@article{hvidsten_comprehensive_2009,
	title = {A {Comprehensive} {Analysis} of the {Structure}-{Function} {Relationship} in {Proteins} {Based} on {Local} {Structure} {Similarity}},
	volume = {4},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0006266},
	doi = {10/bwtcf5},
	abstract = {Background Sequence similarity to characterized proteins provides testable functional hypotheses for less than 50\% of the proteins identified by genome sequencing projects. With structural genomics it is believed that structural similarities may give functional hypotheses for many of the remaining proteins. Methodology/Principal Findings We provide a systematic analysis of the structure-function relationship in proteins using the novel concept of local descriptors of protein structure. A local descriptor is a small substructure of a protein which includes both short- and long-range interactions. We employ a library of commonly reoccurring local descriptors general enough to assemble most existing protein structures. We then model the relationship between these local shapes and Gene Ontology using rule-based learning. Our IF-THEN rule model offers legible, high resolution descriptions that combine local substructures and is able to discriminate functions even for functionally versatile folds such as the frequently occurring TIM barrel and Rossmann fold. By evaluating the predictive performance of the model, we provide a comprehensive quantification of the structure-function relationship based only on local structure similarity. Our findings are, among others, that conserved structure is a stronger prerequisite for enzymatic activity than for binding specificity, and that structure-based predictions complement sequence-based predictions. The model is capable of generating correct hypotheses, as confirmed by a literature study, even when no significant sequence similarity to characterized proteins exists. Conclusions/Significance Our approach offers a new and complete description and quantification of the structure-function relationship in proteins. By demonstrating how our predictions offer higher sensitivity than using global structure, and complement the use of sequence, we show that the presented ideas could advance the development of meta-servers in function prediction.},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {PLOS ONE},
	author = {Hvidsten, Torgeir R. and Lægreid, Astrid and Kryshtafovych, Andriy and Andersson, Gunnar and Fidelis, Krzysztof and Komorowski, Jan},
	month = jul,
	year = {2009},
	keywords = {Forecasting, Gene ontologies, Protein domains, Protein folding, Protein structure, Protein structure prediction, Structural genomics, Structural proteins},
	pages = {e6266},
}

Background Sequence similarity to characterized proteins provides testable functional hypotheses for less than 50% of the proteins identified by genome sequencing projects. With structural genomics it is believed that structural similarities may give functional hypotheses for many of the remaining proteins. Methodology/Principal Findings We provide a systematic analysis of the structure-function relationship in proteins using the novel concept of local descriptors of protein structure. A local descriptor is a small substructure of a protein which includes both short- and long-range interactions. We employ a library of commonly reoccurring local descriptors general enough to assemble most existing protein structures. We then model the relationship between these local shapes and Gene Ontology using rule-based learning. Our IF-THEN rule model offers legible, high resolution descriptions that combine local substructures and is able to discriminate functions even for functionally versatile folds such as the frequently occurring TIM barrel and Rossmann fold. By evaluating the predictive performance of the model, we provide a comprehensive quantification of the structure-function relationship based only on local structure similarity. Our findings are, among others, that conserved structure is a stronger prerequisite for enzymatic activity than for binding specificity, and that structure-based predictions complement sequence-based predictions. The model is capable of generating correct hypotheses, as confirmed by a literature study, even when no significant sequence similarity to characterized proteins exists. Conclusions/Significance Our approach offers a new and complete description and quantification of the structure-function relationship in proteins. By demonstrating how our predictions offer higher sensitivity than using global structure, and complement the use of sequence, we show that the presented ideas could advance the development of meta-servers in function prediction.

@article{leul_phylogeny_2009,
	title = {The phylogeny of uptake hydrogenases in {Frankia}},
	volume = {12},
	issn = {1618-1905},
	doi = {10.2436/20.1501.01.78},
	abstract = {Uptake hydrogenase is an enzyme that is beneficial for nitrogen fixation in bacteria. Recent studies have shown that Frankia sp. has two sets of uptake hydrogenase genes, organized in synton 1 and synton 2. In the present study, phylogenetic analysis of the structural subunits of hydrogenase syntons 1 and 2 showed a distinct clustering pattern between the proteins of Frankia strains that were isolated from different host plants and non-Frankia organisms. The structural subunits of hydrogenase synton 1 of Frankia sp. CpI1, Frankia alni ACN14a, and F. alni AvCI1 were grouped together while those of Frankia spp. CcI3, KB5, UGL140104, and UGL011102 formed another group. The structural subunits of hydrogenase synton 2 of F. alni ACN14a and Frankia spp. CcI3 and BCU110501 grouped together, but those of Frankia spp. KB5 and CpI1, F. alni ArI3, and F. alniAvCI1 comprised a separate group. The structural subunits of hydrogenase syntons 1 and 2 of Frankia sp. EAN1pec were more closely related to those of non-Frankia bacteria, i.e., Streptomyces avermitilis and Anaeromyxobacter sp., respectively, than to those of other Frankia strains, suggesting the occurrence of lateral gene transfer between these organisms. In addition, the accessory Hyp proteins of hydrogenase syntons 1 and 2 of F. alni ACN14a and Frankia sp. CcI3 were shown to be phylogenetically more related to each other than to those of Frankia EAN1pec.},
	language = {eng},
	number = {1},
	journal = {International Microbiology: The Official Journal of the Spanish Society for Microbiology},
	author = {Leul, Melakeselam and Normand, Philippe and Sellstedt, Anita},
	month = mar,
	year = {2009},
	pmid = {19440980},
	keywords = {Bacterial Proteins, Frankia, Genome, Bacterial, Geography, Hydroxyproline, Nitrogen Fixation, Oxidoreductases, Phylogeny},
	pages = {23--28},
}

Uptake hydrogenase is an enzyme that is beneficial for nitrogen fixation in bacteria. Recent studies have shown that Frankia sp. has two sets of uptake hydrogenase genes, organized in synton 1 and synton 2. In the present study, phylogenetic analysis of the structural subunits of hydrogenase syntons 1 and 2 showed a distinct clustering pattern between the proteins of Frankia strains that were isolated from different host plants and non-Frankia organisms. The structural subunits of hydrogenase synton 1 of Frankia sp. CpI1, Frankia alni ACN14a, and F. alni AvCI1 were grouped together while those of Frankia spp. CcI3, KB5, UGL140104, and UGL011102 formed another group. The structural subunits of hydrogenase synton 2 of F. alni ACN14a and Frankia spp. CcI3 and BCU110501 grouped together, but those of Frankia spp. KB5 and CpI1, F. alni ArI3, and F. alniAvCI1 comprised a separate group. The structural subunits of hydrogenase syntons 1 and 2 of Frankia sp. EAN1pec were more closely related to those of non-Frankia bacteria, i.e., Streptomyces avermitilis and Anaeromyxobacter sp., respectively, than to those of other Frankia strains, suggesting the occurrence of lateral gene transfer between these organisms. In addition, the accessory Hyp proteins of hydrogenase syntons 1 and 2 of F. alni ACN14a and Frankia sp. CcI3 were shown to be phylogenetically more related to each other than to those of Frankia EAN1pec.

@article{rae_five_2009,
	title = {Five {QTL} hotspots for yield in short rotation coppice bioenergy poplar: {The} {Poplar} {Biomass} {Loci}},
	volume = {9},
	copyright = {2009 Rae et al; licensee BioMed Central Ltd.},
	issn = {1471-2229},
	shorttitle = {Five {QTL} hotspots for yield in short rotation coppice bioenergy poplar},
	url = {https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-9-23},
	doi = {10/dj94rg},
	abstract = {Concern over land use for non-food bioenergy crops requires breeding programmes that focus on producing biomass on the minimum amount of land that is economically-viable. To achieve this, the maximum potential yield per hectare is a key target for improvement. For long lived tree species, such as poplar, this requires an understanding of the traits that contribute to biomass production and their genetic control. An important aspect of this for long lived plants is an understanding of genetic interactions at different developmental stages, i.e. how genes or genetic regions impact on yield over time. QTL mapping identified regions of genetic control for biomass yield. We mapped consistent QTL across multiple coppice cycles and identified five robust QTL hotspots on linkage groups III, IV, X, XIV and XIX, calling these 'Poplar Biomass Loci' (PBL 1–5). In total 20\% of the variation in final harvest biomass yield was explained by mapped QTL. We also investigated the genetic correlations between yield related traits to identify 'early diagnostic' indicators of yield showing that early biomass was a reasonable predictor of coppice yield and that leaf size, cell number and stem and sylleptic branch number were also valuable traits. These findings provide insight into the genetic control of biomass production and correlation to 'early diagnostic' traits determining yield in poplar SRC for bioenergy. QTL hotspots serve as useful targets for directed breeding for improved biomass productivity that may also be relevant across additional poplar hybrids.},
	language = {en},
	number = {1},
	urldate = {2021-08-20},
	journal = {BMC Plant Biology},
	author = {Rae, Anne M. and Street, Nathaniel Robert and Robinson, Kathryn Megan and Harris, Nicole and Taylor, Gail},
	month = dec,
	year = {2009},
	note = {Number: 1
Publisher: BioMed Central},
	keywords = {Biomass Yield, Linkage Group VIIIa, Short Rotation Coppice, Stem Number, Sylleptic Branch},
	pages = {1--13},
}

Concern over land use for non-food bioenergy crops requires breeding programmes that focus on producing biomass on the minimum amount of land that is economically-viable. To achieve this, the maximum potential yield per hectare is a key target for improvement. For long lived tree species, such as poplar, this requires an understanding of the traits that contribute to biomass production and their genetic control. An important aspect of this for long lived plants is an understanding of genetic interactions at different developmental stages, i.e. how genes or genetic regions impact on yield over time. QTL mapping identified regions of genetic control for biomass yield. We mapped consistent QTL across multiple coppice cycles and identified five robust QTL hotspots on linkage groups III, IV, X, XIV and XIX, calling these 'Poplar Biomass Loci' (PBL 1–5). In total 20% of the variation in final harvest biomass yield was explained by mapped QTL. We also investigated the genetic correlations between yield related traits to identify 'early diagnostic' indicators of yield showing that early biomass was a reasonable predictor of coppice yield and that leaf size, cell number and stem and sylleptic branch number were also valuable traits. These findings provide insight into the genetic control of biomass production and correlation to 'early diagnostic' traits determining yield in poplar SRC for bioenergy. QTL hotspots serve as useful targets for directed breeding for improved biomass productivity that may also be relevant across additional poplar hybrids.

@article{ubeda-tomas_gibberellin_2009,
	title = {Gibberellin {Signaling} in the {Endodermis} {Controls} {Arabidopsis} {Root} {Meristem} {Size}},
	volume = {19},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982209012962},
	doi = {10/dfm6hq},
	language = {en},
	number = {14},
	urldate = {2021-06-08},
	journal = {Current Biology},
	author = {Ubeda-Tomás, Susana and Federici, Fernán and Casimiro, Ilda and Beemster, Gerrit T.S. and Bhalerao, Rishikesh P. and Swarup, Ranjan and Doerner, Peter and Haseloff, Jim and Bennett, Malcolm J.},
	month = jul,
	year = {2009},
	pages = {1194--1199},
}

@article{finley_hierarchical_2009,
	title = {Hierarchical {Spatial} {Modeling} of {Additive} and {Dominance} {Genetic} {Variance} for {Large} {Spatial} {Trial} {Datasets}},
	volume = {65},
	issn = {0006341X},
	url = {http://doi.wiley.com/10.1111/j.1541-0420.2008.01115.x},
	doi = {10/c9kcrv},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Biometrics},
	author = {Finley, Andrew O. and Banerjee, Sudipto and Waldmann, Patrik and Ericsson, Tore},
	month = jun,
	year = {2009},
	pages = {441--451},
}

@article{loha_genetic_2009,
	title = {Genetic variation among and within populations of {Cordia} africana in seed size and germination responses to constant temperatures},
	volume = {165},
	issn = {0014-2336, 1573-5060},
	url = {http://link.springer.com/10.1007/s10681-008-9806-2},
	doi = {10/b5hz8g},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Euphytica},
	author = {Loha, Abraham and Tigabu, Mulualem and Fries, Anders},
	month = jan,
	year = {2009},
	pages = {189--196},
}

@incollection{ruelland_chapter_2009,
	title = {Chapter 2 {Cold} {Signalling} and {Cold} {Acclimation} in {Plants}},
	volume = {49},
	isbn = {978-0-12-374735-8},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0065229608006022},
	language = {en},
	urldate = {2021-06-08},
	booktitle = {Advances in {Botanical} {Research}},
	publisher = {Elsevier},
	author = {Ruelland, Eric and Vaultier, Marie-Noelle and Zachowski, Alain and Hurry, Vaughan},
	year = {2009},
	doi = {10.1016/S0065-2296(08)00602-2},
	pages = {35--150},
}

@article{van_der_merwe_decreased_2009,
	title = {Decreased {Mitochondrial} {Activities} of {Malate} {Dehydrogenase} and {Fumarase} in {Tomato} {Lead} to {Altered} {Root} {Growth} and {Architecture} via {Diverse} {Mechanisms}},
	volume = {149},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/149/2/653/6107909},
	doi = {10/dnz8fc},
	abstract = {Abstract
            Transgenic tomato (Solanum lycopersicum) plants in which either mitochondrial malate dehydrogenase or fumarase was antisense inhibited have previously been characterized to exhibit altered photosynthetic metabolism. Here, we demonstrate that these manipulations also resulted in differences in root growth, with both transgenics being characterized by a dramatic reduction of root dry matter deposition and respiratory activity but opposite changes with respect to root area. A range of physiological, molecular, and biochemical experiments were carried out in order to determine whether changes in root morphology were due to altered metabolism within the root itself, alterations in the nature of the transformants' root exudation, consequences of alteration in the efficiency of photoassimilate delivery to the root, or a combination of these factors. Grafting experiments in which the transformants were reciprocally grafted to wild-type controls suggested that root length and area were determined by the aerial part of the plant but that biomass was not. Despite the transgenic roots displaying alteration in the expression of phytohormone-associated genes, evaluation of the levels of the hormones themselves revealed that, with the exception of gibberellins, they were largely unaltered. When taken together, these combined experiments suggest that root biomass and growth are retarded by root-specific alterations in metabolism and gibberellin contents. These data are discussed in the context of current models of root growth and biomass partitioning.},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {van der Merwe, Margaretha J. and Osorio, Sonia and Moritz, Thomas and Nunes-Nesi, Adriano and Fernie, Alisdair R.},
	month = feb,
	year = {2009},
	pages = {653--669},
}

Abstract Transgenic tomato (Solanum lycopersicum) plants in which either mitochondrial malate dehydrogenase or fumarase was antisense inhibited have previously been characterized to exhibit altered photosynthetic metabolism. Here, we demonstrate that these manipulations also resulted in differences in root growth, with both transgenics being characterized by a dramatic reduction of root dry matter deposition and respiratory activity but opposite changes with respect to root area. A range of physiological, molecular, and biochemical experiments were carried out in order to determine whether changes in root morphology were due to altered metabolism within the root itself, alterations in the nature of the transformants' root exudation, consequences of alteration in the efficiency of photoassimilate delivery to the root, or a combination of these factors. Grafting experiments in which the transformants were reciprocally grafted to wild-type controls suggested that root length and area were determined by the aerial part of the plant but that biomass was not. Despite the transgenic roots displaying alteration in the expression of phytohormone-associated genes, evaluation of the levels of the hormones themselves revealed that, with the exception of gibberellins, they were largely unaltered. When taken together, these combined experiments suggest that root biomass and growth are retarded by root-specific alterations in metabolism and gibberellin contents. These data are discussed in the context of current models of root growth and biomass partitioning.

@article{wu_arabidopsis_2009,
	title = {The {Arabidopsis} {IRX10} and {IRX10}-{LIKE} glycosyltransferases are critical for glucuronoxylan biosynthesis during secondary cell wall formation},
	volume = {57},
	issn = {09607412, 1365313X},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2008.03724.x},
	doi = {10/d3pdnp},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Wu, Ai-Min and Rihouey, Christophe and Seveno, Martial and Hörnblad, Emma and Singh, Sunil Kumar and Matsunaga, Toshiro and Ishii, Tadashi and Lerouge, Patrice and Marchant, Alan},
	month = feb,
	year = {2009},
	pages = {718--731},
}

@article{zida_long-term_2009,
	title = {Long-term effects of prescribed early fire, grazing and selective tree cutting on seedling populations in the {Sudanian} savanna of {Burkina} {Faso}},
	volume = {47},
	issn = {01416707, 13652028},
	url = {http://doi.wiley.com/10.1111/j.1365-2028.2008.01011.x},
	doi = {10/b7w6qg},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {African Journal of Ecology},
	author = {Zida, Didier and Tigabu, Mulualem and Sawadogo, Louis and Tiveau, Daniel and Odén, Per Christer},
	month = mar,
	year = {2009},
	pages = {97--108},
}

@article{wiedermann_can_2009,
	title = {Can small-scale experiments predict ecosystem responses? {An} example from peatlands},
	volume = {118},
	issn = {00301299, 16000706},
	shorttitle = {Can small-scale experiments predict ecosystem responses?},
	url = {http://doi.wiley.com/10.1111/j.1600-0706.2008.17129.x},
	doi = {10/dxrvzs},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Oikos},
	author = {Wiedermann, Magdalena M. and Gunnarsson, Urban and Nilsson, Mats B. and Nordin, Annika and Ericson, Lars},
	month = mar,
	year = {2009},
	pages = {449--456},
}

@article{gronlund_modular_2009,
	title = {Modular gene expression in {Poplar}: a multilayer network approach},
	volume = {181},
	issn = {0028-646X, 1469-8137},
	shorttitle = {Modular gene expression in {Poplar}},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2008.02668.x},
	doi = {10/fm5ggr},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {New Phytologist},
	author = {Grönlund, Andreas and Bhalerao, Rishikesh P. and Karlsson, Jan},
	month = jan,
	year = {2009},
	pages = {315--322},
}

@article{gorzsas_speciation_2009,
	series = {New {Perspectives} on {Vanadium} {Biochemistry}},
	title = {Speciation in aqueous vanadate–ligand and peroxovanadate–ligand systems},
	volume = {103},
	issn = {0162-0134},
	url = {https://www.sciencedirect.com/science/article/pii/S0162013408003036},
	doi = {10/dzgrws},
	abstract = {In the present focused review, the speciation studies of aqueous vanadate–ligand (L) and peroxovanadate–L systems are addressed. The paper focuses solely on the systems studied at our department in the context of potential insulin-enhancing effects, including the following ligands: imidazole, alanylhistidine, alanylserine, lactate, picolinate, citrate, phosphate, maltol, and uridine. We summarise the results of detailed and thorough potentiometric (glass electrode) and 51V NMR (Bruker AMX-500MHz) spectroscopic studies, performed at 25°C in 0.150M Na(Cl), a medium representing human blood. The importance of experimental conditions is discussed and illustrated. A detailed overview of our methodology, based on combining potentiometric and 51V integral and chemical shift data by means of the computer program LAKE, is also given. We list the important steps of equilibrium analysis and the kinds of information available from different sets of NMR spectra. The ligand picolinate is chosen to exemplify our working method, but conclusions are drawn from all systems, reviewing trends and common features. An overview of all systems is given in two tables, including e.g. types and number of species formed. Previously unpublished modelling results at physiological conditions are also shown for all peroxovanadate–ligand systems.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Journal of Inorganic Biochemistry},
	author = {Gorzsás, András and Andersson, Ingegärd and Pettersson, Lage},
	month = apr,
	year = {2009},
	keywords = {51V NMR, Alanylhistidine, Alanylserine, Aqueous speciation, Citrate, Imidazole, Lactate, Maltol, Peroxovanadates, Phosphate, Physiological conditions, Picolinate, Uridine, Vanadates},
	pages = {517--526},
}

In the present focused review, the speciation studies of aqueous vanadate–ligand (L) and peroxovanadate–L systems are addressed. The paper focuses solely on the systems studied at our department in the context of potential insulin-enhancing effects, including the following ligands: imidazole, alanylhistidine, alanylserine, lactate, picolinate, citrate, phosphate, maltol, and uridine. We summarise the results of detailed and thorough potentiometric (glass electrode) and 51V NMR (Bruker AMX-500MHz) spectroscopic studies, performed at 25°C in 0.150M Na(Cl), a medium representing human blood. The importance of experimental conditions is discussed and illustrated. A detailed overview of our methodology, based on combining potentiometric and 51V integral and chemical shift data by means of the computer program LAKE, is also given. We list the important steps of equilibrium analysis and the kinds of information available from different sets of NMR spectra. The ligand picolinate is chosen to exemplify our working method, but conclusions are drawn from all systems, reviewing trends and common features. An overview of all systems is given in two tables, including e.g. types and number of species formed. Previously unpublished modelling results at physiological conditions are also shown for all peroxovanadate–ligand systems.

@article{klevebring_genome-wide_2009,
	title = {Genome-wide profiling of populus small {RNAs}},
	volume = {10},
	issn = {1471-2164},
	doi = {10/d7t35k},
	abstract = {BACKGROUND: Short RNAs, and in particular microRNAs, are important regulators of gene expression both within defined regulatory pathways and at the epigenetic scale. We investigated the short RNA (sRNA) population (18-24 nt) of the transcriptome of green leaves from the sequenced Populus trichocarpa using a concatenation strategy in combination with 454 sequencing.
RESULTS: The most abundant size class of sRNAs were 24 nt. Long Terminal Repeats were particularly associated with 24 nt sRNAs. Additionally, some repetitive elements were associated with 22 nt sRNAs. We identified an sRNA hot-spot on chromosome 19, overlapping a region containing both the proposed sex-determining locus and a major cluster of NBS-LRR genes. A number of phased siRNA loci were identified, a subset of which are predicted to target PPR and NBS-LRR disease resistance genes, classes of genes that have been significantly expanded in Populus. Additional loci enriched for sRNA production were identified and characterised. We identified 15 novel predicted microRNAs (miRNAs), including miRNA*sequences, and identified a novel locus that may encode a dual miRNA or a miRNA and short interfering RNAs (siRNAs).
CONCLUSIONS: The short RNA population of P. trichocarpa is at least as complex as that of Arabidopsis thaliana. We provide a first genome-wide view of short RNA production for P. trichocarpa and identify new, non-conserved miRNAs.},
	language = {eng},
	journal = {BMC genomics},
	author = {Klevebring, Daniel and Street, Nathaniel R. and Fahlgren, Noah and Kasschau, Kristin D. and Carrington, James C. and Lundeberg, Joakim and Jansson, Stefan},
	month = dec,
	year = {2009},
	pmid = {20021695},
	pmcid = {PMC2811130},
	keywords = {Chromosomes, Plant, Genome, Plant, Genome-Wide Association Study, MicroRNAs, Plant Leaves, Populus, RNA, Plant, RNA, Small Interfering},
	pages = {620},
}

BACKGROUND: Short RNAs, and in particular microRNAs, are important regulators of gene expression both within defined regulatory pathways and at the epigenetic scale. We investigated the short RNA (sRNA) population (18-24 nt) of the transcriptome of green leaves from the sequenced Populus trichocarpa using a concatenation strategy in combination with 454 sequencing. RESULTS: The most abundant size class of sRNAs were 24 nt. Long Terminal Repeats were particularly associated with 24 nt sRNAs. Additionally, some repetitive elements were associated with 22 nt sRNAs. We identified an sRNA hot-spot on chromosome 19, overlapping a region containing both the proposed sex-determining locus and a major cluster of NBS-LRR genes. A number of phased siRNA loci were identified, a subset of which are predicted to target PPR and NBS-LRR disease resistance genes, classes of genes that have been significantly expanded in Populus. Additional loci enriched for sRNA production were identified and characterised. We identified 15 novel predicted microRNAs (miRNAs), including miRNA*sequences, and identified a novel locus that may encode a dual miRNA or a miRNA and short interfering RNAs (siRNAs). CONCLUSIONS: The short RNA population of P. trichocarpa is at least as complex as that of Arabidopsis thaliana. We provide a first genome-wide view of short RNA production for P. trichocarpa and identify new, non-conserved miRNAs.

@article{hanson_sugar_2009,
	title = {Sugar perception and signaling--an update},
	volume = {12},
	issn = {1879-0356},
	doi = {10/b87fkq},
	abstract = {Sugars act as potent signaling molecules in plants. Several sugar sensors, including the highly studied glucose sensor HEXOKINASE1 (HXK1), have been identified or proposed. Many additional sensors likely exist, as plants respond to other sugars and sugar metabolites, such as sucrose and trehalose 6-phosphate. Sugar sensing and signaling is a highly complex process resulting in many changes in physiology and development and is integrated with other signaling pathways in plants such as those for inorganic nutrients, hormones, and different stress factors. Importantly, KIN10 and KIN11 protein kinases are central in coordinating several of the responses to sugars and stress. bZIP transcription factors were found to mediate effects of sugar signaling on gene expression and metabolite content.},
	language = {eng},
	number = {5},
	journal = {Current Opinion in Plant Biology},
	author = {Hanson, Johannes and Smeekens, Sjef},
	month = oct,
	year = {2009},
	pmid = {19716759},
	keywords = {Basic-Leucine Zipper Transcription Factors, Carbohydrate Metabolism, Gene Expression Regulation, Plant, Hexokinase, Plant Development, Plant Proteins, Plants, Signal Transduction, Sucrose, Sugar Phosphates, Trehalose},
	pages = {562--567},
}

Sugars act as potent signaling molecules in plants. Several sugar sensors, including the highly studied glucose sensor HEXOKINASE1 (HXK1), have been identified or proposed. Many additional sensors likely exist, as plants respond to other sugars and sugar metabolites, such as sucrose and trehalose 6-phosphate. Sugar sensing and signaling is a highly complex process resulting in many changes in physiology and development and is integrated with other signaling pathways in plants such as those for inorganic nutrients, hormones, and different stress factors. Importantly, KIN10 and KIN11 protein kinases are central in coordinating several of the responses to sugars and stress. bZIP transcription factors were found to mediate effects of sugar signaling on gene expression and metabolite content.

@article{hummel_sucrose-mediated_2009,
	title = {Sucrose-mediated translational control},
	volume = {104},
	issn = {1095-8290},
	doi = {10/bwnw47},
	abstract = {BACKGROUND: Environmental factors greatly impact plant gene expression and concentrations of cellular metabolites such as sugars and amino acids. The changed metabolite concentrations affect the expression of many genes both transcriptionally and post-transcriptionally.
RECENT PROGRESS: Sucrose acts as a signalling molecule in the control of translation of the S1 class basic leucine zipper transcription factor (bZIP) genes. In these genes the main bZIP open reading frames (ORFs) are preceded by upstream open reading frames (uORFs). The presence of uORFs generally inhibits translation of the following ORF but can also be instrumental in specific translational control. bZIP11, a member of the S1 class bZIP genes, harbours four uORFs of which uORF2 is required for translational control in response to sucrose concentrations. This uORF encodes the Sucrose Control peptide (SC-peptide), which is evolutionarily conserved among all S1 class bZIP genes in different plant species. Arabidopsis thaliana bZIP11 and related bZIP genes seem to be important regulators of metabolism. These proteins are targets of the Snf1-related protein kinase 1 (SnRK1) KIN10 and KIN11, which are responsive to energy deprivation as well as to various stresses. In response to energy deprivation, ribosomal biogenesis is repressed to preserve cellular function and maintenance. Other key regulators of ribosomal biogenesis such as the protein kinase Target of Rapamycin (TOR) are tightly regulated in response to stress.
CONCLUSIONS: Plants use translational control of gene expression to optimize growth and development in response to stress as well as to energy deprivation. This Botanical Briefing discusses the role of sucrose signalling in the translational control of bZIP11 and the regulation of ribosomal biogenesis in response to metabolic changes and stress conditions.},
	language = {eng},
	number = {1},
	journal = {Annals of Botany},
	author = {Hummel, Maureen and Rahmani, Fatima and Smeekens, Sjef and Hanson, Johannes},
	month = jul,
	year = {2009},
	pmid = {19376782},
	pmcid = {PMC2706714},
	keywords = {Arabidopsis, Basic-Leucine Zipper Transcription Factors, Gene Expression Regulation, Plant, Open Reading Frames, Plant Proteins, Sucrose},
	pages = {1--7},
}

BACKGROUND: Environmental factors greatly impact plant gene expression and concentrations of cellular metabolites such as sugars and amino acids. The changed metabolite concentrations affect the expression of many genes both transcriptionally and post-transcriptionally. RECENT PROGRESS: Sucrose acts as a signalling molecule in the control of translation of the S1 class basic leucine zipper transcription factor (bZIP) genes. In these genes the main bZIP open reading frames (ORFs) are preceded by upstream open reading frames (uORFs). The presence of uORFs generally inhibits translation of the following ORF but can also be instrumental in specific translational control. bZIP11, a member of the S1 class bZIP genes, harbours four uORFs of which uORF2 is required for translational control in response to sucrose concentrations. This uORF encodes the Sucrose Control peptide (SC-peptide), which is evolutionarily conserved among all S1 class bZIP genes in different plant species. Arabidopsis thaliana bZIP11 and related bZIP genes seem to be important regulators of metabolism. These proteins are targets of the Snf1-related protein kinase 1 (SnRK1) KIN10 and KIN11, which are responsive to energy deprivation as well as to various stresses. In response to energy deprivation, ribosomal biogenesis is repressed to preserve cellular function and maintenance. Other key regulators of ribosomal biogenesis such as the protein kinase Target of Rapamycin (TOR) are tightly regulated in response to stress. CONCLUSIONS: Plants use translational control of gene expression to optimize growth and development in response to stress as well as to energy deprivation. This Botanical Briefing discusses the role of sucrose signalling in the translational control of bZIP11 and the regulation of ribosomal biogenesis in response to metabolic changes and stress conditions.

@article{rahmani_sucrose_2009,
	title = {Sucrose control of translation mediated by an upstream open reading frame-encoded peptide},
	volume = {150},
	issn = {0032-0889},
	doi = {10/dzt95k},
	abstract = {Regulation of gene expression through translational control is common in many organisms. The Arabidopsis (Arabidopsis thaliana) transcription factor bZIP11 is translational repressed in response to sucrose (Suc), resulting in Suc-regulated changes in amino acid metabolism. The 5' leader of the bZIP11 mRNA harbors several upstream open reading frames (uORFs), of which the second uORF is well conserved among bZIP11 homologous genes. The uORF2 element encodes a Suc control peptide (SC-peptide) of 28 residues that is sufficient for imposing Suc-induced repression of translation (SIRT) on a heterologous mRNA. Detailed analysis of the SC-peptide suggests that it functions as an attenuator peptide. Results suggest that the SC-peptide inhibits bZIP11 translation in response to high Suc levels by stalling the ribosome on the mRNA. The conserved noncanonical AUG contexts of bZIP11 uORFs allow inefficient translational initiation of the uORF, resulting in translation initiation of the scanning ribosome at the AUG codon of the bZIP11 main ORF. The results presented show that Suc-dependent signaling mediates differential translation of mRNAs containing SC-peptides encoding uORFs.},
	language = {eng},
	number = {3},
	journal = {Plant Physiology},
	author = {Rahmani, Fatemeh and Hummel, Maureen and Schuurmans, Jolanda and Wiese-Klinkenberg, Anika and Smeekens, Sjef and Hanson, Johannes},
	month = jul,
	year = {2009},
	pmid = {19403731},
	pmcid = {PMC2705056},
	keywords = {Amino Acid Sequence, Arabidopsis, Arabidopsis Proteins, Base Sequence, Basic-Leucine Zipper Transcription Factors, Conserved Sequence, Gene Expression Regulation, Plant, Molecular Sequence Data, Open Reading Frames, Protein Biosynthesis, RNA, Messenger, Sequence Analysis, RNA, Sucrose},
	pages = {1356--1367},
}

Regulation of gene expression through translational control is common in many organisms. The Arabidopsis (Arabidopsis thaliana) transcription factor bZIP11 is translational repressed in response to sucrose (Suc), resulting in Suc-regulated changes in amino acid metabolism. The 5' leader of the bZIP11 mRNA harbors several upstream open reading frames (uORFs), of which the second uORF is well conserved among bZIP11 homologous genes. The uORF2 element encodes a Suc control peptide (SC-peptide) of 28 residues that is sufficient for imposing Suc-induced repression of translation (SIRT) on a heterologous mRNA. Detailed analysis of the SC-peptide suggests that it functions as an attenuator peptide. Results suggest that the SC-peptide inhibits bZIP11 translation in response to high Suc levels by stalling the ribosome on the mRNA. The conserved noncanonical AUG contexts of bZIP11 uORFs allow inefficient translational initiation of the uORF, resulting in translation initiation of the scanning ribosome at the AUG codon of the bZIP11 main ORF. The results presented show that Suc-dependent signaling mediates differential translation of mRNAs containing SC-peptides encoding uORFs.

@article{weltmeier_expression_2009,
	title = {Expression patterns within the {Arabidopsis} {C}/{S1} {bZIP} transcription factor network: availability of heterodimerization partners controls gene expression during stress response and development},
	volume = {69},
	issn = {0167-4412},
	shorttitle = {Expression patterns within the {Arabidopsis} {C}/{S1} {bZIP} transcription factor network},
	doi = {10/dqff6q},
	abstract = {Members of the Arabidopsis group C/S1 basic leucine zipper (bZIP) transcription factor (TF) network are proposed to implement transcriptional reprogramming of plant growth in response to energy deprivation and environmental stresses. The four group C and five group S1 members form specific heterodimers and are, therefore, considered to cooperate functionally. For example, the interplay of C/S1 bZIP TFs in regulating seed maturation genes was analyzed by expression studies and target gene regulation in both protoplasts and transgenic plants. The abundance of the heterodimerization partners significantly affects target gene transcription. Therefore, a detailed analysis of the developmental and stress related expression patterns was performed by comparing promoter: GUS and transcription data. The idea that the C/S1 network plays a role in the allocation of nutrients is supported by the defined and partially overlapping expression patterns in sink leaves, seeds and anthers. Accordingly, metabolic signals strongly affect bZIP expression on the transcriptional and/or post-transcriptional level. Sucrose induced repression of translation (SIRT) was demonstrated for all group S1 bZIPs. In particular, transcription of group S1 genes strongly responds to various abiotic stresses, such as salt (AtbZIP1) or cold (AtbZIP44). In summary, heterodimerization and expression data provide a basic framework to further determine the functional impact of the C/S1 network in regulating the plant energy balance and nutrient allocation.},
	language = {eng},
	number = {1-2},
	journal = {Plant Molecular Biology},
	author = {Weltmeier, Fridtjof and Rahmani, Fatima and Ehlert, Andrea and Dietrich, Katrin and Schütze, Katia and Wang, Xuan and Chaban, Christina and Hanson, Johannes and Teige, Markus and Harter, Klaus and Vicente-Carbajosa, Jesus and Smeekens, Sjef and Dröge-Laser, Wolfgang},
	month = jan,
	year = {2009},
	pmid = {18841482},
	pmcid = {PMC2709229},
	keywords = {Arabidopsis, Basic-Leucine Zipper Transcription Factors, Dimerization, Gene Expression Regulation, Plant, Stress, Physiological},
	pages = {107--119},
}

Members of the Arabidopsis group C/S1 basic leucine zipper (bZIP) transcription factor (TF) network are proposed to implement transcriptional reprogramming of plant growth in response to energy deprivation and environmental stresses. The four group C and five group S1 members form specific heterodimers and are, therefore, considered to cooperate functionally. For example, the interplay of C/S1 bZIP TFs in regulating seed maturation genes was analyzed by expression studies and target gene regulation in both protoplasts and transgenic plants. The abundance of the heterodimerization partners significantly affects target gene transcription. Therefore, a detailed analysis of the developmental and stress related expression patterns was performed by comparing promoter: GUS and transcription data. The idea that the C/S1 network plays a role in the allocation of nutrients is supported by the defined and partially overlapping expression patterns in sink leaves, seeds and anthers. Accordingly, metabolic signals strongly affect bZIP expression on the transcriptional and/or post-transcriptional level. Sucrose induced repression of translation (SIRT) was demonstrated for all group S1 bZIPs. In particular, transcription of group S1 genes strongly responds to various abiotic stresses, such as salt (AtbZIP1) or cold (AtbZIP44). In summary, heterodimerization and expression data provide a basic framework to further determine the functional impact of the C/S1 network in regulating the plant energy balance and nutrient allocation.

@article{robert_powerful_2009,
	title = {Powerful partners: {Arabidopsis} and chemical genomics},
	volume = {7},
	issn = {1543-8120},
	shorttitle = {Powerful partners},
	doi = {10/fwnm6m},
	abstract = {Chemical genomics (i.e. genomics scale chemical genetics) approaches capitalize on the ability of low molecular mass molecules to modify biological processes. Such molecules are used to modify the activity of a protein or a pathway in a manner that it is tunable and reversible. Bioactive chemicals resulting from forward or reverse chemical screens can be useful in understanding and dissecting complex biological processes due to the essentially limitless variation in structure and activities inherent in chemical space. A major advantage of this approach as a powerful addition to conventional plant genetics is the fact that chemical genomics can address loss-of-function lethality and redundancy. Furthermore, the ability of chemicals to be added at will and to act quickly can permit the study of processes that are highly dynamic such as endomembrane trafficking. An important aspect of utilizing small molecules effectively is to characterize bioactive chemicals in detail including an understanding of structure-activity relationships and the identification of active and inactive analogs. Bioactive chemicals can be useful as reagents to probe biological pathways directly. However, the identification of cognate targets and their pathways is also informative and can be achieved by screens for genetic resistance or hypersensitivity in Arabidopsis thaliana or other organisms from which the results can be translated to plants. In addition, there are approaches utilizing "tagged" chemical libraries that possess reactive moieties permitting the immobilization of active compounds. This opens the possibility for biochemical purification of putative cognate targets. We will review approaches to screen for bioactive chemicals that affect biological processes in Arabidopsis and provide several examples of the power and challenges inherent in this new approach in plant biology.},
	language = {eng},
	journal = {The Arabidopsis Book},
	author = {Robert, Stéphanie and Raikhel, Natasha V. and Hicks, Glenn R.},
	year = {2009},
	pmid = {22303245},
	pmcid = {PMC3243329},
	pages = {e0109},
}

Chemical genomics (i.e. genomics scale chemical genetics) approaches capitalize on the ability of low molecular mass molecules to modify biological processes. Such molecules are used to modify the activity of a protein or a pathway in a manner that it is tunable and reversible. Bioactive chemicals resulting from forward or reverse chemical screens can be useful in understanding and dissecting complex biological processes due to the essentially limitless variation in structure and activities inherent in chemical space. A major advantage of this approach as a powerful addition to conventional plant genetics is the fact that chemical genomics can address loss-of-function lethality and redundancy. Furthermore, the ability of chemicals to be added at will and to act quickly can permit the study of processes that are highly dynamic such as endomembrane trafficking. An important aspect of utilizing small molecules effectively is to characterize bioactive chemicals in detail including an understanding of structure-activity relationships and the identification of active and inactive analogs. Bioactive chemicals can be useful as reagents to probe biological pathways directly. However, the identification of cognate targets and their pathways is also informative and can be achieved by screens for genetic resistance or hypersensitivity in Arabidopsis thaliana or other organisms from which the results can be translated to plants. In addition, there are approaches utilizing "tagged" chemical libraries that possess reactive moieties permitting the immobilization of active compounds. This opens the possibility for biochemical purification of putative cognate targets. We will review approaches to screen for bioactive chemicals that affect biological processes in Arabidopsis and provide several examples of the power and challenges inherent in this new approach in plant biology.

@article{elo_stem_2009,
	title = {Stem cell function during plant vascular development},
	volume = {20},
	issn = {10849521},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1084952109001748},
	doi = {10/fqztz4},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {Seminars in Cell \& Developmental Biology},
	author = {Elo, A. and Immanen, J. and Nieminen, K. and Helariutta, Y.},
	month = dec,
	year = {2009},
	pages = {1097--1106},
}

@article{drakakaki_chemical_2009,
	title = {Chemical dissection of endosomal pathways},
	volume = {4},
	issn = {1559-2316},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2634075/},
	abstract = {Membrane trafficking and associated signal transduction pathways are critical for plant development and responses to environment. These transduction pathways, including those for brassinosteroids and auxins, require endocytosis to endosomes and recycling back to the plasma membrane. A major challenge toward understanding these processes and their biological roles has been the highly dynamic nature of endomembrane trafficking. To effectively study endocytosis and recycling, which occur in a time frame of minutes, bioactive chemicals provide a powerful and exacting tool. Pharmacological inhibitors such as Brefeldin A (BFA) and the newly identified Endosidin 1 (ES1) have been used to define endosome compartments. ES1 is a clear example of the ability of chemicals to dissect even distinct subpopulations of endosomes involved in trafficking and signal transduction. The ability to characterize and dissect such highly dynamic pathways in a temporal and spatial manner is possible only using pharmacological reagents which can act rapidly and reversibly.},
	number = {1},
	urldate = {2021-06-08},
	journal = {Plant Signaling \& Behavior},
	author = {Drakakaki, Georgia and Robert, Stéphanie and Raikhel, Natasha V and Hicks, Glenn R},
	month = jan,
	year = {2009},
	pmid = {19704710},
	pmcid = {PMC2634075},
	pages = {57--62},
}

Membrane trafficking and associated signal transduction pathways are critical for plant development and responses to environment. These transduction pathways, including those for brassinosteroids and auxins, require endocytosis to endosomes and recycling back to the plasma membrane. A major challenge toward understanding these processes and their biological roles has been the highly dynamic nature of endomembrane trafficking. To effectively study endocytosis and recycling, which occur in a time frame of minutes, bioactive chemicals provide a powerful and exacting tool. Pharmacological inhibitors such as Brefeldin A (BFA) and the newly identified Endosidin 1 (ES1) have been used to define endosome compartments. ES1 is a clear example of the ability of chemicals to dissect even distinct subpopulations of endosomes involved in trafficking and signal transduction. The ability to characterize and dissect such highly dynamic pathways in a temporal and spatial manner is possible only using pharmacological reagents which can act rapidly and reversibly.

@article{van_der_merwe_role_2009,
	title = {The role and regulation of the tricarboxylic acid cycle in {Solanum} lycopersicum roots},
	volume = {75},
	issn = {02546299},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0254629909001203},
	doi = {10/d84qt3},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {South African Journal of Botany},
	author = {Van der Merwe, M.J. and Osorio, S. and Moritz, T. and Nunes-Nesi, A. and Fernie, A.R.},
	month = apr,
	year = {2009},
	pages = {424},
}

@article{ibatullin_real-time_2009,
	title = {A {Real}-{Time} {Fluorogenic} {Assay} for the {Visualization} of {Glycoside} {Hydrolase} {Activity} in {Planta}},
	volume = {151},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/151/4/1741-1750/6109797},
	doi = {10/b6s8sm},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Ibatullin, Farid M. and Banasiak, Alicja and Baumann, Martin J. and Greffe, Lionel and Takahashi, Junko and Mellerowicz, Ewa J. and Brumer, Harry},
	month = dec,
	year = {2009},
	pages = {1741--1750},
}

@article{granlund_tl29_2009,
	title = {The {TL29} {Protein} is {Lumen} {Located}, {Associated} with {PSII} and {Not} an {Ascorbate} {Peroxidase}},
	volume = {50},
	issn = {1471-9053, 0032-0781},
	url = {https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/pcp134},
	doi = {10/czm8h2},
	language = {en},
	number = {11},
	urldate = {2021-06-08},
	journal = {Plant and Cell Physiology},
	author = {Granlund, Irene and Storm, Patrik and Schubert, Maria and García-Cerdán, José G. and Funk, Christiane and Schröder, Wolfgang P.},
	month = nov,
	year = {2009},
	pages = {1898--1910},
}

@article{nilsson_plant_2009,
	title = {Plant {Evolution}: {Measuring} the {Length} of the {Day}},
	volume = {19},
	issn = {09609822},
	shorttitle = {Plant {Evolution}},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982209006782},
	doi = {10/bd48qv},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {Current Biology},
	author = {Nilsson, Ove},
	month = apr,
	year = {2009},
	pages = {R302--R303},
}

@article{felten_ectomycorrhizal_2009,
	title = {The {Ectomycorrhizal} {Fungus} \textit{{Laccaria} bicolor} {Stimulates} {Lateral} {Root} {Formation} in {Poplar} and {Arabidopsis} through {Auxin} {Transport} and {Signaling}},
	volume = {151},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/151/4/1991/6109870},
	doi = {10/dsjkhv},
	abstract = {Abstract
            The early phase of the interaction between tree roots and ectomycorrhizal fungi, prior to symbiosis establishment, is accompanied by a stimulation of lateral root (LR) development. We aimed to identify gene networks that regulate LR development during the early signal exchanges between poplar (Populus tremula × Populus alba) and the ectomycorrhizal fungus Laccaria bicolor with a focus on auxin transport and signaling pathways. Our data demonstrated that increased LR development in poplar and Arabidopsis (Arabidopsis thaliana) interacting with L. bicolor is not dependent on the ability of the plant to form ectomycorrhizae. LR stimulation paralleled an increase in auxin accumulation at root apices. Blocking plant polar auxin transport with 1-naphthylphthalamic acid inhibited LR development and auxin accumulation. An oligoarray-based transcript profile of poplar roots exposed to molecules released by L. bicolor revealed the differential expression of 2,945 genes, including several components of polar auxin transport (PtaPIN and PtaAUX genes), auxin conjugation (PtaGH3 genes), and auxin signaling (PtaIAA genes). Transcripts of PtaPIN9, the homolog of Arabidopsis AtPIN2, and several PtaIAAs accumulated specifically during the early interaction phase. Expression of these rapidly induced genes was repressed by 1-naphthylphthalamic acid. Accordingly, LR stimulation upon contact with L. bicolor in Arabidopsis transgenic plants defective in homologs of these genes was decreased or absent. Furthermore, in Arabidopsis pin2, the root apical auxin increase during contact with the fungus was modified. We propose a model in which fungus-induced auxin accumulation at the root apex stimulates LR formation through a mechanism involving PtaPIN9-dependent auxin redistribution together with PtaIAA-based auxin signaling.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Felten, Judith and Kohler, Annegret and Morin, Emmanuelle and Bhalerao, Rishikesh P. and Palme, Klaus and Martin, Francis and Ditengou, Franck A. and Legué, Valérie},
	month = dec,
	year = {2009},
	pages = {1991--2005},
}

Abstract The early phase of the interaction between tree roots and ectomycorrhizal fungi, prior to symbiosis establishment, is accompanied by a stimulation of lateral root (LR) development. We aimed to identify gene networks that regulate LR development during the early signal exchanges between poplar (Populus tremula × Populus alba) and the ectomycorrhizal fungus Laccaria bicolor with a focus on auxin transport and signaling pathways. Our data demonstrated that increased LR development in poplar and Arabidopsis (Arabidopsis thaliana) interacting with L. bicolor is not dependent on the ability of the plant to form ectomycorrhizae. LR stimulation paralleled an increase in auxin accumulation at root apices. Blocking plant polar auxin transport with 1-naphthylphthalamic acid inhibited LR development and auxin accumulation. An oligoarray-based transcript profile of poplar roots exposed to molecules released by L. bicolor revealed the differential expression of 2,945 genes, including several components of polar auxin transport (PtaPIN and PtaAUX genes), auxin conjugation (PtaGH3 genes), and auxin signaling (PtaIAA genes). Transcripts of PtaPIN9, the homolog of Arabidopsis AtPIN2, and several PtaIAAs accumulated specifically during the early interaction phase. Expression of these rapidly induced genes was repressed by 1-naphthylphthalamic acid. Accordingly, LR stimulation upon contact with L. bicolor in Arabidopsis transgenic plants defective in homologs of these genes was decreased or absent. Furthermore, in Arabidopsis pin2, the root apical auxin increase during contact with the fungus was modified. We propose a model in which fungus-induced auxin accumulation at the root apex stimulates LR formation through a mechanism involving PtaPIN9-dependent auxin redistribution together with PtaIAA-based auxin signaling.

@article{krzeslowska_pectinous_2009,
	title = {Pectinous cell wall thickenings formation—{A} response of moss protonemata cells to lead},
	volume = {65},
	issn = {00988472},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0098847208000658},
	doi = {10/dtk55h},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Environmental and Experimental Botany},
	author = {Krzeslowska, M and Lenartowska, M and Mellerowicz, E and Samardakiewicz, S and Wozny, A},
	month = jan,
	year = {2009},
	pages = {119--131},
}

@article{pesaresi_mutants_2009,
	title = {Mutants, {Overexpressors}, and {Interactors} of {Arabidopsis} {Plastocyanin} {Isoforms}: {Revised} {Roles} of {Plastocyanin} in {Photosynthetic} {Electron} {Flow} and {Thylakoid} {Redox} {State}},
	volume = {2},
	issn = {16742052},
	shorttitle = {Mutants, {Overexpressors}, and {Interactors} of {Arabidopsis} {Plastocyanin} {Isoforms}},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1674205214604676},
	doi = {10/frhmt4},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Molecular Plant},
	author = {Pesaresi, Paolo and Scharfenberg, Michael and Weigel, Martin and Granlund, Irene and Schröder, Wolfgang P. and Finazzi, Giovanni and Rappaport, Fabrice and Masiero, Simona and Furini, Antonella and Jahns, Peter and Leister, Dario},
	month = mar,
	year = {2009},
	pages = {236--248},
}

@article{pacurar_model_2009,
	title = {Model organisms - {A} journey from the dawn of biological research to the post-genomic era},
	volume = {14},
	abstract = {The study of models organisms has been the core of biological research for many decades. The amount of information collected from the research conducted on these species in the laboratories across the world is enormous, and the progress made in all fields of biology is highly tributary to them. Historically, the big breakthroughs that represent milestones in biological research go hand in hand with the discovery and development of different model organism species. The aim of this review is to underline the most important contributions brought to science by the 'classical models' and, further, to draw attention to newcomers in the field, that are expected to fill up the gaps and answer the most specific question we face in biology in the post-genomic era.},
	journal = {Romanian Biotechnological Letters Biological Sciences REVIEW},
	author = {Pacurar, Daniel},
	month = jan,
	year = {2009},
	keywords = {⛔ No DOI found},
	pages = {4087--4094},
}

The study of models organisms has been the core of biological research for many decades. The amount of information collected from the research conducted on these species in the laboratories across the world is enormous, and the progress made in all fields of biology is highly tributary to them. Historically, the big breakthroughs that represent milestones in biological research go hand in hand with the discovery and development of different model organism species. The aim of this review is to underline the most important contributions brought to science by the 'classical models' and, further, to draw attention to newcomers in the field, that are expected to fill up the gaps and answer the most specific question we face in biology in the post-genomic era.

@article{kumar_juvenile-mature_2009,
	title = {Juvenile-mature wood transition in pine: correlation between wood properties and candidate gene expression profiles},
	volume = {166},
	issn = {0014-2336, 1573-5060},
	shorttitle = {Juvenile-mature wood transition in pine},
	url = {http://link.springer.com/10.1007/s10681-008-9815-1},
	doi = {10/d5vgsg},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Euphytica},
	author = {Kumar, Manoj and Saranpää, Pekka and Barnett, John R. and Wilkinson, Michael J.},
	month = apr,
	year = {2009},
	pages = {341--355},
}

@article{dettmer_hormone_2009,
	title = {Hormone interactions during vascular development},
	volume = {69},
	issn = {0167-4412, 1573-5028},
	url = {http://link.springer.com/10.1007/s11103-008-9374-9},
	doi = {10/dctr8m},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Molecular Biology},
	author = {Dettmer, Jan and Elo, Annakaisa and Helariutta, Ykä},
	month = mar,
	year = {2009},
	pages = {347--360},
}

@article{hallander_optimization_2009,
	title = {Optimization of selection contribution and mate allocations in monoecious tree breeding populations},
	volume = {10},
	issn = {1471-2156},
	url = {https://bmcgenet.biomedcentral.com/articles/10.1186/1471-2156-10-70},
	doi = {10/bp98q7},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Genetics},
	author = {Hallander, Jon and Waldmann, Patrik},
	month = dec,
	year = {2009},
	pages = {70},
}

@article{nordin_complex_2009,
	title = {Complex {Biotic} {Interactions} {Drive} {Long}-{Term} {Vegetation} {Change} in a {Nitrogen} {Enriched} {Boreal} {Forest}},
	volume = {12},
	issn = {1432-9840, 1435-0629},
	url = {http://link.springer.com/10.1007/s10021-009-9287-8},
	doi = {10/dtjs7b},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {Ecosystems},
	author = {Nordin, Annika and Strengbom, Joachim and Forsum, Åsa and Ericson, Lars},
	month = nov,
	year = {2009},
	pages = {1204--1211},
}

@article{mcdonnell_ethylene_2009,
	title = {Ethylene levels are regulated by a plant encoded 1-aminocyclopropane-1-carboxylic acid deaminase},
	volume = {136},
	issn = {00319317, 13993054},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2009.01208.x},
	doi = {10/bmrpvv},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {McDonnell, Lisa and Plett, Jonathan M. and Andersson-Gunnerås, Sara and Kozela, Christopher and Dugardeyn, Jasper and Van Der Straeten, Dominique and Glick, Bernard R. and Sundberg, Björn and Regan, Sharon},
	month = may,
	year = {2009},
	pages = {94--109},
}

@article{ingelsson_peptidylprolyl_2009,
	title = {Peptidyl–{Prolyl} {Isomerase} {Activity} in {Chloroplast} {Thylakoid} {Lumen} is a {Dispensable} {Function} of {Immunophilins} in {Arabidopsis} thaliana},
	volume = {50},
	issn = {1471-9053, 0032-0781},
	url = {https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/pcp122},
	doi = {10/b5nq9q},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {Plant and Cell Physiology},
	author = {Ingelsson, Björn and Shapiguzov, Alexey and Kieselbach, Thomas and Vener, Alexander V.},
	month = oct,
	year = {2009},
	pages = {1801--1814},
}

@article{gapare_genetic_2009,
	title = {Genetic correlations among juvenile wood quality and growth traits and implications for selection strategy in {Pinus} radiata {D}. {Don}},
	volume = {66},
	issn = {1286-4560, 1297-966X},
	url = {http://link.springer.com/10.1051/forest/2009044},
	doi = {10/bbnt8q},
	abstract = {Juvenile wood quality in Pinus radiata is affected by factors such as low density, stiffness, and high microfibril angle, spiral grain, and shrinkage. Adverse genetic correlations between growth and wood quality traits remain as one of the main constraints in radiata pine advanced generation selection breeding program.},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Annals of Forest Science},
	author = {Gapare, Washington J. and Baltunis, Brian S. and Ivković, Miloš and Wu, Harry X.},
	month = jan,
	year = {2009},
	pages = {606--606},
}

Juvenile wood quality in Pinus radiata is affected by factors such as low density, stiffness, and high microfibril angle, spiral grain, and shrinkage. Adverse genetic correlations between growth and wood quality traits remain as one of the main constraints in radiata pine advanced generation selection breeding program.

@article{li_generation_2009,
	title = {Generation and analysis of expressed sequence tags from six developing xylem libraries in {Pinus} radiata {D}. {Don}},
	volume = {10},
	issn = {1471-2164},
	doi = {10/b946xz},
	abstract = {BACKGROUND: Wood is a major renewable natural resource for the timber, fibre and bioenergy industry. Pinus radiata D. Don is the most important commercial plantation tree species in Australia and several other countries; however, genomic resources for this species are very limited in public databases. Our primary objective was to sequence a large number of expressed sequence tags (ESTs) from genes involved in wood formation in radiata pine.
RESULTS: Six developing xylem cDNA libraries were constructed from earlywood and latewood tissues sampled at juvenile (7 yrs), transition (11 yrs) and mature (30 yrs) ages, respectively. These xylem tissues represent six typical development stages in a rotation period of radiata pine. A total of 6,389 high quality ESTs were collected from 5,952 cDNA clones. Assembly of 5,952 ESTs from 5' end sequences generated 3,304 unigenes including 952 contigs and 2,352 singletons. About 97.0\% of the 5,952 ESTs and 96.1\% of the unigenes have matches in the UniProt and TIGR databases. Of the 3,174 unigenes with matches, 42.9\% were not assigned GO (Gene Ontology) terms and their functions are unknown or unclassified. More than half (52.1\%) of the 5,952 ESTs have matches in the Pfam database and represent 772 known protein families. About 18.0\% of the 5,952 ESTs matched cell wall related genes in the MAIZEWALL database, representing all 18 categories, 91 of all 174 families and possibly 557 genes. Fifteen cell wall-related genes are ranked in the 30 most abundant genes, including CesA, tubulin, AGP, SAMS, actin, laccase, CCoAMT, MetE, phytocyanin, pectate lyase, cellulase, SuSy, expansin, chitinase and UDP-glucose dehydrogenase. Based on the PlantTFDB database 41 of the 64 transcription factor families in the poplar genome were identified as being involved in radiata pine wood formation. Comparative analysis of GO term abundance revealed a distinct transcriptome in juvenile earlywood formation compared to other stages of wood development.
CONCLUSION: The first large scale genomic resource in radiata pine was generated from six developing xylem cDNA libraries. Cell wall-related genes and transcription factors were identified. Juvenile earlywood has a distinct transcriptome, which is likely to contribute to the undesirable properties of juvenile wood in radiata pine. The publicly available resource of radiata pine will also be valuable for gene function studies and comparative genomics in forest trees.},
	language = {eng},
	journal = {BMC genomics},
	author = {Li, Xinguo and Wu, Harry X. and Dillon, Shannon K. and Southerton, Simon G.},
	month = jan,
	year = {2009},
	pmid = {19159482},
	pmcid = {PMC2636829},
	keywords = {Cell Wall, Expressed Sequence Tags, Gene Expression Profiling, Gene Expression Regulation, Plant, Gene Library, Genes, Plant, Genome, Plant, Genomics, Pinus, RNA, Plant, Transcription Factors, Xylem},
	pages = {41},
}

BACKGROUND: Wood is a major renewable natural resource for the timber, fibre and bioenergy industry. Pinus radiata D. Don is the most important commercial plantation tree species in Australia and several other countries; however, genomic resources for this species are very limited in public databases. Our primary objective was to sequence a large number of expressed sequence tags (ESTs) from genes involved in wood formation in radiata pine. RESULTS: Six developing xylem cDNA libraries were constructed from earlywood and latewood tissues sampled at juvenile (7 yrs), transition (11 yrs) and mature (30 yrs) ages, respectively. These xylem tissues represent six typical development stages in a rotation period of radiata pine. A total of 6,389 high quality ESTs were collected from 5,952 cDNA clones. Assembly of 5,952 ESTs from 5' end sequences generated 3,304 unigenes including 952 contigs and 2,352 singletons. About 97.0% of the 5,952 ESTs and 96.1% of the unigenes have matches in the UniProt and TIGR databases. Of the 3,174 unigenes with matches, 42.9% were not assigned GO (Gene Ontology) terms and their functions are unknown or unclassified. More than half (52.1%) of the 5,952 ESTs have matches in the Pfam database and represent 772 known protein families. About 18.0% of the 5,952 ESTs matched cell wall related genes in the MAIZEWALL database, representing all 18 categories, 91 of all 174 families and possibly 557 genes. Fifteen cell wall-related genes are ranked in the 30 most abundant genes, including CesA, tubulin, AGP, SAMS, actin, laccase, CCoAMT, MetE, phytocyanin, pectate lyase, cellulase, SuSy, expansin, chitinase and UDP-glucose dehydrogenase. Based on the PlantTFDB database 41 of the 64 transcription factor families in the poplar genome were identified as being involved in radiata pine wood formation. Comparative analysis of GO term abundance revealed a distinct transcriptome in juvenile earlywood formation compared to other stages of wood development. CONCLUSION: The first large scale genomic resource in radiata pine was generated from six developing xylem cDNA libraries. Cell wall-related genes and transcription factors were identified. Juvenile earlywood has a distinct transcriptome, which is likely to contribute to the undesirable properties of juvenile wood in radiata pine. The publicly available resource of radiata pine will also be valuable for gene function studies and comparative genomics in forest trees.

@article{zhang_discussion_2009,
	title = {Discussion on {Role} of {Forest} to {Control} {Agricultural} {Non}-{Point} {Source} {Pollution} in {Taihu} {Lake} {Basin}-{Based} on {Source}-{Sink} {Analysis}},
	volume = {1},
	copyright = {http://creativecommons.org/licenses/by/4.0/},
	url = {http://www.scirp.org/Journal/Paperabs.aspx?paperid=865},
	doi = {10/cfkp6v},
	abstract = {Taihu Lake is located at the center of Changjiang delta region, the Lake and its effluent rivers are important water sources for 40 million around inhabitants and rapidly increasing industrial factories in Shanghai, Ji-angsu and Zhejiang. The pollutants originate mainly from acidy rain, home sewage of the vast number of inhabitants, livestock manure, agricultural fertilizers \& pesticides applied over fields in the drainage basin, and the industrial sewage. Due to the kinds of pollutants, the Lake water is getting highly eutrophic, with frequent blooms of blue-green algae. Compared with point-source pollutants, diffuse pollution is much com-plicated and difficult to control. Thus combating non-point pollution (NPP) is paid much great attention. Based on analysis on source-sink of NPP in Taihu Lake basin, it is concluded that the function of forests on NPP control is multiple and important by both source reduction and sink expansion. The primary objective of planting trees through constructing forested wetlands and establishing riparian forest buffers is to control soil \& water erosion, decrease agrochemicals application, and improve farming conditions in the region of Taihu Lake basin. Moreover forests help to intercept acidy rain, protect streambanks, uptake nutrients, hold up pollutants and provide habitat for wildlife.},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Journal of Water Resource and Protection},
	author = {Zhang, Jianfeng and Jiang, Jingmin and Zhang, Zhijian and Shan, Qihua and Chen, Guangcai and Wang, Ying and Xu, Yonghui and Wu, Harry and Abarquez, Aljoy},
	month = nov,
	year = {2009},
	note = {Number: 5
Publisher: Scientific Research Publishing},
	pages = {345--350},
}

Taihu Lake is located at the center of Changjiang delta region, the Lake and its effluent rivers are important water sources for 40 million around inhabitants and rapidly increasing industrial factories in Shanghai, Ji-angsu and Zhejiang. The pollutants originate mainly from acidy rain, home sewage of the vast number of inhabitants, livestock manure, agricultural fertilizers & pesticides applied over fields in the drainage basin, and the industrial sewage. Due to the kinds of pollutants, the Lake water is getting highly eutrophic, with frequent blooms of blue-green algae. Compared with point-source pollutants, diffuse pollution is much com-plicated and difficult to control. Thus combating non-point pollution (NPP) is paid much great attention. Based on analysis on source-sink of NPP in Taihu Lake basin, it is concluded that the function of forests on NPP control is multiple and important by both source reduction and sink expansion. The primary objective of planting trees through constructing forested wetlands and establishing riparian forest buffers is to control soil & water erosion, decrease agrochemicals application, and improve farming conditions in the region of Taihu Lake basin. Moreover forests help to intercept acidy rain, protect streambanks, uptake nutrients, hold up pollutants and provide habitat for wildlife.

@article{baltunis_comparisons_2009,
	title = {Comparisons of genetic parameters and clonal value predictions from clonal trials and seedling base population trials of radiata pine},
	volume = {5},
	issn = {1614-2950},
	url = {https://doi.org/10.1007/s11295-008-0172-y},
	doi = {10/bwq6cq},
	abstract = {Different methods for predicting clonal values were explored for diameter growth (diameter at breast height (DBH)) in a radiata pine clonal forestry program: (1) clones were analyzed with a full model in which the total genetic variation was partitioned into additive, dominance, and epistasis (Clone Only—Full Model); (2) clones were analyzed together with seedling base population data (Clone Plus Seedling (CPS)), and (3) clones were analyzed with a reduced model in which the only genetic term was the total genetic variance (Clone Only—Reduced Model). DBH was assessed at age 5 for clones and between ages 4 to 13 at the seedling trials. Significant additive, dominance, and epistatic genetic effects were estimated for DBH using the CPS model. Nonadditive genetic effects for DBH were 87\% as large as additive genetic effects. Narrow-sense (\$\${\textbackslash}hat h{\textasciicircum}2 \$\$) and broad-sense (\$\${\textbackslash}hat H{\textasciicircum}2 \$\$) heritability estimates for DBH using the CPS model were 0.14 ± 0.01 and 0.26 ± 0.01, respectively. Accuracy of predicted clonal values increased 4\% by combining the clone and seedling data over using clonal data alone, resulting in greater confidence in the predicted genetic performance of clones. Our results indicate that exploiting nonadditive genetic effects in clonal varieties will generate greater gains than that typically obtainable from conventional family-based forestry of radiata pine. The predicted genetic gain for DBH from deployment of the top 5\% of clones was 24.0\%—an improvement of more than 100\% over family forestry at the same selection intensity. We conclude that it is best practice to predict clonal values by incorporating seedling base population data in the clonal analysis.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Baltunis, Brian S. and Wu, Harry X. and Dungey, Heidi S. and Mullin, T. J. “Tim” and Brawner, Jeremy T.},
	month = jan,
	year = {2009},
	pages = {269--278},
}

Different methods for predicting clonal values were explored for diameter growth (diameter at breast height (DBH)) in a radiata pine clonal forestry program: (1) clones were analyzed with a full model in which the total genetic variation was partitioned into additive, dominance, and epistasis (Clone Only—Full Model); (2) clones were analyzed together with seedling base population data (Clone Plus Seedling (CPS)), and (3) clones were analyzed with a reduced model in which the only genetic term was the total genetic variance (Clone Only—Reduced Model). DBH was assessed at age 5 for clones and between ages 4 to 13 at the seedling trials. Significant additive, dominance, and epistatic genetic effects were estimated for DBH using the CPS model. Nonadditive genetic effects for DBH were 87% as large as additive genetic effects. Narrow-sense ($$\hat h\textasciicircum2 $$) and broad-sense ($$\hat H\textasciicircum2 $$) heritability estimates for DBH using the CPS model were 0.14 ± 0.01 and 0.26 ± 0.01, respectively. Accuracy of predicted clonal values increased 4% by combining the clone and seedling data over using clonal data alone, resulting in greater confidence in the predicted genetic performance of clones. Our results indicate that exploiting nonadditive genetic effects in clonal varieties will generate greater gains than that typically obtainable from conventional family-based forestry of radiata pine. The predicted genetic gain for DBH from deployment of the top 5% of clones was 24.0%—an improvement of more than 100% over family forestry at the same selection intensity. We conclude that it is best practice to predict clonal values by incorporating seedling base population data in the clonal analysis.

@article{meng_domain-specific_2009,
	title = {Domain-specific determinants of catalysis/substrate binding and the oligomerization status of barley {UDP}-glucose pyrophosphorylase},
	volume = {1794},
	issn = {15709639},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1570963909002039},
	doi = {10/fjsv4f},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics},
	author = {Meng, Meng and Fitzek, Elisabeth and Gajowniczek, Agnieszka and Wilczynska, Malgorzata and Kleczkowski, Leszek A.},
	month = dec,
	year = {2009},
	pages = {1734--1742},
}

@article{serrato_changing_2009,
	title = {Changing sugar partitioning in {FBPase}-manipulated plants},
	volume = {60},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/erp066},
	doi = {10/fhtwcd},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Serrato, A. J. and de Dios Barajas-Lopez, J. and Chueca, A. and Sahrawy, M.},
	month = jul,
	year = {2009},
	pages = {2923--2931},
}

@article{boutte_cellular_2009,
	title = {Cellular processes relying on sterol function in plants},
	volume = {12},
	issn = {13695266},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S136952660900137X},
	doi = {10/cjv44b},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Current Opinion in Plant Biology},
	author = {Boutté, Yohann and Grebe, Markus},
	month = dec,
	year = {2009},
	pages = {705--713},
}

@article{damkjaer_photosystem_2009,
	title = {The {Photosystem} {II} {Light}-{Harvesting} {Protein} {Lhcb3} {Affects} the {Macrostructure} of {Photosystem} {II} and the {Rate} of {State} {Transitions} in \textit{{Arabidopsis}}},
	volume = {21},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/21/10/3245/6096237},
	doi = {10/fb96fz},
	abstract = {Abstract
            The main trimeric light-harvesting complex of higher plants (LHCII) consists of three different Lhcb proteins (Lhcb1-3). We show that Arabidopsis thaliana T-DNA knockout plants lacking Lhcb3 (koLhcb3) compensate for the lack of Lhcb3 by producing increased amounts of Lhcb1 and Lhcb2. As in wild-type plants, LHCII-photosystem II (PSII) supercomplexes were present in Lhcb3 knockout plants (koLhcb3), and preservation of the LHCII trimers (M trimers) indicates that the Lhcb3 in M trimers has been replaced by Lhcb1 and/or Lhcb2. However, the rotational position of the M LHCII trimer was altered, suggesting that the Lhcb3 subunit affects the macrostructural arrangement of the LHCII antenna. The absence of Lhcb3 did not result in any significant alteration in PSII efficiency or qE type of nonphotochemical quenching, but the rate of transition from State 1 to State 2 was increased in koLhcb3, although the final extent of state transition was unchanged. The level of phosphorylation of LHCII was increased in the koLhcb3 plants compared with wild-type plants in both State 1 and State 2. The relative increase in phosphorylation upon transition from State 1 to State 2 was also significantly higher in koLhcb3. It is suggested that the main function of Lhcb3 is to modulate the rate of state transitions.},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Damkjær, Jakob T. and Kereïche, Sami and Johnson, Matthew P. and Kovacs, Laszlo and Kiss, Anett Z. and Boekema, Egbert J. and Ruban, Alexander V. and Horton, Peter and Jansson, Stefan},
	month = dec,
	year = {2009},
	pages = {3245--3256},
}

Abstract The main trimeric light-harvesting complex of higher plants (LHCII) consists of three different Lhcb proteins (Lhcb1-3). We show that Arabidopsis thaliana T-DNA knockout plants lacking Lhcb3 (koLhcb3) compensate for the lack of Lhcb3 by producing increased amounts of Lhcb1 and Lhcb2. As in wild-type plants, LHCII-photosystem II (PSII) supercomplexes were present in Lhcb3 knockout plants (koLhcb3), and preservation of the LHCII trimers (M trimers) indicates that the Lhcb3 in M trimers has been replaced by Lhcb1 and/or Lhcb2. However, the rotational position of the M LHCII trimer was altered, suggesting that the Lhcb3 subunit affects the macrostructural arrangement of the LHCII antenna. The absence of Lhcb3 did not result in any significant alteration in PSII efficiency or qE type of nonphotochemical quenching, but the rate of transition from State 1 to State 2 was increased in koLhcb3, although the final extent of state transition was unchanged. The level of phosphorylation of LHCII was increased in the koLhcb3 plants compared with wild-type plants in both State 1 and State 2. The relative increase in phosphorylation upon transition from State 1 to State 2 was also significantly higher in koLhcb3. It is suggested that the main function of Lhcb3 is to modulate the rate of state transitions.

@article{wuolikainen_optimization_2009,
	title = {Optimization of procedures for collecting and storing of {CSF} for studying the metabolome in {ALS}},
	volume = {10},
	issn = {1748-2968, 1471-180X},
	url = {http://www.tandfonline.com/doi/full/10.1080/17482960902871009},
	doi = {10/cjcnvg},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Amyotrophic Lateral Sclerosis},
	author = {Wuolikainen, Anna and Hedenström, Mattias and Moritz, Thomas and Marklund, Stefan L. and Antti, Henrik and Andersen, Peter M.},
	month = jan,
	year = {2009},
	pages = {229--236},
}

@article{redestig_compensation_2009,
	title = {Compensation for {Systematic} {Cross}-{Contribution} {Improves} {Normalization} of {Mass} {Spectrometry} {Based} {Metabolomics} {Data}},
	volume = {81},
	issn = {0003-2700, 1520-6882},
	url = {https://pubs.acs.org/doi/10.1021/ac901143w},
	doi = {10/fr25p2},
	language = {en},
	number = {19},
	urldate = {2021-06-08},
	journal = {Analytical Chemistry},
	author = {Redestig, Henning and Fukushima, Atsushi and Stenlund, Hans and Moritz, Thomas and Arita, Masanori and Saito, Kazuki and Kusano, Miyako},
	month = oct,
	year = {2009},
	pages = {7974--7980},
}

@article{gutierrez_phenotypic_2009,
	title = {Phenotypic {Plasticity} of {Adventitious} {Rooting} in \textit{{Arabidopsis}} {Is} {Controlled} by {Complex} {Regulation} of {AUXIN} {RESPONSE} {FACTOR} {Transcripts} and {MicroRNA} {Abundance}},
	volume = {21},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/21/10/3119/6096289},
	doi = {10/c7kpnr},
	abstract = {Abstract
            The development of shoot-borne roots, or adventitious roots, is indispensable for mass propagation of elite genotypes. It is a complex genetic trait with a high phenotypic plasticity due to multiple endogenous and environmental regulatory factors. We demonstrate here that a subtle balance of activator and repressor AUXIN RESPONSE FACTOR (ARF) transcripts controls adventitious root initiation. Moreover, microRNA activity appears to be required for fine-tuning of this process. Thus, ARF17, a target of miR160, is a negative regulator, and ARF6 and ARF8, targets of miR167, are positive regulators of adventitious rooting. The three ARFs display overlapping expression domains, interact genetically, and regulate each other's expression at both transcriptional and posttranscriptional levels by modulating miR160 and miR167 availability. This complex regulatory network includes an unexpected feedback regulation of microRNA homeostasis by direct and nondirect target transcription factors. These results provide evidence of microRNA control of phenotypic variability and are a significant step forward in understanding the molecular mechanisms regulating adventitious rooting.},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Gutierrez, Laurent and Bussell, John D. and Păcurar, Daniel I. and Schwambach, Josèli and Păcurar, Monica and Bellini, Catherine},
	month = dec,
	year = {2009},
	pages = {3119--3132},
}

Abstract The development of shoot-borne roots, or adventitious roots, is indispensable for mass propagation of elite genotypes. It is a complex genetic trait with a high phenotypic plasticity due to multiple endogenous and environmental regulatory factors. We demonstrate here that a subtle balance of activator and repressor AUXIN RESPONSE FACTOR (ARF) transcripts controls adventitious root initiation. Moreover, microRNA activity appears to be required for fine-tuning of this process. Thus, ARF17, a target of miR160, is a negative regulator, and ARF6 and ARF8, targets of miR167, are positive regulators of adventitious rooting. The three ARFs display overlapping expression domains, interact genetically, and regulate each other's expression at both transcriptional and posttranscriptional levels by modulating miR160 and miR167 availability. This complex regulatory network includes an unexpected feedback regulation of microRNA homeostasis by direct and nondirect target transcription factors. These results provide evidence of microRNA control of phenotypic variability and are a significant step forward in understanding the molecular mechanisms regulating adventitious rooting.

@article{belin_abscisic_2009,
	title = {Abscisic {Acid} {Represses} {Growth} of the \textit{{Arabidopsis}} {Embryonic} {Axis} after {Germination} by {Enhancing} {Auxin} {Signaling}},
	volume = {21},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/21/8/2253/6095468},
	doi = {10/bwsn9b},
	abstract = {Abstract
            Under unfavorable environmental conditions, the stress phytohormone ABA inhibits the developmental transition from an embryo in a dry seed into a young seedling. We developed a genetic screen to isolate Arabidopsis thaliana mutants whose early seedling development is resistant to ABA. Here, we report the identification of a recessive mutation in AUXIN RESISTANT1 (AUX1), encoding a cellular auxin influx carrier. Although auxin is a major morphogenesis hormone in plants, little is known about ABA–auxin interactions during early seedling growth. We show that aux1 and pin2 mutants are insensitive to ABA-dependent repression of embryonic axis (hypocotyl and radicle) elongation. Genetic and physiological experiments show that this involves auxin transport to the embryonic axis elongation zone, where ABA enhances the activity of an auxin-responsive promoter. We propose that ABA represses embryonic axis elongation by potentiating auxin signaling in its elongation zone. This involves repression of the AUXIN INDUCIBLE (Aux/IAA) gene AXR2/IAA7, encoding a key component of ABA- and auxin-dependent responses during postgerminative growth.},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Belin, Christophe and Megies, Christian and Hauserová, Eva and Lopez-Molina, Luis},
	month = oct,
	year = {2009},
	pages = {2253--2268},
}

Abstract Under unfavorable environmental conditions, the stress phytohormone ABA inhibits the developmental transition from an embryo in a dry seed into a young seedling. We developed a genetic screen to isolate Arabidopsis thaliana mutants whose early seedling development is resistant to ABA. Here, we report the identification of a recessive mutation in AUXIN RESISTANT1 (AUX1), encoding a cellular auxin influx carrier. Although auxin is a major morphogenesis hormone in plants, little is known about ABA–auxin interactions during early seedling growth. We show that aux1 and pin2 mutants are insensitive to ABA-dependent repression of embryonic axis (hypocotyl and radicle) elongation. Genetic and physiological experiments show that this involves auxin transport to the embryonic axis elongation zone, where ABA enhances the activity of an auxin-responsive promoter. We propose that ABA represses embryonic axis elongation by potentiating auxin signaling in its elongation zone. This involves repression of the AUXIN INDUCIBLE (Aux/IAA) gene AXR2/IAA7, encoding a key component of ABA- and auxin-dependent responses during postgerminative growth.

@article{rawat_reveille1_2009,
	title = {{REVEILLE1}, a {Myb}-like transcription factor, integrates the circadian clock and auxin pathways},
	volume = {106},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0813035106},
	doi = {10/bwffw9},
	language = {en},
	number = {39},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Rawat, R. and Schwartz, J. and Jones, M. A. and Sairanen, I. and Cheng, Y. and Andersson, C. R. and Zhao, Y. and Ljung, K. and Harmer, S. L.},
	month = sep,
	year = {2009},
	pages = {16883--16888},
}

@article{prusinkiewicz_control_2009,
	title = {Control of bud activation by an auxin transport switch},
	volume = {106},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0906696106},
	doi = {10/d5w9ft},
	language = {en},
	number = {41},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Prusinkiewicz, P. and Crawford, S. and Smith, R. S. and Ljung, K. and Bennett, T. and Ongaro, V. and Leyser, O.},
	month = oct,
	year = {2009},
	pages = {17431--17436},
}

@article{hedenstrom_identification_2009,
	title = {Identification of {Lignin} and {Polysaccharide} {Modifications} in {Populus} {Wood} by {Chemometric} {Analysis} of {2D} {NMR} {Spectra} from {Dissolved} {Cell} {Walls}},
	volume = {2},
	issn = {16742052},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1674205214607097},
	doi = {10/cv5zgn},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Molecular Plant},
	author = {Hedenström, Mattias and Wiklund-Lindström, Susanne and Öman, Tommy and Lu, Fachuang and Gerber, Lorenz and Schatz, Paul and Sundberg, Björn and Ralph, John},
	month = sep,
	year = {2009},
	pages = {933--942},
}

@article{endo_identifying_2009,
	title = {Identifying {New} {Components} {Participating} in the {Secondary} {Cell} {Wall} {Formation} of {Vessel} {Elements} in \textit{{Zinnia}} and \textit{{Arabidopsis}}},
	volume = {21},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/21/4/1155/6095257},
	doi = {10/cmhrbv},
	abstract = {Abstract
            Xylem vessel elements are hollow cellular units that assemble end-to-end to form a continuous vessel throughout the plant body; the xylem vessel is strengthened by the xylem elements' reinforced secondary cell walls (SCWs). This work aims to unravel the contribution of unknown actors in xylem vessel differentiation using the model in vitro cell culture system of Zinnia elegans differentiating cell cultures and the model in vivo system of Arabidopsis thaliana plants. Tracheary Element  Differentiation-Related6 (TED6) and TED7 were selected based on an RNA interference (RNAi) screen in the Zinnia system. RNAi reduction of TED6 and 7 delayed tracheary element (TE) differentiation and co-overexpression of TED6 and 7 increased TE differentiation in cultured Zinnia cells. Arabidopsis TED6 and 7 were expressed preferentially in differentiating vessel elements in seedlings. Aberrant SCW formation of root vessel elements was induced by transient RNAi of At TED7 alone and enhanced by inhibition of both TED6 and 7. Protein–protein interactions were demonstrated between TED6 and a subunit of the SCW-related cellulose synthase complex. Our strategy has succeeded in finding two novel components in SCW formation and has opened the door for in-depth analysis of their molecular functions.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Endo, Satoshi and Pesquet, Edouard and Yamaguchi, Masatoshi and Tashiro, Gen and Sato, Mayuko and Toyooka, Kiminori and Nishikubo, Nobuyuki and Udagawa-Motose, Makiko and Kubo, Minoru and Fukuda, Hiroo and Demura, Taku},
	month = may,
	year = {2009},
	pages = {1155--1165},
}

Abstract Xylem vessel elements are hollow cellular units that assemble end-to-end to form a continuous vessel throughout the plant body; the xylem vessel is strengthened by the xylem elements' reinforced secondary cell walls (SCWs). This work aims to unravel the contribution of unknown actors in xylem vessel differentiation using the model in vitro cell culture system of Zinnia elegans differentiating cell cultures and the model in vivo system of Arabidopsis thaliana plants. Tracheary Element  Differentiation-Related6 (TED6) and TED7 were selected based on an RNA interference (RNAi) screen in the Zinnia system. RNAi reduction of TED6 and 7 delayed tracheary element (TE) differentiation and co-overexpression of TED6 and 7 increased TE differentiation in cultured Zinnia cells. Arabidopsis TED6 and 7 were expressed preferentially in differentiating vessel elements in seedlings. Aberrant SCW formation of root vessel elements was induced by transient RNAi of At TED7 alone and enhanced by inhibition of both TED6 and 7. Protein–protein interactions were demonstrated between TED6 and a subunit of the SCW-related cellulose synthase complex. Our strategy has succeeded in finding two novel components in SCW formation and has opened the door for in-depth analysis of their molecular functions.

@article{tromas_auxin_2009,
	title = {The {AUXIN} {BINDING} {PROTEIN} 1 {Is} {Required} for {Differential} {Auxin} {Responses} {Mediating} {Root} {Growth}},
	volume = {4},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0006648},
	doi = {10/drhr8k},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Tromas, Alexandre and Braun, Nils and Muller, Philippe and Khodus, Tatyana and Paponov, Ivan A. and Palme, Klaus and Ljung, Karin and Lee, Ji-Young and Benfey, Philip and Murray, James A. H. and Scheres, Ben and Perrot-Rechenmann, Catherine},
	editor = {Newbigin, Edward},
	month = sep,
	year = {2009},
	pages = {e6648},
}

@article{lewis_auxin_2009,
	title = {Auxin transport into cotyledons and cotyledon growth depend similarly on the {ABCB19} {Multidrug} {Resistance}-like transporter},
	volume = {60},
	issn = {09607412, 1365313X},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2009.03941.x},
	doi = {10/bf6r5r},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Lewis, Daniel R. and Wu, Guosheng and Ljung, Karin and Spalding, Edgar P.},
	month = oct,
	year = {2009},
	pages = {91--101},
}

@article{igamberdiev_metabolic_2009,
	title = {Metabolic systems maintain stable non-equilibrium via thermodynamic buffering},
	volume = {31},
	issn = {02659247},
	url = {http://doi.wiley.com/10.1002/bies.200900057},
	doi = {10/csrg2d},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {BioEssays},
	author = {Igamberdiev, Abir U. and Kleczkowski, Leszek A.},
	month = oct,
	year = {2009},
	pages = {1091--1099},
}

@article{seveno_structural_2009,
	title = {Structural characterisation of the pectic polysaccharide rhamnogalacturonan {II} using an acidic fingerprinting methodology},
	volume = {230},
	issn = {0032-0935, 1432-2048},
	url = {http://link.springer.com/10.1007/s00425-009-0996-1},
	doi = {10/ccm93h},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Planta},
	author = {Séveno, Martial and Voxeur, Aline and Rihouey, Christophe and Wu, Ai-Min and Ishii, Tadashi and Chevalier, Christian and Ralet, Marie Christine and Driouich, Azeddine and Marchant, Alan and Lerouge, Patrice},
	month = oct,
	year = {2009},
	pages = {947--957},
}

@article{varghese_changes_2009,
	title = {Changes in growth performance and fecundity of {Eucalyptus} camaldulensis and {E}. tereticornis during domestication in southern {India}},
	volume = {5},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-009-0215-z},
	doi = {10/b65z83},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Varghese, M. and Kamalakannan, R. and Harwood, C. E. and Lindgren, D. and McDonald, M. W.},
	month = oct,
	year = {2009},
	pages = {629--640},
}

@article{galindo_metabolomic_2009,
	title = {Metabolomic evaluation of pulsed electric field-induced stress on potato tissue},
	volume = {230},
	issn = {0032-0935, 1432-2048},
	url = {http://link.springer.com/10.1007/s00425-009-0950-2},
	doi = {10/bg94jg},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Planta},
	author = {Galindo, Federico Gómez and Dejmek, Petr and Lundgren, Krister and Rasmusson, Allan G. and Vicente, António and Moritz, Thomas},
	month = aug,
	year = {2009},
	pages = {469--479},
}

@article{andreazza_production_2009,
	title = {Production of imidazole alkaloids in cell cultures of jaborandi as affected by the medium {pH}},
	volume = {31},
	issn = {0141-5492, 1573-6776},
	url = {http://link.springer.com/10.1007/s10529-008-9895-y},
	doi = {10/bbf8bs},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Biotechnology Letters},
	author = {Andreazza, N. L. and Abreu, I. N. and Sawaya, A. C. H. F. and Eberlin, M. N. and Mazzafera, P.},
	month = apr,
	year = {2009},
	pages = {607--614},
}

@article{fei_fe_2009,
	title = {An {Fe} {Deficiency} {Responsive} {Element} with a {Core} {Sequence} of {TGGCA} {Regulates} the {Expression} of {FEA1} in {Chlamydomonas} reinharditii},
	volume = {146},
	issn = {0021-924X},
	url = {https://academic.oup.com/jb/article-lookup/doi/10.1093/jb/mvp056},
	doi = {10/d7z4nm},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Journal of Biochemistry},
	author = {Fei, X. and Eriksson, M. and Yang, J. and Deng, X.},
	month = aug,
	year = {2009},
	pages = {157--166},
}

@incollection{bishopp_chapter_2009,
	title = {Chapter 1 {Cytokinin} {Signaling} {During} {Root} {Development}},
	volume = {276},
	isbn = {978-0-12-374807-2},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1937644809760010},
	language = {en},
	urldate = {2021-06-08},
	booktitle = {International {Review} of {Cell} and {Molecular} {Biology}},
	publisher = {Elsevier},
	author = {Bishopp, Anthony and Help, Hanna and Helariutta, Ykä},
	year = {2009},
	doi = {10.1016/S1937-6448(09)76001-0},
	pages = {1--48},
}

@article{ali_quantification_2009,
	title = {Quantification of indole-3-acetic acid from plant associated {Bacillus} spp. and their phytostimulatory effect on {Vigna} radiata ({L}.)},
	volume = {25},
	issn = {0959-3993, 1573-0972},
	url = {http://link.springer.com/10.1007/s11274-008-9918-9},
	doi = {10/fjqgq7},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {World Journal of Microbiology and Biotechnology},
	author = {Ali, Basharat and Sabri, Anjum Nasim and Ljung, Karin and Hasnain, Shahida},
	month = mar,
	year = {2009},
	pages = {519--526},
}

@article{mauriat_analyses_2009,
	title = {Analyses of {GA20ox}- and {GID1}-over-expressing aspen suggest that gibberellins play two distinct roles in wood formation},
	volume = {58},
	issn = {1365-313X},
	doi = {10/cqnj6n},
	abstract = {Gibberellins (GAs) are involved in many aspects of plant development, including shoot growth, flowering and wood formation. Increased levels of bioactive GAs are known to induce xylogenesis and xylem fiber elongation in aspen. However, there is currently little information on the response pathway(s) that mediate GA effects on wood formation. Here we characterize an important element of the GA pathway in hybrid aspen: the GA receptor, GID1. Four orthologs of GID1 were identified in Populus tremula x P. tremuloides (PttGID1.1-1.4). These were functional when expressed in Arabidopsis thaliana, and appear to present a degree of sub-functionalization in hybrid aspen. PttGID1.1 and PttGID1.3 were over-expressed in independent lines of hybrid aspen using either the 35S promoter or a xylem-specific promoter (LMX5). The 35S:PttGID1 over-expressors shared several phenotypic traits previously described in 35S:AtGA20ox1 over-expressors, including rapid growth, increased elongation, and increased xylogenesis. However, their xylem fibers were not elongated, unlike those of 35S:AtGA20ox1 plants. Similar differences in the xylem fiber phenotype were observed when PttGID1.1, PttGID1.3 or AtGA20ox1 were expressed under the control of the LMX5 promoter, suggesting either that PttGID1.1 and PttGID1.3 play no role in fiber elongation or that GA homeostasis is strongly controlled when GA signaling is altered. Our data suggest that GAs are required in two distinct wood-formation processes that have tissue-specific signaling pathways: xylogenesis, as mediated by GA signaling in the cambium, and fiber elongation in the developing xylem.},
	language = {eng},
	number = {6},
	journal = {The Plant Journal: For Cell and Molecular Biology},
	author = {Mauriat, Mélanie and Moritz, Thomas},
	month = jun,
	year = {2009},
	pmid = {19228336},
	keywords = {Amino Acid Sequence, Arabidopsis, Cloning, Molecular, Gene Expression Regulation, Enzymologic, Gene Expression Regulation, Plant, Gibberellins, Mixed Function Oxygenases, Molecular Sequence Data, Plant Proteins, Plants, Genetically Modified, Populus, Promoter Regions, Genetic, RNA, Plant, Receptors, Cell Surface, Sequence Alignment, Wood},
	pages = {989--1003},
}

Gibberellins (GAs) are involved in many aspects of plant development, including shoot growth, flowering and wood formation. Increased levels of bioactive GAs are known to induce xylogenesis and xylem fiber elongation in aspen. However, there is currently little information on the response pathway(s) that mediate GA effects on wood formation. Here we characterize an important element of the GA pathway in hybrid aspen: the GA receptor, GID1. Four orthologs of GID1 were identified in Populus tremula x P. tremuloides (PttGID1.1-1.4). These were functional when expressed in Arabidopsis thaliana, and appear to present a degree of sub-functionalization in hybrid aspen. PttGID1.1 and PttGID1.3 were over-expressed in independent lines of hybrid aspen using either the 35S promoter or a xylem-specific promoter (LMX5). The 35S:PttGID1 over-expressors shared several phenotypic traits previously described in 35S:AtGA20ox1 over-expressors, including rapid growth, increased elongation, and increased xylogenesis. However, their xylem fibers were not elongated, unlike those of 35S:AtGA20ox1 plants. Similar differences in the xylem fiber phenotype were observed when PttGID1.1, PttGID1.3 or AtGA20ox1 were expressed under the control of the LMX5 promoter, suggesting either that PttGID1.1 and PttGID1.3 play no role in fiber elongation or that GA homeostasis is strongly controlled when GA signaling is altered. Our data suggest that GAs are required in two distinct wood-formation processes that have tissue-specific signaling pathways: xylogenesis, as mediated by GA signaling in the cambium, and fiber elongation in the developing xylem.

@article{pacurar_turning_2009,
	title = {Turning a {Wild} {Plant} {Into} a {Model} - {A} deja vu {Story}},
	volume = {37},
	doi = {10.15835/nbha3713215},
	abstract = {In the past two decades we have witnessed how a useless wild weed has been transformed from an anonymous into a model plant, probably the most widely “cultivated” plant species. The process has been rather slow in the beginning, very laborious on the way, extremely expensive and time consuming, but the outcome is priceless – the knowledge that is most likely to frame and fill the blueprint of the first artificial plant, as system biology promises. The plant species is Arabidopsis thaliana and the “growers” are highly qualified researchers worldwide. This review introduces a new anonymous – Brachypodium distachyon – that raised big hopes for addressing specific problems of fundamental and practical biology in temperate cereals and forage grasses, and is rapidly becoming a “sweetheart” for the researchers working with these crops, and not only.},
	journal = {Notulae Botanicae Horti Agrobotanici Cluj-Napoca},
	author = {Pacurar, Daniel},
	month = jun,
	year = {2009},
	keywords = {⚠️ Invalid DOI},
}

In the past two decades we have witnessed how a useless wild weed has been transformed from an anonymous into a model plant, probably the most widely “cultivated” plant species. The process has been rather slow in the beginning, very laborious on the way, extremely expensive and time consuming, but the outcome is priceless – the knowledge that is most likely to frame and fill the blueprint of the first artificial plant, as system biology promises. The plant species is Arabidopsis thaliana and the “growers” are highly qualified researchers worldwide. This review introduces a new anonymous – Brachypodium distachyon – that raised big hopes for addressing specific problems of fundamental and practical biology in temperate cereals and forage grasses, and is rapidly becoming a “sweetheart” for the researchers working with these crops, and not only.

@article{savadogo_examination_2009,
	title = {Examination of multiple disturbances effects on herbaceous vegetation communities in the {Sudanian} savanna-woodland of {West} {Africa}},
	volume = {204},
	issn = {03672530},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0367253008001527},
	doi = {10/dgg8ts},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Flora - Morphology, Distribution, Functional Ecology of Plants},
	author = {Savadogo, Patrice and Tigabu, Mulualem and Sawadogo, Louis and Odén, Per Christer},
	month = jan,
	year = {2009},
	pages = {409--422},
}

@article{ratnaparkhe_identification_2009,
	title = {Identification and characterization of a matrix metalloproteinase ({Pta1}-{MMP}) expressed during {Loblolly} pine ({Pinus} taeda) seed development, germination completion, and early seedling establishment},
	volume = {230},
	issn = {0032-0935, 1432-2048},
	url = {http://link.springer.com/10.1007/s00425-009-0949-8},
	doi = {10/bdrzhz},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Planta},
	author = {Ratnaparkhe, Supriya M. and Egertsdotter, E. M. Ulrika and Flinn, Barry S.},
	month = jul,
	year = {2009},
	pages = {339--354},
}

@article{fries_genetic_2009,
	title = {Genetic parameters for early wood and latewood densities and development with increasing age in {Scots} pine},
	volume = {66},
	issn = {1286-4560, 1297-966X},
	url = {http://link.springer.com/10.1051/forest/2009019},
	doi = {10/d4txwk},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Annals of Forest Science},
	author = {Fries, Anders and Ericsson, Tore},
	month = jan,
	year = {2009},
	pages = {404--404},
}

@article{chorell_predictive_2009,
	title = {Predictive {Metabolomics} {Evaluation} of {Nutrition}-{Modulated} {Metabolic} {Stress} {Responses} in {Human} {Blood} {Serum} {During} the {Early} {Recovery} {Phase} of {Strenuous} {Physical} {Exercise}},
	volume = {8},
	issn = {1535-3893, 1535-3907},
	url = {https://pubs.acs.org/doi/10.1021/pr900081q},
	doi = {10/fn674z},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Journal of Proteome Research},
	author = {Chorell, Elin and Moritz, Thomas and Branth, Stefan and Antti, Henrik and Svensson, Michael B.},
	month = jun,
	year = {2009},
	pages = {2966--2977},
}

@article{babst_local_2009,
	title = {Local and systemic transcriptome responses to herbivory and jasmonic acid in {Populus}},
	volume = {5},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-009-0200-6},
	doi = {10/fmhhv9},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Babst, Benjamin A. and Sjödin, Andreas and Jansson, Stefan and Orians, Colin M.},
	month = jul,
	year = {2009},
	pages = {459--474},
}

@article{gronlund_evolution_2009,
	title = {Evolution of rogue waves in interacting wave systems},
	volume = {86},
	issn = {0295-5075, 1286-4854},
	url = {https://iopscience.iop.org/article/10.1209/0295-5075/86/24001},
	doi = {10/fd7qs5},
	number = {2},
	urldate = {2021-06-08},
	journal = {EPL (Europhysics Letters)},
	author = {Grönlund, A. and Eliasson, B. and Marklund, M.},
	month = apr,
	year = {2009},
	pages = {24001},
}

@article{cain_novel_2009,
	title = {A novel extended family of stromal thioredoxins},
	volume = {70},
	issn = {0167-4412, 1573-5028},
	url = {http://link.springer.com/10.1007/s11103-009-9471-4},
	doi = {10/dm9h3t},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Plant Molecular Biology},
	author = {Cain, Peter and Hall, Michael and Schröder, Wolfgang P. and Kieselbach, Thomas and Robinson, Colin},
	month = jun,
	year = {2009},
	pages = {273--281},
}

@article{ishida_ectomycorrhizal_2009,
	title = {Ectomycorrhizal fungal community in alkaline-saline soil in northeastern {China}},
	volume = {19},
	issn = {0940-6360, 1432-1890},
	url = {http://link.springer.com/10.1007/s00572-008-0219-9},
	doi = {10/d6329j},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Mycorrhiza},
	author = {Ishida, Takahide A. and Nara, Kazuhide and Ma, Shurong and Takano, Tetsuo and Liu, Shenkui},
	month = jun,
	year = {2009},
	pages = {329--335},
}

@article{kumar_update_2009,
	title = {An update on the nomenclature for the cellulose synthase genes in {Populus}},
	volume = {14},
	issn = {13601385},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1360138509000958},
	doi = {10/b7d42j},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Trends in Plant Science},
	author = {Kumar, Manoj and Thammannagowda, Shivegowda and Bulone, Vincent and Chiang, Vincent and Han, Kyung-Hwan and Joshi, Chandrashekhar P. and Mansfield, Shawn D. and Mellerowicz, Ewa and Sundberg, Björn and Teeri, Tuula and Ellis, Brian E.},
	month = may,
	year = {2009},
	pages = {248--254},
}

@article{petersson_auxin_2009,
	title = {An {Auxin} {Gradient} and {Maximum} in the \textit{{Arabidopsis}} {Root} {Apex} {Shown} by {High}-{Resolution} {Cell}-{Specific} {Analysis} of {IAA} {Distribution} and {Synthesis}},
	volume = {21},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/21/6/1659/6095411},
	doi = {10/ddgn83},
	abstract = {Abstract
            Local concentration gradients of the plant growth regulator auxin (indole-3-acetic acid [IAA]) are thought to instruct the positioning of organ primordia and stem cell niches and to direct cell division, expansion, and differentiation. High-resolution measurements of endogenous IAA concentrations in support of the gradient hypothesis are required to substantiate this hypothesis. Here, we introduce fluorescence-activated cell sorting of green fluorescent protein–marked cell types combined with highly sensitive mass spectrometry methods as a novel means for analyses of IAA distribution and metabolism at cellular resolution. Our results reveal the presence of IAA concentration gradients within the Arabidopsis thaliana root tip with a distinct maximum in the organizing quiescent center of the root apex. We also demonstrate that the root apex provides an important source of IAA and that cells of all types display a high synthesis capacity, suggesting a substantial contribution of local biosynthesis to auxin homeostasis in the root tip. Our results indicate that local biosynthesis and polar transport combine to produce auxin gradients and maxima in the root tip.},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Petersson, Sara V. and Johansson, Annika I. and Kowalczyk, Mariusz and Makoveychuk, Alexander and Wang, Jean Y. and Moritz, Thomas and Grebe, Markus and Benfey, Philip N. and Sandberg, Göran and Ljung, Karin},
	month = aug,
	year = {2009},
	pages = {1659--1668},
}

Abstract Local concentration gradients of the plant growth regulator auxin (indole-3-acetic acid [IAA]) are thought to instruct the positioning of organ primordia and stem cell niches and to direct cell division, expansion, and differentiation. High-resolution measurements of endogenous IAA concentrations in support of the gradient hypothesis are required to substantiate this hypothesis. Here, we introduce fluorescence-activated cell sorting of green fluorescent protein–marked cell types combined with highly sensitive mass spectrometry methods as a novel means for analyses of IAA distribution and metabolism at cellular resolution. Our results reveal the presence of IAA concentration gradients within the Arabidopsis thaliana root tip with a distinct maximum in the organizing quiescent center of the root apex. We also demonstrate that the root apex provides an important source of IAA and that cells of all types display a high synthesis capacity, suggesting a substantial contribution of local biosynthesis to auxin homeostasis in the root tip. Our results indicate that local biosynthesis and polar transport combine to produce auxin gradients and maxima in the root tip.

@article{onischenko_role_2009,
	title = {Role of the {Ndc1} interaction network in yeast nuclear pore complex assembly and maintenance},
	volume = {185},
	issn = {1540-8140, 0021-9525},
	url = {https://rupress.org/jcb/article/185/3/475/35521/Role-of-the-Ndc1-interaction-network-in-yeast},
	doi = {10/dzdj23},
	abstract = {The nuclear pore complex (NPC) mediates all nucleocytoplasmic transport, yet its structure and biogenesis remain poorly understood. In this study, we have functionally characterized interaction partners of the yeast transmembrane nucleoporin Ndc1. Ndc1 forms a distinct complex with the transmembrane proteins Pom152 and Pom34 and two alternative complexes with the soluble nucleoporins Nup53 and Nup59, which in turn bind to Nup170 and Nup157. The transmembrane and soluble Ndc1-binding partners have redundant functions at the NPC, and disruption of both groups of interactions causes defects in Ndc1 targeting and in NPC structure accompanied by significant pore dilation. Using photoconvertible fluorescent protein fusions, we further show that the depletion of Pom34 in cells that lack NUP53 and NUP59 blocks new NPC assembly and leads to the reversible accumulation of newly made nucleoporins in cytoplasmic foci. Therefore, Ndc1 together with its interaction partners are collectively essential for the biosynthesis and structural integrity of yeast NPCs.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Journal of Cell Biology},
	author = {Onischenko, Evgeny and Stanton, Leslie H. and Madrid, Alexis S. and Kieselbach, Thomas and Weis, Karsten},
	month = may,
	year = {2009},
	pages = {475--491},
}

The nuclear pore complex (NPC) mediates all nucleocytoplasmic transport, yet its structure and biogenesis remain poorly understood. In this study, we have functionally characterized interaction partners of the yeast transmembrane nucleoporin Ndc1. Ndc1 forms a distinct complex with the transmembrane proteins Pom152 and Pom34 and two alternative complexes with the soluble nucleoporins Nup53 and Nup59, which in turn bind to Nup170 and Nup157. The transmembrane and soluble Ndc1-binding partners have redundant functions at the NPC, and disruption of both groups of interactions causes defects in Ndc1 targeting and in NPC structure accompanied by significant pore dilation. Using photoconvertible fluorescent protein fusions, we further show that the depletion of Pom34 in cells that lack NUP53 and NUP59 blocks new NPC assembly and leads to the reversible accumulation of newly made nucleoporins in cytoplasmic foci. Therefore, Ndc1 together with its interaction partners are collectively essential for the biosynthesis and structural integrity of yeast NPCs.

@article{granlund_light_2009,
	title = {Light {Induced} {Changes} in {Protein} {Expression} and {Uniform} {Regulation} of {Transcription} in the {Thylakoid} {Lumen} of {Arabidopsis} thaliana},
	volume = {4},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0005649},
	doi = {10/ck4nsw},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Granlund, Irene and Hall, Michael and Kieselbach, Thomas and Schröder, Wolfgang P.},
	editor = {Holm, Magnus},
	month = may,
	year = {2009},
	pages = {e5649},
}

@article{meng_udp-glucose_2009,
	title = {{UDP}-{Glucose} {Pyrophosphorylase} is not {Rate} {Limiting}, but is {Essential} in {Arabidopsis}},
	volume = {50},
	issn = {0032-0781, 1471-9053},
	url = {https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/pcp052},
	doi = {10/cwnt2d},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Plant and Cell Physiology},
	author = {Meng, M. and Geisler, M. and Johansson, H. and Harholt, J. and Scheller, H. V. and Mellerowicz, E. J. and Kleczkowski, L. A.},
	month = may,
	year = {2009},
	pages = {998--1011},
}

@article{sorefan_regulated_2009,
	title = {A regulated auxin minimum is required for seed dispersal in {Arabidopsis}},
	volume = {459},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/articles/nature07875},
	doi = {10/dwbb4c},
	language = {en},
	number = {7246},
	urldate = {2021-06-08},
	journal = {Nature},
	author = {Sorefan, Karim and Girin, Thomas and Liljegren, Sarah J. and Ljung, Karin and Robles, Pedro and Galván-Ampudia, Carlos S. and Offringa, Remko and Friml, Jiří and Yanofsky, Martin F. and Østergaard, Lars},
	month = may,
	year = {2009},
	pages = {583--586},
}

@article{sani_magicangle_2009,
	title = {Magic‐angle phosphorus {NMR} of functional mitochondria: \textit{in situ} monitoring of lipid response under apoptotic‐like stress},
	volume = {23},
	issn = {0892-6638, 1530-6860},
	shorttitle = {Magic‐angle phosphorus {NMR} of functional mitochondria},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1096/fj.09-134114},
	doi = {10/b8cdxs},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {The FASEB Journal},
	author = {Sani, Marc‐Antoine and Keech, Olivier and Gardeström, Per and Dufourc, Erick J. and Gröbner, Gerhard},
	month = sep,
	year = {2009},
	pages = {2872--2878},
}

@incollection{belostotsky_comparison_2009,
	address = {Totowa, NJ},
	title = {Comparison of {Quantitative} {Metabolite} {Imaging} {Tools} and {Carbon}-13 {Techniques} for {Fluxomics}},
	volume = {553},
	isbn = {978-1-60327-562-0 978-1-60327-563-7},
	url = {http://link.springer.com/10.1007/978-1-60327-563-7_19},
	urldate = {2021-06-08},
	booktitle = {Plant {Systems} {Biology}},
	publisher = {Humana Press},
	author = {Niittylae, Totte and Chaudhuri, Bhavna and Sauer, Uwe and Frommer, Wolf B.},
	editor = {Belostotsky, Dmitry A.},
	year = {2009},
	doi = {10.1007/978-1-60327-563-7_19},
	note = {Series Title: Methods in Molecular Biology™},
	pages = {355--372},
}

@article{yanamandra_amyloid_2009,
	title = {Amyloid {Formation} by the {Pro}-{Inflammatory} {S100A8}/{A9} {Proteins} in the {Ageing} {Prostate}},
	volume = {4},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0005562},
	doi = {10/cq9jr4},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Yanamandra, Kiran and Alexeyev, Oleg and Zamotin, Vladimir and Srivastava, Vaibhav and Shchukarev, Andrei and Brorsson, Ann-Christin and Tartaglia, Gian Gaetano and Vogl, Thomas and Kayed, Rakez and Wingsle, Gunnar and Olsson, Jan and Dobson, Christopher M. and Bergh, Anders and Elgh, Fredrik and Morozova-Roche, Ludmilla A.},
	editor = {Gazit, Ehud},
	month = may,
	year = {2009},
	pages = {e5562},
}

@article{eysteinsson_variation_2009,
	title = {Variation in spring and autumn frost tolerance among provenances of {Russian} larches ( \textit{{Larix}} {Mill}.)},
	volume = {24},
	issn = {0282-7581, 1651-1891},
	url = {https://www.tandfonline.com/doi/full/10.1080/02827580902773470},
	doi = {10/cq92w4},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Scandinavian Journal of Forest Research},
	author = {Eysteinsson, Thröstur and Karlman, Lars and Fries, Anders and Martinsson, Owe and Skúlason, Brynjar},
	month = apr,
	year = {2009},
	pages = {100--110},
}

@article{akerstrom_effects_2009,
	title = {Effects of {Sampling} {Time} and {Nitrogen} {Fertilization} on {Anthocyanidin} {Levels} in \textit{{Vaccinium} myrtillus} {Fruits}},
	volume = {57},
	issn = {0021-8561, 1520-5118},
	url = {https://pubs.acs.org/doi/10.1021/jf8037743},
	doi = {10/d4w256},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Journal of Agricultural and Food Chemistry},
	author = {Åkerström, Andreas and Forsum, Åsa and Rumpunen, Kimmo and Jäderlund, Anders and Bång, Ulla},
	month = apr,
	year = {2009},
	pages = {3340--3345},
}

@article{ikeda_local_2009,
	title = {Local auxin biosynthesis modulates gradient-directed planar polarity in {Arabidopsis}},
	volume = {11},
	issn = {1465-7392, 1476-4679},
	url = {http://www.nature.com/articles/ncb1879},
	doi = {10/bdkdmx},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Nature Cell Biology},
	author = {Ikeda, Yoshihisa and Men, Shuzhen and Fischer, Urs and Stepanova, Anna N. and Alonso, José M. and Ljung, Karin and Grebe, Markus},
	month = jun,
	year = {2009},
	pages = {731--738},
}

@article{lundmark_low_2009,
	title = {Low temperature maximizes growth of {Crocus} vernus ({L}.) {Hill} via changes in carbon partitioning and corm development},
	volume = {60},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/erp103},
	doi = {10/c9zwbh},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Lundmark, M. and Hurry, V. and Lapointe, L.},
	month = may,
	year = {2009},
	pages = {2203--2213},
}

@article{chibani_comparative_2009,
	title = {Comparative {Genomic} {Study} of the {Thioredoxin} {Family} in {Photosynthetic} {Organisms} with {Emphasis} on {Populus} trichocarpa},
	volume = {2},
	issn = {16742052},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1674205214604731},
	doi = {10/bhd78p},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Molecular Plant},
	author = {Chibani, Kamel and Wingsle, Gunnar and Jacquot, Jean-Pierre and Gelhaye, Eric and Rouhier, Nicolas},
	month = mar,
	year = {2009},
	pages = {308--322},
}

@article{bjorkholm_using_2009,
	title = {Using multi-data hidden {Markov} models trained on local neighborhoods of protein structure to predict residue–residue contacts},
	volume = {25},
	issn = {1460-2059, 1367-4803},
	url = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btp149},
	doi = {10/cpbqwm},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {Bioinformatics},
	author = {Björkholm, Patrik and Daniluk, Pawel and Kryshtafovych, Andriy and Fidelis, Krzysztof and Andersson, Robin and Hvidsten, Torgeir R.},
	month = may,
	year = {2009},
	pages = {1264--1270},
}

@article{takahashi_korrigan1_2009,
	title = {{KORRIGAN1} and its {Aspen} {Homolog} {PttCel9A1} {Decrease} {Cellulose} {Crystallinity} in {Arabidopsis} {Stems}},
	volume = {50},
	issn = {1471-9053, 0032-0781},
	url = {https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/pcp062},
	doi = {10/djcxr3},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Plant and Cell Physiology},
	author = {Takahashi, Junko and Rudsander, Ulla J. and Hedenström, Mattias and Banasiak, Alicja and Harholt, Jesper and Amelot, Nicolas and Immerzeel, Peter and Ryden, Peter and Endo, Satoshi and Ibatullin, Farid M. and Brumer, Harry and del Campillo, Elena and Master, Emma R. and Vibe Scheller, Henrik and Sundberg, Björn and Teeri, Tuula T. and Mellerowicz, Ewa J.},
	month = jun,
	year = {2009},
	pages = {1099--1115},
}

@article{ali_auxin_2009,
	title = {Auxin production by plant associated bacteria: impact on endogenous {IAA} content and growth of \textit{{Triticum} aestivum} {L}.},
	volume = {48},
	issn = {02668254, 1472765X},
	shorttitle = {Auxin production by plant associated bacteria},
	url = {http://doi.wiley.com/10.1111/j.1472-765X.2009.02565.x},
	doi = {10/djz756},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Letters in Applied Microbiology},
	author = {Ali, B. and Sabri, A.N. and Ljung, K. and Hasnain, S.},
	month = may,
	year = {2009},
	pages = {542--547},
}

@article{love_ethylene_2009,
	title = {Ethylene is an endogenous stimulator of cell division in the cambial meristem of {Populus}},
	volume = {106},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0811660106},
	doi = {10/b8hrnm},
	language = {en},
	number = {14},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Love, J. and Bjorklund, S. and Vahala, J. and Hertzberg, M. and Kangasjarvi, J. and Sundberg, B.},
	month = apr,
	year = {2009},
	pages = {5984--5989},
}

@article{waldmann_easy_2009,
	title = {{EASY} {AND} {FLEXIBLE} {BAYESIAN} {INFERENCE} {OF} {QUANTITATIVE} {GENETIC} {PARAMETERS}},
	volume = {63},
	issn = {00143820, 15585646},
	url = {http://doi.wiley.com/10.1111/j.1558-5646.2009.00645.x},
	doi = {10/bqdxn9},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Evolution},
	author = {Waldmann, Patrik},
	month = jun,
	year = {2009},
	pages = {1640--1643},
}

@article{hvidsten_local_2009,
	title = {Local descriptors of protein structure: {A} systematic analysis of the sequence-structure relationship in proteins using short- and long-range interactions},
	volume = {75},
	issn = {08873585, 10970134},
	shorttitle = {Local descriptors of protein structure},
	url = {http://doi.wiley.com/10.1002/prot.22296},
	doi = {10/b6zxhz},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Proteins: Structure, Function, and Bioinformatics},
	author = {Hvidsten, Torgeir R. and Kryshtafovych, Andriy and Fidelis, Krzysztof},
	month = jun,
	year = {2009},
	pages = {870--884},
}

@article{garcia-gil_joint_2009,
	title = {Joint analysis of spatial genetic structure and inbreeding in a managed population of {Scots} pine},
	volume = {103},
	issn = {0018-067X, 1365-2540},
	url = {http://www.nature.com/articles/hdy200933},
	doi = {10/ff4qg7},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Heredity},
	author = {García-Gil, M R and Olivier, F and Kamruzzahan, S and Waldmann, P},
	month = jul,
	year = {2009},
	pages = {90--96},
}

@article{fracheboud_control_2009,
	title = {The {Control} of {Autumn} {Senescence} in {European} {Aspen}},
	volume = {149},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/149/4/1982/6107938},
	doi = {10/b8n86h},
	abstract = {Abstract
            The initiation, progression, and natural variation of autumn senescence in European aspen (Populus tremula) was investigated by monitoring chlorophyll degradation in (1) trees growing in natural stands and (2) cloned trees growing in a greenhouse under various light regimes. The main trigger for the initiation of autumn senescence in aspen is the shortening photoperiod, but there was a large degree of variation in the onset of senescence, both within local populations and among trees originating from different populations, where it correlated with the latitude of their respective origins. The variation for onset of senescence with a population was much larger than the variation of bud set. Once started, autumn senescence was accelerated by low temperature and longer nights, and clones that started to senescence late had a faster senescence. Bud set and autumn senescence appeared to be under the control of two independent critical photoperiods, but senescence could not be initiated until a certain time after bud set, suggesting that bud set and growth arrest are important for the trees to acquire competence to respond to the photoperiodic trigger to undergo autumn senescence. A timetable of events related to bud set and autumn senescence is presented.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Fracheboud, Yvan and Luquez, Virginia and Björkén, Lars and Sjödin, Andreas and Tuominen, Hannele and Jansson, Stefan},
	month = apr,
	year = {2009},
	pages = {1982--1991},
}

Abstract The initiation, progression, and natural variation of autumn senescence in European aspen (Populus tremula) was investigated by monitoring chlorophyll degradation in (1) trees growing in natural stands and (2) cloned trees growing in a greenhouse under various light regimes. The main trigger for the initiation of autumn senescence in aspen is the shortening photoperiod, but there was a large degree of variation in the onset of senescence, both within local populations and among trees originating from different populations, where it correlated with the latitude of their respective origins. The variation for onset of senescence with a population was much larger than the variation of bud set. Once started, autumn senescence was accelerated by low temperature and longer nights, and clones that started to senescence late had a faster senescence. Bud set and autumn senescence appeared to be under the control of two independent critical photoperiods, but senescence could not be initiated until a certain time after bud set, suggesting that bud set and growth arrest are important for the trees to acquire competence to respond to the photoperiodic trigger to undergo autumn senescence. A timetable of events related to bud set and autumn senescence is presented.

@article{hallander_optimum_2009,
	title = {Optimum contribution selection in large general tree breeding populations with an application to {Scots} pine},
	volume = {118},
	issn = {0040-5752, 1432-2242},
	url = {http://link.springer.com/10.1007/s00122-009-0968-7},
	doi = {10/d99z6c},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Theoretical and Applied Genetics},
	author = {Hallander, Jon and Waldmann, Patrik},
	month = apr,
	year = {2009},
	pages = {1133--1142},
}

@article{srivastava_alternative_2009,
	title = {Alternative {Splicing} {Studies} of the {Reactive} {Oxygen} {Species} {Gene} {Network} in \textit{{Populus}} {Reveal} {Two} {Isoforms} of {High}-{Isoelectric}-{Point} {Superoxide} {Dismutase}},
	volume = {149},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/149/4/1848/6107952},
	doi = {10/d5fkf9},
	abstract = {Abstract
            Recent evidence has shown that alternative splicing (AS) is widely involved in the regulation of gene expression, substantially extending the diversity of numerous proteins. In this study, a subset of expressed sequence tags representing members of the reactive oxygen species gene network was selected from the PopulusDB database to investigate AS mechanisms in Populus. Examples of all known types of AS were detected, but intron retention was the most common. Interestingly, the closest Arabidopsis (Arabidopsis thaliana) homologs of half of the AS genes identified in Populus are not reportedly alternatively spliced. Two genes encoding the protein of most interest in our study (high-isoelectric-point superoxide dismutase [hipI-SOD]) have been found in black cottonwood (Populus trichocarpa), designated PthipI-SODC1 and PthipI-SODC2. Analysis of the expressed sequence tag libraries has indicated the presence of two transcripts of PthipI-SODC1 (hipI-SODC1b and hipI-SODC1s). Alignment of these sequences with the PthipI-SODC1 gene showed that hipI-SODC1b was 69 bp longer than hipI-SODC1s due to an AS event involving the use of an alternative donor splice site in the sixth intron. Transcript analysis showed that the splice variant hipI-SODC1b was differentially expressed, being clearly expressed in cambial and xylem, but not phloem, regions. In addition, immunolocalization and mass spectrometric data confirmed the presence of hipI-SOD proteins in vascular tissue. The functionalities of the spliced gene products were assessed by expressing recombinant hipI-SOD proteins and in vitro SOD activity assays.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Srivastava, Vaibhav and Srivastava, Manoj Kumar and Chibani, Kamel and Nilsson, Robert and Rouhier, Nicolas and Melzer, Michael and Wingsle, Gunnar},
	month = apr,
	year = {2009},
	pages = {1848--1859},
}

Abstract Recent evidence has shown that alternative splicing (AS) is widely involved in the regulation of gene expression, substantially extending the diversity of numerous proteins. In this study, a subset of expressed sequence tags representing members of the reactive oxygen species gene network was selected from the PopulusDB database to investigate AS mechanisms in Populus. Examples of all known types of AS were detected, but intron retention was the most common. Interestingly, the closest Arabidopsis (Arabidopsis thaliana) homologs of half of the AS genes identified in Populus are not reportedly alternatively spliced. Two genes encoding the protein of most interest in our study (high-isoelectric-point superoxide dismutase [hipI-SOD]) have been found in black cottonwood (Populus trichocarpa), designated PthipI-SODC1 and PthipI-SODC2. Analysis of the expressed sequence tag libraries has indicated the presence of two transcripts of PthipI-SODC1 (hipI-SODC1b and hipI-SODC1s). Alignment of these sequences with the PthipI-SODC1 gene showed that hipI-SODC1b was 69 bp longer than hipI-SODC1s due to an AS event involving the use of an alternative donor splice site in the sixth intron. Transcript analysis showed that the splice variant hipI-SODC1b was differentially expressed, being clearly expressed in cambial and xylem, but not phloem, regions. In addition, immunolocalization and mass spectrometric data confirmed the presence of hipI-SOD proteins in vascular tissue. The functionalities of the spliced gene products were assessed by expressing recombinant hipI-SOD proteins and in vitro SOD activity assays.

@article{wientjes_role_2009,
	title = {The {Role} of {Lhca} {Complexes} in the {Supramolecular} {Organization} of {Higher} {Plant} {Photosystem} {I}},
	volume = {284},
	issn = {00219258},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0021925820324923},
	doi = {10/bpvfwk},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {Journal of Biological Chemistry},
	author = {Wientjes, Emilie and Oostergetel, Gert T. and Jansson, Stefan and Boekema, Egbert J. and Croce, Roberta},
	month = mar,
	year = {2009},
	pages = {7803--7810},
}

@article{courtois-moreau_unique_2009,
	title = {A unique program for cell death in xylem fibers of \textit{{Populus}} stem},
	volume = {58},
	issn = {09607412, 1365313X},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2008.03777.x},
	doi = {10/bqdrgm},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Courtois-Moreau, Charleen L. and Pesquet, Edouard and Sjödin, Andreas and Muñiz, Luis and Bollhöner, Benjamin and Kaneda, Minako and Samuels, Lacey and Jansson, Stefan and Tuominen, Hannele},
	month = apr,
	year = {2009},
	pages = {260--274},
}

@article{hytonen_gibberellin_2009,
	title = {Gibberellin mediates daylength-controlled differentiation of vegetative meristems in strawberry ({Fragaria} × ananassa {Duch})},
	volume = {9},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-9-18},
	doi = {10/fk39gx},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Hytönen, Timo and Elomaa, Paula and Moritz, Thomas and Junttila, Olavi},
	year = {2009},
	pages = {18},
}

@article{mathieu_repression_2009,
	title = {Repression of flowering by the {miR172} target {SMZ}},
	volume = {7},
	issn = {1545-7885},
	doi = {10/dcc259},
	abstract = {A small mobile protein, encoded by the FLOWERING LOCUS T (FT) locus, plays a central role in the control of flowering. FT is regulated positively by CONSTANS (CO), the output of the photoperiod pathway, and negatively by FLC, which integrates the effects of prolonged cold exposure. Here, we reveal the mechanisms of regulation by the microRNA miR172 target SCHLAFMUTZE (SMZ), a potent repressor of flowering. Whole-genome mapping of SMZ binding sites demonstrates not only direct regulation of FT, but also of many other flowering time regulators acting both upstream and downstream of FT, indicating an important role of miR172 and its targets in fine tuning the flowering response. A role for the miR172/SMZ module as a rheostat in flowering time is further supported by SMZ binding to several other genes encoding miR172 targets. Finally, we show that the action of SMZ is completely dependent on another floral repressor, FLM, providing the first direct connection between two important classes of flowering time regulators, AP2- and MADS-domain proteins.},
	language = {eng},
	number = {7},
	journal = {PLoS biology},
	author = {Mathieu, Johannes and Yant, Levi J. and Mürdter, Felix and Küttner, Frank and Schmid, Markus},
	month = jul,
	year = {2009},
	pmid = {19582143},
	pmcid = {PMC2701598},
	keywords = {Agrobacterium tumefaciens, Arabidopsis, Arabidopsis Proteins, Chromatin Immunoprecipitation, DNA-Binding Proteins, Flowers, Gene Expression Regulation, Plant, Genes, Reporter, MADS Domain Proteins, Meristem, MicroRNAs, Mutant Proteins, Oligonucleotide Array Sequence Analysis, Photoperiod, Plant Leaves, Plants, Genetically Modified, Protein Biosynthesis, RNA, Messenger, RNA, Plant, Reproduction, Transcription Factors, Transformation, Genetic},
	pages = {e1000148},
}

A small mobile protein, encoded by the FLOWERING LOCUS T (FT) locus, plays a central role in the control of flowering. FT is regulated positively by CONSTANS (CO), the output of the photoperiod pathway, and negatively by FLC, which integrates the effects of prolonged cold exposure. Here, we reveal the mechanisms of regulation by the microRNA miR172 target SCHLAFMUTZE (SMZ), a potent repressor of flowering. Whole-genome mapping of SMZ binding sites demonstrates not only direct regulation of FT, but also of many other flowering time regulators acting both upstream and downstream of FT, indicating an important role of miR172 and its targets in fine tuning the flowering response. A role for the miR172/SMZ module as a rheostat in flowering time is further supported by SMZ binding to several other genes encoding miR172 targets. Finally, we show that the action of SMZ is completely dependent on another floral repressor, FLM, providing the first direct connection between two important classes of flowering time regulators, AP2- and MADS-domain proteins.

@article{yant_just_2009,
	title = {Just say no: floral repressors help {Arabidopsis} bide the time},
	volume = {12},
	issn = {1879-0356},
	shorttitle = {Just say no},
	doi = {10/cnm97d},
	abstract = {Floral repressors ensure correct reproductive timing by safeguarding against premature flowering. In the past decade, several mechanisms of floral repression have come to light. Discrimination between direct and indirect repressors has been facilitated by increasing the use of chromatin immunoprecipitation assays. Certain MADS-domain transcription factors such as SHORT VEGETATIVE PHASE and FLOWERING LOCUS C bind directly to target euchromatin to repress specific loci including FLOWERING LOCUS T (FT) and FD. The AP2-domain transcription factor TEMPRANILLO 1 has also been shown to directly repress FT by binding its 5' UTR. We highlight emerging systems level approaches, including genome-scale direct binding studies (ChIP-chip and ChIP-Seq), which stand out in their promise to elucidate the complex network underlying the transition to flowering at an unprecedented level.},
	language = {eng},
	number = {5},
	journal = {Current Opinion in Plant Biology},
	author = {Yant, Levi and Mathieu, Johannes and Schmid, Markus},
	month = oct,
	year = {2009},
	pmid = {19695946},
	keywords = {Arabidopsis, Arabidopsis Proteins, Chromatin Immunoprecipitation, Flowers, Gene Expression Regulation, Plant, MADS Domain Proteins, Plant Leaves, Plant Shoots, Repressor Proteins, Transcription Factors},
	pages = {580--586},
}

Floral repressors ensure correct reproductive timing by safeguarding against premature flowering. In the past decade, several mechanisms of floral repression have come to light. Discrimination between direct and indirect repressors has been facilitated by increasing the use of chromatin immunoprecipitation assays. Certain MADS-domain transcription factors such as SHORT VEGETATIVE PHASE and FLOWERING LOCUS C bind directly to target euchromatin to repress specific loci including FLOWERING LOCUS T (FT) and FD. The AP2-domain transcription factor TEMPRANILLO 1 has also been shown to directly repress FT by binding its 5' UTR. We highlight emerging systems level approaches, including genome-scale direct binding studies (ChIP-chip and ChIP-Seq), which stand out in their promise to elucidate the complex network underlying the transition to flowering at an unprecedented level.

@article{saavedra_characterization_2009,
	title = {Characterization of {Phosphatidylinositol} {Phosphate} {Kinases} from the {Moss} {Physcomitrella} patens: {PpPIPK1} and {PpPIPK2}},
	volume = {50},
	issn = {0032-0781, 1471-9053},
	shorttitle = {Characterization of {Phosphatidylinositol} {Phosphate} {Kinases} from the {Moss} {Physcomitrella} patens},
	url = {https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/pcp018},
	doi = {10/dbfsgw},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Plant and Cell Physiology},
	author = {Saavedra, L. and Balbi, V. and Dove, S. K. and Hiwatashi, Y. and Mikami, K. and Sommarin, M.},
	month = jan,
	year = {2009},
	pages = {595--609},
}

@article{jimenez_deep_2009,
	title = {Deep shade alters the acclimation response to moderate water stress in {Quercus} suber {L}.},
	volume = {82},
	issn = {0015-752X, 1464-3626},
	url = {https://academic.oup.com/forestry/article-lookup/doi/10.1093/forestry/cpp008},
	doi = {10/c83j4p},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Forestry},
	author = {Jimenez, M. D. and Pardos, M. and Puertolas, J. and Kleczkowski, L. A. and Pardos, J. A.},
	month = jul,
	year = {2009},
	pages = {285--298},
}

@article{sjodin_populus_2009,
	title = {The \textit{{Populus}} {Genome} {Integrative} {Explorer} ({PopGenIE}): a new resource for exploring the \textit{{Populus}} genome},
	volume = {182},
	issn = {0028-646X, 1469-8137},
	shorttitle = {The \textit{{Populus}} {Genome} {Integrative} {Explorer} ({PopGenIE})},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2009.02807.x},
	doi = {10/bwmrwk},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Sjödin, Andreas and Street, Nathaniel Robert and Sandberg, Göran and Gustafsson, Petter and Jansson, Stefan},
	month = jun,
	year = {2009},
	pages = {1013--1025},
}

@article{zackrisson_nitrogen_2009,
	title = {Nitrogen fixation in mixed {Hylocomium} splendens moss communities},
	volume = {160},
	issn = {0029-8549, 1432-1939},
	url = {http://link.springer.com/10.1007/s00442-009-1299-8},
	doi = {10/csd825},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Oecologia},
	author = {Zackrisson, O. and DeLuca, T. H. and Gentili, F. and Sellstedt, A. and Jäderlund, A.},
	month = may,
	year = {2009},
	pages = {309--319},
}

@article{guenin_normalization_2009,
	title = {Normalization of {qRT}-{PCR} data: the necessity of adopting a systematic, experimental conditions-specific, validation of references},
	volume = {60},
	issn = {0022-0957, 1460-2431},
	shorttitle = {Normalization of {qRT}-{PCR} data},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/ern305},
	doi = {10/bf946c},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Guenin, S. and Mauriat, M. and Pelloux, J. and Van Wuytswinkel, O. and Bellini, C. and Gutierrez, L.},
	month = jan,
	year = {2009},
	pages = {487--493},
}

@article{nasholm_uptake_2009,
	title = {Uptake of organic nitrogen by plants},
	volume = {182},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2008.02751.x},
	doi = {10/dvgkdt},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Näsholm, Torgny and Kielland, Knut and Ganeteg, Ulrika},
	month = apr,
	year = {2009},
	pages = {31--48},
}

@article{atkin_temperature_2009,
	title = {Temperature dependence of respiration in roots colonized by arbuscular mycorrhizal fungi},
	volume = {182},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2008.02727.x},
	doi = {10/djs8g3},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Atkin, Owen K. and Sherlock, David and Fitter, Alastair H. and Jarvis, Susan and Hughes, John K. and Campbell, Catherine and Hurry, Vaughan and Hodge, Angela},
	month = apr,
	year = {2009},
	pages = {188--199},
}

@article{prasad_sapkota_species_2009,
	title = {Species diversity and regeneration of old-growth seasonally dry {Shorea} robusta forests following gap formation},
	volume = {20},
	issn = {1007-662X, 1993-0607},
	url = {http://link.springer.com/10.1007/s11676-009-0002-6},
	doi = {10/dttpfw},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Journal of Forestry Research},
	author = {Prasad Sapkota, Indra and Tigabu, Mulualem and Christer Odén, Per},
	month = feb,
	year = {2009},
	pages = {7--14},
}

@article{frenkel_improper_2009,
	title = {Improper excess light energy dissipation in {Arabidopsis} results in a metabolic reprogramming},
	volume = {9},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/1471-2229-9-12},
	doi = {10/ffdbr8},
	abstract = {Plant performance is affected by the level of expression of PsbS, a key photoprotective protein involved in the process of feedback de-excitation (FDE), or the qE component of non-photochemical quenching, NPQ.},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Frenkel, Martin and Külheim, Carsten and Jänkänpää, Hanna Johansson and Skogström, Oskar and Dall'Osto, Luca and Ågren, Jon and Bassi, Roberto and Moritz, Thomas and Moen, Jon and Jansson, Stefan},
	month = jan,
	year = {2009},
	keywords = {Herbivore Preference, Partial Little Square Discriminant Analysis, Partial Little Square Discriminant Analysis Model, Photooxidative Stress, Photosynthetic Light Reaction},
	pages = {12},
}

Plant performance is affected by the level of expression of PsbS, a key photoprotective protein involved in the process of feedback de-excitation (FDE), or the qE component of non-photochemical quenching, NPQ.

@article{lindahl_disulphide_2009,
	title = {Disulphide proteomes and interactions with thioredoxin on the track towards understanding redox regulation in chloroplasts and cyanobacteria},
	volume = {72},
	issn = {18743919},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1874391909000104},
	doi = {10/fgnxw7},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Journal of Proteomics},
	author = {Lindahl, Marika and Kieselbach, Thomas},
	month = apr,
	year = {2009},
	pages = {416--438},
}

@article{wiedermann_ecophysiological_2009,
	title = {Ecophysiological adjustment of two \textit{{Sphagnum}} species in response to anthropogenic nitrogen deposition},
	volume = {181},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2008.02628.x},
	doi = {10/fdmwzb},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Wiedermann, Magdalena M. and Gunnarsson, Urban and Ericson, Lars and Nordin, Annika},
	month = jan,
	year = {2009},
	pages = {208--217},
}

@article{garcia-cerdan_antisense_2009,
	title = {Antisense {Inhibition} of the {PsbX} {Protein} {Affects} {PSII} {Integrity} in the {Higher} {Plant} {Arabidopsis} thaliana},
	volume = {50},
	issn = {1471-9053, 0032-0781},
	url = {https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/pcn188},
	doi = {10/fbkmdx},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Plant and Cell Physiology},
	author = {García-Cerdán, José G. and Sveshnikov, Dmitry and Dewez, David and Jansson, Stefan and Funk, Christiane and Schröder, Wolfgang P.},
	month = feb,
	year = {2009},
	pages = {191--202},
}

@article{wabnik_gene_2009,
	title = {Gene expression trends and protein features effectively complement each other in gene function prediction},
	volume = {25},
	issn = {1460-2059, 1367-4803},
	url = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btn625},
	doi = {10/dmdhqs},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Bioinformatics},
	author = {Wabnik, Krzysztof and Hvidsten, Torgeir R. and Kedzierska, Anna and Van Leene, Jelle and De Jaeger, Geert and Beemster, Gerrit T. S. and Komorowski, Jan and Kuiper, Martin T. R.},
	month = feb,
	year = {2009},
	pages = {322--330},
}

@article{hansson_chlorophyll_2009,
	title = {Chlorophyll limitation in plants remodels and balances the photosynthetic apparatus by changing the accumulation of photosystems {I} and {II} through two different approaches},
	volume = {135},
	issn = {00319317, 13993054},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2008.01181.x},
	doi = {10/d2tn7g},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {Hansson, Andreas and Jensen, Poul E.},
	month = feb,
	year = {2009},
	pages = {214--228},
}

@article{stenlund_unlocking_2009,
	title = {Unlocking {Interpretation} in {Near} {Infrared} {Multivariate} {Calibrations} by {Orthogonal} {Partial} {Least} {Squares}},
	volume = {81},
	issn = {0003-2700, 1520-6882},
	url = {https://pubs.acs.org/doi/10.1021/ac801803e},
	doi = {10/d6m7ss},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Analytical Chemistry},
	author = {Stenlund, Hans and Johansson, Erik and Gottfries, Johan and Trygg, Johan},
	month = jan,
	year = {2009},
	pages = {203--209},
}

@article{bylesjo_integrated_2009,
	title = {Integrated {Analysis} of {Transcript}, {Protein} and {Metabolite} {Data} {To} {Study} {Lignin} {Biosynthesis} in {Hybrid} {Aspen}},
	volume = {8},
	issn = {1535-3893, 1535-3907},
	url = {https://pubs.acs.org/doi/10.1021/pr800298s},
	doi = {10/ddqkpn},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Journal of Proteome Research},
	author = {Bylesjö, Max and Nilsson, Robert and Srivastava, Vaibhav and Grönlund, Andreas and Johansson, Annika I. and Jansson, Stefan and Karlsson, Jan and Moritz, Thomas and Wingsle, Gunnar and Trygg, Johan},
	month = jan,
	year = {2009},
	pages = {199--210},
}

@article{lindgren_unequal_2009,
	title = {Unequal deployment of clones to seed orchards by considering genetic gain, relatedness and gene diversity},
	volume = {82},
	issn = {0015-752X, 1464-3626},
	url = {https://academic.oup.com/forestry/article-lookup/doi/10.1093/forestry/cpn033},
	doi = {10/bt7cth},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Forestry},
	author = {Lindgren, D. and Danusevicius, D. and Rosvall, O.},
	month = jan,
	year = {2009},
	pages = {17--28},
}

@incollection{scherer_bioinformatic_2009,
	address = {Chichester, UK},
	title = {Bioinformatic {Strategies} for {cDNA}-{Microarray} {Data} {Processing}},
	isbn = {978-0-470-68598-3 978-0-470-74138-2},
	url = {http://doi.wiley.com/10.1002/9780470685983.ch6},
	abstract = {Pre-processing plays a vital role in cDNA-microarray data analysis. Without proper preprocessing it is likely that the biological conclusions will be misleading. However, there are many alternatives and in order to choose a proper pre-processing procedure it is necessary to understand the effect of different methods. This chapter discusses several pre-processing steps, including image analysis, background correction, normalization, and filtering. Spike-in data are used to illustrate how different procedures affect the analytical ability to detect differentially expressed genes and estimate their regulation. The result shows that pre-processing has a major impact on both the experiment’s sensitivity and its bias. However, general recommendations are hard to give, since pre-processing consists of several actions that are highly dependent on each other. Furthermore, it is likely that pre-processing have a major impact on downstream analysis, such as clustering and classification, and pre-processing methods should be developed and evaluated with this in mind.},
	language = {en},
	urldate = {2021-06-08},
	booktitle = {Batch {Effects} and {Noise} in {Microarray} {Experiments}},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Fahln, Jessica and Landfors, Mattias and Freyhult, Eva and Bylesj, Max and Trygg, Johan and Hvidsten, Torgeir R and Rydn, Patrik},
	editor = {Scherer, Andreas},
	month = oct,
	year = {2009},
	doi = {10.1002/9780470685983.ch6},
	pages = {61--74},
}

Pre-processing plays a vital role in cDNA-microarray data analysis. Without proper preprocessing it is likely that the biological conclusions will be misleading. However, there are many alternatives and in order to choose a proper pre-processing procedure it is necessary to understand the effect of different methods. This chapter discusses several pre-processing steps, including image analysis, background correction, normalization, and filtering. Spike-in data are used to illustrate how different procedures affect the analytical ability to detect differentially expressed genes and estimate their regulation. The result shows that pre-processing has a major impact on both the experiment’s sensitivity and its bias. However, general recommendations are hard to give, since pre-processing consists of several actions that are highly dependent on each other. Furthermore, it is likely that pre-processing have a major impact on downstream analysis, such as clustering and classification, and pre-processing methods should be developed and evaluated with this in mind.

@article{albrectsen_large_2009,
	title = {Large scale geographic clines of parasite damage to \textit{{Populus} tremula} {L}},
	issn = {09067590, 16000587},
	url = {http://doi.wiley.com/10.1111/j.1600-0587.2009.05982.x},
	doi = {10/c38874},
	language = {en},
	urldate = {2021-06-08},
	journal = {Ecography},
	author = {Albrectsen, Benedicte R. and Witzell, Johanna and Robinson, Kathryn M. and Wulff, Sören and Luquez, Virginia M. C. and Ågren, Rickard and Jansson, Stefan},
	month = oct,
	year = {2009},
}