@article{zeng_mutations_2025,
	title = {Mutations in the floral regulator gene {HUA2} restore flowering to the {Arabidopsis} trehalose 6-phosphate synthase1 (tps1) mutant},
	volume = {198},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiaf225},
	doi = {10.1093/plphys/kiaf225},
	abstract = {Plant growth and development are regulated by many factors, including carbohydrate availability and signaling. Trehalose 6-phosphate (T6P), which is synthesized by TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1), is positively associated with and functions as a signal that informs the cell about the carbohydrate status. Mutations in TPS1 negatively affect the growth and development of Arabidopsis (Arabidopsis thaliana), and complete loss-of-function alleles are embryo-lethal, which can be overcome using inducible expression of TPS1 (GVG::TPS1) during embryogenesis. Using ethyl methane sulfonate mutagenesis in combination with genome re-sequencing, we have identified several alleles in the floral regulator gene HUA2 that restore flowering in tps1-2 GVG::TPS1. Genetic analyses using an HUA2 T-DNA insertion allele, hua2-4, confirmed this finding. RNA-seq analyses demonstrated that hua2-4 has widespread effects on the tps1-2 GVG::TPS1 transcriptome, including key genes and pathways involved in regulating flowering. Higher order mutants combining tps1-2 GVG::TPS1 and hua2-4 with alleles in the key flowering time regulators FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), and FLOWERING LOCUS C (FLC) were constructed to analyze the role of HUA2 during floral transition in tps1-2 in more detail. Our findings demonstrate that loss of HUA2 can restore flowering in tps1-2 GVG::TPS1, in part through activation of FT, with contributions from the upstream regulators SOC1 and FLC. Interestingly, we found that mutation of FLC is sufficient to induce flowering in tps1-2 GVG::TPS1. Furthermore, we observed that mutations in HUA2 modulate carbohydrate signaling and that this regulation might contribute to flowering in hua2-4 tps1-2 GVG::TPS1.},
	number = {2},
	urldate = {2025-06-27},
	journal = {Plant Physiology},
	author = {Zeng, Liping and Zacharaki, Vasiliki and van Es, Sam W and Wang, Yanwei and Schmid, Markus},
	month = jun,
	year = {2025},
	pages = {kiaf225},
}

Plant growth and development are regulated by many factors, including carbohydrate availability and signaling. Trehalose 6-phosphate (T6P), which is synthesized by TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1), is positively associated with and functions as a signal that informs the cell about the carbohydrate status. Mutations in TPS1 negatively affect the growth and development of Arabidopsis (Arabidopsis thaliana), and complete loss-of-function alleles are embryo-lethal, which can be overcome using inducible expression of TPS1 (GVG::TPS1) during embryogenesis. Using ethyl methane sulfonate mutagenesis in combination with genome re-sequencing, we have identified several alleles in the floral regulator gene HUA2 that restore flowering in tps1-2 GVG::TPS1. Genetic analyses using an HUA2 T-DNA insertion allele, hua2-4, confirmed this finding. RNA-seq analyses demonstrated that hua2-4 has widespread effects on the tps1-2 GVG::TPS1 transcriptome, including key genes and pathways involved in regulating flowering. Higher order mutants combining tps1-2 GVG::TPS1 and hua2-4 with alleles in the key flowering time regulators FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), and FLOWERING LOCUS C (FLC) were constructed to analyze the role of HUA2 during floral transition in tps1-2 in more detail. Our findings demonstrate that loss of HUA2 can restore flowering in tps1-2 GVG::TPS1, in part through activation of FT, with contributions from the upstream regulators SOC1 and FLC. Interestingly, we found that mutation of FLC is sufficient to induce flowering in tps1-2 GVG::TPS1. Furthermore, we observed that mutations in HUA2 modulate carbohydrate signaling and that this regulation might contribute to flowering in hua2-4 tps1-2 GVG::TPS1.

@article{gil-munoz_implications_2025,
	title = {Implications of {Breeding} for {Growth} on {Drought} {Tolerance} in {Scots} {Pine} ({Pinus} sylvestris {L}.)—{Insights} {From} {Metabolomics} and {High}-{Throughput} {Plant} {Architecture} {Analysis}},
	volume = {18},
	copyright = {© 2025 The Author(s). Evolutionary Applications published by John Wiley \& Sons Ltd.},
	issn = {1752-4571},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.70122},
	doi = {10.1111/eva.70122},
	abstract = {Drought has been identified as one of the important environmental factors in the context of climate change due to its interaction with other biotic and abiotic stresses. However, only a few studies have reported the effect of breeding on forest adaptability to climate change. Using a common garden experiment with seedlings from families of Scots pine (Pinus sylvestris L.) from northern Sweden, we have found differences in drought tolerance between seedlings from breeding stands and those from natural forests. We performed a genetic analysis including high-throughput image-based phenotyping of seedling canopy and root traits and conducted metabolomic and hormone analyses with the aerial parts of the seedlings. Our results indicate that root architecture traits associated with drought tolerance exhibit moderate to high heritability. Analyses of seedling architecture reveal that families from breeding stands have higher drought resistance but lower genetic variation than the ones from natural forests, especially in the case of canopy traits. Metabolomic and hormone analyses of the aerial parts of the seedlings also support that the breeding stands may have a higher capacity to withstand or deal with drought conditions as compared to the natural forests. For example, increase in abscisic acid along with increase in tryptophan and auxin conjugates in the breeding stands compared to the natural forests under drought conditions may contribute to alleviation of drought response in the breeding stands. The methodology employed to evaluate drought tolerance and plant architecture in this study might be useful for future research and forest management focused on climate change adaptability.},
	language = {en},
	number = {6},
	urldate = {2025-06-27},
	journal = {Evolutionary Applications},
	author = {Gil-Muñoz, Francisco and Ranade, Sonali Sachin and Hayatgheibi, Haleh and Niemi, Juha and Östlund, Lars and García-Gil, María Rosario},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.70122},
	keywords = {abscisic acid, drought, metabolomics, root architecture, scots pine},
	pages = {e70122},
}

Drought has been identified as one of the important environmental factors in the context of climate change due to its interaction with other biotic and abiotic stresses. However, only a few studies have reported the effect of breeding on forest adaptability to climate change. Using a common garden experiment with seedlings from families of Scots pine (Pinus sylvestris L.) from northern Sweden, we have found differences in drought tolerance between seedlings from breeding stands and those from natural forests. We performed a genetic analysis including high-throughput image-based phenotyping of seedling canopy and root traits and conducted metabolomic and hormone analyses with the aerial parts of the seedlings. Our results indicate that root architecture traits associated with drought tolerance exhibit moderate to high heritability. Analyses of seedling architecture reveal that families from breeding stands have higher drought resistance but lower genetic variation than the ones from natural forests, especially in the case of canopy traits. Metabolomic and hormone analyses of the aerial parts of the seedlings also support that the breeding stands may have a higher capacity to withstand or deal with drought conditions as compared to the natural forests. For example, increase in abscisic acid along with increase in tryptophan and auxin conjugates in the breeding stands compared to the natural forests under drought conditions may contribute to alleviation of drought response in the breeding stands. The methodology employed to evaluate drought tolerance and plant architecture in this study might be useful for future research and forest management focused on climate change adaptability.

@article{zhong_maize_2025,
	title = {A maize near-isogenic line population designed for gene discovery and characterization of allelic effects},
	volume = {122},
	copyright = {© 2025 The Author(s). The Plant Journal published by Society for Experimental Biology and John Wiley \& Sons Ltd.},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.70228},
	doi = {10.1111/tpj.70228},
	abstract = {In this study, we characterized a panel of 1264 maize near-isogenic lines (NILs), developed from crosses between 18 diverse inbred lines and the recurrent parent B73, referred to as nested NILs (nNILs). In this study, 888 of the nNILs were genotyped using genotyping-by-sequencing (GBS). Subsequently, 24 of these nNILs, and all the parental lines, were re-genotyped using a high-density single nucleotide polymorphism (SNP) chip. A novel pipeline for calling introgressions, which does not rely on knowing the donor parent of each nNIL, was developed based on a hidden Markov model (HMM) algorithm. By comparing the introgressions detected using GBS data with those identified using chip data, we optimized the HMM parameters for analyzing the entire nNIL population. A total of 2969 introgressions were identified across the 888 nNILs. Individual introgression blocks ranged from 21 bp to 204 Mbp, with an average size of 17 Mbp. By comparing SNP genotypes within introgressed segments to the known genotypes of the donor lines, we determined that in about one third of the lines, the identity of the donors did not match expectation based on their pedigrees. We characterized the entire nNIL population for three foliar diseases. Using these data, we mapped a number of quantitative trait loci (QTL) for disease resistance in the nNIL population and observed extensive variation in effects among the alleles from different donor parents at most QTL identified. This population will be of significant utility for dissecting complex agronomic traits and allelic series in maize.},
	language = {en},
	number = {5},
	urldate = {2025-07-07},
	journal = {The Plant Journal},
	author = {Zhong, Tao and Mullens, Alex and Morales, Laura and Swarts, Kelly L. and Stafstrom, William C. and He, Yijian and Sermons, Shannon M and Yang, Qin and Lopez-Zuniga, Luis O. and Rucker, Elizabeth and Thomason, Wade E. and Nelson, Rebecca J. and Jamann, Tiffany and Balint-Kurti, Peter J. and Holland, James B.},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.70228},
	keywords = {allelic series, disease resistance, maize, near isogenic line},
	pages = {e70228},
}

In this study, we characterized a panel of 1264 maize near-isogenic lines (NILs), developed from crosses between 18 diverse inbred lines and the recurrent parent B73, referred to as nested NILs (nNILs). In this study, 888 of the nNILs were genotyped using genotyping-by-sequencing (GBS). Subsequently, 24 of these nNILs, and all the parental lines, were re-genotyped using a high-density single nucleotide polymorphism (SNP) chip. A novel pipeline for calling introgressions, which does not rely on knowing the donor parent of each nNIL, was developed based on a hidden Markov model (HMM) algorithm. By comparing the introgressions detected using GBS data with those identified using chip data, we optimized the HMM parameters for analyzing the entire nNIL population. A total of 2969 introgressions were identified across the 888 nNILs. Individual introgression blocks ranged from 21 bp to 204 Mbp, with an average size of 17 Mbp. By comparing SNP genotypes within introgressed segments to the known genotypes of the donor lines, we determined that in about one third of the lines, the identity of the donors did not match expectation based on their pedigrees. We characterized the entire nNIL population for three foliar diseases. Using these data, we mapped a number of quantitative trait loci (QTL) for disease resistance in the nNIL population and observed extensive variation in effects among the alleles from different donor parents at most QTL identified. This population will be of significant utility for dissecting complex agronomic traits and allelic series in maize.

@article{chubanava_nad_2025,
	title = {{NAD} depletion in skeletal muscle does not compromise muscle function or accelerate aging},
	issn = {1550-4131},
	url = {https://www.sciencedirect.com/science/article/pii/S1550413125002128},
	doi = {10.1016/j.cmet.2025.04.002},
	abstract = {Nicotinamide adenine dinucleotide (NAD) is a ubiquitous electron carrier essential for energy metabolism and post-translational modification of numerous regulatory proteins. Dysregulations of NAD metabolism are widely regarded as detrimental to health, with NAD depletion commonly implicated in aging. However, the extent to which cellular NAD concentration can decline without adverse consequences remains unclear. To investigate this, we generated a mouse model in which nicotinamide phosphoribosyltransferase (NAMPT)-mediated NAD+ biosynthesis was disrupted in adult skeletal muscle. The intervention resulted in an 85\% reduction in muscle NAD+ abundance while maintaining tissue integrity and functionality, as demonstrated by preserved muscle morphology, contractility, and exercise tolerance. This absence of functional impairments was further supported by intact mitochondrial respiratory capacity and unaltered muscle transcriptomic and proteomic profiles. Furthermore, lifelong NAD depletion did not accelerate muscle aging or impair whole-body metabolism. Collectively, these findings suggest that NAD depletion does not contribute to age-related decline in skeletal muscle function.},
	urldate = {2025-05-09},
	journal = {Cell Metabolism},
	author = {Chubanava, Sabina and Karavaeva, Iuliia and Ehrlich, Amy M. and Justicia, Roger M. and Basse, Astrid L. and Kulik, Ivan and Dalbram, Emilie and Ahwazi, Danial and Heaselgrave, Samuel R. and Trošt, Kajetan and Stocks, Ben and Hodek, Ondřej and Rodrigues, Raissa N. and Havelund, Jesper F. and Schlabs, Farina L. and Larsen, Steen and Yonamine, Caio Y. and Henriquez-Olguín, Carlos and Giustarini, Daniela and Rossi, Ranieri and Gerhart-Hines, Zachary and Moritz, Thomas and Zierath, Juleen R. and Sakamoto, Kei and Jensen, Thomas E. and Færgeman, Nils J. and Lavery, Gareth G. and Deshmukh, Atul S. and Treebak, Jonas T.},
	month = apr,
	year = {2025},
	keywords = {NAD biosynthesis, NAD metabolism, NAMPT, aging, epigenetic clock, exercise, mitochondrial supercomplexes, nicotinamide, reactive oxygen species, skeletal muscle},
}

Nicotinamide adenine dinucleotide (NAD) is a ubiquitous electron carrier essential for energy metabolism and post-translational modification of numerous regulatory proteins. Dysregulations of NAD metabolism are widely regarded as detrimental to health, with NAD depletion commonly implicated in aging. However, the extent to which cellular NAD concentration can decline without adverse consequences remains unclear. To investigate this, we generated a mouse model in which nicotinamide phosphoribosyltransferase (NAMPT)-mediated NAD+ biosynthesis was disrupted in adult skeletal muscle. The intervention resulted in an 85% reduction in muscle NAD+ abundance while maintaining tissue integrity and functionality, as demonstrated by preserved muscle morphology, contractility, and exercise tolerance. This absence of functional impairments was further supported by intact mitochondrial respiratory capacity and unaltered muscle transcriptomic and proteomic profiles. Furthermore, lifelong NAD depletion did not accelerate muscle aging or impair whole-body metabolism. Collectively, these findings suggest that NAD depletion does not contribute to age-related decline in skeletal muscle function.

@article{tian_plantlncboost_2025,
	title = {{PlantLncBoost}: key features for plant {lncRNA} identification and significant improvement in accuracy and generalization},
	copyright = {© 2025 The Author(s). New Phytologist © 2025 New Phytologist Foundation.},
	issn = {1469-8137},
	shorttitle = {{PlantLncBoost}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.70211},
	doi = {10.1111/nph.70211},
	abstract = {Long noncoding RNAs (lncRNAs) are critical regulators of numerous biological processes in plants. Nevertheless, their identification is challenging due to the low sequence conservation across various species. Existing computational methods for lncRNA identification often face difficulties in generalizing across diverse plant species, highlighting the need for more robust and versatile identification models. Here, we present PlantLncBoost, a novel computational tool designed to improve the generalization in plant lncRNA identification. By integrating advanced gradient boosting algorithms with comprehensive feature selection, our approach achieves both high accuracy and generalizability. We conducted an extensive analysis of 1662 features and identified three key features – ORF coverage, complex Fourier average, and atomic Fourier amplitude – that effectively distinguish lncRNAs from mRNAs. We assessed the performance of PlantLncBoost using comprehensive datasets from 20 plant species. The model exhibited exceptional performance, with an accuracy of 96.63\%, a sensitivity of 98.42\%, and a specificity of 94.93\%, significantly outperforming existing tools. Further analysis revealed that the features we selected effectively capture the differences between lncRNAs and mRNAs across a variety of plant species. PlantLncBoost represents a significant advancement in plant lncRNA identification. It is freely accessible on GitHub (https://github.com/xuechantian/PlantLncBoost) and has been integrated into a comprehensive analysis pipeline, Plant-LncRNA-pipeline v.2 (https://github.com/xuechantian/Plant-LncRNA-pipeline-v2).},
	language = {en},
	urldate = {2025-05-30},
	journal = {New Phytologist},
	author = {Tian, Xue-Chan and Nie, Shuai and Domingues, Douglas and Rossi Paschoal, Alexandre and Jiang, Li-Bo and Mao, Jian-Feng},
	month = may,
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.70211},
	keywords = {Fourier transform, ORF coverage, feature selection, gradient boosting algorithms, long noncoding RNAs (lncRNAs), model selection},
}

Long noncoding RNAs (lncRNAs) are critical regulators of numerous biological processes in plants. Nevertheless, their identification is challenging due to the low sequence conservation across various species. Existing computational methods for lncRNA identification often face difficulties in generalizing across diverse plant species, highlighting the need for more robust and versatile identification models. Here, we present PlantLncBoost, a novel computational tool designed to improve the generalization in plant lncRNA identification. By integrating advanced gradient boosting algorithms with comprehensive feature selection, our approach achieves both high accuracy and generalizability. We conducted an extensive analysis of 1662 features and identified three key features – ORF coverage, complex Fourier average, and atomic Fourier amplitude – that effectively distinguish lncRNAs from mRNAs. We assessed the performance of PlantLncBoost using comprehensive datasets from 20 plant species. The model exhibited exceptional performance, with an accuracy of 96.63%, a sensitivity of 98.42%, and a specificity of 94.93%, significantly outperforming existing tools. Further analysis revealed that the features we selected effectively capture the differences between lncRNAs and mRNAs across a variety of plant species. PlantLncBoost represents a significant advancement in plant lncRNA identification. It is freely accessible on GitHub (https://github.com/xuechantian/PlantLncBoost) and has been integrated into a comprehensive analysis pipeline, Plant-LncRNA-pipeline v.2 (https://github.com/xuechantian/Plant-LncRNA-pipeline-v2).

@article{safronov_independent_2025,
	title = {Independent evolution of betulin biosynthesis in {Inonotus} obliquus},
	volume = {15},
	copyright = {2025 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-025-05414-1},
	doi = {10.1038/s41598-025-05414-1},
	abstract = {Chaga mushroom (Inonotus obliquus) is a fungal species in the family Hymenochaetaceae (Basidiomycota) and the causative agent of white rot decay in Betula species. We assembled a high-quality 50.7 Mbp genome from PacBio sequencing and identified a lineage-specific whole genome duplication event approximately 1.3 million years ago, which has contributed to a major increase in biochemical diversity in the species through preferential retention of cytochrome P450 superfamily members. Secondary metabolism has further evolved through small-scale segmental duplications, such as tandem duplications within fungal biosynthetic gene clusters. Metabolomic fingerprinting confirmed increased complexity in terpene biosynthesis chemistry compared to related species that lacked the duplication event. This metabolic diversity may have arisen from co-evolution with the primary host species, which evolved high betulin content in its bark 4–8 million years ago.},
	language = {en},
	number = {1},
	urldate = {2025-07-04},
	journal = {Scientific Reports},
	author = {Safronov, Omid and Bal, Güleycan Lutfullahoglu and Sipari, Nina and Wilkens, Maya and Safdari, Pezhman and Smolander, Olli-Pekka and Laine, Pia K. and Lihavainen, Jenna and Silvan, Niko and Rajaraman, Sitaram and Paulin, Lars G. and Teeri, Teemu H. and Auvinen, Petri and Sarjala, Tytti and Overmyer, Kirk and Richter, Uwe and Salojärvi, Jarkko},
	month = jul,
	year = {2025},
	note = {Publisher: Nature Publishing Group},
	keywords = {Coevolution, Genomics, Molecular evolution},
	pages = {21319},
}

Chaga mushroom (Inonotus obliquus) is a fungal species in the family Hymenochaetaceae (Basidiomycota) and the causative agent of white rot decay in Betula species. We assembled a high-quality 50.7 Mbp genome from PacBio sequencing and identified a lineage-specific whole genome duplication event approximately 1.3 million years ago, which has contributed to a major increase in biochemical diversity in the species through preferential retention of cytochrome P450 superfamily members. Secondary metabolism has further evolved through small-scale segmental duplications, such as tandem duplications within fungal biosynthetic gene clusters. Metabolomic fingerprinting confirmed increased complexity in terpene biosynthesis chemistry compared to related species that lacked the duplication event. This metabolic diversity may have arisen from co-evolution with the primary host species, which evolved high betulin content in its bark 4–8 million years ago.

@article{liu_genomic_2025,
	title = {Genomic insights into the evolution of {Chinese} sweetgum and its autumn leaf coloration},
	volume = {198},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiaf218},
	doi = {10.1093/plphys/kiaf218},
	abstract = {Chinese sweetgum (Liquidambar formosana) is valued as a source of resin and timber and is an important ornamental tree due to its showy fall foliage. Here, we report the chromosome-level assembly of the Chinese sweetgum genome. Phylogenomic analyses showed the basal phylogenetic position of Chinese sweetgum in core eudicots. Comparative genomic analyses revealed that the well-known gamma event in the common ancestors of core eudicots is evident in the Chinese sweetgum genome, and ancestral triplicated blocks resulting from that event are more intact in Chinese sweetgum than in grapevine (Vitis vinifera). Because of its conserved genome structure, very slow rate of evolution, and basal phylogenetic position, the Chinese sweetgum genome is a good reference for comparative genome studies. Further, we reconstructed the entire metabolic pathway for anthocyanins and potential regulatory networks of autumn leaf coloration of this species via metabolomics and transcriptomics. The transcription factors LfMYB69, basic helix–loop–helix (LfbHLH4), and WD40-repeat (LfWDR1) may collectively regulate the transcription of anthocyanin biosynthetic genes. The regulation of chalcone synthase genes (LfCHS1-3) and dihydroflavonol 4-reductase genes (LfDFR1-2) by the LfMYB69–LfbHLH4–LfWDR1 complex was confirmed by luciferase assays. Epigenomic analyses revealed that 5 structural genes, including LfCHS1, and 2 regulatory LfMYBs are epigenetically regulated. This study expands our understanding of autumn leaf coloration and provides valuable genomic resources for comparative biology, breeding, and biotechnology.},
	number = {2},
	urldate = {2025-06-13},
	journal = {Plant Physiology},
	author = {Liu, Ping-Li and Jing, Zhao-Yang and Zhang, Ren-Gang and Chen, Ye and Zhu, Zhixin and Zhang, Xi and Jiang, Chen-Kun and Li, Ruili and Xie, Jian-Bo and Niu, Shihui and Zhang, Jinfeng and Kong, Lisheng and Zhao, Jian and Ma, Yongpeng and Zeisler-Diehl, Viktoria V and Schreiber, Lukas and Karahara, Ichirou and Mao, Jian-Feng and Jiao, Yuannian and Ge, Song and Lin, Jinxing},
	month = jun,
	year = {2025},
	pages = {kiaf218},
}

Chinese sweetgum (Liquidambar formosana) is valued as a source of resin and timber and is an important ornamental tree due to its showy fall foliage. Here, we report the chromosome-level assembly of the Chinese sweetgum genome. Phylogenomic analyses showed the basal phylogenetic position of Chinese sweetgum in core eudicots. Comparative genomic analyses revealed that the well-known gamma event in the common ancestors of core eudicots is evident in the Chinese sweetgum genome, and ancestral triplicated blocks resulting from that event are more intact in Chinese sweetgum than in grapevine (Vitis vinifera). Because of its conserved genome structure, very slow rate of evolution, and basal phylogenetic position, the Chinese sweetgum genome is a good reference for comparative genome studies. Further, we reconstructed the entire metabolic pathway for anthocyanins and potential regulatory networks of autumn leaf coloration of this species via metabolomics and transcriptomics. The transcription factors LfMYB69, basic helix–loop–helix (LfbHLH4), and WD40-repeat (LfWDR1) may collectively regulate the transcription of anthocyanin biosynthetic genes. The regulation of chalcone synthase genes (LfCHS1-3) and dihydroflavonol 4-reductase genes (LfDFR1-2) by the LfMYB69–LfbHLH4–LfWDR1 complex was confirmed by luciferase assays. Epigenomic analyses revealed that 5 structural genes, including LfCHS1, and 2 regulatory LfMYBs are epigenetically regulated. This study expands our understanding of autumn leaf coloration and provides valuable genomic resources for comparative biology, breeding, and biotechnology.

@article{li_ecophysiological_2025,
	title = {Ecophysiological transition mediated by hybridization in a hybrid pine species complex},
	issn = {2468-2659},
	url = {https://www.sciencedirect.com/science/article/pii/S2468265925000952},
	doi = {10.1016/j.pld.2025.05.009},
	abstract = {Hybridization is a driving force in ecological transitions and speciation, yet direct evidence linking it to adaptive differentiation in natural systems remains limited. This study evaluates the role of hybridization in the speciation of Pinus densata, a keystone forest species on the southeastern Tibetan Plateau. By creating artificial interspecific F1s and a long-term common garden experiment on the plateau, we provide in situ assessments on 44 growth and physiological traits across four seasons, along with RNA sequencing. We found significant phenotypic divergence between P. densata and its putative parental species P. tabuliformis and P. yunnanensis, with P. densata demonstrating superior growth and dynamic balance between photosynthesis and photoprotection. The F1s closely resembled P. densata in most traits. Gene expression revealed 19\%–10\% of 34,000 examined genes as differentially expressed in P. densata and F1s relative to mid-parent expression values. Both additive (4\%) and non-additive gene actions (5\%–6\% in F1s, 10\%–12\% in P. densata) were common, while transgressive expression occurred more frequently in the stabilized natural hybrids, illustrating transcriptomic reprogramming brought by hybridization and further divergence by natural selection. We provide compelling evidence for hybridization-derived phenotypic divergence at both physiological and gene expression levels that could have contributed to the adaptation of P. densata to high plateau habitat where both parental species have low fitness. The altered physiology and gene expression in hybrids serve both as a substrate for novel ecological adaptation and as a mechanism for the initiation of reproductive isolation.},
	urldate = {2025-07-04},
	journal = {Plant Diversity},
	author = {Li, Zhi-Chao and Xu, Chao-Qun and Zhao, Wei and Nie, Shuai and Bao, Yu-Tao and Liu, Hui and Xing, Zhen and Mao, Jian-Feng and Wang, Xiao-Ru},
	month = may,
	year = {2025},
	keywords = {Ecological divergence, Gene action, Homoploid hybrid speciation, Physiological traits, RNA-Seq, Tibetan plateau},
}

Hybridization is a driving force in ecological transitions and speciation, yet direct evidence linking it to adaptive differentiation in natural systems remains limited. This study evaluates the role of hybridization in the speciation of Pinus densata, a keystone forest species on the southeastern Tibetan Plateau. By creating artificial interspecific F1s and a long-term common garden experiment on the plateau, we provide in situ assessments on 44 growth and physiological traits across four seasons, along with RNA sequencing. We found significant phenotypic divergence between P. densata and its putative parental species P. tabuliformis and P. yunnanensis, with P. densata demonstrating superior growth and dynamic balance between photosynthesis and photoprotection. The F1s closely resembled P. densata in most traits. Gene expression revealed 19%–10% of 34,000 examined genes as differentially expressed in P. densata and F1s relative to mid-parent expression values. Both additive (4%) and non-additive gene actions (5%–6% in F1s, 10%–12% in P. densata) were common, while transgressive expression occurred more frequently in the stabilized natural hybrids, illustrating transcriptomic reprogramming brought by hybridization and further divergence by natural selection. We provide compelling evidence for hybridization-derived phenotypic divergence at both physiological and gene expression levels that could have contributed to the adaptation of P. densata to high plateau habitat where both parental species have low fitness. The altered physiology and gene expression in hybrids serve both as a substrate for novel ecological adaptation and as a mechanism for the initiation of reproductive isolation.

@incollection{gupta_nanomaterial-based_2025,
	address = {Cham},
	title = {Nanomaterial-{Based} {Sensors} and {Monitoring} {Devices} for {Water} {Quality} {Assessment}},
	isbn = {978-3-031-82794-5},
	url = {https://doi.org/10.1007/978-3-031-82794-5_13},
	abstract = {Industrialization, urbanization, and modern globalization increased the amount of pollutants in aquatic bodies, lowering the water purity. Surface and pollution of groundwater occur due to emerging pollutants, which result in drinking water scarcity. Plants and aquatic life, as well as human health, are significantly impacted by water contaminants, to ensure that natural aquifers provide clean, safe water and to comprehend how water contaminants change over time and space. Therefore, water quality monitoring has grown in significance during the past few years. Traditional methods of measuring water quality parameters are being replaced by new ideas and approaches. In the current era of sensors, biosensors, optical sensors, and microelectronic mechanical systems (MEMS) are significant sensing methods for detecting various water quality parameters. In addition, these sensors have a fast response time, excellent selectivity, sensitivity, affordability, and ease of use. This chapter focuses on the use of nanomaterial-based optical, electronic, and electrochemical sensors for the quick identification of water contaminants, such as microorganisms, anions, heavy metals, etc. There is a need for major development in the identification of pollutants in water due to the limits of present sensing technology. The benefits of sensing technologies based on nanomaterials are emphasized. The latest developments in nanomaterial-based sensors for quick detection of water contaminants have been discussed.},
	language = {en},
	urldate = {2025-07-04},
	booktitle = {Nano-solutions for {Sustainable} {Water} and {Wastewater} {Management}: {From} {Monitoring} to {Treatment}},
	publisher = {Springer Nature Switzerland},
	author = {Gupta, Urvashi and Jindal, Tanu and Tyagi, Jagriti and Salam, Menaka Devi and Saxena, Ananya and Upadhyay, Divya and Mishra, Arti and Shukla, Smriti},
	editor = {Garg, Manoj Chandra and Rajput, Vishnu D. and Minkina, Tatiana and Himanshu, Sushil Kumar},
	year = {2025},
	doi = {10.1007/978-3-031-82794-5_13},
	pages = {299--323},
}

Industrialization, urbanization, and modern globalization increased the amount of pollutants in aquatic bodies, lowering the water purity. Surface and pollution of groundwater occur due to emerging pollutants, which result in drinking water scarcity. Plants and aquatic life, as well as human health, are significantly impacted by water contaminants, to ensure that natural aquifers provide clean, safe water and to comprehend how water contaminants change over time and space. Therefore, water quality monitoring has grown in significance during the past few years. Traditional methods of measuring water quality parameters are being replaced by new ideas and approaches. In the current era of sensors, biosensors, optical sensors, and microelectronic mechanical systems (MEMS) are significant sensing methods for detecting various water quality parameters. In addition, these sensors have a fast response time, excellent selectivity, sensitivity, affordability, and ease of use. This chapter focuses on the use of nanomaterial-based optical, electronic, and electrochemical sensors for the quick identification of water contaminants, such as microorganisms, anions, heavy metals, etc. There is a need for major development in the identification of pollutants in water due to the limits of present sensing technology. The benefits of sensing technologies based on nanomaterials are emphasized. The latest developments in nanomaterial-based sensors for quick detection of water contaminants have been discussed.

@article{ma_ca2_2025,
	title = {Ca2+ waves and ethylene/{JA} crosstalk orchestrate wound responses in {Arabidopsis} roots},
	volume = {26},
	issn = {1469-221X},
	url = {https://www.embopress.org/doi/full/10.1038/s44319-025-00471-z},
	doi = {10.1038/s44319-025-00471-z},
	abstract = {Wounding triggers complex and multi-faceted responses in plants. Among these, calcium (Ca2+) waves serve as an immediate and localized response to strong stimuli, such as nematode infection or laser ablation. Here, we investigate the propagation patterns of Ca2+ waves induced by laser ablation and observe that glutamate-receptor-like channels (GLR3.3/GLR3.6), the stretch-activated anion channel MSL10, and the mechanosensitive Ca2+-permeable channels MCA1/MCA2 influence this process. These channels contribute to ethylene-associated signaling pathways, potentially through the WRKY33-ACS6 regulatory network. Furthermore, our findings show that ACC/ethylene signaling modulates Ca2+ wave propagation following laser ablation. Ethylene perception and synthesis at the site of damage regulate the local jasmonate response, which displays tissue-specific patterns upon laser ablation. Overall, our data provide new insights into the molecular and cellular processes underlying plant responses to localized damage, highlighting the roles of specific ion channels and hormone signaling pathways in shaping these responses in Arabidopsis roots.},
	number = {12},
	urldate = {2025-06-27},
	journal = {EMBO reports},
	author = {Ma, Xuemin and Hasan, M Shamim and Anjam, Muhammad Shahzad and Mahmud, Sakil and Bhattacharyya, Sabarna and Vothknecht, Ute C and Mendy, Badou and Grundler, Florian M W and Marhavý, Peter},
	month = jun,
	year = {2025},
	note = {Num Pages: 3203
Publisher: John Wiley \& Sons, Ltd},
	keywords = {Ca2+ Wave, Ethylene, Jasmonate, Laser Ablation},
	pages = {3187--3203},
}

Wounding triggers complex and multi-faceted responses in plants. Among these, calcium (Ca2+) waves serve as an immediate and localized response to strong stimuli, such as nematode infection or laser ablation. Here, we investigate the propagation patterns of Ca2+ waves induced by laser ablation and observe that glutamate-receptor-like channels (GLR3.3/GLR3.6), the stretch-activated anion channel MSL10, and the mechanosensitive Ca2+-permeable channels MCA1/MCA2 influence this process. These channels contribute to ethylene-associated signaling pathways, potentially through the WRKY33-ACS6 regulatory network. Furthermore, our findings show that ACC/ethylene signaling modulates Ca2+ wave propagation following laser ablation. Ethylene perception and synthesis at the site of damage regulate the local jasmonate response, which displays tissue-specific patterns upon laser ablation. Overall, our data provide new insights into the molecular and cellular processes underlying plant responses to localized damage, highlighting the roles of specific ion channels and hormone signaling pathways in shaping these responses in Arabidopsis roots.

@article{mikko_sequencing_2025,
	title = {Sequencing airborne {DNA} to monitor crop pathogens and pests},
	volume = {0},
	issn = {2589-0042},
	url = {https://www.cell.com/iscience/abstract/S2589-0042(25)01173-3},
	doi = {10.1016/j.isci.2025.112912},
	language = {English},
	number = {0},
	urldate = {2025-06-27},
	journal = {iScience},
	author = {Mikko, Amanda and Villegas, Jose Antonio and Svensson, Daniel and Karlsson, Edvin and Esseen, Per-Anders and Albrectsen, Benedicte Riber and Lundin, Ola and Forsman, Mats and Berlin, Anna and Stenberg, Per},
	month = jun,
	year = {2025},
	note = {Publisher: Elsevier},
	keywords = {Airborne eDNA, metagenomics, non-targeted surveillance, pathogen surveillance, plant pathogens, plant pests},
}

@article{kumar_shape_2025,
	title = {“{Shape} of {Cell}”—{An} {Auxin} and {Cell} {Wall} {Duet}},
	volume = {177},
	copyright = {© 2025 The Author(s). 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.70294},
	doi = {10.1111/ppl.70294},
	abstract = {Understanding the mechanisms underlying cell shape acquisition is of fundamental importance in plant science, as this process ultimately defines the structure and function of plant organs. Plants produce cells of diverse shapes and sizes, including pavement cells and stomata of leaves, elongated epidermal cells of the hypocotyl, and cells with outgrowths such as root hairs, and so forth. Plant cells experience mechanical forces of variable magnitude during their development and interaction with neighboring cells and the surrounding environment. From the time of cytokinesis, they are encaged in a complex cell wall matrix, which offers mechanical support and enables directional growth and a differential rate of expansion towards adjacent cells via its mechanochemical heterogeneity. The phytohormone auxin is well characterized for its role in cell expansion and cell elasticity. The interaction between dynamic auxin redistribution and the mechanical properties of the cell wall within tissues drives the development of specific cell shapes. Here, we focus on the regulatory feedback loop involving auxin activity, its influence on cell wall chemistry and mechanical properties, and the coordination of cell shape formation. Integrating insights from molecular and cell biology, biophysics, and computational modeling, we explore the mechanistic link between auxin signaling and cell wall dynamics in shaping plant cells.},
	language = {en},
	number = {3},
	urldate = {2025-06-13},
	journal = {Physiologia Plantarum},
	author = {Kumar, Vinod and Yadav, Sandeep and Heymans, Adrien and Robert, Stéphanie},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70294},
	keywords = {auxin, cell shape, cell wall, cytoskeleton, mechanical stress},
	pages = {e70294},
}

Understanding the mechanisms underlying cell shape acquisition is of fundamental importance in plant science, as this process ultimately defines the structure and function of plant organs. Plants produce cells of diverse shapes and sizes, including pavement cells and stomata of leaves, elongated epidermal cells of the hypocotyl, and cells with outgrowths such as root hairs, and so forth. Plant cells experience mechanical forces of variable magnitude during their development and interaction with neighboring cells and the surrounding environment. From the time of cytokinesis, they are encaged in a complex cell wall matrix, which offers mechanical support and enables directional growth and a differential rate of expansion towards adjacent cells via its mechanochemical heterogeneity. The phytohormone auxin is well characterized for its role in cell expansion and cell elasticity. The interaction between dynamic auxin redistribution and the mechanical properties of the cell wall within tissues drives the development of specific cell shapes. Here, we focus on the regulatory feedback loop involving auxin activity, its influence on cell wall chemistry and mechanical properties, and the coordination of cell shape formation. Integrating insights from molecular and cell biology, biophysics, and computational modeling, we explore the mechanistic link between auxin signaling and cell wall dynamics in shaping plant cells.

@article{faleiro_assessment_2025,
	title = {Assessment of the impact of biodegradable lignin nanoparticles encapsulating {IAA} on tomato development: from seed to fruit},
	volume = {25},
	issn = {1471-2229},
	shorttitle = {Assessment of the impact of biodegradable lignin nanoparticles encapsulating {IAA} on tomato development},
	url = {https://doi.org/10.1186/s12870-025-06539-1},
	doi = {10.1186/s12870-025-06539-1},
	abstract = {Polymeric nanoparticles have emerged as promising nanocarriers for plant growth regulators (PGRs) in agriculture, enhancing plant growth and boosting fruit and cereal yields. Among these, lignin nanoparticles (LNPs) stand out due to their biodegradability and low production cost. However, few studies have evaluated the biological effects of LNPs encapsulating PGRs — particularly their dose-dependent impacts across the entire plant life cycle. Therefore, our study aims to evaluate the efficiency of lignin nanoparticles (LNPs) encapsulating indole-3-acetic acid (IAA) compared with free application of the hormone. We employed a multidisciplinary approach to comprehensively assess the impacts of different LNPs-IAA concentrations. Germination tests and morphometric analyses were conducted, along with anatomical analyses of seeds, seedlings, and vegetative organs using light microscopy. Confocal microscopy analyses to examine LNP uptake and translocation. Additionally, leaf gas exchange parameters and photosynthetic pigment levels were measured. The lignin nanoparticles were also characterized in terms of length, polydispersity index, zeta potential and encapsulation efficiency. All variables were subjected to normality tests, variance analysis, and post-hoc tests. Structural analysis revealed that LNP application did not alter overall plant anatomy architecture, except for inducing differences in xylem area among vegetative organs. Additionally, LNPs were rapidly absorbed by seeds in less than 5 h and were transported exclusively via the apoplastic pathway. The composition of lignin nanoparticles influenced germination rates and time. Application with lower concentrations showed minimal statistical significance, whereas higher concentrations exhibited phytotoxic effects. Thus, our study highlights the critical importance of optimizing nanocarrier concentrations for plant growth enhancement, demonstrating that lignin nanoparticles (LNPs) represent a promising nanoformulation for bioactive compound encapsulation.},
	number = {1},
	urldate = {2025-06-13},
	journal = {BMC Plant Biology},
	author = {Faleiro, Rodrigo and Tessmer, Magda Andreia and Santo Pereira, Anderson Espirito and Fraceto, Leonardo Fernandes and Rampasso, Marcelle Sanches and Miranda, Marcela Trevenzoli and Pissolato, Maria Dolores and Cassola, Fábio and Ribeiro, Rafael Vasconcelos and Mayer, Juliana Lischka Sampaio},
	month = jun,
	year = {2025},
	keywords = {Crop science, Encapsulation, Nanotechnology, Plant growth regulators, Sustainability},
	pages = {768},
}

Polymeric nanoparticles have emerged as promising nanocarriers for plant growth regulators (PGRs) in agriculture, enhancing plant growth and boosting fruit and cereal yields. Among these, lignin nanoparticles (LNPs) stand out due to their biodegradability and low production cost. However, few studies have evaluated the biological effects of LNPs encapsulating PGRs — particularly their dose-dependent impacts across the entire plant life cycle. Therefore, our study aims to evaluate the efficiency of lignin nanoparticles (LNPs) encapsulating indole-3-acetic acid (IAA) compared with free application of the hormone. We employed a multidisciplinary approach to comprehensively assess the impacts of different LNPs-IAA concentrations. Germination tests and morphometric analyses were conducted, along with anatomical analyses of seeds, seedlings, and vegetative organs using light microscopy. Confocal microscopy analyses to examine LNP uptake and translocation. Additionally, leaf gas exchange parameters and photosynthetic pigment levels were measured. The lignin nanoparticles were also characterized in terms of length, polydispersity index, zeta potential and encapsulation efficiency. All variables were subjected to normality tests, variance analysis, and post-hoc tests. Structural analysis revealed that LNP application did not alter overall plant anatomy architecture, except for inducing differences in xylem area among vegetative organs. Additionally, LNPs were rapidly absorbed by seeds in less than 5 h and were transported exclusively via the apoplastic pathway. The composition of lignin nanoparticles influenced germination rates and time. Application with lower concentrations showed minimal statistical significance, whereas higher concentrations exhibited phytotoxic effects. Thus, our study highlights the critical importance of optimizing nanocarrier concentrations for plant growth enhancement, demonstrating that lignin nanoparticles (LNPs) represent a promising nanoformulation for bioactive compound encapsulation.

@article{gran_unravelling_2025,
	title = {Unravelling the dynamics of seed-stored {mRNAs} during seed priming},
	copyright = {© 2025 The Author(s). New Phytologist © 2025 New Phytologist Foundation.},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.70098},
	doi = {10.1111/nph.70098},
	abstract = {Seed priming is a pre-sowing treatment that enables more efficient and uniform seed germination; however, it negatively affects seed longevity. In this work, the mRNA dynamics underlying a hydropriming treatment have been investigated. Polysome profiling was performed on seeds during different stages of hydropriming. Ribosome nascent chain complex sequencing (RNC-seq) elucidated transcriptomic and translatomic changes during the priming treatment. In contrast to mature dry seeds, hydroprimed seeds contain more mRNA-ribosome complexes, suggesting that the mRNAs that need to be translated during germination are already associated with ribosomes in the primed seeds, leading to a quicker restart of translation and thus faster germination upon re-imbibition. As a result of priming, seeds lose part of their stress-related transcriptome. This work highlights genes that might play a role in increasing the rate of germination after priming.},
	language = {en},
	urldate = {2025-03-28},
	journal = {New Phytologist},
	author = {Gran, Patricija and Visscher, Tessa W. and Bai, Bing and Nijveen, Harm and Mahboubi, Amir and Bakermans, Lars L. and Willems, Leo A. J. and Bentsink, Leónie},
	month = mar,
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.70098},
	keywords = {Arabidopsis thaliana, RNC-seq, germination, hydropriming, longevity, mRNA dynamics, polysome profiling, seeds},
}

Seed priming is a pre-sowing treatment that enables more efficient and uniform seed germination; however, it negatively affects seed longevity. In this work, the mRNA dynamics underlying a hydropriming treatment have been investigated. Polysome profiling was performed on seeds during different stages of hydropriming. Ribosome nascent chain complex sequencing (RNC-seq) elucidated transcriptomic and translatomic changes during the priming treatment. In contrast to mature dry seeds, hydroprimed seeds contain more mRNA-ribosome complexes, suggesting that the mRNAs that need to be translated during germination are already associated with ribosomes in the primed seeds, leading to a quicker restart of translation and thus faster germination upon re-imbibition. As a result of priming, seeds lose part of their stress-related transcriptome. This work highlights genes that might play a role in increasing the rate of germination after priming.

@article{holloway-phillips_is_2025,
	title = {Is {Photosynthesis}-{Derived} {NADPH} {Really} a {Source} of {2H}-{Depleted} {Hydrogen} in {Plant} {Compounds}?},
	volume = {48},
	copyright = {© 2025 John Wiley \& Sons Ltd.},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.15403},
	doi = {10.1111/pce.15403},
	abstract = {statement We provide evidence that photosynthetically produced NADPH is not the major source of 2H-depletion in carbohydrates.},
	number = {6},
	urldate = {2025-05-23},
	journal = {Plant, Cell \& Environment},
	author = {Holloway-Phillips, Meisha and Tcherkez, Guillaume and Wieloch, Thomas and Lehmann, Marco M. and Werner, Roland A.},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.15403},
	pages = {4083--4098},
}

statement We provide evidence that photosynthetically produced NADPH is not the major source of 2H-depletion in carbohydrates.

@article{di_fino_cellular_2025,
	title = {Cellular damage triggers mechano-chemical control of cell wall dynamics and patterned cell divisions in plant healing},
	volume = {60},
	issn = {1534-5807},
	url = {https://www.sciencedirect.com/science/article/pii/S1534580724007718},
	doi = {10.1016/j.devcel.2024.12.032},
	abstract = {Reactivation of cell division is crucial for the regeneration of damaged tissues, which is a fundamental process across all multicellular organisms. However, the mechanisms underlying the activation of cell division in plants during regeneration remain poorly understood. Here, we show that single-cell endodermal ablation generates a transient change in the local mechanical pressure on neighboring pericycle cells to activate patterned cell division that is crucial for tissue regeneration in Arabidopsis roots. Moreover, we provide strong evidence that this process relies on the phytohormone ethylene. Thus, our results highlight a previously unrecognized role of mechano-chemical control in patterned cell division during regeneration in plants.},
	number = {10},
	urldate = {2025-05-23},
	journal = {Developmental Cell},
	author = {Di Fino, Luciano Martín and Anjam, Muhammad Shahzad and Besten, Maarten and Mentzelopoulou, Andriani and Papadakis, Vassilis and Zahid, Nageena and Baez, Luis Alonso and Trozzi, Nicola and Majda, Mateusz and Ma, Xuemin and Hamann, Thorsten and Sprakel, Joris and Moschou, Panagiotis N. and Smith, Richard S. and Marhavý, Peter},
	month = may,
	year = {2025},
	keywords = {cell division, cell wall, ethylene, mechanobiology, pectin, regeneration, single-cell laser ablation, xylem-pole-pericycle},
	pages = {1411--1422.e6},
}

Reactivation of cell division is crucial for the regeneration of damaged tissues, which is a fundamental process across all multicellular organisms. However, the mechanisms underlying the activation of cell division in plants during regeneration remain poorly understood. Here, we show that single-cell endodermal ablation generates a transient change in the local mechanical pressure on neighboring pericycle cells to activate patterned cell division that is crucial for tissue regeneration in Arabidopsis roots. Moreover, we provide strong evidence that this process relies on the phytohormone ethylene. Thus, our results highlight a previously unrecognized role of mechano-chemical control in patterned cell division during regeneration in plants.

@article{moe_marked_2025,
	title = {Marked mucosal lipid shifts in treatment refractory inflammatory bowel disease: a lipidomic study},
	volume = {25},
	issn = {1471-230X},
	shorttitle = {Marked mucosal lipid shifts in treatment refractory inflammatory bowel disease},
	url = {https://doi.org/10.1186/s12876-025-03944-6},
	doi = {10.1186/s12876-025-03944-6},
	abstract = {Mechanisms causing non-response to biological agents in IBD remain to be fully understood. Thus, we aimed to characterize the lipid profile in treatment refractory non-immunogenic patients with adequate trough-levels.},
	number = {1},
	urldate = {2025-05-23},
	journal = {BMC Gastroenterology},
	author = {Moe, Øystein K. and Gao, Qian and Geng, Dawei and Jensen, Einar and Goll, Rasmus and Nestegard, Oddmund and Gundersen, Mona D. and Florholmen, Jon R. and Moritz, T.},
	month = may,
	year = {2025},
	keywords = {Biological therapy, Inflammatory bowel disease, Lipids, Non-response},
	pages = {389},
}

Mechanisms causing non-response to biological agents in IBD remain to be fully understood. Thus, we aimed to characterize the lipid profile in treatment refractory non-immunogenic patients with adequate trough-levels.

@article{liang_pan-genome_2025,
	title = {Pan-{Genome} {Analysis} {Reveals} {Local} {Adaptation} to {Climate} {Driven} by {Introgression} in {Oak} {Species}},
	volume = {42},
	issn = {1537-1719},
	url = {https://doi.org/10.1093/molbev/msaf088},
	doi = {10.1093/molbev/msaf088},
	abstract = {The genetic base of local adaptation has been extensively studied in natural populations. However, a comprehensive genome-wide perspective on the contribution of structural variants (SVs) and adaptive introgression to local adaptation remains limited. In this study, we performed de novo assembly and annotation of 22 representative accessions of Quercus variabilis, identifying a total of 543,372 SVs. These SVs play crucial roles in shaping genomic structure and influencing gene expression. By analyzing range-wide genomic data, we identified both SNPs and SVs associated with local adaptation in Q. variabilis and Quercus acutissima. Notably, SV-outliers exhibit selection signals that did not overlap with SNP-outliers, indicating that SNP-based analyses may not detect the same candidate genes associated with SV-outliers. Remarkably, 29\%−37\% of candidate SNPs were located in a 250 kb region on chromosome 9, referred to as Chr9-ERF. This region contains 8 duplicated ethylene-responsive factor (ERF) genes, which may have contributed to local adaptation of Q. variabilis and Q. acutissima. We also found that a considerable number of candidate SNPs were shared between Q. variabilis and Q. acutissima in the Chr9-ERF region, suggesting a pattern of repeated selection. We further demonstrated that advantageous variants in this region were introgressed from western populations of Q. acutissima into Q. variabilis, providing compelling evidence that introgression facilitates local adaptation. This study offers a valuable genomic resource for future studies on oak species and highlights the importance of pan-genome analysis in understating mechanism driving adaptation and evolution.},
	number = {5},
	urldate = {2025-05-16},
	journal = {Molecular Biology and Evolution},
	author = {Liang, Yi-Ye and Liu, Hui and Lin, Qiong-Qiong and Shi, Yong and Zhou, Biao-Feng and Wang, Jing-Shu and Chen, Xue-Yan and Shen, Zhao and Qiao, Liang-Jing and Niu, Jing-Wei and Ling, Shao-Jun and Luo, Wen-Ji and Zhao, Wei and Liu, Jian-Feng and Kuang, Yuan-Wen and Ingvarsson, Pär K and Guo, Ya-Long and Wang, Baosheng},
	month = may,
	year = {2025},
	pages = {msaf088},
}

The genetic base of local adaptation has been extensively studied in natural populations. However, a comprehensive genome-wide perspective on the contribution of structural variants (SVs) and adaptive introgression to local adaptation remains limited. In this study, we performed de novo assembly and annotation of 22 representative accessions of Quercus variabilis, identifying a total of 543,372 SVs. These SVs play crucial roles in shaping genomic structure and influencing gene expression. By analyzing range-wide genomic data, we identified both SNPs and SVs associated with local adaptation in Q. variabilis and Quercus acutissima. Notably, SV-outliers exhibit selection signals that did not overlap with SNP-outliers, indicating that SNP-based analyses may not detect the same candidate genes associated with SV-outliers. Remarkably, 29%−37% of candidate SNPs were located in a 250 kb region on chromosome 9, referred to as Chr9-ERF. This region contains 8 duplicated ethylene-responsive factor (ERF) genes, which may have contributed to local adaptation of Q. variabilis and Q. acutissima. We also found that a considerable number of candidate SNPs were shared between Q. variabilis and Q. acutissima in the Chr9-ERF region, suggesting a pattern of repeated selection. We further demonstrated that advantageous variants in this region were introgressed from western populations of Q. acutissima into Q. variabilis, providing compelling evidence that introgression facilitates local adaptation. This study offers a valuable genomic resource for future studies on oak species and highlights the importance of pan-genome analysis in understating mechanism driving adaptation and evolution.

@article{koehler_node_2025,
	title = {Node of origin matters: comparative analysis of soil water limitation effects on nodal root anatomy in maize ({Zea} mays {L}.)},
	issn = {0305-7364},
	shorttitle = {Node of origin matters},
	url = {https://doi.org/10.1093/aob/mcaf075},
	doi = {10.1093/aob/mcaf075},
	urldate = {2025-05-16},
	journal = {Annals of Botany},
	author = {Koehler, Tina and Kim, Yunhee and Tung, Shu-Yin and Heymans, Adrien and Tyborski, Nicolas and Steiner, Franziska and Wild, Andreas J and Pausch, Johanna and Ahmed, Mutez A and Schneider, Hannah M},
	month = may,
	year = {2025},
	pages = {mcaf075},
}

@article{biancucci_mutations_2025,
	title = {Mutations in {HEADING} {DATE} 1 affect transcription and cell wall composition in rice},
	volume = {197},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiaf120},
	doi = {10.1093/plphys/kiaf120},
	abstract = {Plants utilize environmental information to modify their developmental trajectories for optimal survival and reproduction. Over a century ago, day length (photoperiod) was identified as a major factor influencing developmental transitions, particularly the shift from vegetative to reproductive growth. In rice (Oryza sativa), exposure to day lengths shorter than a critical threshold accelerates flowering, while longer days inhibit this process. This response is mediated by HEADING DATE 1 (Hd1), a zinc finger transcription factor that is central in the photoperiodic flowering network. Hd1 acts as a repressor of flowering under long days but functions as a promoter of flowering under short days. However, how global transcription of genes downstream of Hd1 changes in response to the photoperiod is still not fully understood. Furthermore, it is unclear whether Hd1 target genes are solely involved in flowering time control or mediate additional functions. In this study, we utilized RNA-Seq to analyze the transcriptome of hd1 mutants under both long and short day conditions. We identified genes involved in the phenylpropanoid pathway that are deregulated under long days in the mutant. Quantitative profiling of cell wall components and abiotic stress assays suggested that Hd1 is involved in processes considered unrelated to flowering control. This indicates that day length perception and responses are intertwined with physiological processes beyond flowering.},
	number = {4},
	urldate = {2025-05-09},
	journal = {Plant Physiology},
	author = {Biancucci, Marco and Chirivì, Daniele and Baldini, Alessio and Badenhorst, Eugene and Dobetti, Fabio and Khahani, Bahman and Formentin, Elide and Eguen, Tenai and Turck, Franziska and Moore, John P and Tavakol, Elahe and Wenkel, Stephan and Lo Schiavo, Fiorella and Ezquer, Ignacio and Brambilla, Vittoria and Horner, David and Chiara, Matteo and Perrella, Giorgio and Betti, Camilla and Fornara, Fabio},
	month = apr,
	year = {2025},
	pages = {kiaf120},
}

Plants utilize environmental information to modify their developmental trajectories for optimal survival and reproduction. Over a century ago, day length (photoperiod) was identified as a major factor influencing developmental transitions, particularly the shift from vegetative to reproductive growth. In rice (Oryza sativa), exposure to day lengths shorter than a critical threshold accelerates flowering, while longer days inhibit this process. This response is mediated by HEADING DATE 1 (Hd1), a zinc finger transcription factor that is central in the photoperiodic flowering network. Hd1 acts as a repressor of flowering under long days but functions as a promoter of flowering under short days. However, how global transcription of genes downstream of Hd1 changes in response to the photoperiod is still not fully understood. Furthermore, it is unclear whether Hd1 target genes are solely involved in flowering time control or mediate additional functions. In this study, we utilized RNA-Seq to analyze the transcriptome of hd1 mutants under both long and short day conditions. We identified genes involved in the phenylpropanoid pathway that are deregulated under long days in the mutant. Quantitative profiling of cell wall components and abiotic stress assays suggested that Hd1 is involved in processes considered unrelated to flowering control. This indicates that day length perception and responses are intertwined with physiological processes beyond flowering.

@article{asao_leaf_2025,
	title = {Leaf nonstructural carbohydrate residence time, not concentration, correlates with leaf functional traits following the leaf economic spectrum in woody plants},
	volume = {246},
	copyright = {© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.20315},
	doi = {10.1111/nph.20315},
	abstract = {Nonstructural carbohydrate (NSC) concentrations might reflect the strategies described in the leaf economic spectrum (LES) due to their dependence on photosynthesis and respiration. We examined if NSC concentrations correlate with leaf structure, chemistry, and physiology traits for 114 species from 19 sites and 5 biomes around the globe. Total leaf NSC concentrations varied greatly from 16 to 199 mg g−1 dry mass and were mostly independent of leaf gas exchange and the LES traits. By contrast, leaf NSC residence time was shorter in species with higher rates of photosynthesis, following the fast-slow strategies in the LES. An average leaf held an amount of NSCs that could sustain one night of leaf respiration and could be replenished in just a few hours of photosynthesis under saturating light, indicating that most daily carbon gain is exported. Our results suggest that NSC export is clearly linked to the economics of return on resource investment.},
	language = {en},
	number = {4},
	urldate = {2025-05-09},
	journal = {New Phytologist},
	author = {Asao, Shinichi and Way, Danielle A. and Turnbull, Matthew H. and Stitt, Mark and McDowell, Nate G. and Reich, Peter B. and Bloomfield, Keith J. and Zaragoza-Castells, Joana and Creek, Danielle and O'Sullivan, Odhran and Crous, Kristine Y. and Egerton, John J.G. and Mirotchnick, Nicholas and Weerasinghe, Lasantha K. and Griffin, Kevin L. and Hurry, Vaughan and Meir, Patrick and Sitch, Stephen and Atkin, Owen K.},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.20315},
	keywords = {export, leaf economic spectrum, leaf functional traits, nonstructural carbohydrate, residence time},
	pages = {1505--1519},
}

Nonstructural carbohydrate (NSC) concentrations might reflect the strategies described in the leaf economic spectrum (LES) due to their dependence on photosynthesis and respiration. We examined if NSC concentrations correlate with leaf structure, chemistry, and physiology traits for 114 species from 19 sites and 5 biomes around the globe. Total leaf NSC concentrations varied greatly from 16 to 199 mg g−1 dry mass and were mostly independent of leaf gas exchange and the LES traits. By contrast, leaf NSC residence time was shorter in species with higher rates of photosynthesis, following the fast-slow strategies in the LES. An average leaf held an amount of NSCs that could sustain one night of leaf respiration and could be replenished in just a few hours of photosynthesis under saturating light, indicating that most daily carbon gain is exported. Our results suggest that NSC export is clearly linked to the economics of return on resource investment.

@article{guo_near-gapless_2025,
	title = {Near-gapless telomere-to-telomere reference nuclear genome and variable mitochondrial genome of \textit{{Amborella} trichopoda}},
	issn = {1673-8527},
	url = {https://www.sciencedirect.com/science/article/pii/S1673852725001250},
	doi = {10.1016/j.jgg.2025.04.016},
	urldate = {2025-05-09},
	journal = {Journal of Genetics and Genomics},
	author = {Guo, Zhonglong and Guo, Jing-Fang and Wei, Zhi-Yan and Zhang, Ren-Gang and McMahan, Scott and Nie, Shuai and Yan, Xue-Mei and Zhou, Shan-Shan and Yun, Quan-Zheng and Wu, Jia-Yi and Ge, Jing and Yang, Yong and Xue, Jia-Yu and Mao, Jian-Feng},
	month = may,
	year = {2025},
}

@article{xiao_protein_2025,
	title = {The protein kinases {KIPK} and {KIPK}-{LIKE1} suppress overbending during negative hypocotyl gravitropic growth in {Arabidopsis}},
	volume = {37},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koaf056},
	doi = {10.1093/plcell/koaf056},
	abstract = {Plants use environmental cues to orient organ and plant growth, such as the direction of gravity or the direction, quantity, and quality of light. During the germination of Arabidopsis thaliana seeds in soil, negative gravitropism responses direct hypocotyl elongation such that the seedling can reach the light for photosynthesis and autotrophic growth. Similarly, hypocotyl elongation in the soil also requires mechanisms to efficiently grow around obstacles such as soil particles. Here, we identify KIPK (KINESIN-LIKE CALMODULIN-BINDING PROTEIN-INTERACTING PROTEIN KINASE) and the paralogous KIPKL1 (KIPK-LIKE1) as genetically redundant regulators of gravitropic hypocotyl bending. Moreover, we demonstrate that the homologous KIPKL2 (KIPK-LIKE2), which shows strong sequence similarity, must be functionally distinct. KIPK and KIPKL1 are polarly localized plasma membrane-associated proteins that can activate PIN-FORMED auxin transporters. KIPK and KIPKL1 are required to efficiently align hypocotyl growth with the gravity vector when seedling hypocotyls are grown on media plates or in soil, where contact with soil particles and obstacle avoidance impede direct negative gravitropic growth. Therefore, the polar KIPK and KIPKL1 kinases have different biological functions from the related AGC1 family kinases D6PK (D6 PROTEIN KINASE) or PAX (PROTEIN KINASE ASSOCIATED WITH BRX).},
	number = {4},
	urldate = {2025-04-25},
	journal = {The Plant Cell},
	author = {Xiao, Yao and Zourelidou, Melina and Bassukas, Alkistis E Lanassa and Weller, Benjamin and Janacek, Dorina P and Šimura, Jan and Ljung, Karin and Hammes, Ulrich Z and Li, Jia and Schwechheimer, Claus},
	month = apr,
	year = {2025},
	pages = {koaf056},
}

Plants use environmental cues to orient organ and plant growth, such as the direction of gravity or the direction, quantity, and quality of light. During the germination of Arabidopsis thaliana seeds in soil, negative gravitropism responses direct hypocotyl elongation such that the seedling can reach the light for photosynthesis and autotrophic growth. Similarly, hypocotyl elongation in the soil also requires mechanisms to efficiently grow around obstacles such as soil particles. Here, we identify KIPK (KINESIN-LIKE CALMODULIN-BINDING PROTEIN-INTERACTING PROTEIN KINASE) and the paralogous KIPKL1 (KIPK-LIKE1) as genetically redundant regulators of gravitropic hypocotyl bending. Moreover, we demonstrate that the homologous KIPKL2 (KIPK-LIKE2), which shows strong sequence similarity, must be functionally distinct. KIPK and KIPKL1 are polarly localized plasma membrane-associated proteins that can activate PIN-FORMED auxin transporters. KIPK and KIPKL1 are required to efficiently align hypocotyl growth with the gravity vector when seedling hypocotyls are grown on media plates or in soil, where contact with soil particles and obstacle avoidance impede direct negative gravitropic growth. Therefore, the polar KIPK and KIPKL1 kinases have different biological functions from the related AGC1 family kinases D6PK (D6 PROTEIN KINASE) or PAX (PROTEIN KINASE ASSOCIATED WITH BRX).

@article{aydin_probing_2025,
	title = {Probing substrate water access through the {O1} channel of {Photosystem} {II} by single site mutations and membrane inlet mass spectrometry},
	volume = {163},
	issn = {1573-5079},
	url = {https://doi.org/10.1007/s11120-025-01147-4},
	doi = {10.1007/s11120-025-01147-4},
	abstract = {Light-driven water oxidation by photosystem II sustains life on Earth by providing the electrons and protons for the reduction of CO2 to carbohydrates and the molecular oxygen we breathe. The inorganic core of the oxygen evolving complex is made of the earth-abundant elements manganese, calcium and oxygen (Mn4CaO5 cluster), and is situated in a binding pocket that is connected to the aqueous surrounding via water-filled channels that allow water intake and proton egress. Recent serial crystallography and infrared spectroscopy studies performed with PSII isolated from Thermosynechococcus vestitus (T. vestitus) support that one of these channels, the O1 channel, facilitates water access to the Mn4CaO5 cluster during its S2→S3 and S3→S4→S0 state transitions, while a subsequent CryoEM study concluded that this channel is blocked in the cyanobacterium Synechocystis sp. PCC 6803, questioning the role of the O1 channel in water delivery. Employing site-directed mutagenesis we modified the two O1 channel bottleneck residues D1-E329 and CP43-V410 (T. vestitus numbering) and probed water access and substrate exchange via time resolved membrane inlet mass spectrometry. Our data demonstrates that water reaches the Mn4CaO5 cluster via the O1 channel in both wildtype and mutant PSII. In addition, the detailed analysis provides functional insight into the intricate protein-water-cofactor network near the Mn4CaO5 cluster that includes the pentameric, near planar ‘water wheel’ of the O1 channel.},
	language = {en},
	number = {3},
	urldate = {2025-04-25},
	journal = {Photosynthesis Research},
	author = {Aydin, A. Orkun and de Lichtenberg, Casper and Liang, Feiyan and Forsman, Jack and Graça, André T. and Chernev, Petko and Zhu, Shaochun and Mateus, André and Magnuson, Ann and Cheah, Mun Hon and Schröder, Wolfgang P. and Ho, Felix and Lindblad, Peter and Debus, Richard J. and Mamedov, Fikret and Messinger, Johannes},
	month = apr,
	year = {2025},
	keywords = {CP43-V410, D1-E329, O1 channel, Oxygen evolving complex, Photosystem II, Substrate water exchange, Synechocystis sp. PCC 6803, Water delivery, Water oxidation, Water wheel},
	pages = {28},
}

Light-driven water oxidation by photosystem II sustains life on Earth by providing the electrons and protons for the reduction of CO2 to carbohydrates and the molecular oxygen we breathe. The inorganic core of the oxygen evolving complex is made of the earth-abundant elements manganese, calcium and oxygen (Mn4CaO5 cluster), and is situated in a binding pocket that is connected to the aqueous surrounding via water-filled channels that allow water intake and proton egress. Recent serial crystallography and infrared spectroscopy studies performed with PSII isolated from Thermosynechococcus vestitus (T. vestitus) support that one of these channels, the O1 channel, facilitates water access to the Mn4CaO5 cluster during its S2→S3 and S3→S4→S0 state transitions, while a subsequent CryoEM study concluded that this channel is blocked in the cyanobacterium Synechocystis sp. PCC 6803, questioning the role of the O1 channel in water delivery. Employing site-directed mutagenesis we modified the two O1 channel bottleneck residues D1-E329 and CP43-V410 (T. vestitus numbering) and probed water access and substrate exchange via time resolved membrane inlet mass spectrometry. Our data demonstrates that water reaches the Mn4CaO5 cluster via the O1 channel in both wildtype and mutant PSII. In addition, the detailed analysis provides functional insight into the intricate protein-water-cofactor network near the Mn4CaO5 cluster that includes the pentameric, near planar ‘water wheel’ of the O1 channel.

@article{mazumdar_damage_2025,
	title = {Damage activates \textit{{EXG1}} and \textit{{RLP44}} to suppress vascular differentiation during regeneration in \textit{{Arabidopsis}}},
	volume = {6},
	issn = {2590-3462},
	url = {https://www.sciencedirect.com/science/article/pii/S2590346225000185},
	doi = {10.1016/j.xplc.2025.101256},
	abstract = {Plants possess remarkable regenerative abilities to form de novo vasculature after damage and in response to pathogens that invade and withdraw nutrients. To identify common factors that affect vascular formation upon stress, we searched for Arabidopsis thaliana genes differentially expressed upon Agrobacterium infection, nematode infection, and plant grafting. One such gene is cell wall-related and highly induced by all three stresses, which we named ENHANCED XYLEM AND GRAFTING1 (EXG1), since its mutations promote ectopic xylem formation in a vascular cell induction system and enhance graft formation. Further observations revealed that exg1 mutants show inhibited cambium development and callus formation but enhanced tissue attachment, syncytium size, phloem reconnection, and xylem formation. Given that brassinosteroids also promote xylem differentiation, we analyzed brassinosteroid-related genes and found that mutations in RLP44 encoding a receptor-like protein cause similar regeneration-related phenotypes as mutations in EXG1. Like EXG1, RLP44 expression is also induced by grafting and wounding. Mutations in EXG1 and RLP44 affect the expression of many genes in common, including those related to cell walls and genes important for vascular regeneration. Our results suggest that EXG1 integrates information from wounding or pathogen stress and functions with RLP44 to suppress vascular differentiation during regeneration and healing.},
	number = {4},
	urldate = {2025-04-22},
	journal = {Plant Communications},
	author = {Mazumdar, Shamik and Augstein, Frauke and Zhang, Ai and Musseau, Constance and Anjam, Muhammad Shahzad and Marhavy, Peter and Melnyk, Charles W.},
	month = apr,
	year = {2025},
	keywords = {Cell wall, Grafting, Regeneration, Stress, Wounding, Xylem, cell wall, grafting, regeneration, stress, wounding, xylem},
	pages = {101256},
}

Plants possess remarkable regenerative abilities to form de novo vasculature after damage and in response to pathogens that invade and withdraw nutrients. To identify common factors that affect vascular formation upon stress, we searched for Arabidopsis thaliana genes differentially expressed upon Agrobacterium infection, nematode infection, and plant grafting. One such gene is cell wall-related and highly induced by all three stresses, which we named ENHANCED XYLEM AND GRAFTING1 (EXG1), since its mutations promote ectopic xylem formation in a vascular cell induction system and enhance graft formation. Further observations revealed that exg1 mutants show inhibited cambium development and callus formation but enhanced tissue attachment, syncytium size, phloem reconnection, and xylem formation. Given that brassinosteroids also promote xylem differentiation, we analyzed brassinosteroid-related genes and found that mutations in RLP44 encoding a receptor-like protein cause similar regeneration-related phenotypes as mutations in EXG1. Like EXG1, RLP44 expression is also induced by grafting and wounding. Mutations in EXG1 and RLP44 affect the expression of many genes in common, including those related to cell walls and genes important for vascular regeneration. Our results suggest that EXG1 integrates information from wounding or pathogen stress and functions with RLP44 to suppress vascular differentiation during regeneration and healing.

@article{bogacz_x-ray_2025,
	title = {X-ray {Absorption} {Spectroscopy} of {Dilute} {Metalloenzymes} at {X}-ray {Free}-{Electron} {Lasers} in a {Shot}-by-{Shot} {Mode}},
	volume = {16},
	url = {https://doi.org/10.1021/acs.jpclett.5c00399},
	doi = {10.1021/acs.jpclett.5c00399},
	abstract = {X-ray absorption spectroscopy (XAS) of 3d transition metals provides important electronic structure information for many fields. However, X-ray-induced radiation damage under physiological temperature has prevented using this method to study dilute aqueous systems, such as metalloenzymes, as the catalytic reaction proceeds. Here we present a new approach to enable operando XAS of dilute biological samples and demonstrate its feasibility with K-edge XAS spectra from the Mn cluster in photosystem II and the Fe–S centers in photosystem I. This approach combines highly efficient sample delivery strategies and a robust signal normalization method with high-transmission Bragg diffraction-based spectrometers at X-ray free-electron lasers (XFELs) in a damage-free, shot-by-shot mode. These photon-out spectrometers have been optimized for discriminating the metal Mn/Fe Kα fluorescence signals from the overwhelming scattering background present on currently available detectors for XFELs that lack suitable energy discrimination. We quantify the enhanced performance metrics of the spectrometer and discuss its potential applications for acquiring time-resolved XAS spectra of biological samples during their reactions at XFELs.},
	number = {15},
	urldate = {2025-04-22},
	journal = {The Journal of Physical Chemistry Letters},
	author = {Bogacz, Isabel and Szilagyi, Erzsi and Makita, Hiroki and Simon, Philipp S. and Zhang, Miao and Doyle, Margaret D. and Chatterjee, Kuntal and Kretzschmar, Moritz and Chernev, Petko and Croy, Nicholas and Cheah, Mun-Hon and Dasgupta, Medhanjali and Nangca, Isabela and Fransson, Thomas and Bhowmick, Asmit and Brewster, Aaron S. and Sauter, Nicholas K. and Owada, Shigeki and Tono, Kensuke and Zerdane, Serhane and Oggenfuss, Alexander and Babich, Danylo and Sander, Mathias and Mankowsky, Roman and Lemke, Henrik T. and Gee, Leland B. and Sato, Takahiro and Kroll, Thomas and Messinger, Johannes and Alonso-Mori, Roberto and Bergmann, Uwe and Sokaras, Dimosthenis and Yachandra, Vittal K. and Kern, Jan and Yano, Junko},
	month = apr,
	year = {2025},
	note = {Publisher: American Chemical Society},
	pages = {3778--3787},
}

X-ray absorption spectroscopy (XAS) of 3d transition metals provides important electronic structure information for many fields. However, X-ray-induced radiation damage under physiological temperature has prevented using this method to study dilute aqueous systems, such as metalloenzymes, as the catalytic reaction proceeds. Here we present a new approach to enable operando XAS of dilute biological samples and demonstrate its feasibility with K-edge XAS spectra from the Mn cluster in photosystem II and the Fe–S centers in photosystem I. This approach combines highly efficient sample delivery strategies and a robust signal normalization method with high-transmission Bragg diffraction-based spectrometers at X-ray free-electron lasers (XFELs) in a damage-free, shot-by-shot mode. These photon-out spectrometers have been optimized for discriminating the metal Mn/Fe Kα fluorescence signals from the overwhelming scattering background present on currently available detectors for XFELs that lack suitable energy discrimination. We quantify the enhanced performance metrics of the spectrometer and discuss its potential applications for acquiring time-resolved XAS spectra of biological samples during their reactions at XFELs.

@article{nair_elf3_2025,
	title = {{ELF3} coordinates temperature and photoperiodic control of seasonal growth in hybrid aspen},
	volume = {35},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982225001903},
	doi = {10.1016/j.cub.2025.02.027},
	abstract = {Timely growth cessation before winter is crucial for the survival of perennial plants in temperate and boreal regions. Short photoperiod (SP) and low temperature (LT) are major seasonal cues regulating growth cessation. SP, sensed in the leaves, initiates growth cessation by downregulating FLOWERING LOCUS T 2 (FT2) expression, but how LT regulates seasonal growth is unclear. Genetic and cell biological approaches identified a hybrid aspen EARLY FLOWERING 3(ELF3) ortholog with a prion-like domain (PrLD) that undergoes LT-responsive phase separation as a key mediator of LT-induced growth cessation. In contrast with SP, LT acts independently of FT2 downregulation and targets the AIL1-BRC1 transcription factor network and hormonal pathways via ELF3 to induce growth cessation. Intriguingly, ELF3 also functions in SP-mediated growth cessation by downregulating FT2 in leaves. Our work thus reveals a previously unrecognized role of ELF3 in growth cessation and in coordinating temperature and photoperiodic pathways to enable robust adaptation to seasonal change.},
	number = {7},
	urldate = {2025-04-11},
	journal = {Current Biology},
	author = {Nair, Aswin and Maurya, Jay P. and Pandey, Shashank K. and Singh, Rajesh Kumar and Miskolczi, Pal C. and Aryal, Bibek and Bhalerao, Rishikesh P.},
	month = apr,
	year = {2025},
	keywords = {EARLY FLOWERING 3(ELF3), FLOWERING LOCUS T (FT), growth cessation, hybrid aspen, perennial trees, seasonal growth},
	pages = {1484--1494.e2},
}

Timely growth cessation before winter is crucial for the survival of perennial plants in temperate and boreal regions. Short photoperiod (SP) and low temperature (LT) are major seasonal cues regulating growth cessation. SP, sensed in the leaves, initiates growth cessation by downregulating FLOWERING LOCUS T 2 (FT2) expression, but how LT regulates seasonal growth is unclear. Genetic and cell biological approaches identified a hybrid aspen EARLY FLOWERING 3(ELF3) ortholog with a prion-like domain (PrLD) that undergoes LT-responsive phase separation as a key mediator of LT-induced growth cessation. In contrast with SP, LT acts independently of FT2 downregulation and targets the AIL1-BRC1 transcription factor network and hormonal pathways via ELF3 to induce growth cessation. Intriguingly, ELF3 also functions in SP-mediated growth cessation by downregulating FT2 in leaves. Our work thus reveals a previously unrecognized role of ELF3 in growth cessation and in coordinating temperature and photoperiodic pathways to enable robust adaptation to seasonal change.

@article{bag_photosynthetic_2025,
	title = {Photosynthetic advantages of conifers in the boreal forest},
	volume = {30},
	issn = {1360-1385},
	url = {https://www.sciencedirect.com/science/article/pii/S1360138524003005},
	doi = {10.1016/j.tplants.2024.10.018},
	abstract = {Boreal conifers – the ‘Christmas trees’ – maintain their green needles over the winter by retaining their chlorophyll. These conifers face the toughest challenge in February and March, when subzero temperatures coincide with high solar radiation. To balance the light energy they harvest with the light energy they utilise, conifers deploy various mechanisms in parallel. These include, thylakoid destacking, which facilitates direct energy transfer from Photosystem II (PSII) to Photosystem I (PSI), and excess energy dissipation through sustained nonphotochemical quenching (NPQ). Additionally, they upregulate alternative electron transport pathways to safely reroute excess electrons while maintaining ATP production. From an evolutionary and ecological perspective, we consider these mechanisms as part of a comprehensive photosynthetic alteration, which enhances our understanding of winter acclimation in conifers and their dominance in the boreal forests.},
	number = {4},
	urldate = {2025-04-11},
	journal = {Trends in Plant Science},
	author = {Bag, Pushan and Ivanov, Alexander G. and Huner, Norman P. and Jansson, Stefan},
	month = apr,
	year = {2025},
	keywords = {alternative electron transport, conifers, direct energy transfer, flavodiiron proteins, nonphotochemical quenching (NPQ), photosystems},
	pages = {409--423},
}

Boreal conifers – the ‘Christmas trees’ – maintain their green needles over the winter by retaining their chlorophyll. These conifers face the toughest challenge in February and March, when subzero temperatures coincide with high solar radiation. To balance the light energy they harvest with the light energy they utilise, conifers deploy various mechanisms in parallel. These include, thylakoid destacking, which facilitates direct energy transfer from Photosystem II (PSII) to Photosystem I (PSI), and excess energy dissipation through sustained nonphotochemical quenching (NPQ). Additionally, they upregulate alternative electron transport pathways to safely reroute excess electrons while maintaining ATP production. From an evolutionary and ecological perspective, we consider these mechanisms as part of a comprehensive photosynthetic alteration, which enhances our understanding of winter acclimation in conifers and their dominance in the boreal forests.

@article{marien_natures_2025,
	title = {Nature’s {Master} of {Ceremony}: {The} {Populus} {Circadian} {Clock} as {Orchestrator} of {Tree} {Growth} and {Phenology}},
	volume = {2},
	copyright = {2025 The Author(s)},
	issn = {2948-281X},
	shorttitle = {Nature’s {Master} of {Ceremony}},
	url = {https://www.nature.com/articles/s44323-025-00034-4},
	doi = {10.1038/s44323-025-00034-4},
	abstract = {Understanding the timely regulation of plant growth and phenology is crucial for assessing a terrestrial ecosystem’s productivity and carbon budget. The circadian clock, a system of genetic oscillators, acts as ‘Master of Ceremony’ during plant physiological processes. The mechanism is particularly elusive in trees despite its relevance. The primary and secondary tree growth, leaf senescence, bud set, and bud burst timing were investigated in 68 constructs transformed into Populus hybrids and compared with untransformed or transformed controls grown in natural or controlled conditions. The results were analyzed using generalized additive models with ordered-factor-smooth interaction smoothers. This meta-analysis shows that several genetic components are associated with the clock. Especially core clock-regulated genes affected tree growth and phenology in both controlled and field conditions. Our results highlight the importance of field trials and the potential of using the clock to generate trees with improved characteristics for sustainable silviculture (e.g., reprogrammed to new photoperiodic regimes and increased growth).},
	language = {en},
	number = {1},
	urldate = {2025-04-11},
	journal = {npj Biological Timing and Sleep},
	author = {Mariën, Bertold and Robinson, Kathryn M. and Jurca, Manuela and Michelson, Ingrid H. and Takata, Naoki and Kozarewa, Iwanka and Pin, Pierre A. and Ingvarsson, Pär K. and Moritz, Thomas and Ibáñez, Cristian and Nilsson, Ove and Jansson, Stefan and Penfield, Steve and Yu, Jun and Eriksson, Maria E.},
	month = apr,
	year = {2025},
	note = {Publisher: Nature Publishing Group},
	keywords = {Biological techniques, Plant sciences},
	pages = {1--19},
}

Understanding the timely regulation of plant growth and phenology is crucial for assessing a terrestrial ecosystem’s productivity and carbon budget. The circadian clock, a system of genetic oscillators, acts as ‘Master of Ceremony’ during plant physiological processes. The mechanism is particularly elusive in trees despite its relevance. The primary and secondary tree growth, leaf senescence, bud set, and bud burst timing were investigated in 68 constructs transformed into Populus hybrids and compared with untransformed or transformed controls grown in natural or controlled conditions. The results were analyzed using generalized additive models with ordered-factor-smooth interaction smoothers. This meta-analysis shows that several genetic components are associated with the clock. Especially core clock-regulated genes affected tree growth and phenology in both controlled and field conditions. Our results highlight the importance of field trials and the potential of using the clock to generate trees with improved characteristics for sustainable silviculture (e.g., reprogrammed to new photoperiodic regimes and increased growth).

@article{dikaya_arabidopsis_2025,
	title = {The {Arabidopsis} thaliana core splicing factor {PORCUPINE}/{SmE1} requires intron-mediated expression},
	volume = {20},
	doi = {10.1371/journal.pone.0318163},
	abstract = {Plants are prone to genome duplications and tend to preserve multiple gene copies. This is also the case for the genes encoding the Sm proteins of Arabidopsis thaliana (L). The Sm proteins are best known for their roles in RNA processing such as pre-mRNA splicing and nonsense-mediated mRNA decay. In this study, we have taken a closer look at the phylogeny and differential regulation of the SmE-coding genes found in A. thaliana, PCP/SmE1, best known for its cold-sensitive phenotype, and its paralog, PCPL/SmE2. The phylogeny of the PCP homologs in the green lineage shows that SmE duplications happened multiple times independently in different plant clades and that the duplication that gave rise to PCP and PCPL occurred only in the Brassicaceae family. Our analysis revealed that A. thaliana PCP and PCPL proteins, which only differ in two amino acids, exhibit a very high level of functional conservation and can perform the same function in the cell. However, our results indicate that PCP is the prevailing copy of the two SmE genes in A. thaliana as it is more highly expressed and that the main difference between PCP and PCPL resides in their transcriptional regulation, which is strongly linked to intronic sequences. Our results provide insight into the complex mechanisms that underlie the differentiation of the paralogous gene expression as an adaptation to stress. © 2025 Dikaya et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.},
	number = {3 March},
	journal = {PLoS ONE},
	author = {Dikaya, V. and Rojas-Murcia, N. and Benstein, R.M. and Eiserhardt, W.L. and Schmid, M.},
	year = {2025},
	keywords = {Arabidopsis thaliana, Gene expression, Genomics, Introns, Phenotypes, Phylogenetic analysis, Seedlings, Sequence alignment},
}

Plants are prone to genome duplications and tend to preserve multiple gene copies. This is also the case for the genes encoding the Sm proteins of Arabidopsis thaliana (L). The Sm proteins are best known for their roles in RNA processing such as pre-mRNA splicing and nonsense-mediated mRNA decay. In this study, we have taken a closer look at the phylogeny and differential regulation of the SmE-coding genes found in A. thaliana, PCP/SmE1, best known for its cold-sensitive phenotype, and its paralog, PCPL/SmE2. The phylogeny of the PCP homologs in the green lineage shows that SmE duplications happened multiple times independently in different plant clades and that the duplication that gave rise to PCP and PCPL occurred only in the Brassicaceae family. Our analysis revealed that A. thaliana PCP and PCPL proteins, which only differ in two amino acids, exhibit a very high level of functional conservation and can perform the same function in the cell. However, our results indicate that PCP is the prevailing copy of the two SmE genes in A. thaliana as it is more highly expressed and that the main difference between PCP and PCPL resides in their transcriptional regulation, which is strongly linked to intronic sequences. Our results provide insight into the complex mechanisms that underlie the differentiation of the paralogous gene expression as an adaptation to stress. © 2025 Dikaya et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

@article{jiang_incorporating_2025,
	title = {Incorporating genetic load contributes to predicting {Arabidopsis} thaliana’s response to climate change},
	volume = {16},
	copyright = {2025 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-025-58021-z},
	doi = {10.1038/s41467-025-58021-z},
	abstract = {Understanding how species respond to climate change can facilitate species conservation and crop breeding. Current prediction frameworks about population vulnerability focused on predicting range shifts or local adaptation but ignored genetic load, which is also crucial for adaptation. By analyzing 1115 globally distributed Arabidopsis thaliana natural accessions, we find that effective population size (Ne) is the major contributor of genetic load variation, both along genome and among populations, and can explain 74-94\% genetic load variation in natural populations. Intriguingly, Ne affects genetic load by changing both effectiveness of purifying selection and GC biased gene conversion strength. In particular, by incorporating genetic load, genetic offset and species distribution models (SDM), we predict that, the populations at species’ range edge are generally at higher risk. The populations at the eastern range perform poorer in all aspects, southern range have higher genetic offset and lower SDM suitability, while northern range have higher genetic load. Among the diverse natural populations, the Yangtze River basin population is the most vulnerable population under future climate change. Overall, here we deciphered the driving forces of genetic load in A. thaliana, and incorporated SDM, local adaptation and genetic load to predict the fate of populations under future climate change.},
	language = {en},
	number = {1},
	urldate = {2025-04-04},
	journal = {Nature Communications},
	author = {Jiang, Juan and Chen, Jia-Fu and Li, Xin-Tong and Wang, Li and Mao, Jian-Feng and Wang, Bao-Sheng and Guo, Ya-Long},
	month = mar,
	year = {2025},
	note = {Publisher: Nature Publishing Group},
	keywords = {Conservation biology, Evolutionary genetics, Molecular evolution, Population genetics},
	pages = {2752},
}

Understanding how species respond to climate change can facilitate species conservation and crop breeding. Current prediction frameworks about population vulnerability focused on predicting range shifts or local adaptation but ignored genetic load, which is also crucial for adaptation. By analyzing 1115 globally distributed Arabidopsis thaliana natural accessions, we find that effective population size (Ne) is the major contributor of genetic load variation, both along genome and among populations, and can explain 74-94% genetic load variation in natural populations. Intriguingly, Ne affects genetic load by changing both effectiveness of purifying selection and GC biased gene conversion strength. In particular, by incorporating genetic load, genetic offset and species distribution models (SDM), we predict that, the populations at species’ range edge are generally at higher risk. The populations at the eastern range perform poorer in all aspects, southern range have higher genetic offset and lower SDM suitability, while northern range have higher genetic load. Among the diverse natural populations, the Yangtze River basin population is the most vulnerable population under future climate change. Overall, here we deciphered the driving forces of genetic load in A. thaliana, and incorporated SDM, local adaptation and genetic load to predict the fate of populations under future climate change.

@article{casanova-saez_suitable_2025,
	title = {A suitable strategy to find {IAA} metabolism mutants},
	volume = {177},
	copyright = {© 2025 The Author(s). 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.70166},
	doi = {10.1111/ppl.70166},
	abstract = {Indole-3-acetic acid (IAA), the most common form of auxin, is involved in a great range of plant physiological processes. IAA is synthesized from the amino acid tryptophan and can be transported and inactivated in a myriad of ways. Despite intense research efforts, there are still dark corners in our comprehension of IAA metabolism and its interplays with other pathways. Genetic screens are a powerful tool for unbiasedly looking for new players in a given biological process. However, pleiotropism of auxin-related phenotypes and indirect effects make it necessary to incorporate additional screening steps to specifically find mutants affected in IAA homeostasis. We previously developed and validated a high-throughput methodology to simultaneously quantify IAA, key precursors, and inactive forms from as little as 10 mg of fresh tissue. We have carried out a genetic screening to identify mutants involved in IAA metabolism. Auxin reporters DR5pro:VENUS and 35Spro:DII-VENUS were EMS-mutagenized and subjected to a parallel morphological and reporter-signal pre-screen. We then obtained the auxin metabolite profile of 325 M3 selected lines and used multivariate data analysis to identify potential IAA-metabolism mutants. To test the screening design, we identified the causal mutations in three of the candidate lines by mapping-by-sequencing: dii365.3, dii571.1 and dr693. These carry new alleles of CYP83A1, MIAO, and SUPERROOT2, respectively, all of which have been previously involved in auxin homeostasis. Our results support the suitability of this approach to find new genes involved in IAA metabolism.},
	language = {en},
	number = {2},
	urldate = {2025-04-04},
	journal = {Physiologia Plantarum},
	author = {Casanova-Sáez, Rubén and Pěnčík, Aleš and Muñoz-Viana, Rafael and Brunoni, Federica and Pinto, Rui and Novák, Ondřej and Ljung, Karin and Mateo-Bonmatí, Eduardo},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70166},
	pages = {e70166},
}

Indole-3-acetic acid (IAA), the most common form of auxin, is involved in a great range of plant physiological processes. IAA is synthesized from the amino acid tryptophan and can be transported and inactivated in a myriad of ways. Despite intense research efforts, there are still dark corners in our comprehension of IAA metabolism and its interplays with other pathways. Genetic screens are a powerful tool for unbiasedly looking for new players in a given biological process. However, pleiotropism of auxin-related phenotypes and indirect effects make it necessary to incorporate additional screening steps to specifically find mutants affected in IAA homeostasis. We previously developed and validated a high-throughput methodology to simultaneously quantify IAA, key precursors, and inactive forms from as little as 10 mg of fresh tissue. We have carried out a genetic screening to identify mutants involved in IAA metabolism. Auxin reporters DR5pro:VENUS and 35Spro:DII-VENUS were EMS-mutagenized and subjected to a parallel morphological and reporter-signal pre-screen. We then obtained the auxin metabolite profile of 325 M3 selected lines and used multivariate data analysis to identify potential IAA-metabolism mutants. To test the screening design, we identified the causal mutations in three of the candidate lines by mapping-by-sequencing: dii365.3, dii571.1 and dr693. These carry new alleles of CYP83A1, MIAO, and SUPERROOT2, respectively, all of which have been previously involved in auxin homeostasis. Our results support the suitability of this approach to find new genes involved in IAA metabolism.

@article{wu_population_2025,
	title = {Population genomics of \textit{{Marchantia} polymorpha} subsp. \textit{ruderalis} reveals evidence of climate adaptation},
	volume = {35},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982225000089},
	doi = {10.1016/j.cub.2025.01.008},
	abstract = {Sexual reproduction results in the development of haploid and diploid cell states during the life cycle. In bryophytes, the dominant multicellular haploid phase produces motile sperm that swim through water to the egg to effect fertilization from which a relatively small diploid phase develops. In angiosperms, the reduced multicellular haploid phase produces non-motile sperm that is delivered to the egg through a pollen tube to effect fertilization from which the dominant diploid phase develops. These different life cycle characteristics are likely to impact the distribution of genetic variation among populations. However, little is known about the distribution of genetic variation among wild populations of bryophytes. To investigate how genetic variation is distributed among populations of a bryophyte and to establish the foundation for population genetics research in bryophytes, we described the genetic diversity of collections of Marchantia polymorpha subsp. ruderalis, a cosmopolitan ruderal liverwort. We identified 78 genetically unique (non-clonal) from a total of 209 sequenced accessions collected from 37 sites in Europe and Japan. There was no detectable population structure among European populations but significant genetic differentiation between Japanese and European populations. By associating genetic variation across the genome with global climate data, we showed that temperature and precipitation influence the frequency of potentially adaptive alleles. This collection establishes the core of an experimental platform that exploits natural genetic variation to answer diverse questions in biology.},
	number = {5},
	urldate = {2025-03-28},
	journal = {Current Biology},
	author = {Wu, Shuangyang and Jandrasits, Katharina and Swarts, Kelly and Roetzer, Johannes and Akimcheva, Svetlana and Shimamura, Masaki and Hisanaga, Tetsuya and Berger, Frédéric and Dolan, Liam},
	month = mar,
	year = {2025},
	pages = {970--980.e3},
}

Sexual reproduction results in the development of haploid and diploid cell states during the life cycle. In bryophytes, the dominant multicellular haploid phase produces motile sperm that swim through water to the egg to effect fertilization from which a relatively small diploid phase develops. In angiosperms, the reduced multicellular haploid phase produces non-motile sperm that is delivered to the egg through a pollen tube to effect fertilization from which the dominant diploid phase develops. These different life cycle characteristics are likely to impact the distribution of genetic variation among populations. However, little is known about the distribution of genetic variation among wild populations of bryophytes. To investigate how genetic variation is distributed among populations of a bryophyte and to establish the foundation for population genetics research in bryophytes, we described the genetic diversity of collections of Marchantia polymorpha subsp. ruderalis, a cosmopolitan ruderal liverwort. We identified 78 genetically unique (non-clonal) from a total of 209 sequenced accessions collected from 37 sites in Europe and Japan. There was no detectable population structure among European populations but significant genetic differentiation between Japanese and European populations. By associating genetic variation across the genome with global climate data, we showed that temperature and precipitation influence the frequency of potentially adaptive alleles. This collection establishes the core of an experimental platform that exploits natural genetic variation to answer diverse questions in biology.

@article{ranade_metabolomic_2025,
	title = {Metabolomic profiling of shade response and in silico analysis of {PAL} homologs imply the potential presence of bifunctional ammonia lyases in conifers},
	volume = {177},
	copyright = {© 2025 The Author(s). 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.70175},
	doi = {10.1111/ppl.70175},
	abstract = {Norway spruce and Scots pine show enhanced lignin synthesis under shade, along with differential expression of defense-related genes that render disease resilience. In general, phenylalanine (Phe) is the precursor for lignin synthesis in plants, and tyrosine (Tyr) forms an additional lignin precursor specifically in grasses. Phenylalanine ammonia-lyase (PAL) and tyrosine ammonia-lyase (TAL) from the lignin biosynthesis pathway use either Phe or Tyr as precursors for lignin production, respectively. Grasses possess a bifunctional phenylalanine/tyrosine ammonia-lyase (PTAL) that potentially can use both Phe and Tyr for lignin biosynthesis. Metabolomic profiles of seedlings revealed higher levels of Phe and Tyr under shade in Scots pine, while Norway spruce showed differential regulation of only Tyr under shade. Sequence analysis and phylogeny of PAL homologs in the two conifers, coupled with correlation of up-regulation of precursors for lignin synthesis (Phe/Tyr) and enhanced lignin synthesis along with differential expression of PAL homologs under shade, suggest the potential presence of a bifunctional ammonia-lyases (BAL) in conifers. This finding is novel and comparable to PTALs in grasses. Exome sequence analysis revealed a latitudinal variation in allele frequencies of SNPs from coding regions of putative PAL and BAL in Norway spruce, which may impact enzyme activity affecting lignin synthesis. Metabolomic analysis additionally identified metabolites involved in plant immunity, defense and stress response.},
	language = {en},
	number = {2},
	urldate = {2025-03-28},
	journal = {Physiologia Plantarum},
	author = {Ranade, Sonali Sachin and García-Gil, María Rosario},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70175},
	pages = {e70175},
}

Norway spruce and Scots pine show enhanced lignin synthesis under shade, along with differential expression of defense-related genes that render disease resilience. In general, phenylalanine (Phe) is the precursor for lignin synthesis in plants, and tyrosine (Tyr) forms an additional lignin precursor specifically in grasses. Phenylalanine ammonia-lyase (PAL) and tyrosine ammonia-lyase (TAL) from the lignin biosynthesis pathway use either Phe or Tyr as precursors for lignin production, respectively. Grasses possess a bifunctional phenylalanine/tyrosine ammonia-lyase (PTAL) that potentially can use both Phe and Tyr for lignin biosynthesis. Metabolomic profiles of seedlings revealed higher levels of Phe and Tyr under shade in Scots pine, while Norway spruce showed differential regulation of only Tyr under shade. Sequence analysis and phylogeny of PAL homologs in the two conifers, coupled with correlation of up-regulation of precursors for lignin synthesis (Phe/Tyr) and enhanced lignin synthesis along with differential expression of PAL homologs under shade, suggest the potential presence of a bifunctional ammonia-lyases (BAL) in conifers. This finding is novel and comparable to PTALs in grasses. Exome sequence analysis revealed a latitudinal variation in allele frequencies of SNPs from coding regions of putative PAL and BAL in Norway spruce, which may impact enzyme activity affecting lignin synthesis. Metabolomic analysis additionally identified metabolites involved in plant immunity, defense and stress response.

@article{jonsson_asymmetry_2025,
	title = {The asymmetry engine: how plants harness asymmetries to shape their bodies},
	volume = {245},
	copyright = {© 2025 The Author(s). New Phytologist © 2025 New Phytologist Foundation.},
	issn = {1469-8137},
	shorttitle = {The asymmetry engine},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.20413},
	doi = {10.1111/nph.20413},
	abstract = {Plant development depends on growth asymmetry to establish body plans and adapt to environmental stimuli. We explore how plants initiate, propagate, and regulate organ-wide growth asymmetries. External cues, such as light and gravity, and internal signals, including stochastic cellular growth variability, drive these asymmetries. The plant hormone auxin orchestrates growth asymmetry through its distribution and transport. Mechanochemical feedback loops, exemplified by apical hook formation, further amplify growth asymmetries, illustrating the dynamic interplay between biochemical signals and physical forces. Growth asymmetry itself can serve as a continuous cue, influencing subsequent growth decisions. By examining specific cellular programs and their responses to asymmetric cues, we propose that the decision to either amplify or dampen these asymmetries is key to shaping plant organs.},
	language = {en},
	number = {6},
	urldate = {2025-01-31},
	journal = {New Phytologist},
	author = {Jonsson, Kristoffer and Routier-Kierzkowska, Anne-Lise and Bhalerao, Rishikesh P.},
	month = jan,
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.20413},
	keywords = {auxin, cell wall, development, feedback mechanisms, growth coordination, mechanics, morphogenesis, tropism},
	pages = {2422--2427},
}

Plant development depends on growth asymmetry to establish body plans and adapt to environmental stimuli. We explore how plants initiate, propagate, and regulate organ-wide growth asymmetries. External cues, such as light and gravity, and internal signals, including stochastic cellular growth variability, drive these asymmetries. The plant hormone auxin orchestrates growth asymmetry through its distribution and transport. Mechanochemical feedback loops, exemplified by apical hook formation, further amplify growth asymmetries, illustrating the dynamic interplay between biochemical signals and physical forces. Growth asymmetry itself can serve as a continuous cue, influencing subsequent growth decisions. By examining specific cellular programs and their responses to asymmetric cues, we propose that the decision to either amplify or dampen these asymmetries is key to shaping plant organs.

@article{bhalerao_intercellular_2025,
	title = {Intercellular communication: {Regulation} of plasmodesmata},
	volume = {35},
	issn = {0960-9822},
	shorttitle = {Intercellular communication},
	url = {https://www.cell.com/current-biology/abstract/S0960-9822(24)01642-7},
	doi = {10.1016/j.cub.2024.12.002},
	language = {English},
	number = {4},
	urldate = {2025-02-28},
	journal = {Current Biology},
	author = {Bhalerao, Rishikesh P.},
	month = feb,
	year = {2025},
	pmid = {39999783},
	note = {Publisher: Elsevier},
	pages = {R143--R145},
}

@article{boussardon_atypical_2025,
	title = {The atypical proteome of mitochondria from mature pollen grains},
	volume = {35},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982224017056},
	doi = {10.1016/j.cub.2024.12.037},
	abstract = {To propagate their genetic material, flowering plants rely on the production of large amounts of pollen grains that are capable of germinating on a compatible stigma. Pollen germination and pollen tube growth are thought to be extremely energy-demanding processes. This raises the question of whether mitochondria from pollen grains are specifically tuned to support this developmental process. To address this question, we isolated mitochondria from both mature pollen and floral buds using the isolation of mitochondria tagged in specific cell-type (IMTACT) strategy and examined their respective proteomes. Strikingly, mitochondria from mature pollen grains have lost many proteins required for genome maintenance, gene expression, and translation. Conversely, a significant accumulation of proteins associated with the tricarboxylic acid (TCA) cycle, the electron transport chain (ETC), and Ca2+ homeostasis was observed. This supports the current model in which pollen requires large quantities of ATP for tube growth but also identifies an unexpected depletion of the gene expression machinery, aligned with the fact that the mitochondrial genome is actively degraded during pollen maturation. Altogether, our results uncover that mitochondria from mature pollen grains are strategically prepared for action by increasing their respiratory capacity and dismantling their gene expression machinery, which raises new questions about the assembly of respiratory complexes in pollen mitochondria, as they rely on the integration of proteins coded by the nuclear and mitochondrial genomes. In addition, the approach described here opens a new range of possibilities for studying mitochondria during pollen development and in pollen-specific mitochondrial events.},
	number = {4},
	urldate = {2025-02-28},
	journal = {Current Biology},
	author = {Boussardon, Clément and Simon, Matthieu and Carrie, Chris and Fuszard, Matthew and Meyer, Etienne H. and Budar, Françoise and Keech, Olivier},
	month = feb,
	year = {2025},
	pages = {776--787.e5},
}

To propagate their genetic material, flowering plants rely on the production of large amounts of pollen grains that are capable of germinating on a compatible stigma. Pollen germination and pollen tube growth are thought to be extremely energy-demanding processes. This raises the question of whether mitochondria from pollen grains are specifically tuned to support this developmental process. To address this question, we isolated mitochondria from both mature pollen and floral buds using the isolation of mitochondria tagged in specific cell-type (IMTACT) strategy and examined their respective proteomes. Strikingly, mitochondria from mature pollen grains have lost many proteins required for genome maintenance, gene expression, and translation. Conversely, a significant accumulation of proteins associated with the tricarboxylic acid (TCA) cycle, the electron transport chain (ETC), and Ca2+ homeostasis was observed. This supports the current model in which pollen requires large quantities of ATP for tube growth but also identifies an unexpected depletion of the gene expression machinery, aligned with the fact that the mitochondrial genome is actively degraded during pollen maturation. Altogether, our results uncover that mitochondria from mature pollen grains are strategically prepared for action by increasing their respiratory capacity and dismantling their gene expression machinery, which raises new questions about the assembly of respiratory complexes in pollen mitochondria, as they rely on the integration of proteins coded by the nuclear and mitochondrial genomes. In addition, the approach described here opens a new range of possibilities for studying mitochondria during pollen development and in pollen-specific mitochondrial events.

@article{petri_exploring_2025,
	series = {Special issue: {Microproteins}},
	title = {Exploring the world of small proteins in plant biology and bioengineering},
	volume = {41},
	issn = {0168-9525},
	url = {https://www.sciencedirect.com/science/article/pii/S0168952524002129},
	doi = {10.1016/j.tig.2024.09.004},
	abstract = {Small proteins are ubiquitous in all kingdoms of life. MicroProteins, initially characterized as small proteins with protein interaction domains that enable them to interact with larger multidomain proteins, frequently modulate the function of these proteins. The study of these small proteins has contributed to a greater comprehension of protein regulation. In addition to sequence homology, sequence-divergent small proteins have the potential to function as microProtein mimics, binding to structurally related proteins. Moreover, a multitude of other small proteins encoded by short open reading frames (sORFs) and peptides, derived from diverse sources such as long noncoding RNAs (lncRNAs) and miRNAs, contribute to a variety of biological processes. The potential of small proteins is evident, offering promising avenues for bioengineering that could revolutionize crop performance and reduce reliance on agrochemicals in future agriculture.},
	number = {2},
	urldate = {2025-02-28},
	journal = {Trends in Genetics},
	author = {Petri, Louise and Van Humbeeck, Anne and Niu, Huanying and Ter Waarbeek, Casper and Edwards, Ashleigh and Chiurazzi, Maurizio Junior and Vittozzi, Ylenia and Wenkel, Stephan},
	month = feb,
	year = {2025},
	keywords = {lncRNA, microProteins, sORFs, transcription factor},
	pages = {170--180},
}

Small proteins are ubiquitous in all kingdoms of life. MicroProteins, initially characterized as small proteins with protein interaction domains that enable them to interact with larger multidomain proteins, frequently modulate the function of these proteins. The study of these small proteins has contributed to a greater comprehension of protein regulation. In addition to sequence homology, sequence-divergent small proteins have the potential to function as microProtein mimics, binding to structurally related proteins. Moreover, a multitude of other small proteins encoded by short open reading frames (sORFs) and peptides, derived from diverse sources such as long noncoding RNAs (lncRNAs) and miRNAs, contribute to a variety of biological processes. The potential of small proteins is evident, offering promising avenues for bioengineering that could revolutionize crop performance and reduce reliance on agrochemicals in future agriculture.

@article{street_data-driven_2025,
	title = {Data-driven resources and computational tools in non-model plant species},
	volume = {177},
	copyright = {© 2025 Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70133},
	doi = {10.1111/ppl.70133},
	language = {en},
	number = {1},
	urldate = {2025-02-28},
	journal = {Physiologia Plantarum},
	author = {Street, Nathaniel R.},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70133},
	pages = {e70133},
}

@article{hogberg_improved_2025,
	title = {Improved methodology for tracing a pulse of {13C}-labelled tree photosynthate carbon to ectomycorrhizal roots, other soil biota and soil processes in the field},
	volume = {45},
	issn = {1758-4469},
	url = {https://doi.org/10.1093/treephys/tpae169},
	doi = {10.1093/treephys/tpae169},
	abstract = {Isotopic pulse-labelling of photosynthate allows tracing of carbon (C) from tree canopies to below-ground biota and calculations of its turnover in roots and recipient soil microorganisms. A high concentration of label is desirable but is difficult to achieve in field studies of intact ecosystem patches with trees. Moreover, root systems of trees overlap considerably in most forests, which requires a large labelled area to minimize the impact of C allocated below-ground by un-labelled trees. We describe a method which combines a high level of labelling at ambient concentrations of CO2, [CO2], with undisturbed root systems and a model to account for root C and root-derived C from un-labelled trees. We raised 5-m-tall chambers, each covering 50 m2 of ground (volume 250 m3) in a young boreal Pinus sylvestris L. forest with up to 5 m tall trees. Rather than a conventional single release of 13CO2, we used five consecutive releases, each followed by a draw-down period, thus avoiding high [CO2]. Hence, we elevated successively the 13CO2 from 1.1 to 23 atom\% after the first release to 61 atom\% after the fifth, while maintaining [CO2] below 500 p.p.m. during 4–4.5 h of labelling. The average abundance of 13CO2 was as high as 42 atom\%. We used the central 10 m2 of the 50 m2 area for sampling of roots and other soil biota. We modelled the dilution of labelled C across the plots by un-labelled C from roots of trees outside the area. In the central 10 m2 area, {\textasciitilde}85\% of roots and root-associated biota received C from labelled trees. In summary, we elevated the labelling of roots and associated soil biota four-fold compared with previous studies and described the commonly overlooked impact of roots from un-labelled trees outside the labelled area.},
	number = {1},
	urldate = {2025-02-21},
	journal = {Tree Physiology},
	author = {Högberg, Peter and Klatt, Christian and Franklin, Oskar and Henriksson, Nils and Lim, Hyungwoo and Inselsbacher, Erich and Hurry, Vaughan and Näsholm, Torgny and Högberg, Mona N},
	month = jan,
	year = {2025},
	pages = {tpae169},
}

Isotopic pulse-labelling of photosynthate allows tracing of carbon (C) from tree canopies to below-ground biota and calculations of its turnover in roots and recipient soil microorganisms. A high concentration of label is desirable but is difficult to achieve in field studies of intact ecosystem patches with trees. Moreover, root systems of trees overlap considerably in most forests, which requires a large labelled area to minimize the impact of C allocated below-ground by un-labelled trees. We describe a method which combines a high level of labelling at ambient concentrations of CO2, [CO2], with undisturbed root systems and a model to account for root C and root-derived C from un-labelled trees. We raised 5-m-tall chambers, each covering 50 m2 of ground (volume 250 m3) in a young boreal Pinus sylvestris L. forest with up to 5 m tall trees. Rather than a conventional single release of 13CO2, we used five consecutive releases, each followed by a draw-down period, thus avoiding high [CO2]. Hence, we elevated successively the 13CO2 from 1.1 to 23 atom% after the first release to 61 atom% after the fifth, while maintaining [CO2] below 500 p.p.m. during 4–4.5 h of labelling. The average abundance of 13CO2 was as high as 42 atom%. We used the central 10 m2 of the 50 m2 area for sampling of roots and other soil biota. We modelled the dilution of labelled C across the plots by un-labelled C from roots of trees outside the area. In the central 10 m2 area, ~85% of roots and root-associated biota received C from labelled trees. In summary, we elevated the labelling of roots and associated soil biota four-fold compared with previous studies and described the commonly overlooked impact of roots from un-labelled trees outside the labelled area.

@article{kokla_long-distance_2025,
	title = {A long-distance inhibitory system regulates haustoria numbers in parasitic plants},
	volume = {122},
	url = {https://www.pnas.org/doi/10.1073/pnas.2424557122},
	doi = {10.1073/pnas.2424557122},
	abstract = {The ability of parasitic plants to withdraw nutrients from their hosts depends on the formation of an infective structure known as the haustorium. How parasites regulate their haustoria numbers is poorly understood, and here, we uncovered that existing haustoria in the facultative parasitic plants Phtheirospermum japonicum and Parentucellia viscosa suppressed the formation of new haustoria located on distant roots. Using Phtheirospermum, we found that this effect depended on the formation of mature haustoria and could be induced through the application of external nutrients. To understand the molecular basis of this root plasticity, we analyzed hormone response and found that existing infections upregulated cytokinin-responsive genes first at the haustoria and then more distantly in Phtheirospermum shoots. We observed that infections increased endogenous cytokinin levels in Phtheirospermum roots and shoots, and this increase appeared relevant since local treatments with exogenous cytokinins blocked the formation of both locally and distantly formed haustoria. In addition, local overexpression of a cytokinin-degrading enzyme in Phtheirospermum prevented this systemic interhaustoria repression and increased haustoria numbers locally. We propose that a long-distance signal produced by haustoria negatively regulates future haustoria, and in Phtheirospermum, such a signaling system is mediated by a local increase in cytokinin to regulate haustoria numbers and balance nutrient acquisition.},
	number = {8},
	urldate = {2025-02-21},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Kokla, Anna and Leso, Martina and Šimura, Jan and Wärdig, Cecilia and Hayashi, Marina and Nishii, Naoshi and Tsuchiya, Yuichiro and Ljung, Karin and Melnyk, Charles W.},
	month = feb,
	year = {2025},
	note = {Publisher: Proceedings of the National Academy of Sciences},
	pages = {e2424557122},
}

The ability of parasitic plants to withdraw nutrients from their hosts depends on the formation of an infective structure known as the haustorium. How parasites regulate their haustoria numbers is poorly understood, and here, we uncovered that existing haustoria in the facultative parasitic plants Phtheirospermum japonicum and Parentucellia viscosa suppressed the formation of new haustoria located on distant roots. Using Phtheirospermum, we found that this effect depended on the formation of mature haustoria and could be induced through the application of external nutrients. To understand the molecular basis of this root plasticity, we analyzed hormone response and found that existing infections upregulated cytokinin-responsive genes first at the haustoria and then more distantly in Phtheirospermum shoots. We observed that infections increased endogenous cytokinin levels in Phtheirospermum roots and shoots, and this increase appeared relevant since local treatments with exogenous cytokinins blocked the formation of both locally and distantly formed haustoria. In addition, local overexpression of a cytokinin-degrading enzyme in Phtheirospermum prevented this systemic interhaustoria repression and increased haustoria numbers locally. We propose that a long-distance signal produced by haustoria negatively regulates future haustoria, and in Phtheirospermum, such a signaling system is mediated by a local increase in cytokinin to regulate haustoria numbers and balance nutrient acquisition.

@article{jewaria_reduced_2025,
	title = {Reduced {RG}-{II} pectin dimerization disrupts differential growth by attenuating hormonal regulation},
	volume = {11},
	url = {https://www.science.org/doi/10.1126/sciadv.ads0760},
	doi = {10.1126/sciadv.ads0760},
	abstract = {Defects in cell wall integrity (CWI) profoundly affect plant growth, although, underlying mechanisms are not well understood. We show that in Arabidopsis mur1 mutant, CWI defects from compromising dimerization of RG-II pectin, a key component of cell wall, attenuate the expression of auxin response factors ARF7-ARF19. As a result, polar auxin transport components are misexpressed, disrupting auxin response asymmetry, leading to defective apical hook development. Accordingly, mur1 hook defects are suppressed by enhancing ARF7 expression. In addition, expression of brassinosteroid biosynthesis genes is down-regulated in mur1 mutant, and supplementing brassinosteroid or enhancing brassinosteroid signaling suppresses mur1 hook defects. Intriguingly, brassinosteroid enhances RG-II dimerization, showing hormonal feedback to the cell wall. Our results thus reveal a previously unrecognized link between cell wall defects from reduced RG-II dimerization and growth regulation mediated via modulation of auxin-brassinosteroid pathways in early seedling development.},
	number = {7},
	urldate = {2025-02-20},
	journal = {Science Advances},
	author = {Jewaria, Pawan Kumar and Aryal, Bibek and Begum, Rifat Ara and Wang, Yaowei and Sancho-Andrés, Gloria and Baba, Abu Imran and Yu, Meng and Li, Xiaojuan and Lin, Jinxing and Fry, Stephen C. and Verger, Stephane and Russinova, Eugenia and Jonsson, Kristoffer and Bhalerao, Rishikesh P.},
	month = feb,
	year = {2025},
	note = {Publisher: American Association for the Advancement of Science},
	pages = {eads0760},
}

Defects in cell wall integrity (CWI) profoundly affect plant growth, although, underlying mechanisms are not well understood. We show that in Arabidopsis mur1 mutant, CWI defects from compromising dimerization of RG-II pectin, a key component of cell wall, attenuate the expression of auxin response factors ARF7-ARF19. As a result, polar auxin transport components are misexpressed, disrupting auxin response asymmetry, leading to defective apical hook development. Accordingly, mur1 hook defects are suppressed by enhancing ARF7 expression. In addition, expression of brassinosteroid biosynthesis genes is down-regulated in mur1 mutant, and supplementing brassinosteroid or enhancing brassinosteroid signaling suppresses mur1 hook defects. Intriguingly, brassinosteroid enhances RG-II dimerization, showing hormonal feedback to the cell wall. Our results thus reveal a previously unrecognized link between cell wall defects from reduced RG-II dimerization and growth regulation mediated via modulation of auxin-brassinosteroid pathways in early seedling development.

@article{jeong_spectral_2025,
	title = {Spectral unmixing of hyperspectral images revealed pine wilt disease sensitive endmembers},
	volume = {177},
	copyright = {© 2025 Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70090},
	doi = {10.1111/ppl.70090},
	abstract = {Throughout the entire cycle of leaf phenological events, leaf colour undergoes changes that are influenced by either abiotic stress or biotic infection. These changes in colouration are closely linked to the quantity and quality of photosynthetic pigments, which directly impact the primary productivity of plants. Therefore, monitoring and quantifying leaf colouration changes are crucial for distinguishing damage caused by pine wilt nematodes from natural tree senescence. In this study, a hyperspectral camera sensor was employed for the non-invasive and non-destructive evaluation of needle colour changes in coniferous trees grown in field tests. Three distinct needle colour variations of six coniferous tree species were selected and monitored using a hyperspectral sensor: those displaying seasonal autumn colours, undergoing nematode-infected necrosis processes, and experiencing natural death. To mitigate the inherently mixed spectral properties of hyperspectral data, endmembers were extracted from individual images using the Purity Pixel Index algorithm under the assumption of linear mixing of endmembers. From a total of 1,321 endmembers extracted from 378 hyperspectral images of six pine species, eight endmembers were ultimately chosen to reconstruct hyperspectral images and generate abundance maps. Among these eight endmembers, four represent varying levels of photosynthetic pigment contents—ranging from very low to high. Consequently, these coniferous endmembers hold promise for assessing seasonal leaf phenology and the extent of damage in pine trees infected by pine wilt nematodes. This comprehensive approach underscores the effectiveness of spectral unmixing of hyperspectral images in advancing precision forestry through meticulous coniferous needle trait analysis.},
	language = {en},
	number = {1},
	urldate = {2025-02-07},
	journal = {Physiologia Plantarum},
	author = {Jeong, Seok Won and Lee, Il Hwan and Kim, Yang-Gil and Kang, Kyu-Suk and Shim, Donghwan and Hurry, Vaughan and Ivanov, Alexander G. and Park, Youn-Il},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70090},
	pages = {e70090},
}

Throughout the entire cycle of leaf phenological events, leaf colour undergoes changes that are influenced by either abiotic stress or biotic infection. These changes in colouration are closely linked to the quantity and quality of photosynthetic pigments, which directly impact the primary productivity of plants. Therefore, monitoring and quantifying leaf colouration changes are crucial for distinguishing damage caused by pine wilt nematodes from natural tree senescence. In this study, a hyperspectral camera sensor was employed for the non-invasive and non-destructive evaluation of needle colour changes in coniferous trees grown in field tests. Three distinct needle colour variations of six coniferous tree species were selected and monitored using a hyperspectral sensor: those displaying seasonal autumn colours, undergoing nematode-infected necrosis processes, and experiencing natural death. To mitigate the inherently mixed spectral properties of hyperspectral data, endmembers were extracted from individual images using the Purity Pixel Index algorithm under the assumption of linear mixing of endmembers. From a total of 1,321 endmembers extracted from 378 hyperspectral images of six pine species, eight endmembers were ultimately chosen to reconstruct hyperspectral images and generate abundance maps. Among these eight endmembers, four represent varying levels of photosynthetic pigment contents—ranging from very low to high. Consequently, these coniferous endmembers hold promise for assessing seasonal leaf phenology and the extent of damage in pine trees infected by pine wilt nematodes. This comprehensive approach underscores the effectiveness of spectral unmixing of hyperspectral images in advancing precision forestry through meticulous coniferous needle trait analysis.

@article{ding_insights_2025,
	title = {Insights into \textit{{PeERF168}} gene in slash pine terpene biosynthesis: {Integrating} high-throughput phenotyping, {GWAS}, and transgenic studies},
	volume = {300},
	issn = {0141-8130},
	shorttitle = {Insights into \textit{{PeERF168}} gene in slash pine terpene biosynthesis},
	url = {https://www.sciencedirect.com/science/article/pii/S0141813025002776},
	doi = {10.1016/j.ijbiomac.2025.139728},
	abstract = {Resin biosynthesis in conifer is a complex process, controlled by multiple quantitative trait loci (QTLs). Quantifying resin components is traditionally expensive and labor-intensive. In this study, we employed near infrared (NIR) spectroscopy to quantify resin components in Slash pine using 240 genotypes. A partial least squares regression model was applied to identify the characteristic bands responsed to variations in Alpha and Beta pinene levels. Genome-wide association study (GWAS) identified 35 significant SNPs involved in terpenoid precursor biosynthesis, transport, modification, and abiotic stress resistance. eQTL mapping co-localized four candidate genes: PeCHITINASE (c166891.graph\_c0), PeGLYCOSYLTRANSFERASE (c160167.graph\_c0), PeASIL2 (c324347.graph\_c0), and PeERF168 (c311225.graph\_c0). Mutations in two SNPs increased the expression of PeASIL2 and PeERF168, leading to higher levels of Alpha and Beta pinene. Further heterologous transformation experiments confirmed that the PeERF168 gene regulates the concentration of both monoterpenes and sesquiterpenes. These findings provide valuable insights into the molecular mechanisms of resin biosynthesis, facilitating cost-effective gene discovery through high-throughput resin component detection and genomics integration, with substantial potential to enhance molecular breeding and improve resin yield and quality.},
	urldate = {2025-01-31},
	journal = {International Journal of Biological Macromolecules},
	author = {Ding, Xianyin and Diao, Shu and Zhang, Yini and Luan, Qifu and Li, Yanjie and Jiang, Jingmin and Wu, Harry X.},
	month = apr,
	year = {2025},
	keywords = {GWAS, High-throughput phenotyping, Slash pine, Terpene biosynthesis, eQTL mapping},
	pages = {139728},
}

Resin biosynthesis in conifer is a complex process, controlled by multiple quantitative trait loci (QTLs). Quantifying resin components is traditionally expensive and labor-intensive. In this study, we employed near infrared (NIR) spectroscopy to quantify resin components in Slash pine using 240 genotypes. A partial least squares regression model was applied to identify the characteristic bands responsed to variations in Alpha and Beta pinene levels. Genome-wide association study (GWAS) identified 35 significant SNPs involved in terpenoid precursor biosynthesis, transport, modification, and abiotic stress resistance. eQTL mapping co-localized four candidate genes: PeCHITINASE (c166891.graph_c0), PeGLYCOSYLTRANSFERASE (c160167.graph_c0), PeASIL2 (c324347.graph_c0), and PeERF168 (c311225.graph_c0). Mutations in two SNPs increased the expression of PeASIL2 and PeERF168, leading to higher levels of Alpha and Beta pinene. Further heterologous transformation experiments confirmed that the PeERF168 gene regulates the concentration of both monoterpenes and sesquiterpenes. These findings provide valuable insights into the molecular mechanisms of resin biosynthesis, facilitating cost-effective gene discovery through high-throughput resin component detection and genomics integration, with substantial potential to enhance molecular breeding and improve resin yield and quality.

@article{baral_typhon_2025,
	title = {{TYPHON} proteins are {RAB}-dependent mediators of the trans-{Golgi} network secretory pathway},
	volume = {37},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koae280},
	doi = {10.1093/plcell/koae280},
	abstract = {The trans-Golgi network (TGN), a key compartment in endomembrane trafficking, participates in both secretion to and endocytosis from the plasma membrane. Consequently, the TGN plays a key role in plant growth and development. Understanding how proteins are sorted for secretion or endocytic recycling at the TGN is critical for elucidating mechanisms of plant development. We previously showed that the protein ECHIDNA is essential for phytohormonal control of hypocotyl bending because it mediates secretion of cell wall components and the auxin influx carrier AUXIN RESISTANT 1 (AUX1) from the TGN. Despite the critical role of ECHIDNA in TGN-mediated trafficking, its mode of action remains unknown in Arabidopsis (Arabidopsis thaliana). We therefore performed a suppressor screen on the ech mutant. Here, we report the identification of TGN-localized TYPHON 1 (TPN1) and TPN2 proteins. A single amino acid change in either TPN protein causes dominant suppression of the ech mutant's defects in growth and AUX1 secretion, while also restoring wild-type (WT)-like ethylene-responsive hypocotyl bending. Importantly, genetic and cell biological evidence shows that TPN1 acts through RAS-ASSOCIATED BINDING H1b (RABH1b), a TGN-localized RAB-GTPase. These results provide insights into ECHIDNA-mediated secretory trafficking of cell wall and auxin carriers at the TGN, as well as its role in controlling plant growth.},
	number = {1},
	urldate = {2025-01-20},
	journal = {The Plant Cell},
	author = {Baral, Anirban and Gendre, Delphine and Aryal, Bibek and Fougère, Louise and Di Fino, Luciano Martin and Ohori, Chihiro and Sztojka, Bernadette and Uemura, Tomohiro and Ueda, Takashi and Marhavý, Peter and Boutté, Yohann and Bhalerao, Rishikesh P},
	month = jan,
	year = {2025},
	pages = {koae280},
}

The trans-Golgi network (TGN), a key compartment in endomembrane trafficking, participates in both secretion to and endocytosis from the plasma membrane. Consequently, the TGN plays a key role in plant growth and development. Understanding how proteins are sorted for secretion or endocytic recycling at the TGN is critical for elucidating mechanisms of plant development. We previously showed that the protein ECHIDNA is essential for phytohormonal control of hypocotyl bending because it mediates secretion of cell wall components and the auxin influx carrier AUXIN RESISTANT 1 (AUX1) from the TGN. Despite the critical role of ECHIDNA in TGN-mediated trafficking, its mode of action remains unknown in Arabidopsis (Arabidopsis thaliana). We therefore performed a suppressor screen on the ech mutant. Here, we report the identification of TGN-localized TYPHON 1 (TPN1) and TPN2 proteins. A single amino acid change in either TPN protein causes dominant suppression of the ech mutant's defects in growth and AUX1 secretion, while also restoring wild-type (WT)-like ethylene-responsive hypocotyl bending. Importantly, genetic and cell biological evidence shows that TPN1 acts through RAS-ASSOCIATED BINDING H1b (RABH1b), a TGN-localized RAB-GTPase. These results provide insights into ECHIDNA-mediated secretory trafficking of cell wall and auxin carriers at the TGN, as well as its role in controlling plant growth.

@article{wieloch_new_2025,
	title = {New insights into the mechanisms of plant isotope fractionation from combined analysis of intramolecular {13C} and deuterium abundances in {Pinus} nigra tree-ring glucose},
	volume = {245},
	copyright = {© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.20113},
	doi = {10.1111/nph.20113},
	abstract = {Understanding isotope fractionation mechanisms is fundamental for analyses of plant ecophysiology and paleoclimate based on tree-ring isotope data. To gain new insights into isotope fractionation, we analysed intramolecular 13C discrimination in tree-ring glucose (Δi′, i = C-1 to C-6) and metabolic deuterium fractionation at H1 and H2 (εmet) combinedly. This dual-isotope approach was used for isotope-signal deconvolution. We found evidence for metabolic processes affecting Δ1′ and Δ3′, which respond to air vapour pressure deficit (VPD), and processes affecting Δ1′, Δ2′, and εmet, which respond to precipitation but not VPD. These relationships exhibit change points dividing a period of homeostasis (1961–1980) from a period of metabolic adjustment (1983–1995). Homeostasis may result from sufficient groundwater availability. Additionally, we found Δ5′ and Δ6′ relationships with radiation and temperature, which are temporally stable and consistent with previously proposed isotope fractionation mechanisms. Based on the multitude of climate covariables, intramolecular carbon isotope analysis has a remarkable potential for climate reconstruction. While isotope fractionation beyond leaves is currently considered to be constant, we propose significant parts of the carbon and hydrogen isotope variation in tree-ring glucose originate in stems (precipitation-dependent signals). As basis for follow-up studies, we propose mechanisms introducing Δ1′, Δ2′, Δ3′, and εmet variability.},
	language = {en},
	number = {3},
	urldate = {2025-01-10},
	journal = {New Phytologist},
	author = {Wieloch, Thomas and Holloway-Phillips, Meisha and Yu, Jun and Niittylä, Totte},
	month = feb,
	year = {2025},
	keywords = {carbon stable isotopes, hydrogen stable isotopes, intramolecular isotope analysis, isotope fractionation mechanisms, leaf water status, plant–environment interactions, stem water status, tree rings},
	pages = {1000--1017},
}

Understanding isotope fractionation mechanisms is fundamental for analyses of plant ecophysiology and paleoclimate based on tree-ring isotope data. To gain new insights into isotope fractionation, we analysed intramolecular 13C discrimination in tree-ring glucose (Δi′, i = C-1 to C-6) and metabolic deuterium fractionation at H1 and H2 (εmet) combinedly. This dual-isotope approach was used for isotope-signal deconvolution. We found evidence for metabolic processes affecting Δ1′ and Δ3′, which respond to air vapour pressure deficit (VPD), and processes affecting Δ1′, Δ2′, and εmet, which respond to precipitation but not VPD. These relationships exhibit change points dividing a period of homeostasis (1961–1980) from a period of metabolic adjustment (1983–1995). Homeostasis may result from sufficient groundwater availability. Additionally, we found Δ5′ and Δ6′ relationships with radiation and temperature, which are temporally stable and consistent with previously proposed isotope fractionation mechanisms. Based on the multitude of climate covariables, intramolecular carbon isotope analysis has a remarkable potential for climate reconstruction. While isotope fractionation beyond leaves is currently considered to be constant, we propose significant parts of the carbon and hydrogen isotope variation in tree-ring glucose originate in stems (precipitation-dependent signals). As basis for follow-up studies, we propose mechanisms introducing Δ1′, Δ2′, Δ3′, and εmet variability.

@article{sivan_modification_2025,
	title = {Modification of xylan in secondary walls alters cell wall biosynthesis and wood formation programs and improves saccharification},
	volume = {23},
	copyright = {© 2024 The Author(s). Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley \& Sons Ltd.},
	issn = {1467-7652},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.14487},
	doi = {10.1111/pbi.14487},
	abstract = {Wood of broad-leaf tree species is a valued source of renewable biomass for biorefinery and a target for genetic improvement efforts to reduce its recalcitrance. Glucuronoxylan (GX) plays a key role in recalcitrance through its interactions with cellulose and lignin. To reduce recalcitrance, we modified wood GX by expressing GH10 and GH11 endoxylanases from Aspergillus nidulans in hybrid aspen (Populus tremula L. × tremuloides Michx.) and targeting the enzymes to cell wall. The xylanases reduced tree height, modified cambial activity by increasing phloem and reducing xylem production, and reduced secondary wall deposition. Xylan molecular weight was decreased, and the spacing between acetyl and MeGlcA side chains was reduced in transgenic lines. The transgenic trees produced hypolignified xylem having thin secondary walls and deformed vessels. Glucose yields of enzymatic saccharification without pretreatment almost doubled indicating decreased recalcitrance. The transcriptomics, hormonomics and metabolomics data provided evidence for activation of cytokinin and ethylene signalling pathways, decrease in ABA levels, transcriptional suppression of lignification and a subset of secondary wall biosynthetic program, including xylan glucuronidation and acetylation machinery. Several candidate genes for perception of impairment in xylan integrity were detected. These candidates could provide a new target for uncoupling negative growth effects from reduced recalcitrance. In conclusion, our study supports the hypothesis that xylan modification generates intrinsic signals and evokes novel pathways regulating tree growth and secondary wall biosynthesis.},
	language = {en},
	number = {1},
	urldate = {2024-10-25},
	journal = {Plant Biotechnology Journal},
	author = {Sivan, Pramod and Urbancsok, János and Donev, Evgeniy N. and Derba-Maceluch, Marta and Barbut, Félix R. and Yassin, Zakiya and Gandla, Madhavi L. and Mitra, Madhusree and Heinonen, Saara E. and Šimura, Jan and Cermanová, Kateřina and Karady, Michal and Scheepers, Gerhard and Jönsson, Leif J. and Master, Emma R. and Vilaplana, Francisco and Mellerowicz, Ewa J.},
	month = jan,
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.14487},
	keywords = {Glucuronoxylan, fungal xylanases, lignocellulose, secondary cell wall, transgenic aspen, wood development},
	pages = {174--197},
}

Wood of broad-leaf tree species is a valued source of renewable biomass for biorefinery and a target for genetic improvement efforts to reduce its recalcitrance. Glucuronoxylan (GX) plays a key role in recalcitrance through its interactions with cellulose and lignin. To reduce recalcitrance, we modified wood GX by expressing GH10 and GH11 endoxylanases from Aspergillus nidulans in hybrid aspen (Populus tremula L. × tremuloides Michx.) and targeting the enzymes to cell wall. The xylanases reduced tree height, modified cambial activity by increasing phloem and reducing xylem production, and reduced secondary wall deposition. Xylan molecular weight was decreased, and the spacing between acetyl and MeGlcA side chains was reduced in transgenic lines. The transgenic trees produced hypolignified xylem having thin secondary walls and deformed vessels. Glucose yields of enzymatic saccharification without pretreatment almost doubled indicating decreased recalcitrance. The transcriptomics, hormonomics and metabolomics data provided evidence for activation of cytokinin and ethylene signalling pathways, decrease in ABA levels, transcriptional suppression of lignification and a subset of secondary wall biosynthetic program, including xylan glucuronidation and acetylation machinery. Several candidate genes for perception of impairment in xylan integrity were detected. These candidates could provide a new target for uncoupling negative growth effects from reduced recalcitrance. In conclusion, our study supports the hypothesis that xylan modification generates intrinsic signals and evokes novel pathways regulating tree growth and secondary wall biosynthesis.

@article{wieloch_shining_2025,
	title = {Shining a new light on the classical concepts of carbon-isotope dendrochronology},
	volume = {245},
	copyright = {© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.20258},
	doi = {10.1111/nph.20258},
	abstract = {Retrospective information about plant ecophysiology and the climate system are key inputs in Earth system and vegetation models. Dendrochronology provides such information with large spatiotemporal coverage, and carbon-isotope analysis across tree-ring series is among the most advanced dendrochronological tools. For the past 70 years, this analysis was performed on whole molecules and, to this day, 13C discrimination during carbon assimilation is invoked to explain isotope variation and associated climate signals. However, recently it was reported that tree-ring glucose exhibits multiple isotope signals at the intramolecular level (see Wieloch et al., 2025). Here, I estimated the signals' contribution to whole-molecule isotope variation and found that downstream processes in leaf and stem metabolism each introduce more variation than carbon assimilation. Moreover, downstream processes introduce most of the climate information. These findings are inconsistent with the classical concepts/practices of carbon-isotope dendrochronology. More importantly, intramolecular tree-ring isotope analysis promises novel insights into forest metabolism and the climate of the past.},
	language = {en},
	number = {3},
	urldate = {2025-01-10},
	journal = {New Phytologist},
	author = {Wieloch, Thomas},
	month = feb,
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.20258},
	keywords = {carbon stable isotopes, dendrochronology, intramolecular isotope analysis, paleoclimate reconstruction, plant carbon fluxes, tree rings, water-use efficiency, whole-molecule isotope analysis},
	pages = {939--944},
}

Retrospective information about plant ecophysiology and the climate system are key inputs in Earth system and vegetation models. Dendrochronology provides such information with large spatiotemporal coverage, and carbon-isotope analysis across tree-ring series is among the most advanced dendrochronological tools. For the past 70 years, this analysis was performed on whole molecules and, to this day, 13C discrimination during carbon assimilation is invoked to explain isotope variation and associated climate signals. However, recently it was reported that tree-ring glucose exhibits multiple isotope signals at the intramolecular level (see Wieloch et al., 2025). Here, I estimated the signals' contribution to whole-molecule isotope variation and found that downstream processes in leaf and stem metabolism each introduce more variation than carbon assimilation. Moreover, downstream processes introduce most of the climate information. These findings are inconsistent with the classical concepts/practices of carbon-isotope dendrochronology. More importantly, intramolecular tree-ring isotope analysis promises novel insights into forest metabolism and the climate of the past.

@article{renzi_epigenetic_2025,
	title = {Epigenetic suppression of creatine kinase {B} in adipocytes links endoplasmic reticulum stress to obesity-associated inflammation},
	volume = {92},
	issn = {2212-8778},
	url = {https://www.sciencedirect.com/science/article/pii/S2212877824002138},
	doi = {10.1016/j.molmet.2024.102082},
	abstract = {In white adipose tissue, disturbed creatine metabolism through reduced creatine kinase B (CKB) transcription contributes to obesity-related inflammation. However, the mechanisms regulating CKB expression in human white adipocytes remain unclear. By screening conditions perturbed in obesity, we identified endoplasmic reticulum (ER) stress as a key suppressor of CKB transcription across multiple cell types. Through follow-up studies, we found that ER stress through the IRE1–XBP1s pathway, promotes CKB promoter methylation via the methyltransferase DNMT3A. This epigenetic change represses CKB transcription, shifting metabolism towards glycolysis and increasing the production of the pro-inflammatory chemokine CCL2. We validated our findings in vivo, demonstrating that individuals living with obesity show an inverse relationship between CKB expression and promoter methylation in white adipocytes, along with elevated CCL2 secretion. Overall, our study uncovers a regulatory axis where ER stress drives inflammation in obesity by reducing CKB abundance, and consequently altering the bioenergetic state of the cell.},
	urldate = {2025-01-10},
	journal = {Molecular Metabolism},
	author = {Renzi, Gianluca and Vlassakev, Ivan and Hansen, Mattias and Higos, Romane and Lecoutre, Simon and Elmastas, Merve and Hodek, Ondrej and Moritz, Thomas and Alaeddine, Lynn M. and Frendo–Cumbo, Scott and Dahlman, Ingrid and Kerr, Alastair and Maqdasy, Salwan and Mejhert, Niklas and Rydén, Mikael},
	month = feb,
	year = {2025},
	keywords = {Chromatin remodeling, Creatine pathway, Glycolysis, Immunometabolism, Tunicamycin},
	pages = {102082},
}

In white adipose tissue, disturbed creatine metabolism through reduced creatine kinase B (CKB) transcription contributes to obesity-related inflammation. However, the mechanisms regulating CKB expression in human white adipocytes remain unclear. By screening conditions perturbed in obesity, we identified endoplasmic reticulum (ER) stress as a key suppressor of CKB transcription across multiple cell types. Through follow-up studies, we found that ER stress through the IRE1–XBP1s pathway, promotes CKB promoter methylation via the methyltransferase DNMT3A. This epigenetic change represses CKB transcription, shifting metabolism towards glycolysis and increasing the production of the pro-inflammatory chemokine CCL2. We validated our findings in vivo, demonstrating that individuals living with obesity show an inverse relationship between CKB expression and promoter methylation in white adipocytes, along with elevated CCL2 secretion. Overall, our study uncovers a regulatory axis where ER stress drives inflammation in obesity by reducing CKB abundance, and consequently altering the bioenergetic state of the cell.

@article{farci_characterization_2025,
	title = {Characterization of {SARS}-{CoV}-2 nucleocapsid protein oligomers},
	volume = {217},
	issn = {1047-8477},
	url = {https://www.sciencedirect.com/science/article/pii/S1047847724001023},
	doi = {10.1016/j.jsb.2024.108162},
	abstract = {Oligomers of the SARS-CoV-2 nucleocapsid (N) protein are characterized by pronounced instability resulting in fast degradation. This property likely relates to two contrasting behaviors of the N protein: genome stabilization through a compact nucleocapsid during cell evasion and genome release by nucleocapsid disassembling during infection. In vivo, the N protein forms rounded complexes of high molecular mass from its interaction with the viral genome. To study the N protein and understand its instability, we analyzed degradation profiles under different conditions by size-exclusion chromatography and characterized samples by mass spectrometry and cryo-electron microscopy. We identified self-cleavage properties of the N protein based on specific Proprotein convertases activities, with Cl- playing a key role in modulating stability and degradation. These findings allowed isolation of a stable oligomeric complex of N, for which we report the 3D structure at ∼6.8 Å resolution. Findings are discussed considering available knowledge about the coronaviruses’ infection cycle.},
	number = {1},
	urldate = {2025-01-10},
	journal = {Journal of Structural Biology},
	author = {Farci, Domenica and Graça, André T. and Hall, Michael and Haniewicz, Patrycja and Kereïche, Sami and Faull, Peter and Kirkpatrick, Joanna and Tramontano, Enzo and Schröder, Wolfgang P. and Piano, Dario},
	month = mar,
	year = {2025},
	keywords = {Covid-19, Cryo-electron microscopy, Furin, Nucleocapsid protein, Proprotein convertases, SARS-CoV-2, Self-cleavage},
	pages = {108162},
}

Oligomers of the SARS-CoV-2 nucleocapsid (N) protein are characterized by pronounced instability resulting in fast degradation. This property likely relates to two contrasting behaviors of the N protein: genome stabilization through a compact nucleocapsid during cell evasion and genome release by nucleocapsid disassembling during infection. In vivo, the N protein forms rounded complexes of high molecular mass from its interaction with the viral genome. To study the N protein and understand its instability, we analyzed degradation profiles under different conditions by size-exclusion chromatography and characterized samples by mass spectrometry and cryo-electron microscopy. We identified self-cleavage properties of the N protein based on specific Proprotein convertases activities, with Cl- playing a key role in modulating stability and degradation. These findings allowed isolation of a stable oligomeric complex of N, for which we report the 3D structure at ∼6.8 Å resolution. Findings are discussed considering available knowledge about the coronaviruses’ infection cycle.

@article{kleczkowski_adenylate-driven_2025,
	title = {Adenylate-driven equilibration of both ribo- and deoxyribonucleotides is under magnesium control: {Quantification} of the {Mg2}+-signal},
	volume = {304},
	issn = {0176-1617},
	shorttitle = {Adenylate-driven equilibration of both ribo- and deoxyribonucleotides is under magnesium control},
	url = {https://www.sciencedirect.com/science/article/pii/S0176161724002116},
	doi = {10.1016/j.jplph.2024.154380},
	abstract = {Nucleoside mono-, di- and triphosphates (NMP, NDP, and NTP) and their deoxy-counterparts (dNMP, dNDP, dNTP) are involved in energy metabolism and are the building blocks of RNA and DNA, respectively. The production of NTP and dNTP is carried out by several NMP kinases (NMPK) and NDP kinases (NDPK). All NMPKs are fully reversible and use defined Mg-free and Mg-complexed nucleotides in both directions of their reactions, with Mg2+ controlling the ratios of Mg-free and Mg-complexed reactants. Their activities are driven by adenylates produced by adenylate kinase which controls the direction of NMPK and NDPK reactions, depending on the energy status of a cell. This enzymatic machinery is localized in the cytosol, mitochondria, and plastids, i.e. compartments with high energy budgets and where (except for cytosol) RNA and DNA synthesis occur. Apparent equilibrium constants of NMPKs, based on total nucleotide contents, are [Mg2+]-dependent. This allows for an indirect estimation of internal [Mg2+], which constitutes a signal of the energetic status of a given tissue/cell/compartment. Adenylates contribute the most to this Mg2+-signal, followed by uridylates, guanylates, and cytidylates, with deoxynucleotides’ contribution deemed negligible. A method to quantify the Mg2+-signal, using nucleotide datasets, is discussed.},
	urldate = {2025-01-10},
	journal = {Journal of Plant Physiology},
	author = {Kleczkowski, Leszek A. and Igamberdiev, Abir U.},
	month = jan,
	year = {2025},
	keywords = {Adenylate kinase, Equilibrium constant, Guanylate kinase, Magnesium signaling, Thymidylate kinase, Uridylate-cytidylate kinase},
	pages = {154380},
}

Nucleoside mono-, di- and triphosphates (NMP, NDP, and NTP) and their deoxy-counterparts (dNMP, dNDP, dNTP) are involved in energy metabolism and are the building blocks of RNA and DNA, respectively. The production of NTP and dNTP is carried out by several NMP kinases (NMPK) and NDP kinases (NDPK). All NMPKs are fully reversible and use defined Mg-free and Mg-complexed nucleotides in both directions of their reactions, with Mg2+ controlling the ratios of Mg-free and Mg-complexed reactants. Their activities are driven by adenylates produced by adenylate kinase which controls the direction of NMPK and NDPK reactions, depending on the energy status of a cell. This enzymatic machinery is localized in the cytosol, mitochondria, and plastids, i.e. compartments with high energy budgets and where (except for cytosol) RNA and DNA synthesis occur. Apparent equilibrium constants of NMPKs, based on total nucleotide contents, are [Mg2+]-dependent. This allows for an indirect estimation of internal [Mg2+], which constitutes a signal of the energetic status of a given tissue/cell/compartment. Adenylates contribute the most to this Mg2+-signal, followed by uridylates, guanylates, and cytidylates, with deoxynucleotides’ contribution deemed negligible. A method to quantify the Mg2+-signal, using nucleotide datasets, is discussed.

@article{spitzer_aboveground_2025,
	title = {Aboveground and belowground trait coordination across twelve boreal forest tree species},
	volume = {15},
	copyright = {2024 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-024-84162-0},
	doi = {10.1038/s41598-024-84162-0},
	abstract = {The existence of trait coordination in roots and leaves has recently been debated, with studies reaching opposing conclusions. Here, we assessed trait coordination across twelve boreal tree species. We show that there is only partial evidence for above-belowground coordination for “fast-slow” economic traits across boreal tree species, i.e., while N content in leaves and roots were positively correlated, as well as dry matter content, root dry matter content and leaf N had no significant relationship. For resource acquisition traits (i.e. related to light capture and nutrient uptake) we did not find strong evidence for trait coordination, as specific root length and specific leaf area were not positively correlated. We further show that site only explained between 0 and 7\% of the total trait variation, while within-site variation contributed substantially to the total trait variation for a large number of traits (1.6–96\%), and more so for morphological root traits than leaf traits. This likely influences the strength of above-belowground trait coordination found across species in our study. Understanding sources of trait variation and above-belowground trait relationships can contribute to improving global and regional C cycling models. However, fine-scale environmental variability should be accounted for given its importance for driving trait variation.},
	language = {en},
	number = {1},
	urldate = {2025-01-10},
	journal = {Scientific Reports},
	author = {Spitzer, Clydecia M. and Jämtgård, Sandra and Larsson, Marcus J. and Gundale, Michael J.},
	month = jan,
	year = {2025},
	note = {Publisher: Nature Publishing Group},
	keywords = {Ecology, Plant sciences},
	pages = {680},
}

The existence of trait coordination in roots and leaves has recently been debated, with studies reaching opposing conclusions. Here, we assessed trait coordination across twelve boreal tree species. We show that there is only partial evidence for above-belowground coordination for “fast-slow” economic traits across boreal tree species, i.e., while N content in leaves and roots were positively correlated, as well as dry matter content, root dry matter content and leaf N had no significant relationship. For resource acquisition traits (i.e. related to light capture and nutrient uptake) we did not find strong evidence for trait coordination, as specific root length and specific leaf area were not positively correlated. We further show that site only explained between 0 and 7% of the total trait variation, while within-site variation contributed substantially to the total trait variation for a large number of traits (1.6–96%), and more so for morphological root traits than leaf traits. This likely influences the strength of above-belowground trait coordination found across species in our study. Understanding sources of trait variation and above-belowground trait relationships can contribute to improving global and regional C cycling models. However, fine-scale environmental variability should be accounted for given its importance for driving trait variation.

@article{miranda-cervantes_pantothenate_2025,
	title = {Pantothenate kinase 4 controls skeletal muscle substrate metabolism},
	volume = {16},
	copyright = {2025 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-024-55036-w},
	doi = {10.1038/s41467-024-55036-w},
	abstract = {Metabolic flexibility in skeletal muscle is essential for maintaining healthy glucose and lipid metabolism, and its dysfunction is closely linked to metabolic diseases. Exercise enhances metabolic flexibility, making it an important tool for discovering mechanisms that promote metabolic health. Here we show that pantothenate kinase 4 (PanK4) is a new conserved exercise target with high abundance in muscle. Muscle-specific deletion of PanK4 impairs fatty acid oxidation which is related to higher intramuscular acetyl-CoA and malonyl-CoA levels. Elevated acetyl-CoA levels persist regardless of feeding state and are associated with whole-body glucose intolerance, reduced insulin-stimulated glucose uptake in glycolytic muscle, and impaired glucose uptake during exercise. Conversely, increasing PanK4 levels in glycolytic muscle lowers acetyl-CoA and enhances glucose uptake. Our findings highlight PanK4 as an important regulator of acetyl-CoA levels, playing a key role in both muscle lipid and glucose metabolism.},
	language = {en},
	number = {1},
	urldate = {2025-01-10},
	journal = {Nature Communications},
	author = {Miranda-Cervantes, Adriana and Fritzen, Andreas M. and Raun, Steffen H. and Hodek, Ondřej and Møller, Lisbeth L. V. and Johann, Kornelia and Deisen, Luisa and Gregorevic, Paul and Gudiksen, Anders and Artati, Anna and Adamski, Jerzy and Andersen, Nicoline R. and Sigvardsen, Casper M. and Carl, Christian S. and Voldstedlund, Christian T. and Kjøbsted, Rasmus and Hauck, Stefanie M. and Schjerling, Peter and Jensen, Thomas E. and Cebrian-Serrano, Alberto and Jähnert, Markus and Gottmann, Pascal and Burtscher, Ingo and Lickert, Heiko and Pilegaard, Henriette and Schürmann, Annette and Tschöp, Matthias H. and Moritz, Thomas and Müller, Timo D. and Sylow, Lykke and Kiens, Bente and Richter, Erik A. and Kleinert, Maximilian},
	month = jan,
	year = {2025},
	note = {Publisher: Nature Publishing Group},
	keywords = {Diabetes, Fat metabolism, Homeostasis, Metabolomics},
	pages = {345},
}

Metabolic flexibility in skeletal muscle is essential for maintaining healthy glucose and lipid metabolism, and its dysfunction is closely linked to metabolic diseases. Exercise enhances metabolic flexibility, making it an important tool for discovering mechanisms that promote metabolic health. Here we show that pantothenate kinase 4 (PanK4) is a new conserved exercise target with high abundance in muscle. Muscle-specific deletion of PanK4 impairs fatty acid oxidation which is related to higher intramuscular acetyl-CoA and malonyl-CoA levels. Elevated acetyl-CoA levels persist regardless of feeding state and are associated with whole-body glucose intolerance, reduced insulin-stimulated glucose uptake in glycolytic muscle, and impaired glucose uptake during exercise. Conversely, increasing PanK4 levels in glycolytic muscle lowers acetyl-CoA and enhances glucose uptake. Our findings highlight PanK4 as an important regulator of acetyl-CoA levels, playing a key role in both muscle lipid and glucose metabolism.

@article{larsson_conversion_2025,
	title = {Conversion of unmanaged boreal forest to even-aged management has a stronger effect on carbon stocks in the organic layer than the mineral soil},
	volume = {578},
	issn = {0378-1127},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112724007709},
	doi = {10.1016/j.foreco.2024.122458},
	abstract = {Forest management can impact forest carbon stocks, above- and belowground. The even-aged management practice removes the aboveground carbon stock at harvest, which is thereafter restored as the new forest stand establishes. The effects of even-aged management on forest soils in earlier unmanaged stands are however less well understood, and it has been suggested that large carbon losses may occur. In this study we use a unique paired sampling approach of stands in north inland Sweden. Half of the sampled stands had been clear cut within the previous 54 years, and half were left unmanaged. Our results show that clear-cut harvesting and subsequent transformation of unmanaged stands into even-aged management resulted in lower aboveground carbon stock in the living trees. For the soil there was weak evidence for a loss of c. 15 \% of the carbon stock in the organic layer. No evidence of an effect in the more stabilized soil organic carbon within the mineral soil layers was found.},
	urldate = {2025-01-10},
	journal = {Forest Ecology and Management},
	author = {Larsson, Marcus and Dahl, Jenny and Lundmark, Tomas and Gundale, Michael J. and Lim, Hyungwoo and Nordin, Annika},
	month = feb,
	year = {2025},
	keywords = {Boreal forest, Carbon sink, Ecosystem carbon stock, Forest management, Soil organic carbon, Unmanaged forests},
	pages = {122458},
}

Forest management can impact forest carbon stocks, above- and belowground. The even-aged management practice removes the aboveground carbon stock at harvest, which is thereafter restored as the new forest stand establishes. The effects of even-aged management on forest soils in earlier unmanaged stands are however less well understood, and it has been suggested that large carbon losses may occur. In this study we use a unique paired sampling approach of stands in north inland Sweden. Half of the sampled stands had been clear cut within the previous 54 years, and half were left unmanaged. Our results show that clear-cut harvesting and subsequent transformation of unmanaged stands into even-aged management resulted in lower aboveground carbon stock in the living trees. For the soil there was weak evidence for a loss of c. 15 % of the carbon stock in the organic layer. No evidence of an effect in the more stabilized soil organic carbon within the mineral soil layers was found.

@article{yu_integration_2025,
	title = {Integration of {Mitoflash} and {Time}-{Series} {Transcriptomics} {Facilitates} {Energy} {Dynamics} {Tracking} and {Substrate} {Supply} {Analysis} of {Floral} {Thermogenesis} in {Lotus}},
	volume = {48},
	copyright = {© 2024 John Wiley \& Sons Ltd.},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.15185},
	doi = {10.1111/pce.15185},
	abstract = {The high biosynthetic and energetic demands of floral thermogenesis render thermogenic plants the ideal systems to characterize energy metabolism in plants, but real-time tracking of energy metabolism in plant cells remains challenging. In this study, a new method was developed for tracking the mitochondrial energy metabolism at the single mitochondria level by real-time imaging of mitochondrial superoxide production (i.e., mitoflash). Using this method, we observed the increased mitoflash frequencies in the receptacles of Nelumbo nucifera Gaertn. at the thermogenic stages. This increase, combined with the higher expression of antioxidant response-related genes identified through time-series transcriptomics at the same stages, shows us a new regulatory mechanism for plant redox balance. Furthermore, we found that the upregulation of respiratory metabolism-related genes during the thermogenic stages not only correlates with changes in mitoflash frequency but also underscores the critical roles of these pathways in ensuring adequate substrate supply for thermogenesis. Metabolite analysis revealed that sugars are likely one of the substrates for thermogenesis and may be transported over long distances by sugar transporters. Taken together, our findings demonstrate that mitoflash is a reliable tool for tracking energy metabolism in thermogenic plants and contributes to our understanding of the regulatory mechanisms underlying floral thermogenesis.},
	language = {en},
	number = {1},
	urldate = {2024-12-06},
	journal = {Plant, Cell \& Environment},
	author = {Yu, Miao and Wang, Siqin and Gu, Ge and Shi, Tian-Le and Zhang, Jin and Jia, Yaping and Ma, Qi and Porth, Ilga and Mao, Jian-Feng and Wang, Ruohan},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.15185},
	keywords = {Nelumbo nucifera, energy metabolism, floral thermogenesis, mitochondrial flash, respiratory substrate, time-series transcriptomics},
	pages = {893--906},
}

The high biosynthetic and energetic demands of floral thermogenesis render thermogenic plants the ideal systems to characterize energy metabolism in plants, but real-time tracking of energy metabolism in plant cells remains challenging. In this study, a new method was developed for tracking the mitochondrial energy metabolism at the single mitochondria level by real-time imaging of mitochondrial superoxide production (i.e., mitoflash). Using this method, we observed the increased mitoflash frequencies in the receptacles of Nelumbo nucifera Gaertn. at the thermogenic stages. This increase, combined with the higher expression of antioxidant response-related genes identified through time-series transcriptomics at the same stages, shows us a new regulatory mechanism for plant redox balance. Furthermore, we found that the upregulation of respiratory metabolism-related genes during the thermogenic stages not only correlates with changes in mitoflash frequency but also underscores the critical roles of these pathways in ensuring adequate substrate supply for thermogenesis. Metabolite analysis revealed that sugars are likely one of the substrates for thermogenesis and may be transported over long distances by sugar transporters. Taken together, our findings demonstrate that mitoflash is a reliable tool for tracking energy metabolism in thermogenic plants and contributes to our understanding of the regulatory mechanisms underlying floral thermogenesis.

@article{bas_influence_2025,
	title = {Influence of {TEMPO} on preparation of softwood nanofibrils and their hydrogel network properties},
	volume = {348},
	issn = {0144-8617},
	url = {https://www.sciencedirect.com/science/article/pii/S0144861724010385},
	doi = {10.1016/j.carbpol.2024.122812},
	abstract = {From an economic and environmental perspective, the use of less chemicals in the production of cellulose nanofibrils (CNFs) is advantageous. In this study, we investigated the oxidation (TEMPO/NaClO2/NaClO, pH 6.8) of softwood (SW) particles with varying amounts of TEMPO (16, 8 or 0 mg g−1 of wood). Following, TEMPO-oxidized SW nanofibrils (TO-SWNFs) were obtained by nanofibrillation and their size, morphology, and crystallite size were assessed. Hydrogel networks of TO-SWNFs were prepared and mechanical properties were measured in dH2O and phosphate buffered saline (PBS) to compare their performance for possible biomedical applications such as wound dressings. The results reveal that the presence of TEMPO is of importance for TO-SWNF network properties, presenting higher eq. H2O absorption (≈2500 \%) and elongation at break (≈10 \%) with good wet strength (≈180 kPa). In addition, a decrease in use of TEMPO catalyst from 16 to 8 mg g−1 of wood is possible, without detrimental effects on hydrogel network properties (dH2O absorption ≈ 2000 \%, elongation at break ≈ 13 \%, wet strength ≈ 190 kPa) related to applications as wound dressings.},
	urldate = {2024-10-18},
	journal = {Carbohydrate Polymers},
	author = {Baş, Yağmur and Berglund, Linn and Stevanic, Jasna S. and Scheepers, Gerhard and Niittylä, Totte and Oksman, Kristiina},
	month = jan,
	year = {2025},
	keywords = {Absorption, Cellulose nanofibrils, Hydrogel network, TEMPO-oxidation, Wood},
	pages = {122812},
}

From an economic and environmental perspective, the use of less chemicals in the production of cellulose nanofibrils (CNFs) is advantageous. In this study, we investigated the oxidation (TEMPO/NaClO2/NaClO, pH 6.8) of softwood (SW) particles with varying amounts of TEMPO (16, 8 or 0 mg g−1 of wood). Following, TEMPO-oxidized SW nanofibrils (TO-SWNFs) were obtained by nanofibrillation and their size, morphology, and crystallite size were assessed. Hydrogel networks of TO-SWNFs were prepared and mechanical properties were measured in dH2O and phosphate buffered saline (PBS) to compare their performance for possible biomedical applications such as wound dressings. The results reveal that the presence of TEMPO is of importance for TO-SWNF network properties, presenting higher eq. H2O absorption (≈2500 %) and elongation at break (≈10 %) with good wet strength (≈180 kPa). In addition, a decrease in use of TEMPO catalyst from 16 to 8 mg g−1 of wood is possible, without detrimental effects on hydrogel network properties (dH2O absorption ≈ 2000 %, elongation at break ≈ 13 %, wet strength ≈ 190 kPa) related to applications as wound dressings.