@article{renstrom_high-resolution_2025,
	title = {High-resolution imaging of the physical and chemical properties of {Populus} wood using {SilviScan}™ and near-infrared spectroscopy},
	volume = {-1},
	issn = {0928-1541, 2294-1932},
	url = {https://brill.com/view/journals/iawa/aop/article-10.1163-22941932-bja10179/article-10.1163-22941932-bja10179.xml},
	doi = {10.1163/22941932-bja10179},
	abstract = {Summary Spatial information on wood structure and chemistry is crucial for understanding wood functionality. We present a high-throughput and high-resolution near-infrared (NIR) method for combined imaging of the physical and chemical properties of stem sections from Populus trees. Pyrolysis-GC/MS data was used for sensitive and spatially resolved calibration of wood chemistry while SilviScan™ analyses provided reference data for wood physical properties with 25 μm resolution for wood density and 0.2–2.0 mm for microfibril angle (MFA). NIR prediction models were trained and calibrated on material from both field- and greenhouse-grown trees. Thus, the method was developed for NIR imaging of stem samples as small as 4 mm in diameter with an image resolution of 0.03 mm for small-diameter samples and 0.5 mm for samples with multiple annual rings. The NIR model performance, tested against data not used in the training set, reached the coefficient of determination ( R pred 2 ) values for wood density and MFA of 0.60 and 0.72, respectively. The NIR models for wood chemistry showed R pred 2 values of 0.78 and 0.77 for carbohydrates and lignin, respectively. Models for the G-, S- and H-type lignin had R pred 2 values between 0.58 and 0.86. In addition, we developed a prediction model for the determination of tension wood distribution. According to this model, tension wood was frequently observed in young greenhouse samples, which might explain the higher variation found in the chemical and physical properties of wood in greenhouse-grown compared to field-grown trees. The study also demonstrated that NIR-model estimations in image format can capture spatial variations that are not detectable in bulk analyses of wood properties. Examples of the method applied to greenhouse-grown trees highlight the efforts to develop NIR models with good prediction accuracies based on high-resolution data.},
	language = {eng},
	number = {aop},
	urldate = {2025-08-18},
	journal = {IAWA Journal},
	author = {Renström, Anna and Scheepers, Gerhard and Yassin, Zakiya and Grahn, Thomas and Sivan, Pramod and Niittylä, Totte and Mellerowicz, Ewa J. and Tuominen, Hannele},
	month = feb,
	year = {2025},
	note = {Publisher: Brill},
	keywords = {NIR prediction models, NIR-imaging, Py-GC/MS, SilviScan, wood chemistry, wood properties},
	pages = {1--16},
}

Summary Spatial information on wood structure and chemistry is crucial for understanding wood functionality. We present a high-throughput and high-resolution near-infrared (NIR) method for combined imaging of the physical and chemical properties of stem sections from Populus trees. Pyrolysis-GC/MS data was used for sensitive and spatially resolved calibration of wood chemistry while SilviScan™ analyses provided reference data for wood physical properties with 25 μm resolution for wood density and 0.2–2.0 mm for microfibril angle (MFA). NIR prediction models were trained and calibrated on material from both field- and greenhouse-grown trees. Thus, the method was developed for NIR imaging of stem samples as small as 4 mm in diameter with an image resolution of 0.03 mm for small-diameter samples and 0.5 mm for samples with multiple annual rings. The NIR model performance, tested against data not used in the training set, reached the coefficient of determination ( R pred 2 ) values for wood density and MFA of 0.60 and 0.72, respectively. The NIR models for wood chemistry showed R pred 2 values of 0.78 and 0.77 for carbohydrates and lignin, respectively. Models for the G-, S- and H-type lignin had R pred 2 values between 0.58 and 0.86. In addition, we developed a prediction model for the determination of tension wood distribution. According to this model, tension wood was frequently observed in young greenhouse samples, which might explain the higher variation found in the chemical and physical properties of wood in greenhouse-grown compared to field-grown trees. The study also demonstrated that NIR-model estimations in image format can capture spatial variations that are not detectable in bulk analyses of wood properties. Examples of the method applied to greenhouse-grown trees highlight the efforts to develop NIR models with good prediction accuracies based on high-resolution data.

@article{cervela-cardona_metabolism_2025,
	title = {Metabolism in {Sync}: {The} {Circadian} {Clock}, a {Central} {Hub} for {Light}-{Driven} {Chloroplastic} and {Mitochondrial} {Entrainment}},
	volume = {14},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2223-7747},
	shorttitle = {Metabolism in {Sync}},
	url = {https://www.mdpi.com/2223-7747/14/16/2464},
	doi = {10.3390/plants14162464},
	abstract = {Plants align their physiology with daily environmental cycles through the circadian clock, which integrates light and metabolic signals to optimize growth and stress responses. While light entrainment has been extensively studied, emerging evidence highlights the central role of metabolism—particularly from chloroplasts and mitochondria—in tuning circadian rhythms. In this review, we explore the bidirectional relationship between organelle metabolism and the circadian clock, focusing on how metabolic signals such as sugars, ROS, and organic acids function as entrainment cues. We discuss how the clock regulates organelle function at multiple levels, including transcriptional, translational, and post-translational mechanisms, and how organelle-derived signals feedback to modulate core clock components through retrograde pathways. Special attention is given to the integration of chloroplast and mitochondrial signals, emphasizing their synergistic roles in maintaining cellular homeostasis. Drawing on the “three-body problem” analogy, we illustrate the dynamic and reciprocal interactions among light, clock, and metabolism. This perspective underscores the need to reframe the circadian system, not merely as light-driven but also as a central integrator of energy status and environmental cues. Understanding this integrated network is essential to improve plant performance and resilience under fluctuating environmental conditions.},
	language = {en},
	number = {16},
	urldate = {2025-08-15},
	journal = {Plants},
	author = {Cervela-Cardona, Luis and Francisco, Marta and Strand, Åsa},
	month = jan,
	year = {2025},
	note = {Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {chloroplast–mitochondria crosstalk, circadian clock, light signaling, metabolic entrainment, plant energy metabolism, retrograde signaling},
	pages = {2464},
}

Plants align their physiology with daily environmental cycles through the circadian clock, which integrates light and metabolic signals to optimize growth and stress responses. While light entrainment has been extensively studied, emerging evidence highlights the central role of metabolism—particularly from chloroplasts and mitochondria—in tuning circadian rhythms. In this review, we explore the bidirectional relationship between organelle metabolism and the circadian clock, focusing on how metabolic signals such as sugars, ROS, and organic acids function as entrainment cues. We discuss how the clock regulates organelle function at multiple levels, including transcriptional, translational, and post-translational mechanisms, and how organelle-derived signals feedback to modulate core clock components through retrograde pathways. Special attention is given to the integration of chloroplast and mitochondrial signals, emphasizing their synergistic roles in maintaining cellular homeostasis. Drawing on the “three-body problem” analogy, we illustrate the dynamic and reciprocal interactions among light, clock, and metabolism. This perspective underscores the need to reframe the circadian system, not merely as light-driven but also as a central integrator of energy status and environmental cues. Understanding this integrated network is essential to improve plant performance and resilience under fluctuating environmental conditions.

@article{zhang_unraveling_2025,
	title = {Unraveling {Nitrogen} {Uptake} and {Metabolism}: {Gene} {Families}, {Expression} {Dynamics}, and {Functional} {Insights} in {Aspen} ({Populus} tremula)},
	issn = {1758-4469},
	shorttitle = {Unraveling {Nitrogen} {Uptake} and {Metabolism}},
	url = {https://doi.org/10.1093/treephys/tpaf099},
	doi = {10.1093/treephys/tpaf099},
	abstract = {The influence of nitrogen on wood formation is well established. To gain insight into the underlying molecular mechanism, we first identified genes in fourteen gene families that are involved in nitrogen uptake and metabolism in European aspen (Populus tremula L.) genome annotation. Gene expression data from a de novo RNA sequencing (RNA-seq) analysis and data available from the AspWood database (plantgenie.org) provided putative candidate genes for the uptake of nitrate, ammonium and amino acids from the xylem sap as well as their further assimilation in the secondary xylem tissues of the stem. For a population-wide analysis of the nitrogen-related genes, we utilized RNA-seq data from the cambial region of the stems of 5-year-old aspen trees, representing 99 natural aspen accessions, and compared the expression of the nitrogen-related genes to stem diameter. Novel regulatory interactions were identified in expression quantitative loci and co-expression network analyses in these data. The expression of certain nitrate and amino acid transporters correlated negatively with stem diameter, suggesting that excessive nitrogen retrieval from the xylem sap suppresses radial growth of the stem. The expression of a glutamine synthetase correlated with the expression of these transporters, a link further supported by increased plant growth in transgenic glutamine synthetase overexpressing trees. This study provides insight into the genetic basis of nitrogen uptake and assimilation and its connection to wood formation, providing interesting targets for improving nitrogen use efficiency and growth of aspen trees.},
	urldate = {2025-08-15},
	journal = {Tree Physiology},
	author = {Zhang, Yupeng and Choudhary, Shruti and Renström, Anna and Luomaranta, Mikko and Chantreau, Maxime and Fleig, Verena and Gaboreanu, Ioana and Grones, Carolin and Nilsson, Ove and Robinson, Kathryn M and Tuominen, Hannele},
	month = aug,
	year = {2025},
	pages = {tpaf099},
}

The influence of nitrogen on wood formation is well established. To gain insight into the underlying molecular mechanism, we first identified genes in fourteen gene families that are involved in nitrogen uptake and metabolism in European aspen (Populus tremula L.) genome annotation. Gene expression data from a de novo RNA sequencing (RNA-seq) analysis and data available from the AspWood database (plantgenie.org) provided putative candidate genes for the uptake of nitrate, ammonium and amino acids from the xylem sap as well as their further assimilation in the secondary xylem tissues of the stem. For a population-wide analysis of the nitrogen-related genes, we utilized RNA-seq data from the cambial region of the stems of 5-year-old aspen trees, representing 99 natural aspen accessions, and compared the expression of the nitrogen-related genes to stem diameter. Novel regulatory interactions were identified in expression quantitative loci and co-expression network analyses in these data. The expression of certain nitrate and amino acid transporters correlated negatively with stem diameter, suggesting that excessive nitrogen retrieval from the xylem sap suppresses radial growth of the stem. The expression of a glutamine synthetase correlated with the expression of these transporters, a link further supported by increased plant growth in transgenic glutamine synthetase overexpressing trees. This study provides insight into the genetic basis of nitrogen uptake and assimilation and its connection to wood formation, providing interesting targets for improving nitrogen use efficiency and growth of aspen trees.

@article{bizjak-johansson_arginine-ironhexametaphosphate_2025,
	title = {Arginine-iron–hexametaphosphate complex as a novel nitrogen plant nutrition reducing nitrate leaching in {Scots} pine ({Pinus} sylvestris) seedling production},
	volume = {15},
	copyright = {2025 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-025-15665-7},
	doi = {10.1038/s41598-025-15665-7},
	abstract = {The industrial production of conifer seedlings in nurseries uses large amounts of fertilizers to ensure their proper growth and accurate nutrient status. However, inorganic nitrogen fertilization leads to nitrate leaching, which has negative environmental consequences. An alternative solution could be the use of controlled-release fertilizers that supply nutrients over longer periods and hence have a lower environmental impact. This study analysed the performance of a novel arginine–iron–hexametaphosphate complex on Scots pine (Pinus sylvestris) seedlings. The complex was characterized using a wide range of analytical tools, indicating that it is a precipitated complex rather than a crystalline compound. Plant growth on arginine–iron–hexametaphosphate was comparable to a commercial inorganic nitrogen controlled-release fertilizer but with significantly lower nitrate leaching. A nitrogen budget of seedlings and growth substrate showed that seedlings had acquired nitrogen in excess of the amount of nitrogen present at the start of the experiment, and this excess nitrogen was smaller in seedlings grown on the inorganic fertilizer. Measurements of acetylene reduction in seedlings indicated low but measurable rates of nitrogen fixation, potentially contributing to the excess nitrogen. Together, the results showed that the arginine–iron–hexametaphosphate complex is a good alternative to commonly used fertilizers and can contribute to sustainable seedling production.},
	language = {en},
	number = {1},
	urldate = {2025-08-15},
	journal = {Scientific Reports},
	author = {Bizjak-Johansson, Tinkara and Bozaghian Bäckman, Marjan and Nilsson, Lina and Holmlund, Mattias and Skoglund, Nils and Näsholm, Torgny and Gratz, Regina},
	month = aug,
	year = {2025},
	note = {Publisher: Nature Publishing Group},
	keywords = {Plant development, Plant physiology},
	pages = {29619},
}

The industrial production of conifer seedlings in nurseries uses large amounts of fertilizers to ensure their proper growth and accurate nutrient status. However, inorganic nitrogen fertilization leads to nitrate leaching, which has negative environmental consequences. An alternative solution could be the use of controlled-release fertilizers that supply nutrients over longer periods and hence have a lower environmental impact. This study analysed the performance of a novel arginine–iron–hexametaphosphate complex on Scots pine (Pinus sylvestris) seedlings. The complex was characterized using a wide range of analytical tools, indicating that it is a precipitated complex rather than a crystalline compound. Plant growth on arginine–iron–hexametaphosphate was comparable to a commercial inorganic nitrogen controlled-release fertilizer but with significantly lower nitrate leaching. A nitrogen budget of seedlings and growth substrate showed that seedlings had acquired nitrogen in excess of the amount of nitrogen present at the start of the experiment, and this excess nitrogen was smaller in seedlings grown on the inorganic fertilizer. Measurements of acetylene reduction in seedlings indicated low but measurable rates of nitrogen fixation, potentially contributing to the excess nitrogen. Together, the results showed that the arginine–iron–hexametaphosphate complex is a good alternative to commonly used fertilizers and can contribute to sustainable seedling production.

@article{wang_ribosome_2025,
	title = {Ribosome biogenesis in plants requires the nuclear envelope and mitochondria localized {OPENER} complex},
	volume = {16},
	copyright = {2025 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-025-62652-7},
	doi = {10.1038/s41467-025-62652-7},
	abstract = {Eukaryotic ribosome biogenesis proceeds from nucleolus to cytosol assisted by various assembly factors. The process is evolutionarily conserved across eukaryotes but differences between the kingdoms are emerging. Here, we describe how the OPENER (OPNR) protein complex is required for 60S ribosome assembly in the model plant Arabidopsis thaliana. The complex is observed on both nuclear envelope and mitochondria, and contains OPNR, OPENER ASSOCIATED PROTEIN 1 (OAP1), OAP2, Cell Division Cycle 48 D (CDC48D) and Calmodulin-interacting protein 111 (CIP111). Depletion of the OPNR complex components results in reproductive lethality and cytoplasmic retention of assembly factors on 60S ribosomes. Subsequent biochemical analyses and structural modelling suggest that OPNR, OAP1 and OAP2 form a claw-like trimer which grabs the ribosome assembly factor RIBOSOMAL PROTEIN L24C (RPL24C) on the pre-60S ribosome. Our results reveal previously unrecognised subcellular complexity of ribosome biogenesis in plants, and point to mitochondria association as a feature to ensure sufficient translational capacity.},
	language = {en},
	number = {1},
	urldate = {2025-08-12},
	journal = {Nature Communications},
	author = {Wang, Wei and Mahboubi, Amir and Zhu, Shaochun and Hanson, Johannes and Mateus, André and Niittylä, Totte},
	month = aug,
	year = {2025},
	note = {Publisher: Nature Publishing Group},
	keywords = {Plant cell biology, Plant molecular biology, Ribosome},
	pages = {7301},
}

Eukaryotic ribosome biogenesis proceeds from nucleolus to cytosol assisted by various assembly factors. The process is evolutionarily conserved across eukaryotes but differences between the kingdoms are emerging. Here, we describe how the OPENER (OPNR) protein complex is required for 60S ribosome assembly in the model plant Arabidopsis thaliana. The complex is observed on both nuclear envelope and mitochondria, and contains OPNR, OPENER ASSOCIATED PROTEIN 1 (OAP1), OAP2, Cell Division Cycle 48 D (CDC48D) and Calmodulin-interacting protein 111 (CIP111). Depletion of the OPNR complex components results in reproductive lethality and cytoplasmic retention of assembly factors on 60S ribosomes. Subsequent biochemical analyses and structural modelling suggest that OPNR, OAP1 and OAP2 form a claw-like trimer which grabs the ribosome assembly factor RIBOSOMAL PROTEIN L24C (RPL24C) on the pre-60S ribosome. Our results reveal previously unrecognised subcellular complexity of ribosome biogenesis in plants, and point to mitochondria association as a feature to ensure sufficient translational capacity.