Publications 2006

@article{yano_where_2006,
	title = {Where {Water} {Is} {Oxidized} to {Dioxygen}: {Structure} of the {Photosynthetic} {Mn4Ca} {Cluster}},
	volume = {314},
	shorttitle = {Where {Water} {Is} {Oxidized} to {Dioxygen}},
	url = {https://www.science.org/doi/10.1126/science.1128186},
	doi = {10.1126/science.1128186},
	abstract = {The oxidation of water to dioxygen is catalyzed within photosystem II (PSII) by a Mn4Ca cluster, the structure of which remains elusive. Polarized extended x-ray absorption fine structure (EXAFS) measurements on PSII single crystals constrain the Mn4Ca cluster geometry to a set of three similar high-resolution structures. Combining polarized EXAFS and x-ray diffraction data, the cluster was placed within PSII, taking into account the overall trend of the electron density of the metal site and the putative ligands. The structure of the cluster from the present study is unlike either the 3.0 or 3.5 angstrom–resolution x-ray structures or other previously proposed models.},
	number = {5800},
	urldate = {2024-11-29},
	journal = {Science},
	author = {Yano, Junko and Kern, Jan and Sauer, Kenneth and Latimer, Matthew J. and Pushkar, Yulia and Biesiadka, Jacek and Loll, Bernhard and Saenger, Wolfram and Messinger, Johannes and Zouni, Athina and Yachandra, Vittal K.},
	month = nov,
	year = {2006},
	note = {Publisher: American Association for the Advancement of Science},
	pages = {821--825},
}

The oxidation of water to dioxygen is catalyzed within photosystem II (PSII) by a Mn4Ca cluster, the structure of which remains elusive. Polarized extended x-ray absorption fine structure (EXAFS) measurements on PSII single crystals constrain the Mn4Ca cluster geometry to a set of three similar high-resolution structures. Combining polarized EXAFS and x-ray diffraction data, the cluster was placed within PSII, taking into account the overall trend of the electron density of the metal site and the putative ligands. The structure of the cluster from the present study is unlike either the 3.0 or 3.5 angstrom–resolution x-ray structures or other previously proposed models.

@article{shevela_characterization_2006,
	title = {Characterization of the water oxidizing complex of photosystem {II} of the {Chl} d-containing cyanobacterium {Acaryochloris} marina via its reactivity towards endogenous electron donors and acceptors},
	volume = {8},
	issn = {1463-9084},
	url = {https://pubs.rsc.org/en/content/articlelanding/2006/cp/b604389e},
	doi = {10.1039/B604389E},
	abstract = {Acaroychloris (A.) marina is a unique oxygen evolving organism that contains a large amount of chlorophyll d (Chl d) and only very few Chl a molecules. This feature raises questions on the nature of the photoactive pigment, which supports light-induced oxidative water splitting in Photosystem II (PS II). In this study, flash-induced oxygen evolution patterns (FIOPs) were measured to address the question whether the Si state transition probabilities and/or the redox-potentials of the water oxidizing complex (WOC) in its different Si states are altered in A. marina cells compared to that of spinach thylakoids. The analysis of the obtained data within the framework of different versions of the Kok model reveals that in light activated A. marina cells the miss probability is similar compared to spinach thylakoids. This finding indicates that the redox-potentials and kinetics within the WOC, of the reaction center (P680) and of YZ are virtually the same for both organisms. This conclusion is strongly supported by lifetime measurements of the S2 and S3 states. Virtually identical time constants were obtained for the slow phase of deactivation. Kinetic differences in the fast phase of S2 and S3 decay between A. marina cells and spinach thylakoids reflect a shift of the Em of YD/YoxD to lower values in the former compared to the latter organisms, as revealed by the observation of an opposite change in the kinetics of S0 oxidation to S1 by YoxD. A slightly increased double hit probability in A. marina cells is indicative of a faster QA− to QB electron transfer in these cells compared to spinach thylakoids.},
	language = {en},
	number = {29},
	urldate = {2024-11-29},
	journal = {Physical Chemistry Chemical Physics},
	author = {Shevela, Dmitriy and Nöring, Birgit and Eckert, Hann-Jörg and Messinger, Johannes and Renger, Gernot},
	month = jul,
	year = {2006},
	note = {Publisher: The Royal Society of Chemistry},
	pages = {3460--3466},
}

Acaroychloris (A.) marina is a unique oxygen evolving organism that contains a large amount of chlorophyll d (Chl d) and only very few Chl a molecules. This feature raises questions on the nature of the photoactive pigment, which supports light-induced oxidative water splitting in Photosystem II (PS II). In this study, flash-induced oxygen evolution patterns (FIOPs) were measured to address the question whether the Si state transition probabilities and/or the redox-potentials of the water oxidizing complex (WOC) in its different Si states are altered in A. marina cells compared to that of spinach thylakoids. The analysis of the obtained data within the framework of different versions of the Kok model reveals that in light activated A. marina cells the miss probability is similar compared to spinach thylakoids. This finding indicates that the redox-potentials and kinetics within the WOC, of the reaction center (P680) and of YZ are virtually the same for both organisms. This conclusion is strongly supported by lifetime measurements of the S2 and S3 states. Virtually identical time constants were obtained for the slow phase of deactivation. Kinetic differences in the fast phase of S2 and S3 decay between A. marina cells and spinach thylakoids reflect a shift of the Em of YD/YoxD to lower values in the former compared to the latter organisms, as revealed by the observation of an opposite change in the kinetics of S0 oxidation to S1 by YoxD. A slightly increased double hit probability in A. marina cells is indicative of a faster QA− to QB electron transfer in these cells compared to spinach thylakoids.

@article{eriksson_ga4_2006,
	title = {{GA4} {Is} the {Active} {Gibberellin} in the {Regulation} of {LEAFY} {Transcription} and {Arabidopsis} {Floral} {Initiation}},
	volume = {18},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.106.042317},
	doi = {10.1105/tpc.106.042317},
	abstract = {Flower initiation in Arabidopsis thaliana under noninductive short-day conditions is dependent on the biosynthesis of the plant hormone gibberellin (GA). This dependency can be explained, at least partly, by GA regulation of the flower meristem identity gene LEAFY (LFY) and the flowering time gene SUPPRESSOR OF CONSTANS1. Although it is well established that GA4 is the active GA in the regulation of Arabidopsis shoot elongation, the identity of the GA responsible for the regulation of Arabidopsis flowering has not been established. Through a combination of GA quantifications and sensitivity assays, we show that GA4 is the active GA in the regulation of LFY transcription and Arabidopsis flowering time under short-day conditions. The levels of GA4 and sucrose increase dramatically in the shoot apex shortly before floral initiation, and the regulation of genes involved in GA metabolism suggests that this increase is possibly due to transport of GAs and sucrose from outside sources to the shoot apex. Our results demonstrate that in the dicot Arabidopsis, in contrast with the monocot Lolium temulentum, GA4 is the active GA in the regulation of both shoot elongation and flower initiation.},
	number = {9},
	urldate = {2024-10-07},
	journal = {The Plant Cell},
	author = {Eriksson, Sven and Böhlenius, Henrik and Moritz, Thomas and Nilsson, Ove},
	month = sep,
	year = {2006},
	pages = {2172--2181},
}

Flower initiation in Arabidopsis thaliana under noninductive short-day conditions is dependent on the biosynthesis of the plant hormone gibberellin (GA). This dependency can be explained, at least partly, by GA regulation of the flower meristem identity gene LEAFY (LFY) and the flowering time gene SUPPRESSOR OF CONSTANS1. Although it is well established that GA4 is the active GA in the regulation of Arabidopsis shoot elongation, the identity of the GA responsible for the regulation of Arabidopsis flowering has not been established. Through a combination of GA quantifications and sensitivity assays, we show that GA4 is the active GA in the regulation of LFY transcription and Arabidopsis flowering time under short-day conditions. The levels of GA4 and sucrose increase dramatically in the shoot apex shortly before floral initiation, and the regulation of genes involved in GA metabolism suggests that this increase is possibly due to transport of GAs and sucrose from outside sources to the shoot apex. Our results demonstrate that in the dicot Arabidopsis, in contrast with the monocot Lolium temulentum, GA4 is the active GA in the regulation of both shoot elongation and flower initiation.

@article{laubinger_arabidopsis_2006,
	title = {Arabidopsis {SPA} proteins regulate photoperiodic flowering and interact with the floral inducer {CONSTANS} to regulate its stability},
	volume = {133},
	issn = {0950-1991},
	url = {https://doi.org/10.1242/dev.02481},
	doi = {10.1242/dev.02481},
	abstract = {The four-member SPA protein family of Arabidopsis acts in concert with the E3 ubiquitin ligase COP1 to suppress photomorphogenesis in dark-grown seedlings. Here, we demonstrate that SPA proteins are, moreover, essential for photoperiodic flowering. Mutations in SPA1 cause phyA-independent early flowering under short day (SD) but not long day (LD) conditions, and this phenotype is enhanced by additional loss of SPA3 and SPA4 function. These spa1 spa3 spa4 triple mutants flower at the same time in LD and SD, indicating that the SPA gene family is essential for the inhibition of flowering under non-inductive SD. Among the four SPA genes, SPA1 is necessary and sufficient for normal photoperiodic flowering. Early flowering of SD-grown spa mutant correlates with strongly increased FT transcript levels, whereas COtranscript levels are not altered. Epistasis analysis demonstrates that both early flowering and FT induction in spa1 mutants is fully dependent on CO. Consistent with this finding, SPA proteins interact physically with CO in vitro and in vivo, suggesting that SPA proteins regulate CO protein function. Domain mapping shows that the SPA1-CO interaction requires the CCT-domain of CO, but is independent of the B-box type Zn fingers of CO. We further show that spa1 spa3 spa4 mutants exhibit strongly increased CO protein levels, which are not caused by a change in COgene expression. Taken together, our results suggest, that SPA proteins regulate photoperiodic flowering by controlling the stability of the floral inducer CO.},
	number = {16},
	urldate = {2022-11-30},
	journal = {Development},
	author = {Laubinger, Sascha and Marchal, Virginie and Gentilhomme, José and Wenkel, Stephan and Adrian, Jessika and Jang, Seonghoe and Kulajta, Carmen and Braun, Helen and Coupland, George and Hoecker, Ute},
	month = aug,
	year = {2006},
	pages = {3213--3222},
}

The four-member SPA protein family of Arabidopsis acts in concert with the E3 ubiquitin ligase COP1 to suppress photomorphogenesis in dark-grown seedlings. Here, we demonstrate that SPA proteins are, moreover, essential for photoperiodic flowering. Mutations in SPA1 cause phyA-independent early flowering under short day (SD) but not long day (LD) conditions, and this phenotype is enhanced by additional loss of SPA3 and SPA4 function. These spa1 spa3 spa4 triple mutants flower at the same time in LD and SD, indicating that the SPA gene family is essential for the inhibition of flowering under non-inductive SD. Among the four SPA genes, SPA1 is necessary and sufficient for normal photoperiodic flowering. Early flowering of SD-grown spa mutant correlates with strongly increased FT transcript levels, whereas COtranscript levels are not altered. Epistasis analysis demonstrates that both early flowering and FT induction in spa1 mutants is fully dependent on CO. Consistent with this finding, SPA proteins interact physically with CO in vitro and in vivo, suggesting that SPA proteins regulate CO protein function. Domain mapping shows that the SPA1-CO interaction requires the CCT-domain of CO, but is independent of the B-box type Zn fingers of CO. We further show that spa1 spa3 spa4 mutants exhibit strongly increased CO protein levels, which are not caused by a change in COgene expression. Taken together, our results suggest, that SPA proteins regulate photoperiodic flowering by controlling the stability of the floral inducer CO.

@article{wenkel_constans_2006,
	title = {{CONSTANS} and the {CCAAT} {Box} {Binding} {Complex} {Share} a {Functionally} {Important} {Domain} and {Interact} to {Regulate} {Flowering} of {Arabidopsis}},
	volume = {18},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.106.043299},
	doi = {10.1105/tpc.106.043299},
	abstract = {The CCT (for CONSTANS, CONSTANS-LIKE, TOC1) domain is found in 45 Arabidopsis thaliana proteins involved in processes such as photoperiodic flowering, light signaling, and regulation of circadian rhythms. We show that this domain exhibits similarities to yeast HEME ACTIVATOR PROTEIN2 (HAP2), which is a subunit of the HAP2/HAP3/HAP5 trimeric complex that binds to CCAAT boxes in eukaryotic promoters. Moreover, we demonstrate that CONSTANS (CO), which promotes Arabidopsis flowering, interacts with At HAP3 and At HAP5 in yeast, in vitro, and in planta. Mutations in CO that delay flowering affect residues highly conserved between CCT and the DNA binding domain of HAP2. Taken together, these data suggest that CO might replace At HAP2 in the HAP complex to form a trimeric CO/At HAP3/At HAP5 complex. Flowering was delayed by overexpression of At HAP2 or At HAP3 throughout the plant or in phloem companion cells, where CO is expressed. This phenotype was correlated with reduced abundance of FLOWERING LOCUS T (FT) mRNA and no change in CO mRNA levels. At HAP2 or At HAP3 overexpression may therefore impair formation of a CO/At HAP3/At HAP5 complex leading to reduced expression of FT. During plant evolution, the number of genes encoding HAP proteins was greatly amplified, and these proteins may have acquired novel functions, such as mediating the effect of CCT domain proteins on gene expression.},
	number = {11},
	urldate = {2022-11-30},
	journal = {The Plant Cell},
	author = {Wenkel, Stephan and Turck, Franziska and Singer, Kamy and Gissot, Lionel and Le Gourrierec, José and Samach, Alon and Coupland, George},
	month = nov,
	year = {2006},
	pages = {2971--2984},
}

The CCT (for CONSTANS, CONSTANS-LIKE, TOC1) domain is found in 45 Arabidopsis thaliana proteins involved in processes such as photoperiodic flowering, light signaling, and regulation of circadian rhythms. We show that this domain exhibits similarities to yeast HEME ACTIVATOR PROTEIN2 (HAP2), which is a subunit of the HAP2/HAP3/HAP5 trimeric complex that binds to CCAAT boxes in eukaryotic promoters. Moreover, we demonstrate that CONSTANS (CO), which promotes Arabidopsis flowering, interacts with At HAP3 and At HAP5 in yeast, in vitro, and in planta. Mutations in CO that delay flowering affect residues highly conserved between CCT and the DNA binding domain of HAP2. Taken together, these data suggest that CO might replace At HAP2 in the HAP complex to form a trimeric CO/At HAP3/At HAP5 complex. Flowering was delayed by overexpression of At HAP2 or At HAP3 throughout the plant or in phloem companion cells, where CO is expressed. This phenotype was correlated with reduced abundance of FLOWERING LOCUS T (FT) mRNA and no change in CO mRNA levels. At HAP2 or At HAP3 overexpression may therefore impair formation of a CO/At HAP3/At HAP5 complex leading to reduced expression of FT. During plant evolution, the number of genes encoding HAP proteins was greatly amplified, and these proteins may have acquired novel functions, such as mediating the effect of CCT domain proteins on gene expression.

@article{drakakaki_arabidopsis_2006,
	title = {Arabidopsis {Reversibly} {Glycosylated} {Polypeptides} 1 and 2 {Are} {Essential} for {Pollen} {Development}},
	volume = {142},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.106.086363},
	doi = {10.1104/pp.106.086363},
	abstract = {Reversibly glycosylated polypeptides (RGPs) have been implicated in polysaccharide biosynthesis. To date, to our knowledge, no direct evidence exists for the involvement of RGPs in a particular biochemical process. The Arabidopsis (Arabidopsis thaliana) genome contains five RGP genes out of which RGP1 and RGP2 share the highest sequence identity. We characterized the native expression pattern of Arabidopsis RGP1 and RGP2 and used reverse genetics to investigate their respective functions. Although both genes are ubiquitously expressed, the highest levels are observed in actively growing tissues and in mature pollen, in particular. RGPs showed cytoplasmic and transient association with Golgi. In addition, both proteins colocalized in the same compartments and coimmunoprecipitated from plant cell extracts. Single-gene disruptions did not show any obvious morphological defects under greenhouse conditions, whereas the double-insertion mutant could not be recovered. We present evidence that the double mutant is lethal and demonstrate the critical role of RGPs, particularly in pollen development. Detailed analysis demonstrated that mutant pollen development is associated with abnormally enlarged vacuoles and a poorly defined inner cell wall layer, which consequently results in disintegration of the pollen structure during pollen mitosis I. Taken together, our results indicate that RGP1 and RGP2 are required during microspore development and pollen mitosis, either affecting cell division and/or vacuolar integrity.},
	number = {4},
	urldate = {2021-10-21},
	journal = {Plant Physiology},
	author = {Drakakaki, Georgia and Zabotina, Olga and Delgado, Ivan and Robert, Stéphanie and Keegstra, Kenneth and Raikhel, Natasha},
	month = dec,
	year = {2006},
	pages = {1480--1492},
}

Reversibly glycosylated polypeptides (RGPs) have been implicated in polysaccharide biosynthesis. To date, to our knowledge, no direct evidence exists for the involvement of RGPs in a particular biochemical process. The Arabidopsis (Arabidopsis thaliana) genome contains five RGP genes out of which RGP1 and RGP2 share the highest sequence identity. We characterized the native expression pattern of Arabidopsis RGP1 and RGP2 and used reverse genetics to investigate their respective functions. Although both genes are ubiquitously expressed, the highest levels are observed in actively growing tissues and in mature pollen, in particular. RGPs showed cytoplasmic and transient association with Golgi. In addition, both proteins colocalized in the same compartments and coimmunoprecipitated from plant cell extracts. Single-gene disruptions did not show any obvious morphological defects under greenhouse conditions, whereas the double-insertion mutant could not be recovered. We present evidence that the double mutant is lethal and demonstrate the critical role of RGPs, particularly in pollen development. Detailed analysis demonstrated that mutant pollen development is associated with abnormally enlarged vacuoles and a poorly defined inner cell wall layer, which consequently results in disintegration of the pollen structure during pollen mitosis I. Taken together, our results indicate that RGP1 and RGP2 are required during microspore development and pollen mitosis, either affecting cell division and/or vacuolar integrity.

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

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

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

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

@article{tuskan_genome_2006,
	title = {The genome of black cottonwood, {Populus} trichocarpa ({Torr}. \& {Gray})},
	volume = {313},
	issn = {0036-8075},
	doi = {10/c7hs34},
	abstract = {We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.},
	language = {English},
	number = {5793},
	journal = {Science},
	author = {Tuskan, G. A. and DiFazio, S. and Jansson, S. and Bohlmann, J. and Grigoriev, I. and Hellsten, U. and Putnam, N. and Ralph, S. and Rombauts, S. and Salamov, A. and Schein, J. and Sterck, L. and Aerts, A. and Bhalerao, Rishikesh P. and Bhalerao, R. P. and Blaudez, D. and Boerjan, W. and Brun, A. and Brunner, A. and Busov, V. and Campbell, M. and Carlson, J. and Chalot, M. and Chapman, J. and Chen, G.-L. and Cooper, D. and Coutinho, P. M. and Couturier, J. and Covert, S. and Cronk, Q. and Cunningham, R. and Davis, J. and Degroeve, S. and Dejardin, A. and dePamphilis, C. and Detter, J. and Dirks, B. and Dubchak, I. and Duplessis, S. and Ehlting, J. and Ellis, B. and Gendler, K. and Goodstein, D. and Gribskov, M. and Grimwood, J. and Groover, A. and Gunter, L. and Hamberger, B. and Heinze, B. and Helariutta, Y. and Henrissat, B. and Holligan, D. and Holt, R. and Huang, W. and Islam-Faridi, N. and Jones, S. and Jones-Rhoades, M. and Jorgensen, R. and Joshi, C. and Kangasjarvi, J. and Karlsson, J. and Kelleher, C. and Kirkpatrick, R. and Kirst, M. and Kohler, A. and Kalluri, U. and Larimer, F. and Leebens-Mack, J. and Leple, J.-C. and Locascio, P. and Lou, Y. and Lucas, S. and Martin, F. and Montanini, B. and Napoli, C. and Nelson, D. R. and Nelson, C. and Nieminen, K. and Nilsson, O. and Pereda, V. and Peter, G. and Philippe, R. and Pilate, G. and Poliakov, A. and Razumovskaya, J. and Richardson, P. and Rinaldi, C. and Ritland, K. and Rouze, P. and Ryaboy, D. and Schmutz, J. and Schrader, J. and Segerman, B. and Shin, H. and Siddiqui, A. and Sterky, F. and Terry, A. and Tsai, C.-J. and Uberbacher, E. and Unneberg, P. and Vahala, J. and Wall, K. and Wessler, S. and Yang, G. and Yin, T. and Douglas, C. and Marra, M. and Sandberg, G. and Van de Peer, Y. and Rokhsar, D.},
	month = sep,
	year = {2006},
	note = {Place: Washington
Publisher: Amer Assoc Advancement Science
WOS:000240498900035},
	keywords = {arabidopsis-thaliana, cinnamyl alcohol-dehydrogenase, gene-expression, gravitational induction, hybrid poplar, lignin biosynthesis, phenylpropanoid metabolism, quaking   aspen, resistance genes, transcriptional regulators},
	pages = {1596--1604},
}

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

@article{pettko-szandtner_activation_2006,
	title = {Activation of an alfalfa cyclin-dependent kinase inhibitor by calmodulin-like domain protein kinase},
	volume = {46},
	issn = {0960-7412},
	doi = {10/b4vt9r},
	abstract = {Kip- related proteins ( KRPs) play a central role in the regulation of the cell cycle and differentiation through modulation of cyclin- dependent kinase ( CDK) functions. We have identified a CDK inhibitor gene from Medicago truncatula ( Mt) by a yeast two- hybrid screen. The KRPMt gene was expressed in all plant organs and cultured cells, and its transcripts accumulated after abscisic acid and NaCl treatment. The KRPMt protein exhibits seven conserved sequence domains and a PEST motif that is also detected in various Arabidopsis KRPs. In the yeast two- hybrid test, the KRPMt protein interacted with CDK ( Medsa; CDKA; 1) and D- type cyclins. However, in the pull- down assays, B- type CDK complexes were also detectable. Recombinant KRPMt differentially inhibited various alfalfa CDK complexes in phosphorylation assays. The immunoprecipitated Medsa; CDKA; 1/ A; 2 complex was strongly inhibited, whereas the mitotic Medsa; CDKB2; 1 complex was the most sensitive to inhibition. Function of Medsa; CDKB1; 1 complex was not inhibited by the KRPMt protein. The mitotic Medsa; CYCB2 and Medsa; CYCA2; 1 complexes responded weakly to this inhibitor protein. Kinase complexes from G2/ M cells showed increased sensitivity towards the inhibitor compared with those isolated from G1/ S- phase cells. In vitro phosphorylation of Medicago retinoblastoma- related protein was also reduced in the presence of KRPMt. Phosphorylation of this inhibitor protein by the recombinant calmodulin- like domain protein kinase ( MsCPK3) resulted in enhanced inhibition of CDK function. The data presented emphasize the selective sensitivity of various cyclin- dependent kinase complexes to this inhibitor protein, and suggest a role for CDK inhibitors and CPKs in cross- talk between Ca2+ signalling and regulation of cell- cycle progression in plants.},
	language = {English},
	number = {1},
	journal = {Plant Journal},
	author = {Pettko-Szandtner, A. and Meszaros, T. and Horvath, G. V. and Bakó, L. and Csordas-Toth, E. and Blastyak, A. and Zhiponova, M. and Miskolczi, P. and Dudits, D.},
	month = apr,
	year = {2006},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000236035700008},
	keywords = {Ca2+ signalling, abscisic acid, arabidopsis-thaliana, calcium, cell cycle, cyclin-dependent kinase, expression, gene family, ick1, in-vitro, medicago-sativa, phosphorylation, plant-cell cycle, retinoblastoma-related protein},
	pages = {111--123},
}

Kip- related proteins ( KRPs) play a central role in the regulation of the cell cycle and differentiation through modulation of cyclin- dependent kinase ( CDK) functions. We have identified a CDK inhibitor gene from Medicago truncatula ( Mt) by a yeast two- hybrid screen. The KRPMt gene was expressed in all plant organs and cultured cells, and its transcripts accumulated after abscisic acid and NaCl treatment. The KRPMt protein exhibits seven conserved sequence domains and a PEST motif that is also detected in various Arabidopsis KRPs. In the yeast two- hybrid test, the KRPMt protein interacted with CDK ( Medsa; CDKA; 1) and D- type cyclins. However, in the pull- down assays, B- type CDK complexes were also detectable. Recombinant KRPMt differentially inhibited various alfalfa CDK complexes in phosphorylation assays. The immunoprecipitated Medsa; CDKA; 1/ A; 2 complex was strongly inhibited, whereas the mitotic Medsa; CDKB2; 1 complex was the most sensitive to inhibition. Function of Medsa; CDKB1; 1 complex was not inhibited by the KRPMt protein. The mitotic Medsa; CYCB2 and Medsa; CYCA2; 1 complexes responded weakly to this inhibitor protein. Kinase complexes from G2/ M cells showed increased sensitivity towards the inhibitor compared with those isolated from G1/ S- phase cells. In vitro phosphorylation of Medicago retinoblastoma- related protein was also reduced in the presence of KRPMt. Phosphorylation of this inhibitor protein by the recombinant calmodulin- like domain protein kinase ( MsCPK3) resulted in enhanced inhibition of CDK function. The data presented emphasize the selective sensitivity of various cyclin- dependent kinase complexes to this inhibitor protein, and suggest a role for CDK inhibitors and CPKs in cross- talk between Ca2+ signalling and regulation of cell- cycle progression in plants.

@article{sjodin_upsc-base_2006,
	title = {{UPSC}-{BASE} - {Populus} transcriptomics online},
	volume = {48},
	issn = {0960-7412},
	doi = {10/cxqkhm},
	abstract = {The increasing accessibility and use of microarrays in transcriptomics has accentuated the need for purpose-designed storage and analysis tools. Here we present UPSC-BASE, a database for analysis and storage of Populus DNA microarray data. A microarray analysis pipeline has also been established to allow consistent and efficient analysis (from small to large scale) of samples in various experimental designs. A range of optimized experimental protocols is provided for each step in generating the data. Within UPSC-BASE, researchers can perform standard and advanced microarray analysis procedures in a user-friendly environment. Background corrections, normalizations, quality-control tools, visualizations, hypothesis tests and export tools are provided without requirements for expert-level knowledge. Although the database has been developed primarily for handling Populus DNA microarrays, most of the tools are generic and can be used for other types of microarray. UPSC-BASE is also a repository of Populus microarray information, providing data from 21 experiments on a total of 407 microarray hybridizations in the public domain of the database. There are also an additional 10 experiments containing 347 hybridizations, where the automatically analysed data are searchable.},
	language = {English},
	number = {5},
	journal = {Plant Journal},
	author = {Sjodin, Andreas and Bylesjo, Max and Skogstrom, Oskar and Eriksson, Daniel and Nilsson, Peter and Ryden, Patrik and Jansson, Stefan and Karlsson, Jan},
	month = dec,
	year = {2006},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000242042900013},
	keywords = {bioconductor, cdna microarray data, database, design, expression profiling, functional genomics, gene-expression patterns, genomics, microarray, normalization, poplar, resource, sequence tags, tool, transcriptome},
	pages = {806--817},
}

The increasing accessibility and use of microarrays in transcriptomics has accentuated the need for purpose-designed storage and analysis tools. Here we present UPSC-BASE, a database for analysis and storage of Populus DNA microarray data. A microarray analysis pipeline has also been established to allow consistent and efficient analysis (from small to large scale) of samples in various experimental designs. A range of optimized experimental protocols is provided for each step in generating the data. Within UPSC-BASE, researchers can perform standard and advanced microarray analysis procedures in a user-friendly environment. Background corrections, normalizations, quality-control tools, visualizations, hypothesis tests and export tools are provided without requirements for expert-level knowledge. Although the database has been developed primarily for handling Populus DNA microarrays, most of the tools are generic and can be used for other types of microarray. UPSC-BASE is also a repository of Populus microarray information, providing data from 21 experiments on a total of 407 microarray hybridizations in the public domain of the database. There are also an additional 10 experiments containing 347 hybridizations, where the automatically analysed data are searchable.

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

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

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

@article{wilson_energy_2006,
	title = {Energy balance, organellar redox status, and acclimation to environmental stress},
	volume = {84},
	issn = {0008-4026},
	url = {http://www.nrcresearchpress.com/doi/10.1139/B06-098},
	doi = {10/dgfh8b},
	abstract = {In plants and algal cells, changes in light intensity can induce intrachloroplastic and retrograde regulation of gene expression in response to changes in the plastoquinone redox status. We review the evidence in support of the thesis that the chloroplast acts as a general sensor of cellular energy imbalance sensed through the plastoquinone pool. Alteration in cellular energy balance caused by chloroplast or mitochondrial metabolism can induce intracellular signalling to affect chloroplastic and nuclear gene expression in response, not only to light intensity, but to a myriad of abiotic stresses. In addition, this chloroplastic redox sensing also appears to have a broader impact, affecting long-distance systemic signalling related to plant growth and development. The organization of the respiratory electron transport chains of mitochondria and heterotrophic prokaryotes is comparable to that of chloroplast thylakoid membranes, and the redox state of the respiratory ubiquinone pool is a well-documented cellular energy sensor. Thus, modulation of electron transport component redox status by abiotic stress regulates organellar as well as nuclear gene expression. From the evidence presented, we suggest that the photosynthetic and respiratory machinery in prokaryotic and eukaryotic organisms have a dual function: primary cellular energy transformation, and global environmental sensing.},
	language = {en},
	number = {9},
	urldate = {2021-06-11},
	journal = {Canadian Journal of Botany},
	author = {Wilson, Kenneth E. and Ivanov, Alexander G. and Öquist, Gunnar and Grodzinski, Bernard and Sarhan, Fathey and Huner, Norman P.A.},
	month = sep,
	year = {2006},
	pages = {1355--1370},
}

In plants and algal cells, changes in light intensity can induce intrachloroplastic and retrograde regulation of gene expression in response to changes in the plastoquinone redox status. We review the evidence in support of the thesis that the chloroplast acts as a general sensor of cellular energy imbalance sensed through the plastoquinone pool. Alteration in cellular energy balance caused by chloroplast or mitochondrial metabolism can induce intracellular signalling to affect chloroplastic and nuclear gene expression in response, not only to light intensity, but to a myriad of abiotic stresses. In addition, this chloroplastic redox sensing also appears to have a broader impact, affecting long-distance systemic signalling related to plant growth and development. The organization of the respiratory electron transport chains of mitochondria and heterotrophic prokaryotes is comparable to that of chloroplast thylakoid membranes, and the redox state of the respiratory ubiquinone pool is a well-documented cellular energy sensor. Thus, modulation of electron transport component redox status by abiotic stress regulates organellar as well as nuclear gene expression. From the evidence presented, we suggest that the photosynthetic and respiratory machinery in prokaryotic and eukaryotic organisms have a dual function: primary cellular energy transformation, and global environmental sensing.

@article{ivanov_acclimation_2006,
	title = {Acclimation to temperature and irradiance modulates {PSII} charge recombination},
	volume = {580},
	issn = {0014-5793},
	doi = {10/fq4dds},
	abstract = {Acclimation of wild type and the chlorina F2 mutant of barley to either high light or low temperature results in a 2- to 3-fold increase in non-photochemical quenching which occurred independently of either energy-dependent quenching (qE), xanthophyll cycle-mediated antenna quenching or state transitions. Results of in vivo thermoluminescence measurements used to address this conundrum indicated that excitation pressure regulates the temperature gap for S(2)Q(B)(-) and S(2)Q(A)(-) charge recombinations within photosystem II reaction centers. This is discussed in terms of photoprotection through non-radiative charge recombination. (c) 2006 Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies.},
	language = {English},
	number = {11},
	journal = {Febs Letters},
	author = {Ivanov, A. G. and Sane, P. V. and Krol, M. and Gray, G. R. and Balseris, A. and Savitch, L. V. and Oquist, G. and Huner, N. P. A.},
	month = may,
	year = {2006},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000237686400041},
	keywords = {acclimation, antenna, charge recombination, chlorophyll fluorescence, energy-dissipation, irradiance, light, photoinhibition, photosynthesis, photosystem-ii, pool size, protein, psii, temperature, thermoluminescence},
	pages = {2797--2802},
}

Acclimation of wild type and the chlorina F2 mutant of barley to either high light or low temperature results in a 2- to 3-fold increase in non-photochemical quenching which occurred independently of either energy-dependent quenching (qE), xanthophyll cycle-mediated antenna quenching or state transitions. Results of in vivo thermoluminescence measurements used to address this conundrum indicated that excitation pressure regulates the temperature gap for S(2)Q(B)(-) and S(2)Q(A)(-) charge recombinations within photosystem II reaction centers. This is discussed in terms of photoprotection through non-radiative charge recombination. (c) 2006 Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies.

@article{gentili_effects_2006,
	title = {Effects of phosphorus and nitrogen on nodulation are seen already at the stage of early cortical cell divisions in {Alnus} incana},
	volume = {98},
	issn = {0305-7364},
	doi = {10/drq8mp},
	abstract = {Background and Aims The present work aimed to study early stages of nodulation in a chronological sequence and to study phosphorus and nitrogen effects on early stages of nodulation in Alnus incana infected by Frankia. A method was developed to quantify early nodulation stages in intact root systems in the root hair-infected actinorhizal plant A. incana. Plant tissue responses were followed every 2 d until 14 d after inoculation. Cortical cell divisions were already seen 2 d after inoculation with Frankia. Cortical cell division areas, prenodules, nodule primordia and emerging nodules were quantified as host responses to infection. Methods Seedlings were grown in pouches and received different levels of phosphorus and nitrogen. Four levels of phosphorus (from 0.03 to 1 mm P) and two levels of nitrogen (0.71 and 6.45 mm N) were used to study P and N effects on these early stages of nodule development. Key Results P at a medium concentration (0.1 mm) stimulated cell divisions in the cortex and a number of prenodules, nodule primordia and emerging nodules as compared with higher or lower P levels. A high N level inhibited early cell divisions in the cortex, and this was particularly evident when the length of cell division areas and presence of the nodulation stages were related to root length. Conclusions Extended cortical cell division areas were found that have not been previously shown in A. incana. The results show that effects of P and N are already expressed at the stage when the first cortical cell divisions are induced by Frankia.},
	language = {English},
	number = {2},
	journal = {Annals of Botany},
	author = {Gentili, Francesco and Wall, Luis G. and Huss-Danell, Kerstin},
	month = aug,
	year = {2006},
	note = {Place: Oxford
Publisher: Oxford Univ Press
WOS:000239630500004},
	keywords = {Alnus incana, Frankia, cortical cell division area, endophyte, fine-structure, frankia, hippophae, n-2 fixation, nitrate, nitrogen, nodulation, nodule development, phosphorus, split-root systems, symbiosis, ultrastructure},
	pages = {309--315},
}

Background and Aims The present work aimed to study early stages of nodulation in a chronological sequence and to study phosphorus and nitrogen effects on early stages of nodulation in Alnus incana infected by Frankia. A method was developed to quantify early nodulation stages in intact root systems in the root hair-infected actinorhizal plant A. incana. Plant tissue responses were followed every 2 d until 14 d after inoculation. Cortical cell divisions were already seen 2 d after inoculation with Frankia. Cortical cell division areas, prenodules, nodule primordia and emerging nodules were quantified as host responses to infection. Methods Seedlings were grown in pouches and received different levels of phosphorus and nitrogen. Four levels of phosphorus (from 0.03 to 1 mm P) and two levels of nitrogen (0.71 and 6.45 mm N) were used to study P and N effects on these early stages of nodule development. Key Results P at a medium concentration (0.1 mm) stimulated cell divisions in the cortex and a number of prenodules, nodule primordia and emerging nodules as compared with higher or lower P levels. A high N level inhibited early cell divisions in the cortex, and this was particularly evident when the length of cell division areas and presence of the nodulation stages were related to root length. Conclusions Extended cortical cell division areas were found that have not been previously shown in A. incana. The results show that effects of P and N are already expressed at the stage when the first cortical cell divisions are induced by Frankia.

@article{geisler_universal_2006,
	title = {A universal algorithm for genome-wide in silicio identification of biologically significant gene promoter putative cis-regulatory-elements; identification of new elements for reactive oxygen species and sucrose signaling in {Arabidopsis}},
	volume = {45},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2005.02634.x},
	doi = {10/dpnz4f},
	abstract = {Short motifs of many cis-regulatory elements (CREs) can be found in the promoters of most Arabidopsis genes, and this raises the question of how their presence can confer specific regulation. We developed a universal algorithm to test the biological significance of CREs by first identifying every Arabidopsis gene with a CRE and then statistically correlating the presence or absence of the element with the gene expression profile on multiple DNA microarrays. This algorithm was successfully verified for previously characterized abscisic acid, ethylene, sucrose and drought responsive CREs in Arabidopsis, showing that the presence of these elements indeed correlates with treatment-specific gene induction. Later, we used standard motif sampling methods to identify 128 putative motifs induced by excess light, reactive oxygen species and sucrose. Our algorithm was able to filter 20 out of 128 novel CREs which significantly correlated with gene induction by either heat, reactive oxygen species and/or sucrose. The position, orientation and sequence specificity of CREs was tested in silicio by analyzing the expression of genes with naturally occurring sequence variations. In three novel CREs the forward orientation correlated with sucrose induction and the reverse orientation with sucrose suppression. The functionality of the predicted novel CREs was experimentally confirmed using Arabidopsis cell-suspension cultures transformed with short promoter fragments or artificial promoters fused with the GUS reporter gene. Our genome-wide analysis opens up new possibilities for in silicio verification of the biological significance of newly discovered CREs, and allows for subsequent selection of such CREs for experimental studies.},
	language = {en},
	number = {3},
	urldate = {2021-06-11},
	journal = {The Plant Journal},
	author = {Geisler, Matt and Kleczkowski, Leszek A. and Karpinski, Stanislaw},
	year = {2006},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2005.02634.x},
	keywords = {DNA microarray analysis, cis-regulatory-element, hormonal signaling, promoter, reactive oxygen species, sucrose},
	pages = {384--398},
}

Short motifs of many cis-regulatory elements (CREs) can be found in the promoters of most Arabidopsis genes, and this raises the question of how their presence can confer specific regulation. We developed a universal algorithm to test the biological significance of CREs by first identifying every Arabidopsis gene with a CRE and then statistically correlating the presence or absence of the element with the gene expression profile on multiple DNA microarrays. This algorithm was successfully verified for previously characterized abscisic acid, ethylene, sucrose and drought responsive CREs in Arabidopsis, showing that the presence of these elements indeed correlates with treatment-specific gene induction. Later, we used standard motif sampling methods to identify 128 putative motifs induced by excess light, reactive oxygen species and sucrose. Our algorithm was able to filter 20 out of 128 novel CREs which significantly correlated with gene induction by either heat, reactive oxygen species and/or sucrose. The position, orientation and sequence specificity of CREs was tested in silicio by analyzing the expression of genes with naturally occurring sequence variations. In three novel CREs the forward orientation correlated with sucrose induction and the reverse orientation with sucrose suppression. The functionality of the predicted novel CREs was experimentally confirmed using Arabidopsis cell-suspension cultures transformed with short promoter fragments or artificial promoters fused with the GUS reporter gene. Our genome-wide analysis opens up new possibilities for in silicio verification of the biological significance of newly discovered CREs, and allows for subsequent selection of such CREs for experimental studies.

@article{kepinski_integrating_2006,
	title = {Integrating hormone signaling and patterning mechanisms in plant development},
	volume = {9},
	issn = {1369-5266},
	doi = {10/c7fvkt},
	abstract = {Plant growth and development are driven by the bustling integration of a vast number of signals, among which plant hormones dominate. Understanding the role of hormones in particular developmental events requires their integration with developmental regulators known to be specific to those events. Using the increasing number of tools that can be utilized to probe hormone biosynthesis, transport and response, several recent studies have taken such an integrative approach, and in so doing have contributed to a clearer picture of precisely how hormones control plant development.},
	language = {English},
	number = {1},
	journal = {Current Opinion in Plant Biology},
	author = {Kepinski, S.},
	month = feb,
	year = {2006},
	note = {Place: London
Publisher: Current Biology Ltd
WOS:000235089300005},
	keywords = {arabidopsis root, dependent auxin   gradients, gibberellin biosynthetic gene, lateral root development, leaf development, shoot apical meristem, stem-cell   niche, tobacco homeobox gene, transcriptional repression, transgenic tobacco},
	pages = {28--34},
}

Plant growth and development are driven by the bustling integration of a vast number of signals, among which plant hormones dominate. Understanding the role of hormones in particular developmental events requires their integration with developmental regulators known to be specific to those events. Using the increasing number of tools that can be utilized to probe hormone biosynthesis, transport and response, several recent studies have taken such an integrative approach, and in so doing have contributed to a clearer picture of precisely how hormones control plant development.

@article{ruonala_transitions_2006,
	title = {Transitions in the functioning of the shoot apical meristem in birch ({Betula} pendula) involve ethylene},
	volume = {46},
	issn = {0960-7412},
	doi = {10/dmkh9w},
	abstract = {In many trees, a short photoperiod (SD) triggers substantial physiological adjustments necessary for over-wintering. We have used transgenic ethylene-insensitive birches (Betula pendula), which express the Arabidopsis ethylene receptor gene ETR1 carrying the dominant mutation etr1-1, to investigate the role of ethylene in SD-induced responses in the shoot apical meristem (SAM). Under SD, the ethylene-insensitive trees ceased elongation growth comparably to the wild-type. In contrast, the formation of terminal buds, which in trees is typically induced by SD, was abolished. However, although delayed, endo-dormancy did eventually develop in the ethylene-insensitive trees. This, together with the rapid resumption of growth in the ethylene-insensitive trees after transfer from non-permissive to permissive conditions suggests that ethylene facilitates the SD-induced terminal bud formation, as well as growth arrest. In addition, apical buds of the ethylene-insensitive birch did not accumulate abscisic acid (ABA) under SD, suggesting interaction between ethylene and ABA signalling in the bud. Alterations in SAM functioning were further exemplified by reduced apical dominance and early flowering in ethylene-insensitive birches. Gene expression analysis of shoot apices revealed that the ethylene-insensitive birch lacked the marked increase in expression of a beta-xylosidase gene typical to the SD-exposed wild-type. The ethylene-dependent beta-xylosidase gene expression is hypothesized to relate to modification of cell walls in terminal buds during SD-induced growth cessation. Our results suggest that ethylene is involved in terminal bud formation and in the timely suppression of SAM activity, not only in the shoot apex, but also in axillary and reproductive meristems.},
	language = {English},
	number = {4},
	journal = {Plant Journal},
	author = {Ruonala, R. and Rinne, P. L. H. and Baghour, M. and Moritz, T. and Tuominen, H. and Kangasjarvi, J.},
	month = may,
	year = {2006},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000237098000008},
	keywords = {abscisic-acid, apical dominance, arabidopsis-thaliana, beta-xylosidase gene, birch, bud dormancy, cell-wall metabolism, dormancy, ethylene, expression, flowering, freezing   tolerance, induction, lateral bud growth, response pathway, xylosidase},
	pages = {628--640},
}

In many trees, a short photoperiod (SD) triggers substantial physiological adjustments necessary for over-wintering. We have used transgenic ethylene-insensitive birches (Betula pendula), which express the Arabidopsis ethylene receptor gene ETR1 carrying the dominant mutation etr1-1, to investigate the role of ethylene in SD-induced responses in the shoot apical meristem (SAM). Under SD, the ethylene-insensitive trees ceased elongation growth comparably to the wild-type. In contrast, the formation of terminal buds, which in trees is typically induced by SD, was abolished. However, although delayed, endo-dormancy did eventually develop in the ethylene-insensitive trees. This, together with the rapid resumption of growth in the ethylene-insensitive trees after transfer from non-permissive to permissive conditions suggests that ethylene facilitates the SD-induced terminal bud formation, as well as growth arrest. In addition, apical buds of the ethylene-insensitive birch did not accumulate abscisic acid (ABA) under SD, suggesting interaction between ethylene and ABA signalling in the bud. Alterations in SAM functioning were further exemplified by reduced apical dominance and early flowering in ethylene-insensitive birches. Gene expression analysis of shoot apices revealed that the ethylene-insensitive birch lacked the marked increase in expression of a beta-xylosidase gene typical to the SD-exposed wild-type. The ethylene-dependent beta-xylosidase gene expression is hypothesized to relate to modification of cell walls in terminal buds during SD-induced growth cessation. Our results suggest that ethylene is involved in terminal bud formation and in the timely suppression of SAM activity, not only in the shoot apex, but also in axillary and reproductive meristems.

@article{geisler-lee_poplar_2006,
	title = {Poplar carbohydrate-active enzymes. {Gene} identification and expression analyses},
	volume = {140},
	issn = {0032-0889},
	doi = {10/bj9bkd},
	abstract = {Over 1,600 genes encoding carbohydrate-active enzymes (CAZymes) in the Populus trichocarpa (Torr.\&Gray) genome were identified based on sequence homology, annotated, and grouped into families of glycosyltransferases, glycoside hydrolases, carbohydrate esterases, polysaccharide lyases, and expansins. Poplar ( Populus spp.) had approximately 1.6 times more CAZyme genes than Arabidopsis ( Arabidopsis thaliana). Whereas most families were proportionally increased, xylan and pectin-related families were underrepresented and the GT1 family of secondary metabolite-glycosylating enzymes was overrepresented in poplar. CAZyme gene expression in poplar was analyzed using a collection of 100,000 expressed sequence tags from 17 different tissues and compared to microarray data for poplar and Arabidopsis. Expression of genes involved in pectin and hemicellulose metabolism was detected in all tissues, indicating a constant maintenance of transcripts encoding enzymes remodeling the cell wall matrix. The most abundant transcripts encoded sucrose synthases that were specifically expressed in wood-forming tissues along with cellulose synthase and homologs of KORRIGAN and ELP1. Woody tissues were the richest source of various other CAZyme transcripts, demonstrating the importance of this group of enzymes for xylogenesis. In contrast, there was little expression of genes related to starch metabolism during wood formation, consistent with the preferential flux of carbon to cell wall biosynthesis. Seasonally dormant meristems of poplar showed a high prevalence of transcripts related to starch metabolism and surprisingly retained transcripts of some cell wall synthesis enzymes. The data showed profound changes in CAZyme transcriptomes in different poplar tissues and pointed to some key differences in CAZyme genes and their regulation between herbaceous and woody plants.},
	language = {English},
	number = {3},
	journal = {Plant Physiology},
	author = {Geisler-Lee, J. and Geisler, M. and Coutinho, P. M. and Segerman, B. and Nishikubo, N. and Takahashi, J. and Aspeborg, H. and Djerbi, S. and Master, E. and Andersson-Gunneras, S. and Sundberg, B. and Karpinski, S. and Teeri, T. T. and Kleczkowski, L. A. and Henrissat, B. and Mellerowicz, E. J.},
	month = mar,
	year = {2006},
	note = {Place: Rockville
Publisher: Amer Soc Plant Biologists
WOS:000235868900014},
	keywords = {arabidopsis, callose synthase, cell-walls, cellulose, family, hybrid aspen, multiple sequence alignment, pectin methylesterases, populus, sucrose},
	pages = {946--962},
}

Over 1,600 genes encoding carbohydrate-active enzymes (CAZymes) in the Populus trichocarpa (Torr.&Gray) genome were identified based on sequence homology, annotated, and grouped into families of glycosyltransferases, glycoside hydrolases, carbohydrate esterases, polysaccharide lyases, and expansins. Poplar ( Populus spp.) had approximately 1.6 times more CAZyme genes than Arabidopsis ( Arabidopsis thaliana). Whereas most families were proportionally increased, xylan and pectin-related families were underrepresented and the GT1 family of secondary metabolite-glycosylating enzymes was overrepresented in poplar. CAZyme gene expression in poplar was analyzed using a collection of 100,000 expressed sequence tags from 17 different tissues and compared to microarray data for poplar and Arabidopsis. Expression of genes involved in pectin and hemicellulose metabolism was detected in all tissues, indicating a constant maintenance of transcripts encoding enzymes remodeling the cell wall matrix. The most abundant transcripts encoded sucrose synthases that were specifically expressed in wood-forming tissues along with cellulose synthase and homologs of KORRIGAN and ELP1. Woody tissues were the richest source of various other CAZyme transcripts, demonstrating the importance of this group of enzymes for xylogenesis. In contrast, there was little expression of genes related to starch metabolism during wood formation, consistent with the preferential flux of carbon to cell wall biosynthesis. Seasonally dormant meristems of poplar showed a high prevalence of transcripts related to starch metabolism and surprisingly retained transcripts of some cell wall synthesis enzymes. The data showed profound changes in CAZyme transcriptomes in different poplar tissues and pointed to some key differences in CAZyme genes and their regulation between herbaceous and woody plants.

@article{klimmek_abundantly_2006,
	title = {Abundantly and rarely expressed {Lhc} protein genes exhibit distinct regulation patterns in plants},
	volume = {140},
	issn = {0032-0889},
	doi = {10/fbrp2z},
	abstract = {We have analyzed gene regulation of the Lhc supergene family in poplar ( Populus spp.) and Arabidopsis ( Arabidopsis thaliana) using digital expression profiling. Multivariate analysis of the tissue-specific, environmental, and developmental Lhc expression patterns in Arabidopsis and poplar was employed to characterize four rarely expressed Lhc genes, Lhca5, Lhca6, Lhcb7, and Lhcb4.3. Those genes have high expression levels under different conditions and in different tissues than the abundantly expressed Lhca1 to 4 and Lhcb1 to 6 genes that code for the 10 major types of higher plant light-harvesting proteins. However, in some of the datasets analyzed, the Lhcb4 and Lhcb6 genes as well as an Arabidopsis gene not present in poplar ( Lhcb2.3) exhibited minor differences to the main cooperative Lhc gene expression pattern. The pattern of the rarely expressed Lhc genes was always found to be more similar to that of PsbS and the various light-harvesting- like genes, which might indicate distinct physiological functions for the rarely and abundantly expressed Lhc proteins. The previously undetected Lhcb7 gene encodes a novel plant Lhcb-type protein that possibly contains an additional, fourth, transmembrane N-terminal helix with a highly conserved motif. As the Lhcb4.3 gene seems to be present only in Eurosid species and as its regulation pattern varies significantly from that of Lhcb4.1 and Lhcb4.2, we conclude it to encode a distinct Lhc protein type, Lhcb8.},
	language = {English},
	number = {3},
	journal = {Plant Physiology},
	author = {Klimmek, F. and Sjodin, A. and Noutsos, C. and Leister, D. and Jansson, S.},
	month = mar,
	year = {2006},
	note = {Place: Rockville
Publisher: Amer Soc Plant Biologists
WOS:000235868900001},
	keywords = {a/b-binding proteins, arabidopsis, chloroplast transit   peptides, draft sequence, energy-dissipation, light-harvesting-complex, membrane-proteins, photosystem-ii, pigment-binding, posttranscriptional   mechanisms},
	pages = {793--804},
}

We have analyzed gene regulation of the Lhc supergene family in poplar ( Populus spp.) and Arabidopsis ( Arabidopsis thaliana) using digital expression profiling. Multivariate analysis of the tissue-specific, environmental, and developmental Lhc expression patterns in Arabidopsis and poplar was employed to characterize four rarely expressed Lhc genes, Lhca5, Lhca6, Lhcb7, and Lhcb4.3. Those genes have high expression levels under different conditions and in different tissues than the abundantly expressed Lhca1 to 4 and Lhcb1 to 6 genes that code for the 10 major types of higher plant light-harvesting proteins. However, in some of the datasets analyzed, the Lhcb4 and Lhcb6 genes as well as an Arabidopsis gene not present in poplar ( Lhcb2.3) exhibited minor differences to the main cooperative Lhc gene expression pattern. The pattern of the rarely expressed Lhc genes was always found to be more similar to that of PsbS and the various light-harvesting- like genes, which might indicate distinct physiological functions for the rarely and abundantly expressed Lhc proteins. The previously undetected Lhcb7 gene encodes a novel plant Lhcb-type protein that possibly contains an additional, fourth, transmembrane N-terminal helix with a highly conserved motif. As the Lhcb4.3 gene seems to be present only in Eurosid species and as its regulation pattern varies significantly from that of Lhcb4.1 and Lhcb4.2, we conclude it to encode a distinct Lhc protein type, Lhcb8.

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

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

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

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

@article{sorin_proteomic_2006,
	title = {Proteomic analysis of different mutant genotypes of {Arabidopsis} led to the identification of 11 proteins correlating with adventitious root development},
	volume = {140},
	issn = {0032-0889},
	doi = {10/bqsw6z},
	abstract = {A lack of competence to form adventitious roots by cuttings or explants in vitro occurs routinely and is an obstacle for the clonal propagation and rapid fixation of elite genotypes. Adventitious rooting is known to be a quantitative genetic trait. We performed a proteomic analysis of Arabidopsis ( Arabidopsis thaliana) mutants affected in their ability to develop adventitious roots in order to identify associated molecular markers that could be used to select genotypes for their rooting ability and/or to get further insight into the molecular mechanisms controlling adventitious rooting. Comparison of two-dimensional gel electrophoresis protein profiles resulted in the identification of 11 proteins whose abundance could be either positively or negatively correlated with endogenous auxin content, the number of adventitious root primordia, and/or the number of mature adventitious roots. One protein was negatively correlated only to the number of root primordia and two were negatively correlated to the number of mature adventitious roots. Two putative chaperone proteins were positively correlated only to the number of primordia, and, interestingly, three auxin-inducible GH3-like proteins were positively correlated with the number of mature adventitious roots. The others were correlated with more than one parameter. The 11 proteins are predicted to be involved in different biological processes, including the regulation of auxin homeostasis and light-associated metabolic pathways. The results identify regulatory pathways associated with adventitious root formation and represent valuable markers that might be used for the future identification of genotypes with better rooting abilities.},
	language = {English},
	number = {1},
	journal = {Plant Physiology},
	author = {Sorin, C. and Negroni, L. and Balliau, T. and Corti, H. and Jacquemot, M. P. and Davanture, M. and Sandberg, G. and Zivy, M. and Bellini, C.},
	month = jan,
	year = {2006},
	note = {Place: Rockville
Publisher: Amer Soc Plant Biologists
WOS:000234492100031},
	keywords = {ago1, auxin, cuttings, cyp83b1, cytochrome-p450, expression, genetic-analysis, glucosinolate biosynthesis, light, locus},
	pages = {349--364},
}

A lack of competence to form adventitious roots by cuttings or explants in vitro occurs routinely and is an obstacle for the clonal propagation and rapid fixation of elite genotypes. Adventitious rooting is known to be a quantitative genetic trait. We performed a proteomic analysis of Arabidopsis ( Arabidopsis thaliana) mutants affected in their ability to develop adventitious roots in order to identify associated molecular markers that could be used to select genotypes for their rooting ability and/or to get further insight into the molecular mechanisms controlling adventitious rooting. Comparison of two-dimensional gel electrophoresis protein profiles resulted in the identification of 11 proteins whose abundance could be either positively or negatively correlated with endogenous auxin content, the number of adventitious root primordia, and/or the number of mature adventitious roots. One protein was negatively correlated only to the number of root primordia and two were negatively correlated to the number of mature adventitious roots. Two putative chaperone proteins were positively correlated only to the number of primordia, and, interestingly, three auxin-inducible GH3-like proteins were positively correlated with the number of mature adventitious roots. The others were correlated with more than one parameter. The 11 proteins are predicted to be involved in different biological processes, including the regulation of auxin homeostasis and light-associated metabolic pathways. The results identify regulatory pathways associated with adventitious root formation and represent valuable markers that might be used for the future identification of genotypes with better rooting abilities.

@article{sohlberg_sty1_2006,
	title = {{STY1} regulates auxin homeostasis and affects apical-basal patterning of the {Arabidopsis} gynoecium},
	volume = {47},
	issn = {0960-7412},
	doi = {10/btq2v8},
	abstract = {Gynoecia of the Arabidopsis mutant sty1-1 display abnormal style morphology and altered vascular patterning. These phenotypes, which are enhanced in the sty1-1 sty2-1 double mutant, suggest that auxin homeostasis or signalling might be affected by mutations in STY1 and STY2, both members of the SHI gene family. Chemical inhibition of polar auxin transport (PAT) severely affects the apical-basal patterning of the gynoecium, as do mutations in the auxin transport/signalling genes PIN1, PID and ETT. Here we show that the apical-basal patterning of sty1-1 and sty1-1 sty2-1 gynoecia is hypersensitive to reductions in PAT, and that sty1-1 enhances the PAT inhibition-like phenotypes of pin1-5, pid-8 and ett-1 gynoecia. Furthermore, we show that STY1 activates transcription of the flavin monooxygenase-encoding gene THREAD/YUCCA4, involved in auxin biosynthesis, and that changes in expression of STY1 and related genes lead to altered auxin homeostasis. Our results suggest that STY1 and related genes promote normal development of the style and affect apical-basal patterning of the gynoecium through regulation of auxin homeostasis.},
	language = {English},
	number = {1},
	journal = {Plant Journal},
	author = {Sohlberg, Joel J. and Myrenas, Mattias and Kuusk, Sandra and Lagercrantz, Ulf and Kowalczyk, Mariusz and Sandberg, Goran and Sundberg, Eva},
	month = jul,
	year = {2006},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000238256700010},
	keywords = {Arabidopsis, auxin, biosynthesis, efflux, gene-expression, gibberellin responses, gradients, gynoecium, lateral root-formation, patterning, protein, sty1, system, tissues, transport, yucca},
	pages = {112--123},
}

Gynoecia of the Arabidopsis mutant sty1-1 display abnormal style morphology and altered vascular patterning. These phenotypes, which are enhanced in the sty1-1 sty2-1 double mutant, suggest that auxin homeostasis or signalling might be affected by mutations in STY1 and STY2, both members of the SHI gene family. Chemical inhibition of polar auxin transport (PAT) severely affects the apical-basal patterning of the gynoecium, as do mutations in the auxin transport/signalling genes PIN1, PID and ETT. Here we show that the apical-basal patterning of sty1-1 and sty1-1 sty2-1 gynoecia is hypersensitive to reductions in PAT, and that sty1-1 enhances the PAT inhibition-like phenotypes of pin1-5, pid-8 and ett-1 gynoecia. Furthermore, we show that STY1 activates transcription of the flavin monooxygenase-encoding gene THREAD/YUCCA4, involved in auxin biosynthesis, and that changes in expression of STY1 and related genes lead to altered auxin homeostasis. Our results suggest that STY1 and related genes promote normal development of the style and affect apical-basal patterning of the gynoecium through regulation of auxin homeostasis.

@article{persson_uptake_2006,
	title = {Uptake, metabolism and distribution of organic and inorganic nitrogen sources by {Pinus} sylvestris},
	volume = {57},
	issn = {0022-0957},
	doi = {10/cr5p6b},
	abstract = {Although an increasing number of studies show that many plant species have the capacity to take up amino acids from exogenous sources, the importance of such uptake for plant nitrogen nutrition is largely unknown. Moreover, little is known regarding metabolism and distribution of amino acid-N following uptake or of the regulation of these processes in response to plant nitrogen status. Here results are presented from a study following uptake, metabolism, and distribution of nitrogen from NO3-, NH4+, Glu, or Ala in Scots pine (Pinus sylvestris L). In a parallel experiment, Ala uptake, processing, and shoot allocation were also monitored following a range of pretreatments intended to alter plant C- and N-status. Uptake data, metabolite profiles, N fluxes through metabolite pools and tissues, as well as alanine aminotransferase activity are presented. The results show that uptake of the organic N sources was equal to or larger than NH4+ uptake, while NO3- uptake was comparatively low. Down-regulation of Ala uptake in response to pretreatments with NH4NO3 or methionine sulphoximine (MSX) indicates similarities between amino acid and inorganic N uptake regulation. N derived from amino acid uptake exhibited a rapid flux through the amino acid pool following uptake. Relative shoot allocation of amino acid-N was equal to that of NH(4)(+)but smaller than for NO3-. Increased N status as well as MSX treatment significantly increased relative shoot allocation of Ala-N suggesting that NH4+ may have a role in the regulation of shoot allocation of amino acid-N.},
	language = {English},
	number = {11},
	journal = {Journal of Experimental Botany},
	author = {Persson, Jorgen and Gardestrom, Per and Nasholm, Torgny},
	month = aug,
	year = {2006},
	note = {Place: Oxford
Publisher: Oxford Univ Press
WOS:000239901500018},
	keywords = {acquisition, alanine, alanine aminotransferase, amino acid uptake, amino-acid-uptake, ammonium, arabidopsis, assimilation, boreal forest plants, carbon, expression, glutamic acid, nitrate, regulation, transport},
	pages = {2651--2659},
}

Although an increasing number of studies show that many plant species have the capacity to take up amino acids from exogenous sources, the importance of such uptake for plant nitrogen nutrition is largely unknown. Moreover, little is known regarding metabolism and distribution of amino acid-N following uptake or of the regulation of these processes in response to plant nitrogen status. Here results are presented from a study following uptake, metabolism, and distribution of nitrogen from NO3-, NH4+, Glu, or Ala in Scots pine (Pinus sylvestris L). In a parallel experiment, Ala uptake, processing, and shoot allocation were also monitored following a range of pretreatments intended to alter plant C- and N-status. Uptake data, metabolite profiles, N fluxes through metabolite pools and tissues, as well as alanine aminotransferase activity are presented. The results show that uptake of the organic N sources was equal to or larger than NH4+ uptake, while NO3- uptake was comparatively low. Down-regulation of Ala uptake in response to pretreatments with NH4NO3 or methionine sulphoximine (MSX) indicates similarities between amino acid and inorganic N uptake regulation. N derived from amino acid uptake exhibited a rapid flux through the amino acid pool following uptake. Relative shoot allocation of amino acid-N was equal to that of NH(4)(+)but smaller than for NO3-. Increased N status as well as MSX treatment significantly increased relative shoot allocation of Ala-N suggesting that NH4+ may have a role in the regulation of shoot allocation of amino acid-N.

@article{kopecny_probing_2006,
	title = {Probing cytokinin homeostasis in {Arabidopsis} thaliana by constitutively overexpressing two forms of the maize cytokinin oxidase/dehydrogenase 1 gene},
	volume = {171},
	issn = {0168-9452},
	doi = {10/d8cm9d},
	abstract = {Engineering transgenic plants with reduced cytokinin (Ck) contents is away to analyze the role of these hormones in growth and development. Cytokinin oxidase/dehydrogenase (CKO) genes are good candidates to promote Ck deficiency. They code for enzymes degrading Cks and generally belong to multigene families. Plants constitutively expressing naturally occurring CKO genes that code for secreted or vacuolar enzymes have been described. We report on Arabidopsis transgenics constitutively overexpressing the secreted native form or an engineered non-secreted form of the maize CKO1{\textbackslash} enzyme. Severity of phenotype symptoms (increased root system, reduced size of aerial parts and defects in seed development) was clearly correlated with the level of enzyme activity. Aerial part was especially affected in plants overexpressing the non-secreted enzyme, even at low activity level. In all strong overexpressers, zeatin-type metabolites were highly depleted compared to isopentenyladenine-type metabolites. AtIPT genes involved in Ck biosynthesis were found to be up-regulated in those transgenics while all AtCKO genes were down-regulated except At5g21482, coding for a putative cytoplasmic enzyme. Cytokinin deficiency in transgenics was not counter-balanced by a higher sensitivity: expression of a cytokinin receptor and type-A response regulators was decreased as well as plant response to benzyladenine. (c) 2006 Elsevier Ireland Ltd. All rights reserved.},
	language = {English},
	number = {1},
	journal = {Plant Science},
	author = {Kopecny, David and Tarkowski, Petr and Majira, Amel and Bouchez-Mahiout, Isabelle and Nogue, Fabien and Lauriere, Michel and Sandberg, Goran and Laloue, Michel and Houba-Herin, Nicole},
	month = jul,
	year = {2006},
	note = {Place: Clare
Publisher: Elsevier Ireland Ltd
WOS:000238454800013},
	keywords = {Arabidopsis thaliana, biosynthesis, cytokinin oxidase/dehydrogenase, derivatization, expression, homeostasis, maize, o-glucosyltransferase, overexpresser, oxidase, oxidase/dehydrogenase, plants, response regulator, root-meristem, zea-mays},
	pages = {114--122},
}

Engineering transgenic plants with reduced cytokinin (Ck) contents is away to analyze the role of these hormones in growth and development. Cytokinin oxidase/dehydrogenase (CKO) genes are good candidates to promote Ck deficiency. They code for enzymes degrading Cks and generally belong to multigene families. Plants constitutively expressing naturally occurring CKO genes that code for secreted or vacuolar enzymes have been described. We report on Arabidopsis transgenics constitutively overexpressing the secreted native form or an engineered non-secreted form of the maize CKO1\ enzyme. Severity of phenotype symptoms (increased root system, reduced size of aerial parts and defects in seed development) was clearly correlated with the level of enzyme activity. Aerial part was especially affected in plants overexpressing the non-secreted enzyme, even at low activity level. In all strong overexpressers, zeatin-type metabolites were highly depleted compared to isopentenyladenine-type metabolites. AtIPT genes involved in Ck biosynthesis were found to be up-regulated in those transgenics while all AtCKO genes were down-regulated except At5g21482, coding for a putative cytoplasmic enzyme. Cytokinin deficiency in transgenics was not counter-balanced by a higher sensitivity: expression of a cytokinin receptor and type-A response regulators was decreased as well as plant response to benzyladenine. (c) 2006 Elsevier Ireland Ltd. All rights reserved.

@article{king_regulation_2006,
	title = {Regulation of flowering in the long-day grass {Lolium} temulentum by {Gibberellins} and the {FLOWERING} {LOCUS} {T} gene},
	volume = {141},
	issn = {0032-0889},
	doi = {10/bc3fw3},
	abstract = {Seasonal control of flowering often involves leaf sensing of daylength coupled to time measurement and generation and transport of florigenic signals to the shoot apex. We show that transmitted signals in the grass Lolium temulentum may include gibberellins ( GAs) and the FLOWERING LOCUS T ( FT) gene. Within 2 h of starting a florally inductive long day ( LD), expression of a 20-oxidase GA biosynthetic gene increases in the leaf; its product, GA 20, then increases 5.7-fold versus short day; its substrate, GA 19, decreases equivalently; and a bioactive product, GA 5, increases 4-fold. A link between flowering, LD, GAs, and GA biosynthesis is shown in three ways: ( 1) applied GA 19 became florigenic on exposure to LD; ( 2) expression of LtGA20ox1, an important GA biosynthetic gene, increased in a florally effective LD involving incandescent lamps, but not with noninductive fluorescent lamps; and ( 3) paclobutrazol, an inhibitor of an early step of GA biosynthesis, blocked flowering, but only if applied before the LD. Expression studies of a 2-oxidase catabolic gene showed no changes favoring a GA increase. Thus, the early LD increase in leaf GA 5 biosynthesis, coupled with subsequent doubling in GA 5 content at the shoot apex, provides a substantial trail of evidence for GA 5 as a LD florigen. LD signaling may also involve transport of FT mRNA or protein because expression of LtFT and LtCONSTANS increased rapidly, substantially ({\textgreater} 80-fold for FT), and independently of GA. However, because a LD from fluorescent lamps induced LtFT expression but not flowering, the nature of the light response of FT requires clarification.},
	language = {English},
	number = {2},
	journal = {Plant Physiology},
	author = {King, Rod W. and Moritz, Thomas and Evans, Lloyd T. and Martin, Jerome and Andersen, Claus H. and Blundell, Cheryl and Kardailsky, Igor and Chandler, Peter M.},
	month = jun,
	year = {2006},
	note = {Place: Rockville
Publisher: Amer Soc Plant Biologists
WOS:000238168800025},
	keywords = {20-oxidase, biosynthesis, expression, in-vitro, inflorescence initiation, metabolism, molecular-cloning, photoperiod, shoot apices, stem   elongation},
	pages = {498--507},
}

Seasonal control of flowering often involves leaf sensing of daylength coupled to time measurement and generation and transport of florigenic signals to the shoot apex. We show that transmitted signals in the grass Lolium temulentum may include gibberellins ( GAs) and the FLOWERING LOCUS T ( FT) gene. Within 2 h of starting a florally inductive long day ( LD), expression of a 20-oxidase GA biosynthetic gene increases in the leaf; its product, GA 20, then increases 5.7-fold versus short day; its substrate, GA 19, decreases equivalently; and a bioactive product, GA 5, increases 4-fold. A link between flowering, LD, GAs, and GA biosynthesis is shown in three ways: ( 1) applied GA 19 became florigenic on exposure to LD; ( 2) expression of LtGA20ox1, an important GA biosynthetic gene, increased in a florally effective LD involving incandescent lamps, but not with noninductive fluorescent lamps; and ( 3) paclobutrazol, an inhibitor of an early step of GA biosynthesis, blocked flowering, but only if applied before the LD. Expression studies of a 2-oxidase catabolic gene showed no changes favoring a GA increase. Thus, the early LD increase in leaf GA 5 biosynthesis, coupled with subsequent doubling in GA 5 content at the shoot apex, provides a substantial trail of evidence for GA 5 as a LD florigen. LD signaling may also involve transport of FT mRNA or protein because expression of LtFT and LtCONSTANS increased rapidly, substantially (\textgreater 80-fold for FT), and independently of GA. However, because a LD from fluorescent lamps induced LtFT expression but not flowering, the nature of the light response of FT requires clarification.

@article{igamberdiev_function_2006,
	title = {Function of mitochondria during the transition of barley protoplasts from low light to high light},
	volume = {224},
	issn = {0032-0935},
	doi = {10/brwsbr},
	abstract = {Mitochondrial contribution to photosynthetic metabolism during the transition from low light (25-100 mu mol quanta m(-2) s(-1), limiting photosynthesis) to high light (500 mu mol quanta m(-2) s(-1), saturating photosynthesis) was investigated in protoplasts from barley (Hordeum vulgare) leaves. After the light shift, photosynthetic oxygen evolution rate increased rapidly during the first 30-40 s and then declined up to 60-70 s after which the rate increased to a new steady-state after 80-110 s. Rapid fractionation of protoplasts was used to follow changes in sub-cellular distribution of key metabolites during the light shift and the activation state of chloroplastic NADP-dependent malate dehydrogenase (EC 1.1.1.82) was measured. Although oligomycin (an inhibitor of the mitochondrial ATP synthase) affected the metabolite content of protoplasts following the light shift, the first oxygen burst was not affected. However, the transition to the new steady-state was delayed. Rotenone (an inhibitor of mitochondrial complex I) had similar, but less pronounced effect as oligomycin. From the analysis of metabolite content and sub-cellular distribution we suggest that the decrease in oxygen evolution following the first oxygen burst is due to phosphate limitation in the chloroplast stroma. For the recovery the control protoplasts can utilize ATP supplied by mitochondrial oxidative phosphorylation to quickly overcome the limitation in stromal phosphate and to increase the content of Calvin cycle metabolites. The oligomycin-treated protoplasts were deficient in cytosolic ATP and thereby unable to support Calvin cycle operation. This resulted in a delayed capacity to adjust to a sudden increase in light intensity.},
	language = {English},
	number = {1},
	journal = {Planta},
	author = {Igamberdiev, Abir U. and Shen, Tongyun and Gardestrom, Per},
	month = jun,
	year = {2006},
	note = {Place: New York
Publisher: Springer
WOS:000237826100019},
	keywords = {Hordeum, activation state, chloroplast enzymes, hordeum-vulgare protoplasts, leaf protoplasts, leaves, lightflecks, metabolite levels, mitochondria, nadp-malate dehydrogenase, oligomycin, oscillations, photosynthetic   induction, rapid fractionation, rotenone},
	pages = {196--204},
}

Mitochondrial contribution to photosynthetic metabolism during the transition from low light (25-100 mu mol quanta m(-2) s(-1), limiting photosynthesis) to high light (500 mu mol quanta m(-2) s(-1), saturating photosynthesis) was investigated in protoplasts from barley (Hordeum vulgare) leaves. After the light shift, photosynthetic oxygen evolution rate increased rapidly during the first 30-40 s and then declined up to 60-70 s after which the rate increased to a new steady-state after 80-110 s. Rapid fractionation of protoplasts was used to follow changes in sub-cellular distribution of key metabolites during the light shift and the activation state of chloroplastic NADP-dependent malate dehydrogenase (EC 1.1.1.82) was measured. Although oligomycin (an inhibitor of the mitochondrial ATP synthase) affected the metabolite content of protoplasts following the light shift, the first oxygen burst was not affected. However, the transition to the new steady-state was delayed. Rotenone (an inhibitor of mitochondrial complex I) had similar, but less pronounced effect as oligomycin. From the analysis of metabolite content and sub-cellular distribution we suggest that the decrease in oxygen evolution following the first oxygen burst is due to phosphate limitation in the chloroplast stroma. For the recovery the control protoplasts can utilize ATP supplied by mitochondrial oxidative phosphorylation to quickly overcome the limitation in stromal phosphate and to increase the content of Calvin cycle metabolites. The oligomycin-treated protoplasts were deficient in cytosolic ATP and thereby unable to support Calvin cycle operation. This resulted in a delayed capacity to adjust to a sudden increase in light intensity.

@article{kevei_forward_2006,
	title = {Forward genetic analysis of the circadian clock separates the multiple functions of {ZEITLUPE}},
	volume = {140},
	issn = {0032-0889},
	doi = {10/bx2pxd},
	abstract = {The circadian system of Arabidopsis ( Arabidopsis thaliana) includes feedback loops of gene regulation that generate 24-h oscillations. Components of these loops remain to be identified; none of the known components is completely understood, including ZEITLUPE (ZTL), a gene implicated in regulated protein degradation. ztl mutations affect both circadian and developmental responses to red light, possibly through ZTL interaction with PHYTOCHROME B (PHYB). We conducted a large-scale genetic screen that identified additional clock-affecting loci. Other mutants recovered include 11 new ztl alleles encompassing mutations in each of the ZTL protein domains. Each mutation lengthened the circadian period, even in darkgrown seedlings entrained to temperature cycles. A mutation of the LIGHT, OXYGEN, VOLTAGE (LOV)/Period-ARNT-Sim ( PAS) domain was unique in retaining wild-type responses to red light both for the circadian period and for control of hypocotyl elongation. This uncoupling of ztl phenotypes indicates that interactions of ZTL protein with multiple factors must be disrupted to generate the full ztl mutant phenotype. Protein interaction assays showed that the ztl mutant phenotypes were not fully explained by impaired interactions with previously described partner proteins Arabidopsis S-phase kinase-related protein 1, TIMING OF CAB EXPRESSION 1, and PHYB. Interaction with PHYB was unaffected by mutation of any ZTL domain. Mutation of the kelch repeat domain affected protein binding at both the LOV/PAS and the F-box domains, indicating that interaction among ZTL domains leads to the strong phenotypes of kelch mutations. Forward genetics continues to provide insight regarding both known and newly discovered components of the circadian system, although current approaches have saturated mutations at some loci.},
	language = {English},
	number = {3},
	journal = {Plant Physiology},
	author = {Kevei, E. and Gyula, P. and Hall, A. and Kozma-Bognar, L. and Kim, W. Y. and Eriksson, M. E. and Toth, R. and Hanano, S. and Feher, B. and Southern, M. M. and Bastow, R. M. and Viczian, A. and Hibberd, V. and Davis, S. J. and Somers, D. E. and Nagy, F. and Millar, A. J.},
	month = mar,
	year = {2006},
	note = {Place: Rockville
Publisher: Amer Soc Plant Biologists
WOS:000235868900013},
	keywords = {arabidopsis-thaliana, degradation, encodes, flowering time, light, photoreceptors, phytochrome interacting factor-3, protein, rhythms, system},
	pages = {933--945},
}

The circadian system of Arabidopsis ( Arabidopsis thaliana) includes feedback loops of gene regulation that generate 24-h oscillations. Components of these loops remain to be identified; none of the known components is completely understood, including ZEITLUPE (ZTL), a gene implicated in regulated protein degradation. ztl mutations affect both circadian and developmental responses to red light, possibly through ZTL interaction with PHYTOCHROME B (PHYB). We conducted a large-scale genetic screen that identified additional clock-affecting loci. Other mutants recovered include 11 new ztl alleles encompassing mutations in each of the ZTL protein domains. Each mutation lengthened the circadian period, even in darkgrown seedlings entrained to temperature cycles. A mutation of the LIGHT, OXYGEN, VOLTAGE (LOV)/Period-ARNT-Sim ( PAS) domain was unique in retaining wild-type responses to red light both for the circadian period and for control of hypocotyl elongation. This uncoupling of ztl phenotypes indicates that interactions of ZTL protein with multiple factors must be disrupted to generate the full ztl mutant phenotype. Protein interaction assays showed that the ztl mutant phenotypes were not fully explained by impaired interactions with previously described partner proteins Arabidopsis S-phase kinase-related protein 1, TIMING OF CAB EXPRESSION 1, and PHYB. Interaction with PHYB was unaffected by mutation of any ZTL domain. Mutation of the kelch repeat domain affected protein binding at both the LOV/PAS and the F-box domains, indicating that interaction among ZTL domains leads to the strong phenotypes of kelch mutations. Forward genetics continues to provide insight regarding both known and newly discovered components of the circadian system, although current approaches have saturated mutations at some loci.

@article{benschop_long-term_2006,
	title = {Long-term submergence-induced elongation in {Rumex} palustris requires abscisic acid-dependent biosynthesis of gibberellin},
	volume = {141},
	issn = {0032-0889},
	doi = {10/fpnvsb},
	abstract = {Rumex palustris (polygonceae) responds to complete submergence with enhanced elongation of its youngest petioles. This process requires the presence of gibberellin (GA) and is associated with an increase in the concentration of GA 1 in elongating petioles. We have examined how GA biosynthesis was regulated in submerged plants. Therefore, cDNAs encoding GA-biosynthetic enzymes GA20-oxidase and GA3-oxidase, and the GA-deactivating enzyme GA2-oxidase were cloned from R. palustris and the kinetics of transcription of the corresponding genes was determined during a 24 h submergence period. The submergence-induced elongation response could be separated into several phases: (1) during the first phase of 4 h, petiole elongation was insensitive to GA; (2) from 4 to 6 h onward growth was limited by GA; and (3) from 15 h onward underwater elongation was dependent, but not limited by GA. Submergence induced an increase of GA 1 concentration, as well as enhanced transcript levels of RpGA3ox1. Exogenous abscisic acid repressed the transcript levels of RpGA20ox1 and RpGA3ox1 and thus inhibited the submergence-induced increase in GA(1). Abscisic acid had no effect on the tissue responsiveness to GA.},
	language = {English},
	number = {4},
	journal = {Plant Physiology},
	author = {Benschop, Joris J. and Bou, Jordi and Peeters, Anton J. M. and Wagemaker, Niels and Guhl, Kerstin and Ward, Dennis and Hedden, Peter and Moritz, Thomas and Voesenek, Laurentius A. C. J.},
	month = aug,
	year = {2006},
	note = {Place: Rockville
Publisher: Amer Soc Plant Biologists
WOS:000239636800044},
	keywords = {20-oxidase genes, arabidopsis, ethylene, expression, pea, petiole elongation, plant, rice, shoot elongation, stem elongation},
	pages = {1644--1652},
}

Rumex palustris (polygonceae) responds to complete submergence with enhanced elongation of its youngest petioles. This process requires the presence of gibberellin (GA) and is associated with an increase in the concentration of GA 1 in elongating petioles. We have examined how GA biosynthesis was regulated in submerged plants. Therefore, cDNAs encoding GA-biosynthetic enzymes GA20-oxidase and GA3-oxidase, and the GA-deactivating enzyme GA2-oxidase were cloned from R. palustris and the kinetics of transcription of the corresponding genes was determined during a 24 h submergence period. The submergence-induced elongation response could be separated into several phases: (1) during the first phase of 4 h, petiole elongation was insensitive to GA; (2) from 4 to 6 h onward growth was limited by GA; and (3) from 15 h onward underwater elongation was dependent, but not limited by GA. Submergence induced an increase of GA 1 concentration, as well as enhanced transcript levels of RpGA3ox1. Exogenous abscisic acid repressed the transcript levels of RpGA20ox1 and RpGA3ox1 and thus inhibited the submergence-induced increase in GA(1). Abscisic acid had no effect on the tissue responsiveness to GA.

@article{louvet_comprehensive_2006,
	title = {Comprehensive expression profiling of the pectin methylesterase gene family during silique development in {Arabidopsis} thaliana},
	volume = {224},
	issn = {0032-0935},
	doi = {10/fkncxm},
	abstract = {Pectin methylesterases (PME, EC. 3.1.1.11) are enzymes that demethylesterify plant cell wall pectins in muro. In Arabidopsis thaliana, putative PME proteins are thought to be encoded by a 66-member gene family. This study used real-time RT-PCR to gain an overview of the expression of the entire family at eight silique developmental stages, in flower buds and in vegetative tissue in the Arabidopsis. Only 15\% of the PMEs were not expressed at any of the developmental stages studied. Among expressed PMEs, expression data could be clustered into five distinct groups: 19 PMEs highly or uniquely expressed in floral buds, 4 PMEs uniquely expressed at mid-silique developmental stages, 16 PMEs highly or uniquely expressed in silique at late developmental stages, 16 PMEs mostly ubiquitously expressed, and 1 PME with a specific expression pattern, i.e. not expressed during early silique development. Comparison of expression and phylogenetic profiles showed that, within phylogenetic group 2, all but one PME belong to the floral bud expression group. Similar results were shown for a subset of one of the phylogenetic group, which differed from others by containing most of the PMEs that do not possess any PRO part next to their catalytic part. Expression data were confirmed by two promoter:GUS transgenic plant analysis revealing a PME expressed in pollen and one in young seeds. Our results highlight the high diversity of PME expression profiles. They are discussed with regard to the role of PMEs in fruit development and cell growth.},
	language = {English},
	number = {4},
	journal = {Planta},
	author = {Louvet, Romain and Cavel, Emilie and Gutierrez, Laurent and Guenin, Stephanie and Roger, David and Gillet, Francoise and Guerineau, Francois and Pelloux, Jerome},
	month = sep,
	year = {2006},
	note = {Place: New York
Publisher: Springer
WOS:000240063100006},
	keywords = {arabidopsis, brassinosteroid-regulated genes, cell wall, cell-wall, esterification, fruit, methyl-esterase, microarray analysis, pattern, pectin methylesterase, pollen-tube growth, real-time RT-PCR, reveals, silique, transcription factors},
	pages = {782--791},
}

Pectin methylesterases (PME, EC. 3.1.1.11) are enzymes that demethylesterify plant cell wall pectins in muro. In Arabidopsis thaliana, putative PME proteins are thought to be encoded by a 66-member gene family. This study used real-time RT-PCR to gain an overview of the expression of the entire family at eight silique developmental stages, in flower buds and in vegetative tissue in the Arabidopsis. Only 15% of the PMEs were not expressed at any of the developmental stages studied. Among expressed PMEs, expression data could be clustered into five distinct groups: 19 PMEs highly or uniquely expressed in floral buds, 4 PMEs uniquely expressed at mid-silique developmental stages, 16 PMEs highly or uniquely expressed in silique at late developmental stages, 16 PMEs mostly ubiquitously expressed, and 1 PME with a specific expression pattern, i.e. not expressed during early silique development. Comparison of expression and phylogenetic profiles showed that, within phylogenetic group 2, all but one PME belong to the floral bud expression group. Similar results were shown for a subset of one of the phylogenetic group, which differed from others by containing most of the PMEs that do not possess any PRO part next to their catalytic part. Expression data were confirmed by two promoter:GUS transgenic plant analysis revealing a PME expressed in pollen and one in young seeds. Our results highlight the high diversity of PME expression profiles. They are discussed with regard to the role of PMEs in fruit development and cell growth.

@article{grebe_acid_2006,
	title = {Acid growth and plant development - {Response}},
	volume = {311},
	issn = {0036-8075},
	language = {English},
	number = {5763},
	journal = {Science},
	author = {Grebe, M.},
	month = feb,
	year = {2006},
	note = {Place: Washington
Publisher: Amer Assoc Advancement Science
WOS:000235456900023},
	keywords = {arabidopsis, auxin, elongation growth, h+-atpase, ⛔ No DOI found},
	pages = {953--954},
}

@article{bohlenius_coft_2006,
	title = {{CO}/{FT} regulatory module controls timing of flowering and seasonal growth cessation in trees},
	volume = {312},
	issn = {0036-8075},
	doi = {10/csznqf},
	abstract = {Forest trees display a perennial growth behavior characterized by a multiple-year delay in flowering and, in temperate regions, an annual cycling between growth and dormancy. We show here that the CO/FT regulatory module, which controls flowering time in response to variations in daylength in annual plants, controls flowering in aspen trees. Unexpectedly, however, it also controls the short-day-induced growth cessation and bud set occurring in the fall. This regulatory mechanism can explain the ecogenetic variation in a highly adaptive trait: the critical daylength for growth cessation displayed by aspen trees sampled across a latitudinal gradient spanning northern Europe.},
	language = {English},
	number = {5776},
	journal = {Science},
	author = {Bohlenius, H. and Huang, T. and Charbonnel-Campaa, L. and Brunner, A. M. and Jansson, S. and Strauss, S. H. and Nilsson, O.},
	month = may,
	year = {2006},
	note = {Place: Washington
Publisher: Amer Assoc Advancement Science
WOS:000237628800042},
	keywords = {arabidopsis, aspen populus-tremula, black cottonwood, bud set, candidate gene, ft, induction, phytochrome, protein, shoot   apex},
	pages = {1040--1043},
}

Forest trees display a perennial growth behavior characterized by a multiple-year delay in flowering and, in temperate regions, an annual cycling between growth and dormancy. We show here that the CO/FT regulatory module, which controls flowering time in response to variations in daylength in annual plants, controls flowering in aspen trees. Unexpectedly, however, it also controls the short-day-induced growth cessation and bud set occurring in the fall. This regulatory mechanism can explain the ecogenetic variation in a highly adaptive trait: the critical daylength for growth cessation displayed by aspen trees sampled across a latitudinal gradient spanning northern Europe.

@article{reuille_computer_2006,
	title = {Computer simulations reveal properties of the cell-cell signaling network at the shoot apex in {Arabidopsis}},
	volume = {103},
	copyright = {Copyright © 2006, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/103/5/1627},
	doi = {10/dc72k6},
	abstract = {The active transport of the plant hormone auxin plays a major role in the initiation of organs at the shoot apex. Polar localized membrane proteins of the PIN1 family facilitate this transport, and recent observations suggest that auxin maxima created by these proteins are at the basis of organ initiation. This hypothesis is based on the visual, qualitative characterization of the complex distribution patterns of the PIN1 protein in Arabidopsis. To take these analyses further, we investigated the properties of the patterns using computational modeling. The simulations reveal previously undescribed properties of PIN1 distribution. In particular, they suggest an important role for the meristem summit in the distribution of auxin. We confirm these predictions by further experimentation and propose a detailed model for the dynamics of auxin fluxes at the shoot apex.},
	language = {en},
	number = {5},
	urldate = {2021-06-11},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Reuille, Pierre Barbier de and Bohn-Courseau, Isabelle and Ljung, Karin and Morin, Halima and Carraro, Nicola and Godin, Christophe and Traas, Jan},
	month = jan,
	year = {2006},
	pmid = {16432202},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	keywords = {auxin, modeling, shoot meristem},
	pages = {1627--1632},
}

The active transport of the plant hormone auxin plays a major role in the initiation of organs at the shoot apex. Polar localized membrane proteins of the PIN1 family facilitate this transport, and recent observations suggest that auxin maxima created by these proteins are at the basis of organ initiation. This hypothesis is based on the visual, qualitative characterization of the complex distribution patterns of the PIN1 protein in Arabidopsis. To take these analyses further, we investigated the properties of the patterns using computational modeling. The simulations reveal previously undescribed properties of PIN1 distribution. In particular, they suggest an important role for the meristem summit in the distribution of auxin. We confirm these predictions by further experimentation and propose a detailed model for the dynamics of auxin fluxes at the shoot apex.

@article{svalastog_comparative_2006,
	title = {Comparative analysis of the risk-handling procedures for gene technology applications in medical and plant science},
	volume = {12},
	issn = {1353-3452},
	doi = {10/b58tj9},
	abstract = {In this paper we analyse how the risks associated with research on transgenic plants are regulated in Sweden. The paper outlines the way in which pilot projects in the plant sciences are overseen in Sweden, and discusses the international and national background to the current regulatory system. The historical, and hitherto unexplored, reasons for the evolution of current administrative and legislative procedures in plant science are of particular interest. Specifically, we discuss similarities and differences in the regulation of medicine and plant science, and we examine the tendency towards dichotomizing risk-focusing on social/ethical risks in medicine and biological risks in plant science. The context of this article is the Synpraxia research project, an inter-disciplinary program combining expertise in sciences and the humanities.},
	language = {English},
	number = {3},
	journal = {Science and Engineering Ethics},
	author = {Svalastog, Anna Lydia and Gustafsson, Petter and Jansson, Stefan},
	month = jul,
	year = {2006},
	note = {Place: Guildford
Publisher: Opragen Publications
WOS:000239947700006},
	keywords = {World War II, gene technology, medical ethics, plant science, public   opinion},
	pages = {465--479},
}

In this paper we analyse how the risks associated with research on transgenic plants are regulated in Sweden. The paper outlines the way in which pilot projects in the plant sciences are overseen in Sweden, and discusses the international and national background to the current regulatory system. The historical, and hitherto unexplored, reasons for the evolution of current administrative and legislative procedures in plant science are of particular interest. Specifically, we discuss similarities and differences in the regulation of medicine and plant science, and we examine the tendency towards dichotomizing risk-focusing on social/ethical risks in medicine and biological risks in plant science. The context of this article is the Synpraxia research project, an inter-disciplinary program combining expertise in sciences and the humanities.

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

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

@article{dharmasiri_axr4_2006,
	title = {{AXR4} is required for localization of the auxin influx facilitator {AUX1}},
	volume = {312},
	issn = {0036-8075},
	doi = {10/djwj2k},
	abstract = {The AUX1 and PIN auxin influx and efflux facilitators are key regulators of root growth and development. For root gravitropism to occur, AUX1 and PIN2 must transport auxin via the lateral root cap to elongating epidermal cells. Genetic studies suggest that AXR4 functions in the same pathway as AUX1. Here we show that AXR4 is a previously unidentified accessory protein of the endoplasmic reticulum (ER) that regulates localization of AUX1 but not of PIN proteins. Loss of AXR4 resulted in abnormal accumulation of AUX1 in the ER of epidermal cells, indicating that the axr4 agravitropic phenotype is caused by defective AUX1 trafficking in the root epidermis.},
	language = {English},
	number = {5777},
	journal = {Science},
	author = {Dharmasiri, S. and Swarup, R. and Mockaitis, K. and Dharmasiri, N. and Singh, S. K. and Kowalchyk, M. and Marchant, A. and Mills, S. and Sandberg, G. and Bennett, M. J. and Estelle, M.},
	month = may,
	year = {2006},
	note = {Place: Washington
Publisher: Amer Assoc Advancement Science
WOS:000237957400055},
	keywords = {arabidopsis, growth, mechanism, pathways, permease aux1, proteins, resistant mutants, root gravitropism, transport},
	pages = {1218--1220},
}

The AUX1 and PIN auxin influx and efflux facilitators are key regulators of root growth and development. For root gravitropism to occur, AUX1 and PIN2 must transport auxin via the lateral root cap to elongating epidermal cells. Genetic studies suggest that AXR4 functions in the same pathway as AUX1. Here we show that AXR4 is a previously unidentified accessory protein of the endoplasmic reticulum (ER) that regulates localization of AUX1 but not of PIN proteins. Loss of AXR4 resulted in abnormal accumulation of AUX1 in the ER of epidermal cells, indicating that the axr4 agravitropic phenotype is caused by defective AUX1 trafficking in the root epidermis.

@article{mahonen_cytokinin_2006,
	title = {Cytokinin signaling and its inhibitor {AHP6} regulate cell fate during vascular development},
	volume = {311},
	issn = {0036-8075},
	doi = {10/b8d3hd},
	abstract = {The cell lineages that form the transporting tissues (xylem and phloem) and the intervening pluripotent procambial tissue originate from stem cells near the root tip. We demonstrate that in Arabidopsis, cytokinin phytohormones negatively regulate protoxylem specification. AHP6, an inhibitory pseudophosphotransfer protein, counteracts cytokinin signaling, allowing protoxylem formation. Conversely, cytokinin signaling negatively regulates the spatial domain of AHP6 expression. Thus, by controlling the identity of cell lineages, the reciprocal interaction of cytokinin signaling and its spatially specific modulator regulates proliferation and differentiation of cell lineages during vascular development, demonstrating a previously unrecognized regulatory circuit underlying meristem organization.},
	language = {English},
	number = {5757},
	journal = {Science},
	author = {Mahonen, A. P. and Bishopp, A. and Higuchi, M. and Nieminen, K. M. and Kinoshita, K. and Tormakangas, K. and Ikeda, Y. and Oka, A. and Kakimoto, T. and Helariutta, Y.},
	month = jan,
	year = {2006},
	note = {Place: Washington
Publisher: Amer Assoc Advancement Science
WOS:000234546300041},
	keywords = {arabidopsis-thaliana, differentiation, expression, growth, histidine kinase, receptor, root, transduction},
	pages = {94--98},
}

The cell lineages that form the transporting tissues (xylem and phloem) and the intervening pluripotent procambial tissue originate from stem cells near the root tip. We demonstrate that in Arabidopsis, cytokinin phytohormones negatively regulate protoxylem specification. AHP6, an inhibitory pseudophosphotransfer protein, counteracts cytokinin signaling, allowing protoxylem formation. Conversely, cytokinin signaling negatively regulates the spatial domain of AHP6 expression. Thus, by controlling the identity of cell lineages, the reciprocal interaction of cytokinin signaling and its spatially specific modulator regulates proliferation and differentiation of cell lineages during vascular development, demonstrating a previously unrecognized regulatory circuit underlying meristem organization.

@article{achard_integration_2006,
	title = {Integration of plant responses to environmentally activated phytohormonal signals},
	volume = {311},
	issn = {0036-8075},
	doi = {10/fd7637},
	abstract = {Plants live in fixed locations and survive adversity by integrating growth responses to diverse environmental signals. Here, we show that the nuclear-localized growth-repressing DELLA proteins of Arabidopsis integrate responses to independent hormonal and environmental signals of adverse conditions. The growth restraint conferred by DELLA proteins is beneficial and promotes survival. We propose that DELLAs permit flexible and appropriate modulation of plant growth in response to changes in natural environments.},
	language = {English},
	number = {5757},
	journal = {Science},
	author = {Achard, P. and Cheng, H. and De Grauwe, L. and Decat, J. and Schoutteten, H. and Moritz, T. and Van Der Straeten, D. and Peng, J. R. and Harberd, N. P.},
	month = jan,
	year = {2006},
	note = {Place: Washington
Publisher: Amer Assoc Advancement Science
WOS:000234546300040},
	keywords = {arabidopsis-thaliana, floral   development, gene-expression, gibberellin response, growth, modulation, overexpression, protein, transcription factor, transduction},
	pages = {91--94},
}

Plants live in fixed locations and survive adversity by integrating growth responses to diverse environmental signals. Here, we show that the nuclear-localized growth-repressing DELLA proteins of Arabidopsis integrate responses to independent hormonal and environmental signals of adverse conditions. The growth restraint conferred by DELLA proteins is beneficial and promotes survival. We propose that DELLAs permit flexible and appropriate modulation of plant growth in response to changes in natural environments.

@article{li_comparison_2006,
	title = {Comparison of phenotype and combined index selection at optimal breeding population size considering gain and gene diversity},
	volume = {55},
	issn = {0037-5349},
	doi = {10/gkj9x2},
	abstract = {A breeding program was simulated in this study. Two alternative ways of selecting the breeding population for the following generation was compared. Phenotypic selection, which means to select just on the individual performance, and combined index selection, which means selection on predicted breeding value for each individual obtained by weighting family average and individual phenotype, were compared. The plant number (testing resource) and gene diversity (status number, Ns) were kept constant, but the breeding population size was variable and chosen for maximizing gain for the particular breeding scenario. At low and medium heritability phenotypic selection was inferior to combined index selection. Only when heritability was high phenotypic selection was as efficient (generation 1) as or more efficient (generation 5) than combined index selection. This contrasts to earlier studies done under constant breeding population size, where selection methods appeared similar. The advantage in gain of combined index selection is usually at a larger breeding population size. At limited heritability and breeding population size the difference is considerable. When breeding population size was kept rather small ({\textless} 100), and the heritability limited, combined index selection can result in slightly higher gain than phenotypic selection at the same gene diversity, but this was at the cost of a much larger breeding population. Phenotypic selection and combined index selection appears as rather similar for many cases in this simple model used in this study. Considering other advantages with phenotypic selection, it may often be regarded as a competitive alternative.},
	language = {English},
	number = {1},
	journal = {Silvae Genetica},
	author = {Li, H. and Lindgren, D.},
	year = {2006},
	note = {Place: Warsaw
Publisher: Sciendo
WOS:000237561500003},
	keywords = {breeding   population size, gene diversity, genetic gain, heritability, selection efficiency, status number, strategies},
	pages = {13--19},
}

A breeding program was simulated in this study. Two alternative ways of selecting the breeding population for the following generation was compared. Phenotypic selection, which means to select just on the individual performance, and combined index selection, which means selection on predicted breeding value for each individual obtained by weighting family average and individual phenotype, were compared. The plant number (testing resource) and gene diversity (status number, Ns) were kept constant, but the breeding population size was variable and chosen for maximizing gain for the particular breeding scenario. At low and medium heritability phenotypic selection was inferior to combined index selection. Only when heritability was high phenotypic selection was as efficient (generation 1) as or more efficient (generation 5) than combined index selection. This contrasts to earlier studies done under constant breeding population size, where selection methods appeared similar. The advantage in gain of combined index selection is usually at a larger breeding population size. At limited heritability and breeding population size the difference is considerable. When breeding population size was kept rather small (\textless 100), and the heritability limited, combined index selection can result in slightly higher gain than phenotypic selection at the same gene diversity, but this was at the cost of a much larger breeding population. Phenotypic selection and combined index selection appears as rather similar for many cases in this simple model used in this study. Considering other advantages with phenotypic selection, it may often be regarded as a competitive alternative.

@article{fries_estimating_2006,
	title = {Estimating genetic parameters for wood density of {Scots} pine ({Pinus} sylvestris {L}.)},
	volume = {55},
	issn = {0037-5349},
	doi = {10/gkj9x3},
	abstract = {Wood density was analysed and annual ring width was measured on increment cores from 1400 trees in a 30-year-old full-sib progeny test of Scots pine (Pinus sylvestris L.) in north Sweden. Genetic parameters for wood density were analysed separately for ten outer annual rings, and for simple averages of the five most recent years. The evaluation included genetic correlations with height and stem diameter. Heritabilities of density estimated separately for each annual ring was 0.14-0.26 without any age trend, and jointly for the ten or five latest rings 0.30-0.33; for height growth it was 0.30-0.42 and for stem diameter 0.11-0.13. Additive genetic correlations with height and stem diameter were negative with the simplest statistical model ((r) over cap (A) = -0.425 and 0.511, respectively) but vanished or diminished when ring width was added as covariate. Density breeding values calculated for the parent trees for each of ten annual rings separately varied considerably between parent trees and between years, tending to increase with increasing age, with a substantial increase between the ages 14 to 16 years from the pith. This age fits well with literature data on the change from juvenile to mature wood. The genetic correlation for wood density between rings from different years was high: (r) over cap (A) = 0.8 ten years apart, increasing to 1.0 for neighbouring rings. The high genetic correlations for wood density between the innermost and outermost annual rings indicate possible strong covariation between juvenile and/or transition wood and mature wood. The annual variation in wood density in relation to genetic regulation, phenology, environmental conditions, and development from juvenile to mature age is discussed.},
	language = {English},
	number = {2},
	journal = {Silvae Genetica},
	author = {Fries, A. and Ericsson, T.},
	year = {2006},
	note = {Place: Warsaw
Publisher: De Gruyter Poland Sp Zoo
WOS:000238884400007},
	keywords = {annual ring density, annual ring width, breeding value, genetic   correlation, growth   rhythm, heritability, juvenile, juvenile wood, mature wood, multitrait REML, progeny test, quality, radiata pine, repeated-measurement model, taeda, tracheid transverse dimensions, traits, tree, wood density},
	pages = {84--92},
}

Wood density was analysed and annual ring width was measured on increment cores from 1400 trees in a 30-year-old full-sib progeny test of Scots pine (Pinus sylvestris L.) in north Sweden. Genetic parameters for wood density were analysed separately for ten outer annual rings, and for simple averages of the five most recent years. The evaluation included genetic correlations with height and stem diameter. Heritabilities of density estimated separately for each annual ring was 0.14-0.26 without any age trend, and jointly for the ten or five latest rings 0.30-0.33; for height growth it was 0.30-0.42 and for stem diameter 0.11-0.13. Additive genetic correlations with height and stem diameter were negative with the simplest statistical model ((r) over cap (A) = -0.425 and 0.511, respectively) but vanished or diminished when ring width was added as covariate. Density breeding values calculated for the parent trees for each of ten annual rings separately varied considerably between parent trees and between years, tending to increase with increasing age, with a substantial increase between the ages 14 to 16 years from the pith. This age fits well with literature data on the change from juvenile to mature wood. The genetic correlation for wood density between rings from different years was high: (r) over cap (A) = 0.8 ten years apart, increasing to 1.0 for neighbouring rings. The high genetic correlations for wood density between the innermost and outermost annual rings indicate possible strong covariation between juvenile and/or transition wood and mature wood. The annual variation in wood density in relation to genetic regulation, phenology, environmental conditions, and development from juvenile to mature age is discussed.

@article{andersson-gunneras_biosynthesis_2006,
	title = {Biosynthesis of cellulose-enriched tension wood in {Populus}: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis},
	volume = {45},
	issn = {1365-313X},
	shorttitle = {Biosynthesis of cellulose-enriched tension wood in {Populus}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2005.02584.x},
	doi = {10/fkwhm3},
	abstract = {Stems and branches of angiosperm trees form tension wood (TW) when exposed to a gravitational stimulus. One of the main characteristics of TW, which distinguishes it from normal wood, is the formation of fibers with a thick inner gelatinous cell wall layer mainly composed of crystalline cellulose. Hence TW is enriched in cellulose, and deficient in lignin and hemicelluloses. An expressed sequence tag library made from TW-forming tissues in Populus tremula (L.) × tremuloides (Michx.) and data from transcript profiling using microarray and metabolite analysis were obtained during TW formation in Populus tremula (L.) in two growing seasons. The data were examined with the aim of identifying the genes responsible for the change in carbon (C) flow into various cell wall components, and the mechanisms important for the formation of the gelatinous cell wall layer (G-layer). A specific effort was made to identify carbohydrate-active enzymes with a putative function in cell wall biosynthesis. An increased C flux to cellulose was suggested by a higher abundance of sucrose synthase transcripts. However, genes related to the cellulose biosynthetic machinery were not generally affected, although the expression of secondary wall-specific CesA genes was modified in both directions. Other pathways for which the data suggested increased activity included lipid and glucosamine biosynthesis and the pectin degradation machinery. In addition, transcripts encoding fasciclin-like arabinogalactan proteins were particularly increased and found to lack true Arabidopsis orthologs. Major pathways for which the transcriptome and metabolome analysis suggested decreased activity were the pathway for C flux through guanosine 5′-diphosphate (GDP) sugars to mannans, the pentose phosphate pathway, lignin biosynthesis, and biosynthesis of cell wall matrix carbohydrates. Several differentially expressed auxin- and ethylene-related genes and transcription factors were also identified.},
	language = {en},
	number = {2},
	urldate = {2021-06-11},
	journal = {The Plant Journal},
	author = {Andersson-Gunnerås, Sara and Mellerowicz, Ewa J. and Love, Jonathan and Segerman, Bo and Ohmiya, Yasunori and Coutinho, Pedro M. and Nilsson, Peter and Henrissat, Bernard and Moritz, Thomas and Sundberg, Björn},
	year = {2006},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2005.02584.x},
	keywords = {cell walls, cellulose, development, hemicellulose, lignin, poplar},
	pages = {144--165},
}

Stems and branches of angiosperm trees form tension wood (TW) when exposed to a gravitational stimulus. One of the main characteristics of TW, which distinguishes it from normal wood, is the formation of fibers with a thick inner gelatinous cell wall layer mainly composed of crystalline cellulose. Hence TW is enriched in cellulose, and deficient in lignin and hemicelluloses. An expressed sequence tag library made from TW-forming tissues in Populus tremula (L.) × tremuloides (Michx.) and data from transcript profiling using microarray and metabolite analysis were obtained during TW formation in Populus tremula (L.) in two growing seasons. The data were examined with the aim of identifying the genes responsible for the change in carbon (C) flow into various cell wall components, and the mechanisms important for the formation of the gelatinous cell wall layer (G-layer). A specific effort was made to identify carbohydrate-active enzymes with a putative function in cell wall biosynthesis. An increased C flux to cellulose was suggested by a higher abundance of sucrose synthase transcripts. However, genes related to the cellulose biosynthetic machinery were not generally affected, although the expression of secondary wall-specific CesA genes was modified in both directions. Other pathways for which the data suggested increased activity included lipid and glucosamine biosynthesis and the pectin degradation machinery. In addition, transcripts encoding fasciclin-like arabinogalactan proteins were particularly increased and found to lack true Arabidopsis orthologs. Major pathways for which the transcriptome and metabolome analysis suggested decreased activity were the pathway for C flux through guanosine 5′-diphosphate (GDP) sugars to mannans, the pentose phosphate pathway, lignin biosynthesis, and biosynthesis of cell wall matrix carbohydrates. Several differentially expressed auxin- and ethylene-related genes and transcription factors were also identified.

@article{zarter_winter_2006,
	title = {Winter acclimation of {PsbS} and related proteins in the evergreen {Arctostaphylos} uva-ursi as influenced by altitude and light environment},
	volume = {29},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-3040.2005.01466.x},
	doi = {10/dffrdg},
	abstract = {The evergreen groundcover bearberry (Arctostaphylos uva-ursi[L.] Sprengel) was characterized over two successive years (2002–2004) from both sun-exposed and shaded sites at a montane ponderosa pine and subalpine forest community of 1900- and 2800-m-high altitudes, respectively. During summer, photosynthetic capacities and pre-dawn photosystem II (PSII) efficiency were similarly high in all four populations, and in winter, only the sun-exposed and shaded populations at 2800 m exhibited complete down-regulation of photosynthetic oxygen evolution capacity and consistent sustained down-regulation of PSII efficiency. This photosynthetic down-regulation at high altitude involved a substantial decrease in PSII components [pheophytin, D1 protein, oxygen evolving complex ([OEC)], a strong up-regulation of several anti-early-light-inducible protein (Elip)- and anti-high-light-inducible protein (Hlip)-reactive bands and a warm-sustained retention of zeaxanthin and antheraxanthin (Z + A). PsbS, the protein modulating the rapid engagement and disengagement of Z + A in energy dissipation, exhibited its most pronounced winter increases in the shade at 1900 m, and thus apparently assumes a greater role in providing rapidly reversible zeaxanthin-dependent photoprotection during winter when light becomes excessive in the shaded population, which remains photosynthetically active. It is attractive to hypothesize that PsbS relatives (Elips/Hlips) may be involved in sustained zeaxanthin-dependent photoprotection under the more extreme winter conditions at 2800 m.},
	language = {en},
	number = {5},
	urldate = {2021-06-11},
	journal = {Plant, Cell \& Environment},
	author = {Zarter, C. Ryan and Adams, William W. and Ebbert, Volker and Adamska, Iwona and Jansson, Stefan and Demmig-Adams, Barbara},
	year = {2006},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-3040.2005.01466.x},
	keywords = {D1 protein, Elip, Hlip, OEC, PsbS, energy dissipation, photoinhibition, photosynthesis, winter stress, zeaxanthin},
	pages = {869--878},
}

The evergreen groundcover bearberry (Arctostaphylos uva-ursi[L.] Sprengel) was characterized over two successive years (2002–2004) from both sun-exposed and shaded sites at a montane ponderosa pine and subalpine forest community of 1900- and 2800-m-high altitudes, respectively. During summer, photosynthetic capacities and pre-dawn photosystem II (PSII) efficiency were similarly high in all four populations, and in winter, only the sun-exposed and shaded populations at 2800 m exhibited complete down-regulation of photosynthetic oxygen evolution capacity and consistent sustained down-regulation of PSII efficiency. This photosynthetic down-regulation at high altitude involved a substantial decrease in PSII components [pheophytin, D1 protein, oxygen evolving complex ([OEC)], a strong up-regulation of several anti-early-light-inducible protein (Elip)- and anti-high-light-inducible protein (Hlip)-reactive bands and a warm-sustained retention of zeaxanthin and antheraxanthin (Z + A). PsbS, the protein modulating the rapid engagement and disengagement of Z + A in energy dissipation, exhibited its most pronounced winter increases in the shade at 1900 m, and thus apparently assumes a greater role in providing rapidly reversible zeaxanthin-dependent photoprotection during winter when light becomes excessive in the shaded population, which remains photosynthetically active. It is attractive to hypothesize that PsbS relatives (Elips/Hlips) may be involved in sustained zeaxanthin-dependent photoprotection under the more extreme winter conditions at 2800 m.

@article{sveshnikov_excitation_2006,
	title = {Excitation energy partitioning and quenching during cold acclimation in {Scots} pine},
	volume = {26},
	issn = {0829-318X},
	doi = {10/fhsdwn},
	abstract = {We studied the influence of two irradiances on cold acclimation and recovery of photosynthesis in Scots pine (Pinus sylvestris L.) seedlings to assess mechanisms for quenching the excess energy captured by the photosynthetic apparatus. A shift in temperature from 20 to 5 degrees C caused a greater decrease in photosynthetic activity, measured by chlorophyll fluorescence and oxygen evolution, in plants exposed to moderate light (350 mu mol m(-2) s(-1)) than in shaded plants (50 mu mol m(-2) s(-1)). In response to the temperature shift, maximal photochemical efficiency of photosystem II (PSII), measured as the ratio of variable to maximal chlorophyll fluorescence (F-v/F-m) of dark-adapted samples, decreased to 70\% in exposed seedlings, whereas shaded seedlings maintained F-v/F-m close to initial values. After a further temperature decrease to-5 C, only 8\% of initial F-v/F-m remained in exposed plants, whereas shaded plants retained 40\% of initial F-v/F-m. Seven days after transfer from-5 to 20 degrees C, recovery of photochemical efficiency was more complete in the shaded plants than in the exposed plants (87 and 65\% of the initial F-v/F-m value, respectively). In response to cold stress, the estimated functional absorption cross section per remaining PSII reaction center increased at both irradiances, but the increase was more pronounced in exposed seedlings. Estimates of energy partitioning in the needles showed a much higher dissipative component in the exposed seedlings at low temperatures, pointing to stronger development of non-photochemical quenching at moderate irradiances. The de-epoxidation state of the xanthophyll cycle pigments increased in exposed seedlings at 5 degrees C, contributing to the quenching capacity, whereas significant de-epoxidation in the shaded plants was observed only when temperatures decreased to -5 degrees C. Thermoluminescence (TL) measurements of PSII revealed that charge recombinations between the second oxidation state of Mn-cluster S-2 and the semireduced secondary electron acceptor quinone Q(B)(-) (S(2)Q(B)(-)) were shifted to lower temperatures in cold-acclimated seedlings compared with control seedlings and this effect depended on irradiance. Concomitant with this. cold-acclimated seedlings demonstrated a significant shift in the S2 recombination with primary acceptor Q(A)(-) (S(2)Q(A)(-)) characteristic TL emission peak to higher temperatures, thus narrowing the redox potential gap between S(2)Q(B)(-) and S(2)Q(A)(-), which might result in increased probability for non-radiative radical pair recombination between the PSII reaction center chlorophyll a (P680(+)) and Q(A)(-) (P680(+)Q(A)(-)) (reaction center quenching) in cold-acclimated seedlings. In Scots pine seedlings, mechanisms of quenching excess light energy in winter therefore involve light-dependent regulation of reaction center content and both reaction center-based and antenna-based quenching of excess light energy, enabling them to withstand high excitation pressure under northern winter conditions.},
	language = {English},
	number = {3},
	journal = {Tree Physiology},
	author = {Sveshnikov, D. and Ensminger, I. and Ivanov, A. G. and Campbell, D. and Lloyd, J. and Funk, C. and Huner, N. P. A. and Oquist, G.},
	month = mar,
	year = {2006},
	note = {Place: Oxford
Publisher: Oxford Univ Press
WOS:000235728100006},
	keywords = {Pinus sylvestris, antenna quenching, chlorophyll fluorescence, cold stress, down-regulation, electron transport, freezing temperatures, high light levels, induced photoinhibition, low-temperature, photosynthetic electron-transport, photosystem-ii, reaction center quenching, seasonal-changes, winter depression},
	pages = {325--336},
}

We studied the influence of two irradiances on cold acclimation and recovery of photosynthesis in Scots pine (Pinus sylvestris L.) seedlings to assess mechanisms for quenching the excess energy captured by the photosynthetic apparatus. A shift in temperature from 20 to 5 degrees C caused a greater decrease in photosynthetic activity, measured by chlorophyll fluorescence and oxygen evolution, in plants exposed to moderate light (350 mu mol m(-2) s(-1)) than in shaded plants (50 mu mol m(-2) s(-1)). In response to the temperature shift, maximal photochemical efficiency of photosystem II (PSII), measured as the ratio of variable to maximal chlorophyll fluorescence (F-v/F-m) of dark-adapted samples, decreased to 70% in exposed seedlings, whereas shaded seedlings maintained F-v/F-m close to initial values. After a further temperature decrease to-5 C, only 8% of initial F-v/F-m remained in exposed plants, whereas shaded plants retained 40% of initial F-v/F-m. Seven days after transfer from-5 to 20 degrees C, recovery of photochemical efficiency was more complete in the shaded plants than in the exposed plants (87 and 65% of the initial F-v/F-m value, respectively). In response to cold stress, the estimated functional absorption cross section per remaining PSII reaction center increased at both irradiances, but the increase was more pronounced in exposed seedlings. Estimates of energy partitioning in the needles showed a much higher dissipative component in the exposed seedlings at low temperatures, pointing to stronger development of non-photochemical quenching at moderate irradiances. The de-epoxidation state of the xanthophyll cycle pigments increased in exposed seedlings at 5 degrees C, contributing to the quenching capacity, whereas significant de-epoxidation in the shaded plants was observed only when temperatures decreased to -5 degrees C. Thermoluminescence (TL) measurements of PSII revealed that charge recombinations between the second oxidation state of Mn-cluster S-2 and the semireduced secondary electron acceptor quinone Q(B)(-) (S(2)Q(B)(-)) were shifted to lower temperatures in cold-acclimated seedlings compared with control seedlings and this effect depended on irradiance. Concomitant with this. cold-acclimated seedlings demonstrated a significant shift in the S2 recombination with primary acceptor Q(A)(-) (S(2)Q(A)(-)) characteristic TL emission peak to higher temperatures, thus narrowing the redox potential gap between S(2)Q(B)(-) and S(2)Q(A)(-), which might result in increased probability for non-radiative radical pair recombination between the PSII reaction center chlorophyll a (P680(+)) and Q(A)(-) (P680(+)Q(A)(-)) (reaction center quenching) in cold-acclimated seedlings. In Scots pine seedlings, mechanisms of quenching excess light energy in winter therefore involve light-dependent regulation of reaction center content and both reaction center-based and antenna-based quenching of excess light energy, enabling them to withstand high excitation pressure under northern winter conditions.

@article{wei_stepwise_2006,
	title = {Stepwise penalty index selection from populations with a hierarchical structure},
	volume = {55},
	issn = {0037-5349},
	doi = {10/gkj9xx},
	abstract = {By adding a penalty to a candidate's breeding value for its relationship with the selected individuals, two indexes were constructed as criteria for stepwise selection of superior individuals from populations with a hierarchical structure. The relationship was expressed in terms of either family contribution or group coancestry. One of the indexes was derived from an optimal selection model. A stepwise procedure that screened superior individuals one by one was introduced to make selection based on these indexes possible. Two penalty selection methods exclusively maximized gain at given coancestry. Both methods produced all identical solutions in most of the populations simulated, and were nearly equivalent in the remaining populations, particularly when heritability was high and the population structure was simple. A better balance between gain and coancestry following penalty index selection can be obtained by avoiding the two extreme solutions: combined-index and within-family selection, and using simple mating designs rather than complex ones.},
	language = {English},
	number = {2},
	journal = {Silvae Genetica},
	author = {Wei, R.-P. and Lindgren, D.},
	year = {2006},
	note = {Place: Warsaw
Publisher: De Gruyter Poland Sp Zoo
WOS:000238884400004},
	keywords = {breeding value, decisions, diversity, families, family contribution, gain, group   coancestry, group coancestry, including genetic-relationships, mating designs, penalty index, prediction, size, status number},
	pages = {62--70},
}

By adding a penalty to a candidate's breeding value for its relationship with the selected individuals, two indexes were constructed as criteria for stepwise selection of superior individuals from populations with a hierarchical structure. The relationship was expressed in terms of either family contribution or group coancestry. One of the indexes was derived from an optimal selection model. A stepwise procedure that screened superior individuals one by one was introduced to make selection based on these indexes possible. Two penalty selection methods exclusively maximized gain at given coancestry. Both methods produced all identical solutions in most of the populations simulated, and were nearly equivalent in the remaining populations, particularly when heritability was high and the population structure was simple. A better balance between gain and coancestry following penalty index selection can be obtained by avoiding the two extreme solutions: combined-index and within-family selection, and using simple mating designs rather than complex ones.

@article{varghese_impact_2006,
	title = {Impact of fertility variation on gene diversity and drift in two clonal seed orchards of teak ({Tectona} grandis linn. {F}.)},
	volume = {31},
	issn = {0169-4286},
	doi = {10/czff8g},
	abstract = {Two 25 year old teak clonal seed orchards comprising 15 (CSO-I) and 20 clones (CSO-II), respectively, selected mostly from moist forests of Western Ghats (latitude 10 degrees N) in southern India, were evaluated for fertility, offspring diversity, and genetic drift. The orchards differed in fertility of clones as well as flower and fruit production per ramet. Fertility was highly skewed in CSO-II, where one clone (originating from higher latitude -17 degrees N, in Eastern Ghats of peninsular India) produced 55\% of the fruits and 68\% of the flowers in the orchard, in contrast to a similar contribution from four most fertile clones in CSO-I. Fertility variation, measured as `sibling coefficient' (1.7 in CSO-I and 8.3 in CSO-II), was high in CSO-II resulting in high coancestry and low effective population size (3 times lower than CSO-I) in the seed crop. In CSO-I, 58\% of the clones contributed effectively to seed production compared to only 12\% effective contribution resulting in eight times higher genetic drift in CSO-II. Placing limits on how much seed can be collected per clone might be useful in restricting over representation of highly reproductive clones thereby increasing genetic diversity in the seed crop.},
	language = {English},
	number = {3},
	journal = {New Forests},
	author = {Varghese, M. and Nicodemus, A. and Nagarajan, B. and Lindgren, D.},
	month = may,
	year = {2006},
	note = {Place: Dordrecht
Publisher: Springer
WOS:000237441700013},
	keywords = {clone, coancestry, cone, crops, number, pollen, pollination, seed production, sibling coefficient, status number},
	pages = {497--512},
}

Two 25 year old teak clonal seed orchards comprising 15 (CSO-I) and 20 clones (CSO-II), respectively, selected mostly from moist forests of Western Ghats (latitude 10 degrees N) in southern India, were evaluated for fertility, offspring diversity, and genetic drift. The orchards differed in fertility of clones as well as flower and fruit production per ramet. Fertility was highly skewed in CSO-II, where one clone (originating from higher latitude -17 degrees N, in Eastern Ghats of peninsular India) produced 55% of the fruits and 68% of the flowers in the orchard, in contrast to a similar contribution from four most fertile clones in CSO-I. Fertility variation, measured as `sibling coefficient' (1.7 in CSO-I and 8.3 in CSO-II), was high in CSO-II resulting in high coancestry and low effective population size (3 times lower than CSO-I) in the seed crop. In CSO-I, 58% of the clones contributed effectively to seed production compared to only 12% effective contribution resulting in eight times higher genetic drift in CSO-II. Placing limits on how much seed can be collected per clone might be useful in restricting over representation of highly reproductive clones thereby increasing genetic diversity in the seed crop.

@article{freeman_depletion_2006,
	title = {Depletion of abundant proteins from non-human primate serum for biomarker studies},
	volume = {6},
	copyright = {Copyright © 2006 WILEY-VCH Verlag GmbH \& Co. KGaA, Weinheim},
	issn = {1615-9861},
	url = {https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/abs/10.1002/pmic.200500717},
	doi = {10/c5xnd4},
	abstract = {Non-human primates are an important biomedical research model organism and offer great promise for serum biomarker proteomic studies. However, potential obstacles to these studies include affinity serum depletion methods based on human antigens, depletion methods altering quantitation, and incomplete non-human primate genome sequences for protein identification. In the present study, high-abundance protein removal from monkey serum using a human multiple affinity removal system (MARS) was shown to be specific and did not alter quantitation. Depleted serum also demonstrated greater sensitivity for previously masked, lower-abundance proteins.},
	language = {en},
	number = {10},
	urldate = {2021-06-11},
	journal = {PROTEOMICS},
	author = {Freeman, Willard M. and Lull, Melinda E. and Guilford, Michael T. and Vrana, Kent E.},
	year = {2006},
	note = {\_eprint: https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/pdf/10.1002/pmic.200500717},
	keywords = {2-DE, Affinity chromatography, Biomarker, Non-human primate, Serum},
	pages = {3109--3113},
}

Non-human primates are an important biomedical research model organism and offer great promise for serum biomarker proteomic studies. However, potential obstacles to these studies include affinity serum depletion methods based on human antigens, depletion methods altering quantitation, and incomplete non-human primate genome sequences for protein identification. In the present study, high-abundance protein removal from monkey serum using a human multiple affinity removal system (MARS) was shown to be specific and did not alter quantitation. Depleted serum also demonstrated greater sensitivity for previously masked, lower-abundance proteins.

@article{friml_apicalbasal_2006,
	title = {Apical–basal polarity: why plant cells don't standon their heads},
	volume = {11},
	issn = {1360-1385},
	shorttitle = {Apical–basal polarity},
	url = {https://www.sciencedirect.com/science/article/pii/S1360138505002980},
	doi = {10/cx2md8},
	language = {en},
	number = {1},
	urldate = {2021-06-11},
	journal = {Trends in Plant Science},
	author = {Friml, Jiří and Benfey, Philip and Benková, Eva and Bennett, Malcolm and Berleth, Thomas and Geldner, Niko and Grebe, Markus and Heisler, Marcus and Hejátko, Jan and Jürgens, Gerd and Laux, Thomas and Lindsey, Keith and Lukowitz, Wolfgang and Luschnig, Christian and Offringa, Remko and Scheres, Ben and Swarup, Ranjan and Torres-Ruiz, Ramón and Weijers, Dolf and Zažímalová, Eva},
	month = jan,
	year = {2006},
	pages = {12--14},
}

@article{waldmann_comparison_2006,
	title = {Comparison of {REML} and {Gibbs} sampling estimates of multi-trait genetic parameters in {Scots} pine},
	volume = {112},
	issn = {0040-5752},
	doi = {10/bhbmvm},
	abstract = {Multi-trait (co)variance estimation is an important topic in plant and animal breeding. In this study we compare estimates obtained with restricted maximum likelihood (REML) and Bayesian Gibbs sampling of simulated data and of three traits (diameter, height and branch angle) from a 26-year-old partial diallel progeny test of Scots pine (Pinus sylvestris L.). Based on the results from the simulated data we can conclude that the REML estimates are accurate but the mode of posterior distributions from the Gibbs sampling can be overestimated depending on the level of the heritability. The mean and median of the posteriors were considerably higher than the expected values of the heritabilities. The confidence intervals calculated with the delta method were biased downwardly. The highest probablity density (HPD) interval provides a better interval estimate, but could be slightly biased at the lower level. Similar differences between REML and Gibbs sampling estimates were found for the Scots pine data. We conclude that further simulation studies are needed in order to evaluate the effect of different priors on (co)variance components in the genetic individual model.},
	language = {English},
	number = {8},
	journal = {Theoretical and Applied Genetics},
	author = {Waldmann, Patrik and Ericsson, Tore},
	month = may,
	year = {2006},
	note = {Place: New York
Publisher: Springer
WOS:000237509700005},
	keywords = {animal-models, bayesian-inference, confidence-intervals, heritability, information, ratio, restricted maximum-likelihood, selection, variance-components},
	pages = {1441--1451},
}

Multi-trait (co)variance estimation is an important topic in plant and animal breeding. In this study we compare estimates obtained with restricted maximum likelihood (REML) and Bayesian Gibbs sampling of simulated data and of three traits (diameter, height and branch angle) from a 26-year-old partial diallel progeny test of Scots pine (Pinus sylvestris L.). Based on the results from the simulated data we can conclude that the REML estimates are accurate but the mode of posterior distributions from the Gibbs sampling can be overestimated depending on the level of the heritability. The mean and median of the posteriors were considerably higher than the expected values of the heritabilities. The confidence intervals calculated with the delta method were biased downwardly. The highest probablity density (HPD) interval provides a better interval estimate, but could be slightly biased at the lower level. Similar differences between REML and Gibbs sampling estimates were found for the Scots pine data. We conclude that further simulation studies are needed in order to evaluate the effect of different priors on (co)variance components in the genetic individual model.

@article{varghese_linear_2006,
	title = {Linear thinning in a clonal test of eucalyptus {Camaldulensis} for conversion to a clonal seed orchard},
	volume = {18},
	issn = {0128-1283},
	abstract = {In this study, we Used linear deployment technique to carry out genetic thinning of clones and ramets in a three-year-old clonal test of Eucalyptus camaldulensis for converting it to a seed orchard. Four different Strategies, namely, truncation selection and three linear thinning options, were employed to have a balanced representation of clones in the orchard. Three linear strategies were considered, namely, to retain the same ramet number, to keep the gain same or to keep the diversity same Lis with truncation Selection. The gain and diversity that can be achieved with the different options were studied Using suitable intercept and slope values for the linear deployment line. Linear deployment. retaining the same ramet, number was efficient in conserving diversity compared with the Second strategy of keeping genetic gain the same as truncation selection. The third strategy which provided maximum gain at the same diversity as truncation selection was suggested to be the most balanced method of thinning the orchard as it provided high gain and reasonable diversity and adequate options for further thinning based on later observations including fertility Simple mass selection for height growth was as effective as the second linear strategy in terms of both genetic gain and diversity.},
	language = {English},
	number = {2},
	journal = {Journal of Tropical Forest Science},
	author = {Varghese, M. and Lindgren, D. and Ravi, N.},
	month = apr,
	year = {2006},
	note = {Place: Kuala Lumpur
Publisher: Forest Research Inst Malaysia
WOS:000237432400003},
	keywords = {diversity, genetic gain, genetic thinning, linear deployment, mass selection, number, proportions, truncation selection, ⛔ No DOI found},
	pages = {102--108},
}

In this study, we Used linear deployment technique to carry out genetic thinning of clones and ramets in a three-year-old clonal test of Eucalyptus camaldulensis for converting it to a seed orchard. Four different Strategies, namely, truncation selection and three linear thinning options, were employed to have a balanced representation of clones in the orchard. Three linear strategies were considered, namely, to retain the same ramet number, to keep the gain same or to keep the diversity same Lis with truncation Selection. The gain and diversity that can be achieved with the different options were studied Using suitable intercept and slope values for the linear deployment line. Linear deployment. retaining the same ramet, number was efficient in conserving diversity compared with the Second strategy of keeping genetic gain the same as truncation selection. The third strategy which provided maximum gain at the same diversity as truncation selection was suggested to be the most balanced method of thinning the orchard as it provided high gain and reasonable diversity and adequate options for further thinning based on later observations including fertility Simple mass selection for height growth was as effective as the second linear strategy in terms of both genetic gain and diversity.

@article{strand_height_2006,
	title = {Height growth of planted conifer seedlings in relation to solar radiation and position in {Scots} pine shelterwood},
	volume = {224},
	issn = {0378-1127},
	doi = {10/fgp7q6},
	abstract = {Seedlings of different provenances of Scots pine (Pinus sylvestris L.), lodgepole pine (Pinus contorta Dougl., var. latifolia Engelm.) and Norway spruce (Picea abies (L.) Karst.) were planted in three Scots pine shelterwoods (125, 65 and 43 stems ha(-1)) and a clear-cut, all in northern Sweden. The sites were mounded and planting took place during 2 consecutive years (1988 and 1989). The solar radiation experienced by the individual seedlings was determined using a simulation model. Height development of the seedlings was examined during their first 6 years after planting. During the final 3 years of the study, height growth of Norway spruce was relatively poor, both in the shelterwoods and the clear-cut area. Height growth of lodgepole pine was significantly greater than that of Scots pine, both in the shelterwoods and the clear-cut. In contrast to Norway spruce, Scots pine and lodgepole pine displayed significantly greater height growth in the clear-cut than in the shelterwoods. For all three species in the shelterwoods, regression analyses showed that height growth was more strongly correlated with the distance to the nearest tree than with the amount of radiation reaching the ground, i.e. growth was reduced in the vicinity of shelter trees. Therefore, we conclude that the significant reduction in height growth of seedlings of Scots pine and lodgepole pine in Scots pine shelterwoods was partially caused by factors associated with the distance to the nearest shelter tree. Because the substrate was a nitrogen-poor sandy soil, we suggest that root competition for mineral nutrients, especially nitrogen, accounts for the reduction in height growth. (c) 2006 Elsevier B.V. All rights reserved.},
	language = {English},
	number = {3},
	journal = {Forest Ecology and Management},
	author = {Strand, M. and Lofvenius, M. O. and Bergsten, U. and Lundmark, T. and Rosvall, O.},
	month = apr,
	year = {2006},
	note = {Place: Amsterdam
Publisher: Elsevier Science Bv
WOS:000236477600006},
	keywords = {Norway spruce, asymmetric crowns, british-columbia, discontinuous canopies, douglas-fir, height growths Scots pine, light availability, lodgepole pine, norway spruce stand, resource availability, shelterwood, solar radiation, southern finland, spatial-distribution, sub-alpine fir},
	pages = {258--265},
}

Seedlings of different provenances of Scots pine (Pinus sylvestris L.), lodgepole pine (Pinus contorta Dougl., var. latifolia Engelm.) and Norway spruce (Picea abies (L.) Karst.) were planted in three Scots pine shelterwoods (125, 65 and 43 stems ha(-1)) and a clear-cut, all in northern Sweden. The sites were mounded and planting took place during 2 consecutive years (1988 and 1989). The solar radiation experienced by the individual seedlings was determined using a simulation model. Height development of the seedlings was examined during their first 6 years after planting. During the final 3 years of the study, height growth of Norway spruce was relatively poor, both in the shelterwoods and the clear-cut area. Height growth of lodgepole pine was significantly greater than that of Scots pine, both in the shelterwoods and the clear-cut. In contrast to Norway spruce, Scots pine and lodgepole pine displayed significantly greater height growth in the clear-cut than in the shelterwoods. For all three species in the shelterwoods, regression analyses showed that height growth was more strongly correlated with the distance to the nearest tree than with the amount of radiation reaching the ground, i.e. growth was reduced in the vicinity of shelter trees. Therefore, we conclude that the significant reduction in height growth of seedlings of Scots pine and lodgepole pine in Scots pine shelterwoods was partially caused by factors associated with the distance to the nearest shelter tree. Because the substrate was a nitrogen-poor sandy soil, we suggest that root competition for mineral nutrients, especially nitrogen, accounts for the reduction in height growth. (c) 2006 Elsevier B.V. All rights reserved.

@article{street_genetics_2006,
	title = {The genetics and genomics of the drought response in {Populus}},
	volume = {48},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2006.02864.x},
	doi = {10/fj53r5},
	abstract = {The genetic nature of tree adaptation to drought stress was examined by utilizing variation in the drought response of a full-sib second generation (F2) mapping population from a cross between Populus trichocarpa (93-968) and P. deltoides Bart (ILL-129) and known to be highly divergent for a vast range of phenotypic traits. We combined phenotyping, quantitative trait loci (QTL) analysis and microarray experiments to demonstrate that ‘genetical genomics’ can be used to provide information on adaptation at the species level. The grandparents and F2 population were subjected to soil drying, and contrasting responses to drought across genotypes, including leaf coloration, expansion and abscission, were observed, and QTL for these traits mapped. A subset of extreme genotypes exhibiting extreme sensitivity and insensitivity to drought on the basis of leaf abscission were defined, and microarray experiments conducted on these genotypes and the grandparent species. The extreme genotype groups induced a different set of genes: 215 and 125 genes differed in their expression response between groups in control and drought, respectively, suggesting species adaptation at the gene expression level. Co-location of differentially expressed genes with drought-specific and drought-responsive QTLs was examined, and these may represent candidate genes contributing to the variation in drought response.},
	language = {en},
	number = {3},
	urldate = {2021-06-11},
	journal = {The Plant Journal},
	author = {Street, Nathaniel Robert and Skogström, Oskar and Sjödin, Andreas and Tucker, James and Rodríguez-Acosta, Maricela and Nilsson, Peter and Jansson, Stefan and Taylor, Gail},
	year = {2006},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2006.02864.x},
	keywords = {QTL, drought, microarray, poplar, transcriptome},
	pages = {321--341},
}

The genetic nature of tree adaptation to drought stress was examined by utilizing variation in the drought response of a full-sib second generation (F2) mapping population from a cross between Populus trichocarpa (93-968) and P. deltoides Bart (ILL-129) and known to be highly divergent for a vast range of phenotypic traits. We combined phenotyping, quantitative trait loci (QTL) analysis and microarray experiments to demonstrate that ‘genetical genomics’ can be used to provide information on adaptation at the species level. The grandparents and F2 population were subjected to soil drying, and contrasting responses to drought across genotypes, including leaf coloration, expansion and abscission, were observed, and QTL for these traits mapped. A subset of extreme genotypes exhibiting extreme sensitivity and insensitivity to drought on the basis of leaf abscission were defined, and microarray experiments conducted on these genotypes and the grandparent species. The extreme genotype groups induced a different set of genes: 215 and 125 genes differed in their expression response between groups in control and drought, respectively, suggesting species adaptation at the gene expression level. Co-location of differentially expressed genes with drought-specific and drought-responsive QTLs was examined, and these may represent candidate genes contributing to the variation in drought response.

@article{tarkowski_cytokinins_2006,
	title = {Cytokinins in the perianth, carpels, and developing fruit of {Helleborus} niger {L}.},
	volume = {57},
	issn = {0022-0957},
	doi = {10/ckvwt2},
	abstract = {Reproductive development in the Christmas rose (Helleborus niger L.) differs from that in commonly investigated model plants in two important aspects: (i) the perianth develops a photosynthetic system after fertilization, and persists until seed ripening; and (ii) the ripe seed contains an immature embryo which continues to mature off the mother plant. The possible roles of cytokinins in these processes are investigated here by analysing extracts of the perianth and the carpels/maturing fruit prepared during anthesis and four stages of post-floral development. trans-Zeatin, dihydrozeatin, N-6-(Delta(2)-isopentenyl)adenine, and their ribosides were identified by tandem mass spectrometry. Single ion monitoring in the presence of deuterated internal standards demonstrated the additional presence of the corresponding riboside-5'-monophosphates, O-glucosides, and 9-glucosides, and afforded quantitative data on the whole set of endogenous cytokinins. Fruit cytokinins were mostly localized in the seeds. Their overall concentrations increased dramatically during early seed development and remained high for 6-8 weeks, until shortly before seed ripening (the last time point covered in this work). Overall cytokinin levels in the perianth did not change markedly in the period covered, but the level of N-6-(Delta(2)-isopentenyl)adenine-type cytokinins appeared to increase slightly and transiently during the greening phase. The perianths of unpollinated or depistillated flowers, which survived, but did not pass through the complete greening process, contained significantly less cytokinins than observed in fruit-bearing flowers. This suggests that perianth greening requires defined cytokinin levels and supports the role of the developing fruit in their maintenance.},
	language = {English},
	number = {10},
	journal = {Journal of Experimental Botany},
	author = {Tarkowski, Petr and Tarkowska, Danuse and Novak, Ondrej and Mihaljevic, Snjezana and Magnus, Volker and Strnad, Miroslav and Salopek-Sondi, Branka},
	year = {2006},
	note = {Place: Oxford
Publisher: Oxford Univ Press
WOS:000239389700011},
	keywords = {Christmas rose, Helleborus niger L., arabidopsis-thaliana, chromoplasts, culture, cytokinin identification and quantification, expression, fruit and   seed development, kinetin, perianth greening, photosynthesis, plants, senescence, specificity, tissue},
	pages = {2237--2247},
}

Reproductive development in the Christmas rose (Helleborus niger L.) differs from that in commonly investigated model plants in two important aspects: (i) the perianth develops a photosynthetic system after fertilization, and persists until seed ripening; and (ii) the ripe seed contains an immature embryo which continues to mature off the mother plant. The possible roles of cytokinins in these processes are investigated here by analysing extracts of the perianth and the carpels/maturing fruit prepared during anthesis and four stages of post-floral development. trans-Zeatin, dihydrozeatin, N-6-(Delta(2)-isopentenyl)adenine, and their ribosides were identified by tandem mass spectrometry. Single ion monitoring in the presence of deuterated internal standards demonstrated the additional presence of the corresponding riboside-5'-monophosphates, O-glucosides, and 9-glucosides, and afforded quantitative data on the whole set of endogenous cytokinins. Fruit cytokinins were mostly localized in the seeds. Their overall concentrations increased dramatically during early seed development and remained high for 6-8 weeks, until shortly before seed ripening (the last time point covered in this work). Overall cytokinin levels in the perianth did not change markedly in the period covered, but the level of N-6-(Delta(2)-isopentenyl)adenine-type cytokinins appeared to increase slightly and transiently during the greening phase. The perianths of unpollinated or depistillated flowers, which survived, but did not pass through the complete greening process, contained significantly less cytokinins than observed in fruit-bearing flowers. This suggests that perianth greening requires defined cytokinin levels and supports the role of the developing fruit in their maintenance.

@article{talyzina_molecular_2006,
	title = {Molecular evolution of a small gene family of wound inducible {Kunitz} trypsin inhibitors in {Populus}},
	volume = {63},
	issn = {0022-2844},
	doi = {10/c8zn3d},
	abstract = {Maximum likelihood models of codon substitutions were used to analyze the molecular evolution of a Kunitz trypsin inhibitor (KTI) gene family in Populus and Salix. The methods support previous assertions that the KTI genes comprise a rapidly evolving gene family. Models that allow for codon specific estimates of the ratio of nonsynonymous to synonymous substitutions (omega) among sites detect positive Darwinian selection at several sites in the KTI protein. In addition, branch-specific maximum likelihood models show that there is significant heterogeneity in omega among branches of the KTI phylogeny. In particular, omega is substantially higher following duplication than speciation. There is also evidence for significant rate heterogeneity following gene duplication, suggesting different evolutionary rates in newly arisen gene duplicates. The results indicate uneven evolutionary rates both between sites in the KTI protein and among different lineages in the KTI phylogeny, which is incompatible with a neutral model of sequence evolution.},
	language = {English},
	number = {1},
	journal = {Journal of Molecular Evolution},
	author = {Talyzina, Nina M. and Ingvarsson, Par K.},
	month = jul,
	year = {2006},
	note = {Place: New York
Publisher: Springer
WOS:000238711900010},
	keywords = {Kunitz trypsin inhibitor, Populus, amino-acid sites, arabidopsis-thaliana, codon-substitution models, disease resistance   genes, duplicate genes, gene duplication, herbivore defense, maximum likelihood, plasminogen-activator, positive selection, proteins, rapid evolution, serine-protease inhibitor},
	pages = {108--119},
}

Maximum likelihood models of codon substitutions were used to analyze the molecular evolution of a Kunitz trypsin inhibitor (KTI) gene family in Populus and Salix. The methods support previous assertions that the KTI genes comprise a rapidly evolving gene family. Models that allow for codon specific estimates of the ratio of nonsynonymous to synonymous substitutions (omega) among sites detect positive Darwinian selection at several sites in the KTI protein. In addition, branch-specific maximum likelihood models show that there is significant heterogeneity in omega among branches of the KTI phylogeny. In particular, omega is substantially higher following duplication than speciation. There is also evidence for significant rate heterogeneity following gene duplication, suggesting different evolutionary rates in newly arisen gene duplicates. The results indicate uneven evolutionary rates both between sites in the KTI protein and among different lineages in the KTI phylogeny, which is incompatible with a neutral model of sequence evolution.

@article{gapare_genetic_2006,
	title = {Genetic control of the time of transition from juvenile to mature wood in {Pinus} radiata {D}. {Don}},
	volume = {63},
	copyright = {INRA, EDP Sciences},
	issn = {1286-4560, 1297-966X},
	url = {http://dx.doi.org/10.1051/forest:2006070},
	doi = {10/c9gr4h},
	abstract = {Annals of Forest Science, is a source of information about current developments and trends in forest research and forestry},
	language = {en},
	number = {8},
	urldate = {2021-06-11},
	journal = {Annals of Forest Science},
	author = {Gapare, Washington J. and Wu, Harry X. and Abarquez, Aljoy},
	month = dec,
	year = {2006},
	note = {Publisher: EDP Sciences},
	pages = {871--878},
}

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

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

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

@article{lucinski_lhca5_2006,
	title = {Lhca5 interaction with plant photosystem {I}},
	volume = {580},
	copyright = {FEBS Letters 580 (2006) 1873-3468 © 2015 Federation of European Biochemical Societies},
	issn = {1873-3468},
	url = {https://febs.onlinelibrary.wiley.com/doi/abs/10.1016/j.febslet.2006.10.063},
	doi = {10.1016/j.febslet.2006.10.063},
	abstract = {In the outer antenna (LHCI) of higher plant photosystem I (PSI) four abundantly expressed light-harvesting protein of photosystem I (Lhca)-type proteins are organized in two heterodimeric domains (Lhca1/Lhca4 and Lhca2/Lhca3). Our cross-linking studies on PSI-LHCI preparations from wildtype Arabidopsis and pea plants indicate an exclusive interaction of the rarely expressed Lhca5 light-harvesting protein with LHCI in the Lhca2/Lhca3-site. In PSI particles with an altered LHCI composition Lhca5 assembles in the Lhca1/Lhca4 site, partly as a homodimer. This flexibility indicates a binding-competitive model for the LHCI assembly in plants regulated by molecular interactions of the Lhca proteins with the PSI core.},
	language = {en},
	number = {27},
	urldate = {2021-06-11},
	journal = {FEBS Letters},
	author = {Lucinski, Robert and Schmid, Volkmar H. R. and Jansson, Stefan and Klimmek, Frank},
	year = {2006},
	note = {\_eprint: https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/j.febslet.2006.10.063},
	keywords = {Cross-linking, LHCI, Lhca, Lhca5, Light-harvesting complex I, PSI, Photosystem I, chl, chlorophyll, depleted in Lhca protein, light-harvesting complex I, light-harvesting protein of photosystem I, photosystem I, wildtype, wt, ΔLhca},
	pages = {6485--6488},
}

In the outer antenna (LHCI) of higher plant photosystem I (PSI) four abundantly expressed light-harvesting protein of photosystem I (Lhca)-type proteins are organized in two heterodimeric domains (Lhca1/Lhca4 and Lhca2/Lhca3). Our cross-linking studies on PSI-LHCI preparations from wildtype Arabidopsis and pea plants indicate an exclusive interaction of the rarely expressed Lhca5 light-harvesting protein with LHCI in the Lhca2/Lhca3-site. In PSI particles with an altered LHCI composition Lhca5 assembles in the Lhca1/Lhca4 site, partly as a homodimer. This flexibility indicates a binding-competitive model for the LHCI assembly in plants regulated by molecular interactions of the Lhca proteins with the PSI core.

@article{albrectsen_micro_2006,
	title = {From micro towards the macro scale},
	volume = {172},
	issn = {0028-646X},
	doi = {10.1111/j.1469-8137.2006.01869.x},
	language = {English},
	number = {1},
	journal = {New Phytologist},
	author = {Albrectsen, Benedicte R. and Jansson, Stefan},
	year = {2006},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000239988100003},
	keywords = {arabidopsis, biofuel, coevolution, developmental biology, diversity, genes, plant defence   strategy, plants, scientific outreach, small RNA},
	pages = {7--10},
}

@article{benova-kakosova_galactoglucomannans_2006,
	title = {Galactoglucomannans {Increase} {Cell} {Population} {Density} and {Alter} the {Protoxylem}/{Metaxylem} {Tracheary} {Element} {Ratio} in {Xylogenic} {Cultures} of {Zinnia}},
	volume = {142},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.106.085712},
	doi = {10.1104/pp.106.085712},
	abstract = {Xylogenic cultures of zinnia (Zinnia elegans) provide a unique opportunity to study signaling pathways of tracheary element (TE) differentiation. In vitro TEs differentiate into either protoxylem (PX)-like TEs characterized by annular/helical secondary wall thickening or metaxylem (MX)-like TEs with reticulate/scalariform/pitted thickening. The factors that determine these different cell fates are largely unknown. We show here that supplementing zinnia cultures with exogenous galactoglucomannan oligosaccharides (GGMOs) derived from spruce (Picea abies) xylem had two major effects: an increase in cell population density and a decrease in the ratio of PX to MX TEs. In an attempt to link these two effects, the consequence of the plane of cell division on PX-MX differentiation was assessed. Although GGMOs did not affect the plane of cell division per se, they significantly increased the proportion of longitudinally divided cells differentiating into MX. To test the biological significance of these findings, we have determined the presence of mannan-containing oligosaccharides in zinnia cultures in vitro. Immunoblot assays indicated that β-1,4-mannosyl epitopes accumulate specifically in TE-inductive media. These epitopes were homogeneously distributed within the thickened secondary walls of TEs when the primary cell wall was weakly labeled. Using polysaccharide analysis carbohydrate gel electrophoresis, glucomannans were specifically detected in cell walls of differentiating zinnia cultures. Finally, zinnia macroarrays probed with cDNAs from cells cultured in the presence or absence of GGMOs indicated that significantly more genes were down-regulated rather than up-regulated by GGMOs. This study constitutes a major step in the elucidation of signaling mechanisms of PX- and MX-specific genetic programs in zinnia.},
	number = {2},
	urldate = {2021-06-11},
	journal = {Plant Physiology},
	author = {Beňová-Kákošová, Anna and Digonnet, Catherine and Goubet, Florence and Ranocha, Philippe and Jauneau, Alain and Pesquet, Edouard and Barbier, Odile and Zhang, Zhinong and Capek, Peter and Dupree, Paul and Lišková, Desana and Goffner, Deborah},
	month = oct,
	year = {2006},
	pages = {696--709},
}

Xylogenic cultures of zinnia (Zinnia elegans) provide a unique opportunity to study signaling pathways of tracheary element (TE) differentiation. In vitro TEs differentiate into either protoxylem (PX)-like TEs characterized by annular/helical secondary wall thickening or metaxylem (MX)-like TEs with reticulate/scalariform/pitted thickening. The factors that determine these different cell fates are largely unknown. We show here that supplementing zinnia cultures with exogenous galactoglucomannan oligosaccharides (GGMOs) derived from spruce (Picea abies) xylem had two major effects: an increase in cell population density and a decrease in the ratio of PX to MX TEs. In an attempt to link these two effects, the consequence of the plane of cell division on PX-MX differentiation was assessed. Although GGMOs did not affect the plane of cell division per se, they significantly increased the proportion of longitudinally divided cells differentiating into MX. To test the biological significance of these findings, we have determined the presence of mannan-containing oligosaccharides in zinnia cultures in vitro. Immunoblot assays indicated that β-1,4-mannosyl epitopes accumulate specifically in TE-inductive media. These epitopes were homogeneously distributed within the thickened secondary walls of TEs when the primary cell wall was weakly labeled. Using polysaccharide analysis carbohydrate gel electrophoresis, glucomannans were specifically detected in cell walls of differentiating zinnia cultures. Finally, zinnia macroarrays probed with cDNAs from cells cultured in the presence or absence of GGMOs indicated that significantly more genes were down-regulated rather than up-regulated by GGMOs. This study constitutes a major step in the elucidation of signaling mechanisms of PX- and MX-specific genetic programs in zinnia.

@article{bilir_growth_2006,
	title = {Growth characters and number of strobili in clonal seed orchards of {Pinus} sylvestris},
	volume = {152},
	issn = {0014-2336},
	doi = {10.1007/s10681-006-9216-2},
	abstract = {Observations were made on six grafts for each of 25 clones in three Scots pine (Pinus sylvestris) seed orchards in Turkey. The characters studied were number of female and male strobili, height below and above the longest branch, total height; diameter at base and breast height, crown diameter, and number of branches. Variation, broad-sense heritability (H-2) and correlations between characters were estimated. Variation among clones was lower than among grafts within clone for all characters. The genetic variation for number of strobili varied between 0 and 17\% of total variation, while that for growth characters values varied between 2 and 13\%. The number of female strobili appeared more variable among trees than the number of male strobili. H-2 was not consistently high for any character or seed orchard. The number of strobili increased with the size of the tree, but not dramatically. Correlations between measures of tree size (both on clone level and individual graft level) and the number of strobili were in the magnitude r approximate to 0.3. Diameter at breast height seems a reasonable predictor for number of strobili.},
	language = {English},
	number = {2},
	journal = {Euphytica},
	author = {Bilir, Nebi and Prescher, Finnvid and Ayan, Sezgin and Lindgren, Dag},
	month = nov,
	year = {2006},
	note = {Place: Dordrecht
Publisher: Springer
WOS:000242606500015},
	keywords = {Scots pine, brutia, fertility variation, flowering, gene diversity, graft size, heritability, impact, scots pine, turkey, variation},
	pages = {293--301},
}

Observations were made on six grafts for each of 25 clones in three Scots pine (Pinus sylvestris) seed orchards in Turkey. The characters studied were number of female and male strobili, height below and above the longest branch, total height; diameter at base and breast height, crown diameter, and number of branches. Variation, broad-sense heritability (H-2) and correlations between characters were estimated. Variation among clones was lower than among grafts within clone for all characters. The genetic variation for number of strobili varied between 0 and 17% of total variation, while that for growth characters values varied between 2 and 13%. The number of female strobili appeared more variable among trees than the number of male strobili. H-2 was not consistently high for any character or seed orchard. The number of strobili increased with the size of the tree, but not dramatically. Correlations between measures of tree size (both on clone level and individual graft level) and the number of strobili were in the magnitude r approximate to 0.3. Diameter at breast height seems a reasonable predictor for number of strobili.

@article{bishopp_signs_2006,
	title = {Signs of change: hormone receptors that regulate plant development},
	volume = {133},
	issn = {0950-1991},
	shorttitle = {Signs of change},
	doi = {10.1242/dev.02359},
	abstract = {Hormonal signalling plays a pivotal role in almost every aspect of plant development, and of high priority has been to identify the receptors that perceive these hormones. In the past seven months, the receptors for the plant hormones auxin, gibberellins and abscisic acid have been identified. These join the receptors that have previously been identified for ethylene, brassinosteroids and cytokinins. This review therefore comes at an exciting time for plant developmental biology, as the new findings shed light on our current understanding of the structure and function of the various hormone receptors, their related signalling pathways and their role in regulating plant development.},
	language = {English},
	number = {10},
	journal = {Development},
	author = {Bishopp, A. and Mahonen, A. P. and Helariutta, Y.},
	month = may,
	year = {2006},
	note = {Place: Cambridge
Publisher: Company Biologists Ltd
WOS:000237208300001},
	keywords = {arabidopsis-thaliana, auxin-response, brassinosteroid receptors, cytokinin receptor, f-box subunit, gene-expression, histidine   kinase, raf-like kinase, scf e3 complex, signaling pathway},
	pages = {1857--1869},
}

Hormonal signalling plays a pivotal role in almost every aspect of plant development, and of high priority has been to identify the receptors that perceive these hormones. In the past seven months, the receptors for the plant hormones auxin, gibberellins and abscisic acid have been identified. These join the receptors that have previously been identified for ethylene, brassinosteroids and cytokinins. This review therefore comes at an exciting time for plant developmental biology, as the new findings shed light on our current understanding of the structure and function of the various hormone receptors, their related signalling pathways and their role in regulating plant development.

@article{bylesjo_masqot-gui_2006,
	title = {{MASQOT}-{GUI}: spot quality assessment for the two-channel microarray platform},
	volume = {22},
	issn = {1367-4803},
	shorttitle = {{MASQOT}-{GUI}},
	url = {https://doi.org/10.1093/bioinformatics/btl434},
	doi = {10.1093/bioinformatics/btl434},
	abstract = {Summary: MASQOT-GUI provides an open-source, platform-independent software pipeline for two-channel microarray spot quality control. This includes gridding, segmentation, quantification, quality assessment and data visualization. It hosts a set of independent applications, with interactions between the tools as well as import and export support for external software. The implementation of automated multivariate quality control assessment, which is a unique feature of MASQOT-GUI, is based on the previously documented and evaluated MASQOT methodology. Further abilities of the application are outlined and illustrated.Availability: MASQOT-GUI is Java-based and licensed under the GNU LGPL. Source code and installation files are available for download at Contact: This email address is being protected from spambots. You need JavaScript enabled to view it. information: Supplementary data are available at Bioinformatics online},
	number = {20},
	urldate = {2021-06-11},
	journal = {Bioinformatics},
	author = {Bylesjö, Max and Sjödin, Andreas and Eriksson, Daniel and Antti, Henrik and Moritz, Thomas and Jansson, Stefan and Trygg, Johan},
	month = oct,
	year = {2006},
	pages = {2554--2555},
}

Summary: MASQOT-GUI provides an open-source, platform-independent software pipeline for two-channel microarray spot quality control. This includes gridding, segmentation, quantification, quality assessment and data visualization. It hosts a set of independent applications, with interactions between the tools as well as import and export support for external software. The implementation of automated multivariate quality control assessment, which is a unique feature of MASQOT-GUI, is based on the previously documented and evaluated MASQOT methodology. Further abilities of the application are outlined and illustrated.Availability: MASQOT-GUI is Java-based and licensed under the GNU LGPL. Source code and installation files are available for download at Contact: This email address is being protected from spambots. You need JavaScript enabled to view it. information: Supplementary data are available at Bioinformatics online

@article{ciereszko_phosphate_2006,
	title = {Phosphate deficiency-dependent upregulation of {UDP}-glucose pyrophosphorylase genes is insensitive to {ABA} and ethylene status in {Arabidopsis} leaves},
	volume = {28},
	issn = {1861-1664},
	url = {https://doi.org/10.1007/BF02706620},
	doi = {10.1007/BF02706620},
	abstract = {The effects of inorganic phosphate (Pi) deficiency and ABA/ethylene status on expression of UDP-glucose pyrophosphorylase (UGPase) genes (Ugp), involved in sucrose/polysaccharide metabolism, were investigated. Both wild-type (wt), aba and abi mutants (ABA-deficient and -in-sensitive), etr, ein and eto (ethylene resistant and overproducing) grown on Pi-deficient and complete nutrient solution, as well as phol (Pi-deficient) mutants of Arabidopsis thaliana were used for experiments. Generally, Pi-deficiency conditions (including mannose feeding to decrease cytosolic Pi pool) resulted in an increase of Ugp expression in the leaves, under all experimental conditions. Mutant backgrounds reflecting differences in ABA or ethylene status/ sensitivity had no effect on the level of Ugp up-regulation by Pi-stress. Furthermore, feeding ABA to the leaves of wt and pho1 plants had no effect on Ugp expression, regardless of the sucrose status in the leaves. The data suggest that Pi deficiency leading to up-regulation of Ugp acts independently of ABA and ethylene status.},
	language = {en},
	number = {5},
	urldate = {2021-06-11},
	journal = {Acta Physiologiae Plantarum},
	author = {Ciereszko, Iwona and Kleczkowski, Leszek A.},
	month = oct,
	year = {2006},
	pages = {387--393},
}

The effects of inorganic phosphate (Pi) deficiency and ABA/ethylene status on expression of UDP-glucose pyrophosphorylase (UGPase) genes (Ugp), involved in sucrose/polysaccharide metabolism, were investigated. Both wild-type (wt), aba and abi mutants (ABA-deficient and -in-sensitive), etr, ein and eto (ethylene resistant and overproducing) grown on Pi-deficient and complete nutrient solution, as well as phol (Pi-deficient) mutants of Arabidopsis thaliana were used for experiments. Generally, Pi-deficiency conditions (including mannose feeding to decrease cytosolic Pi pool) resulted in an increase of Ugp expression in the leaves, under all experimental conditions. Mutant backgrounds reflecting differences in ABA or ethylene status/ sensitivity had no effect on the level of Ugp up-regulation by Pi-stress. Furthermore, feeding ABA to the leaves of wt and pho1 plants had no effect on Ugp expression, regardless of the sucrose status in the leaves. The data suggest that Pi deficiency leading to up-regulation of Ugp acts independently of ABA and ethylene status.

@article{demmig-adams_modulation_2006,
	title = {Modulation of {PsbS} and flexible vs sustained energy dissipation by light environment in different species},
	volume = {127},
	issn = {0031-9317},
	doi = {10.1111/j.1399-3054.2006.00698.x},
	abstract = {Contrasting acclimation strategies of photosynthesis and photoprotection were identified for annual mesophytes (spinach, pumpkin, and Arabidopsis) vs the tropical evergreen Monstera deliciosa. The annual species utilized full sunlight for photosynthesis to a much greater extent than the evergreen species. Conversely, the evergreen species exhibited a greater capacity for photoprotective thermal energy dissipation as well as a greater expression of the PsbS protein in full sun than the annual species. In all species, the majority of thermal energy dissipation [assessed as non-photochemical fluorescence quenching (NPQ)] was the flexible, Delta pH-dependent form of NPQ over the entire range of growth light environments. However, in response to a transfer of shade-grown plants to high light, the evergreen species exhibited a high level of sustained thermal dissipation (ql), but the annual species did not. This sustained energy dissipation in the evergreen species was not Delta pH-dependent nor did the low level of PsbS in shade leaves increase upon transfer to high light for several days. Sustained Delta pH-independent NPQ was correlated (a) initially, with sustained DI protein phosphorylation and xanthophyll cycle arrest and U subsequently, with an accumulation over several days of PsbS-related one-helix proteins and newly synthesized zeaxanthin and lutein.},
	language = {English},
	number = {4},
	journal = {Physiologia Plantarum},
	author = {Demmig-Adams, Barbara and Ebbert, Volker and Mellman, David L. and Mueh, Kristine E. and Schaffer, Lisa and Funk, Christiane and Zarter, C. Ryan and Adamska, Iwona and Jansson, Stefan and Adams III, William W.},
	month = aug,
	year = {2006},
	note = {Place: Hoboken
Publisher: Wiley-Blackwell
WOS:000239561900014},
	keywords = {arabidopsis-thaliana, chlorophyll   fluorescence, excess excitation, inducible polypeptides, overwintering evergreens, photosystem-ii, protein, shade leaves, synechocystis pcc6803, xanthophyll cycle},
	pages = {670--680},
}

Contrasting acclimation strategies of photosynthesis and photoprotection were identified for annual mesophytes (spinach, pumpkin, and Arabidopsis) vs the tropical evergreen Monstera deliciosa. The annual species utilized full sunlight for photosynthesis to a much greater extent than the evergreen species. Conversely, the evergreen species exhibited a greater capacity for photoprotective thermal energy dissipation as well as a greater expression of the PsbS protein in full sun than the annual species. In all species, the majority of thermal energy dissipation [assessed as non-photochemical fluorescence quenching (NPQ)] was the flexible, Delta pH-dependent form of NPQ over the entire range of growth light environments. However, in response to a transfer of shade-grown plants to high light, the evergreen species exhibited a high level of sustained thermal dissipation (ql), but the annual species did not. This sustained energy dissipation in the evergreen species was not Delta pH-dependent nor did the low level of PsbS in shade leaves increase upon transfer to high light for several days. Sustained Delta pH-independent NPQ was correlated (a) initially, with sustained DI protein phosphorylation and xanthophyll cycle arrest and U subsequently, with an accumulation over several days of PsbS-related one-helix proteins and newly synthesized zeaxanthin and lutein.

@article{esmon_gradient_2006,
	title = {A gradient of auxin and auxin-dependent transcription precedes tropic growth responses},
	volume = {103},
	copyright = {Copyright © 2006, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/103/1/236},
	doi = {10.1073/pnas.0507127103},
	abstract = {Plants, although sessile, can reorient growth axes in response to changing environmental conditions. Phototropism and gravitropism represent adaptive growth responses induced by changes in light direction and growth axis orientation relative to gravitational direction, respectively. The nearly 80-year-old Cholodny–Went theory [Went, F. W. \& Thimann, K. V. (1937) Phytohormones (Macmillan, New York)] predicts that formation of a gradient of the plant morphogen auxin is central to the establishment of tropic curvature. Loss of tropic responses in seedling stems of Arabidopsis thaliana mutants lacking the auxin-regulated transcriptional activator NPH4/ARF7 has further suggested that a gradient of gene expression represents an essential output from the auxin gradient. Yet the molecular identities of such output components, which are likely to encode proteins directly involved in growth control, have remained elusive. Here we report the discovery of a suite of tropic stimulus-induced genes in Brassica oleracea that are responsive to an auxin gradient and exhibit morphologically graded expression concomitant with, or before, observable curvature responses. These results provide compelling molecular support for the Cholodny–Went theory and suggest that morphologically graded transcription represents an important mechanism for interpreting tropically stimulated gradients of auxin. Intriguingly, two of the tropic stimulus-induced genes, EXPA1 and EXPA8, encode enzymes involved in cell wall extension, a response prerequisite for differential growth leading to curvatures, and are up-regulated before curvature in the flank that will elongate. This observation suggests that morphologically graded transcription likely leads to the graded expression of proteins whose activities can directly regulate the establishment and modulation of tropic curvatures.},
	language = {en},
	number = {1},
	urldate = {2021-06-11},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Esmon, C. Alex and Tinsley, Amanda G. and Ljung, Karin and Sandberg, Goran and Hearne, Leonard B. and Liscum, Emmanuel},
	month = jan,
	year = {2006},
	pmid = {16371470},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	keywords = {NPH4/ARF7, gravitropism, phototropism},
	pages = {236--241},
}

Plants, although sessile, can reorient growth axes in response to changing environmental conditions. Phototropism and gravitropism represent adaptive growth responses induced by changes in light direction and growth axis orientation relative to gravitational direction, respectively. The nearly 80-year-old Cholodny–Went theory [Went, F. W. & Thimann, K. V. (1937) Phytohormones (Macmillan, New York)] predicts that formation of a gradient of the plant morphogen auxin is central to the establishment of tropic curvature. Loss of tropic responses in seedling stems of Arabidopsis thaliana mutants lacking the auxin-regulated transcriptional activator NPH4/ARF7 has further suggested that a gradient of gene expression represents an essential output from the auxin gradient. Yet the molecular identities of such output components, which are likely to encode proteins directly involved in growth control, have remained elusive. Here we report the discovery of a suite of tropic stimulus-induced genes in Brassica oleracea that are responsive to an auxin gradient and exhibit morphologically graded expression concomitant with, or before, observable curvature responses. These results provide compelling molecular support for the Cholodny–Went theory and suggest that morphologically graded transcription represents an important mechanism for interpreting tropically stimulated gradients of auxin. Intriguingly, two of the tropic stimulus-induced genes, EXPA1 and EXPA8, encode enzymes involved in cell wall extension, a response prerequisite for differential growth leading to curvatures, and are up-regulated before curvature in the flank that will elongate. This observation suggests that morphologically graded transcription likely leads to the graded expression of proteins whose activities can directly regulate the establishment and modulation of tropic curvatures.

@article{ferreira_proteome_2006,
	title = {Proteome profiling of {Populus} euphratica {Oliv}. {Upon} heat stress},
	volume = {98},
	issn = {0305-7364},
	doi = {10.1093/aob/mcl106},
	abstract = {Background and Aims Populus euphratica is a light-demanding species ecologically characterized as a pioneer. It grows in shelter belts along riversides, being part of the natural desert forest ecosystems in China and Middle Eastern countries. It is able to survive extreme temperatures, drought and salt stress, marking itself out as an important plant species to study the mechanisms responsible for survival of woody plants under heat stress. 9 Methods Heat effects were evaluated through electrolyte leakage on leaf discs, and LT50 was determined to occur above 50 degrees C. Protein accumulation profiles of leaves from young plants submitted to 42/37 degrees C for 3 d in a phytotron were determined through 2D-PAGE, and a total of 45\% of up- and downregulated proteins were detected. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF)/TOF analysis, combined with searches in different databases, enabled the identification of 82\% of the selected spots. Key Results Short-term upregulated proteins are related to membrane destabilization and cytoskeleton restructuring, sulfur assimilation, thiamine and hydrophobic amino acid biosynthesis, and protein stability. Long-term upregulated proteins are involved in redox homeostasis and photosynthesis. Late downregulated proteins are involved mainly in carbon metabolism. Conclusions Moderate heat response involves proteins related to lipid biogenesis, cytoskeleton structure, sulfate assimilation, thiamine and hydrophobic amino acid biosynthesis, and nuclear transport. Photostasis is achieved through carbon metabolism adjustment, a decrease of photosystem II (PSII) abundance and an increase of PSI contribution to photosynthetic linear electron flow. Thioredoxin h may have a special role in this process in P. euphratica upon moderate heat exposure.},
	language = {English},
	number = {2},
	journal = {Annals of Botany},
	author = {Ferreira, Silvia and Hjerno, Karin and Larsen, Martin and Wingsle, Gunnar and Larsen, Peter and Fey, Stephen and Roepstorff, Peter and Pais, Maria Salome},
	month = aug,
	year = {2006},
	note = {Place: Oxford
Publisher: Oxford Univ Press
WOS:000239630500008},
	keywords = {Populus euphratica, arabidopsis-thaliana, binding-protein, biosynthetic-pathway, carbon metabolism, escherichia-coli, gene-expression, high-temperature, mass spectrometry, mass-spectrometry, membrane-proteins, moderate heat stress, proteome   profiling, salt stress, sequence databases},
	pages = {361--377},
}

Background and Aims Populus euphratica is a light-demanding species ecologically characterized as a pioneer. It grows in shelter belts along riversides, being part of the natural desert forest ecosystems in China and Middle Eastern countries. It is able to survive extreme temperatures, drought and salt stress, marking itself out as an important plant species to study the mechanisms responsible for survival of woody plants under heat stress. 9 Methods Heat effects were evaluated through electrolyte leakage on leaf discs, and LT50 was determined to occur above 50 degrees C. Protein accumulation profiles of leaves from young plants submitted to 42/37 degrees C for 3 d in a phytotron were determined through 2D-PAGE, and a total of 45% of up- and downregulated proteins were detected. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF)/TOF analysis, combined with searches in different databases, enabled the identification of 82% of the selected spots. Key Results Short-term upregulated proteins are related to membrane destabilization and cytoskeleton restructuring, sulfur assimilation, thiamine and hydrophobic amino acid biosynthesis, and protein stability. Long-term upregulated proteins are involved in redox homeostasis and photosynthesis. Late downregulated proteins are involved mainly in carbon metabolism. Conclusions Moderate heat response involves proteins related to lipid biogenesis, cytoskeleton structure, sulfate assimilation, thiamine and hydrophobic amino acid biosynthesis, and nuclear transport. Photostasis is achieved through carbon metabolism adjustment, a decrease of photosystem II (PSII) abundance and an increase of PSI contribution to photosynthetic linear electron flow. Thioredoxin h may have a special role in this process in P. euphratica upon moderate heat exposure.

@article{fischer_vectorial_2006,
	title = {Vectorial {Information} for {Arabidopsis} {Planar} {Polarity} {Is} {Mediated} by {Combined} {AUX1}, {EIN2}, and {GNOM} {Activity}},
	volume = {16},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982206022044},
	doi = {10.1016/j.cub.2006.08.091},
	abstract = {Cell polarity is commonly coordinated within the plane of a single tissue layer (planar polarity), and hair positioning has been exploited as a simple marker for planar polarization of animal epithelia [1]. The root epidermis of the plant Arabidopsis similarly reveals planar polarity of hair localization close to root tip-oriented (basal) ends of hair-forming cells 2, 3, 4. Hair position is directed toward a concentration maximum of the hormone auxin in the root tip 4, 5, but mechanisms driving this plant-specific planar polarity remain elusive. Here, we report that combinatorial action of the auxin influx carrier AUX16, 7, ETHYLENE-INSENSITIVE2 (EIN2) [8], and GNOM[9] genes mediates the vector for coordinate hair positioning. In aux1;ein2;gnomeb triple mutant roots, hairs display axial (apical or basal) instead of coordinate polar (basal) position, and recruitment of Rho-of-Plant (ROP) GTPases to the hair initiation site 10, 11 reveals the same polar-to-axial switch. The auxin concentration gradient is virtually abolished in aux1;ein2;gnomeb roots, where locally applied auxin can coordinate hair positioning. Moreover, auxin overproduction in sectors of wild-type roots enhances planar ROP and hair polarity over long and short distances. Hence, auxin may provide vectorial information for planar polarity that requires combinatorial AUX1, EIN2, and GNOM activity upstream of ROP positioning.},
	language = {en},
	number = {21},
	urldate = {2021-06-11},
	journal = {Current Biology},
	author = {Fischer, Urs and Ikeda, Yoshihisa and Ljung, Karin and Serralbo, Olivier and Singh, Manoj and Heidstra, Renze and Palme, Klaus and Scheres, Ben and Grebe, Markus},
	month = nov,
	year = {2006},
	keywords = {DEVBIO},
	pages = {2143--2149},
}

Cell polarity is commonly coordinated within the plane of a single tissue layer (planar polarity), and hair positioning has been exploited as a simple marker for planar polarization of animal epithelia [1]. The root epidermis of the plant Arabidopsis similarly reveals planar polarity of hair localization close to root tip-oriented (basal) ends of hair-forming cells 2, 3, 4. Hair position is directed toward a concentration maximum of the hormone auxin in the root tip 4, 5, but mechanisms driving this plant-specific planar polarity remain elusive. Here, we report that combinatorial action of the auxin influx carrier AUX16, 7, ETHYLENE-INSENSITIVE2 (EIN2) [8], and GNOM[9] genes mediates the vector for coordinate hair positioning. In aux1;ein2;gnomeb triple mutant roots, hairs display axial (apical or basal) instead of coordinate polar (basal) position, and recruitment of Rho-of-Plant (ROP) GTPases to the hair initiation site 10, 11 reveals the same polar-to-axial switch. The auxin concentration gradient is virtually abolished in aux1;ein2;gnomeb roots, where locally applied auxin can coordinate hair positioning. Moreover, auxin overproduction in sectors of wild-type roots enhances planar ROP and hair polarity over long and short distances. Hence, auxin may provide vectorial information for planar polarity that requires combinatorial AUX1, EIN2, and GNOM activity upstream of ROP positioning.

@article{forsum_nitrogen_2006,
	title = {Nitrogen utilization by {Hylocomium} splendens in a boreal forest fertilization experiment},
	volume = {20},
	issn = {0269-8463},
	doi = {10.1111/j.1365-2435.2006.01127.x},
	abstract = {1. Nitrogen uptake in the terricolous bryophyte Hylocomium splendens (Hedw.) B.S.G. was studied in a boreal forest long-term N-treatment experiment including control plots, N-addition plots (50 kg N ha(-1) year(-1) for 8 years) and recovery plots (50 kg N ha(-1) year(-1) for 5 years and thereafter no N addition for 3 years). 2.A main objective was to explore whether the N treatments changed bryophyte uptake of different inorganic and organic N forms. In addition, we estimated the contribution of N from throughfall precipitation to the bryophyte N supply. 3. The results demonstrated that bryophyte N uptake was similar in all the long-term N-treatment plots. Hylocomium splendens took up more N-15 labelled NH4+ than NO3- or glycine when these N forms were applied in situ by the spraying of solutions with N concentrations similar to those in precipitation. 4. Analysis of the precipitation collected beneath the closed tree canopy from late May to early October revealed that it contributed 2.0 kg N ha(-1) during the period studied, distributed between NH4+ (78\%), amino acid N (17\%) and NO3- (5\%). 5. The study highlights that, in addition to analyses of NH4+ and NO3- (normally included in standard environmental monitoring of precipitation), analysis of amino acid N must be performed to account fully for the precipitation N input to bryophytes in boreal forest ecosystems.},
	language = {English},
	number = {3},
	journal = {Functional Ecology},
	author = {Forsum, A. and Dahlman, L. and Nasholm, T. and Nordin, A.},
	month = jun,
	year = {2006},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000238185400002},
	keywords = {amino acids, amino-acids, ammonium, arginine, atmospheric deposition, canopy interactions, growth, nitrate, organic nitrogen, pinus-sylvestris, responses, soluble carbohydrates, sphagnum, throughfall, vegetation},
	pages = {421--426},
}

1. Nitrogen uptake in the terricolous bryophyte Hylocomium splendens (Hedw.) B.S.G. was studied in a boreal forest long-term N-treatment experiment including control plots, N-addition plots (50 kg N ha(-1) year(-1) for 8 years) and recovery plots (50 kg N ha(-1) year(-1) for 5 years and thereafter no N addition for 3 years). 2.A main objective was to explore whether the N treatments changed bryophyte uptake of different inorganic and organic N forms. In addition, we estimated the contribution of N from throughfall precipitation to the bryophyte N supply. 3. The results demonstrated that bryophyte N uptake was similar in all the long-term N-treatment plots. Hylocomium splendens took up more N-15 labelled NH4+ than NO3- or glycine when these N forms were applied in situ by the spraying of solutions with N concentrations similar to those in precipitation. 4. Analysis of the precipitation collected beneath the closed tree canopy from late May to early October revealed that it contributed 2.0 kg N ha(-1) during the period studied, distributed between NH4+ (78%), amino acid N (17%) and NO3- (5%). 5. The study highlights that, in addition to analyses of NH4+ and NO3- (normally included in standard environmental monitoring of precipitation), analysis of amino acid N must be performed to account fully for the precipitation N input to bryophytes in boreal forest ecosystems.

@article{fritz_fitness_2006,
	title = {Fitness and genetic architecture of parent and hybrid willows in common gardens},
	volume = {60},
	issn = {0014-3820},
	doi = {10.1554/05-343.1},
	abstract = {Models of hybrid zone dynamics incorporate different patterns of hybrid fitness relative to parental species fitness. An important but understudied source of variation underlying these fitness differences is the environment. We investigated the performance of two willow species and their F-1, F-2, and backcross hybrids using a common-garden experiment with six replicated gardens that differed in soil moisture. Aboveground biomass, catkin production, seed production per catkin, and seed germination rate were significantly different among genetic classes. For aboveground biomass and catkin production, hybrids generally had intermediate or inferior performance compared to parent species. Salix eriocephala had the highest performance for all performance measures, but in two gardens F, plants had superior or equal performance for aboveground biomass and female catkin production. Salix eriocephala and backcrosses to S. eriocephala had the highest numbers of filled seeds per catkin and the highest estimates of total fitness in all gardens. Measures of filled seeds per catkin and germination rate tend to support the model of endogenous hybrid unfitness, and these two measures had major effects on estimates of total seed production per catkin. We also estimated how the two willow species differ genetically in these fitness measures using line cross analysis. We found a complex genetic architecture underlying the fitness differences between species that involved additive, dominance, and epistatic genetic effects for all fitness measures. The environment was important in the expression of these genetic differences, because the type of epistasis differed among the gardens for aboveground biomass and for female catkin production. These findings suggest that fine-scale environmental variation can have a significant impact on hybrid fitness in hybrid zones where parents and hybrids are widely interspersed.},
	language = {English},
	number = {6},
	journal = {Evolution},
	author = {Fritz, Robert S. and Hochwender, Cris G. and Albrectsen, Benedicte R. and Czesak, Mary Ellen},
	month = jun,
	year = {2006},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000238969900010},
	keywords = {epistasis, evolution, fitness, genetic architecture, growth, herbivores, hybrid, hybrid zone, inbreeding depression, natural   hybridization, nutrition, pinus-radiata, responses, sagebrush artemisia-tridentata, willow, zone},
	pages = {1215--1227},
}

Models of hybrid zone dynamics incorporate different patterns of hybrid fitness relative to parental species fitness. An important but understudied source of variation underlying these fitness differences is the environment. We investigated the performance of two willow species and their F-1, F-2, and backcross hybrids using a common-garden experiment with six replicated gardens that differed in soil moisture. Aboveground biomass, catkin production, seed production per catkin, and seed germination rate were significantly different among genetic classes. For aboveground biomass and catkin production, hybrids generally had intermediate or inferior performance compared to parent species. Salix eriocephala had the highest performance for all performance measures, but in two gardens F, plants had superior or equal performance for aboveground biomass and female catkin production. Salix eriocephala and backcrosses to S. eriocephala had the highest numbers of filled seeds per catkin and the highest estimates of total fitness in all gardens. Measures of filled seeds per catkin and germination rate tend to support the model of endogenous hybrid unfitness, and these two measures had major effects on estimates of total seed production per catkin. We also estimated how the two willow species differ genetically in these fitness measures using line cross analysis. We found a complex genetic architecture underlying the fitness differences between species that involved additive, dominance, and epistatic genetic effects for all fitness measures. The environment was important in the expression of these genetic differences, because the type of epistasis differed among the gardens for aboveground biomass and for female catkin production. These findings suggest that fine-scale environmental variation can have a significant impact on hybrid fitness in hybrid zones where parents and hybrids are widely interspersed.

@article{garcia-lorenzo_protease_2006,
	title = {Protease gene families in {Populus} and {Arabidopsis}},
	volume = {6},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/1471-2229-6-30},
	doi = {10.1186/1471-2229-6-30},
	abstract = {Proteases play key roles in plants, maintaining strict protein quality control and degrading specific sets of proteins in response to diverse environmental and developmental stimuli. Similarities and differences between the proteases expressed in different species may give valuable insights into their physiological roles and evolution.},
	number = {1},
	urldate = {2021-06-11},
	journal = {BMC Plant Biology},
	author = {García-Lorenzo, Maribel and Sjödin, Andreas and Jansson, Stefan and Funk, Christiane},
	month = dec,
	year = {2006},
	keywords = {Leaf Senescence, Protease Family, Protease Gene, Putative Protease, Tension Wood},
	pages = {30},
}

Proteases play key roles in plants, maintaining strict protein quality control and degrading specific sets of proteins in response to diverse environmental and developmental stimuli. Similarities and differences between the proteases expressed in different species may give valuable insights into their physiological roles and evolution.

@article{gonzalez-rivas_species_2006,
	title = {Species {Composition}, {Diversity} and {Local} uses of {Tropical} {Dry} {Deciduous} and {Gallery} {Forests} in {Nicaragua}},
	volume = {15},
	issn = {1572-9710},
	url = {https://doi.org/10.1007/s10531-005-2632-0},
	doi = {10.1007/s10531-005-2632-0},
	abstract = {The floristic composition and diversity of tropical dry deciduous and gallery forests were studied in Chacocente Wildlife Refuge, located on the Pacific coast in Nicaragua during 1994 and 2000. Density, dominance and frequency as well as species and family important values were computed to characterize the floristic composition. A variety of diversity measures were also calculated to examine heterogeneity in each forest community. A total of 29 families, 49 genera and 59 species were represented in 2 ha dry deciduous forest. In the gallery forest, the number of families, genera and species recorded in 2000 inventory was 33, 48 and 58, respectively and slightly higher than the 1994 inventory. The number of stems ⩽ 10 cm dbh varied from 451 to 489 per hectare in the deciduous forest, and from 283 to 298 per hectare in the gallery forest. The basal area was much larger for species in the gallery than dry deciduous forest. Fabaceae, sub family Papilionoideae, was the most specious family in the deciduous forest while Meliaceae was the dominant family in the gallery forest. Similarity in species composition and abundance between deciduous and gallery forests was low. In terms of species diversity, the gallery forest was found more diverse than the deciduous forest using Fisher's diversity index. Both forest communities were characterized by a typical inverse J shape. Therefore, emphasis should be given to the protection of rare species, i.e. as the forests are still under continued human pressure, an immediate action should be taken to conserve the remaining flora.},
	language = {en},
	number = {4},
	urldate = {2021-06-11},
	journal = {Biodiversity \& Conservation},
	author = {González-Rivas, Benigno and Tigabu, Mulualem and Gerhardt, Karin and Castro-Marín, Guillermo and Odén, Per Christer},
	month = apr,
	year = {2006},
	pages = {1509--1527},
}

The floristic composition and diversity of tropical dry deciduous and gallery forests were studied in Chacocente Wildlife Refuge, located on the Pacific coast in Nicaragua during 1994 and 2000. Density, dominance and frequency as well as species and family important values were computed to characterize the floristic composition. A variety of diversity measures were also calculated to examine heterogeneity in each forest community. A total of 29 families, 49 genera and 59 species were represented in 2 ha dry deciduous forest. In the gallery forest, the number of families, genera and species recorded in 2000 inventory was 33, 48 and 58, respectively and slightly higher than the 1994 inventory. The number of stems ⩽ 10 cm dbh varied from 451 to 489 per hectare in the deciduous forest, and from 283 to 298 per hectare in the gallery forest. The basal area was much larger for species in the gallery than dry deciduous forest. Fabaceae, sub family Papilionoideae, was the most specious family in the deciduous forest while Meliaceae was the dominant family in the gallery forest. Similarity in species composition and abundance between deciduous and gallery forests was low. In terms of species diversity, the gallery forest was found more diverse than the deciduous forest using Fisher's diversity index. Both forest communities were characterized by a typical inverse J shape. Therefore, emphasis should be given to the protection of rare species, i.e. as the forests are still under continued human pressure, an immediate action should be taken to conserve the remaining flora.

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

@article{hedman_proteomic_2006,
	title = {Proteomic identification of glucocorticoid receptor interacting proteins},
	volume = {6},
	issn = {1615-9853},
	doi = {10.1002/pmic.200500266},
	abstract = {The glucocorticoid receptor (GR) acts as a ligand dependent transcription factor but can also cross talk with other signaling pathways via protein-protein interactions. In this paper we describe methods to study novel cytosolic GR interacting proteins, using mAb based immunoaffinity chromatography of GR from rat liver cytosol. Co-purifying proteins were identified by 2-DE in combination with MALDI-TOF-MS. Non-liganded/non-activated and in vitro liganded/ activated GR, respectively, co-purifies with specific sets of proteins. Of these 34 were conclusively identified, seven have previously been reported to be part of the GR-complex, revealing 27 new possible interacting candidates for the GR-complex. Of the novel GR interacting proteins the major vault protein, TATA binding interacting protein 49a and glycoprotein PP63 were of special interest. Furthermore, using 2-D DIGE we show that the set of proteins interacting with nonliganded GR is distinctly different in protein amount compared to the proteins found with liganded/activated GR. This suggests the presence of different GR complexes in the cell, which was further substantiated by the finding of several separate GR native protein complexes, "GR-receptosomes", using blue native gel electrophoresis. Our findings suggest the existence of several new mechanisms for GR signaling and regulation.},
	language = {English},
	number = {10},
	journal = {Proteomics},
	author = {Hedman, Erik and Widen, Christina and Asadi, Abolfazl and Dinnetz, Ingrid and Schroder, Wolfgang P. and Gustafsson, Jan-ke and Wikstrom, Ann-Charlotte},
	month = may,
	year = {2006},
	note = {Place: Hoboken
Publisher: Wiley
WOS:000238010400018},
	keywords = {2-D blue native-PAGE, 2-d dige, 2-de, Animals, Antibodies, Monoclonal, Cell Line, Tumor, Chromatography, Affinity, Cytosol, Electrophoresis, Gel, Two-Dimensional, Electrophoresis, Polyacrylamide Gel, Immunoblotting, Ligands, Liver, Protein Interaction Mapping, Proteome, Rats, Receptors, Glucocorticoid, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, dna-binding, electrophoresis, glucocorticoid receptor, heat-shock-protein, kappa-b, living cells, localization, maldi-tof, mechanism, polyacrylamide-gels, rat, tyrosine kinase},
	pages = {3114--3126},
}

The glucocorticoid receptor (GR) acts as a ligand dependent transcription factor but can also cross talk with other signaling pathways via protein-protein interactions. In this paper we describe methods to study novel cytosolic GR interacting proteins, using mAb based immunoaffinity chromatography of GR from rat liver cytosol. Co-purifying proteins were identified by 2-DE in combination with MALDI-TOF-MS. Non-liganded/non-activated and in vitro liganded/ activated GR, respectively, co-purifies with specific sets of proteins. Of these 34 were conclusively identified, seven have previously been reported to be part of the GR-complex, revealing 27 new possible interacting candidates for the GR-complex. Of the novel GR interacting proteins the major vault protein, TATA binding interacting protein 49a and glycoprotein PP63 were of special interest. Furthermore, using 2-D DIGE we show that the set of proteins interacting with nonliganded GR is distinctly different in protein amount compared to the proteins found with liganded/activated GR. This suggests the presence of different GR complexes in the cell, which was further substantiated by the finding of several separate GR native protein complexes, "GR-receptosomes", using blue native gel electrophoresis. Our findings suggest the existence of several new mechanisms for GR signaling and regulation.

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

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

@article{horvath_ebp1_2006,
	title = {{EBP1} regulates organ size through cell growth and proliferation in plants},
	volume = {25},
	issn = {0261-4189},
	url = {https://www.embopress.org/doi/full/10.1038/sj.emboj.7601362},
	doi = {10.1038/sj.emboj.7601362},
	abstract = {Plant organ size shows remarkable uniformity within species indicating strong endogenous control. We have identified a plant growth regulatory gene, functionally and structurally homologous to human EBP1. Plant EBP1 levels are tightly regulated; gene expression is highest in developing organs and correlates with genes involved in ribosome biogenesis and function. EBP1 protein is stabilised by auxin. Elevating or decreasing EBP1 levels in transgenic plants results in a dose-dependent increase or reduction in organ growth, respectively. During early stages of organ development, EBP1 promotes cell proliferation, influences cell-size threshold for division and shortens the period of meristematic activity. In postmitotic cells, it enhances cell expansion. EBP1 is required for expression of cell cycle genes; CyclinD3;1, ribonucleotide reductase 2 and the cyclin-dependent kinase B1;1. The regulation of these genes by EBP1 is dose and auxin dependent and might rely on the effect of EBP1 to reduce RBR1 protein level. We argue that EBP1 is a conserved, dose-dependent regulator of cell growth that is connected to meristematic competence and cell proliferation via regulation of RBR1 level.},
	number = {20},
	urldate = {2021-06-11},
	journal = {The EMBO Journal},
	author = {Horváth, Beatrix M and Magyar, Zoltán and Zhang, Yuexing and Hamburger, Anne W and Bakó, László and Visser, Richard GF and Bachem, Christian WB and Bögre, László},
	month = oct,
	year = {2006},
	note = {Publisher: John Wiley \& Sons, Ltd},
	keywords = {EBP1, arabidopsis, cell growth, cell proliferation, cycle regulation, differential gene-expression, division, ebp1, erbb-3   binding-protein, expansion, leaf, organ growth, organogenesis, potato-tuber development, ribosome biogenesis, transcription factor},
	pages = {4909--4920},
}

Plant organ size shows remarkable uniformity within species indicating strong endogenous control. We have identified a plant growth regulatory gene, functionally and structurally homologous to human EBP1. Plant EBP1 levels are tightly regulated; gene expression is highest in developing organs and correlates with genes involved in ribosome biogenesis and function. EBP1 protein is stabilised by auxin. Elevating or decreasing EBP1 levels in transgenic plants results in a dose-dependent increase or reduction in organ growth, respectively. During early stages of organ development, EBP1 promotes cell proliferation, influences cell-size threshold for division and shortens the period of meristematic activity. In postmitotic cells, it enhances cell expansion. EBP1 is required for expression of cell cycle genes; CyclinD3;1, ribonucleotide reductase 2 and the cyclin-dependent kinase B1;1. The regulation of these genes by EBP1 is dose and auxin dependent and might rely on the effect of EBP1 to reduce RBR1 protein level. We argue that EBP1 is a conserved, dose-dependent regulator of cell growth that is connected to meristematic competence and cell proliferation via regulation of RBR1 level.

@article{igamberdiev_equilibration_2006,
	title = {Equilibration of adenylates in the mitochondrial intermembrane space maintains respiration and regulates cytosolic metabolism},
	volume = {57},
	issn = {0022-0957},
	doi = {10.1093/jxb/erl006},
	abstract = {Adenylate kinase (AK) uses one each of Mg-complexed and free adenylates as substrates in both directions of its reaction. It is very active in the mitochondrial intermembrane space (IMS), but is absent from the mitochondrial matrix where low [ADP] upon intensive respiration limits the respiratory rate. AK activity in the IMS is linked to ATP/ADP exchange across the inner mitochondrial membrane by using ATP (imported from the matrix) and AMP as substrates, the latter provided by apyrase and other AMP-generating reactions. The ADP formed by AK is exported to the matrix (in exchange for ATP), providing a mechanism for regeneration of ADP during respiration. From the AK equilibrium, and taking pH values characteristic of subcellular compartments, [Mg2+] in the IMS is calculated as 0.4-0.5 mM and in the cytosol as 0.2-0.3 mM, whereas the MgATP:MgADP ratio in the IMS and cytosol is 6-9 and 10-15, respectively. These represent optimal conditions for transport of adenylates (via the maintenance of an ATP(free):ADP(free) ratio close to 1) and mitochondrial respiratory rates (via the maintenance of submillimolar [ADP(free)] in the IMS). This, in turn, has important consequences for mitochondrial and cytosolic metabolism, including regulation of the protein phosphorylation rate (via changes in the MgATP:AMP(free) ratio) and allosteric regulation of mitochondrial and cytosolic enzymes. Metabolomic consequences are discussed in connection with the calculation of metabolic fluxes from subcompartmental distributions of total adenylates and Mg2+.},
	language = {English},
	number = {10},
	journal = {Journal of Experimental Botany},
	author = {Igamberdiev, Abir U. and Kleczkowski, Leszek A.},
	year = {2006},
	note = {Place: Oxford
Publisher: Oxford Univ Press
WOS:000239389700001},
	keywords = {activated protein-kinase, adenylate kinase, apyrase, atp synthase, dynamic compartmentation, energy-charge, free magnesium, glutamine-synthetase, intermembrane space, magnesium, metabolomics, mitochondrion, oxidative-phosphorylation, pisum-sativum, plant-cells, respiration, spinach-chloroplasts},
	pages = {2133--2141},
}

Adenylate kinase (AK) uses one each of Mg-complexed and free adenylates as substrates in both directions of its reaction. It is very active in the mitochondrial intermembrane space (IMS), but is absent from the mitochondrial matrix where low [ADP] upon intensive respiration limits the respiratory rate. AK activity in the IMS is linked to ATP/ADP exchange across the inner mitochondrial membrane by using ATP (imported from the matrix) and AMP as substrates, the latter provided by apyrase and other AMP-generating reactions. The ADP formed by AK is exported to the matrix (in exchange for ATP), providing a mechanism for regeneration of ADP during respiration. From the AK equilibrium, and taking pH values characteristic of subcellular compartments, [Mg2+] in the IMS is calculated as 0.4-0.5 mM and in the cytosol as 0.2-0.3 mM, whereas the MgATP:MgADP ratio in the IMS and cytosol is 6-9 and 10-15, respectively. These represent optimal conditions for transport of adenylates (via the maintenance of an ATP(free):ADP(free) ratio close to 1) and mitochondrial respiratory rates (via the maintenance of submillimolar [ADP(free)] in the IMS). This, in turn, has important consequences for mitochondrial and cytosolic metabolism, including regulation of the protein phosphorylation rate (via changes in the MgATP:AMP(free) ratio) and allosteric regulation of mitochondrial and cytosolic enzymes. Metabolomic consequences are discussed in connection with the calculation of metabolic fluxes from subcompartmental distributions of total adenylates and Mg2+.

@article{ingvarsson_clinal_2006,
	title = {Clinal variation in {phyB2}, a candidate gene for day-length-induced growth cessation and bud set, across a latitudinal gradient in {European} aspen ({Populus} tremula)},
	volume = {172},
	issn = {0016-6731},
	doi = {10.1534/genetics.105.047522},
	abstract = {The initiation of growth cessation and dormancy represents a Critical ecological and evolutionary tradeoff between survival and growth in most. forest trees. The Most important environmental cue regulating the initiation of dormancy is a shortening of the photoperiod and phytochrome genes have been implicated in short-day-induced bud set and growth cessation in Populus. We characterized patterns of DNA sequence variation at the putative candidate gene phyB2 in 4 populations of European aspen (Populus tremula) and scored single-nucleotide polymorphisms in an additional 12 populations collected along a latitudinal gradient in Sweden. We also measured bud set from a subset Of these trees in a growth chamber experiment. Buds set. showed significant clinal variation With latitude, explaining similar to 90\% Of the population variation in bud Set. A sliding-window scan of phyB2 identified six putative regions with enhanced population differentiation and four SNPs showed significant clinal variation. The clinal variation at individual SNPs is suggestive of all adaptive response in phyB2 to local photoperiodic conditions. Three of four SNPs showing clinal variation were located in regions With excessive genetic differentiation, demonstrating that searching for regions of high genetic differentiation call be useful for identifying sites putatively involved in local adaptation.},
	language = {English},
	number = {3},
	journal = {Genetics},
	author = {Ingvarsson, P. K. and Garcia, M. V. and Hall, D. and Luquez, V. and Jansson, S.},
	month = mar,
	year = {2006},
	note = {Place: Bethesda
Publisher: Genetics Society America
WOS:000236668100040},
	keywords = {adaptation, arabidopsis, coalescent, linkage disequilibrium, nucleotide diversity, phenology, polymorphism, populations, quantitative trait loci, selection},
	pages = {1845--1853},
}

The initiation of growth cessation and dormancy represents a Critical ecological and evolutionary tradeoff between survival and growth in most. forest trees. The Most important environmental cue regulating the initiation of dormancy is a shortening of the photoperiod and phytochrome genes have been implicated in short-day-induced bud set and growth cessation in Populus. We characterized patterns of DNA sequence variation at the putative candidate gene phyB2 in 4 populations of European aspen (Populus tremula) and scored single-nucleotide polymorphisms in an additional 12 populations collected along a latitudinal gradient in Sweden. We also measured bud set from a subset Of these trees in a growth chamber experiment. Buds set. showed significant clinal variation With latitude, explaining similar to 90% Of the population variation in bud Set. A sliding-window scan of phyB2 identified six putative regions with enhanced population differentiation and four SNPs showed significant clinal variation. The clinal variation at individual SNPs is suggestive of all adaptive response in phyB2 to local photoperiodic conditions. Three of four SNPs showing clinal variation were located in regions With excessive genetic differentiation, demonstrating that searching for regions of high genetic differentiation call be useful for identifying sites putatively involved in local adaptation.

@article{ivanov_digalactosyl-diacylglycerol_2006,
	title = {Digalactosyl-diacylglycerol deficiency impairs the capacity for photosynthetic intersystem electron transport and state transitions in {Arabidopsis} thaliana due to photosystem {I} acceptor-side limitations},
	volume = {47},
	issn = {0032-0781},
	doi = {10.1093/pcp/pcj089},
	abstract = {Compared with wild type, the dgd1 mutant of Arabidopsis thaliana exhibited a lower amount of PSI-related Chl-protein complexes and lower abundance of the PSI-associated polypeptides, PsaA, PsaB, PsaC, PsaL and PsaH, with no changes in the levels of Lhca1-4. Functionally, the dgd1 mutant exhibited a significantly lower light-dependent, steady-state oxidation level of P700 (P700(+)) in vivo, a higher intersystem electron pool size, restricted linear electron transport and a higher rate of reduction of P700(+) in the dark, indicating an increased capacity for PSI cyclic electron transfer compared with the wild type. Concomitantly, the dgd1 mutant exhibited a higher sensitivity to and incomplete recovery of photoinhibition of PSI. Furthermore, dgd1 exhibited a lower capacity to undergo state transitions compared with the wild type, which was associated with a higher reduction state of the plastoquinone (PQ) pool. We conclude that digalactosyl-diacylglycerol (DGDG) deficiency results in PSI acceptor-side limitations that alter the flux of electrons through the photosynthetic electron chain and impair the regulation of distribution of excitation energy between the photosystems. These results are discussed in terms of thylakoid membrane domain reorganization in response to DGDG deficiency in A. thaliana.},
	language = {eng},
	number = {8},
	journal = {Plant \& Cell Physiology},
	author = {Ivanov, Alexander G. and Hendrickson, Luke and Krol, Marianna and Selstam, Eva and Oquist, Gunnar and Hurry, Vaughan and Huner, Norman P. A.},
	month = aug,
	year = {2006},
	pmid = {16854937},
	keywords = {Arabidopsis, Arabidopsis dgd1 mutant, Electron Transport, Galactolipids, Photosynthesis, Photosystem I Protein Complex, Thylakoids, chlorophyll fluorescence, dgd1 mutant, digalactosyl-diacylglycerol, excitation-energy, leaves, light-harvesting complex, lipid-content, membranes, p700, photoinhibition, plants, protein, redox state, state transitions},
	pages = {1146--1157},
}

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

@article{ivanov_iron_2006,
	title = {Iron {Deficiency} in {Cyanobacteria} {Causes} {Monomerization} of {Photosystem} {I} {Trimers} and {Reduces} the {Capacity} for {State} {Transitions} and the {Effective} {Absorption} {Cross} {Section} of {Photosystem} {I} in {Vivo}},
	volume = {141},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.106.082339},
	doi = {10.1104/pp.106.082339},
	abstract = {The induction of the isiA (CP43′) protein in iron-stressed cyanobacteria is accompanied by the formation of a ring of 18 CP43′ proteins around the photosystem I (PSI) trimer and is thought to increase the absorption cross section of PSI within the CP43′-PSI supercomplex. In contrast to these in vitro studies, our in vivo measurements failed to demonstrate any increase of the PSI absorption cross section in two strains (Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803) of iron-stressed cells. We report that iron-stressed cells exhibited a reduced capacity for state transitions and limited dark reduction of the plastoquinone pool, which accounts for the increase in PSII-related 685 nm chlorophyll fluorescence under iron deficiency. This was accompanied by lower abundance of the NADP-dehydrogenase complex and the PSI-associated subunit PsaL, as well as a reduced amount of phosphatidylglycerol. Nondenaturating polyacrylamide gel electrophoresis separation of the chlorophyll-protein complexes indicated that the monomeric form of PSI is favored over the trimeric form of PSI under iron stress. Thus, we demonstrate that the induction of CP43′ does not increase the PSI functional absorption cross section of whole cells in vivo, but rather, induces monomerization of PSI trimers and reduces the capacity for state transitions. We discuss the role of CP43′ as an effective energy quencher to photoprotect PSII and PSI under unfavorable environmental conditions in cyanobacteria in vivo.},
	number = {4},
	urldate = {2021-06-11},
	journal = {Plant Physiology},
	author = {Ivanov, Alexander G. and Krol, Marianna and Sveshnikov, Dmitry and Selstam, Eva and Sandström, Stefan and Koochek, Maryam and Park, Youn-Il and Vasil'ev, Sergej and Bruce, Doug and Öquist, Gunnar and Huner, Norman P.A.},
	month = aug,
	year = {2006},
	pages = {1436--1445},
}

The induction of the isiA (CP43′) protein in iron-stressed cyanobacteria is accompanied by the formation of a ring of 18 CP43′ proteins around the photosystem I (PSI) trimer and is thought to increase the absorption cross section of PSI within the CP43′-PSI supercomplex. In contrast to these in vitro studies, our in vivo measurements failed to demonstrate any increase of the PSI absorption cross section in two strains (Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803) of iron-stressed cells. We report that iron-stressed cells exhibited a reduced capacity for state transitions and limited dark reduction of the plastoquinone pool, which accounts for the increase in PSII-related 685 nm chlorophyll fluorescence under iron deficiency. This was accompanied by lower abundance of the NADP-dehydrogenase complex and the PSI-associated subunit PsaL, as well as a reduced amount of phosphatidylglycerol. Nondenaturating polyacrylamide gel electrophoresis separation of the chlorophyll-protein complexes indicated that the monomeric form of PSI is favored over the trimeric form of PSI under iron stress. Thus, we demonstrate that the induction of CP43′ does not increase the PSI functional absorption cross section of whole cells in vivo, but rather, induces monomerization of PSI trimers and reduces the capacity for state transitions. We discuss the role of CP43′ as an effective energy quencher to photoprotect PSII and PSI under unfavorable environmental conditions in cyanobacteria in vivo.

@article{jonsson_predictive_2006,
	title = {Predictive metabolite profiling applying hierarchical multivariate curve resolution to {GC}-{MS} datas - {A} potential tool for multi-parametric diagnosis},
	volume = {5},
	issn = {1535-3893},
	doi = {10.1021/pr0600071},
	abstract = {A method for predictive metabolite profiling based on resolution of GC-MS data followed by multivariate data analysis is presented and applied to three different biofluid data sets (rat urine, aspen leaf extracts, and human blood plasma). Hierarchical multivariate curve resolution (H-MCR) was used to simultaneously resolve the GC-MS data into pure profiles, describing the relative metabolite concentrations between samples, for multivariate analysis. Here, we present an extension of the H-MCR method allowing treatment of independent samples according to processing parameters estimated from a set of training samples. Predictions or inclusion of the new samples, based on their metabolite profiles, into an existing model could then be carried out, which is a requirement for a working application within, e. g., clinical diagnosis. Apart from allowing treatment and prediction of independent samples the proposed method also reduces the time for the curve resolution process since only a subset of representative samples have to be processed while the remaining samples can be treated according to the obtained processing parameters. The time required for resolving the 30 training samples in the rat urine example was approximately 13 h, while the treatment of the 30 test samples according to the training parameters required only approximately 30 s per sample ( similar to 15 min in total). In addition, the presented results show that the suggested approach works for describing metabolic changes in different biofluids, indicating that this is a general approach for high-throughput predictive metabolite profiling, which could have important applications in areas such as plant functional genomics, drug toxicity, treatment efficacy and early disease diagnosis.},
	language = {English},
	number = {6},
	journal = {Journal of Proteome Research},
	author = {Jonsson, Par and Johansson, Elin Sjovik and Wuolikainen, Anna and Lindberg, Johan and Schuppe-Koistinen, Ina and Kusano, Miyako and Sjostrom, Michael and Trygg, Johan and Moritz, Thomas and Antti, Henrik},
	month = jun,
	year = {2006},
	note = {Place: Washington
Publisher: Amer Chemical Soc
WOS:000237973400012},
	keywords = {chemometrics, chromatography, clinical diagnosis, components, curve resolution, design, gc-ms, genomics, h-mcr, high-throughput, identifying differences, metabolic profiling, metabolomics, metabonomics, o-pls, projections, samples, strategy},
	pages = {1407--1414},
}

A method for predictive metabolite profiling based on resolution of GC-MS data followed by multivariate data analysis is presented and applied to three different biofluid data sets (rat urine, aspen leaf extracts, and human blood plasma). Hierarchical multivariate curve resolution (H-MCR) was used to simultaneously resolve the GC-MS data into pure profiles, describing the relative metabolite concentrations between samples, for multivariate analysis. Here, we present an extension of the H-MCR method allowing treatment of independent samples according to processing parameters estimated from a set of training samples. Predictions or inclusion of the new samples, based on their metabolite profiles, into an existing model could then be carried out, which is a requirement for a working application within, e. g., clinical diagnosis. Apart from allowing treatment and prediction of independent samples the proposed method also reduces the time for the curve resolution process since only a subset of representative samples have to be processed while the remaining samples can be treated according to the obtained processing parameters. The time required for resolving the 30 training samples in the rat urine example was approximately 13 h, while the treatment of the 30 test samples according to the training parameters required only approximately 30 s per sample ( similar to 15 min in total). In addition, the presented results show that the suggested approach works for describing metabolic changes in different biofluids, indicating that this is a general approach for high-throughput predictive metabolite profiling, which could have important applications in areas such as plant functional genomics, drug toxicity, treatment efficacy and early disease diagnosis.

@article{keller_arabidopsis_2006,
	title = {Arabidopsis {REGULATOR} {OF} {AXILLARY} {MERISTEMS1} controls a leaf axil stem cell niche and modulates vegetative development},
	volume = {18},
	issn = {1040-4651},
	doi = {10.1105/tpc.105.038588},
	abstract = {Shoot branching is a major determinant of variation in plant stature. Branches, which form secondary growth axes, originate from stem cells activated in leaf axils. The initial steps by which axillary meristems (AMs) are specified and their stem cells organized are still poorly understood. We identified gain- and loss-of-function alleles at the Arabidopsis thaliana REGULATOR OF AXILLARY MERISTEMS1 (RAX1) locus. RAX1 is encoded by the Myb-like transcription factor MYB37 and is an Arabidopsis homolog of the tomato ( Solanum lycopersicum) Blind gene. RAX1 is transiently expressed in a small central domain within the boundary zone separating shoot apical meristem and leaf primordia early in leaf primordium development. RAX1 genetically interacts with CUP-SHAPED COTYLEDON (CUC) genes and is required for the expression of CUC2 in the RAX1 expression domain, suggesting that RAX1 acts through CUC2. We propose that RAX1 functions to positionally specify a stem cell niche for AM formation. RAX1 also affects the timing of developmental phase transitions by negatively regulating gibberellic acid levels in the shoot apex. RAX1 thus defines a novel activity that links the specification of AM formation with the modulation of the rate of progression through developmental phases.},
	language = {English},
	number = {3},
	journal = {Plant Cell},
	author = {Keller, T. and Abbott, J. and Moritz, T. and Doerner, P.},
	month = mar,
	year = {2006},
	note = {Place: Rockville
Publisher: Amer Soc Plant Biologists
WOS:000236004900009},
	keywords = {arabidopsis-thaliana, cup-shaped-cotyledon, expression, gene   family, gibberellin, growth, initiation, organogenesis, shoot apical meristem, t-dna},
	pages = {598--611},
}

Shoot branching is a major determinant of variation in plant stature. Branches, which form secondary growth axes, originate from stem cells activated in leaf axils. The initial steps by which axillary meristems (AMs) are specified and their stem cells organized are still poorly understood. We identified gain- and loss-of-function alleles at the Arabidopsis thaliana REGULATOR OF AXILLARY MERISTEMS1 (RAX1) locus. RAX1 is encoded by the Myb-like transcription factor MYB37 and is an Arabidopsis homolog of the tomato ( Solanum lycopersicum) Blind gene. RAX1 is transiently expressed in a small central domain within the boundary zone separating shoot apical meristem and leaf primordia early in leaf primordium development. RAX1 genetically interacts with CUP-SHAPED COTYLEDON (CUC) genes and is required for the expression of CUC2 in the RAX1 expression domain, suggesting that RAX1 acts through CUC2. We propose that RAX1 functions to positionally specify a stem cell niche for AM formation. RAX1 also affects the timing of developmental phase transitions by negatively regulating gibberellic acid levels in the shoot apex. RAX1 thus defines a novel activity that links the specification of AM formation with the modulation of the rate of progression through developmental phases.

@article{kovacs_lack_2006,
	title = {Lack of the {Light}-{Harvesting} {Complex} {CP24} {Affects} the {Structure} and {Function} of the {Grana} {Membranes} of {Higher} {Plant} {Chloroplasts}},
	volume = {18},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.106.045641},
	doi = {10.1105/tpc.106.045641},
	abstract = {The photosystem II (PSII) light-harvesting antenna in higher plants contains a number of highly conserved gene products whose function is unknown. Arabidopsis thaliana plants depleted of one of these, the CP24 light-harvesting complex, have been analyzed. CP24-deficient plants showed a decrease in light-limited photosynthetic rate and growth, but the pigment and protein content of the thylakoid membranes were otherwise almost unchanged. However, there was a major change in the macroorganization of PSII within these membranes; electron microscopy and image analysis revealed the complete absence of the C2S2M2 light-harvesting complex II (LHCII)/PSII supercomplex predominant in wild-type plants. Instead, only C2S2 supercomplexes, which are deficient in the LHCIIb M-trimers, were found. Spectroscopic analysis confirmed the disruption of the wild-type macroorganization of PSII. It was found that the functions of the PSII antenna were disturbed: connectivity between PSII centers was reduced, and maximum photochemical yield was lowered; rapidly reversible nonphotochemical quenching was inhibited; and the state transitions were altered kinetically. CP24 is therefore an important factor in determining the structure and function of the PSII light-harvesting antenna, providing the linker for association of the M-trimer into the PSII complex, allowing a specific macroorganization that is necessary both for maximum quantum efficiency and for photoprotective dissipation of excess excitation energy.},
	number = {11},
	urldate = {2021-06-11},
	journal = {The Plant Cell},
	author = {Kovács, László and Damkjær, Jakob and Kereïche, Sami and Ilioaia, Cristian and Ruban, Alexander V. and Boekema, Egbert J. and Jansson, Stefan and Horton, Peter},
	month = nov,
	year = {2006},
	pages = {3106--3120},
}

The photosystem II (PSII) light-harvesting antenna in higher plants contains a number of highly conserved gene products whose function is unknown. Arabidopsis thaliana plants depleted of one of these, the CP24 light-harvesting complex, have been analyzed. CP24-deficient plants showed a decrease in light-limited photosynthetic rate and growth, but the pigment and protein content of the thylakoid membranes were otherwise almost unchanged. However, there was a major change in the macroorganization of PSII within these membranes; electron microscopy and image analysis revealed the complete absence of the C2S2M2 light-harvesting complex II (LHCII)/PSII supercomplex predominant in wild-type plants. Instead, only C2S2 supercomplexes, which are deficient in the LHCIIb M-trimers, were found. Spectroscopic analysis confirmed the disruption of the wild-type macroorganization of PSII. It was found that the functions of the PSII antenna were disturbed: connectivity between PSII centers was reduced, and maximum photochemical yield was lowered; rapidly reversible nonphotochemical quenching was inhibited; and the state transitions were altered kinetically. CP24 is therefore an important factor in determining the structure and function of the PSII light-harvesting antenna, providing the linker for association of the M-trimer into the PSII complex, allowing a specific macroorganization that is necessary both for maximum quantum efficiency and for photoprotective dissipation of excess excitation energy.

@article{kruys_phylogenetic_2006,
	title = {Phylogenetic relationships of coprophilous {Pleosporales} ({Dothideomycetes}, {Ascomycota}), and the classification of some bitunicate taxa of unknown position},
	volume = {110},
	issn = {0953-7562},
	doi = {10.1016/j.mycres.2006.03.002},
	abstract = {The purpose of this study was to investigate the natural relationships within the large bitunicate order Pleosporales, with special focus on the coprophilous families Delitschiaceae, Phaeotrichaceae and Sporormiaceae. Parsimony and Bayesian analyses were performed using nSSU, nLSU and mtSSU rDNA sequence data. We also investigated the placement of a number of taxa with uncertain position. Our results showed that Pleosporales, including Delitschiaceae, Sporormiaceae, Zopfiaceae and Testudiriaceae, form a monophyletic group with strong support. Although Delitschiaceae has been considered a synonym of Sporormiaceae, the two families do not form one monophyletic group. Similarly, Zopfiaceae and Testudinaceae should be retained as separate families as they did not group together or with Phaeotrichaceae or Sporormiaceae. Zopfiaceae and Delitchiaceae did group together, but without significant support. Eremodothis angulata (currently in Testudinaceae) is closely related to Westerdykella in Sporormiaceae. Phaeotrichaceae and Venturiaceae formed a group with strong BS support on a branch outside Pleosporales, but an alternative topology including Phaeotrichaceae and Venturiaceae within Pleospotales could not be rejected. All taxa in the present study that were placed with uncertain position in Dothideomycetes/Chaetothyriomycetes in the current classification by Eriksson, grouped within the monophyletic Dothideomycetes. (c) 2006 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.},
	language = {English},
	journal = {Mycological Research},
	author = {Kruys, Asa and Eriksson, Ove E. and Wedin, Mats},
	month = may,
	year = {2006},
	note = {Patent Number: 5
Place: Oxford
Publisher: Elsevier Sci Ltd
WOS:000239396700004},
	keywords = {18S rDNA, 26S rDNA, Loculoascomycetes, amplification, evolution, fungi, genus, lsu rdna, origins, pcr primers, performance, phylogenentics, ribosomal dna, sequences, ssu, systematics},
	pages = {527--536},
}

The purpose of this study was to investigate the natural relationships within the large bitunicate order Pleosporales, with special focus on the coprophilous families Delitschiaceae, Phaeotrichaceae and Sporormiaceae. Parsimony and Bayesian analyses were performed using nSSU, nLSU and mtSSU rDNA sequence data. We also investigated the placement of a number of taxa with uncertain position. Our results showed that Pleosporales, including Delitschiaceae, Sporormiaceae, Zopfiaceae and Testudiriaceae, form a monophyletic group with strong support. Although Delitschiaceae has been considered a synonym of Sporormiaceae, the two families do not form one monophyletic group. Similarly, Zopfiaceae and Testudinaceae should be retained as separate families as they did not group together or with Phaeotrichaceae or Sporormiaceae. Zopfiaceae and Delitchiaceae did group together, but without significant support. Eremodothis angulata (currently in Testudinaceae) is closely related to Westerdykella in Sporormiaceae. Phaeotrichaceae and Venturiaceae formed a group with strong BS support on a branch outside Pleosporales, but an alternative topology including Phaeotrichaceae and Venturiaceae within Pleospotales could not be rejected. All taxa in the present study that were placed with uncertain position in Dothideomycetes/Chaetothyriomycetes in the current classification by Eriksson, grouped within the monophyletic Dothideomycetes. (c) 2006 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

@article{lamien_mistletoe_2006,
	title = {Mistletoe impact on {Shea} tree ({Vitellaria} paradoxa {C}.{F}. {Gaertn}.) flowering and fruiting behaviour in savanna area from {Burkina} {Faso}},
	volume = {55},
	issn = {0098-8472},
	url = {https://www.sciencedirect.com/science/article/pii/S0098847204001364},
	doi = {10.1016/j.envexpbot.2004.10.010},
	abstract = {Vitellaria paradoxa C.F. Gaertn., Sapotaceae family, is a characteristic species of the woody flora in savanna woodland of Africa. The fresh pulp of its fruits and the butter extracted from the kernels play an important social and economic role in rural areas. However, about 95\% of the trees in natural stands are infected with Mistletoes, which are plant parasites. The objective of this study was to assess the impact of this type of parasite on the flowering and fruiting behaviour of the infected branches. For the flowering and fruiting follow-up, 46 infected branches and 46 healthy ones selected on 30 trees located in cropping areas were tagged. The infected branch diameters before and after the attachment point of the parasite and the size of the stump of the parasite were measured. The number of reproductive organs of the on-year fruit bearing shoots was counted each week during the blossom period. Pearson's correlation coefficients were estimated to measure the association between the infected branch morphological parameters and the number of reproductive organs. General Linear Model ANOVA and Student's paired sample test were performed to compare the reproduction index of the infected to healthy branches. The data did not show sufficient evidence that indicate negative association between the infected branch morphological parameters and the reproduction index. No significant difference was observed between the flowering and fruiting behaviour of infected branches and that of healthy ones. The possible reasons of these results are discussed.},
	language = {en},
	number = {1},
	urldate = {2021-06-11},
	journal = {Environmental and Experimental Botany},
	author = {Lamien, N. and Boussim, J. I. and Nygard, R. and Ouédraogo, J. S. and Odén, P. C. and Guinko, S.},
	month = jan,
	year = {2006},
	keywords = {Burkina Faso, Fruit production, Impact, Mistletoes},
	pages = {142--148},
}

Vitellaria paradoxa C.F. Gaertn., Sapotaceae family, is a characteristic species of the woody flora in savanna woodland of Africa. The fresh pulp of its fruits and the butter extracted from the kernels play an important social and economic role in rural areas. However, about 95% of the trees in natural stands are infected with Mistletoes, which are plant parasites. The objective of this study was to assess the impact of this type of parasite on the flowering and fruiting behaviour of the infected branches. For the flowering and fruiting follow-up, 46 infected branches and 46 healthy ones selected on 30 trees located in cropping areas were tagged. The infected branch diameters before and after the attachment point of the parasite and the size of the stump of the parasite were measured. The number of reproductive organs of the on-year fruit bearing shoots was counted each week during the blossom period. Pearson's correlation coefficients were estimated to measure the association between the infected branch morphological parameters and the number of reproductive organs. General Linear Model ANOVA and Student's paired sample test were performed to compare the reproduction index of the infected to healthy branches. The data did not show sufficient evidence that indicate negative association between the infected branch morphological parameters and the reproduction index. No significant difference was observed between the flowering and fruiting behaviour of infected branches and that of healthy ones. The possible reasons of these results are discussed.

@article{loha_provenance_2006,
	title = {Provenance variation in seed morphometric traits, germination, and seedling growth of {Cordia} africana {Lam}},
	volume = {32},
	issn = {0169-4286},
	doi = {10.1007/s11056-005-3872-2},
	abstract = {Patterns of genetic variation in Cordia africana, a tropical timber species, were evaluated at the population level. Bulk seed samples were collected from six natural populations in Ethiopia and examined for variations in seed morphometric traits, seed germination, and seedling growth at nursery stage. Analysis of variance revealed significant differences among provenances in all studied attributes except root collar diameter after 4 months of growth. The provenance effect, as determined by broad sense heritability, was 71-98\% for seed morphometric traits, 80\% for germination capacity, 42\% for germination energy, 57-58\% for seedling height and 3-13\% for root collar diameter. Seed weight showed a significant positive correlation with altitude and negative correlation with mean annual temperature of seed origin. Germination energy was significantly correlated with longitude and mean annual rainfall. Seedling parameters and geo-climatic variables of seed origin were fairly correlated. A significant intercharacter correlation was found between seed length and seed weight, between root collar diameter at the age of 4 months and seed length and weight, as well as between seedling height after 4 and 8 months of growth. It can be concluded that the observed patterns of variation will have implications for genetic resources conservation and tree improvement.},
	language = {English},
	number = {1},
	journal = {New Forests},
	author = {Loha, Abraham and Tigabu, Mulualem and Teketay, Demel and Lundkvist, Kenneth and Fries, Anders},
	month = jul,
	year = {2006},
	note = {Place: Dordrecht
Publisher: Springer
WOS:000238780200006},
	keywords = {Ethiopia, attributes, clones, ethiopia, frost hardiness, genetic variation, genetic-variation, gmelina-arborea, growth capacity, populations, seed weight, selection, tree, trials, tropical   trees, viability},
	pages = {71--86},
}

Patterns of genetic variation in Cordia africana, a tropical timber species, were evaluated at the population level. Bulk seed samples were collected from six natural populations in Ethiopia and examined for variations in seed morphometric traits, seed germination, and seedling growth at nursery stage. Analysis of variance revealed significant differences among provenances in all studied attributes except root collar diameter after 4 months of growth. The provenance effect, as determined by broad sense heritability, was 71-98% for seed morphometric traits, 80% for germination capacity, 42% for germination energy, 57-58% for seedling height and 3-13% for root collar diameter. Seed weight showed a significant positive correlation with altitude and negative correlation with mean annual temperature of seed origin. Germination energy was significantly correlated with longitude and mean annual rainfall. Seedling parameters and geo-climatic variables of seed origin were fairly correlated. A significant intercharacter correlation was found between seed length and seed weight, between root collar diameter at the age of 4 months and seed length and weight, as well as between seedling height after 4 and 8 months of growth. It can be concluded that the observed patterns of variation will have implications for genetic resources conservation and tree improvement.

@article{mateo_controlled_2006,
	title = {Controlled levels of salicylic acid are required for optimal photosynthesis and redox homeostasis},
	volume = {57},
	issn = {0022-0957},
	doi = {10.1093/jxb/erj196},
	abstract = {Sudden exposure of plants to high light (HL) leads to metabolic and physiological disruption of the photosynthetic cells. Changes in ROS content, adjustment of photosynthetic processes and the antioxidant pools and, ultimately, gene induction are essential components for a successful acclimation to the new light conditions. The influence of salicylic acid (SA) on plant growth, short-term acclimation to HL, and on the redox homeostasis of Arabidopsis thaliana leaves was assessed here. The dwarf phenotype displayed by mutants with high SA content (cpr1-1, cpr5-1, cpr6-1, and dnd1-1) was less pronounced when these plants were grown in HL, suggesting that the inhibitory effect of SA on growth was partly overcome at higher light intensities. Moreover, higher SA content affected energy conversion processes in low light, but did not impair short-term acclimation to HL. On the other hand, mutants with low foliar SA content (NahG and sid2-2) were impaired in acclimation to transient exposure to HL and thus predisposed to oxidative stress. Low and high SA levels were strictly correlated to a lower and higher foliar H2O2 content, respectively. Furthermore high SA was also associated with higher GSH contents, suggesting a tight correlation between SA, H2O2 and GSH contents in plants. These observations implied an essential role of SA in the acclimation processes and in regulating the redox homeostasis of the cell. Implications for the role of SA in pathogen defence signalling are also discussed.},
	language = {English},
	number = {8},
	journal = {Journal of Experimental Botany},
	author = {Mateo, Alfonso and Funck, Dietmar and Muhlenbock, Per and Kular, Baldeep and Mullineaux, Philip M. and Karpinski, Stanislaw},
	year = {2006},
	note = {Place: Oxford
Publisher: Oxford Univ Press
WOS:000238768200020},
	keywords = {Arabidopsis, arabidopsis-thaliana, chlorophyll   fluorescence, cross tolerance, defence reactions, defense responses, gene-expression, glutathione, glutathione-reductase, hydrogen   peroxide, hydrogen-peroxide, induced stomatal closure, light acclimation, oxidative stress, phaseolus-vulgaris l., photooxidative stress, photosynthesis, redox signalling, salicylic acid, systemic acquired-resistance},
	pages = {1795--1807},
}

Sudden exposure of plants to high light (HL) leads to metabolic and physiological disruption of the photosynthetic cells. Changes in ROS content, adjustment of photosynthetic processes and the antioxidant pools and, ultimately, gene induction are essential components for a successful acclimation to the new light conditions. The influence of salicylic acid (SA) on plant growth, short-term acclimation to HL, and on the redox homeostasis of Arabidopsis thaliana leaves was assessed here. The dwarf phenotype displayed by mutants with high SA content (cpr1-1, cpr5-1, cpr6-1, and dnd1-1) was less pronounced when these plants were grown in HL, suggesting that the inhibitory effect of SA on growth was partly overcome at higher light intensities. Moreover, higher SA content affected energy conversion processes in low light, but did not impair short-term acclimation to HL. On the other hand, mutants with low foliar SA content (NahG and sid2-2) were impaired in acclimation to transient exposure to HL and thus predisposed to oxidative stress. Low and high SA levels were strictly correlated to a lower and higher foliar H2O2 content, respectively. Furthermore high SA was also associated with higher GSH contents, suggesting a tight correlation between SA, H2O2 and GSH contents in plants. These observations implied an essential role of SA in the acclimation processes and in regulating the redox homeostasis of the cell. Implications for the role of SA in pathogen defence signalling are also discussed.

@article{mohapatra_occurrence_2006,
	series = {{IHEC} 2005 and {COST} {Action} 841 {Final} {Meeting}},
	title = {Occurrence and characterisation of the hydrogen-evolving enzyme in {Frankia} sp.},
	volume = {31},
	issn = {0360-3199},
	url = {https://www.sciencedirect.com/science/article/pii/S036031990600214X},
	doi = {10.1016/j.ijhydene.2006.06.009},
	abstract = {An increase in hydrogen evolution from the hydrogen-evolving enzyme in the actinomycete Frankia was recorded in the presence of nickel. Immunogold localisation analysis of the intracellular distribution of hydrogenase proteins indicated that they were evenly distributed in the membranes and cytosol of both hyphae and vesicles. In addition, molecular characterisation of the hydrogen-evolving enzyme at the proteomic level, using two-dimensional gel electrophoresis combined with mass spectrometry, confirmed that the Frankia hydrogen-evolving enzyme is similar to the cyanobacterial bidirectional hydrogenase of Anabena siamensis.},
	language = {en},
	number = {11},
	urldate = {2021-06-11},
	journal = {International Journal of Hydrogen Energy},
	author = {Mohapatra, A. and Leul, M. and Sandström, G. and Sellstedt, A.},
	month = sep,
	year = {2006},
	keywords = {Frankia, Hydrogen, Hydrogen-evolving hydrogenase, Nickel, bidirectional hydrogenase, classification, cloning, expression, genes, hydrogen, hydrogen-evolving hydrogenase, kb5, localization, nickel, nife hydrogenase, rhodococcus-opacus},
	pages = {1445--1451},
}

An increase in hydrogen evolution from the hydrogen-evolving enzyme in the actinomycete Frankia was recorded in the presence of nickel. Immunogold localisation analysis of the intracellular distribution of hydrogenase proteins indicated that they were evenly distributed in the membranes and cytosol of both hyphae and vesicles. In addition, molecular characterisation of the hydrogen-evolving enzyme at the proteomic level, using two-dimensional gel electrophoresis combined with mass spectrometry, confirmed that the Frankia hydrogen-evolving enzyme is similar to the cyanobacterial bidirectional hydrogenase of Anabena siamensis.

@article{mouillon_structural_2006,
	title = {Structural investigation of disordered stress proteins. {Comparison} of full-length dehydrins with isolated peptides of their conserved segments},
	volume = {141},
	issn = {0032-0889},
	doi = {10.1104/pp.106.079848},
	abstract = {Dehydrins constitute a class of intrinsically disordered proteins that are expressed under conditions of water-related stress. Characteristic of the dehydrins are some highly conserved stretches of seven to 17 residues that are repetitively scattered in their sequences, the K-, S-, Y-, and Lys-rich segments. In this study, we investigate the putative role of these segments in promoting structure. The analysis is based on comparative analysis of four full-length dehydrins from Arabidopsis ( Arabidopsis thaliana; Cor47, Lti29, Lti30, and Rab18) and isolated peptide mimics of the K-, Y-, and Lys-rich segments. In physiological buffer, the circular dichroism spectra of the full-length dehydrins reveal overall disordered structures with a variable content of poly-Pro helices, a type of elongated secondary structure relying on bridging water molecules. Similar disordered structures are observed for the isolated peptides of the conserved segments. Interestingly, neither the full-length dehydrins nor their conserved segments are able to adopt specific structure in response to altered temperature, one of the factors that regulate their expression in vivo. There is also no structural response to the addition of metal ions, increased protein concentration, or the protein-stabilizing salt Na2SO4. Taken together, these observations indicate that the dehydrins are not in equilibrium with high-energy folded structures. The result suggests that the dehydrins are highly evolved proteins, selected to maintain high configurational flexibility and to resist unspecific collapse and aggregation. The role of the conserved segments is thus not to promote tertiary structure, but to exert their biological function more locally upon interaction with specific biological targets, for example, by acting as beads on a string for specific recognition, interaction with membranes, or intermolecular scaffolding. In this perspective, it is notable that the Lys-rich segment in Cor47 and Lti29 shows sequence similarity with the animal chaperone HSP90.},
	language = {English},
	number = {2},
	journal = {Plant Physiology},
	author = {Mouillon, Jean-Marie and Gustafsson, Petter and Harryson, Pia},
	month = jun,
	year = {2006},
	note = {Place: Rockville
Publisher: Amer Soc Plant Biologists
WOS:000238168800038},
	keywords = {arabidopsis-thaliana, binding, dehydration, desiccation, embryogenesis-abundant protein, intrinsic disorder, motif, natively unfolded proteins, phosphorylation, polyproline-ii helix},
	pages = {638--650},
}

Dehydrins constitute a class of intrinsically disordered proteins that are expressed under conditions of water-related stress. Characteristic of the dehydrins are some highly conserved stretches of seven to 17 residues that are repetitively scattered in their sequences, the K-, S-, Y-, and Lys-rich segments. In this study, we investigate the putative role of these segments in promoting structure. The analysis is based on comparative analysis of four full-length dehydrins from Arabidopsis ( Arabidopsis thaliana; Cor47, Lti29, Lti30, and Rab18) and isolated peptide mimics of the K-, Y-, and Lys-rich segments. In physiological buffer, the circular dichroism spectra of the full-length dehydrins reveal overall disordered structures with a variable content of poly-Pro helices, a type of elongated secondary structure relying on bridging water molecules. Similar disordered structures are observed for the isolated peptides of the conserved segments. Interestingly, neither the full-length dehydrins nor their conserved segments are able to adopt specific structure in response to altered temperature, one of the factors that regulate their expression in vivo. There is also no structural response to the addition of metal ions, increased protein concentration, or the protein-stabilizing salt Na2SO4. Taken together, these observations indicate that the dehydrins are not in equilibrium with high-energy folded structures. The result suggests that the dehydrins are highly evolved proteins, selected to maintain high configurational flexibility and to resist unspecific collapse and aggregation. The role of the conserved segments is thus not to promote tertiary structure, but to exert their biological function more locally upon interaction with specific biological targets, for example, by acting as beads on a string for specific recognition, interaction with membranes, or intermolecular scaffolding. In this perspective, it is notable that the Lys-rich segment in Cor47 and Lti29 shows sequence similarity with the animal chaperone HSP90.

@article{nordin_responses_2006,
	title = {Responses to ammonium and nitrate additions by boreal plants and their natural enemies},
	volume = {141},
	issn = {0269-7491},
	doi = {10.1016/j.envpol.2005.08.017},
	abstract = {Separate effects of ammonium (NH4+) and nitrate (NO3-) on boreal forest understorey vegetation were investigated in an experiment where 12.5 and 50.0 kg nitrogen (N) hat year' was added to 2 m(2) sized plots during 4 years. The dwarf-shrubs dominating the plant community, Vaccinium myrtillus and V. vitis-idaea, took up little of the added N independent of the chemical form. and their growth did not respond to the N treatments. The grass Deschampsia flexuosa increased from the N additions and most so in response to NO3-. Bryophytes took up predominately NH4+ and there was a negative correlation between moss N concentration and abundance. Plant pathogenic fungi increased from the N additions, but showed no differences in response to the two N forms. Because the relative contribution of NH4+ and NO3- to the total N deposition on a regional scale can vary substantially, the N load a habitat can sustain without substantial changes in the biota should be set considering specific vegetation responses to the predominant N form in deposition. (c) 2005 Elsevier Ltd. All rights reserved.},
	language = {English},
	number = {1},
	journal = {Environmental Pollution},
	author = {Nordin, A. and Strengbom, J. and Ericson, L.},
	month = may,
	year = {2006},
	note = {Place: Oxford
Publisher: Elsevier Sci Ltd
WOS:000236771400018},
	keywords = {N deposition, N form, N uptake, atmospheric nitrogen, bryophytes, community, density, deposition, growth, pathogen, pathogenic fungi, productivity, species-diversity, valdensinia-heterodoxa, vegetation change},
	pages = {167--174},
}

Separate effects of ammonium (NH4+) and nitrate (NO3-) on boreal forest understorey vegetation were investigated in an experiment where 12.5 and 50.0 kg nitrogen (N) hat year' was added to 2 m(2) sized plots during 4 years. The dwarf-shrubs dominating the plant community, Vaccinium myrtillus and V. vitis-idaea, took up little of the added N independent of the chemical form. and their growth did not respond to the N treatments. The grass Deschampsia flexuosa increased from the N additions and most so in response to NO3-. Bryophytes took up predominately NH4+ and there was a negative correlation between moss N concentration and abundance. Plant pathogenic fungi increased from the N additions, but showed no differences in response to the two N forms. Because the relative contribution of NH4+ and NO3- to the total N deposition on a regional scale can vary substantially, the N load a habitat can sustain without substantial changes in the biota should be set considering specific vegetation responses to the predominant N form in deposition. (c) 2005 Elsevier Ltd. All rights reserved.

@article{petersson_prx_2006,
	title = {The {Prx} {Q} protein of {Arabidopsis} thaliana is a member of the luminal chloroplast proteome},
	volume = {580},
	copyright = {FEBS Letters 580 (2006) 1873-3468 © 2015 Federation of European Biochemical Societies},
	issn = {1873-3468},
	url = {https://febs.onlinelibrary.wiley.com/doi/abs/10.1016/j.febslet.2006.10.001},
	doi = {10.1016/j.febslet.2006.10.001},
	abstract = {Peroxiredoxins have been discovered in many organisms ranging from eubacteria to mammals, and their known biological functions include both oxidant defense and signal transduction. The genome of Arabidopsis thaliana encodes for ten individual peroxiredoxins, of which four are located in the chloroplast. The best-characterized member of the chloroplast peroxiredoxins is 2-Cys Prx that is associated with the stroma side of the thylakoid membrane and is considered to participate in antioxidant defense and protection of photosynthesis. This study addressed the chloroplast peroxiredoxin Prx Q and showed that its subcellular location is the lumen of the thylakoid membrane. To get insight in the biological function of the Prx Q protein of Arabidopsis, the protein levels of the Prx Q protein in thylakoid membranes were studied under different light conditions and oxidative stress. A T-DNA knockout mutant of Prx Q did not show any visible phenotype and had normal photosynthetic performance with a slightly increased oxygen evolving activity.},
	language = {en},
	number = {26},
	urldate = {2021-06-11},
	journal = {FEBS Letters},
	author = {Petersson, Ulrika A. and Kieselbach, Thomas and García-Cerdán, José G. and Schröder, Wolfgang P.},
	year = {2006},
	note = {\_eprint: https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/j.febslet.2006.10.001},
	keywords = {PSII, Peroxiredoxin, Photosynthesis},
	pages = {6055--6061},
}

Peroxiredoxins have been discovered in many organisms ranging from eubacteria to mammals, and their known biological functions include both oxidant defense and signal transduction. The genome of Arabidopsis thaliana encodes for ten individual peroxiredoxins, of which four are located in the chloroplast. The best-characterized member of the chloroplast peroxiredoxins is 2-Cys Prx that is associated with the stroma side of the thylakoid membrane and is considered to participate in antioxidant defense and protection of photosynthesis. This study addressed the chloroplast peroxiredoxin Prx Q and showed that its subcellular location is the lumen of the thylakoid membrane. To get insight in the biological function of the Prx Q protein of Arabidopsis, the protein levels of the Prx Q protein in thylakoid membranes were studied under different light conditions and oxidative stress. A T-DNA knockout mutant of Prx Q did not show any visible phenotype and had normal photosynthetic performance with a slightly increased oxygen evolving activity.

@article{pohjanen_statistical_2006,
	title = {Statistical multivariate metabolite profiling for aiding biomarker pattern detection and mechanistic interpretations in {GC}/{MS} based metabolomics},
	volume = {2},
	issn = {1573-3890},
	url = {https://doi.org/10.1007/s11306-006-0032-4},
	doi = {10.1007/s11306-006-0032-4},
	abstract = {A strategy for robust and reliable mechanistic statistical modelling of metabolic responses in relation to drug induced toxicity is presented. The suggested approach addresses two cases commonly occurring within metabonomic toxicology studies, namely; 1) A pre-defined hypothesis about the biological mechanism exists and 2) No such hypothesis exists. GC/MS data from a liver toxicity study consisting of rat urine from control rats and rats exposed to a proprietary AstraZeneca compound were resolved by means of hierarchical multivariate curve resolution (H-MCR) generating 287 resolved chromatographic profiles with corresponding mass spectra. Filtering according to significance in relation to drug exposure rendered in 210 compound profiles, which were subjected to further statistical analysis following correction to account for the control variation over time. These dose related metabolite traces were then used as new observations in the subsequent analyses. For case 1, a multivariate approach, named Target Batch Analysis, based on OPLS regression was applied to correlate all metabolite traces to one or more key metabolites involved in the pre-defined hypothesis. For case 2, principal component analysis (PCA) was combined with hierarchical cluster analysis (HCA) to create a robust and interpretable framework for unbiased mechanistic screening. Both the Target Batch Analysis and the unbiased approach were cross-verified using the other method to ensure that the results did match in terms of detected metabolite traces. This was also the case, implying that this is a working concept for clustering of metabolites in relation to their toxicity induced dynamic profiles regardless if there is a pre-existing hypothesis or not. For each of the methods the detected metabolites were subjected to identification by means of data base comparison as well as verification in the raw data. The proposed strategy should be seen as a general approach for facilitating mechanistic modelling and interpretations in metabolomic studies.},
	language = {en},
	number = {4},
	urldate = {2021-06-11},
	journal = {Metabolomics},
	author = {Pohjanen, Elin and Thysell, Elin and Lindberg, Johan and Schuppe-Koistinen, Ina and Moritz, Thomas and Jonsson, Pär and Antti, Henrik},
	month = dec,
	year = {2006},
	pages = {257--268},
}

A strategy for robust and reliable mechanistic statistical modelling of metabolic responses in relation to drug induced toxicity is presented. The suggested approach addresses two cases commonly occurring within metabonomic toxicology studies, namely; 1) A pre-defined hypothesis about the biological mechanism exists and 2) No such hypothesis exists. GC/MS data from a liver toxicity study consisting of rat urine from control rats and rats exposed to a proprietary AstraZeneca compound were resolved by means of hierarchical multivariate curve resolution (H-MCR) generating 287 resolved chromatographic profiles with corresponding mass spectra. Filtering according to significance in relation to drug exposure rendered in 210 compound profiles, which were subjected to further statistical analysis following correction to account for the control variation over time. These dose related metabolite traces were then used as new observations in the subsequent analyses. For case 1, a multivariate approach, named Target Batch Analysis, based on OPLS regression was applied to correlate all metabolite traces to one or more key metabolites involved in the pre-defined hypothesis. For case 2, principal component analysis (PCA) was combined with hierarchical cluster analysis (HCA) to create a robust and interpretable framework for unbiased mechanistic screening. Both the Target Batch Analysis and the unbiased approach were cross-verified using the other method to ensure that the results did match in terms of detected metabolite traces. This was also the case, implying that this is a working concept for clustering of metabolites in relation to their toxicity induced dynamic profiles regardless if there is a pre-existing hypothesis or not. For each of the methods the detected metabolites were subjected to identification by means of data base comparison as well as verification in the raw data. The proposed strategy should be seen as a general approach for facilitating mechanistic modelling and interpretations in metabolomic studies.

@article{rosso_immutans_2006,
	title = {{IMMUTANS} does not act as a stress-induced safety valve in the protection of the photosynthetic apparatus of {Arabidopsis} during steady-state photosynthesis},
	volume = {142},
	issn = {0032-0889},
	doi = {10.1104/pp.106.085886},
	abstract = {IMMUTANS (IM) encodes a thylakoid membrane protein that has been hypothesized to act as a terminal oxidase that couples the reduction of O(2) to the oxidation of the plastoquinone (PQ) pool of the photosynthetic electron transport chain. Because IM shares sequence similarity to the stress-induced mitochondrial alternative oxidase (AOX), it has been suggested that the protein encoded by IM acts as a safety valve during the generation of excess photosynthetically generated electrons. We combined in vivo chlorophyll fluorescence quenching analyses with measurements of the redox state of P(700) to assess the capacity of IM to compete with photosystem I for intersystem electrons during steady-state photosynthesis in Arabidopsis (Arabidopsis thaliana). Comparisons were made between wild-type plants, im mutant plants, as well as transgenics in which IM protein levels had been overexpressed six (OE-6 x) and 16 (OE-16 x) times. Immunoblots indicated that IM abundance was the only major variant that we could detect between these genotypes. Overexpression of IM did not result in increased capacity to keep the PQ pool oxidized compared to either the wild type or im grown under control conditions (25 degrees C and photosynthetic photon flux density of 150 micromol photons m(-2) s(-1)). Similar results were observed either after 3-d cold stress at 5 degrees C or after full-leaf expansion at 5 degrees C and photosynthetic photon flux density of 150 micromol photons m(-2) s(-1). Furthermore, IM abundance did not enhance protection of either photosystem II or photosystem I from photoinhibition at either 25 degrees C or 5 degrees C. Our in vivo data indicate that modulation of IM expression and polypeptide accumulation does not alter the flux of intersystem electrons to P(700)(+) during steady-state photosynthesis and does not provide any significant photoprotection. In contrast to AOX1a, meta-analyses of published Arabidopsis microarray data indicated that IM expression exhibited minimal modulation in response to myriad abiotic stresses, which is consistent with our functional data. However, IM exhibited significant modulation in response to development in concert with changes in AOX1a expression. Thus, neither our functional analyses of the IM knockout and overexpression lines nor meta-analyses of gene expression support the model that IM acts as a safety valve to regulate the redox state of the PQ pool during stress and acclimation. Rather, IM appears to be strongly regulated by developmental stage of Arabidopsis.},
	language = {eng},
	number = {2},
	journal = {Plant Physiology},
	author = {Rosso, Dominic and Ivanov, Alexander G. and Fu, Aigen and Geisler-Lee, Jane and Hendrickson, Luke and Geisler, Matt and Stewart, Gregory and Krol, Marianna and Hurry, Vaughan and Rodermel, Steven R. and Maxwell, Denis P. and Hüner, Norman P. A.},
	month = oct,
	year = {2006},
	pmid = {16891546},
	pmcid = {PMC1586030},
	keywords = {Acclimatization, Arabidopsis, Arabidopsis Proteins, Cold Temperature, Gene Expression Profiling, Gene Expression Regulation, Plant, Genotype, Mitochondrial Proteins, Molecular Sequence Data, Oxidoreductases, Photosynthesis, Photosystem I Protein Complex, Photosystem II Protein Complex, Plant Proteins, alternative oxidase, chlorophyll-a, electron-transport, gene, in-vitro, intersystem chain, oxidative stress, photosystem-ii, plastid terminal oxidase, redox state},
	pages = {574--585},
}

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

@article{rouhier_engineering_2006,
	title = {Engineering functional artificial hybrid proteins between poplar peroxiredoxin {II} and glutaredoxin or thioredoxin},
	volume = {341},
	issn = {0006-291X},
	doi = {10.1016/j.bbrc.2006.01.099},
	abstract = {The existence of natural peroxiredoxin-glutaredoxin hybrid enzymes in several bacteria is in line with previous findings indicating that poplar peroxiredoxin II can use glutaredoxin as an electron donor. This peroxiredoxin remains however unique since it also uses thioredoxin with a quite good efficiency. Based on the existing fusions, we have created artificial enzymes containing a poplar peroxiredoxin module linked to glutaredoxin or thioredoxin modules. The recombinant fusion enzymes folded properly into non-covalently bound homodimers or homotetramers. Two of the three protein constructs exhibit peroxidase activity, a reaction where the two modules need to function together, but they also display enzymatic activities specific of each module. In addition, mass spectrometry analyses indicate that the Prx module can be both glutathiolated or overoxidized in vitro. This is discussed in the light of the Prx reactivity. (c) 2006 Elsevier Inc. All rights reserved.},
	language = {English},
	number = {4},
	journal = {Biochemical and Biophysical Research Communications},
	author = {Rouhier, N. and Gama, F. and Wingsle, G. and Gelhaye, E. and Gans, P. and Jacquot, J. P.},
	month = mar,
	year = {2006},
	note = {Place: San Diego
Publisher: Academic Press Inc Elsevier Science
WOS:000235699900056},
	keywords = {acid, cdna, dependent peroxidase, donor, expression, glutaredoxin, hydroperoxide, identification, peroxiredoxin, poplar, reductases, reduction, sequence, thioredoxin},
	pages = {1300--1308},
}

The existence of natural peroxiredoxin-glutaredoxin hybrid enzymes in several bacteria is in line with previous findings indicating that poplar peroxiredoxin II can use glutaredoxin as an electron donor. This peroxiredoxin remains however unique since it also uses thioredoxin with a quite good efficiency. Based on the existing fusions, we have created artificial enzymes containing a poplar peroxiredoxin module linked to glutaredoxin or thioredoxin modules. The recombinant fusion enzymes folded properly into non-covalently bound homodimers or homotetramers. Two of the three protein constructs exhibit peroxidase activity, a reaction where the two modules need to function together, but they also display enzymatic activities specific of each module. In addition, mass spectrometry analyses indicate that the Prx module can be both glutathiolated or overoxidized in vitro. This is discussed in the light of the Prx reactivity. (c) 2006 Elsevier Inc. All rights reserved.

@article{ruban_plasticity_2006,
	title = {Plasticity in the composition of the light harvesting antenna of higher plants preserves structural integrity and biological function},
	volume = {281},
	issn = {0021-9258},
	doi = {10.1074/jbc.M511415200},
	abstract = {Arabidopsis plants in which the major trimeric light harvesting complex ( LHCIIb) is eliminated by antisense expression still exhibit the typical macrostructure of photosystem II in the granal membranes. Here the detailed analysis of the composition and the functional state of the light harvesting antennae of both photosystem I and II of these plants is presented. Two new populations of trimers were found, both functional in energy transfer to the PSII reaction center, a homotrimer of CP26 and a heterotrimer of CP26 and Lhcb3. These trimers possess characteristic features thought to be specific for the native LHCIIb trimers they are replacing: the long wavelength form of lutein and at least one extra chlorophyll b, but they were less stable. A new population of loosely bound LHCI was also found, contributing to an increased antenna size for photosystem I, which may in part compensate for the loss of the phosphorylated LHCIIb that can associate with this photosystem. Thus, the loss of LHCIIb has triggered concerted compensatory responses in the composition of antennae of both photosystems. These responses clearly show the importance of LHCIIb in the structure and assembly of the photosynthetic membrane and illustrate the extreme plasticity at the level of the composition of the light harvesting system.},
	language = {English},
	number = {21},
	journal = {Journal of Biological Chemistry},
	author = {Ruban, Alexander V. and Solovieva, Svetlana and Lee, Pamela J. and Ilioaia, Cristian and Wentworth, Mark and Ganeteg, Ulrika and Klimmek, Frank and Chow, Wah Soon and Anderson, Jan M. and Jansson, Stefan and Horton, Peter},
	month = may,
	year = {2006},
	note = {Place: Rockville
Publisher: Amer Soc Biochemistry Molecular Biology Inc
WOS:000237671300051},
	keywords = {a/b-binding-proteins, acclimation, arabidopsis, complex-ii, crystal-structure, energy, photosystem-ii, spectroscopic analysis, supramolecular organization, xanthophylls},
	pages = {14981--14990},
}

Arabidopsis plants in which the major trimeric light harvesting complex ( LHCIIb) is eliminated by antisense expression still exhibit the typical macrostructure of photosystem II in the granal membranes. Here the detailed analysis of the composition and the functional state of the light harvesting antennae of both photosystem I and II of these plants is presented. Two new populations of trimers were found, both functional in energy transfer to the PSII reaction center, a homotrimer of CP26 and a heterotrimer of CP26 and Lhcb3. These trimers possess characteristic features thought to be specific for the native LHCIIb trimers they are replacing: the long wavelength form of lutein and at least one extra chlorophyll b, but they were less stable. A new population of loosely bound LHCI was also found, contributing to an increased antenna size for photosystem I, which may in part compensate for the loss of the phosphorylated LHCIIb that can associate with this photosystem. Thus, the loss of LHCIIb has triggered concerted compensatory responses in the composition of antennae of both photosystems. These responses clearly show the importance of LHCIIb in the structure and assembly of the photosynthetic membrane and illustrate the extreme plasticity at the level of the composition of the light harvesting system.

@article{sivakumar_effects_2006,
	title = {Effects of presowing treatments, desiccation and storage conditions on germination of {Strychnos} nux-vomica seeds, a valuable medicinal plant},
	volume = {32},
	issn = {1573-5095},
	url = {https://doi.org/10.1007/s11056-005-5038-7},
	doi = {10.1007/s11056-005-5038-7},
	abstract = {Seeds of Strychnos nux-vomica have slow and erratic germination; thus different presowing treatments were applied to enhance the germination of its seeds collected from Tamaraikulam, Tamil Nadu, India. In addition, the effects of desiccation and different storage conditions on the germination of S. nux-vomica seeds were investigated. The results show that soaking in 500 ppm gibberellic acid (GA3) for 24 h, incubation of seeds at 40 °C for 3 days and alternate water soaking (16 h) and drying (8 h) for 14 days significantly increased the percentage germination compared to the control. Desiccation of seeds down to 10\% moisture content resulted in better germination. Germination of S. nux-vomica seeds differed significantly between different storage periods, moisture contents of the seed and for first and second order interactions (p{\textless}0.001). The highest germination (92\%) was achieved when seeds with 10\% moisture content were stored at ambient temperature for 30 weeks. Evidence from the present study indicates that S. nux-vomica seeds possess physiological dormancy that can be broken effectively by after-ripening. As seeds of S. nux-vomica are found to be desiccation tolerant, dry seed (10\% moisture content) can be hermitically stored at ambient temperature for 30 weeks without losing their viability.},
	language = {en},
	number = {2},
	urldate = {2021-06-11},
	journal = {New Forests},
	author = {Sivakumar, V. and Anandalakshmi, R. and Warrier, R. R. and Tigabu, M. and Odén, P. C. and Vijayachandran, S. N. and Geetha, S. and Singh, B. G.},
	month = sep,
	year = {2006},
	pages = {121--131},
}

Seeds of Strychnos nux-vomica have slow and erratic germination; thus different presowing treatments were applied to enhance the germination of its seeds collected from Tamaraikulam, Tamil Nadu, India. In addition, the effects of desiccation and different storage conditions on the germination of S. nux-vomica seeds were investigated. The results show that soaking in 500 ppm gibberellic acid (GA3) for 24 h, incubation of seeds at 40 °C for 3 days and alternate water soaking (16 h) and drying (8 h) for 14 days significantly increased the percentage germination compared to the control. Desiccation of seeds down to 10% moisture content resulted in better germination. Germination of S. nux-vomica seeds differed significantly between different storage periods, moisture contents of the seed and for first and second order interactions (p\textless0.001). The highest germination (92%) was achieved when seeds with 10% moisture content were stored at ambient temperature for 30 weeks. Evidence from the present study indicates that S. nux-vomica seeds possess physiological dormancy that can be broken effectively by after-ripening. As seeds of S. nux-vomica are found to be desiccation tolerant, dry seed (10% moisture content) can be hermitically stored at ambient temperature for 30 weeks without losing their viability.

@article{sjogren_structural_2006,
	title = {Structural and functional insights into the chloroplast {ATP}-dependent {Clp} protease in {Arabidopsis}},
	volume = {18},
	issn = {1040-4651},
	doi = {10.1105/tpc.106.044594},
	abstract = {In contrast with the model Escherichia coli Clp protease, the ATP-dependent Clp protease in higher plants has a remarkably diverse proteolytic core consisting of multiple ClpP and ClpR paralogs, presumably arranged within a dual heptameric ring structure. Using antisense lines for the nucleus-encoded ClpP subunit, ClpP6, we show that the Arabidopsis thaliana Clp protease is vital for chloroplast development and function. Repression of ClpP6 produced a proportional decrease in the Clp proteolytic core, causing a chlorotic phenotype in young leaves that lessened upon maturity. Structural analysis of the proteolytic core revealed two distinct subcomplexes that likely correspond to single heptameric rings, one containing the ClpP1 and ClpR1-4 proteins, the other containing ClpP3-6. Proteomic analysis revealed several stromal proteins more abundant in clpP6 antisense lines, suggesting that some are substrates for the Clp protease. A proteolytic assay developed for intact chloroplasts identified potential substrates for the stromal Clp protease in higher plants, most of which were more abundant in young Arabidopsis leaves, consistent with the severity of the chlorotic phenotype observed in the clpP6 antisense lines. The identified substrates all function in more general housekeeping roles such as plastid protein synthesis, folding, and quality control, rather than in metabolic activities such as photosynthesis.},
	language = {eng},
	number = {10},
	journal = {The Plant Cell},
	author = {Sjögren, Lars L. E. and Stanne, Tara M. and Zheng, Bo and Sutinen, Sirkka and Clarke, Adrian K.},
	month = oct,
	year = {2006},
	pmid = {16980539},
	pmcid = {PMC1626633},
	keywords = {Adenosine Triphosphate, Arabidopsis, Chloroplasts, Electrophoresis, Gel, Two-Dimensional, Endopeptidase Clp, Microscopy, Electron, Photosynthesis, Plant Leaves, Protein Conformation, Substrate Specificity, biosynthesis, complex, degradation, ftsh, gene, identification, norway spruce, plant development, proteins, thaliana},
	pages = {2635--2649},
}

In contrast with the model Escherichia coli Clp protease, the ATP-dependent Clp protease in higher plants has a remarkably diverse proteolytic core consisting of multiple ClpP and ClpR paralogs, presumably arranged within a dual heptameric ring structure. Using antisense lines for the nucleus-encoded ClpP subunit, ClpP6, we show that the Arabidopsis thaliana Clp protease is vital for chloroplast development and function. Repression of ClpP6 produced a proportional decrease in the Clp proteolytic core, causing a chlorotic phenotype in young leaves that lessened upon maturity. Structural analysis of the proteolytic core revealed two distinct subcomplexes that likely correspond to single heptameric rings, one containing the ClpP1 and ClpR1-4 proteins, the other containing ClpP3-6. Proteomic analysis revealed several stromal proteins more abundant in clpP6 antisense lines, suggesting that some are substrates for the Clp protease. A proteolytic assay developed for intact chloroplasts identified potential substrates for the stromal Clp protease in higher plants, most of which were more abundant in young Arabidopsis leaves, consistent with the severity of the chlorotic phenotype observed in the clpP6 antisense lines. The identified substrates all function in more general housekeeping roles such as plastid protein synthesis, folding, and quality control, rather than in metabolic activities such as photosynthesis.

@article{stenberg_tall_2006,
	title = {Tall herb herbivory resistance reflects historic exposure to leaf beetles in a boreal archipelago age-gradient},
	volume = {148},
	issn = {0029-8549},
	doi = {10.1007/s00442-006-0390-7},
	abstract = {In this paper, we introduce the coevolution-by-coexistence hypothesis which predicts that the strength of a coevolutionary adaptation will become increasingly apparent as long as the corresponding selection from an interacting counterpart continues. Hence, evolutionary interactions between plants and their herbivores can be studied by comparing discrete plant populations with known history of herbivore colonization. We studied populations of the host plant, Filipendula ulmaria (meadow sweet), on six islands, in a Bothnian archipelago subject to isostatic rebound, that represent a spatio-temporal gradient of coexistence with its two major herbivores, the specialist leaf beetles Galerucella tenella and Altica engstroemi. Regression analyses showed that a number of traits important for insect-plant interactions (leaf concentrations of individual phenolics and condensed tannins, plant height, G. tenella adult feeding and oviposition) were significantly correlated with island age. First, leaf concentrations of condensed tannins and individual phenolics were positively correlated with island age, suggesting that plant resistance increased after herbivore colonization and continued to increase in parallel to increasing time of past coexistence, while plant height showed a reverse negative correlation. Second, a multi-choice experiment with G. tenella showed that both oviposition and leaf consumption of the host plants were negatively correlated with island age. Third, larvae performed poorly on well-defended, older host populations and well on less-defended, younger populations. Thus, no parameter assessed in this study falsifies the coevolution-by-coexistence hypothesis. We conclude that spatio-temporal gradients present in rising archipelagos offer unique opportunities to address evolutionary interactions, but care has to be taken as abiotic (and other biotic) factors may interact in a complicated way.},
	language = {English},
	number = {3},
	journal = {Oecologia},
	author = {Stenberg, Johan A. and Witzell, Johanna and Ericson, Lars},
	month = jun,
	year = {2006},
	note = {Place: New York
Publisher: Springer
WOS:000237796300006},
	keywords = {Filipendula ulmaria, Galerucella tenella, coevolution, competition, consequences, ecological   costs, evolution, fitness, host, insect-plant relationships, pathogen triphragmium-ulmariae, plant-herbivore   interaction, populations, selection gradient},
	pages = {414--425},
}

In this paper, we introduce the coevolution-by-coexistence hypothesis which predicts that the strength of a coevolutionary adaptation will become increasingly apparent as long as the corresponding selection from an interacting counterpart continues. Hence, evolutionary interactions between plants and their herbivores can be studied by comparing discrete plant populations with known history of herbivore colonization. We studied populations of the host plant, Filipendula ulmaria (meadow sweet), on six islands, in a Bothnian archipelago subject to isostatic rebound, that represent a spatio-temporal gradient of coexistence with its two major herbivores, the specialist leaf beetles Galerucella tenella and Altica engstroemi. Regression analyses showed that a number of traits important for insect-plant interactions (leaf concentrations of individual phenolics and condensed tannins, plant height, G. tenella adult feeding and oviposition) were significantly correlated with island age. First, leaf concentrations of condensed tannins and individual phenolics were positively correlated with island age, suggesting that plant resistance increased after herbivore colonization and continued to increase in parallel to increasing time of past coexistence, while plant height showed a reverse negative correlation. Second, a multi-choice experiment with G. tenella showed that both oviposition and leaf consumption of the host plants were negatively correlated with island age. Third, larvae performed poorly on well-defended, older host populations and well on less-defended, younger populations. Thus, no parameter assessed in this study falsifies the coevolution-by-coexistence hypothesis. We conclude that spatio-temporal gradients present in rising archipelagos offer unique opportunities to address evolutionary interactions, but care has to be taken as abiotic (and other biotic) factors may interact in a complicated way.

@incollection{pesquet_zinnia_2006,
	title = {Zinnia elegans is an {Excellent} {Model} for {Xylogenesis}: {In} {Vitro} and {In} {Planta}},
	shorttitle = {Zinnia elegans is an {Excellent} {Model} for {Xylogenesis}},
	author = {Pesquet, Edouard and Jauneau, Alain and Goffner, Deborah},
	month = jan,
	year = {2006},
	pages = {171--178},
}

@incollection{strand_plastid--nucleus_2006,
	address = {Dordrecht},
	series = {Advances in {Photosynthesis} and {Respiration}},
	title = {Plastid-to-{Nucleus} {Signaling}},
	isbn = {978-1-4020-4061-0},
	url = {https://doi.org/10.1007/978-1-4020-4061-0_9},
	abstract = {The function of the eukaryotic cell depends on the regulated and reciprocal interaction between its different compartments. This includes not only the exchange of energy equivalents but also information. Most information exchange flows from the nucleus to the organelles, because the large majority of genes encoding proteins with organellar function are encoded in the nucleus.},
	language = {en},
	urldate = {2021-06-11},
	booktitle = {The {Structure} and {Function} of {Plastids}},
	publisher = {Springer Netherlands},
	author = {Strand, Åsa and Kleine, Tatjana and Chory, Joanne},
	editor = {Wise, Robert R. and Hoober, J. Kenneth},
	year = {2006},
	doi = {10.1007/978-1-4020-4061-0_9},
	keywords = {Chloroplast Development, Nuclear Gene Expression, Photosynthetic Gene Expression, Plastid Signal, Tetrapyrrole Biosynthesis},
	pages = {183--197},
}

The function of the eukaryotic cell depends on the regulated and reciprocal interaction between its different compartments. This includes not only the exchange of energy equivalents but also information. Most information exchange flows from the nucleus to the organelles, because the large majority of genes encoding proteins with organellar function are encoded in the nucleus.

@article{niittyla_similar_2006,
	title = {Similar {Protein} {Phosphatases} {Control} {Starch} {Metabolism} in {Plants} and {Glycogen} {Metabolism} in {Mammals}*},
	volume = {281},
	issn = {0021-9258},
	url = {https://www.sciencedirect.com/science/article/pii/S0021925819466878},
	doi = {10/fvpqmw},
	abstract = {We report that protein phosphorylation is involved in the control of starch metabolism in Arabidopsis leaves at night. sex4 (starch excess 4) mutants, which have strongly reduced rates of starch metabolism, lack a protein predicted to be a dual specificity protein phosphatase. We have shown that this protein is chloroplastic and can bind to glucans and have presented evidence that it acts to regulate the initial steps of starch degradation at the granule surface. Remarkably, the most closely related protein to SEX4 outside the plant kingdom is laforin, a glucan-binding protein phosphatase required for the metabolism of the mammalian storage carbohydrate glycogen and implicated in a severe form of epilepsy (Lafora disease) in humans.},
	language = {en},
	number = {17},
	urldate = {2021-06-10},
	journal = {Journal of Biological Chemistry},
	author = {Niittylä, Totte and Comparot-Moss, Sylviane and Lue, Wei-Ling and Messerli, Gaëlle and Trevisan, Martine and Seymour, Michael D. J. and Gatehouse, John A. and Villadsen, Dorthe and Smith, Steven M. and Chen, Jychian and Zeeman, Samuel C. and Smith, Alison M.},
	month = apr,
	year = {2006},
	pages = {11815--11818},
}

We report that protein phosphorylation is involved in the control of starch metabolism in Arabidopsis leaves at night. sex4 (starch excess 4) mutants, which have strongly reduced rates of starch metabolism, lack a protein predicted to be a dual specificity protein phosphatase. We have shown that this protein is chloroplastic and can bind to glucans and have presented evidence that it acts to regulate the initial steps of starch degradation at the granule surface. Remarkably, the most closely related protein to SEX4 outside the plant kingdom is laforin, a glucan-binding protein phosphatase required for the metabolism of the mammalian storage carbohydrate glycogen and implicated in a severe form of epilepsy (Lafora disease) in humans.

@article{srivastava_downregulation_2006,
	title = {Downregulation of high-isoelectric-point extracellular superoxide dismutase mediates alterations in the metabolism of reactive oxygen species and developmental disturbances in hybrid aspen: {HipI}-{SOD} in hybrid aspen},
	volume = {49},
	issn = {09607412, 1365313X},
	shorttitle = {Downregulation of high-isoelectric-point extracellular superoxide dismutase mediates alterations in the metabolism of reactive oxygen species and developmental disturbances in hybrid aspen},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2006.02943.x},
	doi = {10/fvh67r},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {The Plant Journal},
	author = {Srivastava, Vaibhav and Schinkel, Helga and Witzell, Johanna and Hertzberg, Magnus and Torp, Mikaela and Srivastava, Manoj Kumar and Karpinska, Barbara and Melzer, Michael and Wingsle, Gunnar},
	month = dec,
	year = {2006},
	pages = {135--148},
}

@article{ingvarsson_gene_2006,
	title = {Gene {Expression} and {Protein} {Length} {Influence} {Codon} {Usage} and {Rates} of {Sequence} {Evolution} in {Populus} tremula},
	volume = {24},
	issn = {0737-4038, 1537-1719},
	url = {https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msl212},
	doi = {10/b7prhk},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Molecular Biology and Evolution},
	author = {Ingvarsson, P. K.},
	month = dec,
	year = {2006},
	pages = {836--844},
}

@article{ubeda-tomas_genomic-assisted_2006,
	title = {Genomic-assisted identification of genes involved in secondary growth in {Arabidopsis} utilising transcript profiling of poplar wood-forming tissues},
	volume = {129},
	issn = {00319317, 13993054},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2006.00817.x},
	doi = {10/c4vjzj},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Physiologia Plantarum},
	author = {Ubeda-Tomas, Susana and Edvardsson, Ellinor and Eland, Cathlene and Singh, Sunil Kumar and Zadik, Daniel and Aspeborg, Henrik and Gorzsàs, Andràs and Teeri, Tuula T. and Sundberg, Björn and Persson, Per and Bennett, Malcolm and Marchant, Alan},
	month = nov,
	year = {2006},
	pages = {415--428},
}

@article{normand_genome_2006,
	title = {Genome characteristics of facultatively symbiotic {Frankia} sp. strains reflect host range and host plant biogeography},
	volume = {17},
	issn = {1088-9051},
	url = {http://www.genome.org/cgi/doi/10.1101/gr.5798407},
	doi = {10/bjt4n7},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Genome Research},
	author = {Normand, P. and Lapierre, P. and Tisa, L. S. and Gogarten, J. P. and Alloisio, N. and Bagnarol, E. and Bassi, C. A. and Berry, A. M. and Bickhart, D. M. and Choisne, N. and Couloux, A. and Cournoyer, B. and Cruveiller, S. and Daubin, V. and Demange, N. and Francino, M. P. and Goltsman, E. and Huang, Y. and Kopp, O. R. and Labarre, L. and Lapidus, A. and Lavire, C. and Marechal, J. and Martinez, M. and Mastronunzio, J. E. and Mullin, B. C. and Niemann, J. and Pujic, P. and Rawnsley, T. and Rouy, Z. and Schenowitz, C. and Sellstedt, A. and Tavares, F. and Tomkins, J. P. and Vallenet, D. and Valverde, C. and Wall, L. G. and Wang, Y. and Medigue, C. and Benson, D. R.},
	month = dec,
	year = {2006},
	pages = {7--15},
}

@article{ahad_actin_2006,
	title = {Actin is bundled in activation-tagged tobacco mutants that tolerate aluminum},
	volume = {225},
	issn = {0032-0935, 1432-2048},
	url = {http://link.springer.com/10.1007/s00425-006-0359-0},
	doi = {10/chr7x7},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Planta},
	author = {Ahad, Abdul and Nick, Peter},
	month = dec,
	year = {2006},
	pages = {451--468},
}