@article{merelo_regulation_2016,
	title = {Regulation of {MIR165}/166 by class {II} and class {III} homeodomain leucine zipper proteins establishes leaf polarity},
	volume = {113},
	url = {https://www.pnas.org/doi/10.1073/pnas.1516110113},
	doi = {10.1073/pnas.1516110113},
	abstract = {A defining feature of plant leaves is their flattened shape. This shape depends on an antagonism between the genes that specify adaxial (top) and abaxial (bottom) tissue identity; however, the molecular nature of this antagonism remains poorly understood. Class III homeodomain leucine zipper (HD-ZIP) transcription factors are key mediators in the regulation of adaxial–abaxial patterning. Their expression is restricted adaxially during early development by the abaxially expressed microRNA (MIR)165/166, yet the mechanism that restricts MIR165/166 expression to abaxial leaf tissues remains unknown. Here, we show that class III and class II HD-ZIP proteins act together to repress MIR165/166 via a conserved cis-element in their promoters. Organ morphology and tissue patterning in plants, therefore, depend on a bidirectional repressive circuit involving a set of miRNAs and its targets.},
	number = {42},
	urldate = {2022-11-30},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Merelo, Paz and Ram, Hathi and Pia Caggiano, Monica and Ohno, Carolyn and Ott, Felix and Straub, Daniel and Graeff, Moritz and Cho, Seok Keun and Yang, Seong Wook and Wenkel, Stephan and Heisler, Marcus G.},
	month = oct,
	year = {2016},
	pages = {11973--11978},
}

A defining feature of plant leaves is their flattened shape. This shape depends on an antagonism between the genes that specify adaxial (top) and abaxial (bottom) tissue identity; however, the molecular nature of this antagonism remains poorly understood. Class III homeodomain leucine zipper (HD-ZIP) transcription factors are key mediators in the regulation of adaxial–abaxial patterning. Their expression is restricted adaxially during early development by the abaxially expressed microRNA (MIR)165/166, yet the mechanism that restricts MIR165/166 expression to abaxial leaf tissues remains unknown. Here, we show that class III and class II HD-ZIP proteins act together to repress MIR165/166 via a conserved cis-element in their promoters. Organ morphology and tissue patterning in plants, therefore, depend on a bidirectional repressive circuit involving a set of miRNAs and its targets.

@article{graeff_microprotein-mediated_2016,
	title = {{MicroProtein}-{Mediated} {Recruitment} of {CONSTANS} into a {TOPLESS} {Trimeric} {Complex} {Represses} {Flowering} in {Arabidopsis}},
	volume = {12},
	issn = {1553-7404},
	url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005959},
	doi = {10.1371/journal.pgen.1005959},
	abstract = {MicroProteins are short, single domain proteins that act by sequestering larger, multi-domain proteins into non-functional complexes. MicroProteins have been identified in plants and animals, where they are mostly involved in the regulation of developmental processes. Here we show that two Arabidopsis thaliana microProteins, miP1a and miP1b, physically interact with CONSTANS (CO) a potent regulator of flowering time. The miP1a/b-type microProteins evolved in dicotyledonous plants and have an additional carboxy-terminal PF(V/L)FL motif. This motif enables miP1a/b microProteins to interact with TOPLESS/TOPLESS-RELATED (TPL/TPR) proteins. Interaction of CO with miP1a/b/TPL causes late flowering due to a failure in the induction of FLOWERING LOCUS T (FT) expression under inductive long day conditions. Both miP1a and miP1b are expressed in vascular tissue, where CO and FT are active. Genetically, miP1a/b act upstream of CO thus our findings unravel a novel layer of flowering time regulation via microProtein-inhibition.},
	language = {en},
	number = {3},
	urldate = {2022-11-30},
	journal = {PLOS Genetics},
	author = {Graeff, Moritz and Straub, Daniel and Eguen, Tenai and Dolde, Ulla and Rodrigues, Vandasue and Brandt, Ronny and Wenkel, Stephan},
	month = mar,
	year = {2016},
	keywords = {Arabidopsis thaliana, Flowering plants, Gene expression, Genetically modified plants, Leaves, Protein domains, Transcription factors, Yeast},
	pages = {e1005959},
}

MicroProteins are short, single domain proteins that act by sequestering larger, multi-domain proteins into non-functional complexes. MicroProteins have been identified in plants and animals, where they are mostly involved in the regulation of developmental processes. Here we show that two Arabidopsis thaliana microProteins, miP1a and miP1b, physically interact with CONSTANS (CO) a potent regulator of flowering time. The miP1a/b-type microProteins evolved in dicotyledonous plants and have an additional carboxy-terminal PF(V/L)FL motif. This motif enables miP1a/b microProteins to interact with TOPLESS/TOPLESS-RELATED (TPL/TPR) proteins. Interaction of CO with miP1a/b/TPL causes late flowering due to a failure in the induction of FLOWERING LOCUS T (FT) expression under inductive long day conditions. Both miP1a and miP1b are expressed in vascular tissue, where CO and FT are active. Genetically, miP1a/b act upstream of CO thus our findings unravel a novel layer of flowering time regulation via microProtein-inhibition.

@article{marhavy_targeted_2016,
	title = {Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation},
	volume = {30},
	issn = {0890-9369, 1549-5477},
	url = {http://genesdev.cshlp.org/lookup/doi/10.1101/gad.276964.115},
	doi = {10.1101/gad.276964.115},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Genes \& Development},
	author = {Marhavý, Peter and Montesinos, Juan Carlos and Abuzeineh, Anas and Van Damme, Daniel and Vermeer, Joop E.M. and Duclercq, Jerôme and Rakusová, Hana and Nováková, Petra and Friml, Jiři and Geldner, Niko and Benková, Eva},
	month = feb,
	year = {2016},
	keywords = {auxin, lateral root organogenesis, mechanical forces, meristem proliferation activity},
	pages = {471--483},
}

@article{wang_natural_2016,
	title = {Natural {Selection} and {Recombination} {Rate} {Variation} {Shape} {Nucleotide} {Polymorphism} {Across} the {Genomes} of {Three} {Related} {Populus} {Species}},
	volume = {202},
	issn = {1943-2631},
	url = {https://academic.oup.com/genetics/article/202/3/1185/5930198},
	doi = {10.1534/genetics.115.183152},
	abstract = {Abstract
            A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Genetics},
	author = {Wang, Jing and Street, Nathaniel R and Scofield, Douglas G and Ingvarsson, Pär K},
	month = mar,
	year = {2016},
	pages = {1185--1200},
}

Abstract A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.

@article{galletti_developing_2016,
	title = {Developing a ‘thick skin’: a paradoxical role for mechanical tension in maintaining epidermal integrity?},
	volume = {143},
	issn = {0950-1991},
	shorttitle = {Developing a ‘thick skin’},
	url = {https://doi.org/10.1242/dev.132837},
	doi = {10.1242/dev.132837},
	abstract = {Plant aerial epidermal tissues, like animal epithelia, act as load-bearing layers and hence play pivotal roles in development. The presence of tension in the epidermis has morphogenetic implications for organ shapes but it also constantly threatens the integrity of this tissue. Here, we explore the multi-scale relationship between tension and cell adhesion in the plant epidermis, and we examine how tensile stress perception may act as a regulatory input to preserve epidermal tissue integrity and thus normal morphogenesis. From this, we identify parallels between plant epidermal and animal epithelial tissues and highlight a list of unexplored questions for future research.},
	number = {18},
	urldate = {2021-10-14},
	journal = {Development},
	author = {Galletti, Roberta and Verger, Stéphane and Hamant, Olivier and Ingram, Gwyneth C.},
	month = sep,
	year = {2016},
	pages = {3249--3258},
}

Plant aerial epidermal tissues, like animal epithelia, act as load-bearing layers and hence play pivotal roles in development. The presence of tension in the epidermis has morphogenetic implications for organ shapes but it also constantly threatens the integrity of this tissue. Here, we explore the multi-scale relationship between tension and cell adhesion in the plant epidermis, and we examine how tensile stress perception may act as a regulatory input to preserve epidermal tissue integrity and thus normal morphogenesis. From this, we identify parallels between plant epidermal and animal epithelial tissues and highlight a list of unexplored questions for future research.

@incollection{john_wiley__sons_ltd_plant_2016,
	address = {Chichester, UK},
	title = {Plant {Circadian} {Rhythms}},
	isbn = {978-0-470-01590-2 978-0-470-01617-6},
	url = {http://doi.wiley.com/10.1002/9780470015902.a0020113.pub2},
	language = {en},
	urldate = {2021-06-07},
	booktitle = {{eLS}},
	publisher = {John Wiley \& Sons, Ltd},
	author = {McWatters, Harriet G and Eriksson, Maria E.},
	editor = {{John Wiley \& Sons Ltd}},
	month = may,
	year = {2016},
	doi = {10.1002/9780470015902.a0020113.pub2},
	pages = {1--10},
}

@article{noren_hsp90_2016,
	title = {{HSP90}, {ZTL}, {PRR5} and {HY5} integrate circadian and plastid signaling pathways to regulate {CBF} and {COR} expression.},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/171/2/1392-1406/6115310},
	doi = {10/f3rvjv},
	language = {en},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Noren, Louise and Kindgren, Peter and Stachula, Paulina and Ruhl, Mark and Eriksson, Maria E. and Hurry, Vaughan and Strand, Asa},
	month = apr,
	year = {2016},
	pages = {pp.00374.2016},
}

@article{cruz-santos_role_2016,
	title = {The {Role} of {microRNAs} in {Animal} {Cell} {Reprogramming}},
	volume = {25},
	issn = {1547-3287, 1557-8534},
	url = {https://www.liebertpub.com/doi/10.1089/scd.2015.0359},
	doi = {10/f3rw7p},
	language = {en},
	number = {14},
	urldate = {2021-06-07},
	journal = {Stem Cells and Development},
	author = {Cruz-Santos, María Concepción and Aragón-Raygoza, Alejandro and Espinal-Centeno, Annie and Arteaga-Vázquez, Mario and Cruz-Hernández, Andrés and Bakó, Laszlo and Cruz-Ramírez, Alfredo},
	month = jul,
	year = {2016},
	pages = {1035--1049},
}

@article{klocko_ft_2016,
	title = {{FT} overexpression induces precocious flowering and normal reproductive development in {Eucalyptus}},
	volume = {14},
	copyright = {© 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley \& Sons Ltd},
	issn = {1467-7652},
	url = {https://www.onlinelibrary.wiley.com/doi/abs/10.1111/pbi.12431},
	doi = {10/f78rxh},
	abstract = {Eucalyptus trees are among the most important species for industrial forestry worldwide. However, as with most forest trees, flowering does not begin for one to several years after planting which can limit the rate of conventional and molecular breeding. To speed flowering, we transformed a Eucalyptus grandis × urophylla hybrid (SP7) with a variety of constructs that enable overexpression of FLOWERING LOCUS T (FT). We found that FT expression led to very early flowering, with events showing floral buds within 1–5 months of transplanting to the glasshouse. The most rapid flowering was observed when the cauliflower mosaic virus 35S promoter was used to drive the Arabidopsis thaliana FT gene (AtFT). Early flowering was also observed with AtFT overexpression from a 409S ubiquitin promoter and under heat induction conditions with Populus trichocarpa FT1 (PtFT1) under control of a heat-shock promoter. Early flowering trees grew robustly, but exhibited a highly branched phenotype compared to the strong apical dominance of nonflowering transgenic and control trees. AtFT-induced flowers were morphologically normal and produced viable pollen grains and viable self- and cross-pollinated seeds. Many self-seedlings inherited AtFT and flowered early. FT overexpression-induced flowering in Eucalyptus may be a valuable means for accelerating breeding and genetic studies as the transgene can be easily segregated away in progeny, restoring normal growth and form.},
	language = {en},
	number = {2},
	urldate = {2021-06-21},
	journal = {Plant Biotechnology Journal},
	author = {Klocko, Amy L. and Ma, Cathleen and Robertson, Sarah and Esfandiari, Elahe and Nilsson, Ove and Strauss, Steven H.},
	year = {2016},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.12431},
	keywords = {Eucalypts, Flowering Locus T, breeding, forest biotechnology, genetic engineering, transgenic},
	pages = {808--819},
}

Eucalyptus trees are among the most important species for industrial forestry worldwide. However, as with most forest trees, flowering does not begin for one to several years after planting which can limit the rate of conventional and molecular breeding. To speed flowering, we transformed a Eucalyptus grandis × urophylla hybrid (SP7) with a variety of constructs that enable overexpression of FLOWERING LOCUS T (FT). We found that FT expression led to very early flowering, with events showing floral buds within 1–5 months of transplanting to the glasshouse. The most rapid flowering was observed when the cauliflower mosaic virus 35S promoter was used to drive the Arabidopsis thaliana FT gene (AtFT). Early flowering was also observed with AtFT overexpression from a 409S ubiquitin promoter and under heat induction conditions with Populus trichocarpa FT1 (PtFT1) under control of a heat-shock promoter. Early flowering trees grew robustly, but exhibited a highly branched phenotype compared to the strong apical dominance of nonflowering transgenic and control trees. AtFT-induced flowers were morphologically normal and produced viable pollen grains and viable self- and cross-pollinated seeds. Many self-seedlings inherited AtFT and flowered early. FT overexpression-induced flowering in Eucalyptus may be a valuable means for accelerating breeding and genetic studies as the transgene can be easily segregated away in progeny, restoring normal growth and form.

@article{bennett_connective_2016,
	title = {Connective {Auxin} {Transport} in the {Shoot} {Facilitates} {Communication} between {Shoot} {Apices}},
	volume = {14},
	issn = {1545-7885},
	url = {https://dx.plos.org/10.1371/journal.pbio.1002446},
	doi = {10/f3t29d},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {PLOS Biology},
	author = {Bennett, Tom and Hines, Geneviève and van Rongen, Martin and Waldie, Tanya and Sawchuk, Megan G. and Scarpella, Enrico and Ljung, Karin and Leyser, Ottoline},
	editor = {Reed, Jason},
	month = apr,
	year = {2016},
	pages = {e1002446},
}

@article{gardestrom_origin_2016,
	title = {The origin of cytosolic {ATP} in photosynthetic cells},
	volume = {157},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12455},
	doi = {10/f3rscd},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Gardeström, Per and Igamberdiev, Abir U.},
	month = jul,
	year = {2016},
	pages = {367--379},
}

@article{lien_atlantic_2016,
	title = {The {Atlantic} salmon genome provides insights into rediploidization},
	volume = {533},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/articles/nature17164},
	doi = {10/f3rv45},
	abstract = {Abstract
            
              The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (
              Salmo salar
              ), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.},
	language = {en},
	number = {7602},
	urldate = {2021-06-07},
	journal = {Nature},
	author = {Lien, Sigbjørn and Koop, Ben F. and Sandve, Simen R. and Miller, Jason R. and Kent, Matthew P. and Nome, Torfinn and Hvidsten, Torgeir R. and Leong, Jong S. and Minkley, David R. and Zimin, Aleksey and Grammes, Fabian and Grove, Harald and Gjuvsland, Arne and Walenz, Brian and Hermansen, Russell A. and von Schalburg, Kris and Rondeau, Eric B. and Di Genova, Alex and Samy, Jeevan K. A. and Olav Vik, Jon and Vigeland, Magnus D. and Caler, Lis and Grimholt, Unni and Jentoft, Sissel and Inge Våge, Dag and de Jong, Pieter and Moen, Thomas and Baranski, Matthew and Palti, Yniv and Smith, Douglas R. and Yorke, James A. and Nederbragt, Alexander J. and Tooming-Klunderud, Ave and Jakobsen, Kjetill S. and Jiang, Xuanting and Fan, Dingding and Hu, Yan and Liberles, David A. and Vidal, Rodrigo and Iturra, Patricia and Jones, Steven J. M. and Jonassen, Inge and Maass, Alejandro and Omholt, Stig W. and Davidson, William S.},
	month = may,
	year = {2016},
	pages = {200--205},
}

Abstract The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon ( Salmo salar ), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.

@article{smakowska_lack_2016,
	title = {Lack of {FTSH4} {Protease} {Affects} {Protein} {Carbonylation}, {Mitochondrial} {Morphology}, and {Phospholipid} {Content} in {Mitochondria} of {Arabidopsis}: {New} {Insights} into a {Complex} {Interplay}},
	volume = {171},
	issn = {0032-0889, 1532-2548},
	shorttitle = {Lack of {FTSH4} {Protease} {Affects} {Protein} {Carbonylation}, {Mitochondrial} {Morphology}, and {Phospholipid} {Content} in {Mitochondria} of {Arabidopsis}},
	url = {https://academic.oup.com/plphys/article/171/4/2516-2535/6115245},
	doi = {10/f3r2fs},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Smakowska, Elwira and Skibior-Blaszczyk, Renata and Czarna, Malgorzata and Kolodziejczak, Marta and Kwasniak-Owczarek, Malgorzata and Parys, Katarzyna and Funk, Christiane and Janska, Hanna},
	month = aug,
	year = {2016},
	pages = {2516--2535},
}

@article{schiffthaler_training_2016,
	title = {Training in {High}-{Throughput} {Sequencing}: {Common} {Guidelines} to {Enable} {Material} {Sharing}, {Dissemination}, and {Reusability}},
	volume = {12},
	issn = {1553-7358},
	shorttitle = {Training in {High}-{Throughput} {Sequencing}},
	url = {https://dx.plos.org/10.1371/journal.pcbi.1004937},
	doi = {10/f3sd3h},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {PLOS Computational Biology},
	author = {Schiffthaler, Bastian and Kostadima, Myrto and {NGS Trainer Consortium} and Delhomme, Nicolas and Rustici, Gabriella},
	editor = {Ouellette, Francis},
	month = jun,
	year = {2016},
	pages = {e1004937},
}

@article{von_sydow_psby_2016,
	title = {The {PsbY} protein of {Arabidopsis} {Photosystem} {II} is important for the redox control of cytochrome b 559},
	volume = {1857},
	issn = {00052728},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0005272816305369},
	doi = {10/f3rzx4},
	language = {en},
	number = {9},
	urldate = {2021-06-07},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {von Sydow, Lotta and Schwenkert, Serena and Meurer, Jörg and Funk, Christiane and Mamedov, Fikret and Schröder, Wolfgang P.},
	month = sep,
	year = {2016},
	pages = {1524--1533},
}

@article{hermansen_extracting_2016,
	title = {Extracting functional trends from whole genome duplication events using comparative genomics},
	volume = {18},
	issn = {1480-9222, 1480-9222},
	url = {http://biologicalproceduresonline.biomedcentral.com/articles/10.1186/s12575-016-0041-2},
	doi = {10/f3r25q},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Biological Procedures Online},
	author = {Hermansen, Russell A. and Hvidsten, Torgeir R. and Sandve, Simen Rød and Liberles, David A.},
	month = dec,
	year = {2016},
	pages = {11},
}

@article{sayou_sam_2016,
	title = {A {SAM} oligomerization domain shapes the genomic binding landscape of the {LEAFY} transcription factor},
	volume = {7},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/ncomms11222},
	doi = {10/f3tdv9},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Sayou, Camille and Nanao, Max H. and Jamin, Marc and Posé, David and Thévenon, Emmanuel and Grégoire, Laura and Tichtinsky, Gabrielle and Denay, Grégoire and Ott, Felix and Peirats Llobet, Marta and Schmid, Markus and Dumas, Renaud and Parcy, François},
	month = sep,
	year = {2016},
	pages = {11222},
}

@article{cheregi_insights_2016,
	title = {Insights into the {Cyanobacterial} {Deg}/{HtrA} {Proteases}},
	volume = {7},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2016.00694/full},
	doi = {10/f3rrmt},
	abstract = {Proteins are the main machinery for all living processes in a cell; they provide structural elements, regulate biochemical reactions as enzymes, and are the interface to the outside as receptors and transporters. Like any other machinery proteins have to be assembled correctly and need maintenance after damage, e.g. caused by changes in environmental conditions, genetic mutations, and limitations in the availability of cofactors. Proteases and chaperones help in repair, assembly, and folding of damaged and misfolded protein complexes cost-effective, with low energy investment compared with neo-synthesis. Despite their importance for viability, the specific biological role of most proteases in vivo is largely unknown. Deg/HtrA proteases, a family of serine-type ATP-independent proteases, have been shown in higher plants to be involved in the degradation of the Photosystem II reaction center protein D1. The objective of this review is to highlight the structure and function of their cyanobacterial orthologues. Homology modeling was used to find specific features of the Deg/HtrA proteases of Synechocystis sp. PCC 6803. Based on the available data concerning their location and their physiological substrates we conclude that these Deg proteases not only have important housekeeping and chaperone functions within the cell, but also are needed for remodeling the cell exterior.},
	language = {English},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Cheregi, Otilia and Wagner, Raik and Funk, Christiane},
	year = {2016},
	note = {Publisher: Frontiers},
	keywords = {Chaperone, Cyanobacteria, PSII degradation, Serine Proteases, cell surface, phylogeny, secretion},
}

Proteins are the main machinery for all living processes in a cell; they provide structural elements, regulate biochemical reactions as enzymes, and are the interface to the outside as receptors and transporters. Like any other machinery proteins have to be assembled correctly and need maintenance after damage, e.g. caused by changes in environmental conditions, genetic mutations, and limitations in the availability of cofactors. Proteases and chaperones help in repair, assembly, and folding of damaged and misfolded protein complexes cost-effective, with low energy investment compared with neo-synthesis. Despite their importance for viability, the specific biological role of most proteases in vivo is largely unknown. Deg/HtrA proteases, a family of serine-type ATP-independent proteases, have been shown in higher plants to be involved in the degradation of the Photosystem II reaction center protein D1. The objective of this review is to highlight the structure and function of their cyanobacterial orthologues. Homology modeling was used to find specific features of the Deg/HtrA proteases of Synechocystis sp. PCC 6803. Based on the available data concerning their location and their physiological substrates we conclude that these Deg proteases not only have important housekeeping and chaperone functions within the cell, but also are needed for remodeling the cell exterior.

@article{zheng_local_2016,
	title = {Local auxin metabolism regulates environment-induced hypocotyl elongation},
	volume = {2},
	issn = {2055-0278},
	url = {http://www.nature.com/articles/nplants201625},
	doi = {10/f3t37r},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Nature Plants},
	author = {Zheng, Zuyu and Guo, Yongxia and Novák, Ondřej and Chen, William and Ljung, Karin and Noel, Joseph P. and Chory, Joanne},
	month = apr,
	year = {2016},
	pages = {16025},
}

@article{dejonghe_mitochondrial_2016,
	title = {Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification},
	volume = {7},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/ncomms11710},
	doi = {10/f3r3j2},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Dejonghe, Wim and Kuenen, Sabine and Mylle, Evelien and Vasileva, Mina and Keech, Olivier and Viotti, Corrado and Swerts, Jef and Fendrych, Matyáš and Ortiz-Morea, Fausto Andres and Mishev, Kiril and Delang, Simon and Scholl, Stefan and Zarza, Xavier and Heilmann, Mareike and Kourelis, Jiorgos and Kasprowicz, Jaroslaw and Nguyen, Le Son Long and Drozdzecki, Andrzej and Van Houtte, Isabelle and Szatmári, Anna-Mária and Majda, Mateusz and Baisa, Gary and Bednarek, Sebastian York and Robert, Stéphanie and Audenaert, Dominique and Testerink, Christa and Munnik, Teun and Van Damme, Daniël and Heilmann, Ingo and Schumacher, Karin and Winne, Johan and Friml, Jiří and Verstreken, Patrik and Russinova, Eugenia},
	month = sep,
	year = {2016},
	pages = {11710},
}

@article{pfeiffer_integration_2016,
	title = {Integration of light and metabolic signals for stem cell activation at the shoot apical meristem},
	volume = {5},
	issn = {2050-084X},
	url = {https://elifesciences.org/articles/17023},
	doi = {10/f3r4bk},
	abstract = {A major feature of embryogenesis is the specification of stem cell systems, but in contrast to the situation in most animals, plant stem cells remain quiescent until the postembryonic phase of development. Here, we dissect how light and metabolic signals are integrated to overcome stem cell dormancy at the shoot apical meristem. We show on the one hand that light is able to activate expression of the stem cell inducer WUSCHEL independently of photosynthesis and that this likely involves inter-regional cytokinin signaling. Metabolic signals, on the other hand, are transduced to the meristem through activation of the TARGET OF RAPAMYCIN (TOR) kinase. Surprisingly, TOR is also required for light signal dependent stem cell activation. Thus, the TOR kinase acts as a central integrator of light and metabolic signals and a key regulator of stem cell activation at the shoot apex.
          , 
            Plants are able to grow and develop throughout their lives thanks to groups of stem cells at the tips of their shoots and roots, which can constantly divide to produce new cells. Energy captured from sunlight during a process called photosynthesis is the main source of energy for most plants. Therefore, the amount and quality of light in the environment has a big influence on how plants grow and develop. An enzyme called TOR kinase can sense energy levels in animal cells and regulate many processes including growth and cell division. Plants also have a TOR kinase, but it is less clear if it plays the same role in plants, and whether it can respond to light.
            Plant stem cells only start to divide after the seed germinates. In shoots, a protein called WUSCHEL is required to maintain stem cells in an active state. Here, Pfeiffer et al. studied how shoot stem cells are activated in response to environmental signals in a plant known as Arabidopsis. The experiments show that light is able to activate the production of WUSCHEL independently of photosynthesis via a signal pathway that depends on TOR kinase. The stem cells do not directly sense light; instead other cells detect the light and relay the information to the stem cells with the help of a hormone called cytokinin.
            Further experiments show that information about energy levels in cells is relayed via another signal pathway that also involves the TOR kinase. Therefore, Pfeiffer et al.’s findings suggest that the activation of TOR by light allows plant cells to anticipate how much energy will be available and efficiently tune their growth and development to cope with the environmental conditions. Future challenges are to understand how TOR kinase is regulated by light signals and how this enzyme is able to act on WUSCHEL to trigger stem cell division.},
	language = {en},
	urldate = {2021-06-07},
	journal = {eLife},
	author = {Pfeiffer, Anne and Janocha, Denis and Dong, Yihan and Medzihradszky, Anna and Schöne, Stefanie and Daum, Gabor and Suzaki, Takuya and Forner, Joachim and Langenecker, Tobias and Rempel, Eugen and Schmid, Markus and Wirtz, Markus and Hell, Rüdiger and Lohmann, Jan U},
	month = jul,
	year = {2016},
	pages = {e17023},
}

A major feature of embryogenesis is the specification of stem cell systems, but in contrast to the situation in most animals, plant stem cells remain quiescent until the postembryonic phase of development. Here, we dissect how light and metabolic signals are integrated to overcome stem cell dormancy at the shoot apical meristem. We show on the one hand that light is able to activate expression of the stem cell inducer WUSCHEL independently of photosynthesis and that this likely involves inter-regional cytokinin signaling. Metabolic signals, on the other hand, are transduced to the meristem through activation of the TARGET OF RAPAMYCIN (TOR) kinase. Surprisingly, TOR is also required for light signal dependent stem cell activation. Thus, the TOR kinase acts as a central integrator of light and metabolic signals and a key regulator of stem cell activation at the shoot apex. , Plants are able to grow and develop throughout their lives thanks to groups of stem cells at the tips of their shoots and roots, which can constantly divide to produce new cells. Energy captured from sunlight during a process called photosynthesis is the main source of energy for most plants. Therefore, the amount and quality of light in the environment has a big influence on how plants grow and develop. An enzyme called TOR kinase can sense energy levels in animal cells and regulate many processes including growth and cell division. Plants also have a TOR kinase, but it is less clear if it plays the same role in plants, and whether it can respond to light. Plant stem cells only start to divide after the seed germinates. In shoots, a protein called WUSCHEL is required to maintain stem cells in an active state. Here, Pfeiffer et al. studied how shoot stem cells are activated in response to environmental signals in a plant known as Arabidopsis. The experiments show that light is able to activate the production of WUSCHEL independently of photosynthesis via a signal pathway that depends on TOR kinase. The stem cells do not directly sense light; instead other cells detect the light and relay the information to the stem cells with the help of a hormone called cytokinin. Further experiments show that information about energy levels in cells is relayed via another signal pathway that also involves the TOR kinase. Therefore, Pfeiffer et al.’s findings suggest that the activation of TOR by light allows plant cells to anticipate how much energy will be available and efficiently tune their growth and development to cope with the environmental conditions. Future challenges are to understand how TOR kinase is regulated by light signals and how this enzyme is able to act on WUSCHEL to trigger stem cell division.

@article{noren_circadian_2016,
	title = {Circadian and {Plastid} {Signaling} {Pathways} {Are} {Integrated} to {Ensure} {Correct} {Expression} of the {CBF} and {COR} {Genes} during {Photoperiodic} {Growth}},
	volume = {171},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.16.00374},
	doi = {10/f3rvjv},
	abstract = {The circadian clock synchronizes a wide range of biological processes with the day/night cycle, and correct circadian regulation is essential for photosynthetic activity and plant growth. We describe here a mechanism where a plastid signal converges with the circadian clock to fine-tune the regulation of nuclear gene expression in Arabidopsis (Arabidopsis thaliana). Diurnal oscillations of tetrapyrrole levels in the chloroplasts contribute to the regulation of the nucleus-encoded transcription factors C-REPEAT BINDING FACTORS (CBFs). The plastid signal triggered by tetrapyrrole accumulation inhibits the activity of cytosolic HEAT SHOCK PROTEIN90 and, as a consequence, the maturation and stability of the clock component ZEITLUPE (ZTL). ZTL negatively regulates the transcription factor LONG HYPOCOTYL5 (HY5) and PSEUDO-RESPONSE REGULATOR5 (PRR5). Thus, low levels of ZTL result in a HY5- and PRR5-mediated repression of CBF3 and PRR5-mediated repression of CBF1 and CBF2 expression. The plastid signal thereby contributes to the rhythm of CBF expression and the downstream COLD RESPONSIVE expression during day/night cycles. These findings provide insight into how plastid signals converge with, and impact upon, the activity of well-defined clock components involved in circadian regulation.},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Norén, Louise and Kindgren, Peter and Stachula, Paulina and Rühl, Mark and Eriksson, Maria E. and Hurry, Vaughan and Strand, Åsa},
	month = jun,
	year = {2016},
	pages = {1392--1406},
}

The circadian clock synchronizes a wide range of biological processes with the day/night cycle, and correct circadian regulation is essential for photosynthetic activity and plant growth. We describe here a mechanism where a plastid signal converges with the circadian clock to fine-tune the regulation of nuclear gene expression in Arabidopsis (Arabidopsis thaliana). Diurnal oscillations of tetrapyrrole levels in the chloroplasts contribute to the regulation of the nucleus-encoded transcription factors C-REPEAT BINDING FACTORS (CBFs). The plastid signal triggered by tetrapyrrole accumulation inhibits the activity of cytosolic HEAT SHOCK PROTEIN90 and, as a consequence, the maturation and stability of the clock component ZEITLUPE (ZTL). ZTL negatively regulates the transcription factor LONG HYPOCOTYL5 (HY5) and PSEUDO-RESPONSE REGULATOR5 (PRR5). Thus, low levels of ZTL result in a HY5- and PRR5-mediated repression of CBF3 and PRR5-mediated repression of CBF1 and CBF2 expression. The plastid signal thereby contributes to the rhythm of CBF expression and the downstream COLD RESPONSIVE expression during day/night cycles. These findings provide insight into how plastid signals converge with, and impact upon, the activity of well-defined clock components involved in circadian regulation.

@article{wagner_deletion_2016,
	title = {Deletion of {FtsH11} protease has impact on chloroplast structure and function in \textit{{Arabidopsis} thaliana} when grown under continuous light: {Impact} of {FtsH11} in \textit{{Arabidopsis} thaliana}},
	volume = {39},
	issn = {01407791},
	shorttitle = {Deletion of {FtsH11} protease has impact on chloroplast structure and function in \textit{{Arabidopsis} thaliana} when grown under continuous light},
	url = {http://doi.wiley.com/10.1111/pce.12808},
	doi = {10/f3rwgc},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Wagner, Raik and von Sydow, Lotta and Aigner, Harald and Netotea, Sergiu and Brugière, Sabine and Sjögren, Lars and Ferro, Myriam and Clarke, Adrian and Funk, Christiane},
	month = nov,
	year = {2016},
	pages = {2530--2544},
}

@article{immanen_cytokinin_2016,
	title = {Cytokinin and {Auxin} {Display} {Distinct} but {Interconnected} {Distribution} and {Signaling} {Profiles} to {Stimulate} {Cambial} {Activity}},
	volume = {26},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982216305504},
	doi = {10/f82nd5},
	language = {en},
	number = {15},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Immanen, Juha and Nieminen, Kaisa and Smolander, Olli-Pekka and Kojima, Mikiko and Alonso Serra, Juan and Koskinen, Patrik and Zhang, Jing and Elo, Annakaisa and Mähönen, Ari Pekka and Street, Nathaniel and Bhalerao, Rishikesh P. and Paulin, Lars and Auvinen, Petri and Sakakibara, Hitoshi and Helariutta, Ykä},
	month = aug,
	year = {2016},
	pages = {1990--1997},
}

@article{eyer_24-d_2016,
	title = {2,4-{D} and {IAA} {Amino} {Acid} {Conjugates} {Show} {Distinct} {Metabolism} in {Arabidopsis}},
	volume = {11},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0159269},
	doi = {10/gbpkvw},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Eyer, Luděk and Vain, Thomas and Pařízková, Barbora and Oklestkova, Jana and Barbez, Elke and Kozubíková, Hana and Pospíšil, Tomáš and Wierzbicka, Roksana and Kleine-Vehn, Jürgen and Fránek, Milan and Strnad, Miroslav and Robert, Stéphanie and Novak, Ondrej},
	editor = {Rahman, Abidur},
	month = jul,
	year = {2016},
	pages = {e0159269},
}

@article{budzinski_seasonal_2016,
	title = {Seasonal {Variation} of {Carbon} {Metabolism} in the {Cambial} {Zone} of {Eucalyptus} grandis},
	volume = {7},
	issn = {1664-462X},
	url = {http://journal.frontiersin.org/Article/10.3389/fpls.2016.00932/abstract},
	doi = {10/f3vjsv},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Budzinski, Ilara G. F. and Moon, David H. and Lindén, Pernilla and Moritz, Thomas and Labate, Carlos A.},
	month = jun,
	year = {2016},
}

@article{budzinski_integrated_2016,
	title = {Integrated analysis of gene expression from carbon metabolism, proteome and metabolome, reveals altered primary metabolism in {Eucalyptus} grandis bark, in response to seasonal variation},
	volume = {16},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-016-0839-8},
	doi = {10/f3vbf9},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Plant Biology},
	author = {Budzinski, Ilara Gabriela Frasson and Moon, David H. and Morosini, Júlia Silva and Lindén, Pernilla and Bragatto, Juliano and Moritz, Thomaz and Labate, Carlos Alberto},
	month = dec,
	year = {2016},
	pages = {149},
}

@article{procko_epidermis_2016,
	title = {The epidermis coordinates auxin-induced stem growth in response to shade},
	volume = {30},
	issn = {0890-9369, 1549-5477},
	url = {http://genesdev.cshlp.org/lookup/doi/10.1101/gad.283234.116},
	doi = {10/f3t2tn},
	language = {en},
	number = {13},
	urldate = {2021-06-07},
	journal = {Genes \& Development},
	author = {Procko, Carl and Burko, Yogev and Jaillais, Yvon and Ljung, Karin and Long, Jeff A. and Chory, Joanne},
	month = jul,
	year = {2016},
	pages = {1529--1541},
}

@article{malm_metabolomic_2016,
	title = {Metabolomic {Quality} {Assessment} of {EDTA} {Plasma} and {Serum} {Samples}},
	volume = {14},
	issn = {1947-5535, 1947-5543},
	url = {http://www.liebertpub.com/doi/10.1089/bio.2015.0092},
	doi = {10/f3tq4s},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Biopreservation and Biobanking},
	author = {Malm, Linus and Tybring, Gunnel and Moritz, Thomas and Landin, Britta and Galli, Joakim},
	month = oct,
	year = {2016},
	pages = {416--423},
}

@article{verger_cell_2016,
	title = {Cell adhesion in plants is under the control of putative {O}-fucosyltransferases},
	volume = {143},
	issn = {0950-1991},
	url = {https://doi.org/10.1242/dev.132308},
	doi = {10/f9n5bb},
	abstract = {Cell-to-cell adhesion in plants is mediated by the cell wall and the presence of a pectin-rich middle lamella. However, we know very little about how the plant actually controls and maintains cell adhesion during growth and development and how it deals with the dynamic cell wall remodeling that takes place. Here we investigate the molecular mechanisms that control cell adhesion in plants. We carried out a genetic suppressor screen and a genetic analysis of cell adhesion-defective Arabidopsis thaliana mutants. We identified a genetic suppressor of a cell adhesion defect affecting a putative O-fucosyltransferase. Furthermore, we show that the state of cell adhesion is not directly linked with pectin content in the cell wall but instead is associated with altered pectin-related signaling. Our results suggest that cell adhesion is under the control of a feedback signal from the state of the pectin in the cell wall. Such a mechanism could be necessary for the control and maintenance of cell adhesion during growth and development.},
	number = {14},
	urldate = {2021-06-07},
	journal = {Development},
	author = {Verger, Stéphane and Chabout, Salem and Gineau, Emilie and Mouille, Grégory},
	month = jul,
	year = {2016},
	pages = {2536--2540},
}

Cell-to-cell adhesion in plants is mediated by the cell wall and the presence of a pectin-rich middle lamella. However, we know very little about how the plant actually controls and maintains cell adhesion during growth and development and how it deals with the dynamic cell wall remodeling that takes place. Here we investigate the molecular mechanisms that control cell adhesion in plants. We carried out a genetic suppressor screen and a genetic analysis of cell adhesion-defective Arabidopsis thaliana mutants. We identified a genetic suppressor of a cell adhesion defect affecting a putative O-fucosyltransferase. Furthermore, we show that the state of cell adhesion is not directly linked with pectin content in the cell wall but instead is associated with altered pectin-related signaling. Our results suggest that cell adhesion is under the control of a feedback signal from the state of the pectin in the cell wall. Such a mechanism could be necessary for the control and maintenance of cell adhesion during growth and development.

@article{peviani_phylogeny_2016,
	title = {The phylogeny of {C}/{S1} {bZIP} transcription factors reveals a shared algal ancestry and the pre-angiosperm translational regulation of {S1} transcripts},
	volume = {6},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/srep30444},
	doi = {10/f3sc79},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Peviani, Alessia and Lastdrager, Jeroen and Hanson, Johannes and Snel, Berend},
	month = jul,
	year = {2016},
	pages = {30444},
}

@article{nukarinen_quantitative_2016,
	title = {Quantitative phosphoproteomics reveals the role of the {AMPK} plant ortholog {SnRK1} as a metabolic master regulator under energy deprivation},
	volume = {6},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/srep31697},
	doi = {10/f3rwtq},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Nukarinen, Ella and Nägele, Thomas and Pedrotti, Lorenzo and Wurzinger, Bernhard and Mair, Andrea and Landgraf, Ramona and Börnke, Frederik and Hanson, Johannes and Teige, Markus and Baena-Gonzalez, Elena and Dröge-Laser, Wolfgang and Weckwerth, Wolfram},
	month = aug,
	year = {2016},
	pages = {31697},
}

@article{pacheco-villalobos_effects_2016,
	title = {The {Effects} of {High} {Steady} {State} {Auxin} {Levels} on {Root} {Cell} {Elongation} in {Brachypodium}},
	volume = {28},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/28/5/1009-1024/6098461},
	doi = {10/bhng},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {Pacheco-Villalobos, David and Díaz-Moreno, Sara M. and van der Schuren, Alja and Tamaki, Takayuki and Kang, Yeon Hee and Gujas, Bojan and Novak, Ondrej and Jaspert, Nina and Li, Zhenni and Wolf, Sebastian and Oecking, Claudia and Ljung, Karin and Bulone, Vincent and Hardtke, Christian S.},
	month = may,
	year = {2016},
	pages = {1009--1024},
}

@article{ingvarsson_towards_2016,
	title = {Towards integration of population and comparative genomics in forest trees},
	volume = {212},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.14153},
	doi = {10/f3tpmx},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Ingvarsson, Pär K. and Hvidsten, Torgeir R. and Street, Nathaniel R.},
	month = oct,
	year = {2016},
	pages = {338--344},
}

@article{maaroufi_chronic_2016,
	title = {Chronic {Nitrogen} {Deposition} {Has} a {Minor} {Effect} on the {Quantity} and {Quality} of {Aboveground} {Litter} in a {Boreal} {Forest}},
	volume = {11},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0162086},
	doi = {10/f3tbg7},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Maaroufi, Nadia I. and Nordin, Annika and Palmqvist, Kristin and Gundale, Michael J.},
	editor = {BassiriRad, Hormoz},
	month = aug,
	year = {2016},
	pages = {e0162086},
}

@article{kudahettige_nilsson_adaptability_2016,
	title = {Adaptability of {Trametes} versicolor to the lignocellulosic inhibitors furfural, {HMF}, phenol and levulinic acid during ethanol fermentation},
	volume = {90},
	issn = {09619534},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0961953416300927},
	doi = {10/f3pk4h},
	language = {en},
	urldate = {2021-06-07},
	journal = {Biomass and Bioenergy},
	author = {Kudahettige Nilsson, Rasika L. and Holmgren, Marie and Madavi, Batol and Nilsson, Robert T. and Sellstedt, Anita},
	month = jul,
	year = {2016},
	pages = {95--100},
}

@article{porco_dioxygenase-encoding_2016,
	title = {Dioxygenase-encoding \textit{{AtDAO1}} gene controls {IAA} oxidation and homeostasis in \textit{{Arabidopsis}}},
	volume = {113},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1604375113},
	doi = {10/f3t58q},
	abstract = {Auxin represents a key signal in plants, regulating almost every aspect of their growth and development. Major breakthroughs have been made dissecting the molecular basis of auxin transport, perception, and response. In contrast, how plants control the metabolism and homeostasis of the major form of auxin in plants, indole-3-acetic acid (IAA), remains unclear. In this paper, we initially describe the function of the
              Arabidopsis thaliana
              gene
              DIOXYGENASE FOR AUXIN OXIDATION 1
              (
              AtDAO1
              ). Transcriptional and translational reporter lines revealed that
              AtDAO1
              encodes a highly root-expressed, cytoplasmically localized IAA oxidase. Stable isotope-labeled IAA feeding studies of loss and gain of function
              AtDAO1
              lines showed that this oxidase represents the major regulator of auxin degradation to 2-oxoindole-3-acetic acid (oxIAA) in
              Arabidopsis
              . Surprisingly,
              AtDAO1
              loss and gain of function lines exhibited relatively subtle auxin-related phenotypes, such as altered root hair length. Metabolite profiling of mutant lines revealed that disrupting
              AtDAO1
              regulation resulted in major changes in steady-state levels of oxIAA and IAA conjugates but not IAA. Hence, IAA conjugation and catabolism seem to regulate auxin levels in
              Arabidopsis
              in a highly redundant manner. We observed that transcripts of
              AtDOA1
              IAA oxidase and
              GH3
              IAA-conjugating enzymes are auxin-inducible, providing a molecular basis for their observed functional redundancy. We conclude that the
              AtDAO1
              gene plays a key role regulating auxin homeostasis in
              Arabidopsis
              , acting in concert with
              GH3
              genes, to maintain auxin concentration at optimal levels for plant growth and development.},
	language = {en},
	number = {39},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Porco, Silvana and Pěnčík, Aleš and Rashed, Afaf and Voß, Ute and Casanova-Sáez, Rubén and Bishopp, Anthony and Golebiowska, Agata and Bhosale, Rahul and Swarup, Ranjan and Swarup, Kamal and Peňáková, Pavlína and Novák, Ondřej and Staswick, Paul and Hedden, Peter and Phillips, Andrew L. and Vissenberg, Kris and Bennett, Malcolm J. and Ljung, Karin},
	month = sep,
	year = {2016},
	pages = {11016--11021},
}

Auxin represents a key signal in plants, regulating almost every aspect of their growth and development. Major breakthroughs have been made dissecting the molecular basis of auxin transport, perception, and response. In contrast, how plants control the metabolism and homeostasis of the major form of auxin in plants, indole-3-acetic acid (IAA), remains unclear. In this paper, we initially describe the function of the Arabidopsis thaliana gene DIOXYGENASE FOR AUXIN OXIDATION 1 ( AtDAO1 ). Transcriptional and translational reporter lines revealed that AtDAO1 encodes a highly root-expressed, cytoplasmically localized IAA oxidase. Stable isotope-labeled IAA feeding studies of loss and gain of function AtDAO1 lines showed that this oxidase represents the major regulator of auxin degradation to 2-oxoindole-3-acetic acid (oxIAA) in Arabidopsis . Surprisingly, AtDAO1 loss and gain of function lines exhibited relatively subtle auxin-related phenotypes, such as altered root hair length. Metabolite profiling of mutant lines revealed that disrupting AtDAO1 regulation resulted in major changes in steady-state levels of oxIAA and IAA conjugates but not IAA. Hence, IAA conjugation and catabolism seem to regulate auxin levels in Arabidopsis in a highly redundant manner. We observed that transcripts of AtDOA1 IAA oxidase and GH3 IAA-conjugating enzymes are auxin-inducible, providing a molecular basis for their observed functional redundancy. We conclude that the AtDAO1 gene plays a key role regulating auxin homeostasis in Arabidopsis , acting in concert with GH3 genes, to maintain auxin concentration at optimal levels for plant growth and development.

@article{van_aken_mitochondrial_2016,
	title = {Mitochondrial and {Chloroplast} {Stress} {Responses} {Are} {Modulated} in {Distinct} {Touch} and {Chemical} {Inhibition} {Phases}},
	volume = {171},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/171/3/2150-2165/6115508},
	doi = {10/f3rznf},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Van Aken, Olivier and De Clercq, Inge and Ivanova, Aneta and Law, Simon R. and Van Breusegem, Frank and Millar, A. Harvey and Whelan, James},
	month = jul,
	year = {2016},
	pages = {2150--2165},
}

@article{liebsch_darkinduced_2016,
	title = {Dark‐induced leaf senescence: new insights into a complex light‐dependent regulatory pathway},
	volume = {212},
	issn = {0028-646X, 1469-8137},
	shorttitle = {Dark‐induced leaf senescence},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.14217},
	doi = {10/f3trh7},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Liebsch, Daniela and Keech, Olivier},
	month = nov,
	year = {2016},
	pages = {563--570},
}

@article{mellor_dynamic_2016,
	title = {Dynamic regulation of auxin oxidase and conjugating enzymes \textit{{AtDAO1}} and \textit{{GH3}} modulates auxin homeostasis},
	volume = {113},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1604458113},
	doi = {10/f3t6ch},
	abstract = {The hormone auxin is a key regulator of plant growth and development, and great progress has been made understanding auxin transport and signaling. Here, we show that auxin metabolism and homeostasis are also regulated in a complex manner. The principal auxin degradation pathways in
              Arabidopsis
              include oxidation by
              Arabidopsis thaliana
              gene
              DIOXYGENASE FOR AUXIN OXIDATION 1/2
              (AtDAO1/2) and conjugation by Gretchen Hagen3s (GH3s). Metabolic profiling of
              dao1-1
              root tissues revealed a 50\% decrease in the oxidation product 2-oxoindole-3-acetic acid (oxIAA) and increases in the conjugated forms indole-3-acetic acid aspartic acid (IAA-Asp) and indole-3-acetic acid glutamic acid (IAA-Glu) of 438- and 240-fold, respectively, whereas auxin remains close to the WT. By fitting parameter values to a mathematical model of these metabolic pathways, we show that, in addition to reduced oxidation, both auxin biosynthesis and conjugation are increased in
              dao1-1
              . Transcripts of
              AtDAO1
              and
              GH3
              genes increase in response to auxin over different timescales and concentration ranges. Including this regulation of
              AtDAO1
              and
              GH3
              in an extended model reveals that auxin oxidation is more important for auxin homoeostasis at lower hormone concentrations, whereas auxin conjugation is most significant at high auxin levels. Finally, embedding our homeostasis model in a multicellular simulation to assess the spatial effect of the
              dao1-1
              mutant shows that auxin increases in outer root tissues in agreement with the
              dao1-1
              mutant root hair phenotype. We conclude that auxin homeostasis is dependent on
              AtDAO1
              , acting in concert with
              GH3
              , to maintain auxin at optimal levels for plant growth and development.},
	language = {en},
	number = {39},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Mellor, Nathan and Band, Leah R. and Pěnčík, Aleš and Novák, Ondřej and Rashed, Afaf and Holman, Tara and Wilson, Michael H. and Voß, Ute and Bishopp, Anthony and King, John R. and Ljung, Karin and Bennett, Malcolm J. and Owen, Markus R.},
	month = sep,
	year = {2016},
	pages = {11022--11027},
}

The hormone auxin is a key regulator of plant growth and development, and great progress has been made understanding auxin transport and signaling. Here, we show that auxin metabolism and homeostasis are also regulated in a complex manner. The principal auxin degradation pathways in Arabidopsis include oxidation by Arabidopsis thaliana gene DIOXYGENASE FOR AUXIN OXIDATION 1/2 (AtDAO1/2) and conjugation by Gretchen Hagen3s (GH3s). Metabolic profiling of dao1-1 root tissues revealed a 50% decrease in the oxidation product 2-oxoindole-3-acetic acid (oxIAA) and increases in the conjugated forms indole-3-acetic acid aspartic acid (IAA-Asp) and indole-3-acetic acid glutamic acid (IAA-Glu) of 438- and 240-fold, respectively, whereas auxin remains close to the WT. By fitting parameter values to a mathematical model of these metabolic pathways, we show that, in addition to reduced oxidation, both auxin biosynthesis and conjugation are increased in dao1-1 . Transcripts of AtDAO1 and GH3 genes increase in response to auxin over different timescales and concentration ranges. Including this regulation of AtDAO1 and GH3 in an extended model reveals that auxin oxidation is more important for auxin homoeostasis at lower hormone concentrations, whereas auxin conjugation is most significant at high auxin levels. Finally, embedding our homeostasis model in a multicellular simulation to assess the spatial effect of the dao1-1 mutant shows that auxin increases in outer root tissues in agreement with the dao1-1 mutant root hair phenotype. We conclude that auxin homeostasis is dependent on AtDAO1 , acting in concert with GH3 , to maintain auxin at optimal levels for plant growth and development.

@article{johnsson_cambial_2016,
	title = {Cambial stem cells and their niche},
	volume = {252},
	issn = {01689452},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0168945216302862},
	doi = {10/gjcnkm},
	language = {en},
	urldate = {2021-06-07},
	journal = {Plant Science},
	author = {Johnsson, Christoffer and Fischer, Urs},
	month = nov,
	year = {2016},
	pages = {239--245},
}

@article{wattelet-boyer_enrichment_2016,
	title = {Enrichment of hydroxylated {C24}- and {C26}-acyl-chain sphingolipids mediates {PIN2} apical sorting at trans-{Golgi} network subdomains},
	volume = {7},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/ncomms12788},
	doi = {10/ghtbhj},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Wattelet-Boyer, Valérie and Brocard, Lysiane and Jonsson, Kristoffer and Esnay, Nicolas and Joubès, Jérôme and Domergue, Frédéric and Mongrand, Sébastien and Raikhel, Natasha and Bhalerao, Rishikesh P. and Moreau, Patrick and Boutté, Yohann},
	month = nov,
	year = {2016},
	pages = {12788},
}

@article{soler_woody-preferential_2016,
	title = {The {Woody}-{Preferential} {Gene} {EgMYB88} {Regulates} the {Biosynthesis} of {Phenylpropanoid}-{Derived} {Compounds} in {Wood}},
	volume = {7},
	issn = {1664-462X},
	url = {http://journal.frontiersin.org/Article/10.3389/fpls.2016.01422/abstract},
	doi = {10/f3tcr7},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Soler, Marçal and Plasencia, Anna and Lepikson-Neto, Jorge and Camargo, Eduardo L. O. and Dupas, Annabelle and Ladouce, Nathalie and Pesquet, Edouard and Mounet, Fabien and Larbat, Romain and Grima-Pettenati, Jacqueline},
	month = sep,
	year = {2016},
}

@article{papazian_central_2016,
	title = {Central {Metabolic} {Responses} to {Ozone} and {Herbivory} {Affect} {Photosynthesis} and {Stomatal} {Closure}},
	volume = {172},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/172/3/2057-2078/6115987},
	doi = {10/f3vft5},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Papazian, Stefano and Khaling, Eliezer and Bonnet, Christelle and Lassueur, Steve and Reymond, Philippe and Moritz, Thomas and Blande, James D. and Albrectsen, Benedicte R.},
	month = nov,
	year = {2016},
	pages = {2057--2078},
}

@article{krupinski_model_2016,
	title = {A {Model} {Analysis} of {Mechanisms} for {Radial} {Microtubular} {Patterns} at {Root} {Hair} {Initiation} {Sites}},
	volume = {7},
	issn = {1664-462X},
	url = {http://journal.frontiersin.org/article/10.3389/fpls.2016.01560/full},
	doi = {10/f3t5jz},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Krupinski, Pawel and Bozorg, Behruz and Larsson, André and Pietra, Stefano and Grebe, Markus and Jönsson, Henrik},
	month = oct,
	year = {2016},
}

@article{czaban_direct_2016,
	title = {Direct acquisition of organic {N} by white clover even in the presence of inorganic {N}},
	volume = {407},
	issn = {0032-079X, 1573-5036},
	url = {http://link.springer.com/10.1007/s11104-016-2896-z},
	doi = {10/f3tc8b},
	language = {en},
	number = {1-2},
	urldate = {2021-06-07},
	journal = {Plant and Soil},
	author = {Czaban, Weronika and Jämtgård, Sandra and Näsholm, Torgny and Rasmussen, Jim and Nicolaisen, Mogens and Fomsgaard, Inge S.},
	month = oct,
	year = {2016},
	pages = {91--107},
}

@article{chrobok_dissecting_2016,
	title = {Dissecting the {Metabolic} {Role} of {Mitochondria} during {Developmental} {Leaf} {Senescence}},
	volume = {172},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/172/4/2132-2153/6115841},
	doi = {10/f3vc6g},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Chrobok, Daria and Law, Simon R. and Brouwer, Bastiaan and Lindén, Pernilla and Ziolkowska, Agnieszka and Liebsch, Daniela and Narsai, Reena and Szal, Bozena and Moritz, Thomas and Rouhier, Nicolas and Whelan, James and Gardeström, Per and Keech, Olivier},
	month = dec,
	year = {2016},
	pages = {2132--2153},
}

@article{mao_framework_2016,
	title = {A {Framework} for {Lateral} {Membrane} {Trafficking} and {Polar} {Tethering} of the {PEN3} {ATP}-{Binding} {Cassette} {Transporter}},
	volume = {172},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/172/4/2245-2260/6115810},
	doi = {10/f3vhhs},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Mao, Hailiang and Nakamura, Moritaka and Viotti, Corrado and Grebe, Markus},
	month = dec,
	year = {2016},
	pages = {2245--2260},
}

@article{li_characterization_2016,
	title = {Characterization of a novel β-barrel protein ({AtOM47}) from the mitochondrial outer membrane of \textit{{Arabidopsis} thaliana}},
	volume = {67},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/erw366},
	doi = {10/f9c9wf},
	language = {en},
	number = {21},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Li, Lu and Kubiszewski-Jakubiak, Szymon and Radomiljac, Jordan and Wang, Yan and Law, Simon R. and Keech, Olivier and Narsai, Reena and Berkowitz, Oliver and Duncan, Owen and Murcha, Monika W. and Whelan, James},
	month = nov,
	year = {2016},
	pages = {6061--6075},
}

@article{chen_method_2016,
	title = {Method for accurate fiber length determination from increment cores for large-scale population analyses in {Norway} spruce},
	volume = {70},
	issn = {1437-434X, 0018-3830},
	url = {https://www.degruyter.com/document/doi/10.1515/hf-2015-0138/html},
	doi = {10/f3rwht},
	abstract = {Abstract
            
              Fiber (tracheid) length is an important trait targeted for genetic and silvicultural improvement. Such studies require large-scale non-destructive sampling, and accurate length determination. The standard procedure for non-destructive sampling is to collect increment cores, singularize their cells by maceration, measure them with optical analyzer and apply various corrections to suppress influence of non-fiber particles and cut fibers, as fibers are cut by the corer. The recently developed expectation-maximization method (EM) not only addresses the problem of non-fibers and cut fibers, but also corrects for the sampling bias. Here, the performance of the EM method has been evaluated by comparing it with length-weighing and squared length-weighing, both implemented in fiber analyzers, and with microscopy data for intact fibers, corrected for sampling bias, as the reference. This was done for 12-mm increment cores from 16 Norway spruce (
              Picea abies
              (L.) Karst) trees on fibers from rings 8–11 (counted from pith), representing juvenile wood of interest in breeding programs. The EM-estimates provided mean-fiber-lengths with bias of only +2.7\% and low scatter. Length-weighing and length
              2
              -weighing gave biases of -7.3\% and +9.3\%, respectively, and larger scatter. The suggested EM approach constitutes a more accurate non-destructive method for fiber length (FL) determination, expected to be applicable also to other conifers.},
	number = {9},
	urldate = {2021-06-07},
	journal = {Holzforschung},
	author = {Chen, Zhi-Qiang and Abramowicz, Konrad and Raczkowski, Rafal and Ganea, Stefana and Wu, Harry X. and Lundqvist, Sven-Olof and Mörling, Tommy and de Luna, Sara Sjöstedt and García Gil, María Rosario and Mellerowicz, Ewa J.},
	month = sep,
	year = {2016},
	pages = {829--838},
}

Abstract Fiber (tracheid) length is an important trait targeted for genetic and silvicultural improvement. Such studies require large-scale non-destructive sampling, and accurate length determination. The standard procedure for non-destructive sampling is to collect increment cores, singularize their cells by maceration, measure them with optical analyzer and apply various corrections to suppress influence of non-fiber particles and cut fibers, as fibers are cut by the corer. The recently developed expectation-maximization method (EM) not only addresses the problem of non-fibers and cut fibers, but also corrects for the sampling bias. Here, the performance of the EM method has been evaluated by comparing it with length-weighing and squared length-weighing, both implemented in fiber analyzers, and with microscopy data for intact fibers, corrected for sampling bias, as the reference. This was done for 12-mm increment cores from 16 Norway spruce ( Picea abies (L.) Karst) trees on fibers from rings 8–11 (counted from pith), representing juvenile wood of interest in breeding programs. The EM-estimates provided mean-fiber-lengths with bias of only +2.7% and low scatter. Length-weighing and length 2 -weighing gave biases of -7.3% and +9.3%, respectively, and larger scatter. The suggested EM approach constitutes a more accurate non-destructive method for fiber length (FL) determination, expected to be applicable also to other conifers.

@article{hasselquist_greater_2016,
	title = {Greater carbon allocation to mycorrhizal fungi reduces tree nitrogen uptake in a boreal forest},
	volume = {97},
	issn = {0012-9658 (Print) 0012-9658 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/27220217},
	doi = {10.1890/15-1222.1},
	abstract = {The central role that ectomycorrhizal (EM) symbioses play in the structure and function of boreal forests pivots around the common assumption that carbon (C) and nitrogen (N) are exchanged at rates favorable for plant growth. However, this may not always be the case. It has been hypothesized that the benefits mycorrhizal fungi convey to their host plants strongly depends upon the availability of C and N, both of which are rapidly changing as a result of intensified human land use and climate change. Using large-scale shading and N addition treatments, we assessed the independent and interactive effects of changes in C and N supply on the transfer of N in intact EM associations with -15 yr. old Scots pine trees. To assess the dynamics of N transfer in EM symbioses, we added trace amounts of highly enriched 5NO3(-) label to the EM-dominated mor-layer and followed the fate of the 15N label in tree foliage, fungal chitin on EM root tips, and EM sporocarps. Despite no change in leaf biomass, shading resulted in reduced tree C uptake, ca. 40\% lower fungal biomass on EM root tips, and greater 15N label in tree foliage compared to unshaded control plots, where more 15N label was found in fungal biomass on EM colonized root tips. Short-term addition of N shifted the incorporation of 15N label from EM fungi to tree foliage, despite no significant changes in below-ground tree C allocation to EM fungi. Contrary to the common assumption that C and N are exchanged at rates favorable for plant growth, our results show for the first time that under N-limited conditions greater C allocation to EM fungi in the field results in reduced, not increased, N transfer to host trees. Moreover, given the ubiquitous nature of mycorrhizal symbioses, our results stress the need to incorporate mycorrhizal dynamics into process-based ecosystem models to better predict forest C and N cycles in light of global climate change.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Ecology},
	author = {Hasselquist, N. J. and Metcalfe, D. B. and Inselsbacher, E. and Stangl, Z. and Oren, R. and Nasholm, T. and Hogberg, P.},
	month = apr,
	year = {2016},
	note = {Edition: 2016/05/26},
	keywords = {*Forests, Carbon/*metabolism, Mycorrhizae/*physiology, Nitrogen/*metabolism, Pinus sylvestris/*microbiology/physiology, Symbiosis, Trees/*microbiology/physiology},
	pages = {1012--22},
}

The central role that ectomycorrhizal (EM) symbioses play in the structure and function of boreal forests pivots around the common assumption that carbon (C) and nitrogen (N) are exchanged at rates favorable for plant growth. However, this may not always be the case. It has been hypothesized that the benefits mycorrhizal fungi convey to their host plants strongly depends upon the availability of C and N, both of which are rapidly changing as a result of intensified human land use and climate change. Using large-scale shading and N addition treatments, we assessed the independent and interactive effects of changes in C and N supply on the transfer of N in intact EM associations with -15 yr. old Scots pine trees. To assess the dynamics of N transfer in EM symbioses, we added trace amounts of highly enriched 5NO3(-) label to the EM-dominated mor-layer and followed the fate of the 15N label in tree foliage, fungal chitin on EM root tips, and EM sporocarps. Despite no change in leaf biomass, shading resulted in reduced tree C uptake, ca. 40% lower fungal biomass on EM root tips, and greater 15N label in tree foliage compared to unshaded control plots, where more 15N label was found in fungal biomass on EM colonized root tips. Short-term addition of N shifted the incorporation of 15N label from EM fungi to tree foliage, despite no significant changes in below-ground tree C allocation to EM fungi. Contrary to the common assumption that C and N are exchanged at rates favorable for plant growth, our results show for the first time that under N-limited conditions greater C allocation to EM fungi in the field results in reduced, not increased, N transfer to host trees. Moreover, given the ubiquitous nature of mycorrhizal symbioses, our results stress the need to incorporate mycorrhizal dynamics into process-based ecosystem models to better predict forest C and N cycles in light of global climate change.

@article{van_de_wouwer_chemical_2016,
	title = {Chemical {Genetics} {Uncovers} {Novel} {Inhibitors} of {Lignification}, {Including} \textit{p} -{Iodobenzoic} {Acid} {Targeting} {CINNAMATE}-4-{HYDROXYLASE}},
	volume = {172},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/172/1/198-220/6115558},
	doi = {10.1104/pp.16.00430},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Van de Wouwer, Dorien and Vanholme, Ruben and Decou, Raphaël and Goeminne, Geert and Audenaert, Dominique and Nguyen, Long and Höfer, René and Pesquet, Edouard and Vanholme, Bartel and Boerjan, Wout},
	month = sep,
	year = {2016},
	pages = {198--220},
}

@article{miguel_short-root-like_2016,
	title = {The {SHORT}-{ROOT}-like gene {PtSHR2B} is involved in {Populus} phellogen activity},
	volume = {67},
	issn = {1460-2431},
	doi = {10.1093/jxb/erv547},
	abstract = {SHORT-ROOT (SHR) is a GRAS transcription factor first characterized for its role in the specification of the stem cell niche and radial patterning in Arabidopsis thaliana (At) roots. Three SHR-like genes have been identified in Populus trichocarpa (Pt). PtSHR1 shares high similarity with AtSHR over the entire length of the coding sequence. The two other Populus SHR-like genes, PtSHR2A and PtSHR2B, are shorter in their 5' ends when compared with AtSHR. Unlike PtSHR1, that is expressed throughout the cambial zone of greenhouse-grown Populus trees, PtSHR2Bprom:uidA expression was detected in the phellogen. Additionally, PtSHR1 and PtSHR2B expression patterns markedly differ in the shoot apex and roots of in vitro plants. Transgenic hybrid aspen expressing PtSHR2B under the 35S constitutive promoter showed overall reduced tree growth while the proportion of bark increased relative to the wood. Reverse transcription-quantitative PCR (RT-qPCR) revealed increased transcript levels of cytokinin metabolism and response-related genes in the transgenic plants consistent with an increase of total cytokinin levels. This was confirmed by cytokinin quantification by LC-MS/MS. Our results indicate that PtSHR2B appears to function in the phellogen and therefore in the regulation of phellem and periderm formation, possibly acting through modulation of cytokinin homeostasis. Furthermore, this work points to a functional diversification of SHR after the divergence of the Populus and Arabidopsis lineages. This finding may contribute to selection and breeding strategies of cork oak in which, unlike Populus, the phellogen is active throughout the entire tree lifespan, being at the basis of a highly profitable cork industry.},
	language = {eng},
	number = {5},
	journal = {Journal of Experimental Botany},
	author = {Miguel, Andreia and Milhinhos, Ana and Novák, Ondřej and Jones, Brian and Miguel, Célia M.},
	month = mar,
	year = {2016},
	pmid = {26709311},
	keywords = {Cambium, Cytokinin, Cytokinins, Gene Expression Regulation, Plant, Genes, Plant, Hybridization, Genetic, Phenotype, Plant Proteins, Plant Stems, Plants, Genetically Modified, Populus, Populus tremula×Populus tremuloides, Promoter Regions, Genetic, SHORT-ROOT., Trees, Wood, lateral meristem, phellogen, secondary growth},
	pages = {1545--1555},
}

SHORT-ROOT (SHR) is a GRAS transcription factor first characterized for its role in the specification of the stem cell niche and radial patterning in Arabidopsis thaliana (At) roots. Three SHR-like genes have been identified in Populus trichocarpa (Pt). PtSHR1 shares high similarity with AtSHR over the entire length of the coding sequence. The two other Populus SHR-like genes, PtSHR2A and PtSHR2B, are shorter in their 5' ends when compared with AtSHR. Unlike PtSHR1, that is expressed throughout the cambial zone of greenhouse-grown Populus trees, PtSHR2Bprom:uidA expression was detected in the phellogen. Additionally, PtSHR1 and PtSHR2B expression patterns markedly differ in the shoot apex and roots of in vitro plants. Transgenic hybrid aspen expressing PtSHR2B under the 35S constitutive promoter showed overall reduced tree growth while the proportion of bark increased relative to the wood. Reverse transcription-quantitative PCR (RT-qPCR) revealed increased transcript levels of cytokinin metabolism and response-related genes in the transgenic plants consistent with an increase of total cytokinin levels. This was confirmed by cytokinin quantification by LC-MS/MS. Our results indicate that PtSHR2B appears to function in the phellogen and therefore in the regulation of phellem and periderm formation, possibly acting through modulation of cytokinin homeostasis. Furthermore, this work points to a functional diversification of SHR after the divergence of the Populus and Arabidopsis lineages. This finding may contribute to selection and breeding strategies of cork oak in which, unlike Populus, the phellogen is active throughout the entire tree lifespan, being at the basis of a highly profitable cork industry.

@article{gerber_highthroughput_2016,
	title = {High‐throughput microanalysis of large lignocellulosic sample sets by pyrolysis‐gas chromatography/mass spectrometry},
	volume = {156},
	issn = {0031-9317, 1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/ppl.12397},
	doi = {10.1111/ppl.12397},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Gerber, Lorenz and Öhman, David and Kumar, Manoj and Ranocha, Philippe and Goffner, Deborah and Sundberg, Björn},
	month = feb,
	year = {2016},
	pages = {127--138},
}

@article{engineer_co_2016,
	title = {{CO} 2 {Sensing} and {CO} 2 {Regulation} of {Stomatal} {Conductance}: {Advances} and {Open} {Questions}},
	volume = {21},
	issn = {13601385},
	shorttitle = {{CO} 2 {Sensing} and {CO} 2 {Regulation} of {Stomatal} {Conductance}},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1360138515002290},
	doi = {10.1016/j.tplants.2015.08.014},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Trends in Plant Science},
	author = {Engineer, Cawas B. and Hashimoto-Sugimoto, Mimi and Negi, Juntaro and Israelsson-Nordström, Maria and Azoulay-Shemer, Tamar and Rappel, Wouter-Jan and Iba, Koh and Schroeder, Julian I.},
	month = jan,
	year = {2016},
	pages = {16--30},
}

@article{shaikhali_redox_2016,
	title = {Redox regulation of the {MED28} and {MED32} mediator subunits is important for development and senescence},
	volume = {253},
	issn = {0033-183X, 1615-6102},
	url = {http://link.springer.com/10.1007/s00709-015-0853-y},
	doi = {10.1007/s00709-015-0853-y},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Protoplasma},
	author = {Shaikhali, Jehad and Davoine, Céline and Björklund, Stefan and Wingsle, Gunnar},
	month = may,
	year = {2016},
	pages = {957--963},
}

@article{pawar_expression_2016,
	title = {Expression of fungal acetyl xylan esterase in \textit{{Arabidopsis} thaliana} improves saccharification of stem lignocellulose},
	volume = {14},
	issn = {14677644},
	url = {http://doi.wiley.com/10.1111/pbi.12393},
	doi = {10.1111/pbi.12393},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Biotechnology Journal},
	author = {Pawar, Prashant Mohan-Anupama and Derba-Maceluch, Marta and Chong, Sun-Li and Gómez, Leonardo D. and Miedes, Eva and Banasiak, Alicja and Ratke, Christine and Gaertner, Cyril and Mouille, Grégory and McQueen-Mason, Simon J. and Molina, Antonio and Sellstedt, Anita and Tenkanen, Maija and Mellerowicz, Ewa J.},
	month = jan,
	year = {2016},
	pages = {387--397},
}

@article{steenackers_allelochemical_2016,
	title = {The allelochemical {MDCA} inhibits lignification and affects auxin homeostasis},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/172/2/874-888/6115977},
	doi = {10.1104/pp.15.01972},
	language = {en},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Steenackers, Ward Jan and Cesarino, Igor and Klíma, Petr and Quareshy, Mussa and Vanholme, Ruben and Corneillie, Sander and Kumpf, Robert P. and Van de Wouwer, Dorien and Ljung, Karin and Goeminne, Geert and Novak, Ondrej and Zažímalová, Eva and Napier, Richard M. and Boerjan, Wout A and Vanholme, Bartel},
	month = aug,
	year = {2016},
	pages = {pp.01972.2015},
}

@article{hall_estimation_2016,
	title = {Estimation of number and size of {QTL} effects in forest tree traits},
	volume = {12},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-016-1073-0},
	doi = {10.1007/s11295-016-1073-0},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Tree Genetics \& Genomes},
	author = {Hall, David and Hallingbäck, Henrik R. and Wu, Harry X.},
	month = dec,
	year = {2016},
	pages = {110},
}

@article{santuari_plethora_2016,
	title = {The {PLETHORA} {Gene} {Regulatory} {Network} {Guides} {Growth} and {Cell} {Differentiation} in {Arabidopsis} {Roots}},
	volume = {28},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/28/12/2937-2951/6098272},
	doi = {10.1105/tpc.16.00656},
	language = {en},
	number = {12},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {Santuari, Luca and Sanchez-Perez, Gabino F. and Luijten, Marijn and Rutjens, Bas and Terpstra, Inez and Berke, Lidija and Gorte, Maartje and Prasad, Kalika and Bao, Dongping and Timmermans-Hereijgers, Johanna L.P.M. and Maeo, Kenichiro and Nakamura, Kenzo and Shimotohno, Akie and Pencik, Ales and Novak, Ondrej and Ljung, Karin and van Heesch, Sebastiaan and de Bruijn, Ewart and Cuppen, Edwin and Willemsen, Viola and Mähönen, Ari Pekka and Lukowitz, Wolfgang and Snel, Berend and de Ridder, Dick and Scheres, Ben and Heidstra, Renze},
	month = dec,
	year = {2016},
	pages = {2937--2951},
}

@article{zulfugarov_enhanced_2016,
	title = {Enhanced resistance of {PsbS}-deficient rice ({Oryza} sativa {L}.) to fungal and bacterial pathogens},
	volume = {59},
	issn = {1226-9239, 1867-0725},
	url = {http://link.springer.com/10.1007/s12374-016-0068-6},
	doi = {10.1007/s12374-016-0068-6},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Journal of Plant Biology},
	author = {Zulfugarov, Ismayil S. and Tovuu, Altanzaya and Kim, Chi-Yeol and Xuan Vo, Kieu Thi and Ko, Soo Yeon and Hall, Michael and Seok, Hye-Yeon and Kim, Yeon-Ki and Skogstrom, Oscar and Moon, Yong-Hwan and Jansson, Stefan and Jeon, Jong-Seong and Lee, Choon-Hwan},
	month = dec,
	year = {2016},
	pages = {616--626},
}

@article{cheregi_antibiotic_2016,
	title = {Antibiotic {Disc} {Assay} for {Synechocystis} sp. {PCC6803}},
	volume = {6},
	issn = {2331-8325},
	url = {https://bio-protocol.org/e2071},
	doi = {10.21769/BioProtoc.2071},
	language = {en},
	number = {24},
	urldate = {2021-06-07},
	journal = {BIO-PROTOCOL},
	author = {Cheregi, Otilia and Funk, Christiane},
	year = {2016},
}

@article{decker_aspen_2016,
	title = {Aspen phenylpropanoid genes’ expression levels correlate with genets’ tannin richness and vary both in responses to soil nitrogen and associations with phenolic profiles},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article-lookup/doi/10.1093/treephys/tpw118},
	doi = {10.1093/treephys/tpw118},
	language = {en},
	urldate = {2021-06-07},
	journal = {Tree Physiology},
	author = {Decker, Vicki H.G. and Bandau, Franziska and Gundale, Michael J. and Cole, Christopher T. and Albrectsen, Benedicte R.},
	editor = {Tsai, Chung-Jui},
	month = dec,
	year = {2016},
	pages = {treephys;tpw118v1},
}

@article{ausin_dna_2016,
	title = {{DNA} methylome of the 20-gigabase {Norway} spruce genome},
	volume = {113},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1618019113},
	doi = {10.1073/pnas.1618019113},
	abstract = {DNA methylation plays important roles in many biological processes, such as silencing of transposable elements, imprinting, and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms (flowering plants). However, few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here, we present genome-wide high coverage single-base resolution methylation maps of Norway spruce (
              Picea abies
              ) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing. On average, DNA methylation levels of CG and CHG of Norway spruce were higher than most other plants studied. CHH methylation was found at a relatively low level; however, at least one copy of most of the RNA-directed DNA methylation pathway genes was found in Norway spruce, and CHH methylation was correlated with levels of siRNAs. In comparison with needles, somatic embryogenesis culture cells that are used for clonally propagating spruce trees showed lower levels of CG and CHG methylation but higher level of CHH methylation, suggesting that like in other species, these culture cells show abnormal methylation patterns.},
	language = {en},
	number = {50},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Ausin, Israel and Feng, Suhua and Yu, Chaowei and Liu, Wanlu and Kuo, Hsuan Yu and Jacobsen, Elise L. and Zhai, Jixian and Gallego-Bartolome, Javier and Wang, Lin and Egertsdotter, Ulrika and Street, Nathaniel R. and Jacobsen, Steven E. and Wang, Haifeng},
	month = dec,
	year = {2016},
	pages = {E8106--E8113},
}

DNA methylation plays important roles in many biological processes, such as silencing of transposable elements, imprinting, and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms (flowering plants). However, few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here, we present genome-wide high coverage single-base resolution methylation maps of Norway spruce ( Picea abies ) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing. On average, DNA methylation levels of CG and CHG of Norway spruce were higher than most other plants studied. CHH methylation was found at a relatively low level; however, at least one copy of most of the RNA-directed DNA methylation pathway genes was found in Norway spruce, and CHH methylation was correlated with levels of siRNAs. In comparison with needles, somatic embryogenesis culture cells that are used for clonally propagating spruce trees showed lower levels of CG and CHG methylation but higher level of CHH methylation, suggesting that like in other species, these culture cells show abnormal methylation patterns.

@article{nordstrom_impacts_2016,
	title = {Impacts of global climate change mitigation scenarios on forests and harvesting in {Sweden}},
	volume = {46},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfr-2016-0122},
	doi = {10.1139/cjfr-2016-0122},
	abstract = {Under climate change, the importance of biomass resources is likely to increase and new approaches are needed to analyze future material and energy use of biomass globally and locally. Using Sweden as an example, we present an approach that combines global and national land-use and forest models to analyze impacts of climate change mitigation ambitions on forest management and harvesting in a specific country. National forest impact analyses in Sweden have traditionally focused on supply potential with little reference to international market developments. In this study, we use the global greenhouse gas concentration scenarios from the Intergovernmental Panel for Climate Change to estimate global biomass demand and assess potential implications on harvesting and biodiversity in Sweden. The results show that the short-term demand for wood is close to the full harvesting potential in Sweden in all scenarios. Under high bioenergy demand, harvest levels are projected to stay high over a longer time and particularly impact the harvest levels of pulpwood. The area of old forest in the managed landscape may decrease. This study highlights the importance of global scenarios when discussing national-level analysis and pinpoints trade-offs that policy making in Sweden may need to tackle in the near future.},
	language = {en},
	number = {12},
	urldate = {2021-06-07},
	journal = {Canadian Journal of Forest Research},
	author = {Nordström, Eva-Maria and Forsell, Nicklas and Lundström, Anders and Korosuo, Anu and Bergh, Johan and Havlík, Petr and Kraxner, Florian and Frank, Stefan and Fricko, Oliver and Lundmark, Tomas and Nordin, Annika},
	month = dec,
	year = {2016},
	pages = {1427--1438},
}

Under climate change, the importance of biomass resources is likely to increase and new approaches are needed to analyze future material and energy use of biomass globally and locally. Using Sweden as an example, we present an approach that combines global and national land-use and forest models to analyze impacts of climate change mitigation ambitions on forest management and harvesting in a specific country. National forest impact analyses in Sweden have traditionally focused on supply potential with little reference to international market developments. In this study, we use the global greenhouse gas concentration scenarios from the Intergovernmental Panel for Climate Change to estimate global biomass demand and assess potential implications on harvesting and biodiversity in Sweden. The results show that the short-term demand for wood is close to the full harvesting potential in Sweden in all scenarios. Under high bioenergy demand, harvest levels are projected to stay high over a longer time and particularly impact the harvest levels of pulpwood. The area of old forest in the managed landscape may decrease. This study highlights the importance of global scenarios when discussing national-level analysis and pinpoints trade-offs that policy making in Sweden may need to tackle in the near future.

@article{from_effects_2016,
	title = {Effects of simulated long-term {N} deposition on \textit{{Picea} abies} and \textit{{Pinus} sylvestris} growth in boreal forest},
	volume = {46},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfr-2016-0201},
	doi = {10.1139/cjfr-2016-0201},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Canadian Journal of Forest Research},
	author = {From, F. and Lundmark, T. and Mörling, T. and Pommerening, A. and Nordin, A.},
	month = nov,
	year = {2016},
	pages = {1396--1403},
}

@article{chen_genetic_2016,
	title = {Genetic analysis of fiber dimensions and their correlation with stem diameter and solid-wood properties in {Norway} spruce},
	volume = {12},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-016-1065-0},
	doi = {10.1007/s11295-016-1065-0},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Tree Genetics \& Genomes},
	author = {Chen, Zhi-Qiang and Karlsson, Bo and Mörling, Tommy and Olsson, Lars and Mellerowicz, Ewa J. and Wu, Harry X. and Lundqvist, Sven-Olof and Gil, María Rosario García},
	month = dec,
	year = {2016},
	pages = {123},
}

@article{dobrenel_arabidopsis_2016,
	title = {The {Arabidopsis} {TOR} {Kinase} {Specifically} {Regulates} the {Expression} of {Nuclear} {Genes} {Coding} for {Plastidic} {Ribosomal} {Proteins} and the {Phosphorylation} of the {Cytosolic} {Ribosomal} {Protein} {S6}},
	volume = {7},
	issn = {1664-462X},
	url = {http://journal.frontiersin.org/article/10.3389/fpls.2016.01611/full},
	doi = {10.3389/fpls.2016.01611},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Dobrenel, Thomas and Mancera-Martínez, Eder and Forzani, Céline and Azzopardi, Marianne and Davanture, Marlène and Moreau, Manon and Schepetilnikov, Mikhail and Chicher, Johana and Langella, Olivier and Zivy, Michel and Robaglia, Christophe and Ryabova, Lyubov A. and Hanson, Johannes and Meyer, Christian},
	month = nov,
	year = {2016},
}

@article{zheng_inheritance_2016,
	title = {Inheritance of growth and survival in two 9-year-old, open-pollinated progenies of an advanced breeding population of {Chinese} firs in southeastern {China}},
	volume = {27},
	issn = {1007-662X, 1993-0607},
	url = {http://link.springer.com/10.1007/s11676-016-0250-1},
	doi = {10.1007/s11676-016-0250-1},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Journal of Forestry Research},
	author = {Zheng, Renhua and Hong, Zhou and Su, Shunde and Bian, Liming and Xiao, Hui and Shi, Jisen and Wu, Harry X.},
	month = oct,
	year = {2016},
	pages = {1067--1075},
}

@article{plochinger_functional_2016,
	title = {Functional {Update} of the {Auxiliary} {Proteins} {PsbW}, {PsbY}, {HCF136}, {PsbN}, {TerC} and {ALB3} in {Maintenance} and {Assembly} of {PSII}},
	volume = {7},
	issn = {1664-462X},
	url = {http://journal.frontiersin.org/Article/10.3389/fpls.2016.00423/abstract},
	doi = {10.3389/fpls.2016.00423},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Plöchinger, Magdalena and Schwenkert, Serena and von Sydow, Lotta and Schröder, Wolfgang P. and Meurer, Jörg},
	month = apr,
	year = {2016},
}

@article{fernandez-moreno_efficient_2016,
	title = {An efficient method for medium throughput screening of cuticular wax composition in different plant species},
	volume = {12},
	issn = {1573-3882, 1573-3890},
	url = {http://link.springer.com/10.1007/s11306-016-0982-0},
	doi = {10.1007/s11306-016-0982-0},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Metabolomics},
	author = {Fernandez-Moreno, Josefina-Patricia and Malitsky, Sergey and Lashbrooke, Justin and Biswal, Ajaya Kumar and Racovita, Radu C. and Mellerowicz, Ewa J. and Jetter, Reinhard and Orzaez, Diego and Aharoni, Asaph and Granell, Antonio},
	month = apr,
	year = {2016},
	pages = {73},
}

@article{hodges_perspectives_2016,
	title = {Perspectives for a better understanding of the metabolic integration of photorespiration within a complex plant primary metabolism network},
	volume = {67},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/erw145},
	doi = {10.1093/jxb/erw145},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Hodges, Michael and Dellero, Younès and Keech, Olivier and Betti, Marco and Raghavendra, Agepati S. and Sage, Rowan and Zhu, Xin-Guang and Allen, Doug K. and Weber, Andreas P.M.},
	month = may,
	year = {2016},
	pages = {3015--3026},
}

@article{krzeslowska_pectinous_2016,
	title = {Pectinous cell wall thickenings formation – {A} common defense strategy of plants to cope with {Pb}},
	volume = {214},
	issn = {02697491},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0269749116302858},
	doi = {10.1016/j.envpol.2016.04.019},
	language = {en},
	urldate = {2021-06-07},
	journal = {Environmental Pollution},
	author = {Krzesłowska, Magdalena and Rabęda, Irena and Basińska, Aneta and Lewandowski, Michał and Mellerowicz, Ewa J. and Napieralska, Anna and Samardakiewicz, Sławomir and Woźny, Adam},
	month = jul,
	year = {2016},
	pages = {354--361},
}

@article{pullman_fraser_2016,
	title = {Fraser fir somatic embryogenesis: high frequency initiation, maintenance, embryo development, germination and cryopreservation},
	volume = {47},
	issn = {0169-4286, 1573-5095},
	shorttitle = {Fraser fir somatic embryogenesis},
	url = {http://link.springer.com/10.1007/s11056-016-9525-9},
	doi = {10.1007/s11056-016-9525-9},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {New Forests},
	author = {Pullman, Gerald S. and Olson, Katie and Fischer, Taylor and Egertsdotter, Ulrika and Frampton, John and Bucalo, Kylie},
	month = may,
	year = {2016},
	pages = {453--480},
}

@article{hoenicka_low_2016,
	title = {Low temperatures are required to induce the development of fertile flowers in transgenic male and female early flowering poplar ( \textit{{Populus} tremula} {L}.)},
	volume = {36},
	issn = {0829-318X, 1758-4469},
	url = {https://academic.oup.com/treephys/article-lookup/doi/10.1093/treephys/tpw015},
	doi = {10.1093/treephys/tpw015},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Tree Physiology},
	author = {Hoenicka, Hans and Lehnhardt, Denise and Briones, Valentina and Nilsson, Ove and Fladung, Matthias},
	editor = {Schnitzler, Jörg-Peter},
	month = may,
	year = {2016},
	pages = {667--677},
}

@article{wu_performance_2016,
	title = {Performance of {Seven} {Tree} {Breeding} {Strategies} {Under} {Conditions} of {Inbreeding} {Depression}},
	volume = {6},
	issn = {2160-1836},
	url = {https://academic.oup.com/g3journal/article/6/3/529/6027276},
	doi = {10.1534/g3.115.025767},
	abstract = {Abstract
            In the domestication and breeding of tree species that suffer from inbreeding depression (ID), the long-term performance of different breeding strategies is poorly known. Therefore, seven tree breeding strategies including single population, subline, selfing, and nucleus breeding were simulated using a multi-locus model with additive, partial, and complete dominance allele effects, and with intermediate, U-shaped, and major allele distributions. The strategies were compared for genetic gain, inbreeding accumulation, capacity to show ID, the frequencies and fixations of unfavorable alleles, and genetic variances in breeding and production populations. Measured by genetic gain of production population, the nucleus breeding and the single breeding population with mass selection strategies were equal or superior to subline and single breeding population with within-family selection strategies in all simulated scenarios, in spite of their higher inbreeding coefficients. Inbreeding and cross-breeding effectively decreased ID and could in some scenarios produce genetic gains during the first few generations. However, in all scenarios, considerable fixation of unfavorable alleles rendered the purging performance of selfing and cross-breeding strategies ineffective, and resulted in substantial inferiority in comparison to the other strategies in the long-term.},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {G3 Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Wu, Harry X and Hallingbäck, Henrik R and Sánchez, Leopoldo},
	month = mar,
	year = {2016},
	pages = {529--540},
}

Abstract In the domestication and breeding of tree species that suffer from inbreeding depression (ID), the long-term performance of different breeding strategies is poorly known. Therefore, seven tree breeding strategies including single population, subline, selfing, and nucleus breeding were simulated using a multi-locus model with additive, partial, and complete dominance allele effects, and with intermediate, U-shaped, and major allele distributions. The strategies were compared for genetic gain, inbreeding accumulation, capacity to show ID, the frequencies and fixations of unfavorable alleles, and genetic variances in breeding and production populations. Measured by genetic gain of production population, the nucleus breeding and the single breeding population with mass selection strategies were equal or superior to subline and single breeding population with within-family selection strategies in all simulated scenarios, in spite of their higher inbreeding coefficients. Inbreeding and cross-breeding effectively decreased ID and could in some scenarios produce genetic gains during the first few generations. However, in all scenarios, considerable fixation of unfavorable alleles rendered the purging performance of selfing and cross-breeding strategies ineffective, and resulted in substantial inferiority in comparison to the other strategies in the long-term.

@article{scott_whole_2016,
	title = {Whole genome duplication in coast redwood ( \textit{{Sequoia} sempervirens} ) and its implications for explaining the rarity of polyploidy in conifers},
	volume = {211},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.13930},
	doi = {10.1111/nph.13930},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Scott, Alison Dawn and Stenz, Noah W. M. and Ingvarsson, Pär K. and Baum, David A.},
	month = jul,
	year = {2016},
	pages = {186--193},
}

@article{heskel_convergence_2016,
	title = {Convergence in the temperature response of leaf respiration across biomes and plant functional types},
	volume = {113},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1520282113},
	doi = {10.1073/pnas.1520282113},
	abstract = {Plant respiration constitutes a massive carbon flux to the atmosphere, and a major control on the evolution of the global carbon cycle. It therefore has the potential to modulate levels of climate change due to the human burning of fossil fuels. Neither current physiological nor terrestrial biosphere models adequately describe its short-term temperature response, and even minor differences in the shape of the response curve can significantly impact estimates of ecosystem carbon release and/or storage. Given this, it is critical to establish whether there are predictable patterns in the shape of the respiration–temperature response curve, and thus in the intrinsic temperature sensitivity of respiration across the globe. Analyzing measurements in a comprehensive database for 231 species spanning 7 biomes, we demonstrate that temperature-dependent increases in leaf respiration do not follow a commonly used exponential function. Instead, we find a decelerating function as leaves warm, reflecting a declining sensitivity to higher temperatures that is remarkably uniform across all biomes and plant functional types. Such convergence in the temperature sensitivity of leaf respiration suggests that there are universally applicable controls on the temperature response of plant energy metabolism, such that a single new function can predict the temperature dependence of leaf respiration for global vegetation. This simple function enables straightforward description of plant respiration in the land-surface components of coupled earth system models. Our cross-biome analyses shows significant implications for such fluxes in cold climates, generally projecting lower values compared with previous estimates.},
	language = {en},
	number = {14},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Heskel, Mary A. and O’Sullivan, Odhran S. and Reich, Peter B. and Tjoelker, Mark G. and Weerasinghe, Lasantha K. and Penillard, Aurore and Egerton, John J. G. and Creek, Danielle and Bloomfield, Keith J. and Xiang, Jen and Sinca, Felipe and Stangl, Zsofia R. and Martinez-de la Torre, Alberto and Griffin, Kevin L. and Huntingford, Chris and Hurry, Vaughan and Meir, Patrick and Turnbull, Matthew H. and Atkin, Owen K.},
	month = apr,
	year = {2016},
	pages = {3832--3837},
}

Plant respiration constitutes a massive carbon flux to the atmosphere, and a major control on the evolution of the global carbon cycle. It therefore has the potential to modulate levels of climate change due to the human burning of fossil fuels. Neither current physiological nor terrestrial biosphere models adequately describe its short-term temperature response, and even minor differences in the shape of the response curve can significantly impact estimates of ecosystem carbon release and/or storage. Given this, it is critical to establish whether there are predictable patterns in the shape of the respiration–temperature response curve, and thus in the intrinsic temperature sensitivity of respiration across the globe. Analyzing measurements in a comprehensive database for 231 species spanning 7 biomes, we demonstrate that temperature-dependent increases in leaf respiration do not follow a commonly used exponential function. Instead, we find a decelerating function as leaves warm, reflecting a declining sensitivity to higher temperatures that is remarkably uniform across all biomes and plant functional types. Such convergence in the temperature sensitivity of leaf respiration suggests that there are universally applicable controls on the temperature response of plant energy metabolism, such that a single new function can predict the temperature dependence of leaf respiration for global vegetation. This simple function enables straightforward description of plant respiration in the land-surface components of coupled earth system models. Our cross-biome analyses shows significant implications for such fluxes in cold climates, generally projecting lower values compared with previous estimates.

@article{betti_manipulating_2016,
	title = {Manipulating photorespiration to increase plant productivity: recent advances and perspectives for crop improvement},
	volume = {67},
	issn = {0022-0957, 1460-2431},
	shorttitle = {Manipulating photorespiration to increase plant productivity},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/erw076},
	doi = {10.1093/jxb/erw076},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Betti, Marco and Bauwe, Hermann and Busch, Florian A. and Fernie, Alisdair R. and Keech, Olivier and Levey, Myles and Ort, Donald R. and Parry, Martin A. J. and Sage, Rowan and Timm, Stefan and Walker, Berkley and Weber, Andreas P. M.},
	month = may,
	year = {2016},
	pages = {2977--2988},
}

@article{besya_intrinsic_2016,
	title = {Intrinsic phenotypic stability of a bi-stable auto regulatory gene},
	volume = {6},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/srep22951},
	doi = {10.1038/srep22951},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Besya, Azim-Berdy and Grönlund, Andreas},
	month = sep,
	year = {2016},
	pages = {22951},
}

@article{custers_eu_2016,
	title = {{EU} {Regulations} {Impede} {Market} {Introduction} of {GM} {Forest} {Trees}},
	volume = {21},
	issn = {13601385},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1360138516000315},
	doi = {10.1016/j.tplants.2016.01.015},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Trends in Plant Science},
	author = {Custers, René and Bartsch, Detlef and Fladung, Matthias and Nilsson, Ove and Pilate, Gilles and Sweet, Jeremy and Boerjan, Wout},
	month = apr,
	year = {2016},
	pages = {283--285},
}

@article{dobrenel_tor_2016,
	title = {{TOR} {Signaling} and {Nutrient} {Sensing}},
	volume = {67},
	issn = {1543-5008, 1545-2123},
	url = {http://www.annualreviews.org/doi/10.1146/annurev-arplant-043014-114648},
	doi = {10.1146/annurev-arplant-043014-114648},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Annual Review of Plant Biology},
	author = {Dobrenel, Thomas and Caldana, Camila and Hanson, Johannes and Robaglia, Christophe and Vincentz, Michel and Veit, Bruce and Meyer, Christian},
	month = apr,
	year = {2016},
	pages = {261--285},
}

@article{oyewole_soil_2016,
	title = {Soil diffusive fluxes constitute the bottleneck to tree nitrogen nutrition in a {Scots} pine forest},
	volume = {399},
	issn = {0032-079X, 1573-5036},
	url = {http://link.springer.com/10.1007/s11104-015-2680-5},
	doi = {10.1007/s11104-015-2680-5},
	language = {en},
	number = {1-2},
	urldate = {2021-06-07},
	journal = {Plant and Soil},
	author = {Oyewole, Olusegun Ayodeji and Jämtgård, Sandra and Gruffman, Linda and Inselsbacher, Erich and Näsholm, Torgny},
	month = feb,
	year = {2016},
	pages = {109--120},
}

@article{hall_precision_2016,
	title = {Precision {Automation} of {Cell} {Type} {Classification} and {Sub}-{Cellular} {Fluorescence} {Quantification} from {Laser} {Scanning} {Confocal} {Images}},
	volume = {7},
	issn = {1664-462X},
	url = {http://journal.frontiersin.org/Article/10.3389/fpls.2016.00119/abstract},
	doi = {10.3389/fpls.2016.00119},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Hall, Hardy C. and Fakhrzadeh, Azadeh and Luengo Hendriks, Cris L. and Fischer, Urs},
	month = feb,
	year = {2016},
}

@article{linden_reduced_2016,
	title = {Reduced mitochondrial malate dehydrogenase activity has a strong effect on photorespiratory metabolism as revealed by $^{\textrm{13}}$ {C} labelling},
	volume = {67},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/erw030},
	doi = {10.1093/jxb/erw030},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Lindén, Pernilla and Keech, Olivier and Stenlund, Hans and Gardeström, Per and Moritz, Thomas},
	month = may,
	year = {2016},
	pages = {3123--3135},
}

@article{wang_inactivation_2016,
	title = {Inactivation of {Mitochondrial} {Complex} {I} {Induces} the {Expression} of a {Twin} {Cysteine} {Protein} that {Targets} and {Affects} {Cytosolic}, {Chloroplastidic} and {Mitochondrial} {Function}},
	volume = {9},
	issn = {16742052},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1674205216000113},
	doi = {10.1016/j.molp.2016.01.009},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Molecular Plant},
	author = {Wang, Yan and Lyu, Wenhui and Berkowitz, Oliver and Radomiljac, Jordan D. and Law, Simon R. and Murcha, Monika W. and Carrie, Chris and Teixeira, Pedro F. and Kmiec, Beata and Duncan, Owen and Van Aken, Olivier and Narsai, Reena and Glaser, Elzbieta and Huang, Shaobai and Roessner, Ute and Millar, A. Harvey and Whelan, James},
	month = may,
	year = {2016},
	pages = {696--710},
}

@article{staubert_increased_2016,
	title = {Increased lanosterol turnover: a metabolic burden for daunorubicin-resistant leukemia cells},
	volume = {33},
	issn = {1357-0560, 1559-131X},
	shorttitle = {Increased lanosterol turnover},
	url = {http://link.springer.com/10.1007/s12032-015-0717-5},
	doi = {10.1007/s12032-015-0717-5},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Medical Oncology},
	author = {Stäubert, Claudia and Krakowsky, Rosanna and Bhuiyan, Hasanuzzaman and Witek, Barbara and Lindahl, Anna and Broom, Oliver and Nordström, Anders},
	month = jan,
	year = {2016},
	pages = {6},
}

@article{wuolikainen_multi-platform_2016,
	title = {Multi-platform mass spectrometry analysis of the {CSF} and plasma metabolomes of rigorously matched amyotrophic lateral sclerosis, {Parkinson}'s disease and control subjects},
	volume = {12},
	issn = {1742-206X, 1742-2051},
	url = {http://xlink.rsc.org/?DOI=C5MB00711A},
	doi = {10.1039/C5MB00711A},
	abstract = {Schematic view of the study design and the mass spectrometry platforms used for metabolomics analysis.
          , 
            Amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD) are protein-aggregation diseases that lack clear molecular etiologies. Biomarkers could aid in diagnosis, prognosis, planning of care, drug target identification and stratification of patients into clinical trials. We sought to characterize shared and unique metabolite perturbations between ALS and PD and matched controls selected from patients with other diagnoses, including differential diagnoses to ALS or PD that visited our clinic for a lumbar puncture. Cerebrospinal fluid (CSF) and plasma from rigorously age-, sex- and sampling-date matched patients were analyzed on multiple platforms using gas chromatography (GC) and liquid chromatography (LC)–mass spectrometry (MS). We applied constrained randomization of run orders and orthogonal partial least squares projection to latent structure-effect projections (OPLS-EP) to capitalize upon the study design. The combined platforms identified 144 CSF and 196 plasma metabolites with diverse molecular properties. Creatine was found to be increased and creatinine decreased in CSF of ALS patients compared to matched controls. Glucose was increased in CSF of ALS patients and α-hydroxybutyrate was increased in CSF and plasma of ALS patients compared to matched controls. Leucine, isoleucine and ketoleucine were increased in CSF of both ALS and PD. Together, these studies, in conjunction with earlier studies, suggest alterations in energy utilization pathways and have identified and further validated perturbed metabolites to be used in panels of biomarkers for the diagnosis of ALS and PD.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Molecular BioSystems},
	author = {Wuolikainen, Anna and Jonsson, Pär and Ahnlund, Maria and Antti, Henrik and Marklund, Stefan L. and Moritz, Thomas and Forsgren, Lars and Andersen, Peter M. and Trupp, Miles},
	year = {2016},
	pages = {1287--1298},
}

Schematic view of the study design and the mass spectrometry platforms used for metabolomics analysis. , Amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD) are protein-aggregation diseases that lack clear molecular etiologies. Biomarkers could aid in diagnosis, prognosis, planning of care, drug target identification and stratification of patients into clinical trials. We sought to characterize shared and unique metabolite perturbations between ALS and PD and matched controls selected from patients with other diagnoses, including differential diagnoses to ALS or PD that visited our clinic for a lumbar puncture. Cerebrospinal fluid (CSF) and plasma from rigorously age-, sex- and sampling-date matched patients were analyzed on multiple platforms using gas chromatography (GC) and liquid chromatography (LC)–mass spectrometry (MS). We applied constrained randomization of run orders and orthogonal partial least squares projection to latent structure-effect projections (OPLS-EP) to capitalize upon the study design. The combined platforms identified 144 CSF and 196 plasma metabolites with diverse molecular properties. Creatine was found to be increased and creatinine decreased in CSF of ALS patients compared to matched controls. Glucose was increased in CSF of ALS patients and α-hydroxybutyrate was increased in CSF and plasma of ALS patients compared to matched controls. Leucine, isoleucine and ketoleucine were increased in CSF of both ALS and PD. Together, these studies, in conjunction with earlier studies, suggest alterations in energy utilization pathways and have identified and further validated perturbed metabolites to be used in panels of biomarkers for the diagnosis of ALS and PD.

@article{obudulu_quantitative_2016,
	title = {Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development},
	volume = {17},
	issn = {1471-2164},
	url = {http://www.biomedcentral.com/1471-2164/17/119},
	doi = {10.1186/s12864-016-2458-z},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Obudulu, Ogonna and Bygdell, Joakim and Sundberg, Björn and Moritz, Thomas and Hvidsten, Torgeir R. and Trygg, Johan and Wingsle, Gunnar},
	month = dec,
	year = {2016},
	pages = {119},
}

@article{jiskrova_extra-_2016,
	title = {Extra- and intracellular distribution of cytokinins in the leaves of monocots and dicots},
	volume = {33},
	issn = {18716784},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1871678416000029},
	doi = {10.1016/j.nbt.2015.12.010},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {New Biotechnology},
	author = {Jiskrová, Eva and Novák, Ondřej and Pospíšilová, Hana and Holubová, Katarína and Karády, Michal and Galuszka, Petr and Robert, Stéphanie and Frébort, Ivo},
	month = sep,
	year = {2016},
	pages = {735--742},
}

@article{roberge_socio-ecological_2016,
	title = {Socio-ecological implications of modifying rotation lengths in forestry},
	volume = {45},
	issn = {0044-7447, 1654-7209},
	url = {http://link.springer.com/10.1007/s13280-015-0747-4},
	doi = {10.1007/s13280-015-0747-4},
	language = {en},
	number = {S2},
	urldate = {2021-06-07},
	journal = {Ambio},
	author = {Roberge, Jean-Michel and Laudon, Hjalmar and Björkman, Christer and Ranius, Thomas and Sandström, Camilla and Felton, Adam and Sténs, Anna and Nordin, Annika and Granström, Anders and Widemo, Fredrik and Bergh, Johan and Sonesson, Johan and Stenlid, Jan and Lundmark, Tomas},
	month = feb,
	year = {2016},
	pages = {109--123},
}

@article{laudon_role_2016,
	title = {The role of biogeochemical hotspots, landscape heterogeneity, and hydrological connectivity for minimizing forestry effects on water quality},
	volume = {45},
	issn = {0044-7447, 1654-7209},
	url = {http://link.springer.com/10.1007/s13280-015-0751-8},
	doi = {10.1007/s13280-015-0751-8},
	language = {en},
	number = {S2},
	urldate = {2021-06-07},
	journal = {Ambio},
	author = {Laudon, Hjalmar and Kuglerová, Lenka and Sponseller, Ryan A. and Futter, Martyn and Nordin, Annika and Bishop, Kevin and Lundmark, Tomas and Egnell, Gustaf and Ågren, Anneli M.},
	month = feb,
	year = {2016},
	pages = {152--162},
}

@article{sponseller_nitrogen_2016,
	title = {Nitrogen dynamics in managed boreal forests: {Recent} advances and future research directions},
	volume = {45},
	issn = {0044-7447, 1654-7209},
	shorttitle = {Nitrogen dynamics in managed boreal forests},
	url = {http://link.springer.com/10.1007/s13280-015-0755-4},
	doi = {10.1007/s13280-015-0755-4},
	language = {en},
	number = {S2},
	urldate = {2021-06-07},
	journal = {Ambio},
	author = {Sponseller, Ryan A. and Gundale, Michael J. and Futter, Martyn and Ring, Eva and Nordin, Annika and Näsholm, Torgny and Laudon, Hjalmar},
	month = feb,
	year = {2016},
	pages = {175--187},
}

@article{ding_molecular_2016,
	title = {Molecular regulation of phenology in trees — because the seasons they are a-changin’},
	volume = {29},
	issn = {13695266},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526615001831},
	doi = {10.1016/j.pbi.2015.11.007},
	language = {en},
	urldate = {2021-06-07},
	journal = {Current Opinion in Plant Biology},
	author = {Ding, Jihua and Nilsson, Ove},
	month = feb,
	year = {2016},
	pages = {73--79},
}

@article{pedmale_cryptochromes_2016,
	title = {Cryptochromes {Interact} {Directly} with {PIFs} to {Control} {Plant} {Growth} in {Limiting} {Blue} {Light}},
	volume = {164},
	issn = {00928674},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0092867415016426},
	doi = {10.1016/j.cell.2015.12.018},
	language = {en},
	number = {1-2},
	urldate = {2021-06-07},
	journal = {Cell},
	author = {Pedmale, Ullas V. and Huang, Shao-shan Carol and Zander, Mark and Cole, Benjamin J. and Hetzel, Jonathan and Ljung, Karin and Reis, Pedro A.B. and Sridevi, Priya and Nito, Kazumasa and Nery, Joseph R. and Ecker, Joseph R. and Chory, Joanne},
	month = jan,
	year = {2016},
	pages = {233--245},
}

@article{dekkers_arabidopsis_2016,
	title = {The {Arabidopsis} \textit{{DELAY} {OF} {GERMINATION} 1} gene affects \textit{{ABSCISIC} {ACID} {INSENSITIVE} 5 ({ABI5})} expression and genetically interacts with \textit{{ABI3}} during {Arabidopsis} seed development},
	volume = {85},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.13118},
	doi = {10.1111/tpj.13118},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Dekkers, Bas J.W. and He, Hanzi and Hanson, Johannes and Willems, Leo A.J. and Jamar, Diaan C.L. and Cueff, Gwendal and Rajjou, Loïc and Hilhorst, Henk W.M. and Bentsink, Leónie},
	month = feb,
	year = {2016},
	pages = {451--465},
}

@article{lundmark_comparison_2016,
	title = {Comparison of carbon balances between continuous-cover and clear-cut forestry in {Sweden}},
	volume = {45},
	issn = {0044-7447, 1654-7209},
	url = {http://link.springer.com/10.1007/s13280-015-0756-3},
	doi = {10.1007/s13280-015-0756-3},
	language = {en},
	number = {S2},
	urldate = {2021-06-07},
	journal = {Ambio},
	author = {Lundmark, Tomas and Bergh, Johan and Nordin, Annika and Fahlvik, Nils and Poudel, Bishnu Chandra},
	month = feb,
	year = {2016},
	pages = {203--213},
}

@article{missailidis_serum_2016,
	title = {Serum {Trimethylamine}-{N}-{Oxide} {Is} {Strongly} {Related} to {Renal} {Function} and {Predicts} {Outcome} in {Chronic} {Kidney} {Disease}},
	volume = {11},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0141738},
	doi = {10.1371/journal.pone.0141738},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Missailidis, Catharina and Hällqvist, Jenny and Qureshi, Abdel Rashid and Barany, Peter and Heimbürger, Olof and Lindholm, Bengt and Stenvinkel, Peter and Bergman, Peter},
	editor = {Burdmann, Emmanuel A},
	month = jan,
	year = {2016},
	pages = {e0141738},
}

@article{he_effects_2016,
	title = {Effects of {Parental} {Temperature} and {Nitrate} on {Seed} {Performance} are {Reflected} by {Partly} {Overlapping} {Genetic} and {Metabolic} {Pathways}},
	volume = {57},
	issn = {0032-0781, 1471-9053},
	url = {https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/pcv207},
	doi = {10.1093/pcp/pcv207},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant and Cell Physiology},
	author = {He, Hanzi and Willems, Leo A. J. and Batushansky, Albert and Fait, Aaron and Hanson, Johannes and Nijveen, Harm and Hilhorst, Henk W.M. and Bentsink, Leónie},
	month = mar,
	year = {2016},
	pages = {473--487},
}

@article{escamez_metacaspase9_2016,
	title = {{METACASPASE9} modulates autophagy to confine cell death to the target cells during \textit{{Arabidopsis}} vascular xylem differentiation},
	volume = {5},
	issn = {2046-6390},
	url = {https://journals.biologists.com/bio/article/5/2/122/643/METACASPASE9-modulates-autophagy-to-confine-cell},
	doi = {10.1242/bio.015529},
	abstract = {ABSTRACT
            We uncovered that the level of autophagy in plant cells undergoing programmed cell death determines the fate of the surrounding cells. Our approach consisted of using Arabidopsis thaliana cell cultures capable of differentiating into two different cell types: vascular tracheary elements (TEs) that undergo programmed cell death (PCD) and protoplast autolysis, and parenchymatic non-TEs that remain alive. The TE cell type displayed higher levels of autophagy when expression of the TE-specific METACASPASE9 (MC9) was reduced using RNAi (MC9-RNAi). Misregulation of autophagy in the MC9-RNAi TEs coincided with ectopic death of the non-TEs, implying the existence of an autophagy-dependent intercellular signalling from within the TEs towards the non-TEs. Viability of the non-TEs was restored when AUTOPHAGY2 (ATG2) was downregulated specifically in MC9-RNAi TEs, demonstrating the importance of autophagy in the spatial confinement of cell death. Our results suggest that other eukaryotic cells undergoing PCD might also need to tightly regulate their level of autophagy to avoid detrimental consequences for the surrounding cells.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Biology Open},
	author = {Escamez, Sacha and André, Domenique and Zhang, Bo and Bollhöner, Benjamin and Pesquet, Edouard and Tuominen, Hannele},
	month = feb,
	year = {2016},
	pages = {122--129},
}

ABSTRACT We uncovered that the level of autophagy in plant cells undergoing programmed cell death determines the fate of the surrounding cells. Our approach consisted of using Arabidopsis thaliana cell cultures capable of differentiating into two different cell types: vascular tracheary elements (TEs) that undergo programmed cell death (PCD) and protoplast autolysis, and parenchymatic non-TEs that remain alive. The TE cell type displayed higher levels of autophagy when expression of the TE-specific METACASPASE9 (MC9) was reduced using RNAi (MC9-RNAi). Misregulation of autophagy in the MC9-RNAi TEs coincided with ectopic death of the non-TEs, implying the existence of an autophagy-dependent intercellular signalling from within the TEs towards the non-TEs. Viability of the non-TEs was restored when AUTOPHAGY2 (ATG2) was downregulated specifically in MC9-RNAi TEs, demonstrating the importance of autophagy in the spatial confinement of cell death. Our results suggest that other eukaryotic cells undergoing PCD might also need to tightly regulate their level of autophagy to avoid detrimental consequences for the surrounding cells.

@article{tibiletti_deletion_2016,
	title = {Deletion of the gene family of small chlorophyll-binding proteins ({ScpABCDE}) offsets {C}/{N} homeostasis in {Synechocystis} {PCC} 6803},
	volume = {1857},
	issn = {00052728},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0005272815002431},
	doi = {10.1016/j.bbabio.2015.11.011},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {Tibiletti, Tania and Hernández-Prieto, Miguel A. and Matthijs, Hans C.P. and Niyogi, Krishna K. and Funk, Christiane},
	month = apr,
	year = {2016},
	pages = {396--407},
}

@article{ranade_application_2016,
	title = {Application of monochromatic blue light during germination and hypocotyl development improves outplanted {Scots} pine ({Pinus} sylvestris {L}.) trees performance},
	volume = {361},
	issn = {03781127},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S037811271500657X},
	doi = {10.1016/j.foreco.2015.11.034},
	language = {en},
	urldate = {2021-06-07},
	journal = {Forest Ecology and Management},
	author = {Ranade, Sonali Sachin and García Gil, M.R.},
	month = feb,
	year = {2016},
	pages = {368--374},
}

@article{bernhardsson_present_2016,
	title = {Present genetic structure is congruent with the common origin of distant {Scots} pine populations in its {Romanian} distribution},
	volume = {361},
	issn = {03781127},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378112715006052},
	doi = {10.1016/j.foreco.2015.10.047},
	language = {en},
	urldate = {2021-06-07},
	journal = {Forest Ecology and Management},
	author = {Bernhardsson, C. and Floran, V. and Ganea, S.L. and García-Gil, M.R.},
	month = feb,
	year = {2016},
	pages = {131--143},
}

@article{ranade_non-functional_2016,
	title = {Non-functional plastid ndh gene fragments are present in the nuclear genome of {Norway} spruce ({Picea} abies {L}. {Karsch}): insights from in silico analysis of nuclear and organellar genomes},
	volume = {291},
	issn = {1617-4615, 1617-4623},
	shorttitle = {Non-functional plastid ndh gene fragments are present in the nuclear genome of {Norway} spruce ({Picea} abies {L}. {Karsch})},
	url = {http://link.springer.com/10.1007/s00438-015-1159-7},
	doi = {10.1007/s00438-015-1159-7},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Molecular Genetics and Genomics},
	author = {Ranade, Sonali Sachin and García-Gil, María Rosario and Rosselló, Josep A.},
	month = apr,
	year = {2016},
	pages = {935--941},
}

@article{baral_exploring_2016,
	title = {Exploring exocytosis using chemical genomics},
	volume = {113},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1522317113},
	doi = {10.1073/pnas.1522317113},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Baral, Anirban and Bhalerao, Rishikesh P.},
	month = jan,
	year = {2016},
	pages = {14--16},
}

@incollection{caillaud_ratiometric_2016,
	address = {New York, NY},
	title = {Ratiometric {Fluorescence} {Live} {Imaging} {Analysis} of {Membrane} {Lipid} {Order} in {Arabidopsis} {Mitotic} {Cells} {Using} a {Lipid} {Order}-{Sensitive} {Probe}},
	volume = {1370},
	isbn = {9781493931415 9781493931422},
	url = {http://link.springer.com/10.1007/978-1-4939-3142-2_17},
	urldate = {2021-06-07},
	booktitle = {Plant {Cell} {Division}},
	publisher = {Springer New York},
	author = {Gerbeau-Pissot, Patricia and Der, Christophe and Grebe, Markus and Stanislas, Thomas},
	editor = {Caillaud, Marie-Cécile},
	year = {2016},
	doi = {10.1007/978-1-4939-3142-2_17},
	pages = {227--239},
}

@article{ricroch_challenges_2016,
	title = {Challenges facing {European} agriculture and possible biotechnological solutions},
	volume = {36},
	issn = {0738-8551, 1549-7801},
	url = {https://www.tandfonline.com/doi/full/10.3109/07388551.2015.1055707},
	doi = {10.3109/07388551.2015.1055707},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Critical Reviews in Biotechnology},
	author = {Ricroch, Agnès and Harwood, Wendy and Svobodová, Zdeňka and Sági, László and Hundleby, Penelope and Badea, Elena Marcela and Rosca, Ioan and Cruz, Gabriela and Salema Fevereiro, Manuel Pedro and Marfà Riera, Victoria and Jansson, Stefan and Morandini, Piero and Bojinov, Bojin and Cetiner, Selim and Custers, René and Schrader, Uwe and Jacobsen, Hans-Joerg and Martin-Laffon, Jacqueline and Boisron, Audrey and Kuntz, Marcel},
	month = sep,
	year = {2016},
	pages = {875--883},
}

@article{funda_mating_2016,
	title = {Mating dynamics of {Scots} pine in isolation tents},
	volume = {12},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-016-1074-z},
	doi = {10.1007/s11295-016-1074-z},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Tree Genetics \& Genomes},
	author = {Funda, Tomas and Wennström, Ulfstand and Almqvist, Curt and Andersson Gull, Bengt and Wang, Xiao-Ru},
	month = dec,
	year = {2016},
	pages = {112},
}

@article{bugala_characterization_2016,
	title = {Characterization of newly identified {DnaA} and {DnaB} proteins from {Acetobacter}},
	volume = {167},
	issn = {09232508},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0923250816300730},
	doi = {10.1016/j.resmic.2016.06.010},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Research in Microbiology},
	author = {Bugala, Juraj and Cimová, Viera and Grones, Peter and Grones, Jozef},
	month = oct,
	year = {2016},
	pages = {655--668},
}