@article{mazumdar_damage_2025,
	title = {Damage activates \textit{{EXG1}} and \textit{{RLP44}} to suppress vascular differentiation during regeneration in {Arabidopsis}},
	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 look for 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 was cell wall related and highly induced by all three stresses and was named ENHANCED XYLEM AND GRAFTING1 (EXG1) since mutations in it promoted ectopic xylem formation in Vascular cell Induction culture System Using Arabidopsis Leaves (VISUAL) and enhanced graft formation. Further observations revealed that exg1 mutants 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 a receptor-like protein, RLP44, caused similar regeneration-related phenotypes as mutations in EXG1. Like EXG1, RLP44 expression was induced by grafting and wounding. Mutations in EXG1 and RLP44 affected the expression of many genes in common including those related to cell walls and genes important for vascular regeneration. We propose that EXG1 integrates information from wounding or pathogen stresses and functions with RLP44 to suppress vascular differentiation during regeneration and healing.},
	urldate = {2025-01-24},
	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 = jan,
	year = {2025},
	keywords = {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 look for 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 was cell wall related and highly induced by all three stresses and was named ENHANCED XYLEM AND GRAFTING1 (EXG1) since mutations in it promoted ectopic xylem formation in Vascular cell Induction culture System Using Arabidopsis Leaves (VISUAL) and enhanced graft formation. Further observations revealed that exg1 mutants 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 a receptor-like protein, RLP44, caused similar regeneration-related phenotypes as mutations in EXG1. Like EXG1, RLP44 expression was induced by grafting and wounding. Mutations in EXG1 and RLP44 affected the expression of many genes in common including those related to cell walls and genes important for vascular regeneration. We propose that EXG1 integrates information from wounding or pathogen stresses and functions with RLP44 to suppress vascular differentiation during regeneration and healing.

@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{fino_cellular_2025,
	title = {Cellular damage triggers mechano-chemical control of cell wall dynamics and patterned cell divisions in plant healing},
	volume = {0},
	issn = {1534-5807},
	url = {https://www.cell.com/developmental-cell/abstract/S1534-5807(24)00771-8},
	doi = {10.1016/j.devcel.2024.12.032},
	language = {English},
	number = {0},
	urldate = {2025-01-15},
	journal = {Developmental Cell},
	author = {Fino, Luciano Martín Di 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 = jan,
	year = {2025},
	pmid = {39809282},
	note = {Publisher: Elsevier},
	keywords = {cell division, cell wall, ethylene, mechanobiology, pectin, regeneration, single-cell laser ablation, xylem-pole-pericycle},
}

@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.