Publications 2015

@article{takuno_independent_2015,
	title = {Independent {Molecular} {Basis} of {Convergent} {Highland} {Adaptation} in {Maize}},
	volume = {200},
	issn = {1943-2631},
	url = {https://doi.org/10.1534/genetics.115.178327},
	doi = {10.1534/genetics.115.178327},
	abstract = {Convergent evolution is the independent evolution of similar traits in different species or lineages of the same species; this often is a result of adaptation to similar environments, a process referred to as convergent adaptation. We investigate here the molecular basis of convergent adaptation in maize to highland climates in Mesoamerica and South America, using genome-wide SNP data. Taking advantage of archaeological data on the arrival of maize to the highlands, we infer demographic models for both populations, identifying evidence of a strong bottleneck and rapid expansion in South America. We use these models to then identify loci showing an excess of differentiation as a means of identifying putative targets of natural selection and compare our results to expectations from recently developed theory on convergent adaptation. Consistent with predictions across a wide parameter space, we see limited evidence for convergent evolution at the nucleotide level in spite of strong similarities in overall phenotypes. Instead, we show that selection appears to have predominantly acted on standing genetic variation and that introgression from wild teosinte populations appears to have played a role in highland adaptation in Mexican maize.},
	number = {4},
	urldate = {2024-03-22},
	journal = {Genetics},
	author = {Takuno, Shohei and Ralph, Peter and Swarts, Kelly and Elshire, Rob J and Glaubitz, Jeffrey C and Buckler, Edward S and Hufford, Matthew B and Ross-Ibarra, Jeffrey},
	month = aug,
	year = {2015},
	pages = {1297--1312},
}

Convergent evolution is the independent evolution of similar traits in different species or lineages of the same species; this often is a result of adaptation to similar environments, a process referred to as convergent adaptation. We investigate here the molecular basis of convergent adaptation in maize to highland climates in Mesoamerica and South America, using genome-wide SNP data. Taking advantage of archaeological data on the arrival of maize to the highlands, we infer demographic models for both populations, identifying evidence of a strong bottleneck and rapid expansion in South America. We use these models to then identify loci showing an excess of differentiation as a means of identifying putative targets of natural selection and compare our results to expectations from recently developed theory on convergent adaptation. Consistent with predictions across a wide parameter space, we see limited evidence for convergent evolution at the nucleotide level in spite of strong similarities in overall phenotypes. Instead, we show that selection appears to have predominantly acted on standing genetic variation and that introgression from wild teosinte populations appears to have played a role in highland adaptation in Mexican maize.

@article{simaskova_cytokinin_2015,
	title = {Cytokinin response factors regulate {PIN}-{FORMED} auxin transporters},
	volume = {6},
	issn = {2041-1723 (Electronic) 2041-1723 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26541513},
	doi = {10.1038/ncomms9717},
	abstract = {Auxin and cytokinin are key endogenous regulators of plant development. Although cytokinin-mediated modulation of auxin distribution is a developmentally crucial hormonal interaction, its molecular basis is largely unknown. Here we show a direct regulatory link between cytokinin signalling and the auxin transport machinery uncovering a mechanistic framework for cytokinin-auxin cross-talk. We show that the CYTOKININ RESPONSE FACTORS (CRFs), transcription factors downstream of cytokinin perception, transcriptionally control genes encoding PIN-FORMED (PIN) auxin transporters at a specific PIN CYTOKININ RESPONSE ELEMENT (PCRE) domain. Removal of this cis-regulatory element effectively uncouples PIN transcription from the CRF-mediated cytokinin regulation and attenuates plant cytokinin sensitivity. We propose that CRFs represent a missing cross-talk component that fine-tunes auxin transport capacity downstream of cytokinin signalling to control plant development.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nat Commun},
	author = {Simaskova, M. and O'Brien, J. A. and Khan, M. and Van Noorden, G. and Otvos, K. and Vieten, A. and De Clercq, I. and Van Haperen, J. M. A. and Cuesta, C. and Hoyerova, K. and Vanneste, S. and Marhavý, P. and Wabnik, K. and Van Breusegem, F. and Nowack, M. and Murphy, A. and Friml, J. and Weijers, D. and Beeckman, T. and Benkova, E.},
	month = nov,
	year = {2015},
	note = {Edition: 2015/11/07},
	keywords = {Arabidopsis, Arabidopsis Proteins/*genetics/metabolism, Chromatin Immunoprecipitation, Cytokinins/*metabolism, Gene Expression Regulation, Plant, Green Fluorescent Proteins, Indoleacetic Acids/*metabolism, Membrane Transport Proteins/*genetics/metabolism, Microscopy, Confocal, Plant Roots/metabolism, Plants, Genetically Modified, Real-Time Polymerase Chain Reaction, Response Elements, Signal Transduction, Transcription Factors/*genetics/metabolism},
	pages = {8717},
}

Auxin and cytokinin are key endogenous regulators of plant development. Although cytokinin-mediated modulation of auxin distribution is a developmentally crucial hormonal interaction, its molecular basis is largely unknown. Here we show a direct regulatory link between cytokinin signalling and the auxin transport machinery uncovering a mechanistic framework for cytokinin-auxin cross-talk. We show that the CYTOKININ RESPONSE FACTORS (CRFs), transcription factors downstream of cytokinin perception, transcriptionally control genes encoding PIN-FORMED (PIN) auxin transporters at a specific PIN CYTOKININ RESPONSE ELEMENT (PCRE) domain. Removal of this cis-regulatory element effectively uncouples PIN transcription from the CRF-mediated cytokinin regulation and attenuates plant cytokinin sensitivity. We propose that CRFs represent a missing cross-talk component that fine-tunes auxin transport capacity downstream of cytokinin signalling to control plant development.

@article{chen_coherent_2015,
	title = {A coherent transcriptional feed-forward motif model for mediating auxin-sensitive {PIN3} expression during lateral root development},
	volume = {6},
	issn = {2041-1723 (Electronic) 2041-1723 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26578065},
	doi = {10.1038/ncomms9821},
	abstract = {Multiple plant developmental processes, such as lateral root development, depend on auxin distribution patterns that are in part generated by the PIN-formed family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7 (ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription in planta to steer the early steps of lateral root formation. This regulatory mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli, potentially maintaining and enhancing the robustness of the auxin flux directionality during lateral root development. The cooperative action between canonical auxin signalling and other transcription factors might constitute a general mechanism by which transcriptional auxin-sensitivity can be regulated at a tissue-specific level.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nat Commun},
	author = {Chen, Q. and Liu, Y. and Maere, S. and Lee, E. and Van Isterdael, G. and Xie, Z. and Xuan, W. and Lucas, J. and Vassileva, V. and Kitakura, S. and Marhavý, P. and Wabnik, K. and Geldner, N. and Benkova, E. and Le, J. and Fukaki, H. and Grotewold, E. and Li, C. and Friml, J. and Sack, F. and Beeckman, T. and Vanneste, S.},
	month = nov,
	year = {2015},
	keywords = {*Gene Expression Regulation, Plant, Arabidopsis Proteins/*genetics/metabolism, Arabidopsis/*genetics/growth \& development, Chromatin Immunoprecipitation, Feedback, Physiological, Glucuronidase/metabolism, Organisms, Genetically Modified, Plant Roots/*growth \& development/metabolism, RNA, Messenger/*metabolism, Reverse Transcriptase Polymerase Chain Reaction, Signal Transduction, Transcription Factors/*genetics/metabolism, Transcription, Genetic},
	pages = {8821},
}

Multiple plant developmental processes, such as lateral root development, depend on auxin distribution patterns that are in part generated by the PIN-formed family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7 (ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription in planta to steer the early steps of lateral root formation. This regulatory mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli, potentially maintaining and enhancing the robustness of the auxin flux directionality during lateral root development. The cooperative action between canonical auxin signalling and other transcription factors might constitute a general mechanism by which transcriptional auxin-sensitivity can be regulated at a tissue-specific level.

@article{zhang_isolation_2015,
	title = {Isolation and characterization of thirty-eight microsatellite loci for the {Pinus} wangii, an endangered species},
	volume = {7},
	issn = {1877-7260},
	url = {https://doi.org/10.1007/s12686-014-0379-1},
	doi = {10.1007/s12686-014-0379-1},
	abstract = {Piuns wangii Hu et Cheng is an endangered five-needle pine species, with scattered populations and scare individuals. To study its genetic diversity and better address conservation programs, 506 novel microsatellite markers were developed by mining the transcriptome database of P. lambertiana. 117 loci were able to amplify a fragment of expected size in P. wangii, of which 38 were polymorphic. The number of alleles of these 38 EST-SSRs in 16 individuals varied from 2 to 6, with an average of 2.6. The observed (Ho) and expected (He) heterozygosity values ranged from 0.000 to 1.000 (averaging 0.532) and 0.117–0.693 (averaging 0.394), respectively. Twenty-three loci showed significant departure from HWE after Bonferroni correction. This was the first report of candidate molecular markers on P. wangii, which will facilitate future analyses of genetic diversity and population structure.},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {Conservation Genetics Resources},
	author = {Zhang, Zhi-Yong and Cui, Binbin and Mao, Jian-Feng and Pang, Xiao-Ming and Li, Ying-Yue},
	month = jun,
	year = {2015},
	keywords = {Conservation genetics, Expressed sequence tag (EST), Microsatellites, Pinus wangii},
	pages = {397--398},
}

Piuns wangii Hu et Cheng is an endangered five-needle pine species, with scattered populations and scare individuals. To study its genetic diversity and better address conservation programs, 506 novel microsatellite markers were developed by mining the transcriptome database of P. lambertiana. 117 loci were able to amplify a fragment of expected size in P. wangii, of which 38 were polymorphic. The number of alleles of these 38 EST-SSRs in 16 individuals varied from 2 to 6, with an average of 2.6. The observed (Ho) and expected (He) heterozygosity values ranged from 0.000 to 1.000 (averaging 0.532) and 0.117–0.693 (averaging 0.394), respectively. Twenty-three loci showed significant departure from HWE after Bonferroni correction. This was the first report of candidate molecular markers on P. wangii, which will facilitate future analyses of genetic diversity and population structure.

@article{zhang_novel_2015,
	title = {Novel polymorphic {EST}-derived microsatellite markers for the red-listed five needle pine, {Pinus} dabeshanensis},
	volume = {7},
	issn = {1877-7260},
	url = {https://doi.org/10.1007/s12686-014-0329-y},
	doi = {10.1007/s12686-014-0329-y},
	abstract = {Pinus dabeshanensis is an endangered five needle pine endemic to mid-South of China. This pine finds its very limited natural occurrence in the Dabie mountains area with altitudes ranging 900–1400 m. We identified 3,516 SSR loci from the transcriptome assembly of the congeneric species P. lambertiana, and evaluated 671 loci we found. Finally, 28 novel polymorphic microsatellite markers were developed for P. dabeshanensis. Markers were characterized using 36 individuals, representing all existing populations from across the species geographic range. Species level analysis of these 28 polymorphic markers revealed the mean number per locus was 2.786 (range 2–6) and mean observed and expected heterozygosities were 0.332 (range 0.000–1.000) and 0.316 (range 0.033–0.691), respectively. This study provides the first set of microsatellite markers for the conservation genetics which in turn will facilitate conservation management for this pine.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Conservation Genetics Resources},
	author = {Zhang, Zhi-Yong and Cui, Bin-Bin and Mao, Jian-Feng and Pang, Xiao-Ming and Liu, Hui and Li, Ying-Yue},
	month = mar,
	year = {2015},
	keywords = {Conservation genetics, Five needle pine, Microsatellite, Pinus dabeshanensis},
	pages = {191--192},
}

Pinus dabeshanensis is an endangered five needle pine endemic to mid-South of China. This pine finds its very limited natural occurrence in the Dabie mountains area with altitudes ranging 900–1400 m. We identified 3,516 SSR loci from the transcriptome assembly of the congeneric species P. lambertiana, and evaluated 671 loci we found. Finally, 28 novel polymorphic microsatellite markers were developed for P. dabeshanensis. Markers were characterized using 36 individuals, representing all existing populations from across the species geographic range. Species level analysis of these 28 polymorphic markers revealed the mean number per locus was 2.786 (range 2–6) and mean observed and expected heterozygosities were 0.332 (range 0.000–1.000) and 0.316 (range 0.033–0.691), respectively. This study provides the first set of microsatellite markers for the conservation genetics which in turn will facilitate conservation management for this pine.

@article{pan_optimization_2015,
	title = {Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers},
	volume = {15},
	issn = {1755-0998},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.12342},
	doi = {10.1111/1755-0998.12342},
	abstract = {Flexibility and low cost make genotyping-by-sequencing (GBS) an ideal tool for population genomic studies of nonmodel species. However, to utilize the potential of the method fully, many parameters affecting library quality and single nucleotide polymorphism (SNP) discovery require optimization, especially for conifer genomes with a high repetitive DNA content. In this study, we explored strategies for effective GBS analysis in pine species. We constructed GBS libraries using HpaII, PstI and EcoRI-MseI digestions with different multiplexing levels and examined the effect of restriction enzymes on library complexity and the impact of sequencing depth and size selection of restriction fragments on sequence coverage bias. We tested and compared UNEAK, Stacks and GATK pipelines for the GBS data, and then developed a reference-free SNP calling strategy for haploid pine genomes. Our GBS procedure proved to be effective in SNP discovery, producing 7000–11 000 and 14 751 SNPs within and among three pine species, respectively, from a PstI library. This investigation provides guidance for the design and analysis of GBS experiments, particularly for organisms for which genomic information is lacking.},
	language = {en},
	number = {4},
	urldate = {2023-04-27},
	journal = {Molecular Ecology Resources},
	author = {Pan, Jin and Wang, Baosheng and Pei, Zhi-Yong and Zhao, Wei and Gao, Jie and Mao, Jian-Feng and Wang, Xiao-Ru},
	year = {2015},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.12342},
	keywords = {SNP validation, conifer genome, genotyping-by-sequencing, library preparation parameters, sequencing depth},
	pages = {711--722},
}

Flexibility and low cost make genotyping-by-sequencing (GBS) an ideal tool for population genomic studies of nonmodel species. However, to utilize the potential of the method fully, many parameters affecting library quality and single nucleotide polymorphism (SNP) discovery require optimization, especially for conifer genomes with a high repetitive DNA content. In this study, we explored strategies for effective GBS analysis in pine species. We constructed GBS libraries using HpaII, PstI and EcoRI-MseI digestions with different multiplexing levels and examined the effect of restriction enzymes on library complexity and the impact of sequencing depth and size selection of restriction fragments on sequence coverage bias. We tested and compared UNEAK, Stacks and GATK pipelines for the GBS data, and then developed a reference-free SNP calling strategy for haploid pine genomes. Our GBS procedure proved to be effective in SNP discovery, producing 7000–11 000 and 14 751 SNPs within and among three pine species, respectively, from a PstI library. This investigation provides guidance for the design and analysis of GBS experiments, particularly for organisms for which genomic information is lacking.

@article{ouyang_transcriptome_2015,
	title = {Transcriptome {Analysis} {Reveals} that {Red} and {Blue} {Light} {Regulate} {Growth} and {Phytohormone} {Metabolism} in {Norway} {Spruce} [{Picea} abies ({L}.) {Karst}.]},
	volume = {10},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0127896},
	doi = {10.1371/journal.pone.0127896},
	abstract = {The mechanisms by which different light spectra regulate plant shoot elongation vary, and phytohormones respond differently to such spectrum-associated regulatory effects. Light supplementation can effectively control seedling growth in Norway spruce. However, knowledge of the effective spectrum for promoting growth and phytohormone metabolism in this species is lacking. In this study, 3-year-old Norway spruce clones were illuminated for 12 h after sunset under blue or red light-emitting diode (LED) light for 90 d, and stem increments and other growth traits were determined. Endogenous hormone levels and transcriptome differences in the current needles were assessed to identify genes related to the red and blue light regulatory responses. The results showed that the stem increment and gibberellin (GA) levels of the seedlings illuminated by red light were 8.6\% and 29.0\% higher, respectively, than those of the seedlings illuminated by blue light. The indoleacetic acid (IAA) level of the seedlings illuminated by red light was 54.6\% lower than that of the seedlings illuminated by blue light, and there were no significant differences in abscisic acid (ABA) or zeatin riboside [ZR] between the two groups of seedlings. The transcriptome results revealed 58,736,166 and 60,555,192 clean reads for the blue-light- and red-light-illuminated samples, respectively. Illumina sequencing revealed 21,923 unigenes, and 2744 (approximately 93.8\%) out of 2926 differentially expressed genes (DEGs) were found to be upregulated under blue light. The main KEGG classifications of the DEGs were metabolic pathway (29\%), biosynthesis of secondary metabolites (20.49\%) and hormone signal transduction (8.39\%). With regard to hormone signal transduction, AUXIN-RESISTANT1 (AUX1), AUX/IAA genes, auxin-inducible genes, and early auxin-responsive genes [(auxin response factor (ARF) and small auxin-up RNA (SAUR)] were all upregulated under blue light compared with red light, which might have yielded the higher IAA level. DELLA and phytochrome-interacting factor 3 (PIF3), involved in negative GA signaling, were also upregulated under blue light, which may be related to the lower GA level. Light quality also affects endogenous hormones by influencing secondary metabolism. Blue light promoted phenylpropanoid biosynthesis, phenylalanine metabolism, flavonoid biosynthesis and flavone and flavonol biosynthesis, accompanied by upregulation of most of the genes in their pathways. In conclusion, red light may promote stem growth by regulating biosynthesis of GAs, and blue light may promote flavonoid, lignin, phenylpropanoid and some hormones (such as jasmonic acid) which were related to plant defense in Norway spruce, which might reduce the primary metabolites available for plant growth.},
	language = {en},
	number = {8},
	urldate = {2023-04-27},
	journal = {PLOS ONE},
	author = {OuYang, Fangqun and Mao, Jian-Feng and Wang, Junhui and Zhang, Shougong and Li, Yue},
	month = aug,
	year = {2015},
	note = {Publisher: Public Library of Science},
	keywords = {Biosynthesis, Gene expression, Gibberellins, Light, Metabolic pathways, Plant hormones, Seedlings, Signal transduction},
	pages = {e0127896},
}

The mechanisms by which different light spectra regulate plant shoot elongation vary, and phytohormones respond differently to such spectrum-associated regulatory effects. Light supplementation can effectively control seedling growth in Norway spruce. However, knowledge of the effective spectrum for promoting growth and phytohormone metabolism in this species is lacking. In this study, 3-year-old Norway spruce clones were illuminated for 12 h after sunset under blue or red light-emitting diode (LED) light for 90 d, and stem increments and other growth traits were determined. Endogenous hormone levels and transcriptome differences in the current needles were assessed to identify genes related to the red and blue light regulatory responses. The results showed that the stem increment and gibberellin (GA) levels of the seedlings illuminated by red light were 8.6% and 29.0% higher, respectively, than those of the seedlings illuminated by blue light. The indoleacetic acid (IAA) level of the seedlings illuminated by red light was 54.6% lower than that of the seedlings illuminated by blue light, and there were no significant differences in abscisic acid (ABA) or zeatin riboside [ZR] between the two groups of seedlings. The transcriptome results revealed 58,736,166 and 60,555,192 clean reads for the blue-light- and red-light-illuminated samples, respectively. Illumina sequencing revealed 21,923 unigenes, and 2744 (approximately 93.8%) out of 2926 differentially expressed genes (DEGs) were found to be upregulated under blue light. The main KEGG classifications of the DEGs were metabolic pathway (29%), biosynthesis of secondary metabolites (20.49%) and hormone signal transduction (8.39%). With regard to hormone signal transduction, AUXIN-RESISTANT1 (AUX1), AUX/IAA genes, auxin-inducible genes, and early auxin-responsive genes [(auxin response factor (ARF) and small auxin-up RNA (SAUR)] were all upregulated under blue light compared with red light, which might have yielded the higher IAA level. DELLA and phytochrome-interacting factor 3 (PIF3), involved in negative GA signaling, were also upregulated under blue light, which may be related to the lower GA level. Light quality also affects endogenous hormones by influencing secondary metabolism. Blue light promoted phenylpropanoid biosynthesis, phenylalanine metabolism, flavonoid biosynthesis and flavone and flavonol biosynthesis, accompanied by upregulation of most of the genes in their pathways. In conclusion, red light may promote stem growth by regulating biosynthesis of GAs, and blue light may promote flavonoid, lignin, phenylpropanoid and some hormones (such as jasmonic acid) which were related to plant defense in Norway spruce, which might reduce the primary metabolites available for plant growth.

@article{mao_development_2015,
	title = {Development of 36 novel polymorphic microsatellites for the critically endangered tree {Pinus} squamaia, by transcriptome database mining},
	volume = {7},
	issn = {1877-7260},
	url = {https://doi.org/10.1007/s12686-014-0300-y},
	doi = {10.1007/s12686-014-0300-y},
	abstract = {Pinus squamaia X. W. Li is a critically endangered five-needle pine species, with only 35 wild individuals left. To understand its genetic variability, 506 novel microsatellite markers were developed by mining the transcriptome database of P. lambertiana. 196 loci were able to amplify a fragment of expected size in P. squamaia, of which 36 were polymorphic. The number of alleles of these 36 EST-SSRs in 16 individuals varied from 2 to 4, with an average of 2.2. The observed (Ho) and expected (He) heterozygosity values ranged from 0.000 to 1.000 (averaging 0.564) and 0.061 to 0.500 (averaging 0.356), respectively. Twenty-four loci showed significant departure from HWE after Bonferroni correction. This was the first report of candidate molecular markers on P. squamaia, which will facilitate future analyses of genetic diversity and population structure.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Conservation Genetics Resources},
	author = {Mao, Jian-Feng and Cui, Bin-Bin and Zhang, Zhi-Yong and Liu, Hui and Li, Ying-Yue},
	month = mar,
	year = {2015},
	keywords = {Expressed sequence tag (EST), Microstallites, Pinus lambertiana, Pinus squamaia, Transcriptome},
	pages = {93--94},
}

Pinus squamaia X. W. Li is a critically endangered five-needle pine species, with only 35 wild individuals left. To understand its genetic variability, 506 novel microsatellite markers were developed by mining the transcriptome database of P. lambertiana. 196 loci were able to amplify a fragment of expected size in P. squamaia, of which 36 were polymorphic. The number of alleles of these 36 EST-SSRs in 16 individuals varied from 2 to 4, with an average of 2.2. The observed (Ho) and expected (He) heterozygosity values ranged from 0.000 to 1.000 (averaging 0.564) and 0.061 to 0.500 (averaging 0.356), respectively. Twenty-four loci showed significant departure from HWE after Bonferroni correction. This was the first report of candidate molecular markers on P. squamaia, which will facilitate future analyses of genetic diversity and population structure.

@article{jin_development_2015,
	title = {Development of 23 novel polymorphic {EST}-{SSR} markers for the endangered relict conifer {Metasequoia} glyptostroboides},
	volume = {3},
	issn = {2168-0450},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.3732/apps.1500038},
	doi = {10.3732/apps.1500038},
	abstract = {Premise of the study: Metasequoia glyptostroboides is an endangered relict conifer species endemic to China. In this study, expressed sequence tag–simple sequence repeat (EST-SSR) markers were developed using transcriptome mining for future genetic and functional studies. Methods and Results: We collected 97,565 unigene sequences generated by 454 pyrosequencing. A bioinformatics analysis identified 2087 unique and putative microsatellites, from which 96 novel microsatellite markers were developed. Fifty-three of the 96 primer sets successfully amplified clear fragments of the expected sizes; 23 of those loci were polymorphic. The number of alleles per locus ranged from two to eight, with an average of three, and the observed and expected heterozygosity values ranged from 0 to 1.0 and 0.117 to 0.813, respectively. Conclusions: These microsatellite loci will enrich the genetic resources to develop functional studies and conservation strategies for this endangered relict species.},
	language = {en},
	number = {9},
	urldate = {2023-04-27},
	journal = {Applications in Plant Sciences},
	author = {Jin, Yuqing and Bi, Quanxin and Guan, Wenbin and Mao, Jian-Feng},
	year = {2015},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.3732/apps.1500038},
	keywords = {454 pyrosequencing, Cupressaceae, EST-SSR, Metasequoia glyptostroboides, microsatellite, relict plant},
	pages = {1500038},
}

Premise of the study: Metasequoia glyptostroboides is an endangered relict conifer species endemic to China. In this study, expressed sequence tag–simple sequence repeat (EST-SSR) markers were developed using transcriptome mining for future genetic and functional studies. Methods and Results: We collected 97,565 unigene sequences generated by 454 pyrosequencing. A bioinformatics analysis identified 2087 unique and putative microsatellites, from which 96 novel microsatellite markers were developed. Fifty-three of the 96 primer sets successfully amplified clear fragments of the expected sizes; 23 of those loci were polymorphic. The number of alleles per locus ranged from two to eight, with an average of three, and the observed and expected heterozygosity values ranged from 0 to 1.0 and 0.117 to 0.813, respectively. Conclusions: These microsatellite loci will enrich the genetic resources to develop functional studies and conservation strategies for this endangered relict species.

@article{hu_predicting_2015,
	title = {Predicting {Impacts} of {Future} {Climate} {Change} on the {Distribution} of the {Widespread} {Conifer} {Platycladus} orientalis},
	volume = {10},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0132326},
	doi = {10.1371/journal.pone.0132326},
	abstract = {Chinese thuja (Platycladus orientalis) has a wide but fragmented distribution in China. It is an important conifer tree in reforestation and plays important roles in ecological restoration in the arid mountains of northern China. Based on high-resolution environmental data for current and future scenarios, we modeled the present and future suitable habitat for P. orientalis, evaluated the importance of environmental factors in shaping the species´ distribution, and identified regions of high risk under climate change scenarios. The niche models showed that P. orientalis has suitable habitat of ca. 4.2×106 km2 across most of eastern China and identified annual temperature, monthly minimum and maximum ultraviolet-B radiation and wet-day frequency as the critical factors shaping habitat availability for P. orientalis. Under the low concentration greenhouse gas emissions scenario, the range of the species may increase as global warming intensifies; however, under the higher concentrations of emissions scenario, we predicted a slight expansion followed by contraction in distribution. Overall, the range shift to higher latitudes and elevations would become gradually more significant. The information gained from this study should be an useful reference for implementing long-term conservation and management strategies for the species.},
	language = {en},
	number = {7},
	urldate = {2023-04-27},
	journal = {PLOS ONE},
	author = {Hu, Xian-Ge and Jin, Yuqing and Wang, Xiao-Ru and Mao, Jian-Feng and Li, Yue},
	month = jul,
	year = {2015},
	note = {Publisher: Public Library of Science},
	keywords = {Anthropogenic climate change, China, Climate change, Conifers, Forests, Habitats, Latitude, Ultraviolet B},
	pages = {e0132326},
}

Chinese thuja (Platycladus orientalis) has a wide but fragmented distribution in China. It is an important conifer tree in reforestation and plays important roles in ecological restoration in the arid mountains of northern China. Based on high-resolution environmental data for current and future scenarios, we modeled the present and future suitable habitat for P. orientalis, evaluated the importance of environmental factors in shaping the species´ distribution, and identified regions of high risk under climate change scenarios. The niche models showed that P. orientalis has suitable habitat of ca. 4.2×106 km2 across most of eastern China and identified annual temperature, monthly minimum and maximum ultraviolet-B radiation and wet-day frequency as the critical factors shaping habitat availability for P. orientalis. Under the low concentration greenhouse gas emissions scenario, the range of the species may increase as global warming intensifies; however, under the higher concentrations of emissions scenario, we predicted a slight expansion followed by contraction in distribution. Overall, the range shift to higher latitudes and elevations would become gradually more significant. The information gained from this study should be an useful reference for implementing long-term conservation and management strategies for the species.

@article{bi_efficiently_2015,
	title = {Efficiently developing a large set of polymorphic {EST}-{SSR} markers for {Xanthoceras} sorbifolium by mining raw reads from high-throughput sequencing},
	volume = {7},
	issn = {1877-7260},
	url = {https://doi.org/10.1007/s12686-014-0386-2},
	doi = {10.1007/s12686-014-0386-2},
	abstract = {Yellow-horn (Xanthoceras sorbifolium Bunge) is an economically and ecologically important tree in northern China that is facing severe stress from human activity and the changing climate. Transcriptome-wide or genome-wide genetic markers are required for functional studies and development of conservation strategies based on genetic variation within the species. In this report, using an in silico microsatellite detection and primer design strategy implemented in the computer program QDD, we detected and designed primers for 477 candidate polymorphic EST-SSR (simple sequences repeat in expressed sequence tags) loci by mining raw reads from high-throughput transcriptome sequencing of pooled samples. A total of 48 primer loci were selected randomly and evaluated, of which 29 (60.42 \%) were polymorphic in eight individuals. Based on these results, this development strategy can be used for the development of EST-SSR markers. This large set of marker resources can be used for mining, performing functional studies, and developing conservation strategies for this endangered species.},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {Conservation Genetics Resources},
	author = {Bi, Quanxin and Mao, Jian-Feng and Guan, Wenbin},
	month = jun,
	year = {2015},
	keywords = {EST-SSR, Endangered tree, QDD, Xanthoceras sorbifolium},
	pages = {423--425},
}

Yellow-horn (Xanthoceras sorbifolium Bunge) is an economically and ecologically important tree in northern China that is facing severe stress from human activity and the changing climate. Transcriptome-wide or genome-wide genetic markers are required for functional studies and development of conservation strategies based on genetic variation within the species. In this report, using an in silico microsatellite detection and primer design strategy implemented in the computer program QDD, we detected and designed primers for 477 candidate polymorphic EST-SSR (simple sequences repeat in expressed sequence tags) loci by mining raw reads from high-throughput transcriptome sequencing of pooled samples. A total of 48 primer loci were selected randomly and evaluated, of which 29 (60.42 %) were polymorphic in eight individuals. Based on these results, this development strategy can be used for the development of EST-SSR markers. This large set of marker resources can be used for mining, performing functional studies, and developing conservation strategies for this endangered species.

@article{bi_characterisation_2015,
	title = {Characterisation of {EST}-based {SSR} loci in the endangered tree {Manchurian} fir {Abies} holophylla: a transcriptomic approach},
	volume = {7},
	issn = {1877-7260},
	shorttitle = {Characterisation of {EST}-based {SSR} loci in the endangered tree {Manchurian} fir {Abies} holophylla},
	url = {https://doi.org/10.1007/s12686-014-0384-4},
	doi = {10.1007/s12686-014-0384-4},
	abstract = {The International Union for the Conservation of Nature has declared Abies holophylla maxim an endangered species. In the study described herein, 171 novel microsatellite markers were identified by mining the transcriptomic database of Abies balsamea to develop a practical and realistic conservation strategy. Among these markers, fragments of expected sizes were amplified from 86 loci of which 14 exhibited polymorphism and 34 monomorphism in eight individuals of A. holophylla. The number of alleles in these 14 expressed sequence tag-simple sequence repeats (EST-SSRs) ranged from two to three per locus, and the observed (Ho) and expected heterozygosity (He) values ranged from 0 to 1.0 and 0.117 to 0.594, respectively. Polymorphic information content respectively ranged from 0.110 to 0.511. These polymorphic markers will be useful for evaluating genetic biodiversity and aid in the development of a conservation strategy for this relict species.},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {Conservation Genetics Resources},
	author = {Bi, Quanxin and Jin, Yuqing and Guan, Wenbin and Mao, Jian-Feng},
	month = jun,
	year = {2015},
	keywords = {Abies holophylla, EST-SSR, Endangered tree},
	pages = {415--418},
}

The International Union for the Conservation of Nature has declared Abies holophylla maxim an endangered species. In the study described herein, 171 novel microsatellite markers were identified by mining the transcriptomic database of Abies balsamea to develop a practical and realistic conservation strategy. Among these markers, fragments of expected sizes were amplified from 86 loci of which 14 exhibited polymorphism and 34 monomorphism in eight individuals of A. holophylla. The number of alleles in these 14 expressed sequence tag-simple sequence repeats (EST-SSRs) ranged from two to three per locus, and the observed (Ho) and expected heterozygosity (He) values ranged from 0 to 1.0 and 0.117 to 0.594, respectively. Polymorphic information content respectively ranged from 0.110 to 0.511. These polymorphic markers will be useful for evaluating genetic biodiversity and aid in the development of a conservation strategy for this relict species.

@article{eguen_microproteins_2015,
	title = {{MicroProteins}: small size – big impact},
	volume = {20},
	issn = {1360-1385},
	shorttitle = {{MicroProteins}},
	url = {https://www.cell.com/trends/plant-science/abstract/S1360-1385(15)00140-5},
	doi = {10.1016/j.tplants.2015.05.011},
	language = {English},
	number = {8},
	urldate = {2022-11-30},
	journal = {Trends in Plant Science},
	author = {Eguen, Tenai and Straub, Daniel and Graeff, Moritz and Wenkel, Stephan},
	month = aug,
	year = {2015},
	keywords = {MicroProteins, dominant-negative effect, modulatory regulation, non-functional complexes, short single domain, transcription factor regulation},
	pages = {477--482},
}

@article{xie_meta-analysis_2015,
	title = {Meta-{Analysis} of {Arabidopsis} {KANADI1} {Direct} {Target} {Genes} {Identifies} a {Basic} {Growth}-{Promoting} {Module} {Acting} {Upstream} of {Hormonal} {Signaling} {Pathways}},
	volume = {169},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.15.00764},
	doi = {10.1104/pp.15.00764},
	abstract = {An intricate network of antagonistically acting transcription factors mediates the formation of a flat leaf lamina of Arabidopsis (Arabidopsis thaliana) plants. In this context, members of the class III homeodomain leucine zipper (HD-ZIPIII) transcription factor family specify the adaxial domain (future upper side) of the leaf, while antagonistically acting KANADI transcription factors determine the abaxial domain (future lower side). Here, we used a messenger RNA sequencing approach to identify genes regulated by KANADI1 (KAN1) and subsequently performed a meta-analysis combining our data sets with published genome-wide data sets. Our analysis revealed that KAN1 acts upstream of several genes encoding auxin biosynthetic enzymes. When exposed to shade, we found three YUCCA genes, YUC2, YUC5, and YUC8, to be transcriptionally up-regulated, which correlates with an increase in the levels of free auxin. When ectopically expressed, KAN1 is able to transcriptionally repress these three YUC genes and thereby block shade-induced auxin biosynthesis. Consequently, KAN1 is able to strongly suppress shade-avoidance responses. Taken together, we hypothesize that HD-ZIPIII/KAN form the basis of a basic growth-promoting module. Hypocotyl extension in the shade and outgrowth of new leaves both involve auxin synthesis and signaling, which are under the direct control of HD-ZIPIII/KAN.},
	number = {2},
	urldate = {2022-11-30},
	journal = {Plant Physiology},
	author = {Xie, Yakun and Straub, Daniel and Eguen, Tenai and Brandt, Ronny and Stahl, Mark and Martínez-García, Jaime F. and Wenkel, Stephan},
	month = oct,
	year = {2015},
	pages = {1240--1253},
}

An intricate network of antagonistically acting transcription factors mediates the formation of a flat leaf lamina of Arabidopsis (Arabidopsis thaliana) plants. In this context, members of the class III homeodomain leucine zipper (HD-ZIPIII) transcription factor family specify the adaxial domain (future upper side) of the leaf, while antagonistically acting KANADI transcription factors determine the abaxial domain (future lower side). Here, we used a messenger RNA sequencing approach to identify genes regulated by KANADI1 (KAN1) and subsequently performed a meta-analysis combining our data sets with published genome-wide data sets. Our analysis revealed that KAN1 acts upstream of several genes encoding auxin biosynthetic enzymes. When exposed to shade, we found three YUCCA genes, YUC2, YUC5, and YUC8, to be transcriptionally up-regulated, which correlates with an increase in the levels of free auxin. When ectopically expressed, KAN1 is able to transcriptionally repress these three YUC genes and thereby block shade-induced auxin biosynthesis. Consequently, KAN1 is able to strongly suppress shade-avoidance responses. Taken together, we hypothesize that HD-ZIPIII/KAN form the basis of a basic growth-promoting module. Hypocotyl extension in the shade and outgrowth of new leaves both involve auxin synthesis and signaling, which are under the direct control of HD-ZIPIII/KAN.

@article{marhavy_real-time_2015,
	title = {Real-time {Analysis} of {Lateral} {Root} {Organogenesis} in {Arabidopsis}},
	volume = {5},
	issn = {2331-8325},
	url = {http://www.bio-protocol.org/e1446},
	doi = {10/ggsz3x},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {BIO-PROTOCOL},
	author = {Marhavý, Peter and Benkova, Eva},
	year = {2015},
}

@techreport{wang_variation_2015,
	type = {preprint},
	title = {Variation in linked selection and recombination drive genomic divergence during allopatric speciation of {European} and {American} aspens},
	url = {http://biorxiv.org/lookup/doi/10.1101/029561},
	abstract = {Abstract
          
            Despite the global economic and ecological importance of forest trees, the genomic basis of differential adaptation and speciation in tree species is still poorly understood.
            Populus tremula
            and
            P. tremuloides
            are two of the most widespread tree species in the Northern Hemisphere. Using whole-genome re-sequencing data of 24
            P. tremula
            and 22
            P. tremuloides
            individuals, we find that the two species diverged ∼2.2-3.1 million years ago, coinciding with the severing of the Bering land bridge and the onset of dramatic climatic oscillations during the Pleistocene. Both species have experienced substantial population expansions following long-term declines after species divergence. We detect widespread and heterogeneous genomic differentiation between species, and in accordance with the expectation of allopatric speciation, coalescent simulations suggest that neutral evolutionary processes can account for most of the observed patterns of genomic differentiation. However, there is an excess of regions exhibiting extreme differentiation relative to those expected under demographic simulations, which is indicative of the action of natural selection. Overall genetic differentiation is negatively associated with recombination rate in both species, providing strong support for a role of linked selection in generating the heterogeneous genomic landscape of differentiation between species. Finally, we identify a number of candidate regions and genes that may have been subject to positive and/or balancing selection during the speciation process.},
	language = {en},
	urldate = {2021-06-07},
	institution = {Evolutionary Biology},
	author = {Wang, Jing and Street, Nathaniel R. and Scofield, Douglas G. and Ingvarsson, Pär K.},
	month = oct,
	year = {2015},
	doi = {10.1101/029561},
}

Abstract Despite the global economic and ecological importance of forest trees, the genomic basis of differential adaptation and speciation in tree species is still poorly understood. Populus tremula and P. tremuloides are two of the most widespread tree species in the Northern Hemisphere. Using whole-genome re-sequencing data of 24 P. tremula and 22 P. tremuloides individuals, we find that the two species diverged ∼2.2-3.1 million years ago, coinciding with the severing of the Bering land bridge and the onset of dramatic climatic oscillations during the Pleistocene. Both species have experienced substantial population expansions following long-term declines after species divergence. We detect widespread and heterogeneous genomic differentiation between species, and in accordance with the expectation of allopatric speciation, coalescent simulations suggest that neutral evolutionary processes can account for most of the observed patterns of genomic differentiation. However, there is an excess of regions exhibiting extreme differentiation relative to those expected under demographic simulations, which is indicative of the action of natural selection. Overall genetic differentiation is negatively associated with recombination rate in both species, providing strong support for a role of linked selection in generating the heterogeneous genomic landscape of differentiation between species. Finally, we identify a number of candidate regions and genes that may have been subject to positive and/or balancing selection during the speciation process.

@article{vera-sirera_bhlh-based_2015,
	title = {A {bHLH}-{Based} {Feedback} {Loop} {Restricts} {Vascular} {Cell} {Proliferation} in {Plants}},
	volume = {35},
	issn = {1878-1551 (Electronic) 1534-5807 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26609958},
	doi = {10.1016/j.devcel.2015.10.022},
	abstract = {Control of tissue dimensions in multicellular organisms requires the precise quantitative regulation of mitotic activity. In plants, where cells are immobile, tissue size is achieved through control of both cell division orientation and mitotic rate. The bHLH transcription factor heterodimer formed by target of monopteros5 (TMO5) and lonesome highway (LHW) is a central regulator of vascular width-increasing divisions. An important unanswered question is how its activity is limited to specify vascular tissue dimensions. Here we identify a regulatory network that restricts TMO5/LHW activity. We show that thermospermine synthase ACAULIS5 antagonizes TMO5/LHW activity by promoting the accumulation of SAC51-LIKE (SACL) bHLH transcription factors. SACL proteins heterodimerize with LHW-therefore likely competing with TMO5/LHW interactions-prevent activation of TMO5/LHW target genes, and suppress the over-proliferation caused by excess TMO5/LHW activity. These findings connect two thus-far disparate pathways and provide a mechanistic understanding of the quantitative control of vascular tissue growth.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Dev Cell},
	author = {Vera-Sirera, F. and De Rybel, B. and Urbez, C. and Kouklas, E. and Pesquera, M. and Alvarez-Mahecha, J. C. and Minguet, E. G. and Tuominen, H. and Carbonell, J. and Borst, J. W. and Weijers, D. and Blazquez, M. A.},
	month = nov,
	year = {2015},
	keywords = {*Gene Expression Regulation, Plant, Arabidopsis Proteins/antagonists \& inhibitors/genetics/*metabolism, Arabidopsis/genetics/*growth \& development/metabolism, Basic Helix-Loop-Helix Transcription Factors/antagonists \&, Gene Expression Regulation, Developmental, Plant Roots/*cytology/metabolism, Plants, Genetically Modified/genetics/growth \& development/metabolism, RNA, Messenger/genetics, Real-Time Polymerase Chain Reaction, Reverse Transcriptase Polymerase Chain Reaction, Trans-Activators/antagonists \& inhibitors/genetics/metabolism, Xylem/*cytology/metabolism, inhibitors/genetics/*metabolism},
	pages = {432--43},
}

Control of tissue dimensions in multicellular organisms requires the precise quantitative regulation of mitotic activity. In plants, where cells are immobile, tissue size is achieved through control of both cell division orientation and mitotic rate. The bHLH transcription factor heterodimer formed by target of monopteros5 (TMO5) and lonesome highway (LHW) is a central regulator of vascular width-increasing divisions. An important unanswered question is how its activity is limited to specify vascular tissue dimensions. Here we identify a regulatory network that restricts TMO5/LHW activity. We show that thermospermine synthase ACAULIS5 antagonizes TMO5/LHW activity by promoting the accumulation of SAC51-LIKE (SACL) bHLH transcription factors. SACL proteins heterodimerize with LHW-therefore likely competing with TMO5/LHW interactions-prevent activation of TMO5/LHW target genes, and suppress the over-proliferation caused by excess TMO5/LHW activity. These findings connect two thus-far disparate pathways and provide a mechanistic understanding of the quantitative control of vascular tissue growth.

@article{mahboubi_13c_2015,
	title = {{13C} {Tracking} after {13CO2} {Supply} {Revealed} {Diurnal} {Patterns} of {Wood} {Formation} in {Aspen}},
	volume = {168},
	issn = {1532-2548 (Electronic) 0032-0889 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25931520},
	doi = {10.1104/pp.15.00292},
	abstract = {Wood of trees is formed from carbon assimilated in the photosynthetic tissues. Determining the temporal dynamics of carbon assimilation, subsequent transport into developing wood, and incorporation to cell walls would further our understanding of wood formation in particular and tree growth in general. To investigate these questions, we designed a (13)CO2 labeling system to study carbon transport and incorporation to developing wood of hybrid aspen (Populus tremula x tremuloides). Tracking of (13)C incorporation to wood over a time course using nuclear magnetic resonance spectroscopy revealed diurnal patterns in wood cell wall biosynthesis. The dark period had a differential effect on (13)C incorporation to lignin and cell wall carbohydrates. No (13)C was incorporated into aromatic amino acids of cell wall proteins in the dark, suggesting that cell wall protein biosynthesis ceased during the night. The results show previously unrecognized temporal patterns in wood cell wall biosynthesis, suggest diurnal cycle as a possible cue in the regulation of carbon incorporation to wood, and establish a unique (13)C labeling method for the analysis of wood formation and secondary growth in trees.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Physiol},
	author = {Mahboubi, A. and Linden, P. and Hedenstrom, M. and Moritz, T. and Niittylä, T.},
	month = jun,
	year = {2015},
	keywords = {*Circadian Rhythm, Analysis of Variance, Carbon Dioxide/*metabolism, Carbon Isotopes, Cell Wall/metabolism, Cellulose/metabolism, Magnetic Resonance Spectroscopy, Metabolic Networks and Pathways, Metabolome, Models, Biological, Phloem/metabolism, Plant Leaves/metabolism, Populus/*physiology, Principal Component Analysis, Sucrose/metabolism, Wood/*growth \& development},
	pages = {478--89},
}

Wood of trees is formed from carbon assimilated in the photosynthetic tissues. Determining the temporal dynamics of carbon assimilation, subsequent transport into developing wood, and incorporation to cell walls would further our understanding of wood formation in particular and tree growth in general. To investigate these questions, we designed a (13)CO2 labeling system to study carbon transport and incorporation to developing wood of hybrid aspen (Populus tremula x tremuloides). Tracking of (13)C incorporation to wood over a time course using nuclear magnetic resonance spectroscopy revealed diurnal patterns in wood cell wall biosynthesis. The dark period had a differential effect on (13)C incorporation to lignin and cell wall carbohydrates. No (13)C was incorporated into aromatic amino acids of cell wall proteins in the dark, suggesting that cell wall protein biosynthesis ceased during the night. The results show previously unrecognized temporal patterns in wood cell wall biosynthesis, suggest diurnal cycle as a possible cue in the regulation of carbon incorporation to wood, and establish a unique (13)C labeling method for the analysis of wood formation and secondary growth in trees.

@article{slane_profiling_2015,
	title = {Profiling of embryonic nuclear vs. cellular {RNA} in {Arabidopsis} thaliana},
	volume = {4},
	issn = {2213-5960},
	doi = {10.1016/j.gdata.2015.03.015},
	abstract = {In Arabidopsis, various cell type-specific whole-genome expression analyses have been conducted. However, the vast majority of these were performed with cellular RNA from root tissues or other easily accessible cell types [1]. Nuclear RNA was neglected for a long time as not being representative for transcriptomic studies. In recent years, however, there have been reports describing the validity of nuclear RNA for these types of studies [2,3]. Here we describe the generation, quality assessment and analysis of nuclear transcriptomic data from Arabidopsis embryos published by Slane et al. (2014) [4]. Comparison of nuclear with cellular gene expression demonstrated the usefulness of nuclear transcriptomics.},
	language = {eng},
	journal = {Genomics Data},
	author = {Slane, Daniel and Kong, Jixiang and Schmid, Markus and Jürgens, Gerd and Bayer, Martin},
	month = jun,
	year = {2015},
	pmid = {26484189},
	pmcid = {PMC4536148},
	keywords = {Arabidopsis thaliana, Gene expression, Microarray, Nuclear and cellular transcriptome, Pro-embryo and suspensor transcriptome},
	pages = {96--98},
}

In Arabidopsis, various cell type-specific whole-genome expression analyses have been conducted. However, the vast majority of these were performed with cellular RNA from root tissues or other easily accessible cell types [1]. Nuclear RNA was neglected for a long time as not being representative for transcriptomic studies. In recent years, however, there have been reports describing the validity of nuclear RNA for these types of studies [2,3]. Here we describe the generation, quality assessment and analysis of nuclear transcriptomic data from Arabidopsis embryos published by Slane et al. (2014) [4]. Comparison of nuclear with cellular gene expression demonstrated the usefulness of nuclear transcriptomics.

@article{lutz_modulation_2015,
	title = {Modulation of {Ambient} {Temperature}-{Dependent} {Flowering} in {Arabidopsis} thaliana by {Natural} {Variation} of {FLOWERING} {LOCUS} {M}},
	volume = {11},
	issn = {1553-7404},
	url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005588},
	doi = {10.1371/journal.pgen.1005588},
	abstract = {Plants integrate seasonal cues such as temperature and day length to optimally adjust their flowering time to the environment. Compared to the control of flowering before and after winter by the vernalization and day length pathways, mechanisms that delay or promote flowering during a transient cool or warm period, especially during spring, are less well understood. Due to global warming, understanding this ambient temperature pathway has gained increasing importance. In Arabidopsis thaliana, FLOWERING LOCUS M (FLM) is a critical flowering regulator of the ambient temperature pathway. FLM is alternatively spliced in a temperature-dependent manner and the two predominant splice variants, FLM-ß and FLM-δ, can repress and activate flowering in the genetic background of the A. thaliana reference accession Columbia-0. The relevance of this regulatory mechanism for the environmental adaptation across the entire range of the species is, however, unknown. Here, we identify insertion polymorphisms in the first intron of FLM as causative for accelerated flowering in many natural A. thaliana accessions, especially in cool (15°C) temperatures. We present evidence for a potential adaptive role of this structural variation and link it specifically to changes in the abundance of FLM-ß. Our results may allow predicting flowering in response to ambient temperatures in the Brassicaceae.},
	language = {en},
	number = {10},
	urldate = {2021-10-22},
	journal = {PLOS Genetics},
	author = {Lutz, Ulrich and Posé, David and Pfeifer, Matthias and Gundlach, Heidrun and Hagmann, Jörg and Wang, Congmao and Weigel, Detlef and Mayer, Klaus F. X. and Schmid, Markus and Schwechheimer, Claus},
	year = {2015},
	note = {Publisher: Public Library of Science},
	keywords = {Arabidopsis thaliana, Flowering plants, Gene expression, Genetic loci, Genomics, Introns, Plant genomics, Polymerase chain reaction},
	pages = {e1005588},
}

Plants integrate seasonal cues such as temperature and day length to optimally adjust their flowering time to the environment. Compared to the control of flowering before and after winter by the vernalization and day length pathways, mechanisms that delay or promote flowering during a transient cool or warm period, especially during spring, are less well understood. Due to global warming, understanding this ambient temperature pathway has gained increasing importance. In Arabidopsis thaliana, FLOWERING LOCUS M (FLM) is a critical flowering regulator of the ambient temperature pathway. FLM is alternatively spliced in a temperature-dependent manner and the two predominant splice variants, FLM-ß and FLM-δ, can repress and activate flowering in the genetic background of the A. thaliana reference accession Columbia-0. The relevance of this regulatory mechanism for the environmental adaptation across the entire range of the species is, however, unknown. Here, we identify insertion polymorphisms in the first intron of FLM as causative for accelerated flowering in many natural A. thaliana accessions, especially in cool (15°C) temperatures. We present evidence for a potential adaptive role of this structural variation and link it specifically to changes in the abundance of FLM-ß. Our results may allow predicting flowering in response to ambient temperatures in the Brassicaceae.

@article{eriksson_transgenic_2015,
	title = {Transgenic hybrid aspen trees with increased gibberellin ({GA}) concentrations suggest that {GA} acts in parallel with {FLOWERING} {LOCUS} {T2} to control shoot elongation},
	volume = {205},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.13144},
	doi = {10/f3nxc2},
	abstract = {Bioactive gibberellins (GAs) have been implicated in short day (SD)-induced growth cessation in Populus, because exogenous applications of bioactive GAs to hybrid aspens (Populus tremula × tremuloides) under SD conditions delay growth cessation. However, this effect diminishes with time, suggesting that plants may cease growth following exposure to SDs due to a reduction in sensitivity to GAs. In order to validate and further explore the role of GAs in growth cessation, we perturbed GA biosynthesis or signalling in hybrid aspen plants by overexpressing AtGA20ox1, AtGA2ox2 and PttGID1.3 (encoding GA biosynthesis enzymes and a GA receptor). We found trees with elevated concentrations of bioactive GA, due to overexpression of AtGA20ox1, continued to grow in SD conditions and were insensitive to the level of FLOWERING LOCUS T2 (FT2) expression. As transgenic plants overexpressing the PttGID1.3 GA receptor responded in a wild-type (WT) manner to SD conditions, this insensitivity did not result from limited receptor availability. As high concentrations of bioactive GA during SD conditions were sufficient to sustain shoot elongation growth in hybrid aspen trees, independent of FT2 expression levels, we conclude elongation growth in trees is regulated by both GA- and long day-responsive pathways, similar to the regulation of flowering in Arabidopsis thaliana.},
	language = {en},
	number = {3},
	urldate = {2021-08-31},
	journal = {New Phytologist},
	author = {Eriksson, Maria E. and Hoffman, Daniel and Kaduk, Mateusz and Mauriat, Mélanie and Moritz, Thomas},
	year = {2015},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.13144},
	keywords = {Flowering Locus T2 (FT2), Populus, gibberellins (GA), growth cessation, photoperiod},
	pages = {1288--1295},
}

Bioactive gibberellins (GAs) have been implicated in short day (SD)-induced growth cessation in Populus, because exogenous applications of bioactive GAs to hybrid aspens (Populus tremula × tremuloides) under SD conditions delay growth cessation. However, this effect diminishes with time, suggesting that plants may cease growth following exposure to SDs due to a reduction in sensitivity to GAs. In order to validate and further explore the role of GAs in growth cessation, we perturbed GA biosynthesis or signalling in hybrid aspen plants by overexpressing AtGA20ox1, AtGA2ox2 and PttGID1.3 (encoding GA biosynthesis enzymes and a GA receptor). We found trees with elevated concentrations of bioactive GA, due to overexpression of AtGA20ox1, continued to grow in SD conditions and were insensitive to the level of FLOWERING LOCUS T2 (FT2) expression. As transgenic plants overexpressing the PttGID1.3 GA receptor responded in a wild-type (WT) manner to SD conditions, this insensitivity did not result from limited receptor availability. As high concentrations of bioactive GA during SD conditions were sufficient to sustain shoot elongation growth in hybrid aspen trees, independent of FT2 expression levels, we conclude elongation growth in trees is regulated by both GA- and long day-responsive pathways, similar to the regulation of flowering in Arabidopsis thaliana.

@article{eklund_auxin_2015,
	title = {Auxin {Produced} by the {Indole}-3-{Pyruvic} {Acid} {Pathway} {Regulates} {Development} and {Gemmae} {Dormancy} in the {Liverwort} {Marchantia} polymorpha},
	volume = {27},
	issn = {1532-298X (Electronic) 1040-4651 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26036256},
	doi = {10.1105/tpc.15.00065},
	abstract = {The plant hormone auxin (indole-3-acetic acid [IAA]) has previously been suggested to regulate diverse forms of dormancy in both seed plants and liverworts. Here, we use loss- and gain-of-function alleles for auxin synthesis- and signaling-related genes, as well as pharmacological approaches, to study how auxin regulates development and dormancy in the gametophyte generation of the liverwort Marchantia polymorpha. We found that M. polymorpha possess the smallest known toolkit for the indole-3-pyruvic acid (IPyA) pathway in any land plant and that this auxin synthesis pathway mainly is active in meristematic regions of the thallus. Previously a Trp-independent auxin synthesis pathway has been suggested to produce a majority of IAA in bryophytes. Our results indicate that the Trp-dependent IPyA pathway produces IAA that is essential for proper development of the gametophyte thallus of M. polymorpha. Furthermore, we show that dormancy of gemmae is positively regulated by auxin synthesized by the IPyA pathway in the apex of the thallus. Our results indicate that auxin synthesis, transport, and signaling, in addition to its role in growth and development, have a critical role in regulation of gemmae dormancy in M. polymorpha.},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Plant Cell},
	author = {Eklund, D. M. and Ishizaki, K. and Flores-Sandoval, E. and Kikuchi, S. and Takebayashi, Y. and Tsukamoto, S. and Hirakawa, Y. and Nonomura, M. and Kato, H. and Kouno, M. and Bhalerao, Rishikesh P. and Lagercrantz, U. and Kasahara, H. and Kohchi, T. and Bowman, J. L.},
	month = jun,
	year = {2015},
	note = {Edition: 2015/06/04},
	keywords = {Indoleacetic Acids/*metabolism, Indoles/metabolism, Marchantia/*growth \& development/physiology, Plant Components, Aerial/*growth \& development, Plant Dormancy/*physiology, Plant Growth Regulators/metabolism/*physiology},
	pages = {1650--69},
}

The plant hormone auxin (indole-3-acetic acid [IAA]) has previously been suggested to regulate diverse forms of dormancy in both seed plants and liverworts. Here, we use loss- and gain-of-function alleles for auxin synthesis- and signaling-related genes, as well as pharmacological approaches, to study how auxin regulates development and dormancy in the gametophyte generation of the liverwort Marchantia polymorpha. We found that M. polymorpha possess the smallest known toolkit for the indole-3-pyruvic acid (IPyA) pathway in any land plant and that this auxin synthesis pathway mainly is active in meristematic regions of the thallus. Previously a Trp-independent auxin synthesis pathway has been suggested to produce a majority of IAA in bryophytes. Our results indicate that the Trp-dependent IPyA pathway produces IAA that is essential for proper development of the gametophyte thallus of M. polymorpha. Furthermore, we show that dormancy of gemmae is positively regulated by auxin synthesized by the IPyA pathway in the apex of the thallus. Our results indicate that auxin synthesis, transport, and signaling, in addition to its role in growth and development, have a critical role in regulation of gemmae dormancy in M. polymorpha.

@article{grimberg_transcriptional_2015,
	title = {Transcriptional transitions in {Nicotiana} benthamiana leaves upon induction of oil synthesis by {WRINKLED1} homologs from diverse species and tissues},
	volume = {15},
	issn = {1471-2229 (Electronic) 1471-2229 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26253704},
	doi = {10.1186/s12870-015-0579-1},
	abstract = {BACKGROUND: Carbon accumulation and remobilization are essential mechanisms in plants to ensure energy transfer between plant tissues with different functions or metabolic needs and to support new generations. Knowledge about the regulation of carbon allocation into oil (triacylglycerol) in plant storage tissue can be of great economic and environmental importance for developing new high-yielding oil crops. Here, the effect on global gene expression as well as on physiological changes in leaves transiently expressing five homologs of the transcription factor WRINKLED1 (WRI1) originating from diverse species and tissues; Arabidopsis thaliana and potato (Solanum tuberosum) seed embryo, poplar (Populus trichocarpa) stem cambium, oat (Avena sativa) grain endosperm, and nutsedge (Cyperus esculentus) tuber parenchyma, were studied by agroinfiltration in Nicotiana benthamiana. RESULTS: All WRI1 homologs induced oil accumulation when expressed in leaf tissue. Transcriptome sequencing revealed that all homologs induced the same general patterns with a drastic shift in gene expression profiles of leaves from that of a typical source tissue to a source-limited sink-like tissue: Transcripts encoding enzymes for plastid uptake and metabolism of phosphoenolpyruvate, fatty acid and oil biosynthesis were up-regulated, as were also transcripts encoding starch degradation. Transcripts encoding enzymes in photosynthesis and starch synthesis were instead down-regulated. Moreover, transcripts representing fatty acid degradation were up-regulated indicating that fatty acids might be degraded to feed the increased need to channel carbons into fatty acid synthesis creating a futile cycle. RT-qPCR analysis of leaves expressing Arabidopsis WRI1 showed the temporal trends of transcripts selected as 'markers' for key metabolic pathways one to five days after agroinfiltration. Chlorophyll fluorescence measurements of leaves expressing Arabidopsis WRI1 showed a significant decrease in photosynthesis, even though effect on starch content could not be observed. CONCLUSIONS: This data gives for the first time a general view on the transcriptional transitions in leaf tissue upon induction of oil synthesis by WRI1. This yields important information about what effects WRI1 may exert on global gene expression during seed and embryo development. The results suggest why high oil content in leaf tissue cannot be achieved by solely transcriptional activation by WRI1, which can be essential knowledge in the development of new high-yielding oil crops.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Plant Biol},
	author = {Grimberg, A. and Carlsson, A. S. and Marttila, S. and Bhalerao, Rishikesh P. and Hofvander, P.},
	month = aug,
	year = {2015},
	note = {Edition: 2015/08/09},
	keywords = {*Gene Expression Regulation, Plant, Arabidopsis Proteins/*genetics/metabolism, Avena/genetics/metabolism, Carbohydrate Metabolism, Cyperus/genetics/metabolism, Plant Leaves/genetics/metabolism, Plants, Genetically Modified/genetics/metabolism, Populus/genetics/metabolism, Real-Time Polymerase Chain Reaction, Solanum tuberosum/genetics/metabolism, Tobacco/*genetics/metabolism, Transcription Factors/*genetics/metabolism},
	pages = {192},
}

BACKGROUND: Carbon accumulation and remobilization are essential mechanisms in plants to ensure energy transfer between plant tissues with different functions or metabolic needs and to support new generations. Knowledge about the regulation of carbon allocation into oil (triacylglycerol) in plant storage tissue can be of great economic and environmental importance for developing new high-yielding oil crops. Here, the effect on global gene expression as well as on physiological changes in leaves transiently expressing five homologs of the transcription factor WRINKLED1 (WRI1) originating from diverse species and tissues; Arabidopsis thaliana and potato (Solanum tuberosum) seed embryo, poplar (Populus trichocarpa) stem cambium, oat (Avena sativa) grain endosperm, and nutsedge (Cyperus esculentus) tuber parenchyma, were studied by agroinfiltration in Nicotiana benthamiana. RESULTS: All WRI1 homologs induced oil accumulation when expressed in leaf tissue. Transcriptome sequencing revealed that all homologs induced the same general patterns with a drastic shift in gene expression profiles of leaves from that of a typical source tissue to a source-limited sink-like tissue: Transcripts encoding enzymes for plastid uptake and metabolism of phosphoenolpyruvate, fatty acid and oil biosynthesis were up-regulated, as were also transcripts encoding starch degradation. Transcripts encoding enzymes in photosynthesis and starch synthesis were instead down-regulated. Moreover, transcripts representing fatty acid degradation were up-regulated indicating that fatty acids might be degraded to feed the increased need to channel carbons into fatty acid synthesis creating a futile cycle. RT-qPCR analysis of leaves expressing Arabidopsis WRI1 showed the temporal trends of transcripts selected as 'markers' for key metabolic pathways one to five days after agroinfiltration. Chlorophyll fluorescence measurements of leaves expressing Arabidopsis WRI1 showed a significant decrease in photosynthesis, even though effect on starch content could not be observed. CONCLUSIONS: This data gives for the first time a general view on the transcriptional transitions in leaf tissue upon induction of oil synthesis by WRI1. This yields important information about what effects WRI1 may exert on global gene expression during seed and embryo development. The results suggest why high oil content in leaf tissue cannot be achieved by solely transcriptional activation by WRI1, which can be essential knowledge in the development of new high-yielding oil crops.

@article{marin-de_la_rosa_genome_2015,
	title = {Genome {Wide} {Binding} {Site} {Analysis} {Reveals} {Transcriptional} {Coactivation} of {Cytokinin}-{Responsive} {Genes} by {DELLA} {Proteins}},
	volume = {11},
	issn = {1553-7404 (Electronic) 1553-7390 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26134422},
	doi = {10.1371/journal.pgen.1005337},
	abstract = {The ability of plants to provide a plastic response to environmental cues relies on the connectivity between signaling pathways. DELLA proteins act as hubs that relay environmental information to the multiple transcriptional circuits that control growth and development through physical interaction with transcription factors from different families. We have analyzed the presence of one DELLA protein at the Arabidopsis genome by chromatin immunoprecipitation coupled to large-scale sequencing and we find that it binds at the promoters of multiple genes. Enrichment analysis shows a strong preference for cis elements recognized by specific transcription factor families. In particular, we demonstrate that DELLA proteins are recruited by type-B ARABIDOPSIS RESPONSE REGULATORS (ARR) to the promoters of cytokinin-regulated genes, where they act as transcriptional co-activators. The biological relevance of this mechanism is underpinned by the necessity of simultaneous presence of DELLAs and ARRs to restrict root meristem growth and to promote photomorphogenesis.},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {PLoS Genet},
	author = {Marin-de la Rosa, N. and Pfeiffer, A. and Hill, K. and Locascio, A. and Bhalerao, Rishikesh P. and Miskolczi, P. and Gronlund, A. L. and Wanchoo-Kohli, A. and Thomas, S. G. and Bennett, M. J. and Lohmann, J. U. and Blazquez, M. A. and Alabadi, D.},
	month = jul,
	year = {2015},
	note = {Edition: 2015/07/03},
	keywords = {Arabidopsis Proteins/genetics/*metabolism, Arabidopsis/*embryology, Base Sequence, Binding Sites/genetics, Chromatin Immunoprecipitation, Cytokinins/*metabolism, DNA, Plant/genetics, DNA-Binding Proteins/*metabolism, Gene Expression Regulation, Plant, Plant Development/physiology, Plant Roots/growth \& development, Promoter Regions, Genetic/genetics, Repressor Proteins/genetics/metabolism, Sequence Analysis, DNA, Signal Transduction, Transcription Factors/*metabolism, Transcriptional Activation/*genetics},
	pages = {e1005337},
}

The ability of plants to provide a plastic response to environmental cues relies on the connectivity between signaling pathways. DELLA proteins act as hubs that relay environmental information to the multiple transcriptional circuits that control growth and development through physical interaction with transcription factors from different families. We have analyzed the presence of one DELLA protein at the Arabidopsis genome by chromatin immunoprecipitation coupled to large-scale sequencing and we find that it binds at the promoters of multiple genes. Enrichment analysis shows a strong preference for cis elements recognized by specific transcription factor families. In particular, we demonstrate that DELLA proteins are recruited by type-B ARABIDOPSIS RESPONSE REGULATORS (ARR) to the promoters of cytokinin-regulated genes, where they act as transcriptional co-activators. The biological relevance of this mechanism is underpinned by the necessity of simultaneous presence of DELLAs and ARRs to restrict root meristem growth and to promote photomorphogenesis.

@article{randall_aintegumenta_2015,
	title = {{AINTEGUMENTA} and the {D}-type cyclin {CYCD3};1 regulate root secondary growth and respond to cytokinins},
	volume = {4},
	issn = {2046-6390 (Print) 2046-6390 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26340943},
	doi = {10.1242/bio.013128},
	abstract = {Higher plant vasculature is characterized by two distinct developmental phases. Initially, a well-defined radial primary pattern is established. In eudicots, this is followed by secondary growth, which involves development of the cambium and is required for efficient water and nutrient transport and wood formation. Regulation of secondary growth involves several phytohormones, and cytokinins have been implicated as key players, particularly in the activation of cell proliferation, but the molecular mechanisms mediating this hormonal control remain unknown. Here we show that the genes encoding the transcription factor AINTEGUMENTA (ANT) and the D-type cyclin CYCD3;1 are expressed in the vascular cambium of Arabidopsis roots, respond to cytokinins and are both required for proper root secondary thickening. Cytokinin regulation of ANT and CYCD3 also occurs during secondary thickening of poplar stems, suggesting this represents a conserved regulatory mechanism.},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Biol Open},
	author = {Randall, R. S. and Miyashima, S. and Blomster, T. and Zhang, J. and Elo, A. and Karlberg, A. and Immanen, J. and Nieminen, K. and Lee, J. Y. and Kakimoto, T. and Blajecka, K. and Melnyk, C. W. and Alcasabas, A. and Forzani, C. and Matsumoto-Kitano, M. and Mahonen, A. P. and Bhalerao, Rishikesh P. and Dewitte, W. and Helariutta, Y. and Murray, J. A.},
	month = sep,
	year = {2015},
	note = {Edition: 2015/09/06},
	keywords = {Aintegumenta, Cyclin D, Cytokinins, Root development, Secondary growth},
	pages = {1229--36},
}

Higher plant vasculature is characterized by two distinct developmental phases. Initially, a well-defined radial primary pattern is established. In eudicots, this is followed by secondary growth, which involves development of the cambium and is required for efficient water and nutrient transport and wood formation. Regulation of secondary growth involves several phytohormones, and cytokinins have been implicated as key players, particularly in the activation of cell proliferation, but the molecular mechanisms mediating this hormonal control remain unknown. Here we show that the genes encoding the transcription factor AINTEGUMENTA (ANT) and the D-type cyclin CYCD3;1 are expressed in the vascular cambium of Arabidopsis roots, respond to cytokinins and are both required for proper root secondary thickening. Cytokinin regulation of ANT and CYCD3 also occurs during secondary thickening of poplar stems, suggesting this represents a conserved regulatory mechanism.

@article{tylewicz_dual_2015,
	title = {Dual role of tree florigen activation complex component {FD} in photoperiodic growth control and adaptive response pathways},
	volume = {112},
	issn = {1091-6490 (Electronic) 0027-8424 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25713384},
	doi = {10.1073/pnas.1423440112},
	abstract = {A complex consisting of evolutionarily conserved FD, flowering locus T (FT) proteins is a regulator of floral transition. Intriguingly, FT orthologs are also implicated in developmental transitions distinct from flowering, such as photoperiodic control of bulbing in onions, potato tuberization, and growth cessation in trees. However, whether an FT-FD complex participates in these transitions and, if so, its mode of action, are unknown. We identified two closely related FD homologs, FD-like 1 (FDL1) and FD-like 2 (FDL2), in the model tree hybrid aspen. Using gain of function and RNAi-suppressed FDL1 and FDL2 transgenic plants, we show that FDL1 and FDL2 have distinct functions and a complex consisting of FT and FDL1 mediates in photoperiodic control of seasonal growth. The downstream target of the FT-FD complex in photoperiodic control of growth is Like AP1 (LAP1), a tree ortholog of the floral meristem identity gene APETALA1. Intriguingly, FDL1 also participates in the transcriptional control of adaptive response and bud maturation pathways, independent of its interaction with FT, presumably via interaction with abscisic acid insensitive 3 (ABI3) transcription factor, a component of abscisic acid (ABA) signaling. Our data reveal that in contrast to its primary role in flowering, FD has dual roles in the photoperiodic control of seasonal growth and stress tolerance in trees. Thus, the functions of FT and FD have diversified during evolution, and FD homologs have acquired roles that are independent of their interaction with FT.},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Proc Natl Acad Sci U S A},
	author = {Tylewicz, S. and Tsuji, H. and Miskolczi, P. and Petterle, A. and Azeez, A. and Jonsson, K. and Shimamoto, K. and Bhalerao, Rishikesh P.},
	month = mar,
	year = {2015},
	note = {Edition: 2015/02/26},
	keywords = {*Adaptation, Physiological, *Photoperiod, Florigen/*metabolism, Trees/growth \& development/*physiology, adaptive response, bud set, growth cessation, hybrid aspen, seasonal growth},
	pages = {3140--5},
}

A complex consisting of evolutionarily conserved FD, flowering locus T (FT) proteins is a regulator of floral transition. Intriguingly, FT orthologs are also implicated in developmental transitions distinct from flowering, such as photoperiodic control of bulbing in onions, potato tuberization, and growth cessation in trees. However, whether an FT-FD complex participates in these transitions and, if so, its mode of action, are unknown. We identified two closely related FD homologs, FD-like 1 (FDL1) and FD-like 2 (FDL2), in the model tree hybrid aspen. Using gain of function and RNAi-suppressed FDL1 and FDL2 transgenic plants, we show that FDL1 and FDL2 have distinct functions and a complex consisting of FT and FDL1 mediates in photoperiodic control of seasonal growth. The downstream target of the FT-FD complex in photoperiodic control of growth is Like AP1 (LAP1), a tree ortholog of the floral meristem identity gene APETALA1. Intriguingly, FDL1 also participates in the transcriptional control of adaptive response and bud maturation pathways, independent of its interaction with FT, presumably via interaction with abscisic acid insensitive 3 (ABI3) transcription factor, a component of abscisic acid (ABA) signaling. Our data reveal that in contrast to its primary role in flowering, FD has dual roles in the photoperiodic control of seasonal growth and stress tolerance in trees. Thus, the functions of FT and FD have diversified during evolution, and FD homologs have acquired roles that are independent of their interaction with FT.

@article{pietra_sabre_2015,
	title = {{SABRE} is required for stabilization of root hair patterning in {Arabidopsis} thaliana},
	volume = {153},
	copyright = {© 2014 The Authors. Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.12257},
	doi = {10/f3nj53},
	abstract = {Patterned differentiation of distinct cell types is essential for the development of multicellular organisms. The root epidermis of Arabidopsis thaliana is composed of alternating files of root hair and non-hair cells and represents a model system for studying the control of cell-fate acquisition. Epidermal cell fate is regulated by a network of genes that translate positional information from the underlying cortical cell layer into a specific pattern of differentiated cells. While much is known about the genes of this network, new players continue to be discovered. Here we show that the SABRE (SAB) gene, known to mediate microtubule organization, anisotropic cell growth and planar polarity, has an effect on root epidermal hair cell patterning. Loss of SAB function results in ectopic root hair formation and destabilizes the expression of cell fate and differentiation markers in the root epidermis, including expression of the WEREWOLF (WER) and GLABRA2 (GL2) genes. Double mutant analysis reveal that wer and caprice (cpc) mutants, defective in core components of the epidermal patterning pathway, genetically interact with sab. This suggests that SAB may act on epidermal patterning upstream of WER and CPC. Hence, we provide evidence for a role of SAB in root epidermal patterning by affecting cell-fate stabilization. Our work opens the door for future studies addressing SAB-dependent functions of the cytoskeleton during root epidermal patterning.},
	language = {en},
	number = {3},
	urldate = {2021-06-21},
	journal = {Physiologia Plantarum},
	author = {Pietra, Stefano and Lang, Patricia and Grebe, Markus},
	year = {2015},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.12257},
	pages = {440--453},
}

Patterned differentiation of distinct cell types is essential for the development of multicellular organisms. The root epidermis of Arabidopsis thaliana is composed of alternating files of root hair and non-hair cells and represents a model system for studying the control of cell-fate acquisition. Epidermal cell fate is regulated by a network of genes that translate positional information from the underlying cortical cell layer into a specific pattern of differentiated cells. While much is known about the genes of this network, new players continue to be discovered. Here we show that the SABRE (SAB) gene, known to mediate microtubule organization, anisotropic cell growth and planar polarity, has an effect on root epidermal hair cell patterning. Loss of SAB function results in ectopic root hair formation and destabilizes the expression of cell fate and differentiation markers in the root epidermis, including expression of the WEREWOLF (WER) and GLABRA2 (GL2) genes. Double mutant analysis reveal that wer and caprice (cpc) mutants, defective in core components of the epidermal patterning pathway, genetically interact with sab. This suggests that SAB may act on epidermal patterning upstream of WER and CPC. Hence, we provide evidence for a role of SAB in root epidermal patterning by affecting cell-fate stabilization. Our work opens the door for future studies addressing SAB-dependent functions of the cytoskeleton during root epidermal patterning.

@article{wrzaczek_grim_2015,
	title = {{GRIM} {REAPER} peptide binds to receptor kinase {PRK5} to trigger cell death in {Arabidopsis}},
	volume = {34},
	issn = {0261-4189},
	url = {https://www.embopress.org/doi/full/10.15252/embj.201488582},
	doi = {10/f2wbpv},
	abstract = {Abstract Recognition of extracellular peptides by plasma membrane-localized receptor proteins is commonly used in signal transduction. In plants, very little is known about how extracellular peptides are processed and activated in order to allow recognition by receptors. Here, we show that induction of cell death in planta by a secreted plant protein GRIM REAPER (GRI) is dependent on the activity of the type II metacaspase METACASPASE-9. GRI is cleaved by METACASPASE-9 in vitro resulting in the release of an 11 amino acid peptide. This peptide bound in vivo to the extracellular domain of the plasma membrane-localized, atypical leucine-rich repeat receptor-like kinase POLLEN-SPECIFIC RECEPTOR-LIKE KINASE 5 (PRK5) and was sufficient to induce oxidative stress/ROS-dependent cell death. This shows a signaling pathway in plants from processing and activation of an extracellular protein to recognition by its receptor.},
	number = {1},
	urldate = {2021-06-21},
	journal = {The EMBO Journal},
	author = {Wrzaczek, Michael and Vainonen, Julia P and Stael, Simon and Tsiatsiani, Liana and Help-Rinta-Rahko, Hanna and Gauthier, Adrien and Kaufholdt, David and Bollhöner, Benjamin and Lamminmäki, Airi and Staes, An and Gevaert, Kris and Tuominen, Hannele and Van Breusegem, Frank and Helariutta, Ykä and Kangasjärvi, Jaakko},
	month = jan,
	year = {2015},
	note = {Publisher: John Wiley \& Sons, Ltd},
	keywords = {ligand, protease, receptor-like kinase, secreted protein},
	pages = {55--66},
}

Abstract Recognition of extracellular peptides by plasma membrane-localized receptor proteins is commonly used in signal transduction. In plants, very little is known about how extracellular peptides are processed and activated in order to allow recognition by receptors. Here, we show that induction of cell death in planta by a secreted plant protein GRIM REAPER (GRI) is dependent on the activity of the type II metacaspase METACASPASE-9. GRI is cleaved by METACASPASE-9 in vitro resulting in the release of an 11 amino acid peptide. This peptide bound in vivo to the extracellular domain of the plasma membrane-localized, atypical leucine-rich repeat receptor-like kinase POLLEN-SPECIFIC RECEPTOR-LIKE KINASE 5 (PRK5) and was sufficient to induce oxidative stress/ROS-dependent cell death. This shows a signaling pathway in plants from processing and activation of an extracellular protein to recognition by its receptor.

@article{menard_cellular_2015,
	title = {Cellular interactions during tracheary elements formation and function},
	volume = {23},
	issn = {13695266},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526614001721},
	doi = {10/f3nvfn},
	language = {en},
	urldate = {2021-06-08},
	journal = {Current Opinion in Plant Biology},
	author = {Ménard, Delphine and Pesquet, Edouard},
	month = feb,
	year = {2015},
	pages = {109--115},
}

@article{mellor_modelling_2015,
	title = {Modelling of {Arabidopsis} {LAX3} expression suggests auxin homeostasis},
	volume = {366},
	issn = {00225193},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0022519314006353},
	doi = {10/f3pwnp},
	language = {en},
	urldate = {2021-06-08},
	journal = {Journal of Theoretical Biology},
	author = {Mellor, Nathan and Péret, Benjamin and Porco, Silvana and Sairanen, Ilkka and Ljung, Karin and Bennett, Malcolm and King, John},
	month = feb,
	year = {2015},
	pages = {57--70},
}

@article{du_identification_2015,
	title = {Identification of additive, dominant, and epistatic variation conferred by key genes in cellulose biosynthesis pathway in {Populus} tomentosa},
	volume = {22},
	issn = {1340-2838, 1756-1663},
	url = {https://academic.oup.com/dnaresearch/article-lookup/doi/10.1093/dnares/dsu040},
	doi = {10/f3mv7g},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {DNA Research},
	author = {Du, Q. and Tian, J. and Yang, X. and Pan, W. and Xu, B. and Li, B. and Ingvarsson, P. K. and Zhang, D.},
	month = feb,
	year = {2015},
	pages = {53--67},
}

@incollection{estevez_live_2015,
	address = {New York, NY},
	title = {Live {Cell} {Imaging} of {FM4}-64, a {Tool} for {Tracing} the {Endocytic} {Pathways} in {Arabidopsis} {Root} {Cells}},
	volume = {1242},
	isbn = {978-1-4939-1901-7 978-1-4939-1902-4},
	url = {http://link.springer.com/10.1007/978-1-4939-1902-4_9},
	urldate = {2021-06-08},
	booktitle = {Plant {Cell} {Expansion}},
	publisher = {Springer New York},
	author = {Rigal, Adeline and Doyle, Siamsa M. and Robert, Stéphanie},
	editor = {Estevez, José M.},
	year = {2015},
	doi = {10.1007/978-1-4939-1902-4_9},
	note = {Series Title: Methods in Molecular Biology},
	pages = {93--103},
}

@article{shaikhali_gip1_2015,
	title = {{GIP1} protein is a novel cofactor that regulates {DNA}-binding affinity of redox-regulated members of {bZIP} transcription factors involved in the early stages of {Arabidopsis} development},
	volume = {252},
	issn = {0033-183X, 1615-6102},
	url = {http://link.springer.com/10.1007/s00709-014-0726-9},
	doi = {10/f3pk93},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Protoplasma},
	author = {Shaikhali, Jehad},
	month = may,
	year = {2015},
	pages = {867--883},
}

@article{curtu_fine-scale_2015,
	title = {Fine-scale spatial genetic structure in a multi-oak-species ({Quercus} spp.) forest},
	volume = {8},
	copyright = {(c) SISEF 2015 - The Italian Society of Silviculture and Forest Ecology},
	issn = {1971-7458},
	url = {https://iforest.sisef.org/contents/?id=ifor1150-007},
	doi = {10/gkgdgq},
	abstract = {iForest - Biogeosciences and Forestry, vol. 8, pp. 324-332 (2015)},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {iForest - Biogeosciences and Forestry},
	author = {Curtu, A. L. and Craciunesc, I. and Enescu, C. M. and Vidalis, A. and Sofletea, N.},
	year = {2015},
	pmid = {ifor1150-007},
	note = {Publisher: SISEF - Italian Society of Silviculture and Forest Ecology},
	pages = {324},
}

iForest - Biogeosciences and Forestry, vol. 8, pp. 324-332 (2015)

@article{derbamaceluch_suppression_2015,
	title = {Suppression of xylan endotransglycosylase \textit{{PtxtXyn10A}} affects cellulose microfibril angle in secondary wall in aspen wood},
	volume = {205},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.13099},
	doi = {10/f3n8td},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Derba‐Maceluch, Marta and Awano, Tatsuya and Takahashi, Junko and Lucenius, Jessica and Ratke, Christine and Kontro, Inkeri and Busse‐Wicher, Marta and Kosik, Ondrej and Tanaka, Ryo and Winzéll, Anders and Kallas, Åsa and Leśniewska, Joanna and Berthold, Fredrik and Immerzeel, Peter and Teeri, Tuula T. and Ezcurra, Ines and Dupree, Paul and Serimaa, Ritva and Mellerowicz, Ewa J.},
	month = jan,
	year = {2015},
	pages = {666--681},
}

@article{gendre_journey_2015,
	title = {Journey to the cell surface—the central role of the trans-{Golgi} network in plants},
	volume = {252},
	issn = {0033-183X, 1615-6102},
	url = {http://link.springer.com/10.1007/s00709-014-0693-1},
	doi = {10/f3rqn7},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Protoplasma},
	author = {Gendre, Delphine and Jonsson, Kristoffer and Boutté, Yohann and Bhalerao, Rishikesh P.},
	month = mar,
	year = {2015},
	pages = {385--398},
}

@incollection{clark_biomassbased_2015,
	edition = {1},
	title = {Biomass‐{Based} {Energy} {Production}},
	isbn = {978-1-118-71448-5 978-1-118-71447-8},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9781118714478.ch7},
	abstract = {Today, bioenergy is a practical and increasingly widely available option for heating that is being adopted by many industries and households that are looking to use more sustainable energy sources. Biomass-derived fuels may be solids, liquids, or gases. They can be classified based on the processes used in their production, which include physical upgrading, microbiological processes, thermochemical processes, and chemical processes. The production of solid fuels from renewable resources has become more important due to the growing global demand for energy and environmental concerns. Various microbial processes can be exploited to utilize energy that has been stored in biomass by photosynthesis. Methanol, ethanol, and butanol are liquid biofuels that can be synthesized from biomass and used in both four-stroke gasoline and diesel engines. These alcohols can be prepared from sugarcane, sugar beet, wheat, barley, corn, switch grass, agricultural residues, wood, and many other industrial wastes},
	language = {en},
	urldate = {2021-06-07},
	booktitle = {Introduction to {Chemicals} from {Biomass}},
	publisher = {Wiley},
	author = {Arshadi, Mehrdad and Sellstedt, Anita},
	editor = {Clark, James and Deswarte, Fabien},
	month = feb,
	year = {2015},
	doi = {10.1002/9781118714478.ch7},
	pages = {249--284},
}

Today, bioenergy is a practical and increasingly widely available option for heating that is being adopted by many industries and households that are looking to use more sustainable energy sources. Biomass-derived fuels may be solids, liquids, or gases. They can be classified based on the processes used in their production, which include physical upgrading, microbiological processes, thermochemical processes, and chemical processes. The production of solid fuels from renewable resources has become more important due to the growing global demand for energy and environmental concerns. Various microbial processes can be exploited to utilize energy that has been stored in biomass by photosynthesis. Methanol, ethanol, and butanol are liquid biofuels that can be synthesized from biomass and used in both four-stroke gasoline and diesel engines. These alcohols can be prepared from sugarcane, sugar beet, wheat, barley, corn, switch grass, agricultural residues, wood, and many other industrial wastes

@article{doyle_small_2015,
	title = {Small molecules unravel complex interplay between auxin biology and endomembrane trafficking},
	volume = {66},
	issn = {1460-2431 (Electronic) 0022-0957 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25911743},
	doi = {10/f3p4ct},
	abstract = {The establishment and maintenance of controlled auxin gradients within plant tissues are essential for a multitude of developmental processes. Auxin gradient formation is co-ordinated via local biosynthesis and transport. Cell to cell auxin transport is facilitated and precisely regulated by complex endomembrane trafficking mechanisms that target auxin carrier proteins to their final destinations. In turn, auxin and cross-talk with other phytohormones regulate the endomembrane trafficking of auxin carriers. Dissecting such rapid and complicated processes is challenging for classical genetic experiments due to trafficking pathway diversity, gene functional redundancy, and lethality in loss-of-function mutants. Many of these difficulties can be bypassed via the use of small molecules to modify or disrupt the function or localization of proteins. Here, we will review examples of the knowledge acquired by the use of such chemical tools in this field, outlining the advantages afforded by chemical biology approaches.},
	language = {en},
	number = {16},
	urldate = {2021-06-07},
	journal = {J Exp Bot},
	author = {Doyle, S. M. and Vain, T. and Robert, S.},
	month = aug,
	year = {2015},
	note = {Edition: 2015/04/26},
	keywords = {*Signal Transduction, Auxin carriers, Carrier Proteins/*metabolism, Indoleacetic Acids/*metabolism, Plant Growth Regulators/*metabolism, Plant Proteins/*metabolism, Protein Transport, auxin gradients, auxin transport, chemical biology, endomembrane trafficking, phytohormones.},
	pages = {4971--82},
}

The establishment and maintenance of controlled auxin gradients within plant tissues are essential for a multitude of developmental processes. Auxin gradient formation is co-ordinated via local biosynthesis and transport. Cell to cell auxin transport is facilitated and precisely regulated by complex endomembrane trafficking mechanisms that target auxin carrier proteins to their final destinations. In turn, auxin and cross-talk with other phytohormones regulate the endomembrane trafficking of auxin carriers. Dissecting such rapid and complicated processes is challenging for classical genetic experiments due to trafficking pathway diversity, gene functional redundancy, and lethality in loss-of-function mutants. Many of these difficulties can be bypassed via the use of small molecules to modify or disrupt the function or localization of proteins. Here, we will review examples of the knowledge acquired by the use of such chemical tools in this field, outlining the advantages afforded by chemical biology approaches.

@article{delhomme_serendipitous_2015,
	title = {Serendipitous {Meta}-{Transcriptomics}: {The} {Fungal} {Community} of {Norway} {Spruce} ({Picea} abies)},
	volume = {10},
	issn = {1932-6203 (Electronic) 1932-6203 (Linking)},
	shorttitle = {Serendipitous {Meta}-{Transcriptomics}},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26413905},
	doi = {10/f3m8d5},
	abstract = {After performing de novo transcript assembly of {\textgreater}1 billion RNA-Sequencing reads obtained from 22 samples of different Norway spruce (Picea abies) tissues that were not surface sterilized, we found that assembled sequences captured a mix of plant, lichen, and fungal transcripts. The latter were likely expressed by endophytic and epiphytic symbionts, indicating that these organisms were present, alive, and metabolically active. Here, we show that these serendipitously sequenced transcripts need not be considered merely as contamination, as is common, but that they provide insight into the plant's phyllosphere. Notably, we could classify these transcripts as originating predominantly from Dothideomycetes and Leotiomycetes species, with functional annotation of gene families indicating active growth and metabolism, with particular regards to glucose intake and processing, as well as gene regulation.},
	language = {en},
	number = {9},
	urldate = {2021-06-07},
	journal = {PLoS One},
	author = {Delhomme, N. and Sundstrom, G. and Zamani, N. and Lantz, H. and Lin, Y. C. and Hvidsten, T. R. and Hoppner, M. P. and Jern, P. and Van de Peer, Y. and Lundeberg, J. and Grabherr, M. G. and Street, N. R.},
	month = sep,
	year = {2015},
	note = {Edition: 2015/09/29},
	keywords = {Base Composition/genetics, Fungi/*genetics, Gene Expression Regulation, Fungal, Gene Expression Regulation, Plant, Picea/*genetics/*microbiology, RNA, Messenger/genetics/metabolism, Transcriptome/*genetics},
	pages = {e0139080},
}

After performing de novo transcript assembly of \textgreater1 billion RNA-Sequencing reads obtained from 22 samples of different Norway spruce (Picea abies) tissues that were not surface sterilized, we found that assembled sequences captured a mix of plant, lichen, and fungal transcripts. The latter were likely expressed by endophytic and epiphytic symbionts, indicating that these organisms were present, alive, and metabolically active. Here, we show that these serendipitously sequenced transcripts need not be considered merely as contamination, as is common, but that they provide insight into the plant's phyllosphere. Notably, we could classify these transcripts as originating predominantly from Dothideomycetes and Leotiomycetes species, with functional annotation of gene families indicating active growth and metabolism, with particular regards to glucose intake and processing, as well as gene regulation.

@article{martinez-bello_silencing_2015,
	title = {Silencing {C19}-{GA} 2-oxidases induces parthenocarpic development and inhibits lateral branching in tomato plants},
	volume = {66},
	issn = {1460-2431 (Electronic) 0022-0957 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26093022},
	doi = {10/f3p6nj},
	abstract = {Gibberellins (GAs) are phytohormones that regulate a wide range of developmental processes in plants. Levels of active GAs are regulated by biosynthetic and catabolic enzymes like the GA 2-oxidases (GA2oxs). In tomato (Solanum lycopersicum L.) C19 GA2oxs are encoded by a small multigenic family of five members with some degree of redundancy. In order to investigate their roles in tomato, the silencing of all five genes in transgenic plants was induced. A significant increase in active GA4 content was found in the ovaries of transgenic plants. In addition, the transgenic unfertilized ovaries were much bigger than wild-type ovaries (about 30 times) and a certain proportion (5-37\%) were able to develop parthenocarpically. Among the GA2ox family, genes GA2ox1 and -2 seem to be the most relevant for this phenotype since their expression was induced in unfertilized ovaries and repressed in developing fruits, inversely correlating with ovary growth. Interestingly, transgenic lines exhibited a significant inhibition of branching and a higher content of active GA4 in axillary buds. This phenotype was reverted, in transgenic plants, by the application of paclobutrazol, a GA biosynthesis inhibitor, suggesting a role for GAs as repressors of branching. In summary, this work demonstrates that GA 2-oxidases regulate gibberellin levels in ovaries and axillary buds of tomato plants and their silencing is responsible for parthenocarpic fruit growth and branching inhibition.},
	language = {en},
	number = {19},
	urldate = {2021-06-07},
	journal = {J Exp Bot},
	author = {Martinez-Bello, L. and Moritz, T. and Lopez-Diaz, I.},
	month = sep,
	year = {2015},
	note = {Edition: 2015/06/21},
	keywords = {*Gene Expression Regulation, Plant, Branching, Fruit/genetics/growth \& development/metabolism, GA 2-oxidases, Gene Expression Regulation, Developmental, Gene Silencing, Gibberellins/metabolism, Lycopersicon esculentum/*genetics/*growth \& development/metabolism, Mixed Function Oxygenases/*genetics/metabolism, Plant Proteins/*genetics/metabolism, Plant Stems/genetics/growth \& development/metabolism, Plants, Genetically Modified/genetics/growth \& development/metabolism, Sequence Analysis, DNA, gibberellins, parthenocarpy, silencing, tomato.},
	pages = {5897--910},
}

Gibberellins (GAs) are phytohormones that regulate a wide range of developmental processes in plants. Levels of active GAs are regulated by biosynthetic and catabolic enzymes like the GA 2-oxidases (GA2oxs). In tomato (Solanum lycopersicum L.) C19 GA2oxs are encoded by a small multigenic family of five members with some degree of redundancy. In order to investigate their roles in tomato, the silencing of all five genes in transgenic plants was induced. A significant increase in active GA4 content was found in the ovaries of transgenic plants. In addition, the transgenic unfertilized ovaries were much bigger than wild-type ovaries (about 30 times) and a certain proportion (5-37%) were able to develop parthenocarpically. Among the GA2ox family, genes GA2ox1 and -2 seem to be the most relevant for this phenotype since their expression was induced in unfertilized ovaries and repressed in developing fruits, inversely correlating with ovary growth. Interestingly, transgenic lines exhibited a significant inhibition of branching and a higher content of active GA4 in axillary buds. This phenotype was reverted, in transgenic plants, by the application of paclobutrazol, a GA biosynthesis inhibitor, suggesting a role for GAs as repressors of branching. In summary, this work demonstrates that GA 2-oxidases regulate gibberellin levels in ovaries and axillary buds of tomato plants and their silencing is responsible for parthenocarpic fruit growth and branching inhibition.

@article{zamioudis_rhizobacterial_2015,
	title = {Rhizobacterial volatiles and photosynthesis-related signals coordinate {MYB72} expression in {Arabidopsis} roots during onset of induced systemic resistance and iron-deficiency responses},
	volume = {84},
	issn = {1365-313X (Electronic) 0960-7412 (Linking)},
	shorttitle = {Rhizobacterial volatiles and photosynthesis‐related signals coordinate},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26307542},
	doi = {10/f3m6j7},
	abstract = {In Arabidopsis roots, the transcription factor MYB72 plays a dual role in the onset of rhizobacteria-induced systemic resistance (ISR) and plant survival under conditions of limited iron availability. Previously, it was shown that MYB72 coordinates the expression of a gene module that promotes synthesis and excretion of iron-mobilizing phenolic compounds in the rhizosphere, a process that is involved in both iron acquisition and ISR signaling. Here, we show that volatile organic compounds (VOCs) from ISR-inducing Pseudomonas bacteria are important elicitors of MYB72. In response to VOC treatment, MYB72 is co-expressed with the iron uptake-related genes FERRIC REDUCTION OXIDASE 2 (FRO2) and IRON-REGULATED TRANSPORTER 1 (IRT1) in a manner that is dependent on FER-LIKE IRON DEFICIENCY TRANSCRIPTION FACTOR (FIT), indicating that MYB72 is an intrinsic part of the plant's iron-acquisition response that is typically activated upon iron starvation. However, VOC-induced MYB72 expression is activated independently of iron availability in the root vicinity. Moreover, rhizobacterial VOC-mediated induction of MYB72 requires photosynthesis-related signals, while iron deficiency in the rhizosphere activates MYB72 in the absence of shoot-derived signals. Together, these results show that the ISR- and iron acquisition-related transcription factor MYB72 in Arabidopsis roots is activated by rhizobacterial volatiles and photosynthesis-related signals, and enhances the iron-acquisition capacity of roots independently of the iron availability in the rhizosphere. This work highlights the role of MYB72 in plant processes by which root microbiota simultaneously stimulate systemic immunity and activate the iron-uptake machinery in their host plants.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant J},
	author = {Zamioudis, C. and Korteland, J. and Van Pelt, J. A. and van Hamersveld, M. and Dombrowski, N. and Bai, Y. and Hanson, J. and Van Verk, M. C. and Ling, H. Q. and Schulze-Lefert, P. and Pieterse, C. M.},
	month = oct,
	year = {2015},
	note = {Edition: 2015/08/27},
	keywords = {Arabidopsis Proteins/genetics/*metabolism, Arabidopsis thaliana, Arabidopsis/drug effects/*metabolism, Gene Expression Regulation, Plant/drug effects/genetics, Iron/*deficiency, MYB transcription factor, Photosynthesis/drug effects, Plant Roots/drug effects/*metabolism, Rhizobium/*chemistry, Volatile Organic Compounds/*pharmacology, induced resistance, iron homeostasis, plant growth-promoting rhizobacteria, volatile organic compounds},
	pages = {309--22},
}

In Arabidopsis roots, the transcription factor MYB72 plays a dual role in the onset of rhizobacteria-induced systemic resistance (ISR) and plant survival under conditions of limited iron availability. Previously, it was shown that MYB72 coordinates the expression of a gene module that promotes synthesis and excretion of iron-mobilizing phenolic compounds in the rhizosphere, a process that is involved in both iron acquisition and ISR signaling. Here, we show that volatile organic compounds (VOCs) from ISR-inducing Pseudomonas bacteria are important elicitors of MYB72. In response to VOC treatment, MYB72 is co-expressed with the iron uptake-related genes FERRIC REDUCTION OXIDASE 2 (FRO2) and IRON-REGULATED TRANSPORTER 1 (IRT1) in a manner that is dependent on FER-LIKE IRON DEFICIENCY TRANSCRIPTION FACTOR (FIT), indicating that MYB72 is an intrinsic part of the plant's iron-acquisition response that is typically activated upon iron starvation. However, VOC-induced MYB72 expression is activated independently of iron availability in the root vicinity. Moreover, rhizobacterial VOC-mediated induction of MYB72 requires photosynthesis-related signals, while iron deficiency in the rhizosphere activates MYB72 in the absence of shoot-derived signals. Together, these results show that the ISR- and iron acquisition-related transcription factor MYB72 in Arabidopsis roots is activated by rhizobacterial volatiles and photosynthesis-related signals, and enhances the iron-acquisition capacity of roots independently of the iron availability in the rhizosphere. This work highlights the role of MYB72 in plant processes by which root microbiota simultaneously stimulate systemic immunity and activate the iron-uptake machinery in their host plants.

@article{capovilla_role_2015,
	title = {Role of alternative pre-{mRNA} splicing in temperature signaling},
	volume = {27},
	issn = {1879-0356 (Electronic) 1369-5266 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26190743},
	doi = {10/f3ndbf},
	abstract = {Developmental plasticity enables plants to respond rapidly to changing environmental conditions, such as temperature fluctuations. Understanding how plants measure temperature and integrate this information into developmental programs at the molecular level will be essential to breed thermo-tolerant crop varieties. Recent studies identified alternative splicing (AS) as a possible 'molecular thermometer', allowing plants to quickly adjust the abundance of functional transcripts to environmental perturbations. In this review, recent advances regarding the effects of temperature-responsive AS on plant development will be discussed, with emphasis on the circadian clock and flowering time control. The challenge for the near future will be to understand the molecular mechanisms by which temperature can influence AS regulation.},
	language = {en},
	urldate = {2021-06-07},
	journal = {Curr Opin Plant Biol},
	author = {Capovilla, G. and Pajoro, A. and Immink, R. G. and Schmid, M.},
	month = oct,
	year = {2015},
	note = {Edition: 2015/07/21},
	keywords = {*Alternative Splicing, *Gene Expression Regulation, Plant, *Genes, Regulator, *Plant Development, Circadian Clocks, Flowers/genetics/growth \& development, Plant Proteins/*genetics/metabolism, Temperature},
	pages = {97--103},
}

Developmental plasticity enables plants to respond rapidly to changing environmental conditions, such as temperature fluctuations. Understanding how plants measure temperature and integrate this information into developmental programs at the molecular level will be essential to breed thermo-tolerant crop varieties. Recent studies identified alternative splicing (AS) as a possible 'molecular thermometer', allowing plants to quickly adjust the abundance of functional transcripts to environmental perturbations. In this review, recent advances regarding the effects of temperature-responsive AS on plant development will be discussed, with emphasis on the circadian clock and flowering time control. The challenge for the near future will be to understand the molecular mechanisms by which temperature can influence AS regulation.

@article{staubert_rewired_2015,
	title = {Rewired metabolism in drug-resistant leukemia cells: a metabolic switch hallmarked by reduced dependence on exogenous glutamine},
	volume = {290},
	issn = {1083-351X (Electronic) 0021-9258 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25697355},
	doi = {10/f3nndz},
	abstract = {Cancer cells that escape induction therapy are a major cause of relapse. Understanding metabolic alterations associated with drug resistance opens up unexplored opportunities for the development of new therapeutic strategies. Here, we applied a broad spectrum of technologies including RNA sequencing, global untargeted metabolomics, and stable isotope labeling mass spectrometry to identify metabolic changes in P-glycoprotein overexpressing T-cell acute lymphoblastic leukemia (ALL) cells, which escaped a therapeutically relevant daunorubicin treatment. We show that compared with sensitive ALL cells, resistant leukemia cells possess a fundamentally rewired central metabolism characterized by reduced dependence on glutamine despite a lack of expression of glutamate-ammonia ligase (GLUL), a higher demand for glucose and an altered rate of fatty acid beta-oxidation, accompanied by a decreased pantothenic acid uptake capacity. We experimentally validate our findings by selectively targeting components of this metabolic switch, using approved drugs and starvation approaches followed by cell viability analyses in both the ALL cells and in an acute myeloid leukemia (AML) sensitive/resistant cell line pair. We demonstrate how comparative metabolomics and RNA expression profiling of drug-sensitive and -resistant cells expose targetable metabolic changes and potential resistance markers. Our results show that drug resistance is associated with significant metabolic costs in cancer cells, which could be exploited using new therapeutic strategies.},
	language = {en},
	number = {13},
	urldate = {2021-06-07},
	journal = {J Biol Chem},
	author = {Staubert, C. and Bhuiyan, H. and Lindahl, A. and Broom, O. J. and Zhu, Y. and Islam, S. and Linnarsson, S. and Lehtio, J. and Nordstrom, A.},
	month = mar,
	year = {2015},
	note = {Edition: 2015/02/24},
	keywords = {*Drug Resistance, Neoplasm, 3-Hydroxyacyl CoA Dehydrogenases/metabolism, ATP Binding Cassette Transporter, Subfamily B, Member 1/metabolism, Acetyl-CoA C-Acyltransferase/metabolism, Antineoplastic Agents/*pharmacology, Carbon-Carbon Double Bond Isomerases/metabolism, Cell Line, Tumor, Cyclosporins/pharmacology, Daunorubicin/*pharmacology, Drug Resistance, Drug Synergism, Enoyl-CoA Hydratase/metabolism, Fatty Acids/biosynthesis, Glutamine, Glutamine/*physiology, Glycolysis, Humans, Leukemia, Mass Spectrometry (MS), Metabolism, Metabolome, Metabolomics, Oxidation-Reduction, Pantothenic Acid/metabolism, Perhexiline/pharmacology, RNA, Messenger/genetics/metabolism, Racemases and Epimerases/metabolism, Transcriptome, Transcriptomics, beta-Oxidation},
	pages = {8348--59},
}

Cancer cells that escape induction therapy are a major cause of relapse. Understanding metabolic alterations associated with drug resistance opens up unexplored opportunities for the development of new therapeutic strategies. Here, we applied a broad spectrum of technologies including RNA sequencing, global untargeted metabolomics, and stable isotope labeling mass spectrometry to identify metabolic changes in P-glycoprotein overexpressing T-cell acute lymphoblastic leukemia (ALL) cells, which escaped a therapeutically relevant daunorubicin treatment. We show that compared with sensitive ALL cells, resistant leukemia cells possess a fundamentally rewired central metabolism characterized by reduced dependence on glutamine despite a lack of expression of glutamate-ammonia ligase (GLUL), a higher demand for glucose and an altered rate of fatty acid beta-oxidation, accompanied by a decreased pantothenic acid uptake capacity. We experimentally validate our findings by selectively targeting components of this metabolic switch, using approved drugs and starvation approaches followed by cell viability analyses in both the ALL cells and in an acute myeloid leukemia (AML) sensitive/resistant cell line pair. We demonstrate how comparative metabolomics and RNA expression profiling of drug-sensitive and -resistant cells expose targetable metabolic changes and potential resistance markers. Our results show that drug resistance is associated with significant metabolic costs in cancer cells, which could be exploited using new therapeutic strategies.

@article{from_residual_2015,
	title = {Residual {Long}-{Term} {Effects} of {Forest} {Fertilization} on {Tree} {Growth} and {Nitrogen} {Turnover} in {Boreal} {Forest}},
	volume = {6},
	issn = {1999-4907},
	url = {://WOS:000353775500015},
	doi = {10/f3p5c9},
	abstract = {The growth enhancing effects of forest fertilizer is considered to level off within 10 years of the application, and be restricted to one forest stand rotation. However, fertilizer induced changes in plant community composition has been shown to occur in the following stand rotation. To clarify whether effects of forest fertilization have residual long-term effects, extending into the next rotation, we compared tree growth, needle N concentrations and the availability of mobile soil N in young (10 years) Pinus sylvestris L. and Picea abies (L.) H. Karst. stands. The sites were fertilized with 150 kg center dot N center dot ha(-1) once or twice during the previous stand rotation, or unfertilized. Two fertilization events increased tree height by 24\% compared to the controls. Needle N concentrations of the trees on previously fertilized sites were 15\% higher than those of the controls. Soil N mineralization rates and the amounts of mobile soil NH4-N and NO3-N were higher on sites that were fertilized twice than on control sites. Our study demonstrates that operational forest fertilization can cause residual long-term effects on stand N dynamics, with subsequent effects on tree growth that may be more long-lasting than previously believed, i.e., extending beyond one stand rotation.},
	language = {English},
	number = {4},
	urldate = {2021-06-07},
	journal = {Forests},
	author = {From, F. and Strengbom, J. and Nordin, A.},
	month = apr,
	year = {2015},
	keywords = {availability, biomass, carbon, ground vegetation, picea-abies, pinus-sylvestris, soil},
	pages = {1145--1156},
}

The growth enhancing effects of forest fertilizer is considered to level off within 10 years of the application, and be restricted to one forest stand rotation. However, fertilizer induced changes in plant community composition has been shown to occur in the following stand rotation. To clarify whether effects of forest fertilization have residual long-term effects, extending into the next rotation, we compared tree growth, needle N concentrations and the availability of mobile soil N in young (10 years) Pinus sylvestris L. and Picea abies (L.) H. Karst. stands. The sites were fertilized with 150 kg center dot N center dot ha(-1) once or twice during the previous stand rotation, or unfertilized. Two fertilization events increased tree height by 24% compared to the controls. Needle N concentrations of the trees on previously fertilized sites were 15% higher than those of the controls. Soil N mineralization rates and the amounts of mobile soil NH4-N and NO3-N were higher on sites that were fertilized twice than on control sites. Our study demonstrates that operational forest fertilization can cause residual long-term effects on stand N dynamics, with subsequent effects on tree growth that may be more long-lasting than previously believed, i.e., extending beyond one stand rotation.

@article{cheregi_regulation_2015,
	title = {Regulation of the scp {Genes} in the {Cyanobacterium} {Synechocystis} sp. {PCC} 6803--{What} is {New}?},
	volume = {20},
	issn = {1420-3049 (Electronic) 1420-3049 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26274949},
	doi = {10/f3nfg3},
	abstract = {In the cyanobacterium Synechocystis sp. PCC 6803 there are five genes encoding small CAB-like (SCP) proteins, which have been shown to be up-regulated under stress. Analyses of the promoter sequences of the scp genes revealed the existence of an NtcA binding motif in two scp genes, scpB and scpE. Binding of NtcA, the key transcriptional regulator during nitrogen stress, to the promoter regions was shown by electrophoretic mobility shift assay. The metabolite 2-oxoglutarate did not increase the affinity of NtcA for binding to the promoters of scpB and scpE. A second motif, the HIP1 palindrome 5' GGCGATCGCC 3', was detected in the upstream regions of scpB and scpC. The transcription factor encoded by sll1130 has been suggested to recognize this motif to regulate heat-responsive genes. Our data suggest that HIP1 is not a regulatory element within the scp genes. Further, the presence of the high light regulatory (HLR1) motif was confirmed in scpB-E, in accordance to their induced transcriptions in cells exposed to high light. The HLR1 motif was newly discovered in eight additional genes.},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Molecules},
	author = {Cheregi, O. and Funk, C.},
	month = aug,
	year = {2015},
	note = {Edition: 2015/08/15},
	keywords = {*Gene Expression Regulation, Bacterial, Amino Acid Motifs, Bacterial Proteins/biosynthesis/*genetics/metabolism, DNA-Binding Proteins/biosynthesis/*genetics/metabolism, Electrophoretic Mobility Shift Assay, Genes, Bacterial, Hip1, Ketoglutaric Acids/metabolism, NtcA, Promoter Regions, Genetic, Scp, Synechocystis 6803, Synechocystis/*genetics/metabolism, Transcription Factors/biosynthesis/*genetics/metabolism, Transcriptional Activation, high light regulatory motif (HLR1)},
	pages = {14621--37},
}

In the cyanobacterium Synechocystis sp. PCC 6803 there are five genes encoding small CAB-like (SCP) proteins, which have been shown to be up-regulated under stress. Analyses of the promoter sequences of the scp genes revealed the existence of an NtcA binding motif in two scp genes, scpB and scpE. Binding of NtcA, the key transcriptional regulator during nitrogen stress, to the promoter regions was shown by electrophoretic mobility shift assay. The metabolite 2-oxoglutarate did not increase the affinity of NtcA for binding to the promoters of scpB and scpE. A second motif, the HIP1 palindrome 5' GGCGATCGCC 3', was detected in the upstream regions of scpB and scpC. The transcription factor encoded by sll1130 has been suggested to recognize this motif to regulate heat-responsive genes. Our data suggest that HIP1 is not a regulatory element within the scp genes. Further, the presence of the high light regulatory (HLR1) motif was confirmed in scpB-E, in accordance to their induced transcriptions in cells exposed to high light. The HLR1 motif was newly discovered in eight additional genes.

@article{roberge_relative_2015,
	title = {Relative contributions of set-asides and tree retention to the long-term availability of key forest biodiversity structures at the landscape scale},
	volume = {154},
	issn = {1095-8630 (Electronic) 0301-4797 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25745845},
	doi = {10/f3p26n},
	abstract = {Over previous decades new environmental measures have been implemented in forestry. In Fennoscandia, forest management practices were modified to set aside conservation areas and to retain trees at final felling. In this study we simulated the long-term effects of set-aside establishment and tree retention practices on the future availability of large trees and dead wood, two forest structures of documented importance to biodiversity conservation. Using a forest decision support system (Heureka), we projected the amounts of these structures over 200 years in two managed north Swedish landscapes, under management scenarios with and without set-asides and tree retention. In line with common best practice, we simulated set-asides covering 5\% of the productive area with priority to older stands, as well as approximately 5\% green-tree retention (solitary trees and forest patches) including high-stump creation at final felling. We found that only tree retention contributed to substantial increases in the future density of large (DBH {\textgreater}/=35 cm) deciduous trees, while both measures made significant contributions to the availability of large conifers. It took more than half a century to observe stronger increases in the densities of large deciduous trees as an effect of tree retention. The mean landscape-scale volumes of hard dead wood fluctuated widely, but the conservation measures yielded values which were, on average over the entire simulation period, about 2.5 times as high as for scenarios without these measures. While the density of large conifers increased with time in the landscape initially dominated by younger forest, best practice conservation measures did not avert a long-term decrease in large conifer density in the landscape initially comprised of more old forest. Our results highlight the needs to adopt a long temporal perspective and to consider initial landscape conditions when evaluating the large-scale effects of conservation measures on forest biodiversity.},
	language = {en},
	urldate = {2021-06-07},
	journal = {J Environ Manage},
	author = {Roberge, J. M. and Lamas, T. and Lundmark, T. and Ranius, T. and Felton, A. and Nordin, A.},
	month = may,
	year = {2015},
	note = {Edition: 2015/03/10},
	keywords = {*Biodiversity, *Trees, Biodiversity conservation, Conservation of Natural Resources, Dead wood, Ecosystem, Forest management, Forestry/*methods, Humans, Landscape simulations, Large trees, Sweden, Tree retention, Wood},
	pages = {284--92},
}

Over previous decades new environmental measures have been implemented in forestry. In Fennoscandia, forest management practices were modified to set aside conservation areas and to retain trees at final felling. In this study we simulated the long-term effects of set-aside establishment and tree retention practices on the future availability of large trees and dead wood, two forest structures of documented importance to biodiversity conservation. Using a forest decision support system (Heureka), we projected the amounts of these structures over 200 years in two managed north Swedish landscapes, under management scenarios with and without set-asides and tree retention. In line with common best practice, we simulated set-asides covering 5% of the productive area with priority to older stands, as well as approximately 5% green-tree retention (solitary trees and forest patches) including high-stump creation at final felling. We found that only tree retention contributed to substantial increases in the future density of large (DBH \textgreater/=35 cm) deciduous trees, while both measures made significant contributions to the availability of large conifers. It took more than half a century to observe stronger increases in the densities of large deciduous trees as an effect of tree retention. The mean landscape-scale volumes of hard dead wood fluctuated widely, but the conservation measures yielded values which were, on average over the entire simulation period, about 2.5 times as high as for scenarios without these measures. While the density of large conifers increased with time in the landscape initially dominated by younger forest, best practice conservation measures did not avert a long-term decrease in large conifer density in the landscape initially comprised of more old forest. Our results highlight the needs to adopt a long temporal perspective and to consider initial landscape conditions when evaluating the large-scale effects of conservation measures on forest biodiversity.

@article{robinson_relative_2015,
	title = {Relative impacts of environmental variation and evolutionary history on the nestedness and modularity of tree-herbivore networks},
	volume = {5},
	issn = {2045-7758 (Print) 2045-7758 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26306175},
	doi = {10/f3nt2b},
	abstract = {Nestedness and modularity are measures of ecological networks whose causative effects are little understood. We analyzed antagonistic plant-herbivore bipartite networks using common gardens in two contrasting environments comprised of aspen trees with differing evolutionary histories of defence against herbivores. These networks were tightly connected owing to a high level of specialization of arthropod herbivores that spend a large proportion of the life cycle on aspen. The gardens were separated by ten degrees of latitude with resultant differences in abiotic conditions. We evaluated network metrics and reported similar connectance between gardens but greater numbers of links per species in the northern common garden. Interaction matrices revealed clear nestedness, indicating subsetting of the bipartite interactions into specialist divisions, in both the environmental and evolutionary aspen groups, although nestedness values were only significant in the northern garden. Variation in plant vulnerability, measured as the frequency of herbivore specialization in the aspen population, was significantly partitioned by environment (common garden) but not by evolutionary origin of the aspens. Significant values of modularity were observed in all network matrices. Trait-matching indicated that growth traits, leaf morphology, and phenolic metabolites affected modular structure in both the garden and evolutionary groups, whereas extra-floral nectaries had little influence. Further examination of module configuration revealed that plant vulnerability explained considerable variance in web structure. The contrasting conditions between the two gardens resulted in bottom-up effects of the environment, which most strongly influenced the overall network architecture, however, the aspen groups with dissimilar evolutionary history also showed contrasting degrees of nestedness and modularity. Our research therefore shows that, while evolution does affect the structure of aspen-herbivore bipartite networks, the role of environmental variations is a dominant constraint.},
	language = {en},
	number = {14},
	urldate = {2021-06-07},
	journal = {Ecol Evol},
	author = {Robinson, K. M. and Hauzy, C. and Loeuille, N. and Albrectsen, B. R.},
	month = jul,
	year = {2015},
	note = {Edition: 2015/08/26},
	keywords = {Antagonism, arthropod, aspen, bipartite networks, degree of specialization, modularity, nestedness, trophic strength},
	pages = {2898--915},
}

Nestedness and modularity are measures of ecological networks whose causative effects are little understood. We analyzed antagonistic plant-herbivore bipartite networks using common gardens in two contrasting environments comprised of aspen trees with differing evolutionary histories of defence against herbivores. These networks were tightly connected owing to a high level of specialization of arthropod herbivores that spend a large proportion of the life cycle on aspen. The gardens were separated by ten degrees of latitude with resultant differences in abiotic conditions. We evaluated network metrics and reported similar connectance between gardens but greater numbers of links per species in the northern common garden. Interaction matrices revealed clear nestedness, indicating subsetting of the bipartite interactions into specialist divisions, in both the environmental and evolutionary aspen groups, although nestedness values were only significant in the northern garden. Variation in plant vulnerability, measured as the frequency of herbivore specialization in the aspen population, was significantly partitioned by environment (common garden) but not by evolutionary origin of the aspens. Significant values of modularity were observed in all network matrices. Trait-matching indicated that growth traits, leaf morphology, and phenolic metabolites affected modular structure in both the garden and evolutionary groups, whereas extra-floral nectaries had little influence. Further examination of module configuration revealed that plant vulnerability explained considerable variance in web structure. The contrasting conditions between the two gardens resulted in bottom-up effects of the environment, which most strongly influenced the overall network architecture, however, the aspen groups with dissimilar evolutionary history also showed contrasting degrees of nestedness and modularity. Our research therefore shows that, while evolution does affect the structure of aspen-herbivore bipartite networks, the role of environmental variations is a dominant constraint.

@article{tam_proteomic_2015,
	title = {Proteomic approaches to identify substrates of the three {Deg}/{HtrA} proteases of the cyanobacterium {Synechocystis} sp. {PCC} 6803},
	volume = {468},
	issn = {1470-8728 (Electronic) 0264-6021 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25877158},
	doi = {10/f3pn99},
	abstract = {The family of Deg/HtrA proteases plays an important role in quality control of cellular proteins in a wide range of organisms. In the genome of the cyanobacterium Synechocystis sp. PCC 6803, a model organism for photosynthetic research and renewable energy products, three Deg proteases are encoded, termed HhoA, HhoB and HtrA. In the present study, we compared wild-type (WT) Synechocystis cells with the single insertion mutants DeltahhoA, DeltahhoB and DeltahtrA. Protein expression of the remaining Deg/HtrA proteases was strongly affected in the single insertion mutants. Detailed proteomic studies using DIGE (difference gel electrophoresis) and N-terminal COFRADIC (N-terminal combined fractional diagonal chromatography) revealed that inactivation of a single Deg protease has similar impact on the proteomes of the three mutants; differences to WT were observed in enzymes involved in the major metabolic pathways. Changes in the amount of phosphate permease system Pst-1 were observed only in the insertion mutant DeltahhoB. N-terminal COFRADIC analyses on cell lysates of DeltahhoB confirmed changed amounts of many cell envelope proteins, including the phosphate permease systems, compared with WT. In vitro COFRADIC studies were performed to identify the specificity profiles of the recombinant proteases rHhoA, rHhoB or rHtrA added to the Synechocystis WT proteome. The combined in vivo and in vitro N-terminal COFRADIC datasets propose RbcS as a natural substrate for HhoA, PsbO for HhoB and HtrA and Pbp8 for HtrA. We therefore suggest that each Synechocystis Deg protease protects the cell through different, but connected mechanisms.},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Biochem J},
	author = {Tam, L. X. and Aigner, H. and Timmerman, E. and Gevaert, K. and Funk, C.},
	month = jun,
	year = {2015},
	note = {Edition: 2015/04/17},
	keywords = {Bacterial Proteins/genetics/*metabolism, Gene Deletion, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Heat-Shock Proteins/genetics/*metabolism, Mutagenesis, Insertional, N-terminal combined fractional diagonal chromatography (COFRADIC), Periplasmic Proteins/genetics/*metabolism, Phosphate Transport Proteins/genetics/metabolism, Photosystem II Protein Complex/genetics/*metabolism, Protein Subunits/genetics/metabolism, Proteolysis, Proteomics/methods, Recombinant Proteins/genetics/metabolism, Ribulose-Bisphosphate Carboxylase/genetics/*metabolism, Serine Endopeptidases/genetics/*metabolism, Serine-Type D-Ala-D-Ala Carboxypeptidase/genetics/*metabolism, Substrate Specificity, Synechocystis 6803, Synechocystis/*enzymology/genetics/metabolism, Two-Dimensional Difference Gel Electrophoresis, difference gel electrophoresis (DIGE), expression, proteases},
	pages = {373--84},
}

The family of Deg/HtrA proteases plays an important role in quality control of cellular proteins in a wide range of organisms. In the genome of the cyanobacterium Synechocystis sp. PCC 6803, a model organism for photosynthetic research and renewable energy products, three Deg proteases are encoded, termed HhoA, HhoB and HtrA. In the present study, we compared wild-type (WT) Synechocystis cells with the single insertion mutants DeltahhoA, DeltahhoB and DeltahtrA. Protein expression of the remaining Deg/HtrA proteases was strongly affected in the single insertion mutants. Detailed proteomic studies using DIGE (difference gel electrophoresis) and N-terminal COFRADIC (N-terminal combined fractional diagonal chromatography) revealed that inactivation of a single Deg protease has similar impact on the proteomes of the three mutants; differences to WT were observed in enzymes involved in the major metabolic pathways. Changes in the amount of phosphate permease system Pst-1 were observed only in the insertion mutant DeltahhoB. N-terminal COFRADIC analyses on cell lysates of DeltahhoB confirmed changed amounts of many cell envelope proteins, including the phosphate permease systems, compared with WT. In vitro COFRADIC studies were performed to identify the specificity profiles of the recombinant proteases rHhoA, rHhoB or rHtrA added to the Synechocystis WT proteome. The combined in vivo and in vitro N-terminal COFRADIC datasets propose RbcS as a natural substrate for HhoA, PsbO for HhoB and HtrA and Pbp8 for HtrA. We therefore suggest that each Synechocystis Deg protease protects the cell through different, but connected mechanisms.

@article{cheregi_presence_2015,
	title = {Presence of state transitions in the cryptophyte alga {Guillardia} theta},
	volume = {66},
	issn = {1460-2431 (Electronic) 0022-0957 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26254328},
	doi = {10/f3pqj8},
	abstract = {Plants and algae have developed various regulatory mechanisms for optimal delivery of excitation energy to the photosystems even during fluctuating light conditions; these include state transitions as well as non-photochemical quenching. The former process maintains the balance by redistributing antennae excitation between the photosystems, meanwhile the latter by dissipating excessive excitation inside the antennae. In the present study, these mechanisms have been analysed in the cryptophyte alga Guillardia theta. Photoprotective non-photochemical quenching was observed in cultures only after they had entered the stationary growth phase. These cells displayed a diminished overall photosynthetic efficiency, measured as CO2 assimilation rate and electron transport rate. However, in the logarithmic growth phase G. theta cells redistributed excitation energy via a mechanism similar to state transitions. These state transitions were triggered by blue light absorbed by the membrane integrated chlorophyll a/c antennae, and green light absorbed by the lumenal biliproteins was ineffective. It is proposed that state transitions in G. theta are induced by small re-arrangements of the intrinsic antennae proteins, resulting in their coupling/uncoupling to the photosystems in state 1 or state 2, respectively. G. theta therefore represents a chromalveolate algae able to perform state transitions.},
	language = {en},
	number = {20},
	urldate = {2021-06-07},
	journal = {J Exp Bot},
	author = {Cheregi, O. and Kotabova, E. and Prasil, O. and Schroder, W. P. and Kana, R. and Funk, C.},
	month = oct,
	year = {2015},
	note = {Edition: 2015/08/09},
	keywords = {*Electron Transport, *Photochemical Processes, Blue/low light adaptation, Carbon Dioxide/*metabolism, Cryptophyta/growth \& development/*physiology, Light, Photosynthesis, chlorophyll a/c antenna, cryptophytes, growth stage, non-photochemical quenching, state transitions.},
	pages = {6461--70},
}

Plants and algae have developed various regulatory mechanisms for optimal delivery of excitation energy to the photosystems even during fluctuating light conditions; these include state transitions as well as non-photochemical quenching. The former process maintains the balance by redistributing antennae excitation between the photosystems, meanwhile the latter by dissipating excessive excitation inside the antennae. In the present study, these mechanisms have been analysed in the cryptophyte alga Guillardia theta. Photoprotective non-photochemical quenching was observed in cultures only after they had entered the stationary growth phase. These cells displayed a diminished overall photosynthetic efficiency, measured as CO2 assimilation rate and electron transport rate. However, in the logarithmic growth phase G. theta cells redistributed excitation energy via a mechanism similar to state transitions. These state transitions were triggered by blue light absorbed by the membrane integrated chlorophyll a/c antennae, and green light absorbed by the lumenal biliproteins was ineffective. It is proposed that state transitions in G. theta are induced by small re-arrangements of the intrinsic antennae proteins, resulting in their coupling/uncoupling to the photosystems in state 1 or state 2, respectively. G. theta therefore represents a chromalveolate algae able to perform state transitions.

@article{derbyshire_proteomic_2015,
	title = {Proteomic {Analysis} of {Microtubule} {Interacting} {Proteins} over the {Course} of {Xylem} {Tracheary} {Element} {Formation} in {Arabidopsis}},
	volume = {27},
	issn = {1532-298X (Electronic) 1040-4651 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26432860},
	doi = {10/f3pfjx},
	abstract = {Plant vascular cells, or tracheary elements (TEs), rely on circumferential secondary cell wall thickenings to maintain sap flow. The patterns in which TE thickenings are organized vary according to the underlying microtubule bundles that guide wall deposition. To identify microtubule interacting proteins present at defined stages of TE differentiation, we exploited the synchronous differentiation of TEs in Arabidopsis thaliana suspension cultures. Quantitative proteomic analysis of microtubule pull-downs, using ratiometric (14)N/(15)N labeling, revealed 605 proteins exhibiting differential accumulation during TE differentiation. Microtubule interacting proteins associated with membrane trafficking, protein synthesis, DNA/RNA binding, and signal transduction peaked during secondary cell wall formation, while proteins associated with stress peaked when approaching TE cell death. In particular, CELLULOSE SYNTHASE-INTERACTING PROTEIN1, already associated with primary wall synthesis, was enriched during secondary cell wall formation. RNAi knockdown of genes encoding several of the identified proteins showed that secondary wall formation depends on the coordinated presence of microtubule interacting proteins with nonoverlapping functions: cell wall thickness, cell wall homogeneity, and the pattern and cortical location of the wall are dependent on different proteins. Altogether, proteins linking microtubules to a range of metabolic compartments vary specifically during TE differentiation and regulate different aspects of wall patterning.},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Plant Cell},
	author = {Derbyshire, P. and Menard, D. and Green, P. and Saalbach, G. and Buschmann, H. and Lloyd, C. W. and Pesquet, E.},
	month = oct,
	year = {2015},
	note = {Edition: 2015/10/04},
	keywords = {*Proteomics, *Signal Transduction, Arabidopsis Proteins/genetics/metabolism, Arabidopsis/cytology/genetics/growth \& development/*metabolism, Cell Differentiation, Cell Wall/metabolism, Gene Expression Regulation, Plant, Gene Knockdown Techniques, Microtubule Proteins/genetics/*metabolism, Microtubules/metabolism, Plants, Genetically Modified, RNA Interference, Xylem/cytology/genetics/growth \& development/physiology},
	pages = {2709--26},
}

Plant vascular cells, or tracheary elements (TEs), rely on circumferential secondary cell wall thickenings to maintain sap flow. The patterns in which TE thickenings are organized vary according to the underlying microtubule bundles that guide wall deposition. To identify microtubule interacting proteins present at defined stages of TE differentiation, we exploited the synchronous differentiation of TEs in Arabidopsis thaliana suspension cultures. Quantitative proteomic analysis of microtubule pull-downs, using ratiometric (14)N/(15)N labeling, revealed 605 proteins exhibiting differential accumulation during TE differentiation. Microtubule interacting proteins associated with membrane trafficking, protein synthesis, DNA/RNA binding, and signal transduction peaked during secondary cell wall formation, while proteins associated with stress peaked when approaching TE cell death. In particular, CELLULOSE SYNTHASE-INTERACTING PROTEIN1, already associated with primary wall synthesis, was enriched during secondary cell wall formation. RNAi knockdown of genes encoding several of the identified proteins showed that secondary wall formation depends on the coordinated presence of microtubule interacting proteins with nonoverlapping functions: cell wall thickness, cell wall homogeneity, and the pattern and cortical location of the wall are dependent on different proteins. Altogether, proteins linking microtubules to a range of metabolic compartments vary specifically during TE differentiation and regulate different aspects of wall patterning.

@article{kindgren_predictable_2015,
	title = {Predictable alteration of sequence recognition by {RNA} editing factors from {Arabidopsis}},
	volume = {27},
	issn = {1532-298X (Electronic) 1040-4651 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25649437},
	doi = {10/f64zv2},
	abstract = {RNA editing factors of the pentatricopeptide repeat (PPR) family show a very high degree of sequence specificity in the recognition of their target sites. A molecular basis for target recognition by editing factors has been proposed based on statistical correlations but has not been tested experimentally. To achieve this, we systematically mutated the pentatricopeptide motifs in the Arabidopsis thaliana RNA editing factor CLB19 to investigate their individual contribution to RNA recognition. We find that the motifs contributing significantly to the specificity of binding follow the previously proposed recognition rules, distinguishing primarily between purines and pyrimidines. Our results are consistent with proposals that each motif recognizes one nucleotide in the RNA target with the protein aligned parallel to the RNA and contiguous motifs aligned with contiguous nucleotides such that the final PPR motif aligns four nucleotides upstream of the edited cytidine. By altering S motifs in CLB19 and another editing factor, OTP82, and using the modified proteins to attempt to complement the respective mutants, we demonstrate that we can predictably alter the specificity of these factors in vivo.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Cell},
	author = {Kindgren, P. and Yap, A. and Bond, C. S. and Small, I.},
	month = feb,
	year = {2015},
	note = {Edition: 2015/02/05},
	keywords = {Amino Acid Motifs, Amino Acid Sequence, Arabidopsis Proteins/chemistry/*metabolism, Arabidopsis/*metabolism, Base Sequence, Molecular Sequence Data, Mutation/genetics, Nucleic Acid Conformation, Protein Binding, RNA Editing/*genetics, RNA, Plant/metabolism, RNA-Binding Proteins/chemistry/*metabolism, Recombinant Proteins/metabolism, Sequence Alignment},
	pages = {403--16},
}

RNA editing factors of the pentatricopeptide repeat (PPR) family show a very high degree of sequence specificity in the recognition of their target sites. A molecular basis for target recognition by editing factors has been proposed based on statistical correlations but has not been tested experimentally. To achieve this, we systematically mutated the pentatricopeptide motifs in the Arabidopsis thaliana RNA editing factor CLB19 to investigate their individual contribution to RNA recognition. We find that the motifs contributing significantly to the specificity of binding follow the previously proposed recognition rules, distinguishing primarily between purines and pyrimidines. Our results are consistent with proposals that each motif recognizes one nucleotide in the RNA target with the protein aligned parallel to the RNA and contiguous motifs aligned with contiguous nucleotides such that the final PPR motif aligns four nucleotides upstream of the edited cytidine. By altering S motifs in CLB19 and another editing factor, OTP82, and using the modified proteins to attempt to complement the respective mutants, we demonstrate that we can predictably alter the specificity of these factors in vivo.

@article{ratke_populus_2015,
	title = {Populus {GT43} family members group into distinct sets required for primary and secondary wall xylan biosynthesis and include useful promoters for wood modification},
	volume = {13},
	issn = {1467-7652 (Electronic) 1467-7644 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25100045},
	doi = {10/f3nk7x},
	abstract = {The plant GT43 protein family includes xylosyltransferases that are known to be required for xylan backbone biosynthesis, but have incompletely understood specificities. RT-qPCR and histochemical (GUS) analyses of expression patterns of GT43 members in hybrid aspen, reported here, revealed that three clades of the family have markedly differing specificity towards secondary wall-forming cells (wood and extraxylary fibres). Intriguingly, GT43A and B genes (corresponding to the Arabidopsis IRX9 clade) showed higher specificity for secondary-walled cells than GT43C and D genes (IRX14 clade), although both IRX9 and IRX14 are required for xylosyltransferase activity. The remaining genes, GT43E, F and G (IRX9-L clade), showed broad expression patterns. Transient transactivation analyses of GT43A and B reporters demonstrated that they are activated by PtxtMYB021 and PNAC085 (master secondary wall switches), mediated in PtxtMYB021 activation by an AC element. The high observed secondary cell wall specificity of GT43B expression prompted tests of the efficiency of its promoter (pGT43B), relative to the CaMV 35S (35S) promoter, for overexpressing a xylan acetyl esterase (CE5) or downregulating REDUCED WALL ACETYLATION (RWA) family genes and thus engineering wood acetylation. CE5 expression was weaker when driven by pGT43B, but it reduced wood acetyl content substantially more efficiently than the 35S promoter. RNAi silencing of the RWA family, which was ineffective using 35S, was achieved when using GT43B promoter. These results show the utility of the GT43B promoter for genetically engineering properties of wood and fibres.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Biotechnol J},
	author = {Ratke, C. and Pawar, P. M. and Balasubramanian, V. K. and Naumann, M. and Duncranz, M. L. and Derba-Maceluch, M. and Gorzsas, A. and Endo, S. and Ezcurra, I. and Mellerowicz, E. J.},
	month = jan,
	year = {2015},
	note = {Edition: 2014/08/08},
	keywords = {*Genes, Plant, *Multigene Family, *Promoter Regions, Genetic, Cell Wall/*metabolism, Cloning, Molecular, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Genetic Vectors/metabolism, Glucuronidase/metabolism, Plants, Genetically Modified, Populus/*genetics, Transcriptional Activation/genetics, Wood/genetics/*metabolism, Xylans/*biosynthesis, genetic engineering, poplar, secondary wall, transgenic trees, wood development, xylan biosynthesis},
	pages = {26--37},
}

The plant GT43 protein family includes xylosyltransferases that are known to be required for xylan backbone biosynthesis, but have incompletely understood specificities. RT-qPCR and histochemical (GUS) analyses of expression patterns of GT43 members in hybrid aspen, reported here, revealed that three clades of the family have markedly differing specificity towards secondary wall-forming cells (wood and extraxylary fibres). Intriguingly, GT43A and B genes (corresponding to the Arabidopsis IRX9 clade) showed higher specificity for secondary-walled cells than GT43C and D genes (IRX14 clade), although both IRX9 and IRX14 are required for xylosyltransferase activity. The remaining genes, GT43E, F and G (IRX9-L clade), showed broad expression patterns. Transient transactivation analyses of GT43A and B reporters demonstrated that they are activated by PtxtMYB021 and PNAC085 (master secondary wall switches), mediated in PtxtMYB021 activation by an AC element. The high observed secondary cell wall specificity of GT43B expression prompted tests of the efficiency of its promoter (pGT43B), relative to the CaMV 35S (35S) promoter, for overexpressing a xylan acetyl esterase (CE5) or downregulating REDUCED WALL ACETYLATION (RWA) family genes and thus engineering wood acetylation. CE5 expression was weaker when driven by pGT43B, but it reduced wood acetyl content substantially more efficiently than the 35S promoter. RNAi silencing of the RWA family, which was ineffective using 35S, was achieved when using GT43B promoter. These results show the utility of the GT43B promoter for genetically engineering properties of wood and fibres.

@article{du_multilocus_2015,
	title = {Multilocus analysis of nucleotide variation and speciation in three closely related {Populus} ({Salicaceae}) species},
	volume = {24},
	issn = {1365-294X (Electronic) 0962-1083 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26334549},
	doi = {10/f3mw96},
	abstract = {Historical tectonism and climate oscillations can isolate and contract the geographical distributions of many plant species, and they are even known to trigger species divergence and ultimately speciation. Here, we estimated the nucleotide variation and speciation in three closely related Populus species, Populus tremuloides, P. tremula and P. davidiana, distributed in North America and Eurasia. We analysed the sequence variation in six single-copy nuclear loci and three chloroplast (cpDNA) fragments in 497 individuals sampled from 33 populations of these three species across their geographic distributions. These three Populus species harboured relatively high levels of nucleotide diversity and showed high levels of nucleotide differentiation. Phylogenetic analysis revealed that P. tremuloides diverged earlier than the other two species. The cpDNA haplotype network result clearly illustrated the dispersal route from North America to eastern Asia and then into Europe. Molecular dating results confirmed that the divergence of these three species coincided with the sundering of the Bering land bridge in the late Miocene and a rapid uplift of the Qinghai-Tibetan Plateau around the Miocene/Pliocene boundary. Vicariance-driven successful allopatric speciation resulting from historical tectonism and climate oscillations most likely played roles in the formation of the disjunct distributions and divergence of these three Populus species.},
	language = {en},
	number = {19},
	urldate = {2021-06-07},
	journal = {Mol Ecol},
	author = {Du, S. and Wang, Z. and Ingvarsson, P. K. and Wang, D. and Wang, J. and Wu, Z. and Tembrock, L. R. and Zhang, J.},
	month = oct,
	year = {2015},
	note = {Edition: 2015/09/04},
	keywords = {*Genetic Speciation, *Genetic Variation, *Phylogeny, DNA, Chloroplast/genetics, DNA, Plant/genetics, Genetic Markers, Genetics, Population, Haplotypes, Models, Genetic, Molecular Sequence Data, Populus, Populus/*classification/genetics, Sequence Analysis, DNA, nucleotide differentiation, nucleotide variation, speciation, vicariance},
	pages = {4994--5005},
}

Historical tectonism and climate oscillations can isolate and contract the geographical distributions of many plant species, and they are even known to trigger species divergence and ultimately speciation. Here, we estimated the nucleotide variation and speciation in three closely related Populus species, Populus tremuloides, P. tremula and P. davidiana, distributed in North America and Eurasia. We analysed the sequence variation in six single-copy nuclear loci and three chloroplast (cpDNA) fragments in 497 individuals sampled from 33 populations of these three species across their geographic distributions. These three Populus species harboured relatively high levels of nucleotide diversity and showed high levels of nucleotide differentiation. Phylogenetic analysis revealed that P. tremuloides diverged earlier than the other two species. The cpDNA haplotype network result clearly illustrated the dispersal route from North America to eastern Asia and then into Europe. Molecular dating results confirmed that the divergence of these three species coincided with the sundering of the Bering land bridge in the late Miocene and a rapid uplift of the Qinghai-Tibetan Plateau around the Miocene/Pliocene boundary. Vicariance-driven successful allopatric speciation resulting from historical tectonism and climate oscillations most likely played roles in the formation of the disjunct distributions and divergence of these three Populus species.

@article{hong_measuring_2015,
	title = {Measuring stiffness using acoustic tool for {Scots} pine breeding selection},
	volume = {30},
	issn = {0282-7581},
	url = {://WOS:000352893900012},
	doi = {10/f3rwh9},
	abstract = {Stiffness (modulus of elasticity, MOE) of conifer trees is the most important trait for structural wood products. Finding a fast, reliable and non-destructive way to measure MOE is a priority for screening large progeny trials in tree breeding programmes. For Scots pine, time-of-flight (TOF) velocity measured on standing trees accounted for 47\% of the variation to the benchmark SilviScan-based clearwood MOE (MOEs), under the assumption of constant wood density. If wood density was included, 59\% of the variation was accounted for. The TOF stiffness measurements on standing trees were, however, more related to the clearwood MOEs in the outerwood, and the prediction was the most reliable at breast height compared to the stem base and the top section. Microfibril angle (MFA) had higher correlation with acoustic velocity (VEL) of standing trees than wood density, and among the early, transition and latewood density, the latewood density had the highest correlation with stiffness measurements on standing trees. VEL measured at breast height in combination with wood density was the most reliable predictor of MOE of standing trees for selection and breeding in Scots pine.},
	language = {English},
	number = {4},
	urldate = {2021-06-07},
	journal = {Scandinavian Journal of Forest Research},
	author = {Hong, Z. and Fries, A. and Lundqvist, S. O. and Gull, B. A. and Wu, H. X.},
	month = may,
	year = {2015},
	keywords = {acoustic velocity, economic weights, genetic correlations, logs, mature wood, microfibril angle, modulus of elasticity (moe), non-destructive evaluation, pinus sylvestris, radiata, standing trees, traits, velocity, wood stiffness},
	pages = {363--372},
}

Stiffness (modulus of elasticity, MOE) of conifer trees is the most important trait for structural wood products. Finding a fast, reliable and non-destructive way to measure MOE is a priority for screening large progeny trials in tree breeding programmes. For Scots pine, time-of-flight (TOF) velocity measured on standing trees accounted for 47% of the variation to the benchmark SilviScan-based clearwood MOE (MOEs), under the assumption of constant wood density. If wood density was included, 59% of the variation was accounted for. The TOF stiffness measurements on standing trees were, however, more related to the clearwood MOEs in the outerwood, and the prediction was the most reliable at breast height compared to the stem base and the top section. Microfibril angle (MFA) had higher correlation with acoustic velocity (VEL) of standing trees than wood density, and among the early, transition and latewood density, the latewood density had the highest correlation with stiffness measurements on standing trees. VEL measured at breast height in combination with wood density was the most reliable predictor of MOE of standing trees for selection and breeding in Scots pine.

@article{blumenstein_phenotype_2015,
	title = {Phenotype {MicroArrays} as a complementary tool to next generation sequencing for characterization of tree endophytes},
	volume = {6},
	issn = {1664-302X (Print) 1664-302X (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26441951},
	doi = {10/f3m9xw},
	abstract = {There is an increasing need to calibrate microbial community profiles obtained through next generation sequencing (NGS) with relevant taxonomic identities of the microbes, and to further associate these identities with phenotypic attributes. Phenotype MicroArray (PM) techniques provide a semi-high throughput assay for characterization and monitoring the microbial cellular phenotypes. Here, we present detailed descriptions of two different PM protocols used in our recent studies on fungal endophytes of forest trees, and highlight the benefits and limitations of this technique. We found that the PM approach enables effective screening of substrate utilization by endophytes. However, the technical limitations are multifaceted and the interpretation of the PM data challenging. For the best result, we recommend that the growth conditions for the fungi are carefully standardized. In addition, rigorous replication and control strategies should be employed whether using pre-configured, commercial microwell-plates or in-house designed PM plates for targeted substrate analyses. With these precautions, the PM technique is a valuable tool to characterize the metabolic capabilities of individual endophyte isolates, or successional endophyte communities identified by NGS, allowing a functional interpretation of the taxonomic data. Thus, PM approaches can provide valuable complementary information for NGS studies of fungal endophytes in forest trees.},
	urldate = {2021-06-07},
	journal = {Front Microbiol},
	author = {Blumenstein, K. and Macaya-Sanz, D. and Martin, J. A. and Albrectsen, B. R. and Witzell, J.},
	month = sep,
	year = {2015},
	note = {Edition: 2015/10/07},
	keywords = {Biolog PM, fungal phenotype, fungus-fungus interactions, nutrient utilization, phenolic compounds},
	pages = {1033},
}

There is an increasing need to calibrate microbial community profiles obtained through next generation sequencing (NGS) with relevant taxonomic identities of the microbes, and to further associate these identities with phenotypic attributes. Phenotype MicroArray (PM) techniques provide a semi-high throughput assay for characterization and monitoring the microbial cellular phenotypes. Here, we present detailed descriptions of two different PM protocols used in our recent studies on fungal endophytes of forest trees, and highlight the benefits and limitations of this technique. We found that the PM approach enables effective screening of substrate utilization by endophytes. However, the technical limitations are multifaceted and the interpretation of the PM data challenging. For the best result, we recommend that the growth conditions for the fungi are carefully standardized. In addition, rigorous replication and control strategies should be employed whether using pre-configured, commercial microwell-plates or in-house designed PM plates for targeted substrate analyses. With these precautions, the PM technique is a valuable tool to characterize the metabolic capabilities of individual endophyte isolates, or successional endophyte communities identified by NGS, allowing a functional interpretation of the taxonomic data. Thus, PM approaches can provide valuable complementary information for NGS studies of fungal endophytes in forest trees.

@article{khaling_ozone_2015,
	title = {Ozone affects growth and development of {Pieris} brassicae on the wild host plant {Brassica} nigra},
	volume = {199},
	issn = {1873-6424 (Electronic) 0269-7491 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25645061},
	doi = {10/f3n6fn},
	abstract = {When plants are exposed to ozone they exhibit changes in both primary and secondary metabolism, which may affect their interactions with herbivorous insects. Here we investigated the performance and preferences of the specialist herbivore Pieris brassicae on the wild plant Brassica nigra under elevated ozone conditions. The direct and indirect effects of ozone on the plant-herbivore system were studied. In both cases ozone exposure had a negative effect on P. brassicae development. However, in dual-choice tests larvae preferentially consumed plant material previously fumigated with the highest concentration tested, showing a lack of correlation between larval preference and performance on ozone exposed plants. Metabolomic analysis of leaf material subjected to combinations of ozone and herbivore-feeding, and focussing on known defence metabolites, indicated that P. brassicae behaviour and performance were associated with ozone-induced alterations to glucosinolate and phenolic pools.},
	language = {en},
	urldate = {2021-06-07},
	journal = {Environ Pollut},
	author = {Khaling, E. and Papazian, S. and Poelman, E. H. and Holopainen, J. K. and Albrectsen, B. R. and Blande, J. D.},
	month = apr,
	year = {2015},
	note = {Edition: 2015/02/04},
	keywords = {Air Pollutants/*toxicity, Animals, Brassica nigra, Brassica/drug effects/metabolism, Butterflies/growth \& development/*physiology, Defence compounds, Glucosinolates, Glucosinolates/metabolism, Growth and performance, Herbivory, Larva/growth \& development, Mustard Plant, Ozone exposure, Ozone/*toxicity, Phenolics, Pieris brassicae, Plant Leaves/chemistry/drug effects, Stress, Physiological},
	pages = {119--29},
}

When plants are exposed to ozone they exhibit changes in both primary and secondary metabolism, which may affect their interactions with herbivorous insects. Here we investigated the performance and preferences of the specialist herbivore Pieris brassicae on the wild plant Brassica nigra under elevated ozone conditions. The direct and indirect effects of ozone on the plant-herbivore system were studied. In both cases ozone exposure had a negative effect on P. brassicae development. However, in dual-choice tests larvae preferentially consumed plant material previously fumigated with the highest concentration tested, showing a lack of correlation between larval preference and performance on ozone exposed plants. Metabolomic analysis of leaf material subjected to combinations of ozone and herbivore-feeding, and focussing on known defence metabolites, indicated that P. brassicae behaviour and performance were associated with ozone-induced alterations to glucosinolate and phenolic pools.

@article{ivkovic_pattern_2015,
	title = {Pattern of genotype by environment interaction for radiata pine in southern {Australia}},
	volume = {72},
	issn = {1286-4560, 1297-966X},
	url = {http://link.springer.com/10.1007/s13595-014-0437-6},
	doi = {10/gkf559},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Annals of Forest Science},
	author = {Ivković, Miloš and Gapare, Washington and Yang, Huixiao and Dutkowski, Gregory and Buxton, Peter and Wu, Harry},
	month = may,
	year = {2015},
	pages = {391--401},
}

@article{funda_low_2015,
	title = {Low rates of pollen contamination in a {Scots} pine seed orchard in {Sweden}: the exception or the norm?},
	volume = {30},
	issn = {0282-7581},
	shorttitle = {Low rates of pollen contamination in a {Scots} pine seed orchard in {Sweden}},
	url = {://WOS:000358150200001},
	doi = {10/f3nftx},
	abstract = {We investigated mating structure and gene flow in a clonal seed orchard of Scots pine (Pinus sylvestris L.) over three consecutive pollination seasons (2010-2012) with nine nuclear microsatellite markers. The paternity of 1991 offspring from four maternal parents was assigned to 28 candidate fathers using an exclusion procedure and a likelihood-based method implemented in the program CERVUS. Relative reproductive success was highly variable among pollen parents but consistent across years and ranged from 0.1\% to 18.3\%. Consequently, the seed crops' effective number of fathers was reduced to 52.9\%, 48.8\%, and 45.7\% of the census in the three seasons, respectively. Self-fertilization fluctuated around the orchard's expected value of 5.1\%, reaching 4.05\%, 7.71\%, and 6.61\%, respectively. Pollen contamination was estimated to be 5.64\%, 7.29\%, and 4.89\%, respectively, after correction for cryptic gene flow. CERVUS provided similar results as the exclusion method, but estimates greatly varied depending on the input parameters, mainly the proportion of fathers sampled. These results indicate the studied seed orchard is a well-functioning production population with only minor negative effects of self-fertilization and pollen contamination on the quality of seed crops. Genotyping issues associated with microsatellites as a potential source of false paternity assignment and exclusion are discussed.},
	language = {English},
	number = {7},
	urldate = {2021-06-07},
	journal = {Scandinavian Journal of Forest Research},
	author = {Funda, T. and Wennstrom, U. and Almqvist, C. and Torimaru, T. and Gull, B. A. and Wang, X. R.},
	month = oct,
	year = {2015},
	keywords = {allele, dynamics, genotyping error, mating structure, mating system, microsatellite loci, parentage analysis, paternal contribution, paternity assignment, pedigree reconstruction, pollen contamination, pollination, seed orchard, success},
	pages = {573--586},
}

We investigated mating structure and gene flow in a clonal seed orchard of Scots pine (Pinus sylvestris L.) over three consecutive pollination seasons (2010-2012) with nine nuclear microsatellite markers. The paternity of 1991 offspring from four maternal parents was assigned to 28 candidate fathers using an exclusion procedure and a likelihood-based method implemented in the program CERVUS. Relative reproductive success was highly variable among pollen parents but consistent across years and ranged from 0.1% to 18.3%. Consequently, the seed crops' effective number of fathers was reduced to 52.9%, 48.8%, and 45.7% of the census in the three seasons, respectively. Self-fertilization fluctuated around the orchard's expected value of 5.1%, reaching 4.05%, 7.71%, and 6.61%, respectively. Pollen contamination was estimated to be 5.64%, 7.29%, and 4.89%, respectively, after correction for cryptic gene flow. CERVUS provided similar results as the exclusion method, but estimates greatly varied depending on the input parameters, mainly the proportion of fathers sampled. These results indicate the studied seed orchard is a well-functioning production population with only minor negative effects of self-fertilization and pollen contamination on the quality of seed crops. Genotyping issues associated with microsatellites as a potential source of false paternity assignment and exclusion are discussed.

@article{cheregi_inactivation_2015,
	title = {Inactivation of the {Deg} protease family in the cyanobacterium {Synechocystis} sp. {PCC} 6803 has impact on the outer cell layers},
	volume = {152},
	issn = {1873-2682 (Electronic) 1011-1344 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26051963},
	doi = {10/f3pst3},
	abstract = {The serine type Deg/HtrA proteases are distributed in a wide range of organisms from Escherichia coli to humans. The cyanobacterium Synechocystis sp. PCC 6803 possesses three Deg protease orthologues: HtrA, HhoA and HhoB. Previously we compared Synechocystis 6803 wild type cells exposed to mild or severe stress conditions with a mutant lacking all three Deg proteases and demonstrated that stress had strong impact on the proteomes and metabolomes. To identify the biochemical processes, which this protease family is involved in, here we compared Synechocystis sp. PCC 6803 wild type cells with a mutant lacking all three Deg proteases grown under normal growth conditions (30 degrees C and 40 mumol photons m(-2) s(-1)). Deletion of the Deg proteases lead to the down-regulation of proteins related to the biosynthesis of outer cell layers (e.g. the GDP mannose 4,6-dehydratase) and affected protein secretion. During the late growth phase of the culture Deg proteases were found to be secreted to the extracellular medium of the Synechocystis sp. PCC 6803 wild type strain. While cyanobacterial Deg proteases seem to act mainly in the periplasmic space, deletion of the three proteases influences the proteome and metabolome of the whole cell. Impairments in the outer cell layers of the triple mutant might explain the higher sensitivity toward light and oxidative stress, which was observed earlier by Barker and coworkers.},
	language = {en},
	number = {Pt B},
	urldate = {2021-06-07},
	journal = {J Photochem Photobiol B},
	author = {Cheregi, O. and Miranda, H. and Grobner, G. and Funk, C.},
	month = nov,
	year = {2015},
	note = {Edition: 2015/06/09},
	keywords = {Cyanobacterium, Enzyme Activation, Metabolomic, Metabolomics, Mutation, Protease, Protein secretion, Proteomic, Proteomics, Serine Endopeptidases/genetics/*metabolism, Synechocystis/*cytology/*enzymology/genetics/metabolism},
	pages = {383--94},
}

The serine type Deg/HtrA proteases are distributed in a wide range of organisms from Escherichia coli to humans. The cyanobacterium Synechocystis sp. PCC 6803 possesses three Deg protease orthologues: HtrA, HhoA and HhoB. Previously we compared Synechocystis 6803 wild type cells exposed to mild or severe stress conditions with a mutant lacking all three Deg proteases and demonstrated that stress had strong impact on the proteomes and metabolomes. To identify the biochemical processes, which this protease family is involved in, here we compared Synechocystis sp. PCC 6803 wild type cells with a mutant lacking all three Deg proteases grown under normal growth conditions (30 degrees C and 40 mumol photons m(-2) s(-1)). Deletion of the Deg proteases lead to the down-regulation of proteins related to the biosynthesis of outer cell layers (e.g. the GDP mannose 4,6-dehydratase) and affected protein secretion. During the late growth phase of the culture Deg proteases were found to be secreted to the extracellular medium of the Synechocystis sp. PCC 6803 wild type strain. While cyanobacterial Deg proteases seem to act mainly in the periplasmic space, deletion of the three proteases influences the proteome and metabolome of the whole cell. Impairments in the outer cell layers of the triple mutant might explain the higher sensitivity toward light and oxidative stress, which was observed earlier by Barker and coworkers.

@article{dent_large-scale_2015,
	title = {Large-scale insertional mutagenesis of {Chlamydomonas} supports phylogenomic functional prediction of photosynthetic genes and analysis of classical acetate-requiring mutants},
	volume = {82},
	issn = {1365-313X (Electronic) 0960-7412 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25711437},
	doi = {10/f67nvt},
	abstract = {Chlamydomonas reinhardtii is a unicellular green alga that is a key model organism in the study of photosynthesis and oxidative stress. Here we describe the large-scale generation of a population of insertional mutants that have been screened for phenotypes related to photosynthesis and the isolation of 459 flanking sequence tags from 439 mutants. Recent phylogenomic analysis has identified a core set of genes, named GreenCut2, that are conserved in green algae and plants. Many of these genes are likely to be central to the process of photosynthesis, and they are over-represented by sixfold among the screened insertional mutants, with insertion events isolated in or adjacent to 68 of 597 GreenCut2 genes. This enrichment thus provides experimental support for functional assignments based on previous bioinformatic analysis. To illustrate one of the uses of the population, a candidate gene approach based on genome position of the flanking sequence of the insertional mutant CAL027\_01\_20 was used to identify the molecular basis of the classical C. reinhardtii mutation ac17. These mutations were shown to affect the gene PDH2, which encodes a subunit of the plastid pyruvate dehydrogenase complex. The mutants and associated flanking sequence data described here are publicly available to the research community, and they represent one of the largest phenotyped collections of algal insertional mutants to date.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant J},
	author = {Dent, R. M. and Sharifi, M. N. and Malnoe, A. and Haglund, C. and Calderon, R. H. and Wakao, S. and Niyogi, K. K.},
	month = apr,
	year = {2015},
	note = {Edition: 2015/02/26},
	keywords = {Acetates/metabolism, Chlamydomonas reinhardtii, Chlamydomonas reinhardtii/*genetics/*metabolism, GreenCut, Mutagenesis, Insertional, Mutation, Pdh2, Photosynthesis/*genetics, Plant Proteins/genetics/*metabolism, genomics, insertion mutant, oxidative stress, photosynthesis},
	pages = {337--51},
}

Chlamydomonas reinhardtii is a unicellular green alga that is a key model organism in the study of photosynthesis and oxidative stress. Here we describe the large-scale generation of a population of insertional mutants that have been screened for phenotypes related to photosynthesis and the isolation of 459 flanking sequence tags from 439 mutants. Recent phylogenomic analysis has identified a core set of genes, named GreenCut2, that are conserved in green algae and plants. Many of these genes are likely to be central to the process of photosynthesis, and they are over-represented by sixfold among the screened insertional mutants, with insertion events isolated in or adjacent to 68 of 597 GreenCut2 genes. This enrichment thus provides experimental support for functional assignments based on previous bioinformatic analysis. To illustrate one of the uses of the population, a candidate gene approach based on genome position of the flanking sequence of the insertional mutant CAL027_01_20 was used to identify the molecular basis of the classical C. reinhardtii mutation ac17. These mutations were shown to affect the gene PDH2, which encodes a subunit of the plastid pyruvate dehydrogenase complex. The mutants and associated flanking sequence data described here are publicly available to the research community, and they represent one of the largest phenotyped collections of algal insertional mutants to date.

@article{podgorska_comparison_2015,
	title = {In comparison with nitrate nutrition, ammonium nutrition increases growth of the frostbite1 {Arabidopsis} mutant},
	volume = {38},
	issn = {1365-3040 (Electronic) 0140-7791 (Linking)},
	shorttitle = {In comparison with nitrate nutrition, ammonium nutrition increases growth of the frostbite1 {A} rabidopsis mutant},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25040883},
	doi = {10/f3mzhm},
	abstract = {Ammonium nutrition inhibits the growth of many plant species, including Arabidopsis thaliana. The toxicity of ammonium is associated with changes in the cellular redox state. The cellular oxidant/antioxidant balance is controlled by mitochondrial electron transport chain. In this study, we analysed the redox metabolism of frostbite1 (fro1) plants, which lack mitochondrial respiratory chain complex I. Surprisingly, the growth of fro1 plants increased under ammonium nutrition. Ammonium nutrition increased the reduction level of pyridine nucleotides in the leaves of wild-type plants, but not in the leaves of fro1 mutant plants. The observed higher activities of type II NADH dehydrogenases and cytochrome c oxidase in the mitochondrial electron transport chain may improve the energy metabolism of fro1 plants grown on ammonium. Additionally, the observed changes in reactive oxygen species (ROS) metabolism in the apoplast may be important for determining the growth of fro1 under ammonium nutrition. Moreover, bioinformatic analyses showed that the gene expression changes in fro1 plants significantly overlap with the changes previously observed in plants with a modified apoplastic pH. Overall, the results suggest a pronounced connection between the mitochondrial redox system and the apoplastic pH and ROS levels, which may modify cell wall plasticity and influence growth.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Cell Environ},
	author = {Podgorska, A. and Ostaszewska, M. and Gardestrom, P. and Rasmusson, A. G. and Szal, B.},
	month = jan,
	year = {2015},
	note = {Edition: 2014/07/22},
	keywords = {*Gene Expression Regulation, Plant, Ammonium Compounds/*metabolism, Arabidopsis Proteins/genetics/*metabolism, Arabidopsis/genetics/growth \& development/*metabolism/ultrastructure, Cell Respiration, Electron Transport Complex IV/genetics/metabolism, Energy Metabolism, Homeostasis, Hydrogen-Ion Concentration, Metabolome, Mitochondria/metabolism, Mutation, NADH Dehydrogenase/genetics/*metabolism, Nitrates/*metabolism, Oxidation-Reduction, Plant Leaves/genetics/growth \& development/metabolism/ultrastructure, Reactive Oxygen Species/metabolism, ammonium syndrome, apoplast, apoplastic pH, complex I, dysfunction of mtETC, mitochondria, redox homeostasis, respiration},
	pages = {224--37},
}

Ammonium nutrition inhibits the growth of many plant species, including Arabidopsis thaliana. The toxicity of ammonium is associated with changes in the cellular redox state. The cellular oxidant/antioxidant balance is controlled by mitochondrial electron transport chain. In this study, we analysed the redox metabolism of frostbite1 (fro1) plants, which lack mitochondrial respiratory chain complex I. Surprisingly, the growth of fro1 plants increased under ammonium nutrition. Ammonium nutrition increased the reduction level of pyridine nucleotides in the leaves of wild-type plants, but not in the leaves of fro1 mutant plants. The observed higher activities of type II NADH dehydrogenases and cytochrome c oxidase in the mitochondrial electron transport chain may improve the energy metabolism of fro1 plants grown on ammonium. Additionally, the observed changes in reactive oxygen species (ROS) metabolism in the apoplast may be important for determining the growth of fro1 under ammonium nutrition. Moreover, bioinformatic analyses showed that the gene expression changes in fro1 plants significantly overlap with the changes previously observed in plants with a modified apoplastic pH. Overall, the results suggest a pronounced connection between the mitochondrial redox system and the apoplastic pH and ROS levels, which may modify cell wall plasticity and influence growth.

@article{staubert_hydroxycarboxylic_2015,
	title = {Hydroxycarboxylic acid receptors are essential for breast cancer cells to control their lipid/fatty acid metabolism},
	volume = {6},
	issn = {1949-2553 (Electronic) 1949-2553 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25839160},
	doi = {10/f3n9cg},
	abstract = {Cancer cells exhibit characteristic changes in their metabolism with efforts being made to address them therapeutically. However, targeting metabolic enzymes as such is a major challenge due to their essentiality for normal proliferating cells. The most successful pharmaceutical targets are G protein-coupled receptors (GPCRs), with more than 40\% of all currently available drugs acting through them.We show that, a family of metabolite-sensing GPCRs, the Hydroxycarboxylic acid receptor family (HCAs), is crucial for breast cancer cells to control their metabolism and proliferation.We found HCA1 and HCA3 mRNA expression were significantly increased in breast cancer patient samples and detectable in primary human breast cancer patient cells. Furthermore, siRNA mediated knock-down of HCA3 induced considerable breast cancer cell death as did knock-down of HCA1, although to a lesser extent. Liquid Chromatography Mass Spectrometry based analyses of breast cancer cell medium revealed a role for HCA3 in controlling intracellular lipid/fatty acid metabolism. The presence of etomoxir or perhexiline, both inhibitors of fatty acid beta-oxidation rescues breast cancer cells with knocked-down HCA3 from cell death.Our data encourages the development of drugs acting on cancer-specific metabolite-sensing GPCRs as novel anti-proliferative agents for cancer therapy.},
	number = {23},
	urldate = {2021-06-07},
	journal = {Oncotarget},
	author = {Staubert, C. and Broom, O. J. and Nordstrom, A.},
	month = aug,
	year = {2015},
	note = {Edition: 2015/04/04},
	keywords = {*Lipid Metabolism/drug effects, Breast Neoplasms/drug therapy/genetics/*metabolism/pathology, Carnitine O-Palmitoyltransferase/antagonists \& inhibitors/metabolism, Cell Death, Cell Line, Tumor, Cell Proliferation, Chromatography, Liquid, Enzyme Inhibitors/pharmacology, Epoxy Compounds/pharmacology, Fatty Acids/*metabolism, Female, GPR109a, Gene Expression Regulation, Neoplastic, Gene Knockdown Techniques, Gpr81, HEK293 Cells, Humans, Oxidation-Reduction, Perhexiline/pharmacology, RNA Interference, RNA, Messenger/metabolism, Receptors, G-Protein-Coupled/drug effects/genetics/*metabolism, Receptors, Nicotinic/drug effects/genetics/*metabolism, Signal Transduction, Tandem Mass Spectrometry, Time Factors, Transfection, Tumor Cells, Cultured, cancer metabolism, hydroxycarboxylic acid receptors, metabolite-sensing GPCRs},
	pages = {19706--20},
}

Cancer cells exhibit characteristic changes in their metabolism with efforts being made to address them therapeutically. However, targeting metabolic enzymes as such is a major challenge due to their essentiality for normal proliferating cells. The most successful pharmaceutical targets are G protein-coupled receptors (GPCRs), with more than 40% of all currently available drugs acting through them.We show that, a family of metabolite-sensing GPCRs, the Hydroxycarboxylic acid receptor family (HCAs), is crucial for breast cancer cells to control their metabolism and proliferation.We found HCA1 and HCA3 mRNA expression were significantly increased in breast cancer patient samples and detectable in primary human breast cancer patient cells. Furthermore, siRNA mediated knock-down of HCA3 induced considerable breast cancer cell death as did knock-down of HCA1, although to a lesser extent. Liquid Chromatography Mass Spectrometry based analyses of breast cancer cell medium revealed a role for HCA3 in controlling intracellular lipid/fatty acid metabolism. The presence of etomoxir or perhexiline, both inhibitors of fatty acid beta-oxidation rescues breast cancer cells with knocked-down HCA3 from cell death.Our data encourages the development of drugs acting on cancer-specific metabolite-sensing GPCRs as novel anti-proliferative agents for cancer therapy.

@article{azoulay-shemer_guard_2015,
	title = {Guard cell photosynthesis is critical for stomatal turgor production, yet does not directly mediate {CO2} - and {ABA}-induced stomatal closing},
	volume = {83},
	issn = {1365-313X (Electronic) 0960-7412 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26096271},
	doi = {10/f3pk33},
	abstract = {Stomata mediate gas exchange between the inter-cellular spaces of leaves and the atmosphere. CO2 levels in leaves (Ci) are determined by respiration, photosynthesis, stomatal conductance and atmospheric [CO2 ]. [CO2 ] in leaves mediates stomatal movements. The role of guard cell photosynthesis in stomatal conductance responses is a matter of debate, and genetic approaches are needed. We have generated transgenic Arabidopsis plants that are chlorophyll-deficient in guard cells only, expressing a constitutively active chlorophyllase in a guard cell specific enhancer trap line. Our data show that more than 90\% of guard cells were chlorophyll-deficient. Interestingly, approximately 45\% of stomata had an unusual, previously not-described, morphology of thin-shaped chlorophyll-less stomata. Nevertheless, stomatal size, stomatal index, plant morphology, and whole-leaf photosynthetic parameters (PSII, qP, qN, FV '/FM' ) were comparable with wild-type plants. Time-resolved intact leaf gas-exchange analyses showed a reduction in stomatal conductance and CO2 -assimilation rates of the transgenic plants. Normalization of CO2 responses showed that stomata of transgenic plants respond to [CO2 ] shifts. Detailed stomatal aperture measurements of normal kidney-shaped stomata, which lack chlorophyll, showed stomatal closing responses to [CO2 ] elevation and abscisic acid (ABA), while thin-shaped stomata were continuously closed. Our present findings show that stomatal movement responses to [CO2 ] and ABA are functional in guard cells that lack chlorophyll. These data suggest that guard cell CO2 and ABA signal transduction are not directly modulated by guard cell photosynthesis/electron transport. Moreover, the finding that chlorophyll-less stomata cause a 'deflated' thin-shaped phenotype, suggests that photosynthesis in guard cells is critical for energization and guard cell turgor production.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Plant J},
	author = {Azoulay-Shemer, T. and Palomares, A. and Bagheri, A. and Israelsson-Nordstrom, M. and Engineer, C. B. and Bargmann, B. O. and Stephan, A. B. and Schroeder, J. I.},
	month = aug,
	year = {2015},
	note = {Edition: 2015/06/23},
	keywords = {Abscisic Acid/*metabolism, Arabidopsis thaliana, Arabidopsis/genetics/metabolism/physiology, Carbon Dioxide/*metabolism, Chlorophyll/metabolism, Co 2, Photosynthesis/genetics/*physiology, Plant Leaves/metabolism/physiology, Plant Stomata/genetics/*metabolism/*physiology, Plants, Genetically Modified/genetics/metabolism/physiology, abscisic acid, chlorophyll, chlorophyllase, guard cell, photosynthesis, stomata, turgor},
	pages = {567--81},
}

Stomata mediate gas exchange between the inter-cellular spaces of leaves and the atmosphere. CO2 levels in leaves (Ci) are determined by respiration, photosynthesis, stomatal conductance and atmospheric [CO2 ]. [CO2 ] in leaves mediates stomatal movements. The role of guard cell photosynthesis in stomatal conductance responses is a matter of debate, and genetic approaches are needed. We have generated transgenic Arabidopsis plants that are chlorophyll-deficient in guard cells only, expressing a constitutively active chlorophyllase in a guard cell specific enhancer trap line. Our data show that more than 90% of guard cells were chlorophyll-deficient. Interestingly, approximately 45% of stomata had an unusual, previously not-described, morphology of thin-shaped chlorophyll-less stomata. Nevertheless, stomatal size, stomatal index, plant morphology, and whole-leaf photosynthetic parameters (PSII, qP, qN, FV '/FM' ) were comparable with wild-type plants. Time-resolved intact leaf gas-exchange analyses showed a reduction in stomatal conductance and CO2 -assimilation rates of the transgenic plants. Normalization of CO2 responses showed that stomata of transgenic plants respond to [CO2 ] shifts. Detailed stomatal aperture measurements of normal kidney-shaped stomata, which lack chlorophyll, showed stomatal closing responses to [CO2 ] elevation and abscisic acid (ABA), while thin-shaped stomata were continuously closed. Our present findings show that stomatal movement responses to [CO2 ] and ABA are functional in guard cells that lack chlorophyll. These data suggest that guard cell CO2 and ABA signal transduction are not directly modulated by guard cell photosynthesis/electron transport. Moreover, the finding that chlorophyll-less stomata cause a 'deflated' thin-shaped phenotype, suggests that photosynthesis in guard cells is critical for energization and guard cell turgor production.

@article{chong_glucuronic_2015,
	title = {Glucuronic acid in {Arabidopsis} thaliana xylans carries a novel pentose substituent},
	volume = {79},
	issn = {1879-0003 (Electronic) 0141-8130 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26047894},
	doi = {10/f3pws3},
	abstract = {Glucuronic acids in Arabidopsis thaliana xylans exist in 4-O-methylated (MeGlcA) and non-methylated (GlcA) forms at a ratio of about 3:2. The matrix-assisted laser desorption/ionization mass spectrometry analysis of the endoxylanase liberated acidic oligosaccharides from the Arabidopsis inflorescence stem showed that two peaks with GlcA (GlcA-Xyl4Ac1 and GlcA-Xyl5Ac2) had abnormally high intensities, as well as different tandem mass spectra, than their 4-O-methylated counterparts. These peaks were interestingly enriched in the xylan biosynthesis mutant irx7 and irx9-1. Multi-stages fragmentation analysis using negative ion electrospray-ion trap mass spectrometry indicated that this GlcA was further carrying a pentose residue in the glucuronoxylan-derived oligosaccharide from irx9-1. The structure was also identified in Arabidopsis wild type. The results prove evidence of a new pentose substitution on the GlcA residue of Arabidopsis GX, which is likely present in the primary walls.},
	language = {en},
	urldate = {2021-06-07},
	journal = {Int J Biol Macromol},
	author = {Chong, S. L. and Koutaniemi, S. and Juvonen, M. and Derba-Maceluch, M. and Mellerowicz, E. J. and Tenkanen, M.},
	month = aug,
	year = {2015},
	note = {Edition: 2015/06/07},
	keywords = {Arabidopsis Proteins/chemistry/*genetics, Arabidopsis thaliana, Arabidopsis/*chemistry/genetics, Endo-1,4-beta Xylanases/genetics, Gene Expression Regulation, Plant, Glucuronic Acid/*chemistry/genetics, Glucuronoxylan, Oligosaccharides/chemistry, Pentoses/*chemistry/genetics, Pentosyltransferases/chemistry/*genetics, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Tandem mass spectrometry, Xylans/biosynthesis/chemistry/*genetics},
	pages = {807--12},
}

Glucuronic acids in Arabidopsis thaliana xylans exist in 4-O-methylated (MeGlcA) and non-methylated (GlcA) forms at a ratio of about 3:2. The matrix-assisted laser desorption/ionization mass spectrometry analysis of the endoxylanase liberated acidic oligosaccharides from the Arabidopsis inflorescence stem showed that two peaks with GlcA (GlcA-Xyl4Ac1 and GlcA-Xyl5Ac2) had abnormally high intensities, as well as different tandem mass spectra, than their 4-O-methylated counterparts. These peaks were interestingly enriched in the xylan biosynthesis mutant irx7 and irx9-1. Multi-stages fragmentation analysis using negative ion electrospray-ion trap mass spectrometry indicated that this GlcA was further carrying a pentose residue in the glucuronoxylan-derived oligosaccharide from irx9-1. The structure was also identified in Arabidopsis wild type. The results prove evidence of a new pentose substitution on the GlcA residue of Arabidopsis GX, which is likely present in the primary walls.

@article{kunz_hexokinase_2015,
	title = {Hexokinase 1 is required for glucose-induced repression of {bZIP63}, {At5g22920}, and {BT2} in {Arabidopsis}},
	volume = {6},
	issn = {1664-462X (Print) 1664-462X (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26236323},
	doi = {10/f3n6kb},
	abstract = {Simple sugars, like glucose (Glc) and sucrose (Suc), act as signals to modulate the expression of hundreds of genes in plants. Frequently, however, it remains unclear whether this regulation is induced by the sugars themselves or by their derivatives generated in the course of carbohydrate (CH) metabolism. In the present study, we tested the relevance of different CH metabolism and allocation pathways affecting expression patterns of five selected sugar-responsive genes (bZIP63, At5g22920, BT2, MGD2, and TPS9) in Arabidopsis thaliana. In general, the expression followed diurnal changes in the overall sugar availability. However, under steady growth conditions, this response was hardly impaired in the mutants for CH metabolizing/ transporting proteins (adg1, sex1, sus1-4, sus5/6, and tpt2), including also hexokinase1 (HXK1) loss- and gain-of-function plants-gin2.1 and oe3.2, respectively. In addition, transgenic plants carrying pbZIP63::GUS showed no changes in reporter-gene-expression when grown on sugar under steady-state conditions. In contrast, short-term treatments of agar-grown seedlings with 1\% Glc or Suc induced pbZIP63::GUS repression, which became even more apparent in seedlings grown in liquid media. Subsequent analyses of liquid-grown gin2.1 and oe3.2 seedlings revealed that Glc -dependent regulation of the five selected genes was not affected in gin2.1, whereas it was enhanced in oe3.2 plants for bZIP63, At5g22920, and BT2. The sugar treatments had no effect on ATP/ADP ratio, suggesting that changes in gene expression were not linked to cellular energy status. Overall, the data suggest that HXK1 does not act as Glc sensor controlling bZIP63, At5g22920, and BT2 expression, but it is nevertheless required for the production of a downstream metabolic signal regulating their expression.},
	urldate = {2021-06-07},
	journal = {Front Plant Sci},
	author = {Kunz, S. and Gardestrom, P. and Pesquet, E. and Kleczkowski, L. A.},
	month = jul,
	year = {2015},
	note = {Edition: 2015/08/04},
	keywords = {At5g22920 expression, BT2 expression, bZIP63 expression, diurnal regulation of expression, glucose sensing, hexokinase, sugar regulation of gene expression},
	pages = {525},
}

Simple sugars, like glucose (Glc) and sucrose (Suc), act as signals to modulate the expression of hundreds of genes in plants. Frequently, however, it remains unclear whether this regulation is induced by the sugars themselves or by their derivatives generated in the course of carbohydrate (CH) metabolism. In the present study, we tested the relevance of different CH metabolism and allocation pathways affecting expression patterns of five selected sugar-responsive genes (bZIP63, At5g22920, BT2, MGD2, and TPS9) in Arabidopsis thaliana. In general, the expression followed diurnal changes in the overall sugar availability. However, under steady growth conditions, this response was hardly impaired in the mutants for CH metabolizing/ transporting proteins (adg1, sex1, sus1-4, sus5/6, and tpt2), including also hexokinase1 (HXK1) loss- and gain-of-function plants-gin2.1 and oe3.2, respectively. In addition, transgenic plants carrying pbZIP63::GUS showed no changes in reporter-gene-expression when grown on sugar under steady-state conditions. In contrast, short-term treatments of agar-grown seedlings with 1% Glc or Suc induced pbZIP63::GUS repression, which became even more apparent in seedlings grown in liquid media. Subsequent analyses of liquid-grown gin2.1 and oe3.2 seedlings revealed that Glc -dependent regulation of the five selected genes was not affected in gin2.1, whereas it was enhanced in oe3.2 plants for bZIP63, At5g22920, and BT2. The sugar treatments had no effect on ATP/ADP ratio, suggesting that changes in gene expression were not linked to cellular energy status. Overall, the data suggest that HXK1 does not act as Glc sensor controlling bZIP63, At5g22920, and BT2 expression, but it is nevertheless required for the production of a downstream metabolic signal regulating their expression.

@article{rappaport_gordon_2015,
	title = {Gordon research conference on photosynthesis: from evolution of fundamental mechanisms to radical re-engineering},
	volume = {123},
	issn = {1573-5079 (Electronic) 0166-8595 (Linking)},
	shorttitle = {Gordon research conference on photosynthesis},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25425217},
	doi = {10/gj6zms},
	abstract = {We provide here a News Report on the 2014 Gordon Research Conference on Photosynthesis, with the subtitle "From Evolution of Fundamental Mechanisms to Radical Re-Engineering." It was held at Mount Snow Resort, West Dover, Vermont, during August 10-15, 2014. After the formal sessions ended, four young scientists (Ute Ambruster of USA; Han Bao of USA; Nicoletta Liguori of the Netherlands; and Anat Shperberg-Avni of Israel) were recognized for their research; they each received a book from one of us (G) in memory of Colin A. Wraight (1945-2014), a brilliant and admired scientist who had been very active in the bioenergetics field in general and in past Gordon Conferences in particular, having chaired the 1988 Gordon Conference on Photosynthesis. (See an article on Wraight by one of us (Govindjee) at http://www.life.illinois.edu/plantbio/Features/ColinWraight/ColinWraight.html .).},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Photosynth Res},
	author = {Rappaport, F. and Malnoe, A. and {Govindjee}},
	month = feb,
	year = {2015},
	note = {Edition: 2014/11/27},
	keywords = {*Biological Evolution, *Photosynthesis, Congresses as Topic, Vermont},
	pages = {213--23},
}

We provide here a News Report on the 2014 Gordon Research Conference on Photosynthesis, with the subtitle "From Evolution of Fundamental Mechanisms to Radical Re-Engineering." It was held at Mount Snow Resort, West Dover, Vermont, during August 10-15, 2014. After the formal sessions ended, four young scientists (Ute Ambruster of USA; Han Bao of USA; Nicoletta Liguori of the Netherlands; and Anat Shperberg-Avni of Israel) were recognized for their research; they each received a book from one of us (G) in memory of Colin A. Wraight (1945-2014), a brilliant and admired scientist who had been very active in the bioenergetics field in general and in past Gordon Conferences in particular, having chaired the 1988 Gordon Conference on Photosynthesis. (See an article on Wraight by one of us (Govindjee) at http://www.life.illinois.edu/plantbio/Features/ColinWraight/ColinWraight.html .).

@article{tolu_high-throughput_2015,
	title = {High-throughput characterization of sediment organic matter by pyrolysis-gas chromatography/mass spectrometry and multivariate curve resolution: {A} promising analytical tool in (paleo)limnology},
	volume = {880},
	issn = {1873-4324 (Electronic) 0003-2670 (Linking)},
	shorttitle = {High-throughput characterization of sediment organic matter by pyrolysis–gas chromatography/mass spectrometry and multivariate curve resolution},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26092342},
	doi = {10/f3m37w},
	abstract = {Molecular-level chemical information about organic matter (OM) in sediments helps to establish the sources of OM and the prevalent degradation/diagenetic processes, both essential for understanding the cycling of carbon (C) and of the elements associated with OM (toxic trace metals and nutrients) in lake ecosystems. Ideally, analytical methods for characterizing OM should allow high sample throughput, consume small amounts of sample and yield relevant chemical information, which are essential for multidisciplinary, high-temporal resolution and/or large spatial scale investigations. We have developed a high-throughput analytical method based on pyrolysis-gas chromatography/mass spectrometry and automated data processing to characterize sedimentary OM in sediments. Our method consumes 200 mug of freeze-dried and ground sediment sample. Pyrolysis was performed at 450 degrees C, which was found to avoid degradation of specific biomarkers (e.g., lignin compounds, fresh carbohydrates/cellulose) compared to 650 degrees C, which is in the range of temperatures commonly applied for environmental samples. The optimization was conducted using the top ten sediment samples of an annually resolved sediment record (containing 16-18\% and 1.3-1.9\% of total carbon and nitrogen, respectively). Several hundred pyrolytic compound peaks were detected of which over 200 were identified, which represent different classes of organic compounds (i.e., n-alkanes, n-alkenes, 2-ketones, carboxylic acids, carbohydrates, proteins, other N compounds, (methoxy)phenols, (poly)aromatics, chlorophyll and steroids/hopanoids). Technical reproducibility measured as relative standard deviation of the identified peaks in triplicate analyses was 5.5+/-4.3\%, with 90\% of the RSD values within 10\% and 98\% within 15\%. Finally, a multivariate calibration model was calculated between the pyrolytic degradation compounds and the sediment depth (i.e., sediment age), which is a function of degradation processes and changes in OM source type. This allowed validation of the Py-GC/MS dataset against fundamental processes involved in OM cycling in aquatic ecosystems.},
	language = {en},
	urldate = {2021-06-07},
	journal = {Anal Chim Acta},
	author = {Tolu, J. and Gerber, L. and Boily, J. F. and Bindler, R.},
	month = jun,
	year = {2015},
	note = {Edition: 2015/06/21},
	keywords = {*Gas Chromatography-Mass Spectrometry/standards, Algorithms, Calibration, Chemometric analyses, Environmental Monitoring, Gas chromatography/mass spectrometry, Geologic Sediments/*analysis/chemistry, Hot Temperature, Least-Squares Analysis, Organic Chemicals/*analysis/standards, Organic matter, Pyrolysis, Sediment, Sub-mg sample mass, Time Factors},
	pages = {93--102},
}

Molecular-level chemical information about organic matter (OM) in sediments helps to establish the sources of OM and the prevalent degradation/diagenetic processes, both essential for understanding the cycling of carbon (C) and of the elements associated with OM (toxic trace metals and nutrients) in lake ecosystems. Ideally, analytical methods for characterizing OM should allow high sample throughput, consume small amounts of sample and yield relevant chemical information, which are essential for multidisciplinary, high-temporal resolution and/or large spatial scale investigations. We have developed a high-throughput analytical method based on pyrolysis-gas chromatography/mass spectrometry and automated data processing to characterize sedimentary OM in sediments. Our method consumes 200 mug of freeze-dried and ground sediment sample. Pyrolysis was performed at 450 degrees C, which was found to avoid degradation of specific biomarkers (e.g., lignin compounds, fresh carbohydrates/cellulose) compared to 650 degrees C, which is in the range of temperatures commonly applied for environmental samples. The optimization was conducted using the top ten sediment samples of an annually resolved sediment record (containing 16-18% and 1.3-1.9% of total carbon and nitrogen, respectively). Several hundred pyrolytic compound peaks were detected of which over 200 were identified, which represent different classes of organic compounds (i.e., n-alkanes, n-alkenes, 2-ketones, carboxylic acids, carbohydrates, proteins, other N compounds, (methoxy)phenols, (poly)aromatics, chlorophyll and steroids/hopanoids). Technical reproducibility measured as relative standard deviation of the identified peaks in triplicate analyses was 5.5+/-4.3%, with 90% of the RSD values within 10% and 98% within 15%. Finally, a multivariate calibration model was calculated between the pyrolytic degradation compounds and the sediment depth (i.e., sediment age), which is a function of degradation processes and changes in OM source type. This allowed validation of the Py-GC/MS dataset against fundamental processes involved in OM cycling in aquatic ecosystems.

@article{kucukoglu_cle_2015,
	title = {{CLE} peptide signaling in plants - the power of moving around},
	volume = {155},
	issn = {1399-3054 (Electronic) 0031-9317 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26096704},
	doi = {10.1111/ppl.12358},
	abstract = {The CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (ESR)-RELATED (CLE) gene family encodes small secreted peptide ligands in plants. These peptides function non-cell autonomously through interactions with plasma membrane-associated LEUCINE-RICH REPEAT RECEPTOR-LIKE KINASEs (LRR-RLKs). These interactions are critical for cell-to-cell communications and control a variety of developmental and physiological processes in plants, such as regulation of stem cell proliferation and differentiation in the meristems, embryo and endosperm development, vascular development and autoregulation of nodulation. Here, we review the current knowledge in the field of CLE polypeptide signaling.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Physiol Plant},
	author = {Kucukoglu, M. and Nilsson, O.},
	month = sep,
	year = {2015},
	note = {Edition: 2015/06/23},
	keywords = {*Gene Expression Profiling, Arabidopsis Proteins/classification/*genetics, Arabidopsis/cytology/*genetics/growth \& development, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Meristem/cytology/genetics/growth \& development, Phylogeny, Protein Sorting Signals/*genetics, Signal Transduction/*genetics, Stem Cells/cytology/metabolism},
	pages = {74--87},
}

The CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (ESR)-RELATED (CLE) gene family encodes small secreted peptide ligands in plants. These peptides function non-cell autonomously through interactions with plasma membrane-associated LEUCINE-RICH REPEAT RECEPTOR-LIKE KINASEs (LRR-RLKs). These interactions are critical for cell-to-cell communications and control a variety of developmental and physiological processes in plants, such as regulation of stem cell proliferation and differentiation in the meristems, embryo and endosperm development, vascular development and autoregulation of nodulation. Here, we review the current knowledge in the field of CLE polypeptide signaling.

@article{kindgren_chloroplast_2015,
	title = {Chloroplast transcription, untangling the {Gordian} {Knot}},
	volume = {206},
	issn = {1469-8137 (Electronic) 0028-646X (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25865165},
	doi = {10.1111/nph.13388},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {New Phytol},
	author = {Kindgren, P. and Strand, A.},
	month = may,
	year = {2015},
	note = {Edition: 2015/04/14},
	keywords = {DNA-Directed RNA Polymerases/*chemistry, Plant Proteins/*chemistry, Protein Subunits/*chemistry, Zea mays/*genetics, chloroplast, development, pTAC, plastid encoded RNA polymerase (PEP), plastome, polymerase-associated protein (PAP)},
	pages = {889--891},
}

@article{kiefer_arabidopsis_2015,
	title = {Arabidopsis {AIP1}-2 restricted by {WER}-mediated patterning modulates planar polarity},
	volume = {142},
	issn = {1477-9129 (Electronic) 0950-1991 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25428588},
	doi = {10.1242/dev.111013},
	abstract = {The coordination of cell polarity within the plane of the tissue layer (planar polarity) is crucial for the development of diverse multicellular organisms. Small Rac/Rho-family GTPases and the actin cytoskeleton contribute to planar polarity formation at sites of polarity establishment in animals and plants. Yet, upstream pathways coordinating planar polarity differ strikingly between kingdoms. In the root of Arabidopsis thaliana, a concentration gradient of the phytohormone auxin coordinates polar recruitment of Rho-of-plant (ROP) to sites of polar epidermal hair initiation. However, little is known about cytoskeletal components and interactions that contribute to this planar polarity or about their relation to the patterning machinery. Here, we show that ACTIN7 (ACT7) represents a main actin isoform required for planar polarity of root hair positioning, interacting with the negative modulator ACTIN-INTERACTING PROTEIN1-2 (AIP1-2). ACT7, AIP1-2 and their genetic interaction are required for coordinated planar polarity of ROP downstream of ethylene signalling. Strikingly, AIP1-2 displays hair cell file-enriched expression, restricted by WEREWOLF (WER)-dependent patterning and modified by ethylene and auxin action. Hence, our findings reveal AIP1-2, expressed under control of the WER-dependent patterning machinery and the ethylene signalling pathway, as a modulator of actin-mediated planar polarity.},
	number = {1},
	urldate = {2021-06-07},
	journal = {Development},
	author = {Kiefer, C. S. and Claes, A. R. and Nzayisenga, J. C. and Pietra, S. and Stanislas, T. and Huser, A. and Ikeda, Y. and Grebe, M.},
	month = jan,
	year = {2015},
	note = {Edition: 2014/11/28},
	keywords = {*Body Patterning, *Cell Polarity, Actin, Actins/metabolism, Aip1, Arabidopsis, Arabidopsis Proteins/*metabolism, Arabidopsis/*cytology/*embryology, Carrier Proteins/*metabolism, DNA-Binding Proteins/*metabolism, Epistasis, Genetic, Ethylenes/metabolism, Patterning, Planar polarity, Plant Roots/metabolism, Protein Binding, Saccharomyces cerevisiae/metabolism, Signal Transduction, Werewolf},
	pages = {151--61},
}

The coordination of cell polarity within the plane of the tissue layer (planar polarity) is crucial for the development of diverse multicellular organisms. Small Rac/Rho-family GTPases and the actin cytoskeleton contribute to planar polarity formation at sites of polarity establishment in animals and plants. Yet, upstream pathways coordinating planar polarity differ strikingly between kingdoms. In the root of Arabidopsis thaliana, a concentration gradient of the phytohormone auxin coordinates polar recruitment of Rho-of-plant (ROP) to sites of polar epidermal hair initiation. However, little is known about cytoskeletal components and interactions that contribute to this planar polarity or about their relation to the patterning machinery. Here, we show that ACTIN7 (ACT7) represents a main actin isoform required for planar polarity of root hair positioning, interacting with the negative modulator ACTIN-INTERACTING PROTEIN1-2 (AIP1-2). ACT7, AIP1-2 and their genetic interaction are required for coordinated planar polarity of ROP downstream of ethylene signalling. Strikingly, AIP1-2 displays hair cell file-enriched expression, restricted by WEREWOLF (WER)-dependent patterning and modified by ethylene and auxin action. Hence, our findings reveal AIP1-2, expressed under control of the WER-dependent patterning machinery and the ethylene signalling pathway, as a modulator of actin-mediated planar polarity.

@article{jin_auxin_2015,
	title = {Auxin is a long-range signal that acts independently of ethylene signaling on leaf abscission in {Populus}},
	volume = {6},
	issn = {1664-462X (Print) 1664-462X (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26322071},
	doi = {10.3389/fpls.2015.00634},
	abstract = {Timing of leaf abscission is an important trait for biomass production and seasonal acclimation in deciduous trees. The signaling leading to organ separation, from the external cue (decreasing photoperiod) to ethylene-regulated hydrolysis of the middle lamellae in the abscission zone, is only poorly understood. Data from annual species indicate that the formation of an auxin gradient spanning the abscission zone regulates the timing of abscission. We established an experimental system in Populus to induce leaf shedding synchronously under controlled greenhouse conditions in order to test the function of auxin in leaf abscission. Here, we show that exogenous auxin delayed abscission of dark-induced leaves over short and long distances and that a new auxin response maximum preceded the formation of an abscission zone. Several auxin transporters were down-regulated during abscission and inhibition of polar auxin transport delayed leaf shedding. Ethylene signaling was not involved in the regulation of these auxin transporters and in the formation of an abscission zone, but was required for the expression of hydrolytic enzymes associated with cell separation. Since exogenous auxin delayed abscission in absence of ethylene signaling auxin likely acts independently of ethylene signaling on cell separation.},
	urldate = {2021-06-07},
	journal = {Front Plant Sci},
	author = {Jin, X. and Zimmermann, J. and Polle, A. and Fischer, U.},
	month = aug,
	year = {2015},
	note = {Edition: 2015/09/01},
	keywords = {PIN proteins, Populus, abscission, auxin, cell separation, ethylene},
	pages = {634},
}

Timing of leaf abscission is an important trait for biomass production and seasonal acclimation in deciduous trees. The signaling leading to organ separation, from the external cue (decreasing photoperiod) to ethylene-regulated hydrolysis of the middle lamellae in the abscission zone, is only poorly understood. Data from annual species indicate that the formation of an auxin gradient spanning the abscission zone regulates the timing of abscission. We established an experimental system in Populus to induce leaf shedding synchronously under controlled greenhouse conditions in order to test the function of auxin in leaf abscission. Here, we show that exogenous auxin delayed abscission of dark-induced leaves over short and long distances and that a new auxin response maximum preceded the formation of an abscission zone. Several auxin transporters were down-regulated during abscission and inhibition of polar auxin transport delayed leaf shedding. Ethylene signaling was not involved in the regulation of these auxin transporters and in the formation of an abscission zone, but was required for the expression of hydrolytic enzymes associated with cell separation. Since exogenous auxin delayed abscission in absence of ethylene signaling auxin likely acts independently of ethylene signaling on cell separation.

@article{hong_age_2015,
	title = {Age trend of heritability, genetic correlation, and efficiency of early selection for wood quality traits in {Scots} pine},
	volume = {45},
	issn = {0045-5067},
	url = {://WOS:000357136800004},
	doi = {10.1139/cjfr-2014-0465},
	abstract = {To examine the efficiency of early selection for wood quality traits in the Scots pine (Pinus sylvestris L.) breeding program in Sweden, a total of 778 wood increment cores were sampled from 179 full-sib families in a single progeny trial at 40 years of age. Age trend of inheritance, age-age genetic correlation, and early selection efficiency for eight wood traits including annual ring width, wood density, microfibril angle (MFA), modulus of elasticity (i.e., wood stiffness; MOE), and fibre dimensions were studied. Heritabilities for the eight wood traits reached a plateau between age 5 years and age 15 years, with the highest heritability for radial fibre width and fibre coarseness (similar to 0.6) and the lowest heritability for ring width (similar to 0.2). Heritability reached about 0.4 for both wood density and MFA but only reached about 0.3 for MOE. Genetic correlation from early to reference age 30 years reached a very high level ({\textgreater}0.8) for all eight wood traits at age 5 years. Early selection was effective for wood quality traits in Scots pine, and selection at age 8 years is recommended for MOE in Scots pine.},
	language = {English},
	number = {7},
	urldate = {2021-06-07},
	journal = {Canadian Journal of Forest Research},
	author = {Hong, Z. and Fries, A. and Wu, H. X.},
	month = jul,
	year = {2015},
	keywords = {2 locations, density, early selection, genetic parameters, growth traits, juvenile, mature wood, microfibril angle, parameters, picea-abies, pinus sylvestris, radiata pine, sylvestris, wood properties},
	pages = {817--825},
}

To examine the efficiency of early selection for wood quality traits in the Scots pine (Pinus sylvestris L.) breeding program in Sweden, a total of 778 wood increment cores were sampled from 179 full-sib families in a single progeny trial at 40 years of age. Age trend of inheritance, age-age genetic correlation, and early selection efficiency for eight wood traits including annual ring width, wood density, microfibril angle (MFA), modulus of elasticity (i.e., wood stiffness; MOE), and fibre dimensions were studied. Heritabilities for the eight wood traits reached a plateau between age 5 years and age 15 years, with the highest heritability for radial fibre width and fibre coarseness (similar to 0.6) and the lowest heritability for ring width (similar to 0.2). Heritability reached about 0.4 for both wood density and MFA but only reached about 0.3 for MOE. Genetic correlation from early to reference age 30 years reached a very high level (\textgreater0.8) for all eight wood traits at age 5 years. Early selection was effective for wood quality traits in Scots pine, and selection at age 8 years is recommended for MOE in Scots pine.

@article{ganea_development_2015,
	title = {Development and transferability of two multiplexes {nSSR} in {Scots} pine ({Pinus} sylvestris {L}.)},
	volume = {26},
	issn = {1007-662x},
	url = {://WOS:000354402700012},
	doi = {10.1007/s11676-015-0042-z},
	abstract = {Single sequence repeat (SSR) multiplexing is a semi high-throughput PCR methodology for the analysis of multiple SSRs. We developed two SSR multiplexes selected from SSR loci previously reported in the pine literature and tested the transferability of both SSR multiplexes in nine other pine species. We tested 234 nuclear SSR loci (nSSRs) previously described in the pine literature and selected ten nSSRs following the simple criteria of interpretability and reproducibility. Selected nuclear loci were divided into two nSSRs multiplex sets and their amplification was optimized for three different multiplex PCR methods based on: (a) a custom PCR protocol, (b) a custom protocol with hotstart taq polymerase, and (c) a commercially available kit for SSR multiplexing. To validate their performance, the level of genetic diversity was assessed in three Scots pine natural populations (Hungary, northern Sweden and southern Sweden). In addition, we also tested the transferability of these multiplexes in nine other pine species. We have developed two nSSRs multiplexes of five loci each that will contribute to reduce the costs of nSSR scoring, while increasing the capacity of nSSR loci analysis. Amplification was successful in all three populations (94 \% success) and the level of polymorphism (7.1 alleles/marker) was similar to that previously reported for other Scots pine natural populations. Transferability of both multiplexes was successful for those pine species closely related to Scots pine.},
	language = {English},
	number = {2},
	urldate = {2021-06-07},
	journal = {Journal of Forestry Research},
	author = {Ganea, S. and Ranade, S. S. and Hall, D. and Abrahamsson, S. and Garcia-Gil, M. R.},
	month = jun,
	year = {2015},
	keywords = {evolution, genetic diversity, genetic-structure, mitochondrial-DNA variation, molecular markers, nuclear microsatellite loci, nuclear ssr, pcr, picea-glauca, population-genetics, scots pine, simple sequence repeats, ssr markers, ssr multiplex},
	pages = {361--368},
}

Single sequence repeat (SSR) multiplexing is a semi high-throughput PCR methodology for the analysis of multiple SSRs. We developed two SSR multiplexes selected from SSR loci previously reported in the pine literature and tested the transferability of both SSR multiplexes in nine other pine species. We tested 234 nuclear SSR loci (nSSRs) previously described in the pine literature and selected ten nSSRs following the simple criteria of interpretability and reproducibility. Selected nuclear loci were divided into two nSSRs multiplex sets and their amplification was optimized for three different multiplex PCR methods based on: (a) a custom PCR protocol, (b) a custom protocol with hotstart taq polymerase, and (c) a commercially available kit for SSR multiplexing. To validate their performance, the level of genetic diversity was assessed in three Scots pine natural populations (Hungary, northern Sweden and southern Sweden). In addition, we also tested the transferability of these multiplexes in nine other pine species. We have developed two nSSRs multiplexes of five loci each that will contribute to reduce the costs of nSSR scoring, while increasing the capacity of nSSR loci analysis. Amplification was successful in all three populations (94 % success) and the level of polymorphism (7.1 alleles/marker) was similar to that previously reported for other Scots pine natural populations. Transferability of both multiplexes was successful for those pine species closely related to Scots pine.

@article{doyle_early_2015,
	title = {An early secretory pathway mediated by {GNOM}-{LIKE} 1 and {GNOM} is essential for basal polarity establishment in {Arabidopsis} thaliana},
	volume = {112},
	issn = {1091-6490 (Electronic) 0027-8424 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25646449},
	doi = {10.1073/pnas.1424856112},
	abstract = {Spatial regulation of the plant hormone indole-3-acetic acid (IAA, or auxin) is essential for plant development. Auxin gradient establishment is mediated by polarly localized auxin transporters, including PIN-FORMED (PIN) proteins. Their localization and abundance at the plasma membrane are tightly regulated by endomembrane machinery, especially the endocytic and recycling pathways mediated by the ADP ribosylation factor guanine nucleotide exchange factor (ARF-GEF) GNOM. We assessed the role of the early secretory pathway in establishing PIN1 polarity in Arabidopsis thaliana by pharmacological and genetic approaches. We identified the compound endosidin 8 (ES8), which selectively interferes with PIN1 basal polarity without altering the polarity of apical proteins. ES8 alters the auxin distribution pattern in the root and induces a strong developmental phenotype, including reduced root length. The ARF-GEF-defective mutants gnom-like 1 (gnl1-1) and gnom (van7) are significantly resistant to ES8. The compound does not affect recycling or vacuolar trafficking of PIN1 but leads to its intracellular accumulation, resulting in loss of PIN1 basal polarity at the plasma membrane. Our data confirm a role for GNOM in endoplasmic reticulum (ER)-Golgi trafficking and reveal that a GNL1/GNOM-mediated early secretory pathway selectively regulates PIN1 basal polarity establishment in a manner essential for normal plant development.},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Proc Natl Acad Sci U S A},
	author = {Doyle, S. M. and Haeger, A. and Vain, T. and Rigal, A. and Viotti, C. and Langowska, M. and Ma, Q. and Friml, J. and Raikhel, N. V. and Hicks, G. R. and Robert, S.},
	month = feb,
	year = {2015},
	note = {Edition: 2015/02/04},
	keywords = {Arabidopsis Proteins/metabolism/*physiology, Arabidopsis/growth \& development/*physiology, Endocytosis, Guanine Nucleotide Exchange Factors/*physiology, Membrane Transport Proteins/metabolism, PIN auxin transporters, Protein Transport, chemical genomics, endomembrane trafficking, plasma membrane protein polarity},
	pages = {E806--15},
}

Spatial regulation of the plant hormone indole-3-acetic acid (IAA, or auxin) is essential for plant development. Auxin gradient establishment is mediated by polarly localized auxin transporters, including PIN-FORMED (PIN) proteins. Their localization and abundance at the plasma membrane are tightly regulated by endomembrane machinery, especially the endocytic and recycling pathways mediated by the ADP ribosylation factor guanine nucleotide exchange factor (ARF-GEF) GNOM. We assessed the role of the early secretory pathway in establishing PIN1 polarity in Arabidopsis thaliana by pharmacological and genetic approaches. We identified the compound endosidin 8 (ES8), which selectively interferes with PIN1 basal polarity without altering the polarity of apical proteins. ES8 alters the auxin distribution pattern in the root and induces a strong developmental phenotype, including reduced root length. The ARF-GEF-defective mutants gnom-like 1 (gnl1-1) and gnom (van7) are significantly resistant to ES8. The compound does not affect recycling or vacuolar trafficking of PIN1 but leads to its intracellular accumulation, resulting in loss of PIN1 basal polarity at the plasma membrane. Our data confirm a role for GNOM in endoplasmic reticulum (ER)-Golgi trafficking and reveal that a GNL1/GNOM-mediated early secretory pathway selectively regulates PIN1 basal polarity establishment in a manner essential for normal plant development.

@article{zhang_intrinsic_2015,
	title = {An intrinsic {microRNA} timer regulates progressive decline in shoot regenerative capacity in plants},
	volume = {27},
	issn = {1532-298X (Electronic) 1040-4651 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25649435},
	doi = {10.1105/tpc.114.135186},
	abstract = {Plant cells are totipotent and competent to regenerate from differentiated organs. It has been shown that two phytohormones, auxin and cytokinin, play critical roles within this process. As in animals, the regenerative capacity declines with age in plants, but the molecular basis for this phenomenon remains elusive. Here, we demonstrate that an age-regulated microRNA, miR156, regulates shoot regenerative capacity. As a plant ages, the gradual increase in miR156-targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors leads to the progressive decline in shoot regenerative capacity. In old plants, SPL reduces shoot regenerative capacity by attenuating the cytokinin response through binding with the B-type ARABIDOPSIS RESPONSE REGULATORs, which encode the transcriptional activators in the cytokinin signaling pathway. Consistently, the increased amount of exogenous cytokinin complements the reduced shoot regenerative capacity in old plants. Therefore, the recruitment of age cues in response to cytokinin contributes to shoot regenerative competence.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Cell},
	author = {Zhang, T. Q. and Lian, H. and Tang, H. and Dolezal, K. and Zhou, C. M. and Yu, S. and Chen, J. H. and Chen, Q. and Liu, H. and Ljung, K. and Wang, J. W.},
	month = feb,
	year = {2015},
	note = {Edition: 2015/02/05},
	keywords = {Arabidopsis/genetics/*physiology, Cytokinins/pharmacology, Genes, Plant, MicroRNAs/genetics/*metabolism, Plant Proteins/metabolism, Plant Shoots/*genetics/*physiology, Regeneration/*genetics, Tobacco/genetics/*physiology},
	pages = {349--60},
}

Plant cells are totipotent and competent to regenerate from differentiated organs. It has been shown that two phytohormones, auxin and cytokinin, play critical roles within this process. As in animals, the regenerative capacity declines with age in plants, but the molecular basis for this phenomenon remains elusive. Here, we demonstrate that an age-regulated microRNA, miR156, regulates shoot regenerative capacity. As a plant ages, the gradual increase in miR156-targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors leads to the progressive decline in shoot regenerative capacity. In old plants, SPL reduces shoot regenerative capacity by attenuating the cytokinin response through binding with the B-type ARABIDOPSIS RESPONSE REGULATORs, which encode the transcriptional activators in the cytokinin signaling pathway. Consistently, the increased amount of exogenous cytokinin complements the reduced shoot regenerative capacity in old plants. Therefore, the recruitment of age cues in response to cytokinin contributes to shoot regenerative competence.

@article{yap_aef1mpr25_2015,
	title = {{AEF1}/{MPR25} is implicated in {RNA} editing of plastid {atpF} and mitochondrial nad5, and also promotes {atpF} splicing in {Arabidopsis} and rice},
	volume = {81},
	issn = {1365-313X (Electronic) 0960-7412 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25585673},
	doi = {10.1111/tpj.12756},
	abstract = {RNA editing is an essential mechanism that modifies target cytidines to uridine in both mitochondrial and plastid mRNA. Target sites are recognized by pentatricopeptide repeat (PPR) proteins. Using bioinformatics predictions based on the code describing sequence recognition by PPR proteins, we have identified an Arabidopsis editing factor required for editing of atpF in plastids. A loss-of-function mutation in ATPF EDITING FACTOR 1 (AEF1, AT3G22150) results in severe variegation, presumably due to decreased plastid ATP synthase levels. Loss of editing at the atpF site is coupled with a large decrease in splicing of the atpF transcript, even though the editing site is within an exon and 53 nucleotides distant from the splice site. The rice orthologue of AEF1, MPR25, has been reported to be required for editing of a site in mitochondrial nad5 transcripts, and we confirm that editing of the same site is affected in the Arabidopsis aef1 mutant. We also show that splicing of chloroplast atpF transcripts is affected in the rice mpr25 mutant. AEF1 is thus highly unusual for an RNA editing specificity factor in that it has functions in both organelles.},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Plant J},
	author = {Yap, A. and Kindgren, P. and Colas des Francs-Small, C. and Kazama, T. and Tanz, S. K. and Toriyama, K. and Small, I.},
	month = mar,
	year = {2015},
	note = {Edition: 2015/01/15},
	keywords = {ATP synthase, Arabidopsis Proteins/*genetics/metabolism, Arabidopsis thaliana, Arabidopsis/*genetics/metabolism, Chloroplast Proteins/genetics/metabolism, DNA-Binding Proteins/*genetics/metabolism, Mitochondrial Proteins/genetics/metabolism, Mutation, Oryza/*genetics/metabolism, Plant Proteins/*genetics/metabolism, Plastids/genetics/metabolism, RNA Editing, RNA Splicing, RNA, Chloroplast/genetics, RNA, Messenger/genetics, Transcription Factors/*genetics/metabolism, chloroplast, dual targeting, mitochondria, splicing},
	pages = {661--9},
}

RNA editing is an essential mechanism that modifies target cytidines to uridine in both mitochondrial and plastid mRNA. Target sites are recognized by pentatricopeptide repeat (PPR) proteins. Using bioinformatics predictions based on the code describing sequence recognition by PPR proteins, we have identified an Arabidopsis editing factor required for editing of atpF in plastids. A loss-of-function mutation in ATPF EDITING FACTOR 1 (AEF1, AT3G22150) results in severe variegation, presumably due to decreased plastid ATP synthase levels. Loss of editing at the atpF site is coupled with a large decrease in splicing of the atpF transcript, even though the editing site is within an exon and 53 nucleotides distant from the splice site. The rice orthologue of AEF1, MPR25, has been reported to be required for editing of a site in mitochondrial nad5 transcripts, and we confirm that editing of the same site is affected in the Arabidopsis aef1 mutant. We also show that splicing of chloroplast atpF transcripts is affected in the rice mpr25 mutant. AEF1 is thus highly unusual for an RNA editing specificity factor in that it has functions in both organelles.

@article{vayssieres_development_2015,
	title = {Development of the {Poplar}-{Laccaria} bicolor {Ectomycorrhiza} {Modifies} {Root} {Auxin} {Metabolism}, {Signaling}, and {Response}},
	volume = {169},
	issn = {1532-2548 (Electronic) 0032-0889 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26084921},
	doi = {10.1104/pp.114.255620},
	abstract = {Root systems of host trees are known to establish ectomycorrhizae (ECM) interactions with rhizospheric fungi. This mutualistic association leads to dramatic developmental modifications in root architecture, with the formation of numerous short and swollen lateral roots ensheathed by a fungal mantle. Knowing that auxin plays a crucial role in root development, we investigated how auxin metabolism, signaling, and response are affected in poplar (Populus spp.)-Laccaria bicolor ECM roots. The plant-fungus interaction leads to the arrest of lateral root growth with simultaneous attenuation of the synthetic auxin response element DR5. Measurement of auxin-related metabolites in the free-living partners revealed that the mycelium of L. bicolor produces high concentrations of the auxin indole-3-acetic acid (IAA). Metabolic profiling showed an accumulation of IAA and changes in the indol-3-pyruvic acid-dependent IAA biosynthesis and IAA conjugation and degradation pathways during ECM formation. The global analysis of auxin response gene expression and the regulation of AUXIN SIGNALING F-BOX PROTEIN5, AUXIN/IAA, and AUXIN RESPONSE FACTOR expression in ECM roots suggested that symbiosis-dependent auxin signaling is activated during the colonization by L. bicolor. Taking all this evidence into account, we propose a model in which auxin signaling plays a crucial role in the modification of root growth during ECM formation.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiol},
	author = {Vayssieres, A. and Pencik, A. and Felten, J. and Kohler, A. and Ljung, K. and Martin, F. and Legue, V.},
	month = sep,
	year = {2015},
	note = {Edition: 2015/06/19},
	keywords = {*Signal Transduction/drug effects, Gene Expression Regulation, Plant/drug effects, Indoleacetic Acids/*metabolism/pharmacology, Laccaria/drug effects/*physiology, Metabolome/drug effects, Models, Biological, Multivariate Analysis, Mycorrhizae/drug effects/*physiology, Plant Proteins/metabolism, Plant Roots/drug effects/growth \& development/*metabolism/*microbiology, Populus/drug effects/*microbiology},
	pages = {890--902},
}

Root systems of host trees are known to establish ectomycorrhizae (ECM) interactions with rhizospheric fungi. This mutualistic association leads to dramatic developmental modifications in root architecture, with the formation of numerous short and swollen lateral roots ensheathed by a fungal mantle. Knowing that auxin plays a crucial role in root development, we investigated how auxin metabolism, signaling, and response are affected in poplar (Populus spp.)-Laccaria bicolor ECM roots. The plant-fungus interaction leads to the arrest of lateral root growth with simultaneous attenuation of the synthetic auxin response element DR5. Measurement of auxin-related metabolites in the free-living partners revealed that the mycelium of L. bicolor produces high concentrations of the auxin indole-3-acetic acid (IAA). Metabolic profiling showed an accumulation of IAA and changes in the indol-3-pyruvic acid-dependent IAA biosynthesis and IAA conjugation and degradation pathways during ECM formation. The global analysis of auxin response gene expression and the regulation of AUXIN SIGNALING F-BOX PROTEIN5, AUXIN/IAA, and AUXIN RESPONSE FACTOR expression in ECM roots suggested that symbiosis-dependent auxin signaling is activated during the colonization by L. bicolor. Taking all this evidence into account, we propose a model in which auxin signaling plays a crucial role in the modification of root growth during ECM formation.

@article{sto_conservation_2015,
	title = {Conservation of the abscission signaling peptide {IDA} during {Angiosperm} evolution: withstanding genome duplications and gain and loss of the receptors {HAE}/{HSL2}},
	volume = {6},
	issn = {1664-462X (Print) 1664-462X (Linking)},
	shorttitle = {Conservation of the abscission signaling peptide {IDA} during {Angiosperm} evolution},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26579174},
	doi = {10.3389/fpls.2015.00931},
	abstract = {The peptide INFLORESCENCE DEFICIENT IN ABSCISSION (IDA), which signals through the leucine-rich repeat receptor-like kinases HAESA (HAE) and HAESA-LIKE2 (HSL2), controls different cell separation events in Arabidopsis thaliana. We hypothesize the involvement of this signaling module in abscission processes in other plant species even though they may shed other organs than A. thaliana. As the first step toward testing this hypothesis from an evolutionarily perspective we have identified genes encoding putative orthologs of IDA and its receptors by BLAST searches of publically available protein, nucleotide and genome databases for angiosperms. Genes encoding IDA or IDA-LIKE (IDL) peptides and HSL proteins were found in all investigated species, which were selected as to represent each angiosperm order with available genomic sequences. The 12 amino acids representing the bioactive peptide in A. thaliana have virtually been unchanged throughout the evolution of the angiosperms; however, the number of IDL and HSL genes varies between different orders and species. The phylogenetic analyses suggest that IDA, HSL2, and the related HSL1 gene, were present in the species that gave rise to the angiosperms. HAE has arisen from HSL1 after a genome duplication that took place after the monocot-eudicots split. HSL1 has also independently been duplicated in the monocots, while HSL2 has been lost in gingers (Zingiberales) and grasses (Poales). IDA has been duplicated in eudicots to give rise to functionally divergent IDL peptides. We postulate that the high number of IDL homologs present in the core eudicots is a result of multiple whole genome duplications (WGD). We substantiate the involvement of IDA and HAE/HSL2 homologs in abscission by providing gene expression data of different organ separation events from various species.},
	urldate = {2021-06-07},
	journal = {Front Plant Sci},
	author = {Sto, I. M. and Orr, R. J. and Fooyontphanich, K. and Jin, X. and Knutsen, J. M. and Fischer, U. and Tranbarger, T. J. and Nordal, I. and Aalen, R. B.},
	month = oct,
	year = {2015},
	note = {Edition: 2015/11/19},
	keywords = {Lrr-rlk, Populus, fruit abscission, genome duplication, leaf abscission, oil palm, peptide signaling, phylogeny},
	pages = {931},
}

The peptide INFLORESCENCE DEFICIENT IN ABSCISSION (IDA), which signals through the leucine-rich repeat receptor-like kinases HAESA (HAE) and HAESA-LIKE2 (HSL2), controls different cell separation events in Arabidopsis thaliana. We hypothesize the involvement of this signaling module in abscission processes in other plant species even though they may shed other organs than A. thaliana. As the first step toward testing this hypothesis from an evolutionarily perspective we have identified genes encoding putative orthologs of IDA and its receptors by BLAST searches of publically available protein, nucleotide and genome databases for angiosperms. Genes encoding IDA or IDA-LIKE (IDL) peptides and HSL proteins were found in all investigated species, which were selected as to represent each angiosperm order with available genomic sequences. The 12 amino acids representing the bioactive peptide in A. thaliana have virtually been unchanged throughout the evolution of the angiosperms; however, the number of IDL and HSL genes varies between different orders and species. The phylogenetic analyses suggest that IDA, HSL2, and the related HSL1 gene, were present in the species that gave rise to the angiosperms. HAE has arisen from HSL1 after a genome duplication that took place after the monocot-eudicots split. HSL1 has also independently been duplicated in the monocots, while HSL2 has been lost in gingers (Zingiberales) and grasses (Poales). IDA has been duplicated in eudicots to give rise to functionally divergent IDL peptides. We postulate that the high number of IDL homologs present in the core eudicots is a result of multiple whole genome duplications (WGD). We substantiate the involvement of IDA and HAE/HSL2 homologs in abscission by providing gene expression data of different organ separation events from various species.

@article{stanislas_arabidopsis_2015,
	title = {Arabidopsis {D6PK} is a lipid domain-dependent mediator of root epidermal planar polarity},
	volume = {1},
	issn = {2055-0278 (Electronic) 2055-0278 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/27251533},
	doi = {10.1038/nplants.2015.162},
	abstract = {Development of diverse multicellular organisms relies on coordination of single-cell polarities within the plane of the tissue layer (planar polarity). Cell polarity often involves plasma membrane heterogeneity generated by accumulation of specific lipids and proteins into membrane subdomains. Coordinated hair positioning along Arabidopsis root epidermal cells provides a planar polarity model in plants, but knowledge about the functions of proteo-lipid domains in planar polarity signalling remains limited. Here we show that Rho-of-plant (ROP) 2 and 6, phosphatidylinositol-4-phosphate 5-kinase 3 (PIP5K3), DYNAMIN-RELATED PROTEIN (DRP) 1A and DRP2B accumulate in a sterol-enriched, polar membrane domain during root hair initiation. DRP1A, DRP2B, PIP5K3 and sterols are required for planar polarity and the AGCVIII kinase D6 PROTEIN KINASE (D6PK) is a modulator of this process. D6PK undergoes phosphatidylinositol-4,5-bisphosphate- and sterol-dependent basal-to-planar polarity switching into the polar, lipid-enriched domain just before hair formation, unravelling lipid-dependent D6PK localization during late planar polarity signalling.},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Nat Plants},
	author = {Stanislas, T. and Huser, A. and Barbosa, I. C. and Kiefer, C. S. and Brackmann, K. and Pietra, S. and Gustavsson, A. and Zourelidou, M. and Schwechheimer, C. and Grebe, M.},
	month = nov,
	year = {2015},
	note = {Edition: 2015/01/01},
	pages = {15162},
}

Development of diverse multicellular organisms relies on coordination of single-cell polarities within the plane of the tissue layer (planar polarity). Cell polarity often involves plasma membrane heterogeneity generated by accumulation of specific lipids and proteins into membrane subdomains. Coordinated hair positioning along Arabidopsis root epidermal cells provides a planar polarity model in plants, but knowledge about the functions of proteo-lipid domains in planar polarity signalling remains limited. Here we show that Rho-of-plant (ROP) 2 and 6, phosphatidylinositol-4-phosphate 5-kinase 3 (PIP5K3), DYNAMIN-RELATED PROTEIN (DRP) 1A and DRP2B accumulate in a sterol-enriched, polar membrane domain during root hair initiation. DRP1A, DRP2B, PIP5K3 and sterols are required for planar polarity and the AGCVIII kinase D6 PROTEIN KINASE (D6PK) is a modulator of this process. D6PK undergoes phosphatidylinositol-4,5-bisphosphate- and sterol-dependent basal-to-planar polarity switching into the polar, lipid-enriched domain just before hair formation, unravelling lipid-dependent D6PK localization during late planar polarity signalling.

@article{soolanayakanahally_comparative_2015,
	title = {Comparative physiology of allopatric {Populus} species: geographic clines in photosynthesis, height growth, and carbon isotope discrimination in common gardens},
	volume = {6},
	issn = {1664-462X (Print) 1664-462X (Linking)},
	shorttitle = {Comparative physiology of allopatric {Populus} species},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26236324},
	doi = {10.3389/fpls.2015.00528},
	abstract = {Populus species with wide geographic ranges display strong adaptation to local environments. We studied the clinal patterns in phenology and ecophysiology in allopatric Populus species adapted to similar environments on different continents under common garden settings. As a result of climatic adaptation, both Populus tremula L. and Populus balsamifera L. display latitudinal clines in photosynthetic rates (A), whereby high-latitude trees of P. tremula had higher A compared to low-latitude trees and nearly so in P. balsamifera (p = 0.06). Stomatal conductance (g s) and chlorophyll content index (CCI) follow similar latitudinal trends. However, foliar nitrogen was positively correlated with latitude in P. balsamifera and negatively correlated in P. tremula. No significant trends in carbon isotope composition of the leaf tissue (delta(13)C) were observed for both species; but, intrinsic water-use efficiency (WUEi) was negatively correlated with the latitude of origin in P. balsamifera. In spite of intrinsically higher A, high-latitude trees in both common gardens accomplished less height gain as a result of early bud set. Thus, shoot biomass was determined by height elongation duration (HED), which was well approximated by the number of days available for free growth between bud flush and bud set. We highlight the shortcoming of unreplicated outdoor common gardens for tree improvement and the crucial role of photoperiod in limiting height growth, further complicating interpretation of other secondary effects.},
	language = {English},
	urldate = {2021-06-07},
	journal = {Front Plant Sci},
	author = {Soolanayakanahally, R. Y. and Guy, R. D. and Street, N. R. and Robinson, K. M. and Silim, S. N. and Albrectsen, B. R. and Jansson, S.},
	year = {2015},
	note = {Edition: 2015/08/04},
	keywords = {Photosynthesis, bud set, carbon isotope discrimination, common garden, comparative physiology, latitude, photosynthesis, poplar, water-use efficiency},
	pages = {528},
}

Populus species with wide geographic ranges display strong adaptation to local environments. We studied the clinal patterns in phenology and ecophysiology in allopatric Populus species adapted to similar environments on different continents under common garden settings. As a result of climatic adaptation, both Populus tremula L. and Populus balsamifera L. display latitudinal clines in photosynthetic rates (A), whereby high-latitude trees of P. tremula had higher A compared to low-latitude trees and nearly so in P. balsamifera (p = 0.06). Stomatal conductance (g s) and chlorophyll content index (CCI) follow similar latitudinal trends. However, foliar nitrogen was positively correlated with latitude in P. balsamifera and negatively correlated in P. tremula. No significant trends in carbon isotope composition of the leaf tissue (delta(13)C) were observed for both species; but, intrinsic water-use efficiency (WUEi) was negatively correlated with the latitude of origin in P. balsamifera. In spite of intrinsically higher A, high-latitude trees in both common gardens accomplished less height gain as a result of early bud set. Thus, shoot biomass was determined by height elongation duration (HED), which was well approximated by the number of days available for free growth between bud flush and bud set. We highlight the shortcoming of unreplicated outdoor common gardens for tree improvement and the crucial role of photoperiod in limiting height growth, further complicating interpretation of other secondary effects.

@article{sheng_aberrant_2015,
	title = {Aberrant fat metabolism in {Caenorhabditis} elegans mutants with defects in the defecation motor program},
	volume = {10},
	issn = {1932-6203 (Electronic) 1932-6203 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25849533},
	doi = {10.1371/journal.pone.0124515},
	abstract = {The molecular mechanisms by which dietary fatty acids are absorbed by the intestine, and the way in which the process is regulated are poorly understood. In a genetic screen for mutations affecting fat accumulation in the intestine of Caenorhabditis elegans, nematode worms, we have isolated mutations in the aex-5 gene, which encodes a Kex2/subtilisin-family, Ca2+-sensitive proprotein convertase known to be required for maturation of certain neuropeptides, and for a discrete step in an ultradian rhythmic phenomenon called the defecation motor program. We demonstrate that aex-5 mutants have markedly lower steady-state levels of fat in the intestine, and that this defect is associated with a significant reduction in the rate at which labeled fatty acid derivatives are taken up from the intestinal lumen. Other mutations affecting the defecation motor program also affect steady-state levels of triglycerides, suggesting that the program is required per se for the proper accumulation of neutral lipids. Our results suggest that an important function of the defecation motor program in C. elegans is to promote the uptake of an important class of dietary nutrients. They also imply that modulation of the program might be one way in which worms adjust nutrient uptake in response to altered metabolic status.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {PLoS One},
	author = {Sheng, M. and Hosseinzadeh, A. and Muralidharan, S. V. and Gaur, R. and Selstam, E. and Tuck, S.},
	month = apr,
	year = {2015},
	note = {Edition: 2015/04/08},
	keywords = {*Defecation, Animals, Caenorhabditis elegans Proteins/*genetics, Caenorhabditis elegans/genetics/*metabolism, Dietary Fats/metabolism, Endopeptidases/*genetics, Intestinal Mucosa/metabolism, Lipid Metabolism, Mutation},
	pages = {e0124515},
}

The molecular mechanisms by which dietary fatty acids are absorbed by the intestine, and the way in which the process is regulated are poorly understood. In a genetic screen for mutations affecting fat accumulation in the intestine of Caenorhabditis elegans, nematode worms, we have isolated mutations in the aex-5 gene, which encodes a Kex2/subtilisin-family, Ca2+-sensitive proprotein convertase known to be required for maturation of certain neuropeptides, and for a discrete step in an ultradian rhythmic phenomenon called the defecation motor program. We demonstrate that aex-5 mutants have markedly lower steady-state levels of fat in the intestine, and that this defect is associated with a significant reduction in the rate at which labeled fatty acid derivatives are taken up from the intestinal lumen. Other mutations affecting the defecation motor program also affect steady-state levels of triglycerides, suggesting that the program is required per se for the proper accumulation of neutral lipids. Our results suggest that an important function of the defecation motor program in C. elegans is to promote the uptake of an important class of dietary nutrients. They also imply that modulation of the program might be one way in which worms adjust nutrient uptake in response to altered metabolic status.

@article{shaikhali_biochemical_2015,
	title = {Biochemical and redox characterization of the mediator complex and its associated transcription factor {GeBPL}, a {GLABROUS1} enhancer binding protein},
	volume = {468},
	issn = {1470-8728 (Electronic) 0264-6021 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25877331},
	doi = {10.1042/BJ20150132},
	abstract = {The eukaryotic mediator integrates regulatory signals from promoter-bound transcription factors (TFs) and transmits them to RNA polymerase II (Pol II) machinery. Although redox signalling is important in adjusting plant metabolism and development, nothing is known about a possible redox regulation of mediator. In the present study, using pull-down and yeast two-hybrid assays, we demonstrate the association of mediator (MED) subunits MED10a, MED28 and MED32 with the GLABROUS1 (GL1) enhancer-binding protein-like (GeBPL), a plant-specific TF that binds a promoter containing cryptochrome 1 response element 2 (CryR2) element. All the corresponding recombinant proteins form various types of covalent oligomers linked by intermolecular disulfide bonds that are reduced in vitro by the thioredoxin (TRX) and/or glutathione/glutaredoxin (GRX) systems. The presence of recombinant MED10a, MED28 and MED32 subunits or changes of its redox state affect the DNA-binding capacity of GeBPL suggesting that redox-driven conformational changes might modulate its activity. Overall, these results advance our understanding of how redox signalling affects transcription and identify mediator as a novel actor in redox signalling pathways, relaying or integrating redox changes in combination with specific TFs as GeBPL.},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Biochem J},
	author = {Shaikhali, J. and Davoine, C. and Brannstrom, K. and Rouhier, N. and Bygdell, J. and Bjorklund, S. and Wingsle, G.},
	month = jun,
	year = {2015},
	note = {Edition: 2015/04/17},
	keywords = {Arabidopsis Proteins/genetics/*metabolism, Arabidopsis thaliana, Arabidopsis/*metabolism, CryR2, DNA-Binding Proteins/genetics/*metabolism, GLABROUS1 enhancer-binding protein (GeBP), Glutaredoxins/metabolism, Glutathione/metabolism, Mediator Complex/genetics/*metabolism, Mutagenesis, Site-Directed, Mutation, Oxidation-Reduction, Promoter Regions, Genetic, Protein Subunits/genetics/*metabolism, Recombinant Proteins/metabolism, Response Elements, Thioredoxins/metabolism, Transcription Factors, Two-Hybrid System Techniques, deoxyribonucleic acid (DNA)-binding, mediator, redox},
	pages = {385--400},
}

The eukaryotic mediator integrates regulatory signals from promoter-bound transcription factors (TFs) and transmits them to RNA polymerase II (Pol II) machinery. Although redox signalling is important in adjusting plant metabolism and development, nothing is known about a possible redox regulation of mediator. In the present study, using pull-down and yeast two-hybrid assays, we demonstrate the association of mediator (MED) subunits MED10a, MED28 and MED32 with the GLABROUS1 (GL1) enhancer-binding protein-like (GeBPL), a plant-specific TF that binds a promoter containing cryptochrome 1 response element 2 (CryR2) element. All the corresponding recombinant proteins form various types of covalent oligomers linked by intermolecular disulfide bonds that are reduced in vitro by the thioredoxin (TRX) and/or glutathione/glutaredoxin (GRX) systems. The presence of recombinant MED10a, MED28 and MED32 subunits or changes of its redox state affect the DNA-binding capacity of GeBPL suggesting that redox-driven conformational changes might modulate its activity. Overall, these results advance our understanding of how redox signalling affects transcription and identify mediator as a novel actor in redox signalling pathways, relaying or integrating redox changes in combination with specific TFs as GeBPL.

@article{serk_cooperative_2015,
	title = {Cooperative lignification of xylem tracheary elements},
	volume = {10},
	issn = {1559-2324 (Electronic) 1559-2316 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25761224},
	doi = {10.1080/15592324.2014.1003753},
	abstract = {The development of xylem tracheary elements (TEs)--the hydro-mineral sap conducting cells--has been an evolutionary breakthrough to enable long distance nutrition and upright growth of vascular land plants. To allow sap conduction, TEs form hollow laterally reinforced cylinders by combining programmed cell death and secondary cell wall formation. To ensure their structural resistance for sap conduction, TE cell walls are reinforced with the phenolic polymer lignin, which is deposited after TE cell death by the cooperative supply of monomers and other substrates from the surrounding living cells.},
	language = {eng},
	number = {4},
	journal = {Plant Signal Behav},
	author = {Serk, H. and Gorzsas, A. and Tuominen, H. and Pesquet, E.},
	year = {2015},
	note = {Edition: 2015/03/12},
	keywords = {Arabidopsis, Arabidopsis Proteins, Arabidopsis Proteins/metabolism, Arabidopsis/metabolism, Asteraceae, Asteraceae/*metabolism, Cell Wall, Cell Wall/metabolism, Hypocotyl, Hypocotyl/metabolism, Lignin, Lignin/*metabolism, Time Factors, Xylem, Xylem/*metabolism, lignin, non-cell autonomous process, post-mortem lignification, secondary cell wall, tracheary elements, xylem/wood vessels},
	pages = {e1003753},
}

The development of xylem tracheary elements (TEs)–the hydro-mineral sap conducting cells–has been an evolutionary breakthrough to enable long distance nutrition and upright growth of vascular land plants. To allow sap conduction, TEs form hollow laterally reinforced cylinders by combining programmed cell death and secondary cell wall formation. To ensure their structural resistance for sap conduction, TE cell walls are reinforced with the phenolic polymer lignin, which is deposited after TE cell death by the cooperative supply of monomers and other substrates from the surrounding living cells.

@article{ranade_comparative_2015,
	title = {Comparative in silico analysis of {SSRs} in coding regions of high confidence predicted genes in {Norway} spruce ({Picea} abies) and {Loblolly} pine ({Pinus} taeda)},
	volume = {16},
	issn = {1471-2156 (Electronic) 1471-2156 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26706685},
	doi = {10.1186/s12863-015-0304-y},
	abstract = {BACKGROUND: Microsatellites or simple sequence repeats (SSRs) are DNA sequences consisting of 1-6 bp tandem repeat motifs present in the genome. SSRs are considered to be one of the most powerful tools in genetic studies. We carried out a comparative study of perfect SSR loci belonging to class I ({\textgreater}/=20) and class II ({\textgreater}/=12 and {\textless}20 bp) types located in coding regions of high confidence genes in Picea abies and Pinus taeda. SSRLocator was used to retrieve SSRs from the full length CDS of predicted genes in both species. RESULTS: Trimers were the most abundant motifs in class I followed by hexamers in Picea abies, while trimers and hexamers were equally abundant in Pinus taeda class I SSRs. Hexamers were most frequent within class II SSRs followed by trimers, in both species. Although the frequency of genes containing SSRs was slightly higher in Pinus taeda, SSR counts per Mbp for class I was similar in both species (P-value = 0.22); while for class II SSRs, it was significantly higher in Picea abies (P-value = 0.00009). AT-rich motifs were higher in abundance than the GC-rich motifs, within class II SSRs in both the species (P-values = 10(-9) and 0). With reference to class I SSRs, AT-rich and GC-rich motifs were detected with equal frequency in Pinus taeda (P-value = 0.24); while in Picea abies, GC-rich motifs were detected with higher frequency than the AT-rich motifs (P-value = 0.0005). CONCLUSIONS: Our study gives a comparative overview of the genome SSRs composition based on high confidence genes in the two recently sequenced and economically important conifers and, also provides information on functional molecular markers that can be applied in genetic studies in Pinus and Picea species.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genet},
	author = {Ranade, S. S. and Lin, Y. C. and Van de Peer, Y. and Garcia-Gil, M. R.},
	month = dec,
	year = {2015},
	note = {Edition: 2015/12/27},
	keywords = {*Microsatellite Repeats, Computer Simulation, DNA, Plant/analysis/*genetics, Nucleotide Motifs, Picea/*genetics, Pinus taeda/*genetics},
	pages = {149},
}

BACKGROUND: Microsatellites or simple sequence repeats (SSRs) are DNA sequences consisting of 1-6 bp tandem repeat motifs present in the genome. SSRs are considered to be one of the most powerful tools in genetic studies. We carried out a comparative study of perfect SSR loci belonging to class I (\textgreater/=20) and class II (\textgreater/=12 and \textless20 bp) types located in coding regions of high confidence genes in Picea abies and Pinus taeda. SSRLocator was used to retrieve SSRs from the full length CDS of predicted genes in both species. RESULTS: Trimers were the most abundant motifs in class I followed by hexamers in Picea abies, while trimers and hexamers were equally abundant in Pinus taeda class I SSRs. Hexamers were most frequent within class II SSRs followed by trimers, in both species. Although the frequency of genes containing SSRs was slightly higher in Pinus taeda, SSR counts per Mbp for class I was similar in both species (P-value = 0.22); while for class II SSRs, it was significantly higher in Picea abies (P-value = 0.00009). AT-rich motifs were higher in abundance than the GC-rich motifs, within class II SSRs in both the species (P-values = 10(-9) and 0). With reference to class I SSRs, AT-rich and GC-rich motifs were detected with equal frequency in Pinus taeda (P-value = 0.24); while in Picea abies, GC-rich motifs were detected with higher frequency than the AT-rich motifs (P-value = 0.0005). CONCLUSIONS: Our study gives a comparative overview of the genome SSRs composition based on high confidence genes in the two recently sequenced and economically important conifers and, also provides information on functional molecular markers that can be applied in genetic studies in Pinus and Picea species.

@article{rabeda_colocalization_2015,
	title = {Colocalization of low-methylesterified pectins and {Pb} deposits in the apoplast of aspen roots exposed to lead},
	volume = {205},
	issn = {1873-6424 (Electronic) 0269-7491 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26123720},
	doi = {10.1016/j.envpol.2015.05.048},
	abstract = {Low-methylesterified homogalacturonans have been suggested to play a role in the binding and immobilization of Pb in CW. Using root apices of hybrid aspen, a plant with a high phytoremediation potential, as a model, we demonstrated that the in situ distribution pattern of low-methylesterified homogalacturonan, pectin epitope (JIM5-P), reflects the pattern of Pb occurrence. The region which indicated high JIM5-P level corresponded with "Pb accumulation zone". Moreover, JIM5-P was especially abundant in cell junctions, CWs lining the intercellular spaces and the corners of intercellular spaces indicating the highest accumulation of Pb. Furthermore, JIM5-P and Pb commonly co-localized. The observations indicate that low-methylesterified homogalacturonan is the CW polymer that determines the capacity of CW for Pb sequestration. Our results suggest a promising directions for CW modification for enhancing the efficiency of plant roots in Pb accumulation, an important aspect in the phytoremediation of soils contaminated with trace metals.},
	language = {en},
	urldate = {2021-06-07},
	journal = {Environ Pollut},
	author = {Rabeda, I. and Bilski, H. and Mellerowicz, E. J. and Napieralska, A. and Suski, S. and Wozny, A. and Krzeslowska, M.},
	month = oct,
	year = {2015},
	note = {Edition: 2015/07/01},
	keywords = {Antibodies, Monoclonal/metabolism, Biodegradation, Environmental, Biomarkers/blood, Cell wall, Esterification, Heavy metal, Lead/*metabolism, Pectins/*metabolism, Phytoremediation, Plant Roots/metabolism, Populus, Populus/*metabolism, Soil Pollutants/*metabolism, Tolerance},
	pages = {315--26},
}

Low-methylesterified homogalacturonans have been suggested to play a role in the binding and immobilization of Pb in CW. Using root apices of hybrid aspen, a plant with a high phytoremediation potential, as a model, we demonstrated that the in situ distribution pattern of low-methylesterified homogalacturonan, pectin epitope (JIM5-P), reflects the pattern of Pb occurrence. The region which indicated high JIM5-P level corresponded with "Pb accumulation zone". Moreover, JIM5-P was especially abundant in cell junctions, CWs lining the intercellular spaces and the corners of intercellular spaces indicating the highest accumulation of Pb. Furthermore, JIM5-P and Pb commonly co-localized. The observations indicate that low-methylesterified homogalacturonan is the CW polymer that determines the capacity of CW for Pb sequestration. Our results suggest a promising directions for CW modification for enhancing the efficiency of plant roots in Pb accumulation, an important aspect in the phytoremediation of soils contaminated with trace metals.

@article{petersson_cell-type_2015,
	title = {Cell-type specific metabolic profiling of {Arabidopsis} thaliana protoplasts as a tool for plant systems biology},
	volume = {11},
	issn = {1573-3882 (Print) 1573-3882 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26491421},
	doi = {10.1007/s11306-015-0814-7},
	abstract = {Flow cytometry combined with cell sorting of protoplasts has previously been used successfully for transcript profiling of the Arabidopsis thaliana root. We have developed the technique further, and in this paper we present a robust and reliable method for metabolite profiling in specific cell types isolated from Arabidopsis roots. The method uses a combination of fluorescence-activated cell sorting and gas chromatography-time of flight-mass spectrometry analysis. Cortical and endodermal cells from the green fluorescent protein (GFP)-expressing enhancer trap line J0571 were analysed and compared with non-GFP-expressing cells and intact root tissue. Of the metabolites identified, several showed significant differences in concentration between cell types. Multivariate statistical analysis was used to compare metabolite patterns between cell and tissue types, showing that the patterns differed substantially. Isolation of specific cell populations combined with highly sensitive MS-analysis will be a powerful tool for future studies of plant metabolism, and can also be combined with transcript and protein profiling for in-depth analyses of cellular processes.},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Metabolomics},
	author = {Petersson, S. V. and Linden, P. and Moritz, T. and Ljung, K.},
	month = dec,
	year = {2015},
	note = {Edition: 2015/10/23},
	keywords = {Arabidopsis thaliana, Flow cytometry, Gas chromatography-mass spectrometry, Metabolite profiling, Multivariate statistical analysis, Untargeted metabolomics},
	pages = {1679--1689},
}

Flow cytometry combined with cell sorting of protoplasts has previously been used successfully for transcript profiling of the Arabidopsis thaliana root. We have developed the technique further, and in this paper we present a robust and reliable method for metabolite profiling in specific cell types isolated from Arabidopsis roots. The method uses a combination of fluorescence-activated cell sorting and gas chromatography-time of flight-mass spectrometry analysis. Cortical and endodermal cells from the green fluorescent protein (GFP)-expressing enhancer trap line J0571 were analysed and compared with non-GFP-expressing cells and intact root tissue. Of the metabolites identified, several showed significant differences in concentration between cell types. Multivariate statistical analysis was used to compare metabolite patterns between cell and tissue types, showing that the patterns differed substantially. Isolation of specific cell populations combined with highly sensitive MS-analysis will be a powerful tool for future studies of plant metabolism, and can also be combined with transcript and protein profiling for in-depth analyses of cellular processes.

@article{mamun_bioreactor_2015,
	title = {Bioreactor technology for clonal propagation of plants and metabolite production},
	volume = {10},
	issn = {1674-7984 1674-7992},
	doi = {10.1007/s11515-015-1355-1},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Frontiers in Biology},
	author = {Mamun, Nazmul H. A. and Egertsdotter, Ulrika and Aidun, Cyrus K.},
	month = apr,
	year = {2015},
	note = {Section: 177},
	pages = {177--193},
}

@article{maaroufi_anthropogenic_2015,
	title = {Anthropogenic nitrogen deposition enhances carbon sequestration in boreal soils},
	volume = {21},
	issn = {1365-2486 (Electronic) 1354-1013 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25711504},
	doi = {10.1111/gcb.12904},
	abstract = {It is proposed that carbon (C) sequestration in response to reactive nitrogen (Nr ) deposition in boreal forests accounts for a large portion of the terrestrial sink for anthropogenic CO2 emissions. While studies have helped clarify the magnitude by which Nr deposition enhances C sequestration by forest vegetation, there remains a paucity of long-term experimental studies evaluating how soil C pools respond. We conducted a long-term experiment, maintained since 1996, consisting of three N addition levels (0, 12.5, and 50 kg N ha(-1) yr(-1) ) in the boreal zone of northern Sweden to understand how atmospheric Nr deposition affects soil C accumulation, soil microbial communities, and soil respiration. We hypothesized that soil C sequestration will increase, and soil microbial biomass and soil respiration will decrease, with disproportionately large changes expected compared to low levels of N addition. Our data showed that the low N addition treatment caused a non-significant increase in the organic horizon C pool of {\textasciitilde}15\% and a significant increase of {\textasciitilde}30\% in response to the high N treatment relative to the control. The relationship between C sequestration and N addition in the organic horizon was linear, with a slope of 10 kg C kg(-1) N. We also found a concomitant decrease in total microbial and fungal biomasses and a {\textasciitilde}11\% reduction in soil respiration in response to the high N treatment. Our data complement previous data from the same study system describing aboveground C sequestration, indicating a total ecosystem sequestration rate of 26 kg C kg(-1) N. These estimates are far lower than suggested by some previous modeling studies, and thus will help improve and validate current modeling efforts aimed at separating the effect of multiple global change factors on the C balance of the boreal region.},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Glob Chang Biol},
	author = {Maaroufi, N. I. and Nordin, A. and Hasselquist, N. J. and Bach, L. H. and Palmqvist, K. and Gundale, M. J.},
	month = aug,
	year = {2015},
	note = {Edition: 2015/02/26},
	keywords = {*Carbon Sequestration, *Taiga, Carbon/*analysis, Ecosystem, Nitrogen/*analysis, Soil Microbiology, Soil/chemistry, Sweden, boreal forest, boreal soil, carbon sequestration, carbon sink, nitrogen deposition, soil C pool, soil respiration},
	pages = {3169--80},
}

It is proposed that carbon (C) sequestration in response to reactive nitrogen (Nr ) deposition in boreal forests accounts for a large portion of the terrestrial sink for anthropogenic CO2 emissions. While studies have helped clarify the magnitude by which Nr deposition enhances C sequestration by forest vegetation, there remains a paucity of long-term experimental studies evaluating how soil C pools respond. We conducted a long-term experiment, maintained since 1996, consisting of three N addition levels (0, 12.5, and 50 kg N ha(-1) yr(-1) ) in the boreal zone of northern Sweden to understand how atmospheric Nr deposition affects soil C accumulation, soil microbial communities, and soil respiration. We hypothesized that soil C sequestration will increase, and soil microbial biomass and soil respiration will decrease, with disproportionately large changes expected compared to low levels of N addition. Our data showed that the low N addition treatment caused a non-significant increase in the organic horizon C pool of ~15% and a significant increase of ~30% in response to the high N treatment relative to the control. The relationship between C sequestration and N addition in the organic horizon was linear, with a slope of 10 kg C kg(-1) N. We also found a concomitant decrease in total microbial and fungal biomasses and a ~11% reduction in soil respiration in response to the high N treatment. Our data complement previous data from the same study system describing aboveground C sequestration, indicating a total ecosystem sequestration rate of 26 kg C kg(-1) N. These estimates are far lower than suggested by some previous modeling studies, and thus will help improve and validate current modeling efforts aimed at separating the effect of multiple global change factors on the C balance of the boreal region.

@article{liu_resource_2015,
	title = {A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in {Populus}},
	volume = {82},
	issn = {1365-313X (Electronic) 0960-7412 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25903933},
	doi = {10.1111/tpj.12850},
	abstract = {Identifying transcription factor target genes is essential for modeling the transcriptional networks underlying developmental processes. Here we report a chromatin immunoprecipitation sequencing (ChIP-seq) resource consisting of genome-wide binding regions and associated putative target genes for four Populus homeodomain transcription factors expressed during secondary growth and wood formation. Software code (programs and scripts) for processing the Populus ChIP-seq data are provided within a publically available iPlant image, including tools for ChIP-seq data quality control and evaluation adapted from the human Encyclopedia of DNA Elements (ENCODE) project. Basic information for each transcription factor (including members of Class I KNOX, Class III HD ZIP, BEL1-like families) binding are summarized, including the number and location of binding regions, distribution of binding regions relative to gene features, associated putative target genes, and enriched functional categories of putative target genes. These ChIP-seq data have been integrated within the Populus Genome Integrative Explorer (PopGenIE) where they can be analyzed using a variety of web-based tools. We present an example analysis that shows preferential binding of transcription factor ARBORKNOX1 to the nearest neighbor genes in a pre-calculated co-expression network module, and enrichment for meristem-related genes within this module including multiple orthologs of Arabidopsis KNOTTED-like Arabidopsis 2/6.},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Plant J},
	author = {Liu, L. and Ramsay, T. and Zinkgraf, M. and Sundell, D. and Street, N. R. and Filkov, V. and Groover, A.},
	month = jun,
	year = {2015},
	note = {Edition: 2015/04/24},
	keywords = {Amino Acid Sequence, Binding Sites, Chromatin Immunoprecipitation, Gene Expression Profiling/methods, Gene Expression Regulation, Plant, Gene Regulatory Networks, Genome, Plant, Image Processing, Computer-Assisted, Molecular Sequence Data, Plant Proteins/*genetics/metabolism, Populus trichocarpa, Populus/*genetics/growth \& development, Transcription Factors/genetics/*metabolism, Wood/genetics/*growth \& development, Workflow, cambium, chromatin immunoprecipitation sequencing, secondary growth, transcription factor, wood formation},
	pages = {887--98},
}

Identifying transcription factor target genes is essential for modeling the transcriptional networks underlying developmental processes. Here we report a chromatin immunoprecipitation sequencing (ChIP-seq) resource consisting of genome-wide binding regions and associated putative target genes for four Populus homeodomain transcription factors expressed during secondary growth and wood formation. Software code (programs and scripts) for processing the Populus ChIP-seq data are provided within a publically available iPlant image, including tools for ChIP-seq data quality control and evaluation adapted from the human Encyclopedia of DNA Elements (ENCODE) project. Basic information for each transcription factor (including members of Class I KNOX, Class III HD ZIP, BEL1-like families) binding are summarized, including the number and location of binding regions, distribution of binding regions relative to gene features, associated putative target genes, and enriched functional categories of putative target genes. These ChIP-seq data have been integrated within the Populus Genome Integrative Explorer (PopGenIE) where they can be analyzed using a variety of web-based tools. We present an example analysis that shows preferential binding of transcription factor ARBORKNOX1 to the nearest neighbor genes in a pre-calculated co-expression network module, and enrichment for meristem-related genes within this module including multiple orthologs of Arabidopsis KNOTTED-like Arabidopsis 2/6.

@article{leal_valentim_quantitative_2015,
	title = {A quantitative and dynamic model of the {Arabidopsis} flowering time gene regulatory network},
	volume = {10},
	issn = {1932-6203 (Electronic) 1932-6203 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25719734},
	doi = {10.1371/journal.pone.0116973},
	abstract = {Various environmental signals integrate into a network of floral regulatory genes leading to the final decision on when to flower. Although a wealth of qualitative knowledge is available on how flowering time genes regulate each other, only a few studies incorporated this knowledge into predictive models. Such models are invaluable as they enable to investigate how various types of inputs are combined to give a quantitative readout. To investigate the effect of gene expression disturbances on flowering time, we developed a dynamic model for the regulation of flowering time in Arabidopsis thaliana. Model parameters were estimated based on expression time-courses for relevant genes, and a consistent set of flowering times for plants of various genetic backgrounds. Validation was performed by predicting changes in expression level in mutant backgrounds and comparing these predictions with independent expression data, and by comparison of predicted and experimental flowering times for several double mutants. Remarkably, the model predicts that a disturbance in a particular gene has not necessarily the largest impact on directly connected genes. For example, the model predicts that SUPPRESSOR OF OVEREXPRESSION OF CONSTANS (SOC1) mutation has a larger impact on APETALA1 (AP1), which is not directly regulated by SOC1, compared to its effect on LEAFY (LFY) which is under direct control of SOC1. This was confirmed by expression data. Another model prediction involves the importance of cooperativity in the regulation of APETALA1 (AP1) by LFY, a prediction supported by experimental evidence. Concluding, our model for flowering time gene regulation enables to address how different quantitative inputs are combined into one quantitative output, flowering time.},
	language = {eng},
	number = {2},
	journal = {PLoS One},
	author = {Leal Valentim, F. and Mourik, Sv and Pose, D. and Kim, M. C. and Schmid, M. and van Ham, R. C. and Busscher, M. and Sanchez-Perez, G. F. and Molenaar, J. and Angenent, G. C. and Immink, R. G. and van Dijk, A. D.},
	year = {2015},
	note = {Edition: 2015/02/27},
	keywords = {*Gene Expression Regulation, Plant, *Gene Regulatory Networks, Arabidopsis, Arabidopsis Proteins, Arabidopsis Proteins/genetics/metabolism, Arabidopsis/*genetics/growth \& development, Flowers, Flowers/*genetics/growth \& development, Gene Expression Regulation, Plant, Gene Regulatory Networks, MADS Domain Proteins, MADS Domain Proteins/genetics/metabolism, Models, Genetic, Transcription Factors, Transcription Factors/genetics/metabolism},
	pages = {e0116973},
}

Various environmental signals integrate into a network of floral regulatory genes leading to the final decision on when to flower. Although a wealth of qualitative knowledge is available on how flowering time genes regulate each other, only a few studies incorporated this knowledge into predictive models. Such models are invaluable as they enable to investigate how various types of inputs are combined to give a quantitative readout. To investigate the effect of gene expression disturbances on flowering time, we developed a dynamic model for the regulation of flowering time in Arabidopsis thaliana. Model parameters were estimated based on expression time-courses for relevant genes, and a consistent set of flowering times for plants of various genetic backgrounds. Validation was performed by predicting changes in expression level in mutant backgrounds and comparing these predictions with independent expression data, and by comparison of predicted and experimental flowering times for several double mutants. Remarkably, the model predicts that a disturbance in a particular gene has not necessarily the largest impact on directly connected genes. For example, the model predicts that SUPPRESSOR OF OVEREXPRESSION OF CONSTANS (SOC1) mutation has a larger impact on APETALA1 (AP1), which is not directly regulated by SOC1, compared to its effect on LEAFY (LFY) which is under direct control of SOC1. This was confirmed by expression data. Another model prediction involves the importance of cooperativity in the regulation of APETALA1 (AP1) by LFY, a prediction supported by experimental evidence. Concluding, our model for flowering time gene regulation enables to address how different quantitative inputs are combined into one quantitative output, flowering time.

@article{gorshkova_aspen_2015,
	title = {Aspen {Tension} {Wood} {Fibers} {Contain} beta-(1---{\textgreater} 4)-{Galactans} and {Acidic} {Arabinogalactans} {Retained} by {Cellulose} {Microfibrils} in {Gelatinous} {Walls}},
	volume = {169},
	issn = {1532-2548 (Electronic) 0032-0889 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26378099},
	doi = {10.1104/pp.15.00690},
	abstract = {Contractile cell walls are found in various plant organs and tissues such as tendrils, contractile roots, and tension wood. The tension-generating mechanism is not known but is thought to involve special cell wall architecture. We previously postulated that tension could result from the entrapment of certain matrix polymers within cellulose microfibrils. As reported here, this hypothesis was corroborated by sequential extraction and analysis of cell wall polymers that are retained by cellulose microfibrils in tension wood and normal wood of hybrid aspen (Populus tremula x Populus tremuloides). beta-(1--{\textgreater}4)-Galactan and type II arabinogalactan were the main large matrix polymers retained by cellulose microfibrils that were specifically found in tension wood. Xyloglucan was detected mostly in oligomeric form in the alkali-labile fraction and was enriched in tension wood. beta-(1--{\textgreater}4)-Galactan and rhamnogalacturonan I backbone epitopes were localized in the gelatinous cell wall layer. Type II arabinogalactans retained by cellulose microfibrils had a higher content of (methyl)glucuronic acid and galactose in tension wood than in normal wood. Thus, beta-(1--{\textgreater}4)-galactan and a specialized form of type II arabinogalactan are trapped by cellulose microfibrils specifically in tension wood and, thus, are the main candidate polymers for the generation of tensional stresses by the entrapment mechanism. We also found high beta-galactosidase activity accompanying tension wood differentiation and propose a testable hypothesis that such activity might regulate galactan entrapment and, thus, mechanical properties of cell walls in tension wood.},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant Physiol},
	author = {Gorshkova, T. and Mokshina, N. and Chernova, T. and Ibragimova, N. and Salnikov, V. and Mikshina, P. and Tryfona, T. and Banasiak, A. and Immerzeel, P. and Dupree, P. and Mellerowicz, E. J.},
	month = nov,
	year = {2015},
	note = {Edition: 2015/09/18},
	keywords = {*Models, Biological, Biopolymers/chemistry/metabolism, Cell Wall/chemistry/metabolism, Cellulose/chemistry/*metabolism, Galactans/chemistry/*metabolism, Galactose/metabolism, Gelatin/chemistry/metabolism, Glucans/chemistry/metabolism, Microfibrils/chemistry/*metabolism, Pectins/chemistry/metabolism, Polysaccharides/chemistry/*metabolism, Populus/chemistry/cytology/*metabolism, Wood/chemistry/cytology/metabolism, Xylans/chemistry/metabolism, beta-Galactosidase/metabolism},
	pages = {2048--63},
}

Contractile cell walls are found in various plant organs and tissues such as tendrils, contractile roots, and tension wood. The tension-generating mechanism is not known but is thought to involve special cell wall architecture. We previously postulated that tension could result from the entrapment of certain matrix polymers within cellulose microfibrils. As reported here, this hypothesis was corroborated by sequential extraction and analysis of cell wall polymers that are retained by cellulose microfibrils in tension wood and normal wood of hybrid aspen (Populus tremula x Populus tremuloides). beta-(1–\textgreater4)-Galactan and type II arabinogalactan were the main large matrix polymers retained by cellulose microfibrils that were specifically found in tension wood. Xyloglucan was detected mostly in oligomeric form in the alkali-labile fraction and was enriched in tension wood. beta-(1–\textgreater4)-Galactan and rhamnogalacturonan I backbone epitopes were localized in the gelatinous cell wall layer. Type II arabinogalactans retained by cellulose microfibrils had a higher content of (methyl)glucuronic acid and galactose in tension wood than in normal wood. Thus, beta-(1–\textgreater4)-galactan and a specialized form of type II arabinogalactan are trapped by cellulose microfibrils specifically in tension wood and, thus, are the main candidate polymers for the generation of tensional stresses by the entrapment mechanism. We also found high beta-galactosidase activity accompanying tension wood differentiation and propose a testable hypothesis that such activity might regulate galactan entrapment and, thus, mechanical properties of cell walls in tension wood.

@article{hartmann_crosstalk_2015,
	title = {Crosstalk between {Two} {bZIP} {Signaling} {Pathways} {Orchestrates} {Salt}-{Induced} {Metabolic} {Reprogramming} in {Arabidopsis} {Roots}},
	volume = {27},
	issn = {1532-298X (Electronic) 1040-4651 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26276836},
	doi = {10.1105/tpc.15.00163},
	abstract = {Soil salinity increasingly causes crop losses worldwide. Although roots are the primary targets of salt stress, the signaling networks that facilitate metabolic reprogramming to induce stress tolerance are less understood than those in leaves. Here, a combination of transcriptomic and metabolic approaches was performed in salt-treated Arabidopsis thaliana roots, which revealed that the group S1 basic leucine zipper transcription factors bZIP1 and bZIP53 reprogram primary C- and N-metabolism. In particular, gluconeogenesis and amino acid catabolism are affected by these transcription factors. Importantly, bZIP1 expression reflects cellular stress and energy status in roots. In addition to the well-described abiotic stress response pathway initiated by the hormone abscisic acid (ABA) and executed by SnRK2 (Snf1-RELATED-PROTEIN-KINASE2) and AREB-like bZIP factors, we identify a structurally related ABA-independent signaling module consisting of SnRK1s and S1 bZIPs. Crosstalk between these signaling pathways recruits particular bZIP factor combinations to establish at least four distinct gene expression patterns. Understanding this signaling network provides a framework for securing future crop productivity.},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Plant Cell},
	author = {Hartmann, L. and Pedrotti, L. and Weiste, C. and Fekete, A. and Schierstaedt, J. and Gottler, J. and Kempa, S. and Krischke, M. and Dietrich, K. and Mueller, M. J. and Vicente-Carbajosa, J. and Hanson, J. and Droge-Laser, W.},
	month = aug,
	year = {2015},
	note = {Edition: 2015/08/16},
	keywords = {Abscisic Acid/pharmacology, Amino Acids/metabolism, Arabidopsis Proteins/*genetics/metabolism, Arabidopsis/drug effects/*genetics/metabolism, Basic-Leucine Zipper Transcription Factors/*genetics/metabolism, Calcium/metabolism, Carbohydrate Metabolism/drug effects/genetics, Gene Expression Regulation, Plant/drug effects, Gluconeogenesis/drug effects/genetics, Immunoblotting, Mutation, Plant Growth Regulators/pharmacology, Plant Roots/drug effects/genetics/metabolism, Promoter Regions, Genetic/genetics, Protein Binding/drug effects, Protein-Serine-Threonine Kinases, Reverse Transcriptase Polymerase Chain Reaction, Salt-Tolerant Plants/drug effects/genetics/metabolism, Signal Transduction/drug effects/*genetics, Sodium Chloride/pharmacology, Transcriptome/drug effects/genetics},
	pages = {2244--60},
}

Soil salinity increasingly causes crop losses worldwide. Although roots are the primary targets of salt stress, the signaling networks that facilitate metabolic reprogramming to induce stress tolerance are less understood than those in leaves. Here, a combination of transcriptomic and metabolic approaches was performed in salt-treated Arabidopsis thaliana roots, which revealed that the group S1 basic leucine zipper transcription factors bZIP1 and bZIP53 reprogram primary C- and N-metabolism. In particular, gluconeogenesis and amino acid catabolism are affected by these transcription factors. Importantly, bZIP1 expression reflects cellular stress and energy status in roots. In addition to the well-described abiotic stress response pathway initiated by the hormone abscisic acid (ABA) and executed by SnRK2 (Snf1-RELATED-PROTEIN-KINASE2) and AREB-like bZIP factors, we identify a structurally related ABA-independent signaling module consisting of SnRK1s and S1 bZIPs. Crosstalk between these signaling pathways recruits particular bZIP factor combinations to establish at least four distinct gene expression patterns. Understanding this signaling network provides a framework for securing future crop productivity.

@article{de_wit_contrasting_2015,
	title = {Contrasting growth responses in lamina and petiole during neighbor detection depend on differential auxin responsiveness rather than different auxin levels},
	volume = {208},
	issn = {1469-8137 (Electronic) 0028-646X (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25963518},
	doi = {10.1111/nph.13449},
	abstract = {Foliar shade triggers rapid growth of specific structures that facilitate access of the plant to direct sunlight. In leaves of many plant species, this growth response is complex because, although shade triggers the elongation of petioles, it reduces the growth of the lamina. How the same external cue leads to these contrasting growth responses in different parts of the leaf is not understood. Using mutant analysis, pharmacological treatment and gene expression analyses, we investigated the role of PHYTOCHROME INTERACTING FACTOR7 (PIF7) and the growth-promoting hormone auxin in these contrasting leaf growth responses. Both petiole elongation and lamina growth reduction are dependent on PIF7. The induction of auxin production is both necessary and sufficient to induce opposite growth responses in petioles vs lamina. However, these contrasting growth responses are not caused by different auxin concentrations in the two leaf parts. Our work suggests that a transient increase in auxin levels triggers tissue-specific growth responses in different leaf parts. We provide evidence suggesting that this may be caused by the different sensitivity to auxin in the petiole vs the blade and by tissue-specific gene expression.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {New Phytol},
	author = {de Wit, M. and Ljung, K. and Fankhauser, C.},
	month = oct,
	year = {2015},
	note = {Edition: 2015/05/13},
	keywords = {*Light, Arabidopsis Proteins/*metabolism, Arabidopsis/growth \& development/metabolism/*physiology, DNA-Binding Proteins/*metabolism, Darkness, Gene Expression, Indoleacetic Acids/*metabolism, Phytochrome interacting factor (pif), Plant Leaves/growth \& development/metabolism/*physiology, Xyloglucan endotransglucosylase/hydrolase (xth), auxin, leaf growth, neighbor detection, shade avoidance response},
	pages = {198--209},
}

Foliar shade triggers rapid growth of specific structures that facilitate access of the plant to direct sunlight. In leaves of many plant species, this growth response is complex because, although shade triggers the elongation of petioles, it reduces the growth of the lamina. How the same external cue leads to these contrasting growth responses in different parts of the leaf is not understood. Using mutant analysis, pharmacological treatment and gene expression analyses, we investigated the role of PHYTOCHROME INTERACTING FACTOR7 (PIF7) and the growth-promoting hormone auxin in these contrasting leaf growth responses. Both petiole elongation and lamina growth reduction are dependent on PIF7. The induction of auxin production is both necessary and sufficient to induce opposite growth responses in petioles vs lamina. However, these contrasting growth responses are not caused by different auxin concentrations in the two leaf parts. Our work suggests that a transient increase in auxin levels triggers tissue-specific growth responses in different leaf parts. We provide evidence suggesting that this may be caused by the different sensitivity to auxin in the petiole vs the blade and by tissue-specific gene expression.

@article{chong_active_2015,
	title = {Active fungal {GH115} alpha-glucuronidase produced in {Arabidopsis} thaliana affects only the {UX1}-reactive glucuronate decorations on native glucuronoxylans},
	volume = {15},
	issn = {1472-6750 (Electronic) 1472-6750 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26084671},
	doi = {10.1186/s12896-015-0154-8},
	abstract = {BACKGROUND: Expressing microbial polysaccharide-modifying enzymes in plants is an attractive approach to custom tailor plant lignocellulose and to study the importance of wall structures to plant development. Expression of alpha-glucuronidases in plants to modify the structures of glucuronoxylans has not been yet attempted. Glycoside hydrolase (GH) family 115 alpha-glucuronidases cleave the internal alpha-D-(4-O-methyl)glucopyranosyluronic acid ((Me)GlcA) from xylans or xylooligosaccharides. In this work, a GH115 alpha-glucuronidase from Schizophyllum commune, ScAGU115, was expressed in Arabidopsis thaliana and targeted to apoplast. The transgene effects on native xylans' structures, plant development, and lignocellulose saccharification were evaluated and compared to those of knocked out glucuronyltransferases AtGUX1 and AtGUX2. RESULTS: The ScAGU115 extracted from cell walls of Arabidopsis was active on the internally substituted aldopentaouronic acid (XUXX). The transgenic plants did not show any change in growth or in lignocellulose saccharification. The cell wall (Me)GlcA and other non-cellulosic sugars, as well as the lignin content, remained unchanged. In contrast, the gux1gux2 double mutant showed a 70\% decrease in (Me)GlcA to xylose molar ratio, and, interestingly, a 60\% increase in the xylose content. Whereas ScAGU115-expressing plants exhibited a decreased signal in native secondary walls from the monoclonal antibody UX1 that recognizes (Me)GlcA on non-acetylated xylan, the signal was not affected after wall deacetylation. In contrast, gux1gux2 mutant was lacking UX1 signals in both native and deacetylated cell walls. This indicates that acetyl substitution on the xylopyranosyl residue carrying (Me)GlcA or on the neighboring xylopyranosyl residues may restrict post-synthetic modification of xylans by ScAGU115 in planta. CONCLUSIONS: Active GH115 alpha-glucuronidase has been produced for the first time in plants. The cell wall-targeted ScAGU115 was shown to affect those glucuronate substitutions of xylan, which are accessible to UX1 antibody and constitute a small fraction in Arabidopsis, whereas majority of (Me)GlcA substitutions were resistant, most likely due to the shielding by acetyl groups. Plants expressing ScAGU115 did not show any defects under laboratory conditions indicating that the UX1 epitope of xylan is not essential under these conditions. Moreover the removal of the UX1 xylan epitope does not affect lignocellulose saccharification.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Biotechnol},
	author = {Chong, S. L. and Derba-Maceluch, M. and Koutaniemi, S. and Gomez, L. D. and McQueen-Mason, S. J. and Tenkanen, M. and Mellerowicz, E. J.},
	month = jun,
	year = {2015},
	note = {Edition: 2015/06/19},
	keywords = {Arabidopsis Proteins/genetics/metabolism, Arabidopsis/enzymology, Cell Wall/enzymology, Gene Expression Regulation, Enzymologic, Glucuronates/metabolism, Glucuronic Acid/metabolism, Glycoside Hydrolases/*biosynthesis/genetics, Glycosyltransferases/genetics/metabolism, Lignin/genetics/*metabolism, Oligosaccharides/metabolism, Polysaccharides/metabolism, Schizophyllum/*enzymology, Xylans/*metabolism},
	pages = {56},
}

BACKGROUND: Expressing microbial polysaccharide-modifying enzymes in plants is an attractive approach to custom tailor plant lignocellulose and to study the importance of wall structures to plant development. Expression of alpha-glucuronidases in plants to modify the structures of glucuronoxylans has not been yet attempted. Glycoside hydrolase (GH) family 115 alpha-glucuronidases cleave the internal alpha-D-(4-O-methyl)glucopyranosyluronic acid ((Me)GlcA) from xylans or xylooligosaccharides. In this work, a GH115 alpha-glucuronidase from Schizophyllum commune, ScAGU115, was expressed in Arabidopsis thaliana and targeted to apoplast. The transgene effects on native xylans' structures, plant development, and lignocellulose saccharification were evaluated and compared to those of knocked out glucuronyltransferases AtGUX1 and AtGUX2. RESULTS: The ScAGU115 extracted from cell walls of Arabidopsis was active on the internally substituted aldopentaouronic acid (XUXX). The transgenic plants did not show any change in growth or in lignocellulose saccharification. The cell wall (Me)GlcA and other non-cellulosic sugars, as well as the lignin content, remained unchanged. In contrast, the gux1gux2 double mutant showed a 70% decrease in (Me)GlcA to xylose molar ratio, and, interestingly, a 60% increase in the xylose content. Whereas ScAGU115-expressing plants exhibited a decreased signal in native secondary walls from the monoclonal antibody UX1 that recognizes (Me)GlcA on non-acetylated xylan, the signal was not affected after wall deacetylation. In contrast, gux1gux2 mutant was lacking UX1 signals in both native and deacetylated cell walls. This indicates that acetyl substitution on the xylopyranosyl residue carrying (Me)GlcA or on the neighboring xylopyranosyl residues may restrict post-synthetic modification of xylans by ScAGU115 in planta. CONCLUSIONS: Active GH115 alpha-glucuronidase has been produced for the first time in plants. The cell wall-targeted ScAGU115 was shown to affect those glucuronate substitutions of xylan, which are accessible to UX1 antibody and constitute a small fraction in Arabidopsis, whereas majority of (Me)GlcA substitutions were resistant, most likely due to the shielding by acetyl groups. Plants expressing ScAGU115 did not show any defects under laboratory conditions indicating that the UX1 epitope of xylan is not essential under these conditions. Moreover the removal of the UX1 xylan epitope does not affect lignocellulose saccharification.

@article{capovilla_control_2015,
	title = {Control of flowering by ambient temperature},
	volume = {66},
	issn = {1460-2431 (Electronic) 0022-0957 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25326628},
	doi = {10.1093/jxb/eru416},
	abstract = {The timing of flowering is a crucial decision in the life cycle of plants since favourable conditions are needed to maximize reproductive success and, hence, the survival of the species. It is therefore not surprising that plants constantly monitor endogenous and environmental signals, such as day length (photoperiod) and temperature, to adjust the timing of the floral transition. Temperature in particular has been shown to have a tremendous effect on the timing of flowering: the effect of prolonged periods of cold, called the vernalization response, has been extensively studied and the underlying epigenetic mechanisms are reasonably well understood in Arabidopsis thaliana. In contrast, the effect of moderate changes in ambient growth temperature on the progression of flowering, the thermosensory pathway, is only starting to be understood on the molecular level. Several genes and molecular mechanisms underlying the thermosensory pathway have already been identified and characterized in detail. At a time when global temperature is rising due to climate change, this knowledge will be pivotal to ensure crop production in the future.},
	language = {eng},
	number = {1},
	journal = {J Exp Bot},
	author = {Capovilla, G. and Schmid, M. and Pose, D.},
	month = jan,
	year = {2015},
	note = {Edition: 2014/10/19},
	keywords = {*Plant Development/genetics, *Temperature, Ambient temperature, Arabidopsis, Arabidopsis thaliana, Arabidopsis/genetics/growth \& development, Epigenesis, Genetic, Flowers, Flowers/genetics/*growth \& development, MADS, Mads, Plant Development, Temperature, flowering time, miRNA, thermosensory pathway.},
	pages = {59--69},
}

The timing of flowering is a crucial decision in the life cycle of plants since favourable conditions are needed to maximize reproductive success and, hence, the survival of the species. It is therefore not surprising that plants constantly monitor endogenous and environmental signals, such as day length (photoperiod) and temperature, to adjust the timing of the floral transition. Temperature in particular has been shown to have a tremendous effect on the timing of flowering: the effect of prolonged periods of cold, called the vernalization response, has been extensively studied and the underlying epigenetic mechanisms are reasonably well understood in Arabidopsis thaliana. In contrast, the effect of moderate changes in ambient growth temperature on the progression of flowering, the thermosensory pathway, is only starting to be understood on the molecular level. Several genes and molecular mechanisms underlying the thermosensory pathway have already been identified and characterized in detail. At a time when global temperature is rising due to climate change, this knowledge will be pivotal to ensure crop production in the future.

@article{benson_intact_2015,
	title = {An intact light harvesting complex {I} antenna system is required for complete state transitions in {Arabidopsis}},
	volume = {1},
	issn = {2055-0278 (Electronic) 2055-0278 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/27251716},
	doi = {10.1038/nplants.2015.176},
	abstract = {Efficient photosynthesis depends on maintaining balance between the rate of light-driven electron transport occurring in photosystem I (PSI) and photosystem II (PSII), located in the chloroplast thylakoid membranes. Balance is achieved through a process of 'state transitions' that increases energy transfer towards PSI when PSII is overexcited (state II), and towards PSII when PSI is overexcited (state I). This is achieved through redox control of the phosphorylation state of light-harvesting antenna complex II (LHCII). PSI is served by both LHCII and four light-harvesting antenna complex I (LHCI) subunits, Lhca1, 2, 3 and 4. Here we demonstrate that despite unchanged levels of LHCII phosphorylation, absence of specific Lhca subunits reduces state transitions in Arabidopsis. The severest phenotype-observed in a mutant lacking Lhca4 (DeltaLhca4)-displayed a 69\% reduction compared with the wild type. Yet, surprisingly, the amounts of the PSI-LHCI-LHCII supercomplex isolated by blue native polyacrylamide gel electrophoresis (BN-PAGE) from digitonin-solubilized thylakoids were similar in the wild type and DeltaLhca mutants. Fluorescence excitation spectroscopy revealed that in the wild type this PSI-LHCI-LHCII supercomplex is supplemented by energy transfer from additional LHCII trimers in state II, whose binding is sensitive to digitonin, and which are absent in DeltaLhca4. The grana margins of the thylakoid membrane were found to be the primary site of interaction between this 'extra' LHCII and the PSI-LHCI-LHCII supercomplex in state II. The results suggest that the LHCI complexes mediate energetic interactions between LHCII and PSI in the intact membrane.},
	language = {en},
	number = {12},
	urldate = {2021-06-07},
	journal = {Nat Plants},
	author = {Benson, S. L. and Maheswaran, P. and Ware, M. A. and Hunter, C. N. and Horton, P. and Jansson, S. and Ruban, A. V. and Johnson, M. P.},
	month = nov,
	year = {2015},
	note = {Edition: 2015/01/01},
	pages = {15176},
}

Efficient photosynthesis depends on maintaining balance between the rate of light-driven electron transport occurring in photosystem I (PSI) and photosystem II (PSII), located in the chloroplast thylakoid membranes. Balance is achieved through a process of 'state transitions' that increases energy transfer towards PSI when PSII is overexcited (state II), and towards PSII when PSI is overexcited (state I). This is achieved through redox control of the phosphorylation state of light-harvesting antenna complex II (LHCII). PSI is served by both LHCII and four light-harvesting antenna complex I (LHCI) subunits, Lhca1, 2, 3 and 4. Here we demonstrate that despite unchanged levels of LHCII phosphorylation, absence of specific Lhca subunits reduces state transitions in Arabidopsis. The severest phenotype-observed in a mutant lacking Lhca4 (DeltaLhca4)-displayed a 69% reduction compared with the wild type. Yet, surprisingly, the amounts of the PSI-LHCI-LHCII supercomplex isolated by blue native polyacrylamide gel electrophoresis (BN-PAGE) from digitonin-solubilized thylakoids were similar in the wild type and DeltaLhca mutants. Fluorescence excitation spectroscopy revealed that in the wild type this PSI-LHCI-LHCII supercomplex is supplemented by energy transfer from additional LHCII trimers in state II, whose binding is sensitive to digitonin, and which are absent in DeltaLhca4. The grana margins of the thylakoid membrane were found to be the primary site of interaction between this 'extra' LHCII and the PSI-LHCI-LHCII supercomplex in state II. The results suggest that the LHCI complexes mediate energetic interactions between LHCII and PSI in the intact membrane.

@article{benlloch_crystal_2015,
	title = {Crystal structure and functional characterization of photosystem {II}-associated carbonic anhydrase {CAH3} in {Chlamydomonas} reinhardtii},
	volume = {167},
	issn = {1532-2548 (Electronic) 0032-0889 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25617045},
	doi = {10.1104/pp.114.253591},
	abstract = {In oxygenic photosynthesis, light energy is stored in the form of chemical energy by converting CO2 and water into carbohydrates. The light-driven oxidation of water that provides the electrons and protons for the subsequent CO2 fixation takes place in photosystem II (PSII). Recent studies show that in higher plants, HCO3 (-) increases PSII activity by acting as a mobile acceptor of the protons produced by PSII. In the green alga Chlamydomonas reinhardtii, a luminal carbonic anhydrase, CrCAH3, was suggested to improve proton removal from PSII, possibly by rapid reformation of HCO3 (-) from CO2. In this study, we investigated the interplay between PSII and CrCAH3 by membrane inlet mass spectrometry and x-ray crystallography. Membrane inlet mass spectrometry measurements showed that CrCAH3 was most active at the slightly acidic pH values prevalent in the thylakoid lumen under illumination. Two crystal structures of CrCAH3 in complex with either acetazolamide or phosphate ions were determined at 2.6- and 2.7-A resolution, respectively. CrCAH3 is a dimer at pH 4.1 that is stabilized by swapping of the N-terminal arms, a feature not previously observed in alpha-type carbonic anhydrases. The structure contains a disulfide bond, and redox titration of CrCAH3 function with dithiothreitol suggested a possible redox regulation of the enzyme. The stimulating effect of CrCAH3 and CO2/HCO3 (-) on PSII activity was demonstrated by comparing the flash-induced oxygen evolution pattern of wild-type and CrCAH3-less PSII preparations. We showed that CrCAH3 has unique structural features that allow this enzyme to maximize PSII activity at low pH and CO2 concentration.},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant Physiol},
	author = {Benlloch, R. and Shevela, D. and Hainzl, T. and Grundstrom, C. and Shutova, T. and Messinger, J. and Samuelsson, G. and Sauer-Eriksson, A. E.},
	month = mar,
	year = {2015},
	note = {Edition: 2015/01/27},
	keywords = {Carbonic Anhydrase Inhibitors/pharmacology, Carbonic Anhydrases/*chemistry/*metabolism, Catalytic Domain, Chlamydomonas reinhardtii/*enzymology, Crystallography, X-Ray, Cysteine/metabolism, Disulfides/metabolism, Hydrogen-Ion Concentration, Mass Spectrometry, Mutation, Oxidation-Reduction/drug effects, Oxygen/metabolism, Photosystem II Protein Complex/*metabolism, Protein Structure, Secondary},
	pages = {950--62},
}

In oxygenic photosynthesis, light energy is stored in the form of chemical energy by converting CO2 and water into carbohydrates. The light-driven oxidation of water that provides the electrons and protons for the subsequent CO2 fixation takes place in photosystem II (PSII). Recent studies show that in higher plants, HCO3 (-) increases PSII activity by acting as a mobile acceptor of the protons produced by PSII. In the green alga Chlamydomonas reinhardtii, a luminal carbonic anhydrase, CrCAH3, was suggested to improve proton removal from PSII, possibly by rapid reformation of HCO3 (-) from CO2. In this study, we investigated the interplay between PSII and CrCAH3 by membrane inlet mass spectrometry and x-ray crystallography. Membrane inlet mass spectrometry measurements showed that CrCAH3 was most active at the slightly acidic pH values prevalent in the thylakoid lumen under illumination. Two crystal structures of CrCAH3 in complex with either acetazolamide or phosphate ions were determined at 2.6- and 2.7-A resolution, respectively. CrCAH3 is a dimer at pH 4.1 that is stabilized by swapping of the N-terminal arms, a feature not previously observed in alpha-type carbonic anhydrases. The structure contains a disulfide bond, and redox titration of CrCAH3 function with dithiothreitol suggested a possible redox regulation of the enzyme. The stimulating effect of CrCAH3 and CO2/HCO3 (-) on PSII activity was demonstrated by comparing the flash-induced oxygen evolution pattern of wild-type and CrCAH3-less PSII preparations. We showed that CrCAH3 has unique structural features that allow this enzyme to maximize PSII activity at low pH and CO2 concentration.

@article{antoniadi_cell-type-specific_2015,
	title = {Cell-{Type}-{Specific} {Cytokinin} {Distribution} within the {Arabidopsis} {Primary} {Root} {Apex}},
	volume = {27},
	issn = {1532-298X (Electronic) 1040-4651 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26152699},
	doi = {10.1105/tpc.15.00176},
	abstract = {Cytokinins (CKs) play a crucial role in many physiological and developmental processes at the levels of individual plant components (cells, tissues, and organs) and by coordinating activities across these parts. High-resolution measurements of intracellular CKs in different plant tissues can therefore provide insights into their metabolism and mode of action. Here, we applied fluorescence-activated cell sorting of green fluorescent protein (GFP)-marked cell types, combined with solid-phase microextraction and an ultra-high-sensitivity mass spectrometry (MS) method for analysis of CK biosynthesis and homeostasis at cellular resolution. This method was validated by series of control experiments, establishing that protoplast isolation and cell sorting procedures did not greatly alter endogenous CK levels. The MS-based method facilitated the quantification of all the well known CK isoprenoid metabolites in four different transgenic Arabidopsis thaliana lines expressing GFP in specific cell populations within the primary root apex. Our results revealed the presence of a CK gradient within the Arabidopsis root tip, with a concentration maximum in the lateral root cap, columella, columella initials, and quiescent center cells. This distribution, when compared with previously published auxin gradients, implies that the well known antagonistic interactions between the two hormone groups are cell type specific.},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Plant Cell},
	author = {Antoniadi, I. and Plackova, L. and Simonovik, B. and Dolezal, K. and Turnbull, C. and Ljung, K. and Novak, O.},
	month = jul,
	year = {2015},
	note = {Edition: 2015/07/15},
	keywords = {Arabidopsis/cytology/*metabolism, Biological Transport, Cell Separation, Cytokinins/*metabolism, Flow Cytometry, Green Fluorescent Proteins/metabolism, Indoleacetic Acids/metabolism, Meristem/metabolism, Metabolome, Miniaturization, Organ Specificity, Plant Roots/cytology/*metabolism, Protoplasts/metabolism, Solid Phase Extraction},
	pages = {1955--67},
}

Cytokinins (CKs) play a crucial role in many physiological and developmental processes at the levels of individual plant components (cells, tissues, and organs) and by coordinating activities across these parts. High-resolution measurements of intracellular CKs in different plant tissues can therefore provide insights into their metabolism and mode of action. Here, we applied fluorescence-activated cell sorting of green fluorescent protein (GFP)-marked cell types, combined with solid-phase microextraction and an ultra-high-sensitivity mass spectrometry (MS) method for analysis of CK biosynthesis and homeostasis at cellular resolution. This method was validated by series of control experiments, establishing that protoplast isolation and cell sorting procedures did not greatly alter endogenous CK levels. The MS-based method facilitated the quantification of all the well known CK isoprenoid metabolites in four different transgenic Arabidopsis thaliana lines expressing GFP in specific cell populations within the primary root apex. Our results revealed the presence of a CK gradient within the Arabidopsis root tip, with a concentration maximum in the lateral root cap, columella, columella initials, and quiescent center cells. This distribution, when compared with previously published auxin gradients, implies that the well known antagonistic interactions between the two hormone groups are cell type specific.

@article{le_hir_disruption_2015,
	title = {Disruption of the {Sugar} {Transporters} {AtSWEET11} and {AtSWEET12} {Affects} {Vascular} {Development} and {Freezing} {Tolerance} in {Arabidopsis}},
	volume = {8},
	issn = {1752-9867 (Electronic) 1674-2052 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26358680},
	doi = {10.1016/j.molp.2015.08.007},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Mol Plant},
	author = {Le Hir, R. and Spinner, L. and Klemens, P. A. and Chakraborti, D. and de Marco, F. and Vilaine, F. and Wolff, N. and Lemoine, R. and Porcheron, B. and Gery, C. and Teoule, E. and Chabout, S. and Mouille, G. and Neuhaus, H. E. and Dinant, S. and Bellini, C.},
	month = nov,
	year = {2015},
	note = {Edition: 2015/09/12},
	keywords = {Adaptation, Physiological, Arabidopsis Proteins/genetics/*physiology, Arabidopsis/growth \& development/metabolism/*physiology, Carbohydrates, Cell Wall/metabolism, Freezing, Membrane Transport Proteins/genetics/*physiology, Phloem/metabolism, Xylem/metabolism},
	pages = {1687--90},
}

@article{latha_gandla_expression_2015,
	title = {Expression of a fungal glucuronoyl esterase in {Populus}: effects on wood properties and saccharification efficiency},
	volume = {112},
	issn = {1873-3700 (Electronic) 0031-9422 (Linking)},
	shorttitle = {Expression of a fungal glucuronoyl esterase in {Populus}},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/24997793},
	doi = {10.1016/j.phytochem.2014.06.002},
	abstract = {The secondary walls of angiosperms contain large amounts of glucuronoxylan that is thought to be covalently linked to lignin via ester bonds between 4-O-methyl-alpha-D-glucuronic acid (4-O-Me-GlcA) moieties in glucuronoxylan and alcohol groups in lignin. This linkage is proposed to be hydrolysed by glucuronoyl esterases (GCEs) secreted by wood-degrading fungi. We report effects of overexpression of a GCE from the white-rot basidiomycete Phanerochaete carnosa, PcGCE, in hybrid aspen (Populus tremula L. x tremuloides Michx.) on the wood composition and the saccharification efficiency. The recombinant enzyme, which was targeted to the plant cell wall using the signal peptide from hybrid aspen cellulase PttCel9B3, was constitutively expressed resulting in the appearance of GCE activity in protein extracts from developing wood. Diffuse reflectance FT-IR spectroscopy and pyrolysis-GC/MS analyses showed significant alternation in wood chemistry of transgenic plants including an increase in lignin content and S/G ratio, and a decrease in carbohydrate content. Sequential wood extractions confirmed a massive (+43\%) increase of Klason lignin, which was accompanied by a ca. 5\% decrease in cellulose, and ca. 20\% decrease in wood extractives. Analysis of the monosaccharide composition using methanolysis showed a reduction of 4-O-Me-GlcA content without a change in Xyl contents in transgenic lines, suggesting that the covalent links between 4-O-Me-GlcA moieties and lignin protect these moieties from degradation. Enzymatic saccharification without pretreatment resulted in significant decreases of the yields of Gal, Glc, Xyl and Man in transgenic lines, consistent with their increased recalcitrance caused by the increased lignin content. In contrast, the enzymatic saccharification after acid pretreatment resulted in Glc yields similar to wild-type despite of their lower cellulose content. These data indicate that whereas PcGCE expression in hybrid aspen increases lignin deposition, the inhibitory effects of lignin are efficiently removed during acid pretreatment, and the extent of wood cellulose conversion during hydrolysis after acid pretreatment is improved in the transgenic lines possible due to reduced cell wall cross-links between cell wall biopolymers by PcGCE.},
	language = {en},
	urldate = {2021-06-07},
	journal = {Phytochemistry},
	author = {Latha Gandla, M. and Derba-Maceluch, M. and Liu, X. and Gerber, L. and Master, E. R. and Mellerowicz, E. J. and Jonsson, L. J.},
	month = apr,
	year = {2015},
	note = {Edition: 2014/07/07},
	keywords = {Ce15, Enzymatic saccharification, Esterases/*genetics/metabolism, Gene Expression, Glucuronic Acid/*metabolism, Glucuronoyl esterase, Hybrid aspen, Hydrolysis, Phanerochaete/*enzymology/*genetics, Polysaccharides/metabolism, Populus, Populus/*genetics, Secondary cell wall, Wood/*chemistry/*metabolism},
	pages = {210--20},
}

The secondary walls of angiosperms contain large amounts of glucuronoxylan that is thought to be covalently linked to lignin via ester bonds between 4-O-methyl-alpha-D-glucuronic acid (4-O-Me-GlcA) moieties in glucuronoxylan and alcohol groups in lignin. This linkage is proposed to be hydrolysed by glucuronoyl esterases (GCEs) secreted by wood-degrading fungi. We report effects of overexpression of a GCE from the white-rot basidiomycete Phanerochaete carnosa, PcGCE, in hybrid aspen (Populus tremula L. x tremuloides Michx.) on the wood composition and the saccharification efficiency. The recombinant enzyme, which was targeted to the plant cell wall using the signal peptide from hybrid aspen cellulase PttCel9B3, was constitutively expressed resulting in the appearance of GCE activity in protein extracts from developing wood. Diffuse reflectance FT-IR spectroscopy and pyrolysis-GC/MS analyses showed significant alternation in wood chemistry of transgenic plants including an increase in lignin content and S/G ratio, and a decrease in carbohydrate content. Sequential wood extractions confirmed a massive (+43%) increase of Klason lignin, which was accompanied by a ca. 5% decrease in cellulose, and ca. 20% decrease in wood extractives. Analysis of the monosaccharide composition using methanolysis showed a reduction of 4-O-Me-GlcA content without a change in Xyl contents in transgenic lines, suggesting that the covalent links between 4-O-Me-GlcA moieties and lignin protect these moieties from degradation. Enzymatic saccharification without pretreatment resulted in significant decreases of the yields of Gal, Glc, Xyl and Man in transgenic lines, consistent with their increased recalcitrance caused by the increased lignin content. In contrast, the enzymatic saccharification after acid pretreatment resulted in Glc yields similar to wild-type despite of their lower cellulose content. These data indicate that whereas PcGCE expression in hybrid aspen increases lignin deposition, the inhibitory effects of lignin are efficiently removed during acid pretreatment, and the extent of wood cellulose conversion during hydrolysis after acid pretreatment is improved in the transgenic lines possible due to reduced cell wall cross-links between cell wall biopolymers by PcGCE.

@article{ranade_fungal_2015,
	title = {Fungal {Infection} {Increases} the {Rate} of {Somatic} {Mutation} in {Scots} {Pine} ({Pinus} sylvestris {L}.)},
	volume = {106},
	issn = {1465-7333 (Electronic) 0022-1503 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25890976},
	doi = {10.1093/jhered/esv017},
	abstract = {Somatic mutations are transmitted during mitosis in developing somatic tissue. Somatic cells bearing the mutations can develop into reproductive (germ) cells and the somatic mutations are then passed on to the next generation of plants. Somatic mutations are a source of variation essential to evolve new defense strategies and adapt to the environment. Stem rust disease in Scots pine has a negative effect on wood quality, and thus adversely affects the economy. It is caused by the 2 most destructive fungal species in Scandinavia: Peridermium pini and Cronartium flaccidum. We studied nuclear genome stability in Scots pine under biotic stress (fungus-infected, 22 trees) compared to a control population (plantation, 20 trees). Stability was assessed as accumulation of new somatic mutations in 10 microsatellite loci selected for genotyping. Microsatellites are widely used as molecular markers in population genetics studies of plants, and are particularly used for detection of somatic mutations as their rate of mutation is of a much higher magnitude when compared with other DNA markers. We report double the rate of somatic mutation per locus in the fungus-infected trees (4.8x10(-3) mutations per locus), as compared to the controls (2.0x10(-3) mutations per locus) when individual samples were analyzed at 10 different microsatellite markers. Pearson's chi-squared test indicated a significant effect of the fungal infection which increased the number of mutations in the fungus-infected trees (chi(2) = 12.9883, df = 1, P = 0.0003134).},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {J Hered},
	author = {Ranade, S. S. and Ganea, L. S. and Razzak, A. M. and Garcia Gil, M. R.},
	month = jul,
	year = {2015},
	note = {Edition: 2015/04/22},
	keywords = {*Mutation Rate, Basidiomycota/*pathogenicity, DNA, Plant/genetics, Genetic Markers, Genetics, Population, Genome, Plant, Genomic Instability, Genotype, Host-Pathogen Interactions/*genetics, Microsatellite Repeats, Mutation, Pinus sylvestris/*genetics/microbiology, Plant Diseases/genetics/*microbiology, Scots pine, Sequence Analysis, DNA, Somatic mutation., Sweden, abiotic stress, microsatellite, simple sequence repeats},
	pages = {386--94},
}

Somatic mutations are transmitted during mitosis in developing somatic tissue. Somatic cells bearing the mutations can develop into reproductive (germ) cells and the somatic mutations are then passed on to the next generation of plants. Somatic mutations are a source of variation essential to evolve new defense strategies and adapt to the environment. Stem rust disease in Scots pine has a negative effect on wood quality, and thus adversely affects the economy. It is caused by the 2 most destructive fungal species in Scandinavia: Peridermium pini and Cronartium flaccidum. We studied nuclear genome stability in Scots pine under biotic stress (fungus-infected, 22 trees) compared to a control population (plantation, 20 trees). Stability was assessed as accumulation of new somatic mutations in 10 microsatellite loci selected for genotyping. Microsatellites are widely used as molecular markers in population genetics studies of plants, and are particularly used for detection of somatic mutations as their rate of mutation is of a much higher magnitude when compared with other DNA markers. We report double the rate of somatic mutation per locus in the fungus-infected trees (4.8x10(-3) mutations per locus), as compared to the controls (2.0x10(-3) mutations per locus) when individual samples were analyzed at 10 different microsatellite markers. Pearson's chi-squared test indicated a significant effect of the fungal infection which increased the number of mutations in the fungus-infected trees (chi(2) = 12.9883, df = 1, P = 0.0003134).

@article{de_la_torre_genetic_2015,
	title = {Genetic architecture and genomic patterns of gene flow between hybridizing species of {Picea}},
	volume = {115},
	issn = {1365-2540 (Electronic) 0018-067X (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25806545},
	doi = {10.1038/hdy.2015.19},
	abstract = {Hybrid zones provide an opportunity to study the effects of selection and gene flow in natural settings. We employed nuclear microsatellites (single sequence repeat (SSR)) and candidate gene single-nucleotide polymorphism markers (SNPs) to characterize the genetic architecture and patterns of interspecific gene flow in the Picea glauca x P. engelmannii hybrid zone across a broad latitudinal (40-60 degrees) and elevational (350-3500 m) range in western North America. Our results revealed a wide and complex hybrid zone with broad ancestry levels and low interspecific heterozygosity, shaped by asymmetric advanced-generation introgression, and low reproductive barriers between parental species. The clinal variation based on geographic variables, lack of concordance in clines among loci and the width of the hybrid zone points towards the maintenance of species integrity through environmental selection. Congruency between geographic and genomic clines suggests that loci with narrow clines are under strong selection, favoring either one parental species (directional selection) or their hybrids (overdominance) as a result of strong associations with climatic variables such as precipitation as snow and mean annual temperature. Cline movement due to past demographic events (evidenced by allelic richness and heterozygosity shifts from the average cline center) may explain the asymmetry in introgression and predominance of P. engelmannii found in this study. These results provide insights into the genetic architecture and fine-scale patterns of admixture, and identify loci that may be involved in reproductive barriers between the species.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Heredity (Edinb)},
	author = {De La Torre, A. and Ingvarsson, P. K. and Aitken, S. N.},
	month = aug,
	year = {2015},
	note = {Edition: 2015/03/26},
	keywords = {*Gene Flow, *Hybridization, Genetic, British Columbia, DNA, Plant/genetics, Evolution, Molecular, Genetic Loci, Genetics, Population, Genotype, Geography, Microsatellite Repeats, Models, Genetic, Picea/*genetics, Polymorphism, Single Nucleotide, Sequence Analysis, DNA, Southwestern United States},
	pages = {153--64},
}

Hybrid zones provide an opportunity to study the effects of selection and gene flow in natural settings. We employed nuclear microsatellites (single sequence repeat (SSR)) and candidate gene single-nucleotide polymorphism markers (SNPs) to characterize the genetic architecture and patterns of interspecific gene flow in the Picea glauca x P. engelmannii hybrid zone across a broad latitudinal (40-60 degrees) and elevational (350-3500 m) range in western North America. Our results revealed a wide and complex hybrid zone with broad ancestry levels and low interspecific heterozygosity, shaped by asymmetric advanced-generation introgression, and low reproductive barriers between parental species. The clinal variation based on geographic variables, lack of concordance in clines among loci and the width of the hybrid zone points towards the maintenance of species integrity through environmental selection. Congruency between geographic and genomic clines suggests that loci with narrow clines are under strong selection, favoring either one parental species (directional selection) or their hybrids (overdominance) as a result of strong associations with climatic variables such as precipitation as snow and mean annual temperature. Cline movement due to past demographic events (evidenced by allelic richness and heterozygosity shifts from the average cline center) may explain the asymmetry in introgression and predominance of P. engelmannii found in this study. These results provide insights into the genetic architecture and fine-scale patterns of admixture, and identify loci that may be involved in reproductive barriers between the species.

@article{garcia_gil_genetic_2015,
	title = {Genetic diversity and inbreeding in natural and managed populations of {Scots} pine},
	volume = {11},
	issn = {1614-2942 1614-2950},
	doi = {10.1007/s11295-015-0850-5},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Tree Genetics \& Genomes},
	author = {García Gil, M. Rosario and Floran, Valentina and Östlund, Lars and Mullin, T. J. “Tim” and Andersson Gull, Bengt},
	month = apr,
	year = {2015},
	pages = {28},
}

@article{pujic_genome_2015,
	title = {Genome {Sequence} of the {Atypical} {Symbiotic} {Frankia} {R43} {Strain}, a {Nitrogen}-{Fixing} and {Hydrogen}-{Producing} {Actinobacterium}},
	volume = {3},
	issn = {2169-8287 (Print)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26607894},
	doi = {10.1128/genomeA.01387-15},
	abstract = {Frankia strain R43 is a nitrogen-fixing and hydrogen-producing symbiotic actinobacterium that was isolated from nodules of Casuarina cunninghamiana but infects only Elaeagnaceae. This communication reports the genome of the strain R43 and provides insights into the microbe genomics and physiological potentials.},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Genome Announc},
	author = {Pujic, P. and Bolotin, A. and Fournier, P. and Sorokin, A. and Lapidus, A. and Richau, K. H. and Briolay, J. and Mebarki, F. and Normand, P. and Sellstedt, A.},
	month = nov,
	year = {2015},
	note = {Edition: 2015/11/27},
}

Frankia strain R43 is a nitrogen-fixing and hydrogen-producing symbiotic actinobacterium that was isolated from nodules of Casuarina cunninghamiana but infects only Elaeagnaceae. This communication reports the genome of the strain R43 and provides insights into the microbe genomics and physiological potentials.

@article{de_la_torre_genome-wide_2015,
	title = {Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in picea gene families},
	volume = {7},
	issn = {1759-6653 (Electronic) 1759-6653 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25747252},
	doi = {10.1093/gbe/evv044},
	abstract = {The recent sequencing of several gymnosperm genomes has greatly facilitated studying the evolution of their genes and gene families. In this study, we examine the evidence for expression-mediated selection in the first two fully sequenced representatives of the gymnosperm plant clade (Picea abies and Picea glauca). We use genome-wide estimates of gene expression ({\textgreater}50,000 expressed genes) to study the relationship between gene expression, codon bias, rates of sequence divergence, protein length, and gene duplication. We found that gene expression is correlated with rates of sequence divergence and codon bias, suggesting that natural selection is acting on Picea protein-coding genes for translational efficiency. Gene expression, rates of sequence divergence, and codon bias are correlated with the size of gene families, with large multicopy gene families having, on average, a lower expression level and breadth, lower codon bias, and higher rates of sequence divergence than single-copy gene families. Tissue-specific patterns of gene expression were more common in large gene families with large gene expression divergence than in single-copy families. Recent family expansions combined with large gene expression variation in paralogs and increased rates of sequence evolution suggest that some Picea gene families are rapidly evolving to cope with biotic and abiotic stress. Our study highlights the importance of gene expression and natural selection in shaping the evolution of protein-coding genes in Picea species, and sets the ground for further studies investigating the evolution of individual gene families in gymnosperms.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Genome Biol Evol},
	author = {De La Torre, A. R. and Lin, Y. C. and Van de Peer, Y. and Ingvarsson, P. K.},
	month = mar,
	year = {2015},
	note = {Edition: 2015/03/10},
	keywords = {*Codon, *Evolution, Molecular, *Gene Expression, *Multigene Family, Gene Duplication, Genome, Plant, Genomics, Picea/*genetics, Plant Proteins/genetics, codon usage, gene expression, sequence divergence, single-copy genes},
	pages = {1002--15},
}

The recent sequencing of several gymnosperm genomes has greatly facilitated studying the evolution of their genes and gene families. In this study, we examine the evidence for expression-mediated selection in the first two fully sequenced representatives of the gymnosperm plant clade (Picea abies and Picea glauca). We use genome-wide estimates of gene expression (\textgreater50,000 expressed genes) to study the relationship between gene expression, codon bias, rates of sequence divergence, protein length, and gene duplication. We found that gene expression is correlated with rates of sequence divergence and codon bias, suggesting that natural selection is acting on Picea protein-coding genes for translational efficiency. Gene expression, rates of sequence divergence, and codon bias are correlated with the size of gene families, with large multicopy gene families having, on average, a lower expression level and breadth, lower codon bias, and higher rates of sequence divergence than single-copy gene families. Tissue-specific patterns of gene expression were more common in large gene families with large gene expression divergence than in single-copy families. Recent family expansions combined with large gene expression variation in paralogs and increased rates of sequence evolution suggest that some Picea gene families are rapidly evolving to cope with biotic and abiotic stress. Our study highlights the importance of gene expression and natural selection in shaping the evolution of protein-coding genes in Picea species, and sets the ground for further studies investigating the evolution of individual gene families in gymnosperms.

@article{wullschleger_genomics_2015,
	title = {Genomics in a changing arctic: critical questions await the molecular ecologist},
	volume = {24},
	issn = {1365-294X (Electronic) 0962-1083 (Linking)},
	shorttitle = {Genomics in a changing arctic},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25809088},
	doi = {10.1111/mec.13166},
	abstract = {Molecular ecology is poised to tackle a host of interesting questions in the coming years. The Arctic provides a unique and rapidly changing environment with a suite of emerging research needs that can be addressed through genetics and genomics. Here we highlight recent research on boreal and tundra ecosystems and put forth a series of questions related to plant and microbial responses to climate change that can benefit from technologies and analytical approaches contained within the molecular ecologist's toolbox. These questions include understanding (i) the mechanisms of plant acquisition and uptake of N in cold soils, (ii) how these processes are mediated by root traits, (iii) the role played by the plant microbiome in cycling C and nutrients within high-latitude ecosystems and (iv) plant adaptation to extreme Arctic climates. We highlight how contributions can be made in these areas through studies that target model and nonmodel organisms and emphasize that the sequencing of the Populus and Salix genomes provides a valuable resource for scientific discoveries related to the plant microbiome and plant adaptation in the Arctic. Moreover, there exists an exciting role to play in model development, including incorporating genetic and evolutionary knowledge into ecosystem and Earth System Models. In this regard, the molecular ecologist provides a valuable perspective on plant genetics as a driver for community biodiversity, and how ecological and evolutionary forces govern community dynamics in a rapidly changing climate.},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Mol Ecol},
	author = {Wullschleger, S. D. and Breen, A. L. and Iversen, C. M. and Olson, M. S. and Nasholm, T. and Ganeteg, U. and Wallenstein, M. D. and Weston, D. J.},
	month = may,
	year = {2015},
	note = {Edition: 2015/03/27},
	keywords = {*Climate Change, *Forests, *Genomics, *Tundra, Adaptation, Biological, Arctic Regions, Carbon Cycle, Cold Temperature, Genome, Plant, Microbiota, Nitrogen Cycle, Nitrogen/metabolism, Plant Roots/metabolism/microbiology, Plants/genetics/metabolism/microbiology, Populus/genetics, Salix/genetics, boreal forest, climate change, genomics, microbiome, shrubs, tundra},
	pages = {2301--9},
}

Molecular ecology is poised to tackle a host of interesting questions in the coming years. The Arctic provides a unique and rapidly changing environment with a suite of emerging research needs that can be addressed through genetics and genomics. Here we highlight recent research on boreal and tundra ecosystems and put forth a series of questions related to plant and microbial responses to climate change that can benefit from technologies and analytical approaches contained within the molecular ecologist's toolbox. These questions include understanding (i) the mechanisms of plant acquisition and uptake of N in cold soils, (ii) how these processes are mediated by root traits, (iii) the role played by the plant microbiome in cycling C and nutrients within high-latitude ecosystems and (iv) plant adaptation to extreme Arctic climates. We highlight how contributions can be made in these areas through studies that target model and nonmodel organisms and emphasize that the sequencing of the Populus and Salix genomes provides a valuable resource for scientific discoveries related to the plant microbiome and plant adaptation in the Arctic. Moreover, there exists an exciting role to play in model development, including incorporating genetic and evolutionary knowledge into ecosystem and Earth System Models. In this regard, the molecular ecologist provides a valuable perspective on plant genetics as a driver for community biodiversity, and how ecological and evolutionary forces govern community dynamics in a rapidly changing climate.

@article{bandau_genotypic_2015,
	title = {Genotypic {Tannin} {Levels} in {Populus} tremula {Impact} the {Way} {Nitrogen} {Enrichment} {Affects} {Growth} and {Allocation} {Responses} for {Some} {Traits} and {Not} for {Others}},
	volume = {10},
	issn = {1932-6203 (Electronic) 1932-6203 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26488414},
	doi = {10.1371/journal.pone.0140971},
	abstract = {Plant intraspecific variability has been proposed as a key mechanism by which plants adapt to environmental change. In boreal forests where nitrogen availability is strongly limited, nitrogen addition happens indirectly through atmospheric N deposition and directly through industrial forest fertilization. These anthropogenic inputs of N have numerous environmental consequences, including shifts in plant species composition and reductions in plant species diversity. However, we know less about how genetic differences within plant populations determine how species respond to eutrophication in boreal forests. According to plant defense theories, nitrogen addition will cause plants to shift carbon allocation more towards growth and less to chemical defense, potentially enhancing vulnerability to antagonists. Aspens are keystone species in boreal forests that produce condensed tannins to serve as chemical defense. We conducted an experiment using ten Populus tremula genotypes from the Swedish Aspen Collection that express extreme levels of baseline investment into foliar condensed tannins. We investigated whether investment into growth and phenolic defense compounds in young plants varied in response to two nitrogen addition levels, corresponding to atmospheric N deposition and industrial forest fertilization. Nitrogen addition generally caused growth to increase, and tannin levels to decrease; however, individualistic responses among genotypes were found for height growth, biomass of specific tissues, root:shoot ratios, and tissue lignin and N concentrations. A genotype's baseline ability to produce and store condensed tannins also influenced plant responses to N, although this effect was relatively minor. High-tannin genotypes tended to grow less biomass under low nitrogen levels and more at the highest fertilization level. Thus, the ability in aspen to produce foliar tannins is likely associated with a steeper reaction norm of growth responses, which suggests a higher plasticity to nitrogen addition, and potentially an advantage when adapting to higher concentrations of soil nitrogen.},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {PLoS One},
	author = {Bandau, F. and Decker, V. H. and Gundale, M. J. and Albrectsen, B. R.},
	month = oct,
	year = {2015},
	note = {Edition: 2015/10/22},
	keywords = {Adaptation, Physiological/*genetics, Biomass, Eutrophication/*physiology, Forests, Nitrogen/*metabolism, Photosynthesis/physiology, Plant Leaves/chemistry, Plant Roots/chemistry, Plant Shoots/chemistry, Populus/genetics/*growth \& development/metabolism, Soil/chemistry, Tannins/genetics/*metabolism},
	pages = {e0140971},
}

Plant intraspecific variability has been proposed as a key mechanism by which plants adapt to environmental change. In boreal forests where nitrogen availability is strongly limited, nitrogen addition happens indirectly through atmospheric N deposition and directly through industrial forest fertilization. These anthropogenic inputs of N have numerous environmental consequences, including shifts in plant species composition and reductions in plant species diversity. However, we know less about how genetic differences within plant populations determine how species respond to eutrophication in boreal forests. According to plant defense theories, nitrogen addition will cause plants to shift carbon allocation more towards growth and less to chemical defense, potentially enhancing vulnerability to antagonists. Aspens are keystone species in boreal forests that produce condensed tannins to serve as chemical defense. We conducted an experiment using ten Populus tremula genotypes from the Swedish Aspen Collection that express extreme levels of baseline investment into foliar condensed tannins. We investigated whether investment into growth and phenolic defense compounds in young plants varied in response to two nitrogen addition levels, corresponding to atmospheric N deposition and industrial forest fertilization. Nitrogen addition generally caused growth to increase, and tannin levels to decrease; however, individualistic responses among genotypes were found for height growth, biomass of specific tissues, root:shoot ratios, and tissue lignin and N concentrations. A genotype's baseline ability to produce and store condensed tannins also influenced plant responses to N, although this effect was relatively minor. High-tannin genotypes tended to grow less biomass under low nitrogen levels and more at the highest fertilization level. Thus, the ability in aspen to produce foliar tannins is likely associated with a steeper reaction norm of growth responses, which suggests a higher plasticity to nitrogen addition, and potentially an advantage when adapting to higher concentrations of soil nitrogen.

@article{galvao_gibberellic_2015,
	title = {Gibberellic acid signaling is required for ambient temperature-mediated induction of flowering in {Arabidopsis} thaliana},
	volume = {84},
	issn = {1365-313X (Electronic) 0960-7412 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26466761},
	doi = {10.1111/tpj.13051},
	abstract = {Distinct molecular mechanisms integrate changes in ambient temperature into the genetic pathways that govern flowering time in Arabidopsis thaliana. Temperature-dependent eviction of the histone variant H2A.Z from nucleosomes has been suggested to facilitate the expression of FT by PIF4 at elevated ambient temperatures. Here we show that, in addition to PIF4, PIF3 and PIF5, but not PIF1 and PIF6, can promote flowering when expressed specifically in phloem companion cells (PCC), where they can induce FT and its close paralog, TSF. However, despite their strong potential to promote flowering, genetic analyses suggest that the PIF genes seem to have only a minor role in adjusting flowering in response to photoperiod or high ambient temperature. In addition, loss of PIF function only partially suppressed the early flowering phenotype and FT expression of the arp6 mutant, which is defective in H2A.Z deposition. In contrast, the chemical inhibition of gibberellic acid (GA) biosynthesis resulted in a strong attenuation of early flowering and FT expression in arp6. Furthermore, GA was able to induce flowering at low temperature (15 degrees C) independently of FT, TSF, and the PIF genes, probably directly at the shoot apical meristem. Together, our results suggest that the timing of the floral transition in response to ambient temperature is more complex than previously thought and that GA signaling might play a crucial role in this process.},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Plant J},
	author = {Galvao, V. C. and Collani, S. and Horrer, D. and Schmid, M.},
	month = dec,
	year = {2015},
	note = {Edition: 2015/10/16},
	keywords = {Arabidopsis Proteins/genetics/metabolism/physiology, Arabidopsis thaliana, Arabidopsis/genetics/*growth \& development/metabolism, Arp6, Basic Helix-Loop-Helix Transcription Factors/genetics/metabolism/physiology, Flm, Flowers/genetics/growth \& development/metabolism, Ft, Gibberellins/*metabolism/pharmacology, H2a.Z, Histones/metabolism, Microfilament Proteins/genetics/metabolism/physiology, Nucleosomes/metabolism, Phosphatidylethanolamine Binding Protein/genetics/metabolism/physiology, Photoperiod, Pif, Plant Growth Regulators/*metabolism/pharmacology, Signal Transduction, Svp, Temperature, ambient temperature, flowering, gibberellin},
	pages = {949--62},
}

Distinct molecular mechanisms integrate changes in ambient temperature into the genetic pathways that govern flowering time in Arabidopsis thaliana. Temperature-dependent eviction of the histone variant H2A.Z from nucleosomes has been suggested to facilitate the expression of FT by PIF4 at elevated ambient temperatures. Here we show that, in addition to PIF4, PIF3 and PIF5, but not PIF1 and PIF6, can promote flowering when expressed specifically in phloem companion cells (PCC), where they can induce FT and its close paralog, TSF. However, despite their strong potential to promote flowering, genetic analyses suggest that the PIF genes seem to have only a minor role in adjusting flowering in response to photoperiod or high ambient temperature. In addition, loss of PIF function only partially suppressed the early flowering phenotype and FT expression of the arp6 mutant, which is defective in H2A.Z deposition. In contrast, the chemical inhibition of gibberellic acid (GA) biosynthesis resulted in a strong attenuation of early flowering and FT expression in arp6. Furthermore, GA was able to induce flowering at low temperature (15 degrees C) independently of FT, TSF, and the PIF genes, probably directly at the shoot apical meristem. Together, our results suggest that the timing of the floral transition in response to ambient temperature is more complex than previously thought and that GA signaling might play a crucial role in this process.

@incollection{gunawardena_life_2015,
	address = {Cham},
	title = {Life {Beyond} {Death}: {The} {Formation} of {Xylem} {Sap} {Conduits}},
	isbn = {978-3-319-21032-2 978-3-319-21033-9},
	shorttitle = {Life {Beyond} {Death}},
	language = {en},
	urldate = {2021-06-07},
	booktitle = {Plant {Programmed} {Cell} {Death}},
	publisher = {Springer International Publishing},
	author = {Ménard, Delphine and Escamez, Sacha and Tuominen, Hannele and Pesquet, Edouard},
	editor = {Gunawardena, Arunika N. and McCabe, Paul F.},
	year = {2015},
	pages = {55--76},
}

@article{ljung_new_2015,
	title = {New mechanistic links between sugar and hormone signalling networks},
	volume = {25},
	issn = {1879-0356 (Electronic) 1369-5266 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26037392},
	doi = {10.1016/j.pbi.2015.05.022},
	abstract = {Plant growth and development must be coordinated with metabolism, notably with the efficiency of photosynthesis and the uptake of nutrients. This coordination requires local connections between hormonal response and metabolic state, as well as long-distance connections between shoot and root tissues. Recently, several molecular mechanisms have been proposed to explain the integration of sugar signalling with hormone pathways. In this work, DELLA and PIF proteins have emerged as hubs in sugar-hormone cross-regulation networks.},
	language = {en},
	urldate = {2021-06-07},
	journal = {Curr Opin Plant Biol},
	author = {Ljung, K. and Nemhauser, J. L. and Perata, P.},
	month = jun,
	year = {2015},
	note = {Edition: 2015/06/04},
	keywords = {*Plant Physiological Phenomena, *Signal Transduction, Biological Transport, Brassinosteroids/metabolism, Carbohydrate Metabolism, Carbohydrates, Gibberellins/metabolism, Indoleacetic Acids/metabolism, Photosynthesis, Plant Development, Plant Growth Regulators/*metabolism, Plant Roots/growth \& development/metabolism, Plants/*metabolism},
	pages = {130--7},
}

Plant growth and development must be coordinated with metabolism, notably with the efficiency of photosynthesis and the uptake of nutrients. This coordination requires local connections between hormonal response and metabolic state, as well as long-distance connections between shoot and root tissues. Recently, several molecular mechanisms have been proposed to explain the integration of sugar signalling with hormone pathways. In this work, DELLA and PIF proteins have emerged as hubs in sugar-hormone cross-regulation networks.

@article{brackin_nitrogen_2015,
	title = {Nitrogen fluxes at the root-soil interface show a mismatch of nitrogen fertilizer supply and sugarcane root uptake capacity},
	volume = {5},
	issn = {2045-2322 (Electronic) 2045-2322 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26496834},
	doi = {10.1038/srep15727},
	abstract = {Globally only approximately 50\% of applied nitrogen (N) fertilizer is captured by crops, and the remainder can cause pollution via runoff and gaseous emissions. Synchronizing soil N supply and crop demand will address this problem, however current soil analysis methods provide little insight into delivery and acquisition of N forms by roots. We used microdialysis, a novel technique for in situ quantification of soil nutrient fluxes, to measure N fluxes in sugarcane cropping soils receiving different fertilizer regimes, and compare these with N uptake capacities of sugarcane roots. We show that in fertilized sugarcane soils, fluxes of inorganic N exceed the uptake capacities of sugarcane roots by several orders of magnitude. Contrary, fluxes of organic N closely matched roots' uptake capacity. These results indicate root uptake capacity constrains plant acquisition of inorganic N. This mismatch between soil N supply and root N uptake capacity is a likely key driver for low N efficiency in the studied crop system. Our results also suggest that (i) the relative contribution of inorganic N for plant nutrition may be overestimated when relying on soil extracts as indicators for root-available N, and (ii) organic N may contribute more to crop N supply than is currently assumed.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Sci Rep},
	author = {Brackin, R. and Nasholm, T. and Robinson, N. and Guillou, S. and Vinall, K. and Lakshmanan, P. and Schmidt, S. and Inselsbacher, E.},
	month = oct,
	year = {2015},
	note = {Edition: 2015/10/27},
	keywords = {Amino Acids/metabolism, Ammonium Compounds/chemistry/metabolism, Crops, Agricultural, Kinetics, Nitrogen Isotopes/analysis, Nitrogen/analysis/*metabolism, Plant Roots/metabolism, Saccharum/growth \& development/*metabolism, Soil/*chemistry},
	pages = {15727},
}

Globally only approximately 50% of applied nitrogen (N) fertilizer is captured by crops, and the remainder can cause pollution via runoff and gaseous emissions. Synchronizing soil N supply and crop demand will address this problem, however current soil analysis methods provide little insight into delivery and acquisition of N forms by roots. We used microdialysis, a novel technique for in situ quantification of soil nutrient fluxes, to measure N fluxes in sugarcane cropping soils receiving different fertilizer regimes, and compare these with N uptake capacities of sugarcane roots. We show that in fertilized sugarcane soils, fluxes of inorganic N exceed the uptake capacities of sugarcane roots by several orders of magnitude. Contrary, fluxes of organic N closely matched roots' uptake capacity. These results indicate root uptake capacity constrains plant acquisition of inorganic N. This mismatch between soil N supply and root N uptake capacity is a likely key driver for low N efficiency in the studied crop system. Our results also suggest that (i) the relative contribution of inorganic N for plant nutrition may be overestimated when relying on soil extracts as indicators for root-available N, and (ii) organic N may contribute more to crop N supply than is currently assumed.

@article{hedwall_nitrogen-retention_2015,
	title = {Nitrogen-retention capacity in a fertilized forest after clear-cutting - the effect of forest-floor vegetation},
	volume = {45},
	issn = {0045-5067},
	url = {://WOS:000347297500015},
	doi = {10.1139/cjfr-2014-0281},
	abstract = {Forest fertilization with nitrogen (N) has several benefits to society such as increased wood production and carbon sequestration. There are, however, concerns about N leakage, particularly following clear-cutting. The forest-floor vegetation may increase the N retention of forest ecosystems; however, very few studies have quantified the amount of vegetation required. We studied the relationship between vegetation cover and risk of N leakage, estimated by the amounts of ammonium-N and nitrate-N retained on ion-exchange capsules in the soil, during 4 years following the clear-cutting and harvesting of logging residues in a previously fertilized forest in southern Sweden. Previous fertilization increased the amount of nitrate-N captured on the capsules, whereas the amount of ammonium-N decreased. The vascular vegetation cover increased from almost zero to approximately 25\% independent of fertilization. The amount of ammonium-N and nitrate-N retained on the capsules was already reduced by 50\%-75\% at 20\% vegetation cover, and by 30\%-40\% cover, it approached zero, independent of the number of years since clear-cutting. The vegetation may impede tree-seedling establishment, implying a trade-off between seedling growth and N-retention capacity. However, our results indicate that maximum N retention may be achieved at a relatively low vegetation cover, which could be accomplished with less intrusive scarification methods than currently used.},
	language = {English},
	number = {1},
	urldate = {2021-06-07},
	journal = {Canadian Journal of Forest Research},
	author = {Hedwall, P. O. and Bergh, J. and Nordin, A.},
	month = jan,
	year = {2015},
	keywords = {deposition, forest fertilization, ground vegetation, immobilization, intensities, management, nitrate, nitrogen, norway spruce, nutrient leakage, water},
	pages = {130--134},
}

Forest fertilization with nitrogen (N) has several benefits to society such as increased wood production and carbon sequestration. There are, however, concerns about N leakage, particularly following clear-cutting. The forest-floor vegetation may increase the N retention of forest ecosystems; however, very few studies have quantified the amount of vegetation required. We studied the relationship between vegetation cover and risk of N leakage, estimated by the amounts of ammonium-N and nitrate-N retained on ion-exchange capsules in the soil, during 4 years following the clear-cutting and harvesting of logging residues in a previously fertilized forest in southern Sweden. Previous fertilization increased the amount of nitrate-N captured on the capsules, whereas the amount of ammonium-N decreased. The vascular vegetation cover increased from almost zero to approximately 25% independent of fertilization. The amount of ammonium-N and nitrate-N retained on the capsules was already reduced by 50%-75% at 20% vegetation cover, and by 30%-40% cover, it approached zero, independent of the number of years since clear-cutting. The vegetation may impede tree-seedling establishment, implying a trade-off between seedling growth and N-retention capacity. However, our results indicate that maximum N retention may be achieved at a relatively low vegetation cover, which could be accomplished with less intrusive scarification methods than currently used.

@article{blumenstein_nutritional_2015,
	title = {Nutritional niche overlap potentiates the use of endophytes in biocontrol of a tree disease},
	volume = {60},
	issn = {1386-6141},
	url = {://WOS:000360999800007},
	doi = {10.1007/s10526-015-9668-1},
	abstract = {Asymptomatic endophytic fungi are often regarded as potent biocontrol agents in plants, but the competitive interactions between endophytes and other microbes within the same host plant are poorly understood. We tested a hypothesis that as compared to asymptomatic endophytes, an aggressive pathogen inhabiting the same host is able to utilize carbon substrates more efficiently. Using phenotype microarray, we determined the carbon utilization profiles of the highly virulent Dutch elm disease (DED) pathogen Ophiostoma novo-ulmi, and four asymptomatic elm (Ulmus spp.) endophyte isolates that were selected based on their differential association to the DED-susceptibility pattern of the host elms. The competitive interactions between isolates were evaluated using a niche overlap index. In contrast to our hypothesis, the studied endophytes exhibited extensive niche overlap with the pathogen, suggesting that some endophyte strains might protect elms against DED-pathogen through competition for substrates and provide new tools for biocontrol of DED.},
	language = {English},
	number = {5},
	urldate = {2021-06-07},
	journal = {Biocontrol},
	author = {Blumenstein, K. and Albrectsen, B. R. and Martin, J. A. and Hultberg, M. and Sieber, T. N. and Helander, M. and Witzell, J.},
	month = oct,
	year = {2015},
	keywords = {aureobasidium-pullulans, biocontrol, biological-control, carbon utilization profile, competition, dutch elm disease, endophytic fungi, fungal endophytes, growth, niche differentiation hypothesis, niche tradeoff, ophiostoma-ulmi, populations, resistance, virulence},
	pages = {655--667},
}

Asymptomatic endophytic fungi are often regarded as potent biocontrol agents in plants, but the competitive interactions between endophytes and other microbes within the same host plant are poorly understood. We tested a hypothesis that as compared to asymptomatic endophytes, an aggressive pathogen inhabiting the same host is able to utilize carbon substrates more efficiently. Using phenotype microarray, we determined the carbon utilization profiles of the highly virulent Dutch elm disease (DED) pathogen Ophiostoma novo-ulmi, and four asymptomatic elm (Ulmus spp.) endophyte isolates that were selected based on their differential association to the DED-susceptibility pattern of the host elms. The competitive interactions between isolates were evaluated using a niche overlap index. In contrast to our hypothesis, the studied endophytes exhibited extensive niche overlap with the pathogen, suggesting that some endophyte strains might protect elms against DED-pathogen through competition for substrates and provide new tools for biocontrol of DED.

@article{zwiewka_osmotic_2015,
	title = {Osmotic {Stress} {Modulates} the {Balance} between {Exocytosis} and {Clathrin}-{Mediated} {Endocytosis} in {Arabidopsis} thaliana},
	volume = {8},
	issn = {1752-9867 (Electronic) 1674-2052 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25795554},
	doi = {10.1016/j.molp.2015.03.007},
	abstract = {The sessile life style of plants creates the need to deal with an often adverse environment, in which water availability can change on a daily basis, challenging the cellular physiology and integrity. Changes in osmotic conditions disrupt the equilibrium of the plasma membrane: hypoosmotic conditions increase and hyperosmotic environment decrease the cell volume. Here, we show that short-term extracellular osmotic treatments are closely followed by a shift in the balance between endocytosis and exocytosis in root meristem cells. Acute hyperosmotic treatments (ionic and nonionic) enhance clathrin-mediated endocytosis simultaneously attenuating exocytosis, whereas hypoosmotic treatments have the opposite effects. In addition to clathrin recruitment to the plasma membrane, components of early endocytic trafficking are essential during hyperosmotic stress responses. Consequently, growth of seedlings defective in elements of clathrin or early endocytic machinery is more sensitive to hyperosmotic treatments. We also found that the endocytotic response to a change of osmotic status in the environment is dominant over the presumably evolutionary more recent regulatory effect of plant hormones, such as auxin. These results imply that osmotic perturbation influences the balance between endocytosis and exocytosis acting through clathrin-mediated endocytosis. We propose that tension on the plasma membrane determines the addition or removal of membranes at the cell surface, thus preserving cell integrity.},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Mol Plant},
	author = {Zwiewka, M. and Nodzynski, T. and Robert, S. and Vanneste, S. and Friml, J.},
	month = aug,
	year = {2015},
	note = {Edition: 2015/03/22},
	keywords = {*Endocytosis/drug effects, *Exocytosis/drug effects, *Osmotic Pressure/drug effects, Adaptation, Physiological/drug effects, Arabidopsis Proteins/metabolism, Arabidopsis/*cytology/drug effects/*metabolism, Cell Membrane/drug effects/metabolism, Clathrin/*metabolism, Gene Knockdown Techniques, Indoleacetic Acids/pharmacology, Mutation/genetics, auxin, clathrin-mediated endocytosis, osmotic stress, protein trafficking},
	pages = {1175--87},
}

The sessile life style of plants creates the need to deal with an often adverse environment, in which water availability can change on a daily basis, challenging the cellular physiology and integrity. Changes in osmotic conditions disrupt the equilibrium of the plasma membrane: hypoosmotic conditions increase and hyperosmotic environment decrease the cell volume. Here, we show that short-term extracellular osmotic treatments are closely followed by a shift in the balance between endocytosis and exocytosis in root meristem cells. Acute hyperosmotic treatments (ionic and nonionic) enhance clathrin-mediated endocytosis simultaneously attenuating exocytosis, whereas hypoosmotic treatments have the opposite effects. In addition to clathrin recruitment to the plasma membrane, components of early endocytic trafficking are essential during hyperosmotic stress responses. Consequently, growth of seedlings defective in elements of clathrin or early endocytic machinery is more sensitive to hyperosmotic treatments. We also found that the endocytotic response to a change of osmotic status in the environment is dominant over the presumably evolutionary more recent regulatory effect of plant hormones, such as auxin. These results imply that osmotic perturbation influences the balance between endocytosis and exocytosis acting through clathrin-mediated endocytosis. We propose that tension on the plasma membrane determines the addition or removal of membranes at the cell surface, thus preserving cell integrity.

@incollection{anderson_role_2015,
	address = {Cham},
	title = {Role of the {Circadian} {Clock} in {Cold} {Acclimation} and {Winter} {Dormancy} in {Perennial} {Plants}},
	isbn = {978-3-319-14450-4 978-3-319-14451-1},
	url = {http://link.springer.com/10.1007/978-3-319-14451-1_3},
	language = {en},
	urldate = {2021-06-07},
	booktitle = {Advances in {Plant} {Dormancy}},
	publisher = {Springer International Publishing},
	author = {Johansson, Mikael and Ramos-Sánchez, José M. and Conde, Daniel and Ibáñez, Cristian and Takata, Naoki and Allona, Isabel and Eriksson, Maria E.},
	editor = {Anderson, James V.},
	year = {2015},
	doi = {10.1007/978-3-319-14451-1_3},
	pages = {51--74},
}

@article{mair_snrk1-triggered_2015,
	title = {{SnRK1}-triggered switch of {bZIP63} dimerization mediates the low-energy response in plants},
	volume = {4},
	issn = {2050-084X (Electronic) 2050-084X (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26263501},
	doi = {10.7554/eLife.05828},
	abstract = {Metabolic adjustment to changing environmental conditions, particularly balancing of growth and defense responses, is crucial for all organisms to survive. The evolutionary conserved AMPK/Snf1/SnRK1 kinases are well-known metabolic master regulators in the low-energy response in animals, yeast and plants. They act at two different levels: by modulating the activity of key metabolic enzymes, and by massive transcriptional reprogramming. While the first part is well established, the latter function is only partially understood in animals and not at all in plants. Here we identified the Arabidopsis transcription factor bZIP63 as key regulator of the starvation response and direct target of the SnRK1 kinase. Phosphorylation of bZIP63 by SnRK1 changed its dimerization preference, thereby affecting target gene expression and ultimately primary metabolism. A bzip63 knock-out mutant exhibited starvation-related phenotypes, which could be functionally complemented by wild type bZIP63, but not by a version harboring point mutations in the identified SnRK1 target sites.},
	language = {en},
	urldate = {2021-06-07},
	journal = {Elife},
	author = {Mair, A. and Pedrotti, L. and Wurzinger, B. and Anrather, D. and Simeunovic, A. and Weiste, C. and Valerio, C. and Dietrich, K. and Kirchler, T. and Nagele, T. and Vicente Carbajosa, J. and Hanson, J. and Baena-Gonzalez, E. and Chaban, C. and Weckwerth, W. and Droge-Laser, W. and Teige, M.},
	month = aug,
	year = {2015},
	note = {Edition: 2015/08/12},
	keywords = {*Gene Expression Regulation, Plant, *Protein Multimerization, Adaptation, Physiological, Arabidopsis Proteins/*metabolism, Arabidopsis/*genetics/metabolism, Basic-Leucine Zipper Transcription Factors/deficiency/*metabolism, Gene Knockout Techniques, Genetic Complementation Test, Phosphorylation, Protein Processing, Post-Translational, Protein-Serine-Threonine Kinases/*metabolism, SnRK1 kinase, arabidopsis, bZIP transcription factor, cell biology, metabolic reprogramming, plant biology},
	pages = {e05828},
}

Metabolic adjustment to changing environmental conditions, particularly balancing of growth and defense responses, is crucial for all organisms to survive. The evolutionary conserved AMPK/Snf1/SnRK1 kinases are well-known metabolic master regulators in the low-energy response in animals, yeast and plants. They act at two different levels: by modulating the activity of key metabolic enzymes, and by massive transcriptional reprogramming. While the first part is well established, the latter function is only partially understood in animals and not at all in plants. Here we identified the Arabidopsis transcription factor bZIP63 as key regulator of the starvation response and direct target of the SnRK1 kinase. Phosphorylation of bZIP63 by SnRK1 changed its dimerization preference, thereby affecting target gene expression and ultimately primary metabolism. A bzip63 knock-out mutant exhibited starvation-related phenotypes, which could be functionally complemented by wild type bZIP63, but not by a version harboring point mutations in the identified SnRK1 target sites.

@article{henriksson_stem_2015,
	title = {Stem compression reversibly reduces phloem transport in {Pinus} sylvestris trees},
	volume = {35},
	issn = {1758-4469 (Electronic) 0829-318X (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26377876},
	doi = {10.1093/treephys/tpv078},
	abstract = {Manipulating tree belowground carbon (C) transport enables investigation of the ecological and physiological roles of tree roots and their associated mycorrhizal fungi, as well as a range of other soil organisms and processes. Girdling remains the most reliable method for manipulating this flux and it has been used in numerous studies. However, girdling is destructive and irreversible. Belowground C transport is mediated by phloem tissue, pressurized through the high osmotic potential resulting from its high content of soluble sugars. We speculated that phloem transport may be reversibly blocked through the application of an external pressure on tree stems. Thus, we here introduce a technique based on compression of the phloem, which interrupts belowground flow of assimilates, but allows trees to recover when the external pressure is removed. Metal clamps were wrapped around the stems and tightened to achieve a pressure theoretically sufficient to collapse the phloem tissue, thereby aiming to block transport. The compression's performance was tested in two field experiments: a (13)C canopy labelling study conducted on small Scots pine (Pinus sylvestris L.) trees [2-3 m tall, 3-7 cm diameter at breast height (DBH)] and a larger study involving mature pines ( approximately 15 m tall, 15-25 cm DBH) where stem respiration, phloem and root carbohydrate contents, and soil CO2 efflux were measured. The compression's effectiveness was demonstrated by the successful blockage of (13)C transport. Stem compression doubled stem respiration above treatment, reduced soil CO2 efflux by 34\% and reduced phloem sucrose content by 50\% compared with control trees. Stem respiration and soil CO2 efflux returned to normal within 3 weeks after pressure release, and (13)C labelling revealed recovery of phloem function the following year. Thus, we show that belowground phloem C transport can be reduced by compression, and we also demonstrate that trees recover after treatment, resuming C transport in the phloem.},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Tree Physiol},
	author = {Henriksson, N. and Tarvainen, L. and Lim, H. and Tor-Ngern, P. and Palmroth, S. and Oren, R. and Marshall, J. and Nasholm, T.},
	month = oct,
	year = {2015},
	note = {Edition: 2015/09/18},
	keywords = {Biological Transport, Carbon/*metabolism, Phloem/*metabolism, Pinus sylvestris/*metabolism, Plant Roots/metabolism, Plant Stems/*metabolism, Pressure, Trees/metabolism, belowground carbon transport, carbon partitioning, carbon-13, girdling, soil respiration, stem respiration},
	pages = {1075--85},
}

Manipulating tree belowground carbon (C) transport enables investigation of the ecological and physiological roles of tree roots and their associated mycorrhizal fungi, as well as a range of other soil organisms and processes. Girdling remains the most reliable method for manipulating this flux and it has been used in numerous studies. However, girdling is destructive and irreversible. Belowground C transport is mediated by phloem tissue, pressurized through the high osmotic potential resulting from its high content of soluble sugars. We speculated that phloem transport may be reversibly blocked through the application of an external pressure on tree stems. Thus, we here introduce a technique based on compression of the phloem, which interrupts belowground flow of assimilates, but allows trees to recover when the external pressure is removed. Metal clamps were wrapped around the stems and tightened to achieve a pressure theoretically sufficient to collapse the phloem tissue, thereby aiming to block transport. The compression's performance was tested in two field experiments: a (13)C canopy labelling study conducted on small Scots pine (Pinus sylvestris L.) trees [2-3 m tall, 3-7 cm diameter at breast height (DBH)] and a larger study involving mature pines ( approximately 15 m tall, 15-25 cm DBH) where stem respiration, phloem and root carbohydrate contents, and soil CO2 efflux were measured. The compression's effectiveness was demonstrated by the successful blockage of (13)C transport. Stem compression doubled stem respiration above treatment, reduced soil CO2 efflux by 34% and reduced phloem sucrose content by 50% compared with control trees. Stem respiration and soil CO2 efflux returned to normal within 3 weeks after pressure release, and (13)C labelling revealed recovery of phloem function the following year. Thus, we show that belowground phloem C transport can be reduced by compression, and we also demonstrate that trees recover after treatment, resuming C transport in the phloem.

@article{kurepin_stress-related_2015,
	title = {Stress-related hormones and glycinebetaine interplay in protection of photosynthesis under abiotic stress conditions},
	volume = {126},
	issn = {1573-5079 (Electronic) 0166-8595 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25823797},
	doi = {10.1007/s11120-015-0125-x},
	abstract = {Plants subjected to abiotic stresses such as extreme high and low temperatures, drought or salinity, often exhibit decreased vegetative growth and reduced reproductive capabilities. This is often associated with decreased photosynthesis via an increase in photoinhibition, and accompanied by rapid changes in endogenous levels of stress-related hormones such as abscisic acid (ABA), salicylic acid (SA) and ethylene. However, certain plant species and/or genotypes exhibit greater tolerance to abiotic stress because they are capable of accumulating endogenous levels of the zwitterionic osmolyte-glycinebetaine (GB). The accumulation of GB via natural production, exogenous application or genetic engineering, enhances plant osmoregulation and thus increases abiotic stress tolerance. The final steps of GB biosynthesis occur in chloroplasts where GB has been shown to play a key role in increasing the protection of soluble stromal and lumenal enzymes, lipids and proteins, of the photosynthetic apparatus. In addition, we suggest that the stress-induced GB biosynthesis pathway may well serve as an additional or alternative biochemical sink, one which consumes excess photosynthesis-generated electrons, thus protecting photosynthetic apparatus from overreduction. Glycinebetaine biosynthesis in chloroplasts is up-regulated by increases in endogenous ABA or SA levels. In this review, we propose and discuss a model describing the close interaction and synergistic physiological effects of GB and ABA in the process of cold acclimation of higher plants.},
	language = {en},
	number = {2-3},
	urldate = {2021-06-07},
	journal = {Photosynth Res},
	author = {Kurepin, L. V. and Ivanov, A. G. and Zaman, M. and Pharis, R. P. and Allakhverdiev, S. I. and Hurry, V. and Huner, N. P.},
	month = dec,
	year = {2015},
	note = {Edition: 2015/04/01},
	keywords = {*Acclimatization, *Stress, Physiological, Abscisic Acid/*metabolism, Abscisic acid, Betaine/*metabolism, Cold Temperature, Cold acclimation, Droughts, Environmental stress, Glycinebetaine, Photosynthesis/*drug effects/physiology, Photosynthetic apparatus, Plant Growth Regulators/*metabolism, Plant hormones, Salinity},
	pages = {221--35},
}

Plants subjected to abiotic stresses such as extreme high and low temperatures, drought or salinity, often exhibit decreased vegetative growth and reduced reproductive capabilities. This is often associated with decreased photosynthesis via an increase in photoinhibition, and accompanied by rapid changes in endogenous levels of stress-related hormones such as abscisic acid (ABA), salicylic acid (SA) and ethylene. However, certain plant species and/or genotypes exhibit greater tolerance to abiotic stress because they are capable of accumulating endogenous levels of the zwitterionic osmolyte-glycinebetaine (GB). The accumulation of GB via natural production, exogenous application or genetic engineering, enhances plant osmoregulation and thus increases abiotic stress tolerance. The final steps of GB biosynthesis occur in chloroplasts where GB has been shown to play a key role in increasing the protection of soluble stromal and lumenal enzymes, lipids and proteins, of the photosynthetic apparatus. In addition, we suggest that the stress-induced GB biosynthesis pathway may well serve as an additional or alternative biochemical sink, one which consumes excess photosynthesis-generated electrons, thus protecting photosynthetic apparatus from overreduction. Glycinebetaine biosynthesis in chloroplasts is up-regulated by increases in endogenous ABA or SA levels. In this review, we propose and discuss a model describing the close interaction and synergistic physiological effects of GB and ABA in the process of cold acclimation of higher plants.

@article{zhang_subcellular_2015,
	title = {Subcellular {Localization} of {Carotenoid} {Biosynthesis} in {Synechocystis} sp. {PCC} 6803},
	volume = {10},
	issn = {1932-6203 (Electronic) 1932-6203 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26083372},
	doi = {10.1371/journal.pone.0130904},
	abstract = {The biosynthesis pathway of carotenoids in cyanobacteria is partly described. However, the subcellular localization of individual steps is so far unknown. Carotenoid analysis of different membrane subfractions in Synechocystis sp. PCC6803 shows that "light" plasma membranes have a high carotenoid/protein ratio, when compared to "heavier" plasma membranes or thylakoids. The localization of CrtQ and CrtO, two well-defined carotenoid synthesis pathway enzymes in Synechocystis, was studied by epitope tagging and western blots. Both enzymes are locally more abundant in plasma membranes than in thylakoids, implying that the plasma membrane has higher synthesis rates of beta-carotene precursor molecules and echinenone.},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {PLoS One},
	author = {Zhang, L. and Selao, T. T. and Selstam, E. and Norling, B.},
	month = jun,
	year = {2015},
	note = {Edition: 2015/06/18},
	keywords = {Bacterial Proteins/*metabolism, Biosynthetic Pathways, Carotenoids/*biosynthesis, Cell Membrane/*chemistry/metabolism, Chromatography, High Pressure Liquid, Subcellular Fractions, Synechocystis/growth \& development/*metabolism},
	pages = {e0130904},
}

The biosynthesis pathway of carotenoids in cyanobacteria is partly described. However, the subcellular localization of individual steps is so far unknown. Carotenoid analysis of different membrane subfractions in Synechocystis sp. PCC6803 shows that "light" plasma membranes have a high carotenoid/protein ratio, when compared to "heavier" plasma membranes or thylakoids. The localization of CrtQ and CrtO, two well-defined carotenoid synthesis pathway enzymes in Synechocystis, was studied by epitope tagging and western blots. Both enzymes are locally more abundant in plasma membranes than in thylakoids, implying that the plasma membrane has higher synthesis rates of beta-carotene precursor molecules and echinenone.

@article{kleczkowski_sugar_2015,
	title = {Sugar {Activation} for {Production} of {Nucleotide} {Sugars} as {Substrates} for {Glycosyltransferases} in {Plants}},
	volume = {62},
	issn = {1344-7882, 1880-7291},
	url = {https://www.jstage.jst.go.jp/article/jag/62/2/62_jag.JAG-2015_003/_article},
	doi = {10.5458/jag.jag.JAG-2015_003},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Journal of Applied Glycoscience},
	author = {Kleczkowski, Leszek A. and Decker, Daniel},
	year = {2015},
	pages = {25--36},
}

@article{barros_cell_2015,
	title = {The cell biology of lignification in higher plants},
	volume = {115},
	issn = {1095-8290 (Electronic) 0305-7364 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25878140},
	doi = {10.1093/aob/mcv046},
	abstract = {BACKGROUND: Lignin is a polyphenolic polymer that strengthens and waterproofs the cell wall of specialized plant cell types. Lignification is part of the normal differentiation programme and functioning of specific cell types, but can also be triggered as a response to various biotic and abiotic stresses in cells that would not otherwise be lignifying. SCOPE: Cell wall lignification exhibits specific characteristics depending on the cell type being considered. These characteristics include the timing of lignification during cell differentiation, the palette of associated enzymes and substrates, the sub-cellular deposition sites, the monomeric composition and the cellular autonomy for lignin monomer production. This review provides an overview of the current understanding of lignin biosynthesis and polymerization at the cell biology level. CONCLUSIONS: The lignification process ranges from full autonomy to complete co-operation depending on the cell type. The different roles of lignin for the function of each specific plant cell type are clearly illustrated by the multiple phenotypic defects exhibited by knock-out mutants in lignin synthesis, which may explain why no general mechanism for lignification has yet been defined. The range of phenotypic effects observed include altered xylem sap transport, loss of mechanical support, reduced seed protection and dispersion, and/or increased pest and disease susceptibility.},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Ann Bot},
	author = {Barros, J. and Serk, H. and Granlund, I. and Pesquet, E.},
	month = jun,
	year = {2015},
	note = {Edition: 2015/04/17},
	keywords = {*Gene Expression Regulation, Plant, Arabidopsis thaliana, Arabidopsis/genetics/metabolism, Cell Wall/metabolism, Embryophyta/*genetics/*metabolism, Lignin, Lignin/*metabolism, laccases, lignification, monolignols, non-cell autonomous processes, peroxidases, plant cell wall},
	pages = {1053--74},
}

BACKGROUND: Lignin is a polyphenolic polymer that strengthens and waterproofs the cell wall of specialized plant cell types. Lignification is part of the normal differentiation programme and functioning of specific cell types, but can also be triggered as a response to various biotic and abiotic stresses in cells that would not otherwise be lignifying. SCOPE: Cell wall lignification exhibits specific characteristics depending on the cell type being considered. These characteristics include the timing of lignification during cell differentiation, the palette of associated enzymes and substrates, the sub-cellular deposition sites, the monomeric composition and the cellular autonomy for lignin monomer production. This review provides an overview of the current understanding of lignin biosynthesis and polymerization at the cell biology level. CONCLUSIONS: The lignification process ranges from full autonomy to complete co-operation depending on the cell type. The different roles of lignin for the function of each specific plant cell type are clearly illustrated by the multiple phenotypic defects exhibited by knock-out mutants in lignin synthesis, which may explain why no general mechanism for lignification has yet been defined. The range of phenotypic effects observed include altered xylem sap transport, loss of mechanical support, reduced seed protection and dispersion, and/or increased pest and disease susceptibility.

@article{voss_circadian_2015,
	title = {The circadian clock rephases during lateral root organ initiation in {Arabidopsis} thaliana},
	volume = {6},
	issn = {2041-1723 (Electronic) 2041-1723 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26144255},
	doi = {10.1038/ncomms8641},
	abstract = {The endogenous circadian clock enables organisms to adapt their growth and development to environmental changes. Here we describe how the circadian clock is employed to coordinate responses to the key signal auxin during lateral root (LR) emergence. In the model plant, Arabidopsis thaliana, LRs originate from a group of stem cells deep within the root, necessitating that new organs emerge through overlying root tissues. We report that the circadian clock is rephased during LR development. Metabolite and transcript profiling revealed that the circadian clock controls the levels of auxin and auxin-related genes including the auxin response repressor IAA14 and auxin oxidase AtDAO2. Plants lacking or overexpressing core clock components exhibit LR emergence defects. We conclude that the circadian clock acts to gate auxin signalling during LR development to facilitate organ emergence.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nat Commun},
	author = {Voss, U. and Wilson, M. H. and Kenobi, K. and Gould, P. D. and Robertson, F. C. and Peer, W. A. and Lucas, M. and Swarup, K. and Casimiro, I. and Holman, T. J. and Wells, D. M. and Peret, B. and Goh, T. and Fukaki, H. and Hodgman, T. C. and Laplaze, L. and Halliday, K. J. and Ljung, K. and Murphy, A. S. and Hall, A. J. and Webb, A. A. and Bennett, M. J.},
	month = jul,
	year = {2015},
	note = {Edition: 2015/07/07},
	keywords = {Arabidopsis Proteins/genetics/metabolism, Arabidopsis/*growth \& development, Circadian Clocks/*physiology, Gene Expression Regulation, Plant/*physiology, Gravitropism, Indoleacetic Acids/metabolism, Mutation, Oxidoreductases/genetics/metabolism, Plant Roots/*physiology, Time Factors, Transcription Factors/genetics/metabolism, Transcriptome},
	pages = {7641},
}

The endogenous circadian clock enables organisms to adapt their growth and development to environmental changes. Here we describe how the circadian clock is employed to coordinate responses to the key signal auxin during lateral root (LR) emergence. In the model plant, Arabidopsis thaliana, LRs originate from a group of stem cells deep within the root, necessitating that new organs emerge through overlying root tissues. We report that the circadian clock is rephased during LR development. Metabolite and transcript profiling revealed that the circadian clock controls the levels of auxin and auxin-related genes including the auxin response repressor IAA14 and auxin oxidase AtDAO2. Plants lacking or overexpressing core clock components exhibit LR emergence defects. We conclude that the circadian clock acts to gate auxin signalling during LR development to facilitate organ emergence.

@article{matrosova_ht1_2015,
	title = {The {HT1} protein kinase is essential for red light-induced stomatal opening and genetically interacts with {OST1} in red light and {CO2} -induced stomatal movement responses},
	volume = {208},
	issn = {1469-8137 (Electronic) 0028-646X (Linking)},
	shorttitle = {The},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26192339},
	doi = {10.1111/nph.13566},
	abstract = {The question of whether red light-induced stomatal opening is mediated by a photosynthesis-derived reduction in intercellular [CO2 ] (Ci ) remains controversial and genetic analyses are needed. The Arabidopsis thaliana protein kinase HIGH TEMPERATURE 1 (HT1) is a negative regulator of [CO2 ]-induced stomatal closing and ht1-2 mutant plants do not show stomatal opening to low [CO2 ]. The protein kinase mutant ost1-3 exhibits slowed stomatal responses to CO2 . The functions of HT1 and OPEN STOMATA 1 (OST1) to changes in red, blue light or [CO2 ] were analyzed. For comparison we assayed recessive ca1ca4 carbonic anhydrase double mutant plants, based on their slowed stomatal response to CO2 . Here, we report a strong impairment in ht1 in red light-induced stomatal opening whereas blue light was able to induce stomatal opening. The effects on photosynthetic performance in ht1 were restored when stomatal limitation of CO2 uptake, by control of [Ci ], was eliminated. HT1 was found to interact genetically with OST1 both during red light- and low [CO2 ]-induced stomatal opening. Analyses of ca1ca4 plants suggest that more than a low [Ci ]-dependent pathway may function in red light-induced stomatal opening. These results demonstrate that HT1 is essential for red light-induced stomatal opening and interacts genetically with OST1 during stomatal responses to red light and altered [CO2 ].},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {New Phytol},
	author = {Matrosova, A. and Bogireddi, H. and Mateo-Penas, A. and Hashimoto-Sugimoto, M. and Iba, K. and Schroeder, J. I. and Israelsson-Nordstrom, M.},
	month = dec,
	year = {2015},
	note = {Edition: 2015/07/21},
	keywords = {*Genes, Plant, *Light, *Plant Stomata, Arabidopsis Proteins/*genetics/metabolism, Arabidopsis thaliana, Arabidopsis/*genetics/metabolism, Carbon Dioxide/*metabolism, High temperature 1 (ht1), Mutation, Open stomata 1 (ost1), Photosynthesis/*genetics, Protein Kinases/*genetics/metabolism, Signal Transduction, low [CO2], photosynthesis, red light, stomata},
	pages = {1126--37},
}

The question of whether red light-induced stomatal opening is mediated by a photosynthesis-derived reduction in intercellular [CO2 ] (Ci ) remains controversial and genetic analyses are needed. The Arabidopsis thaliana protein kinase HIGH TEMPERATURE 1 (HT1) is a negative regulator of [CO2 ]-induced stomatal closing and ht1-2 mutant plants do not show stomatal opening to low [CO2 ]. The protein kinase mutant ost1-3 exhibits slowed stomatal responses to CO2 . The functions of HT1 and OPEN STOMATA 1 (OST1) to changes in red, blue light or [CO2 ] were analyzed. For comparison we assayed recessive ca1ca4 carbonic anhydrase double mutant plants, based on their slowed stomatal response to CO2 . Here, we report a strong impairment in ht1 in red light-induced stomatal opening whereas blue light was able to induce stomatal opening. The effects on photosynthetic performance in ht1 were restored when stomatal limitation of CO2 uptake, by control of [Ci ], was eliminated. HT1 was found to interact genetically with OST1 both during red light- and low [CO2 ]-induced stomatal opening. Analyses of ca1ca4 plants suggest that more than a low [Ci ]-dependent pathway may function in red light-induced stomatal opening. These results demonstrate that HT1 is essential for red light-induced stomatal opening and interacts genetically with OST1 during stomatal responses to red light and altered [CO2 ].

@article{sundell_plant_2015,
	title = {The {Plant} {Genome} {Integrative} {Explorer} {Resource}: {PlantGenIE}.org},
	volume = {208},
	issn = {1469-8137 (Electronic) 0028-646X (Linking)},
	shorttitle = {The {Plant} {Genome} {Integrative} {Explorer} {Resource}},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26192091},
	doi = {10.1111/nph.13557},
	abstract = {Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {New Phytol},
	author = {Sundell, D. and Mannapperuma, C. and Netotea, S. and Delhomme, N. and Lin, Y. C. and Sjodin, A. and Van de Peer, Y. and Jansson, S. and Hvidsten, T. R. and Street, N. R.},
	month = dec,
	year = {2015},
	note = {Edition: 2015/07/21},
	keywords = {*Databases, Factual, *Genes, Plant, *Genome, Plant, Arabidopsis/*genetics, Computational Biology, Forests, Gene Expression, Genomics/methods, Internet, Models, Biological, Populus, Populus/*genetics, RNA, Plant, Sequence Analysis, DNA, Tracheophyta/*genetics, Trees/*genetics, annotation, coexpression, conifer, database, genome browser, transcriptomics, web resource},
	pages = {1149--56},
}

Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight.

@article{kindgren_recovery_2015,
	title = {The {Recovery} of {Plastid} {Function} {Is} {Required} for {Optimal} {Response} to {Low} {Temperatures} in {Arabidopsis}},
	volume = {10},
	issn = {1932-6203 (Electronic) 1932-6203 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26366569},
	doi = {10.1371/journal.pone.0138010},
	abstract = {Cold acclimation is an essential response in higher plants to survive freezing temperatures. Here, we report that two independent mutant alleles of the H-subunit of Mg-chelatase, CHLH, gun5-1 and cch in Arabidopsis are sensitive to low temperatures. Plants were grown in photoperiodic conditions and exposed to low temperatures for short- and long-term periods. Tetrapyrrole biosynthesis was initially significantly inhibited in response to low temperature but recovered in wild type (Col-0), although the tetrapyrrole levels were lower in cold compared to control conditions. The gun5-1 and cch alleles showed an inability to recover chlorophyll biosynthesis in addition to a significant decrease in freezing tolerance. We found that the impaired plastid function in the CHLH mutant plants resulted in compromised de novo protein synthesis at low temperatures. The expression of the transcription factors CBF1-3 was super-induced in gun5-1 and cch mutant alleles but expression levels of their target genes, COR15a, COR47 and COR78 were similar or even lower compared to Col-0. In addition, the protein levels of COR15a were lower in gun5-1 and cch and a general defect in protein synthesis could be seen in the gun5-1 mutant following a 35S labelling experiment performed at low temperature. Taken together, our results demonstrate the importance of a functional chloroplast for the cold acclimation process and further suggest that impaired plastid function could result in inhibition of protein synthesis at low temperature.},
	language = {en},
	number = {9},
	urldate = {2021-06-07},
	journal = {PLoS One},
	author = {Kindgren, P. and Dubreuil, C. and Strand, A.},
	month = sep,
	year = {2015},
	note = {Edition: 2015/09/15},
	keywords = {*Mutation, Acclimatization/*physiology, Alleles, Arabidopsis Proteins/*biosynthesis/genetics, Arabidopsis/genetics/*metabolism, Cold Temperature, Cold-Shock Response/*physiology, Plastids/genetics/*metabolism, Protein Biosynthesis/physiology, Transcription, Genetic/physiology},
	pages = {e0138010},
}

Cold acclimation is an essential response in higher plants to survive freezing temperatures. Here, we report that two independent mutant alleles of the H-subunit of Mg-chelatase, CHLH, gun5-1 and cch in Arabidopsis are sensitive to low temperatures. Plants were grown in photoperiodic conditions and exposed to low temperatures for short- and long-term periods. Tetrapyrrole biosynthesis was initially significantly inhibited in response to low temperature but recovered in wild type (Col-0), although the tetrapyrrole levels were lower in cold compared to control conditions. The gun5-1 and cch alleles showed an inability to recover chlorophyll biosynthesis in addition to a significant decrease in freezing tolerance. We found that the impaired plastid function in the CHLH mutant plants resulted in compromised de novo protein synthesis at low temperatures. The expression of the transcription factors CBF1-3 was super-induced in gun5-1 and cch mutant alleles but expression levels of their target genes, COR15a, COR47 and COR78 were similar or even lower compared to Col-0. In addition, the protein levels of COR15a were lower in gun5-1 and cch and a general defect in protein synthesis could be seen in the gun5-1 mutant following a 35S labelling experiment performed at low temperature. Taken together, our results demonstrate the importance of a functional chloroplast for the cold acclimation process and further suggest that impaired plastid function could result in inhibition of protein synthesis at low temperature.

@article{coudert_three_2015,
	title = {Three ancient hormonal cues co-ordinate shoot branching in a moss},
	volume = {4},
	issn = {2050-084X (Electronic) 2050-084X (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25806686},
	doi = {10.7554/eLife.06808},
	abstract = {Shoot branching is a primary contributor to plant architecture, evolving independently in flowering plant sporophytes and moss gametophytes. Mechanistic understanding of branching is largely limited to flowering plants such as Arabidopsis, which have a recent evolutionary origin. We show that in gametophytic shoots of Physcomitrella, lateral branches arise by re-specification of epidermal cells into branch initials. A simple model co-ordinating the activity of leafy shoot tips can account for branching patterns, and three known and ancient hormonal regulators of sporophytic branching interact to generate the branching pattern- auxin, cytokinin and strigolactone. The mode of auxin transport required in branch patterning is a key divergence point from known sporophytic pathways. Although PIN-mediated basipetal auxin transport regulates branching patterns in flowering plants, this is not so in Physcomitrella, where bi-directional transport is required to generate realistic branching patterns. Experiments with callose synthesis inhibitors suggest plasmodesmal connectivity as a potential mechanism for transport.},
	language = {en},
	urldate = {2021-06-07},
	journal = {Elife},
	author = {Coudert, Y. and Palubicki, W. and Ljung, K. and Novak, O. and Leyser, O. and Harrison, C. J.},
	month = mar,
	year = {2015},
	note = {Edition: 2015/03/26},
	keywords = {Biological Transport/drug effects, Body Patterning/drug effects, Bryopsida/drug effects/*growth \& development, Cytokinins/biosynthesis, Gene Expression Regulation, Plant/drug effects, Indoleacetic Acids/metabolism/pharmacology, Lactones/pharmacology, Models, Biological, Morphogenesis/*drug effects, Mutation/genetics, Physcomitrella, Plant Epidermis/cytology/growth \& development, Plant Growth Regulators/*pharmacology, Plant Proteins/metabolism, Plant Shoots/drug effects/*growth \& development, Plants, Genetically Modified, apical dominance, branching, developmental biology, gametophyte, plant biology, stem cells},
	pages = {e06808},
}

Shoot branching is a primary contributor to plant architecture, evolving independently in flowering plant sporophytes and moss gametophytes. Mechanistic understanding of branching is largely limited to flowering plants such as Arabidopsis, which have a recent evolutionary origin. We show that in gametophytic shoots of Physcomitrella, lateral branches arise by re-specification of epidermal cells into branch initials. A simple model co-ordinating the activity of leafy shoot tips can account for branching patterns, and three known and ancient hormonal regulators of sporophytic branching interact to generate the branching pattern- auxin, cytokinin and strigolactone. The mode of auxin transport required in branch patterning is a key divergence point from known sporophytic pathways. Although PIN-mediated basipetal auxin transport regulates branching patterns in flowering plants, this is not so in Physcomitrella, where bi-directional transport is required to generate realistic branching patterns. Experiments with callose synthesis inhibitors suggest plasmodesmal connectivity as a potential mechanism for transport.

@article{felten_vibrational_2015,
	title = {Vibrational spectroscopic image analysis of biological material using multivariate curve resolution-alternating least squares ({MCR}-{ALS})},
	volume = {10},
	issn = {1750-2799 (Electronic) 1750-2799 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25569330},
	doi = {10.1038/nprot.2015.008},
	abstract = {Raman and Fourier transform IR (FTIR) microspectroscopic images of biological material (tissue sections) contain detailed information about their chemical composition. The challenge lies in identifying changes in chemical composition, as well as locating and assigning these changes to different conditions (pathology, anatomy, environmental or genetic factors). Multivariate data analysis techniques are ideal for decrypting such information from the data. This protocol provides a user-friendly pipeline and graphical user interface (GUI) for data pre-processing and unmixing of pixel spectra into their contributing pure components by multivariate curve resolution-alternating least squares (MCR-ALS) analysis. The analysis considers the full spectral profile in order to identify the chemical compounds and to visualize their distribution across the sample to categorize chemically distinct areas. Results are rapidly achieved (usually {\textless}30-60 min per image), and they are easy to interpret and evaluate both in terms of chemistry and biology, making the method generally more powerful than principal component analysis (PCA) or heat maps of single-band intensities. In addition, chemical and biological evaluation of the results by means of reference matching and segmentation maps (based on k-means clustering) is possible.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Nat Protoc},
	author = {Felten, J. and Hall, H. and Jaumot, J. and Tauler, R. and de Juan, A. and Gorzsas, A.},
	month = feb,
	year = {2015},
	note = {Edition: 2015/01/09},
	keywords = {*Multivariate Analysis, *Spectroscopy, Fourier Transform Infrared, *Spectrum Analysis, Raman, Animals, Image Processing, Computer-Assisted/*methods, Islets of Langerhans/chemistry, Least-Squares Analysis, Mice, Inbred C57BL, Populus/chemistry, User-Computer Interface, Xylem/chemistry},
	pages = {217--40},
}

Raman and Fourier transform IR (FTIR) microspectroscopic images of biological material (tissue sections) contain detailed information about their chemical composition. The challenge lies in identifying changes in chemical composition, as well as locating and assigning these changes to different conditions (pathology, anatomy, environmental or genetic factors). Multivariate data analysis techniques are ideal for decrypting such information from the data. This protocol provides a user-friendly pipeline and graphical user interface (GUI) for data pre-processing and unmixing of pixel spectra into their contributing pure components by multivariate curve resolution-alternating least squares (MCR-ALS) analysis. The analysis considers the full spectral profile in order to identify the chemical compounds and to visualize their distribution across the sample to categorize chemically distinct areas. Results are rapidly achieved (usually \textless30-60 min per image), and they are easy to interpret and evaluate both in terms of chemistry and biology, making the method generally more powerful than principal component analysis (PCA) or heat maps of single-band intensities. In addition, chemical and biological evaluation of the results by means of reference matching and segmentation maps (based on k-means clustering) is possible.

@article{ditengou_volatile_2015,
	title = {Volatile signalling by sesquiterpenes from ectomycorrhizal fungi reprogrammes root architecture},
	volume = {6},
	issn = {2041-1723 (Electronic) 2041-1723 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25703994},
	doi = {10.1038/ncomms7279},
	abstract = {The mutualistic association of roots with ectomycorrhizal fungi promotes plant health and is a hallmark of boreal and temperate forests worldwide. In the pre-colonization phase, before direct contact, lateral root (LR) production is massively stimulated, yet little is known about the signals exchanged during this step. Here, we identify sesquiterpenes (SQTs) as biologically active agents emitted by Laccaria bicolor while interacting with Populus or Arabidopsis. We show that inhibition of fungal SQT production by lovastatin strongly reduces LR proliferation and that (-)-thujopsene, a low-abundance SQT, is sufficient to stimulate LR formation in the absence of the fungus. Further, we show that the ectomycorrhizal ascomycote, Cenococcum geophilum, which cannot synthesize SQTs, does not promote LRs. We propose that the LR-promoting SQT signal creates a win-win situation by enhancing the root surface area for plant nutrient uptake and by improving fungal access to plant-derived carbon via root exudates.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nat Commun},
	author = {Ditengou, F. A. and Muller, A. and Rosenkranz, M. and Felten, J. and Lasok, H. and van Doorn, M. M. and Legue, V. and Palme, K. and Schnitzler, J. P. and Polle, A.},
	month = feb,
	year = {2015},
	note = {Edition: 2015/02/24},
	keywords = {*Sesquiterpenes, Arabidopsis, Ascomycota, Indoleacetic Acids/metabolism, Laccaria/*physiology, Mycorrhizae/*physiology, Plant Roots/*growth \& development/metabolism, Populus/*growth \& development, Superoxides/metabolism, Symbiosis, Volatile Organic Compounds},
	pages = {6279},
}

The mutualistic association of roots with ectomycorrhizal fungi promotes plant health and is a hallmark of boreal and temperate forests worldwide. In the pre-colonization phase, before direct contact, lateral root (LR) production is massively stimulated, yet little is known about the signals exchanged during this step. Here, we identify sesquiterpenes (SQTs) as biologically active agents emitted by Laccaria bicolor while interacting with Populus or Arabidopsis. We show that inhibition of fungal SQT production by lovastatin strongly reduces LR proliferation and that (-)-thujopsene, a low-abundance SQT, is sufficient to stimulate LR formation in the absence of the fungus. Further, we show that the ectomycorrhizal ascomycote, Cenococcum geophilum, which cannot synthesize SQTs, does not promote LRs. We propose that the LR-promoting SQT signal creates a win-win situation by enhancing the root surface area for plant nutrient uptake and by improving fungal access to plant-derived carbon via root exudates.

@article{sundstrom_whiteboard_2015,
	title = {Whiteboard: a framework for the programmatic visualization of complex biological analyses},
	volume = {31},
	issn = {1367-4811 (Electronic) 1367-4803 (Linking)},
	shorttitle = {Whiteboard},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25661541},
	doi = {10.1093/bioinformatics/btv078},
	abstract = {UNLABELLED: Whiteboard is a class library implemented in C++ that enables visualization to be tightly coupled with computation when analyzing large and complex datasets. AVAILABILITY AND IMPLEMENTATION: the C++ source code, coding samples and documentation are freely available under the Lesser General Public License from http://whiteboard-class.sourceforge.net/.},
	language = {en},
	number = {12},
	urldate = {2021-06-07},
	journal = {Bioinformatics},
	author = {Sundstrom, G. and Zamani, N. and Grabherr, M. G. and Mauceli, E.},
	month = jun,
	year = {2015},
	note = {Edition: 2015/02/11},
	keywords = {*Computer Graphics, *Programming Languages, *Software, Computational Biology/*methods, Databases, Factual, Humans, Information Storage and Retrieval},
	pages = {2054--5},
}

UNLABELLED: Whiteboard is a class library implemented in C++ that enables visualization to be tightly coupled with computation when analyzing large and complex datasets. AVAILABILITY AND IMPLEMENTATION: the C++ source code, coding samples and documentation are freely available under the Lesser General Public License from http://whiteboard-class.sourceforge.net/.

@article{xu_yeast_2015,
	title = {Yeast {Elongator} protein {Elp1p} does not undergo proteolytic processing in exponentially growing cells},
	volume = {4},
	issn = {2045-8827 (Electronic) 2045-8827 (Linking)},
	shorttitle = {Yeast},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26407534},
	doi = {10.1002/mbo3.285},
	abstract = {In eukaryotic organisms, Elongator is a six-subunit protein complex required for the formation of 5-carbamoylmethyl (ncm(5) ) and 5-methylcarboxymethyl (mcm(5) ) side chains on uridines present at the wobble position (U34 ) of tRNA. The open reading frame encoding the largest Elongator subunit Elp1p has two in-frame 5' AUG methionine codons separated by 48 nucleotides. Here, we show that the second AUG acts as the start codon of translation. Furthermore, Elp1p was previously shown to exist in two major forms of which one was generated by proteolysis of full-length Elp1p and this proteolytic cleavage was suggested to regulate Elongator complex activity. In this study, we found that the vacuolar protease Prb1p was responsible for the cleavage of Elp1p. The cleavage occurs between residues 203 (Lys) and 204 (Ala) as shown by amine reactive Tandem Mass Tag followed by LC-MS/MS (liquid chromatography mass spectrometry) analysis. However, using a modified protein extraction procedure, including trichloroacetic acid, only full-length Elp1p was observed, showing that truncation of Elp1p is an artifact occurring during protein extraction. Consequently, our results indicate that N-terminal truncation of Elp1p is not likely to regulate Elongator complex activity.},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Microbiologyopen},
	author = {Xu, H. and Bygdell, J. and Wingsle, G. and Bystrom, A. S.},
	month = dec,
	year = {2015},
	note = {Edition: 2015/09/27},
	keywords = {Amino Acid Sequence, Elongator complex, Elp1p, Histone Acetyltransferases/chemistry/genetics/*metabolism, Molecular Sequence Data, Peptide Elongation Factors/chemistry/genetics/*metabolism, Prb1p, Protein Structure, Tertiary, Proteolysis, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism, Saccharomyces cerevisiae/chemistry/genetics/growth \& development/*metabolism, Tandem Mass Spectrometry, tRNA modification},
	pages = {867--78},
}

In eukaryotic organisms, Elongator is a six-subunit protein complex required for the formation of 5-carbamoylmethyl (ncm(5) ) and 5-methylcarboxymethyl (mcm(5) ) side chains on uridines present at the wobble position (U34 ) of tRNA. The open reading frame encoding the largest Elongator subunit Elp1p has two in-frame 5' AUG methionine codons separated by 48 nucleotides. Here, we show that the second AUG acts as the start codon of translation. Furthermore, Elp1p was previously shown to exist in two major forms of which one was generated by proteolysis of full-length Elp1p and this proteolytic cleavage was suggested to regulate Elongator complex activity. In this study, we found that the vacuolar protease Prb1p was responsible for the cleavage of Elp1p. The cleavage occurs between residues 203 (Lys) and 204 (Ala) as shown by amine reactive Tandem Mass Tag followed by LC-MS/MS (liquid chromatography mass spectrometry) analysis. However, using a modified protein extraction procedure, including trichloroacetic acid, only full-length Elp1p was observed, showing that truncation of Elp1p is an artifact occurring during protein extraction. Consequently, our results indicate that N-terminal truncation of Elp1p is not likely to regulate Elongator complex activity.

@article{stavrinidou_electronic_2015,
	title = {Electronic plants},
	volume = {1},
	issn = {2375-2548},
	url = {https://advances.sciencemag.org/lookup/doi/10.1126/sciadv.1501136},
	doi = {10.1126/sciadv.1501136},
	abstract = {The roots, stems, leaves, and vascular circuitry of higher plants are responsible for conveying the chemical signals that regulate growth and functions. From a certain perspective, these features are analogous to the contacts, interconnections, devices, and wires of discrete and integrated electronic circuits. Although many attempts have been made to augment plant function with electroactive materials, plants’ “circuitry” has never been directly merged with electronics. We report analog and digital organic electronic circuits and devices manufactured in living plants. The four key components of a circuit have been achieved using the xylem, leaves, veins, and signals of the plant as the template and integral part of the circuit elements and functions. With integrated and distributed electronics in plants, one can envisage a range of applications including precision recording and regulation of physiology, energy harvesting from photosynthesis, and alternatives to genetic modification for plant optimization.},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Science Advances},
	author = {Stavrinidou, Eleni and Gabrielsson, Roger and Gomez, Eliot and Crispin, Xavier and Nilsson, Ove and Simon, Daniel T. and Berggren, Magnus},
	month = nov,
	year = {2015},
	keywords = {conducting polymers, organic bioelectronics, plants},
	pages = {e1501136},
}

The roots, stems, leaves, and vascular circuitry of higher plants are responsible for conveying the chemical signals that regulate growth and functions. From a certain perspective, these features are analogous to the contacts, interconnections, devices, and wires of discrete and integrated electronic circuits. Although many attempts have been made to augment plant function with electroactive materials, plants’ “circuitry” has never been directly merged with electronics. We report analog and digital organic electronic circuits and devices manufactured in living plants. The four key components of a circuit have been achieved using the xylem, leaves, veins, and signals of the plant as the template and integral part of the circuit elements and functions. With integrated and distributed electronics in plants, one can envisage a range of applications including precision recording and regulation of physiology, energy harvesting from photosynthesis, and alternatives to genetic modification for plant optimization.

@article{chen_estimating_2015,
	title = {Estimating solid wood properties using {Pilodyn} and acoustic velocity on standing trees of {Norway} spruce},
	volume = {72},
	issn = {1286-4560},
	url = {://WOS:000354388400010},
	doi = {10.1007/s13595-015-0458-9},
	abstract = {Strong genetic correlations were observed between Pilodyn measurement and wood density, and between acoustic velocity and MFA. Combination of Pilodyn penetration and acoustic velocity measurements from standing trees can provide reliable prediction of stiffness of Norway spruce for breeding selection.
Traditional methods for the estimation of solid wood quality traits of standing tree such as wood density, microfibril angle (MFA), and modulus of elasticity (MOE) are time-consuming and expensive, which render them unsuitable for rapidly screening a large number of trees in tree breeding programs.
This study aims to evaluate the suitability of using Pilodyn penetration and acoustic velocity (nondestructive evaluation) to assess wood density, MFA, and MOE for Norway spruce.
Pilodyn penetration and Hitman acoustic velocity, as well as wood density, MFA, and MOE using benchmark SilviScan were measured on 5618 standing trees of 524 open-pollinated families in two 21-year-old Norway spruce (Picea abies) progeny trials in southern Sweden.
Strong genetic correlations were observed between Pilodyn measurement and wood density (r (g) = -0.96), and between acoustic velocity and MFA (r (g) = -0.94). Combination of Pilodyn penetration and Hitman acoustic velocity measurements () obtained from standing trees showed a genetic correlation with benchmark MOE of 0.99. This combined had higher selection efficiency for benchmark MOE (92 \%) compared to 58-60 \% using acoustic velocity alone and 78 \% using Pilodyn penetration alone.
Combination of Pilodyn penetration with Hitman acoustic velocity provided very high selection efficiency for the three most important quality traits for wood mechanical properties in Norway spruce.},
	language = {English},
	number = {4},
	urldate = {2021-06-07},
	journal = {Annals of Forest Science},
	author = {Chen, Z. Q. and Karlsson, B. and Lundqvist, S. O. and Gil, M. R. G. and Olsson, L. and Wu, H. X.},
	month = jun,
	year = {2015},
	keywords = {douglas-fir, genetic-improvement, mature wood, microfibril angle, modulus of elasticity, near-infrared spectroscopy, new-zealand, nondestructive evaluation, norway spruce, picea-abies, pinus-radiata, quality traits, rapid assessment, stiffness, wood density},
	pages = {499--508},
}

Strong genetic correlations were observed between Pilodyn measurement and wood density, and between acoustic velocity and MFA. Combination of Pilodyn penetration and acoustic velocity measurements from standing trees can provide reliable prediction of stiffness of Norway spruce for breeding selection. Traditional methods for the estimation of solid wood quality traits of standing tree such as wood density, microfibril angle (MFA), and modulus of elasticity (MOE) are time-consuming and expensive, which render them unsuitable for rapidly screening a large number of trees in tree breeding programs. This study aims to evaluate the suitability of using Pilodyn penetration and acoustic velocity (nondestructive evaluation) to assess wood density, MFA, and MOE for Norway spruce. Pilodyn penetration and Hitman acoustic velocity, as well as wood density, MFA, and MOE using benchmark SilviScan were measured on 5618 standing trees of 524 open-pollinated families in two 21-year-old Norway spruce (Picea abies) progeny trials in southern Sweden. Strong genetic correlations were observed between Pilodyn measurement and wood density (r (g) = -0.96), and between acoustic velocity and MFA (r (g) = -0.94). Combination of Pilodyn penetration and Hitman acoustic velocity measurements () obtained from standing trees showed a genetic correlation with benchmark MOE of 0.99. This combined had higher selection efficiency for benchmark MOE (92 %) compared to 58-60 % using acoustic velocity alone and 78 % using Pilodyn penetration alone. Combination of Pilodyn penetration with Hitman acoustic velocity provided very high selection efficiency for the three most important quality traits for wood mechanical properties in Norway spruce.

@article{hummel_proteomic_2015,
	title = {Proteomic {LC}-{MS} analysis of {Arabidopsis} cytosolic ribosomes: {Identification} of ribosomal protein paralogs and re-annotation of the ribosomal protein genes},
	volume = {128},
	issn = {1876-7737 (Electronic) 1874-3919 (Linking)},
	shorttitle = {Proteomic {LC}–{MS} analysis of {Arabidopsis} cytosolic ribosomes},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26232565},
	doi = {10.1016/j.jprot.2015.07.004},
	abstract = {UNLABELLED: Arabidopsis thaliana cytosolic ribosomes are large complexes containing eighty-one distinct ribosomal proteins (r-proteins), four ribosomal RNAs (rRNA) and a plethora of associated (non-ribosomal) proteins. In plants, r-proteins of cytosolic ribosomes are each encoded by two to seven different expressed and similar genes, forming an r-protein family. Distinctions in the r-protein coding sequences of gene family members are a source of variation between ribosomes. We performed proteomic investigation of actively translating cytosolic ribosomes purified using both immunopurification and a classic sucrose cushion centrifugation-based protocol from plants of different developmental stages. Both 1D and 2D LC-MS(E) with data-independent acquisition as well as conventional data-dependent MS/MS procedures were applied. This approach provided detailed identification of 165 r-protein paralogs with high coverage based on proteotypic peptides. The detected r-proteins were the products of the majority (68\%) of the 242 cytosolic r-protein genes encoded by the genome. A total of 70 distinct r-proteins were identified. Based on these results and information from DNA microarray and ribosome footprint profiling studies a re-annotation of Arabidopsis r-proteins and genes is proposed. This compendium of the cytosolic r-protein proteome will serve as a template for future investigations on the dynamic structure and function of plant ribosomes. BIOLOGICAL SIGNIFICANCE: Translation is one of the most energy demanding processes in a living cell and is therefore carefully regulated. Translational activity is tightly linked to growth control and growth regulating mechanism. Recently established translational profiling technologies, including the profiling of mRNAs associated with polysomes and the mapping of ribosome footprints on mRNAs, have revealed that the expression of gene expression is often fine-tuned by differential translation of gene transcripts. The eukaryotic ribosome, the hub of these important processes, consists of close to eighty different proteins (depending on species) and four large RNAs assembled into two highly conserved subunits. In plants and to lesser extent in yeast, the r-proteins are encoded by more than one actively transcribed gene. As r-protein gene paralogs frequently do not encode identical proteins and are regulated by growth conditions and development, in vivo ribosomes are heterogeneous in their protein content. The regulatory and physiological importance of this heterogeneity is unknown. Here, an improved annotation of the more than two hundred r-protein genes of Arabidopsis is presented that combines proteomic and advanced mRNA expression data. This proteomic investigation and re-annotation of Arabidopsis ribosomes establish a base for future investigations of translational control in plants.},
	language = {en},
	urldate = {2021-06-07},
	journal = {J Proteomics},
	author = {Hummel, M. and Dobrenel, T. and Cordewener, J. J. and Davanture, M. and Meyer, C. and Smeekens, S. J. and Bailey-Serres, J. and America, T. A. and Hanson, J.},
	month = oct,
	year = {2015},
	note = {Edition: 2015/08/02},
	keywords = {A. thaliana, Amino Acid Sequence, Arabidopsis Proteins/*metabolism, Arabidopsis/*metabolism, Chromatography, Liquid/*methods, Data-independent acquisition, Dia, Gene Expression Profiling/methods, Lc-ms, Mass Spectrometry/*methods, Molecular Sequence Data, Paralogs, Proteome/chemistry/metabolism, Ribosomal Proteins/*chemistry/*metabolism, Ribosomal protein, Ribosomes},
	pages = {436--49},
}

UNLABELLED: Arabidopsis thaliana cytosolic ribosomes are large complexes containing eighty-one distinct ribosomal proteins (r-proteins), four ribosomal RNAs (rRNA) and a plethora of associated (non-ribosomal) proteins. In plants, r-proteins of cytosolic ribosomes are each encoded by two to seven different expressed and similar genes, forming an r-protein family. Distinctions in the r-protein coding sequences of gene family members are a source of variation between ribosomes. We performed proteomic investigation of actively translating cytosolic ribosomes purified using both immunopurification and a classic sucrose cushion centrifugation-based protocol from plants of different developmental stages. Both 1D and 2D LC-MS(E) with data-independent acquisition as well as conventional data-dependent MS/MS procedures were applied. This approach provided detailed identification of 165 r-protein paralogs with high coverage based on proteotypic peptides. The detected r-proteins were the products of the majority (68%) of the 242 cytosolic r-protein genes encoded by the genome. A total of 70 distinct r-proteins were identified. Based on these results and information from DNA microarray and ribosome footprint profiling studies a re-annotation of Arabidopsis r-proteins and genes is proposed. This compendium of the cytosolic r-protein proteome will serve as a template for future investigations on the dynamic structure and function of plant ribosomes. BIOLOGICAL SIGNIFICANCE: Translation is one of the most energy demanding processes in a living cell and is therefore carefully regulated. Translational activity is tightly linked to growth control and growth regulating mechanism. Recently established translational profiling technologies, including the profiling of mRNAs associated with polysomes and the mapping of ribosome footprints on mRNAs, have revealed that the expression of gene expression is often fine-tuned by differential translation of gene transcripts. The eukaryotic ribosome, the hub of these important processes, consists of close to eighty different proteins (depending on species) and four large RNAs assembled into two highly conserved subunits. In plants and to lesser extent in yeast, the r-proteins are encoded by more than one actively transcribed gene. As r-protein gene paralogs frequently do not encode identical proteins and are regulated by growth conditions and development, in vivo ribosomes are heterogeneous in their protein content. The regulatory and physiological importance of this heterogeneity is unknown. Here, an improved annotation of the more than two hundred r-protein genes of Arabidopsis is presented that combines proteomic and advanced mRNA expression data. This proteomic investigation and re-annotation of Arabidopsis ribosomes establish a base for future investigations of translational control in plants.

@article{igamberdiev_optimization_2015,
	title = {Optimization of {ATP} synthase function in mitochondria and chloroplasts via the adenylate kinase equilibrium},
	volume = {6},
	issn = {1664-462X (Print) 1664-462X (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25674099},
	doi = {10.3389/fpls.2015.00010},
	abstract = {The bulk of ATP synthesis in plants is performed by ATP synthase, the main bioenergetics engine of cells, operating both in mitochondria and in chloroplasts. The reaction mechanism of ATP synthase has been studied in detail for over half a century; however, its optimal performance depends also on the steady delivery of ATP synthase substrates and the removal of its products. For mitochondrial ATP synthase, we analyze here the provision of stable conditions for (i) the supply of ADP and Mg(2+), supported by adenylate kinase (AK) equilibrium in the intermembrane space, (ii) the supply of phosphate via membrane transporter in symport with H(+), and (iii) the conditions of outflow of ATP by adenylate transporter carrying out the exchange of free adenylates. We also show that, in chloroplasts, AK equilibrates adenylates and governs Mg(2+) contents in the stroma, optimizing ATP synthase and Calvin cycle operation, and affecting the import of inorganic phosphate in exchange with triose phosphates. It is argued that chemiosmosis is not the sole component of ATP synthase performance, which also depends on AK-mediated equilibrium of adenylates and Mg(2+), adenylate transport, and phosphate release and supply.},
	urldate = {2021-06-07},
	journal = {Front Plant Sci},
	author = {Igamberdiev, A. U. and Kleczkowski, L. A.},
	month = jan,
	year = {2015},
	note = {Edition: 2015/02/13},
	keywords = {ATP synthase, adenylate kinase, chemiosmosis, chloroplasts, magnesium, mitochondria},
	pages = {10},
}

The bulk of ATP synthesis in plants is performed by ATP synthase, the main bioenergetics engine of cells, operating both in mitochondria and in chloroplasts. The reaction mechanism of ATP synthase has been studied in detail for over half a century; however, its optimal performance depends also on the steady delivery of ATP synthase substrates and the removal of its products. For mitochondrial ATP synthase, we analyze here the provision of stable conditions for (i) the supply of ADP and Mg(2+), supported by adenylate kinase (AK) equilibrium in the intermembrane space, (ii) the supply of phosphate via membrane transporter in symport with H(+), and (iii) the conditions of outflow of ATP by adenylate transporter carrying out the exchange of free adenylates. We also show that, in chloroplasts, AK equilibrates adenylates and governs Mg(2+) contents in the stroma, optimizing ATP synthase and Calvin cycle operation, and affecting the import of inorganic phosphate in exchange with triose phosphates. It is argued that chemiosmosis is not the sole component of ATP synthase performance, which also depends on AK-mediated equilibrium of adenylates and Mg(2+), adenylate transport, and phosphate release and supply.