Publications 2013

@article{romay_comprehensive_2013,
	title = {Comprehensive genotyping of the {USA} national maize inbred seed bank},
	volume = {14},
	issn = {1474-760X},
	url = {https://doi.org/10.1186/gb-2013-14-6-r55},
	doi = {10.1186/gb-2013-14-6-r55},
	abstract = {Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world.},
	number = {6},
	urldate = {2024-03-22},
	journal = {Genome Biology},
	author = {Romay, Maria C. and Millard, Mark J. and Glaubitz, Jeffrey C. and Peiffer, Jason A. and Swarts, Kelly L. and Casstevens, Terry M. and Elshire, Robert J. and Acharya, Charlotte B. and Mitchell, Sharon E. and Flint-Garcia, Sherry A. and McMullen, Michael D. and Holland, James B. and Buckler, Edward S. and Gardner, Candice A.},
	month = jun,
	year = {2013},
	keywords = {Diversity, Genotyping by sequencing, Germplasm, Maize, Public},
	pages = {R55},
}

Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world.

@article{nookaraju_designing_2013,
	title = {Designing {Cell} {Walls} for {Improved} {Bioenergy} {Production}},
	volume = {6},
	issn = {1674-2052},
	url = {https://www.sciencedirect.com/science/article/pii/S1674205214608741},
	doi = {10.1093/mp/sss111},
	number = {1},
	urldate = {2023-11-14},
	journal = {Molecular Plant},
	author = {Nookaraju, Akula and Pandey, Shashank K. and Bae, Hyeun-Jong and Joshi, Chandrashekhar P.},
	month = jan,
	year = {2013},
	pages = {8--10},
}

@article{liang_seedling_2013,
	title = {Seedling performance of {Pinus} densata and its parental population in the habitat of {P}. tabuliformis},
	volume = {37},
	issn = {1005-264X},
	url = {https://www.plant-ecology.com/EN/10.3724/SP.J.1258.2013.00016},
	doi = {10.3724/SP.J.1258.2013.00016},
	abstract = {Aims Pinus densata is the natural diploid hybrid of P. tabuliformis an...},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {Chinese Journal of Plant Ecology},
	author = {Liang, Dong and Mao, Jian-Feng and Zhao, Wei and Zhou, Xian-Qing and Yuan, Yuan and Wang, Li-Ming and Xing, Fang-Qian and Wang, Xiao-Ru and Li, Yue},
	month = aug,
	year = {2013},
	pages = {150},
}

Aims Pinus densata is the natural diploid hybrid of P. tabuliformis an...

@article{wang_impact_2013,
	title = {Impact of {Geography} and {Climate} on the {Genetic} {Differentiation} of the {Subtropical} {Pine} {Pinus} yunnanensis},
	volume = {8},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067345},
	doi = {10.1371/journal.pone.0067345},
	abstract = {Southwest China is a biodiversity hotspot characterized by complex topography, heterogeneous regional climates and rich flora. The processes and driving factors underlying this hotspot remain to be explicitly tested across taxa to gain a general understanding of the evolution of biodiversity and speciation in the region. In this study, we examined the role played by historically neutral processes, geography and environment in producing the current genetic diversity of the subtropical pine Pinus yunnanensis. We used genetic and ecological methods to investigate the patterns of genetic differentiation and ecological niche divergence across the distribution range of this species. We found both continuous genetic differentiation over the majority of its range, and discrete isolated local clusters. The discrete differentiation between two genetic groups in the west and east peripheries is consistent with niche divergence and geographical isolation of these groups. In the central area of the species’ range, population structure was shaped mainly by neutral processes and geography rather than by ecological selection. These results show that geographical and environmental factors together created stronger and more discrete genetic differentiation than isolation by distance alone, and illustrate the importance of ecological factors in forming or maintaining genetic divergence across a complex landscape. Our findings differ from other phylogenetic studies that identified the historical drainage system in the region as the primary factor shaping population structure, and highlight the heterogeneous contributions that geography and environment have made to genetic diversity among taxa in southwest China.},
	language = {en},
	number = {6},
	urldate = {2023-04-27},
	journal = {PLOS ONE},
	author = {Wang, Baosheng and Mao, Jian-Feng and Zhao, Wei and Wang, Xiao-Ru},
	month = jun,
	year = {2013},
	note = {Publisher: Public Library of Science},
	keywords = {Biogeography, Ecological niches, Environmental geography, Mitochondrial DNA, Paleogenetics, Phylogeography, Population genetics, Rivers},
	pages = {e67345},
}

Southwest China is a biodiversity hotspot characterized by complex topography, heterogeneous regional climates and rich flora. The processes and driving factors underlying this hotspot remain to be explicitly tested across taxa to gain a general understanding of the evolution of biodiversity and speciation in the region. In this study, we examined the role played by historically neutral processes, geography and environment in producing the current genetic diversity of the subtropical pine Pinus yunnanensis. We used genetic and ecological methods to investigate the patterns of genetic differentiation and ecological niche divergence across the distribution range of this species. We found both continuous genetic differentiation over the majority of its range, and discrete isolated local clusters. The discrete differentiation between two genetic groups in the west and east peripheries is consistent with niche divergence and geographical isolation of these groups. In the central area of the species’ range, population structure was shaped mainly by neutral processes and geography rather than by ecological selection. These results show that geographical and environmental factors together created stronger and more discrete genetic differentiation than isolation by distance alone, and illustrate the importance of ecological factors in forming or maintaining genetic divergence across a complex landscape. Our findings differ from other phylogenetic studies that identified the historical drainage system in the region as the primary factor shaping population structure, and highlight the heterogeneous contributions that geography and environment have made to genetic diversity among taxa in southwest China.

@article{merelo_genome-wide_2013,
	title = {Genome-{Wide} {Identification} of {KANADI1} {Target} {Genes}},
	volume = {8},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0077341},
	doi = {10.1371/journal.pone.0077341},
	abstract = {Plant organ development and polarity establishment is mediated by the action of several transcription factors. Among these, the KANADI (KAN) subclade of the GARP protein family plays important roles in polarity-associated processes during embryo, shoot and root patterning. In this study, we have identified a set of potential direct target genes of KAN1 through a combination of chromatin immunoprecipitation/DNA sequencing (ChIP-Seq) and genome-wide transcriptional profiling using tiling arrays. Target genes are over-represented for genes involved in the regulation of organ development as well as in the response to auxin. KAN1 affects directly the expression of several genes previously shown to be important in the establishment of polarity during lateral organ and vascular tissue development. We also show that KAN1 controls through its target genes auxin effects on organ development at different levels: transport and its regulation, and signaling. In addition, KAN1 regulates genes involved in the response to abscisic acid, jasmonic acid, brassinosteroids, ethylene, cytokinins and gibberellins. The role of KAN1 in organ polarity is antagonized by HD-ZIPIII transcription factors, including REVOLUTA (REV). A comparison of their target genes reveals that the REV/KAN1 module acts in organ patterning through opposite regulation of shared targets. Evidence of mutual repression between closely related family members is also shown.},
	language = {en},
	number = {10},
	urldate = {2022-11-30},
	journal = {PLOS ONE},
	author = {Merelo, Paz and Xie, Yakun and Brand, Lucas and Ott, Felix and Weigel, Detlef and Bowman, John L. and Heisler, Marcus G. and Wenkel, Stephan},
	month = oct,
	year = {2013},
	keywords = {Auxins, DNA transcription, Gene expression, Gene regulation, Leaves, Organogenesis, Transcription factors, Transcriptional control},
	pages = {e77341},
}

Plant organ development and polarity establishment is mediated by the action of several transcription factors. Among these, the KANADI (KAN) subclade of the GARP protein family plays important roles in polarity-associated processes during embryo, shoot and root patterning. In this study, we have identified a set of potential direct target genes of KAN1 through a combination of chromatin immunoprecipitation/DNA sequencing (ChIP-Seq) and genome-wide transcriptional profiling using tiling arrays. Target genes are over-represented for genes involved in the regulation of organ development as well as in the response to auxin. KAN1 affects directly the expression of several genes previously shown to be important in the establishment of polarity during lateral organ and vascular tissue development. We also show that KAN1 controls through its target genes auxin effects on organ development at different levels: transport and its regulation, and signaling. In addition, KAN1 regulates genes involved in the response to abscisic acid, jasmonic acid, brassinosteroids, ethylene, cytokinins and gibberellins. The role of KAN1 in organ polarity is antagonized by HD-ZIPIII transcription factors, including REVOLUTA (REV). A comparison of their target genes reveals that the REV/KAN1 module acts in organ patterning through opposite regulation of shared targets. Evidence of mutual repression between closely related family members is also shown.

@article{brandt_control_2013,
	series = {Developmental plasticity and adaptation in plants},
	title = {Control of stem cell homeostasis via interlocking {microRNA} and {microProtein} feedback loops},
	volume = {130},
	issn = {0925-4773},
	url = {https://www.sciencedirect.com/science/article/pii/S0925477312000603},
	doi = {10.1016/j.mod.2012.06.007},
	abstract = {Stem cells in the shoot apex of plants produce cells required for the formation of new leaves. Adult leaves are composed of multiple tissue layers arranged along the dorso-ventral (adaxial/abaxial) axis. Class III homeodomain leucine zipper (HD-ZIPIII) transcription factors play an important role in the set-up of leaf polarity in plants. Loss of HD-ZIPIII function results in strongly misshapen leaves and in severe cases fosters the consumption of the apical stem cells, thus causing a growth arrest in mutant plants. HD-ZIPIII mRNA is under tight control by microRNAs 165/166. In addition to the microRNA-action a second layer of regulation is established by LITTLE ZIPPER (ZPR)-type microProteins, which can interact with HD-ZIPIII proteins, forming attenuated protein complexes. Here we show that REVOLUTA (REV, a member of the HD-ZIPIII family) directly regulates the expression of ARGONAUTE10 (AGO10), ZPR1 and ZPR3. Because AGO10 was shown to dampen microRNA165/6 function, REV establishes a positive feedback loop on its own activity. Since ZPR-type microProteins are known to reduce HD-ZIPIII protein activity, REV concomitantly establishes a negative feedback loop. We propose that the interconnection of these microRNA/microProtein feedback loops regulates polarity set-up and stem cell activity in plants.},
	language = {en},
	number = {1},
	urldate = {2022-11-30},
	journal = {Mechanisms of Development},
	author = {Brandt, Ronny and Xie, Yakun and Musielak, Thomas and Graeff, Moritz and Stierhof, York-Dieter and Huang, Hai and Liu, Chun-Ming and Wenkel, Stephan},
	month = jan,
	year = {2013},
	keywords = {AGO10, HD-ZIPIII transcription factors, LITTLE ZIPPER, Shoot apical meristem, microProteins, microRNAs},
	pages = {25--33},
}

Stem cells in the shoot apex of plants produce cells required for the formation of new leaves. Adult leaves are composed of multiple tissue layers arranged along the dorso-ventral (adaxial/abaxial) axis. Class III homeodomain leucine zipper (HD-ZIPIII) transcription factors play an important role in the set-up of leaf polarity in plants. Loss of HD-ZIPIII function results in strongly misshapen leaves and in severe cases fosters the consumption of the apical stem cells, thus causing a growth arrest in mutant plants. HD-ZIPIII mRNA is under tight control by microRNAs 165/166. In addition to the microRNA-action a second layer of regulation is established by LITTLE ZIPPER (ZPR)-type microProteins, which can interact with HD-ZIPIII proteins, forming attenuated protein complexes. Here we show that REVOLUTA (REV, a member of the HD-ZIPIII family) directly regulates the expression of ARGONAUTE10 (AGO10), ZPR1 and ZPR3. Because AGO10 was shown to dampen microRNA165/6 function, REV establishes a positive feedback loop on its own activity. Since ZPR-type microProteins are known to reduce HD-ZIPIII protein activity, REV concomitantly establishes a negative feedback loop. We propose that the interconnection of these microRNA/microProtein feedback loops regulates polarity set-up and stem cell activity in plants.

@article{calderon_conserved_2013,
	title = {A {Conserved} {Rubredoxin} {Is} {Necessary} for {Photosystem} {II} {Accumulation} in {Diverse} {Oxygenic} {Photoautotrophs}},
	volume = {288},
	issn = {00219258},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0021925820490738},
	doi = {10/f5qnnj},
	abstract = {In oxygenic photosynthesis, two photosystems work in tandem to harvest light energy and generate NADPH and ATP. Photosystem II (PSII), the protein-pigment complex that uses light energy to catalyze the splitting of water, is assembled from its component parts in a tightly regulated process that requires a number of assembly factors. The 2pac mutant of the unicellular green alga Chlamydomonas reinhardtii was isolated and found to have no detectable PSII activity, whereas other components of the photosynthetic electron transport chain, including photosystem I, were still functional. PSII activity was fully restored by complementation with the RBD1 gene, which encodes a small iron-sulfur protein known as a rubredoxin. Phylogenetic evidence supports the hypothesis that this rubredoxin and its orthologs are unique to oxygenic phototrophs and distinct from rubredoxins in Archaea and bacteria (excluding cyanobacteria). Knockouts of the rubredoxin orthologs in the cyanobacterium Synechocystis sp. PCC 6803 and the plant Arabidopsis thaliana were also found to be specifically affected in PSII accumulation. Taken together, our data suggest that this rubredoxin is necessary for normal PSII activity in a diverse set of organisms that perform oxygenic photosynthesis},
	language = {en},
	number = {37},
	urldate = {2021-06-08},
	journal = {Journal of Biological Chemistry},
	author = {Calderon, Robert H. and García-Cerdán, José G. and Malnoë, Alizée and Cook, Ron and Russell, James J. and Gaw, Cynthia and Dent, Rachel M. and de Vitry, Catherine and Niyogi, Krishna K.},
	month = sep,
	year = {2013},
	pages = {26688--26696},
}

In oxygenic photosynthesis, two photosystems work in tandem to harvest light energy and generate NADPH and ATP. Photosystem II (PSII), the protein-pigment complex that uses light energy to catalyze the splitting of water, is assembled from its component parts in a tightly regulated process that requires a number of assembly factors. The 2pac mutant of the unicellular green alga Chlamydomonas reinhardtii was isolated and found to have no detectable PSII activity, whereas other components of the photosynthetic electron transport chain, including photosystem I, were still functional. PSII activity was fully restored by complementation with the RBD1 gene, which encodes a small iron-sulfur protein known as a rubredoxin. Phylogenetic evidence supports the hypothesis that this rubredoxin and its orthologs are unique to oxygenic phototrophs and distinct from rubredoxins in Archaea and bacteria (excluding cyanobacteria). Knockouts of the rubredoxin orthologs in the cyanobacterium Synechocystis sp. PCC 6803 and the plant Arabidopsis thaliana were also found to be specifically affected in PSII accumulation. Taken together, our data suggest that this rubredoxin is necessary for normal PSII activity in a diverse set of organisms that perform oxygenic photosynthesis

@article{lafonplacette_methylome_2013,
	title = {Methylome of {DNase} {I} sensitive chromatin in {Populus} trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene-body {DNA} methylation in open chromatin state},
	volume = {197},
	issn = {0028-646X, 1469-8137},
	shorttitle = {Methylome of {\textless}span style="font-variant},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.12026},
	doi = {10/f22v74},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Lafon‐Placette, Clément and Faivre‐Rampant, Patricia and Delaunay, Alain and Street, Nathaniel and Brignolas, Franck and Maury, Stéphane},
	month = jan,
	year = {2013},
	pages = {416--430},
}

@article{bussell_requirement_2013,
	title = {Requirement for the plastidial oxidative pentose phosphate pathway for nitrate assimilation in {Arabidopsis}},
	volume = {75},
	copyright = {© 2013 The Authors The Plant Journal © 2013 John Wiley \& Sons Ltd},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.12222},
	doi = {10/f46xkb},
	abstract = {Sugar metabolism and the oxidative pentose phosphate pathway (OPPP) are strongly implicated in N assimilation, although the relationship between them and the roles of the plastidial and cytosolic OPPP have not been established genetically. We studied a knock-down mutant of the plastid-localized OPPP enzyme 6-phosphogluconolactonase 3 (PGL3). pgl3-1 plants exhibited relatively greater resource allocation to roots but were smaller than the wild type. They had a lower content of amino acids and free in leaves than the wild type, despite exhibiting comparable photosynthetic rates and efficiency, and normal levels of many other primary metabolites. When N-deprived plants were fed via the roots with , pgl3-1 exhibited normal induction of OPPP and nitrate assimilation genes in roots, and amino acids in roots and shoots were labeled with 15N at least as rapidly as in the wild type. However, when N-replete plants were fed via the roots with sucrose, expression of specific OPPP and N assimilation genes in roots increased in the wild type but not in pgl3-1. Thus, sugar-dependent expression of N assimilation genes requires OPPP activity and the specificity of the effect of the pgl3-1 mutation on N assimilation genes establishes that it is not the result of general energy deficiency or accumulation of toxic intermediates. We conclude that expression of specific nitrate assimilation genes in the nucleus of root cells is positively regulated by a signal emanating from OPPP activity in the plastid.},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {The Plant Journal},
	author = {Bussell, John D. and Keech, Olivier and Fenske, Ricarda and Smith, Steven M.},
	year = {2013},
	keywords = {6-phosphogluconolactonase, Arabidopsis thaliana, nitrate, nitrogen assimilation, oxidative pentose phosphate pathway, plastid},
	pages = {578--591},
}

Sugar metabolism and the oxidative pentose phosphate pathway (OPPP) are strongly implicated in N assimilation, although the relationship between them and the roles of the plastidial and cytosolic OPPP have not been established genetically. We studied a knock-down mutant of the plastid-localized OPPP enzyme 6-phosphogluconolactonase 3 (PGL3). pgl3-1 plants exhibited relatively greater resource allocation to roots but were smaller than the wild type. They had a lower content of amino acids and free in leaves than the wild type, despite exhibiting comparable photosynthetic rates and efficiency, and normal levels of many other primary metabolites. When N-deprived plants were fed via the roots with , pgl3-1 exhibited normal induction of OPPP and nitrate assimilation genes in roots, and amino acids in roots and shoots were labeled with 15N at least as rapidly as in the wild type. However, when N-replete plants were fed via the roots with sucrose, expression of specific OPPP and N assimilation genes in roots increased in the wild type but not in pgl3-1. Thus, sugar-dependent expression of N assimilation genes requires OPPP activity and the specificity of the effect of the pgl3-1 mutation on N assimilation genes establishes that it is not the result of general energy deficiency or accumulation of toxic intermediates. We conclude that expression of specific nitrate assimilation genes in the nucleus of root cells is positively regulated by a signal emanating from OPPP activity in the plastid.

@article{mahboubi_aspen_2013,
	title = {Aspen {SUCROSE} {TRANSPORTER3} {Allocates} {Carbon} into {Wood} {Fibers}},
	volume = {163},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/163/4/1729-1740/6111119},
	doi = {10/f24j68},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {PLANT PHYSIOLOGY},
	author = {Mahboubi, A. and Ratke, C. and Gorzsas, A. and Kumar, M. and Mellerowicz, E. J. and Niittylä, T.},
	month = dec,
	year = {2013},
	pages = {1729--1740},
}

@article{leoni_very_2013,
	title = {Very rapid phosphorylation kinetics suggest a unique role for {Lhcb2} during state transitions in {Arabidopsis}},
	volume = {76},
	issn = {0960-7412, 1365-313X},
	shorttitle = {Very rapid phosphorylation kinetics suggest a unique role for {\textless}span style="font-variant},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.12297},
	doi = {10/f23mzn},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Leoni, Claudia and Pietrzykowska, Malgorzata and Kiss, Anett Z. and Suorsa, Marjaana and Ceci, Luigi R. and Aro, Eva‐Mari and Jansson, Stefan},
	month = oct,
	year = {2013},
	pages = {236--246},
}

@article{schallenberg-rudinger_dyw-protein_2013,
	title = {A {DYW}-protein knockout in {Physcomitrella} affects two closely spaced mitochondrial editing sites and causes a severe developmental phenotype},
	volume = {76},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.12304},
	doi = {10/f5fkxs},
	abstract = {RNA-binding pentatricopeptide repeat (PPR) proteins carrying a carboxy-terminal DYW domain similar to cytidine deaminases have been characterized as site-specific factors for C-to-U RNA editing in plant organelles. Here we report that knockout of DYW-PPR\_65 in Physcomitrella patens causes a severe developmental phenotype in the moss and specifically affects two editing sites located 18 nucleotides apart on the mitochondrial ccmFC mRNA. Intriguingly, PPR\_71, another DYW-type PPR, had been identified previously as an editing factor specifically affecting only the downstream editing site, ccmFCeU122SF. The now characterized PPR\_65 binds specifically only to the upstream target site, ccmFCeU103PS, in full agreement with a recent RNA-recognition code for PPR arrays. The functional interference between the two editing events may be caused by a combination of three factors: (i) the destabilization of an RNA secondary structure interfering with PPR\_71 binding by prior binding of PPR\_65; (ii) the resulting upstream C–U conversion; or (iii) a direct interaction between the two DYW proteins. Indeed, we find the Physcomitrella DYW-PPRs to interact in yeast-two-hybrid assays. The moss DYW-PPRs also interact yet more strongly with MORF (Multiple Organellar RNA editing Factor)/RIP (RNA editing factor interacting proteins) proteins of Arabidopsis known to be general editing factors in flowering plants, although MORF homologues are entirely absent in the moss. Finally, we demonstrate binding of Physcomitrella DYW-PPR\_98, for which no KO lines could be raised, to its predicted target sequence upstream of editing site atp9eU92SL. Together with the functional characterization of DYW-PPR\_65, this completes the assignment of RNA editing factors to all editing sites in the Physcomitrella mitochondrial transcriptome.},
	language = {en},
	number = {3},
	urldate = {2021-09-02},
	journal = {The Plant Journal},
	author = {Schallenberg-Rüdinger, Mareike and Kindgren, Peter and Zehrmann, Anja and Small, Ian and Knoop, Volker},
	year = {2013},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.12304},
	keywords = {Cytidine deaminase, DYW domain, Pentatricopeptide repeat proteins, Physcomitrella patens, Plant mitochondrial RNA editing, RNA-binding code},
	pages = {420--432},
}

RNA-binding pentatricopeptide repeat (PPR) proteins carrying a carboxy-terminal DYW domain similar to cytidine deaminases have been characterized as site-specific factors for C-to-U RNA editing in plant organelles. Here we report that knockout of DYW-PPR_65 in Physcomitrella patens causes a severe developmental phenotype in the moss and specifically affects two editing sites located 18 nucleotides apart on the mitochondrial ccmFC mRNA. Intriguingly, PPR_71, another DYW-type PPR, had been identified previously as an editing factor specifically affecting only the downstream editing site, ccmFCeU122SF. The now characterized PPR_65 binds specifically only to the upstream target site, ccmFCeU103PS, in full agreement with a recent RNA-recognition code for PPR arrays. The functional interference between the two editing events may be caused by a combination of three factors: (i) the destabilization of an RNA secondary structure interfering with PPR_71 binding by prior binding of PPR_65; (ii) the resulting upstream C–U conversion; or (iii) a direct interaction between the two DYW proteins. Indeed, we find the Physcomitrella DYW-PPRs to interact in yeast-two-hybrid assays. The moss DYW-PPRs also interact yet more strongly with MORF (Multiple Organellar RNA editing Factor)/RIP (RNA editing factor interacting proteins) proteins of Arabidopsis known to be general editing factors in flowering plants, although MORF homologues are entirely absent in the moss. Finally, we demonstrate binding of Physcomitrella DYW-PPR_98, for which no KO lines could be raised, to its predicted target sequence upstream of editing site atp9eU92SL. Together with the functional characterization of DYW-PPR_65, this completes the assignment of RNA editing factors to all editing sites in the Physcomitrella mitochondrial transcriptome.

@article{boutte_echidna-mediated_2013,
	title = {{ECHIDNA}-mediated post-{Golgi} trafficking of auxin carriers for differential cell elongation},
	volume = {110},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1309057110},
	doi = {10/f2z6v9},
	language = {en},
	number = {40},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Boutte, Y. and Jonsson, K. and McFarlane, H. E. and Johnson, E. and Gendre, D. and Swarup, R. and Friml, J. and Samuels, L. and Robert, S. and Bhalerao, Rishikesh P.},
	month = oct,
	year = {2013},
	pages = {16259--16264},
}

@article{duan_endodermal_2013,
	title = {Endodermal {ABA} {Signaling} {Promotes} {Lateral} {Root} {Quiescence} during {Salt} {Stress} in \textit{{Arabidopsis}} {Seedlings}},
	volume = {25},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/25/1/324/6097782},
	doi = {10/f2zqb8},
	abstract = {Abstract
            The endodermal tissue layer is found in the roots of vascular plants and functions as a semipermeable barrier, regulating the transport of solutes from the soil into the vascular stream. As a gateway for solutes, the endodermis may also serve as an important site for sensing and responding to useful or toxic substances in the environment. Here, we show that high salinity, an environmental stress widely impacting agricultural land, regulates growth of the seedling root system through a signaling network operating primarily in the endodermis. We report that salt stress induces an extended quiescent phase in postemergence lateral roots (LRs) whereby the rate of growth is suppressed for several days before recovery begins. Quiescence is correlated with sustained abscisic acid (ABA) response in LRs and is dependent upon genes necessary for ABA biosynthesis, signaling, and transcriptional regulation. We use a tissue-specific strategy to identify the key cell layers where ABA signaling acts to regulate growth. In the endodermis, misexpression of the ABA insensitive1-1 mutant protein, which dominantly inhibits ABA signaling, leads to a substantial recovery in LR growth under salt stress conditions. Gibberellic acid signaling, which antagonizes the ABA pathway, also acts primarily in the endodermis, and we define the crosstalk between these two hormones. Our results identify the endodermis as a gateway with an ABA-dependent guard, which prevents root growth into saline environments.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Duan, Lina and Dietrich, Daniela and Ng, Chong Han and Chan, Penny Mei Yeen and Bhalerao, Rishikesh P. and Bennett, Malcolm J. and Dinneny, José R.},
	month = feb,
	year = {2013},
	pages = {324--341},
}

Abstract The endodermal tissue layer is found in the roots of vascular plants and functions as a semipermeable barrier, regulating the transport of solutes from the soil into the vascular stream. As a gateway for solutes, the endodermis may also serve as an important site for sensing and responding to useful or toxic substances in the environment. Here, we show that high salinity, an environmental stress widely impacting agricultural land, regulates growth of the seedling root system through a signaling network operating primarily in the endodermis. We report that salt stress induces an extended quiescent phase in postemergence lateral roots (LRs) whereby the rate of growth is suppressed for several days before recovery begins. Quiescence is correlated with sustained abscisic acid (ABA) response in LRs and is dependent upon genes necessary for ABA biosynthesis, signaling, and transcriptional regulation. We use a tissue-specific strategy to identify the key cell layers where ABA signaling acts to regulate growth. In the endodermis, misexpression of the ABA insensitive1-1 mutant protein, which dominantly inhibits ABA signaling, leads to a substantial recovery in LR growth under salt stress conditions. Gibberellic acid signaling, which antagonizes the ABA pathway, also acts primarily in the endodermis, and we define the crosstalk between these two hormones. Our results identify the endodermis as a gateway with an ABA-dependent guard, which prevents root growth into saline environments.

@article{nystedt_norway_2013,
	title = {The {Norway} spruce genome sequence and conifer genome evolution},
	volume = {497},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/articles/nature12211},
	doi = {10/f2zsx6},
	language = {en},
	number = {7451},
	urldate = {2021-06-08},
	journal = {Nature},
	author = {Nystedt, Björn and Street, Nathaniel R. and Wetterbom, Anna and Zuccolo, Andrea and Lin, Yao-Cheng and Scofield, Douglas G. and Vezzi, Francesco and Delhomme, Nicolas and Giacomello, Stefania and Alexeyenko, Andrey and Vicedomini, Riccardo and Sahlin, Kristoffer and Sherwood, Ellen and Elfstrand, Malin and Gramzow, Lydia and Holmberg, Kristina and Hällman, Jimmie and Keech, Olivier and Klasson, Lisa and Koriabine, Maxim and Kucukoglu, Melis and Käller, Max and Luthman, Johannes and Lysholm, Fredrik and Niittylä, Totte and Olson, Åke and Rilakovic, Nemanja and Ritland, Carol and Rosselló, Josep A. and Sena, Juliana and Svensson, Thomas and Talavera-López, Carlos and Theißen, Günter and Tuominen, Hannele and Vanneste, Kevin and Wu, Zhi-Qiang and Zhang, Bo and Zerbe, Philipp and Arvestad, Lars and Bhalerao, Rishikesh P. and Bohlmann, Joerg and Bousquet, Jean and Garcia Gil, Rosario and Hvidsten, Torgeir R. and de Jong, Pieter and MacKay, John and Morgante, Michele and Ritland, Kermit and Sundberg, Björn and Lee Thompson, Stacey and Van de Peer, Yves and Andersson, Björn and Nilsson, Ove and Ingvarsson, Pär K. and Lundeberg, Joakim and Jansson, Stefan},
	month = may,
	year = {2013},
	pages = {579--584},
}

@article{petterle_daylength_2013,
	title = {Daylength mediated control of seasonal growth patterns in perennial trees},
	volume = {16},
	issn = {13695266},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526613000241},
	doi = {10/f2zsrv},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Current Opinion in Plant Biology},
	author = {Petterle, Anna and Karlberg, Anna and Bhalerao, Rishikesh P.},
	month = jun,
	year = {2013},
	pages = {301--306},
}

@article{le_hir_abcg9_2013,
	title = {{ABCG9}, {ABCG11} and {ABCG14} {ABC} transporters are required for vascular development in {Arabidopsis}},
	volume = {76},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.12334},
	doi = {10/f22xd4},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Le Hir, Rozenn and Sorin, Clément and Chakraborti, Dipankar and Moritz, Thomas and Schaller, Hubert and Tellier, Frédérique and Robert, Stéphanie and Morin, Halima and Bakó, Laszlo and Bellini, Catherine},
	month = dec,
	year = {2013},
	pages = {811--824},
}

@article{ranade_pinus_2013,
	title = {Pinus taeda {cDNA} {Microarray} as a {Tool} for {Candidate} {Gene} {Identification} for {Local} {Red}/{Far}-{Red} {Light} {Adaptive} {Response} in {Pinus} sylvestris},
	volume = {4},
	copyright = {http://creativecommons.org/licenses/by/4.0/},
	url = {http://www.scirp.org/Journal/Paperabs.aspx?paperid=28683},
	doi = {10/gjcmm4},
	abstract = {Light quality response is a vital environmental cue regulating plant development. Conifers, like angiosperms, respond to the changes in light quality including the level of red (R) and far-red (FR) light, which follows a latitudinal cline. R and FR wavelengths form a significant component of the entire plant life cycle, including the initial developmental stages such as seed germination, cotyledon expansion and hypocotyl elongation. With an aim to identify differentially expressed candidate genes, which would provide a clue regarding genes involved in the local adaptive response in Scots pine (Pinus sylvestris) with reference to red/far-red light; we performed a global expression analysis of Scots pine hypocotyls grown under two light treatments, continuous R (cR) and continuous FR (cFR) light; using Pinus taeda cDNA microarrays on bulked hypocotyl tissues from different individuals, which represented different genotypes. This experiment was performed with the seeds collected from northern part of Sweden (Ylinen, 68?N). Interestingly, gene expression pattern with reference to cryptochrome1, a blue light photoreceptor, was relatively high under cFR as compared to cR light treatment. Additionally, the microarray data analysis also revealed expression of 405 genes which was enhanced under cR light treatment; while the expression of 239 genes was enhanced under the cFR light treatment. Differentially expressed genes were re-annotated using Blast2GO tool. These results indicated that cR light acts as promoting factor whereas cFR antagonises the effect in most of the processes like C/N metabolism, photosynthesis and cell wall metabolism which is in accordance with former findings in Arabidopsis. We propose cryptochrome1 as a strong candidate gene to study the adaptive cline response under R and FR light in Scots pine as it shows a differential expression under the two light conditions.},
	language = {en},
	number = {3},
	urldate = {2021-06-21},
	journal = {American Journal of Plant Sciences},
	author = {Ranade, Sonali S. and Abrahamsson, Sara and Niemi, Juha and García-Gil, María Rosario},
	month = mar,
	year = {2013},
	note = {Number: 3
Publisher: Scientific Research Publishing},
	pages = {479--493},
}

Light quality response is a vital environmental cue regulating plant development. Conifers, like angiosperms, respond to the changes in light quality including the level of red (R) and far-red (FR) light, which follows a latitudinal cline. R and FR wavelengths form a significant component of the entire plant life cycle, including the initial developmental stages such as seed germination, cotyledon expansion and hypocotyl elongation. With an aim to identify differentially expressed candidate genes, which would provide a clue regarding genes involved in the local adaptive response in Scots pine (Pinus sylvestris) with reference to red/far-red light; we performed a global expression analysis of Scots pine hypocotyls grown under two light treatments, continuous R (cR) and continuous FR (cFR) light; using Pinus taeda cDNA microarrays on bulked hypocotyl tissues from different individuals, which represented different genotypes. This experiment was performed with the seeds collected from northern part of Sweden (Ylinen, 68?N). Interestingly, gene expression pattern with reference to cryptochrome1, a blue light photoreceptor, was relatively high under cFR as compared to cR light treatment. Additionally, the microarray data analysis also revealed expression of 405 genes which was enhanced under cR light treatment; while the expression of 239 genes was enhanced under the cFR light treatment. Differentially expressed genes were re-annotated using Blast2GO tool. These results indicated that cR light acts as promoting factor whereas cFR antagonises the effect in most of the processes like C/N metabolism, photosynthesis and cell wall metabolism which is in accordance with former findings in Arabidopsis. We propose cryptochrome1 as a strong candidate gene to study the adaptive cline response under R and FR light in Scots pine as it shows a differential expression under the two light conditions.

@article{bollhoner_post_2013,
	title = {Post mortem function of {AtMC9} in xylem vessel elements},
	volume = {200},
	copyright = {© 2013 The Authors. New Phytologist © 2013 New Phytologist Trust},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.12387},
	doi = {10/f228vk},
	abstract = {Cell death of xylem elements is manifested by rupture of the tonoplast and subsequent autolysis of the cellular contents. Metacaspases have been implicated in various forms of plant cell death but regulation and execution of xylem cell death by metacaspases remains unknown. Analysis of the type II metacaspase gene family in Arabidopsis thaliana supported the function of METACASPASE 9 (AtMC9) in xylem cell death. Progression of xylem cell death was analysed in protoxylem vessel elements of 3-d-old atmc9 mutant roots using reporter gene analysis and electron microscopy. Protoxylem cell death was normally initiated in atmc9 mutant lines, but detailed electron microscopic analyses revealed a role for AtMC9 in clearance of the cell contents post mortem, that is after tonoplast rupture. Subcellular localization of fluorescent AtMC9 reporter fusions supported a post mortem role for AtMC9. Further, probe-based activity profiling suggested a function of AtMC9 on activities of papain-like cysteine proteases. Our data demonstrate that the function of AtMC9 in xylem cell death is to degrade vessel cell contents after vacuolar rupture. We further provide evidence on a proteolytic cascade in post mortem autolysis of xylem vessel elements and suggest that AtMC9 is part of this cascade.},
	language = {en},
	number = {2},
	urldate = {2021-06-21},
	journal = {New Phytologist},
	author = {Bollhöner, Benjamin and Zhang, Bo and Stael, Simon and Denancé, Nicolas and Overmyer, Kirk and Goffner, Deborah and Breusegem, Frank Van and Tuominen, Hannele},
	year = {2013},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.12387},
	keywords = {Arabidopsis thaliana, autolysis, metacaspase, protease, vessel element, xylem cell death},
	pages = {498--510},
}

Cell death of xylem elements is manifested by rupture of the tonoplast and subsequent autolysis of the cellular contents. Metacaspases have been implicated in various forms of plant cell death but regulation and execution of xylem cell death by metacaspases remains unknown. Analysis of the type II metacaspase gene family in Arabidopsis thaliana supported the function of METACASPASE 9 (AtMC9) in xylem cell death. Progression of xylem cell death was analysed in protoxylem vessel elements of 3-d-old atmc9 mutant roots using reporter gene analysis and electron microscopy. Protoxylem cell death was normally initiated in atmc9 mutant lines, but detailed electron microscopic analyses revealed a role for AtMC9 in clearance of the cell contents post mortem, that is after tonoplast rupture. Subcellular localization of fluorescent AtMC9 reporter fusions supported a post mortem role for AtMC9. Further, probe-based activity profiling suggested a function of AtMC9 on activities of papain-like cysteine proteases. Our data demonstrate that the function of AtMC9 in xylem cell death is to degrade vessel cell contents after vacuolar rupture. We further provide evidence on a proteolytic cascade in post mortem autolysis of xylem vessel elements and suggest that AtMC9 is part of this cascade.

@article{gendre_trans-golgi_2013,
	title = {Trans-{Golgi} {Network} {Localized} {ECHIDNA}/{Ypt} {Interacting} {Protein} {Complex} {Is} {Required} for the {Secretion} of {Cell} {Wall} {Polysaccharides} in {Arabidopsis}},
	volume = {25},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.113.112482},
	doi = {10/f22fqp},
	abstract = {The secretion of cell wall polysaccharides through the trans-Golgi network (TGN) is required for plant cell elongation. However, the components mediating the post-Golgi secretion of pectin and hemicellulose, the two major cell wall polysaccharides, are largely unknown. We identified evolutionarily conserved YPT/RAB GTPase Interacting Protein 4a (YIP4a) and YIP4b (formerly YIP2), which form a TGN-localized complex with ECHIDNA (ECH) in Arabidopsis thaliana. The localization of YIP4 and ECH proteins at the TGN is interdependent and influences the localization of VHA-a1 and SYP61, which are key components of the TGN. YIP4a and YIP4b act redundantly, and the yip4a yip4b double mutants have a cell elongation defect. Genetic, biochemical, and cell biological analyses demonstrate that the ECH/YIP4 complex plays a key role in TGN-mediated secretion of pectin and hemicellulose to the cell wall in dark-grown hypocotyls and in secretory cells of the seed coat. In keeping with these observations, Fourier transform infrared microspectroscopy analysis revealed that the ech and yip4a yip4b mutants exhibit changes in their cell wall composition. Overall, our results reveal a TGN subdomain defined by ECH/YIP4 that is required for the secretion of pectin and hemicellulose and distinguishes the role of the TGN in secretion from its roles in endocytic and vacuolar trafficking.},
	number = {7},
	urldate = {2021-06-21},
	journal = {The Plant Cell},
	author = {Gendre, Delphine and McFarlane, Heather E. and Johnson, Errin and Mouille, Gregory and Sjödin, Andreas and Oh, Jaesung and Levesque-Tremblay, Gabriel and Watanabe, Yoichiro and Samuels, Lacey and Bhalerao, Rishikesh P.},
	month = jul,
	year = {2013},
	pages = {2633--2646},
}

The secretion of cell wall polysaccharides through the trans-Golgi network (TGN) is required for plant cell elongation. However, the components mediating the post-Golgi secretion of pectin and hemicellulose, the two major cell wall polysaccharides, are largely unknown. We identified evolutionarily conserved YPT/RAB GTPase Interacting Protein 4a (YIP4a) and YIP4b (formerly YIP2), which form a TGN-localized complex with ECHIDNA (ECH) in Arabidopsis thaliana. The localization of YIP4 and ECH proteins at the TGN is interdependent and influences the localization of VHA-a1 and SYP61, which are key components of the TGN. YIP4a and YIP4b act redundantly, and the yip4a yip4b double mutants have a cell elongation defect. Genetic, biochemical, and cell biological analyses demonstrate that the ECH/YIP4 complex plays a key role in TGN-mediated secretion of pectin and hemicellulose to the cell wall in dark-grown hypocotyls and in secretory cells of the seed coat. In keeping with these observations, Fourier transform infrared microspectroscopy analysis revealed that the ech and yip4a yip4b mutants exhibit changes in their cell wall composition. Overall, our results reveal a TGN subdomain defined by ECH/YIP4 that is required for the secretion of pectin and hemicellulose and distinguishes the role of the TGN in secretion from its roles in endocytic and vacuolar trafficking.

@article{pollier_protein_2013,
	title = {The protein quality control system manages plant defence compound synthesis},
	volume = {504},
	issn = {1476-4687},
	doi = {10/f5jcsn},
	abstract = {Jasmonates are ubiquitous oxylipin-derived phytohormones that are essential in the regulation of many development, growth and defence processes. Across the plant kingdom, jasmonates act as elicitors of the production of bioactive secondary metabolites that serve in defence against attackers. Knowledge of the conserved jasmonate perception and early signalling machineries is increasing, but the downstream mechanisms that regulate defence metabolism remain largely unknown. Here we show that, in the legume Medicago truncatula, jasmonate recruits the endoplasmic-reticulum-associated degradation (ERAD) quality control system to manage the production of triterpene saponins, widespread bioactive compounds that share a biogenic origin with sterols. An ERAD-type RING membrane-anchor E3 ubiquitin ligase is co-expressed with saponin synthesis enzymes to control the activity of 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), the rate-limiting enzyme in the supply of the ubiquitous terpene precursor isopentenyl diphosphate. Thus, unrestrained bioactive saponin accumulation is prevented and plant development and integrity secured. This control apparatus is equivalent to the ERAD system that regulates sterol synthesis in yeasts and mammals but that uses distinct E3 ubiquitin ligases, of the HMGR degradation 1 (HRD1) type, to direct destruction of HMGR. Hence, the general principles for the management of sterol and triterpene saponin biosynthesis are conserved across eukaryotes but can be controlled by divergent regulatory cues.},
	language = {eng},
	number = {7478},
	journal = {Nature},
	author = {Pollier, Jacob and Moses, Tessa and González-Guzmán, Miguel and De Geyter, Nathan and Lippens, Saskia and Vanden Bossche, Robin and Marhavý, Peter and Kremer, Anna and Morreel, Kris and Guérin, Christopher J. and Tava, Aldo and Oleszek, Wieslaw and Thevelein, Johan M. and Campos, Narciso and Goormachtig, Sofie and Goossens, Alain},
	month = dec,
	year = {2013},
	pmid = {24213631},
	keywords = {Cells, Cultured, Endoplasmic Reticulum-Associated Degradation, Gene Expression Profiling, Gene Expression Regulation, Plant, Gene Silencing, Genetic Complementation Test, Medicago truncatula, Microscopy, Electron, Scanning, Molecular Sequence Data, Mutation, Plant Growth Regulators, Plant Roots, Saccharomyces cerevisiae, Saponins, Signal Transduction, Ubiquitin-Protein Ligases},
	pages = {148--152},
}

Jasmonates are ubiquitous oxylipin-derived phytohormones that are essential in the regulation of many development, growth and defence processes. Across the plant kingdom, jasmonates act as elicitors of the production of bioactive secondary metabolites that serve in defence against attackers. Knowledge of the conserved jasmonate perception and early signalling machineries is increasing, but the downstream mechanisms that regulate defence metabolism remain largely unknown. Here we show that, in the legume Medicago truncatula, jasmonate recruits the endoplasmic-reticulum-associated degradation (ERAD) quality control system to manage the production of triterpene saponins, widespread bioactive compounds that share a biogenic origin with sterols. An ERAD-type RING membrane-anchor E3 ubiquitin ligase is co-expressed with saponin synthesis enzymes to control the activity of 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), the rate-limiting enzyme in the supply of the ubiquitous terpene precursor isopentenyl diphosphate. Thus, unrestrained bioactive saponin accumulation is prevented and plant development and integrity secured. This control apparatus is equivalent to the ERAD system that regulates sterol synthesis in yeasts and mammals but that uses distinct E3 ubiquitin ligases, of the HMGR degradation 1 (HRD1) type, to direct destruction of HMGR. Hence, the general principles for the management of sterol and triterpene saponin biosynthesis are conserved across eukaryotes but can be controlled by divergent regulatory cues.

@article{srivastava_onpls_2013,
	title = {{OnPLS} integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic {hipI}- superoxide dismutase {Populus} plants},
	volume = {14},
	issn = {1471-2164},
	url = {https://doi.org/10.1186/1471-2164-14-893},
	doi = {10/f2zk6q},
	abstract = {Reactive oxygen species (ROS) are involved in the regulation of diverse physiological processes in plants, including various biotic and abiotic stress responses. Thus, oxidative stress tolerance mechanisms in plants are complex, and diverse responses at multiple levels need to be characterized in order to understand them. Here we present system responses to oxidative stress in Populus by integrating data from analyses of the cambial region of wild-type controls and plants expressing high-isoelectric-point superoxide dismutase (hipI-SOD) transcripts in antisense orientation showing a higher production of superoxide. The cambium, a thin cell layer, generates cells that differentiate to form either phloem or xylem and is hypothesized to be a major reason for phenotypic perturbations in the transgenic plants. Data from multiple platforms including transcriptomics (microarray analysis), proteomics (UPLC/QTOF-MS), and metabolomics (GC-TOF/MS, UPLC/MS, and UHPLC-LTQ/MS) were integrated using the most recent development of orthogonal projections to latent structures called OnPLS. OnPLS is a symmetrical multi-block method that does not depend on the order of analysis when more than two blocks are analysed. Significantly affected genes, proteins and metabolites were then visualized in painted pathway diagrams.},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Srivastava, Vaibhav and Obudulu, Ogonna and Bygdell, Joakim and Löfstedt, Tommy and Rydén, Patrik and Nilsson, Robert and Ahnlund, Maria and Johansson, Annika and Jonsson, Pär and Freyhult, Eva and Qvarnström, Johanna and Karlsson, Jan and Melzer, Michael and Moritz, Thomas and Trygg, Johan and Hvidsten, Torgeir R. and Wingsle, Gunnar},
	month = dec,
	year = {2013},
	keywords = {OnPLS, Oxidative stress, Poplar, Statistical integration, Systems biology},
	pages = {893},
}

Reactive oxygen species (ROS) are involved in the regulation of diverse physiological processes in plants, including various biotic and abiotic stress responses. Thus, oxidative stress tolerance mechanisms in plants are complex, and diverse responses at multiple levels need to be characterized in order to understand them. Here we present system responses to oxidative stress in Populus by integrating data from analyses of the cambial region of wild-type controls and plants expressing high-isoelectric-point superoxide dismutase (hipI-SOD) transcripts in antisense orientation showing a higher production of superoxide. The cambium, a thin cell layer, generates cells that differentiate to form either phloem or xylem and is hypothesized to be a major reason for phenotypic perturbations in the transgenic plants. Data from multiple platforms including transcriptomics (microarray analysis), proteomics (UPLC/QTOF-MS), and metabolomics (GC-TOF/MS, UPLC/MS, and UHPLC-LTQ/MS) were integrated using the most recent development of orthogonal projections to latent structures called OnPLS. OnPLS is a symmetrical multi-block method that does not depend on the order of analysis when more than two blocks are analysed. Significantly affected genes, proteins and metabolites were then visualized in painted pathway diagrams.

@article{yu_root_2013,
	title = {{ROOT} {ULTRAVIOLET} {B}-{SENSITIVE1}/{WEAK} {AUXIN} {RESPONSE3} {Is} {Essential} for {Polar} {Auxin} {Transport} in {Arabidopsis}},
	volume = {162},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/162/2/965/6110776},
	doi = {10/f3rt2n},
	abstract = {Abstract
            The phytohormone auxin regulates virtually every aspect of plant development. To identify new genes involved in auxin activity, a genetic screen was performed for Arabidopsis (Arabidopsis thaliana) mutants with altered expression of the auxin-responsive reporter DR5rev:GFP. One of the mutants recovered in the screen, designated as weak auxin response3 (wxr3), exhibits much lower DR5rev:GFP expression when treated with the synthetic auxin 2,4-dichlorophenoxyacetic acid and displays severe defects in root development. The wxr3 mutant decreases polar auxin transport and results in a disruption of the asymmetric auxin distribution. The levels of the auxin transporters AUXIN1 and PIN-FORMED are dramatically reduced in the wxr3 root tip. Molecular analyses demonstrate that WXR3 is ROOT ULTRAVIOLET B-SENSITIVE1 (RUS1), a member of the conserved Domain of Unknown Function647 protein family found in diverse eukaryotic organisms. Our data suggest that RUS1/WXR3 plays an essential role in the regulation of polar auxin transport by maintaining the proper level of auxin transporters on the plasma membrane.},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Yu, Hong and Karampelias, Michael and Robert, Stephanie and Peer, Wendy Ann and Swarup, Ranjan and Ye, Songqing and Ge, Lei and Cohen, Jerry and Murphy, Angus and Friml, Jirí and Estelle, Mark},
	month = may,
	year = {2013},
	pages = {965--976},
}

Abstract The phytohormone auxin regulates virtually every aspect of plant development. To identify new genes involved in auxin activity, a genetic screen was performed for Arabidopsis (Arabidopsis thaliana) mutants with altered expression of the auxin-responsive reporter DR5rev:GFP. One of the mutants recovered in the screen, designated as weak auxin response3 (wxr3), exhibits much lower DR5rev:GFP expression when treated with the synthetic auxin 2,4-dichlorophenoxyacetic acid and displays severe defects in root development. The wxr3 mutant decreases polar auxin transport and results in a disruption of the asymmetric auxin distribution. The levels of the auxin transporters AUXIN1 and PIN-FORMED are dramatically reduced in the wxr3 root tip. Molecular analyses demonstrate that WXR3 is ROOT ULTRAVIOLET B-SENSITIVE1 (RUS1), a member of the conserved Domain of Unknown Function647 protein family found in diverse eukaryotic organisms. Our data suggest that RUS1/WXR3 plays an essential role in the regulation of polar auxin transport by maintaining the proper level of auxin transporters on the plasma membrane.

@article{rigas_root_2013,
	title = {Root gravitropism and root hair development constitute coupled developmental responses regulated by auxin homeostasis in the \textit{{Arabidopsis}} root apex},
	volume = {197},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.12092},
	doi = {10/f22m5k},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Rigas, Stamatis and Ditengou, Franck Anicet and Ljung, Karin and Daras, Gerasimos and Tietz, Olaf and Palme, Klaus and Hatzopoulos, Polydefkis},
	month = mar,
	year = {2013},
	pages = {1130--1141},
}

@article{fernie_perspectives_2013,
	title = {Perspectives on plant photorespiratory metabolism},
	volume = {15},
	issn = {14358603},
	url = {http://doi.wiley.com/10.1111/j.1438-8677.2012.00693.x},
	doi = {10/f2364c},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Biology},
	author = {Fernie, A. R. and Bauwe, H. and Eisenhut, M. and Florian, A. and Hanson, D. T. and Hagemann, M. and Keech, O. and Mielewczik, M. and Nikoloski, Z. and Peterhänsel, C. and Roje, S. and Sage, R. and Timm, S. and von Cammerer, S. and Weber, A. P. M. and Westhoff, P.},
	editor = {Rennenberg, H.},
	month = jul,
	year = {2013},
	pages = {748--753},
}

@article{sairanen_soluble_2013,
	title = {Soluble {Carbohydrates} {Regulate} {Auxin} {Biosynthesis} via {PIF} {Proteins} in \textit{{Arabidopsis}}},
	volume = {24},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/24/12/4907/6098068},
	doi = {10/f2z2pm},
	abstract = {Abstract
            Plants are necessarily highly competitive and have finely tuned mechanisms to adjust growth and development in accordance with opportunities and limitations in their environment. Sugars from photosynthesis form an integral part of this growth control process, acting as both an energy source and as signaling molecules in areas targeted for growth. The plant hormone auxin similarly functions as a signaling molecule and a driver of growth and developmental processes. Here, we show that not only do the two act in concert but that auxin metabolism is itself regulated by the availability of free sugars. The regulation of the biosynthesis and degradation of the main auxin, indole-3-acetic acid (IAA), by sugars requires changes in the expression of multiple genes and metabolites linked to several IAA biosynthetic pathways. The induction also involves members of the recently described central regulator PHYTOCHROME-INTERACTING FACTOR transcription factor family. Linking these three known regulators of growth provides a model for the dynamic coordination of responses to a changing environment.},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Sairanen, Ilkka and Novák, Ondřej and Pěnčík, Aleš and Ikeda, Yoshihisa and Jones, Brian and Sandberg, Göran and Ljung, Karin},
	month = jan,
	year = {2013},
	pages = {4907--4916},
}

Abstract Plants are necessarily highly competitive and have finely tuned mechanisms to adjust growth and development in accordance with opportunities and limitations in their environment. Sugars from photosynthesis form an integral part of this growth control process, acting as both an energy source and as signaling molecules in areas targeted for growth. The plant hormone auxin similarly functions as a signaling molecule and a driver of growth and developmental processes. Here, we show that not only do the two act in concert but that auxin metabolism is itself regulated by the availability of free sugars. The regulation of the biosynthesis and degradation of the main auxin, indole-3-acetic acid (IAA), by sugars requires changes in the expression of multiple genes and metabolites linked to several IAA biosynthetic pathways. The induction also involves members of the recently described central regulator PHYTOCHROME-INTERACTING FACTOR transcription factor family. Linking these three known regulators of growth provides a model for the dynamic coordination of responses to a changing environment.

@article{peterhansel_engineering_2013,
	title = {Engineering photorespiration: current state and future possibilities},
	volume = {15},
	issn = {14358603},
	shorttitle = {Engineering photorespiration},
	url = {http://doi.wiley.com/10.1111/j.1438-8677.2012.00681.x},
	doi = {10/f22k83},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Biology},
	author = {Peterhansel, C. and Krause, K. and Braun, H.-P. and Espie, G. S. and Fernie, A. R. and Hanson, D. T. and Keech, O. and Maurino, V. G. and Mielewczik, M. and Sage, R. F.},
	month = jul,
	year = {2013},
	pages = {754--758},
}

@article{tiwari_physiological_2013,
	title = {Physiological and morphological changes during early and later stages of fruit growth in \textit{{Capsicum} annuum}},
	volume = {147},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2012.01673.x},
	doi = {10/f23jvb},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {Tiwari, Aparna and Vivian-Smith, Adam and Ljung, Karin and Offringa, Remko and Heuvelink, Ep},
	month = mar,
	year = {2013},
	pages = {396--406},
}

@article{miranda_co-expression_2013,
	title = {Co-expression analysis, proteomic and metabolomic study on the impact of a {Deg}/{HtrA} protease triple mutant in {Synechocystis} sp. {PCC} 6803 exposed to temperature and high light stress},
	volume = {78},
	issn = {18743919},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1874391912006926},
	doi = {10/f2z4z6},
	language = {en},
	urldate = {2021-06-08},
	journal = {Journal of Proteomics},
	author = {Miranda, Hélder and Cheregi, Otilia and Netotea, Sergiu and Hvidsten, Torgeir R. and Moritz, Thomas and Funk, Christiane},
	month = jan,
	year = {2013},
	pages = {294--311},
}

@article{ohman_myb103_2013,
	title = {{MYB103} is required for \textit{{FERULATE}-5-{HYDROXYLASE}} expression and syringyl lignin biosynthesis in {Arabidopsis} stems},
	volume = {73},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.12018},
	doi = {10/f24jdb},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Öhman, David and Demedts, Brecht and Kumar, Manoj and Gerber, Lorenz and Gorzsás, András and Goeminne, Geert and Hedenström, Mattias and Ellis, Brian and Boerjan, Wout and Sundberg, Björn},
	month = jan,
	year = {2013},
	pages = {63--76},
}

@article{isabel_second-generation_2013,
	title = {A second-generation diagnostic single nucleotide polymorphism ({SNP})-based assay, optimized to distinguish among eight poplar ({Populus} {L}.) species and their early hybrids},
	volume = {9},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-012-0569-5},
	doi = {10/f22fcx},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Isabel, Nathalie and Lamothe, Manuel and Thompson, Stacey Lee},
	month = apr,
	year = {2013},
	pages = {621--626},
}

@article{barajas-lopez_plastid--nucleus_2013,
	series = {Protein {Import} and {Quality} {Control} in {Mitochondria} and {Plastids}},
	title = {Plastid-to-nucleus communication, signals controlling the running of the plant cell},
	volume = {1833},
	issn = {0167-4889},
	url = {https://www.sciencedirect.com/science/article/pii/S0167488912001772},
	doi = {10/f24h6j},
	abstract = {The presence of genes encoding organellar proteins in both the nucleus and the organelle necessitates tight coordination of expression by the different genomes, and this has led to the evolution of sophisticated intracellular signaling networks. Organelle-to-nucleus signaling, or retrograde control, coordinates the expression of nuclear genes encoding organellar proteins with the metabolic and developmental state of the organelle. Complex networks of retrograde signals orchestrate major changes in nuclear gene expression and coordinate cellular activities and assist the cell during plant development and stress responses. It has become clear that, even though the chloroplast depends on the nucleus for its function, plastid signals play important roles in an array of different cellular processes vital to the plant. Hence, the chloroplast exerts significant control over the running of the cell. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Biochimica et Biophysica Acta (BBA) - Molecular Cell Research},
	author = {Barajas-López, Juan de Dios and Blanco, Nicolás E. and Strand, Åsa},
	month = feb,
	year = {2013},
	keywords = {Photosynthesis, Plastids, Redox, Retrograde, Signaling, Stress},
	pages = {425--437},
}

The presence of genes encoding organellar proteins in both the nucleus and the organelle necessitates tight coordination of expression by the different genomes, and this has led to the evolution of sophisticated intracellular signaling networks. Organelle-to-nucleus signaling, or retrograde control, coordinates the expression of nuclear genes encoding organellar proteins with the metabolic and developmental state of the organelle. Complex networks of retrograde signals orchestrate major changes in nuclear gene expression and coordinate cellular activities and assist the cell during plant development and stress responses. It has become clear that, even though the chloroplast depends on the nucleus for its function, plastid signals play important roles in an array of different cellular processes vital to the plant. Hence, the chloroplast exerts significant control over the running of the cell. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.

@article{kuhlmann_exploring_2013,
	title = {Exploring the {Nitrogen} {Ingestion} of {Aphids} — {A} {New} {Method} {Using} {Electrical} {Penetration} {Graph} and {15N} {Labelling}},
	volume = {8},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0083085},
	doi = {10/f2z8kn},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Kuhlmann, Franziska and Opitz, Sebastian E. W. and Inselsbacher, Erich and Ganeteg, Ulrika and Näsholm, Torgny and Ninkovic, Velemir},
	editor = {Wilkinson, Thomas L.},
	month = dec,
	year = {2013},
	pages = {e83085},
}

@article{li_transcriptome_2013,
	title = {Transcriptome profiling of radiata pine branches reveals new insights into reaction wood formation with implications in plant gravitropism},
	volume = {14},
	issn = {1471-2164},
	url = {http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-768},
	doi = {10/f23ncd},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Genomics},
	author = {Li, Xinguo and Yang, Xiaohui and Wu, Harry X},
	year = {2013},
	pages = {768},
}

@article{immanen_characterization_2013,
	title = {Characterization of cytokinin signaling and homeostasis gene families in two hardwood tree species: {Populus} trichocarpa and {Prunus} persica},
	volume = {14},
	issn = {1471-2164},
	shorttitle = {Characterization of cytokinin signaling and homeostasis gene families in two hardwood tree species},
	url = {http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-885},
	doi = {10/f237jw},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Genomics},
	author = {Immanen, Juha and Nieminen, Kaisa and Duchens Silva, Héctor and Rodríguez Rojas, Fernanda and Meisel, Lee A and Silva, Herman and Albert, Victor A and Hvidsten, Torgeir R and Helariutta, Ykä},
	year = {2013},
	pages = {885},
}

@article{ranocha_arabidopsis_2013,
	title = {Arabidopsis {WAT1} is a vacuolar auxin transport facilitator required for auxin homoeostasis},
	volume = {4},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/ncomms3625},
	doi = {10/f23w2p},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Nature Communications},
	author = {Ranocha, Philippe and Dima, Oana and Nagy, Réka and Felten, Judith and Corratgé-Faillie, Claire and Novák, Ondřej and Morreel, Kris and Lacombe, Benoît and Martinez, Yves and Pfrunder, Stephanie and Jin, Xu and Renou, Jean-Pierre and Thibaud, Jean-Baptiste and Ljung, Karin and Fischer, Urs and Martinoia, Enrico and Boerjan, Wout and Goffner, Deborah},
	month = dec,
	year = {2013},
	pages = {2625},
}

@article{norman_novo_2013,
	title = {De {Novo} {SNP} {Discovery} in the {Scandinavian} {Brown} {Bear} ({Ursus} arctos)},
	volume = {8},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0081012},
	doi = {10/f23hc8},
	language = {en},
	number = {11},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Norman, Anita J. and Street, Nathaniel R. and Spong, Göran},
	editor = {Caramelli, David},
	month = nov,
	year = {2013},
	pages = {e81012},
}

@article{gundale_impact_2013,
	title = {The impact of simulated chronic nitrogen deposition on the biomass and {N} $_{\textrm{2}}$ -fixation activity of two boreal feather moss–cyanobacteria associations},
	volume = {9},
	issn = {1744-9561, 1744-957X},
	url = {https://royalsocietypublishing.org/doi/10.1098/rsbl.2013.0797},
	doi = {10/f23kcz},
	abstract = {Bryophytes achieve substantial biomass and play several key functional roles in boreal forests that can influence how carbon (C) and nitrogen (N) cycling respond to atmospheric deposition of reactive nitrogen (N
              r
              ). They associate with cyanobacteria that fix atmospheric N
              2
              , and downregulation of this process may offset anthropogenic N
              r
              inputs to boreal systems. Bryophytes also promote soil C accumulation by thermally insulating soils, and changes in their biomass influence soil C dynamics. Using a unique large-scale (0.1 ha forested plots), long-term experiment (16 years) in northern Sweden where we simulated anthropogenic N
              r
              deposition, we measured the biomass and N
              2
              -fixation response of two bryophyte species, the feather mosses
              Hylocomium splendens
              and
              Pleurozium schreberi
              . Our data show that the biomass declined for both species; however, N
              2
              -fixation rates per unit mass and per unit area declined only for
              H. splendens
              . The low and high treatments resulted in a 29\% and 54\% reduction in total feather moss biomass, and a 58\% and 97\% reduction in total N
              2
              -fixation rate per unit area, respectively. These results help to quantify the sensitivity of feather moss biomass and N
              2
              fixation to chronic N
              r
              deposition, which is relevant for modelling ecosystem C and N balances in boreal ecosystems.},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Biology Letters},
	author = {Gundale, Michael J. and Bach, Lisbet H. and Nordin, Annika},
	month = dec,
	year = {2013},
	pages = {20130797},
}

Bryophytes achieve substantial biomass and play several key functional roles in boreal forests that can influence how carbon (C) and nitrogen (N) cycling respond to atmospheric deposition of reactive nitrogen (N r ). They associate with cyanobacteria that fix atmospheric N 2 , and downregulation of this process may offset anthropogenic N r inputs to boreal systems. Bryophytes also promote soil C accumulation by thermally insulating soils, and changes in their biomass influence soil C dynamics. Using a unique large-scale (0.1 ha forested plots), long-term experiment (16 years) in northern Sweden where we simulated anthropogenic N r deposition, we measured the biomass and N 2 -fixation response of two bryophyte species, the feather mosses Hylocomium splendens and Pleurozium schreberi . Our data show that the biomass declined for both species; however, N 2 -fixation rates per unit mass and per unit area declined only for H. splendens . The low and high treatments resulted in a 29% and 54% reduction in total feather moss biomass, and a 58% and 97% reduction in total N 2 -fixation rate per unit area, respectively. These results help to quantify the sensitivity of feather moss biomass and N 2 fixation to chronic N r deposition, which is relevant for modelling ecosystem C and N balances in boreal ecosystems.

@article{manabe_reduced_2013,
	title = {Reduced {Wall} {Acetylation} {Proteins} {Play} {Vital} and {Distinct} {Roles} in {Cell} {Wall} \textit{{O}} -{Acetylation} in {Arabidopsis}},
	volume = {163},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/163/3/1107/6112718},
	doi = {10/f2zn5j},
	abstract = {Abstract
            The Reduced Wall Acetylation (RWA) proteins are involved in cell wall acetylation in plants. Previously, we described a single mutant, rwa2, which has about 20\% lower level of O-acetylation in leaf cell walls and no obvious growth or developmental phenotype. In this study, we generated double, triple, and quadruple loss-of-function mutants of all four members of the RWA family in Arabidopsis (Arabidopsis thaliana). In contrast to rwa2, the triple and quadruple rwa mutants display severe growth phenotypes revealing the importance of wall acetylation for plant growth and development. The quadruple rwa mutant can be completely complemented with the RWA2 protein expressed under 35S promoter, indicating the functional redundancy of the RWA proteins. Nevertheless, the degree of acetylation of xylan, (gluco)mannan, and xyloglucan as well as overall cell wall acetylation is affected differently in different combinations of triple mutants, suggesting their diversity in substrate preference. The overall degree of wall acetylation in the rwa quadruple mutant was reduced by 63\% compared with the wild type, and histochemical analysis of the rwa quadruple mutant stem indicates defects in cell differentiation of cell types with secondary cell walls.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Manabe, Yuzuki and Verhertbruggen, Yves and Gille, Sascha and Harholt, Jesper and Chong, Sun-Li and Pawar, Prashant Mohan-Anupama and Mellerowicz, Ewa J. and Tenkanen, Maija and Cheng, Kun and Pauly, Markus and Scheller, Henrik Vibe},
	month = oct,
	year = {2013},
	pages = {1107--1117},
}

Abstract The Reduced Wall Acetylation (RWA) proteins are involved in cell wall acetylation in plants. Previously, we described a single mutant, rwa2, which has about 20% lower level of O-acetylation in leaf cell walls and no obvious growth or developmental phenotype. In this study, we generated double, triple, and quadruple loss-of-function mutants of all four members of the RWA family in Arabidopsis (Arabidopsis thaliana). In contrast to rwa2, the triple and quadruple rwa mutants display severe growth phenotypes revealing the importance of wall acetylation for plant growth and development. The quadruple rwa mutant can be completely complemented with the RWA2 protein expressed under 35S promoter, indicating the functional redundancy of the RWA proteins. Nevertheless, the degree of acetylation of xylan, (gluco)mannan, and xyloglucan as well as overall cell wall acetylation is affected differently in different combinations of triple mutants, suggesting their diversity in substrate preference. The overall degree of wall acetylation in the rwa quadruple mutant was reduced by 63% compared with the wild type, and histochemical analysis of the rwa quadruple mutant stem indicates defects in cell differentiation of cell types with secondary cell walls.

@article{richau_structural_2013,
	title = {Structural and gene expression analyses of uptake hydrogenases and other proteins involved in nitrogenase protection in {Frankia}},
	volume = {38},
	issn = {0250-5991, 0973-7138},
	url = {http://link.springer.com/10.1007/s12038-013-9372-1},
	doi = {10/f2z2tc},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Journal of Biosciences},
	author = {Richau, Kh and Kudahettige, Rl and Pujic, P and Kudahettige, Np and Sellstedt, A},
	month = nov,
	year = {2013},
	pages = {703--712},
}

@article{pietra_arabidopsis_2013,
	title = {Arabidopsis {SABRE} and {CLASP} interact to stabilize cell division plane orientation and planar polarity},
	volume = {4},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/ncomms3779},
	doi = {10/f24gtc},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Nature Communications},
	author = {Pietra, Stefano and Gustavsson, Anna and Kiefer, Christian and Kalmbach, Lothar and Hörstedt, Per and Ikeda, Yoshihisa and Stepanova, Anna N. and Alonso, Jose M. and Grebe, Markus},
	month = dec,
	year = {2013},
	pages = {2779},
}

@article{vahala_genomewide_2013,
	title = {A genome‐wide screen for ethylene‐induced {Ethylene} {Response} {Factors} ( {\textless}span style="font-variant:small-caps;"{\textgreater}{ERF}{\textless}/span{\textgreater} s) in hybrid aspen stem identifies \textit{ {\textless}span style="font-variant:small-caps;"{\textgreater}{ERF}{\textless}/span{\textgreater} } genes that modify stem growth and wood properties},
	volume = {200},
	issn = {0028-646X, 1469-8137},
	shorttitle = {A genome‐wide screen for ethylene‐induced {Ethylene} {Response} {Factors} ( {\textless}span style="font-variant},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.12386},
	doi = {10/f2zvjg},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Vahala, Jorma and Felten, Judith and Love, Jonathan and Gorzsás, András and Gerber, Lorenz and Lamminmäki, Airi and Kangasjärvi, Jaakko and Sundberg, Björn},
	month = oct,
	year = {2013},
	pages = {511--522},
}

@article{podgorska_long-term_2013,
	title = {Long-term ammonium nutrition of \textit{{Arabidopsis}} increases the extrachloroplastic {NAD}({P}){H}/{NAD}({P}) $^{\textrm{+}}$ ratio and mitochondrial reactive oxygen species level in leaves but does not impair photosynthetic capacity: {NH} $_{\textrm{4}}$ $^{\textrm{+}}$ nutrition and leaf redox homeostasis},
	issn = {01407791},
	shorttitle = {Long-term ammonium nutrition of \textit{{Arabidopsis}} increases the extrachloroplastic {NAD}({P}){H}/{NAD}({P}) $^{\textrm{+}}$ ratio and mitochondrial reactive oxygen species level in leaves but does not impair photosynthetic capacity},
	url = {http://doi.wiley.com/10.1111/pce.12113},
	doi = {10/f23dxm},
	language = {en},
	urldate = {2021-06-08},
	journal = {Plant, Cell \& Environment},
	author = {PODGóRSKA, Anna and Gieczewska, Katarzyna and ŁUKAWSKA-KUźMA, Katarzyna and Rasmusson, Allan G. and GARDESTRöM, Per and Szal, BOżENA},
	month = jun,
	year = {2013},
	pages = {n/a--n/a},
}

@article{pencik_regulation_2013,
	title = {Regulation of {Auxin} {Homeostasis} and {Gradients} in \textit{{Arabidopsis}} {Roots} through the {Formation} of the {Indole}-3-{Acetic} {Acid} {Catabolite} 2-{Oxindole}-3-{Acetic} {Acid}},
	volume = {25},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/25/10/3858-3870/6099549},
	doi = {10/f2zn6c},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Pěnčík, Aleš and Simonovik, Biljana and Petersson, Sara V. and Henyková, Eva and Simon, Sibu and Greenham, Kathleen and Zhang, Yi and Kowalczyk, Mariusz and Estelle, Mark and Zažímalová, Eva and Novák, Ondřej and Sandberg, Göran and Ljung, Karin},
	month = oct,
	year = {2013},
	pages = {3858--3870},
}

@incollection{audenaert_use_2013,
	address = {Hoboken, NJ},
	title = {The {Use} of {Chemical} {Biology} to {Study} {Plant} {Cellular} {Processes}: {Subcellular} {Trafficking}},
	isbn = {978-1-118-74292-1 978-0-470-94669-5},
	shorttitle = {The {Use} of {Chemical} {Biology} to {Study} {Plant} {Cellular} {Processes}},
	url = {http://doi.wiley.com/10.1002/9781118742921.ch5.2},
	language = {en},
	urldate = {2021-06-08},
	booktitle = {Plant {Chemical} {Biology}},
	publisher = {John Wiley \& Sons, Inc},
	author = {Haeger, Ash and Łangowska, Malgorzata and Robert, Stéphanie},
	editor = {Audenaert, Dominique and Overvoorde, Paul},
	month = nov,
	year = {2013},
	doi = {10.1002/9781118742921.ch5.2},
	pages = {218--231},
}

@article{hedwall_does_2013,
	title = {Does background nitrogen deposition affect the response of boreal vegetation to fertilization?},
	volume = {173},
	issn = {0029-8549, 1432-1939},
	url = {http://link.springer.com/10.1007/s00442-013-2638-3},
	doi = {10/f23wzh},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Oecologia},
	author = {Hedwall, P. O. and Nordin, A. and Strengbom, J. and Brunet, J. and Olsson, B.},
	month = oct,
	year = {2013},
	pages = {615--624},
}

@article{peret_sequential_2013,
	title = {Sequential induction of auxin efflux and influx carriers regulates lateral root emergence},
	volume = {9},
	issn = {1744-4292, 1744-4292},
	url = {https://onlinelibrary.wiley.com/doi/10.1038/msb.2013.43},
	doi = {10/f2pc8d},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Molecular Systems Biology},
	author = {Péret, Benjamin and Middleton, Alistair M and French, Andrew P and Larrieu, Antoine and Bishopp, Anthony and Njo, Maria and Wells, Darren M and Porco, Silvana and Mellor, Nathan and Band, Leah R and Casimiro, Ilda and Kleine‐Vehn, Jürgen and Vanneste, Steffen and Sairanen, Ilkka and Mallet, Romain and Sandberg, Göran and Ljung, Karin and Beeckman, Tom and Benkova, Eva and Friml, Jiří and Kramer, Eric and King, John R and De Smet, Ive and Pridmore, Tony and Owen, Markus and Bennett, Malcolm J},
	month = jan,
	year = {2013},
	pages = {699},
}

@article{ruggeberg_enhanced_2013,
	title = {Enhanced cellulose orientation analysis in complex model plant tissues},
	volume = {183},
	issn = {10478477},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1047847713001810},
	doi = {10/f2ztwv},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Journal of Structural Biology},
	author = {Rüggeberg, Markus and Saxe, Friederike and Metzger, Till H. and Sundberg, Björn and Fratzl, Peter and Burgert, Ingo},
	month = sep,
	year = {2013},
	pages = {419--428},
}

@article{pacheco-villalobos_disturbed_2013,
	title = {Disturbed {Local} {Auxin} {Homeostasis} {Enhances} {Cellular} {Anisotropy} and {Reveals} {Alternative} {Wiring} of {Auxin}-ethylene {Crosstalk} in {Brachypodium} distachyon {Seminal} {Roots}},
	volume = {9},
	issn = {1553-7404},
	url = {https://dx.plos.org/10.1371/journal.pgen.1003564},
	doi = {10/f236vj},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {PLoS Genetics},
	author = {Pacheco-Villalobos, David and Sankar, Martial and Ljung, Karin and Hardtke, Christian S.},
	editor = {Yu, Hao},
	month = jun,
	year = {2013},
	pages = {e1003564},
}

@article{huesgen_proteomic_2013,
	title = {Proteomic {Amino}-{Termini} {Profiling} {Reveals} {Targeting} {Information} for {Protein} {Import} into {Complex} {Plastids}},
	volume = {8},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0074483},
	doi = {10/f23w6c},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Huesgen, Pitter F. and Alami, Meriem and Lange, Philipp F. and Foster, Leonard J. and Schröder, Wolfgang P. and Overall, Christopher M. and Green, Beverley R.},
	editor = {Scorrano, Luca},
	month = sep,
	year = {2013},
	pages = {e74483},
}

@article{moubayidin_spatial_2013,
	title = {Spatial {Coordination} between {Stem} {Cell} {Activity} and {Cell} {Differentiation} in the {Root} {Meristem}},
	volume = {26},
	issn = {15345807},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1534580713003882},
	doi = {10/f23ftm},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Developmental Cell},
	author = {Moubayidin, Laila and Di Mambro, Riccardo and Sozzani, Rosangela and Pacifici, Elena and Salvi, Elena and Terpstra, Inez and Bao, Dongping and van Dijken, Anja and Dello Ioio, Raffaele and Perilli, Serena and Ljung, Karin and Benfey, Philip N. and Heidstra, Renze and Costantino, Paolo and Sabatini, Sabrina},
	month = aug,
	year = {2013},
	pages = {405--415},
}

@article{mcfarlane_cell_2013,
	title = {Cell {Wall} {Polysaccharides} are {Mislocalized} to the {Vacuole} in echidna {Mutants}},
	volume = {54},
	issn = {1471-9053, 0032-0781},
	url = {https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/pct129},
	doi = {10/f23zf4},
	language = {en},
	number = {11},
	urldate = {2021-06-08},
	journal = {Plant and Cell Physiology},
	author = {McFarlane, Heather E. and Watanabe, Yoichiro and Gendre, Delphine and Carruthers, Kimberley and Levesque-Tremblay, Gabriel and Haughn, George W. and Bhalerao, Rishikesh P. and Samuels, Lacey},
	month = nov,
	year = {2013},
	pages = {1867--1880},
}

@article{lin_effect_2013,
	title = {Effect of genotype by spacing interaction on radiata pine genetic parameters for height and diameter growth},
	volume = {304},
	issn = {03781127},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378112713003149},
	doi = {10/f23mtw},
	language = {en},
	urldate = {2021-06-08},
	journal = {Forest Ecology and Management},
	author = {Lin, Yuanzhen and Yang, Huixiao and Ivković, Miloš and Gapare, Washington J. and Colin Matheson, A. and Wu, Harry X.},
	month = sep,
	year = {2013},
	pages = {204--211},
}

@article{milhinhos_thermospermine_2013,
	title = {Thermospermine levels are controlled by an auxin-dependent feedback loop mechanism in \textit{{Populus}} xylem},
	volume = {75},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.12231},
	doi = {10/f22nbr},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Milhinhos, Ana and Prestele, Jakob and Bollhöner, Benjamin and Matos, Andreia and Vera-Sirera, Francisco and Rambla, José L. and Ljung, Karin and Carbonell, Juan and Blázquez, Miguel A. and Tuominen, Hannele and Miguel, Célia M.},
	month = aug,
	year = {2013},
	pages = {685--698},
}

@article{haniewicz_isolation_2013,
	title = {Isolation of monomeric photosystem {II} that retains the subunit {PsbS}},
	volume = {118},
	issn = {0166-8595, 1573-5079},
	url = {http://link.springer.com/10.1007/s11120-013-9914-2},
	doi = {10/f226cb},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Photosynthesis Research},
	author = {Haniewicz, Patrycja and De Sanctis, Daniele and Büchel, Claudia and Schröder, Wolfgang P. and Loi, Maria Cecilia and Kieselbach, Thomas and Bochtler, Matthias and Piano, Dario},
	month = dec,
	year = {2013},
	pages = {199--207},
}

@article{klemens_overexpression_2013,
	title = {Overexpression of the {Vacuolar} {Sugar} {Carrier} \textit{{AtSWEET16}} {Modifies} {Germination}, {Growth}, and {Stress} {Tolerance} in {Arabidopsis}},
	volume = {163},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/163/3/1338/6112737},
	doi = {10/f23t2h},
	abstract = {Abstract
            Here, we report that SUGARS WILL EVENTUALLY BE EXPORTED TRANSPORTER (SWEET16) from Arabidopsis (Arabidopsis thaliana) is a vacuole-located carrier, transporting glucose (Glc), fructose (Fru), and sucrose (Suc) after heterologous expression in Xenopus laevis oocytes. The SWEET16 gene, similar to the homologs gene SWEET17, is mainly expressed in vascular parenchyma cells. Application of Glc, Fru, or Suc, as well as cold, osmotic stress, or low nitrogen, provoke the down-regulation of SWEET16 messenger RNA accumulation. SWEET16 overexpressors (35SPro:SWEET16) showed a number of peculiarities related to differences in sugar accumulation, such as less Glc, Fru, and Suc at the end of the night. Under cold stress, 35SPro:SWEET16 plants are unable to accumulate Fru, while under nitrogen starvation, both Glc and Fru, but not Suc, were less abundant. These changes of individual sugars indicate that the consequences of an increased SWEET16 activity are dependent upon the type of external stimulus. Remarkably, 35SPro:SWEET16 lines showed improved germination and increased freezing tolerance. The latter observation, in combination with the modified sugar levels, points to a superior function of Glc and Suc for frost tolerance. 35SPro:SWEET16 plants exhibited increased growth efficiency when cultivated on soil and showed improved nitrogen use efficiency when nitrate was sufficiently available, while under conditions of limiting nitrogen, wild-type biomasses were higher than those of 35SPro:SWEET16 plants. Our results identify SWEET16 as a vacuolar sugar facilitator, demonstrate the substantial impact of SWEET16 overexpression on various critical plant traits, and imply that SWEET16 activity must be tightly regulated to allow optimal Arabidopsis development under nonfavorable conditions.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Klemens, Patrick A.W. and Patzke, Kathrin and Deitmer, Joachim and Spinner, Lara and Le Hir, Rozenn and Bellini, Catherine and Bedu, Magali and Chardon, Fabien and Krapp, Anne and Neuhaus, H. Ekkehard},
	month = oct,
	year = {2013},
	pages = {1338--1352},
}

Abstract Here, we report that SUGARS WILL EVENTUALLY BE EXPORTED TRANSPORTER (SWEET16) from Arabidopsis (Arabidopsis thaliana) is a vacuole-located carrier, transporting glucose (Glc), fructose (Fru), and sucrose (Suc) after heterologous expression in Xenopus laevis oocytes. The SWEET16 gene, similar to the homologs gene SWEET17, is mainly expressed in vascular parenchyma cells. Application of Glc, Fru, or Suc, as well as cold, osmotic stress, or low nitrogen, provoke the down-regulation of SWEET16 messenger RNA accumulation. SWEET16 overexpressors (35SPro:SWEET16) showed a number of peculiarities related to differences in sugar accumulation, such as less Glc, Fru, and Suc at the end of the night. Under cold stress, 35SPro:SWEET16 plants are unable to accumulate Fru, while under nitrogen starvation, both Glc and Fru, but not Suc, were less abundant. These changes of individual sugars indicate that the consequences of an increased SWEET16 activity are dependent upon the type of external stimulus. Remarkably, 35SPro:SWEET16 lines showed improved germination and increased freezing tolerance. The latter observation, in combination with the modified sugar levels, points to a superior function of Glc and Suc for frost tolerance. 35SPro:SWEET16 plants exhibited increased growth efficiency when cultivated on soil and showed improved nitrogen use efficiency when nitrate was sufficiently available, while under conditions of limiting nitrogen, wild-type biomasses were higher than those of 35SPro:SWEET16 plants. Our results identify SWEET16 as a vacuolar sugar facilitator, demonstrate the substantial impact of SWEET16 overexpression on various critical plant traits, and imply that SWEET16 activity must be tightly regulated to allow optimal Arabidopsis development under nonfavorable conditions.

@article{viotti_endoplasmic_2013,
	title = {The {Endoplasmic} {Reticulum} {Is} the {Main} {Membrane} {Source} for {Biogenesis} of the {Lytic} {Vacuole} in \textit{{Arabidopsis}}},
	volume = {25},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/25/9/3434/6097922},
	doi = {10/f22zxf},
	abstract = {Abstract
            Vacuoles are multifunctional organelles essential for the sessile lifestyle of plants. Despite their central functions in cell growth, storage, and detoxification, knowledge about mechanisms underlying their biogenesis and associated protein trafficking pathways remains limited. Here, we show that in meristematic cells of the Arabidopsis thaliana root, biogenesis of vacuoles as well as the trafficking of sterols and of two major tonoplast proteins, the vacuolar H+-pyrophosphatase and the vacuolar H+-adenosinetriphosphatase, occurs independently of endoplasmic reticulum (ER)–Golgi and post-Golgi trafficking. Instead, both pumps are found in provacuoles that structurally resemble autophagosomes but are not formed by the core autophagy machinery. Taken together, our results suggest that vacuole biogenesis and trafficking of tonoplast proteins and lipids can occur directly from the ER independent of Golgi function.},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Viotti, Corrado and Krüger, Falco and Krebs, Melanie and Neubert, Christoph and Fink, Fabian and Lupanga, Upendo and Scheuring, David and Boutté, Yohann and Frescatada-Rosa, Márcia and Wolfenstetter, Susanne and Sauer, Norbert and Hillmer, Stefan and Grebe, Markus and Schumacher, Karin},
	month = oct,
	year = {2013},
	pages = {3434--3449},
}

Abstract Vacuoles are multifunctional organelles essential for the sessile lifestyle of plants. Despite their central functions in cell growth, storage, and detoxification, knowledge about mechanisms underlying their biogenesis and associated protein trafficking pathways remains limited. Here, we show that in meristematic cells of the Arabidopsis thaliana root, biogenesis of vacuoles as well as the trafficking of sterols and of two major tonoplast proteins, the vacuolar H+-pyrophosphatase and the vacuolar H+-adenosinetriphosphatase, occurs independently of endoplasmic reticulum (ER)–Golgi and post-Golgi trafficking. Instead, both pumps are found in provacuoles that structurally resemble autophagosomes but are not formed by the core autophagy machinery. Taken together, our results suggest that vacuole biogenesis and trafficking of tonoplast proteins and lipids can occur directly from the ER independent of Golgi function.

@article{simon_defining_2013,
	title = {Defining the selectivity of processes along the auxin response chain: a study using auxin analogues},
	volume = {200},
	issn = {0028-646X, 1469-8137},
	shorttitle = {Defining the selectivity of processes along the auxin response chain},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.12437},
	doi = {10/f3p46z},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Simon, Sibu and Kubeš, Martin and Baster, Pawel and Robert, Stéphanie and Dobrev, Petre Ivanov and Friml, Jiří and Petrášek, Jan and Zažímalová, Eva},
	month = dec,
	year = {2013},
	pages = {1034--1048},
}

@article{gruffman_organic_2013,
	title = {Organic nitrogen uptake of {Scots} pine seedlings is independent of current carbohydrate supply},
	volume = {33},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article-lookup/doi/10.1093/treephys/tpt041},
	doi = {10/f22v4r},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Tree Physiology},
	author = {Gruffman, L. and Palmroth, S. and Nasholm, T.},
	month = jun,
	year = {2013},
	pages = {590--600},
}

@article{wang_arabidopsis_2013,
	title = {The {Arabidopsis} {LRR}-{RLK}, {PXC1}, is a regulator of secondary wall formation correlated with the {TDIF}-{PXY}/{TDR}-{WOX4} signaling pathway},
	volume = {13},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-13-94},
	doi = {10/f225hg},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Wang, Jiehua and Kucukoglu, Melis and Zhang, Linbin and Chen, Peng and Decker, Daniel and Nilsson, Ove and Jones, Brian and Sandberg, Göran and Zheng, Bo},
	year = {2013},
	pages = {94},
}

@article{moschou_caspase-related_2013,
	title = {The {Caspase}-{Related} {Protease} {Separase} ({EXTRA} {SPINDLE} {POLES}) {Regulates} {Cell} {Polarity} and {Cytokinesis} in {Arabidopsis}[{C}][{W}]},
	volume = {25},
	issn = {1040-4651},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3723619/},
	doi = {10/f24kgw},
	abstract = {Separase is responsible for segregation of daughter chromatids during cell division in all eukaryotes. Here it is reported that in addition to regulating chromatid segregation, the plant homolog of separase regulates vesicle trafficking essential for the cytokinesis and establishment of cell polarity during tissue and organ patterning., Vesicle trafficking plays an important role in cell division, establishment of cell polarity, and translation of environmental cues to developmental responses. However, the molecular mechanisms regulating vesicle trafficking remain poorly understood. Here, we report that the evolutionarily conserved caspase-related protease separase (EXTRA SPINDLE POLES [ESP]) is required for the establishment of cell polarity and cytokinesis in Arabidopsis
thaliana. At the cellular level, separase colocalizes with microtubules and RabA2a (for RAS GENES FROM RAT BRAINA2a) GTPase-positive structures. Separase facilitates polar targeting of the auxin efflux carrier PIN-FORMED2 (PIN2) to the rootward side of the root cortex cells. Plants with the radially swollen4 (rsw4) allele with compromised separase activity, in addition to mitotic failure, display isotropic cell growth, perturbation of auxin gradient formation, slower gravitropic response in roots, and cytokinetic failure. Measurements of the dynamics of vesicle markers on the cell plate revealed an overall reduction of the delivery rates of KNOLLE and RabA2a GTPase in separase-deficient roots. Furthermore, dissociation of the clathrin light chain, a protein that plays major role in the formation of coated vesicles, was slower in rsw4 than in the control. Our results demonstrate that separase is a key regulator of vesicle trafficking, which is indispensable for cytokinesis and the establishment of cell polarity.},
	number = {6},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Moschou, Panagiotis N. and Smertenko, Andrei P. and Minina, Elena A. and Fukada, Kazutake and Savenkov, Eugene I. and Robert, Stephanie and Hussey, Patrick J. and Bozhkov, Peter V.},
	month = jun,
	year = {2013},
	pmid = {23898031},
	pmcid = {PMC3723619},
	pages = {2171--2186},
}

Separase is responsible for segregation of daughter chromatids during cell division in all eukaryotes. Here it is reported that in addition to regulating chromatid segregation, the plant homolog of separase regulates vesicle trafficking essential for the cytokinesis and establishment of cell polarity during tissue and organ patterning., Vesicle trafficking plays an important role in cell division, establishment of cell polarity, and translation of environmental cues to developmental responses. However, the molecular mechanisms regulating vesicle trafficking remain poorly understood. Here, we report that the evolutionarily conserved caspase-related protease separase (EXTRA SPINDLE POLES [ESP]) is required for the establishment of cell polarity and cytokinesis in Arabidopsis thaliana. At the cellular level, separase colocalizes with microtubules and RabA2a (for RAS GENES FROM RAT BRAINA2a) GTPase-positive structures. Separase facilitates polar targeting of the auxin efflux carrier PIN-FORMED2 (PIN2) to the rootward side of the root cortex cells. Plants with the radially swollen4 (rsw4) allele with compromised separase activity, in addition to mitotic failure, display isotropic cell growth, perturbation of auxin gradient formation, slower gravitropic response in roots, and cytokinetic failure. Measurements of the dynamics of vesicle markers on the cell plate revealed an overall reduction of the delivery rates of KNOLLE and RabA2a GTPase in separase-deficient roots. Furthermore, dissociation of the clathrin light chain, a protein that plays major role in the formation of coated vesicles, was slower in rsw4 than in the control. Our results demonstrate that separase is a key regulator of vesicle trafficking, which is indispensable for cytokinesis and the establishment of cell polarity.

@article{kurepin_role_2013,
	title = {Role of {CBFs} as {Integrators} of {Chloroplast} {Redox}, {Phytochrome} and {Plant} {Hormone} {Signaling} during {Cold} {Acclimation}},
	volume = {14},
	issn = {1422-0067},
	url = {http://www.mdpi.com/1422-0067/14/6/12729},
	doi = {10/f23sbq},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {International Journal of Molecular Sciences},
	author = {Kurepin, Leonid and Dahal, Keshav and Savitch, Leonid and Singh, Jas and Bode, Rainer and Ivanov, Alexander and Hurry, Vaughan and Hüner, Norman},
	month = jun,
	year = {2013},
	pages = {12729--12763},
}

@article{geshi_galactosyltransferase_2013,
	title = {A galactosyltransferase acting on arabinogalactan protein glycans is essential for embryo development in {Arabidopsis}},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.12281},
	doi = {10/gkgdks},
	language = {en},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Geshi, Naomi and Johansen, Jorunn N. and Dilokpimol, Adiphol and Rolland, Aurélia and Belcram, Katia and Verger, Stéphane and Kotake, Toshihisa and Tsumuraya, Yoichi and Kaneko, Satoshi and Tryfona, Theodora and Dupree, Paul and Scheller, Henrik V. and Höfte, Herman and Mouille, Gregory},
	month = aug,
	year = {2013},
	pages = {n/a--n/a},
}

@article{shevela_efficiency_2013,
	title = {Efficiency of photosynthetic water oxidation at ambient and depleted levels of inorganic carbon},
	volume = {117},
	issn = {0166-8595, 1573-5079},
	url = {http://link.springer.com/10.1007/s11120-013-9875-5},
	doi = {10/f2zpf2},
	language = {en},
	number = {1-3},
	urldate = {2021-06-08},
	journal = {Photosynthesis Research},
	author = {Shevela, Dmitriy and Nöring, Birgit and Koroidov, Sergey and Shutova, Tatiana and Samuelsson, Göran and Messinger, Johannes},
	month = nov,
	year = {2013},
	pages = {401--412},
}

@article{miedes_xyloglucan_2013,
	title = {Xyloglucan endotransglucosylase/hydrolase ({XTH}) overexpression affects growth and cell wall mechanics in etiolated {Arabidopsis} hypocotyls},
	volume = {64},
	issn = {1460-2431, 0022-0957},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/ert107},
	doi = {10/f244cc},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Miedes, Eva and Suslov, Dmitry and Vandenbussche, Filip and Kenobi, Kim and Ivakov, Alexander and Van Der Straeten, Dominique and Lorences, Ester P. and Mellerowicz, Ewa J. and Verbelen, Jean-Pierre and Vissenberg, Kris},
	month = may,
	year = {2013},
	pages = {2481--2497},
}

@article{hallingback_genetic_2013,
	title = {Genetic information from progeny trials: a comparison between progenies generated by open pollination and by controlled crosses},
	volume = {9},
	issn = {1614-2942, 1614-2950},
	shorttitle = {Genetic information from progeny trials},
	url = {http://link.springer.com/10.1007/s11295-012-0588-2},
	doi = {10/f24bh4},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Hallingbäck, Henrik R. and Jansson, Gunnar},
	month = jun,
	year = {2013},
	pages = {731--740},
}

@article{genneback_using_2013,
	title = {Using {OPLS}-{DA} to find new hypotheses in vast amounts of gene expression data — {Studying} the progression of cardiac hypertrophy in the heart of aorta ligated rat},
	volume = {522},
	issn = {03781119},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378111913002527},
	doi = {10/f2zw4b},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Gene},
	author = {Gennebäck, Nina and Malm, Linus and Hellman, Urban and Waldenström, Anders and Mörner, Stellan},
	month = jun,
	year = {2013},
	pages = {27--36},
}

@article{cecchetti_auxin_2013,
	title = {Auxin controls {Arabidopsis} anther dehiscence by regulating endothecium lignification and jasmonic acid biosynthesis},
	volume = {74},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.12130},
	doi = {10/f23td7},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Cecchetti, Valentina and Altamura, Maria Maddalena and Brunetti, Patrizia and Petrocelli, Valentina and Falasca, Giuseppina and Ljung, Karin and Costantino, Paolo and Cardarelli, Maura},
	month = may,
	year = {2013},
	pages = {411--422},
}

@article{tanaka_cell_2013,
	title = {Cell {Polarity} and {Patterning} by {PIN} {Trafficking} through {Early} {Endosomal} {Compartments} in {Arabidopsis} thaliana},
	volume = {9},
	issn = {1553-7404},
	url = {https://dx.plos.org/10.1371/journal.pgen.1003540},
	doi = {10/gbc9jh},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {PLoS Genetics},
	author = {Tanaka, Hirokazu and Kitakura, Saeko and Rakusová, Hana and Uemura, Tomohiro and Feraru, Mugurel I. and De Rycke, Riet and Robert, Stéphanie and Kakimoto, Tatsuo and Friml, Jiří},
	editor = {Luschnig, Christian},
	month = may,
	year = {2013},
	pages = {e1003540},
}

@article{le_hir_plant-specific_2013,
	title = {The {Plant}-{Specific} {Dof} {Transcription} {Factors} {Family}: {New} {Players} {Involved} in {Vascular} {System} {Development} and {Functioning} in {Arabidopsis}},
	volume = {4},
	issn = {1664-462X},
	shorttitle = {The {Plant}-{Specific} {Dof} {Transcription} {Factors} {Family}},
	url = {http://journal.frontiersin.org/article/10.3389/fpls.2013.00164/abstract},
	doi = {10/f2ztrr},
	urldate = {2021-06-08},
	journal = {Frontiers in Plant Science},
	author = {Le Hir, Rozenn and Bellini, Catherine},
	year = {2013},
}

@article{pawar_acetylation_2013,
	title = {Acetylation of woody lignocellulose: significance and regulation},
	volume = {4},
	issn = {1664-462X},
	shorttitle = {Acetylation of woody lignocellulose},
	url = {http://journal.frontiersin.org/article/10.3389/fpls.2013.00118/abstract},
	doi = {10/f236bp},
	urldate = {2021-06-08},
	journal = {Frontiers in Plant Science},
	author = {Pawar, Prashant Mohan-Anupama and Koutaniemi, Sanna and Tenkanen, Maija and Mellerowicz, Ewa J.},
	year = {2013},
}

@article{gronlund_transcription_2013,
	title = {Transcription factor binding kinetics constrain noise suppression via negative feedback},
	volume = {4},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/ncomms2867},
	doi = {10/f23pk6},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Nature Communications},
	author = {Grönlund, Andreas and Lötstedt, Per and Elf, Johan},
	month = oct,
	year = {2013},
	pages = {1864},
}

@article{sauer_auxin_2013,
	title = {Auxin: simply complicated},
	volume = {64},
	issn = {1460-2431, 0022-0957},
	shorttitle = {Auxin},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/ert139},
	doi = {10/f3pxg2},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Sauer, Michael and Robert, Stéphanie and Kleine-Vehn, Jürgen},
	month = jun,
	year = {2013},
	pages = {2565--2577},
}

@article{rosquete_auxin_2013,
	title = {An {Auxin} {Transport} {Mechanism} {Restricts} {Positive} {Orthogravitropism} in {Lateral} {Roots}},
	volume = {23},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982213003667},
	doi = {10/f4w5br},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {Current Biology},
	author = {Rosquete, Michel Ruiz and von Wangenheim, Daniel and Marhavý, Peter and Barbez, Elke and Stelzer, Ernst H.K. and Benková, Eva and Maizel, Alexis and Kleine-Vehn, Jürgen},
	month = may,
	year = {2013},
	pages = {817--822},
}

@article{pose_temperature-dependent_2013,
	title = {Temperature-dependent regulation of flowering by antagonistic {FLM} variants},
	volume = {503},
	issn = {1476-4687},
	doi = {10/f5h734},
	abstract = {The appropriate timing of flowering is crucial for plant reproductive success. It is therefore not surprising that intricate genetic networks have evolved to perceive and integrate both endogenous and environmental signals, such as carbohydrate and hormonal status, photoperiod and temperature. In contrast to our detailed understanding of the vernalization pathway, little is known about how flowering time is controlled in response to changes in the ambient growth temperature. In Arabidopsis thaliana, the MADS-box transcription factor genes FLOWERING LOCUS M (FLM) and SHORT VEGETATIVE PHASE (SVP) have key roles in this process. FLM is subject to temperature-dependent alternative splicing. Here we report that the two main FLM protein splice variants, FLM-β and FLM-δ, compete for interaction with the floral repressor SVP. The SVP-FLM-β complex is predominately formed at low temperatures and prevents precocious flowering. By contrast, the competing SVP-FLM-δ complex is impaired in DNA binding and acts as a dominant-negative activator of flowering at higher temperatures. Our results show a new mechanism that controls the timing of the floral transition in response to changes in ambient temperature. A better understanding of how temperature controls the molecular mechanisms of flowering will be important to cope with current changes in global climate.},
	language = {eng},
	number = {7476},
	journal = {Nature},
	author = {Posé, David and Verhage, Leonie and Ott, Felix and Yant, Levi and Mathieu, Johannes and Angenent, Gerco C. and Immink, Richard G. H. and Schmid, Markus},
	month = nov,
	year = {2013},
	pmid = {24067612},
	keywords = {Alternative Splicing, Arabidopsis, Arabidopsis Proteins, DNA-Binding Proteins, Flowers, Gene Expression Regulation, Plant, MADS Domain Proteins, Plants, Genetically Modified, Protein Binding, Protein Isoforms, Temperature, Time Factors, Transcription Factors},
	pages = {414--417},
}

The appropriate timing of flowering is crucial for plant reproductive success. It is therefore not surprising that intricate genetic networks have evolved to perceive and integrate both endogenous and environmental signals, such as carbohydrate and hormonal status, photoperiod and temperature. In contrast to our detailed understanding of the vernalization pathway, little is known about how flowering time is controlled in response to changes in the ambient growth temperature. In Arabidopsis thaliana, the MADS-box transcription factor genes FLOWERING LOCUS M (FLM) and SHORT VEGETATIVE PHASE (SVP) have key roles in this process. FLM is subject to temperature-dependent alternative splicing. Here we report that the two main FLM protein splice variants, FLM-β and FLM-δ, compete for interaction with the floral repressor SVP. The SVP-FLM-β complex is predominately formed at low temperatures and prevents precocious flowering. By contrast, the competing SVP-FLM-δ complex is impaired in DNA binding and acts as a dominant-negative activator of flowering at higher temperatures. Our results show a new mechanism that controls the timing of the floral transition in response to changes in ambient temperature. A better understanding of how temperature controls the molecular mechanisms of flowering will be important to cope with current changes in global climate.

@article{lee_regulation_2013,
	title = {Regulation of temperature-responsive flowering by {MADS}-box transcription factor repressors},
	volume = {342},
	issn = {1095-9203},
	doi = {10/f5fmt6},
	abstract = {Changes in ambient temperature affect flowering time in plants; understanding this phenomenon will be crucial for buffering agricultural systems from the effects of climate change. Here, we show that levels of FLM-β, an alternatively spliced form of the flowering repressor FLOWERING LOCUS M, increase at lower temperatures, repressing flowering. FLM-β interacts with SHORT VEGETATIVE PHASE (SVP); SVP is degraded at high temperatures, reducing the abundance of the SVP-FLM-β repressor complex and, thus, allowing the plant to flower. The svp and flm mutants show temperature-insensitive flowering in different temperature ranges. Control of SVP-FLM-β repressor complex abundance via transcriptional and splicing regulation of FLM and posttranslational regulation of SVP protein stability provides an efficient, rapid mechanism for plants to respond to ambient temperature changes.},
	language = {eng},
	number = {6158},
	journal = {Science (New York, N.Y.)},
	author = {Lee, Jeong Hwan and Ryu, Hak-Seung and Chung, Kyung Sook and Posé, David and Kim, Soonkap and Schmid, Markus and Ahn, Ji Hoon},
	month = nov,
	year = {2013},
	pmid = {24030492},
	keywords = {Alternative Splicing, Arabidopsis, Arabidopsis Proteins, Flowers, Gene Expression Regulation, Plant, MADS Domain Proteins, Molecular Sequence Data, Mutation, Repressor Proteins, Temperature, Transcription Factors},
	pages = {628--632},
}

Changes in ambient temperature affect flowering time in plants; understanding this phenomenon will be crucial for buffering agricultural systems from the effects of climate change. Here, we show that levels of FLM-β, an alternatively spliced form of the flowering repressor FLOWERING LOCUS M, increase at lower temperatures, repressing flowering. FLM-β interacts with SHORT VEGETATIVE PHASE (SVP); SVP is degraded at high temperatures, reducing the abundance of the SVP-FLM-β repressor complex and, thus, allowing the plant to flower. The svp and flm mutants show temperature-insensitive flowering in different temperature ranges. Control of SVP-FLM-β repressor complex abundance via transcriptional and splicing regulation of FLM and posttranslational regulation of SVP protein stability provides an efficient, rapid mechanism for plants to respond to ambient temperature changes.

@article{wahl_regulation_2013,
	title = {Regulation of flowering by trehalose-6-phosphate signaling in {Arabidopsis} thaliana},
	volume = {339},
	issn = {1095-9203},
	doi = {10/f4kxph},
	abstract = {The timing of the induction of flowering determines to a large extent the reproductive success of plants. Plants integrate diverse environmental and endogenous signals to ensure the timely transition from vegetative growth to flowering. Carbohydrates are thought to play a crucial role in the regulation of flowering, and trehalose-6-phosphate (T6P) has been suggested to function as a proxy for carbohydrate status in plants. The loss of TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1) causes Arabidopsis thaliana to flower extremely late, even under otherwise inductive environmental conditions. This suggests that TPS1 is required for the timely initiation of flowering. We show that the T6P pathway affects flowering both in the leaves and at the shoot meristem, and integrate TPS1 into the existing genetic framework of flowering-time control.},
	language = {eng},
	number = {6120},
	journal = {Science (New York, N.Y.)},
	author = {Wahl, Vanessa and Ponnu, Jathish and Schlereth, Armin and Arrivault, Stéphanie and Langenecker, Tobias and Franke, Annika and Feil, Regina and Lunn, John E. and Stitt, Mark and Schmid, Markus},
	month = feb,
	year = {2013},
	pmid = {23393265},
	keywords = {Arabidopsis, Arabidopsis Proteins, Circadian Rhythm, Flowers, Gene Expression Regulation, Plant, Glucosyltransferases, Meristem, MicroRNAs, Phosphatidylethanolamine Binding Protein, Photoperiod, Plant Leaves, Plant Shoots, Signal Transduction, Sugar Phosphates, Trehalose},
	pages = {704--707},
}

The timing of the induction of flowering determines to a large extent the reproductive success of plants. Plants integrate diverse environmental and endogenous signals to ensure the timely transition from vegetative growth to flowering. Carbohydrates are thought to play a crucial role in the regulation of flowering, and trehalose-6-phosphate (T6P) has been suggested to function as a proxy for carbohydrate status in plants. The loss of TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1) causes Arabidopsis thaliana to flower extremely late, even under otherwise inductive environmental conditions. This suggests that TPS1 is required for the timely initiation of flowering. We show that the T6P pathway affects flowering both in the leaves and at the shoot meristem, and integrate TPS1 into the existing genetic framework of flowering-time control.

@article{bernhardsson_geographic_2013,
	title = {Geographic structure in metabolome and herbivore community co-occurs with genetic structure in plant defence genes},
	volume = {16},
	issn = {1461023X},
	url = {http://doi.wiley.com/10.1111/ele.12114},
	doi = {10/f25rz6},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Ecology Letters},
	author = {Bernhardsson, Carolina and Robinson, Kathryn M. and Abreu, Ilka N. and Jansson, Stefan and Albrectsen, Benedicte R. and Ingvarsson, Pär K.},
	editor = {Eubanks, Micky},
	month = jun,
	year = {2013},
	pages = {791--798},
}

@article{zheng_coordination_2013,
	title = {Coordination of auxin and ethylene biosynthesis by the aminotransferase {VAS1}},
	volume = {9},
	issn = {1552-4450, 1552-4469},
	url = {http://www.nature.com/articles/nchembio.1178},
	doi = {10/f234vk},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Nature Chemical Biology},
	author = {Zheng, Zuyu and Guo, Yongxia and Novák, Ondřej and Dai, Xinhua and Zhao, Yunde and Ljung, Karin and Noel, Joseph P and Chory, Joanne},
	month = apr,
	year = {2013},
	pages = {244--246},
}

@article{chardon_leaf_2013,
	title = {Leaf {Fructose} {Content} {Is} {Controlled} by the {Vacuolar} {Transporter} {SWEET17} in {Arabidopsis}},
	volume = {23},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S096098221300287X},
	doi = {10/f24bg2},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Current Biology},
	author = {Chardon, Fabien and Bedu, Magali and Calenge, Fanny and Klemens, Patrick A.W. and Spinner, Lara and Clement, Gilles and Chietera, Giorgiana and Léran, Sophie and Ferrand, Marina and Lacombe, Benoit and Loudet, Olivier and Dinant, Sylvie and Bellini, Catherine and Neuhaus, H. Ekkehard and Daniel-Vedele, Françoise and Krapp, Anne},
	month = apr,
	year = {2013},
	pages = {697--702},
}

@article{pesquet_non-cell-autonomous_2013,
	title = {Non-{Cell}-{Autonomous} {Postmortem} {Lignification} of {Tracheary} {Elements} in \textit{{Zinnia} elegans}},
	volume = {25},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/25/4/1314/6100539},
	doi = {10/f22bdv},
	abstract = {Abstract
            Postmortem lignification of xylem tracheary elements (TEs) has been debated for decades. Here, we provide evidence in Zinnia elegans  TE cell cultures, using pharmacological inhibitors and in intact Z. elegans plants using Fourier transform infrared microspectroscopy, that TE lignification occurs postmortem (i.e., after TE programmed cell death). In situ RT-PCR verified expression of the lignin monomer biosynthetic cinnamoyl CoA reductase and cinnamyl alcohol dehydrogenase in not only the lignifying TEs but also in the unlignified non-TE cells of Z. elegans  TE cell cultures and in living, parenchymatic xylem cells that surround TEs in stems. These cells were also shown to have the capacity to synthesize and transport lignin monomers and reactive oxygen species to the cell walls of dead TEs. Differential gene expression analysis in Z. elegans  TE cell cultures and concomitant functional analysis in Arabidopsis thaliana resulted in identification of several genes that were expressed in the non-TE cells and that affected lignin chemistry on the basis of pyrolysis–gas chromatography/mass spectrometry analysis. These data suggest that living, parenchymatic xylem cells contribute to TE lignification in a non-cell-autonomous manner, thus enabling the postmortem lignification of TEs.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Pesquet, Edouard and Zhang, Bo and Gorzsás, András and Puhakainen, Tuula and Serk, Henrik and Escamez, Sacha and Barbier, Odile and Gerber, Lorenz and Courtois-Moreau, Charleen and Alatalo, Edward and Paulin, Lars and Kangasjärvi, Jaakko and Sundberg, Björn and Goffner, Deborah and Tuominen, Hannele},
	month = may,
	year = {2013},
	pages = {1314--1328},
}

Abstract Postmortem lignification of xylem tracheary elements (TEs) has been debated for decades. Here, we provide evidence in Zinnia elegans  TE cell cultures, using pharmacological inhibitors and in intact Z. elegans plants using Fourier transform infrared microspectroscopy, that TE lignification occurs postmortem (i.e., after TE programmed cell death). In situ RT-PCR verified expression of the lignin monomer biosynthetic cinnamoyl CoA reductase and cinnamyl alcohol dehydrogenase in not only the lignifying TEs but also in the unlignified non-TE cells of Z. elegans  TE cell cultures and in living, parenchymatic xylem cells that surround TEs in stems. These cells were also shown to have the capacity to synthesize and transport lignin monomers and reactive oxygen species to the cell walls of dead TEs. Differential gene expression analysis in Z. elegans  TE cell cultures and concomitant functional analysis in Arabidopsis thaliana resulted in identification of several genes that were expressed in the non-TE cells and that affected lignin chemistry on the basis of pyrolysis–gas chromatography/mass spectrometry analysis. These data suggest that living, parenchymatic xylem cells contribute to TE lignification in a non-cell-autonomous manner, thus enabling the postmortem lignification of TEs.

@article{ivkovic_influence_2013,
	title = {Influence of cambial age and climate on ring width and wood density in {Pinus} radiata families},
	volume = {70},
	issn = {1286-4560, 1297-966X},
	url = {http://link.springer.com/10.1007/s13595-013-0290-z},
	doi = {10/f4zz7w},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Annals of Forest Science},
	author = {Ivković, Miloš and Gapare, Washington and Wu, Harry and Espinoza, Sergio and Rozenberg, Philippe},
	month = jul,
	year = {2013},
	pages = {525--534},
}

@article{barajas-lopez_papp5_2013,
	title = {{PAPP5} {Is} {Involved} in the {Tetrapyrrole} {Mediated} {Plastid} {Signalling} during {Chloroplast} {Development}},
	volume = {8},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0060305},
	doi = {10/f223sf},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Barajas-López, Juan de Dios and Kremnev, Dmitry and Shaikhali, Jehad and Piñas-Fernández, Aurora and Strand, Åsa},
	editor = {Pandey, Girdhar Kumar},
	month = mar,
	year = {2013},
	pages = {e60305},
}

@article{ng_cyclin-dependent_2013,
	title = {Cyclin-dependent {Kinase} {E1} ({CDKE1}) {Provides} a {Cellular} {Switch} in {Plants} between {Growth} and {Stress} {Responses}},
	volume = {288},
	issn = {00219258},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0021925820464580},
	doi = {10/f2z2ws},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Journal of Biological Chemistry},
	author = {Ng, Sophia and Giraud, Estelle and Duncan, Owen and Law, Simon R. and Wang, Yan and Xu, Lin and Narsai, Reena and Carrie, Chris and Walker, Hayden and Day, David A. and Blanco, Nicolás E. and Strand, Åsa and Whelan, James and Ivanova, Aneta},
	month = feb,
	year = {2013},
	pages = {3449--3459},
}

@article{wind_abi4_2013,
	title = {{ABI4}: versatile activator and repressor},
	volume = {18},
	issn = {13601385},
	shorttitle = {{ABI4}},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1360138512002312},
	doi = {10/f22p4f},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Trends in Plant Science},
	author = {Wind, Julia J. and Peviani, Alessia and Snel, Berend and Hanson, Johannes and Smeekens, Sjef C.},
	month = mar,
	year = {2013},
	pages = {125--132},
}

@article{orians_how_2013,
	title = {How slug herbivory of juvenile hybrid willows alters chemistry, growth and subsequent susceptibility to diverse plant enemies},
	volume = {112},
	issn = {1095-8290, 0305-7364},
	url = {https://academic.oup.com/aob/article-lookup/doi/10.1093/aob/mct002},
	doi = {10/f228d8},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Annals of Botany},
	author = {Orians, Colin M. and Fritz, Robert S. and Hochwender, Cris G. and Albrectsen, Benedicte R. and Czesak, Mary Ellen},
	month = aug,
	year = {2013},
	pages = {757--765},
}

@article{sellstedt_aspects_2013,
	title = {Aspects of nitrogen-fixing \textit{{Actinobacteria}} , in particular free-living and symbiotic \textit{{Frankia}}},
	volume = {342},
	issn = {03781097},
	url = {https://academic.oup.com/femsle/article-lookup/doi/10.1111/1574-6968.12116},
	doi = {10/f23gh6},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {FEMS Microbiology Letters},
	author = {Sellstedt, Anita and Richau, Kerstin H.},
	month = may,
	year = {2013},
	pages = {179--186},
}

@article{abrahamsson_maternal_2013,
	title = {Maternal heterozygosity and progeny fitness association in an inbred {Scots} pine population},
	volume = {141},
	issn = {0016-6707, 1573-6857},
	url = {http://link.springer.com/10.1007/s10709-013-9704-y},
	doi = {10/f2242n},
	language = {en},
	number = {1-3},
	urldate = {2021-06-08},
	journal = {Genetica},
	author = {Abrahamsson, S. and Ahlinder, J. and Waldmann, P. and García-Gil, M. R.},
	month = mar,
	year = {2013},
	pages = {41--50},
}

@article{businge_effect_2013,
	title = {The effect of carbohydrates and osmoticum on storage reserve accumulation and germination of {Norway} spruce somatic embryos},
	volume = {149},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12039},
	doi = {10/f2zr7w},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {Businge, Edward and Bygdell, Joakim and Wingsle, Gunnar and Moritz, Thomas and Egertsdotter, Ulrika},
	month = oct,
	year = {2013},
	pages = {273--285},
}

@article{ljung_auxin_2013,
	title = {Auxin metabolism and homeostasis during plant development},
	volume = {140},
	issn = {1477-9129, 0950-1991},
	url = {https://journals.biologists.com/dev/article/140/5/943/45952/Auxin-metabolism-and-homeostasis-during-plant},
	doi = {10/f23cpj},
	abstract = {Auxin plays important roles during the entire life span of a plant. This small organic acid influences cell division, cell elongation and cell differentiation, and has great impact on the final shape and function of cells and tissues in all higher plants. Auxin metabolism is not well understood but recent discoveries, reviewed here, have started to shed light on the processes that regulate the synthesis and degradation of this important plant hormone.},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Development},
	author = {Ljung, Karin},
	month = mar,
	year = {2013},
	pages = {943--950},
}

Auxin plays important roles during the entire life span of a plant. This small organic acid influences cell division, cell elongation and cell differentiation, and has great impact on the final shape and function of cells and tissues in all higher plants. Auxin metabolism is not well understood but recent discoveries, reviewed here, have started to shed light on the processes that regulate the synthesis and degradation of this important plant hormone.

@article{ranade_ecotypic_2013,
	title = {Ecotypic variation in response to light spectra in {Scots} pine ({Pinus} sylvestris {L}.)},
	volume = {33},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article-lookup/doi/10.1093/treephys/tps131},
	doi = {10/f23q2k},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Tree Physiology},
	author = {Ranade, S. S. and Garcia-Gil, M. R.},
	month = feb,
	year = {2013},
	pages = {195--201},
}

@article{cox_reflections_2013,
	title = {Reflections on substrate water and dioxygen formation},
	volume = {1827},
	issn = {00052728},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0005272813000170},
	doi = {10/f2zvnx},
	language = {en},
	number = {8-9},
	urldate = {2021-06-08},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {Cox, Nicholas and Messinger, Johannes},
	month = aug,
	year = {2013},
	pages = {1020--1030},
}

@article{storm_refolding_2013,
	title = {Refolding and {Enzyme} {Kinetic} {Studies} on the {Ferrochelatase} of the {Cyanobacterium} {Synechocystis} sp. {PCC} 6803},
	volume = {8},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0055569},
	doi = {10/f23fpb},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Storm, Patrik and Tibiletti, Tania and Hall, Michael and Funk, Christiane},
	editor = {Subramanyam, Rajagopal},
	month = feb,
	year = {2013},
	pages = {e55569},
}

@article{nasholm_are_2013,
	title = {Are ectomycorrhizal fungi alleviating or aggravating nitrogen limitation of tree growth in boreal forests?},
	volume = {198},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.12139},
	doi = {10/f2zz5x},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Näsholm, Torgny and Högberg, Peter and Franklin, Oskar and Metcalfe, Daniel and Keel, Sonja G. and Campbell, Catherine and Hurry, Vaughan and Linder, Sune and Högberg, Mona N.},
	month = apr,
	year = {2013},
	pages = {214--221},
}

@article{johansson_jankanpaa_non-photochemical_2013,
	title = {Non-{Photochemical} {Quenching} {Capacity} in {Arabidopsis} thaliana {Affects} {Herbivore} {Behaviour}},
	volume = {8},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0053232},
	doi = {10/f22s4s},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Johansson Jänkänpää, Hanna and Frenkel, Martin and Zulfugarov, Ismayil and Reichelt, Michael and Krieger-Liszkay, Anja and Mishra, Yogesh and Gershenzon, Jonathan and Moen, Jon and Lee, Choon-Hwan and Jansson, Stefan},
	editor = {Tran, Lam-Son Phan},
	month = jan,
	year = {2013},
	pages = {e53232},
}

@article{dhooghe_sulphur_2013,
	title = {Sulphur limitation provokes physiological and leaf proteome changes in oilseed rape that lead to perturbation of sulphur, carbon and oxidative metabolisms},
	volume = {13},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-13-23},
	doi = {10/gbcv4c},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {D’Hooghe, Philippe and Escamez, Sacha and Trouverie, Jacques and Avice, Jean-Christophe},
	year = {2013},
	pages = {23},
}

@article{hedwall_can_2013,
	title = {Can thinning alleviate negative effects of fertilization on boreal forest floor vegetation?},
	volume = {310},
	issn = {03781127},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378112713005677},
	doi = {10/f236wd},
	language = {en},
	urldate = {2021-06-08},
	journal = {Forest Ecology and Management},
	author = {Hedwall, P.-O. and Strengbom, J. and Nordin, A.},
	month = dec,
	year = {2013},
	pages = {382--392},
}