat (Triticum aestivum L. cv. Monopol) were cold acclimated under controlled conditions to induce frost hardiness. Lodgepole pine responded to cold acclimation by partial inhibition of photosynthesis with an associated partial loss of photosystem II reaction centres, and a reduction in needle chlorophyll content. This was accompanied by a low daily carbon gain, and the development of a high and sustained capacity for non-photochemical quenching of absorbed light. This sustained dissipation of absorbed light as heat correlated with an increased de-epoxidation of the xanthophyll cycle pigments forming the quenching forms antheraxanthin and zeaxanthin. In addition, the PsbS protein known to bind chlorophyll and the xanthophyll cycle pigments increased strongly during cold acclimation of pine. In contrast, winter wheat maintained high photosynthetic rates, showed no loss of chlorophyll content per leaf area, and exhibited a high daily carbon gain and a minimal non-photochemical quenching after cold acclimation. In accordance, cold acclimation of wheat neither increased the de-epoxidation of the xanthophylls nor the content of the PsbS protein. These different responses of photosynthesis to cold acclimation are correlated with pine, reducing its need for assimilates when entering dormancy associated with termination of primary growth, whereas winter wheat maintains a high need for assimilates as it continues to grow and develop throughout the cold-acclimation period. It appears that without evolving a sustained ability for controlled dissipation of absorbed light as heat throughout the winter, winter green conifers would not have managed to adapt and establish themselves so successfully in the cold climatic zones of the northern hemisphere.},
	language = {en},
	number = {6},
	urldate = {2021-10-19},
	journal = {Plant, Cell \& Environment},
	author = {Savitch, L. V. and Leonardos, E. D. and Krol, M. and Jansson, S. and Grodzinski, B. and Huner, N. P. A. and Öquist, G.},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-3040.2002.00861.x},
	keywords = {Pinus contorta, PsbS protein, Triticum aestivum, cold acclimation, dormancy, evergreen, frost hardening, photo-inhibition, photosynthesis, xanthophyll cycle},
	pages = {761--771},
}

Seedlings of Lodgepole pine (Pinus contorta L.) and winter wheat (Triticum aestivum L. cv. Monopol) were cold acclimated under controlled conditions to induce frost hardiness. Lodgepole pine responded to cold acclimation by partial inhibition of photosynthesis with an associated partial loss of photosystem II reaction centres, and a reduction in needle chlorophyll content. This was accompanied by a low daily carbon gain, and the development of a high and sustained capacity for non-photochemical quenching of absorbed light. This sustained dissipation of absorbed light as heat correlated with an increased de-epoxidation of the xanthophyll cycle pigments forming the quenching forms antheraxanthin and zeaxanthin. In addition, the PsbS protein known to bind chlorophyll and the xanthophyll cycle pigments increased strongly during cold acclimation of pine. In contrast, winter wheat maintained high photosynthetic rates, showed no loss of chlorophyll content per leaf area, and exhibited a high daily carbon gain and a minimal non-photochemical quenching after cold acclimation. In accordance, cold acclimation of wheat neither increased the de-epoxidation of the xanthophylls nor the content of the PsbS protein. These different responses of photosynthesis to cold acclimation are correlated with pine, reducing its need for assimilates when entering dormancy associated with termination of primary growth, whereas winter wheat maintains a high need for assimilates as it continues to grow and develop throughout the cold-acclimation period. It appears that without evolving a sustained ability for controlled dissipation of absorbed light as heat throughout the winter, winter green conifers would not have managed to adapt and establish themselves so successfully in the cold climatic zones of the northern hemisphere.

@article{wullschleger_genomics_2002,
	title = {Genomics and {Forest} {Biology}: {Populus} {Emerges} as the {Perennial} {Favorite}},
	volume = {14},
	issn = {1040-4651},
	shorttitle = {Genomics and {Forest} {Biology}},
	url = {https://doi.org/10.1105/tpc.141120},
	doi = {10/bwdnsd},
	abstract = {Forest biologists have developed strong justifications for why trees should be viewed as model systems in plant biology, including the obvious challenges in extrapolating findings from annual, herbaceous plants to organisms that are distinguished by perennial growth, large size, complex crown architecture, extensive secondary xylem, dormancy, and juvenile–mature phase changes (Bradshaw et al., 2000; Taylor, 2002). Similar justification has been used to argue why the genome of a tree should be sequenced. The U.S. Department of Energy (DOE), Office of Science, announced earlier this year plans to sequence the first tree genome, that of the black cottonwood (Populus trichocarpa) (Figure 1) Figure 1.Populus: A Model System for Tree Genomics.At left, 7-year-old hybrid poplars being harvested in western Oregon. Top right, expression of a poplar DEFICIENS homolog in female floral meristems of black cottonwood (Sheppard et al., 2000); bottom right, germinating pollen grains being tested for viability using a fluorescent stain. .},
	number = {11},
	urldate = {2021-10-19},
	journal = {The Plant Cell},
	author = {Wullschleger, Stan D. and Jansson, Stefan and Taylor, Gail},
	month = nov,
	year = {2002},
	pages = {2651--2655},
}

Forest biologists have developed strong justifications for why trees should be viewed as model systems in plant biology, including the obvious challenges in extrapolating findings from annual, herbaceous plants to organisms that are distinguished by perennial growth, large size, complex crown architecture, extensive secondary xylem, dormancy, and juvenile–mature phase changes (Bradshaw et al., 2000; Taylor, 2002). Similar justification has been used to argue why the genome of a tree should be sequenced. The U.S. Department of Energy (DOE), Office of Science, announced earlier this year plans to sequence the first tree genome, that of the black cottonwood (Populus trichocarpa) (Figure 1) Figure 1.Populus: A Model System for Tree Genomics.At left, 7-year-old hybrid poplars being harvested in western Oregon. Top right, expression of a poplar DEFICIENS homolog in female floral meristems of black cottonwood (Sheppard et al., 2000); bottom right, germinating pollen grains being tested for viability using a fluorescent stain. .

@article{moyle_environmental_2002,
	title = {Environmental and auxin regulation of wood formation involves members of the {Aux}/{IAA} gene family in hybrid aspen},
	volume = {31},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-313X.2002.01386.x},
	doi = {10/fw3n8w},
	abstract = {Indole acetic acid (IAA/auxin) profoundly affects wood formation but the molecular mechanism of auxin action in this process remains poorly understood. We have cloned cDNAs for eight members of the Aux/IAA gene family from hybrid aspen (Populus tremula L. × Populus tremuloides Michx.) that encode potential mediators of the auxin signal transduction pathway. These genes designated as PttIAA1-PttIAA8 are auxin inducible but differ in their requirement of de novo protein synthesis for auxin induction. The auxin induction of the PttIAA genes is also developmentally controlled as evidenced by the loss of their auxin inducibility during leaf maturation. The PttIAA genes are differentially expressed in the cell types of a developmental gradient comprising the wood-forming tissues. Interestingly, the expression of the PttIAA genes is downregulated during transition of the active cambium into dormancy, a process in which meristematic cells of the cambium lose their sensitivity to auxin. Auxin-regulated developmental reprogramming of wood formation during the induction of tension wood is accompanied by changes in the expression of PttIAA genes. The distinct tissue-specific expression patterns of the auxin inducible PttIAA genes in the cambial region together with the change in expression during dormancy transition and tension wood formation suggest a role for these genes in mediating cambial responses to auxin and xylem development.},
	language = {en},
	number = {6},
	urldate = {2021-10-19},
	journal = {The Plant Journal},
	author = {Moyle, Richard and Schrader, Jarmo and Stenberg, Anneli and Olsson, Olof and Saxena, Sangeeta and Sandberg, Göran and Bhalerao, Rishikesh P},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313X.2002.01386.x},
	keywords = {Aux, IAA proteins, auxin, development, dormancy, tension wood, wood formation},
	pages = {675--685},
}

Indole acetic acid (IAA/auxin) profoundly affects wood formation but the molecular mechanism of auxin action in this process remains poorly understood. We have cloned cDNAs for eight members of the Aux/IAA gene family from hybrid aspen (Populus tremula L. × Populus tremuloides Michx.) that encode potential mediators of the auxin signal transduction pathway. These genes designated as PttIAA1-PttIAA8 are auxin inducible but differ in their requirement of de novo protein synthesis for auxin induction. The auxin induction of the PttIAA genes is also developmentally controlled as evidenced by the loss of their auxin inducibility during leaf maturation. The PttIAA genes are differentially expressed in the cell types of a developmental gradient comprising the wood-forming tissues. Interestingly, the expression of the PttIAA genes is downregulated during transition of the active cambium into dormancy, a process in which meristematic cells of the cambium lose their sensitivity to auxin. Auxin-regulated developmental reprogramming of wood formation during the induction of tension wood is accompanied by changes in the expression of PttIAA genes. The distinct tissue-specific expression patterns of the auxin inducible PttIAA genes in the cambial region together with the change in expression during dormancy transition and tension wood formation suggest a role for these genes in mediating cambial responses to auxin and xylem development.

@article{bellec_pasticcino2_2002,
	title = {Pasticcino2 is a protein tyrosine phosphatase-like involved in cell proliferation and differentiation in {Arabidopsis}},
	volume = {32},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-313X.2002.01456.x},
	doi = {10/cgckd9},
	abstract = {The pasticcino2 (pas2) mutant shows impaired embryo and seedling development associated with cell de-differentiation and proliferation. This process is specifically enhanced in presence of cytokinins leading to callus-like structure of the apical part of the seedling. Cell proliferation concerns localized and stochastic nodules of dividing cells. In absence of cytokinins, cell proliferation leads to small calli on stems but, most often, cell proliferation is associated with post-genital organ fusion. The PAS2 gene was identified by positional cloning. PAS2 expression was found in every plant organ and was not regulated by PAS1 and PAS3 genes. PAS2 encodes the Arabidopsis member of the protein tyrosine phosphatase-like (Ptpl) family, a new PTP family originally described in mice and humans and characterized by a mutated PTP active site. This family of proteins has a yeast homolog that is essential for cell viability. The absence of yeast PAS2 homolog can be functionally replaced by the Arabidopsis PAS2 protein, demonstrating that PAS2 function is conserved between higher and lower eukaryotes.},
	language = {en},
	number = {5},
	urldate = {2021-10-19},
	journal = {The Plant Journal},
	author = {Bellec, Yannick and Harrar, Yaël and Butaeye, Christelle and Darnet, Sylvain and Bellini, Catherine and Faure, Jean-Denis},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313X.2002.01456.x},
	keywords = {Ptpl, YJL097w, cytokinins, protein tyrosine phosphatase, tumor},
	pages = {713--722},
}

The pasticcino2 (pas2) mutant shows impaired embryo and seedling development associated with cell de-differentiation and proliferation. This process is specifically enhanced in presence of cytokinins leading to callus-like structure of the apical part of the seedling. Cell proliferation concerns localized and stochastic nodules of dividing cells. In absence of cytokinins, cell proliferation leads to small calli on stems but, most often, cell proliferation is associated with post-genital organ fusion. The PAS2 gene was identified by positional cloning. PAS2 expression was found in every plant organ and was not regulated by PAS1 and PAS3 genes. PAS2 encodes the Arabidopsis member of the protein tyrosine phosphatase-like (Ptpl) family, a new PTP family originally described in mice and humans and characterized by a mutated PTP active site. This family of proteins has a yeast homolog that is essential for cell viability. The absence of yeast PAS2 homolog can be functionally replaced by the Arabidopsis PAS2 protein, demonstrating that PAS2 function is conserved between higher and lower eukaryotes.

@article{jackson_over-expression_2002,
	title = {Over-expression of an {Arabidopsis} gene encoding a glucosyltransferase of indole-3-acetic acid: phenotypic characterisation of transgenic lines},
	volume = {32},
	issn = {1365-313X},
	shorttitle = {Over-expression of an {Arabidopsis} gene encoding a glucosyltransferase of indole-3-acetic acid},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-313X.2002.01445.x},
	doi = {10/bcmjjd},
	abstract = {An analysis of the multigene family of Group 1 glucosyltransferases (UGTs) of Arabidopsis thaliana revealed a gene, UGT84B1, whose recombinant product glucosylated indole-3-acetic acid (IAA) in vitro. Transgenic Arabidopsis plants constitutively over-expressing UGT84B1 under the control of the CaMV 35S promoter have been constructed and their phenotype analysed. The transgenic lines displayed a number of changes that resembled those described previously in lines in which auxin levels were depleted. A root elongation assay was used as a measure of auxin sensitivity. A reduced sensitivity of the transgenic lines compared to wild-type was observed when IAA was applied. In contrast, application of 2,4-dichlorophenoxyacetic acid (2,4-D), previously demonstrated not to be a substrate for UGT84B1, led to a wild-type response. These data suggested that the catalytic specificity of the recombinant enzyme in vitro was maintained in planta. This was further confirmed when levels of IAA metabolites and conjugates were measured in extracts of the transgenic plants and 1-O-IAGlc was found to be elevated to approximately 50 pg mg−1 FW, compared to the trace levels characteristic of wild-type plants. Surprisingly, in the same extracts, levels of free IAA were also found to have accumulated to some 70 pg mg−1 FW compared to approximately 15 pg mg−1 FW in extracts of wild-type plants. Analysis of leaves at different developmental stages revealed the auxin gradient, typical of wild-type plants, was not observed in the transgenic lines, with free IAA levels in the apex and youngest leaves at a lower level compared to wild-type. In total, the data reveal that significant changes in auxin homeostasis can be caused by overproduction of an IAA-conjugating enzyme.},
	language = {en},
	number = {4},
	urldate = {2021-10-19},
	journal = {The Plant Journal},
	author = {Jackson, Rosamond G. and Kowalczyk, Mariusz and Li, Yi and Higgins, Gillian and Ross, Joe and Sandberg, Göran and Bowles, Dianna J.},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313X.2002.01445.x},
	keywords = {auxin, conjugation, glucosyltransferase, metabolism, plant hormones},
	pages = {573--583},
}

An analysis of the multigene family of Group 1 glucosyltransferases (UGTs) of Arabidopsis thaliana revealed a gene, UGT84B1, whose recombinant product glucosylated indole-3-acetic acid (IAA) in vitro. Transgenic Arabidopsis plants constitutively over-expressing UGT84B1 under the control of the CaMV 35S promoter have been constructed and their phenotype analysed. The transgenic lines displayed a number of changes that resembled those described previously in lines in which auxin levels were depleted. A root elongation assay was used as a measure of auxin sensitivity. A reduced sensitivity of the transgenic lines compared to wild-type was observed when IAA was applied. In contrast, application of 2,4-dichlorophenoxyacetic acid (2,4-D), previously demonstrated not to be a substrate for UGT84B1, led to a wild-type response. These data suggested that the catalytic specificity of the recombinant enzyme in vitro was maintained in planta. This was further confirmed when levels of IAA metabolites and conjugates were measured in extracts of the transgenic plants and 1-O-IAGlc was found to be elevated to approximately 50 pg mg−1 FW, compared to the trace levels characteristic of wild-type plants. Surprisingly, in the same extracts, levels of free IAA were also found to have accumulated to some 70 pg mg−1 FW compared to approximately 15 pg mg−1 FW in extracts of wild-type plants. Analysis of leaves at different developmental stages revealed the auxin gradient, typical of wild-type plants, was not observed in the transgenic lines, with free IAA levels in the apex and youngest leaves at a lower level compared to wild-type. In total, the data reveal that significant changes in auxin homeostasis can be caused by overproduction of an IAA-conjugating enzyme.

@article{dolezal_identification_2002,
	title = {Identification of aromatic cytokinins in suspension cultured photoautotrophic cells of {Chenopodium} rubrum by capillary liquid chromatography/frit – fast atom bombardment mass spectrometry},
	volume = {36},
	issn = {1573-5087},
	url = {https://doi.org/10.1023/A:1015027906046},
	doi = {10/bnfzdw},
	abstract = {Two previously unrecorded endogenous cytokinin metabolites,6-[2-(β-D-glucopyranosyloxy)benzylamino]purine and6-[2-(β-D-glucopyranosyloxy)benzylamino]-2-methylthiopurine, wereidentified, together with 6-benzylamino-9-β-D-glucopyranosylpurine(BAP9G),from Chenopodium rubrum cells, grown autotrophically insuspension culture. The new metabolites belong to the aromatic class ofcytokinins, in which an aromatic side chain is attached at theN6-position of the adenine species. The identification was performedby capillary-liquid chromatography/frit-fast atom bombardment - massspectrometry (LC/FAB MS) after pre-column derivatisation and the structuralelucidation was confirmed by organic synthesis. Cytokinin activity of thecompounds was tested in an Amaranthus bioassay. Theendogenous synthesis of the identified compounds was verified byin vivo deuterium labelling of the analysed cytokininspecies, thereby for the first time providing absolute evidence for theendogenous origin of these compounds.},
	language = {en},
	number = {2},
	urldate = {2021-10-19},
	journal = {Plant Growth Regulation},
	author = {Doležal, Karel and Åstot, Crister and Hanuš, Jan and Holub, Jan and Peters, Wilfried and Beck, Erwin and Strnad, Miroslav and Sandberg, Göran},
	month = feb,
	year = {2002},
	pages = {181--189},
}

Two previously unrecorded endogenous cytokinin metabolites,6-[2-(β-D-glucopyranosyloxy)benzylamino]purine and6-[2-(β-D-glucopyranosyloxy)benzylamino]-2-methylthiopurine, wereidentified, together with 6-benzylamino-9-β-D-glucopyranosylpurine(BAP9G),from Chenopodium rubrum cells, grown autotrophically insuspension culture. The new metabolites belong to the aromatic class ofcytokinins, in which an aromatic side chain is attached at theN6-position of the adenine species. The identification was performedby capillary-liquid chromatography/frit-fast atom bombardment - massspectrometry (LC/FAB MS) after pre-column derivatisation and the structuralelucidation was confirmed by organic synthesis. Cytokinin activity of thecompounds was tested in an Amaranthus bioassay. Theendogenous synthesis of the identified compounds was verified byin vivo deuterium labelling of the analysed cytokininspecies, thereby for the first time providing absolute evidence for theendogenous origin of these compounds.

@article{von_aderkas_abscisic_2002,
	title = {Abscisic acid and its influence on development of the embryonal root cap, storage product and secondary metabolite accumulation in hybrid larch somatic embryos},
	volume = {69},
	issn = {1573-5044},
	url = {https://doi.org/10.1023/A:1015245627220},
	doi = {10/fr6k4f},
	abstract = {Somatic embryos of Larix × leptoeuropaea were grown on modified MSG media with 60 μM abscisic acid (ABA). These were compared to control embryos raised on the same medium without ABA. Transmission electron microscopy demonstrated that zonation of polyphenol production as well as presence of extracellular mucilage was markedly different in embryos raised with and without ABA. Idioblasts were found in subepidermal and pith regions of hypocotyls and among the subepidermal cells of cotyledons in embryos matured on ABA, but not in embryos matured without ABA. The embryonal root caps of ABA-treated embryos had substantial deposition of lipids and proteins in both the column and inner pericolumn regions, but not in the outer layer of the pericolumn. Control embryos showed no accumulation of proteins or lipids, but an increase in polyphenol accumulation, which had spread to the epidermal and sub-epidermal layers of the cotyledons and hypocotyl. Starch accumulation was similar over the course of development in embryos treated with or without ABA. Using gas chromatography-selected reaction monitoring mass spectrometry, it was shown that concentrations of ABA averaged 186 ± 17 μg g−1 dry weight (DW) in embryos raised on medium supplemented with this plant growth regulator, versus an average concentration of 55 ± 19 μg g−1 DW in embryos raised in the absence of ABA. No difference in ABA concentration was found between the root cap and the rest of ABA-treated embryos.},
	language = {en},
	number = {2},
	urldate = {2021-10-19},
	journal = {Plant Cell, Tissue and Organ Culture},
	author = {von Aderkas, Patrick and Rohr, René and Sundberg, Björn and Gutmann, Markus and Dumont-BéBoux, Nicole and Lelu, Marie-Anne},
	month = may,
	year = {2002},
	pages = {111--120},
}

Somatic embryos of Larix × leptoeuropaea were grown on modified MSG media with 60 μM abscisic acid (ABA). These were compared to control embryos raised on the same medium without ABA. Transmission electron microscopy demonstrated that zonation of polyphenol production as well as presence of extracellular mucilage was markedly different in embryos raised with and without ABA. Idioblasts were found in subepidermal and pith regions of hypocotyls and among the subepidermal cells of cotyledons in embryos matured on ABA, but not in embryos matured without ABA. The embryonal root caps of ABA-treated embryos had substantial deposition of lipids and proteins in both the column and inner pericolumn regions, but not in the outer layer of the pericolumn. Control embryos showed no accumulation of proteins or lipids, but an increase in polyphenol accumulation, which had spread to the epidermal and sub-epidermal layers of the cotyledons and hypocotyl. Starch accumulation was similar over the course of development in embryos treated with or without ABA. Using gas chromatography-selected reaction monitoring mass spectrometry, it was shown that concentrations of ABA averaged 186 ± 17 μg g−1 dry weight (DW) in embryos raised on medium supplemented with this plant growth regulator, versus an average concentration of 55 ± 19 μg g−1 DW in embryos raised in the absence of ABA. No difference in ABA concentration was found between the root cap and the rest of ABA-treated embryos.

@article{lennartsson_causes_2002,
	title = {Causes of variation in cold hardiness among fast-growing willows ({Salix} spp.) with particular reference to their inherent rates of cold hardening},
	volume = {25},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-3040.2002.00902.x},
	doi = {10/bcrgt2},
	abstract = {Causes of variation in cold hardiness in the autumn were assessed among closely related, fast-growing clones of willow of northern/continental and southern/maritime origins, under controlled regimes and natural conditions. Cold hardiness was assessed by controlled freezing followed by injury analysis, based on measurements of chlorophyll fluorescence (stems) and electrolyte leakage (leaves). During growth at a given temperature, the cold hardiness of the clones' stems was negatively correlated with their rate of growth. This apparently phenotypic variation was independent of temperature and, hence, the absolute growth rate. At later stages, cold hardiness of stems varied mainly with respect to genetic differences in the timing and rate of cold hardening. Cold hardening began up to 7 weeks earlier in northern/continental clones, and their rates of hardening in cool temperature regimes were up to three times higher than in southern/maritime clones. Ranking of clones with respect to rates was essentially the same whether natural or abrupt reductions of day length were used to trigger cold hardening. Results closely agreed with those of a previous field trial. Comparisons of rates at cool and warm temperatures suggest that cold hardening became increasingly dependent on cool temperatures with time. Increasing sucrose-to-glucose ratios, and especially dry-to-fresh weight ratios, paralleled early cold hardening. Before leaves were shed in the autumn they underwent cold hardening in parallel with stems, eventually allowing them to tolerate temperatures down to −10 °C.},
	language = {en},
	number = {10},
	urldate = {2021-10-19},
	journal = {Plant, Cell \& Environment},
	author = {Lennartsson, M. and Ögren, E.},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-3040.2002.00902.x},
	keywords = {Salix, chlorophyll fluorescence, cold hardiness, cold resistance, growth rhythm, willow},
	pages = {1279--1288},
}

Causes of variation in cold hardiness in the autumn were assessed among closely related, fast-growing clones of willow of northern/continental and southern/maritime origins, under controlled regimes and natural conditions. Cold hardiness was assessed by controlled freezing followed by injury analysis, based on measurements of chlorophyll fluorescence (stems) and electrolyte leakage (leaves). During growth at a given temperature, the cold hardiness of the clones' stems was negatively correlated with their rate of growth. This apparently phenotypic variation was independent of temperature and, hence, the absolute growth rate. At later stages, cold hardiness of stems varied mainly with respect to genetic differences in the timing and rate of cold hardening. Cold hardening began up to 7 weeks earlier in northern/continental clones, and their rates of hardening in cool temperature regimes were up to three times higher than in southern/maritime clones. Ranking of clones with respect to rates was essentially the same whether natural or abrupt reductions of day length were used to trigger cold hardening. Results closely agreed with those of a previous field trial. Comparisons of rates at cool and warm temperatures suggest that cold hardening became increasingly dependent on cool temperatures with time. Increasing sucrose-to-glucose ratios, and especially dry-to-fresh weight ratios, paralleled early cold hardening. Before leaves were shed in the autumn they underwent cold hardening in parallel with stems, eventually allowing them to tolerate temperatures down to −10 °C.

@article{moseley_reciprocal_2002,
	title = {Reciprocal {Expression} of {Two} {Candidate} {Di}-{Iron} {Enzymes} {Affecting} {Photosystem} {I} and {Light}-{Harvesting} {Complex} {Accumulation}},
	volume = {14},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.010420},
	doi = {10/d4c8zx},
	abstract = {Crd1 (Copper response defect 1), which is required for the maintenance of photosystem I and its associated light-harvesting complexes in copper-deficient (−Cu) and oxygen-deficient (−O2) Chlamydomonas reinhardtii cells, is localized to the thylakoid membrane. A related protein, Cth1 (Copper target homolog 1), is shown to have a similar but not identical function by genetic suppressor analysis of gain-of-function sct1 (suppressor of copper target 1) strains that are transposon-containing alleles at CTH1. The pattern of Crd1 versus Cth1 accumulation is reciprocal; Crd1 abundance is increased in −Cu or −O2 cells, whereas Cth1 accumulates in copper-sufficient (+Cu), oxygenated cells. This expression pattern is determined by a single trans-acting regulatory locus, CRR1 (COPPER RESPONSE REGULATOR 1), which activates transcription in −Cu cells. In +Cu cells, a 2.1-kb Cth1 mRNA is produced and translated, whereas Crd1 is transcribed only at basal levels, leading to Cth1 accumulation in +Cu cells. In −Cu cells, CRR1 function determines the activation of Crd1 expression and the production of an alternative 3.1-kb Cth1 mRNA that is extended at the 5′ end relative to the 2.1-kb mRNA. Synthesis of the 3.1-kb mRNA, which encodes six small upstream open reading frames that possibly result in poor translation, blocks the downstream promoter through transcriptional occlusion. Fluorescence analysis of wild-type, crd1, and sct1 strains indicates that copper-responsive adjustment of the Cth1:Crd1 ratio results in modification of the interactions between photosystem I and associated light-harvesting complexes. The tightly coordinated CRR1-dependent regulation of isoenzymes Cth1 and Crd1 reinforces the notion that copper plays a specific role in the maintenance of chlorophyll proteins.},
	number = {3},
	urldate = {2021-10-19},
	journal = {The Plant Cell},
	author = {Moseley, Jeffrey L. and Page, M. Dudley and Alder, Nancy P. and Eriksson, Mats and Quinn, Jeanette and Soto, Feiris and Theg, Steven M. and Hippler, Michael and Merchant, Sabeeha},
	month = mar,
	year = {2002},
	pages = {673--688},
}

Crd1 (Copper response defect 1), which is required for the maintenance of photosystem I and its associated light-harvesting complexes in copper-deficient (−Cu) and oxygen-deficient (−O2) Chlamydomonas reinhardtii cells, is localized to the thylakoid membrane. A related protein, Cth1 (Copper target homolog 1), is shown to have a similar but not identical function by genetic suppressor analysis of gain-of-function sct1 (suppressor of copper target 1) strains that are transposon-containing alleles at CTH1. The pattern of Crd1 versus Cth1 accumulation is reciprocal; Crd1 abundance is increased in −Cu or −O2 cells, whereas Cth1 accumulates in copper-sufficient (+Cu), oxygenated cells. This expression pattern is determined by a single trans-acting regulatory locus, CRR1 (COPPER RESPONSE REGULATOR 1), which activates transcription in −Cu cells. In +Cu cells, a 2.1-kb Cth1 mRNA is produced and translated, whereas Crd1 is transcribed only at basal levels, leading to Cth1 accumulation in +Cu cells. In −Cu cells, CRR1 function determines the activation of Crd1 expression and the production of an alternative 3.1-kb Cth1 mRNA that is extended at the 5′ end relative to the 2.1-kb mRNA. Synthesis of the 3.1-kb mRNA, which encodes six small upstream open reading frames that possibly result in poor translation, blocks the downstream promoter through transcriptional occlusion. Fluorescence analysis of wild-type, crd1, and sct1 strains indicates that copper-responsive adjustment of the Cth1:Crd1 ratio results in modification of the interactions between photosystem I and associated light-harvesting complexes. The tightly coordinated CRR1-dependent regulation of isoenzymes Cth1 and Crd1 reinforces the notion that copper plays a specific role in the maintenance of chlorophyll proteins.

@article{schrick_interactions_2002,
	title = {Interactions between sterol biosynthesis genes in embryonic development of {Arabidopsis}},
	volume = {31},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-313X.2002.01333.x},
	doi = {10/fv724z},
	abstract = {The sterol biosynthesis pathway of Arabidopsis produces a large set of structurally related phytosterols including sitosterol and campesterol, the latter being the precursor of the brassinosteroids (BRs). While BRs are implicated as phytohormones in post-embryonic growth, the functions of other types of steroid molecules are not clear. Characterization of the fackel (fk) mutants provided the first hint that sterols play a role in plant embryogenesis. FK encodes a sterol C-14 reductase that acts upstream of all known enzymatic steps corresponding to BR biosynthesis mutants. Here we report that genetic screens for fk-like seedling and embryonic phenotypes have identified two additional genes coding for sterol biosynthesis enzymes: CEPHALOPOD (CPH), a C-24 sterol methyl transferase, and HYDRA1 (HYD1), a sterol C-8,7 isomerase. We describe genetic interactions between cph, hyd1 and fk, and studies with 15-azasterol, an inhibitor of sterol C-14 reductase. Our experiments reveal that FK and HYD1 act sequentially, whereas CPH acts independently of these genes to produce essential sterols. Similar experiments indicate that the BR biosynthesis gene DWF1 acts independently of FK, whereas BR receptor gene BRI1 acts downstream of FK to promote post-embryonic growth. We found embryonic patterning defects in cph mutants and describe a GC–MS analysis of cph tissues which suggests that steroid molecules in addition to BRs play critical roles during plant embryogenesis. Taken together, our results imply that the sterol biosynthesis pathway is not a simple linear pathway but a complex network of enzymes that produce essential steroid molecules for plant growth and development.},
	language = {en},
	number = {1},
	urldate = {2021-10-19},
	journal = {The Plant Journal},
	author = {Schrick, Kathrin and Mayer, Ulrike and Martin, Gottfried and Bellini, Catherine and Kuhnt, Christine and Schmidt, Jürgen and Jürgens, Gerd},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313X.2002.01333.x},
	keywords = {15-azasterol, Arabidopsis, GC–MS, brassinosteroids., embryogenesis, sterols},
	pages = {61--73},
}

The sterol biosynthesis pathway of Arabidopsis produces a large set of structurally related phytosterols including sitosterol and campesterol, the latter being the precursor of the brassinosteroids (BRs). While BRs are implicated as phytohormones in post-embryonic growth, the functions of other types of steroid molecules are not clear. Characterization of the fackel (fk) mutants provided the first hint that sterols play a role in plant embryogenesis. FK encodes a sterol C-14 reductase that acts upstream of all known enzymatic steps corresponding to BR biosynthesis mutants. Here we report that genetic screens for fk-like seedling and embryonic phenotypes have identified two additional genes coding for sterol biosynthesis enzymes: CEPHALOPOD (CPH), a C-24 sterol methyl transferase, and HYDRA1 (HYD1), a sterol C-8,7 isomerase. We describe genetic interactions between cph, hyd1 and fk, and studies with 15-azasterol, an inhibitor of sterol C-14 reductase. Our experiments reveal that FK and HYD1 act sequentially, whereas CPH acts independently of these genes to produce essential sterols. Similar experiments indicate that the BR biosynthesis gene DWF1 acts independently of FK, whereas BR receptor gene BRI1 acts downstream of FK to promote post-embryonic growth. We found embryonic patterning defects in cph mutants and describe a GC–MS analysis of cph tissues which suggests that steroid molecules in addition to BRs play critical roles during plant embryogenesis. Taken together, our results imply that the sterol biosynthesis pathway is not a simple linear pathway but a complex network of enzymes that produce essential steroid molecules for plant growth and development.

@article{bhalerao_shoot-derived_2002,
	title = {Shoot-derived auxin is essential for early lateral root emergence in {Arabidopsis} seedlings},
	volume = {29},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.0960-7412.2001.01217.x},
	doi = {10/cjt66p},
	abstract = {Lateral root formation is profoundly affected by auxins. Here we present data which indicate that light influences the formation of indole-3-acetic acid (IAA) in germinating Arabidopsis seedlings. IAA transported from the developing leaves to the root system is detectable as a short-lived pulse in the roots and is required for the emergence of the lateral root primordia (LRP) during early seedling development. LRP emergence is inhibited by the removal of apical tissues prior to detection of the IAA pulse in the root, but this treatment has minimal effects on LRP initiation. Our results identify the first developing true leaves as the most likely source for the IAA required for the first emergence of the LRP, as removal of cotyledons has only a minor effect on LRP emergence in contrast to removal of the leaves. A basipetal IAA concentration gradient with high levels of IAA in the root tip appears to control LRP initiation, in contrast to their emergence. A significant increase in the ability of the root system to synthesize IAA is observed 10 days after germination, and this in turn is reflected in the reduced dependence of the lateral root emergence on aerial tissue-derived auxin at this stage. We propose a model for lateral root formation during early seedling development that can be divided into two phases: (i) an LRP initiation phase dependent on a root tip-localized IAA source, and (ii) an LRP emergence phase dependent on leaf-derived IAA up to 10 days after germination.},
	language = {en},
	number = {3},
	urldate = {2021-10-19},
	journal = {The Plant Journal},
	author = {Bhalerao, Rishikesh P. and Eklöf, Jan and Ljung, Karin and Marchant, Alan and Bennett, Malcolm and Sandberg, Göran},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.0960-7412.2001.01217.x},
	keywords = {Arabidopsis thaliana, IAA, auxin, lateral root},
	pages = {325--332},
}

Lateral root formation is profoundly affected by auxins. Here we present data which indicate that light influences the formation of indole-3-acetic acid (IAA) in germinating Arabidopsis seedlings. IAA transported from the developing leaves to the root system is detectable as a short-lived pulse in the roots and is required for the emergence of the lateral root primordia (LRP) during early seedling development. LRP emergence is inhibited by the removal of apical tissues prior to detection of the IAA pulse in the root, but this treatment has minimal effects on LRP initiation. Our results identify the first developing true leaves as the most likely source for the IAA required for the first emergence of the LRP, as removal of cotyledons has only a minor effect on LRP emergence in contrast to removal of the leaves. A basipetal IAA concentration gradient with high levels of IAA in the root tip appears to control LRP initiation, in contrast to their emergence. A significant increase in the ability of the root system to synthesize IAA is observed 10 days after germination, and this in turn is reflected in the reduced dependence of the lateral root emergence on aerial tissue-derived auxin at this stage. We propose a model for lateral root formation during early seedling development that can be divided into two phases: (i) an LRP initiation phase dependent on a root tip-localized IAA source, and (ii) an LRP emergence phase dependent on leaf-derived IAA up to 10 days after germination.

@article{ljung_biosynthesis_2002,
	title = {Biosynthesis, conjugation, catabolism and homeostasis of indole-3-acetic acid in {Arabidopsis} thaliana},
	volume = {49},
	issn = {1573-5028},
	url = {https://doi.org/10.1023/A:1015298812300},
	doi = {10/bws57n},
	language = {en},
	number = {3},
	urldate = {2021-10-19},
	journal = {Plant Molecular Biology},
	author = {Ljung, Karin and Hull, Anna K. and Kowalczyk, Mariusz and Marchant, Alan and Celenza, John and Cohen, Jerry D. and Sandberg, Göran},
	month = jun,
	year = {2002},
	pages = {249--272},
}

@article{quinn_oxygen_2002,
	title = {Oxygen {Deficiency} {Responsive} {Gene} {Expression} {inChlamydomonas} reinhardtii through a {Copper}-{Sensing} {Signal} {Transduction} {Pathway}},
	volume = {128},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.010694},
	doi = {10/cp86k3},
	abstract = {Chlamydomonas reinhardtii activatesCpx1, Cyc6, and Crd1, encoding, respectively, coproporphyrinogen oxidase, cytochromec  6, and a novel di-iron enzyme when transferred to oxygen-deficient growth conditions. This response is physiologically relevant because C. reinhardtiiexperiences these growth conditions routinely, and furthermore, one of the target genes, Crd1, is functionally required for normal growth under oxygen-depleted conditions. The same genes are activated also in response to copper-deficiency through copper-response elements that function as target sites for a transcriptional activator. The core of the copper-response element, GTAC, is required also for the hypoxic response, as is a trans-acting locus, CRR1. Mercuric ions, which antagonize the copper-deficiency response, also antagonize the oxygen-deficiency response of these target genes. Taken together, these observations suggest that the oxygen- and copper-deficiency responses share signal transduction components. Nevertheless, whereas the copper-response element is sufficient for the nutritional copper response, the oxygen-deficiency response requires, in addition, a second cis-element, indicating that the response to oxygen depletion is not identical to the nutritional copper response. The distinction between the two responses is also supported by comparative analysis of the response of the target genes,Cyc6, Cpx1, and Crd1, to copper versus oxygen deficiency. A Crr1-independent pathway forHyd1 expression in oxygen-depleted C. reinhardtii demonstrates the existence of multiple oxygen/redox-responsive circuits in this model organism.},
	number = {2},
	urldate = {2021-10-19},
	journal = {Plant Physiology},
	author = {Quinn, Jeanette M. and Eriksson, Mats and Moseley, Jeffrey L. and Merchant, Sabeeha},
	month = feb,
	year = {2002},
	pages = {463--471},
}

Chlamydomonas reinhardtii activatesCpx1, Cyc6, and Crd1, encoding, respectively, coproporphyrinogen oxidase, cytochromec  6, and a novel di-iron enzyme when transferred to oxygen-deficient growth conditions. This response is physiologically relevant because C. reinhardtiiexperiences these growth conditions routinely, and furthermore, one of the target genes, Crd1, is functionally required for normal growth under oxygen-depleted conditions. The same genes are activated also in response to copper-deficiency through copper-response elements that function as target sites for a transcriptional activator. The core of the copper-response element, GTAC, is required also for the hypoxic response, as is a trans-acting locus, CRR1. Mercuric ions, which antagonize the copper-deficiency response, also antagonize the oxygen-deficiency response of these target genes. Taken together, these observations suggest that the oxygen- and copper-deficiency responses share signal transduction components. Nevertheless, whereas the copper-response element is sufficient for the nutritional copper response, the oxygen-deficiency response requires, in addition, a second cis-element, indicating that the response to oxygen depletion is not identical to the nutritional copper response. The distinction between the two responses is also supported by comparative analysis of the response of the target genes,Cyc6, Cpx1, and Crd1, to copper versus oxygen deficiency. A Crr1-independent pathway forHyd1 expression in oxygen-depleted C. reinhardtii demonstrates the existence of multiple oxygen/redox-responsive circuits in this model organism.

@article{clarke_amino_2002,
	title = {Amino acid deletions in the cytosolic domains of the chlorophyll a-binding protein {CP47} slow {QA}− oxidation and/or prevent the assembly of {Photosystem} {II}},
	volume = {50},
	issn = {1573-5028},
	url = {https://doi.org/10.1023/A:1019865909130},
	doi = {10/d2jh8m},
	abstract = {The Photosystem II (PSII) core antenna chlorophyll a-binding protein, CP47, contains six membrane-spanning α-helices separated by five hydrophilic loops: A–E. To identify important hydrophilic cytosolic regions, oligonucleotide-directed mutagenesis was employed to introduce short segment deletions into loops B and D, and the C-terminal domain. Four strains carrying deletions of between three and five residues were created in loop B. Two strains, with deletions adjacent to helices II and III, did not assemble PSII; however, the mutants Δ(F123–D125) and Δ(R127–S131) remained photoautotrophic with near wild-type levels of assembled reaction centers. In contrast, all deletions introduced into loop D, connecting helices IV and V, failed to assemble significant levels of PSII and were obligate photoheterotrophic mutants. However, deletions in the C-terminal domain did not prevent the assembly of PSII reaction centers although the mutant Δ(S471–T473), with a deletion adjacent to helix VI, exhibited retarded QA− oxidation kinetics and the PSII-specific herbicide, atrazine, bound less tightly in the Δ(S471–T473) and Δ(F475–D477) strains. Deletions in the C-terminal domain also created mutants with large protein aggregates that were recognized by an antibody raised against the PSII reaction center D1 protein. Low-temperature fluorescence emission spectra of photoautotrophic strains carrying deletions in either the C-terminal domain or loop B did not provide evidence for impaired energy transfer from the phycobilisomes to the PSII reaction center. The data therefore suggest an important structural role for loop D in the assembly of PSII and a potential interaction between the C-terminal domain of CP47 and the PSII reaction center that, when perturbed, results in photoinduced protein aggregates involving the D1 protein.},
	language = {en},
	number = {3},
	urldate = {2021-10-19},
	journal = {Plant Molecular Biology},
	author = {Clarke, Shannon M. and Funk, Christiane and Hendry, Garth S. and Shand, Jackie A. and Wydrzynski, Tom and Eaton-Rye, Julian J.},
	month = oct,
	year = {2002},
	pages = {563--572},
}

The Photosystem II (PSII) core antenna chlorophyll a-binding protein, CP47, contains six membrane-spanning α-helices separated by five hydrophilic loops: A–E. To identify important hydrophilic cytosolic regions, oligonucleotide-directed mutagenesis was employed to introduce short segment deletions into loops B and D, and the C-terminal domain. Four strains carrying deletions of between three and five residues were created in loop B. Two strains, with deletions adjacent to helices II and III, did not assemble PSII; however, the mutants Δ(F123–D125) and Δ(R127–S131) remained photoautotrophic with near wild-type levels of assembled reaction centers. In contrast, all deletions introduced into loop D, connecting helices IV and V, failed to assemble significant levels of PSII and were obligate photoheterotrophic mutants. However, deletions in the C-terminal domain did not prevent the assembly of PSII reaction centers although the mutant Δ(S471–T473), with a deletion adjacent to helix VI, exhibited retarded QA− oxidation kinetics and the PSII-specific herbicide, atrazine, bound less tightly in the Δ(S471–T473) and Δ(F475–D477) strains. Deletions in the C-terminal domain also created mutants with large protein aggregates that were recognized by an antibody raised against the PSII reaction center D1 protein. Low-temperature fluorescence emission spectra of photoautotrophic strains carrying deletions in either the C-terminal domain or loop B did not provide evidence for impaired energy transfer from the phycobilisomes to the PSII reaction center. The data therefore suggest an important structural role for loop D in the assembly of PSII and a potential interaction between the C-terminal domain of CP47 and the PSII reaction center that, when perturbed, results in photoinduced protein aggregates involving the D1 protein.

@article{welling_independent_2002,
	title = {Independent {Activation} of {Cold} {Acclimation} by {Low} {Temperature} and {Short} {Photoperiod} in {Hybrid} {Aspen}},
	volume = {129},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.003814},
	doi = {10/bwp2sf},
	abstract = {Temperate zone woody plants cold acclimate in response to both short daylength (SD) and low temperature (LT). We were able to show that these two environmental cues induce cold acclimation independently by comparing the wild type (WT) and the transgenic hybrid aspen (Populus tremula × Populus tremuloides Michx.) line 22 overexpressing the oat (Avena sativa) PHYTOCHROME A gene. Line 22 was not able to detect the SD and, consequently, did not stop growing in SD conditions. This resulted in an impaired freezing tolerance development under SD. In contrast, exposure to LT resulted in cold acclimation of line 22 to a degree comparable with the WT. In contrast to the WT, line 22 could not dehydrate the overwintering tissues or induce the production of dehydrins (DHN) under SD conditions. Furthermore, abscisic acid (ABA) content of the buds of line 22 were the same under SD and long daylength, whereas prolonged SD exposure decreased the ABA level in the WT. LT exposure resulted in a rapid accumulation of DHN in both the WT and line 22. Similarly, ABA content increased transiently in both the WT and line 22. Our results indicate that phytochrome A is involved in photoperiodic regulation of ABA and DHN levels, but at LT they are regulated by a different mechanism. Although SD and LT induce cold acclimation independently, ABA and DHN may play important roles in both modes of acclimation.},
	number = {4},
	urldate = {2021-10-19},
	journal = {Plant Physiology},
	author = {Welling, Annikki and Moritz, Thomas and Palva, E. Tapio and Junttila, Olavi},
	month = aug,
	year = {2002},
	pages = {1633--1641},
}

Temperate zone woody plants cold acclimate in response to both short daylength (SD) and low temperature (LT). We were able to show that these two environmental cues induce cold acclimation independently by comparing the wild type (WT) and the transgenic hybrid aspen (Populus tremula × Populus tremuloides Michx.) line 22 overexpressing the oat (Avena sativa) PHYTOCHROME A gene. Line 22 was not able to detect the SD and, consequently, did not stop growing in SD conditions. This resulted in an impaired freezing tolerance development under SD. In contrast, exposure to LT resulted in cold acclimation of line 22 to a degree comparable with the WT. In contrast to the WT, line 22 could not dehydrate the overwintering tissues or induce the production of dehydrins (DHN) under SD conditions. Furthermore, abscisic acid (ABA) content of the buds of line 22 were the same under SD and long daylength, whereas prolonged SD exposure decreased the ABA level in the WT. LT exposure resulted in a rapid accumulation of DHN in both the WT and line 22. Similarly, ABA content increased transiently in both the WT and line 22. Our results indicate that phytochrome A is involved in photoperiodic regulation of ABA and DHN levels, but at LT they are regulated by a different mechanism. Although SD and LT induce cold acclimation independently, ABA and DHN may play important roles in both modes of acclimation.

@article{xu_small_2002,
	title = {Small {Cab}-like proteins regulating tetrapyrrole biosynthesis in the cyanobacterium {Synechocystis} sp. {PCC} 6803},
	volume = {49},
	issn = {1573-5028},
	url = {https://doi.org/10.1023/A:1014900806905},
	doi = {10/cw2469},
	abstract = {In the cyanobacterium Synechocystis sp. PCC 6803 five open reading frames (scpA–scpE) have been identified that code for single-helix proteins resembling helices I and III of chlorophyll a/b-binding (Cab) antenna proteins from higher plants. They have been named SCPs (small Cab-like proteins). Deletion of a single scp gene in a wild-type or in a photosystem I-less (PS I-less) strain has little effect. However, the effects of functional deletion of scpB or scpE were remarkable under conditions where chlorophyll availability was limited. When cells of a strain lacking PS I and chlL (coding for a polypeptide needed for light-independent protochlorophyllide reduction) were grown in darkness, the phycobilin and protochlorophyllide levels decreased upon deletion of scpB or scpE and the protoheme level was reduced in the strain lacking scpE. Addition of δ-aminolevulinic acid (ALA) in darkness drastically increased the level of Mg-protoporphyrin IX and Mg-protoporphyrin IX monomethyl ester in the PS I-less/chlL−/scpE− strain, whereas PChlide accumulated in the PS I-less/chlL−/scpB− strain. In the PS I-less/chlL− control strain ALA supplementation did not lead to large changes in the levels of tetrapyrrole biosynthesis intermediates. We propose that ScpE and ScpB regulate tetrapyrrole biosynthesis as a function of pigment availability. This regulation occurs primarily at an early step of tetrapyrrole biosynthesis, prior to ALA. In view of the conserved nature of chlorophyll-binding sites in these proteins, it seems likely that regulation by SCPs occurs as a function of chlorophyll availability, with SCPs activating chlorophyll biosynthesis steps when they do not have pigments bound.},
	language = {en},
	number = {2},
	urldate = {2021-10-19},
	journal = {Plant Molecular Biology},
	author = {Xu, Hong and Vavilin, Dmitrii and Funk, Christiane and Vermaas, Wim},
	month = may,
	year = {2002},
	pages = {149--160},
}

In the cyanobacterium Synechocystis sp. PCC 6803 five open reading frames (scpA–scpE) have been identified that code for single-helix proteins resembling helices I and III of chlorophyll a/b-binding (Cab) antenna proteins from higher plants. They have been named SCPs (small Cab-like proteins). Deletion of a single scp gene in a wild-type or in a photosystem I-less (PS I-less) strain has little effect. However, the effects of functional deletion of scpB or scpE were remarkable under conditions where chlorophyll availability was limited. When cells of a strain lacking PS I and chlL (coding for a polypeptide needed for light-independent protochlorophyllide reduction) were grown in darkness, the phycobilin and protochlorophyllide levels decreased upon deletion of scpB or scpE and the protoheme level was reduced in the strain lacking scpE. Addition of δ-aminolevulinic acid (ALA) in darkness drastically increased the level of Mg-protoporphyrin IX and Mg-protoporphyrin IX monomethyl ester in the PS I-less/chlL−/scpE− strain, whereas PChlide accumulated in the PS I-less/chlL−/scpB− strain. In the PS I-less/chlL− control strain ALA supplementation did not lead to large changes in the levels of tetrapyrrole biosynthesis intermediates. We propose that ScpE and ScpB regulate tetrapyrrole biosynthesis as a function of pigment availability. This regulation occurs primarily at an early step of tetrapyrrole biosynthesis, prior to ALA. In view of the conserved nature of chlorophyll-binding sites in these proteins, it seems likely that regulation by SCPs occurs as a function of chlorophyll availability, with SCPs activating chlorophyll biosynthesis steps when they do not have pigments bound.

@article{sehnke_evolution_2002,
	title = {Evolution and isoform specificity of plant 14-3-3 proteins},
	volume = {50},
	issn = {0167-4412},
	doi = {10/d728pb},
	abstract = {The 14-3-3 proteins, once thought of as obscure mammalian brain proteins, are fast becoming recognized as major regulators of plant primary metabolism and of other cellular processes. Their presence as large gene families in plants underscores their essential role in plant physiology. We have examined the Arabidopsis thaliana 14-3-3 gene family, which currently is the largest and most complete 14-3-3 family with at least 12 expressed members and 15 genes from the now completed Arabidopsis thaliana genome project. The phylogenetic branching of this family serves as the prototypical model for comparison with other large plant 14-3-3 families and as such may serve to rationalize clustering in a biological context. Equally important for ascribing common functions for the various 14-3-3 isoforms is determining an isoform-specific correlation with localization and target partnering. A summary of localization information available in the literature is presented. In an effort to identify specific 14-3-3 isoform location and participation in cellular processes, we have produced a panel of isoform-specific antibodies to Arabidopsis thaliana 14-3-3s and present initial immunolocalization studies that suggest biologically relevant, discriminative partnering of 14-3-3 isoforms.},
	language = {eng},
	number = {6},
	journal = {Plant Molecular Biology},
	author = {Sehnke, Paul C. and Rosenquist, Magnus and Alsterfjord, Magnus and DeLille, Justin and Sommarin, Marianne and Larsson, Christer and Ferl, Robert J.},
	month = dec,
	year = {2002},
	pmid = {12516868},
	keywords = {14-3-3 Proteins, Arabidopsis, Evolution, Molecular, Microscopy, Fluorescence, Non-programmatic, Phylogeny, Plant Proteins, Protein Binding, Protein Isoforms, Tyrosine 3-Monooxygenase},
	pages = {1011--1018},
}

The 14-3-3 proteins, once thought of as obscure mammalian brain proteins, are fast becoming recognized as major regulators of plant primary metabolism and of other cellular processes. Their presence as large gene families in plants underscores their essential role in plant physiology. We have examined the Arabidopsis thaliana 14-3-3 gene family, which currently is the largest and most complete 14-3-3 family with at least 12 expressed members and 15 genes from the now completed Arabidopsis thaliana genome project. The phylogenetic branching of this family serves as the prototypical model for comparison with other large plant 14-3-3 families and as such may serve to rationalize clustering in a biological context. Equally important for ascribing common functions for the various 14-3-3 isoforms is determining an isoform-specific correlation with localization and target partnering. A summary of localization information available in the literature is presented. In an effort to identify specific 14-3-3 isoform location and participation in cellular processes, we have produced a panel of isoform-specific antibodies to Arabidopsis thaliana 14-3-3s and present initial immunolocalization studies that suggest biologically relevant, discriminative partnering of 14-3-3 isoforms.

@article{matheson_inbreeding_2002,
	title = {Inbreeding in {Pinus} radiata {III}: the effect of inbreeding on age-age correlation and early selection efficiency},
	shorttitle = {Inbreeding in {Pinus} radiata {III}},
	abstract = {A breeding strategy involving inbreeding followed by crossbreeding of inbreds requires that the production of superior inbred lines must be possible, but crosses between lines should exhibit heterosis, inbreeding should not substantially delay reproduction, and early selection between lines to be effective. Age-age correlation and the effectiveness of early selection have been extensively reported for outcrossed populations of different species, but there are no reports for inbred populations. In this study, age-age correlations based on both family means and individual trees were investigated and compared in radiata pine populations with five different inbreeding levels (F = 0, 0.125, 0.25, 0.5 and 0.75). Trends in additive genetic variance, environmental variance, heritability and age-age additive genetic correlations were estimated from an outcrossed population (F = 0). For cross-sectional area at breast height, additive genetic variance increased from 3.7\% at age 3 to 29.4\% at age 5, remained at about 30\% up to age 10, then declined to 15.6\% at age 13.},
	number = {51},
	urldate = {2021-11-22},
	journal = {Silvae Genetica},
	author = {Matheson, A. Colin and Wu, Harry X. and Spencer, David J. and Raymond, Carolyn A. and Griffin, A. Rod},
	year = {2002},
	keywords = {⛔ No DOI found},
	pages = {115--122},
}

A breeding strategy involving inbreeding followed by crossbreeding of inbreds requires that the production of superior inbred lines must be possible, but crosses between lines should exhibit heterosis, inbreeding should not substantially delay reproduction, and early selection between lines to be effective. Age-age correlation and the effectiveness of early selection have been extensively reported for outcrossed populations of different species, but there are no reports for inbred populations. In this study, age-age correlations based on both family means and individual trees were investigated and compared in radiata pine populations with five different inbreeding levels (F = 0, 0.125, 0.25, 0.5 and 0.75). Trends in additive genetic variance, environmental variance, heritability and age-age additive genetic correlations were estimated from an outcrossed population (F = 0). For cross-sectional area at breast height, additive genetic variance increased from 3.7% at age 3 to 29.4% at age 5, remained at about 30% up to age 10, then declined to 15.6% at age 13.

@article{eriksson_daylength_2002,
	title = {Daylength and spatial expression of a gibberellin 20-oxidase isolated from hybrid aspen ({Populus} tremula {L}. × {P}. tremuloides {Michx}.)},
	volume = {214},
	issn = {1432-2048},
	url = {https://doi.org/10.1007/s00425-001-0703-3},
	doi = {10/bn4z3p},
	abstract = {Physiologically active gibberellins (GAs) are key regulators of shoot growth in trees. To investigate this mechanism of GA-controlled growth in hybrid aspen, we cloned cDNAs encoding gibberellin 20-oxidase (GA 20-oxidase), a key, highly regulated enzyme in the biosynthesis of GAs. Clones were isolated from leaf and cambium cDNA libraries using probes generated by polymerase chain reaction, based on conserved domains of GA 20-oxidases. Upon expression in Escherichia coli, the GST-fusion protein was shown to oxidise GA12 as well as oxidising the 13-hydroxylated substrate GA53, successively to GA9 and GA20, respectively. The gene PttGA20ox1 was expressed in meristematic cells and growing tissues such as expanding internodes, leaves and roots. The expression was negatively regulated by both GA4 and overexpression of phytochrome A. RNA analysis also showed that the expression was down-regulated in late-expanding leaf tissue in response to short days (SDs). Actively growing tissues such as early elongating internodes, petioles and leaf blades had the highest levels of C19-GAs. Upon transfer to SDs an accumulation of GA19 was observed in early elongating internodes and leaf blades. The levels of C19-GAs were also to some extent changed upon transfer to SDs. The levels of GA20 were down-regulated in internodes, and those of GA1 were significantly reduced in early expanding leaf blades. In roots the metabolites GA19 and GA8 decreased upon shifts to SDs, while GA20 accumulated slightly. The down-regulation of GA 20-oxidase activity in response to SDs was further indicated by studies of [14C]GA12 metabolism in shoots, demonstrating that the substrate for GA 20-oxidase, [14C]GA53, accumulates in SDs.},
	language = {en},
	number = {6},
	urldate = {2021-10-19},
	journal = {Planta},
	author = {Eriksson, Maria E. and Moritz, Thomas},
	month = apr,
	year = {2002},
	pages = {920--930},
}

Physiologically active gibberellins (GAs) are key regulators of shoot growth in trees. To investigate this mechanism of GA-controlled growth in hybrid aspen, we cloned cDNAs encoding gibberellin 20-oxidase (GA 20-oxidase), a key, highly regulated enzyme in the biosynthesis of GAs. Clones were isolated from leaf and cambium cDNA libraries using probes generated by polymerase chain reaction, based on conserved domains of GA 20-oxidases. Upon expression in Escherichia coli, the GST-fusion protein was shown to oxidise GA12 as well as oxidising the 13-hydroxylated substrate GA53, successively to GA9 and GA20, respectively. The gene PttGA20ox1 was expressed in meristematic cells and growing tissues such as expanding internodes, leaves and roots. The expression was negatively regulated by both GA4 and overexpression of phytochrome A. RNA analysis also showed that the expression was down-regulated in late-expanding leaf tissue in response to short days (SDs). Actively growing tissues such as early elongating internodes, petioles and leaf blades had the highest levels of C19-GAs. Upon transfer to SDs an accumulation of GA19 was observed in early elongating internodes and leaf blades. The levels of C19-GAs were also to some extent changed upon transfer to SDs. The levels of GA20 were down-regulated in internodes, and those of GA1 were significantly reduced in early expanding leaf blades. In roots the metabolites GA19 and GA8 decreased upon shifts to SDs, while GA20 accumulated slightly. The down-regulation of GA 20-oxidase activity in response to SDs was further indicated by studies of [14C]GA12 metabolism in shoots, demonstrating that the substrate for GA 20-oxidase, [14C]GA53, accumulates in SDs.

@article{slesak_redox_2002,
	series = {Free radicals and oxidative stress in plants: {A} new insight},
	title = {Redox control of oxidative stress responses in the {C3}–{CAM} intermediate plant {Mesembryanthemum} crystallinum},
	volume = {40},
	issn = {0981-9428},
	url = {https://www.sciencedirect.com/science/article/pii/S0981942802014092},
	doi = {10/bwj7s9},
	abstract = {Crassulacean acid metabolism (CAM) is named after the Crassulaceae family of succulent plants, in which this type of metabolism was first discovered at the beginning of the 19th century. In recent years, Mesembryanthemum crystallinum, a facultative halophyte and C3–CAM intermediate plant, has become a favoured plant for studying stress response mechanisms during C3–CAM shifts. Recent studies in this and related areas can provide a new model of how such mechanisms could operate for acclimation to high salinity or excess excitation energy. These include roles for photosynthetic electron transport chain components and reactive oxygen species. The diurnal rhythms of catalase, superoxide dismutase and some CAM-related enzyme activities are discussed in relation to the protective role of photorespiration during C3–CAM transition. The role of excess excitation energy and redox events in the proximity of photosystem II (PSII) in regulation of ascorbate peroxidase (APX), superoxide dismutase (SOD): copper/zinc SOD (Cu/ZnSOD), iron SOD (FeSOD), and NAD(P)-malic enzyme gene expression are also discussed. We suggest a model in which the chloroplast plays a major role in regulation of acclimation to high salinity and/or excess exitation energy.},
	language = {en},
	number = {6},
	urldate = {2021-10-19},
	journal = {Plant Physiology and Biochemistry},
	author = {Ślesak, Ireneusz and Miszalski, Zbigniew and Karpinska, Barbara and Niewiadomska, Ewa and Ratajczak, Rafael and Karpinski, Stanislaw},
	month = jun,
	year = {2002},
	keywords = {Crassulacean acid metabolism, Oxidative stress, Photosynthesis, Redox sensing, Salt stress, Superoxide dismutase},
	pages = {669--677},
}

Crassulacean acid metabolism (CAM) is named after the Crassulaceae family of succulent plants, in which this type of metabolism was first discovered at the beginning of the 19th century. In recent years, Mesembryanthemum crystallinum, a facultative halophyte and C3–CAM intermediate plant, has become a favoured plant for studying stress response mechanisms during C3–CAM shifts. Recent studies in this and related areas can provide a new model of how such mechanisms could operate for acclimation to high salinity or excess excitation energy. These include roles for photosynthetic electron transport chain components and reactive oxygen species. The diurnal rhythms of catalase, superoxide dismutase and some CAM-related enzyme activities are discussed in relation to the protective role of photorespiration during C3–CAM transition. The role of excess excitation energy and redox events in the proximity of photosystem II (PSII) in regulation of ascorbate peroxidase (APX), superoxide dismutase (SOD): copper/zinc SOD (Cu/ZnSOD), iron SOD (FeSOD), and NAD(P)-malic enzyme gene expression are also discussed. We suggest a model in which the chloroplast plays a major role in regulation of acclimation to high salinity and/or excess exitation energy.

@article{ciereszko_glucose_2002,
	title = {Glucose and mannose regulate the expression of a major sucrose synthase gene in {Arabidopsis} via hexokinase-dependent mechanisms},
	volume = {40},
	issn = {0981-9428},
	url = {https://www.sciencedirect.com/science/article/pii/S0981942802014523},
	doi = {10/ct2hnm},
	abstract = {Sucrose synthase (SuSy) is an important enzyme involved in sucrose synthesis/breakdown in all plants. Sus1, a major SuSy gene in Arabidopsis thaliana, was upregulated by sucrose, glucose and D-mannose, but not 3-O-methylglucose, when those compounds were fed to excised leaves. Mannose was more effective than glucose or sucrose in the induction of Sus1, with strong effects observed at a concentration as low as 20 mM. When fed to the excised leaves, N-acetyl-glucosamine, an inhibitor of hexokinase (HXK) enzymatic activity, decreased sucrose- and glucose-dependent, but not mannose-dependent, upregulation of Sus1. The sucrose/glucose-dependent Sus1 expression was strongly induced in transgenic Arabidopsis HXK-overexpressing (OE) plants, whereas mannose-dependent Sus1 expression markedly decreased in OE, but not in HXK-“antisense”, Arabidopsis plants. Feeding with sucrose resulted in a marked increase of glucose content in leaves, suggesting that it is glucose rather than sucrose that serves as a signal in upregulating Sus1 expression in sucrose-fed plants. The data suggest that Sus1 is regulated by a HXK-dependent pathway, with glucose and mannose effects differentially sensed/transmitted via the HXK step.},
	language = {en},
	number = {11},
	urldate = {2021-10-19},
	journal = {Plant Physiology and Biochemistry},
	author = {Ciereszko, Iwona and Kleczkowski, Leszek A.},
	month = nov,
	year = {2002},
	keywords = {Arabidopsis thaliana, Gene expression, Sucrose synthesis, Sus1, UDP-glucose synthesis},
	pages = {907--911},
}

Sucrose synthase (SuSy) is an important enzyme involved in sucrose synthesis/breakdown in all plants. Sus1, a major SuSy gene in Arabidopsis thaliana, was upregulated by sucrose, glucose and D-mannose, but not 3-O-methylglucose, when those compounds were fed to excised leaves. Mannose was more effective than glucose or sucrose in the induction of Sus1, with strong effects observed at a concentration as low as 20 mM. When fed to the excised leaves, N-acetyl-glucosamine, an inhibitor of hexokinase (HXK) enzymatic activity, decreased sucrose- and glucose-dependent, but not mannose-dependent, upregulation of Sus1. The sucrose/glucose-dependent Sus1 expression was strongly induced in transgenic Arabidopsis HXK-overexpressing (OE) plants, whereas mannose-dependent Sus1 expression markedly decreased in OE, but not in HXK-“antisense”, Arabidopsis plants. Feeding with sucrose resulted in a marked increase of glucose content in leaves, suggesting that it is glucose rather than sucrose that serves as a signal in upregulating Sus1 expression in sucrose-fed plants. The data suggest that Sus1 is regulated by a HXK-dependent pathway, with glucose and mannose effects differentially sensed/transmitted via the HXK step.

@article{ciereszko_expression_2002,
	title = {Expression of genes for sucrose synthase and {UDP}-glucose pyrophosphorylase under changing conditions of {Pi} and sucrose (in {Polish}) ({Zeszyty} {Problemowe} {Postepow} {Nauk} {Rolniczych} 481: 281-287)},
	volume = {481},
	shorttitle = {Expression of genes for sucrose synthase and {UDP}-glucose pyrophosphorylase under changing conditions of {Pi} and sucrose (in {Polish}) ({Zeszyty} {Problemowe} {Postepow} {Nauk} {Rolniczych} 481},
	abstract = {The effect of inorganic phosphate (Pi) level and carbohydrate/osmotic status on expression of genes encoding UDP-glucose pyrophosphorylase (Ugp) and sucrose synthase (Sus1) were investigated in Arabidopsis thaliana (L.) HEYNH. leaves. Phosphate deficiency strongly induced Ugp gene expression and had no influence on the level of Sus1 transcript in the leaves of Arabidopsis. Feeding leaves with Pi, at the concentration of 20-200 mmol-dm⁻³, increased Sus1 expression and had no significant effect on Ugp transcript level. Genes for UDP-glucose pyrophosphorylase and sucrose synthase were found to be strongly regulated by sugar and sugar/osmoticum, respectively. The increase of Ugp and Sus1 expression after feeding of sucrose to the leaves of pho1 mutant of Arabidopsis was not significantly higher than the transcripts level in wild-type plants. Sucrose, exogenously provided to the leaves of pho2 mutant had lower effect on Ugp transcript level than in wild-type plants, however Sus1 upregulation was higher in pho2 than in w-t. Sucrose-related induction of Ugp was inhibited by okadaic acid, an inhibitor of protein phosphatases; on the other hand, Sus1 expression was enhanced after okadaic acid treatment. The obtained results suggest that Ugp and Sus1 genes expression, both P- modulated and sugar/osmoticum-dependent, are regulated via distinct sensing mechanisms and distinct signaling pathways and are closely involved in homeos- tatic readjustments of plant responses to environmental stresses.},
	author = {Ciereszko, Iwona and Kleczkowski, Leszek},
	month = jan,
	year = {2002},
	pages = {281--287},
}

The effect of inorganic phosphate (Pi) level and carbohydrate/osmotic status on expression of genes encoding UDP-glucose pyrophosphorylase (Ugp) and sucrose synthase (Sus1) were investigated in Arabidopsis thaliana (L.) HEYNH. leaves. Phosphate deficiency strongly induced Ugp gene expression and had no influence on the level of Sus1 transcript in the leaves of Arabidopsis. Feeding leaves with Pi, at the concentration of 20-200 mmol-dm⁻³, increased Sus1 expression and had no significant effect on Ugp transcript level. Genes for UDP-glucose pyrophosphorylase and sucrose synthase were found to be strongly regulated by sugar and sugar/osmoticum, respectively. The increase of Ugp and Sus1 expression after feeding of sucrose to the leaves of pho1 mutant of Arabidopsis was not significantly higher than the transcripts level in wild-type plants. Sucrose, exogenously provided to the leaves of pho2 mutant had lower effect on Ugp transcript level than in wild-type plants, however Sus1 upregulation was higher in pho2 than in w-t. Sucrose-related induction of Ugp was inhibited by okadaic acid, an inhibitor of protein phosphatases; on the other hand, Sus1 expression was enhanced after okadaic acid treatment. The obtained results suggest that Ugp and Sus1 genes expression, both P- modulated and sugar/osmoticum-dependent, are regulated via distinct sensing mechanisms and distinct signaling pathways and are closely involved in homeos- tatic readjustments of plant responses to environmental stresses.

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

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

@article{danusevicius_efficiency_2002,
	title = {Efficiency of selection based on phenotype, clone and progeny testing in long-term breeding},
	volume = {51},
	abstract = {The overall goal for long-term breeding was formulated as maximising annual progress in group merit (GMG/Y) at a given annual budget. Group merit is a weighted average of breeding value and gene diversity. Breeding strategies based on testing of phenotypes, clones or progeny for selection of parents for next breeding cycle were optimised as regards testing time and test entry size. The dependence of GMG/Y on genetic parameters, cost and time components was investigated. Numeric values were chosen with long-term breeding of Norway spruce in mind. The highest GMG/Y under the most likely parameter values for clone, phenotype and progeny strategies was 0.250\%, 0.152\% and 0.139\%, respectively. The clone strategy was the best over the whole range of considered cases, except for the scenario with high narrow-sense heritability, for which the phenotype strategy was the most efficient. Except for low narrow-sense heritability, the phenotype strategy was the second best, but superiority of the phenotype strategy over progeny strategy was usually small. If reproductive maturity of the test parents could be shortened to below about 12 years, the progeny strategy may be better than the phenotype strategy. Comparably high costs (per parent) seem to be acceptable for promoting early sexual maturity. Narrow-sense heritability, additive variance at mature age, rotation age, plant-dependent cost and the time needed to produce the test plants had the strongest effect on GMG/Y. The clone strategy became less superior at high dominance variance. Short rotation age favoured the clone and phenotype strategies. Reduction of cost per test plant was especially beneficial for the clonal and progeny strategies.},
	journal = {Silvae Genetica},
	author = {Danusevicius, Darius and Lindgren, D.},
	month = jan,
	year = {2002},
	pages = {19--26},
}

The overall goal for long-term breeding was formulated as maximising annual progress in group merit (GMG/Y) at a given annual budget. Group merit is a weighted average of breeding value and gene diversity. Breeding strategies based on testing of phenotypes, clones or progeny for selection of parents for next breeding cycle were optimised as regards testing time and test entry size. The dependence of GMG/Y on genetic parameters, cost and time components was investigated. Numeric values were chosen with long-term breeding of Norway spruce in mind. The highest GMG/Y under the most likely parameter values for clone, phenotype and progeny strategies was 0.250%, 0.152% and 0.139%, respectively. The clone strategy was the best over the whole range of considered cases, except for the scenario with high narrow-sense heritability, for which the phenotype strategy was the most efficient. Except for low narrow-sense heritability, the phenotype strategy was the second best, but superiority of the phenotype strategy over progeny strategy was usually small. If reproductive maturity of the test parents could be shortened to below about 12 years, the progeny strategy may be better than the phenotype strategy. Comparably high costs (per parent) seem to be acceptable for promoting early sexual maturity. Narrow-sense heritability, additive variance at mature age, rotation age, plant-dependent cost and the time needed to produce the test plants had the strongest effect on GMG/Y. The clone strategy became less superior at high dominance variance. Short rotation age favoured the clone and phenotype strategies. Reduction of cost per test plant was especially beneficial for the clonal and progeny strategies.

@article{strand_impacts_2002,
	title = {Impacts of seasonal air and soil temperatures on photosynthesis in {Scots} pine trees},
	volume = {22},
	issn = {0829-318X},
	url = {https://doi.org/10.1093/treephys/22.12.839},
	doi = {10.1093/treephys/22.12.839},
	abstract = {Seasonal courses of light-saturated rate of net photosynthesis (A360) and stomatal conductance (gs) were examined in detached 1-year-old needles of Scots pine (Pinus sylvestris L.) from early April to mid-November. To evaluate the effects of soil frost and low soil temperatures on gas exchange, the extent and duration of soil frost, as well as the onset of soil warming, were manipulated in the field. During spring, early summer and autumn, the patterns of A360 and gs in needles from the control and warm-soil plots were generally strongly related to daily mean air temperatures and the frequency of severe frosts. The warm-soil treatment had little effect on gas exchange, although mean soil temperature in the warm-soil plot was 3.8 °C higher than in the control plot during spring and summer, indicating that A360 and gs in needles from control trees were not limited by low soil temperature alone. In contrast, prolonged exposure to soil temperatures slightly above 0 °C severely restricted recovery of A360 and especially gs in needles from the cold-soil treatment during spring and early summer; however, full recovery of both A360 and gs occurred in late summer. We conclude that inhibition of A360 by low soil temperatures is related to both stomatal closure and effects on the biochemistry of photosynthesis, the relative importance of which appeared to vary during spring and early summer. During the autumn, soil temperatures as low as 8 °C did not affect either A360 or gs.},
	number = {12},
	urldate = {2021-10-19},
	journal = {Tree Physiology},
	author = {Strand, Martin and Lundmark, Tomas and Söderbergh, Ingrid and Mellander, Per-Erik},
	month = aug,
	year = {2002},
	pages = {839--847},
}

Seasonal courses of light-saturated rate of net photosynthesis (A360) and stomatal conductance (gs) were examined in detached 1-year-old needles of Scots pine (Pinus sylvestris L.) from early April to mid-November. To evaluate the effects of soil frost and low soil temperatures on gas exchange, the extent and duration of soil frost, as well as the onset of soil warming, were manipulated in the field. During spring, early summer and autumn, the patterns of A360 and gs in needles from the control and warm-soil plots were generally strongly related to daily mean air temperatures and the frequency of severe frosts. The warm-soil treatment had little effect on gas exchange, although mean soil temperature in the warm-soil plot was 3.8 °C higher than in the control plot during spring and summer, indicating that A360 and gs in needles from control trees were not limited by low soil temperature alone. In contrast, prolonged exposure to soil temperatures slightly above 0 °C severely restricted recovery of A360 and especially gs in needles from the cold-soil treatment during spring and early summer; however, full recovery of both A360 and gs occurred in late summer. We conclude that inhibition of A360 by low soil temperatures is related to both stomatal closure and effects on the biochemistry of photosynthesis, the relative importance of which appeared to vary during spring and early summer. During the autumn, soil temperatures as low as 8 °C did not affect either A360 or gs.

@article{chaffey_understanding_2002,
	title = {Understanding the role of the cytoskeleton in wood formation in angiosperm trees: hybrid aspen ({Populus} tremula × {P}. tremuloides) as the model species},
	volume = {22},
	issn = {0829-318X},
	shorttitle = {Understanding the role of the cytoskeleton in wood formation in angiosperm trees},
	url = {https://doi.org/10.1093/treephys/22.4.239},
	doi = {10.1093/treephys/22.4.239},
	abstract = {The involvement of microfilaments and microtubules in the development of the radial and axial components of secondary xylem (wood) in hybrid aspen (Populus tremula L. × P. tremuloidesMichx.) was studied by indirect immunofluorescent localization techniques. In addition to cambial cells, the differentiated cell types considered were early- and late-wood vessel elements, axial parenchyma, normal-wood fibers and gelatinous fibers, and contact and isolation ray cells. Microfilaments were rare in ray cambial cells, but were abundant and axially arranged in their derivatives once cell elongation had begun, and persisted in that orientation in mature ray cells. Microfilaments were axially arranged in fusiform cambial cells and persisted in that orientation in all xylem derivatives of those cells. Microtubules were randomly oriented in ray and fusiform cells of the cambial zone. Dense arrays of parallel-aligned microtubules were oriented near axially in the developing gelatinous fibers, but at a wide range of angles in normal-wood fibers. Ellipses of microfilaments were associated with pit development in fiber cells and isolation ray cells. Rings of co-localized microtubules and microfilaments were associated with developing inter-vessel bordered pits and vessel-contact ray cell contact pits, and, in the case of bordered pits, these rings decreased in diameter as the over-arching pit border increased in size. Although only microtubules were seen at the periphery of the perforation plate of vessel elements, a prominent meshwork of microfilaments overlaid the perforation plate itself. A consensus view of the roles of the cytoskeleton during wood formation in angiosperm trees is presented.},
	number = {4},
	urldate = {2021-10-19},
	journal = {Tree Physiology},
	author = {Chaffey, Nigel and Barlow, Peter and Sundberg, Björn},
	month = mar,
	year = {2002},
	pages = {239--249},
}

The involvement of microfilaments and microtubules in the development of the radial and axial components of secondary xylem (wood) in hybrid aspen (Populus tremula L. × P. tremuloidesMichx.) was studied by indirect immunofluorescent localization techniques. In addition to cambial cells, the differentiated cell types considered were early- and late-wood vessel elements, axial parenchyma, normal-wood fibers and gelatinous fibers, and contact and isolation ray cells. Microfilaments were rare in ray cambial cells, but were abundant and axially arranged in their derivatives once cell elongation had begun, and persisted in that orientation in mature ray cells. Microfilaments were axially arranged in fusiform cambial cells and persisted in that orientation in all xylem derivatives of those cells. Microtubules were randomly oriented in ray and fusiform cells of the cambial zone. Dense arrays of parallel-aligned microtubules were oriented near axially in the developing gelatinous fibers, but at a wide range of angles in normal-wood fibers. Ellipses of microfilaments were associated with pit development in fiber cells and isolation ray cells. Rings of co-localized microtubules and microfilaments were associated with developing inter-vessel bordered pits and vessel-contact ray cell contact pits, and, in the case of bordered pits, these rings decreased in diameter as the over-arching pit border increased in size. Although only microtubules were seen at the periphery of the perforation plate of vessel elements, a prominent meshwork of microfilaments overlaid the perforation plate itself. A consensus view of the roles of the cytoskeleton during wood formation in angiosperm trees is presented.

@article{shchukarev_xps_2002,
	title = {{XPS} study of living tree},
	volume = {34},
	issn = {1096-9918},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/sia.1301},
	doi = {10.1002/sia.1301},
	abstract = {X-ray photoelectron spectroscopy (XPS) was used to study the distribution of elements and main wood components (cellulose and lignin) within the wood and at the bark/wood interface of a living hybrid aspen stem. The hybrid aspen was grown upright in a greenhouse and then tilted at ∼45° to induce tension wood formation and upright bending of the stem. The wood between the pith and the bark on the upper side of the tilted stem was analysed. Changes in the middle lamella/S1 layer chemical composition, which corresponded to the transition from normal wood produced during upright stem growth to tension wood produced upon stem tilting, were observed. Such changes were related to the lower lignin and higher cellulose/hemicellulose contents in the tension wood. A non-uniform radial distribution of nitrogen (amino acids, proteins) within the stem was also noted. At the bark/wood interface the presence of inorganic elements (Ca, K and P) and a significant increase in nitrogen were found. The opposite wood side of the tree was enriched in lignin and fatty acids. It was shown that application of XPS imaging to a very rough surface of wood split allows the inhomogeneous lateral lignin distribution to be visualized. Copyright © 2002 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {1},
	urldate = {2021-10-19},
	journal = {Surface and Interface Analysis},
	author = {Shchukarev, Andrei and Sundberg, Björn and Mellerowicz, Ewa and Persson, Per},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/sia.1301},
	keywords = {XPS, XPS imaging, cellulose, lignin, wood, x-ray photoelectron spectroscopy},
	pages = {284--288},
}

X-ray photoelectron spectroscopy (XPS) was used to study the distribution of elements and main wood components (cellulose and lignin) within the wood and at the bark/wood interface of a living hybrid aspen stem. The hybrid aspen was grown upright in a greenhouse and then tilted at ∼45° to induce tension wood formation and upright bending of the stem. The wood between the pith and the bark on the upper side of the tilted stem was analysed. Changes in the middle lamella/S1 layer chemical composition, which corresponded to the transition from normal wood produced during upright stem growth to tension wood produced upon stem tilting, were observed. Such changes were related to the lower lignin and higher cellulose/hemicellulose contents in the tension wood. A non-uniform radial distribution of nitrogen (amino acids, proteins) within the stem was also noted. At the bark/wood interface the presence of inorganic elements (Ca, K and P) and a significant increase in nitrogen were found. The opposite wood side of the tree was enriched in lignin and fatty acids. It was shown that application of XPS imaging to a very rough surface of wood split allows the inhomogeneous lateral lignin distribution to be visualized. Copyright © 2002 John Wiley & Sons, Ltd.

@article{kang_using_2002,
	title = {Using single family in reforestation: {Gene} diversity concerns},
	volume = {51},
	shorttitle = {Using single family in reforestation},
	abstract = {Formulae for gene diversity measured by status number (group coancestry) for seeds collected from a single clone in a clonal seed orchard were derived. The formulae considered: number of seeds collected, ratio of seeds from selfing, fertility variation of pollen parents, relatedness among pollen parents and amount of pollination by alien fathers from outside the seed orchard (pollen contamination). The results showed that the status number of seeds collected from a single clone generally varied between 2 and 4 in most cases. Typically it was close to 4, thus close to that of an "ideal" half-sib family. Relatedness among pollen parents and selfing decreased status number and gene diversity while pollen contamination increased it. Effect of the level of pollen contamination and fertility variation among pollen parents on gene diversity of crops from the same seed parent was usually small. High degree of relatedness and selfing can be important. If there were few pollen parents, the gene diversity depended greatly on relatedness, selfing and fertility variation. However, if there were many pollen parents (about 10 or more), these factors were not important. The influence of the number of pollen parents was discussed.},
	journal = {Silvae Genetica},
	author = {Kang, Kyu-Suk and Lai, H.-L and Lindgren, Dag},
	month = jan,
	year = {2002},
	pages = {65--72},
}

Formulae for gene diversity measured by status number (group coancestry) for seeds collected from a single clone in a clonal seed orchard were derived. The formulae considered: number of seeds collected, ratio of seeds from selfing, fertility variation of pollen parents, relatedness among pollen parents and amount of pollination by alien fathers from outside the seed orchard (pollen contamination). The results showed that the status number of seeds collected from a single clone generally varied between 2 and 4 in most cases. Typically it was close to 4, thus close to that of an "ideal" half-sib family. Relatedness among pollen parents and selfing decreased status number and gene diversity while pollen contamination increased it. Effect of the level of pollen contamination and fertility variation among pollen parents on gene diversity of crops from the same seed parent was usually small. High degree of relatedness and selfing can be important. If there were few pollen parents, the gene diversity depended greatly on relatedness, selfing and fertility variation. However, if there were many pollen parents (about 10 or more), these factors were not important. The influence of the number of pollen parents was discussed.

@article{kulheim_rapid_2002,
	title = {Rapid {Regulation} of {Light} {Harvesting} and {Plant} {Fitness} in the {Field}},
	volume = {297},
	url = {https://www.science.org/lookup/doi/10.1126/science.1072359},
	doi = {10.1126/science.1072359},
	number = {5578},
	urldate = {2021-10-19},
	journal = {Science},
	author = {Külheim, Carsten and Ågren, Jon and Jansson, Stefan},
	month = jul,
	year = {2002},
	note = {Publisher: American Association for the Advancement of Science},
	pages = {91--93},
}

@article{wennstrom_effects_2002,
	title = {Effects of {Seed} {Weight} and {Seed} {Type} on {Early} {Seedling} {Growth} of {Pinus} sylvestris under {Harsh} and {Optimal} {Conditions}},
	volume = {17},
	issn = {0282-7581},
	url = {https://doi.org/10.1080/028275802753626764},
	doi = {10.1080/028275802753626764},
	abstract = {The effects of seed weight and seed type on seedling growth of Pinus sylvestris (L.) were studied by seeding individually weighed orchard and stand seed in different mixtures under harsh (direct seeding in field) and optimal (seeding in nursery) conditions. In the nursery experiment an increase in the seed weight from 3 to 7 mg increased the seedling height by 10-27\% and total weight by 27-113\%, and decreased the height/diameter ratio by 5-6\% after 2 yrs. With elimination of seed weight effects, orchard seedlings were 2\% taller than stand seedlings in year 2. Without elimination of seed weight effects, orchard seedlings were 7-13\% taller. In the field experiment an increase in the seed weight from 3 to 7 mg increased seedling height by 18-65\%, stem volume by 81-274\% and the number of top-buds by 23-34\% in year 5. After elimination of seed weight effects, orchard seedlings were 7-13\% taller than stand seedlings and without elimination of seed weight effects 20-21\% taller after 5 yrs. Even after elimination of both seed weight and genetic effects orchard seedlings were 3-9\% larger than stand seedlings in the field experiment. In conclusion, the influence of seed weight and seed type on growth traits and slenderness is highly significant and the influence seems to be greater in harsh conditions.},
	number = {2},
	urldate = {2021-10-19},
	journal = {Scandinavian Journal of Forest Research},
	author = {Wennström, Ulfstand and Bergsten, Urban and Nilsson, Jan-Erik},
	month = jan,
	year = {2002},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/028275802753626764},
	keywords = {Allocation, Biomass, Competition, Direct, Growth, Orchard, Pine, Scots, Seed, Seeding, Stand},
	pages = {118--130},
}

The effects of seed weight and seed type on seedling growth of Pinus sylvestris (L.) were studied by seeding individually weighed orchard and stand seed in different mixtures under harsh (direct seeding in field) and optimal (seeding in nursery) conditions. In the nursery experiment an increase in the seed weight from 3 to 7 mg increased the seedling height by 10-27% and total weight by 27-113%, and decreased the height/diameter ratio by 5-6% after 2 yrs. With elimination of seed weight effects, orchard seedlings were 2% taller than stand seedlings in year 2. Without elimination of seed weight effects, orchard seedlings were 7-13% taller. In the field experiment an increase in the seed weight from 3 to 7 mg increased seedling height by 18-65%, stem volume by 81-274% and the number of top-buds by 23-34% in year 5. After elimination of seed weight effects, orchard seedlings were 7-13% taller than stand seedlings and without elimination of seed weight effects 20-21% taller after 5 yrs. Even after elimination of both seed weight and genetic effects orchard seedlings were 3-9% larger than stand seedlings in the field experiment. In conclusion, the influence of seed weight and seed type on growth traits and slenderness is highly significant and the influence seems to be greater in harsh conditions.

@article{ingvarsson_genealogical_2002,
	title = {Genealogical evidence for epidemics of selfish genes},
	volume = {99},
	issn = {0027-8424},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC123245/},
	doi = {10.1073/pnas.172318099},
	abstract = {Some genetic elements spread infectiously in populations by increasing their rate of genetic transmission at the expense of other genes in the genome. These so-called selfish genetic elements comprise a substantial portion of eukaryotic genomes and have long been viewed as a potent evolutionary force. Despite this view, little is known about the evolutionary history of selfish genetic elements in natural populations, or their genetic effects on other portions of the genome. Here we use nuclear and chloroplast gene genealogies in two species of Silene to show the historical pattern of selection on a well known selfish genetic element, cytoplasmic male sterility. We provide evidence that evolution of cytoplasmic male sterility has been characterized by frequent turnovers of mutations in natural populations, thus supporting an epidemic model for the evolution of selfish genes, where new mutations repeatedly arise and rapidly sweep through populations.},
	number = {17},
	urldate = {2021-10-19},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Ingvarsson, Pär K. and Taylor, Douglas R.},
	month = aug,
	year = {2002},
	pmid = {12177435},
	pmcid = {PMC123245},
	pages = {11265--11269},
}

Some genetic elements spread infectiously in populations by increasing their rate of genetic transmission at the expense of other genes in the genome. These so-called selfish genetic elements comprise a substantial portion of eukaryotic genomes and have long been viewed as a potent evolutionary force. Despite this view, little is known about the evolutionary history of selfish genetic elements in natural populations, or their genetic effects on other portions of the genome. Here we use nuclear and chloroplast gene genealogies in two species of Silene to show the historical pattern of selection on a well known selfish genetic element, cytoplasmic male sterility. We provide evidence that evolution of cytoplasmic male sterility has been characterized by frequent turnovers of mutations in natural populations, thus supporting an epidemic model for the evolution of selfish genes, where new mutations repeatedly arise and rapidly sweep through populations.

@article{persson_regulation_2002,
	title = {Regulation of amino acid uptake in conifers by exogenous and endogenous nitrogen},
	volume = {215},
	issn = {1432-2048},
	url = {https://doi.org/10.1007/s00425-002-0786-5},
	doi = {10.1007/s00425-002-0786-5},
	abstract = {Although an accumulating amount of research clearly indicates that plants are capable of taking up exogenous amino acids, the actual importance of such organic N sources for plant N nutrition is under debate. In this study, we show that amino acid uptake by Scots pine (Pinus sylvestris L.) is significantly decreased by elevated internal NH4+ levels, while it increases following exposure to exogenous amino acids. Furthermore, amino acid uptake is larger in N-deficient plants than in plants grown with a large access of N. The regulatory pattern of amino acid uptake shows important similarities to the regulation of NO3– and NH4+ transport as well as to the regulation of yeast amino acid transporters. In addition, our data suggest that uptake may be regulated by factors not originating from N metabolism. The up-regulation of uptake in response to N deficiency suggests that amino acid uptake may be a significant contributor to the N economy of P. sylvestris.},
	language = {en},
	number = {4},
	urldate = {2021-10-19},
	journal = {Planta},
	author = {Persson, Jörgen and Näsholm, Torgny},
	month = aug,
	year = {2002},
	pages = {639--644},
}

Although an accumulating amount of research clearly indicates that plants are capable of taking up exogenous amino acids, the actual importance of such organic N sources for plant N nutrition is under debate. In this study, we show that amino acid uptake by Scots pine (Pinus sylvestris L.) is significantly decreased by elevated internal NH4+ levels, while it increases following exposure to exogenous amino acids. Furthermore, amino acid uptake is larger in N-deficient plants than in plants grown with a large access of N. The regulatory pattern of amino acid uptake shows important similarities to the regulation of NO3– and NH4+ transport as well as to the regulation of yeast amino acid transporters. In addition, our data suggest that uptake may be regulated by factors not originating from N metabolism. The up-regulation of uptake in response to N deficiency suggests that amino acid uptake may be a significant contributor to the N economy of P. sylvestris.

@article{peng_molecular_2002,
	title = {Molecular and physiological characterization of {Arabidopsis} {GAI} alleles obtained in targeted {Ds}-tagging experiments},
	volume = {214},
	issn = {1432-2048},
	url = {https://doi.org/10.1007/s004250100643},
	doi = {10.1007/s004250100643},
	abstract = {Bioactive gibberellin (GA) is an essential regulator of vascular plant development. The GAI gene of Arabidopsis thaliana (L.) Heynh. encodes a product (GAI) that is involved in GA signalling. The dominant mutant gai allele encodes an altered product (gai) that confers reduced GA responses, dwarfism, and elevated endogenous GA levels. Recessive, presumed loss-of-function alleles of GAI confer normal height and resistance to the GA biosynthesis inhibitor paclobutrazol. One explanation for these observations is that GAI is a growth repressor whose activity is opposed by GA, whilst gai retains a constitutive repressor activity that is less affected by GA. Previously, we described gai-t6, a mutant allele which contains an insertion of a maize Ds transposable element into gai. Here we describe the molecular and physiological characterization of two further alleles (gai-t5, gai-t7) identified during the Ds mutagenesis experiment. These alleles confer paclobutrazol resistance and normal endogenous GA levels. Thus the phenotype conferred by gai-t5, gai-t6 and gai-t7 is not due to elevated GA levels, but is due to loss of gai, a constitutively active plant growth repressor.},
	language = {en},
	number = {4},
	urldate = {2021-10-19},
	journal = {Planta},
	author = {Peng, Jinrong and Richards, Donald E. and Moritz, Thomas and Ezura, Hiroshi and Carol, Pierre and Harberd, Nicholas P.},
	month = feb,
	year = {2002},
	pages = {591--596},
}

Bioactive gibberellin (GA) is an essential regulator of vascular plant development. The GAI gene of Arabidopsis thaliana (L.) Heynh. encodes a product (GAI) that is involved in GA signalling. The dominant mutant gai allele encodes an altered product (gai) that confers reduced GA responses, dwarfism, and elevated endogenous GA levels. Recessive, presumed loss-of-function alleles of GAI confer normal height and resistance to the GA biosynthesis inhibitor paclobutrazol. One explanation for these observations is that GAI is a growth repressor whose activity is opposed by GA, whilst gai retains a constitutive repressor activity that is less affected by GA. Previously, we described gai-t6, a mutant allele which contains an insertion of a maize Ds transposable element into gai. Here we describe the molecular and physiological characterization of two further alleles (gai-t5, gai-t7) identified during the Ds mutagenesis experiment. These alleles confer paclobutrazol resistance and normal endogenous GA levels. Thus the phenotype conferred by gai-t5, gai-t6 and gai-t7 is not due to elevated GA levels, but is due to loss of gai, a constitutively active plant growth repressor.

@article{ivanov_seasonal_2002,
	title = {Seasonal responses of photosynthetic electron transport in {Scots} pine ({Pinus} sylvestris {L}.) studied by thermoluminescence},
	volume = {215},
	issn = {1432-2048},
	url = {https://doi.org/10.1007/s00425-002-0765-x},
	doi = {10.1007/s00425-002-0765-x},
	abstract = {The potential of photosynthesis to recover from winter stress was studied by following the thermoluminescence (TL) and chlorophyll fluorescence changes of winter pine needles during the exposure to room temperature (20 °C) and an irradiance of 100 µmol m–2 s–1. TL measurements of photosystem II (PSII) revealed that the S2QB– charge recombinations (the B-band) were shifted to lower temperatures in winter pine needles, while the S2QA– recombinations (the Q-band) remained close to 0 °C. This was accompanied by a drastically reduced (65\%) PSII photochemical efficiency measured as Fv/Fm, and a 20-fold faster rate of the fluorescence transient from Fo to Fm as compared to summer pine. A strong positive correlation between the increase in the photochemical efficiency of PSII and the increase in the relative contribution of the B-band was found during the time course of the recovery process. The seasonal dynamics of TL in Scots pine needles studied under field conditions revealed that between November and April, the contribution of the Q- and B-bands to the overall TL emission was very low (less than 5\%). During spring, the relative contribution of the Q- and B-bands, corresponding to charge recombination events between the acceptor and donor sides of PSII, rapidly increased, reaching maximal values in late July. A sharp decline of the B-band was observed in late summer, followed by a gradual decrease, reaching minimal values in November. Possible mechanisms of the seasonally induced changes in the redox properties of S2/S3QB– recombinations are discussed. It is proposed that the lowered redox potential of QB in winter needles increases the population of QA–, thus enhancing the probability for non-radiative P680+QA– recombination. This is suggested to enhance the radiationless dissipation of excess light within the PSII reaction center during cold acclimation and during cold winter periods.},
	language = {en},
	number = {3},
	urldate = {2021-10-19},
	journal = {Planta},
	author = {Ivanov, A. and Sane, P. and Zeinalov, Y. and Simidjiev, I. and Huner, N. and Öquist, G.},
	month = jul,
	year = {2002},
	pages = {457--465},
}

The potential of photosynthesis to recover from winter stress was studied by following the thermoluminescence (TL) and chlorophyll fluorescence changes of winter pine needles during the exposure to room temperature (20 °C) and an irradiance of 100 µmol m–2 s–1. TL measurements of photosystem II (PSII) revealed that the S2QB– charge recombinations (the B-band) were shifted to lower temperatures in winter pine needles, while the S2QA– recombinations (the Q-band) remained close to 0 °C. This was accompanied by a drastically reduced (65%) PSII photochemical efficiency measured as Fv/Fm, and a 20-fold faster rate of the fluorescence transient from Fo to Fm as compared to summer pine. A strong positive correlation between the increase in the photochemical efficiency of PSII and the increase in the relative contribution of the B-band was found during the time course of the recovery process. The seasonal dynamics of TL in Scots pine needles studied under field conditions revealed that between November and April, the contribution of the Q- and B-bands to the overall TL emission was very low (less than 5%). During spring, the relative contribution of the Q- and B-bands, corresponding to charge recombination events between the acceptor and donor sides of PSII, rapidly increased, reaching maximal values in late July. A sharp decline of the B-band was observed in late summer, followed by a gradual decrease, reaching minimal values in November. Possible mechanisms of the seasonally induced changes in the redox properties of S2/S3QB– recombinations are discussed. It is proposed that the lowered redox potential of QB in winter needles increases the population of QA–, thus enhancing the probability for non-radiative P680+QA– recombination. This is suggested to enhance the radiationless dissipation of excess light within the PSII reaction center during cold acclimation and during cold winter periods.

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

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

@article{mullineaux_signal_2002,
	title = {Signal transduction in response to excess light: getting out of the chloroplast},
	volume = {5},
	issn = {1369-5266},
	shorttitle = {Signal transduction in response to excess light},
	url = {https://www.sciencedirect.com/science/article/pii/S1369526601002266},
	doi = {10.1016/S1369-5266(01)00226-6},
	abstract = {Plants are continually in danger of absorbing more light energy than they can use productively for their metabolism. Acclimation to environmental conditions therefore includes the development of mechanisms for dissipating or avoiding the accumulation of such excess excitation energy. Acclimation could be controlled by many signal transduction pathways that would be initiated by the perception of excess excitation energy both inside and outside the chloroplast. Recent studies in related areas provide models of how these signalling pathways could operate in acclimation to excess light. Components of photosynthetic electron transport chains, reactive oxygen species, redox-responsive protein kinases, thiol-regulated enzymes, chlorophyll precursors and chloroplast-envelope electron transport chains all have roles in these models.},
	language = {en},
	number = {1},
	urldate = {2021-10-19},
	journal = {Current Opinion in Plant Biology},
	author = {Mullineaux, Philip and Karpinski, Stanislaw},
	month = feb,
	year = {2002},
	keywords = {abiotic stress, antioxidants, chloroplast, electron transport (photosynthetic), excess excitation energy, excess light, metabolic sinks, quenching (photochemical and non-photochemical), reactive oxygen species, signal transduction},
	pages = {43--48},
}

Plants are continually in danger of absorbing more light energy than they can use productively for their metabolism. Acclimation to environmental conditions therefore includes the development of mechanisms for dissipating or avoiding the accumulation of such excess excitation energy. Acclimation could be controlled by many signal transduction pathways that would be initiated by the perception of excess excitation energy both inside and outside the chloroplast. Recent studies in related areas provide models of how these signalling pathways could operate in acclimation to excess light. Components of photosynthetic electron transport chains, reactive oxygen species, redox-responsive protein kinases, thiol-regulated enzymes, chlorophyll precursors and chloroplast-envelope electron transport chains all have roles in these models.

@article{mattsson_nickel_2002,
	title = {Nickel {Affects} {Activity} {More} {Than} {Expression} of {Hydrogenase} {Protein} in {Frankia}},
	volume = {44},
	issn = {1432-0991},
	url = {https://doi.org/10.1007/s00284-001-0056-y},
	doi = {10.1007/s00284-001-0056-y},
	language = {en},
	number = {2},
	urldate = {2021-10-19},
	journal = {Current Microbiology},
	author = {Mattsson, Ulrika and Sellstedt, Anita},
	month = feb,
	year = {2002},
	pages = {88--93},
}

@article{grebe_cell_2002,
	title = {Cell {Polarity} {Signaling} in {Arabidopsis} {Involves} a {BFA}-{Sensitive} {Auxin} {Influx} {Pathway}},
	volume = {12},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982202006541},
	doi = {10.1016/S0960-9822(02)00654-1},
	abstract = {Coordination of cell and tissue polarity commonly involves directional signaling [1]. In the Arabidopsis root epidermis, cell polarity is revealed by basal, root tip-oriented, hair outgrowth from hair-forming cells (trichoblasts) [2]. The plant hormone auxin displays polar movements 1, 3 and accumulates at maximum concentration in the root tip 4, 5. The application of polar auxin transport inhibitors [3] evokes changes in trichoblast polarity only at high concentrations and after long-term application 2, 4. Thus, it remains open whether components of the auxin transport machinery mediate establishment of trichoblast polarity. Here we report that the presumptive auxin influx carrier AUX1 6, 7 contributes to apical-basal hair cell polarity. AUX1 function is required for polarity changes induced by exogenous application of the auxin 2,4-D, a preferential influx carrier substrate. Similar to aux1 mutants, the vesicle trafficking inhibitor brefeldin A (BFA) interferes with polar hair initiation, and AUX1 function is required for BFA-mediated polarity changes. Consistently, BFA inhibits membrane trafficking of AUX1, trichoblast hyperpolarization induced by 2,4-D, and alters the distal auxin maximum. Our results identify AUX1 as one component of a novel BFA-sensitive auxin transport pathway polarizing cells toward a hormone maximum.},
	language = {en},
	number = {4},
	urldate = {2021-10-19},
	journal = {Current Biology},
	author = {Grebe, Markus and Friml, Jiří and Swarup, Ranjan and Ljung, Karin and Sandberg, Göran and Terlou, Maarten and Palme, Klaus and Bennett, Malcolm J. and Scheres, Ben},
	month = feb,
	year = {2002},
	pages = {329--334},
}

Coordination of cell and tissue polarity commonly involves directional signaling [1]. In the Arabidopsis root epidermis, cell polarity is revealed by basal, root tip-oriented, hair outgrowth from hair-forming cells (trichoblasts) [2]. The plant hormone auxin displays polar movements 1, 3 and accumulates at maximum concentration in the root tip 4, 5. The application of polar auxin transport inhibitors [3] evokes changes in trichoblast polarity only at high concentrations and after long-term application 2, 4. Thus, it remains open whether components of the auxin transport machinery mediate establishment of trichoblast polarity. Here we report that the presumptive auxin influx carrier AUX1 6, 7 contributes to apical-basal hair cell polarity. AUX1 function is required for polarity changes induced by exogenous application of the auxin 2,4-D, a preferential influx carrier substrate. Similar to aux1 mutants, the vesicle trafficking inhibitor brefeldin A (BFA) interferes with polar hair initiation, and AUX1 function is required for BFA-mediated polarity changes. Consistently, BFA inhibits membrane trafficking of AUX1, trichoblast hyperpolarization induced by 2,4-D, and alters the distal auxin maximum. Our results identify AUX1 as one component of a novel BFA-sensitive auxin transport pathway polarizing cells toward a hormone maximum.

@article{keun_analytical_2002,
	title = {Analytical {Reproducibility} in {1H} {NMR}-{Based} {Metabonomic} {Urinalysis}},
	volume = {15},
	issn = {0893-228X},
	url = {https://doi.org/10.1021/tx0255774},
	doi = {10.1021/tx0255774},
	abstract = {Metabonomic analysis of biofluids and tissues utilizing high-resolution NMR spectroscopy and chemometric techniques has proven valuable in characterizing the biochemical response to toxicity for many xenobiotics. To assess the analytical reproducibility of metabonomic protocols, sample preparation and NMR data acquisition were performed at two sites (one using a 500 MHz and the other using a 600 MHz system) using two identical (split) sets of urine samples from an 8-day acute study of hydrazine toxicity in the rat. Despite the difference in spectrometer operating frequency, both datasets were extremely similar when analyzed using principal components analysis (PCA) and gave near-identical descriptions of the metabolic responses to hydrazine treatment. The main consistent difference between the datasets was related to the efficiency of water resonance suppression in the spectra. In a 4-PC model of both datasets combined, describing all systematic dose- and time-related variation (88\% of the total variation), differences between the two datasets accounted for only 3\% of the total modeled variance compared to ca. 15\% for normal physiological (pre-dose) variation. Furthermore, {\textless}3\% of spectra displayed distinct inter-site differences, and these were clearly identified as outliers in their respective dose-group PCA models. No samples produced clear outliers in both datasets, suggesting that the outliers observed did not reflect an unusual sample composition, but rather sporadic differences in sample preparation leading to, for example, very dilute samples. Estimations of the relative concentrations of citrate, hippurate, and taurine were in {\textgreater}95\% correlation (r2) between sites, with an analytical error comparable to normal physiological variation in concentration (4−8\%). The excellent analytical reproducibility and robustness of metabonomic techniques demonstrated here are highly competitive compared to the best proteomic analyses and are in significant contrast to genomic microarray platforms, both of which are complementary techniques for predictive and mechanistic toxicology. These results have implications for the quantitative interpretation of metabonomic data, and the establishment of quality control criteria for both regulatory agencies and for integrating data obtained at different sites.},
	number = {11},
	urldate = {2021-10-19},
	journal = {Chemical Research in Toxicology},
	author = {Keun, Hector C. and Ebbels, Timothy M. D. and Antti, Henrik and Bollard, Mary E. and Beckonert, Olaf and Schlotterbeck, Götz and Senn, Hans and Niederhauser, Urs and Holmes, Elaine and Lindon, John C. and Nicholson, Jeremy K.},
	month = nov,
	year = {2002},
	note = {Publisher: American Chemical Society},
	pages = {1380--1386},
}

Metabonomic analysis of biofluids and tissues utilizing high-resolution NMR spectroscopy and chemometric techniques has proven valuable in characterizing the biochemical response to toxicity for many xenobiotics. To assess the analytical reproducibility of metabonomic protocols, sample preparation and NMR data acquisition were performed at two sites (one using a 500 MHz and the other using a 600 MHz system) using two identical (split) sets of urine samples from an 8-day acute study of hydrazine toxicity in the rat. Despite the difference in spectrometer operating frequency, both datasets were extremely similar when analyzed using principal components analysis (PCA) and gave near-identical descriptions of the metabolic responses to hydrazine treatment. The main consistent difference between the datasets was related to the efficiency of water resonance suppression in the spectra. In a 4-PC model of both datasets combined, describing all systematic dose- and time-related variation (88% of the total variation), differences between the two datasets accounted for only 3% of the total modeled variance compared to ca. 15% for normal physiological (pre-dose) variation. Furthermore, \textless3% of spectra displayed distinct inter-site differences, and these were clearly identified as outliers in their respective dose-group PCA models. No samples produced clear outliers in both datasets, suggesting that the outliers observed did not reflect an unusual sample composition, but rather sporadic differences in sample preparation leading to, for example, very dilute samples. Estimations of the relative concentrations of citrate, hippurate, and taurine were in \textgreater95% correlation (r2) between sites, with an analytical error comparable to normal physiological variation in concentration (4−8%). The excellent analytical reproducibility and robustness of metabonomic techniques demonstrated here are highly competitive compared to the best proteomic analyses and are in significant contrast to genomic microarray platforms, both of which are complementary techniques for predictive and mechanistic toxicology. These results have implications for the quantitative interpretation of metabonomic data, and the establishment of quality control criteria for both regulatory agencies and for integrating data obtained at different sites.

@article{friml_atpin4_2002,
	title = {{AtPIN4} {Mediates} {Sink}-{Driven} {Auxin} {Gradients} and {Root} {Patterning} in {Arabidopsis}},
	volume = {108},
	issn = {0092-8674},
	url = {https://www.sciencedirect.com/science/article/pii/S0092867402006566},
	doi = {10.1016/S0092-8674(02)00656-6},
	abstract = {In contrast to animals, little is known about pattern formation in plants. Physiological and genetic data suggest the involvement of the phytohormone auxin in this process. Here, we characterize a novel member of the PIN family of putative auxin efflux carriers, Arabidopsis PIN4, that is localized in developing and mature root meristems. Atpin4 mutants are defective in establishment and maintenance of endogenous auxin gradients, fail to canalize externally applied auxin, and display various patterning defects in both embryonic and seedling roots. We propose a role for AtPIN4 in generating a sink for auxin below the quiescent center of the root meristem that is essential for auxin distribution and patterning.},
	language = {en},
	number = {5},
	urldate = {2021-10-19},
	journal = {Cell},
	author = {Friml, Jiřı́ and Benková, Eva and Blilou, Ikram and Wisniewska, Justyna and Hamann, Thorsten and Ljung, Karin and Woody, Scott and Sandberg, Goran and Scheres, Ben and Jürgens, Gerd and Palme, Klaus},
	month = mar,
	year = {2002},
	pages = {661--673},
}

In contrast to animals, little is known about pattern formation in plants. Physiological and genetic data suggest the involvement of the phytohormone auxin in this process. Here, we characterize a novel member of the PIN family of putative auxin efflux carriers, Arabidopsis PIN4, that is localized in developing and mature root meristems. Atpin4 mutants are defective in establishment and maintenance of endogenous auxin gradients, fail to canalize externally applied auxin, and display various patterning defects in both embryonic and seedling roots. We propose a role for AtPIN4 in generating a sink for auxin below the quiescent center of the root meristem that is essential for auxin distribution and patterning.

@article{beckwith-hall_application_2002,
	title = {Application of orthogonal signal correction to minimise the effects of physical and biological variation in high resolution {1H} {NMR} spectra of biofluids},
	volume = {127},
	issn = {1364-5528},
	url = {https://pubs.rsc.org/en/content/articlelanding/2002/an/b205128c},
	doi = {10.1039/B205128C},
	abstract = {1H nuclear magnetic resonance (NMR)-based metabonomics is a well-established technique used to analyse and interpret complex multiparametric metabolic data, and has a wide number of applications in the development of pharmaceuticals. However, interpretation of biological data can be confounded by extraneous variation in the data such as fluctuations in either experimental conditions or in physiological status. Here we have shown the novel application of a data filtering method, orthogonal signal correction (OSC), to biofluid NMR data to minimise the influence of inter- and intra-spectrometer variation during data acquisition, and also to minimise innate physiological variation. The removal of orthogonal variation exposed features of interest in the NMR data and facilitated interpretation of the derived multivariate models. Furthermore, analysis of the orthogonal variation provided an explanation of the systematic analytical/biological changes responsible for confounding the original NMR data.},
	language = {en},
	number = {10},
	urldate = {2021-10-19},
	journal = {Analyst},
	author = {Beckwith-Hall, Bridgette M. and Brindle, Joanne T. and Barton, Richard H. and Coen, Muireann and Holmes, Elaine and Nicholson, Jeremy K. and Antti, Henrik},
	month = oct,
	year = {2002},
	note = {Publisher: The Royal Society of Chemistry},
	pages = {1283--1288},
}

1H nuclear magnetic resonance (NMR)-based metabonomics is a well-established technique used to analyse and interpret complex multiparametric metabolic data, and has a wide number of applications in the development of pharmaceuticals. However, interpretation of biological data can be confounded by extraneous variation in the data such as fluctuations in either experimental conditions or in physiological status. Here we have shown the novel application of a data filtering method, orthogonal signal correction (OSC), to biofluid NMR data to minimise the influence of inter- and intra-spectrometer variation during data acquisition, and also to minimise innate physiological variation. The removal of orthogonal variation exposed features of interest in the NMR data and facilitated interpretation of the derived multivariate models. Furthermore, analysis of the orthogonal variation provided an explanation of the systematic analytical/biological changes responsible for confounding the original NMR data.

@article{ferris_leaf_2002,
	title = {Leaf stomatal and epidermal cell development: identification of putative quantitative trait loci in relation to elevated carbon dioxide concentration in poplar},
	volume = {22},
	issn = {0829-318X},
	shorttitle = {Leaf stomatal and epidermal cell development},
	url = {https://doi.org/10.1093/treephys/22.9.633},
	doi = {10.1093/treephys/22.9.633},
	abstract = {Genetic variation in stomatal initiation and density, and epidermal cell size and number were examined in a hybrid pedigree of Populus trichocarpa T. \& G. and P. deltoides Marsh in both ambient ([aCO2]) and elevated ([eCO2]) concentrations of CO2. We aimed to link anatomical traits with the underlying genetic map of F2 Family 331, composed of 350 markers across 19 linkage groups. Leaf stomatal and epidermal cell traits showed pronounced differences between the original parents. We considered the following traits in the F2 population: stomatal density (SD), stomatal index (SI), epidermal cell area (ECA) and the number of epidermal cells per leaf (ECN). In [eCO2], adaxial SD and SI were reduced in the F2 population, whereas ECA increased and ECN remained unchanged. In [aCO2], four putative quantitative trait loci (QTL) with logarithm of the odds ratio (LOD) scores greater than 2.9 were found for stomatal traits on linkage group B: adaxial SI (LOD scores of 5.4 and 5.2); abaxial SI (LOD score of 3.3); and SD (LOD score of 3.2). These results imply that QTL for SI and SD share linkage group B and are under genetic control. More moderate LOD scores (LOD scores \>/= 2.5) suggest QTL for SI on linkage groups A and B and for SD on linkage groups B, D and X with a probable co-locating quantitative trait locus for SI and SD on linkage group D (position 46.3 cM). The QTL in both [aCO2] and [eCO2] for adaxial SD were co-located on linkage group X (LOD scores of 3.5 and 2.6, respectively) indicating a similar response across both treatments. Putative QTL were located on linkage group A (position 89.2 cM) for both leaf size and ECN in [aCO2] and for ECA at almost the same position. The data provide preliminary evidence that leaf stomatal and cell traits are amenable to QTL analysis.},
	number = {9},
	urldate = {2021-10-19},
	journal = {Tree Physiology},
	author = {Ferris, Rachel and Long, L. and Bunn, S. M. and Robinson, K. M. and Bradshaw, H. D. and Rae, A. M. and Taylor, Gail},
	month = jun,
	year = {2002},
	pages = {633--640},
}

Genetic variation in stomatal initiation and density, and epidermal cell size and number were examined in a hybrid pedigree of Populus trichocarpa T. & G. and P. deltoides Marsh in both ambient ([aCO2]) and elevated ([eCO2]) concentrations of CO2. We aimed to link anatomical traits with the underlying genetic map of F2 Family 331, composed of 350 markers across 19 linkage groups. Leaf stomatal and epidermal cell traits showed pronounced differences between the original parents. We considered the following traits in the F2 population: stomatal density (SD), stomatal index (SI), epidermal cell area (ECA) and the number of epidermal cells per leaf (ECN). In [eCO2], adaxial SD and SI were reduced in the F2 population, whereas ECA increased and ECN remained unchanged. In [aCO2], four putative quantitative trait loci (QTL) with logarithm of the odds ratio (LOD) scores greater than 2.9 were found for stomatal traits on linkage group B: adaxial SI (LOD scores of 5.4 and 5.2); abaxial SI (LOD score of 3.3); and SD (LOD score of 3.2). These results imply that QTL for SI and SD share linkage group B and are under genetic control. More moderate LOD scores (LOD scores >/= 2.5) suggest QTL for SI on linkage groups A and B and for SD on linkage groups B, D and X with a probable co-locating quantitative trait locus for SI and SD on linkage group D (position 46.3 cM). The QTL in both [aCO2] and [eCO2] for adaxial SD were co-located on linkage group X (LOD scores of 3.5 and 2.6, respectively) indicating a similar response across both treatments. Putative QTL were located on linkage group A (position 89.2 cM) for both leaf size and ECN in [aCO2] and for ECA at almost the same position. The data provide preliminary evidence that leaf stomatal and cell traits are amenable to QTL analysis.

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

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

@article{rojdestvenski_segregation_2002,
	title = {Segregation of {Photosystems} in {Thylakoid} {Membranes} as a {Critical} {Phenomenon}},
	volume = {82},
	issn = {0006-3495},
	url = {https://www.sciencedirect.com/science/article/pii/S0006349502755240},
	doi = {10.1016/S0006-3495(02)75524-0},
	abstract = {The distribution of the two photosystems, PSI and PSII, in grana and stroma lamellae of the chloroplast membranes is not uniform. PSII are mainly concentrated in grana and PSI in stroma thylakoids. The dynamics and factors controlling the spatial segregation of PSI and PSII are generally not well understood, and here we address the segregation of photosystems in thylakoid membranes by means of a molecular dynamics method. The lateral segregation of photosystems was studied assuming a model comprising a two-dimensional (in-plane), two-component, many-body system with periodic boundary conditions and competing interactions between the photosystems in the thylakoid membrane. PSI and PSII are represented by particles with different values of negative charge. The pair interactions between particles include a screened Coulomb repulsive part and an exponentially decaying attractive part. The modeling results suggest a complicated phase behavior of the system, including quasi-crystalline phase of randomly distributed complexes of PSII and PSI at low ionic screening, well defined clustered state of segregated complexes at high screening, and in addition, an intermediate agglomerate phase where the photosystems tend to aggregate together without segregation. The calculations demonstrated that the ordering of photosystems within the membrane was the result of interplay between electrostatic and lipid-mediated interactions. At some values of the model parameters the segregation can be represented visually as well as by analyzing the correlation functions of the configuration.},
	language = {en},
	number = {4},
	urldate = {2021-10-19},
	journal = {Biophysical Journal},
	author = {Rojdestvenski, Igor and Ivanov, Alexander G. and Cottam, M. G. and Borodich, Andrei and Huner, Norman P. A. and Öquist, Gunnar},
	month = apr,
	year = {2002},
	pages = {1719--1730},
}

The distribution of the two photosystems, PSI and PSII, in grana and stroma lamellae of the chloroplast membranes is not uniform. PSII are mainly concentrated in grana and PSI in stroma thylakoids. The dynamics and factors controlling the spatial segregation of PSI and PSII are generally not well understood, and here we address the segregation of photosystems in thylakoid membranes by means of a molecular dynamics method. The lateral segregation of photosystems was studied assuming a model comprising a two-dimensional (in-plane), two-component, many-body system with periodic boundary conditions and competing interactions between the photosystems in the thylakoid membrane. PSI and PSII are represented by particles with different values of negative charge. The pair interactions between particles include a screened Coulomb repulsive part and an exponentially decaying attractive part. The modeling results suggest a complicated phase behavior of the system, including quasi-crystalline phase of randomly distributed complexes of PSII and PSI at low ionic screening, well defined clustered state of segregated complexes at high screening, and in addition, an intermediate agglomerate phase where the photosystems tend to aggregate together without segregation. The calculations demonstrated that the ordering of photosystems within the membrane was the result of interplay between electrostatic and lipid-mediated interactions. At some values of the model parameters the segregation can be represented visually as well as by analyzing the correlation functions of the configuration.

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

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

@article{johansson_molecular_2002,
	title = {Molecular cloning and characterization of a {cDNA} encoding poplar {UDP}-glucose dehydrogenase, a key gene of hemicellulose/pectin formation},
	volume = {1576},
	issn = {0167-4781},
	url = {https://www.sciencedirect.com/science/article/pii/S0167478102002920},
	doi = {10.1016/S0167-4781(02)00292-0},
	abstract = {Plant UDP-glucose dehydrogenase (UGDH) is an important enzyme in the formation of hemicellulose and pectin, the components of newly formed cell walls. A cDNA clone (Ugdh) corresponding to UGDH was isolated from a cDNA library prepared from cambial zone of poplar (Populus tremula x tremuloides). Within the 1824-nucleotide (nt)-long clone, an open reading frame encoded a protein of 481 amino acids (aa), with a calculated molecular weight of 53.1 kDa. The derived aa sequence showed 90\% and 63\% identity with UGDHs from soybean and bovine liver, respectively, and had highly conserved aa motifs believed to be of importance for nt binding and catalytic efficiency. In poplar, the Ugdh corresponds to one or two genes, as found by genomic Southern analysis. The gene was expressed predominantly in differentiating xylem and young leaves, with little expression in the phloem zone of the stem. The expression pattern matched that of UGDH protein, as found by immunoblotting. In leaves, the Ugdh expression was upregulated by a short-term feeding with sucrose, sorbitol and polyethylene glycol, and this effect was to some extent mimicked by light exposure. The data suggest that Ugdh is regulated via an osmoticum-dependent pathway, possibly related to the availability of osmotically active carbohydrate precursors to UDP-glucose, a substrate of UGDH.},
	language = {en},
	number = {1},
	urldate = {2021-10-19},
	journal = {Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression},
	author = {Johansson, Henrik and Sterky, Fredrik and Amini, Bahram and Lundeberg, Joakim and Kleczkowski, Leszek A.},
	month = jun,
	year = {2002},
	keywords = {Glucuronate, Hemicellulose, Pectin, UDP-glucose metabolism, Wood formation},
	pages = {53--58},
}

Plant UDP-glucose dehydrogenase (UGDH) is an important enzyme in the formation of hemicellulose and pectin, the components of newly formed cell walls. A cDNA clone (Ugdh) corresponding to UGDH was isolated from a cDNA library prepared from cambial zone of poplar (Populus tremula x tremuloides). Within the 1824-nucleotide (nt)-long clone, an open reading frame encoded a protein of 481 amino acids (aa), with a calculated molecular weight of 53.1 kDa. The derived aa sequence showed 90% and 63% identity with UGDHs from soybean and bovine liver, respectively, and had highly conserved aa motifs believed to be of importance for nt binding and catalytic efficiency. In poplar, the Ugdh corresponds to one or two genes, as found by genomic Southern analysis. The gene was expressed predominantly in differentiating xylem and young leaves, with little expression in the phloem zone of the stem. The expression pattern matched that of UGDH protein, as found by immunoblotting. In leaves, the Ugdh expression was upregulated by a short-term feeding with sucrose, sorbitol and polyethylene glycol, and this effect was to some extent mimicked by light exposure. The data suggest that Ugdh is regulated via an osmoticum-dependent pathway, possibly related to the availability of osmotically active carbohydrate precursors to UDP-glucose, a substrate of UGDH.

@article{ciereszko_effects_2002,
	title = {Effects of phosphate deficiency and sugars on expression of rab18 in {Arabidopsis}: hexokinase-dependent and okadaic acid-sensitive transduction of the sugar signal},
	volume = {1579},
	issn = {0167-4781},
	shorttitle = {Effects of phosphate deficiency and sugars on expression of rab18 in {Arabidopsis}},
	url = {https://www.sciencedirect.com/science/article/pii/S016747810200502X},
	doi = {10.1016/S0167-4781(02)00502-X},
	abstract = {The lack of phosphorus in the nutrient medium increased the expression of rab18, an abscisic acid (ABA)-responsive gene, in leaves of Arabidopsis thaliana. The expression of this gene was also upregulated after feeding the excised leaves with d-mannose and sucrose for both wild-type (wt) and aba1 (ABA-deficient) mutant plants. For aba1 mutants, both the phosphate deficiency and sugar effects on rab18 were weaker than in wt plants, suggesting possible involvement of both ABA-dependent and ABA-independent components in signalling. Transgenic Arabidopsis plants with increased hexokinase (HXK) expression had a much higher sucrose-dependent level of rab18 mRNA, implying the HXK involvement in sensing/transmitting the sugar signal. Sucrose-related induction of rab18 was completely inhibited by okadaic acid (OKA), suggesting the involvement of specific protein phosphatase(s) in transduction of the sugar signal. The results suggest that rab18 is regulated via interaction of a plethora of signals, including ABA, sugar and phosphate deficiency, and that the sugar effect is transmitted via a HXK-pathway, involving OKA-sensitive component(s). The findings prompt caution in linking the expression of rab18 solely to ABA signalling.},
	language = {en},
	number = {1},
	urldate = {2021-10-19},
	journal = {Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression},
	author = {Ciereszko, Iwona and Kleczkowski, Leszek A},
	month = nov,
	year = {2002},
	keywords = {Gene expression, Mannose, Phosphate stress, Sucrose, mutant},
	pages = {43--49},
}

The lack of phosphorus in the nutrient medium increased the expression of rab18, an abscisic acid (ABA)-responsive gene, in leaves of Arabidopsis thaliana. The expression of this gene was also upregulated after feeding the excised leaves with d-mannose and sucrose for both wild-type (wt) and aba1 (ABA-deficient) mutant plants. For aba1 mutants, both the phosphate deficiency and sugar effects on rab18 were weaker than in wt plants, suggesting possible involvement of both ABA-dependent and ABA-independent components in signalling. Transgenic Arabidopsis plants with increased hexokinase (HXK) expression had a much higher sucrose-dependent level of rab18 mRNA, implying the HXK involvement in sensing/transmitting the sugar signal. Sucrose-related induction of rab18 was completely inhibited by okadaic acid (OKA), suggesting the involvement of specific protein phosphatase(s) in transduction of the sugar signal. The results suggest that rab18 is regulated via interaction of a plethora of signals, including ABA, sugar and phosphate deficiency, and that the sugar effect is transmitted via a HXK-pathway, involving OKA-sensitive component(s). The findings prompt caution in linking the expression of rab18 solely to ABA signalling.

@article{martz_oligomerization_2002,
	title = {Oligomerization status, with the monomer as active species, defines catalytic efficiency of {UDP}-glucose pyrophosphorylase},
	volume = {367},
	issn = {0264-6021},
	url = {https://doi.org/10.1042/bj20020772},
	doi = {10.1042/bj20020772},
	abstract = {Barley UDP-glucose pyrophosphorylase (UGPase), a key enzyme for the synthesis of sucrose, cellulose and other saccharides, was expressed in Escherichia coli and purified. Using both native electrophoresis and gel filtration, the recombinant and crude leaf UGPase proteins were found to exist as a mixture of monomers, dimers and higher-order polymers. In order to understand the molecular basis for the oligomerization of UGPase, a conserved Cys residue was replaced (C99S mutant) and several amino acids were substituted (LIV to NIN, KK to LL and LLL to NNN) in a conserved hydrophobic domain (amino acids 117—138). The C99S mutant had about half the Vmax of the wild-type and a 12-fold higher Km for PPi, whereas NIN and LL mutations lowered the Vmax by 12- and 2-fold, respectively, with relatively small effects on substrate Km values (the NNN mutant was insoluble/inactive). The NIN mutation resulted in a low-activity oligomerized enzyme form, with very little monomer formation. Activity staining on native PAGE gels as well as gel-filtration studies demonstrated that the monomer was the sole enzymically active form. Possible implications of the oligomerization status of UGPase for post-translational regulation of the enzyme are discussed.},
	number = {1},
	urldate = {2021-10-19},
	journal = {Biochemical Journal},
	author = {MARTZ, Françoise and WILCZYNSKA, Malgorzata and KLECZKOWSKI, Leszek A.},
	month = oct,
	year = {2002},
	pages = {295--300},
}

Barley UDP-glucose pyrophosphorylase (UGPase), a key enzyme for the synthesis of sucrose, cellulose and other saccharides, was expressed in Escherichia coli and purified. Using both native electrophoresis and gel filtration, the recombinant and crude leaf UGPase proteins were found to exist as a mixture of monomers, dimers and higher-order polymers. In order to understand the molecular basis for the oligomerization of UGPase, a conserved Cys residue was replaced (C99S mutant) and several amino acids were substituted (LIV to NIN, KK to LL and LLL to NNN) in a conserved hydrophobic domain (amino acids 117—138). The C99S mutant had about half the Vmax of the wild-type and a 12-fold higher Km for PPi, whereas NIN and LL mutations lowered the Vmax by 12- and 2-fold, respectively, with relatively small effects on substrate Km values (the NNN mutant was insoluble/inactive). The NIN mutation resulted in a low-activity oligomerized enzyme form, with very little monomer formation. Activity staining on native PAGE gels as well as gel-filtration studies demonstrated that the monomer was the sole enzymically active form. Possible implications of the oligomerization status of UGPase for post-translational regulation of the enzyme are discussed.

@article{garcia_reliable_2002,
	title = {Reliable and easy screening technique for salt tolerance of citrus rootstocks under controlled environments},
	volume = {53},
	issn = {1444-9838},
	url = {https://www.publish.csiro.au/ar/ar01071},
	doi = {10.1071/ar01071},
	abstract = {Three salt tolerance experiments using 5 common citrus rootstocks were carried out to find a reliable and easy screening technique for salt tolerance in breeding programs. The experiments were: (1) in vitro seed culture where salt tolerance was mainly evaluated as germination percentage, (2) hydroponic culture of 2-month-old seedlings where salt tolerance was mainly evaluated as survival percentage, and (3) hydroponic culture of satsuma-rootstock combinations where salt tolerance was evaluated by leaf and fruit characters. Treatments were: 4 mm K2CO3 and 0-100 mm NaCl in Expt 1; 3.5 mm K2CO3 and 0-50 mm NaCl, with and without K2CO3, in Expt 2; and 25 mm NaCl in Expt 3. Volkamer lemon was the most salt-sensitive genotype during seed germination (Expt 1), whereas Troyer citrange was the most sensitive when used as rootstock of satsuma (Expt 3). For seedling survival (Expt 2), the trifoliate orange variety Flying dragon showed the highest survival percentage, and chloride content of satsuma leaves and fruit juice were high on this rootstock under salinity (Expt 3). Alkalinity (pH = 8.5) greatly affected seedling survival of Cleopatra mandarin and Volkamer lemon (Expt 2), probably due to major disturbances in seedling nutrition. Analysis of trait values for the rootstocks in the different saline treatments in both the in vitro germination and the seedling survival experiments revealed some significant changes compared with control conditions. Most of these changes were not consistent between genotypes, except for chloride concentration in both shoot ([Cl]s) and root ([Cl]r). The ordering of genotypes for salt tolerance found in the literature, which corresponds to the ordering as chloride excluders in our satsuma Expt 3, agrees with the inverse ordering of genotypes regarding the increment of both [Cl]s and the ratio [Cl]s/[Cl]r from control to low salinity, but does not agree with salt tolerance measured as a percentage of germination or seedling survival. The increments of both [Cl]s and the ratio [Cl]s/[Cl]r from control to low salinity are suggested as criteria for early selection of salt-tolerant citrus rootstocks. Three salt tolerance mechanisms have been observed: chloride exclusion, water saving, and accumulation of soluble solids. They all seem to be presented by Cleopatra mandarin when used as rootstock, supporting its utilisation as donor of salt tolerance in breeding programs of citrus rootstocks.},
	language = {en},
	number = {6},
	urldate = {2021-10-19},
	journal = {Australian Journal of Agricultural Research},
	author = {García, M. R. and Bernet, G. P. and Puchades, J. and Gómez, I. and Carbonell, E. A. and Asins, M. J.},
	year = {2002},
	note = {Publisher: CSIRO PUBLISHING},
	pages = {653--662},
}

Three salt tolerance experiments using 5 common citrus rootstocks were carried out to find a reliable and easy screening technique for salt tolerance in breeding programs. The experiments were: (1) in vitro seed culture where salt tolerance was mainly evaluated as germination percentage, (2) hydroponic culture of 2-month-old seedlings where salt tolerance was mainly evaluated as survival percentage, and (3) hydroponic culture of satsuma-rootstock combinations where salt tolerance was evaluated by leaf and fruit characters. Treatments were: 4 mm K2CO3 and 0-100 mm NaCl in Expt 1; 3.5 mm K2CO3 and 0-50 mm NaCl, with and without K2CO3, in Expt 2; and 25 mm NaCl in Expt 3. Volkamer lemon was the most salt-sensitive genotype during seed germination (Expt 1), whereas Troyer citrange was the most sensitive when used as rootstock of satsuma (Expt 3). For seedling survival (Expt 2), the trifoliate orange variety Flying dragon showed the highest survival percentage, and chloride content of satsuma leaves and fruit juice were high on this rootstock under salinity (Expt 3). Alkalinity (pH = 8.5) greatly affected seedling survival of Cleopatra mandarin and Volkamer lemon (Expt 2), probably due to major disturbances in seedling nutrition. Analysis of trait values for the rootstocks in the different saline treatments in both the in vitro germination and the seedling survival experiments revealed some significant changes compared with control conditions. Most of these changes were not consistent between genotypes, except for chloride concentration in both shoot ([Cl]s) and root ([Cl]r). The ordering of genotypes for salt tolerance found in the literature, which corresponds to the ordering as chloride excluders in our satsuma Expt 3, agrees with the inverse ordering of genotypes regarding the increment of both [Cl]s and the ratio [Cl]s/[Cl]r from control to low salinity, but does not agree with salt tolerance measured as a percentage of germination or seedling survival. The increments of both [Cl]s and the ratio [Cl]s/[Cl]r from control to low salinity are suggested as criteria for early selection of salt-tolerant citrus rootstocks. Three salt tolerance mechanisms have been observed: chloride exclusion, water saving, and accumulation of soluble solids. They all seem to be presented by Cleopatra mandarin when used as rootstock, supporting its utilisation as donor of salt tolerance in breeding programs of citrus rootstocks.

@article{holmes_chemometric_2002,
	title = {Chemometric contributions to the evolution of metabonomics: mathematical solutions to characterising and interpreting complex biological {NMR} spectra},
	volume = {127},
	issn = {1364-5528},
	shorttitle = {Chemometric contributions to the evolution of metabonomics},
	url = {https://pubs.rsc.org/en/content/articlelanding/2002/an/b208254n},
	doi = {10.1039/B208254N},
	abstract = {The pharmaceutical industry has embraced emerging technologies such as genomics, proteomics and metabonomics over the past decade with a view to minimizing attrition and expanding drug development pipelines. Metabonomic technology, based on the multivariate analysis of complex biological profiles generated from spectroscopic instruments, has enabled the construction of successful expert systems for toxicity screening and disease diagnosis. Here we describe the evolution of chemometric and bioinformatic methodologies to accommodate the multi- and megavariate data generated by high resolution NMR spectroscopy of biofluids, tissues and cell cultures and explore their potential role in mining, modeling and predicting metabolic data.},
	language = {en},
	number = {12},
	urldate = {2021-10-19},
	journal = {Analyst},
	author = {Holmes, E. and Antti, H.},
	month = dec,
	year = {2002},
	note = {Publisher: The Royal Society of Chemistry},
	pages = {1549--1557},
}

The pharmaceutical industry has embraced emerging technologies such as genomics, proteomics and metabonomics over the past decade with a view to minimizing attrition and expanding drug development pipelines. Metabonomic technology, based on the multivariate analysis of complex biological profiles generated from spectroscopic instruments, has enabled the construction of successful expert systems for toxicity screening and disease diagnosis. Here we describe the evolution of chemometric and bioinformatic methodologies to accommodate the multi- and megavariate data generated by high resolution NMR spectroscopy of biofluids, tissues and cell cultures and explore their potential role in mining, modeling and predicting metabolic data.

@article{azmi_metabolic_2002,
	title = {Metabolic trajectory characterisation of xenobiotic-induced hepatotoxic lesions using statistical batch processing of {NMR} data},
	volume = {127},
	issn = {1364-5528},
	url = {https://pubs.rsc.org/en/content/articlelanding/2002/an/b109430k},
	doi = {10.1039/B109430K},
	abstract = {Multivariate statistical batch processing (BP) analysis of 1H NMR urine spectra was employed to establish time-dependent metabolic variations in animals treated with the model hepatotoxin, α-naphthylisothiocyanate (ANIT). ANIT (100 mg kg−1) was administered orally to rats (n = 5) and urine samples were collected from dosed and matching control rats at time-points up to 168 h post-dose. Urine samples were measured via1H NMR spectroscopy and partial least squares (PLS) based batch processing analysis was used to interpret the spectral data, treating each rat as an individual batch comprising a series of timed urine samples. A model defining the mean urine profile over the 7 day study period was established, together with model confidence limits (±3 standard deviation), for the control group. Samples obtained from ANIT treated animals were evaluated using the control model. Time-dependent deviations from the control model were evident in all ANIT treated animals consisting of glycosuria, bile aciduria, an initial decrease in taurine levels followed by taurinuria and a reduction of tricarboxylic acid cycle intermediate excretion. BP provided an efficient means of visualising the biochemical response to ANIT in terms of both inter-animal variation and net variation in metabolite excretion profiles. BP also allowed multivariate statistical limits for normality to be established and provided a template for defining the sequence of time-dependent metabolic consequences of toxicity in NMR based metabonomic studies.},
	language = {en},
	number = {2},
	urldate = {2021-10-19},
	journal = {Analyst},
	author = {Azmi, Jahanara and Griffin, Julian L. and Antti, Henrik and Shore, Richard F. and Johansson, Erik and Nicholson, Jeremy K. and Holmes, Elaine},
	month = jan,
	year = {2002},
	note = {Publisher: The Royal Society of Chemistry},
	pages = {271--276},
}

Multivariate statistical batch processing (BP) analysis of 1H NMR urine spectra was employed to establish time-dependent metabolic variations in animals treated with the model hepatotoxin, α-naphthylisothiocyanate (ANIT). ANIT (100 mg kg−1) was administered orally to rats (n = 5) and urine samples were collected from dosed and matching control rats at time-points up to 168 h post-dose. Urine samples were measured via1H NMR spectroscopy and partial least squares (PLS) based batch processing analysis was used to interpret the spectral data, treating each rat as an individual batch comprising a series of timed urine samples. A model defining the mean urine profile over the 7 day study period was established, together with model confidence limits (±3 standard deviation), for the control group. Samples obtained from ANIT treated animals were evaluated using the control model. Time-dependent deviations from the control model were evident in all ANIT treated animals consisting of glycosuria, bile aciduria, an initial decrease in taurine levels followed by taurinuria and a reduction of tricarboxylic acid cycle intermediate excretion. BP provided an efficient means of visualising the biochemical response to ANIT in terms of both inter-animal variation and net variation in metabolite excretion profiles. BP also allowed multivariate statistical limits for normality to be established and provided a template for defining the sequence of time-dependent metabolic consequences of toxicity in NMR based metabonomic studies.

@article{berglund_chemometric_2002,
	title = {Chemometric tools in bioinformatics.},
	volume = {224},
	issn = {0065-7727},
	url = {https://www.webofscience.com/wos/woscc/full-record/WOS:000177422202571?SID=E6OBdVIk3N3sJssnJl2},
	language = {English},
	urldate = {2021-10-19},
	journal = {Abstracts of Papers of the American Chemical Society},
	author = {Berglund, A. and Pettersson, F.},
	month = aug,
	year = {2002},
	note = {Patent Number: 1
Place: Washington
Publisher: Amer Chemical Soc
WOS:000177422202571},
	pages = {U506--U506},
}

@article{van_zyl_heterologous_2002,
	title = {Heterologous {Array} {Analysis} in {Pinaceae}: {Hybridization} of {Pinus} taeda {cDNA} {Arrays} with {cDNA} from {Needles} and {Embryogenic} {Cultures} of {P}. taeda, {P}. sylvestris or {Picea} abies},
	volume = {3},
	issn = {2314-436X},
	shorttitle = {Heterologous {Array} {Analysis} in {Pinaceae}},
	url = {https://www.hindawi.com/journals/ijg/2002/186124/},
	doi = {10.1002/cfg.199},
	abstract = {Hybridization of labelled cDNA from various cell types with high-density arrays of expressed sequence tags is a powerful technique for investigating gene expression. Few conifer cDNA libraries have been sequenced. Because of the high level of sequence conservation between Pinus and Picea we have investigated the use of arrays from one genus for studies of gene expression in the other. The partial cDNAs from 384 identifiable genes expressed in differentiating xylem of Pinus taeda were printed on nylon membranes in randomized replicates. These were hybridized with labelled cDNA from needles or embryogenic cultures of Pinus taeda, P. sylvestris and Picea abies, and with labelled cDNA from leaves of Nicotiana tabacum. The Spearman correlation of gene expression for pairs of conifer species was high for needles (r2 = 0.78 − 0.86), and somewhat lower for embryogenic cultures (r2 = 0.68 − 0.83). The correlation of gene expression for tobacco leaves and needles of each of the three conifer species was lower but sufficiently high (r2 = 0.52 − 0.63) to suggest that many partial gene sequences are conserved in angiosperms and gymnosperms. Heterologous probing was further used to identify tissue-specific gene expression over species boundaries. To evaluate the significance of differences in gene expression, conventional parametric tests were compared with permutation tests after four methods of normalization. Permutation tests after Z-normalization provide the highest degree of discrimination but may enhance the probability of type I errors. It is concluded that arrays of cDNA from loblolly pine are useful for studies of gene expression in other pines or spruces.},
	language = {en},
	number = {4},
	urldate = {2021-10-19},
	journal = {Comparative and Functional Genomics},
	author = {van Zyl, Leonel and von Arnold, Sara and Bozhkov, Peter and Chen, Yongzhong and Egertsdotter, Ulrika and MacKay, John and Sederoff, Ronald R. and Shen, Jing and Zelena, Lyubov and Clapham, David H.},
	year = {2002},
	note = {Publisher: Hindawi},
	pages = {306--318},
}

Hybridization of labelled cDNA from various cell types with high-density arrays of expressed sequence tags is a powerful technique for investigating gene expression. Few conifer cDNA libraries have been sequenced. Because of the high level of sequence conservation between Pinus and Picea we have investigated the use of arrays from one genus for studies of gene expression in the other. The partial cDNAs from 384 identifiable genes expressed in differentiating xylem of Pinus taeda were printed on nylon membranes in randomized replicates. These were hybridized with labelled cDNA from needles or embryogenic cultures of Pinus taeda, P. sylvestris and Picea abies, and with labelled cDNA from leaves of Nicotiana tabacum. The Spearman correlation of gene expression for pairs of conifer species was high for needles (r2 = 0.78 − 0.86), and somewhat lower for embryogenic cultures (r2 = 0.68 − 0.83). The correlation of gene expression for tobacco leaves and needles of each of the three conifer species was lower but sufficiently high (r2 = 0.52 − 0.63) to suggest that many partial gene sequences are conserved in angiosperms and gymnosperms. Heterologous probing was further used to identify tissue-specific gene expression over species boundaries. To evaluate the significance of differences in gene expression, conventional parametric tests were compared with permutation tests after four methods of normalization. Permutation tests after Z-normalization provide the highest degree of discrimination but may enhance the probability of type I errors. It is concluded that arrays of cDNA from loblolly pine are useful for studies of gene expression in other pines or spruces.

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

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

@article{wu_study_2002,
	title = {Study of early selection in tree breeding 4. {Efficiency} of {Marker}-{Aided} {Early} {Selection} ({MAES})},
	volume = {51},
	abstract = {One of the main attractions of Marker-Aided Selection (MAS) in tree breeding is its potential for early selection through juvenile traits as Marker-Aided Early Selection (MAES). The theoretical advantages of incorporating molecular markers into early selection in tree breeding are examined. Equations were derived to answer the following questions: (1) how effective is the use of markers for early selection relative to conventional late (mature) selection? (2) what is the efficiency of using markers for early selection relative to early selection based on morphological traits? (3) how effective is incorporating markers into an early selection index relative to an early selection index based on morphological traits alone? (4) what are the efficiencies when MAS is used only for within-family selection in the combined family and within family selection approach, relative to selection using combined family and within family phenotypic information alone? and (5) how effective is selection when MAES is used for within-family selection only in the combined family and within family early selection approach, relative to early selection using combined family and within family phenotypic information alone? These equations could be used to compare relative efficiencies of MAES and QAES (QTL-Aided Early Selection) relative to traditional phenotypic selection in breeding programs. For Marker-Aided Early Selection or QTL-Aided Early Selection to be applicable in tree breeding populations, it may be necessary to demonstrate that efficiency from MAES or QAES is higher than efficiency of early selection using less expensive early phenotypic traits. Furthermore, the relative efficiency of MAES or QAES is higher when genetic correlation of early-mature trait and/or heritability of the early trait is lower and is less for full-sib family than for half-sib family selection.},
	journal = {Silvae Genetica},
	author = {Wu, H.X.},
	month = jan,
	year = {2002},
	keywords = {⛔ No DOI found},
	pages = {261--269},
}

One of the main attractions of Marker-Aided Selection (MAS) in tree breeding is its potential for early selection through juvenile traits as Marker-Aided Early Selection (MAES). The theoretical advantages of incorporating molecular markers into early selection in tree breeding are examined. Equations were derived to answer the following questions: (1) how effective is the use of markers for early selection relative to conventional late (mature) selection? (2) what is the efficiency of using markers for early selection relative to early selection based on morphological traits? (3) how effective is incorporating markers into an early selection index relative to an early selection index based on morphological traits alone? (4) what are the efficiencies when MAS is used only for within-family selection in the combined family and within family selection approach, relative to selection using combined family and within family phenotypic information alone? and (5) how effective is selection when MAES is used for within-family selection only in the combined family and within family early selection approach, relative to early selection using combined family and within family phenotypic information alone? These equations could be used to compare relative efficiencies of MAES and QAES (QTL-Aided Early Selection) relative to traditional phenotypic selection in breeding programs. For Marker-Aided Early Selection or QTL-Aided Early Selection to be applicable in tree breeding populations, it may be necessary to demonstrate that efficiency from MAES or QAES is higher than efficiency of early selection using less expensive early phenotypic traits. Furthermore, the relative efficiency of MAES or QAES is higher when genetic correlation of early-mature trait and/or heritability of the early trait is lower and is less for full-sib family than for half-sib family selection.

@article{wu_inbreeding_2002,
	title = {Inbreeding in {Pinus} radiata. {IV}: the effect of inbreeding on wood density},
	volume = {59},
	copyright = {INRA, EDP Sciences},
	issn = {1286-4560, 1297-966X},
	shorttitle = {Inbreeding in {Pinus} radiata. {IV}},
	url = {http://dx.doi.org/10.1051/forest:2002041},
	doi = {10/c8jbk5},
	abstract = {Annals of Forest Science, is a source of information about current developments and trends in forest research and forestry},
	language = {en},
	number = {5-6},
	urldate = {2021-08-26},
	journal = {Annals of Forest Science},
	author = {Wu, Harry X. and Matheson, A. Colin and Abarquez, Aljoy},
	month = jul,
	year = {2002},
	note = {Publisher: EDP Sciences},
	pages = {557--562},
}

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

@article{hanson_expression_2002,
	title = {The expression pattern of the homeobox gene {ATHB13} reveals a conservation of transcriptional regulatory mechanisms between {Arabidopsis} and hybrid aspen},
	volume = {21},
	issn = {1432-203X},
	url = {https://doi.org/10.1007/s00299-002-0476-6},
	doi = {10/cvzt76},
	abstract = {ATHB13 belongs to a family of homeodomain leucine zipper (HDZip) transcription factors in Arabidopsis thaliana. To understand the temporal and spatial distribution of ATHB13 gene expression, we examined the ATHB13 promoter activity by means of fusions to the uidA (GUS, β-glucuronidase) reporter gene in transgenic plants. The strongest promoter activity was detected in the vasculature of the basal portion of petioles for both rosette leaves and cotyledons and at the base of cauline leaves. Activity was also detected in the stem at the base of the cauline leaf in an area corresponding to the leaf gap in the vasculature. In flowers, promoter activity was also present in the receptacle and in the stigma. Transformation of the same promoter-GUS construct into hybrid aspen (Populus tremula × P. tremuloides) resulted in an analogous expression pattern in the petioles of leaves. The similarity of these expression patterns indicates that the trans-acting factors responsible for ATHB13 expression are conserved between aspen and Arabidopsis. The conserved expression pattern of the highly specific Arabidopsis ATHB13 promoter in hybrid aspen demonstrates the potential utility of Arabidopsis promoters for tissue-specific expression in angiosperm trees.},
	language = {en},
	number = {1},
	urldate = {2021-08-26},
	journal = {Plant Cell Reports},
	author = {Hanson, J. and Regan, S. and Engström, P.},
	month = jul,
	year = {2002},
	pages = {81--89},
}

ATHB13 belongs to a family of homeodomain leucine zipper (HDZip) transcription factors in Arabidopsis thaliana. To understand the temporal and spatial distribution of ATHB13 gene expression, we examined the ATHB13 promoter activity by means of fusions to the uidA (GUS, β-glucuronidase) reporter gene in transgenic plants. The strongest promoter activity was detected in the vasculature of the basal portion of petioles for both rosette leaves and cotyledons and at the base of cauline leaves. Activity was also detected in the stem at the base of the cauline leaf in an area corresponding to the leaf gap in the vasculature. In flowers, promoter activity was also present in the receptacle and in the stigma. Transformation of the same promoter-GUS construct into hybrid aspen (Populus tremula × P. tremuloides) resulted in an analogous expression pattern in the petioles of leaves. The similarity of these expression patterns indicates that the trans-acting factors responsible for ATHB13 expression are conserved between aspen and Arabidopsis. The conserved expression pattern of the highly specific Arabidopsis ATHB13 promoter in hybrid aspen demonstrates the potential utility of Arabidopsis promoters for tissue-specific expression in angiosperm trees.

@article{ciavatta_promoter_2002,
	title = {A promoter from the loblolly pine {PtNIP1};1 gene directs expression in an early-embryogenesis and suspensor-specific fashion},
	volume = {215},
	issn = {1432-2048},
	url = {https://doi.org/10.1007/s00425-002-0822-5},
	doi = {10/b3zcr8},
	abstract = {The PtNIP1;1 gene encodes an aquaglyceroporin that is expressed early in embryogenesis and appears to be expressed preferentially in the suspensor [V.T. Ciavatta et al. (2001) Plant Physiol 127:211–224]. An 899-bp fragment 5′ to the PtNIP1;1 open reading frame (NIP-899) was cloned from loblolly pine (Pinus taeda L.) genomic DNA and fused to the β-glucuronidase (GUS) reporter gene. The resulting plasmid, pNIP-GUS, was transformed into Norway spruce (Picea abies L.) embryogenic cultures by co-bombarding with a plasmid containing a bar gene construct as a selectable marker. The identity of lines selected on medium containing the herbicide Basta and showing β-glucuronidase activity was confirmed by polymerase chain reaction as harboring GUS. Histochemical GUS assays of these lines revealed GUS activity in all cells of proembryogenic masses. During early embryogeny, GUS staining was intense in the suspensor region but not detectable in embryonal masses. GUS staining was absent by mid-embryogeny. By contrast, a control transgenic line, transformed with EuCAD-GUS, expressed GUS throughout embryo development. These results suggest that NIP-899 contains elements that drive early embryogenesis-specific expression and suspensor-specific expression. This is the first example of a suspensor-specific promoter in conifers.},
	language = {en},
	number = {4},
	urldate = {2021-08-26},
	journal = {Planta},
	author = {Ciavatta, Vincent T. and Egertsdotter, Ulrika and Clapham, David and von Arnold, Sara and Cairney, John},
	month = aug,
	year = {2002},
	pages = {694--698},
}

The PtNIP1;1 gene encodes an aquaglyceroporin that is expressed early in embryogenesis and appears to be expressed preferentially in the suspensor [V.T. Ciavatta et al. (2001) Plant Physiol 127:211–224]. An 899-bp fragment 5′ to the PtNIP1;1 open reading frame (NIP-899) was cloned from loblolly pine (Pinus taeda L.) genomic DNA and fused to the β-glucuronidase (GUS) reporter gene. The resulting plasmid, pNIP-GUS, was transformed into Norway spruce (Picea abies L.) embryogenic cultures by co-bombarding with a plasmid containing a bar gene construct as a selectable marker. The identity of lines selected on medium containing the herbicide Basta and showing β-glucuronidase activity was confirmed by polymerase chain reaction as harboring GUS. Histochemical GUS assays of these lines revealed GUS activity in all cells of proembryogenic masses. During early embryogeny, GUS staining was intense in the suspensor region but not detectable in embryonal masses. GUS staining was absent by mid-embryogeny. By contrast, a control transgenic line, transformed with EuCAD-GUS, expressed GUS throughout embryo development. These results suggest that NIP-899 contains elements that drive early embryogenesis-specific expression and suspensor-specific expression. This is the first example of a suspensor-specific promoter in conifers.