@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{ma_ca2_2025,
	title = {Ca2+ waves and ethylene/{JA} crosstalk orchestrate wound responses in {Arabidopsis} roots},
	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.},
	urldate = {2025-05-20},
	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 = may,
	year = {2025},
	note = {Num Pages: 17
Publisher: John Wiley \& Sons, Ltd},
	keywords = {Ca2+ Wave, Ethylene, Jasmonate, Laser Ablation},
	pages = {1--17},
}

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{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.