Publications 2018

@article{kremling_dysregulation_2018,
	title = {Dysregulation of expression correlates with rare-allele burden and fitness loss in maize},
	volume = {555},
	copyright = {2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/nature25966},
	doi = {10.1038/nature25966},
	abstract = {A multi-tissue gene expression resource representative of the genotypic and phenotypic diversity of modern inbred maize reveals the effect of rare alleles and evolutionary history on the regulation of gene expression.},
	language = {en},
	number = {7697},
	urldate = {2024-03-22},
	journal = {Nature},
	author = {Kremling, Karl A. G. and Chen, Shu-Yun and Su, Mei-Hsiu and Lepak, Nicholas K. and Romay, M. Cinta and Swarts, Kelly L. and Lu, Fei and Lorant, Anne and Bradbury, Peter J. and Buckler, Edward S.},
	month = mar,
	year = {2018},
	note = {Publisher: Nature Publishing Group},
	keywords = {Agricultural genetics, Gene regulation, Rare variants},
	pages = {520--523},
}

A multi-tissue gene expression resource representative of the genotypic and phenotypic diversity of modern inbred maize reveals the effect of rare alleles and evolutionary history on the regulation of gene expression.

@article{bilinski_parallel_2018,
	title = {Parallel altitudinal clines reveal trends in adaptive evolution of genome size in {Zea} mays},
	volume = {14},
	issn = {1553-7404},
	url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007162},
	doi = {10.1371/journal.pgen.1007162},
	abstract = {While the vast majority of genome size variation in plants is due to differences in repetitive sequence, we know little about how selection acts on repeat content in natural populations. Here we investigate parallel changes in intraspecific genome size and repeat content of domesticated maize (Zea mays) landraces and their wild relative teosinte across altitudinal gradients in Mesoamerica and South America. We combine genotyping, low coverage whole-genome sequence data, and flow cytometry to test for evidence of selection on genome size and individual repeat abundance. We find that population structure alone cannot explain the observed variation, implying that clinal patterns of genome size are maintained by natural selection. Our modeling additionally provides evidence of selection on individual heterochromatic knob repeats, likely due to their large individual contribution to genome size. To better understand the phenotypes driving selection on genome size, we conducted a growth chamber experiment using a population of highland teosinte exhibiting extensive variation in genome size. We find weak support for a positive correlation between genome size and cell size, but stronger support for a negative correlation between genome size and the rate of cell production. Reanalyzing published data of cell counts in maize shoot apical meristems, we then identify a negative correlation between cell production rate and flowering time. Together, our data suggest a model in which variation in genome size is driven by natural selection on flowering time across altitudinal clines, connecting intraspecific variation in repetitive sequence to important differences in adaptive phenotypes.},
	language = {en},
	number = {5},
	urldate = {2024-03-22},
	journal = {PLOS Genetics},
	author = {Bilinski, Paul and Albert, Patrice S. and Berg, Jeremy J. and Birchler, James A. and Grote, Mark N. and Lorant, Anne and Quezada, Juvenal and Swarts, Kelly and Yang, Jinliang and Ross-Ibarra, Jeffrey},
	month = may,
	year = {2018},
	note = {Publisher: Public Library of Science},
	keywords = {Fish genomics, Inbreeding, Invertebrate genomics, Leaves, Maize, Natural selection, Plant genomics, Transposable elements},
	pages = {e1007162},
}

While the vast majority of genome size variation in plants is due to differences in repetitive sequence, we know little about how selection acts on repeat content in natural populations. Here we investigate parallel changes in intraspecific genome size and repeat content of domesticated maize (Zea mays) landraces and their wild relative teosinte across altitudinal gradients in Mesoamerica and South America. We combine genotyping, low coverage whole-genome sequence data, and flow cytometry to test for evidence of selection on genome size and individual repeat abundance. We find that population structure alone cannot explain the observed variation, implying that clinal patterns of genome size are maintained by natural selection. Our modeling additionally provides evidence of selection on individual heterochromatic knob repeats, likely due to their large individual contribution to genome size. To better understand the phenotypes driving selection on genome size, we conducted a growth chamber experiment using a population of highland teosinte exhibiting extensive variation in genome size. We find weak support for a positive correlation between genome size and cell size, but stronger support for a negative correlation between genome size and the rate of cell production. Reanalyzing published data of cell counts in maize shoot apical meristems, we then identify a negative correlation between cell production rate and flowering time. Together, our data suggest a model in which variation in genome size is driven by natural selection on flowering time across altitudinal clines, connecting intraspecific variation in repetitive sequence to important differences in adaptive phenotypes.

@article{drapek_minimum_2018,
	title = {Minimum requirements for changing and maintaining endodermis cell identity in the {Arabidopsis} root},
	volume = {4},
	issn = {2055-0278},
	url = {http://www.nature.com/articles/s41477-018-0213-y},
	doi = {10/gd9kpt},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Nature Plants},
	author = {Drapek, Colleen and Sparks, Erin E. and Marhavý, Peter and Taylor, Isaiah and Andersen, Tonni G. and Hennacy, Jessica H. and Geldner, Niko and Benfey, Philip N.},
	month = aug,
	year = {2018},
	pages = {586--595},
}

@article{pandey_lbd18_2018,
	title = {{LBD18} uses a dual mode of a positive feedback loop to regulate {ARF} expression and transcriptional activity in {Arabidopsis}},
	volume = {95},
	copyright = {© 2018 The Authors The Plant Journal © 2018 John Wiley \& Sons Ltd},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.13945},
	doi = {10.1111/tpj.13945},
	abstract = {A hierarchy of transcriptional regulators controlling lateral root formation in Arabidopsis thaliana has been identified, including the AUXIN RESPONSE FACTOR 7 (ARF7)/ARF19-LATERAL ORGAN BOUNDARIES DOMAIN 16 (LBD16)/LBD18 transcriptional network; however, their feedback regulation mechanisms are not known. Here we show that LBD18 controls ARF activity using the dual mode of a positive feedback loop. We showed that ARF7 and ARF19 directly bind AuxRE in the LBD18 promoter. A variety of molecular and biochemical experiments demonstrated that LBD18 binds a specific DNA motif in the ARF19 promoter to regulate its expression in vivo as well as in vitro. LBD18 interacts with ARFs including ARF7 and ARF19 via the Phox and Bem1 domain of ARF to enhance the transcriptional activity of ARF7 on AuxRE, and competes with auxin/indole-3-acetic acid (IAA) repressors for ARF binding, overriding the negative feedback loop exerted by Aux/IAA repressors. Taken together, these results show that LBD18 and ARFs form a double positive feedback loop, and that LBD18 uses the dual mode of a positive feedback loop by binding directly to the ARF19 promoter and through the protein–protein interactions with ARF7 and ARF19. This novel mechanism of feedback loops may constitute a robust feedback mechanism that ensures continued lateral root growth in response to auxin in Arabidopsis.},
	language = {en},
	number = {2},
	urldate = {2023-11-14},
	journal = {The Plant Journal},
	author = {Pandey, Shashank K. and Lee, Han Woo and Kim, Min-Jung and Cho, Chuloh and Oh, Eunkyoo and Kim, Jungmook},
	year = {2018},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.13945},
	keywords = {Arabidopsis thaliana, auxin, feedback regulation, lateral root development, protein–protein interaction, transcriptional regulation},
	pages = {233--251},
}

A hierarchy of transcriptional regulators controlling lateral root formation in Arabidopsis thaliana has been identified, including the AUXIN RESPONSE FACTOR 7 (ARF7)/ARF19-LATERAL ORGAN BOUNDARIES DOMAIN 16 (LBD16)/LBD18 transcriptional network; however, their feedback regulation mechanisms are not known. Here we show that LBD18 controls ARF activity using the dual mode of a positive feedback loop. We showed that ARF7 and ARF19 directly bind AuxRE in the LBD18 promoter. A variety of molecular and biochemical experiments demonstrated that LBD18 binds a specific DNA motif in the ARF19 promoter to regulate its expression in vivo as well as in vitro. LBD18 interacts with ARFs including ARF7 and ARF19 via the Phox and Bem1 domain of ARF to enhance the transcriptional activity of ARF7 on AuxRE, and competes with auxin/indole-3-acetic acid (IAA) repressors for ARF binding, overriding the negative feedback loop exerted by Aux/IAA repressors. Taken together, these results show that LBD18 and ARFs form a double positive feedback loop, and that LBD18 uses the dual mode of a positive feedback loop by binding directly to the ARF19 promoter and through the protein–protein interactions with ARF7 and ARF19. This novel mechanism of feedback loops may constitute a robust feedback mechanism that ensures continued lateral root growth in response to auxin in Arabidopsis.

@article{pandey_coiled-coil_2018,
	title = {Coiled-coil motif in {LBD16} and {LBD18} transcription factors are critical for dimerization and biological function in arabidopsis},
	volume = {13},
	issn = {null},
	url = {https://doi.org/10.1080/15592324.2017.1411450},
	doi = {10.1080/15592324.2017.1411450},
	abstract = {The LATERAL ORGAN BOUNDARIES (LOB) DOMAIN (LBD) gene family members encode a class of plant-specific transcription factors that play important roles in many different aspects of plant growth and development. The LBD proteins contain a conserved LOB domain harboring a Leu zipper-like coiled-coil motif, which has been predicted to mediate protein-protein interactions among the LBD family members. Dimerization of transcription factors is crucial for the modulation of their DNA-binding affinity, specificity, and diversity, contributing to the transcriptional regulation of distinct cellular and biological responses. Our various molecular and biochemical experiments with genetic approaches on LBD16 and LBD18, which are known to control lateral root development in Arabidopsis, demonstrated that the conserved Leu or Val residues in the coiled-coil motifs of these transcription factors are critical for their dimerization as well as the transcriptional regulation to display their biological functions during lateral root formation. We further showed that beside the coiled-coil motif, the carboxyl-terminal region in LBD18 acts as an additional dimerization domain. These findings provide a molecular framework for the homo- and hetero-dimerization of the LBD family proteins for displaying their distinct and diverse biological functions in plants.},
	number = {1},
	urldate = {2023-11-14},
	journal = {Plant Signaling \& Behavior},
	author = {Pandey, Shashank K. and Kim, Jungmook},
	month = jan,
	year = {2018},
	pmid = {29227192},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/15592324.2017.1411450},
	keywords = {Arabidopsis, LBD16, LBD18, coiled-coil motif, lateral organ boundaries domain, lateral root development, protein-protein interactions, transcriptional regulation},
	pages = {e1411450},
}

The LATERAL ORGAN BOUNDARIES (LOB) DOMAIN (LBD) gene family members encode a class of plant-specific transcription factors that play important roles in many different aspects of plant growth and development. The LBD proteins contain a conserved LOB domain harboring a Leu zipper-like coiled-coil motif, which has been predicted to mediate protein-protein interactions among the LBD family members. Dimerization of transcription factors is crucial for the modulation of their DNA-binding affinity, specificity, and diversity, contributing to the transcriptional regulation of distinct cellular and biological responses. Our various molecular and biochemical experiments with genetic approaches on LBD16 and LBD18, which are known to control lateral root development in Arabidopsis, demonstrated that the conserved Leu or Val residues in the coiled-coil motifs of these transcription factors are critical for their dimerization as well as the transcriptional regulation to display their biological functions during lateral root formation. We further showed that beside the coiled-coil motif, the carboxyl-terminal region in LBD18 acts as an additional dimerization domain. These findings provide a molecular framework for the homo- and hetero-dimerization of the LBD family proteins for displaying their distinct and diverse biological functions in plants.

@article{xia_combining_2018,
	title = {Combining mitochondrial and nuclear genome analyses to dissect the effects of colonization, environment, and geography on population structure in {Pinus} tabuliformis},
	volume = {11},
	issn = {1752-4571},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.12697},
	doi = {10.1111/eva.12697},
	abstract = {The phylogeographic histories of plants in East Asia are complex and shaped by both past large-scale climatic oscillations and dramatic tectonic events. The impact of these historic events, as well as ecological adaptation, on the distribution of biodiversity remains to be elucidated. Pinus tabuliformis is the dominant coniferous tree in northern China, with a large distribution across wide environmental gradients. We examined genetic variation in this species using genotyping-by-sequencing and mitochondrial (mt) DNA markers. We found population structure on both nuclear and mt genomes with a geographic pattern that corresponds well with the landscape of northern China. To understand the contributions of environment, geography, and colonization history to the observed population structure, we performed ecological niche modeling and partitioned the among-population genomic variance into isolation by environment (IBE), isolation by distance (IBD), and isolation by colonization (IBC). We used mtDNA, which is transmitted by seeds in pine, to reflect colonization. We found little impact of IBE, IBD, and IBC on variation in neutral SNPs, but significant impact of IBE on a group of outlier loci. The lack of IBC illustrates that the maternal history can be quickly eroded from the nuclear genome by high rates of gene flow. Our results suggest that genomic variation in P. tabuliformis is largely affected by neutral and stochastic processes, and the signature of local adaptation is visible only at robust outlier loci. This study enriches our understanding on the complex evolutionary forces that shape the distribution of genetic variation in plant taxa in northern China, and guides breeding, conservation, and reforestation programs for P. tabuliformis.},
	language = {en},
	number = {10},
	urldate = {2023-04-27},
	journal = {Evolutionary Applications},
	author = {Xia, Hanhan and Wang, Baosheng and Zhao, Wei and Pan, Jin and Mao, Jian-Feng and Wang, Xiao-Ru},
	year = {2018},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.12697},
	keywords = {demographic history, genotyping-by-sequencing, local adaptation, niche modeling, population structure},
	pages = {1931--1945},
}

The phylogeographic histories of plants in East Asia are complex and shaped by both past large-scale climatic oscillations and dramatic tectonic events. The impact of these historic events, as well as ecological adaptation, on the distribution of biodiversity remains to be elucidated. Pinus tabuliformis is the dominant coniferous tree in northern China, with a large distribution across wide environmental gradients. We examined genetic variation in this species using genotyping-by-sequencing and mitochondrial (mt) DNA markers. We found population structure on both nuclear and mt genomes with a geographic pattern that corresponds well with the landscape of northern China. To understand the contributions of environment, geography, and colonization history to the observed population structure, we performed ecological niche modeling and partitioned the among-population genomic variance into isolation by environment (IBE), isolation by distance (IBD), and isolation by colonization (IBC). We used mtDNA, which is transmitted by seeds in pine, to reflect colonization. We found little impact of IBE, IBD, and IBC on variation in neutral SNPs, but significant impact of IBE on a group of outlier loci. The lack of IBC illustrates that the maternal history can be quickly eroded from the nuclear genome by high rates of gene flow. Our results suggest that genomic variation in P. tabuliformis is largely affected by neutral and stochastic processes, and the signature of local adaptation is visible only at robust outlier loci. This study enriches our understanding on the complex evolutionary forces that shape the distribution of genetic variation in plant taxa in northern China, and guides breeding, conservation, and reforestation programs for P. tabuliformis.

@article{huang_development_2018,
	title = {Development of high transferability {cpSSR} markers for individual identification and genetic investigation in {Cupressaceae} species},
	volume = {8},
	issn = {2045-7758},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.4053},
	doi = {10.1002/ece3.4053},
	abstract = {Given the low substitution rate in plastomes, the polymorphic and codominant nature of chloroplast SSRs (cpSSRs) makes them ideal markers, complementing their nuclear counterpart. In Cupressaceae, cpSSRs are mostly paternally inherited, thus, they are useful in mating systems and pollen flow studies. Using e-PCR, 92 SSR loci were identified across six Cupressaceae plastomes, and primers were designed for 26 loci with potential interspecific transferability. The 26 developed cpSSRs were polymorphic in four genera, Platycladus, Sabina, Juniperus, and Cupressus and are suitable for Cupressaceae molecular genetic studies and utilization. We genotyped 192 Platycladus orientalis samples from a core breeding population using 10 of the developed cpSSRs and 10 nuclear SSRs, and these individuals were identified with high confidence. The developed cpSSRs can be used in (1) a marker-assisted breeding scheme, specifically when paternity identification is required, (2) population genetics investigations, and (3) biogeography of Cupressaceae and unraveling the genetic relationships between related species.},
	language = {en},
	number = {10},
	urldate = {2023-04-27},
	journal = {Ecology and Evolution},
	author = {Huang, Li-Sha and Sun, Yan-Qiang and Jin, Yuqing and Gao, Qiong and Hu, Xian-Ge and Gao, Fu-Ling and Yang, Xiao-Lei and Zhu, Ji-Jun and El-Kassaby, Yousry A. and Mao, Jian-Feng},
	year = {2018},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.4053},
	keywords = {Cupressaceae, chloroplast SSRs, genetic diversity, haplotype, mating system, paternity test},
	pages = {4967--4977},
}

Given the low substitution rate in plastomes, the polymorphic and codominant nature of chloroplast SSRs (cpSSRs) makes them ideal markers, complementing their nuclear counterpart. In Cupressaceae, cpSSRs are mostly paternally inherited, thus, they are useful in mating systems and pollen flow studies. Using e-PCR, 92 SSR loci were identified across six Cupressaceae plastomes, and primers were designed for 26 loci with potential interspecific transferability. The 26 developed cpSSRs were polymorphic in four genera, Platycladus, Sabina, Juniperus, and Cupressus and are suitable for Cupressaceae molecular genetic studies and utilization. We genotyped 192 Platycladus orientalis samples from a core breeding population using 10 of the developed cpSSRs and 10 nuclear SSRs, and these individuals were identified with high confidence. The developed cpSSRs can be used in (1) a marker-assisted breeding scheme, specifically when paternity identification is required, (2) population genetics investigations, and (3) biogeography of Cupressaceae and unraveling the genetic relationships between related species.

@article{huang_pollination_2018,
	title = {Pollination dynamics in a {Platycladus} orientalis seed orchard as revealed by partial pedigree reconstruction},
	volume = {48},
	issn = {0045-5067},
	url = {https://cdnsciencepub.com/doi/10.1139/cjfr-2018-0077},
	doi = {10.1139/cjfr-2018-0077},
	abstract = {Pollination dynamics was studied in a first-generation Platycladus orientalis (L.) Franco seed orchard with pedigree reconstruction using eight nuclear and four chloroplast SSRs. The pedigree reconstruction assigned 371 of 448 studied seeds to one of the orchard’s 192 candidate male parents and showed a high level of outcrossing and pollen contamination in the orchard’s seed crop. While the orchard’s seed population showed greater allelic richness compared with the parental population, a few alleles present in the parental population were missing in the seed crop. Additionally, we detected no significant correlation between male reproductive energy (pollen yield) and male reproductive success; however, uneven parental contribution was also observed. Pollen management practices were recommended to ensure the maintenance of genetic diversity in the seed crops and increase in genetic gain.},
	number = {8},
	urldate = {2023-04-27},
	journal = {Canadian Journal of Forest Research},
	author = {Huang, Li-Sha and Song, Jiayin and Sun, Yan-Qiang and Gao, Qiong and Jiao, Si-Qian and Zhou, Shan-Shan and Jin, Yuqing and Yang, Xiao-Lei and Zhu, Ji-Jun and Gao, Fu-Ling and El-Kassaby, Yousry A. and Mao, Jian-Feng},
	month = aug,
	year = {2018},
	note = {Publisher: NRC Research Press},
	pages = {952--957},
}

Pollination dynamics was studied in a first-generation Platycladus orientalis (L.) Franco seed orchard with pedigree reconstruction using eight nuclear and four chloroplast SSRs. The pedigree reconstruction assigned 371 of 448 studied seeds to one of the orchard’s 192 candidate male parents and showed a high level of outcrossing and pollen contamination in the orchard’s seed crop. While the orchard’s seed population showed greater allelic richness compared with the parental population, a few alleles present in the parental population were missing in the seed crop. Additionally, we detected no significant correlation between male reproductive energy (pollen yield) and male reproductive success; however, uneven parental contribution was also observed. Pollen management practices were recommended to ensure the maintenance of genetic diversity in the seed crops and increase in genetic gain.

@article{dong_high-quality_2018,
	title = {High-quality assembly of the reference genome for scarlet sage, {Salvia} splendens, an economically important ornamental plant},
	volume = {7},
	issn = {2047-217X},
	url = {https://doi.org/10.1093/gigascience/giy068},
	doi = {10.1093/gigascience/giy068},
	abstract = {Salvia splendens Ker-Gawler, scarlet or tropical sage, is a tender herbaceous perennial widely introduced and seen in public gardens all over the world. With few molecular resources, breeding is still restricted to traditional phenotypic selection, and the genetic mechanisms underlying phenotypic variation remain unknown. Hence, a high-quality reference genome will be very valuable for marker-assisted breeding, genome editing, and molecular genetics.We generated 66 Gb and 37 Gb of raw DNA sequences, respectively, from whole-genome sequencing of a largely homozygous scarlet sage inbred line using Pacific Biosciences (PacBio) single-molecule real-time and Illumina HiSeq sequencing platforms. The PacBio de novo assembly yielded a final genome with a scaffold N50 size of 3.12 Mb and a total length of 808 Mb. The repetitive sequences identified accounted for 57.52\% of the genome sequence, and  54,008 protein-coding genes were predicted collectively with ab initio and homology-based gene prediction from the masked genome. The divergence time between S. splendens and Salvia miltiorrhiza was estimated at 28.21 million years ago (Mya). Moreover, 3,797 species-specific genes and 1,187 expanded gene families were identified for the scarlet sage genome.We provide the first genome sequence and gene annotation for the scarlet sage. The availability of these resources will be of great importance for further breeding strategies, genome editing, and comparative genomics among related species.},
	number = {7},
	urldate = {2023-04-27},
	journal = {GigaScience},
	author = {Dong, Ai-Xiang and Xin, Hai-Bo and Li, Zi-Jing and Liu, Hui and Sun, Yan-Qiang and Nie, Shuai and Zhao, Zheng-Nan and Cui, Rong-Feng and Zhang, Ren-Gang and Yun, Quan-Zheng and Wang, Xin-Ning and Maghuly, Fatemeh and Porth, Ilga and Cong, Ri-Chen and Mao, Jian-Feng},
	month = jul,
	year = {2018},
	pages = {giy068},
}

Salvia splendens Ker-Gawler, scarlet or tropical sage, is a tender herbaceous perennial widely introduced and seen in public gardens all over the world. With few molecular resources, breeding is still restricted to traditional phenotypic selection, and the genetic mechanisms underlying phenotypic variation remain unknown. Hence, a high-quality reference genome will be very valuable for marker-assisted breeding, genome editing, and molecular genetics.We generated 66 Gb and 37 Gb of raw DNA sequences, respectively, from whole-genome sequencing of a largely homozygous scarlet sage inbred line using Pacific Biosciences (PacBio) single-molecule real-time and Illumina HiSeq sequencing platforms. The PacBio de novo assembly yielded a final genome with a scaffold N50 size of 3.12 Mb and a total length of 808 Mb. The repetitive sequences identified accounted for 57.52% of the genome sequence, and  54,008 protein-coding genes were predicted collectively with ab initio and homology-based gene prediction from the masked genome. The divergence time between S. splendens and Salvia miltiorrhiza was estimated at 28.21 million years ago (Mya). Moreover, 3,797 species-specific genes and 1,187 expanded gene families were identified for the scarlet sage genome.We provide the first genome sequence and gene annotation for the scarlet sage. The availability of these resources will be of great importance for further breeding strategies, genome editing, and comparative genomics among related species.

@article{melida_non-branched_2018,
	title = {Non-branched β-1,3-glucan oligosaccharides trigger immune responses in {Arabidopsis}},
	volume = {93},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.13755},
	doi = {10.1111/tpj.13755},
	abstract = {Fungal cell walls, which are essential for environmental adaptation and host colonization by the fungus, have been evolutionarily selected by plants and animals as a source of microbe-associated molecular patterns (MAMPs) that, upon recognition by host pattern recognition receptors (PRRs), trigger immune responses conferring disease resistance. Chito-oligosaccharides [β-1,4-N-acetylglucosamine oligomers, (GlcNAc)n] are the only glycosidic structures from fungal walls that have been well-demonstrated to function as MAMPs in plants. Perception of (GlcNAc)4–8 by Arabidopsis involves CERK1, LYK4 and LYK5, three of the eight members of the LysM PRR family. We found that a glucan-enriched wall fraction from the pathogenic fungus Plectosphaerella cucumerina which was devoid of GlcNAc activated immune responses in Arabidopsis wild-type plants but not in the cerk1 mutant. Using this differential response, we identified the non-branched 1,3-β-d-(Glc) hexasaccharide as a major fungal MAMP. Recognition of 1,3-β-d-(Glc)6 was impaired in cerk1 but not in mutants defective in either each of the LysM PRR family members or in the PRR-co-receptor BAK1. Transcriptomic analyses of Arabidopsis plants treated with 1,3-β-d-(Glc)6 further demonstrated that this fungal MAMP triggers the expression of immunity-associated genes. In silico docking analyses with molecular mechanics and solvation energy calculations corroborated that CERK1 can bind 1,3-β-d-(Glc)6 at effective concentrations similar to those of (GlcNAc)4. These data support that plants, like animals, have selected as MAMPs the linear 1,3-β-d-glucans present in the walls of fungi and oomycetes. Our data also suggest that CERK1 functions as an immune co-receptor for linear 1,3-β-d-glucans in a similar way to its proposed function in the recognition of fungal chito-oligosaccharides and bacterial peptidoglycan MAMPs.},
	language = {en},
	number = {1},
	urldate = {2023-03-10},
	journal = {The Plant Journal},
	author = {Mélida, Hugo and Sopeña-Torres, Sara and Bacete, Laura and Garrido-Arandia, María and Jordá, Lucía and López, Gemma and Muñoz-Barrios, Antonio and Pacios, Luis F. and Molina, Antonio},
	year = {2018},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.13755},
	keywords = {BAK1, CERK, cell wall, chitin, glucan, necrotrophic fungi, plant immunity},
	pages = {34--49},
}

Fungal cell walls, which are essential for environmental adaptation and host colonization by the fungus, have been evolutionarily selected by plants and animals as a source of microbe-associated molecular patterns (MAMPs) that, upon recognition by host pattern recognition receptors (PRRs), trigger immune responses conferring disease resistance. Chito-oligosaccharides [β-1,4-N-acetylglucosamine oligomers, (GlcNAc)n] are the only glycosidic structures from fungal walls that have been well-demonstrated to function as MAMPs in plants. Perception of (GlcNAc)4–8 by Arabidopsis involves CERK1, LYK4 and LYK5, three of the eight members of the LysM PRR family. We found that a glucan-enriched wall fraction from the pathogenic fungus Plectosphaerella cucumerina which was devoid of GlcNAc activated immune responses in Arabidopsis wild-type plants but not in the cerk1 mutant. Using this differential response, we identified the non-branched 1,3-β-d-(Glc) hexasaccharide as a major fungal MAMP. Recognition of 1,3-β-d-(Glc)6 was impaired in cerk1 but not in mutants defective in either each of the LysM PRR family members or in the PRR-co-receptor BAK1. Transcriptomic analyses of Arabidopsis plants treated with 1,3-β-d-(Glc)6 further demonstrated that this fungal MAMP triggers the expression of immunity-associated genes. In silico docking analyses with molecular mechanics and solvation energy calculations corroborated that CERK1 can bind 1,3-β-d-(Glc)6 at effective concentrations similar to those of (GlcNAc)4. These data support that plants, like animals, have selected as MAMPs the linear 1,3-β-d-glucans present in the walls of fungi and oomycetes. Our data also suggest that CERK1 functions as an immune co-receptor for linear 1,3-β-d-glucans in a similar way to its proposed function in the recognition of fungal chito-oligosaccharides and bacterial peptidoglycan MAMPs.

@article{gonneau_receptor_2018,
	title = {Receptor {Kinase} {THESEUS1} {Is} a {Rapid} {Alkalinization} {Factor} 34 {Receptor} in {Arabidopsis}},
	volume = {28},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982218307115},
	doi = {10.1016/j.cub.2018.05.075},
	abstract = {The growth of plants, like that of other walled organisms, depends on the ability of the cell wall to yield without losing its integrity. In this context, plant cells can sense the perturbation of their walls and trigger adaptive modifications in cell wall polymer interactions. Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) THESEUS1 (THE1) was previously shown in Arabidopsis to trigger growth inhibition and defense responses upon perturbation of the cell wall, but so far, neither the ligand nor the role of the receptor in normal development was known. Here, we report that THE1 is a receptor for the peptide rapid alkalinization factor (RALF) 34 and that this signaling module has a role in the fine-tuning of lateral root initiation. We also show that RALF34-THE1 signaling depends, at least for some responses, on FERONIA (FER), another RALF receptor involved in a variety of processes, including immune signaling, mechanosensing, and reproduction [1]. Together, the results show that RALF34 and THE1 are part of a signaling network that integrates information on the integrity of the cell wall with the coordination of normal morphogenesis.},
	language = {en},
	number = {15},
	urldate = {2023-03-10},
	journal = {Current Biology},
	author = {Gonneau, Martine and Desprez, Thierry and Martin, Marjolaine and Doblas, Verónica G. and Bacete, Laura and Miart, Fabien and Sormani, Rodnay and Hématy, Kian and Renou, Julien and Landrein, Benoit and Murphy, Evan and Van De Cotte, Brigitte and Vernhettes, Samantha and De Smet, Ive and Höfte, Herman},
	month = aug,
	year = {2018},
	keywords = {FERONIA, cell wall, lateral root initiation, rapid alkalinization factor},
	pages = {2452--2458.e4},
}

The growth of plants, like that of other walled organisms, depends on the ability of the cell wall to yield without losing its integrity. In this context, plant cells can sense the perturbation of their walls and trigger adaptive modifications in cell wall polymer interactions. Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) THESEUS1 (THE1) was previously shown in Arabidopsis to trigger growth inhibition and defense responses upon perturbation of the cell wall, but so far, neither the ligand nor the role of the receptor in normal development was known. Here, we report that THE1 is a receptor for the peptide rapid alkalinization factor (RALF) 34 and that this signaling module has a role in the fine-tuning of lateral root initiation. We also show that RALF34-THE1 signaling depends, at least for some responses, on FERONIA (FER), another RALF receptor involved in a variety of processes, including immune signaling, mechanosensing, and reproduction [1]. Together, the results show that RALF34 and THE1 are part of a signaling network that integrates information on the integrity of the cell wall with the coordination of normal morphogenesis.

@article{bacete_plant_2018,
	title = {Plant cell wall-mediated immunity: cell wall changes trigger disease resistance responses},
	volume = {93},
	issn = {1365-313X},
	shorttitle = {Plant cell wall-mediated immunity},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.13807},
	doi = {10.1111/tpj.13807},
	abstract = {Plants have evolved a repertoire of monitoring systems to sense plant morphogenesis and to face environmental changes and threats caused by different attackers. These systems integrate different signals into overreaching triggering pathways which coordinate developmental and defence-associated responses. The plant cell wall, a dynamic and complex structure surrounding every plant cell, has emerged recently as an essential component of plant monitoring systems, thus expanding its function as a passive defensive barrier. Plants have a dedicated mechanism for maintaining cell wall integrity (CWI) which comprises a diverse set of plasma membrane-resident sensors and pattern recognition receptors (PRRs). The PRRs perceive plant-derived ligands, such as peptides or wall glycans, known as damage-associated molecular patterns (DAMPs). These DAMPs function as ‘danger’ alert signals activating DAMP-triggered immunity (DTI), which shares signalling components and responses with the immune pathways triggered by non-self microbe-associated molecular patterns that mediate disease resistance. Alteration of CWI by impairment of the expression or activity of proteins involved in cell wall biosynthesis and/or remodelling, as occurs in some plant cell wall mutants, or by wall damage due to colonization by pathogens/pests, activates specific defensive and growth responses. Our current understanding of how these alterations of CWI are perceived by the wall monitoring systems is scarce and few plant sensors/PRRs and DAMPs have been characterized. The identification of these CWI sensors and PRR–DAMP pairs will help us to understand the immune functions of the wall monitoring system, and might allow the breeding of crop varieties and the design of agricultural strategies that would enhance crop disease resistance.},
	language = {en},
	number = {4},
	urldate = {2023-03-10},
	journal = {The Plant Journal},
	author = {Bacete, Laura and Mélida, Hugo and Miedes, Eva and Molina, Antonio},
	year = {2018},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.13807},
	keywords = {Arabidopsis, DAMP, PRR, cell wall, cell wall integrity, cell wall mutant, disease resistance, immunity, wall sensor},
	pages = {614--636},
}

Plants have evolved a repertoire of monitoring systems to sense plant morphogenesis and to face environmental changes and threats caused by different attackers. These systems integrate different signals into overreaching triggering pathways which coordinate developmental and defence-associated responses. The plant cell wall, a dynamic and complex structure surrounding every plant cell, has emerged recently as an essential component of plant monitoring systems, thus expanding its function as a passive defensive barrier. Plants have a dedicated mechanism for maintaining cell wall integrity (CWI) which comprises a diverse set of plasma membrane-resident sensors and pattern recognition receptors (PRRs). The PRRs perceive plant-derived ligands, such as peptides or wall glycans, known as damage-associated molecular patterns (DAMPs). These DAMPs function as ‘danger’ alert signals activating DAMP-triggered immunity (DTI), which shares signalling components and responses with the immune pathways triggered by non-self microbe-associated molecular patterns that mediate disease resistance. Alteration of CWI by impairment of the expression or activity of proteins involved in cell wall biosynthesis and/or remodelling, as occurs in some plant cell wall mutants, or by wall damage due to colonization by pathogens/pests, activates specific defensive and growth responses. Our current understanding of how these alterations of CWI are perceived by the wall monitoring systems is scarce and few plant sensors/PRRs and DAMPs have been characterized. The identification of these CWI sensors and PRR–DAMP pairs will help us to understand the immune functions of the wall monitoring system, and might allow the breeding of crop varieties and the design of agricultural strategies that would enhance crop disease resistance.

@article{dolde_synthetic_2018,
	title = {Synthetic {MicroProteins}: {Versatile} {Tools} for {Posttranslational} {Regulation} of {Target} {Proteins}},
	volume = {176},
	issn = {0032-0889},
	shorttitle = {Synthetic {MicroProteins}},
	url = {https://doi.org/10.1104/pp.17.01743},
	doi = {10.1104/pp.17.01743},
	abstract = {MicroProteins are small, single-domain proteins that regulate multidomain proteins by sequestering them into novel, often nonproductive, complexes. Several microProteins have been identified in plants and animals, most of which negatively regulate transcription factors. MicroProtein candidates that potentially target a wide range of different protein classes were recently identified in a computational approach. Here, we classified all Arabidopsis (Arabidopsis thaliana) microProteins and developed a synthetic microProtein approach to target specific protein classes, such as hydrolases, receptors, and lyases, in a proof-of-concept approach. Our findings reveal that microProteins can be used to influence different physiological processes, which makes them useful tools for posttranslational regulation in plants and potentially also in animals.},
	number = {4},
	urldate = {2022-11-30},
	journal = {Plant Physiology},
	author = {Dolde, Ulla and Rodrigues, Vandasue and Straub, Daniel and Bhati, Kaushal Kumar and Choi, Sukwon and Yang, Seong Wook and Wenkel, Stephan},
	month = apr,
	year = {2018},
	pages = {3136--3145},
}

MicroProteins are small, single-domain proteins that regulate multidomain proteins by sequestering them into novel, often nonproductive, complexes. Several microProteins have been identified in plants and animals, most of which negatively regulate transcription factors. MicroProtein candidates that potentially target a wide range of different protein classes were recently identified in a computational approach. Here, we classified all Arabidopsis (Arabidopsis thaliana) microProteins and developed a synthetic microProtein approach to target specific protein classes, such as hydrolases, receptors, and lyases, in a proof-of-concept approach. Our findings reveal that microProteins can be used to influence different physiological processes, which makes them useful tools for posttranslational regulation in plants and potentially also in animals.

@article{bhati_approaches_2018,
	title = {Approaches to identify and characterize {microProteins} and their potential uses in biotechnology},
	volume = {75},
	issn = {1420-9071},
	url = {https://doi.org/10.1007/s00018-018-2818-8},
	doi = {10.1007/s00018-018-2818-8},
	abstract = {MicroProteins are small proteins that contain a single protein domain and are related to larger, often multi-domain proteins. At the molecular level, microProteins act by interfering with the formation of higher order protein complexes. In the past years, several microProteins have been identified in plants and animals that strongly influence biological processes. Due to their ability to act as dominant regulators in a targeted manner, microProteins have a high potential for biotechnological use. In this review, we present different ways in which microProteins are generated and we elaborate on techniques used to identify and characterize them. Finally, we give an outlook on possible applications in biotechnology.},
	language = {en},
	number = {14},
	urldate = {2022-11-30},
	journal = {Cellular and Molecular Life Sciences},
	author = {Bhati, Kaushal Kumar and Blaakmeer, Anko and Paredes, Esther Botterweg and Dolde, Ulla and Eguen, Tenai and Hong, Shin-Young and Rodrigues, Vandasue and Straub, Daniel and Sun, Bin and Wenkel, Stephan},
	month = jul,
	year = {2018},
	keywords = {Complex, Inhibition, MiPFinder, MicroProtein, Protein–protein interaction, Small proteins, Targets},
	pages = {2529--2536},
}

MicroProteins are small proteins that contain a single protein domain and are related to larger, often multi-domain proteins. At the molecular level, microProteins act by interfering with the formation of higher order protein complexes. In the past years, several microProteins have been identified in plants and animals that strongly influence biological processes. Due to their ability to act as dominant regulators in a targeted manner, microProteins have a high potential for biotechnological use. In this review, we present different ways in which microProteins are generated and we elaborate on techniques used to identify and characterize them. Finally, we give an outlook on possible applications in biotechnology.

@article{zhang_spatiotemporal_2018,
	title = {Spatiotemporal control of axillary meristem formation by interacting transcriptional regulators},
	volume = {145},
	issn = {0950-1991},
	url = {https://doi.org/10.1242/dev.158352},
	doi = {10.1242/dev.158352},
	abstract = {Branching is a common feature of plant development. In seed plants, axillary meristems (AMs) initiate in leaf axils to enable lateral shoot branching. AM initiation requires a high level of expression of the meristem marker SHOOT MERISTEMLESS (STM) in the leaf axil. Here, we show that modules of interacting transcriptional regulators control STM expression and AM initiation. Two redundant AP2-type transcription factors, DORNRÖSCHEN (DRN) and DORNRÖSCHEN-LIKE (DRNL), control AM initiation by regulating STM expression. DRN and DRNL directly upregulate STM expression in leaf axil meristematic cells, as does another transcription factor, REVOLUTA (REV). The activation of STM expression by DRN/DRNL depends on REV, and vice versa. DRN/DRNL and REV have overlapping expression patterns and protein interactions in the leaf axil, which are required for the upregulation of STM expression. Furthermore, LITTLE ZIPPER3, another REV-interacting protein, is expressed in the leaf axil and interferes with the DRN/DRNL-REV interaction to negatively modulate STM expression. Our results support a model in which interacting transcriptional regulators fine-tune the expression of STM to precisely regulate AM initiation. Thus, shoot branching recruits the same conserved protein complexes used in embryogenesis and leaf polarity patterning.},
	number = {24},
	urldate = {2022-11-30},
	journal = {Development},
	author = {Zhang, Cui and Wang, Jin and Wenkel, Stephan and Chandler, John W. and Werr, Wolfgang and Jiao, Yuling},
	month = dec,
	year = {2018},
	pages = {dev158352},
}

Branching is a common feature of plant development. In seed plants, axillary meristems (AMs) initiate in leaf axils to enable lateral shoot branching. AM initiation requires a high level of expression of the meristem marker SHOOT MERISTEMLESS (STM) in the leaf axil. Here, we show that modules of interacting transcriptional regulators control STM expression and AM initiation. Two redundant AP2-type transcription factors, DORNRÖSCHEN (DRN) and DORNRÖSCHEN-LIKE (DRNL), control AM initiation by regulating STM expression. DRN and DRNL directly upregulate STM expression in leaf axil meristematic cells, as does another transcription factor, REVOLUTA (REV). The activation of STM expression by DRN/DRNL depends on REV, and vice versa. DRN/DRNL and REV have overlapping expression patterns and protein interactions in the leaf axil, which are required for the upregulation of STM expression. Furthermore, LITTLE ZIPPER3, another REV-interacting protein, is expressed in the leaf axil and interferes with the DRN/DRNL-REV interaction to negatively modulate STM expression. Our results support a model in which interacting transcriptional regulators fine-tune the expression of STM to precisely regulate AM initiation. Thus, shoot branching recruits the same conserved protein complexes used in embryogenesis and leaf polarity patterning.

@article{malnoe_plastid_2018,
	title = {The {Plastid} {Lipocalin} {LCNP} {Is} {Required} for {Sustained} {Photoprotective} {Energy} {Dissipation} in {Arabidopsis}},
	volume = {30},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/30/1/196-208/6100355},
	doi = {10/gc3tvv},
	abstract = {Light utilization is finely tuned in photosynthetic organisms to prevent cellular damage. The dissipation of excess absorbed light energy, a process termed nonphotochemical quenching (NPQ), plays an important role in photoprotection. Little is known about the sustained or slowly reversible form(s) of NPQ and whether they are photoprotective, in part due to the lack of mutants. The Arabidopsis thaliana suppressor of quenching1 (soq1) mutant exhibits enhanced sustained NPQ, which we term qH. To identify molecular players involved in qH, we screened for suppressors of soq1 and isolated mutants affecting either chlorophyllide a oxygenase or the chloroplastic lipocalin, now renamed plastid lipocalin (LCNP). Analysis of the mutants confirmed that qH is localized to the peripheral antenna (LHCII) of photosystem II and demonstrated that LCNP is required for qH, either directly (by forming NPQ sites) or indirectly (by modifying the LHCII membrane environment). qH operates under stress conditions such as cold and high light and is photoprotective, as it reduces lipid peroxidation levels. We propose that, under stress conditions, LCNP protects the thylakoid membrane by enabling sustained NPQ in LHCII, thereby preventing singlet oxygen stress.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {Malnoë, Alizée and Schultink, Alex and Shahrasbi, Sanya and Rumeau, Dominique and Havaux, Michel and Niyogi, Krishna K.},
	month = jan,
	year = {2018},
	pages = {196--208},
}

Light utilization is finely tuned in photosynthetic organisms to prevent cellular damage. The dissipation of excess absorbed light energy, a process termed nonphotochemical quenching (NPQ), plays an important role in photoprotection. Little is known about the sustained or slowly reversible form(s) of NPQ and whether they are photoprotective, in part due to the lack of mutants. The Arabidopsis thaliana suppressor of quenching1 (soq1) mutant exhibits enhanced sustained NPQ, which we term qH. To identify molecular players involved in qH, we screened for suppressors of soq1 and isolated mutants affecting either chlorophyllide a oxygenase or the chloroplastic lipocalin, now renamed plastid lipocalin (LCNP). Analysis of the mutants confirmed that qH is localized to the peripheral antenna (LHCII) of photosystem II and demonstrated that LCNP is required for qH, either directly (by forming NPQ sites) or indirectly (by modifying the LHCII membrane environment). qH operates under stress conditions such as cold and high light and is photoprotective, as it reduces lipid peroxidation levels. We propose that, under stress conditions, LCNP protects the thylakoid membrane by enabling sustained NPQ in LHCII, thereby preventing singlet oxygen stress.

@article{malnoe_photoinhibition_2018,
	title = {Photoinhibition or photoprotection of photosynthesis? {Update} on the (newly termed) sustained quenching component {qH}},
	volume = {154},
	issn = {00988472},
	shorttitle = {Photoinhibition or photoprotection of photosynthesis?},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0098847218301862},
	doi = {10.1016/j.envexpbot.2018.05.005},
	abstract = {Non-photochemical quenching (NPQ) of chlorophyll fluorescence is a valuable feature for the study of photosynthetic organisms’ light utilization and dissipation. However, all too often NPQ is simply equated with the harmless dissipation of excess absorbed light energy as heat. This is not always the case as some processes cause NPQ without thermal dissipation. Photoinhibitory quenching, qI, is sustained NPQ that continuously depresses the commonly used fluorescence parameter “quantum yield of photosystem II (PSII)”, or Fv/Fm, and is often viewed as a result of PSII core inactivation due to D1 damage. Inactivated PSII cores might have a photoprotective role but that is not the topic of the present review. Instead, this review focuses on a sustained photoprotective antenna quenching component, which we have termed qH, and summarizes the recently uncovered molecular players of this sustained form of NPQ.},
	language = {en},
	urldate = {2021-06-07},
	journal = {Environmental and Experimental Botany},
	author = {Malnoë, Alizée},
	month = oct,
	year = {2018},
	pages = {123--133},
}

Non-photochemical quenching (NPQ) of chlorophyll fluorescence is a valuable feature for the study of photosynthetic organisms’ light utilization and dissipation. However, all too often NPQ is simply equated with the harmless dissipation of excess absorbed light energy as heat. This is not always the case as some processes cause NPQ without thermal dissipation. Photoinhibitory quenching, qI, is sustained NPQ that continuously depresses the commonly used fluorescence parameter “quantum yield of photosystem II (PSII)”, or Fv/Fm, and is often viewed as a result of PSII core inactivation due to D1 damage. Inactivated PSII cores might have a photoprotective role but that is not the topic of the present review. Instead, this review focuses on a sustained photoprotective antenna quenching component, which we have termed qH, and summarizes the recently uncovered molecular players of this sustained form of NPQ.

@article{marhava_molecular_2018,
	title = {A molecular rheostat adjusts auxin flux to promote root protophloem differentiation},
	volume = {558},
	copyright = {2018 Macmillan Publishers Ltd., part of Springer Nature},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/s41586-018-0186-z},
	doi = {10.1038/s41586-018-0186-z},
	abstract = {Auxin influences plant development through several distinct concentration-dependent effects1. In the Arabidopsis root tip, polar auxin transport by PIN-FORMED (PIN) proteins creates a local auxin accumulation that is required for the maintenance of the stem-cell niche2–4. Proximally, stem-cell daughter cells divide repeatedly before they eventually differentiate. This developmental gradient is accompanied by a gradual decrease in auxin levels as cells divide, and subsequently by a gradual increase as the cells differentiate5,6. However, the timing of differentiation is not uniform across cell files. For instance, developing protophloem sieve elements (PPSEs) differentiate as neighbouring cells still divide. Here we show that PPSE differentiation involves local steepening of the post-meristematic auxin gradient. BREVIS RADIX (BRX) and PROTEIN KINASE ASSOCIATED WITH BRX (PAX) are interacting plasma-membrane-associated, polarly localized proteins that co-localize with PIN proteins at the rootward end of developing PPSEs. Both brx and pax mutants display impaired PPSE differentiation. Similar to other AGC-family kinases, PAX activates PIN-mediated auxin efflux, whereas BRX strongly dampens this stimulation. Efficient BRX plasma-membrane localization depends on PAX, but auxin negatively regulates BRX plasma-membrane association and promotes PAX activity. Thus, our data support a model in which BRX and PAX are elements of a molecular rheostat that modulates auxin flux through developing PPSEs, thereby timing PPSE differentiation.},
	language = {en},
	number = {7709},
	urldate = {2022-05-02},
	journal = {Nature},
	author = {Marhava, P. and Bassukas, A. E. L. and Zourelidou, M. and Kolb, M. and Moret, B. and Fastner, A. and Schulze, W. X. and Cattaneo, P. and Hammes, U. Z. and Schwechheimer, C. and Hardtke, C. S.},
	month = jun,
	year = {2018},
	note = {Number: 7709
Publisher: Nature Publishing Group},
	keywords = {Auxin, Cell fate, Root apical meristem},
	pages = {297--300},
}

Auxin influences plant development through several distinct concentration-dependent effects1. In the Arabidopsis root tip, polar auxin transport by PIN-FORMED (PIN) proteins creates a local auxin accumulation that is required for the maintenance of the stem-cell niche2–4. Proximally, stem-cell daughter cells divide repeatedly before they eventually differentiate. This developmental gradient is accompanied by a gradual decrease in auxin levels as cells divide, and subsequently by a gradual increase as the cells differentiate5,6. However, the timing of differentiation is not uniform across cell files. For instance, developing protophloem sieve elements (PPSEs) differentiate as neighbouring cells still divide. Here we show that PPSE differentiation involves local steepening of the post-meristematic auxin gradient. BREVIS RADIX (BRX) and PROTEIN KINASE ASSOCIATED WITH BRX (PAX) are interacting plasma-membrane-associated, polarly localized proteins that co-localize with PIN proteins at the rootward end of developing PPSEs. Both brx and pax mutants display impaired PPSE differentiation. Similar to other AGC-family kinases, PAX activates PIN-mediated auxin efflux, whereas BRX strongly dampens this stimulation. Efficient BRX plasma-membrane localization depends on PAX, but auxin negatively regulates BRX plasma-membrane association and promotes PAX activity. Thus, our data support a model in which BRX and PAX are elements of a molecular rheostat that modulates auxin flux through developing PPSEs, thereby timing PPSE differentiation.

@incollection{gietl_ricinosomes_2018,
	title = {Ricinosomes and {Aleurain}-{Containing} {Vacuoles} ({ACVs}): {Protease}-{Storing} {Organelles}},
	isbn = {978-1-119-31299-4},
	shorttitle = {Ricinosomes and {Aleurain}-{Containing} {Vacuoles} ({ACVs})},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9781119312994.apr0039},
	abstract = {The sections in this article are},
	language = {en},
	urldate = {2021-10-22},
	booktitle = {Annual {Plant} {Reviews} online},
	publisher = {American Cancer Society},
	author = {Gietl, Christine and Schmid, Markus and Simpson, David},
	year = {2018},
	doi = {10.1002/9781119312994.apr0039},
	note = {Section: 5
\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781119312994.apr0039},
	keywords = {Aleurone cell, aleurain-containing vacuoles, cotyledons, cysteine endopeptidase, endosperm, programmed cell death, ricinosomes},
	pages = {96--118},
}

The sections in this article are

@article{michelson_autumn_2018,
	title = {Autumn senescence in aspen is not triggered by day length},
	volume = {162},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12593},
	doi = {10.1111/ppl.12593},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Michelson, Ingrid H. and Ingvarsson, Pär K. and Robinson, Kathryn M. and Edlund, Erik and Eriksson, Maria E. and Nilsson, Ove and Jansson, Stefan},
	month = jan,
	year = {2018},
	pages = {123--134},
}

@article{tylewicz_photoperiodic_2018,
	title = {Photoperiodic control of seasonal growth is mediated by {ABA} acting on cell-cell communication},
	volume = {360},
	issn = {0036-8075, 1095-9203},
	url = {https://www.sciencemag.org/lookup/doi/10.1126/science.aan8576},
	doi = {10/gc8wcn},
	language = {en},
	number = {6385},
	urldate = {2021-06-07},
	journal = {Science},
	author = {Tylewicz, S. and Petterle, A. and Marttila, S. and Miskolczi, P. and Azeez, A. and Singh, R. K. and Immanen, J. and Mähler, N. and Hvidsten, T. R. and Eklund, D. M. and Bowman, J. L. and Helariutta, Y. and Bhalerao, Rishikesh P.},
	month = apr,
	year = {2018},
	pages = {212--215},
}

@article{caballero-perez_transcriptional_2018,
	title = {Transcriptional landscapes of {Axolotl} ({Ambystoma} mexicanum)},
	volume = {433},
	issn = {00121606},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0012160617302786},
	doi = {10/gcwm2z},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Developmental Biology},
	author = {Caballero-Pérez, Juan and Espinal-Centeno, Annie and Falcon, Francisco and García-Ortega, Luis F. and Curiel-Quesada, Everardo and Cruz-Hernández, Andrés and Bakó, Laszlo and Chen, Xuemei and Martínez, Octavio and Alberto Arteaga-Vázquez, Mario and Herrera-Estrella, Luis and Cruz-Ramírez, Alfredo},
	month = jan,
	year = {2018},
	pages = {227--239},
}

@article{ding_gigantea-like_2018,
	title = {{GIGANTEA}-like genes control seasonal growth cessation in {Populus}},
	volume = {218},
	copyright = {© 2018 The Authors. New Phytologist © 2018 New Phytologist Trust},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.15087},
	doi = {10/gdt24k},
	abstract = {Survival of trees growing in temperate zones requires cycling between active growth and dormancy. This involves growth cessation in the autumn triggered by a photoperiod shorter than the critical day length. Variations in GIGANTEA (GI)-like genes have been associated with phenology in a range of different tree species, but characterization of the functions of these genes in the process is still lacking. We describe the identification of the Populus orthologs of GI and their critical role in short-day-induced growth cessation. Using ectopic expression and silencing, gene expression analysis, protein interaction and chromatin immunoprecipitation experiments, we show that PttGIs are likely to act in a complex with PttFKF1s (FLAVIN-BINDING, KELCH REPEAT, F-BOX 1) and PttCDFs (CYCLING DOF FACTOR) to control the expression of PttFT2, the key gene regulating short-day-induced growth cessation in Populus. In contrast to Arabidopsis, in which the GI-CONSTANS (CO)-FLOWERING LOCUS T (FT) regulon is a crucial day-length sensor for flowering time, our study suggests that, in Populus, PttCO-independent regulation of PttFT2 by PttGI is more important in the photoperiodic control of growth cessation and bud set.},
	language = {en},
	number = {4},
	urldate = {2021-06-21},
	journal = {New Phytologist},
	author = {Ding, Jihua and Böhlenius, Henrik and Rühl, Mark Georg and Chen, Peng and Sane, Shashank and Zambrano, Jose A. and Zheng, Bo and Eriksson, Maria E. and Nilsson, Ove},
	year = {2018},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15087},
	keywords = {FLOWERING LOCUS (FT), GIGANTEA (GI), Populus, growth cessation, photoperiod},
	pages = {1491--1503},
}

Survival of trees growing in temperate zones requires cycling between active growth and dormancy. This involves growth cessation in the autumn triggered by a photoperiod shorter than the critical day length. Variations in GIGANTEA (GI)-like genes have been associated with phenology in a range of different tree species, but characterization of the functions of these genes in the process is still lacking. We describe the identification of the Populus orthologs of GI and their critical role in short-day-induced growth cessation. Using ectopic expression and silencing, gene expression analysis, protein interaction and chromatin immunoprecipitation experiments, we show that PttGIs are likely to act in a complex with PttFKF1s (FLAVIN-BINDING, KELCH REPEAT, F-BOX 1) and PttCDFs (CYCLING DOF FACTOR) to control the expression of PttFT2, the key gene regulating short-day-induced growth cessation in Populus. In contrast to Arabidopsis, in which the GI-CONSTANS (CO)-FLOWERING LOCUS T (FT) regulon is a crucial day-length sensor for flowering time, our study suggests that, in Populus, PttCO-independent regulation of PttFT2 by PttGI is more important in the photoperiodic control of growth cessation and bud set.

@article{allario_ptxtpme1_2018,
	title = {{PtxtPME1} and homogalacturonans influence xylem hydraulic properties in poplar},
	volume = {163},
	copyright = {© 2018 Scandinavian Plant Physiology Society},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.12702},
	doi = {10/gcxrch},
	abstract = {While the xylem hydraulic properties, such as vulnerability to cavitation (VC), are of paramount importance in drought resistance, their genetic determinants remain unexplored. There is evidence that pectins and their methylation pattern are involved, but the detail of their involvement and the corresponding genes need to be clarified. We analyzed the hydraulic properties of the 35S::PME1 transgenic aspen that ectopically under- or over-express a xylem-abundant pectin methyl esterase, PtxtPME1. We also produced and analyzed 4CL1::PGII transgenic poplars expressing a fungal polygalacturonase, AnPGII, under the control of the Ptxa4CL1 promoter that is active in the developing xylem after xylem cell expansion. Both the 35S::PME1 under- and over-expressing aspen lines developed xylem with lower-specific hydraulic conductivity and lower VC, while the 4CL1::PGII plants developed xylem with a higher VC. These xylem hydraulic changes were associated with modifications in xylem structure or in intervessel pit structure that can result in changes in mechanical behavior of the pit membrane. This study shows that homogalacturonans and their methylation pattern influence xylem hydraulic properties, through its effect on xylem cell expansion and on intervessel pit properties and it show a role for PtxtPME1 in the xylem hydraulic properties.},
	language = {en},
	number = {4},
	urldate = {2021-06-21},
	journal = {Physiologia Plantarum},
	author = {Allario, Thierry and Tixier, Aude and Awad, Hosam and Lemaire, Cedric and Brunel, Nicole and Badel, Eric and Barigah, Têtè S. and Julien, Jean-Louis and Peyret, Pierre and Mellerowicz, Ewa J. and Cochard, Herve and Herbette, Stephane},
	year = {2018},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.12702},
	pages = {502--515},
}

While the xylem hydraulic properties, such as vulnerability to cavitation (VC), are of paramount importance in drought resistance, their genetic determinants remain unexplored. There is evidence that pectins and their methylation pattern are involved, but the detail of their involvement and the corresponding genes need to be clarified. We analyzed the hydraulic properties of the 35S::PME1 transgenic aspen that ectopically under- or over-express a xylem-abundant pectin methyl esterase, PtxtPME1. We also produced and analyzed 4CL1::PGII transgenic poplars expressing a fungal polygalacturonase, AnPGII, under the control of the Ptxa4CL1 promoter that is active in the developing xylem after xylem cell expansion. Both the 35S::PME1 under- and over-expressing aspen lines developed xylem with lower-specific hydraulic conductivity and lower VC, while the 4CL1::PGII plants developed xylem with a higher VC. These xylem hydraulic changes were associated with modifications in xylem structure or in intervessel pit structure that can result in changes in mechanical behavior of the pit membrane. This study shows that homogalacturonans and their methylation pattern influence xylem hydraulic properties, through its effect on xylem cell expansion and on intervessel pit properties and it show a role for PtxtPME1 in the xylem hydraulic properties.

@article{nakamura_outer_2018,
	title = {Outer, inner and planar polarity in the {Arabidopsis} root},
	volume = {41},
	issn = {13695266},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526617301024},
	doi = {10/gc764h},
	language = {en},
	urldate = {2021-06-07},
	journal = {Current Opinion in Plant Biology},
	author = {Nakamura, Moritaka and Grebe, Markus},
	month = feb,
	year = {2018},
	pages = {46--53},
}

@article{nakamura_auxin_2018,
	title = {Auxin and {ROP} {GTPase} {Signaling} of {Polar} {Nuclear} {Migration} in {Root} {Epidermal} {Hair} {Cells}},
	volume = {176},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/176/1/378-391/6117182},
	doi = {10/gct4b2},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Nakamura, Moritaka and Claes, Andrea R. and Grebe, Tobias and Hermkes, Rebecca and Viotti, Corrado and Ikeda, Yoshihisa and Grebe, Markus},
	month = jan,
	year = {2018},
	pages = {378--391},
}

@article{bai_combined_2018,
	title = {Combined transcriptome and translatome analyses reveal a role for tryptophan-dependent auxin biosynthesis in the control of \textit{{DOG1}} -dependent seed dormancy},
	volume = {217},
	issn = {0028646X},
	url = {http://doi.wiley.com/10.1111/nph.14885},
	doi = {10/gcwrgv},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Bai, Bing and Novák, Ondřej and Ljung, Karin and Hanson, Johannes and Bentsink, Leónie},
	month = feb,
	year = {2018},
	pages = {1077--1085},
}

@article{waller_sharing_2018,
	title = {Sharing resources for mutual benefit: crosstalk between disciplines deepens the understanding of mycorrhizal symbioses across scales},
	volume = {217},
	issn = {0028646X},
	shorttitle = {Sharing resources for mutual benefit},
	url = {http://doi.wiley.com/10.1111/nph.14912},
	doi = {10/ghbzdd},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Waller, Lauren P. and Felten, Judith and Hiiesalu, Inga and Vogt-Schilb, Hélène},
	month = jan,
	year = {2018},
	pages = {29--32},
}

@article{ma_auxin_2018,
	title = {Auxin signaling: a big question to be addressed by small molecules},
	volume = {69},
	issn = {0022-0957, 1460-2431},
	shorttitle = {Auxin signaling},
	url = {https://academic.oup.com/jxb/article/69/2/313/4641657},
	doi = {10/gct4mb},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Ma, Qian and Grones, Peter and Robert, Stéphanie},
	month = jan,
	year = {2018},
	pages = {313--328},
}

@article{hernandez-verdeja_retrograde_2018,
	title = {Retrograde {Signals} {Navigate} the {Path} to {Chloroplast} {Development}},
	volume = {176},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.17.01299},
	doi = {10/gc8tpr},
	abstract = {Light is the main source of energy for life on Earth, and plants and algae are able to convert light energy, through photosynthesis, into chemical energy that can be used by all organisms. The photosynthetic reactions are housed in the chloroplasts, but the chloroplasts also are the site for synthesis of essential compounds like fatty acids, vitamins, amino acids, and tetrapyrroles. Given their essential role, the correct formation and function of chloroplasts is vital for the growth and development of plants and algae, and hence for almost all organisms. Chloroplasts evolved from an endosymbiotic event where a photosynthetic prokaryotic organism was acquired by a proeukaryotic cell. With time, the photosynthetic prokaryote lost or transferred most of its genes to the host genome. As a result, plastid protein complexes, such as the photosynthetic complexes, are encoded by genes of both the nuclear and plastid genomes. This division of genetic information requires a precise coordination between the two genomes to achieve proper plastid development and function. Plastid development and gene expression are under nuclear control, in what is referred to as anterograde control. However, there also is a signaling system originating in the plastids, so-called retrograde signals, transmitting information about the developmental and functional state of the plastids to the nucleus to regulate nuclear gene expression. Retrograde signaling is a complex network of signals that can be divided into “biogenic control,” referring to signals generated by the plastid as it develops from a proplastid or etioplast into a chloroplast, and “operational control” signals, including those generated from a mature chloroplast in response to environmental perturbations (Chan et al., 2016).},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Hernández-Verdeja, Tamara and Strand, Åsa},
	month = feb,
	year = {2018},
	pages = {967--976},
}

Light is the main source of energy for life on Earth, and plants and algae are able to convert light energy, through photosynthesis, into chemical energy that can be used by all organisms. The photosynthetic reactions are housed in the chloroplasts, but the chloroplasts also are the site for synthesis of essential compounds like fatty acids, vitamins, amino acids, and tetrapyrroles. Given their essential role, the correct formation and function of chloroplasts is vital for the growth and development of plants and algae, and hence for almost all organisms. Chloroplasts evolved from an endosymbiotic event where a photosynthetic prokaryotic organism was acquired by a proeukaryotic cell. With time, the photosynthetic prokaryote lost or transferred most of its genes to the host genome. As a result, plastid protein complexes, such as the photosynthetic complexes, are encoded by genes of both the nuclear and plastid genomes. This division of genetic information requires a precise coordination between the two genomes to achieve proper plastid development and function. Plastid development and gene expression are under nuclear control, in what is referred to as anterograde control. However, there also is a signaling system originating in the plastids, so-called retrograde signals, transmitting information about the developmental and functional state of the plastids to the nucleus to regulate nuclear gene expression. Retrograde signaling is a complex network of signals that can be divided into “biogenic control,” referring to signals generated by the plastid as it develops from a proplastid or etioplast into a chloroplast, and “operational control” signals, including those generated from a mature chloroplast in response to environmental perturbations (Chan et al., 2016).

@article{liu_vacuole_2018,
	title = {Vacuole {Integrity} {Maintained} by {DUF300} {Proteins} {Is} {Required} for {Brassinosteroid} {Signaling} {Regulation}},
	volume = {11},
	issn = {1674-2052},
	url = {https://www.sciencedirect.com/science/article/pii/S1674205217303854},
	doi = {10/gdbfj5},
	abstract = {Brassinosteroid (BR) hormone signaling controls multiple processes during plant growth and development and is initiated at the plasma membrane through the receptor kinase BRASSINOSTEROID INSENSITIVE1 (BRI1) together with co-receptors such as BRI1-ASSOCIATED RECEPTOR KINASE1 (BAK1). BRI1 abundance is regulated by endosomal recycling and vacuolar targeting, but the role of vacuole-related proteins in BR receptor dynamics and BR responses remains elusive. Here, we show that the absence of two DUF300 domain-containing tonoplast proteins, LAZARUS1 (LAZ1) and LAZ1 HOMOLOG1 (LAZ1H1), causes vacuole morphology defects, growth inhibition, and constitutive activation of BR signaling. Intriguingly, tonoplast accumulation of BAK1 was substantially increased and appeared causally linked to enhanced BRI1 trafficking and degradation in laz1 laz1h1 plants. Since unrelated vacuole mutants exhibited normal BR responses, our findings indicate that DUF300 proteins play distinct roles in the regulation of BR signaling by maintaining vacuole integrity required to balance subcellular BAK1 pools and BR receptor distribution.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Molecular Plant},
	author = {Liu, Qinsong and Vain, Thomas and Viotti, Corrado and Doyle, Siamsa M. and Tarkowská, Danuše and Novák, Ondřej and Zipfel, Cyril and Sitbon, Folke and Robert, Stéphanie and Hofius, Daniel},
	month = apr,
	year = {2018},
	keywords = {DUF300 proteins, brassinosteroid signaling, tonoplast, vacuole integrity},
	pages = {553--567},
}

Brassinosteroid (BR) hormone signaling controls multiple processes during plant growth and development and is initiated at the plasma membrane through the receptor kinase BRASSINOSTEROID INSENSITIVE1 (BRI1) together with co-receptors such as BRI1-ASSOCIATED RECEPTOR KINASE1 (BAK1). BRI1 abundance is regulated by endosomal recycling and vacuolar targeting, but the role of vacuole-related proteins in BR receptor dynamics and BR responses remains elusive. Here, we show that the absence of two DUF300 domain-containing tonoplast proteins, LAZARUS1 (LAZ1) and LAZ1 HOMOLOG1 (LAZ1H1), causes vacuole morphology defects, growth inhibition, and constitutive activation of BR signaling. Intriguingly, tonoplast accumulation of BAK1 was substantially increased and appeared causally linked to enhanced BRI1 trafficking and degradation in laz1 laz1h1 plants. Since unrelated vacuole mutants exhibited normal BR responses, our findings indicate that DUF300 proteins play distinct roles in the regulation of BR signaling by maintaining vacuole integrity required to balance subcellular BAK1 pools and BR receptor distribution.

@article{dubreuil_establishment_2018,
	title = {Establishment of {Photosynthesis} through {Chloroplast} {Development} {Is} {Controlled} by {Two} {Distinct} {Regulatory} {Phases}},
	volume = {176},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/176/2/1199-1214/6117139},
	doi = {10/gb2hj6},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Dubreuil, Carole and Jin, Xu and Barajas-López, Juan de Dios and Hewitt, Timothy C. and Tanz, Sandra K. and Dobrenel, Thomas and Schröder, Wolfgang P. and Hanson, Johannes and Pesquet, Edouard and Grönlund, Andreas and Small, Ian and Strand, Åsa},
	month = feb,
	year = {2018},
	pages = {1199--1214},
}

@article{eklund_evolutionarily_2018,
	title = {An {Evolutionarily} {Conserved} {Abscisic} {Acid} {Signaling} {Pathway} {Regulates} {Dormancy} in the {Liverwort} {Marchantia} polymorpha},
	volume = {28},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982218313472},
	doi = {10/gfpxm6},
	language = {en},
	number = {22},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Eklund, D. Magnus and Kanei, Masakazu and Flores-Sandoval, Eduardo and Ishizaki, Kimitsune and Nishihama, Ryuichi and Kohchi, Takayuki and Lagercrantz, Ulf and Bhalerao, Rishikesh P. and Sakata, Yoichi and Bowman, John L.},
	month = nov,
	year = {2018},
	pages = {3691--3699.e3},
}

@article{dubreuil_local_2018,
	title = {A {Local} {Auxin} {Gradient} {Regulates} {Root} {Cap} {Self}-{Renewal} and {Size} {Homeostasis}},
	volume = {28},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982218307607},
	doi = {10/gdwtc4},
	language = {en},
	number = {16},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Dubreuil, Carole and Jin, Xu and Grönlund, Andreas and Fischer, Urs},
	month = aug,
	year = {2018},
	pages = {2581--2587.e3},
}

@article{edwards_circadian_2018,
	title = {Circadian clock components control daily growth activities by modulating cytokinin levels and cell division-associated gene expression in \textit{{Populus}} trees: {Control} of growth in {Populus}.},
	volume = {41},
	issn = {01407791},
	shorttitle = {Circadian clock components control daily growth activities by modulating cytokinin levels and cell division-associated gene expression in \textit{{Populus}} trees},
	url = {http://doi.wiley.com/10.1111/pce.13185},
	doi = {10/gd8xdq},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Edwards, Kieron D. and Takata, Naoki and Johansson, Mikael and Jurca, Manuela and Novák, Ondřej and Hényková, Eva and Liverani, Silvia and Kozarewa, Iwanka and Strnad, Miroslav and Millar, Andrew J. and Ljung, Karin and Eriksson, Maria E.},
	month = jun,
	year = {2018},
	pages = {1468--1482},
}

@article{donev_engineering_2018,
	title = {Engineering {Non}-cellulosic {Polysaccharides} of {Wood} for the {Biorefinery}},
	volume = {9},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2018.01537/full},
	doi = {10/gjcq6g},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Donev, Evgeniy and Gandla, Madhavi Latha and Jönsson, Leif J. and Mellerowicz, Ewa J.},
	month = oct,
	year = {2018},
	pages = {1537},
}

@article{decker_structure-activity_2018,
	title = {The structure-activity relationship of the salicylimide derived inhibitors of {UDP}-sugar producing pyrophosphorylases},
	issn = {1559-2324},
	url = {https://www.tandfonline.com/doi/full/10.1080/15592324.2018.1507406},
	doi = {10/gjdv5h},
	language = {en},
	urldate = {2021-06-07},
	journal = {Plant Signaling \& Behavior},
	author = {Decker, Daniel and Öberg, Christopher and Kleczkowski, Leszek A.},
	month = aug,
	year = {2018},
	pages = {1--3},
}

@article{diaz_redox_2018,
	title = {Redox regulation of {PEP} activity during seedling establishment in {Arabidopsis} thaliana},
	volume = {9},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-017-02468-2},
	doi = {10/gcthqp},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Díaz, Manuel Guinea and Hernández-Verdeja, Tamara and Kremnev, Dmitry and Crawford, Tim and Dubreuil, Carole and Strand, Åsa},
	month = dec,
	year = {2018},
	pages = {50},
}

@article{dahrendorf_analysis_2018,
	title = {Analysis of {Nitrogen} {Utilization} {Capability} during the {Proliferation} and {Maturation} {Phases} of {Norway} {Spruce} ({Picea} abies ({L}.) {H}.{Karst}.) {Somatic} {Embryogenesis}},
	volume = {9},
	issn = {1999-4907},
	url = {http://www.mdpi.com/1999-4907/9/6/288},
	doi = {10/gdw3gf},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Forests},
	author = {Dahrendorf, Julia and Clapham, David and Egertsdotter, Ulrika},
	month = may,
	year = {2018},
	pages = {288},
}

@article{chen_efficiency_2018,
	title = {Efficiency of using spatial analysis for {Norway} spruce progeny tests in {Sweden}},
	volume = {75},
	issn = {1286-4560, 1297-966X},
	url = {http://link.springer.com/10.1007/s13595-017-0680-8},
	doi = {10/gdfmxt},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Annals of Forest Science},
	author = {Chen, Zhiqiang and Helmersson, Andreas and Westin, Johan and Karlsson, Bo and Wu, Harry X.},
	month = mar,
	year = {2018},
	pages = {2},
}

@article{chen_accuracy_2018,
	title = {Accuracy of genomic selection for growth and wood quality traits in two control-pollinated progeny trials using exome capture as the genotyping platform in {Norway} spruce},
	volume = {19},
	issn = {1471-2164},
	url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-5256-y},
	doi = {10/ghk9pc},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Chen, Zhi-Qiang and Baison, John and Pan, Jin and Karlsson, Bo and Andersson, Bengt and Westin, Johan and García-Gil, María Rosario and Wu, Harry X.},
	month = dec,
	year = {2018},
	pages = {946},
}

@article{chen_atlht1_2018,
	title = {{AtLHT1} {Transporter} {Can} {Facilitate} the {Uptake} and {Translocation} of a {Glycinergic}–{Chlorantraniliprole} {Conjugate} in \textit{{Arabidopsis} thaliana}},
	volume = {66},
	issn = {0021-8561, 1520-5118},
	url = {https://pubs.acs.org/doi/10.1021/acs.jafc.8b03591},
	doi = {10/gfr229},
	language = {en},
	number = {47},
	urldate = {2021-06-07},
	journal = {Journal of Agricultural and Food Chemistry},
	author = {Chen, Yan and Yan, Ying and Ren, Zhan-Fu and Ganeteg, Ulrika and Yao, Guang-Kai and Li, Zi-Lin and Huang, Tian and Li, Jia-Hui and Tian, Yong-Qing and Lin, Fei and Xu, Han-Hong},
	month = nov,
	year = {2018},
	pages = {12527--12535},
}

@article{chahtane_leafy_2018,
	title = {{LEAFY} activity is post-transcriptionally regulated by {BLADE} {ON} {PETIOLE2} and {CULLIN3} in {Arabidopsis}},
	volume = {220},
	issn = {0028646X},
	url = {http://doi.wiley.com/10.1111/nph.15329},
	doi = {10/gfcdwc},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Chahtane, Hicham and Zhang, Bo and Norberg, Mikael and LeMasson, Marie and Thévenon, Emmanuel and Bakó, László and Benlloch, Reyes and Holmlund, Mattias and Parcy, François and Nilsson, Ove and Vachon, Gilles},
	month = oct,
	year = {2018},
	pages = {579--592},
}

@article{chen_early_2018,
	title = {Early selection for resistance to {Heterobasidion} parviporum in {Norway} spruce is not likely to adversely affect growth and wood quality traits in late-age performance},
	volume = {137},
	issn = {1612-4669, 1612-4677},
	url = {http://link.springer.com/10.1007/s10342-018-1120-5},
	doi = {10/gdmzbk},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {European Journal of Forest Research},
	author = {Chen, Zhi-Qiang and Lundén, Karl and Karlsson, Bo and Vos, Ingrid and Olson, Åke and Lundqvist, Sven-Olof and Stenlid, Jan and Wu, Harry X. and García Gil, María Rosario and Elfstrand, Malin},
	month = aug,
	year = {2018},
	pages = {517--525},
}

@article{capovilla_porcupine_2018,
	title = {{PORCUPINE} regulates development in response to temperature through alternative splicing},
	volume = {4},
	issn = {2055-0278},
	url = {http://www.nature.com/articles/s41477-018-0176-z},
	doi = {10/gd9hnk},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Nature Plants},
	author = {Capovilla, Giovanna and Delhomme, Nicolas and Collani, Silvio and Shutava, Iryna and Bezrukov, Ilja and Symeonidi, Efthymia and de Francisco Amorim, Marcella and Laubinger, Sascha and Schmid, Markus},
	month = aug,
	year = {2018},
	pages = {534--539},
}

@article{bollhoner_function_2018,
	title = {The function of two type {II} metacaspases in woody tissues of \textit{{Populus}} trees},
	volume = {217},
	issn = {0028646X},
	url = {http://doi.wiley.com/10.1111/nph.14945},
	doi = {10/gczh42},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Bollhöner, Benjamin and Jokipii-Lukkari, Soile and Bygdell, Joakim and Stael, Simon and Adriasola, Mathilda and Muñiz, Luis and Van Breusegem, Frank and Ezcurra, Inés and Wingsle, Gunnar and Tuominen, Hannele},
	month = mar,
	year = {2018},
	pages = {1551--1565},
}

@article{armezzani_transcriptional_2018,
	title = {Transcriptional induction of cell wall remodelling genes is coupled to microtubule-driven growth isotropy at the shoot apex in {Arabidopsis}},
	issn = {1477-9129, 0950-1991},
	url = {https://journals.biologists.com/dev/article/doi/10.1242/dev.162255/264733/Transcriptional-induction-of-cell-wall-remodelling},
	doi = {10/gdhnxm},
	abstract = {The shoot apical meristem of higher plants continuously generates new tissues and organs through complex changes in growth rates and directions of its individual cells. Cell growth, driven by turgor pressure, largely depends on the cell walls, which allow cell expansion through synthesis and structural changes. A previous study revealed a major contribution of wall isotropy in organ emergence, through the disorganization of cortical microtubules. We show here that this disorganization is coupled with the transcriptional control of genes involved in wall remodelling. Some of these genes are induced when microtubules are disorganized and cells shift to isotropic growth. Mechanical modelling shows that this coupling has the potential to compensate for reduced cell expansion rates induced by the shift to isotropic growth. Reciprocally, cell wall loosening induced by different treatments or altered cell wall composition promotes a disruption of microtubule alignment. Our data thus indicate the existence of a regulatory module activated during organ outgrowth, linking microtubule arrangements to cell wall remodelling.},
	language = {en},
	urldate = {2021-06-07},
	journal = {Development},
	author = {Armezzani, Alessia and Abad, Ursula and Ali, Olivier and Robin, Amélie Andres and Vachez, Laetitia and Larrieu, Antoine and Mellerowicz, Ewa J. and Taconnat, Ludivine and Battu, Virginie and Stanislas, Thomas and Liu, Mengying and Vernoux, Teva and Traas, Jan and Sassi, Massimiliano},
	month = jan,
	year = {2018},
	pages = {dev.162255},
}

The shoot apical meristem of higher plants continuously generates new tissues and organs through complex changes in growth rates and directions of its individual cells. Cell growth, driven by turgor pressure, largely depends on the cell walls, which allow cell expansion through synthesis and structural changes. A previous study revealed a major contribution of wall isotropy in organ emergence, through the disorganization of cortical microtubules. We show here that this disorganization is coupled with the transcriptional control of genes involved in wall remodelling. Some of these genes are induced when microtubules are disorganized and cells shift to isotropic growth. Mechanical modelling shows that this coupling has the potential to compensate for reduced cell expansion rates induced by the shift to isotropic growth. Reciprocally, cell wall loosening induced by different treatments or altered cell wall composition promotes a disruption of microtubule alignment. Our data thus indicate the existence of a regulatory module activated during organ outgrowth, linking microtubule arrangements to cell wall remodelling.

@article{bhosale_mechanistic_2018,
	title = {A mechanistic framework for auxin dependent {Arabidopsis} root hair elongation to low external phosphate},
	volume = {9},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-018-03851-3},
	doi = {10/gdfv4v},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Bhosale, Rahul and Giri, Jitender and Pandey, Bipin K. and Giehl, Ricardo F. H. and Hartmann, Anja and Traini, Richard and Truskina, Jekaterina and Leftley, Nicola and Hanlon, Meredith and Swarup, Kamal and Rashed, Afaf and Voß, Ute and Alonso, Jose and Stepanova, Anna and Yun, Jeonga and Ljung, Karin and Brown, Kathleen M. and Lynch, Jonathan P. and Dolan, Liam and Vernoux, Teva and Bishopp, Anthony and Wells, Darren and von Wirén, Nicolaus and Bennett, Malcolm J. and Swarup, Ranjan},
	month = dec,
	year = {2018},
	pages = {1409},
}

@article{allakhverdiev_vyacheslav_2018,
	title = {Vyacheslav ({Slava}) {Klimov} (1945–2017): {A} scientist par excellence, a great human being, a friend, and a {Renaissance} man},
	volume = {136},
	issn = {0166-8595, 1573-5079},
	shorttitle = {Vyacheslav ({Slava}) {Klimov} (1945–2017)},
	url = {http://link.springer.com/10.1007/s11120-017-0440-5},
	doi = {10/gc7tqz},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Photosynthesis Research},
	author = {Allakhverdiev, Suleyman I. and Zharmukhamedov, Sergey K. and Rodionova, Margarita V. and Shuvalov, Vladimir A. and Dismukes, Charles and Shen, Jian-Ren and Barber, James and Samuelsson, Göran and {Govindjee}},
	month = apr,
	year = {2018},
	pages = {1--16},
}

@article{akhter_integrative_2018,
	title = {Integrative {Analysis} of {Three} {RNA} {Sequencing} {Methods} {Identifies} {Mutually} {Exclusive} {Exons} of {MADS}-{Box} {Isoforms} {During} {Early} {Bud} {Development} in {Picea} abies},
	volume = {9},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2018.01625/full},
	doi = {10/gh967n},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Akhter, Shirin and Kretzschmar, Warren W. and Nordal, Veronika and Delhomme, Nicolas and Street, Nathaniel R. and Nilsson, Ove and Emanuelsson, Olof and Sundström, Jens F.},
	month = nov,
	year = {2018},
	pages = {1625},
}

@article{agostinelli_pedunculate_2018,
	title = {Pedunculate {Oaks} ({Quercus} robur {L}.) {Differing} in {Vitality} as {Reservoirs} for {Fungal} {Biodiversity}},
	volume = {9},
	issn = {1664-302X},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2018.01758/full},
	doi = {10/gd4djv},
	urldate = {2021-06-07},
	journal = {Frontiers in Microbiology},
	author = {Agostinelli, Marta and Cleary, Michelle and Martín, Juan A. and Albrectsen, Benedicte R. and Witzell, Johanna},
	month = aug,
	year = {2018},
	pages = {1758},
}

@article{albrectsen_both_2018,
	title = {Both plant genotype and herbivory shape aspen endophyte communities},
	volume = {187},
	issn = {0029-8549, 1432-1939},
	url = {http://link.springer.com/10.1007/s00442-018-4097-3},
	doi = {10/gdrvmw},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Oecologia},
	author = {Albrectsen, Benedicte Riber and Siddique, Abu Bakar and Decker, Vicki Huizu Guo and Unterseher, Martin and Robinson, Kathryn M.},
	month = jun,
	year = {2018},
	pages = {535--545},
}

@article{verger_tension-adhesion_2018,
	title = {A tension-adhesion feedback loop in plant epidermis},
	volume = {7},
	issn = {2050-084X},
	url = {https://doi.org/10.7554/eLife.34460},
	doi = {10/gdd8s2},
	abstract = {Mechanical forces have emerged as coordinating signals for most cell functions. Yet, because forces are invisible, mapping tensile stress patterns in tissues remains a major challenge in all kingdoms. Here we take advantage of the adhesion defects in the Arabidopsis mutant quasimodo1 (qua1) to deduce stress patterns in tissues. By reducing the water potential and epidermal tension in planta, we rescued the adhesion defects in qua1, formally associating gaping and tensile stress patterns in the mutant. Using suboptimal water potential conditions, we revealed the relative contributions of shape- and growth-derived stress in prescribing maximal tension directions in aerial tissues. Consistently, the tension patterns deduced from the gaping patterns in qua1 matched the pattern of cortical microtubules, which are thought to align with maximal tension, in wild-type organs. Conversely, loss of epidermis continuity in the qua1 mutant hampered supracellular microtubule alignments, revealing that coordination through tensile stress requires cell-cell adhesion.},
	urldate = {2021-06-07},
	journal = {eLife},
	author = {Verger, Stéphane and Long, Yuchen and Boudaoud, Arezki and Hamant, Olivier},
	editor = {Hardtke, Christian S and Bergmann, Dominique C},
	month = apr,
	year = {2018},
	note = {Publisher: eLife Sciences Publications, Ltd},
	keywords = {cell adhesion, mechanical stress, microtubules, plant organs},
	pages = {e34460},
}

Mechanical forces have emerged as coordinating signals for most cell functions. Yet, because forces are invisible, mapping tensile stress patterns in tissues remains a major challenge in all kingdoms. Here we take advantage of the adhesion defects in the Arabidopsis mutant quasimodo1 (qua1) to deduce stress patterns in tissues. By reducing the water potential and epidermal tension in planta, we rescued the adhesion defects in qua1, formally associating gaping and tensile stress patterns in the mutant. Using suboptimal water potential conditions, we revealed the relative contributions of shape- and growth-derived stress in prescribing maximal tension directions in aerial tissues. Consistently, the tension patterns deduced from the gaping patterns in qua1 matched the pattern of cortical microtubules, which are thought to align with maximal tension, in wild-type organs. Conversely, loss of epidermis continuity in the qua1 mutant hampered supracellular microtubule alignments, revealing that coordination through tensile stress requires cell-cell adhesion.

@article{verger_plant_2018,
	title = {Plant {Physiology}: {FERONIA} {Defends} the {Cell} {Walls} against {Corrosion}},
	volume = {28},
	issn = {0960-9822},
	shorttitle = {Plant {Physiology}},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982218300769},
	doi = {10/gc3gx6},
	abstract = {A new study uncovers the role of wall sensing and remodeling in the plant response to salt stress, identifying the FERONIA receptor kinase as a key player in that process, likely through direct sensing of cell wall pectins.},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Verger, Stéphane and Hamant, Olivier},
	month = mar,
	year = {2018},
	pages = {R215--R217},
}

A new study uncovers the role of wall sensing and remodeling in the plant response to salt stress, identifying the FERONIA receptor kinase as a key player in that process, likely through direct sensing of cell wall pectins.

@article{varadharajan_grayling_2018,
	title = {The {Grayling} {Genome} {Reveals} {Selection} on {Gene} {Expression} {Regulation} after {Whole}-{Genome} {Duplication}},
	volume = {10},
	issn = {1759-6653},
	url = {https://academic.oup.com/gbe/article/10/10/2785/5098299},
	doi = {10/gd97nr},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Genome Biology and Evolution},
	author = {Varadharajan, Srinidhi and Sandve, Simen R and Gillard, Gareth B and Tørresen, Ole K and Mulugeta, Teshome D and Hvidsten, Torgeir R and Lien, Sigbjørn and Asbjørn Vøllestad, Leif and Jentoft, Sissel and Nederbragt, Alexander J and Jakobsen, Kjetill S},
	editor = {Van De Peer, Yves},
	month = oct,
	year = {2018},
	pages = {2785--2800},
}

@article{verger_image_2018,
	title = {An {Image} {Analysis} {Pipeline} to {Quantify} {Emerging} {Cracks} in {Materials} or {Adhesion} {Defects} in {Living} {Tissues}},
	volume = {8},
	issn = {2331-8325},
	url = {https://bio-protocol.org/e3036},
	doi = {10/gkf56f},
	language = {en},
	number = {19},
	urldate = {2021-06-07},
	journal = {BIO-PROTOCOL},
	author = {Verger, Stéphane and Cerutti, Guillaume and Hamant, Olivier},
	year = {2018},
}

@article{van_der_schuren_broad_2018,
	title = {Broad spectrum developmental role of {Brachypodium} {AUX1}},
	volume = {219},
	issn = {0028646X},
	url = {http://doi.wiley.com/10.1111/nph.15332},
	doi = {10/gd3g53},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {van der Schuren, Alja and Voiniciuc, Catalin and Bragg, Jennifer and Ljung, Karin and Vogel, John and Pauly, Markus and Hardtke, Christian S.},
	month = sep,
	year = {2018},
	pages = {1216--1223},
}

@article{ursache_protocol_2018,
	title = {A protocol for combining fluorescent proteins with histological stains for diverse cell wall components},
	volume = {93},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.13784},
	doi = {10/gkf56d},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Ursache, Robertas and Andersen, Tonni Grube and Marhavý, Peter and Geldner, Niko},
	month = jan,
	year = {2018},
	pages = {399--412},
}

@article{torell_metabolic_2018,
	title = {Metabolic {Profiling} of {Multiorgan} {Samples}: {Evaluation} of {MODY5}/{RCAD} {Mutant} {Mice}},
	volume = {17},
	issn = {1535-3893, 1535-3907},
	shorttitle = {Metabolic {Profiling} of {Multiorgan} {Samples}},
	url = {https://pubs.acs.org/doi/10.1021/acs.jproteome.7b00821},
	doi = {10/gdxhnh},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Journal of Proteome Research},
	author = {Torell, Frida and Bennett, Kate and Cereghini, Silvia and Fabre, Mélanie and Rännar, Stefan and Lundstedt-Enkel, Katrin and Moritz, Thomas and Haumaitre, Cécile and Trygg, Johan and Lundstedt, Torbjörn},
	month = jul,
	year = {2018},
	pages = {2293--2306},
}

@article{tibiletti_stress-induced_2018,
	title = {The stress-induced {SCP}/{HLIP} family of small light-harvesting-like proteins ({ScpABCDE}) protects {Photosystem} {II} from photoinhibitory damages in the cyanobacterium {Synechocystis} sp. {PCC} 6803},
	volume = {135},
	issn = {0166-8595, 1573-5079},
	url = {http://link.springer.com/10.1007/s11120-017-0426-3},
	doi = {10/gcxqh5},
	language = {en},
	number = {1-3},
	urldate = {2021-06-07},
	journal = {Photosynthesis Research},
	author = {Tibiletti, Tania and Rehman, Ateeq Ur and Vass, Imre and Funk, Christiane},
	month = mar,
	year = {2018},
	pages = {103--114},
}

@article{tan_genomic_2018,
	title = {Genomic relationships reveal significant dominance effects for growth in hybrid {Eucalyptus}},
	volume = {267},
	issn = {01689452},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0168945217307847},
	doi = {10/gc3n47},
	language = {en},
	urldate = {2021-06-07},
	journal = {Plant Science},
	author = {Tan, Biyue and Grattapaglia, Dario and Wu, Harry X. and Ingvarsson, Pär K.},
	month = feb,
	year = {2018},
	pages = {84--93},
}

@article{sun_editing_2018,
	title = {Editing of {Chloroplast} rps14 by {PPR} {Editing} {Factor} {EMB2261} {Is} {Essential} for {Arabidopsis} {Development}},
	volume = {9},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2018.00841/full},
	doi = {10/gkf56c},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Sun, Yueming K. and Gutmann, Bernard and Yap, Aaron and Kindgren, Peter and Small, Ian},
	month = jun,
	year = {2018},
	pages = {841},
}

@article{singh_genetic_2018,
	title = {A genetic network mediating the control of bud break in hybrid aspen},
	volume = {9},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-018-06696-y},
	doi = {10/gffvjm},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Singh, Rajesh Kumar and Maurya, Jay P. and Azeez, Abdul and Miskolczi, Pal and Tylewicz, Szymon and Stojkovič, Katja and Delhomme, Nicolas and Busov, Victor and Bhalerao, Rishikesh P.},
	month = dec,
	year = {2018},
	pages = {4173},
}

@article{speth_arabidopsis_2018,
	title = {Arabidopsis {RNA} processing factor {SERRATE} regulates the transcription of intronless genes},
	volume = {7},
	issn = {2050-084X},
	url = {https://elifesciences.org/articles/37078},
	doi = {10/gd7w68},
	abstract = {Intron splicing increases proteome complexity, promotes RNA stability, and enhances transcription. However, introns and the concomitant need for splicing extend the time required for gene expression and can cause an undesirable delay in the activation of genes. Here, we show that the plant microRNA processing factor SERRATE (SE) plays an unexpected and pivotal role in the regulation of intronless genes. Arabidopsis SE associated with more than 1000, mainly intronless, genes in a transcription-dependent manner. Chromatin-bound SE liaised with paused and elongating polymerase II complexes and promoted their association with intronless target genes. Our results indicate that stress-responsive genes contain no or few introns, which negatively affects their expression strength, but that some genes circumvent this limitation via a novel SE-dependent transcriptional activation mechanism. Transcriptome analysis of a Drosophila mutant defective in ARS2, the metazoan homologue of SE, suggests that SE/ARS2 function in regulating intronless genes might be conserved across kingdoms.},
	language = {en},
	urldate = {2021-06-07},
	journal = {eLife},
	author = {Speth, Corinna and Szabo, Emese Xochitl and Martinho, Claudia and Collani, Silvio and zur Oven-Krockhaus, Sven and Richter, Sandra and Droste-Borel, Irina and Macek, Boris and Stierhof, York-Dieter and Schmid, Markus and Liu, Chang and Laubinger, Sascha},
	month = aug,
	year = {2018},
	pages = {e37078},
}

Intron splicing increases proteome complexity, promotes RNA stability, and enhances transcription. However, introns and the concomitant need for splicing extend the time required for gene expression and can cause an undesirable delay in the activation of genes. Here, we show that the plant microRNA processing factor SERRATE (SE) plays an unexpected and pivotal role in the regulation of intronless genes. Arabidopsis SE associated with more than 1000, mainly intronless, genes in a transcription-dependent manner. Chromatin-bound SE liaised with paused and elongating polymerase II complexes and promoted their association with intronless target genes. Our results indicate that stress-responsive genes contain no or few introns, which negatively affects their expression strength, but that some genes circumvent this limitation via a novel SE-dependent transcriptional activation mechanism. Transcriptome analysis of a Drosophila mutant defective in ARS2, the metazoan homologue of SE, suggests that SE/ARS2 function in regulating intronless genes might be conserved across kingdoms.

@article{strengbom_trade-offs_2018,
	title = {Trade-offs in the multi-use potential of managed boreal forests},
	volume = {55},
	issn = {00218901},
	url = {http://doi.wiley.com/10.1111/1365-2664.13019},
	doi = {10/gc4hkp},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Journal of Applied Ecology},
	author = {Strengbom, Joachim and Axelsson, E. Petter and Lundmark, Tomas and Nordin, Annika},
	editor = {Villard, Marc-André},
	month = mar,
	year = {2018},
	pages = {958--966},
}

@article{shanks_role_2018,
	title = {Role of \textit{{BASIC} {PENTACYSTEINE}} transcription factors in a subset of cytokinin signaling responses},
	volume = {95},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.13962},
	doi = {10/gdqkns},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Shanks, Carly M. and Hecker, Andreas and Cheng, Chia-Yi and Brand, Luise and Collani, Silvio and Schmid, Markus and Schaller, G. Eric and Wanke, Dierk and Harter, Klaus and Kieber, Joseph J.},
	month = aug,
	year = {2018},
	pages = {458--473},
}

@article{simura_plant_2018,
	title = {Plant {Hormonomics}: {Multiple} {Phytohormone} {Profiling} by {Targeted} {Metabolomics}},
	volume = {177},
	issn = {1532-2548},
	shorttitle = {Plant {Hormonomics}},
	url = {https://academic.oup.com/plphys/article/177/2/476/6117035},
	doi = {10/gdrpsw},
	abstract = {Abstract
            Phytohormones are physiologically important small molecules that play essential roles in intricate signaling networks that regulate diverse processes in plants. We present a method for the simultaneous targeted profiling of 101 phytohormone-related analytes from minute amounts of fresh plant material (less than 20 mg). Rapid and nonselective extraction, fast one-step sample purification, and extremely sensitive ultra-high-performance liquid chromatography-tandem mass spectrometry enable concurrent quantification of the main phytohormone classes: cytokinins, auxins, brassinosteroids, gibberellins, jasmonates, salicylates, and abscisates. We validated this hormonomic approach in salt-stressed and control Arabidopsis (Arabidopsis thaliana) seedlings, quantifying a total of 43 endogenous compounds in both root and shoot samples. Subsequent multivariate statistical data processing and cross-validation with transcriptomic data highlighted the main hormone metabolites involved in plant adaptation to salt stress.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Šimura, Jan and Antoniadi, Ioanna and Široká, Jitka and Tarkowská, Danu¡e and Strnad, Miroslav and Ljung, Karin and Novák, Ondřej},
	month = jun,
	year = {2018},
	pages = {476--489},
}

Abstract Phytohormones are physiologically important small molecules that play essential roles in intricate signaling networks that regulate diverse processes in plants. We present a method for the simultaneous targeted profiling of 101 phytohormone-related analytes from minute amounts of fresh plant material (less than 20 mg). Rapid and nonselective extraction, fast one-step sample purification, and extremely sensitive ultra-high-performance liquid chromatography-tandem mass spectrometry enable concurrent quantification of the main phytohormone classes: cytokinins, auxins, brassinosteroids, gibberellins, jasmonates, salicylates, and abscisates. We validated this hormonomic approach in salt-stressed and control Arabidopsis (Arabidopsis thaliana) seedlings, quantifying a total of 43 endogenous compounds in both root and shoot samples. Subsequent multivariate statistical data processing and cross-validation with transcriptomic data highlighted the main hormone metabolites involved in plant adaptation to salt stress.

@article{seyfferth_ethylene-related_2018,
	title = {Ethylene-{Related} {Gene} {Expression} {Networks} in {Wood} {Formation}},
	volume = {9},
	issn = {1664-462X},
	url = {http://journal.frontiersin.org/article/10.3389/fpls.2018.00272/full},
	doi = {10/gc7vds},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Seyfferth, Carolin and Wessels, Bernard and Jokipii-Lukkari, Soile and Sundberg, Björn and Delhomme, Nicolas and Felten, Judith and Tuominen, Hannele},
	month = mar,
	year = {2018},
	pages = {272},
}

@article{sapala_why_2018,
	title = {Why plants make puzzle cells, and how their shape emerges},
	volume = {7},
	issn = {2050-084X},
	url = {https://doi.org/10.7554/eLife.32794},
	doi = {10/gc3w3z},
	abstract = {The shape and function of plant cells are often highly interdependent. The puzzle-shaped cells that appear in the epidermis of many plants are a striking example of a complex cell shape, however their functional benefit has remained elusive. We propose that these intricate forms provide an effective strategy to reduce mechanical stress in the cell wall of the epidermis. When tissue-level growth is isotropic, we hypothesize that lobes emerge at the cellular level to prevent formation of large isodiametric cells that would bulge under the stress produced by turgor pressure. Data from various plant organs and species support the relationship between lobes and growth isotropy, which we test with mutants where growth direction is perturbed. Using simulation models we show that a mechanism actively regulating cellular stress plausibly reproduces the development of epidermal cell shape. Together, our results suggest that mechanical stress is a key driver of cell-shape morphogenesis.},
	urldate = {2021-06-07},
	journal = {eLife},
	author = {Sapala, Aleksandra and Runions, Adam and Routier-Kierzkowska, Anne-Lise and Das Gupta, Mainak and Hong, Lilan and Hofhuis, Hugo and Verger, Stéphane and Mosca, Gabriella and Li, Chun-Biu and Hay, Angela and Hamant, Olivier and Roeder, Adrienne HK and Tsiantis, Miltos and Prusinkiewicz, Przemyslaw and Smith, Richard S},
	editor = {McCormick, Sheila},
	month = feb,
	year = {2018},
	note = {Publisher: eLife Sciences Publications, Ltd},
	keywords = {growth, modelling, morphogenesis, organ shape, pavement cells, plant development},
	pages = {e32794},
}

The shape and function of plant cells are often highly interdependent. The puzzle-shaped cells that appear in the epidermis of many plants are a striking example of a complex cell shape, however their functional benefit has remained elusive. We propose that these intricate forms provide an effective strategy to reduce mechanical stress in the cell wall of the epidermis. When tissue-level growth is isotropic, we hypothesize that lobes emerge at the cellular level to prevent formation of large isodiametric cells that would bulge under the stress produced by turgor pressure. Data from various plant organs and species support the relationship between lobes and growth isotropy, which we test with mutants where growth direction is perturbed. Using simulation models we show that a mechanism actively regulating cellular stress plausibly reproduces the development of epidermal cell shape. Together, our results suggest that mechanical stress is a key driver of cell-shape morphogenesis.

@article{sandve_subfunctionalization_2018,
	title = {Subfunctionalization versus neofunctionalization after whole-genome duplication},
	volume = {50},
	issn = {1061-4036, 1546-1718},
	url = {http://www.nature.com/articles/s41588-018-0162-4},
	doi = {10/gd8pbv},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Nature Genetics},
	author = {Sandve, Simen R. and Rohlfs, Rori V. and Hvidsten, Torgeir R.},
	month = jul,
	year = {2018},
	pages = {908--909},
}

@article{ravikumar_independent_2018,
	title = {Independent yet overlapping pathways ensure the robustness and responsiveness of trans-{Golgi} network functions in \textit{{Arabidopsis}}},
	volume = {145},
	issn = {1477-9129, 0950-1991},
	url = {https://journals.biologists.com/dev/article/145/21/dev169201/48526/Independent-yet-overlapping-pathways-ensure-the},
	doi = {10/gfqn3d},
	abstract = {ABSTRACT
            The trans-Golgi-network (TGN) has essential housekeeping functions in secretion, endocytosis and protein sorting, but also more specialized functions in plant development. How the robustness of basal TGN function is ensured while specialized functions are differentially regulated is poorly understood. Here, we investigate two key regulators of TGN structure and function, ECHIDNA and the Transport Protein Particle II (TRAPPII) tethering complex. An analysis of physical, network and genetic interactions suggests that two network communities are implicated in TGN function and that ECHIDNA and TRAPPII belong to distinct yet overlapping pathways. Whereas ECHIDNA and TRAPPII colocalized at the TGN in interphase cells, their localization diverged in dividing cells. Moreover, ECHIDNA and TRAPPII localization patterns were mutually independent. TGN structure, endocytosis and sorting decisions were differentially impacted in echidna and trappii mutants. Our analyses point to a partitioning of specialized TGN functions, with ECHIDNA being required for cell elongation and TRAPPII for cytokinesis. Two independent pathways able to compensate for each other might contribute to the robustness of TGN housekeeping functions and to the responsiveness and fine tuning of its specialized functions.},
	language = {en},
	number = {21},
	urldate = {2021-06-07},
	journal = {Development},
	author = {Ravikumar, Raksha and Kalbfuß, Nils and Gendre, Delphine and Steiner, Alexander and Altmann, Melina and Altmann, Stefan and Rybak, Katarzyna and Edelmann, Holger and Stephan, Friederike and Lampe, Marko and Facher, Eva and Wanner, Gerhard and Falter-Braun, Pascal and Bhalerao, Rishikesh P. and Assaad, Farhah F.},
	month = nov,
	year = {2018},
	pages = {dev169201},
}

ABSTRACT The trans-Golgi-network (TGN) has essential housekeeping functions in secretion, endocytosis and protein sorting, but also more specialized functions in plant development. How the robustness of basal TGN function is ensured while specialized functions are differentially regulated is poorly understood. Here, we investigate two key regulators of TGN structure and function, ECHIDNA and the Transport Protein Particle II (TRAPPII) tethering complex. An analysis of physical, network and genetic interactions suggests that two network communities are implicated in TGN function and that ECHIDNA and TRAPPII belong to distinct yet overlapping pathways. Whereas ECHIDNA and TRAPPII colocalized at the TGN in interphase cells, their localization diverged in dividing cells. Moreover, ECHIDNA and TRAPPII localization patterns were mutually independent. TGN structure, endocytosis and sorting decisions were differentially impacted in echidna and trappii mutants. Our analyses point to a partitioning of specialized TGN functions, with ECHIDNA being required for cell elongation and TRAPPII for cytokinesis. Two independent pathways able to compensate for each other might contribute to the robustness of TGN housekeeping functions and to the responsiveness and fine tuning of its specialized functions.

@article{reza_transcriptome_2018,
	title = {Transcriptome analysis of embryonic domains in {Norway} spruce reveals potential regulators of suspensor cell death},
	volume = {13},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0192945},
	doi = {10/gc8wb4},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Reza, Salim H. and Delhomme, Nicolas and Street, Nathaniel R. and Ramachandran, Prashanth and Dalman, Kerstin and Nilsson, Ove and Minina, Elena A. and Bozhkov, Peter V.},
	editor = {Sun, Meng-xiang},
	month = mar,
	year = {2018},
	pages = {e0192945},
}

@article{roberge_modified_2018,
	title = {Modified forest rotation lengths: {Long}-term effects on landscape-scale habitat availability for specialized species},
	volume = {210},
	issn = {03014797},
	shorttitle = {Modified forest rotation lengths},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0301479717311908},
	doi = {10/gc5jnj},
	language = {en},
	urldate = {2021-06-07},
	journal = {Journal of Environmental Management},
	author = {Roberge, Jean-Michel and Öhman, Karin and Lämås, Tomas and Felton, Adam and Ranius, Thomas and Lundmark, Tomas and Nordin, Annika},
	month = mar,
	year = {2018},
	pages = {1--9},
}

@article{ratke_downregulating_2018,
	title = {Downregulating aspen xylan biosynthetic {GT43} genes in developing wood stimulates growth via reprograming of the transcriptome},
	volume = {219},
	issn = {0028646X},
	url = {http://doi.wiley.com/10.1111/nph.15160},
	doi = {10/gdmzzr},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Ratke, Christine and Terebieniec, Barbara K. and Winestrand, Sandra and Derba-Maceluch, Marta and Grahn, Thomas and Schiffthaler, Bastian and Ulvcrona, Thomas and Özparpucu, Merve and Rüggeberg, Markus and Lundqvist, Sven-Olof and Street, Nathaniel R. and Jönsson, Leif J. and Mellerowicz, Ewa J.},
	month = jul,
	year = {2018},
	pages = {230--245},
}

@article{randriamanana_does_2018,
	title = {Does fungal endophyte inoculation affect the responses of aspen seedlings to carbon dioxide enrichment?},
	volume = {33},
	issn = {17545048},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1754504817301861},
	doi = {10/gdkfq9},
	language = {en},
	urldate = {2021-06-07},
	journal = {Fungal Ecology},
	author = {Randriamanana, Tendry R. and Nissinen, Katri and Ovaskainen, Anu and Lavola, Anu and Peltola, Heli and Albrectsen, Benedicte and Julkunen-Tiitto, Riitta},
	month = jun,
	year = {2018},
	pages = {24--31},
}

@article{colesie_can_2018,
	title = {Can {Antarctic} lichens acclimatize to changes in temperature?},
	volume = {24},
	issn = {1354-1013, 1365-2486},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.13984},
	doi = {10.1111/gcb.13984},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Global Change Biology},
	author = {Colesie, Claudia and Büdel, Burkhard and Hurry, Vaughan and Green, Thomas George Allan},
	month = mar,
	year = {2018},
	pages = {1123--1135},
}

@article{crawford_role_2018,
	title = {The role of retrograde signals during plant stress responses},
	volume = {69},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erx481},
	doi = {10.1093/jxb/erx481},
	abstract = {Chloroplast and mitochondria not only provide the energy to the plant cell but due to the sensitivity of organellar processes to perturbations caused by abiotic stress, they are also key cellular sensors of environmental fluctuations. Abiotic stresses result in reduced photosynthetic efficiency and thereby reduced energy supply for cellular processes. Thus, in order to acclimate to stress, plants must re-program gene expression and cellular metabolism to divert energy from growth and developmental processes to stress responses. To restore cellular energy homeostasis following exposure to stress, the activities of the organelles must be tightly co-ordinated with the transcriptional re-programming in the nucleus. Thus, communication between the organelles and the nucleus, so-called retrograde signalling, is essential to direct the energy use correctly during stress exposure. Stress-triggered retrograde signals are mediated by reactive oxygen species and metabolites including β-cyclocitral, MEcPP (2-C-methyl-d-erythritol 2,4-cyclodiphosphate), PAP (3ʹ-phosphoadenosine 5ʹ-phosphate), and intermediates of the tetrapyrrole biosynthesis pathway. However, for the plant cell to respond optimally to environmental stress, these stress-triggered retrograde signalling pathways must be integrated with the cytosolic stress signalling network. We hypothesize that the Mediator transcriptional co-activator complex may play a key role as a regulatory hub in the nucleus, integrating the complex stress signalling networks originating in different cellular compartments.},
	number = {11},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Crawford, Tim and Lehotai, Nóra and Strand, Åsa},
	month = may,
	year = {2018},
	pages = {2783--2795},
}

Chloroplast and mitochondria not only provide the energy to the plant cell but due to the sensitivity of organellar processes to perturbations caused by abiotic stress, they are also key cellular sensors of environmental fluctuations. Abiotic stresses result in reduced photosynthetic efficiency and thereby reduced energy supply for cellular processes. Thus, in order to acclimate to stress, plants must re-program gene expression and cellular metabolism to divert energy from growth and developmental processes to stress responses. To restore cellular energy homeostasis following exposure to stress, the activities of the organelles must be tightly co-ordinated with the transcriptional re-programming in the nucleus. Thus, communication between the organelles and the nucleus, so-called retrograde signalling, is essential to direct the energy use correctly during stress exposure. Stress-triggered retrograde signals are mediated by reactive oxygen species and metabolites including β-cyclocitral, MEcPP (2-C-methyl-d-erythritol 2,4-cyclodiphosphate), PAP (3ʹ-phosphoadenosine 5ʹ-phosphate), and intermediates of the tetrapyrrole biosynthesis pathway. However, for the plant cell to respond optimally to environmental stress, these stress-triggered retrograde signalling pathways must be integrated with the cytosolic stress signalling network. We hypothesize that the Mediator transcriptional co-activator complex may play a key role as a regulatory hub in the nucleus, integrating the complex stress signalling networks originating in different cellular compartments.

@article{klemencic_type_2018,
	title = {Type {III} metacaspases: calcium-dependent activity proposes new function for the p10 domain},
	volume = {218},
	issn = {0028646X},
	shorttitle = {Type {III} metacaspases},
	url = {http://doi.wiley.com/10.1111/nph.14660},
	doi = {10.1111/nph.14660},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Klemenčič, Marina and Funk, Christiane},
	month = may,
	year = {2018},
	pages = {1179--1191},
}

@article{felten_ethylene_2018,
	title = {Ethylene signaling induces gelatinous layers with typical features of tension wood in hybrid aspen},
	volume = {218},
	issn = {0028646X},
	url = {http://doi.wiley.com/10.1111/nph.15078},
	doi = {10.1111/nph.15078},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Felten, Judith and Vahala, Jorma and Love, Jonathan and Gorzsás, András and Rüggeberg, Markus and Delhomme, Nicolas and Leśniewska, Joanna and Kangasjärvi, Jaakko and Hvidsten, Torgeir R. and Mellerowicz, Ewa J. and Sundberg, Björn},
	month = may,
	year = {2018},
	pages = {999--1014},
}

@article{ferro_isolation_2018,
	title = {Isolation and characterization of microalgal strains for biomass production and wastewater reclamation in {Northern} {Sweden}},
	volume = {32},
	issn = {22119264},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2211926417308330},
	doi = {10.1016/j.algal.2018.03.006},
	language = {en},
	urldate = {2021-06-07},
	journal = {Algal Research},
	author = {Ferro, Lorenza and Gentili, Francesco G. and Funk, Christiane},
	month = jun,
	year = {2018},
	pages = {44--53},
}

@article{ferro_subarctic_2018,
	title = {Subarctic microalgal strains treat wastewater and produce biomass at low temperature and short photoperiod},
	volume = {35},
	issn = {22119264},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2211926418302273},
	doi = {10.1016/j.algal.2018.08.031},
	language = {en},
	urldate = {2021-06-07},
	journal = {Algal Research},
	author = {Ferro, Lorenza and Gorzsás, András and Gentili, Francesco G. and Funk, Christiane},
	month = nov,
	year = {2018},
	pages = {160--167},
}

@article{fundova_non-destructive_2018,
	title = {Non-destructive wood density assessment of {Scots} pine ({Pinus} sylvestris {L}.) using {Resistograph} and {Pilodyn}},
	volume = {13},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0204518},
	doi = {10.1371/journal.pone.0204518},
	language = {en},
	number = {9},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Fundova, Irena and Funda, Tomas and Wu, Harry X.},
	editor = {Gomory, Dusan},
	month = sep,
	year = {2018},
	pages = {e0204518},
}

@article{giri_rice_2018,
	title = {Rice auxin influx carrier {OsAUX1} facilitates root hair elongation in response to low external phosphate},
	volume = {9},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-018-03850-4},
	doi = {10.1038/s41467-018-03850-4},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Giri, Jitender and Bhosale, Rahul and Huang, Guoqiang and Pandey, Bipin K. and Parker, Helen and Zappala, Susan and Yang, Jing and Dievart, Anne and Bureau, Charlotte and Ljung, Karin and Price, Adam and Rose, Terry and Larrieu, Antoine and Mairhofer, Stefan and Sturrock, Craig J. and White, Philip and Dupuy, Lionel and Hawkesford, Malcolm and Perin, Christophe and Liang, Wanqi and Peret, Benjamin and Hodgman, Charlie T. and Lynch, Jonathan and Wissuwa, Matthias and Zhang, Dabing and Pridmore, Tony and Mooney, Sacha J. and Guiderdoni, Emmanuel and Swarup, Ranjan and Bennett, Malcolm J.},
	month = dec,
	year = {2018},
	pages = {1408},
}

@article{grimberg_storage_2018,
	title = {Storage lipid accumulation is controlled by photoperiodic signal acting via regulators of growth cessation and dormancy in hybrid aspen},
	volume = {219},
	issn = {0028646X},
	url = {http://doi.wiley.com/10.1111/nph.15197},
	doi = {10.1111/nph.15197},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Grimberg, Åsa and Lager, Ida and Street, Nathaniel R. and Robinson, Kathryn M. and Marttila, Salla and Mähler, Niklas and Ingvarsson, Pär K. and Bhalerao, Rishikesh P.},
	month = jul,
	year = {2018},
	pages = {619--630},
}

@article{haas_microbial_2018,
	title = {Microbial community response to growing season and plant nutrient optimisation in a boreal {Norway} spruce forest},
	volume = {125},
	issn = {00380717},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0038071718302335},
	doi = {10.1016/j.soilbio.2018.07.005},
	language = {en},
	urldate = {2021-06-07},
	journal = {Soil Biology and Biochemistry},
	author = {Haas, Julia C. and Street, Nathaniel R. and Sjödin, Andreas and Lee, Natuschka M. and Högberg, Mona N. and Näsholm, Torgny and Hurry, Vaughan},
	month = oct,
	year = {2018},
	pages = {197--209},
}

@article{hayatgheibi_genetic_2018,
	title = {Genetic control of transition from juvenile to mature wood with respect to microfibril angle in {Norway} spruce ( \textit{{Picea} abies} ) and lodgepole pine ( \textit{{Pinus} contorta} )},
	volume = {48},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfr-2018-0140},
	doi = {10.1139/cjfr-2018-0140},
	abstract = {Genetic control of microfibril angle (MFA) transition from juvenile wood to mature wood was evaluated in Norway spruce (Picea abies (L.) Karst) and lodgepole pine (Pinus contorta Douglas ex Loudon). Increment cores were collected at breast height (1.3 m) from 5664 trees in two 21-year-old Norway spruce progeny trials in southern Sweden and from 823 trees in two lodgepole pine progeny trials, aged 34–35 years, in northern Sweden. Radial variations in MFA from pith to bark were measured for each core using SilviScan. To estimate MFA transition from juvenile wood to mature wood, a threshold level of MFA 20° was considered, and six different regression functions were fitted to the MFA profile of each tree after exclusion of outliers, following three steps. The narrow-sense heritability estimates (h
              2
              ) obtained for MFA transition were highest based on the slope function, ranging from 0.21 to 0.23 for Norway spruce and from 0.34 to 0.53 for lodgepole pine, while h
              2
              were mostly non-significant based on the logistic function, under all exclusion methods. Results of this study indicate that it is possible to select for an earlier MFA transition from juvenile wood to mature wood in Norway spruce and lodgepole pine selective breeding programs, as the genetic gains (ΔG) obtained in direct selection of this trait were very high in both species.},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Canadian Journal of Forest Research},
	author = {Hayatgheibi, Haleh and Forsberg, Nils Erik Gustaf and Lundqvist, Sven-Olof and Mörling, Tommy and Mellerowicz, Ewa J. and Karlsson, Bo and Wu, Harry X. and García-Gil, M. Rosario},
	month = nov,
	year = {2018},
	pages = {1358--1365},
}

Genetic control of microfibril angle (MFA) transition from juvenile wood to mature wood was evaluated in Norway spruce (Picea abies (L.) Karst) and lodgepole pine (Pinus contorta Douglas ex Loudon). Increment cores were collected at breast height (1.3 m) from 5664 trees in two 21-year-old Norway spruce progeny trials in southern Sweden and from 823 trees in two lodgepole pine progeny trials, aged 34–35 years, in northern Sweden. Radial variations in MFA from pith to bark were measured for each core using SilviScan. To estimate MFA transition from juvenile wood to mature wood, a threshold level of MFA 20° was considered, and six different regression functions were fitted to the MFA profile of each tree after exclusion of outliers, following three steps. The narrow-sense heritability estimates (h 2 ) obtained for MFA transition were highest based on the slope function, ranging from 0.21 to 0.23 for Norway spruce and from 0.34 to 0.53 for lodgepole pine, while h 2 were mostly non-significant based on the logistic function, under all exclusion methods. Results of this study indicate that it is possible to select for an earlier MFA transition from juvenile wood to mature wood in Norway spruce and lodgepole pine selective breeding programs, as the genetic gains (ΔG) obtained in direct selection of this trait were very high in both species.

@article{hedwall_interplay_2018,
	title = {Interplay between {N}-form and {N}-dose influences ecosystem effects of {N} addition to boreal forest},
	volume = {423},
	issn = {0032-079X, 1573-5036},
	url = {http://link.springer.com/10.1007/s11104-017-3444-1},
	doi = {10.1007/s11104-017-3444-1},
	language = {en},
	number = {1-2},
	urldate = {2021-06-07},
	journal = {Plant and Soil},
	author = {Hedwall, Per-Ola and Gruffman, Linda and Ishida, Takahide and From, Fredrik and Lundmark, Tomas and Näsholm, Torgny and Nordin, Annika},
	month = feb,
	year = {2018},
	pages = {385--395},
}

@article{horn_growth_2018,
	title = {Growth and survival relationships of 71 tree species with nitrogen and sulfur deposition across the conterminous {U}.{S}.},
	volume = {13},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0205296},
	doi = {10.1371/journal.pone.0205296},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Horn, Kevin J. and Thomas, R. Quinn and Clark, Christopher M. and Pardo, Linda H. and Fenn, Mark E. and Lawrence, Gregory B. and Perakis, Steven S. and Smithwick, Erica A. H. and Baldwin, Douglas and Braun, Sabine and Nordin, Annika and Perry, Charles H. and Phelan, Jennifer N. and Schaberg, Paul G. and St. Clair, Samuel B. and Warby, Richard and Watmough, Shaun},
	editor = {Loustau, Denis},
	month = oct,
	year = {2018},
	pages = {e0205296},
}

@article{igamberdiev_glycerate_2018,
	title = {The {Glycerate} and {Phosphorylated} {Pathways} of {Serine} {Synthesis} in {Plants}: {The} {Branches} of {Plant} {Glycolysis} {Linking} {Carbon} and {Nitrogen} {Metabolism}},
	volume = {9},
	issn = {1664-462X},
	shorttitle = {The {Glycerate} and {Phosphorylated} {Pathways} of {Serine} {Synthesis} in {Plants}},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2018.00318/full},
	doi = {10.3389/fpls.2018.00318},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Igamberdiev, Abir U. and Kleczkowski, Leszek A.},
	month = mar,
	year = {2018},
	pages = {318},
}

@article{jamtgard_optimising_2018,
	title = {Optimising methods for the recovery and quantification of di- and tripeptides in soil},
	volume = {56},
	issn = {1838-675X},
	url = {http://www.publish.csiro.au/?paper=SR17279},
	doi = {10.1071/SR17279},
	abstract = {Di- and tripeptides are intermediaries in the nitrogen cycle and are likely to have roles in the soil–microbe–plant continuum, but they have hitherto been difficult to measure in soils. To lay the base for future studies of oligopeptides in soil, we added 10 known di- and tripeptides with diverse chemical properties to forest and agricultural soils and then recovered the peptides by means of induced diffusive fluxes using microdialysis, a minimally-intrusive soil sampling technique. The concentration of the peptides recovered with the probes was 25–39\% (relative recovery) of the concentration in the external solution, and followed the same trend as previously observed for amino acids, with smaller peptides (e.g. Gly-Gly) recovered at a higher rate than larger ones (e.g. Tyr-Phe). After derivatisation with AccQ-Tag™, a standard method for amino acids, peptides were analysed by ultra-high-pressure liquid chromatography-triple quadrupole mass spectrometry. Multiple reaction monitoring mass spectrometry was used to quantify specific peptides with a short run time of 15 min and a detection limit of 0.01–0.02 pmol injected (0.005–0.01 pmol µL–1) for the different peptides. This methodology allowed successful analysis of all standard di- and tripeptides tested here. We conclude that microdialysis in combination with UHPLC-MS will allow measurement of plant-relevant fluxes of di- and tripeptides in undisturbed soil.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Soil Research},
	author = {Jämtgård, Sandra and Robinson, Nicole and Moritz, Thomas and Colgrave, Michelle L. and Schmidt, Susanne},
	year = {2018},
	pages = {404},
}

Di- and tripeptides are intermediaries in the nitrogen cycle and are likely to have roles in the soil–microbe–plant continuum, but they have hitherto been difficult to measure in soils. To lay the base for future studies of oligopeptides in soil, we added 10 known di- and tripeptides with diverse chemical properties to forest and agricultural soils and then recovered the peptides by means of induced diffusive fluxes using microdialysis, a minimally-intrusive soil sampling technique. The concentration of the peptides recovered with the probes was 25–39% (relative recovery) of the concentration in the external solution, and followed the same trend as previously observed for amino acids, with smaller peptides (e.g. Gly-Gly) recovered at a higher rate than larger ones (e.g. Tyr-Phe). After derivatisation with AccQ-Tag™, a standard method for amino acids, peptides were analysed by ultra-high-pressure liquid chromatography-triple quadrupole mass spectrometry. Multiple reaction monitoring mass spectrometry was used to quantify specific peptides with a short run time of 15 min and a detection limit of 0.01–0.02 pmol injected (0.005–0.01 pmol µL–1) for the different peptides. This methodology allowed successful analysis of all standard di- and tripeptides tested here. We conclude that microdialysis in combination with UHPLC-MS will allow measurement of plant-relevant fluxes of di- and tripeptides in undisturbed soil.

@article{jansson_gene-edited_2018,
	title = {Gene-edited plants on the plate: the ‘{CRISPR} cabbage story’},
	volume = {164},
	issn = {00319317},
	shorttitle = {Gene-edited plants on the plate},
	url = {http://doi.wiley.com/10.1111/ppl.12754},
	doi = {10.1111/ppl.12754},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Jansson, Stefan},
	month = dec,
	year = {2018},
	pages = {396--405},
}

@article{jansson_gene-edited_2018,
	title = {Gene-edited plants: {What} is happening now?},
	volume = {164},
	issn = {00319317},
	shorttitle = {Gene-edited plants},
	url = {http://doi.wiley.com/10.1111/ppl.12853},
	doi = {10.1111/ppl.12853},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Jansson, Stefan},
	month = dec,
	year = {2018},
	pages = {370--371},
}

@article{jiang_design_2018,
	title = {Design of a {New} {Glutamine}–{Fipronil} {Conjugate} with α-{Amino} {Acid} {Function} and {Its} {Uptake} by \textit{{A}. thaliana} {Lysine} {Histidine} {Transporter} 1 ( \textit{{AtLHT1}} )},
	volume = {66},
	issn = {0021-8561, 1520-5118},
	url = {https://pubs.acs.org/doi/10.1021/acs.jafc.8b02287},
	doi = {10.1021/acs.jafc.8b02287},
	language = {en},
	number = {29},
	urldate = {2021-06-07},
	journal = {Journal of Agricultural and Food Chemistry},
	author = {Jiang, Xunyuan and Xie, Yun and Ren, Zhanfu and Ganeteg, Ulrika and Lin, Fei and Zhao, Chen and Xu, Hanhong},
	month = jul,
	year = {2018},
	pages = {7597--7605},
}

@article{jokipii-lukkari_transcriptional_2018,
	title = {Transcriptional {Roadmap} to {Seasonal} {Variation} in {Wood} {Formation} of {Norway} {Spruce}},
	volume = {176},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/176/4/2851-2870/6117009},
	doi = {10.1104/pp.17.01590},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Jokipii-Lukkari, Soile and Delhomme, Nicolas and Schiffthaler, Bastian and Mannapperuma, Chanaka and Prestele, Jakob and Nilsson, Ove and Street, Nathaniel R. and Tuominen, Hannele},
	month = apr,
	year = {2018},
	pages = {2851--2870},
}

@article{kania_inhibitor_2018,
	title = {The {Inhibitor} {Endosidin} 4 {Targets} {SEC7} {Domain}-{Type} {ARF} {GTPase} {Exchange} {Factors} and {Interferes} with {Subcellular} {Trafficking} in {Eukaryotes}},
	volume = {30},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/30/10/2553-2572/6099476},
	doi = {10.1105/tpc.18.00127},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {Kania, Urszula and Nodzyński, Tomasz and Lu, Qing and Hicks, Glenn R. and Nerinckx, Wim and Mishev, Kiril and Peurois, François and Cherfils, Jacqueline and De Rycke, Riet and Grones, Peter and Robert, Stéphanie and Russinova, Eugenia and Friml, Jiří},
	month = oct,
	year = {2018},
	pages = {2553--2572},
}

@article{kawde_photo-electrochemical_2018,
	title = {Photo-electrochemical hydrogen production from neutral phosphate buffer and seawater using micro-structured p-{Si} photo-electrodes functionalized by solution-based methods},
	volume = {2},
	issn = {2398-4902},
	url = {http://xlink.rsc.org/?DOI=C8SE00291F},
	doi = {10.1039/C8SE00291F},
	abstract = {Micro-structured p-Si/TiO
              2
              /NiO
              x
              allows for efficient photoelectrochemical H
              2
              production from seawater.
            
          , 
            
              Solar fuels such as H
              2
              generated from sunlight and seawater using earth-abundant materials are expected to be a crucial component of a next generation renewable energy mix. We herein report a systematic analysis of the photo-electrochemical performance of TiO
              2
              coated, microstructured p-Si photo-electrodes (p-Si/TiO
              2
              ) that were functionalized with CoO
              x
              and NiO
              x
              for H
              2
              generation. These photocathodes were synthesized from commercial p-Si wafers employing wet chemical methods. In neutral phosphate buffer and standard 1 sun illumination, the p-Si/TiO
              2
              /NiO
              x
              photoelectrode showed a photocurrent density of −1.48 mA cm
              −2
              at zero bias (0 V
              RHE
              ), which was three times and 15 times better than the photocurrent densities of p-Si/TiO
              2
              /CoO
              x
              and p-Si/TiO
              2
              , respectively. No decline in activity was observed over a five hour test period, yielding a Faradaic efficiency of 96\% for H
              2
              production. Based on the electrochemical characterizations and the high energy resolution fluorescence detected X-ray absorption near edge structure (HERFD-XANES) and emission spectroscopy measurements performed at the Ti Kα
              1
              fluorescence line, the superior performance of the p-Si/TiO
              2
              /NiO
              x
              photoelectrode was attributed to improved charge transfer properties induced by the NiO
              x
              coating on the protective TiO
              2
              layer, in combination with a higher catalytic activity of NiO
              x
              for H
              2
              -evolution. Moreover, we report here an excellent photo-electrochemical performance of p-Si/TiO
              2
              /NiO
              x
              photoelectrode in corrosive artificial seawater (pH 8.4) with an unprecedented photocurrent density of 10 mA cm
              −2
              at an applied potential of −0.7 V
              RHE
              , and of 20 mA cm
              −2
              at −0.9 V
              RHE
              . The applied bias photon-to-current conversion efficiency (ABPE) at −0.7 V
              RHE
              and 10 mA cm
              −2
              was found to be 5.1\%.},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Sustainable Energy \& Fuels},
	author = {Kawde, Anurag and Annamalai, Alagappan and Amidani, Lucia and Boniolo, Manuel and Kwong, Wai Ling and Sellstedt, Anita and Glatzel, Pieter and Wågberg, Thomas and Messinger, Johannes},
	year = {2018},
	pages = {2215--2223},
}

Micro-structured p-Si/TiO 2 /NiO x allows for efficient photoelectrochemical H 2 production from seawater. , Solar fuels such as H 2 generated from sunlight and seawater using earth-abundant materials are expected to be a crucial component of a next generation renewable energy mix. We herein report a systematic analysis of the photo-electrochemical performance of TiO 2 coated, microstructured p-Si photo-electrodes (p-Si/TiO 2 ) that were functionalized with CoO x and NiO x for H 2 generation. These photocathodes were synthesized from commercial p-Si wafers employing wet chemical methods. In neutral phosphate buffer and standard 1 sun illumination, the p-Si/TiO 2 /NiO x photoelectrode showed a photocurrent density of −1.48 mA cm −2 at zero bias (0 V RHE ), which was three times and 15 times better than the photocurrent densities of p-Si/TiO 2 /CoO x and p-Si/TiO 2 , respectively. No decline in activity was observed over a five hour test period, yielding a Faradaic efficiency of 96% for H 2 production. Based on the electrochemical characterizations and the high energy resolution fluorescence detected X-ray absorption near edge structure (HERFD-XANES) and emission spectroscopy measurements performed at the Ti Kα 1 fluorescence line, the superior performance of the p-Si/TiO 2 /NiO x photoelectrode was attributed to improved charge transfer properties induced by the NiO x coating on the protective TiO 2 layer, in combination with a higher catalytic activity of NiO x for H 2 -evolution. Moreover, we report here an excellent photo-electrochemical performance of p-Si/TiO 2 /NiO x photoelectrode in corrosive artificial seawater (pH 8.4) with an unprecedented photocurrent density of 10 mA cm −2 at an applied potential of −0.7 V RHE , and of 20 mA cm −2 at −0.9 V RHE . The applied bias photon-to-current conversion efficiency (ABPE) at −0.7 V RHE and 10 mA cm −2 was found to be 5.1%.

@article{kieselbach_proteomic_2018,
	title = {Proteomic analysis of the phycobiliprotein antenna of the cryptophyte alga {Guillardia} theta cultured under different light intensities},
	volume = {135},
	issn = {0166-8595, 1573-5079},
	url = {http://link.springer.com/10.1007/s11120-017-0400-0},
	doi = {10.1007/s11120-017-0400-0},
	language = {en},
	number = {1-3},
	urldate = {2021-06-07},
	journal = {Photosynthesis Research},
	author = {Kieselbach, Thomas and Cheregi, Otilia and Green, Beverley R. and Funk, Christiane},
	month = mar,
	year = {2018},
	pages = {149--163},
}

@article{kindgren_transcriptional_2018,
	title = {Transcriptional read-through of the long non-coding {RNA} {SVALKA} governs plant cold acclimation},
	volume = {9},
	copyright = {2018 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-018-07010-6},
	doi = {10.1038/s41467-018-07010-6},
	abstract = {Most DNA in the genomes of higher organisms does not encode proteins, yet much is transcribed by RNA polymerase II (RNAPII) into long non-coding RNAs (lncRNAs). The biological significance of most lncRNAs is largely unclear. Here, we identify a lncRNA (SVALKA) in a cold-sensitive region of the Arabidopsis genome. Mutations in SVALKA affect CBF1 expression and freezing tolerance. RNAPII read-through transcription of SVALKA results in a cryptic lncRNA overlapping CBF1 on the antisense strand, termed asCBF1. Our molecular dissection reveals that CBF1 is suppressed by RNAPII collision stemming from the SVALKA-asCBF1 lncRNA cascade. The SVALKA-asCBF1 cascade provides a mechanism to tightly control CBF1 expression and timing that could be exploited to maximize freezing tolerance with mitigated fitness costs. Our results provide a compelling example of local gene regulation by lncRNA transcription having a profound impact on the ability of plants to appropriately acclimate to challenging environmental conditions.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Kindgren, Peter and Ard, Ryan and Ivanov, Maxim and Marquardt, Sebastian},
	month = nov,
	year = {2018},
	note = {Number: 1
Publisher: Nature Publishing Group},
	pages = {4561},
}

Most DNA in the genomes of higher organisms does not encode proteins, yet much is transcribed by RNA polymerase II (RNAPII) into long non-coding RNAs (lncRNAs). The biological significance of most lncRNAs is largely unclear. Here, we identify a lncRNA (SVALKA) in a cold-sensitive region of the Arabidopsis genome. Mutations in SVALKA affect CBF1 expression and freezing tolerance. RNAPII read-through transcription of SVALKA results in a cryptic lncRNA overlapping CBF1 on the antisense strand, termed asCBF1. Our molecular dissection reveals that CBF1 is suppressed by RNAPII collision stemming from the SVALKA-asCBF1 lncRNA cascade. The SVALKA-asCBF1 cascade provides a mechanism to tightly control CBF1 expression and timing that could be exploited to maximize freezing tolerance with mitigated fitness costs. Our results provide a compelling example of local gene regulation by lncRNA transcription having a profound impact on the ability of plants to appropriately acclimate to challenging environmental conditions.

@article{klapwijk_capturing_2018,
	title = {Capturing complexity: {Forests}, decision-making and climate change mitigation action},
	volume = {52},
	issn = {09593780},
	shorttitle = {Capturing complexity},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0959378017312815},
	doi = {10.1016/j.gloenvcha.2018.07.012},
	language = {en},
	urldate = {2021-06-07},
	journal = {Global Environmental Change},
	author = {Klapwijk, M.J. and Boberg, J. and Bergh, J. and Bishop, K. and Björkman, C. and Ellison, D. and Felton, A. and Lidskog, R. and Lundmark, T. and Keskitalo, E.C.H. and Sonesson, J. and Nordin, A. and Nordström, E.-M. and Stenlid, J. and Mårald, E.},
	month = sep,
	year = {2018},
	pages = {238--247},
}

@article{klemencic_structural_2018,
	title = {Structural and functional diversity of caspase homologues in non-metazoan organisms},
	volume = {255},
	issn = {0033-183X, 1615-6102},
	url = {http://link.springer.com/10.1007/s00709-017-1145-5},
	doi = {10.1007/s00709-017-1145-5},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Protoplasma},
	author = {Klemenčič, Marina and Funk, Christiane},
	month = jan,
	year = {2018},
	pages = {387--397},
}

@article{kong_simultaneous_2018,
	title = {Simultaneous determination of ribonucleoside and deoxyribonucleoside triphosphates in biological samples by hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry},
	volume = {46},
	issn = {0305-1048, 1362-4962},
	url = {https://academic.oup.com/nar/article/46/11/e66/4937551},
	doi = {10.1093/nar/gky203},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Nucleic Acids Research},
	author = {Kong, Ziqing and Jia, Shaodong and Chabes, Anna Lena and Appelblad, Patrik and Lundmark, Richard and Moritz, Thomas and Chabes, Andrei},
	month = jun,
	year = {2018},
	pages = {e66--e66},
}

@article{kumar_med7_2018,
	title = {The {MED7} subunit paralogs of {Mediator} function redundantly in development of etiolated seedlings in {Arabidopsis}},
	volume = {96},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.14052},
	doi = {10.1111/tpj.14052},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Kumar, Koppolu Raja Rajesh and Blomberg, Jeanette and Björklund, Stefan},
	month = nov,
	year = {2018},
	pages = {578--594},
}

@article{kurepin_contrasting_2018,
	title = {Contrasting acclimation abilities of two dominant boreal conifers to elevated {CO} $_{\textrm{2}}$ and temperature: {CO} $_{\textrm{2}}$ and warming effects on spruce and pine},
	volume = {41},
	issn = {01407791},
	shorttitle = {Contrasting acclimation abilities of two dominant boreal conifers to elevated {CO} $_{\textrm{2}}$ and temperature},
	url = {http://doi.wiley.com/10.1111/pce.13158},
	doi = {10.1111/pce.13158},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Kurepin, Leonid V. and Stangl, Zsofia R. and Ivanov, Alexander G. and Bui, Vi and Mema, Marin and Hüner, Norman P.A. and Öquist, Gunnar and Way, Danielle and Hurry, Vaughan},
	month = jun,
	year = {2018},
	pages = {1331--1345},
}

@article{lage_algal_2018,
	title = {Algal {Biomass} from {Wastewater} and {Flue} {Gases} as a {Source} of {Bioenergy}},
	volume = {11},
	issn = {1996-1073},
	url = {http://www.mdpi.com/1996-1073/11/3/664},
	doi = {10.3390/en11030664},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Energies},
	author = {Lage, Sandra and Gojkovic, Zivan and Funk, Christiane and Gentili, Francesco},
	month = mar,
	year = {2018},
	pages = {664},
}

@article{law_darkened_2018,
	title = {Darkened {Leaves} {Use} {Different} {Metabolic} {Strategies} for {Senescence} and {Survival}},
	volume = {177},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/177/1/132-150/6116945},
	doi = {10.1104/pp.18.00062},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Law, Simon R. and Chrobok, Daria and Juvany, Marta and Delhomme, Nicolas and Lindén, Pernilla and Brouwer, Bastiaan and Ahad, Abdul and Moritz, Thomas and Jansson, Stefan and Gardeström, Per and Keech, Olivier},
	month = may,
	year = {2018},
	pages = {132--150},
}

@article{lin_functional_2018,
	title = {Functional and evolutionary genomic inferences in \textit{{Populus}} through genome and population sequencing of {American} and {European} aspen},
	volume = {115},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1801437115},
	doi = {10.1073/pnas.1801437115},
	abstract = {The
              Populus
              genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily
              Populus trichocarpa
              (Torr. \& Gray), which was the first tree with a whole-genome assembly. To further advance evolutionary and functional genomic analyses in
              Populus
              , we produced genome assemblies and population genetics resources of two aspen species,
              Populus tremula
              L. and
              Populus tremuloides
              Michx. The two aspen species have distributions spanning the Northern Hemisphere, where they are keystone species supporting a wide variety of dependent communities and produce a diverse array of secondary metabolites. Our analyses show that the two aspens share a similar genome structure and a highly conserved gene content with
              P. trichocarpa
              but display substantially higher levels of heterozygosity. Based on population resequencing data, we observed widespread positive and negative selection acting on both coding and noncoding regions. Furthermore, patterns of genetic diversity and molecular evolution in aspen are influenced by a number of features, such as expression level, coexpression network connectivity, and regulatory variation. To maximize the community utility of these resources, we have integrated all presented data within the PopGenIE web resource (
              PopGenIE.org
              ).},
	language = {en},
	number = {46},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Lin, Yao-Cheng and Wang, Jing and Delhomme, Nicolas and Schiffthaler, Bastian and Sundström, Görel and Zuccolo, Andrea and Nystedt, Björn and Hvidsten, Torgeir R. and de la Torre, Amanda and Cossu, Rosa M. and Hoeppner, Marc P. and Lantz, Henrik and Scofield, Douglas G. and Zamani, Neda and Johansson, Anna and Mannapperuma, Chanaka and Robinson, Kathryn M. and Mähler, Niklas and Leitch, Ilia J. and Pellicer, Jaume and Park, Eung-Jun and Van Montagu, Marc and Van de Peer, Yves and Grabherr, Manfred and Jansson, Stefan and Ingvarsson, Pär K. and Street, Nathaniel R.},
	month = nov,
	year = {2018},
	pages = {E10970--E10978},
}

The Populus genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily Populus trichocarpa (Torr. & Gray), which was the first tree with a whole-genome assembly. To further advance evolutionary and functional genomic analyses in Populus , we produced genome assemblies and population genetics resources of two aspen species, Populus tremula L. and Populus tremuloides Michx. The two aspen species have distributions spanning the Northern Hemisphere, where they are keystone species supporting a wide variety of dependent communities and produce a diverse array of secondary metabolites. Our analyses show that the two aspens share a similar genome structure and a highly conserved gene content with P. trichocarpa but display substantially higher levels of heterozygosity. Based on population resequencing data, we observed widespread positive and negative selection acting on both coding and noncoding regions. Furthermore, patterns of genetic diversity and molecular evolution in aspen are influenced by a number of features, such as expression level, coexpression network connectivity, and regulatory variation. To maximize the community utility of these resources, we have integrated all presented data within the PopGenIE web resource ( PopGenIE.org ).

@article{lundmark_carbon_2018,
	title = {Carbon balance in production forestry in relation to rotation length},
	volume = {48},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfr-2017-0410},
	doi = {10.1139/cjfr-2017-0410},
	abstract = {The choice of a rotation length is an integral part of even-aged forest management regimes. In this study, we simulated stand development and carbon pools in four even-aged stands representing the two most common tree species in Fennoscandia, Norway spruce (Picea abies (L.) Karst.) and Scots pine (Pinus sylvestris L.), growing on high- and low-productivity sites. We hypothesized that increased rotation lengths (+10, +20, and +30 years) in comparison with today’s practice would increase forests’ average carbon stock during a rotation cycle but decrease the average yield. The results showed that for spruce, a moderate increase in rotation length (+10 years) increased both average standing carbon stock and average yield. For the longer alternatives (+20 and +30 years) for spruce and for all pine alternatives, prolonging rotation lengths resulted in increased average standing carbon stocks but decreased average yield, resulting in decreased carbon storage in forest products and decreased substitution effects. Decreasing the rotation lengths (–10 years) always resulted in both decreased average standing carbon stocks and decreased yields. We conclude that a moderate increase of rotation lengths may slightly increase forests’ climate benefits for spruce sites, but for all other alternatives, there was a trade-off between the temporary gain of increasing carbon stocks and the permanent loss in productivity and, consequently, substitution potential.},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Canadian Journal of Forest Research},
	author = {Lundmark, Tomas and Poudel, Bishnu Chandra and Stål, Gustav and Nordin, Annika and Sonesson, Johan},
	month = jun,
	year = {2018},
	pages = {672--678},
}

The choice of a rotation length is an integral part of even-aged forest management regimes. In this study, we simulated stand development and carbon pools in four even-aged stands representing the two most common tree species in Fennoscandia, Norway spruce (Picea abies (L.) Karst.) and Scots pine (Pinus sylvestris L.), growing on high- and low-productivity sites. We hypothesized that increased rotation lengths (+10, +20, and +30 years) in comparison with today’s practice would increase forests’ average carbon stock during a rotation cycle but decrease the average yield. The results showed that for spruce, a moderate increase in rotation length (+10 years) increased both average standing carbon stock and average yield. For the longer alternatives (+20 and +30 years) for spruce and for all pine alternatives, prolonging rotation lengths resulted in increased average standing carbon stocks but decreased average yield, resulting in decreased carbon storage in forest products and decreased substitution effects. Decreasing the rotation lengths (–10 years) always resulted in both decreased average standing carbon stocks and decreased yields. We conclude that a moderate increase of rotation lengths may slightly increase forests’ climate benefits for spruce sites, but for all other alternatives, there was a trade-off between the temporary gain of increasing carbon stocks and the permanent loss in productivity and, consequently, substitution potential.

@article{lundqvist_age_2018,
	title = {Age and weather effects on between and within ring variations of number, width and coarseness of tracheids and radial growth of young {Norway} spruce},
	volume = {137},
	issn = {1612-4669, 1612-4677},
	url = {http://link.springer.com/10.1007/s10342-018-1136-x},
	doi = {10.1007/s10342-018-1136-x},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {European Journal of Forest Research},
	author = {Lundqvist, Sven-Olof and Seifert, Stefan and Grahn, Thomas and Olsson, Lars and García-Gil, Maria Rosario and Karlsson, Bo and Seifert, Thomas},
	month = oct,
	year = {2018},
	pages = {719--743},
}

@article{maaroufi_nutrient_2018,
	title = {Nutrient optimization of tree growth alters structure and function of boreal soil food webs},
	volume = {428},
	issn = {03781127},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378112718301142},
	doi = {10.1016/j.foreco.2018.06.034},
	language = {en},
	urldate = {2021-06-07},
	journal = {Forest Ecology and Management},
	author = {Maaroufi, Nadia I. and Palmqvist, Kristin and Bach, Lisbet H. and Bokhorst, Stef and Liess, Antonia and Gundale, Michael J. and Kardol, Paul and Nordin, Annika and Meunier, Cédric L.},
	month = nov,
	year = {2018},
	pages = {46--56},
}

@article{mahboubi_sucrose_2018,
	title = {Sucrose transport and carbon fluxes during wood formation},
	volume = {164},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12729},
	doi = {10.1111/ppl.12729},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Mahboubi, Amir and Niittylä, Totte},
	month = sep,
	year = {2018},
	pages = {67--81},
}

@article{majda_role_2018,
	title = {The {Role} of {Auxin} in {Cell} {Wall} {Expansion}},
	volume = {19},
	issn = {1422-0067},
	url = {http://www.mdpi.com/1422-0067/19/4/951},
	doi = {10.3390/ijms19040951},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {International Journal of Molecular Sciences},
	author = {Majda, Mateusz and Robert, Stéphanie},
	month = mar,
	year = {2018},
	pages = {951},
}

@article{mamun_improved_2018,
	title = {Improved and synchronized maturation of {Norway} spruce ({Picea} abies ({L}.) {H}.{Karst}.) somatic embryos in temporary immersion bioreactors},
	volume = {54},
	issn = {1054-5476, 1475-2689},
	url = {http://link.springer.com/10.1007/s11627-018-9911-4},
	doi = {10.1007/s11627-018-9911-4},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {In Vitro Cellular \& Developmental Biology - Plant},
	author = {Mamun, Nazmul H. A. and Aidun, Cyrus K. and Egertsdotter, Ulrika},
	month = dec,
	year = {2018},
	pages = {612--620},
}

@article{maurya_environmentally_2018,
	title = {Environmentally {Sensitive} {Molecular} {Switches} {Drive} {Poplar} {Phenology}},
	volume = {9},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2018.01873/full},
	doi = {10.3389/fpls.2018.01873},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Maurya, Jay P. and Triozzi, Paolo M. and Bhalerao, Rishikesh P. and Perales, Mariano},
	month = dec,
	year = {2018},
	pages = {1873},
}

@article{minina_transcriptional_2018,
	title = {Transcriptional stimulation of rate-limiting components of the autophagic pathway improves plant fitness},
	volume = {69},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article/69/6/1415/4818325},
	doi = {10.1093/jxb/ery010},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Minina, Elena A and Moschou, Panagiotis N and Vetukuri, Ramesh R and Sanchez-Vera, Victoria and Cardoso, Catarina and Liu, Qinsong and Elander, Pernilla H and Dalman, Kerstin and Beganovic, Mirela and Lindberg Yilmaz, Jenny and Marmon, Sofia and Shabala, Lana and Suarez, Maria F and Ljung, Karin and Novák, Ondřej and Shabala, Sergey and Stymne, Sten and Hofius, Daniel and Bozhkov, Peter V},
	editor = {Raines, Christine},
	month = mar,
	year = {2018},
	pages = {1415--1432},
}

@article{myouga_stable_2018,
	title = {Stable {Accumulation} of {Photosystem} {II} {Requires} {ONE}-{HELIX} {PROTEIN1} ({OHP1}) of the {Light} {Harvesting}-{Like} {Family}},
	volume = {176},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/176/3/2277-2291/6117119},
	doi = {10.1104/pp.17.01782},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Myouga, Fumiyoshi and Takahashi, Kaori and Tanaka, Ryoichi and Nagata, Noriko and Kiss, Anett Z. and Funk, Christiane and Nomura, Yuko and Nakagami, Hirofumi and Jansson, Stefan and Shinozaki, Kazuo},
	month = mar,
	year = {2018},
	pages = {2277--2291},
}

@article{nzayisenga_mixotrophic_2018,
	title = {Mixotrophic and heterotrophic production of lipids and carbohydrates by a locally isolated microalga using wastewater as a growth medium},
	volume = {257},
	issn = {09608524},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960852418302827},
	doi = {10.1016/j.biortech.2018.02.085},
	language = {en},
	urldate = {2021-06-07},
	journal = {Bioresource Technology},
	author = {Nzayisenga, Jean Claude and Eriksson, Karolina and Sellstedt, Anita},
	month = jun,
	year = {2018},
	pages = {260--265},
}

@article{obudulu_multi-omics_2018,
	title = {A multi-omics approach reveals function of {Secretory} {Carrier}-{Associated} {Membrane} {Proteins} in wood formation of​ ​​{Populus}​​ ​trees},
	volume = {19},
	issn = {1471-2164},
	url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4411-1},
	doi = {10.1186/s12864-017-4411-1},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Obudulu, Ogonna and Mähler, Niklas and Skotare, Tomas and Bygdell, Joakim and Abreu, Ilka N. and Ahnlund, Maria and Latha Gandla, Madhavi and Petterle, Anna and Moritz, Thomas and Hvidsten, Torgeir R. and Jönsson, Leif J. and Wingsle, Gunnar and Trygg, Johan and Tuominen, Hannele},
	month = dec,
	year = {2018},
	pages = {11},
}

@article{orman-ligeza_xerobranching_2018,
	title = {The {Xerobranching} {Response} {Represses} {Lateral} {Root} {Formation} {When} {Roots} {Are} {Not} in {Contact} with {Water}},
	volume = {28},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982218310042},
	doi = {10.1016/j.cub.2018.07.074},
	language = {en},
	number = {19},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Orman-Ligeza, Beata and Morris, Emily C. and Parizot, Boris and Lavigne, Tristan and Babé, Aurelie and Ligeza, Aleksander and Klein, Stephanie and Sturrock, Craig and Xuan, Wei and Novák, Ondřey and Ljung, Karin and Fernandez, Maria A. and Rodriguez, Pedro L. and Dodd, Ian C. and De Smet, Ive and Chaumont, Francois and Batoko, Henri and Périlleux, Claire and Lynch, Jonathan P. and Bennett, Malcolm J. and Beeckman, Tom and Draye, Xavier},
	month = oct,
	year = {2018},
	pages = {3165--3173.e5},
}

@article{pawar_qtl_2018,
	title = {{QTL} {Mapping} of {Wood} {FT}-{IR} {Chemotypes} {Shows} {Promise} for {Improving} {Biofuel} {Potential} in {Short} {Rotation} {Coppice} {Willow} ({Salix} spp.)},
	volume = {11},
	issn = {1939-1242},
	url = {https://doi.org/10.1007/s12155-018-9901-8},
	doi = {10.1007/s12155-018-9901-8},
	abstract = {An increasing interest to convert lignocellulosic biomass into biofuels has highlighted the potential of using willows for this purpose, due to its fast growth in short rotation coppice systems. Here, we use a mapping population of 463 individuals of a cross between Salix viminalis and S. viminalis × S. schwerinii to investigate the genetic background of different wood chemical traits, information of importance for breeding towards different uses of wood. Furthermore, using a subset of the mapping population, the correlation between biogas production and chemical traits was investigated. The phenotyping of wood was carried by Furrier-transformed-Infrared spectrometry (FT-IR) and water content analysis. Quantitative trait loci (QTLs) analysis was used to identify regions in the genome of importance for the phenotypic variation of these chemical traits. We found 27 QTLs for various traits. On linkage group (LG) VI-1, QTLs for signals assigned to G-lignin, lignin, and the S/G ratio were collocated and on LG XIV we found a cluster of QTLs representing signals assigned to lignin, cellulose, hemicellulose, and water. The QTLs explained from 3.4 to 6.9\% of the phenotypic variation indicating a quantitative genetic background where many genes influence the traits. For the biogas production, a positive and negative correlation was seen with the signals assigned to acetyl and lignin, respectively. This study represents a first step in the understanding of the genetic background of wood chemical traits for willows, information needed for complementary studies, mapping of important genes, and for breeding of varieties for biofuel production purposes.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {BioEnergy Research},
	author = {Pawar, Prashant Mohan-Anupama and Schnürer, Anna and Mellerowicz, Ewa J. and Rönnberg-Wästljung, Ann Christin},
	month = jun,
	year = {2018},
	pages = {351--363},
}

An increasing interest to convert lignocellulosic biomass into biofuels has highlighted the potential of using willows for this purpose, due to its fast growth in short rotation coppice systems. Here, we use a mapping population of 463 individuals of a cross between Salix viminalis and S. viminalis × S. schwerinii to investigate the genetic background of different wood chemical traits, information of importance for breeding towards different uses of wood. Furthermore, using a subset of the mapping population, the correlation between biogas production and chemical traits was investigated. The phenotyping of wood was carried by Furrier-transformed-Infrared spectrometry (FT-IR) and water content analysis. Quantitative trait loci (QTLs) analysis was used to identify regions in the genome of importance for the phenotypic variation of these chemical traits. We found 27 QTLs for various traits. On linkage group (LG) VI-1, QTLs for signals assigned to G-lignin, lignin, and the S/G ratio were collocated and on LG XIV we found a cluster of QTLs representing signals assigned to lignin, cellulose, hemicellulose, and water. The QTLs explained from 3.4 to 6.9% of the phenotypic variation indicating a quantitative genetic background where many genes influence the traits. For the biogas production, a positive and negative correlation was seen with the signals assigned to acetyl and lignin, respectively. This study represents a first step in the understanding of the genetic background of wood chemical traits for willows, information needed for complementary studies, mapping of important genes, and for breeding of varieties for biofuel production purposes.

@article{pencik_ultra-rapid_2018,
	title = {Ultra-rapid auxin metabolite profiling for high-throughput mutant screening in {Arabidopsis}},
	volume = {69},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article/69/10/2569/4919650},
	doi = {10.1093/jxb/ery084},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Pěnčík, Aleš and Casanova-Sáez, Rubén and Pilařová, Veronika and Žukauskaitė, Asta and Pinto, Rui and Micol, José Luis and Ljung, Karin and Novák, Ondřej},
	month = apr,
	year = {2018},
	pages = {2569--2579},
}

@article{perring_understanding_2018,
	title = {Understanding context dependency in the response of forest understorey plant communities to nitrogen deposition},
	volume = {242},
	issn = {02697491},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0269749118316610},
	doi = {10.1016/j.envpol.2018.07.089},
	language = {en},
	urldate = {2021-06-07},
	journal = {Environmental Pollution},
	author = {Perring, Michael P. and Diekmann, Martin and Midolo, Gabriele and Schellenberger Costa, David and Bernhardt-Römermann, Markus and Otto, Johanna C.J. and Gilliam, Frank S. and Hedwall, Per-Ola and Nordin, Annika and Dirnböck, Thomas and Simkin, Samuel M. and Máliš, František and Blondeel, Haben and Brunet, Jörg and Chudomelová, Markéta and Durak, Tomasz and De Frenne, Pieter and Hédl, Radim and Kopecký, Martin and Landuyt, Dries and Li, Daijiang and Manning, Peter and Petřík, Petr and Reczyńska, Kamila and Schmidt, Wolfgang and Standovár, Tibor and Świerkosz, Krzysztof and Vild, Ondřej and Waller, Donald M. and Verheyen, Kris},
	month = nov,
	year = {2018},
	pages = {1787--1799},
}

@article{podgorska_nitrogen_2018,
	title = {Nitrogen {Source} {Dependent} {Changes} in {Central} {Sugar} {Metabolism} {Maintain} {Cell} {Wall} {Assembly} in {Mitochondrial} {Complex} {I}-{Defective} frostbite1 and {Secondarily} {Affect} {Programmed} {Cell} {Death}},
	volume = {19},
	issn = {1422-0067},
	url = {http://www.mdpi.com/1422-0067/19/8/2206},
	doi = {10.3390/ijms19082206},
	abstract = {For optimal plant growth, carbon and nitrogen availability needs to be tightly coordinated. Mitochondrial perturbations related to a defect in complex I in the Arabidopsis thalianafrostbite1 (fro1) mutant, carrying a point mutation in the 8-kD Fe-S subunit of NDUFS4 protein, alter aspects of fundamental carbon metabolism, which is manifested as stunted growth. During nitrate nutrition, fro1 plants showed a dominant sugar flux toward nitrogen assimilation and energy production, whereas cellulose integration in the cell wall was restricted. However, when cultured on NH4+ as the sole nitrogen source, which typically induces developmental disorders in plants (i.e., the ammonium toxicity syndrome), fro1 showed improved growth as compared to NO3− nourishing. Higher energy availability in fro1 plants was correlated with restored cell wall assembly during NH4+ growth. To determine the relationship between mitochondrial complex I disassembly and cell wall-related processes, aspects of cell wall integrity and sugar and reactive oxygen species signaling were analyzed in fro1 plants. The responses of fro1 plants to NH4+ treatment were consistent with the inhibition of a form of programmed cell death. Resistance of fro1 plants to NH4+ toxicity coincided with an absence of necrotic lesion in plant leaves.},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {International Journal of Molecular Sciences},
	author = {Podgórska, Anna and Ostaszewska-Bugajska, Monika and Tarnowska, Agata and Burian, Maria and Borysiuk, Klaudia and Gardeström, Per and Szal, Bożena},
	month = jul,
	year = {2018},
	pages = {2206},
}

For optimal plant growth, carbon and nitrogen availability needs to be tightly coordinated. Mitochondrial perturbations related to a defect in complex I in the Arabidopsis thalianafrostbite1 (fro1) mutant, carrying a point mutation in the 8-kD Fe-S subunit of NDUFS4 protein, alter aspects of fundamental carbon metabolism, which is manifested as stunted growth. During nitrate nutrition, fro1 plants showed a dominant sugar flux toward nitrogen assimilation and energy production, whereas cellulose integration in the cell wall was restricted. However, when cultured on NH4+ as the sole nitrogen source, which typically induces developmental disorders in plants (i.e., the ammonium toxicity syndrome), fro1 showed improved growth as compared to NO3− nourishing. Higher energy availability in fro1 plants was correlated with restored cell wall assembly during NH4+ growth. To determine the relationship between mitochondrial complex I disassembly and cell wall-related processes, aspects of cell wall integrity and sugar and reactive oxygen species signaling were analyzed in fro1 plants. The responses of fro1 plants to NH4+ treatment were consistent with the inhibition of a form of programmed cell death. Resistance of fro1 plants to NH4+ toxicity coincided with an absence of necrotic lesion in plant leaves.

@article{prat_wrky23_2018,
	title = {{WRKY23} is a component of the transcriptional network mediating auxin feedback on {PIN} polarity},
	volume = {14},
	issn = {1553-7404},
	url = {https://dx.plos.org/10.1371/journal.pgen.1007177},
	doi = {10.1371/journal.pgen.1007177},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {PLOS Genetics},
	author = {Prát, Tomáš and Hajný, Jakub and Grunewald, Wim and Vasileva, Mina and Molnár, Gergely and Tejos, Ricardo and Schmid, Markus and Sauer, Michael and Friml, Jiří},
	editor = {Strader, Lucia},
	month = jan,
	year = {2018},
	pages = {e1007177},
}

@article{pribil_fine-tuning_2018,
	title = {Fine-{Tuning} of {Photosynthesis} {Requires} {CURVATURE} {THYLAKOID1}-{Mediated} {Thylakoid} {Plasticity}},
	volume = {176},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/176/3/2351-2364/6117159},
	doi = {10.1104/pp.17.00863},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Pribil, Mathias and Sandoval-Ibáñez, Omar and Xu, Wenteng and Sharma, Anurag and Labs, Mathias and Liu, Qiuping and Galgenmüller, Carolina and Schneider, Trang and Wessels, Malgorzata and Matsubara, Shizue and Jansson, Stefan and Wanner, Gerhard and Leister, Dario},
	month = mar,
	year = {2018},
	pages = {2351--2364},
}

@article{rahneshan_unravelling_2018,
	title = {Unravelling salt stress responses in two pistachio ({Pistacia} vera {L}.) genotypes},
	volume = {40},
	issn = {0137-5881, 1861-1664},
	url = {http://link.springer.com/10.1007/s11738-018-2745-1},
	doi = {10.1007/s11738-018-2745-1},
	language = {en},
	number = {9},
	urldate = {2021-06-07},
	journal = {Acta Physiologiae Plantarum},
	author = {Rahneshan, Zahra and Nasibi, Fatemeh and Lakehal, Abdellah and Bellini, Catherine},
	month = sep,
	year = {2018},
	pages = {172},
}

@incollection{varis_norway_2018,
	address = {Cham},
	series = {Forestry {Sciences}},
	title = {Norway {Spruce} {Picea} abies ({L}.) {Karst}},
	isbn = {978-3-319-89483-6},
	url = {https://doi.org/10.1007/978-3-319-89483-6_19},
	abstract = {The increasing use of wood as a source of bioenergy, bio-products and conservation of more natural (old) forests with high biodiversity, compel us to find means to increase forest productivity. Using the best quality regeneration material can increase the economic gain obtained from future silvicultured forests. Norway spruce is an important raw material in the European forest industry and it is the most-planted tree species in Finland. However, there is periodically a lack of high-quality Norway spruce seed due to irregular flowering of the species, as well as pests and pathogens which can lower the productivity of seed orchards. To ensure availability of good-quality forest regeneration material, effective vegetative propagation methods like somatic embryogenesis (SE) can be introduced. SE has become the method of choice for vegetative propagation of conifers (Sutton in Ann For Sci 59:657–661, 2002) due to its high multiplication rate and the maintenance of juvenility via cryopreservation that allows long-term field testing of materials.},
	language = {en},
	urldate = {2021-06-07},
	booktitle = {Step {Wise} {Protocols} for {Somatic} {Embryogenesis} of {Important} {Woody} {Plants}: {Volume} {I}},
	publisher = {Springer International Publishing},
	author = {Varis, Saila},
	editor = {Jain, Shri Mohan and Gupta, Pramod},
	year = {2018},
	doi = {10.1007/978-3-319-89483-6_19},
	pages = {255--267},
}

The increasing use of wood as a source of bioenergy, bio-products and conservation of more natural (old) forests with high biodiversity, compel us to find means to increase forest productivity. Using the best quality regeneration material can increase the economic gain obtained from future silvicultured forests. Norway spruce is an important raw material in the European forest industry and it is the most-planted tree species in Finland. However, there is periodically a lack of high-quality Norway spruce seed due to irregular flowering of the species, as well as pests and pathogens which can lower the productivity of seed orchards. To ensure availability of good-quality forest regeneration material, effective vegetative propagation methods like somatic embryogenesis (SE) can be introduced. SE has become the method of choice for vegetative propagation of conifers (Sutton in Ann For Sci 59:657–661, 2002) due to its high multiplication rate and the maintenance of juvenility via cryopreservation that allows long-term field testing of materials.

@article{voon_atp_2018,
	title = {{ATP} compartmentation in plastids and cytosol of \textit{{Arabidopsis} thaliana} revealed by fluorescent protein sensing},
	volume = {115},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1711497115},
	doi = {10.1073/pnas.1711497115},
	abstract = {Matching ATP:NADPH provision and consumption in the chloroplast is a prerequisite for efficient photosynthesis. In terms of ATP:NADPH ratio, the amount of ATP generated from the linear electron flow does not meet the demand of the Calvin–Benson–Bassham (CBB) cycle. Several different mechanisms to increase ATP availability have evolved, including cyclic electron flow in higher plants and the direct import of mitochondrial-derived ATP in diatoms. By imaging a fluorescent ATP sensor protein expressed in living
              Arabidopsis thaliana
              seedlings, we found that MgATP
              2−
              concentrations were lower in the stroma of mature chloroplasts than in the cytosol, and exogenous ATP was able to enter chloroplasts isolated from 4- and 5-day-old seedlings, but not chloroplasts isolated from 10- or 20-day-old photosynthetic tissues. This observation is in line with the previous finding that the expression of chloroplast nucleotide transporters (NTTs) in
              Arabidopsis
              mesophyll is limited to very young seedlings. Employing a combination of photosynthetic and respiratory inhibitors with compartment-specific imaging of ATP, we corroborate the dependency of stromal ATP production on mitochondrial dissipation of photosynthetic reductant. Our data suggest that, during illumination, the provision and consumption of ATP:NADPH in chloroplasts can be balanced by exporting excess reductants rather than importing ATP from the cytosol.},
	language = {en},
	number = {45},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Voon, Chia Pao and Guan, Xiaoqian and Sun, Yuzhe and Sahu, Abira and Chan, May Ngor and Gardeström, Per and Wagner, Stephan and Fuchs, Philippe and Nietzel, Thomas and Versaw, Wayne K. and Schwarzländer, Markus and Lim, Boon Leong},
	month = nov,
	year = {2018},
	pages = {E10778--E10787},
}

Matching ATP:NADPH provision and consumption in the chloroplast is a prerequisite for efficient photosynthesis. In terms of ATP:NADPH ratio, the amount of ATP generated from the linear electron flow does not meet the demand of the Calvin–Benson–Bassham (CBB) cycle. Several different mechanisms to increase ATP availability have evolved, including cyclic electron flow in higher plants and the direct import of mitochondrial-derived ATP in diatoms. By imaging a fluorescent ATP sensor protein expressed in living Arabidopsis thaliana seedlings, we found that MgATP 2− concentrations were lower in the stroma of mature chloroplasts than in the cytosol, and exogenous ATP was able to enter chloroplasts isolated from 4- and 5-day-old seedlings, but not chloroplasts isolated from 10- or 20-day-old photosynthetic tissues. This observation is in line with the previous finding that the expression of chloroplast nucleotide transporters (NTTs) in Arabidopsis mesophyll is limited to very young seedlings. Employing a combination of photosynthetic and respiratory inhibitors with compartment-specific imaging of ATP, we corroborate the dependency of stromal ATP production on mitochondrial dissipation of photosynthetic reductant. Our data suggest that, during illumination, the provision and consumption of ATP:NADPH in chloroplasts can be balanced by exporting excess reductants rather than importing ATP from the cytosol.

@article{wang_major_2018,
	title = {A major locus controls local adaptation and adaptive life history variation in a perennial plant},
	volume = {19},
	issn = {1474-760X},
	url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1444-y},
	doi = {10.1186/s13059-018-1444-y},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Genome Biology},
	author = {Wang, Jing and Ding, Jihua and Tan, Biyue and Robinson, Kathryn M. and Michelson, Ingrid H. and Johansson, Anna and Nystedt, Björn and Scofield, Douglas G. and Nilsson, Ove and Jansson, Stefan and Street, Nathaniel R. and Ingvarsson, Pär K.},
	month = dec,
	year = {2018},
	pages = {72},
}

@article{zare_gut_2018,
	title = {The gut microbiome participates in transgenerational inheritance of low‐temperature responses in \textit{{Drosophila} melanogaster}},
	volume = {592},
	issn = {0014-5793, 1873-3468},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/1873-3468.13278},
	doi = {10.1002/1873-3468.13278},
	language = {en},
	number = {24},
	urldate = {2021-06-07},
	journal = {FEBS Letters},
	author = {Zare, Aman and Johansson, Anna‐Mia and Karlsson, Edvin and Delhomme, Nicolas and Stenberg, Per},
	month = dec,
	year = {2018},
	pages = {4078--4086},
}

@article{zhang_cellulose_2018,
	title = {Cellulose {Synthase} {Stoichiometry} in {Aspen} {Differs} from {Arabidopsis} and {Norway} {Spruce}},
	volume = {177},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/177/3/1096-1107/6117105},
	doi = {10.1104/pp.18.00394},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Zhang, Xueyang and Dominguez, Pia Guadalupe and Kumar, Manoj and Bygdell, Joakim and Miroshnichenko, Sergey and Sundberg, Björn and Wingsle, Gunnar and Niittylä, Totte},
	month = jul,
	year = {2018},
	pages = {1096--1107},
}

@article{kern_structures_2018,
	title = {Structures of the intermediates of {Kok}’s photosynthetic water oxidation clock},
	volume = {563},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/articles/s41586-018-0681-2},
	doi = {10.1038/s41586-018-0681-2},
	language = {en},
	number = {7731},
	urldate = {2021-06-07},
	journal = {Nature},
	author = {Kern, Jan and Chatterjee, Ruchira and Young, Iris D. and Fuller, Franklin D. and Lassalle, Louise and Ibrahim, Mohamed and Gul, Sheraz and Fransson, Thomas and Brewster, Aaron S. and Alonso-Mori, Roberto and Hussein, Rana and Zhang, Miao and Douthit, Lacey and de Lichtenberg, Casper and Cheah, Mun Hon and Shevela, Dmitry and Wersig, Julia and Seuffert, Ina and Sokaras, Dimosthenis and Pastor, Ernest and Weninger, Clemens and Kroll, Thomas and Sierra, Raymond G. and Aller, Pierre and Butryn, Agata and Orville, Allen M. and Liang, Mengning and Batyuk, Alexander and Koglin, Jason E. and Carbajo, Sergio and Boutet, Sébastien and Moriarty, Nigel W. and Holton, James M. and Dobbek, Holger and Adams, Paul D. and Bergmann, Uwe and Sauter, Nicholas K. and Zouni, Athina and Messinger, Johannes and Yano, Junko and Yachandra, Vittal K.},
	month = nov,
	year = {2018},
	pages = {421--425},
}

@book{roberts_annual_2018,
	edition = {1},
	title = {Annual {Plant} {Reviews} online},
	isbn = {978-1-119-31299-4},
	url = {https://onlinelibrary.wiley.com/doi/book/10.1002/9781119312994},
	language = {en},
	urldate = {2021-06-07},
	publisher = {Wiley},
	editor = {Roberts, Jeremy A},
	month = feb,
	year = {2018},
	doi = {10.1002/9781119312994},
}